text:
2001
}

@Article{2001-Gordon-BRJW,
	Author = "T. P. Gordon and A. I. Bolstad and M. Rischmueller and R. Jonsson and S. A. Waterman",
	Title = "{Autoantibodies in primary Sjögren's syndrome: new insights into mechanisms of autoantibody diversification and disease pathogenesis}",
	Journal = "Autoimmunity",
	Volume = "34",
	Pages = "123–132",
	collection = "cells",
	localfile = "cells/2001 - Autoantibodies in primary Sjogren's syndrome: new insights into mechanisms of autoantibody diversification and disease pathogenesis.pdf",
	year = 2001
}

@Article{2001-Grembecka-KSL,
	Author = "Jolanta Grembecka and Paweł Kędzierski and W. Andrzej Sokalski and Jerzy Leszczyński",
	Title = "{Electrostatic models of inhibitory activity}",
	Journal = "Int. J. Quant. Chem.",
	Volume = "83",
	Number = "3-4",
	Pages = "180–192",
	abstract = "Various models of electrostatic interactions have been applied and tested for several leucine aminopeptidase (LAP) inhibitors interacting with the enzyme active site. Our results indicate that atomic multipoles up to quadrupole moment as M ell as potential derived Merz-Kollman and RESP charges reproduce reasonably the ab initio electrostatic interaction energies and the expectation values of the molecular electrostatic potential. These electrostatic models together with CHELP atomic point charges, yield the satisfactory correlation of the electrostatic interaction energy with the experimental activities of the inhibitors. in contrast to the results obtained from atomic monopoles (Mulliken charges) and atomic dipoles. Reasonable correlation has been also obtained for the simple electrostatic “key-lock” model proposed by Naray-Szabo, in which the LAP active site is represented by set of point charges (”lock”) interacting with the molecular electrostatic potential of each inhibitor (“`key”').",
	cited = "2 (2005-05-23)",
	collection = "enzymes",
	doi = "10.1002/qua.1209",
	localfile = "enzymes/2001 - Electrostatic models of inhibitory activity.pdf",
	year = 2001
}

@Article{2001-Grishin,
	Author = "Nick V. Grishin",
	Title = "{Fold change in evolution of protein structure}",
	Journal = "J. Struct. Biol",
	Volume = "134",
	Pages = "167–185",
	Note = "Has some interesting examples of structural divergence caused by moderate differences in sequence.",
	cited = "224 (2013-07-10)",
	collection = "protein structure",
	doi = "10.1006/jsbi.2001.4335",
	keywords = "homology modeling; protein structure",
	localfile = "protein structure/2001 - Fold change in evolution of protein structures.pdf",
	rating = "2",
	read = "2013-07-08",
	year = 2001
}

@Article{2001-Hernandez-Trujillo-Bader,
	Author = "Jesús Hernández-Trujillo and Richard F. W. Bader",
	Title = "{Properties of atoms in molecules: Construction of one-density matrix from functional group densities}",
	Journal = "J. Chem. Phys.",
	Volume = "115",
	Number = "23",
	Pages = "10595–10607",
	abstract = "The demonstrated transferability of functional groups deﬁned as proper open systems within the theory of atoms in molecules is used to iteratively construct a one-electron density matrix P and its derived electron density distribution. The initial guess at the density used in the ﬁtting procedure is obtained from the addition of the density distributions of groups deﬁned in parent molecules by the maximal matching of their interatomic surfaces. The method thus takes advantage of the observation that the ‘‘zero-ﬂux’’ boundary condition deﬁning a proper open system maximizes the transferability of the density distribution of a given group between molecules, one that is accompanied by a paralleling transferability in all of its properties. The construction is subject to the constraints that P be idempotent and normalized. The method is applied to the construction of P for the molecules HCH2 CH2X, with X CH3, NH2, OH, and F, where the vertical bar denotes the new C–C interatomic surface, the new zero-ﬂux boundary. The densities for the groups HCH2 and CH2X are deﬁned in their dimer molecules, HCH2|CH2H and XCH2|CH2X.",
	collection = "molecular fragmentation",
	doi = "10.1063/1.1418435",
	localfile = "molecular fragmentation/2001 - Properties of atoms in molecules: construction of one-density matrix from functional group densities.pdf",
	shorttitle = "Properties of atoms in molecules",
	year = 2001
}

@Article{2001-Hill-MPHM,
	Author = "David J. Hill and Matthew J. Mio and Ryan B. Prince and Thomas S. Hughes and Jeffrey S. Moore",
	Title = "{A field guide to foldamers}",
	Journal = "Chem. Rev.",
	Volume = "101",
	Number = "12",
	Pages = "3893 – 4011",
	abstract = "(Excerpt) The breadth of structure and function displayed by the molecules of biology is remarkable. Considering that there are only three major biopolymer backbones (proteins, ribonucleic acids, and polysaccharides), nature vividly teaches that copolymer sequence is a powerful way to meet diverse chemical challenges. It is logical then to ask are biomacromolecule building blocks are matchless in their suitability for life? Systematic studies on alternative monomers closely related to those found in nature have provided clues about the fitness of R-amino acids, ribofuranosyl (5′f3′) nucleic acids, and phosphodiester linkages. Yet “why nature is such, and not otherwise”1 is a question that continues to be asked. Looking beyond the biopolymers and their related derivatives however, it is possible to imagine that other chain molecules are capable of similar functions. This prediction has only recently begun to be tested, raising questions of great fundamental interest. On a more practical level, the discovery of new functional polymers clearly has widespread potential for both chemistry and biology.",
	collection = "protein structure",
	doi = "10.1021/cr990120t",
	keywords = "protein folding",
	localfile = "protein structure/2001 - A field guide to foldamers.pdf",
	year = 2001
}

@Article{2001-Hunter-LPU,
	Author = "Christopher A. Hunter and Kevin R. Lawson and Julie Perkins and Christopher J. Urch",
	Title = "{Aromatic interactions}",
	Journal = "J. Chem. Soc. Perkin Trans. 2",
	Number = "5",
	Pages = "651–669",
	abstract = "(Excerpt) Molecular organisation and molecular interactions are the basis of the functional properties of most molecules, and a detailed understanding of non-covalent chemistry is therefore fundamental to interpreting and predicting relationships between chemical structure and function. Molecular recognition processes are inﬂuenced by many diﬀerent factors which make their study complicated. Progress requires a quantitative understanding of these diﬀerent factors. Some key functional group interactions, such as H-bonding, are well-understood. H-bonds are strong, single point interactions with a very well-deﬁned geometry, and their magnitude is determined by the electrostatic forces between the donor hydrogen atom and the acceptor atom. For weaker, less well-deﬁned interactions, the picture is not so clear. In this review, we focus on one such class, aromatic interactions. Here there are multiple points of intermolecular contact, the geometry of interaction is variable, and there are a vast range of diﬀerent functional groups that can be involved. We summarise evidence on the properties of these interactions from a variety of diﬀerent sources, and we apologise for necessarily omitting related work.",
	collection = "stacking",
	doi = "10.1039/b008495f",
	localfile = "molecular stacking/2001 - Aromatic interactions.pdf",
	year = 2001
}

@Article{2001-Jansen-Hesselmann,
	Author = "Georg Jansen and Andreas Heßelmann",
	Title = "{Comment on 'Using {Kohn−Sham} Orbitals in {Symmetry-Adapted} Perturbation Theory To Investigate Intermolecular Interactions'}",
	Journal = "J. Phys. Chem. A",
	Volume = "105",
	Number = "49",
	Pages = "11156–11157",
	collection = "molecular interactions",
	doi = "10.1021/jp0112774",
	localfile = "molecular interactions/2001 - Comment on 'Using Kohn-Sham orbitals in symmetry-adapted perturbation theory to ivestigate intermoleculat interactions'.pdf",
	year = 2001
}

@Article{2001-Kedzierski-Sokalski,
	Author = "Paweł Kędzierski and W. Andrzej Sokalski",
	Title = "{Analysis of the transferability of atomic multipoles for amino acids in modeling macromolecular charge distribution from fragments}",
	Journal = "J. Comp. Chem.",
	Volume = "22",
	Number = "10",
	Pages = "1082–1097",
	abstract = "Cumulative Atomic Multipole Moments were calculated for all natural amino acids and symmetric cyclic hexapeptides within Self-Consisted Field (SCF) and Density Functional Theory (DFT) approaches using a standard 6-31G(d,p) basis set. These data were used to analyze in detail the quality and the conformational and the intermolecular transferability of molecular charge distributions expressed in the atomic multipole form. Intermolecular interaction energies were reproduced reasonably by CAMM transformed from other conformations. Good transferability of CAMM based model was also achieved between similar molecular environments, which opens a route to modeling electrostatic effects in highly symmetric (e.g., crystalline) systems. Transferability deficiencies of various charge distribution models were analyzed and attributed to different levels of multipole expansion.",
	cited = "5 (2005-05-05)",
	collection = "protein amino acids",
	doi = "10.1002/jcc.1068",
	localfile = "protein amino acids/2001 - Analysis of the transferability of atomic multipoles for amino acids in modeling macromolecular charge disitribution from fragments.pdf",
	year = 2001
}

@Article{2001-Kobko-Dannenberg,
	Author = "Nadya Kobko and Joseph J. Dannenberg",
	Title = "{Effect of basis set superposition error (BSSE) upon ab initio calculations of organic transition states}",
	Journal = "J. Phys. Chem. A",
	Volume = "105",
	Pages = "1944–1950",
	abstract = "The transition states (TS) for several organic reactions (concerted Diels-Alder, 1,2-H-atom shift in ethyl radical, and H-atom transfers from methane and propene to methyl radical) have been optimized on potential energy surfaces that include the counterpoise (CP) correction for basis set superposition error (BSSE). Various molecular orbit methods were used (Hartree-Fock (HF), second order Møller–Plesset, and density functional theory (DFT)) using basis sets varying in size from 3-21G to 6-311++G**. We show that the CP-optimized TSs obtained using small basis sets resemble those obtained using the larger basis sets both in energies and geometries. The geometry of the concerted Diels-Alder TS for ethylene and butadiene becomes more compact upon CP-correction, whereas the apparent TS for the 1,2-H-atom shift in ethyl radical is shown to be an artifact of BSSE (at least at the HF and DFT levels). The TSs for the radical abstraction reactions are shown to move toward product upon CP-optimization, The choice of fragments for the CP-correction is discussed. C1 CUNY Hunter Coll, Dept Chem, New York, NY 10021 USA. CUNY, Grad Sch, New York, NY 10021 USA.",
	collection = "basis set superposition",
	doi = "10.1021/jp001970b",
	localfile = "basis set superposition/2001 - Effect of basis set superposition error (BSSE) upon ab initio calcualtions of organic transition states.pdf",
	year = 2001
}

@Article{2001-Koeppel-RLMALPHM,
	Author = "Florence Koeppel and {Jean-François} Riou and Abdelazize Laoui and Patrick Mailliet and Paola B. Arimondo and Delphine Labit and Odile Petitgenet and Claude Helene and {Jean-Louis} Mergny",
	Title = "{Ethidium derivatives bind to G-quartets, inhibit telomerase and act as fluorescent probes for quadruplexes}",
	Journal = "Nucl. Acids Res.",
	Volume = "29",
	Number = "5",
	Pages = "1087–1096",
	abstract = "The telomeric G-rich single-stranded {DNA} can adopt in vitro an intramolecular quadruplex structure, which has been shown to directly inhibit telomerase activity. The reactivation of this enzyme in immortalized and most cancer cells suggests that telomerase is a relevant target in oncology, and telomerase inhibitors have been proposed as new potential anticancer agents. In this paper, we describe ethidium derivatives that stabilize G-quadruplexes. These molecules were shown to increase the melting temperature of an intramolecular quadruplex structure, as shown by fluorescence and absorbance measurements, and to facilitate the formation of intermolecular quadruplex structures. In addition, these molecules may be used to reveal the formation of multi-stranded {DNA} structures by standard fluorescence imaging, and therefore become fluorescent probes of quadruplex structures. This recognition was associated with telomerase inhibition in vitro: these derivatives showed a potent anti-telomerase activity, with {IC50} values of 18-100 {nM} in a standard {TRAP} assay.",
	collection = "nucleic acid intercalation",
	doi = "10.1093/nar",
	localfile = "nucleic acid intercalation/2001 - Ethidium derivatives bind to G-quartets, inhibit telomerase and act as fluorescent probes for quadruplexes.pdf",
	year = 2001
}

@Article{2001-Lane-Jenkins,
	Author = "Andrew N. Lane and Terence C. Jenkins",
	Title = "{Structures and properties of multi-stranded nucleic acids}",
	Journal = "Curr. Org. Chem.",
	Volume = "5",
	Number = "8",
	Pages = "845 – 869",
	abstract = "Nucleic acids exist in a number of Structural states that may comprise one to four strands. Common features involve base-stacking and pairing of complementary bases via H-bonded interactions, although a wide variety of pairing motifs are found in higher-order structures. Another property is the marked flexibility of nucleic acids reflected in their solution behaviour, thermodynamic stability and interactions with proteins and small ligand molecules. The electrostatic properties of a nucleic acid and its ability to pack into high-order structure(s) are largely determined by the anionic phosphodiester backbone. This feature is particularly evident for triple-helical assemblies, where there is close proximity between phosphates and intrinsic thermodynamic stability is strongly influenced by ionic strength. Structural stabilisation of parallel triplexes can also be modulated by the presence of positive charge, achieved through either N3-protonation of cytosine bases or the deliberate incorporation of charged residues into the third strand. Salt effects are also pronounced in four-stranded structures such as the i-motif and G-tetraplex (“quadruplex”) assemblies; indeed, different structures are produced for the latter depending on the nature of the associated cation. High-order nucleic acid structures are currently a focus of intense interest in antisense and antigene strategies toward novel chemotherapeutic agents. An understanding of both their structural details and solution properties is essential for a rational approach to DNA-targeted drug design.",
	collection = "nucleic acids",
	doi = "10.2174/1385272013375157",
	localfile = "nucleic acids/2001 - Structure and properties of multi-stranded nucleic acids.pdf",
	year = 2001
}

