text:
aromatic-aromatic interactions, however, are not yet clear.",
	cited = "125 (2005-04-27)",
	collection = "stacking",
	doi = "10.1021/ja00090a057",
	localfile = "molecular stacking/1994 - Aromatic stacking interactions in aqueous solution.pdf",
	year = 1994
}

@Article{1994-Peek-VSP,
	Author = "R. Peek and W. J. {van Venrooij} and F. Simons and G. Pruijn",
	Title = "{The SS-A/SS-B autoantigenic complex: localization and assembly}",
	Journal = "Clin. Exp. Rheumatol.",
	Volume = "12 suppl 11",
	Pages = "S15–S18",
	collection = "cells",
	localfile = {},
	year = 1994
}

@Article{1994-Strasburger-Sokalski,
	Author = "Krzysztof Strasburger and W. Andrzej Sokalski",
	Title = "{Intramolecular electrostatic interactions studied by cumulative atomic multipole moment expansion with improved convergence}",
	Journal = "Chem. Phys. Lett.",
	Volume = "221",
	Number = "1-2",
	Pages = "129–135",
	abstract = "A novel approach allowing the estimation of intramolecular electrostatic interactions has been applied to evaluate torsional barriers for model HO-OH, CH3-CH, and H2FSi-SiFH2 systems. Interactions between rotated fragments have been estimated from cumulative atomic multipole moments (CAMM) calculated for frozen molecular fragments and compared with corresponding ab initio results. The exclusion of all intersegment components of the global density matrix resulted in considerably improved convergence of the moment-truncated expansion. CAMM generated for different conformers yield similar results, indicating reasonable transferability of frozen fragment CAMM. The close qualitative and quantitative correspondence between atomic multipole and non-empirical ab initio results indicates the dominant electrostatic nature of the intramolecular torsional barriers.",
	cited = "7 (2005-05-05)",
	collection = "molecular electrostatics",
	doi = "10.1016/0009-2614(94)87028-4",
	localfile = "molecular electrostatics/1994 - Intramolecular electrostatic interactions studied by cumulative atomic multipole moment expansion with improved convergence.pdf",
	year = 1994
}

@Article{1995-Bader,
	Author = "Richard F. W. Bader",
	Title = "{Chemistry and the near-sighted nature of the one-electron density matrix}",
	Journal = "Int. J. Quant. Chem.",
	Volume = "56",
	Number = "4",
	Pages = "409–419",
	abstract = "Two different macrospopic pieces of copper have different external potentials and, because of the unique functional relationship between the electron density and the external potential as demanded by density functional theory, should possess different electron density distributions. Experimentally, however, an atom in the bulk exhibits the same electron density in both samples and they possess identical sets of intensive properties. Density functional theory does not account for the fundamental observation underlying the theory of atoms in molecules: that what are apparently identical distributions of charge can be observed for an atom or a grouping of atoms in systems with different external potentials and that these atoms contribute essentially identical amounts to the energies and all other properties of the systems in which they occur. It is shown that, unlike the external potential, the kinetic energy density and the potential energy density, defined by the virial of the Ehrenfest force acting on electron density, are short-range functions. As recorded in the first article on atoms in molecules, they exhibit a local dependence on the electron density that causes them to faithfully mimic the transferability of the atomic charge distributions from one system to another. The electron, the kinetic energy, and the virial densities are all determined directly by the one-electron density matrix, a function termed near-sighted by Professor Kohn. It is this near-sighted property of the one-matrix that underlies the working hypothesis of chemistry - that of a functional group exhibiting a characteristic set of properties. The observations obtained from the theory of atoms in molecules and the atomic theorems it determines demonstrate the existence of a local relationship between the electron density and all properties of a system.",
	collection = "quantum chemistry",
	doi = "10.1002/qua.560560427",
	localfile = "quantum chemistry/1994 - Chemistry and the near-sighted nature of the one-electron density matrix.pdf.pdf",
	year = 1995
}

