text:
.1139/cjc-77-1-86",
	localfile = "molecular fragmentation/1999 - Can there be more than a single definition of an atom in a molecule?.pdf",
	year = 1999
}

@Article{1999-Becker-Stockhausen,
	Author = "U. Becker and M. Stockhausen",
	Title = "{A dielectric relaxation study of some mixtures of mono and dihydric alcohols}",
	Journal = "J. Mol. Liquids",
	Volume = "81",
	Pages = "89–100",
	cited = "22 (2013-04-29)",
	collection = "molecular sovlation",
	doi = "10.1016/S0167-7322(99)00058-6",
	localfile = "molecular solvation/1999 - A dielectric relaxation study of some mixtures of mono and dihydric alcohols.pdf",
	year = 1999
}

@Article{1999-Bruice-Lightstone,
	Author = "Thomas C. Bruice and Felice C. Lightstone",
	Title = "{Ground state and transition state contributions to the rates of intramolecular and enzymatic reactions}",
	Journal = "Acc. Chem. Res.",
	Volume = "32",
	Pages = "127–136",
	abstract = "Reactions within enzyme-substrate (E‚S) complexes share with intramolecular reactions the close proximity of reactants. This proximity effect results in a much larger numerical value of the rate constants when compared to the rate constants of the corresponding bimolecular reaction.",
	collection = "enzymes",
	doi = "10.1021/ar960131y",
	localfile = "enzymes/1999 - Ground state and transition state contributions to the rates of intramolecular and enzymatic reactions.pdf",
	year = 1999
}

@Article{1999-Buchner-BS,
	Author = "Richard Buchner and J. Barthel and J. Stauber",
	Title = "{The dielectric relaxation of water between 0°C and 35°C}",
	Journal = "Chem. Phys. Lett.",
	Volume = "306",
	Number = "1-2",
	Pages = "57–63",
	cited = "186 (2013-04-29)",
	collection = "molecular sovlation",
	doi = "10.1016/S0009-2614(99)00455-8",
	keywords = "water",
	localfile = "molecular solvation/1999 - The dielectric relaxation of water between 0C and 35C.pdf",
	year = 1999
}

@Article{1999-Buchner-HM,
	Author = "Richard Buchner and Glenn T. Hefter and Peter M. May",
	Title = "{Dielectric relaxation of aqueous NaCl solutions}",
	Journal = "J. Phys. Chem. A",
	Volume = "103",
	Number = "1",
	Pages = "1–9",
	cited = "158 (2013-04-29)",
	collection = "molecular solvation",
	doi = "10.1021/jp982977k",
	localfile = "molecular solvation/1999 - Dielectric relaxation of squeous NaCl solutions.pdf",
	year = 1999
}

@Article{1999-Ciatto-DNSV,
	Author = "Carlo Ciatto and Maria L. D'Amico and Giovanni Natile and Fernando Secco and Marcella Venturini",
	Title = "{Intercalation of Proflavine and a Platinum Derivative of Proflavine into Double-Helical Poly(A)}",
	Journal = "Biophys. J.",
	Volume = "77",
	Number = "5",
	Pages = "2717–2724",
	abstract = "The equilibria and kinetics of the interactions of proflavine (PR) and its platinum-containing derivative [{PtCl(tmen)}2{HNC13H7(NHCH2CH2)2}] (PRPt) with double-stranded poly(A) have been investigated by spectrophotometry and Joule temperature-jump relaxation at ionic strength 0.1 M, 25°C, and pH 5.2. Spectrophotometric measurements indicate that base-dye interactions are prevailing. T-jump experiments with polarized light showed that effects due to field-induced alignment could be neglected. Both of the investigated systems display two relaxation effects. The kinetic features of the reaction are discussed in terms of a two-step series mechanism in which a precursor complex DSI is formed in the fast step, which is then converted to a final complex in the slow step.",
	collection = "nucleic acid intercalation",
	doi = "10.1016/S0006-3495(99)77105-5",
	localfile = "nucleic acid intercalation/1999 - Intercalation of proflavine and a platinum derivative of proflavine into double-helical Poly(A).pdf",
	year = 1999
}

@Article{1999-Coppens-ACKNAP,
	Author = "Phillip Coppens and Yuriy Abramov and Michael Carducci and Boris Korjov and Irina Novozhilova and Cristobal Alhambra and Mark R. Pressprich",
	Title = "{Experimental charge densities and intermolecular interactions: electrostatic and topological analysis of DL-histidine}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "121",
	Pages = "2585–2593",
	abstract = "Abstract: A high-resolution, low-temperature X-ray diffraction data set on DL-histidine, collected with a CCD detector, is used in the analysis of molecular bonding and intermolecular interactions. The molecular dipole moment in the crystal is enhanced relative to that from HF and DFT calculations. Topological properties of the molecular electron density differ from theory for the polar bonds but generally agree well for the C-C bonds in the molecule. A major aim of the study is the evaluation of the electrostatic contribution to the intermolecular interactions from the experimental density. The electrostatic interaction energies between pairs of neighboring molecules, as calculated from the experimental density, compare reasonably well with the total interaction energies from supermolecule calculations. The agreement is somewhat improved by the addition of nonelectrostatic repulsion and dispersive terms, which together contribute much less than the electrostatic energy. The electrostatic interaction energy calculated from the CHARMM point-charge force field is often close to the values derived from the experimental charge density, though exceptions occur. In an alternative approach, the topology of the intermolecular charge density is related to the intermolecular interaction energy. The latter approach makes use of a density functional by Abramov (Acta Crystallogr. 1997, A53, 264-272) and a relation between the potential energy density at the bond critical point and the hydrogen bond dissociation energy (Espinosa, et al. Chem. Phys. Lett. 1998, 285, 170-173).",
	collection = "protein amino acids",
	doi = "10.1021/ja983320f",
	localfile = "protein amino acids/1999 - Experimental charge densities and intermolecular interactions: electrostatic and topological analysis of DL-histidine.pdf",
	systems = "histidine",
	year = 1999
}

@Article{1999-Davis-Teague,
	Author = "Andrew M. David and Simon J. Teague",
	Title = "{Hydrogen bonding, hydrophobic interactions, and failure of the rigid receptor hypothesis}",
	Journal = "Angew. Chem. Int. Ed.",
	Volume = "38",
	Pages = "736–749",
	Note = "Looks in detail at the importance of hydrogen bonds, their variability and how they balance hydrophobic interactions.",
	collection = "molecular interactions",
	keywords = "hydrogen bonds; hydrophobic effect",
	localfile = "molecular interactions/1999 - Hydrogen bonding, hydrophobic interactions, and failure of the rigid receptor hypothesis.pdf",
	rating = "2",
	read = "2012-12-10",
	year = 1999
}

@Article{1999-Drolet-Fredrickson,
	Author = "François Drolet and Glenn H. Fredrickson",
	Title = "{Combinatorial screening of complex block copolymer assembly with self-consistent field theory}",
	Journal = "Phys. Rev. Lett.",
	Volume = "83",
	Number = "21",
	Pages = "4317–4320",
	abstract = "We describe a numerical implementation of self-consistent mean ﬁeld theory for block copolymers that requires no assumption of the mesophase symmetry. The method is amenable to massively parallel screening of self-assembly in complex block copolymer systems, characterized by high-dimensional parameter spaces. We illustrate the method by screening for novel mesophases in linear ABCA tetrablock copolymers; several previously unreported mesophases have been identiﬁed. Extension to multicomponent systems, such as blends of block copolymers and homopolymers, is straightforward.",
	collection = "polymers",
	doi = "10.1103/PhysRevLett.83.4317",
	localfile = "polymers/1999 - Combinatorial screening of complex block copolymer assembly with self-consistent field theory.pdf",
	year = 1999
}

@Article{1999-Espinosa-SLL,
	Author = "E. Espinosa and M. Souhassou and H. Lachekar and Claude Lecomte",
	Title = "{Topological analysis of the electron density in hydrogen bonds}",
	Journal = "Acta Cryst. B",
	Volume = "55",
	Pages = "563–572",
	abstract = "Topological analysis of the experimental electron density \&(r) in hydrogen-bonding regions has been carried out for a large number of organic compounds using different multipole models and techniques. Relevant systematic relationships between topological properties at the critical points and the usual geometric parameters are pointed out. Results involving X-ray data only and joint X-ray and neutron data, as well as special hydrogen bonding cases (symmetric, bifurcated, peptide bonds, etc.) are included and analysed in the same framework. A new classi®cation of hydrogen bonds using the positive curvature of the electron density at the critical point $[{\l}ambda\_3(\mathbf{r}\_{CP})]$ is proposed.",
	collection = "hydrogen bonding",
	doi = "10.1107/S0108768199002128",
	localfile = "hydrogen bonding/1999 - Topological analysis of the electron density in hydrogen bonds.pdf",
	year = 1999
}

@Article{1999-Fradera-AB,
	Author = "Xavier Fradera and Maggie A. Austen and Richard F. W. Bader",
	Title = "{The Lewis Model and Beyond}",
	Journal = "J. Phys. Chem. A",
	Volume = "103",
	Number = "2",
	Pages = "304–314",
	abstract = "The electron pair density, in conjunction with the definition of an atom in a molecule, enables one to determine the average number of electron pairs that are localized to each atom and the number that are formed between any given pair of atoms. Thus, it is through the pair density that the Lewis model of electronic structure finds physical expression. The pairing of electrons is a consequence of the Pauli principle whose effect is made manifest through the creation of the Fermi hole. The density describing the spatial distribution of the Fermi hole for an electron of given spin determines how the density of that electron is spread out in space, excluding an equivalent amount of same-spin density. The averaging of the Fermi density over single atoms or pairs of atoms determines the corresponding contributions to the total Fermi correlation. It is these terms that yield the localization and delocalization indices that determine the intra- and interatomic distribution of electron pairs that enables one to compare the pairing predicted by theory with that of a Lewis structure. The agreement is best at the {HartreeFock} level, where the Fermi hole is the sole source of correlation between the electrons. The introduction of the remaining correlation, the Coulomb correlation, disrupts the sharing of electron pairs between the atoms, and its effect is therefore, most pronounced for shared interactions. For example, Coulomb correlation reduces the number of shared pairs in N2 from the {HartreeFock} value of three to just above two. In ionic systems, the electrons are strongly localized within each atomic basin and the effect of Coulomb correlation on the atomic pairing is minimal, approaching zero over each of the atomic basins, as it does for the total molecule.",
	collection = "quantum chemistry",
	doi = "10.1021/jp983362q",
	localfile = "quantum chemistry/1999 - The Lewis model and beyond.pdf",
	year = 1999
}

@Article{1999-Ginzburg-Balazs,
	Author = "Valeriy V. Ginzburg and Anna C. Balazs",
	Title = "{Calculating phase diagrams of polymer-platelet mixtures using density functional theory: implication for polymer/clay composites}",
	Journal = "Macromolecules",
	Volume = "32",
	Pages = "5681–5688",
	abstract = "We analyze the thermodynamics of disklike particles dispersed in a polymer matrix. Using the Somoza-Tarazona free energy functional for thin oblate ellipsoids of revolution in combination with the Flory-Huggins mixing free energy, we obtain a new expression that allows us to describe the complete (liquid, crystalline, and liquid crystalline) phase diagram for the mixture as a function of shape anisotropy κ, polymer chain length N, and the disk-disk interaction parameter, q. It is shown that at large q and/or N positional ordering plays an important role in determining the stability and morphology of such mixtures.",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma990135t",
	localfile = "polymer nanocomposites/1999 - Calculating phase diagrams of polymer-platelet mixtures using density functional theory: implications for polymer-clay composites.pdf",
	year = 1999
}

@Article{1999-Grembecka-KS,
	Author = "Jolanta Grembecka and Paweł Kędzierski and W. Andrzej Sokalski",
	Title = "{Non-empirical analysis of the nature of the inhibitor–active-site interactions in leucine aminopeptidase}",
	Journal = "Chem. Phys. Lett.",
	Volume = "313",
	Number = "1-2",
	Pages = "385–392",
	abstract = "Non-empirical analysis of the physical nature of the intermolecular interactions between several leucine aminopeptidase inhibitors and various constituents of the enzyme active site has been performed using a diner version of the hybrid variation-perturbation decomposition of SCF and MP2 interaction energies. The interaction energy terms obtained at different theory levels have been correlated with experimentally measured activities of the inhibitors, indicating that the more advanced the quantum-chemical method and, the larger the active-site model, the better is the correlation between calculated and measured binding energies. The electrostatic multipole term constitutes the dominant contribution in the total interaction energy, whereas Zn(2+)488 and Lys(2+)262 enzyme residues play the crucial role in the binding of these inhibitors by leucine aminopeptidase.",
	collection = "enzymes",
	doi = "10.1016/S0009-2614(99)01012-X",
	keywords = "active site",
	localfile = "enzymes/1999 - Non-empirical analysis of the nature of the inhibitor-active-site interactions.pdf",
	year = 1999
}

@Article{1999-Hobza-Sponer,
	Author = "Pavel Hobza and Jiří Šponer",
	Title = "{Structure, energetics, and dynamics of the nucleic acid base pairs: nonempirical ab initio calculations}",
	Journal = "Chem. Rev.",
	Volume = "99",
	Number = "11",
	Pages = "3247–3276",
	abstract = "(Excerpt) Living organisms contain a set of instructions that specifies every step required for the organism to construct a replica of itself. This information is stored in deoxyribonucleic acid, DNA, and the respective molecule is thus one of the most important molecules in our life. The discovery of DNA was made in 1869 by Miescher and it took more than 70 years to demonstrate that DNA was the molecule that carried genetic information. A further important step in the study of DNA was made in 1953 by Watson and Crick, who proposed a three-dimensional, right-handed double-helical B-DNA model of the DNA structure.",
	collection = "nucleic acid bases",
	doi = "10.1021/cr9800255",
	localfile = "nucleic acid bases/1999 - Structure, energetics, and dynamics of the nucleic acid base pairs.pdf",
	year = 1999
}