@Article{2001-Lara-Castells-KBDV,
	Author = "M. P. {de {Lara-Castells}} and R. V. Krems and A. A. Buchachenko and G. {Delgado-Barrio} and P. Villarreal",
	Title = "{Complete basis set extrapolation limit for electronic structure calculations: Energetic and nonenergetic properties of {HeBr} and {HeBr[sub} 2] van der Waals dimers}",
	Journal = "J. Chem. Phys.",
	Volume = "115",
	Number = "22",
	Pages = "10438–10449",
	abstract = "The lowest electronic states of the HeBr molecule have been calculated by the ab initio coupled cluster approach in conjunction with a series of increasing size augmented correlation-consistent basis sets of double through quintuple zeta quality. Different extrapolation formulas to the complete basis set limit have been tested by comparing estimated and actual quintuple zeta quality counterpoise corrected interaction energies. Frozen-core approach is checked by performing calculations in which all electrons are correlated. The potential energy surfaces of the HeBr2 van der Waals complex have been obtained from the HeBr potentials by means of the diatomic-in-molecule approach. Finally, transport, scattering, and spectroscopic properties of HeBr and HeBr2 (B) systems derived from ab initio data for different basis sets are examined. It is shown that their convergence closely follows the convergence of corresponding potential energy surfaces.",
	collection = "basis set dependence",
	doi = "10.1063/1.1415078",
	localfile = "basis set dependence/2001 - Complete basis set extrapolation limit for electronic structure calculations.pdf",
	shorttitle = "Complete basis set extrapolation limit for electronic structure calculations",
	year = 2001
}

@Article{2001-Luo-GPG,
	Author = "Ray Luo and Hillary S. R. Gilson and Michael J. Potter and Michael K. Gilson",
	Title = "{The physical basis of nucleic acid base stacking in water}",
	Journal = "Biophys. J.",
	Volume = "80",
	Number = "1",
	Pages = "140–148",
	abstract = "It has been argued that the stacking of adenyl groups in water must be driven primarily by electrostatic interactions, based upon NMR data showing stacking for two adenyl groups joined by a 3-atom linker but not for two naphthyl groups joined by the same linker. in contrast, theoretical work has suggested that adenine stacking is driven primarily by nonelectrostatic forces, and that electrostatic interactions actually produce a net repulsion between adenines stacking in water. The present study provides evidence that the experimental data for the 3-atom-linked bis-adenyl and bis-naphthyl compounds are consistent with the theory indicating that nonelectrostatic interactions drive adenine stacking. First, a theoretical conformational analysis is found to reproduce the observed ranking of the stacking tendencies of the compounds studied experimentally. A geometric analysis identifies two possible reasons, other than stronger electrostatic interactions, why the 3-atom-linked bis-adenyl compounds should stack more than the bis-naphthyl compounds. First, stacked naphthyl groups tend to lie further apart: than stacked adenyl groups, based upon both quantum calculations and crystal structures. This may prevent the bis-naphthyl compound from stacking as extensively as the bis-adenyl compound. Second, geometric analysis shows that more stacked conformations are sterically accessible to the bis-adenyl compound than to the bis-naphthyl compound because the linker is attached to the sides of the adenyl groups, but to the ends of the naphthyl groups. Finally, ab initio quantum mechanics calculations and energy decompositions for relevant conformations of adenine and naphthalene dimers support the view that stacking in these compounds is driven primarily by nonelectrostatic interactions. The present analysis illustrates the importance of considering all aspects of a molecular system when interpreting experimental data, and the value of computer models as an adjunct to chemical intuition.",
	cited = "16 (2005-04-27)",
	collection = "stacking",
	doi = "10.1016/S0006-3495(01)76001-8",
	localfile = "molecular stacking/2001 - The physical basis of nucleic acid base stacking in water.pdf",
	year = 2001
}

@Article{2001-Maroulis,
	Author = "George Maroulis",
	Title = "{Accurate higher electric multipole moments for carbon monoxide}",
	Journal = "Chem. Phys. Lett.",
	Volume = "334",
	Number = "1-3",
	Pages = "214–219",
	collection = "molecular electrostatics",
	doi = "10.1016/S0009-2614(00)01413-5",
	keywords = "basis set superposition error",
	localfile = "molecular electrostatics/2001 - Accurate higher electric multipole moments for carbon monoxide.pdf",
	year = 2001
}

@Article{2001-Martin-Feher,
	Author = "P. A. Martin and M. Feher",
	Title = "{Ab initio calculations on the multipole moments and dipole polarisabilities of the {PO+} molecular ion {(X1[Sigma]+)}}",
	Journal = "J. Mol. Struct.: {THEOCHEM}",
	Volume = "540",
	Number = "1-3",
	Pages = "139–144",
	abstract = "The potential energy, dipole, quadrupole and octopole moments and dipole polarisabilities have been calculated at {CASSCF} level for the ground {X1[Sigma]+} state of the {PO+} molecular ion as a function of internuclear distance. Most of the electrical properties have not previously been calculated and show rapid variations around 5 a.u. due to a perturbation. The calculated vibrational frequency of 1410.4 cm-1 and the integrated {IR} absorption intensity of 984 cm2 mol-1 should lead towards the first observation of the vibrational spectrum.",
	collection = "molecular reactions",
	doi = "10.1016/S0166-1280(00)00727-2",
	localfile = "molecular reactions/2001 - Ab initio calculations on the multipole moments and dipole polarisabilities of the PO+ molecular ion.pdf",
	year = 2001
}

@Article{2001-Murdachaew-Szalewicz,
	Author = "Garold Murdachaew and Krzysztof Szalewicz",
	Title = "{Intermolecular potentials with flexible monomers}",
	Journal = "Faraday Discuss.",
	Volume = "118",
	Pages = "121–142",
	abstract = "Most available intermolecular potentials assume rigid monomers. Such an assumption is a reflection of a trivial observation that if monomer degrees of freedom are considered, the dimensionality of an intermolecular potential increases dramatically even for few-atom monomers. This puts strict limits on the sizes of clusters with flexible monomers that can be treated by ab initio methods since the number of grid points needed to fit a potential surface quickly becomes enormous. Most of the literature flexible-monomer potentials were obtained from the so-called site-site rigid-monomer potentials by simply allowing the sites to move with atomic nuclei as the monomers are deformed. This simple atom-following approach has been investigated in the present work, using water dimer and Ar-HF as test systems, and shown to be not adequate. A method has been proposed which uses properties of isolated flexible monomers to improve upon the atom-following approach without performing any dimer calculations outside the rigid-monomer grid. The method is shown to give for Ar-HF a 3D representation of the dispersion energy that should be adequate for HF motion in the ground and first excited vibrational states.",
	collection = "molecular interactions",
	doi = "10.1039/b009748i",
	localfile = "molecular interactions/2001 - Intermolecular potentials with flexible monomers.pdf",
	year = 2001
}

@Article{2001-Nakatani-MAHS,
	Author = "Kazuhiko Nakatani and Takahiro Matsuno and Kaoru Adachi and Shinya Hagihara and Isao Saito",
	Title = "{Selective Intercalation of Charge Neutral Intercalators into {GG} and {CG} Steps: Implication of {HOMO-LUMO} Interaction for {Sequence-Selective} Drug Intercalation into {DNA}}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "123",
	Number = "24",
	Pages = "5695–5702",
	collection = "nucleic acid intercalation",
	doi = "10.1021/ja003956i",
	keywords = "nucleic acid intercalation",
	localfile = "nucleic acid intercalation/2001 - Selective intercalation of charge neutral intercalators in GG and CG steps: implication of HOMO-LUMO interaction for sequence-selective drug intercalation into DNA.pdf",
	shorttitle = "Selective Intercalation of Charge Neutral Intercalators into {GG} and {CG} Steps",
	year = 2001
}

@Article{2001-Pacios-Gomez,
	Author = "L. F. Pacios and P. C. Gomez",
	Title = "{Atomic charges in conformers of gaseous glycine}",
	Journal = "J. Mol. Struct.: {THEOCHEM}",
	Volume = "544",
	Number = "1-3",
	Pages = "237–251",
	abstract = "The potential energy surface of gaseous glycine determined years ago in ab initio {MP2/6-311++G**} calculations {(A.Császár,} J. Am. Chem. Soc., 114 (1992) 9568) is composed of 13 stable conformers with relative energies within 11 kcal/mol. Glycine being the simplest amino acid and having a large number of conformers with close energies, it offers a stringent benchmark to explore the conformational dependences of properties of interest for further studies on peptides or proteins. The conformational behavior of atomic charges computed with the {MP2/6-311++G**} electron density using population analyses and partition approaches of different nature are analyzed. The behavior of every atom as well as that of molecular fragments {COOH,} {CH2} and {NH2} show that atoms in molecules {(AIM)} and natural population analysis {(NPA)} charges exhibit not only a good conformational independence but also provide a meaningful picture of the electron charge distribution in this system.",
	collection = "protein amino acids",
	doi = "10.1016/S0166-1280(01)00383-9",
	keywords = "glycine",
	localfile = "protein amino acids/2001 - Atomic charges in conformers of gaseous glycine.pdf",
	year = 2001
}

@Article{2001-Paizs-SCDS,
	Author = "Béla Paizs and Pedro Salvador and Attila G. Császár and Miquel Duran and Sándor Suhai",
	Title = "{Intermolecular bond lengths: extrapolation to the basis set limit on uncorrected and BSSE-corrected potential energy hypersurfaces}",
	Journal = "J. Comp. Chem.",
	Volume = "22",
	Number = "2",
	Pages = "196–207",
	collection = "basis set superposition",
	doi = "10.1002/1096-987X(20010130)22:2",
	localfile = "basis set superposition/2001 - Intermolecular bond lengths: extrapolation to the basis set limit on uncorrected adn BSSE-correted potential energy hypersurfaces.pdf",
	year = 2001
}

@Article{2001-Politzer-MP,
	Author = "Peter Politzer and Jane S. Murray and Zenaida Peralta-Inga",
	Title = "{Molecular surface electrostatic potentials in relation to noncovalent interactions in biological systems}",
	Journal = "Int. J. Quant. Chem.",
	Volume = "85",
	Pages = "676–684",
	abstract = "Noncovalent interactions are predominantly electrostatic in nature. It follows that an effective tool for their investigation and elucidation is the electrostatic potential on the molecular surface. We have shown that a variety of condensed phase macroscopic properties can be expressed quantitatively in terms of certain site-speciﬁc and global statistical quantities that characterize the overall pattern of the surface potential. We are now extending this approach to interactions in biological systems. Several applications will be discussed, including initial qualitative studies of dioxins, a series of anticonvulsants and some tetracyclines, the nucleotide bases, and a recent quantitative treatment of the anti-HIV activities of three groups of reverse transcriptase inhibitors.",
	collection = "molecular electrostatics",
	doi = "10.1002/qua.1706",
	localfile = "molecular electrostatics/2001 - Molecular surface electrostatic potnentials in relation to noncovalent interactions in biological systems.pdf",
	year = 2001
}

@Article{2001-Popelier-JK,
	Author = "Paul L. A. Popelier and Laurent Joubert and D. S. Kosov",
	Title = "{Convergence of the electrostatic interaction based on topological atoms}",
	Journal = "J. Phys. Chem. A",
	Volume = "105",
	Number = "35",
	Pages = "8254–8261",
	abstract = "An atom-atom partitioning of the electrostatic energy between unperturbed molecules is proposed on the basis of the topology of the electron density. Atom-atom contributions to the electrostatic energy are computed exactly, i.e., via a novel six-dimensional integration over two atomic basins, and by means of the spherical tensor multipole expansion, up to total interaction rank L = l(A) + l(B) + I = 6. The convergence behavior of the topological multipole expansion is compared with that using distributed multipole analysis (DMA) multipole moments for a set of van der Waals complexes at the B3LYP/6-311+G(2d,p) level. Within the context of the Buckingham-Fowler model it is shown that the topological and DMA multipole moments converge to a very similar interaction energy and geometry (average absolute discrepancy of 1.3 kJ/mol and 1.3 degrees, respectively) and are both in good to excellent agreement with supermolecule calculations.",
	cited = "25 (2005-05-24)",
	collection = "molecular electrostatics",
	doi = "10.1021/jp011511q",
	keywords = "multipole expansion",
	localfile = "molecular electrostatics/2001 - Convergence of the electrostatic interaction based on topological atoms.pdf",
	year = 2001
}

@Article{2001-Popelier-Kosov,
	Author = "Paul L. A. Popelier and D. S. Kosov",
	Title = "{Atom-atom partitioning of intramolecular and intermolecular coulomb energy}",
	Journal = "J. Chem. Phys.",
	Volume = "114",
	Number = "15",
	Pages = "6539–6547",
	abstract = "An atom-atom partitioning of the (super)molecular Coulomb energy is proposed on the basis of the topological partitioning of the electron density. Atom-atom contributions to the molecular intra- and intermolecular Coulomb energy are computed exactly, i.e., via a double integration over atomic basins, and by means of the spherical tensor multipole expansion, up to rank L=l(A)+l(B)+1=5. The convergence of the multipole expansion is able to reproduce the exact interaction energy with an accuracy of 0.1-2.3 kJ/mol at L=5 for atom pairs, each atom belonging to a different molecule constituting a van der Waals complex, and for nonbonded atom-atom interactions in single molecules. The atom-atom contributions do not show a significant basis set dependence (3\%) provided electron correlation and polarization basis functions are included. The proposed atom-atom Coulomb interaction energy can be used both with post-Hartree-Fock wave functions and experimental charge densities in principle. The Coulomb interaction energy between two molecules in a van der Waals complex can be computed by summing the additive atom-atom contributions between the molecules. Our method is able to extract from the supermolecule wave function an estimate of the molecular interaction energy in a complex, without invoking the reference state of free noninteracting molecules. We provide computational details of this method and apply it to (C2H2)(2); (HF)(2); (H2O)(2); butane; 1,3,5-hexatriene; acrolein and urocanic acid, thereby covering a cross section of hydrogen bonds, and covalent bonds with and without charge transfer. (C) 2001 American Institute of Physics.",
	cited = "14 (2005-05-24)",
	collection = "molecular electrostatics",
	doi = "10.1063/1.1356013",
	localfile = "molecular electrostatics/2001 - Atom-atom partitioning of intramolecular and intermolecular coulomb energy.pdf",
	year = 2001
}