@Article{1995-Challacombe-SA,
	Author = "Matt Challacombe and Eric Schwegler and Jan Almlöf",
	Title = "{Recurrence relations for calculation of the cartesian multipole tensor}",
	Journal = "Chem. Phys. Lett.",
	Volume = "241",
	Number = "1-2",
	Pages = "67–72",
	abstract = "We demonstrate that the Cartesian multipole interaction tenser may be evaluated with recurrence relations analogous to the McMurchie-Davidson algorithm for calculation of electron repulsion integrals. With these recursion relations all elements of the Cartesian multipole tenser through order L may be calculated in O(L(4)) CPU time, in contrast to current methods that scale as O(L(6)).",
	cited = "11 (2005-05-20)",
	collection = "molecular electrostatics",
	doi = "10.1016/0009-2614(95)00597-W",
	keywords = "algorithms",
	localfile = "molecular electrostatics/1995 - Recurrence relations for calculations of the Cartesian multipole tensor.pdf",
	rating = "2",
	year = 1995
}

@Article{1995-Cybulski-BCS,
	Author = "Sławomir M. Cybulski and Rudolf Burcl and Grzegorz Chałasiński and Małgorzata M. Szczęśniak",
	Title = "{Partitioning of interaction energy in van der Waals complexes involving excited state species}",
	Journal = "J. Chem. Phys.",
	Volume = "103",
	Pages = "10116",
	abstract = "The partitioning of interaction energy between a closed-shell and an open-shell system is proposed. This allows us to describe the unrestricted Møller–Plesset interaction energy as a sum of fundamental contributions: electrostatic, exchange, induction and dispersion. The supermolecular energies derived within unrestricted Møller–Plesset perturbation theory are analyzed in terms of perturbation theory of intermolecular forces. The latter has been generalized to allow for the description of monomer wave functions within the unrestricted Hartree–Fock approach. The method is applied to the potential energy surfaces for the ﬁrst excited triplet states, $^3A'$ and $^3A''$ , of the He+Cl$\_2$(3$\Pi\_u$) complex. The $^3A'$ and $^3A''$ potential energy surfaces have different shapes. The lower one, $^3A'$ , has a single minimum for the T-shaped structure. The higher one, $^3A''$ , has the global minimum for the T-shaped structure and the secondary minimum for a linear orientation. The calculated well depth for the $^3A'$ state is 31.1 cm$^{-1}$ at the 3.75 Å intersystem separation at the UMP2 level with extended basis set involving bond functions. The $^3A''$ well depth is approximately 2.3 cm$^{-1}$ smaller at this level. This order is reversed by higher correlation effects. The angular and radial behaviors of the individual components of the $^3A'$ and $^3A''$ interaction energies are compared to reveal the different nature of interaction energies in both states. A comparison with the ground state reveals that the $A''$ state has a typical van der Waals character similar to that of the ground state. The $A'$ state, on the other hand, differs considerably from the ground state. The $A'$ and $A''$ states differ primarily in different role of the intramonomer correlation effects.",
	collection = "molecular interactions",
	doi = "10.1063/1.469913",
	localfile = "molecular interactions/1995 - Partitioning of interaction energy in van der Waals complexes involving excited state species: the He(1S)+Cl2(B3piu) interaction.pdf",
	year = 1995
}

@Article{1995-Dapprich-Frenking,
	Author = "Stefan Dapprich and Gernot Frenking",
	Title = "{Investigation of donor-acceptor interactions: a charge decomposition analysis using fragment molecular orbitals}",
	Journal = "J. Phys. Chem.",
	Volume = "99",
	Pages = "9352–9362",
	collection = "molecular fragmentation",
	doi = "10.1021/j100023a009",
	localfile = "molecular fragmentation/1995 - Invesitgation of donor-acceptor interactions: a charge decomposition analysis using fragment molecular orbitals.pdf",
	year = 1995
}

@Article{1995-Freeman-Wimmer,
	Author = "Arthur J. Freeman and Erich Wimmer",
	Title = "{Density functional theory as a major tool in computational materials science}",
	Journal = "Annu. Rev. Mater. Sci.",
	Volume = "25",
	Pages = "7–36",
	abstract = "It is now widely recognized that atomistic simulations-especially those employing density functional theory-are becoming an increasingly important part of materials science today. However, a great variety of approaches and implementations have been developed that make the situ ation confusing not only to the non-expert, but perhaps even to the specialist. For this reason, we describe here the local density formulation of density functional theory in enough detail to provide some understanding of this now fairly well-developed, important, and most successful approach for studying electronic structure phenomena in materials.",
	collection = "quantum chemistry",
	localfile = "quantum chemistry/1995 - Density functional theory as a major tool in computational materials science.pdf",
	year = 1995
}