@Article{1999-Kitaura-IANU,
	Author = "Kazuo Kitaura and Eiji Ikeo and Toshio Asada and Tatsuya Nakano and Masami Uebayasi",
	Title = "{Fragment molecular orbital method: an approximate computational method for large molecules}",
	Journal = "Chem. Phys. Lett.",
	Volume = "313",
	Number = "3-4",
	Pages = "701–706",
	abstract = "We propose an approximate molecular orbital (MO) method for calculating large molecules such as proteins. Our method assigns the electrons of the molecules to fragments, and the MOs of fragments and fragment pairs are calculated to obtain the total energy of the molecule. The method avoids the MO calculation of the whole molecule and is expected to reduce the computational time drastically for large molecules. Numerical calculations were performed on propane, propanol and methylacetamide to demonstrate the accuracy of the method. The optimized geometries and the total energies were in good agreement with those from the ab initio MO calculations.",
	collection = "quantum chemistry",
	doi = "10.1016/S0009-2614(99)00874-X",
	localfile = "quantum chemistry/1999 - Fragment molecular orbital method: an approximate computational method for large molecules.pdf",
	year = 1999
}

@Article{1999-Mavrantzas-BZT,
	Author = "Vlasis G. Mavrantzas and Travis D. Boone and Evangelia Zervopoulou and Doros N. Theodorou",
	Title = "{End-bridging Monte Carlo: a fast algorithm for atomistic simulation of condensed phases of long polymer chains}",
	Journal = "Macromolecules",
	Volume = "32",
	Pages = "5072–5096",
	collection = "polymers",
	doi = "10.1021/ma981745g",
	keywords = "algorithms",
	localfile = "polymers/1999 - End-bridgin Monte Carlo: a fast algorithm for atomistic s imulation of condensed phases of long polymer chains.pdf",
	methods = "MC",
	rating = "2",
	year = 1999
}

@Article{1999-Medhi-MPT,
	Author = "C. Medhi and J. B. O. Mitchell and Sarah L. Price and A. B. Tabor",
	Title = "{Electrostatic factors in {DNA} intercalation}",
	Journal = "Biopolymers",
	Volume = "52",
	Number = "2",
	Pages = "84–93",
	abstract = "The factors that determine the binding of a chromophore between the base pairs in DNA intercalation complexes are dissected The electrostatic potential in the intercalation plane is calculated using an accurate ab initio based distributed multipole electrostatic model for a range of intercalation sires, involving different sequences of base pairs and relative rn isl angles. There will be a significant electrostatic contribution to the binding energy for chromophores with a predominantly positive electrostatic potential, but this varies significantly with sequence, and somewhat with twist angle. The usefulness of these potential maps for understanding the binding of intercalators is explored by calculating the electrostatic Binding energy for 9-aminoacridine, ethidium, and daunomycin in a variety of model binding sites. The electrostatic forces play a major role in the positioning of an intercalating 9-aminoacridine and a significant stabilizing rob in the binding of ethidium in its sterically constrained position, but the intercalation of daunomycin is determined by the side-chain binding. Sequence preferences are likely to be determined by a complex and subtle mixture of effects, with electrostatics being just one component. The electrostatic binding energy is also unlikely to be a major determinant of the twist angle, as its variation with angle is modest for most intercalation sires. Overall the electrostatic potential maps give guidance on how positively charged chromophores can be chemically adapted by heteroatomic substitution to optimise their binding. (C) 2000 John Wiley \& Sons, Inc.",
	collection = "nucleic acid intercalation",
	doi = "10.1002/1097-0282(1999)52:2",
	keywords = "nucleic acid intercalation",
	localfile = "nucleic acid intercalation/1999 - Electrostatic factors in DNA intercalation.pdf",
	rating = "2",
	year = 1999
}

@Article{1999-Pope-DLRTW,
	Author = "Lisa H. Pope and M. C. Davies and C. A. Laughton and C. J. Roberts and S. J. B. Tendler and P. M. Williams",
	Title = "{Intercalation-induced changes in {DNA} supercoiling observed in real-time by atomic force microscopy}",
	Journal = "Anal. Chim. Acta",
	Volume = "400",
	Number = "1-3",
	Pages = "27–32",
	abstract = "Atomic force microscopy {(AFM)} has been employed to observe in real-time and in an aqueous environment the process of ethidium bromide induced supercoiling in individual {DNA} plasmid molecules. Image data reveal both the onset and the progressive presence of plectonemic {DNA} supercoiling. In addition, significant molecular motion of the surface adsorbed {DNA} is observed. These data illustrate the potential of {AFM} in the time-resolved study of biomolecular processes, and hence, provide new insights into biomolecular structure and function.",
	collection = "nucleic acid intercalation",
	doi = "10.1016/S0003-2670(99)00624-8",
	localfile = "nucleic acid intercalation/1999 - Intercalation-induced changes in DNA supercoiling observed in real-time by atomic force microscopy.pdf",
	year = 1999
}

@Article{1999-Qu-Chaires,
	Author = "Xiaogang Qu and Jonathan B. Chaires",
	Title = "{Contrasting Hydration Changes for Ethidium and Daunomycin Binding to {DNA}}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "121",
	Number = "11",
	Pages = "2649–2650",
	collection = "nucleic acid intercalation",
	doi = "10.1021/ja984366b",
	localfile = "nucleic acid intercalation/1999 - Contrasting hydration changes for ethidium and duanomycin binding to DNA.pdf",
	year = 1999
}

@Article{1999-Ren-Chaires,
	Author = "Jinsong S. Ren and Jonathan B. Chaires",
	Title = "{Sequence and structural selectivity of nucleic acid binding ligands}",
	Journal = "Biochemistry",
	Volume = "38",
	Number = "49",
	Pages = "16067 – 16075",
	abstract = "The sequence and structural selectivity of 15 different DNA binding agents was explored using a novel, thermodynamically rigorous, competition dialysis procedure. In the competition dialysis method, 13 different nucleic acid structures were dialyzed against a common ligand solution. More ligand accumulated in the dialysis tube containing the structural form with the highest ligand binding affinity. DNA structural forms included in the assay ranged from single-stranded forms, through a variety of duplex forms, to multistranded tripler and tetraplex forms. Left-handed Z-DNA, RNA, and a DNA-RNA hybrid were also represented. Standard intercalators (ethidium, daunorubicin, and actinomycin D) served as control compounds and were found to show structural binding preferences fully consistent with their previously published behavior. Standard groove binding agents (DAPI,dystamycin, and netropsin) showed a strong preference for AT-rich duplex DNA forms, along with apparently strong binding to the poly(da)-[poly(dT)](2) tripler. Thermal denaturation studies revealed the apparent tripler binding to be complex, and perhaps to result from displacement of the third strand. Putative tripler (BePI, coralyne, and berberine) and tetraplex [H2TmPyP, 5,10,15,20-tetrakis [4-(trimethylammonio)phenyl] -21H,23H-porphine, and N-methyl mesoporphyrin IX] selective agents showed in many cases less dramatic binding selectivity than anticipated from published reports that compared their binding to only a few structural forms. Coralyne was found to bind strongly to single-stranded poly(dA), a novel and previously unreported interaction. Finally, three compounds (berenil, chromomycin A, and pyrenemethylamine) whose structural preferences are largely unknown were examined. Pyrenemethylamine exhibited an unexpected and unprecedented preference for duplex poly(dAdT).",
	collection = "nucleic acid drugs",
	doi = "10.1021/bi992070s",
	localfile = "nucleic acid drugs/1999 - Sequence and structural selectivity of nucleic acid binding ligands.pdf",
	year = 1999
}

@Article{1999-Schutz-HW,
	Author = "Martin Schütz and Georg Hetzer and {Hans-Joachim} Werner",
	Title = "{Low-order scaling local electron correlation methods. I. Linear scaling local {MP2}}",
	Journal = "J. Chem. Phys.",
	Volume = "111",
	Number = "13",
	Pages = "5691–5705",
	abstract = "A new implementation of local second-order Møller–Plesset perturbation theory (LMP2) is presented for which asymptotically all computational resources CPU, memory, and disk scale only linearly with the molecular size. This is achieved by (i) using orbital domains for each electron pair that are independent of molecular size; (ii) classifying the pairs according to a distance criterion and neglecting very distant pairs; (iii) treating distant pairs by a multipole approximation, and (iv) using efﬁcient prescreening algorithms in the integral transformation. The errors caused by the various approximations are negligible. LMP2 calculations on molecules including up to 500 correlated electrons and over 1500 basis functions in C$\_1$ symmetry are reported, all carried out on a single low-cost personal computer.",
	collection = "quantum chemistry",
	doi = "10.1063/1.479957",
	keywords = "electronic structure; algorithms",
	localfile = "quantum chemistry/1999 - Low-order scaling local electron correlation methods. I. Linear scaling local MP2.pdf",
	year = 1999
}

@Article{1999-Sevink-ZVMF,
	Author = "G. J. Agur Sevink and Andrei V. Zvelindovsky and {B. A. C. van} Vlimmeren and N. M. Maurits and Johannes G. E. M. Fraaije",
	Title = "{Dynamics of surface directed mesophase formation in block copolymer melts}",
	Journal = "J. Chem. Phys.",
	Volume = "110",
	Number = "4",
	Pages = "2250–2256",
	abstract = "The dynamic mean-ﬁeld density functional method is adapted to describe phase separation in the presence of geometrical constraints. We observe that inclusion of small ﬁller particles such as rods already has a dramatic effect on the morphology of polymer melts. The effect is comparable to the effect of applied simple steady shear. Mesostructures in the presence of large ﬁller particles such as plates are totally governed by the geometry of the particle. Effects of polymer–surface interactions on morphology formation are investigated in detail.",
	collection = "block copolymers",
	doi = "10.1063/1.477837",
	keywords = "block copolymers; nanoconfinement",
	localfile = "block copolymers/1999 - Dynamics of surface directed mesophase formation in block copolymer melts.pdf",
	year = 1999
}

@Article{1999-Simon-DD,
	Author = "Silvia Simon and Miquel Duran and Joseph J. Dannenberg",
	Title = "{Effect of basis set superposition error on the water dimer surface calculated at Hartree-Fock, Møller–Plesset, and density functional theory levels}",
	Journal = "J. Phys. Chem. A",
	Volume = "103",
	Pages = "1640–1643",
	abstract = "Counterpoise (CP) corrected optimizations of water dimer using the D95++(d,p) basis set at various levels of MP and DFT are presented. The MP2(full) calculations predict an interaction energy of -4.75 kcal/mol, close to the “MP2 limit” and to reported MP2 calculations with much large basis sets. DFT (B3PLYP) CP-corrected optimization provided the best interaction energy (-5.22 kcal/mol). The optimized O ... O separations are larger on the CP-optimized than on the uncorrected surface, as expected. These increases improve the separations predicted by DFT and worsen those predicted by the MP methods. However, the MP2 surface is so flat that the distortions of the O ... O separations needed to make the calculations agree with the experimental value require less than 0.1 kcal/mol.",
	collection = "basis set superposition",
	doi = "10.1021/jp9842188",
	keywords = "water",
	localfile = "basis set superposition/1999 - Effect of basis set superposition error on the water dimer surface calculated at HF, MP, and DFT theory levels.pdf",
	year = 1999
}

@Article{1999-Soo-HJCSM,
	Author = "Philip P. Soo and Biying Huang and Young-Il Jang and Yet-Ming Chiang and Donald R. Sadoway and Anne M. Mayes",
	Title = "{Rubbery block copolymer electrolytes for solid-state rechargeable lithium batteries}",
	Journal = "J. Electrochem. Soc.",
	Volume = "146",
	Number = "1",
	Pages = "32–37",
	collection = "block copolymer nanocomposites",
	doi = "10.1149/1.1391560",
	keywords = "block copolymers; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/1999 - Rubbery block copolymer electrolytes for solid-state rechargeable batteries.pdf",
	year = 1999
}

@Article{1999-Tang-Huang,
	Author = "{Tzyh-Chyang} Tang and {Hsuan-Jung} Huang",
	Title = "{Electrochemical Studies of the Intercalation of Ethidium Bromide to {DNA}}",
	Journal = "Electroanalysis",
	Volume = "11",
	Number = "16",
	Pages = "1185–1190",
	abstract = "Ethidium bromide in a concentration range of 5.7 {nM} to 0.7 {µM} was determined amperometrically with an electrochemically activated glassy carbon electrode. From the relationship derived for the intercalation of {EB} to {DNA} and the equilibrated concentration of free ethidium bromide determined, the binding constant of the {EB-DNA} intercalation was determined. The binding constants found agree very well with those reported in the literature. The linear relationship found for {EB-DNA} intercalation was developed as a new procedure for {DNA} analysis. With the developed method, a detection limit of 0.4 {µM} and a linear dynamic range of 0.4 to 107 {µM} for {dsDNA} analysis can be obtained optimistically.",
	collection = "nucleic acid intercalation",
	doi = "10.1002/(SICI)1521-4109(199911)11:16",
	keywords = "nucleic acid intercalation",
	localfile = "nucleic acid intercalation/1999 - Electrochemical studies of the intercalation of ethidium bromide to DNA.pdf",
	systems = "sthidium bromide",
	year = 1999
}

@Article{1999-Teague-DLO,
	Author = "Simon J. Teague and Andrew M. Davis and Paul D. Leeson and Tudor Oprea",
	Title = "{The design of leadlike combinatorial libraries}",
	Journal = "Angew. Chem. Int. Ed.",
	Volume = "38",
	Number = "24",
	Pages = "3743–3748",
	collection = "cheminformatics",
	doi = "10.1002/(SICI)1521-3773(19991216)38:24",
	keywords = "drug design",
	localfile = "cheminformatics/1999 - The design of leadlike combinatorial libraries.pdf",
	year = 1999
}

@Article{1999-Tsutsumi-FHH,
	Author = "Kiyoharu Tsutsumi and Yoshinori Funaki and Yoshitsugu Hirokawa and Takeji Hashimoto",
	Title = "{Selective incorporation of palladium nanoparticles into microphase-separated domains of poly(2-vinylpyridine)-block-polyisoprene}",
	Journal = "Langmuir",
	Volume = "15",
	Pages = "5200–5203",
	Note = "Bare Pd nanoparticles go into domains, whereas coated with the BCP go to the interface.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/la990246l",
	keywords = "block copolymers; nanoparticle distribution; nanoparticle grafts; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/1999 - Selective incorporation of palladium nanoparticles into microphase-separated domains of poly(2-vinylpyridine)-block-polyisoprene.pdf",
	methods = "TEM",
	rating = "2",
	read = "2012-03-21",
	systems = "Pd@P2VP-PI, Pd-P2VP-PI@P2VP-PI",
	year = 1999
}