@Article{2001-Qu-Chaires,
	Author = "Xiaogang Qu and Jonathan B. Chaires",
	Title = "{Hydration changes for {DNA} intercalation reactions}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "123",
	Number = "1",
	abstract = "The hydration changes that accompany the DNA binding of five intercalators (ethidium, propidium, proflavine, daunomycin, and 7-aminoactinomycin D) were measured by the osmotic stress method with use of the osmolytes betaine, sucrose, and triethylene glycol. Water uptake was found to accompany complex formation for all intercalators except ethidium. The difference in the number of bound water molecules between the complex and the free reactants (∆nw) was different for each intercalator. The values found for ∆nw were the following: propidium, +6; daunomycin, +18; proflavine, +30; and 7-aminoactinomycin D, +32. For ethidium binding to DNA a value of ∆nw ) +0.25((0.3) was found, indicating that within experimental error no water was released or taken up upon complex formation. Intercalation association constants measured in D2O were found to increase relative to values measured in H2O for all compounds except ethidium. A positive correlation between the ratio of binding constants (KD2O/KH2O) and ∆nw was found. These combined studies identify water as an important thermodynamic participant in the formation of certain intercalation complexes.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/ja002793v",
	localfile = "nucleic acid intercalation/2001 - Hydration changes for DNA intercalation reactions.pdf",
	year = 2001
}

@Article{2001-Salvador-PDS,
	Author = "Pedro Salvador and Béla Paizs and Miquel Duran and Sándor Suhai",
	Title = "{On the effect of the BSSE on intermolecular potential energy surfaces. Comparison of a priori and a posteriori BSSE correction schemes}",
	Journal = "J. Comp. Chem.",
	Volume = "22",
	Pages = "765–786",
	abstract = "A comparative study of geometrical parameters is performed on the complexes HF-HF, H2O-H2O, and HF-H2O using 12 different basis sets at the RHF, MP2, and DET (BLYP and B3LYP) levels of theory. The equilibrium geometries were obtained from uncorrected, a posteriori (counterpoise, CP) and a priori (Chemical Hamiltonian Approach, CHA) BSSE-corrected potential energy surfaces. The calculation of equilibrium geometries using the CP and CHA schemes is described in details. The effect of the BSSE on various intermolecular parameters is discussed and the performance of the applied theoretical models is critically evaluated from the BSSE point of view. (C) 2001 John Wiley \& Sons, Inc. C1 German Canc Res Ctr, Dept Mol Biophys, D-69120 Heidelberg, Germany. Univ Girona, Inst Quim Computac, Girona 17071, Catalonia, Spain. Univ Girona, Dept Quim, Girona 17071, Catalonia, Spain. Hungarian Acad Sci, Inst Chem, H-1525 Budapest, Hungary.",
	collection = "basis set superposition",
	doi = "10.1002/jcc.1042",
	localfile = "basis set superposition/2001 - On the effect of the BSSE on intermolecular potential energy surfaces.pdf",
	year = 2001
}

@Article{2001-Sevink-ZFH,
	Author = "G. J. Agur Sevink and Andrei V. Zvelindovsky and Johannes G. E. M. Fraaije and H. P. Huinink",
	Title = "{Morphology of symmetric block copolymer in a cylindrical pore}",
	Journal = "J. Chem. Phys.",
	Volume = "115",
	Number = "17",
	Pages = "8226–8230",
	abstract = "The inﬂuence of conﬁnement on morphology formation in copolymer systems is an important area of interest in theoretical research. We apply dynamic density functional theory to investigate the effect of pores on the morphology formation in a symmetric diblock copolymer system. The pore is represented by a perfect cylindrical tube. Porous systems are important in biology and are gaining interest for applications in nanotechnology. We show that for the pore sizes under investigation two equilibrium morphologies are possible depending on the surface interaction: a perpendicular or slab morphology and a parallel or multiwall tube morphology. The latter is referred to in the article as dartboard morphology. In the dynamic pathway towards this morphology an intermediate metastable helical phase is found. An important observation is that, for a wide range of pore radii and variations of polymer chain length, no mixed parallel/perpendicular morphologies were found: All observed morphologies are insensitive to the pore diameter.",
	collection = "block copolymers",
	doi = "10.1063/1.1403437",
	keywords = "block copolymers; nanoconfinement",
	localfile = "block copolymers/2001 - Morphology of symmetric block copolymer in a cylindrical pore.pdf",
	year = 2001
}

@Article{2001-Sokalski-KG,
	Author = "W. Andrzej Sokalski and Paweł Kędzierski and Jolanta Grembecka",
	Title = "{Ab initio study of the physical nature of interactions between enzyme active site fragments in vacuo}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "3",
	Number = "5",
	Pages = "657–663",
	abstract = "A recently developed direct version of variation-perturbation decomposition of intermolecular interaction energy into electrostatic, exchange, delocalization and correlation components has been used to explore the physical nature of interactions between key fragments of several enzyme active sites and corresponding reactants or inhibitors in vacuo. Despite neglecting solvent effects our results correlate reasonably with available experimental data and indicate the dominant electrostatic nature of inhibitory effects of PheP derivatives in leucine aminopeptidase and pK(a) shifts resulting from amino acid substitutions in mutated subtilisins. The range of applicability of the electrostatic approximation has been examined for the chorismate mutase enzyme.",
	cited = "2 (2005-04-13)",
	collection = "enzymes",
	doi = "10.1039/b007280j",
	keywords = "active site",
	localfile = "enzymes/2001 - Ab initio study of the physical nature of interactions between enzyme active site fragment in vacuo.pdf",
	year = 2001
}

@Article{2001-Sordo,
	Author = "Jóse A. Sordo",
	Title = "{On the use of the Boys-Bernardi function counterpoise procedure to correct barrier heights for basis set superposition error}",
	Journal = "J. Mol. Struct.: {THEOCHEM}",
	Volume = "537",
	Pages = "245–251",
	abstract = "The application of Boys-Bernardi's function counterpoise procedure to correct for the basis set superposition error when computing barrier heights associated with transition structures using well-balanced basis sets is analyzed in detail. It is shown that Emsley et al.'s formulation of the counterpoise method including the fragment relaxation terms may involve considerable errors when the relative orientation of the reference fragments is very different in the two chemical species defining the energy barrier. (C) 2001 Elsevier Science B.V. All rights reserved. C1 Univ Oviedo, Fac Quim, Dept Quim Fis \& Analit, Lab Quim Computac, E-33006 Oviedo, Principado Astu, Spain.",
	collection = "basis set superposition",
	doi = "10.1016/S0166-1280(00)00681-3",
	localfile = "basis set superposition/2001 - On the use of the Boys-Bernardi function counterpoise procedure to correct barrier heights for basis set superposition error.pdf",
	year = 2001
}

@Article{2001-Swart-DS,
	Author = "Marcel Swart and Piet Th. {can Duijnen} and Jaap G. Snijders",
	Title = "{A charge analysis derived from an atomic multipole expansion}",
	Journal = "J. Comp. Chem.",
	Volume = "22",
	Number = "1",
	Pages = "79–88",
	abstract = "A new charge analysis is presented that gives an accurate description of the electrostatic potential from the charge distribution in molecules. This is achieved in three steps: ﬁrst, the total density is written as a sum of atomic densities; next, from these atomic densities a set of atomic multipoles is deﬁned; ﬁnally, these atomic multipoles are reconstructed exactly by distributing charges over all atoms. The method is generally applicable to any method able to provide atomic multipole moments, but in this article we take advantage of the way the electrostatic potential is calculated within the Density Functional Theory framework. We investigated a set of 31 molecules as well as all amino acid residues to test the quality of the method, and found accurate results for the molecular multipole moments directly from the DFT calculations. The deviations from experimental values for the dipole/quadrupole moments are also small. Finally, our Multipole Derived Charges reproduce both the atomic and molecular multipole moments exactly.",
	collection = "molecular electrostatics",
	doi = "10.1002/1096-987X(20010115)22:1",
	keywords = "multipole expansion",
	localfile = "molecular electrostatics/2001 - A charge analysis derived from an atomic multipole expansions.pdf",
	year = 2001
}

@Article{2001-Thompson-GMB,
	Author = "Russell B. Thompson and Valeriy V. Ginzburg and Mark W. Matsen and Anna C. Balazs",
	Title = "{Predicting the mesophases of copolymer-nanoparticle composites}",
	Journal = "Science",
	Volume = "292",
	Pages = "2469–2472",
	Note = "Describes the SCFT/DFT combination and demonstrates some 2D configurations; first big BCP/NP paper.",
	abstract = "The interactions between mesophase-forming copolymers and nanoscopic particles can lead to highly organized hybrid materials. The morphology of such composites depends not only on the characteristics of the copolymers, but also on the features of the nanoparticles. To explore this vast parameter space and predict the mesophases of the hybrids, we have developed a mean ﬁeld theory for mixtures of soft, ﬂexible chains and hard spheres. Applied to diblock-nanoparticle mixtures, the theory predicts ordered phases where particles and diblocks self-assemble into spatially periodic structures. The method can be applied to other copolymer-particle mixtures and can be used to design novel composite architectures.",
	collection = "block copolymer nanocomposites",
	doi = "10.1126/science.1060585",
	keywords = "block copolymers; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2001 - Predicting the mesophases of copolymer-nanoparticle composites.pdf",
	methods = "SCFT/DFT",
	year = 2001
}

@Article{2001-Vardevanyan-AMK,
	Author = "P. O. Vardevanyan and A. P. Antonyan and G. A. Manukyan and A. T. Karapetyan",
	Title = "{Study of ethidium bromide interaction peculiarities with {DNA}}",
	Journal = "Exp. Mol. Med.",
	Volume = "33",
	Number = "4",
	Pages = "205–208",
	abstract = "The helix-coil transition of DNA-ethidium bromide complexes in an interval of ionic strength of 2.0 x 10(-3) M less than or equal to mu(Na+) less than or equal to 2.0 x 10(-2) M has been investigated. It has been revealed that at the certain high ligand-DNA ratios (r(b)) the transition interval of the complex - (DeltaT) becomes equal to that of DNA itself (DeltaT(0)). It has been shown that the values of rb at which deltaDeltaT=DeltaT-DeltaT(0)=0 depends on ionic strength of a solution. Further increasing of ligand concentration leads to its conversion from stabilizer into the destabilizer of the double-stranded DNA.",
	collection = "nucleic acid intercalation",
	localfile = "nucleic acid intercalation/2001 - Study of ethidium bromide interaction peculiarities with DNA.pdf",
	year = 2001
}

@Article{2001-Velde-BBGGSZ,
	Author = "{G. te} Velde and F. Matthias Bickelhaupt and E. J. Baerends and Célia Fonseca Guerra and {S. J. A. van} Gisbergen and Jaap G. Snijders and Tom Ziegler",
	Title = "{Chemistry with {ADF}}",
	Journal = "J. Comp. Chem.",
	Volume = "22",
	Number = "9",
	Pages = "931–967",
	abstract = "We present the theoretical and technical foundations of the Amsterdam Density Functional {(ADF)} program with a survey of the characteristics of the code (numerical integration, density fitting for the Coulomb potential, and {STO} basis functions). Recent developments enhance the efficiency of {ADF} (e.g., parallelization, near {order-N} scaling, {QM/MM)} and its functionality (e.g., {NMR} chemical shifts, {COSMO} solvent effects, {ZORA} relativistic method, excitation energies, frequency-dependent (hyper)polarizabilities, atomic {VDD} charges). In the Applications section we discuss the physical model of the electronic structure and the chemical bond, i.e., the {Kohn-Sham} molecular orbital {(MO)} theory, and illustrate the power of the {Kohn-Sham} {MO} model in conjunction with the {ADF-typical} fragment approach to quantitatively understand and predict chemical phenomena. We review the {ldquoActivation-strain} {TS} interactionrdquo {(ATS)} model of chemical reactivity as a conceptual framework for understanding how activation barriers of various types of (competing) reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis. Finally, we include a brief discussion of exemplary applications in the field of biochemistry (structure and bonding of {DNA)} and of time-dependent density functional theory {(TDDFT)} to indicate how this development further reinforces the {ADF} tools for the analysis of chemical phenomena.",
	collection = "cheminformatics",
	doi = "10.1002/jcc.1056",
	localfile = "cheminformatics/2001 - Chemistry with ADF.pdf",
	year = 2001
}

@Article{2001-Williams-Chabalowski,
	Author = "Hayes L. Williams and Cary F. Chabalowski",
	Title = "{Using {Kohn−Sham} Orbitals in {Symmetry-Adapted} Perturbation Theory to Investigate Intermolecular Interactions}",
	Journal = "J. Phys. Chem. A",
	Volume = "105",
	Number = "3",
	Pages = "646–659",
	abstract = "This is the first reported use of a hybrid method involving density functional theory {(DFT)} and symmetry-adapted perturbation theory {(SAPT)} to calculate intermolecular interactions. This work was stimulated by the reported failures of supermolecular {DFT} calculations to adequately predict intermolecular (and interatomic) interactions, particularly of the van der Waals type. The goals are to develop a hybrid scheme that will calculate intermolecular interaction energies accurately and in a computationally efficient fashion, while including the benefits of the energy decomposition provided by {SAPT.} The computational savings result from replacing the costly perturbation theory treatment with {DFT,} which should include the intramolecular correlation effects on the intermolecular interaction energies. The accuracy of this new hybrid approach (labeled {SAPT(DFT))} is evaluated by comparisons with higher level calculations. The test cases include He2, Ar2, {ArH2,} {(H2O)2,} {(HF)2,} {CO2CH3CN,} and {CO2-dimethylnitramine.} The new approach shows mixed results concerning the accuracy of interaction energies. {SAPT(DFT)} correctly predicts all the qualitative trends in binding energies for all test cases. This is particularly encouraging in dimer systems dominated by dispersive interactions where supermolecular {DFT} fails to predict binding. In addition, the method achieves a drastic reduction (a factor of at least 100) in computational time over the higher level calculations often used to predict these forces. With respect to quantitative accuracy, this initial hybrid scheme, using the very popular exchange-correlation functional {B3LYP,} overestimates the second-order energy components (e.g., induction and dispersion terms) for all of the test cases, and subsequently overestimates the total interaction energy for all dimer systems except those heavily dominated by the electrotstatic interactions. The {SAPT} energy decomposition points to the use of {DFT} virtual orbital eigenvalues in the second-order perturbation terms as the likely cause for this error. These results are consistent with earlier work suggesting that {DFT} canonical virtual orbital energies obtained from commonly used functionals are less than optimal for use in such a perturbative scheme. The first-order interaction energy terms from the {SAPT(DFT)} are found to be generally more accurate than the second-order terms, and agree well with the benchmark values for dimers containing molecules with a permanent electric dipole moment. These first-order terms depend only upon the occupied {MO} eigenvectors, and hence are not affected by the inaccuracies in the {KohnSham} {DFT} virtual orbital eigenvalues. These observations encourage future studies utilizing newly reported functionals, some of which have been developed to directly address problems with {DFT} virtual orbital energies and the asymptotic region of the electron density.",
	collection = "molecular interactions",
	doi = "10.1021/jp003883p",
	localfile = "molecular interactions/2001 - Using Kohn-Sham ortbials in Symmetry-Adapted Perturbation Theory to investigate intermolecular interactions.pdf",
	year = 2001
}