@Article{1995-Gurovich,
	Author = "Eugene Gurovich",
	Title = "{Polymer solutions under electric fields: ellipsoidal correlation holes}",
	Journal = "Macromolecules",
	Volume = "28",
	Pages = "6078–6083",
	collection = "block copolymers",
	doi = "10.1021/ma00122a012",
	localfile = "block copolymers/1995 - Polymer solutions under electric fields: ellipsoidal correlation holes.pdf",
	year = 1995
}

@Article{1995-Gurovich-1,
	Author = "Eugene Gurovich",
	Title = "{Why does an electric field align structures in copolymers?}",
	Journal = "Phys. Rev. Lett.",
	Volume = "74",
	Number = "3",
	Pages = "482–485",
	collection = "block copolymers",
	doi = "10.1103/PhysRevLett.74.482",
	localfile = "block copolymers/1995 - Why does an electirc field align structure in copolymers?.pdf",
	year = 1995
}

@Article{1995-Keech-GM,
	Author = "Catherine L. Keech and Tom P. Gordon and James McCluskey",
	Title = "{Cytoplasmic accumulation of the 52kDa Ro/SS-A nuclear autoantigen in transfected cell lines}",
	Journal = "J. Autoimmunity",
	Volume = "8",
	Pages = "699–712",
	collection = "cells",
	localfile = "cells/1995 - Cytoplasmic accumulation of the 52kDa Ro-SS-A nuclear autoantigen in transfected cell lines.pdf",
	year = 1995
}

@Article{1995-Koch-PS,
	Author = "Uwe Koch and Paul L. A. Popelier and Anthony J. Stone",
	Title = "{Conformational dependence of atomic multipole moments}",
	Journal = "Chem. Phys. Lett.",
	Volume = "238",
	Number = "4-6",
	Pages = "253–260",
	abstract = "The influence of conformational changes on the molecular charge distribution is investigated for three model compounds, We show that local torsional effects, such as rotations about bonds directly connected to the atom of interest, have an important influence on the atomic charge distribution. The description of the electrostatic potential of flexible molecules can be significantly improved if the torsional dependence of the multiple moments is described by a short Fourier series.",
	collection = "molecular electrostatics",
	doi = "10.1016/0009-2614(95)00389-L",
	localfile = "molecular electrostatics/1995 - Conformational dependence of atomic multipole moments.pdf",
	year = 1995
}

@Article{1995-Krausch,
	Author = "Georg Krausch",
	Title = "{Surface induced self assembly in thin polymer films}",
	Journal = "Materials Science and Engineering: R: Reports",
	Volume = "1",
	Pages = "1–94",
	collection = "polymers",
	doi = "10.1016/0927-796X(94)00173-1",
	keywords = "block copolymers; polymer blends; thin films",
	localfile = "polymers/1995 - Surface induced self assembly in thin polymer films.pdf",
	type = "Review",
	year = 1995
}

@Article{1995-Matteoli-Mansoori,
	Author = "Enrico Matteoli and G. Ali Mansoori",
	Title = "{A simple expression for radial distribution functions of pure fluids and mixtures}",
	Journal = "J. Chem. Phys.",
	Volume = "103",
	Number = "11",
	Pages = "4672–4677",
	Note = "Provides a simple two-part expression for the RDF of hard sphere liquids.",
	collection = "statistical mechanics",
	doi = "10.1063/1.470654",
	keywords = "liquid state; radial distribution function",
	localfile = "statistical mechanics/1995 - A simple expression for radial distribution functions of pure fluids and mixtures.pdf",
	rating = "2",
	read = "2012-04-27",
	year = 1995
}