@Article{1999-Vlimmeren-MZSF,
	Author = "{B. A. C. van} Vlimmeren and N. M. Maurits and Andrei V. Zvelindovsky and G. J. Agur Sevink and Johannes G. E. M. Fraaije",
	Title = "{Simulation of {3D} Mesoscale Structure Formation in Concentrated Aqueous Solution of the Triblock Polymer Surfactants {(Ethylene} {Oxide)13(Propylene} {Oxide)30(Ethylene} Oxide)13 and {(Propylene} {Oxide)19(Ethylene} {Oxide)33(Propylene} Oxide)19. Application of Dynamic {Mean-Field} Density Functional Theory}",
	Journal = "Macromolecules",
	Volume = "32",
	Number = "3",
	Pages = "646–656",
	abstract = "We simulate the microphase separation dynamics of aqueous solutions of the triblock polymer surfactants (ethylene oxide)13(propylene oxide)30(ethylene oxide)13 and (propylene oxide)19(ethylene oxide)33(propylene oxide)19 by a dynamic variant of mean-field density functional theory for Gaussian chains. This is the first {3D} mesoscale model for the dynamic behavior of specific complex polymer solutions. Different mesoscale structures (micellar, hexagonal, bicontinuous, and lamellar and dispersed coexisting phases) are formed depending on composition. The numerical results are in good agreement with experiment. The intermediate hexagonal and bicontinuous phases of (ethylene oxide)13(propylene oxide)30(ethylene oxide)13 solution retain a rich defect structure. Concentrated solution (60\%) of (propylene oxide)19(ethylene oxide)33(propylene oxide)19 shows the onset of macrophase separation, with small water droplets dispersed throughout the system. We confirm the experimental observation that the lamellar phase formation does not depend on the block sequence. Quenched from homogeneous state, the kinetics of each system consists of a fast local aggregation stage and subsequent slow rearrangement by defect annihilation. We conclude that the simulation method is a valuable tool for description of {3D} morphology formation in a wide variety of complex polymer liquids.",
	collection = "block copolymers",
	doi = "10.1021/ma980947",
	keywords = "block copolymers",
	localfile = "block copolymers/1999 - Simulation of 3D mesoscale structure formation in concentrated aqueous solution of the triblock polymer surfactants.pdf",
	methods = "DDFT",
	year = 1999
}

@Article{1999-Word-LRR,
	Author = "J. M. Word and S. C. Lovell and J. S. Richardson and D. C. Richardson",
	Title = "{Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation}",
	Journal = "J. Mol. Biol.",
	Volume = "285",
	Number = "4",
	Pages = "1735–1747",
	abstract = "Small-probe contact dot surface analysis, with all explicit hydrogen atoms added and their van der Waals contacts included, was used to choose between the two possible orientations for each of 1554 asparagine (Asn) and glutamine (Gln) side-chain amide groups in a dataset of 100 unrelated, high-quality protein crystal structures at 0.9 to 1.7 Angstrom resolution. For the movable-H groups, each connected, closed set of local H-bonds was optimized for both H-bonds and van der Waals overlaps. In addition to the Asn/Gln “flips”, this process included rotation of OH, SH, NH3+ and methionine methyl II atoms, flip and protonation state of histidine rings, interaction with bound ligands, and a simple model of water interactions. However, except for switching N and O identity for amide flips (or N and C identity for His flips), no non-H atoms were shifted. Even in these very high-quality structures, about 20\% of the Asn/Gln side-chains required a 180 degrees flip to optimize H-bonding and/or to avoid NH2 clashes with neighboring atoms (incorporating a conservative score penalty which, for marginal cases, favors the assignment in the original coordinate file). The programs Reduce, Probe, and Mage provide not only a suggested amide orientation, but also a numerical score comparison, a categorization of the marginal cases, and a direct visualization of all relevant interactions in both orientations. Visual examination allowed confirmation of the raw score assignment for about 40\% of those Asn/Gln flips placed within the “marginal” penalty range by the automated algorithm, while uncovering only a small number of cases whose automated assignment was incorrect because of special circumstances not yet handled by the algorithm. It seems that the H-bond and the atomic-clash criteria independently look at the same structural realities: when both criteria gave a clear answer they agreed every time. But consideration of van der Waals clashes settled many additional cases for which H-bonding was either absent or approximately equivalent for the two main alternatives. With this extra information, 86\% of all side-chain amide groups could be oriented quite unambiguously. In the absence of further experimental data, it would probably be inappropriate to assign many more than this. Some of the remaining 14\% are ambiguous because of coordinate error or inadequacy of the theoretical model, but the great majority of ambiguous cases probably occur as a dynamic mix of both flip states in the actual protein molecule. The software and the 100 coordinate files with all H atoms added and optimized and with amide flips corrected are publicly available.",
	cited = "67 (2005-05-05)",
	collection = "cheminformatics",
	localfile = "cheminformatics/1999 - Using hydrogen atom contacts in the choice of side-chain amide orientation.pdf",
	year = 1999
}

@Article{1999-Yeung-Shi,
	Author = "Chuck Yeung and An-Chang Shi",
	Title = "{Formation of interfaces in incompatible polymer blends: a dynamical mean field study}",
	Journal = "Macromolecules",
	Volume = "32",
	Pages = "3637–3642",
	abstract = "The interdiffusion dynamics of a polymer interface towards its equilibrium profile is studied using a dynamical mean field method, in which the nonequilibrium chemical potentials are evaluated numerically using the full polymer mean field free energy. Our results demonstrated that the interfacial width grows as t1/4 at early times and saturates to the equilibrium thickness at long times, in agreement with previous, more approximate analysis based on Cahn-Hilliard-type theories. Furthermore, we show that the dynamical exponent can only be obtained unequivocally via a scaling analysis. The interdiffusion of a polymer interface in the single phase regime is also studied.",
	collection = "polymers",
	doi = "10.1021/ma981648n",
	localfile = "polymers/1999 - Formation of interfaces in incompatible polymer blends: a dynamical mean field study.pdf",
	year = 1999
}

@Article{2000-Alexandre-Dubois,
	Author = "Michael Alexandre and Philippe Dubois",
	Title = "{Polymer-layered silicate nanocomposites: preparation, properties and uses of a new class of materials}",
	Journal = "Materials Science and Engineering: R: Reports",
	Volume = "28",
	Number = "1-2",
	Pages = "1–63",
	abstract = "This review aims at reporting on very recent developments in syntheses, properties and (future) applications of polymer-layered silicate nanocomposites. This new type of materials, based on smectite clays usually rendered hydrophobic through ionic exchange of the sodium interlayer cation with an onium cation, may be prepared via various synthetic routes comprising exfoliation adsorption, in situ intercalative polymerization and melt intercalation. The whole range of polymer matrices is covered, i.e. thermoplastics, thermosets and elastomers. Two types of structure may be obtained, namely intercalated nanocomposites where the polymer chains are sandwiched in between silicate layers and exfoliated nanocomposites where the separated, individual silicate layers are more or less uniformly dispersed in the polymer matrix. This new family of materials exhibits enhanced properties at very low filler level, usually inferior to 5 wt.\%, such as increased Young's modulus and storage modulus, increase in thermal stability and gas barrier properties and good flame retardancy.",
	collection = "polymer nanocomposites",
	doi = "10.1016/S0927-796X(00)00012-7",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2000 - Polymer-layered silicate nanocomposites: preparation, properties and uses of a new class of materials.pdf",
	year = 2000
}

@Article{2000-Bader,
	Author = "Richard F. W. Bader",
	Title = "{Atomic force microscope as an open system and the Ehrenfest force}",
	Journal = "Phys. Rev. B",
	Volume = "61",
	Number = "11",
	Pages = "7795",
	abstract = "Two systems in contact, such as the tip of an atomic force microscope {(AFM)} and a sample, share a common surface. Each exerts an equal and opposite force on the other determined by the pressure it exerts on every element of the surface of separation, as required by the physics of an open system. In a quantum system, the force exerted on the tip is the Ehrenfest force, a force that is balanced by the pressure exerted on every element of its surface, as determined by the quantum stress tensor. The surface separating the tip from the sample is one of local zero flux in the gradient vector field of the electron density, the surface that separates two neighboring atoms. A zero-flux surface also defines a proper open system, one whose observables are governed by the equations of motion, the equation for the electronic momentum yielding the Ehrenfest force theorem. Thus the force measured in the {AFM} is exerted on a surface determined by the boundaries separating the atoms in the tip from those in the sample, and its response is a consequence of the atomic form of matter. This approach to the determination of the force measured in the {AFM} is contrasted with results reported in the literature that equate it to the {Hellmann-Feyman} forces exerted on the nuclei of the atoms in the tip.",
	collection = "quantum physics",
	doi = "10.1103/PhysRevB.61.7795",
	localfile = "quantum physics/2000 - Atomic force microscope as an open system and the Ehrenfest force.pdf",
	year = 2000
}

@Article{2000-Bader-BH,
	Author = "Richard F. W. Bader and David Bayles and G. L. Heard",
	Title = "{Properties of atoms in molecules: Transition probabilities}",
	Journal = "J. Chem. Phys.",
	Volume = "112",
	Number = "23",
	Pages = "10095–10105",
	abstract = "The transition probability for electric dipole transitions is a measurable property of a system and is therefore, partitionable into atomic contributions using the physics of a proper open system. The derivation of the dressed property density, whose averaging over an atomic basin yields the atomic contribution to a given oscillator strength, is achieved through the development of perturbation theory for an open system. A dressed density describes the local contribution resulting from the interaction of a single electron at some position r, as determined by the relevant observable, averaged over the motions of all of the remaining particles in the system. In the present work, the transition probability density expressed in terms of the relevant transition density, yields a local measure of the associated oscillator strength resulting from the interaction of the entire molecule with a radiation ﬁeld. The deﬁnition of the atomic contributions to the oscillator strength enables one to determine the extent to which a given electronic or vibrational transition is spatially localized to a given atom or functional group. The concepts introduced in this article are applied to the Rydberg-type transitions observed in the electronic excitation of a nonbonding electron in formaldehyde and ammonia. The atomic partitioning of the molecular density distribution and of the molecular properties by surfaces of zero ﬂux in the gradient vector ﬁeld of the electron density, the boundary condition deﬁning the physics of a proper open system, is found to apply to the density distributions of the excited, Rydberg states.",
	collection = "molecular fragmentation",
	doi = "10.1063/1.481651",
	localfile = "molecular fragmentation/2000 - Properties of atoms in molecules: transition probabilities.pdf",
	shorttitle = "Properties of atoms in molecules",
	year = 2000
}

@Article{2000-Bader-Bayles,
	Author = "Richard F. W. Bader and David Bayles",
	Title = "{Properties of Atoms in Molecules: Group Additivity}",
	Journal = "J. Phys. Chem. A",
	Volume = "104",
	Number = "23",
	Pages = "5579–5589",
	abstract = "Every property of a molecule is given by the sum of the contributions from each of its constituent atoms or groups, the groups being defined as proper open systems. The observation of “experimental group additivty” requires that in addition to the properties of the groups being additive, the group and its properties be transferable from one molecule to another, different molecule. It is shown that such transferability of a group and its properties is in general, only apparent, being the result of compensatory transferability wherein the changes in the properties of one group are compensated for by equal but opposite changes in the properties of the adjoining group. These compensating changes are in some cases vanishingly small, but even when the energy changes are in excess of 20 kcal/mol, the experimental heat of formation is still predicted to be additive to within 0.1 kcal/mol. The operation of compensatory transferability is illustrated for the linear homologous series of hydrocarbons and polysilanes and for the formation of pyridine from fragments of benzene and pyrazine. The properties considered are the energy and the delocalization of the electrons, the former determined by the one-electron density matrix and the latter by the pair density. It is shown that the transferability of the degree of localization of the electrons to a given group, a property of the pair density, is a result of the conservation of the delocalization of its electrons over the remaining groups in the molecule. The results presented here emphasize the important observation that all the properties of a proper open systemsa functional groupswhether determined by the first-order density matrix, the pair density, or field-induced charge and current densities, are all functionally related to its form in real space, that is, to its distribution of charge.",
	collection = "molecular fragmentation",
	doi = "10.1021/jp9943631",
	localfile = "molecular fragmentation/2000 - Properties of atoms in molecules: group additivity.pdf",
	shorttitle = "Properties of Atoms in Molecules",
	year = 2000
}

@Article{2000-Bailly-LDL,
	Author = "Christian Bailly and William Laine and Martine Demeunynck and Jean Lhomme",
	Title = "{Enantiospecific Recognition of DNA Sequences by a Proflavine Troger Base}",
	Journal = "Biochem. Biophys. Res. Commun.",
	Volume = "273",
	Number = "2",
	Pages = "681–685",
	abstract = "The DNA interaction of a chiral Troger base derived from proflavine was investigated by DNA melting temperature measurements and complementary biochemical assays. DNase I footprinting experiments demonstrate that the binding of the proflavine-based Troger base is both enantio- and sequence-specific. The (+)-isomer poorly interacts with DNA in a non-sequence-selective fashion. In sharp contrast, the corresponding (-)-isomer recognizes preferentially certain DNA sequences containing both A..T and G..C base pairs, such as the motifs 5'-GTT..AAC and 5'-ATGA..TCAT. This is the first experimental demonstration that acridine-type Tr�ger bases can be used for enantiospecific recognition of DNA sequences.",
	collection = "nucleic acid intercalation",
	doi = "10.1006/bbrc.2000.2997",
	localfile = "nucleic acid intercalation/2000 - Enantiospecific recognition of DNA sequences by a proflavine Troger base.pdf",
	year = 2000
}