@Article{2002-Aarts-TL,
	Author = "D. G. A. L. Aarts and R. Tuinier and H. N. W. Lekkerkerker",
	Title = "{Phase behavior of mixtures of colloidal spheres and excluded-volume polymer chains}",
	Journal = "J. Phys.: Condens. Matter",
	Volume = "14",
	Pages = "7551–7561",
	abstract = "We study the phase behaviour of mixtures of colloidal spheres and polymers that have an excluded-volume interaction dispersed in a (background) solvent using the concept of free volume theory. The depletion layer thickness is calculated from the negative adsorption of polymer segments around a sphere. The correlation length and thermodynamic properties of the excluded-volume interacting polymer chains in solution are taken into account by using results from the renormalization group theory. For small polymer–colloid size ratios the difference from an ideal description of the polymers is small, while for larger size ratios the gas–liquid coexistence region shifts in the direction of higher polymer concentrations and at the same time the liquid–crystal coexistence region becomes more extended. Both the gas–liquid region and the gas–liquid–crystal region become less extended. These features are compared to experiment.",
	collection = "polymers",
	localfile = "polymers/2002 - Phase behavior of mixtures of colloidal spheres and excluded-volume polymer chains.pdf",
	year = 2002
}

@Article{2002-Allen,
	Author = "Frank H. Allen",
	Title = "{The Cambridge Structural Database: a quarter of a million crystal structures and rising}",
	Journal = "Acta Cryst. B",
	Volume = "58",
	Pages = "380–388",
	collection = "crystallography",
	keywords = "crystallgraphy; cheminformatics",
	localfile = "crystallography/2002 - The Cambridge Structural Database: a quarter of a million crystak structures and rising.pdf",
	rating = "2",
	read = "2014-03-25",
	year = 2002
}

@Article{2002-Baeurle,
	Author = "Stephan A. Baeurle",
	Title = "{Method of Gaussian equivalent representation: a new technique for reducing the sign problem of functional integral methods}",
	Journal = "Phys. Rev. Lett.",
	Volume = "89",
	Number = "8",
	Pages = "080602",
	abstract = "We report on the speciﬁc features of the sign problem in the classical auxiliary ﬁeld methodology and the strategies employed for its alleviation. In particular, we focus on a new technique based on the method of Gaussian equivalent representation of Eﬁmov and Nogovitsin [Physica (Amsterdam) 234A, 506 (1996)] with which we could ameliorate the convergence properties signiﬁcantly. We believe that this technique can also provide an interesting possibility to reduce the sign problem of other methods of computer simulation based on a functional integral approach.",
	collection = "statistical mechanics",
	doi = "10.1103/PhysRevLett.89.080602",
	localfile = "statistical mechanics/2002 - Method of Gaussian equivalent representation.pdf",
	year = 2002
}

@Article{2002-Baldeyrou-TBCHCD,
	Author = "Brigitte Baldeyrou and Christelle Tardy and Christian Bailly and Pierre Colson and Claude Houssier and Franck Charmantray and Martine Demeunynck",
	Title = "{Synthesis and DNA interaction of a mixed proflavine-phenanthroline Troger base}",
	Journal = "Eur. J. Med. Chem.",
	Volume = "37",
	Number = "4",
	Pages = "315–322",
	abstract = "We report the synthesis of an asymmetric Troger base containing the two well characterised DNA binding chromophores, proflavine and phenanthroline. The mode of interaction of the hybrid molecule was investigated by circular and linear dichroism experiments and a biochemical assay using DNA topoisomerase I. The data are compatible with a model in which the proflavine moiety intercalates between DNA base pairs and the phenanthroline ring occupies the DNA groove. DNase I cleavage experiments were carried out to investigate the sequence preference of the hybrid ligand and a well resolved footprint was detected at a site encompassing two adjacent 5'-GTC,5-GAC triplets. The sequence preference of the asymmetric molecule is compared to that of the symmetric analogues.",
	collection = "nucleic acid intercalation",
	doi = "10.1016/S0223-5234(02)01356-9",
	localfile = "nucleic acid intercalation/2002 - Synthesis and DNA interaction of a mixed proflavine-phenanthroline Troger base.pdf",
	year = 2002
}

@Article{2002-Berge-JHWEH,
	Author = "Torunn Berge and Nigel S. Jenkins and Richard B. Hopkirk and Michael J. Waring and J. Michael Edwardson and Robert M. Henderson",
	Title = "{Structural perturbations in {DNA} caused by bis-intercalation of ditercalinium visualised by atomic force microscopy}",
	Journal = "Nucl. Acids Res.",
	Volume = "30",
	Number = "13",
	Pages = "2980–2986",
	abstract = "Atomic force microscopy (AFM) has been used to examine perturbations in the tertiary structure of DNA induced by the binding of ditercalinium, a DNA bis-intercalator with strong anti-tumour properties. We report AFM images of plasmid DNA of both circular and linearised forms showing a difference in the formation of supercoils and plectonemic coils caused at least in part by alterations in the superhelical stress upon bis-intercalation. A further investigation of the effects of drug binding performed with 292 bp mixed-sequence DNA fragments, and using increment in contour length as a reliable measure of intercalation, revealed saturation occurring at a point where sufficient drug was present to interact with every other available binding site. Moment analysis based on the distribution of angles between segments along single DNA molecules showed that at this level of bis-intercalation, the apparent persistence length of the molecules was 91.7 +/- 5.7 nm, approximately twice as long as that of naked DNA. We conclude that images of single molecules generated using AFM provide a valuable supplement to solution-based techniques for evaluation of physical properties of biological macromolecules.",
	collection = "nucleic acid intercalation",
	doi = "10.1093/nar",
	localfile = "nucleic acid intercalation/2002 - Structural perturbation in DNA caused by bis-intercalation of ditercalinium visualized by atomiv force microscopy.pdf",
	year = 2002
}

@Article{2002-Bisogno-PM,
	Author = "Tiziana Bisogno and Luciano {De Petroceliis} and Vincenzo {Di Marzo}",
	Title = "{Fatty acid amide hydrolase, an enzyme with many bioactive substrates. Possible therapeutic implications}",
	Journal = "Curr. Pharm. Design",
	Volume = "8",
	Pages = "533–547",
	abstract = "During the last eight years a number of bioactive lipid mediators, the amides or esters of long chain fatty acids, have been discovered or re-discovered. These are: anandamide (N-arachidonoyl-ethanolamine, AEA) and 2-arachidonoylglycerol (2-AG), two endogenous agonists of cannabinoid receptors; oleamide (cis-9-octadecenoamide), a putative endogenous sleep-inducing factor; N-palmitoylethanol amine (PEA), a compound with promising anti-inflammatory and immune-modulatory activity. These compounds are all substrates for the same hydrolytic enzyme, fatty acid amide hydrolase (FAAH), whose molecular characterization was obtained in 1996. The molecular and enzymatic properties, tissue distribution, substrate recognition properties, physiological regulation and biological role of FAAH are discussed in this article, with special emphasis on the possible pharmacological manipulation of the activity of this enzyme with therapeutic purpose.",
	collection = "enzymes",
	localfile = "enzymes/2002 - Fatty acid amide hydrolase, an enzyme with many bioactive substrates. Possible therapeutic implications.pdf",
	year = 2002
}

@Article{2002-Boker-EHKLZUAMK,
	Author = "Alexander Böker and H. Elbs and Helmut Hansel and A. Knoll and Sabine Ludwigs and Heiko Zettl and Volker Urban and V. Arbetz and A. H. E. Muller and Georg Krausch",
	Title = "{Microscopic mechanisms of electric-field-induced alignment of block copolymer microdomains}",
	Journal = "Phys. Rev. Lett.",
	Volume = "89",
	Number = "13",
	Pages = "135502",
	abstract = "We investigate the microscopic mechanisms responsible for microdomain alignment in block copolymer solutions exposed to an electric ﬁeld. Using time-resolved synchrotron small-angle x-ray scattering, we reveal two distinct processes, i.e., grain boundary migration and rotation of entire grains, as the two dominant microscopic mechanisms. The former dominates in weakly segregating systems, while the latter is predominant in strongly segregated systems. The kinetics of the processes are followed as a function of polymer concentration and temperature and are correlated to the solution viscosity.",
	collection = "block copolymers",
	localfile = "block copolymers/2002 - Miscroscopic mechanisms of electirc-field-induced alignment of block copolymer microdomains.pdf",
	year = 2002
}

@Article{2002-Boys-Bernardi,
	Author = "S. Francis Boys and Fernando Bernardi",
	Title = "{The calculation of small molecular interactions by the differences of separate total energies. {S}ome procedures with reduced errors ({R}eprinted from {M}olecular {P}hysics, vol 19, pg 553-566, 1970)}",
	Journal = "Mol. Phys.",
	Volume = "100",
	Number = "1",
	Pages = "65 – 73",
	abstract = "A new direct difference method for the computation of molecular interactions has been based on a bivariational transcorrelated treatment, together with special methods for the balancing of other errors. It appears that these new features can give a strong reduction in the error of the interaction energy, and they seem to be particularly suitable for computations in the important region near the minimum energy. It has been generally accepted that this problem is dominated by unresolved difficulties and the relation of the new methods to these apparent difficulties is analysed here.",
	collection = "basis set superposition",
	doi = "10.1080/00268970110088901",
	keywords = "basis set superposition error",
	localfile = "basis set superposition/2002 - The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors.pdf",
	rating = "3",
	year = 2002
}

@Article{2002-Bracey-HMSC,
	Author = "Michael H. Bracey and Michael A. Hanson and Kim R. Masuda and Raymond C. Stevens and Benjamin F. Cravatt",
	Title = "{Structural adaptations in a membrane enzyme that terminates endocannabinoid signaling}",
	Journal = "Science",
	Volume = "298",
	Pages = "1793–1796",
	abstract = "Cellular communication in the nervous system is mediated by chemical messengers that include amino acids, monoamines, peptide hormones, and lipids. An interesting question is how neurons regulate signals that are transmitted by membrane-embedded lipids. Here, we report the 2.8 angstrom crystal structure of the integral membrane protein fatty acid amide hydrolase (FAAH), an enzyme that degrades members of the endocannabinoid class of signaling lipids and terminates their activity. The structure of FAAH complexed with an arachidonyl inhibitor reveals how a set of discrete structural alterations allows this enzyme, in contrast to soluble hydrolases of the same family, to integrate into cell membranes and establish direct access to the bilayer from its active site.",
	collection = "enzymes",
	doi = "10.1126/science.1076535",
	localfile = "enzymes/2002 - Structural adaptations in a membrane enzyme that terminates endocannabinoid signaling.pdf",
	year = 2002
}

@Article{2002-Bruice,
	Author = "Thomas C. Bruice",
	Title = "{A view at the millenium: the efficiency of enzymatic catalysis}",
	Journal = "Acc. Chem. Res.",
	Volume = "35",
	Number = "3",
	Pages = "139–148",
	abstract = "Binding TS in preference to S and increasing TDeltaS(double dagger) by freezing out motions in E.S and E.TS have been accepted as the driving forces in enzymatic catalysis; however, the smaller value of DeltaG(double dagger) for a one-substrate enzymatic reaction, as compared to its nonenzymatic counterpart, is generally the result of a smaller value of DeltaH(double dagger). Ground-state conformers (E.NACs) are formed in enzymatic reactions that structurally resemble E.TS. E.NACs are in thermal equilibrium with all. other E.S conformers and are turnstiles through which substrate molecules must pass to arrive at the lowest-energy TS. TS in E.TS may or may not be bound tighter than NAC in E.NAC.",
	collection = "enzymes",
	doi = "10.1021/ar0001665",
	localfile = "enzymes/2002 - A view at the millenium: the efficiency of enzymatic catalysis.pdf",
	year = 2002
}

@Article{2002-Coulson-Moult,
	Author = "Andrew F. W. Coulson and John Moult",
	Title = "{A unifold, mesofold and superfold model of protein fold use}",
	Journal = "Proteins: Structure, Function and Genetics",
	Volume = "46",
	Pages = "61–71",
	Note = "Puts forward the claim that alongside a regular exponential distribution of fold population there are unifolds (one sequence per fold) and superfolds (superfamilies).",
	cited = "66 (2013-9-03)",
	collection = "protein structure",
	doi = "10.1002/prot.10011",
	keywords = "protein folds",
	localfile = "protein structure/2002 - A unifold, mesofold and superfold model of protein fold use.pdf",
	read = "2013-08-30",
	year = 2002
}

@Article{2002-DAmico-SV,
	Author = "Maria L. D'Amico and V. Paiotta and Fernando Secco and Marcella Venturini",
	Title = "{A kinetic study of the interacalation of ethidium bromide into poly(A)-poly(U)}",
	Journal = "J. Phys. Chem. B",
	Volume = "106",
	Pages = "12635–12641",
	collection = "nucleic acid intercalation",
	doi = "10.1021/jp025989l",
	localfile = "nucleic acid intercalation/2002 - A kinetic study of the intercalation of ethidium bromide into poly(A)-poly(U).pdf",
	year = 2002
}