@Article{1995-Misra-Honig,
	Author = "Vinod K. Misra and Barry Honig",
	Title = "{On the magnitude of the electrostatic contribution to {ligand-DNA} interactions}",
	Journal = "Proc. Natl. Acad. Sci.",
	Volume = "92",
	Number = "10",
	Pages = "4691–4695",
	abstract = "A model based on the nonlinear {Poisson-Boltzmann} equation is used to study the electrostatic contribution to the binding free energy of a simple intercalating ligand, 3,8-diamino-6-phenylphenanthridine, to {DNA.} We find that the nonlinear {Poisson-Boltzmann} model accurately describes both the absolute magnitude of the {pKa} shift of 3,8-diamino-6-phenylphenanthridine observed upon intercalation and its variation with bulk salt concentration. Since the {pKa} shift is directly related to the total electrostatic binding free energy of the charged and neutral forms of the ligand, the accuracy of the calculations implies that the electrostatic contributions to binding are accurately predicted as well. Based on our results, we have developed a general physical description of the electrostatic contribution to {ligand-DNA} binding in which the electrostatic binding free energy is described as a balance between the coulombic attraction of a ligand to {DNA} and the disruption of solvent upon binding. Long-range coulombic forces associated with highly charged nucleic acids provide a strong driving force for the interaction of cationic ligands with {DNA.} These favorable electrostatic interactions are, however, largely compensated for by unfavorable changes in the solvation of both the ligand and the {DNA} upon binding. The formation of a {ligand-DNA} complex removes both charged and polar groups at the binding interface from pure solvent while it displaces salt from around the nucleic acid. As a result, the total electrostatic binding free energy is quite small. Consequently, nonpolar interactions, such as tight packing and hydrophobic forces, must play a significant role in {ligand-DNA} stability.",
	collection = "nucleic acid intercalation",
	doi = "10.1073/pnas.92.10.4691",
	localfile = "nucleic acid intercalation/1995 - On the magnitude of the electrostatic contribution to ligand-DNA interactions.pdf",
	year = 1995
}

@Article{1995-Naray-Szabo-Ferenczy,
	Author = "Gabor Naray-Szabo and Gyorgy G. Ferenczy",
	Title = "{Molecular electrostatics}",
	Journal = "Chem. Rev.",
	Volume = "95",
	Pages = "829–847",
	abstract = "(Excerpt) In principle, quantum mechanics describes molecular interactions with sufficient accuracy but a t the cost of extremely complicated and time-consuming numerical calculations, especially for large systems. It is therefore desirable to find approximations that lead to a simplified, yet accurate, description of the interaction process. For polar molecules it is classical electrostatics that fulfills the aforementioned goal. In the electrostatic approximation it is the charge density of the isolated molecules that has to be calculated quantum mechanically or by some other approximation. The interaction energy and its dependence on the relative position of the partners is then obtained from these unperturbed charge densities classically.",
	collection = "molecular electrostatics",
	doi = "10.1021/cr00036a002",
	localfile = "molecular electrostatics/1995 - Molecular electrostatics.pdf",
	year = 1995
}

@Article{1995-Onuki-Fukuda,
	Author = "Akira Onuki and Jun-ichi Fukuda",
	Title = "{Electric field effects and form birefringence in diblock copolymers}",
	Journal = "Macromolecules",
	Volume = "28",
	Pages = "8788–8795",
	abstract = "We investigate effects of the electric field on diblock copolymers by assuming an induced dipolar interaction among the composition fluctuations. First, we show that, when a n electric field is applied perpendicularly to lamellae, undulations start to grow if their in-plane wavenumbers are smaller than an electric wavenumber qe proportional to the field. Subsequently, the undulations grow into larger spatial structures, eventually leading to a final square-lattice pattern. Second, we calculate the Maxwell stress tensor due to the electric field to predict a finite shear modulus in a lamellar state oriented by the electric field. Third, we examine form birefringence in disordered and ordered phases. In particular, the lamellar and hexagonal phases are shown to become birefringent on spatial scales longer than the spacing of lamellae or cylinders, even if the constituent monomers are optically isotropic. This gives rise to enhancement of depolarized light scattering from lamellar microstructures, which has indeed been observed recently. Most predictions in this paper are applicable to many situations other than those in the electric field.",
	collection = "block copolymers",
	doi = "10.1021/ma00130a011",
	keywords = "block copolymers; electric fields",
	localfile = "block copolymers/1995 - Electric field effects and form direfringence in diblock copolymers.pdf",
	year = 1995
}

@Article{1995-Polanyi-Zewail,
	Author = "John C. Polanyi and Ahmed H. Zewail",
	Title = "{Direct observation of the transition state}",
	Journal = "Acc. Chem. Res.",
	Volume = "28",
	Pages = "119–132",
	abstract = "The direct observation of the “transition state’’ for chemical reaction clearly merits a place in this series devoted to the “Holy Grails” of chemistry. The transition state is neither one thing, namely, chemical reagents, nor the other, reaction products. Instead it illustrates the mystical event of trans-substantiation.",
	collection = "molecular reactions",
	doi = "10.1021/ar00051a005",
	localfile = "molecular reactions/1995 - Direct observation of the transition state.pdf",
	year = 1995
}