@Article{2000-Balazs-GQPJ,
	Author = "Anna C. Balazs and Valeriy V. Ginzburg and Feng Qiu and Gongwen Peng and David Jasnow",
	Title = "{Multi-scale model for binary mixtures containing nanoscopic particles}",
	Journal = "J. Phys. Chem. B",
	Volume = "104",
	Pages = "3411–3422",
	abstract = "We develop a computer simulation for the dynamic behavior of a phase-separating binary mixture that contains mobile, solid particles. The system models “filled polymers”, which contain not only a blend of different macromolecules, but also solid fillers. We focus on the case where one of the components preferentially wets the surface of the particles. By combining a mesoscopic, coarse-grained description of the fluids with a discrete model for the particles, we show that the addition of hard particles significantly changes both the speed and the morphology of the phase separation. To probe the late-stage properties of the system, we also develop a mean-field rate-equation model for the mixture. The results indicate that the phase separation is arrested in the late stage; the “steady-state” domain size depends strongly on both the particle diffusion constant and the particle concentration. To obtain insight into the effects of processing on the properties of such composites, we also investigated the behavior of the binary fluid/particle mixture under shear. For sufficiently large particle densities, we find that the anisotropic growth caused by the imposed shear is destroyed by the randomly moving particles, and the domains are isotropic in shape even for large shear strains. Finally, we apply our models to mixtures of diblock copolymers and fillers. Overall, our findings reveal how the solid additives can be used to tailor the morphology of the complex mixture, and thereby control the macroscopic properties (such as mechanical integrity) of the composite.",
	collection = "polymer nanocomposites",
	doi = "10.1021/jp993356",
	keywords = "mesophase transitions; nanospheres",
	localfile = "block copolymer nanocomposites/2000 - Multi-scale model for binary mixtures containing nanoscopic particles.pdf",
	year = 2000
}

@Article{2000-Blackburn,
	Author = "Elizabeth H. Blackburn",
	Title = "{Telomere states and cell fates}",
	Journal = "Nature",
	Volume = "408",
	Number = "6808",
	Pages = "53–56",
	abstract = "Telomere length has frequently been used as a means to predict the future life of cells. But by itself it can be a poor indicator of ageing or cell viability. What, then, is the important property of a telomere? Here recent ﬁndings are integrated into a new, probabilistic view of the telomere to explain how and when it can signal not only its own fate but also that of a cell.",
	collection = "cells",
	doi = "10.1038/35040500",
	localfile = "cells/2000 - Telomere states and cell fates.pdf",
	year = 2000
}

@Article{2000-Bondarev-SV,
	Author = "Dmitry A. Bondarev and William J. Skawinski and Carol A. Venanzi",
	Title = "{Nature of Intercalator {Amiloride−Nucelobase} Stacking. An Empirical Potential and ab Initio Electron Correlation Study}",
	Journal = "J. Phys. Chem. B",
	Volume = "104",
	Number = "4",
	Pages = "815–822",
	abstract = "A rigid-body systematic search technique was applied to stacked complexes of the novel {AT-specific} intercalator, amiloride, with each of the four {DNA} bases {(A,} T, C, G) and two {WatsonCrick} base pairs {(AT} and {GC).} Gas-phase calculations were carried out using the Cornell empirical molecular potential with a set of ab initio-optimized atomic charges. At selected points on the ligandnucleobase potential energy surface, empirical intermolecular interaction energy values were found to be in good agreement with the ab initio {MP2/6-31++G(d,p)} energies corrected for basis set superposition errors. This result supports the application of the systematic search technique to larger model systems. The general features of the amiloridebase and amiloridebase pair intermolecular potential energy surfaces were found to be different in the case of adenine and thymine compared to guanine and cytosine, resulting in more orientational and translational freedom for amiloride in the former case. In addition, the interaction of amiloride with adenine and thymine nucleobases is significantly more dispersion-controlled than that with guanine and cytosine, where the electrostatic energy contributes up to a third of the total intermolecular energy. Amiloride in the base pair complexes is overlapped with guanine and adenine. Thymine and cytosine are exposed, and the interaction of the ligand with the pyrimidine nucleobases appears to be exclusively due to electrostatic forces.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/jp9926140",
	localfile = "nucleic acid intercalation/2000 - Nature of intercalator amiloride-nucleobase stacking. An empirical potential and ab initio electron correlation study.pdf",
	year = 2000
}

@Article{2000-Bruice-Benkovic,
	Author = "Thomas C. Bruice and Stephen J. Benkovic",
	Title = "{Chemical basis for enzyme catalysis}",
	Journal = "Biochemistry",
	Volume = "39",
	Number = "21",
	Pages = "6267–6274",
	abstract = "(Excerpt) Some half-century ago Pauling proposed that the lowering of the activation energy in enzyme catalysis stems from the enzyme’s affinity for the transition state exceeding it’s affinity for the substrate. This proposal has great popular appeal and has served as the basis for the design of transition state based inhibitors and for inducing catalytic activity in various molecular templates. Recent investigations, however, have brought into focus the contributions of thermal motions and ground state conformers associated with the Michaelis complex to the rate of enzymatic reactions. A description and analysis of the enzyme-substrate complex characteristics are a focus of this review.",
	collection = "enzymes",
	doi = "10.1021/bi0003689",
	localfile = "enzymes/2000 - Chemical basis for enzyme catalysis.pdf",
	year = 2000
}

@Article{2000-Caseri,
	Author = "Walter Caseri",
	Title = "{Nanocomposites of polymers and metals or semiconductors: historical background and optical properties}",
	Journal = "Macromol. Rapid Commun.",
	Volume = "21",
	Number = "11",
	Pages = "705–722",
	abstract = "(Excerpt) This article deals with composites comprising of polymers and metal or semiconductor particles with average diameters below 50 – 100 nm (nanoparticles, nanosized particles).",
	collection = "polymer nanocomposites",
	doi = "10.1002/1521-3927(20000701)21:11",
	keywords = "optical properties",
	localfile = "polymer nanocomposites/2000 - Nanocomposites of polymers and metals or semiconductors: historical background and optical properties.pdf",
	year = 2000
}

@Article{2000-Chalasinski-Szczesniak,
	Author = "Grzegorz Chałasiński and Małgorzata M. Szczęśniak",
	Title = "{State of the art and challenges of the ab initio theory of intermolecular interactions}",
	Journal = "Chem. Rev.",
	Volume = "100",
	Number = "11",
	Pages = "4227 – 4252",
	abstract = "The past decade has seen explosive growth in experimental and theoretical studies of van der Waals interactions. Considerable progress has been achieved toward understanding the nature of these interactions at the fundamental level. Ab initio theory has played a central role in this progress. The earlier applications of ab initio techniques to this problem concentrated primarily on the qualitative understanding of these interactions. These applications greatly benefited from the partitioning of interaction energy into its fundamental components, such as electrostatic, exchange, induction, and dispersion. The analyses of a large number of model complexes helped to identify the origins of binding and the sources of anisotropy of these interactions. A detailed examination of the interaction energy components and their computational requirements shed new light on the question of how to saturate the basis-set and the correlation effects. Progress in computational capabilities enabled the use of sufficiently large basis sets and highly correlated methods. With the background of these advances, the ab initio theory of intermolecular interactions entered a new quantitative phase. The progress in the accurate predictions of potential-energy surfaces for these interactions has been matched by new treatments of multidimensional fully coupled vibration dynamics, thereby establishing a direct connection to experimental observations.",
	collection = "molecular interactions",
	doi = "10.1021/cr990048z",
	localfile = "molecular interactions/2000 - State of the art and challanges of the ab initio theory of intermolecular interactions.pdf",
	year = 2000
}

@Article{2000-Chen-TT,
	Author = "Wei Chen and Nicholas J. Turro and Donald A. Tomalia",
	Title = "{Using Ethidium Bromide To Probe the Interactions between {DNA} and Dendrimers†}",
	Journal = "Langmuir",
	Volume = "16",
	Number = "1",
	Pages = "15–19",
	abstract = "Investigations have been carried out to probe the interactions between double-stranded {DNA} and amine-terminated, ethylenediamine core polyamidoamine starburst dendrimers generation 2 {(G2),} generation 4 {(G4),} and generation 7 {(G7).} Ethidium bromide is used as a fluorescent probe for this study. Under our experimental conditions, the results show that there is mainly one binding mode between ethidium and {DNAdendrimer} complexes and that dendrimers bind to {DNA} sufficiently strongly that they cannot be displaced by ethidium. In the proposed binding model for {DNAdendrimer} complexes, the {DNA} wraps around G7 dendrimers while the wrapping of {DNA} does not occur for G2 and G4 dendrimers. {DNAdendrimer} interactions display little preference on {DNA} base components. The influence of {pH} and ionic strength is in agreement with electrostatic interactions as the major binding force for {DNAdendrimer} complexes.",
	collection = "nucleic acids",
	doi = "10.1021/la981429v",
	keywords = "dendrimers",
	localfile = "nucleic acids/2000 - Using ethidium bromide to probe the interactions between DNA and dendrimers.pdf",
	year = 2000
}

@Article{2000-Ginzburg-GQPB,
	Author = "Valeriy V. Ginzburg and Corey Gibbons and Feng Qiu and Gongwen Peng and Anna C. Balazs",
	Title = "{Modeling the dynamic behavior of diblock copolymer/particle composites}",
	Journal = "Macromolecules",
	Volume = "33",
	Pages = "6140–6147",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma991065t",
	keywords = "mesophase transitions; nanospheres",
	localfile = "block copolymer nanocomposites/2000 - Modeling the dynamic behavior of diblock copolymer-particle composites.pdf",
	methods = "CDS/BD",
	year = 2000
}

@Article{2000-Ginzburg-SB,
	Author = "Valeriy V. Ginzburg and Chandralekha Singh and Anna C. Balazs",
	Title = "{Theoretical phase diagrams of polymer/clay composites: the role of grafted organic modifiers}",
	Journal = "Macromolecules",
	Volume = "33",
	Pages = "1089–1099",
	abstract = "We combine a density functional theory (DFT) with a self-consistent field model (SCF) to calculate the phase behavior of thin, oblate colloidal particles that are coated with surfactants and dispersed in a polymer melt. These coated particles represent organically modified clay sheets. By integrating the two methods, we can investigate the effect of the surfactants’ characteristics (grafting density Fgr and length Ngr) and the polymer-surfactant interaction energy on the polymer-clay phase diagram. Depending on the values of these critical parameters and the clay volume fraction, φ, the system can be in an isotropic or nematic phase (which corresponds to an exfoliated composite). The system can also form a smectic, crystal, columnar, or “house-of-cards” plastic solid, as well as a two-phase (immiscible) mixture. Using this model, we isolate conditions that lead to the stabilization of the homogeneous, exfoliated phases (the isotropic and nematic regions) and to the narrowing of the immiscible two-phase regions.",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma991324e",
	localfile = "polymer nanocomposites/2000 - Theoretical phase diagrams of polymer-clay composites: the role of grafted organic modifiers.pdf",
	year = 2000
}

@Article{2000-Graves-Velea,
	Author = "David E. Graves and L. M. Velea",
	Title = "{Intercalative binding of small molecules to nucleic acids}",
	Journal = "Curr. Org. Chem.",
	Volume = "4",
	Number = "9",
	Pages = "915–929",
	abstract = "The interactions of small molecules with nucleic acids have provoked considerable interest in the field of anticancer drug design over the past three decades; however, critical information linking the physical-chemical properties associated with these complexes with their biological effectiveness remains unclear. Significant progress has been made towards unraveling the structural and dynamic properties of many ligand-DNA complexes which has provided pivotal insight into the design and development of more effective second and third generation chemotherapeutic agents for the successful treatment of many types of cancer. Interactions of ligands with DNA are studied by a variety of physical and biochemical methods in an effort to determine the chemical and physical basis of novel binding phenomena such as DNA base sequence selectivity, correlation of structure-activity relationships, linkages between the geometry and thermodynamic properties describing drug-DNA complexes, and influences of substituent modifications on the physical, chemical, and biological properties of the drug-DNA complex.",
	collection = "nucleic acid intercalation",
	doi = "10.2174/1385272003375978",
	keywords = "nucleic acids; intercalation",
	localfile = "nucleic acid intercalation/2000 - Intercalative binding of small molecules to nucleic acids.pdf",
	year = 2000
}

@Article{2000-Guckian-SRSTK,
	Author = "Kevin M. Guckian and Barbara A. Schweitzer and Rex X.-F. Ren and Charles J. Sheils and Deborah C. Tahmassebi and Eric T. Kool",
	Title = "{Factors contributing to aromatic stacking in water: evaluation in the context of {DNA}}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "122",
	Number = "10",
	Pages = "2213–2222",
	abstract = "We report the use of thermodynamic measurements in a self-complementary DNA duplex (5'-dXCGCGCG)(2), where X is an unpaired natural or nonnatural deoxynucleoside, to study the forces that stabilize aqueous aromatic stacking in the context of DNA. Thermal denaturation experiments show that the core duplex (lacking X) is formed with a free energy (37 degrees C) of -8.1 kcal mol(-1) in a pH 7.0 buffer containing 1 M Na+ We studied the effects of adding single dangling nucleosides (X) where the aromatic “base” is adenine, guanine, thymine, cytosine, pyrrole, benzene, 4-methylindole, 5-nitroindole, trimethylbenzene, difluorotoluene, naphthalene, phenanthrene, and pyrene. Adding these dangling residues is found to stabilize the duplex by an additional -0.8 to -3.4 kcal mol(-1). At 5 mu M DNA concentration, T-m values range from 41.7 degrees C (core sequence) to 64.1 degrees C (with dangling pyrene residues). For the four natural bases, the order of stacking ability is A > G greater than or equal to T = C. The nonpolar analogues stack more strongly in general than the more polar natural bases. The stacking geometry was confirmed in two cases (X = adenine and pyrene) by 2-D NOESY experiments. Also studied is the effect of ethanol cosolvent on the stacking of natural bases and pyrene. Stacking abilities were compared to calculated values for hydrophobicity, dipole moment, polarizability, and surface area. In general, hydrophobic effects are found to be larger than other effects stabilizing stacking (electrostatic effects, dispersion forces); however, the natural DNA bases are found to be less dependent on hydrophobic effects than are the more nonpolar compounds. The results also point out strategies for the design nucleoside analogues that stack considerably more strongly than the natural bases; such compounds may be useful in stabilizing designed DNA structures and complexes.",
	collection = "stacking",
	doi = "10.1021/ja9934854",
	localfile = "molecular stacking/2000 - Factors contributing to aromatic stacking in water: evaluation in the context of DNA.pdf",
	year = 2000
}