@Article{2002-Dziekonski-SSL,
	Author = "Paweł Dziekoński and W. Andrzej Sokalski and Bartłomiej Szyja and Jerzy Leszczyński",
	Title = "{Physical nature of catalytic effects of Si->Al substitutions in ZMS-5 zeolite for propylene protonation reaction}",
	Journal = "Chem. Phys. Lett.",
	Volume = "364",
	Pages = "133–138",
	collection = "molecular catalysis",
	doi = "10.1016/S0009-2614(02)01280-0",
	localfile = "molecular catalysis/2002 - Physical anture of catalytic effects of Si->Al substitutions in ZMS-5 zeolite for propylene protonation reaction.pdf",
	year = 2002
}

@Article{2002-Fredrickson,
	Author = "Glenn H. Fredrickson",
	Title = "{Dynamics and rheology of inhomogeneous polymeric fluids: a complex Langevin approach}",
	Journal = "J. Chem. Phys.",
	Volume = "117",
	Number = "14",
	Pages = "6810–6820",
	abstract = "A complex Langevin framework is described for carrying out numerical simulations of coupled ﬁeld equations for ﬂow and structure of inhomogeneous polymeric ﬂuids. The formalism permits an exact embedding of the relevant thermodynamic forces into the dynamical equations, regardless of the characteristic length scale of the inhomogeneities in the ﬂuid. As such, it is capable of treating a wide variety of systems, such as dilute and semidilute polymer solutions, microemulsions, block copolymers, and micellar solutions, including those whose equilibrium properties and self-assembly characteristics are not well described by mean-ﬁeld theory. The formalism also integrates with existing molecular and continuum descriptions of coupled stress and species concentration dynamics. In this report, we present the method for the simplest case of a homopolymer solution.",
	collection = "polymers",
	doi = "10.1063/1.1505025",
	localfile = "polymers/2002 - Dynamics and rheology of inhomogeneous polymeric fluids: a complex Langevin approach.pdf",
	year = 2002
}

@Article{2002-Fredrickson-GD,
	Author = "Glenn H. Fredrickson and Venkat Ganesan and François Drolet",
	Title = "{Field-theoretic computer simulation methods for polymers and complex fluids}",
	Journal = "Macromolecules",
	Volume = "35",
	Pages = "16–39",
	abstract = "We review a class of new computer simulation methods for polymeric fluids and other soft condensed matter systems that are based on an underlying field-theoretic description. These methods, while still in an early stage of development, show considerable promise for studying the equilibrium properties of many-component systems capable of intricate self-assembly, such as solutions and blends containing block and graft copolymers. Field-theoretic simulation methods also provide a great deal of flexibility in model building and coarse graining, and appear to be particularly well suited to treat systems with soft, long-range interactions, such as polyelectrolytes. We attempt to connect various related theoretical approaches, such as self-consistent field theory and dynamic density functional theory, within a common framework.",
	collection = "polymers",
	doi = "10.1021/ma011515t",
	localfile = "polymers/2002 - Field-theoretic computer simulations methods for polymers and complex fluids.pdf",
	methods = "FTS",
	type = "Review",
	year = 2002
}

@Article{2002-Glotzer-Paul,
	Author = "Sharon C. Glotzer and Wolfgang Paul",
	Title = "{Molecular and mesoscale simulation methods for polymer materials}",
	Journal = "Ann. Rev. Mater. Res.",
	Volume = "32",
	Pages = "401–436",
	abstract = "Polymers offer a wide spectrum of possibilities for materials applications, in part because of the chemical complexity and variability of the constituent molecules, and in part because they can be blended together with other organic as well as inorganic components. The majority of applications of polymeric materials is based on their excellent mechanical properties, which arise from the long-chain nature of the constituents. Microscopically, this means that polymeric materials are able to respond to external forces in a broad frequency range, i.e., with a broad range of relaxation processes. Computer simulation methods are ideally suited to help to understand these processes and the structural properties that lead to them and to further our ability to predict materials properties and behavior. However, the broad range of timescales and underlying structure prohibits any one single simulation method from capturing all of these processes. This manuscript provides an overview of some of the more popular computational models and methods used today in the ﬁeld of molecular and mesoscale simulation of polymeric materials, ranging from molecular models and methods that treat electronic degrees of freedom to mesoscopic ﬁeld theoretic methods.",
	collection = "polymers",
	doi = "10.1146/annurev.matsci.32.010802.112213",
	localfile = "polymers/2002 - Molecular and mesoscale simulation methods for polymer materials.pdf",
	rating = "2",
	read = "2011-04-06",
	year = 2002
}

@Article{2002-Gora-BRL,
	Author = "Robert W. Góra and Wojciech Bartkowiak and Szczepan Roszak and Jerzy Leszczyński",
	Title = "{A new theoretical insight into the nature of intermolecular interactions in the molecular crystal of urea}",
	Journal = "J. Chem. Phys.",
	Volume = "117",
	Number = "3",
	Pages = "1031–1039",
	abstract = "The nature of interactions in the molecular crystal of urea is analyzed in terms of the interaction energy decomposition. The influence of the electron correlation effects was estimated on the basis of the calculated second order Møller–Plesset corrections and their analysis. In the crystal, the urea molecules form infinite ribbons which reveal strong cooperative effects. The hydrogen-bonded interactions of the orthogonal ribbons do stabilize the crystal, whereas interactions between parallel tapes are repulsive. The stability of the crystal structure is determined by a subtle balance between these two types of interactions. Although, the electron correlation effects are stabilizing, their contribution is rather small in comparison with the total interaction energy.",
	cited = "15 (2005-04-13)",
	collection = "molecular crystals",
	doi = "10.1063/1.1482069",
	localfile = "molecular crystals/2002 - A new theoretical insight into the nature of intermolecular interactions in the molecular crystal of urea.pdf",
	year = 2002
}

@Article{2002-Gudowska-Nowak-Weron,
	Author = "Ewa Gudowska-Nowak and Karina Weron",
	Title = "{Random walk models of electron tunneling in a fluctuating medium}",
	Journal = "Phys. Rev. E",
	Volume = "65",
	Pages = "011103",
	cited = "18 (2013-04-29)",
	collection = "statistics",
	doi = "10.1103/PhysRevE.65.011103",
	localfile = "statistics/2002 - Random walk models of electron tunneling in a fluctuating medium.pdf",
	year = 2002
}

@aritlce{2002-Hanna-GS,
	author = "F. F. Hanna and Bo Gestblom and A. Soliman",
	cited = "13 (2013-04-29)",
	collection = "molecular solvation",
	doi = "10.1016/S0167-7322(01)00284-7",
	journal = "J. Mol. Liquids",
	localfile = "molecular solvation/2002 - Dielectric relaxation study of alcohol-diol(s) mixtures.pdf",
	pages = "27–40",
	title = "{Dielectric relaxation study of alcohol/diol(s) mixtures}",
	volume = "95",
	year = 2002
}

@Article{2002-Haq,
	Author = "Ihtshamul Haq",
	Title = "{Part {II}: {T}he thermodynamics of drug-bipolymer interaction - {T}hermodynamics of drug-{DNA} interactions}",
	Journal = "Arch. Biochem. Biophys.",
	Volume = "403",
	Number = "1",
	Pages = "1 – 15",
	abstract = "Many anticancer, antibiotic, and antiviral drugs exert their primary biological effects by reversibly interacting with nucleic acids. Therefore, these biomolecules represent a major target in drug development strategies designed to produce next generation therapeutics for diseases such as cancer. In order to improve the clinical efficacy of existing drugs and also to design new ones it is necessary to understand the molecular basis of drug-DNA interactions in structural, thermodynamic, and kinetic detail. The past decade has witnessed an increase in the number of rigorous biophysical studies of drug-DNA systems and considerable knowledge has been gained in the energetics of these binding reactions. This is, in part, due to the increased availability of high-sensitivity calorimetric techniques, which have allowed the thermodynamics of drug-DNA interactions to be probed directly and accurately. The focus of this article is to review thermodynamic approaches to examining drug-DNA recognition. Specifically, an overview of a recently developed method of analysis that dissects the binding free energy of these reactions into five component terms is presented. The results of applying this analysis to the DNA binding interactions of both minor groove drugs and intercalators are discussed. The solvent water plays a key role in nucleic acid structure and consequently in the binding of ligands to these biomolecules. Any rational approach to DNA-targeted drug design requires an understanding of how water participates in recognition and binding events. Recent studies examining hydration changes that accompany DNA binding by intercalators will be reviewed. Finally some aspects of cooperativity in drug-DNA interactions are described and the importance of considering cooperative effects when examining these reactions is highlighted. (C) 2002 Elsevier Science (USA). All rights reserved.",
	collection = "nucleic acid drugs",
	doi = "10.1016/S0003-9861(02)00202-3",
	localfile = "nucleic acid drugs/2002 - Part II: The thermodynamics of drug-bipolymer interaction.pdf",
	year = 2002
}

@Article{2002-Hesselmann-Jansen,
	Author = "Andreas Heßelmann and Georg Jansen",
	Title = "{Intermolecular induction and exchange-induction energies from coupled-perturbed {Kohn-Sham} density functional theory}",
	Journal = "Chem. Phys. Lett.",
	Volume = "362",
	Number = "3-4",
	Pages = "319–325",
	collection = "molecular interactions",
	doi = "10.1016/S0009-2614(02)01097-7",
	localfile = "molecular interactions/2002 - Intermolecular induction and exchange-induction energies from coupled-perturbed Kohn-Sham density functional theory.pdf",
	year = 2002
}

@Article{2002-Hobza-Sponer,
	Author = "Pavel Hobza and Jiří Šponer",
	Title = "{Toward true {DNA} base-stacking energies: {MP2},
{CCSD(T)}, and complete basis set calculations}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "124",
	Number = "39",
	Pages = "11802–11808",
	abstract = "Stacking energies in low-energy geometries of pyrimidine, uracil, cytosine, and guanine homodimers were determined by the MP2 and CCSD(T) calculations utilizing a wide range of split-valence, correlation-consistent, and bond-functions basis sets. Complete basis set MP2 (CBS MP2) stacking energies extrapolated using aug-cc-pVXZ (X = D, T, and for pyrimidine dimer Q) basis sets equal to -5.3, -12.3, and -11.2 kcal/mol for the first three dimers, respectively. Higher-order correlation corrections estimated as the difference between MP2 and CCSD(T) stacking energies amount to 2.0, 0.7, and 0.9 kcal/mol and lead to final estimates of the genuine stacking energies for the three dimers of -3.4, -11.6, and -10.4 kcal/mol. The CBS MP2 stacking-energy estimate for guanine dimer (-14.8 kcal/mol) was based on the 6-31G*(0.25) and aug-cc-pVDZ calculations. This simplified extrapolation can be routinely used with a meaningful accuracy around 1 kcal/mol for large aromatic stacking clusters. The final estimate of the guanine stacking energy after the CCSD(T) correction amounts to - 12.9 kcal/mol. The MP2/6-31G*(0.25) method previously used as the standard level to calculate aromatic stacking in hundreds of geometries of nucleobase dimers systematically underestimates the base stacking by ca. 1.0-2.5 kcal/mol per stacked dimer, covering 75-90\% of the intermolecular correlation stabilization. We suggest that this correction is to be considered in calibration of force fields and other cheaper computational methods. The quality of the MP2/6-31G*(0.25) predictions is nevertheless considerably better than suggested on the basis of monomer polarizability calculations. Fast and very accurate estimates of the MP2 aromatic stacking energies can be achieved using the Rl-MP2 method. The CBS MP2 calculations and the CCSD(T) correction, when taken together, bring only marginal changes to the relative stability of H-bonded and stacked base pairs, with a slight shift of ca. 1 kcal/mol in favor of H-bonding. We suggest that the present values are very close to ultimate predictions of the strength of aromatic base stacking of DNA and RNA bases.",
	collection = "stacking",
	doi = "10.1021/ja026759n",
	localfile = "molecular stacking/2002 - Toward true DNA base-stacking energies.pdf",
	year = 2002
}

@Article{2002-Jasper-HTP,
	Author = "Ahren W. Jasper and Michael D. Hack and Donald G. Truhlar and Piotr Piecuch",
	Title = "{Coupled quasidiabatic potential energy surfaces for {LiFH}}",
	Journal = "J. Chem. Phys.",
	Volume = "116",
	Number = "19",
	Pages = "8353–8366",
	collection = "molecular reactions",
	doi = "10.1063/1.1463440",
	localfile = "molecular reactions/2002 - Coupled quasidiabatic potential energy surfaces for LiFH.pdf",
	year = 2002
}

@Article{2002-Joubert-Popelier,
	Author = "Laurent Joubert and Paul L. A. Popelier",
	Title = "{The prediction of energies and geometries of hydrogen bonded {DNA} base-pairs via a topological electrostatic potential}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "4",
	Number = "18",
	Pages = "4353–4359",
	abstract = "We introduce an anisotropic model of electrostatic interaction based on topological atoms obtained from the gradient vector field partitioning of the electron density. High- order electrostatic moments are computed within the compact spherical tensor formalism from ab initio wave functions of rigid geometry- optimized monomers. When combined with a simple hard- sphere or Lennard- Jones potential this topological electrostatic interaction potential correctly predicts the geometries of 27 DNA base- pairs. With the Lennard- Jones( LJ) potential internuclear distances of frontier atoms between base- pairs differ only by 0.08 Angstrom compared to supermolecular calculations at B3LYP/ 6- 31G( d, p) level. The discrepancy for angles involved in hydrogen bond contacts amounts to only 3.5degrees. The topological model globally reproduces the correct ranking in intermolecular interaction energy (6.5 +/- 6.5 kJ mol(-1)). Subsequently we compare the interaction energy profiles of the topological model with distributed multipole analysis, Merz-Kollman charges and the natural population analysis at the B3LYP/ 6- 311+ G( 2d, p) level. The convergence of the topological multipole expansion is somewhat more favorable than that based on DMA but the two models have similar basis set dependence. This work encourages the development of a topological intermolecular potential, which already predicts a reliable geometry of a DNA tetrad in its present form.",
	collection = "nucleic acid bases",
	doi = "10.1039/b204485d",
	localfile = "nucleic acid bases/2002 - The prediction of energies and geometries of hydrogen bonded DNA base-pairs.pdf",
	year = 2002
}