@Article{2000-Hamza-VHM,
	Author = "A. Hamza and Á. Vibók and G. J. Halász and Istvan Mayer",
	Title = "{BSSE-free SCF theories: a comment}",
	Journal = "J. Mol. Struct.: {THEOCHEM}",
	Volume = "501",
	Pages = "427–434",
	abstract = "Some aspects of creating the basis set superposition error (BSSE) problem at the SCF level are briefly discussed. It is stressed that - contrary to the recurring propositions in the literature - the BSSE-problem cannot be properly handled by restricting each molecular orbital to be expanded in the basis of only one of the monomers, because this also excludes the physically important, true charge-transfer effects. The discussion is illustrated by some calculations performed for water dimer and for two pairs of nucleic bases (thymine-adenine and uracil-adenine) which are compared with those in the recent paper of Gianinetti et al. [E. Gianinetti, M. Raimondi, E. Tornaghi, Int. J. Quant. Chem. 60 (1996) 157]. (C) 2000 Elsevier Science B.V. All rights reserved. C1 Lajos Kossuth Univ, Inst Theoret Phys, H-4010 Debrecen, Hungary. Lajos Kossuth Univ, Inst Math \& Informat, H-4010 Debrecen, Hungary. Hungarian Acad Sci, Chem Res Ctr, Inst Chem, H-1525 Budapest, Hungary.",
	collection = "basis set superposition",
	doi = "10.1016/S0166-1280(99)00454-6",
	localfile = "basis set superposition/2000 - BSSE-free SCF theories: a comment.pdf",
	year = 2000
}

@Article{2000-Haq-Ladbury,
	Author = "Ihtshamul Haq and John Ladbury",
	Title = "{Drug-{DNA} recognition: energetics and implications for design}",
	Journal = "J. Mol. Recognit.",
	Volume = "13",
	Number = "4",
	Pages = "188 – 197",
	abstract = "In this article we review thermodynamic studies designed to examine the interaction of low molecular weight ligands or drugs with DNA. Over the past 10 years there has been an increase in the number of rigorous biophysical studies of DNA-drug interactions and considerable insight has been gained into the energetics of these binding reactions. The advent of high-sensitivity calorimetric techniques has meant that the energetics of DNA-drug association reactions can be probed directly and enthalpic and entropic contributions to the binding free energy established, There are two principal consequences arising from this type of work, firstly three-dimensional structures of DNA-drug complexes from X-ray and NMR studies can be put into a thermodynamic context and the energetics responsible for stabilizing the observed structures can be more fully understood. Secondly, any rational approach to structure-based drug design requires a fundamental base of knowledge where structural detail and thermodynamic data on complex formation are intimately linked. Therefore these types of studies allow a set of general guidelines to be established, which can then be used to develop drug design algorithms. In this review we describe recent breakthroughs in duplex DNA-directed drug design and also discuss how similar principles are now being used to target higher-order DNA molecules, for example, tripler (three-stranded) and tetraplex (four-stranded) structures. Copyright (C) 2000 John Wiley \& Sons, Ltd.",
	collection = "nucleic acid drugs",
	doi = "10.1002/1099-1352(200007",
	localfile = "nucleic acid drugs/2000 - Drug-DNA recognition: energetics and implications for design.pdf",
	year = 2000
}

@Article{2000-Hernandez-Trujillo-Bader,
	Author = "Jesús Hernández-Trujillo and Richard F. W. Bader",
	Title = "{Properties of Atoms in Molecules: Atoms Forming Molecules}",
	Journal = "J. Phys. Chem. A",
	Volume = "104",
	Number = "8",
	Pages = "1779–1794",
	abstract = "This paper studies the evolution of the electron densities of two separated atoms into an equilibrium molecular distribution. A range of interactions is considered: from closed-shell with and without charge transfer, through polar-shared, to equally shared interactions. The changes in the density are monitored in terms of the properties of the density at the bond critical point and the shape of the interatomic surface. The effect of these changes on the properties of the atoms defined as proper open systems is determined. The harpoon mechanism operative in the formation of {LiF} is found to exert dramatic effects on the electron density and on the atomic and molecular properties. The virial and the Ehrenfest force theorems in their molecular, atomic, and local forms, together with the {HellmannFeynman} theorem, provide an understanding of the similarities and differences in the bonding resulting from closed-shell, shared, and polar interactions. The effect of the long-range dispersion forces on the electron density and the resulting changes in the kinetic and potential energies, the former decreasing and the latter increasing on the initial approach of the atoms, are investigated. In addition to the changes in the total energy and its kinetic and potential energy components as a function of the internuclear separation R, the atomic contributions to these quantities are also reported. The atomic Ehrenfest force is the force acting on the electron density in an atomic basin and the one measured in an atomic force microscope. It is shown to change from an intially attractive interaction, to a repulsive one at a separation slightly greater than Re where the {HellmannFeynman} forces on the nuclei vanish.",
	collection = "molecular fragmentation",
	doi = "10.1021/jp994096z",
	localfile = "molecular fragmentation/2000 - Properties of atoms in molecules: atoms forming molecules.pdf",
	methods = "QTAIM",
	shorttitle = "Properties of Atoms in Molecules",
	year = 2000
}

@Article{2000-Hodges-Stone,
	Author = "Matthew P. Hodges and Anthony J. Stone",
	Title = "{A new representation of the dispersion interaction}",
	Journal = "Mol. Phys.",
	Volume = "98",
	Number = "5",
	Pages = "275–286",
	abstract = "The conventional formulation of the dispersion energy as a power series in R$^{-1}$ with damping at small R is re-examined. Symmetry-adapted and intermolecular perturbation theory calculations have been performed and compared for the argon dimer. We show that conventional Tang-Toennies damping functions t the data better when exchange as well as charge-overlap effcts are included. We also construct a new representation of the dispersion energy which provides a more accurate, but still quite compact, description of the dispersion energy, and suggest several simpler forms which would be suitable for describing dispersion more accurately in larger systems. Some preliminary results for the HF dimer are also described.",
	collection = "molecular interactions",
	doi = "10.1080/00268970009483291",
	localfile = "molecular interactions/2000 - A new representation of the dispersion interaction.pdf",
	year = 2000
}

@Article{2000-Hodges-Wheatley,
	Author = "Matthew P. Hodges and Richard J. Wheatley",
	Title = "{Flexible multipole models for hydrogen fluoride}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "2",
	Number = "8",
	Pages = "1631–1638",
	abstract = "We use the distributed multipole analysis method to analyse the charge density of the hydrogen fluoride molecule, including variation of the {HF} bond length, and taking into consideration the level of theory, the basis set, and the number of sites used. We also examine the effects of truncating the dimer electrostatic interactions at charge-charge, quadrupole-quadrupole and all interactions up to r-5 dependence in the intermolecular site-site separations. We assess the accuracy of these approximations using both the calculated multipoles and multipoles described by polynomial functions of the bond stretching coordinate. We consider two ranges of the {HF} bond length, one of which should be suitable for calculations of structures and energetics of hydrogen fluoride clusters, and the other for dynamical calculations on the same systems.",
	collection = "molecular electrostatics",
	doi = "10.1039/a910293k",
	localfile = "molecular electrostatics/2000 - Flexible multipole models for hydrogen fluoride.pdf",
	year = 2000
}

@Article{2000-Huh-GB,
	Author = "June Huh and Valeriy V. Ginzburg and Anna C. Balazs",
	Title = "{Thermodynamic behavior of particle/diblock copolymer mixtures: simulation and theory}",
	Journal = "Macromolecules",
	Volume = "33",
	Pages = "8085–8096",
	Note = "Contains phase diagrams as a function of particle size and concentration, and describes new ordered structures for particles comparable to polymer radius of gyration.",
	abstract = "We investigate the influence of hard nanoparticles on the phase behavior of diblock copolymers. Using Monte Carlo simulations, we obtain phase diagrams as a function of the nanoparticle size and concentration. When the size of the nanoparticles becomes comparable to the radius of gyration of the minority (A) block, we observe the formation of new superstructures, where the particles self-assemble inside the copolymer micelles. We develop a theoretical model, based on the strong segregation limit approximation, and show that these self-assembled structures can be either stable or metastable, depending on the particle size and volume fraction. The formation of such phases is due to the interplay between the particle-particle excluded-volume interactions, preferential particle/block-A interactions, and the enthalpic and stretching interactions within the diblock.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma000708y",
	keywords = "mesophase transitions; nanoparticle distribution; nanospheres",
	localfile = "block copolymer nanocomposites/2000 - Thermodynamic behavior of particle-diblock copolymer mixtures: simualation and theory.pdf",
	methods = "SST, MC",
	rating = "2",
	year = 2000
}

@Article{2000-Huinink-BDS,
	Author = "H. P. Huinink and J. C. M. {Brokken-Zijp} and {M. A. van} Dijk and G. J. Agur Sevink",
	Title = "{Asymmetric block copolymers confined in a thin film}",
	Journal = "J. Chem. Phys.",
	Volume = "112",
	Number = "5",
	Pages = "2452–2462",
	abstract = "We have used a dynamic density functional theory DDFT for polymeric systems, to simulate the formation of micro phases in a melt of an asymmetric block copolymer, A n B m ( f A 1/3), both in the bulk and in a thin ﬁlm. In the DDFT model a polymer is represented as a chain of springs and beads. A spring mimics the stretching behavior of a chain fragment and the spring constant is calculated with the Gaussian chain approximation. Simulations were always started from a homogeneous system. We have mainly investigated the ﬁnal morphology, adopted by the system. First, we have studied the bulk behavior. The diblock copolymer forms a hexagonal packed array of A-rich cylinders, embedded in a B-rich matrix. Film calculations have been done by conﬁning a polymer melt in a slit. Both the slit width and surface-polymer interactions were varied. With the outcomes a phase diagram for conﬁned ﬁlms has been constructed. Various phases are predicted: parallel cylinders (C ), perpendicular cylinders (C ), parallel lamellae (L ), and parallel perforated lamellae (CL ). When the ﬁlm surfaces are preferentially wet by either the A or the B block, parallel oriented microdomains are preferred. A perpendicular cylindrical phase is stable when neither the A nor B block preferentially wets the surfaces. The predicted phase diagram is in accordance with experimental data in the literature and explains the experimentally observed differences between ﬁlms of asymmetric block copolymers with only two parameters: the ﬁlm thickness and the energetic preference of the surface for one of the polymer blocks. We have also observed, that conﬁnement speeds up the process of long range ordering of the microdomains",
	collection = "block copolymers",
	doi = "10.1063/1.480811",
	keywords = "block copolymers; thin films",
	localfile = "block copolymers/2000 - Asymmetric block copolymers confined in a thin film.pdf",
	year = 2000
}

@Article{2000-Ioannides-GBB,
	Author = "Demetris Ioannides and Brian D. Golden and Jill P. Buyon and Jean-Claude Bystryn",
	Title = "{Expression of SS-A/Ro and SS-B/La antigens in skin biopsy specimens of patients with photosensitive forms of lupus erythematosus}",
	Journal = "Arch. Dermatol.",
	Volume = "136",
	Number = "3",
	Pages = "340–346",
	collection = "cells",
	localfile = "cells/2000 - Expression of SS-A-Ro and SS-B-La antigens in skin biopsy specimens of patients with photosensitive forms of lupus erythematosus.pdf",
	year = 2000
}

@Article{2000-Jansen,
	Author = "Georg Jansen",
	Title = "{Convergence of multipole expanded intermolecular interaction energies for Gaussian-type-function and Slater-type-function basis sets}",
	Journal = "Theor. Chem. Acc.",
	Volume = "104",
	Pages = "499–506",
	collection = "molecular electrostatics",
	doi = "10.1007/s002140000178",
	localfile = "molecular electrostatics/2000 - Convergence of multipole expanded intermolecular interaction energies for Gaussian-type-function and Slater-type-function basis sets.pdf",
	year = 2000
}

@Article{2000-Jenkins,
	Author = "Terence C. Jenkins",
	Title = "{Targeting multi-stranded {DNA} structures}",
	Journal = "Curr. Med. Chem.",
	Volume = "7",
	Number = "1",
	Pages = "99 – 115",
	abstract = "The design of agents targeted toward a structure-specific molecular recognition of DNA triplexes or tetraplexes (“quadruplexes”) is discussed, where such structures are relevant to antigene-based chemotherapies and the in situ cellular inhibition of telomerase function, respectively. Using principles that stem from the development of earlier synthetic duplex-binding ligands, together with recent findings that probe structure-thermodynamic linkages and kinetic features of stability, a rational approach is developed to exploit the distinct molecular templates offered by these high-order nucleic acid biotarget systems. Such analytical techniques can usefully augment conventional drug design methods, particularly where detailed structural information is unavailable or the mode of binding to form a persistent DNA biotarget-ligand complex is not established. Examples from the author's laboratory are used to illustrate structure-specific (or structure-preferential) recognition and subsequent stabilization of DNA triplexes using intercalative or groove-mediated binding mechanisms, and the successful targeting of DNA tetraplexes using planar extended-aromatic ligands. in each case, chemical manipulation of the molecule by exploiting either (i) geometric isomers, (ii) redistribution of charged groups and/or H-bond donors/acceptors, or (iii) optimization of intermolecular pi-overlap can be used to improve the affinity or specificity of the underlying DNA-drug binding events.",
	collection = "nucleic acid drugs",
	doi = "10.2174/0929867003375551",
	localfile = "nucleic acid drugs/2000 - Targeting multi-stranded DNA structures.pdf",
	year = 2000
}

@Article{2000-Jeziorska-JSJ,
	Author = "Małgorzata Jeziorska and Piotr Jankowski and Krzysztof Szalewicz and Bogumił Jeziorski",
	Title = "{On the optimal choice of monomer geometry in calculations of intermolecular interaction energies: rovibrational spectrum of Ar-HF from two- and three-dimensional potentials}",
	Journal = "J. Chem. Phys.",
	Volume = "113",
	Number = "8",
	Pages = "2957–2968",
	collection = "molecular interactions",
	doi = "10.1063/1.1287058",
	localfile = "molecular interactions/2000 - On the optimal choice of monomer geometry in calculations of intermolecular interaction energies: rovibrational spectrum of Ar-HF from two- and three-dimensional potentials.pdf",
	year = 2000
}

@Article{2000-Kedzierski-SK,
	Author = "Paweł Kędzierski and W. Andrzej Sokalski and Morris Krauss",
	Title = "{Nonempirical analysis of nature of catalytic effects in ribonuclease {A} active site}",
	Journal = "J. Comp. Chem.",
	Volume = "21",
	Number = "6",
	Pages = "432–445",
	abstract = "The physical nature of the catalytic activity exerted by various ribonuclease A active site constituents is analyzed in terms of the differential transition state stabilization approach in which activation barrier changes induced by the molecular environment are expressed by additive components defined in the theory of intermolecular interactions. Electrostatic multipole contributions seem to approximate total catalytic activity well for residues separated by contacts longer than 2.7 Angstrom whereas at shorter distances the remaining exchange and delocalization terms are not negligible. Depending on the reaction step, the same residue may exhibit catalytic or inhibitory activity. (C) 2000 John Wiley \& Sons, Inc.",
	cited = "6 (2005-05-23)",
	collection = "enzymes",
	doi = "10.1002/(SICI)1096-987X(20000430)21:6",
	keywords = "active site",
	localfile = "enzymes/2000 - Nonempirical analysis of nature of catalytic effects in ribonuclease A active site.pdf",
	year = 2000
}

@Article{2000-Klopper-RD,
	Author = "Wim Klopper and {Jeanne G. C. M. van} {Duijneveldt-van de Rijdt} and {Frans B. van} {Duijneveldt}",
	Title = "{Computational determination of equilibrium geometry and dissociation energy of the water dimer}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "2",
	Pages = "2227–2234",
	abstract = "The equilibrium geometry and dissociation energy of the water dimer have been determined as accurately as technically possible. Various quantum chemical methods and high-quality basis sets have been appliedÈthat is, at the level of a nearly complete basis-and both the intermolecular separation and the deformation of the donor and acceptor molecules have been optimized at the level of CCSD(T) theory (coupled-cluster theory with singles and doubles excitations plus a perturbation correction for connected triples).",
	collection = "hydrogen bonding",
	doi = "10.1039/a910312k",
	keywords = "water",
	localfile = "hydrogen bonding/2000 - Computational determination of equilibrium geometry and dissociation energy of the wate dimer.pdf",
	methods = "CCSD(T)",
	systems = "water dimer",
	year = 2000
}

@Article{2000-Kulkarni-CSZ,
	Author = "Amit M. Kulkarni and Avik P. Chatterjee and Kenneth S. Schweizer and Charles F. Zukoski",
	Title = "{Effects of polyethylene gylcol on protein interactions}",
	Journal = "J. Chem. Phys.",
	Volume = "113",
	Number = "21",
	Pages = "9863–9873",
	collection = "polymers",
	doi = "10.1063/1.1321042",
	localfile = "polymers/2000 - Effects of polyethylene glycol on protein interactions.pdf",
	year = 2000
}

@Article{2000-Lane-Jenkins,
	Author = "Andrew N. Lane and Terence C. Jenkins",
	Title = "{Thermodynamics of nucleic acids and their interactions with ligands}",
	Journal = "Q. Rev. Biophys.",
	Volume = "33",
	Number = "3",
	Pages = "255 – 306",
	abstract = "(Excerpt) In recent years the availability of large quantities of pure synthetic DNA and RNA has revolutionised the study of nucleic acids, such that it is now possible to study their conformations, dynamics and large-scale properties, and their interactions with small ligands, proteins and other nucleic acids in unprecedented detail. This has led to the (re)discovery of higher order structures such as triple helices and quartets, and also the catalytic activity of RNA contingent on three-dimensional folding, and the extraordinary speciﬁcity possible with DNA and RNA aptamers.",
	collection = "nucleic acid drugs",
	doi = "10.1017/S0033583500003632",
	localfile = "nucleic acid drugs/2000 - Thermodynamics of nucleic acids and their interactions with ligands.pdf",
	year = 2000
}

@Article{2000-Leininger-AIS,
	Author = "Matthew L. Leininger and Wesley D. Allen and {Henry F. III} Schaefer and C. David Sherrill",
	Title = "{Is Møller–Plesset perturbation theory a convergent ab initio method?}",
	Journal = "J. Chem. Phys.",
	Volume = "112",
	Number = "21",
	Pages = "9213–9222",
	abstract = "Recent studies have seriously questioned the use of higher-order Møller–Plesset perturbation theory (MP$n$) in describing electron correlation in atomic and molecular systems. Here we ﬁrst reinvestigate with improved numerical techniques previously controversial and disturbing MP$n$ energetic series for Ne, F$^{-}$ , HF, BH, C$\_2$ and N$\_2$ . Conspicuously absent in previous work is research on the convergence of MP$n$ spectroscopic constants, and thus complete MP$n$ (energy, $r\_e$ ,${\o}mega\_e$) series were then computed for BH, HF, CN$^{+}$ , C$\_2$ and N$\_2$) through the high orders MP25, MP21, MP13, MP39 and MP19 within the correlation consistent family of basis sets. A persistent, slowly decaying ringing pattern in the C$\_2$ energy series was tracked out to MP155. Finally, new energy series were generated and analyzed through MP167 for Cl$^{-}$ and MP39 for Ar and HCl. The MP$n$ energy and property series variously display rapid or slow convergence, monotonic or oscillatory decay, highly erratic or regular behavior, or early or late divergence, all depending on the chemical system or the choice of one-particle basis set. For oscillatory series the spectroscopic constants computed from low-order MPn methods are often more accurate, with respect to the full conﬁguration interaction FCI limit, than those computed via high-order MP$n$ theory.",
	collection = "quantum chemistry",
	doi = "10.1063/1.481764",
	keywords = "electronic structure",
	localfile = "quantum chemistry/2000 - Is Moller-Plesset perturbation theory a convergent ab initio method.pdf",
	year = 2000
}

@Article{2000-Matta-Bader,
	Author = "Chérif F. Matta and Richard F. W. Bader",
	Title = "{An {Atoms-In-Molecules} study of the genetically-encoded amino acids: I. Effects of conformation and of tautomerization on geometric, atomic, and bond properties}",
	Journal = "Proteins",
	Volume = "40",
	Number = "2",
	Pages = "310–329",
	abstract = "The theory of {Atoms-In-Molecules} {(AIM)} is a partitioning of the real space of a molecule into disjoint atomic constituents as determined by the topology of the electron density, rho(r). This theory identifies an atom in a molecule with a quantum mechanical open system and, consequently, all of the atom's properties are unambiguously defined. {AIM} recovers the basic empirical cornerstone of chemistry: that atoms and functional groups possess characteristic and additive properties that in many cases exhibit a remarkable transferability between different molecules. As a result, the theory enables the theoretical synthesis of a large molecule and the prediction of its properties by joining fragments that are predetermined as open systems. The present article is the first of a series (in preparation) that explore this possibility for polypeptides by determining the transferability of the building blocks: the amino acid residues. Transferability of group properties requires transferability of the electron density rho(r), which in turn requires the transferability of the geometric parameters. This article demonstrates that these parameters are conformation-insensitive for a representative amino acid, leucine, and that the atomic and bond properties exhibit a corresponding transferability. The effects of hydrogen bonding are determined and a set of geometrical conditions for the occurrence of such bonding is identified. The effects of transforming neutral leucine into its zwitter-ionic form on its atomic and bond properties are shown to be localized primarily to the sites of ionization.",
	collection = "protein amino acids",
	doi = "10.1002/(SICI)1097-0134(20000801)40:2",
	localfile = "protein amino acids/2000 - An AIM study of the genetically encoded amino acids: I. Effects of conformatin and of tautomerization on geometric, atomic, and bond properties.pdf",
	shorttitle = "An {Atoms-In-Molecules} study of the genetically-encoded amino acids",
	year = 2000
}

@Article{2000-Michielsen-Raedt,
	Author = "K. Michielsen and H. De Raedt",
	Title = "{Morphological image analysis}",
	Journal = "Comp. Phys. Comm.",
	Volume = "132",
	Pages = "94–103",
	abstract = "We describe a morphological image analysis method to characterize black-and-white images in terms of geometry and topology by means of the Minkowski functionals. We present an algorithm to calculate these functionals in two and three dimensions and apply the method to random point patterns on square and cubic lattices.",
	collection = "informatics",
	doi = "10.1016/S0010-4655(00)00139-9",
	keywords = "algorithms",
	localfile = "informatics/2000 - Morphological image analysis.pdf",
	year = 2000
}

@Article{2000-Mierzwicki-Latajka,
	Author = "Krzysztof Mierzwicki and Zdzisław Latajka",
	Title = "{Basis set superposition error in calculations of nonadditive effects in Li(NH3)(n) and Li(NH3)(n)(+) (n=1-4) clusters}",
	Journal = "Chem. Phys. Lett.",
	Volume = "325",
	Pages = "465–472",
	abstract = "The effect of the basis set superposition error is investigated at both SCF and correlated levels, using the pairwise additive function counterpoise (PAFC), the site-site function counterpoise (SSFC), and the White and Davidson method, for [Li(NH3)(n)](q+)(n = 1-4; q = 0, 1) clusters. The PAFC method gives results surprisingly close to the ones obtained with the SSFC approximation. The SSFC, and White and Davidson methods give the possibility of a meaningful decomposition of the total interaction energy of the many-body cluster into its n-body components. The obtained results show that the White-Davidson method is more correct, and always gives the BSSE corrections with the right sign. Moreover it is presented that the effect of the geometry distortions of the interacting particles is so small, that it can be omitted. (C) 2000 Elsevier Science B.V. All rights reserved. C1 Univ Wroclaw, Fac Chem, PL-50383 Wroclaw, Poland.",
	collection = "basis set superposition",
	doi = "10.1016/S0009-2614(00)00721-1",
	localfile = "basis set superposition/2000 - Basis set superposition error in calculations of nonadditive effects in Li(NH3)n and Li(NH3)n+ (n=1-4) clusters.pdf",
	year = 2000
}

@Article{2000-Mo-GP,
	Author = "Yirong Mo and Jiali Gao and Sigrid D. Peyerimhoff",
	Title = "{Energy decomposition analysis of intermolecular interactions using a block-localized wave function approach}",
	Journal = "J. Chem. Phys.",
	Volume = "112",
	Number = "13",
	Pages = "5530–5538",
	abstract = "An energy decomposition scheme based on the block-localized wave function BLW method is proposed. The key of this scheme is the deﬁnition and the full optimization of the diabatic state wave function, where the charge transfer among interacting molecules is deactivated. The present energy decomposition ED , BLW-ED, method is similar to the Morokuma decomposition scheme in deﬁnition of the energy terms, but differs in implementation and the computational algorithm. In addition, in the BLW-ED approach, the basis set superposition error is fully taken into account. The application of this scheme to the water dimer and the lithium cation–water clusters reveals that there is minimal charge transfer effect in hydrogen-bonded complexes. At the HF/aug-cc-PVTZ level, the electrostatic, polarization, and charge-transfer effects contribute 65\%, 24\%, and 11\%, respectively, to the total bonding energy 3.84 kcal/mol in the water dimer. On the other hand, charge transfer effects are shown to be signiﬁcant in Lewis acid–base complexes such as H3NSO3 and H3NBH3. In this work, the effect of basis sets used on the energy decomposition analysis is addressed and the results manifest that the present energy decomposition scheme is stable with a modest size of basis functions.",
	collection = "molecular interactions",
	doi = "10.1063/1.481185",
	localfile = "molecular interactions/2000 - Energy decomposition analysis of intermolecular interactions using a block-localized wave function approach.pdf",
	year = 2000
}

@Article{2000-Nakano-KSAUK,
	Author = "Tatsuya Nakano and Tsuguchika Kaminuma and Toshiyuki Sato and Yutaka Akiyama and Masami Uebayasi and Kazuo Kitaura",
	Title = "{Fragment molecular orbital method: application to polypeptides}",
	Journal = "Chem. Phys. Lett.",
	Volume = "318",
	Pages = "614–618",
	abstract = "Recently we have proposed the fragment molecular orbital method for calculating large molecules such as proteins. The method, with some modifications for a practical convenience, was applied to the model peptides of (Gly)n and (Ala)n where n=5–20, [Met5]enkephalin (YGGFM), and the synthetic designed peptide ALPHA-1 (acetyl-ELLKKLLEELKG). The calculated total energies compare well with those from the conventional ab initio MO method; the errors were within 2 kcalrmol. It indicates that the fragment MO method is sufficiently accurate and useful to study electronic properties of large molecules.",
	collection = "protein structure",
	localfile = "protein structure/2000 - Fragment molecular orbital method: application to polypeptides.pdf",
	year = 2000
}

@Article{2000-Patricelli-Cravatt,
	Author = "Matthew P. Patricelli and Benjamin F. Cravatt",
	Title = "{Clarifying the catalytic roles of conserved residues in the amidase signature family}",
	Journal = "J. Biol. Chem.",
	Volume = "275",
	Number = "25",
	Pages = "19177–19184",
	abstract = "Fatty acid amide hydrolase (FAAH) is a mammalian integral membrane enzyme responsible for the hydrolysis of a number of neuromodulatory fatty acid amides, including the endogenous cannabinoid anandamide and the sleep-inducing lipid oleamide. FAAH belongs to a large class of hydrolytic enzymes termed the “amidase signature family,” whose members are defined by a conserved stretch of approximately 130 amino acids termed the “amidase signature sequence.” Recently, site-directed mutagenesis studies of FAAH have targeted a limited number of conserved residues in the amidase signature sequence of the enzyme, identifying Ser-241 as the catalytic nucleophile and Lys-142 as an acid/base catalyst. The roles of several other conserved residues with potentially important and/or overlapping catalytic functions have not yet been examined. In this study, we have mutated all potentially catalytic residues in FAAH that are conserved among members of the amidase signature family, and have assessed their individual roles in catalysis through chemical labeling and kinetic methods. Several of these residues appear to serve primarily structural roles, as their mutation produced FAAH variants with considerable catalytic activity but reduced expression in prokaryotic and/or eukaryotic systems. In contrast, five mutations, K142A, S217A, S218A, S241A, and R243A, decreased the amidase activity of FAAH greater than 100-fold without detectably impacting the structural integrity of the enzyme. The pH rate profiles, amide/ester selectivities, and fluorophosphonate reactivities of these mutants revealed distinct catalytic roles for each residue. Of particular interest, one mutant, R243A, displayed uncompromised esterase activity but severely reduced amidase activity, indicating that the amidase and esterase efficiencies of FAAH can be functionally uncoupled. Collectively, these studies provide evidence that amidase signature enzymes represent a large class of serine-lysine catalytic dyad hydrolases whose evolutionary distribution rivals that of the catalytic triad superfamily.",
	collection = "enzymes",
	doi = "10.1074/jbc.M001607200",
	localfile = "enzymes/2000 - Clarifying the catalytic roles of conserved residues in the amidase signature family.pdf",
	year = 2000
}