@Article{2002-Jurlewicz-Weron,
	Author = "Agnieszka Jurlewicz and Karina Weron",
	Title = "{Relaxation of dynamically correlated clusters}",
	Journal = "J. Non-Crystalline Solids",
	Volume = "305",
	Pages = "112–121",
	cited = "35 (2013-04-29)",
	collection = "statistics",
	doi = "10.1016/S0022-3093(02)01087-6",
	localfile = "statistics/2002 - Relaxation of dynamically correlated clusters.pdf",
	year = 2002
}

@Article{2002-Kallberg-OJP,
	Author = "Yvonne Kallberg and Udo Oppermann and Hans Jörnvall AND Bengt Persson",
	Title = "{Short-chain dehydrogenase/reductase (SDR) relationships: a large family with eight clusters common to human, animal, and plant genomes}",
	Journal = "Protein Science",
	Volume = "11",
	Pages = "636–641",
	Note = "A good introduction to the SDR classes, with a table of 47 human SDRs.",
	cited = "116 (2013-09-09)",
	collection = "proteins",
	doi = "10.1110/ps.26902",
	localfile = "proteins/2002 - Short-chain dehydrogenase-reductase (SDR) relationahips: a large family with eight clusters common to human, animal, and plant genomces.pdf",
	rating = "2",
	read = "2013-09-09",
	system = "SDR",
	year = 2002
}

@Article{2002-Knoll-HLKSZM,
	Author = "A. Knoll and A. Horvat and Kateryna S. Lyakhova and Georg Krausch and G. J. Agur Sevink and Andrei V. Zvelindovsky and R. Magerle",
	Title = "{Phase Behavior in Thin Films of {Cylinder-Forming} Block Copolymers}",
	Journal = "Phys. Rev. Lett.",
	Volume = "89",
	Number = "3",
	Pages = "035501",
	abstract = "We have experimentally determined a phase diagram for cylinder-forming polystyrene-block-polybutadien-block-polystyrene triblock copolymer in thin films. The phase behavior can be modeled in great detail by dynamic density functional theory. Deviations from the bulk structure, such as wetting layer, perforated lamella, and lamella, are identified as surface reconstructions. Their stability regions are determined by an interplay between surface fields and confinement effects.",
	collection = "block copolymers",
	doi = "10.1103/PhysRevLett.89.035501",
	keywords = "block copolymers; thin films",
	localfile = "block copolymers/2002 - Phase behavior in thin films of cylinder-forming block copolymers.pdf",
	year = 2002
}

@Article{2002-Krasteva-BSBMYV,
	Author = "Nadejda Krasteva and Isabelle Besnard and Berit Guse and Roland E. Bauer and Klaus Müllen and Akio Yasuda and Tobias Vossmeyer",
	Title = "{Self-assembled gold nanoparticle-dendrimer composite films for vapor sensing applications}",
	Journal = "Nano Lett.",
	Volume = "2",
	Pages = "551–555",
	collection = "nanotechnology",
	doi = "10.1021/nl020242s",
	keywords = "self-assembly; dendrimers",
	localfile = "nanotechnology/2002 - Self-assembled gold nanoparticle-dendrimer composite films for vapor sensing applications.pdf",
	year = 2002
}

@Article{2002-Krautbauer-FAG,
	Author = "Rupert Krautbauer and Stefan Fischerländer and Stephanie Allen and Hermann E. Gaub",
	Title = "{Mechanical fingerprints of DNA drug complexes}",
	Journal = "Single Mol.",
	Volume = "3",
	Number = "2-3",
	Pages = "97–103",
	abstract = "We have investigated in detail the effects of different minor groove binders and intercalators on the mechanical properties of single DNA molecules under mechanical tension. It is known that individual double stranded DNA molecules show a highly cooperative overstretching transition and may be separated into single strands by application of force. Here we detect non-covalent binding to DNA by mechanical means in AFM based single molecule stretching experiments. The binding of small molecules is found to change the mechanical properties of DNA under tension significantly, and the effects of different binding modes and concentrations are compared. The observed forces and widths of the overstretching transition are found to correlate with magnitudes and ranges of temperatures recorded in DNA thermal melting experiments in the presence of each drug.",
	collection = "nucleic acid drugs",
	doi = "10.1002/1438-5171(200206)3:2",
	localfile = "nucleic acid drugs/2002 - Mechanical fingerprints of DNA drug complexes.pdf",
	year = 2002
}

@Article{2002-Krautbauer-PSAG,
	Author = "Rupert Krautbauer and Lisa H. Pope and Tobias E. Schrader and Stephanie Allen and Hermann E. Gaub",
	Title = "{Discriminating small molecule {DNA} binding modes by single molecule force spectroscopy}",
	Journal = "FEBS Letters",
	Volume = "510",
	Number = "3",
	Pages = "154 – 158",
	abstract = "Drugs may interact with double stranded DNA via a variety of binding modes, each mode giving rise to a specific pharmacological function. Here we demonstrate the ability of single molecule force spectroscopy to discriminate between different interaction modes by measuring the mechanical properties of DNA and their modulation upon the binding of small molecules. Due to the unique topology of double stranded DNA and due to its base pair stacking pattern, DNA undergoes several well-characterised structural transitions upon stretching. We show that small molecule binding markedly affects these transitions in ways characteristic to the binding mode and that these effects can be detected at the level of an individual molecule. The minor groove binder berenil, the crosslinker cisplatin and the intercalator ethidium bromide are compared. (C) 2002 Federation of European Biochemical Societies. Published by Elsevier Science B.V. All rights reserved.",
	collection = "nucleic acid drugs",
	doi = "10.1016/S0014-5793(01)03257-4",
	localfile = "nucleic acid drugs/2002 - Discriminating small molecule DNA binding modes by single molecule force spectroscopy.pdf",
	year = 2002
}

@Article{2002-Kyrylyuk-ZSF,
	Author = "A. V. Kyrylyuk and Andrei V. Zvelindovsky and G. J. Agur Sevink and Johannes G. E. M. Fraaije",
	Title = "{Lamellar Alignment of Diblock Copolymers in an Electric Field}",
	Journal = "Macromolecules",
	Volume = "35",
	Number = "4",
	Pages = "1473–1476",
	abstract = "(Excerpt) Applications in nanotechnology have led to an increased interest toward the incorporation of externally applied field in current models for (micro)phase separation. In the past few years a large number of studies have addressed binary fluids, solution, and melt behavior of block copolymers in an external electric field. Diblock copolymers form a variety of structures (lamellae, body-centered-cubic spheres, hexagonally packed cylinders, and gyroids), the morphology of which depends mainly on the temperature and the volume fraction of the polymer blocks. The reorientation of microdomains in the presence of an electric field has been observed experimentally for lamellar and cylindrical microstructures.",
	collection = "block copolymers",
	doi = "10.1021/ma0110756",
	keywords = "alignment",
	localfile = "block copolymers/2002 - Lamellar alignment of diblock copolymers in an electric field.pdf",
	year = 2002
}

@Article{2002-Lee-TJB,
	Author = "Jae Youn Lee and Russell B. Thompson and David Jasnow and Anna C. Balazs",
	Title = "{Effect of nanoscopic particles on the mesophase structure of diblock copolymers}",
	Journal = "Macromolecules",
	Volume = "35",
	Pages = "4855–4858",
	Note = "Shows phase diagrams as a function of particle size and affinity toward one BCP phase.",
	abstract = "(Excerpt) The fabrication of novel biomimetic photonic and electronic materials requires the manipulation of both organic and inorganic materials at the nanometer length scale. One possible means of achieving this level of control is to add inorganic nanoparticles to a melt of diblock copolymers. The microphase separation of the copolymers into nanoscopic, ordered domains could be harnessed to “template” the organization of the particles into nanoplanes, -wires, or -spheres within the polymer matrix",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma0200266",
	keywords = "block copolymers; mesophase transitions; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2002 - Effect of nanoscopic particles on the mesophase structure of diblock copolymers.pdf",
	methods = "SCFT/DFT",
	year = 2002
}

@Article{2002-Lee-TJB-1,
	Author = "Jae Youn Lee and Russell B. Thompson and David Jasnow and Anna C. Balazs",
	Title = "{Entropically driven formation of hierarchically ordered nanocomposites}",
	Journal = "Phys. Rev. Lett.",
	Volume = "89",
	Number = "15",
	Pages = "155503",
	Note = "Similar to article by same authors in Macromolecules in same year, but with bidisperse populations.",
	collection = "block copolymer nanocomposites",
	doi = "10.1103/PhysRevLett.89.155503",
	keywords = "block copolymers; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2002 - Entropically driven formation of hierarchically ordered nanocomposites.pdf",
	methods = "SCFT/DFT",
	rating = "2",
	read = "2012-03-21",
	year = 2002
}

@Article{2002-Lopez-MGM,
	Author = "Jos Luis Lopez and Marcos Mandado and Ana M. Grana and Ricardo A. Mosquera",
	Title = "{Approximate transferability in alkanenitriles}",
	Journal = "Int. J. Quant. Chem.",
	Volume = "86",
	Number = "2",
	Pages = "190–198",
	abstract = "The atomic and bond properties of a series of alkanenitriles were calculated in order to analyze the transferability of the {CN,} methyl, and methylene groups. The calculations were carried out using the atoms in molecules {(AIM)} theory on {RHF/6-31++G**//} {RHF/6-31G**} wave functions obtained for compounds {CN-R} {(R} ranging from H to {C11H23).} Linear correlations between {L(Omega)} and {N(Omega)} were used to establish {N(CH2)} and {N(CH3)} nearly transferable values. Average values and maximum differences to the mean value of several properties were used for classifying the {CN} group. It shows a transferable behavior along the {CN-R} series for {R\>Et.} The methyl group presents specific properties when {R\<Pr.} The methylene groups can be classified considering both their position with respect to the end of the chain and the position with respect to the {CN} group. The atomic energy displays a dependence on the molecular size. Although this behavior does not allow to consider this property as transferable, both the ab initio total electronic molecular energies and the experimental heats of formation can be fitted, by linear regression analysis, as a function of the number of methylene groups.",
	collection = "molecular fragmentation",
	doi = "10.1002/qua.1624",
	localfile = "molecular fragmentation/2002 - Approximate transferability in alkanenitriles.pdf",
	year = 2002
}

@Article{2002-Matsen,
	Author = "Mark W. Matsen",
	Title = "{The standard Gaussian model for block copolymer melts}",
	Journal = "J. Phys.: Condens. Matter",
	Volume = "14",
	Pages = "R21–R47",
	abstract = "As a result of important advances over the last decade, block copolymer melts have become an excellent model system for studying fundamental phenomena associated with molecular self-assembly. During this time, good quantitative agreement has been achieved between theory and experiment in regards to equilibrium phase behaviour, and with it has emerged a thorough understanding in terms of simple intuitive explanations. The theoretical contributions to this effort are largely attributed to mean-ﬁeld calculations on a standard Gaussian model. Here, we review this present understanding of block copolymer phase behaviour, the model and its underlying assumptions, the mean-ﬁeld approximation and its limitations, and the attempts to incorporate ﬂuctuation corrections. Rather than following the traditional rigorous derivations, we present slightly more intuitive and transparent ones in such a way to stress the close connection between the related calculations. In this way, we hope to provide a valuable introduction to block copolymer theory.",
	collection = "polymers",
	keywords = "block copolymers",
	localfile = "polymers/2002 - The standard Gaussian model for block copolymer melts.pdf",
	year = 2002
}

@Article{2002-Matta-Bader,
	Author = "Chérif F. Matta and Richard F. W. Bader",
	Title = "{Atoms-in-molecules study of the genetically encoded amino acids. {II.} Computational study of molecular geometries}",
	Journal = "Proteins",
	Volume = "48",
	Number = "3",
	Pages = "519–538",
	abstract = "The geometries of the 20 genetically encoded amino acids were optimized at the restricted {Hartree-Fock} level of theory using the {6-31+G*} basis set. A detailed comparison showed the calculated geometries to be in excellent agreement with those determined by X-ray crystallography. The study demonstrated that the geometric parameters for the main-chain group and for the bonds and common functional groups of the side-chains exhibit a high degree of transferability among the members of this set of molecules. This geometric transferability is a necessary prerequisite for the corresponding transferability of their electron density distributions and hence of their bond and atomic properties. The transferability of the electron distributions will be demonstrated and exploited in the following paper of this series, which uses the topology of the electron density to define an atom within the quantum theory of atoms in molecules. Particular features of the geometries of the amino acids are discussed. It has been shown, for example, how the apparent anomaly of the {Calpha\&bond;N} bond length in a peptide being shorter than in the charged species {Calpha\&bond;NH+3} is resolved when the charge separation is gauged by the differences in the charges of the Calpha and N atoms as opposed to the use of formal charges. A compilation of literature sources on experimental geometries covering each member of the 20 amino acids is presented. A set of rules for labeling the atoms and bonds, complementing the generally accepted {IUPAC-IUB} rules, is proposed to uniquely identify every atom and bond in the amino acids.",
	collection = "protein amino acids",
	doi = "10.1002/prot.10170",
	localfile = "protein amino acids/2002 - AIM study of the genetically encoded amino acids. II. Computational study of molecular geometries.pdf",
	year = 2002
}

@Article{2002-Menger,
	Author = "Frederic M. Menger",
	Title = "{Supramolecular chemistry and self-assembly}",
	Journal = "Proc. Natl. Acad. Sci.",
	Volume = "99",
	Number = "8",
	Pages = "4818–4822",
	abstract = "(Excerpt) Supramolecular chemistry, broadly speaking, entails the study of intermolecular bonding. The discipline blossomed two decades ago with host–guest systems in which (i) metal ions were complexed to crown ethers and (ii) small molecules (such as urea) were bound to larger hosts by means of multiple hydrogen bonds. One of my favorite examples is cited below.",
	collection = "molecular interactions",
	doi = "10.1073/pnas.062524299",
	localfile = "molecular interactions/2002 - Supramolecular chemistry and self-assembly.pdf",
	shorttitle = "Supramolecular Chemistry And Self-assembly Special Feature",
	year = 2002
}