@Article{2000-Pope-DLRTW,
	Author = "Lisa H. Pope and M. C. Davies and C. A. Laughton and C. J. Roberts and S. J. B. Tendler and P. M. Williams",
	Title = "{Atomic force microscopy studies of intercalation-induced changes in plasmid {DNA} tertiary structure}",
	Journal = "J. Microsc.",
	Volume = "199",
	Number = "1",
	Pages = "68–78",
	abstract = "Structural transitions in the tertiary structure of plasmid {DNA} have been investigated using atomic force microscopy. Changes in superhelical stress were induced by ethidium bromide intercalation, and conformational effects monitored by recording topographic images from {DNA} complexes of various ethidium bromide : base pair stoichiometry. Significant changes in the tertiary structure of individual {DNA} molecules were observed with increasing ethidium bromide concentration. The first distinct conformational transition was from a predominantly relaxed structure to one consisting solely of toroidal supercoils. A further increase in ethidium bromide concentration resulted in the formation of regions of plectonemic supercoiling. The ratio of plectonemic : toroidal supercoiling gradually increased until an extremely tightly interwound structure of solely plectonemic supercoiling was finally adopted. The toroidal form of supercoiling observed in this study is unusual as both atomic force microscopy and electron microscopy techniques have previously shown that plectonemic supercoiling is the predominant form adopted by plasmid {DNA.}",
	collection = "nucleic acid intercalation",
	doi = "10.1046/j.1365-2818.2000.00703.x",
	localfile = "nucleic acid intercalation/2000 - Atomic force microscopy studies of intercalation-induced changes in plasmid DNA tertiary structure.pdf",
	year = 2000
}

@Article{2000-Porter-MT,
	Author = "D. Porter and E. Metcalfe and M. J. K. Thomas",
	Title = "{Nanocomposite fire retardants - a review}",
	Journal = "Fire and Materials",
	Volume = "24",
	Pages = "45–52",
	abstract = "Most fire retardant nanocomposites are made from layered silicates and organic polymers, a variety of methods are used in their synthesis. The mechanism for the fire retardancy of these composites is generally considered to be due to the structure of the char formed during combustion, which enables the char to thermally insulate the polymer and inhibit the formation and escape of volatiles during combustion. Fire retardant nanocomposites require relatively low concentrations of silicates for activity, resulting in low additional costs and weight. Improvements in the bulk physical properties of the polymer can be additional advantages over traditional 5re retardants.",
	collection = "polymer nanocomposites",
	doi = "10.1002/(SICI)1099-1018(200001",
	keywords = "block copolymers; fire retardants",
	localfile = "polymer nanocomposites/2000 - Nanocomposite fire retardants - a review.pdf",
	type = "Review",
	year = 2000
}

@Article{2000-Ren-JC,
	Author = "Jinsong S. Ren and Terence C. Jenkins and Jonathan B. Chaires",
	Title = "{Energetics of {DNA} intercalation reactions}",
	Journal = "Biochemistry",
	Volume = "39",
	Pages = "8439–8447",
	abstract = "Isothermal titration calorimetry has been used to determine the binding enthalpy and heat capacity change (∆Cp) for a series of DNA intercalators, including ethidium, propidium, daunorubicin, and adriamycin. Temperature-dependent binding enthalpies were measured directly for the ligands, from which ∆Cp values of -140 to -160 cal mol-1 K-1 were calculated. Published van’t Hoff plots were reanalyzed to obtain ∆Cp values of -337 to -423 cal mol-1 K-1 for the binding of actinomycin D to several DNA oligonucleotide duplexes with defined sequences. Heat capacity changes for DNA intercalation were found to correlate with the alterations in solvent-accessible surface area calculated from available high-resolution structural data. Multiple linear regression was used to derive the relationship ∆Cp ) 0.382-((0.026)∆Anp - 0.121((0.077)∆Ap cal mol-1 K-1, where ∆Anp and ∆Ap are the binding-induced changes in nonpolar and polar solvent-accessible surface areas (in square angstroms), respectively. The ∆Cp terms were used to estimate the hydrophobic contribution to intercalative binding free energies, yielding values that ranged from -11.2 (ethidium) to -30 kcal mol-1 (actinomycin D). An attempt was made to parse the observed binding free energies of ethidium and propidium into five underlying contributions. Such analysis showed that the DNA binding behavior of these simple intercalators is driven almost equally by hydrophobic effects and van der Waals contacts within the intercalation site.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/bi000474a",
	localfile = "nucleic acid intercalation/2000 - Energetics of DNA intercalation reactions.pdf",
	year = 2000
}

@Article{2000-Rudnicki-KSPL,
	Author = "Witold R. Rudnicki and Małgorzata Kurzepa and Teresa Szczepanik and Waldemar Priebe and Bogdan Lesyng",
	Title = "{A simple model for predicting the free energy of binding between anthracycline antibiotics and DNA}",
	Journal = "Acta Biochim. Pol.",
	Number = "47",
	Pages = "1–9",
	collection = "nucleic acid intercalation",
	localfile = "nucleic acid intercalation/2000 - A simple model for predicting the free energy of binding between anthracycline antibiotics and DNA.pdf",
	year = 2000
}

@Article{2000-Salvador-FD,
	Author = "Pedro Salvador and Xavier Fradera and Miquel Duran",
	Title = "{Effect of basis set superposition error on the electron density of molecular complexes}",
	Journal = "J. Chem. Phys.",
	Volume = "112",
	Pages = "10106–10115",
	abstract = "The Chemical Hamiltonian Approach (CHA) versions of the Roothaan and Kohn-Sham equations, labeled CHA/F and CHA/DFT, respectively, have been used to obtain the basis set superposition error (BSSE)-corrected first-order electron density of the hydrogen fluoride dimer with several basis sets. We have analyzed the effect of BSSE in terms of the electronic relaxation, i.e., the redistribution of the electron density due to the inclusion of the CHA correction at a frozen geometry, along with the subsequent nuclear relaxation process. Critical points of the charge density have been located and characterized to compare the conventional, uncorrected first-order electron density against the BSSE-corrected density at each level of theory. Contour difference maps between BSSE-corrected and uncorrected densities on the molecular plane have also been plotted to gain insight into the effects of BSSE correction on the electron density. (C) 2000 American Institute of Physics. [S0021-9606(00)31423-4]. C1 Univ Girona, Inst Computat Chem, Girona 17071, Catalonia, Spain. Univ Girona, Dept Chem, Girona 17071, Catalonia, Spain.",
	collection = "basis set superposition",
	doi = "10.1063/1.481703",
	localfile = "basis set superposition/2000 - Effect of basis set superposition error on the electron density of molecular complexes.pdf",
	year = 2000
}

@Article{2000-Scerri,
	Author = "Eric R. Scerri",
	Title = "{Philosophy of chemistry – a new interdisciplinary field?}",
	Journal = "J. Chem. Ed.",
	Volume = "77",
	Number = "4",
	Pages = "522",
	abstract = "What could possibly be the connection between chemistry and philosophy, apart from the obvious superficial one of their both representing quests for knowledge? How do contemporary chemists and philosophers generally view one another? These are some of the questions I will try to put before going on to describe the connections that have recently been forged between these two seemingly very diverse fields of academic study.",
	collection = "philosophy",
	doi = "10.1021/ed077p522",
	localfile = "philosophy/2000 - Philosophy of chemistry: a new interdisciplinary field.pdf",
	year = 2000
}

@Article{2000-Schaftenaar-Noordik,
	Author = "G. Schaftenaar and J.H. Noordik",
	Title = "{Molden: a pre- and post-processing program for molecular and electronic structures}",
	Journal = "J. Comput.-Aided Mol. Des.",
	Volume = "14",
	Pages = "123–134",
	collection = "cheminformatics",
	localfile = "cheminformatics/2000 - Molden: a pre- and post-processing program for molecular and electronic structures.pdf",
	url = "http://www.cmbi.kun.nl/molden",
	year = 2000
}

@Article{2000-Srivastava,
	Author = "Vipin Srivastava",
	Title = "{A unified view of the orthogonalization methods}",
	Journal = "J. Phys. A: Math. Gen.",
	Volume = "33",
	Pages = "6219–6222",
	abstract = "The problem of conversion of a given set of linearly independent vectors into a set of mutually orthogonal vectors has been studied for a long time. It ﬁnds wide applications in mathematics, physics and chemistry. The methods involve a straightforward and simple mathematics and differ in the special conditions they satisfy. We present a simple analysis of the orthogonalization methods in terms of the projections of the given vectors on the orthogonalized bases vectors and ﬁnd that the methods possess some powerful properties hitherto unknown. The discovered properties are not only curious but also have algorithmic value in that they enable geometrical constructions of the orthogonal basis sets and the eigenvalues of the metric matrix of the given vector set. These properties also underline the scenarios where the different methods should be applicable. We expect that the present insight should also provide clues to understand certain aspects of cognitive memory, e.g. along the lines of.",
	collection = "quantum chemistry",
	keywords = "algorithms",
	localfile = "quantum chemistry/2000 - A unified view of the orthogonalization methods.pdf",
	year = 2000
}

@Article{2000-Torheyden-Jansen,
	Author = "Martin Torheyden and Georg Jansen",
	Title = "{Interaction energies for the water dimer by supermolecular methods and symmetry-adapted perturbation theory: the role of bond functions and convergence of basis subsets}",
	Journal = "Theor. Chem. Acc.",
	Volume = "104",
	Number = "5",
	Pages = "370 – 384",
	abstract = "Using a systematic series of basis sets in supermolecular and symmetry-adapted intermolecular perturbation theory calculations it is examined how interaction energies of various water dimer structures change upon addition and shifting of bond functions. Their addition to augmented double- and triple-zeta basis sets brings the sum of the electron correlation contributions to the second-order interaction energy nearly to convergence, while accurate first-order electrostatic and exchange contributions require better than augmented quadruple-zeta quality. A scheme which combines the different perturbation energy contributions as computed in different basis subsets performs uniformly well for the various dimer structures. It yields a symmetry-adapted perturbation theory value of -21.08 kJ/mol for the energy of interaction of two vibrationally averaged water molecules compared to -21.29 kJ/mol when the full augmented triple-zeta basis set is used throughout.",
	collection = "hydrogen bonding",
	doi = "10.1007/s002140000152",
	localfile = "hydrogen bonding/2000 - Interaction energies for the water dimer by supermolecular methods and symmetry-adapted perturbation theory: the role of bond functions and convergence of basis subsets.pdf",
	year = 2000
}

@Article{2000-Ueda-PYD,
	Author = "Natsuo Ueda and Robyn A. Puffenbarger and Shozo Yamamoto and Dale G. Deutsch",
	Title = "{The fatty acid amide hydrolase (FAAH)}",
	Journal = "Chem. Phys. Lipids",
	Volume = "108",
	Pages = "107–121",
	abstract = "The topic of this review is fatty acid amide hydrolase (FAAH), one of the best-characterized enzymes involved in the hydrolysis of bioactive lipids such as anandamide, 2-arachidonoylglycerol (2-AG), and oleamide. Herein, we discuss the nomenclature, the various assays that have been developed, the relative activity of the various substrates and the reversibility of the enzyme reactions catalyzed by FAAH. We also describe the cloning of the enzyme from rat and subsequent cDNA isolation from mouse, human, and pig. The proteins and the mRNAs from different species are compared. Cloning the enzyme permitted the puriﬁcation and characterization of recombinant FAAH. The conserved regions of FAAH are described in terms of sequence and function, including the amidase domain which contains the serine catalytic nucleophile, the hydrophobic domain important for self association, and the proline rich domain region, which may be important for subcellular localization. The distribution of FAAH in the major organs of the body is described as well as regional distribution in the brain and its correlation with cannabinoid receptors. Since FAAH is recognized as a drug target, a large number of inhibitors have been synthesized and tested since 1994 and these are reviewed in terms of reversibility, potency, and speciﬁcity for FAAH and cannabinoid receptors.",
	collection = "enzymes",
	localfile = "enzymes/2000 - The fatty acid amide hydrolase (FAAH).pdf",
	systems = "fatty acid amide hydrolase",
	year = 2000
}

@Article{2000-Wommack-Colwell,
	Author = "K. E. Wommack and R. R. Colwell",
	Title = "{Virioplankton: viruses in aquatic ecosystems}",
	Journal = "Microbiol. Mol. Biol. Rev.",
	Volume = "64",
	Number = "1",
	Pages = "69 – 114",
	abstract = "(Excerpt) This review is divided into four sections. The ﬁrst and second sections cover methods for viral direct counting, reports of naturally occurring virioplankton abundance in a variety of aquatic environments, and the correlation between changes in virus abundance and changes in other important ecological parameters. The third examines aspects of aquatic bacteriophage biology which have a signiﬁcant inﬂuence on host infection in aquatic environments. The ﬁnal section focuses on viral infection and lysis, as both a factor in the mortality of host populations and a mechanism inﬂuencing genetic and clonal diversity of host populations. In general, the discussion is focused on in situ measurement of virioplankton populations. Model phage-host systems are included, as appropriate, for background information.",
	collection = "viruses",
	doi = "10.1128/MMBR.64.1.69-114.2000",
	localfile = "viruses/2000 - Virioplankton: viruses in aquatic ecosystems.pdf",
	year = 2000
}