@Article{2002-Morita-KDYTH,
	Author = "Hiroshi Morita and Toshihiro Kawakatsu and Masao Doi and Daisuke Yamaguchi and Mikihito Takenaka and Takeji Hashimoto",
	Title = "{Competition between micro- and macrophase separations in a binary mixture of block copolymers. A dynamic density functional study}",
	Journal = "Macromolecules",
	Volume = "35",
	Pages = "7473–7480",
	collection = "block copolymers",
	doi = "10.1021/ma0203997",
	keywords = "block copolymers",
	localfile = "block copolymers/2002 - Competition between micro- and macrophase separations i na binary mixture of block copolymers. A dynamic density functional study.pdf",
	year = 2002
}

@Article{2002-Mui-THSLWCMMMS,
	Author = "S. C. Mui and P. E. Trapa and B. Huang and Philip P. Soo and M. I. Lozow and T. C. Wang and R. E. Cohen and A. N. Mansour and S. Mukerjee and Anne M. Mayes and Donald R. Sadoway",
	Title = "{Block copolymer-templated nanocomposite electrodes for rechargeable litium matteries}",
	Journal = "J. Electrochem. Soc.",
	Volume = "149",
	Number = "12",
	Pages = "A1610–A1615",
	collection = "block copolymer nanocomposites",
	doi = "10.1149/1.1518482",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2002 - Block Copolymer-Templated Nanocomposite Electrodes for Rechargeable Lithium Batteries.pdf",
	year = 2002
}

@Article{2002-Muller-Plathe,
	Author = "Florian Müller-Plathe",
	Title = "{Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back}",
	Journal = "ChemPhysChem",
	Volume = "3",
	Pages = "754–769",
	abstract = "Polymers can be theoretically and computationally described by models pertaining to different length scales and corresponding time scales. These models have traditionally been used independently of each other. Recently, considerable progress has been made in systematically linking models of different scales. This Review focuses on the generation of lattice and off-lattice coarse-grained polymer models, whose “monomers” correspond to roughly a chemical repeat unit, from chemically detailed atomistic simulations of the same polymers. Computational methods are described as well as applications to polymers in the melt and in solution. The success of multiscale simulations in solving real-world polymer problems that could not be solved in any other way suggests that they will have an important role to play in the future.",
	collection = "coarse graining",
	doi = "10.1002/1439-7641(20020916)3:9",
	keywords = "coarse graining; polymers",
	localfile = "coarse graining/2002 - Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back.pdf",
	type = "Review",
	year = 2002
}

@Article{2002-Murdachaew-SB,
	Author = "Garold Murdachaew and Krzysztof Szalewicz and Robert Bukowski",
	Title = "{Efficient generation of flexible-monomer intermolecular potential energy surfaces}",
	Journal = "Phys. Rev. Lett.",
	Volume = "88",
	Number = "12",
	Pages = "123202",
	abstract = "A new method of generating ﬂexible-monomer intermolecular interaction potentials has been proposed. The method, based on symmetry-adapted perturbation theory, extends a rigid-monomer potential into a ﬂexible-monomer one at a cost negligible compared to performing calculations on a full-dimensional grid (i.e., including internal degrees of freedom of monomers). The nonrigidity effects are accounted for by density-overlap integrals and by asymptotic expansion coefﬁcients. Results for a model system (Ar-HF) demonstrate that the method recovers a substantial portion of these effects.",
	collection = "molecular interactions",
	doi = "10.1103/PhysRevLett.88.123202",
	localfile = "molecular interactions/2002 - Efficient generation of flexible-monomer intermolecular potential energy surfaces.pdf",
	year = 2002
}

@Article{2002-Noguchi-Takasu,
	Author = "Hiroshi Noguchi and Masako Takasu",
	Title = "{Adhesion of nanoparticles to vesicles: a Brownian dynamics simulation}",
	Journal = "Biophys. J.",
	Volume = "83",
	Pages = "299–308",
	abstract = "We studied the interaction of bilayer vesicles and adhesive nanoparticles using a brownian dynamics simulation. The nanoparticles are simple models of proteins aor colloids. The adhering nanoparticle induces the morphological change of the vesicle: budding, formation of two vesicles in which only the outer monolayers are connected, and fission. We also show that the nanoparticle promotes the fusion process: fusion-pore opening from a stalk intermediate, a neck-like structure that only connects outer monolayers of two vesicles. The nanoparticle blends the stalk, and induces the pore opening.",
	collection = "lipid bilayers",
	doi = "10.1016/S0006-3495(02)75170-9",
	keywords = "biological nanocomposites; lipid bilayers; nanospheres",
	localfile = "lipid bilayers/2002 - Adhesion of nanoparticles to vesicles: a Brownian dynamics simulation.pdf",
	methods = "CG BD",
	year = 2002
}

@Article{2002-Oxtoby,
	Author = "David A. Oxtoby",
	Title = "{Density functional methods in the statistical mechanics of materials}",
	Journal = "Ann. Rev. Mater. Res.",
	Volume = "32",
	Pages = "39–52",
	abstract = "Methods of density functional theory in statistical mechanics have been applied extensively over the past 15 years to problems in the equilibrium and dynamic properties of materials. They allow the incorporation of microscopic atomic and molecular forces at a much lower computational cost than direct simulation. This review discusses recent advances in the calculation of density functionals for materials, with particular emphasis on ﬂuids at walls and in porous media, on crystal nucleation and growth from the melt, and on complex ﬂuids and biomolecules. The extension of equilibrium density functional methods to approximate theories of phase transition dynamics is emphasized.",
	collection = "polymers",
	doi = "10.1146/annurev.matsci.32.100401.103425",
	localfile = "polymers/2002 - Density functional methods in the statistical mechanics of materials.pdf",
	year = 2002
}

@Article{2002-Politzer-LC,
	Author = "Peter Politzer and Pat Lane and Monica C. Concha",
	Title = "{Atomic and molecular energies in terms of electrostatic potentials at nuclei}",
	Journal = "Int. J. Quant. Chem.",
	Number = "90",
	Pages = "459–463",
	abstract = "Several formulas, both exact and approximate, that relate atomic and molecular energies to electrostatic potentials at nuclei are discussed in terms of the relative contributions of the nuclear–electronic, nuclear–nuclear, and electronic–electronic interactions. These quantities and related ratios are evaluated at the density functional B3PW91/6-311+G(3df,2pd) level for a group of 24 molecules. A modiﬁed version of an approximate molecular energy expression is tested and found to give improved results.",
	collection = "quantum chemistry",
	doi = "10.1002/qua.10105",
	localfile = "quantum chemistry/2002 - Atomic and molecular energies in terms of elecrtostatic potentials at nuclei.pdf",
	year = 2002
}

@Article{2002-Reha-KRSSESH,
	Author = "David Řeha and Martin Kabeláč and Filip Ryjáček and Jiří Šponer and Judit E. Šponer and Marcus Elstner and Sándor Suhai and Pavel Hobza",
	Title = "{{Intercalators. 1. {N}ature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4 ',6-diaminide-2-phenylindole) and {DNA} base pairs. {A}b initio quantum chemical, density functional theory, and empirical potential study}1}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "124",
	Number = "13",
	Pages = "3366–3376",
	abstract = "Properties of isolated intercalators (ethidium (E), daunomycin (D), ellipticine (EL), and 4,6'-diaminide-2-phenylindole (DAPI)) and their stacking interactions with adenine(...)thymine (AT) and guanine(...)cytosine (GC) nucleic acid base pairs were investigated by means of a nonempirical correlated ab initio method. All intercalators exhibit large charge delocalization, and none of them (including the DAPI dication) exhibits a site with dominant charge. All intercalators have large polarizability and are good electron acceptors, while base pairs are good electron donors. MP2/6-31G*(0.25) stabilization energies of intercalator(...)base pair complexes are large (E(...)AT, 22.4 kcal/mol; D(...)GC, 17.8 kcal/mol; EL(...)GC, 18.2 kcal/mol; DAPI(...)GC, 21.1 kcal/mol) and are well reproduced by modified AMBER potential (van der Waals radii of intercalator atoms are enlarged and their energy depths are increased). Standard AMBER potential underestimates binding, especially for DAPI-containing complexes. Because the DAPI dication is the best electron acceptor (among all intercalators studied), this difference is explained by the importance of the charge-transfer term, which is not included in the AMBER potential. For the neutral EL molecule, the standard AMBER force field provides correct results. The Hartree-Fock and DFT/B3LYP methods, not covering the dispersion energy, fail completely to reveal any energy minimum at the potential energy curve of the E(...)AT complex, and these methods thus cannot be recommended for a study of intercalation process. On the other hand, an approximate version of the DFT method, which was extended to cover London dispersion energy, yields for all complexes very good stabilization energies that are well comparable with referenced ab initio data. Besides the vertical dependence of the interaction, an energy twist dependence of the interaction energy was also investigated by a reference correlated ab initio method and empirical potentials. It is concluded that, despite the cationic (E + 1, D + 1, DAPI + 2) or polar (EL) character of the intercalators investigated, it is the dispersion energy which predominantly contributes to the stability of intercalator(...)DNA base pair complexes. Any procedure which does not cover dispersion energy is thus not suitable for studying the process of intercalation.",
	cited = "43 (2005-04-13)",
	collection = "nucleic acid intercalation",
	doi = "10.1021/ja011490d",
	keywords = "nucleic acid intercalation; aromatic stacking",
	localfile = "nucleic acid intercalation/2002 - Intercalators. 1. Nature of stacking interactions between intercalators and DNA base pairs. Ab initio quantum checmical, density functional theory, and empirical study.pdf",
	year = 2002
}

@Article{2002-Rhodes-IRMTIT,
	Author = "David A. Rhodes and Gudrun Ihrke and Anna T. Reinicke and Georg Malcherek and Michael Towey and David A. Isenberg and John Trowsdale",
	Title = "{The 52 000 MW Ro/SS-A autoantigen in Sjögren's syndrom - systemic lupus erythematosus (Ro52) is an interferon-gamma inducible tripartite motif protein associated with membrane proximal structures}",
	Journal = "Immunology",
	Volume = "106",
	Pages = "246–256",
	collection = "cells",
	localfile = "cells/2002 - The 52 000 MW Ro-SS-A autoantigen in Sjogren's syndrome-systemic lupus erythematosus (Ro52) is an interferon-gamma inducible tripartite motif protein associated with membrane proximal structures.pdf",
	year = 2002
}

@Article{2002-Scerri,
	Author = "Eric R. Scerri",
	Title = "{Have orbitals really been observed?}",
	Journal = "J. Chem. Ed.",
	Volume = "79",
	Number = "3",
	Pages = "310",
	abstract = "(Excerpt) I would like to thank Spence et al. for their response to my article, in which I criticized what I, and others, took to be a claim for the observation of atomic orbitals.",
	collection = "philosophy",
	doi = "10.1021/ed079p310.1",
	localfile = "philosophy/2002 - Have orbitals really been observed.pdf",
	year = 2002
}

@Article{2002-Schmidt-Fuchs,
	Author = "Matthias Schmidt and Matthias Fuchs",
	Title = "{Penetrability in model colloid–polymer mixtures}",
	Journal = "J. Chem. Phys.",
	Volume = "117",
	Number = "13",
	Pages = "6308–6312",
	abstract = "In order to study the effects of penetrability in mixtures of dissimilar particles we consider hard (colloidal) spheres and penetrable spheres. The latter may be taken to represent ideal, noninteracting polymer coils. Polymers and colloids interact by means of a repulsive step-function pair potential, which allows for insertion of colloids into the polymer coil. The potential strength is obtained from scaling arguments for the cross virial coefficient of true colloid–polymer systems. For this model we construct a geometry-based density functional and apply it to bulk fluid demixing. We find that taking into account penetrability leads to a significant stabilization of the mixed phase for large polymer-to-colloid size ratio.",
	collection = "polymer nanocomposites",
	keywords = "polymer nanocomposites",
	localfile = {},
	year = 2002
}

@Article{2002-Sponer-LH,
	Author = "Jiří Šponer and Jerzy Leszczyński and Pavel Hobza",
	Title = "{Electronic properties, hydrogen bonding, stacking, and cation binding of {DNA} and {RNA} bases}",
	Journal = "Biopolymers",
	Volume = "61",
	Number = "1",
	Pages = "3–31",
	abstract = "This review summarizes results concerning molecular interactions of nucleic acid bases as revealed by advanced ab initio quantum chemical (QM) calculations published in last few years. We first explain advantages and limitations of modem QM calculations of nucleobases and provide a brief history of this still rather new field. Then we provide an overview of key electronic properties of standard and selected modified nucleobases, such as their charge distributions, dipole moments, polarizabilities, proton affinities, tautomeric equilibria, and amino group hybridization. Then we continue with hydrogen bonding of nucleobases, by analyzing energetics of standard basepairs,yI mismatched base pairs, thio-base pairs, and others. After this, the nature of aromatic stacking interactions is explained. Also, nonclassical interactions in nucleic acids such as interstrand bifurcated hydrogen bonds, interstrand close amino group contacts, C-H... O interbase contacts, sugars base stacking, intrinsically nonplanar base pairs, out-of-plane hydrogen bonds, and amino-acceptor interactions are commented on. Finally, we overview recent calculations on interactions between nucleic acid bases and metal cations, These studies deal with effects of cation binding on the strength of base pairs, analysis of specific differences among cations, such as the difference between zinc and magnesium, the influence of metalation on protonation and tautomeric equlibria of bases, and cation-pi,T interactions involving nucleobases. In this review, we do not provide methodological details, as these can be found in our preceding reviews. The interrelation between advanced QM approaches and classical molecular dynamics simulations is briefly discussed. (C) 20021 Wiley Periodicals, Inc.",
	collection = "nucleic acid bases",
	doi = "10.1002/1097-0282(2001)61:1",
	localfile = "nucleic acid bases/2002 - Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases.pdf",
	year = 2002
}

@Article{2002-Stone-Alderton,
	Author = "Anthony J. Stone and M. Alderton",
	Title = "{Distributed multipole analysis: methods and applications}",
	Journal = "Mol. Phys.",
	Volume = "100",
	Number = "1",
	Pages = "221–233",
	abstract = "The conventional multipole expansion gives a description of electrostatic interactions which is only useful at long distances. Distributed multipole analysis gives a description which is accurate at all accessible distances, and also gives a much more detailed and instructive picture of the charge distribution. We report our recent investigations into the method and comment on its limitations.",
	collection = "molecular electrostatics",
	doi = "10.1080/00268970110089432",
	keywords = "multipole expansion",
	localfile = "molecular electrostatics/2002 - Distributed multipole analysis: methods and applications.pdf",
	year = 2002
}