@Article{2000-Zewail,
	Author = "Ahmed H. Zewail",
	Title = "{Femtochemistry: atomic-scale dynamics of the chemical bond}",
	Journal = "J. Phys. Chem. A",
	Volume = "104",
	Number = "24",
	Pages = "5660–5694",
	abstract = "This anthology, which is adapted from the Nobel Lecture, gives an overview of the field of Femtochemistry from a personal perspective, encompassing our research at Caltech and focusing on the evolution of techniques, concepts, and new discoveries. In developing femtochemistrysthe study of molecular motions in the ephemeral transition states of physical, chemical, and biological changesswe have harnessed the powerful concept of molecular coherence and developed ultrafast-laser techniques for observing these motions. Femtosecond resolution (1 fs = 10$^{-15}$ s) is the ultimate achievement for studies of the dynamics of the chemical bond at the atomic level. On this time scale, matter wave packets (particle-type) can be created and their coherent evolution as a single-molecule trajectory can be observed. The field began with simple systems of a few atoms and has reached the realm of the very complex in isolated, mesoscopic, and condensed phases and in biological systems such as proteins and DNA. It also offers new possibilities for the control of reactivity and for structural femtochemistry and femtobiology.",
	collection = "molecular reactions",
	doi = "10.1021/jp001460h",
	localfile = "molecular reactions/2000 - Femtochemistry: atomic-scale dynamics of the chemical bond.pdf",
	year = 2000
}

@Article{2000-Zewail-1,
	Author = "Ahmed H. Zewail",
	Title = "{Femtochemistry. Past, present, and future}",
	Journal = "Pure Appl. Chem.",
	Volume = "72",
	Number = "12",
	Pages = "2219–2231",
	abstract = "This review highlights, with a historical perspective, the development of the field, with focus on the evolution since its birth in 1987, the scope of applications in present-time research, and some future developments in femtochemistry and the sibling field, femtobiology.",
	collection = "molecular reactions",
	doi = "10.1351/pac200072122219",
	localfile = "molecular reactions/2000 - Femtochemistry. Past, present, and future.pdf",
	year = 2000
}

@Article{2001-Adam,
	Author = "Stefan Adams",
	Title = "{Relationship between bond valence and bond softness of alkali halides and chalcogenides}",
	Journal = "Acta Cryst. B",
	Volume = "57",
	Pages = "278–287",
	Note = "Good points on the behavior of bond valence sums in the second coordination shell",
	collection = "crystallography",
	doi = "10.1107/S0108768101003068",
	localfile = "crystallography/2001 - Relationship between bond valence and bond softness of alkali halides and chalcogenides.pdf",
	rating = "2",
	read = "2013-02-19",
	year = 2009
}

@Article{2001-Arthanari-Bolton,
	Author = "Haribabu Arthanari and Philip H. Bolton",
	Title = "{Functional and dysfunctional roles of quadruplex {DNA} in cells}",
	Journal = "Chem. Biol.",
	Volume = "8",
	Number = "3",
	Pages = "221 – 230",
	abstract = "A number of biological roles have been proposed for quadruplex, also referred to as G4 or tetraplex, DNA. The presence of quadruplex DNA may lead to errors in some biological processes and be required in others. Proteins that interact with quadruplex DNA have been identified including those that cause Bloom's and Werner's syndromes. There are small molecules that specifically bind to quadruplex DNA, inhibit telomerase, and are cytotoxic towards tumor cells indicating a role for quadruplex DNA in telomere function. It is now possible to make testable proposals for the possible biological implications of quadruplex DNA in replication, transcription: and recombination as well as possible routes to therapeutic intervention.",
	collection = "cells",
	localfile = "cells/2001 - Functional and dysfunctional roles of quadruplex DNA in cells.pdf",
	year = 2001
}

@Article{2001-Bader-Matta,
	Author = "Richard F. W. Bader and Chérif F. Matta",
	Title = "{Properties of atoms in crystals: Dielectric polarization}",
	Journal = "Int. J. Quant. Chem.",
	Volume = "85",
	Number = "4-5",
	Pages = "592–607",
	abstract = "It is shown that the polarization of a molecule or an extended system, permanent or induced can, like all measurable properties, be equated to a sum of atomic contributions. While it has been previously shown that a change in the polarization of a dielectric can be considered a consequence of a geometric quantum phase and obtainable from a Berry phase in a parameter space, such a possibility does not exclude a real space description, stated in terms of the charge distributions of the system's composite atoms or cells. The cells are defined as bounded regions of real space whose properties are described by the physics of a proper open system, a description that applies to any system regardless of the nature of the interactions between the atoms. This approach necessarily leads to the inclusion of a contribution to the polarization arising from the transfer of charge across the boundary of a cell, in addition to that from the cell's internal polarization, thereby correcting the textbook description of polarization that considers only the latter contribution. It is shown that a neutral repeating cell in a dielectric behaves as an atomic capacitor which mimics the macroscopic behavior, with the internal charge transfer leading to the creation of what Feynman terms the ldquosurface polarization charge.rdquo © 2001 John Wiley \& Sons, Inc. Int J Quantum Chem, 2001",
	collection = "molecular fragmentation",
	doi = "10.1002/qua.1540",
	localfile = "molecular fragmentation/2001 - Properties of atoms in crystals: dielectric polarization.pdf",
	shorttitle = "Properties of atoms in crystals",
	year = 2001
}

@Article{2001-Blackburn,
	Author = "Elizabeth H. Blackburn",
	Title = "{Switching and signaling at the telomere}",
	Journal = "Cell",
	Volume = "106",
	Number = "6",
	Pages = "661–673",
	abstract = "This review describes the structure of telomeres, the protective {DNA-protein} complexes at eukaryotic chromosomal ends, and several molecular mechanisms involved in telomere functions. Also discussed are cellular responses to compromising the functions of telomeres and of telomerase, which synthesizes telomeric {DNA.}",
	collection = "nucleic acids",
	doi = "10.1016/S0092-8674(01)00492-5",
	localfile = "nucleic acids/2001 - Switching and singaling at the telomere.pdf",
	year = 2001
}

@Article{2001-Brana-CGPR,
	Author = "M. F. Brano and M. Cacho and A. Gradillas and B. {de Pascual-Teresa} and A. Ramos",
	Title = "{Intercalators as anticancer drugs}",
	Journal = "Curr. Pharm. Design",
	Volume = "7",
	Pages = "1745–1780",
	abstract = "Intercalators are the most important group of compounds that interact reversibly with the DNA double helix. Some of them are valuable drugs currently used for the treatment of ovarian and breast cancers and acute leukemias, while many others are in different phases of clinical trials. Intercalating agents share common structural features such as the presence of planar polyaromatic systems which bind by insertion between DNA base-pairs, with a marked preference for 5'-pyrimidine-purine-3' steps. The chromophores are linked to basic chains that might also play an important role in the affinity and selectivity shown by these compounds. Bisintercalators have two potential intercalating ring systems connected by linkers which can vary in length and rigidity. Nowadays it is well accepted that the antitumor activity of intercalators is closely related to the ability of these compounds to stabilize the DNA-intercalator-topoisomerase II ternary complex. In this work we have carried out a revision of small organic molecules that bind to the DNA molecule via intercalation, and exert their antitumor activity through a proven topoisomerase II inhibition. We have tried to give a general overview of the most recent results in this area, paying special attention to compounds that are currently under clinical trials. Among those are naphthalimides, a group of compounds that has been developed in our laboratory since the 70's.",
	collection = "nucleic acid intercalation",
	localfile = "nucleic acid intercalation/2001 - Intercalators as anticancer drugs.pdf",
	year = 2001
}

@Article{2001-Champoux,
	Author = "James J. Champoux",
	Title = "{D{NA} topoisomerases: {S}tructure, function, and mechanism}",
	Journal = "Ann. Rev. Biochem.",
	Volume = "70",
	Pages = "369 – 413",
	abstract = "DNA topoisomerases solve the topological problems associated with DNA replication, transcription, recombination, and chromatin remodeling by introducing temporary single- or double-strand breaks in the DNA. In addition, these enzymes fine-tune the steady-state level of DNA supercoiling both to facilitate protein interactions with the DNA and to prevent excessive supercoiling that is deleterious. In recent years, the crystal structures of a number of topoisomerase fragments, representing nearly all the known classes of enzymes, have been solved. These structures provide remarkable insights into the mechanisms of these enzymes and complement previous conclusions based on biochemical analyses. Surprisingly, despite little or no sequence homology, both type IA and type ITA topoisomerases from prokaryotes and the type IIA enzymes from eukaryotes share structural folds that appear to reflect functional motifs within critical regions of the enzymes. The type IB enzymes are structurally distinct from all other known topoisomerases but are similar to a class of enzymes referred to as tyrosine recombinases. The structural themes common to all topoisomerases include hinged clamps that open and close to bind DNA, the presence of DNA binding cavities for temporary storage of DNA segments, and the coupling of protein conformational changes to DNA rotation or DNA movement. For the type II topoisomerases, the binding and hydrolysis of ATP further modulate conformational changes in the enzymes to effect changes in DNA topology.",
	collection = "nucleic acids",
	doi = "10.1038/nrm831",
	localfile = "nucleic acids/2001 - DNA topoisomerases: structure, function, and mechanism.pdf",
	year = 2001
}

@Article{2001-Cravatt-DPBGML,
	Author = "Benjamin F. Cravatt and Kristin Demarest and Matthew P. Patricelli and Michael H. Bracey and Dan K. Giang and Billy R. Martin and Aaron H. Lichtman",
	Title = "{Supersensitivity to anandamide and enhanced endogenous cannabinoid signaling in mice lacking fatty acid amide hydrolase4}",
	Journal = "Proc. Natl. Acad. Sci.",
	Volume = "98",
	Number = "16",
	Pages = "9371–9376",
	abstract = "The medicinal properties of marijuana have been recognized for centuries, but clinical and societal acceptance of this drug of abuse as a potential therapeutic agent remains ﬁercely debated. An attractive alternative to marijuana-based therapeutics would be to target the molecular pathways that mediate the effects of this drug. To date, these neural signaling pathways have been shown to comprise a cannabinoid receptor (CB1) that binds the active constituent of marijuana, tetrahydrocannabinol (THC), and a postulated endogenous CB1 ligand anandamide. Although anandamide binds and activates the CB1 receptor in vitro, this compound induces only weak and transient cannabinoid behavioral effects in vivo, possibly a result of its rapid catabolism. Here we show that mice lacking the enzyme fatty acid amide hydrolase (FAAH / ) are severely impaired in their ability to degrade anandamide and when treated with this compound, exhibit an array of intense CB1-dependent behavioral responses, including hypomotility, analgesia, catalepsy, and hypothermia. FAAH / -mice possess 15-fold augmented endogenous brain levels of anandamide and display reduced pain sensation that is reversed by the CB1 antagonist SR141716A. Collectively, these results indicate that FAAH is a key regulator of anandamide signaling in vivo, setting an endogenous cannabinoid tone that modulates pain perception. FAAH may therefore represent an attractive pharmaceutical target for the treatment of pain and neuropsychiatric disorders.",
	collection = "enzymes",
	doi = "10.1073/pnas.161191698",
	localfile = "enzymes/2001 - Supersensitivity to anandamide and enhanced endogenous cannabinoid signaling in mice lacking fatty acid amide hydrolase.pdf",
	year = 2001
}

@Article{2001-Fasolka-Mayes,
	Author = "Michael J. Fasolka and Anne M. Mayes",
	Title = "{Block copolymer thin films: physics and applications}",
	Journal = "Ann. Rev. Mater. Res.",
	Volume = "31",
	Pages = "323–355",
	abstract = "A two-part review of research concerning block copolymer thin films is presented. The first section summarizes experimental and theoretical studies of the fundamental physics of these systems, concentrating upon the forces that govern film morphology. The role of film thickness and surface energetics on the morphology of compositionally symmetric, amorphous diblock copolymer films is emphasized, including considerations of boundary condition symmetry, so-called hybrid structures, and surface chemical expression. Discussions of compositionally asymmetric systems and emerging research areas, e.g., liquid-crystalline and A-B-C triblock systems, are also included. In the second section, technological applications of block copolymer films, e.g., as lithographic masks and photonic materials, are considered. Particular attention is paid to means by which microphase domain order and orientation can be controlled, including exploitation of thickness and surface effects, the application of external fields, and the use of patterned substrates.",
	collection = "block copolymers",
	doi = "10.1146/annurev.matsci.31.1.323",
	keywords = "block copolymers; thin films",
	localfile = "block copolymers/2001 - Block copolymer thin films: physics and applications.pdf",
	type = "Review",
	year = 2001
}

@Article{2001-Gallego-Varani,
	Author = "José Gallego and Gabriele Varani",
	Title = "{Targeting {RNA} with {Small-Molecule} Drugs: Therapeutic Promise and Chemical Challenges}",
	Journal = "Acc. Chem. Res.",
	Volume = "34",
	Number = "10",
	Pages = "836–843",
	abstract = "Researchers’ increasing awareness of the essential role played by RNA in many biological processes and in the progression of disease makes the discovery of new RNA targets an emerging field in drug discovery. Since most existing pharmacologically active compounds bind proteins, RNA provides nearly untapped opportunities for pharmacological development. The elucidation of the structure of the ribosome and other cellular and viral RNA motifs creates the opportunity for discovering new drug-like compounds that inhibit RNA function. However, further advances in understanding the chemistry and structure of RNA recognition are needed before these promises are fulfilled.",
	collection = "nucleic acid drugs",
	doi = "10.1021/ar000118k",
	keywords = "drug discovery",
	localfile = "nucleic acid drugs/2001 - Targeting RNA with small-molecule drugs: therapteutic promise and chemical challenges.pdf",
	shorttitle = "Targeting {RNA} with {Small-Molecule} Drugs",
	year = 2001
}

@Article{2001-Ganesan-Fredrickson,
	Author = "Venkat Ganesan and Glenn H. Fredrickson",
	Title = "{Field-theoretic polymer simulations}",
	Journal = "Europhys. Lett.",
	Volume = "55",
	Number = "6",
	Pages = "814–820",
	abstract = "A method is presented for numerically sampling functional integrals in ﬁeld theory models of polymer solutions and melts. The approach eﬀectively relaxes the mean-ﬁeld approximation in self-consistent ﬁeld theories of equilibrium polymer phases. Viewed from another perspective, the method provides an alternative to conventional particle-based simulations of coarse-grained models of polymers. We demonstrate the technique by applying it to examine ﬂuctuation eﬀects on the order-disorder transition in symmetric diblock copolymer melts. Extensions to more complex polymer blends, copolymers, and solutions are outlined.",
	collection = "polymers",
	doi = "10.1209/epl",
	localfile = "polymers/2001 - Field-theoretic polymer simulations.pdf",
	year =

license: MIT

license_type: permissive

extension: bib