@Article{2002-Sudo-SKY,
	Author = "Seiichi Sudo and Naoki Shinyashiki and Yusuke Kitsuki and Shin Yagihara",
	Title = "{Dielectric relaxation time and relxation time distribution of alcohol-water mixtures}",
	Journal = "J. Phys. Chem. A",
	Volume = "106",
	Pages = "458–464",
	cited = "64 (2013-04-29)",
	collection = "molecular solvation",
	doi = "10.1021/jp013117y",
	localfile = "molecular solvation/2002 - Dielectric relaxation time and relaxation time distribution of alcohol-water mictures.pdf",
	year = 2002
}

@Article{2002-Suppa-KBY,
	Author = "Domenico Suppa and Olga Kuksenok and Anna C. Balazs and J. M. Yeomans",
	Title = "{Phase separation of a binary fluid in the presence of immobile particles: a lattice Boltzmann approach}",
	Journal = "J. Chem. Phys.",
	Volume = "116",
	Number = "14",
	Pages = "6305–6310",
	collection = "interfaces",
	doi = "10.1063/1.1460863",
	keywords = "binary fluids; suspensions",
	localfile = "interfaces/2002 - Phase separation of a binary fluid in the presence of immobile particles: a lattice Boltzmann approach.pdf",
	methods = "LB",
	year = 2002
}

@Article{2002-Szefczyk-SL,
	Author = "Borys Szefczyk and W. Andrzej Sokalski and Jerzy Leszczyński",
	Title = "{Optimal methods for calculation of the amount of intermolecular electron transfer}",
	Journal = "J. Chem. Phys.",
	Volume = "117",
	Number = "15",
	Pages = "6952–6958",
	abstract = "In order to determine the optimal methodology for evaluation of the magnitude of intermolecular charge transfer, several methods have been examined: Mulliken population, natural population analysis, atoms in molecules AIM as well as charges from electrostatic potentials using a grid-based method Chelp and Chelpg procedures using a series of correlation consistent cc-pVXZ X D, T, Q basis sets within LCAO MO SCF, MP2, DFT, and coupled cluster theory levels. In contrast to previous nonconclusive comparative studies, the present calculations reveal close matching of the recently available experimental data for six Lewis acid-base adducts with theoretical values derived from the Chelpg approach, whereas for the remaining methods relative errors are almost doubled. On the other hand, AIM and Chelpg results display the best linear correlation coefﬁcients with the experimental data. Since reasonably accurate Chelpg results could be already obtained with SCF or DFT B3LYP methods using cc-pVDZ, such an approach opens the way to study intermolecular charge transfer in larger molecular systems. Preliminary results obtained within cc-pVDZ basis set and B3LYP functional for pyridine-SO3 complex do not exceed relative error limits observed for other smaller complexes. Analysis of corresponding interaction energy components calculated consistently in the dimer basis set indicates signiﬁcant role of electrostatic, exchange and delocalization contributions, with rather negligible correlation term. In contrast to previous ﬁndings, the experimentally observed amount of transferred charge seems not to correlate with any interaction energy term.",
	collection = "molecular fragmentation",
	doi = "10.1063/1.1508367",
	localfile = "molecular fragmentation/2002 - Optimal methods for calculation of the amount of intermolecular electron transfer.pdf",
	year = 2002
}

@Article{2002-Thompson-GMB,
	Author = "Russell B. Thompson and Valeriy V. Ginzburg and Mark W. Matsen and Anna C. Balazs",
	Title = "{Block copolymer-directed assembly of nanoparticles: forming mesoscopically ordered hybrid materials}",
	Journal = "Macromolecules",
	Volume = "35",
	Pages = "1060–1071",
	Note = "Describes the SCFT/DFT combination, demonstrates some 1D, 2D and 3D configurations and discusses possible extensions.",
	abstract = "Mixtures of diblock copolymers and nanoscopic spherical particles can yield well-ordered hybrid materials, which can be used for separation processes, catalysis, and optoelectronic applications. Predicting the morphologies of these systems is difficult because the final structures depend not only on the characteristics of the copolymer but also on the features of the particles. Combining self-consistent field and density functional theories, we develop a model that allows us to determine the equilibrium or metastable phases of diblock copolymer/spherical nanoparticle composites, without making a priori assumptions about the structure of the system. Using this model, we illustrate various examples where mixtures of diblocks and nanoparticles self-assemble into mesoscopically ordered phases. The model can be generalized to other types of copolymers and particles and can be modified to include homopolymers or solvent molecules. Thus, the technique constitutes a useful tool for determining the structures of a large class of nanocomposites.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma011563d",
	keywords = "block copolymers; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2002 - Block copolymer-directed assembly of nanoparticles: forming mesoscopically ordered hybrid materials.pdf",
	methods = "SCFT/DFT",
	year = 2002
}

@Article{2002-Thompson-LJB,
	Author = "Russell B. Thompson and Jae Youn Lee and David Jasnow and Anna C. Balazs",
	Title = "{Binary hard sphere mixtures in block copolymer melts}",
	Journal = "Phys. Rev. E",
	Volume = "66",
	Pages = "031801",
	collection = "block copolymer nanocomposites",
	doi = "10.1103/PhysRevE.66.031801",
	keywords = "block copolymers; nanoparticle distribution; nanospheres; polydispersity; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2002 - Binary hard sphere mixtures in block copolymer melts.pdf",
	methods = "SCFT/DFT",
	year = 2002
}

@Article{2002-Tsai-MN,
	Author = "Chung-Jung Tsai and Jr. {Jacob V. Maizel} and Ruth Nussinov",
	Title = "{The hydrophobic effect: a new insight from cold denaturation and a two-state water structure}",
	Journal = "Crit. Rev. Biochem. Mol. Biol.",
	Volume = "37",
	Number = "2",
	Pages = "55–69",
	cited = "52 (2013-04-29)",
	collection = "protein structure",
	doi = "10.1080/10409230290771456",
	keywords = "hydrophobic effect; protein folding",
	localfile = "protein structure/2002 - The hydrophobic effect: a new insight from cold denaturation and a two-state water structure.pdf",
	year = 2002
}

@Article{2002-Tschumper-LHVIQ,
	Author = "Gregory S. Tschumper and Matthew L. Leininger and Brian C. Hoffman and Edward F. Valeev and {Henry F. III} Schaefer and Martin Quack",
	Title = "{Anchoring the water dimer potential energy surface with explicitly correlated computations and focal point analyses}",
	Journal = "J. Chem. Phys.",
	Volume = "116",
	Number = "2",
	Pages = "690 – 701",
	abstract = "Ten stationary points on the water dimer potential energy surface have been characterized with the coupled-cluster technique which includes all single and double excitations as well as a perturbative approximation of triple excitations [CCSD(T)]. Using a triple-zeta basis set with two sets of polarization functions augmented with higher angular momentum and diffuse functions [TZ2P(f,d)+dif], the fully optimized geometries and harmonic vibrational frequencies of these ten stationary points were determined at the CCSD(T) theoretical level. In agreement with other ab initio investigations, only one of these ten stationary points is a true minimum. Of the other nine structures, three are transition structures, and the remaining are higher order saddle points. These high-level ab initio results indicate that the lowest lying transition state involved in hydrogen interchange is chiral, of C-1 symmetry rather than C-s as suggested by recently developed 6D potential energy surfaces. The one- and n-particle limits of the electronic energies of these ten stationary points were probed by systematic variation of the atomic orbital basis sets and the treatment of electron correlation within the framework of the focal-point analysis of Allen and co-workers. The one-particle limit was approached via extrapolation of electronic energies computed with the augmented correlation consistent basis sets (aug-cc-pVXZ, X=D-6), and, independently, by estimating the basis set incompleteness effect with the explicitly-correlated second-order Møller–Plesset method (MP2-R12). Electron correlation was evaluated at levels as high as the Brueckner coupled cluster method with double excitations and perturbatively treated triple and quadruple excitations [BD(TQ)]. Core correlation and relativistic effects were also assessed. Consideration of the aforementioned electronic effects as well as basis set superposition error leads to an estimate of 21.0 kJ mol(-1) for the electronic dissociation energy of (H2O)(2). (C) 2002 American Institute of Physics.",
	collection = "hydrogen bonding",
	doi = "10.1063/1.1408302",
	localfile = "hydrogen bonding/2002 - Anchoring the water dimer potential energy surface with explicitly correlated computations and focal point analyses.pdf",
	methods = "CCSD(T)",
	systems = "water dimer",
	year = 2002
}

@Article{2002-Tsori-Andelman,
	Author = "Yoav Tsori and David Andelman",
	Title = "{Thin film diblock copolymers in electric field: transition from perpendicular to parallel lamellae}",
	Journal = "Macromolecules",
	Volume = "35",
	Pages = "5161–5170",
	abstract = "We examine the alignment of thin film diblock copolymers subject to a perpendicular electric field. Two regimes are considered separately: weak segregation and strong segregation. For weakly segregated blocks and below a critical value of the field, Ec, surface interactions stabilize stacking of lamellae in a direction parallel to the surfaces. Above the critical field, a first-order phase transition occurs when lamellae in a direction perpendicular to the confining surfaces (and parallel to the field) become stable. The film morphology is then a superposition of parallel and perpendicular lamellae. In contrast to Helfrich-Hurault instability for smectic liquid crystals, the mode that gets critical first has the natural lamellar periodicity. In addition, undulations of adjacent intermaterial dividing surfaces are out-of-phase with each other. For diblock copolymers in the strong segregation regime, we find two critical fields E1 and E2 > E1. As the field is increased from zero above E1, the region in the middle of the film develops an orientation perpendicular to the walls, while the surface regions still have parallel lamellae. When the field is increased above E2, the perpendicular alignment spans the whole film. In another range of parameters, the transition from parallel to perpendicular orientation is direct.",
	collection = "block copolymers",
	keywords = "block copolymers; electric fields; mesophase transitions",
	localfile = "block copolymers/2002 - Thin film diblock copolymers in electric field: transition from perpendicular to parallel lamellae.pdf",
	rating = "2",
	year = 2002
}

@Article{2002-Tsuzuki-HUMT,
	Author = "Seiji Tsuzuki and Kazumasa Honda and Tadafumi Uchimaru and Masuhiro Mikami and K. Tanabe",
	Title = "{Origin of Attraction and Directionality of the π/π Interaction: Model Chemistry Calculations of Benzene Dimer Interaction}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "124",
	Number = "1",
	Pages = "104–112",
	abstract = "A model chemistry for the evaluation of intermolecular interaction between aromatic molecules (AIMI Model) has been developed. The CCSD(T) interaction energy at the basis set limit has been estimated from the MP2 interaction energy near the basis set limit and the CCSD(T) correction term obtained by using a medium size basis set. The calculated interaction energies of the parallel, T-shaped and slipped-parallel benzene dimers are -1.48, -2.46, and -2.48 kcal/mol, respectively, The substantial attractive interaction in benzene dimer, even where the molecules are well separated, shows that the major source of attraction is not short-range interactions such as charge-transfer but long-range interactions such as electrostatic and dispersion. The inclusion of electron correlation increases attraction significantly. The dispersion interaction is found to be the major source of attraction in the benzene dimer, The orientation dependence of the dimer interaction is mainly controlled by long-range interactions. Although electrostatic interaction is considerably weaker than dispersion interaction, it is highly orientation dependent. Dispersion and electrostatic interactions are both important for the directionality of the benzene dimer interaction.",
	collection = "stacking",
	doi = "10.1021/ja0105212",
	localfile = "molecular stacking/2002 - Origin of attraction and directionality of the pi-pi interaction: model chemistry calculations of benzene Dimer interaction.pdf",
	year = 2002
}

@Article{2002-Voter-MG,
	Author = "Arthur F. Voter and Francesco Montalenti and Timothy C. Germann",
	Title = "{Extending the time scale in atomistic simulation of materials}",
	Journal = "Ann. Rev. Mater. Res.",
	Volume = "32",
	Pages = "321–346",
	abstract = "Obtaining a good atomistic description of diffusion dynamics in materials has been a daunting task owing to the time-scale limitations of the molecular dynamics method. We discuss promising new methods, derived from transition state theory, for accelerating molecular dynamics simulations of these infrequent-event processes. These methods, hyperdynamics, parallel replica dynamics, temperature-accelerated dynamics, and on-the-ﬂy kinetic Monte Carlo, can reach simulation times several orders of magnitude longer than direct molecular dynamics while retaining full atomistic detail. Most applications so far have involved surface diffusion and growth, but it is clear that these methods can address a wide range of materials problems.",
	collection = "molecular dynamics",
	doi = "10.1146/annurev.matsci.32.112601.141541",
	localfile = "molecular dynamics/2002 - Extending the time scale in atomistic simultion of materials.pdf",
	year = 2002
}

@Article{2002-Wang,
	Author = "James C. Wang",
	Title = "{Cellular roles of {DNA} topoisomerases: {A} molecular perspective}",
	Journal = "Nat. Rev. Mol. Cell Biol.",
	Volume = "3",
	Number = "6",
	Pages = "430 – 440",
	abstract = "DNA topoisomerases are the magicians of the DNA world - by allowing DNA strands or double helices to pass through each other, they can solve all of the topological problems of DNA in replication, transcription and other cellular transactions. Extensive biochemical and structural studies over the past three decades have provided molecular models of how the various subfamilies of DNA topoisomerase manipulate DNA. In this review, the cellular roles of these enzymes are examined from a molecular point of view.",
	collection = "nucleic acids",
	doi = "10.1038/nrm831",
	localfile = "nucleic acids/2002 - Cellular roles of DNA topoisomerases: a molecular perspective.pdf",
	year = 2002
}

@Article{2002-Waters,
	Author = "Marcey L. Waters",
	Title = "{Aromatic interactions in model systems}",
	Journal = "Curr. Op. Chem. Biol.",
	Volume = "6",
	Number = "6",
	Pages = "736–741",
	abstract = "A thorough knowledge of noncovalent interactions is crucial to the understanding of biological complexity. One of the less well understood but significant weak interactions in nature is the aromatic interaction. Recent studies have provided new insight into the driving force, stability and selectivity of these interactions. The contribution of sol

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repo_name: langner/library

branch_name: refs/heads/master