@Article{1995-Soga-GZ,
	Author = "K. Geoffrey Soga and Hong Guo and Martin J. Zuckermann",
	Title = "{Polymer brushes in a poor solvent}",
	Journal = "Europhys. Lett.",
	Volume = "29",
	Number = "7",
	Pages = "531–536",
	collection = "polymer brushes",
	doi = "10.1209/0295-5075",
	localfile = "polymer brushes/1995 - Polymer brushes in a poor solvent.pdf",
	year = 1995
}

@Article{1995-Stanton-DM,
	Author = "Robert V. Stanton and Steven L. Dixon and Kenneth M. Jr. Merz",
	Title = "{General formulation for a quantum free energy perturbation study}",
	Journal = "J. Phys. Chem.",
	Volume = "99",
	Pages = "10701–10704",
	abstract = "We describe a general method whereby ab initio and semiempirical quantum mechanical techniques can be used in free energy perturbation simulations in which the number of electrons and atoms are being changed. This involves the introduction of a variable which allows the generation of fractional electrons during the course of a free energy perturbation simulation. Several applications of this new methodology using the semiempirical PM3 method are presented. These examples demonstrate that the technique can be successfully utilized to determine free energy differences in the gas phase. Finally, extension of the methodology to other quantum mechanical approaches and to condensed phases is discussed.",
	collection = "statistical mechanics",
	doi = "10.1021/j100027a004",
	localfile = "statistical mechanics/1995 - General formulation for a quantum free energy perturbation study.pdf",
	year = 1995
}

@Article{1995-Williams-MSJ,
	Author = "Hayes L. Williams and Eric M. Mas and Krzysztof Szalewicz and Bogumił Jeziorski",
	Title = "{On the effectiveness of monomer-centered, dimer-centered, and bond-centered basis functions in calculations of intermolecular interaction energies}",
	Journal = "J. Chem. Phys.",
	Volume = "103",
	Number = "17",
	Pages = "7374–7391",
	abstract = "A range of basis sets differing in the location of basis functions has been explored from the point of view of the effectiveness of calculating the electrostatic, induction, dispersion, and exchange components of intermolecular interaction energies. Possible location strategies range from monomer-centered basis sets, through the dimer-centered ones, to sets with functions centered at the intermolecular bond. It is shown that the most effective approach is to use the so-called ”monomer plus” basis sets containing, in addition to monomer-centered functions and bond functions, a small number of functions centered on the interacting partner. Using such basis sets for He-2 and (H2O)(2) the best values to date have been obtained for several interaction energy components. The conclusions from this work are relevant also for supermolecular calculations of interaction energies.",
	cited = "59 (2005-05-29)",
	collection = "basis set dependence",
	doi = "10.1063/1.470309",
	localfile = "basis set dependence/1995 - On the effectiveness of monomer-centered, dimer-centered, and bond-centered basis functions in calculations of intermolecular interaction energies.pdf",
	year = 1995
}

@Article{1996-Archontis-Karplus,
	Author = "G. Archontis and Martin Karplus",
	Title = "{Cumulant expansion of the free energy: application to free energy derivatives and component analysis}",
	Journal = "J. Chem. Phys.",
	Volume = "105",
	Number = "24",
	Pages = "11246–11260",
	collection = "statistical mechanics",
	doi = "10.1063/1.472921",
	localfile = "statistical mechanics/1996 - Cumulant expansion of the free energy: application to free energy derivatives and component analysis.pdf",
	year = 1996
}

@Article{1996-Bakalarski-GKLL,
	Author = "Grzegorz Bakalarski and Paweł Grochowski and Józef S. Kwiatkowski and Bogdan Lesyng and Jerzy Leszczyński",
	Title = "{Molecular and electrostatic properties of the N-methylated nucleic acid bases by density functional theory}",
	Journal = "Chem. Phys.",
	Volume = "204",
	Pages = "301–311",
	abstract = "Complete geometry optimizations using a density functional theory (DIT) with the combined Becke3 and LYP functional potentials (B3-LYP) and the conventional ab initio Hartree-Fock (HF) method with the 6-31G(d,p) basis set were carried out for the fundamental tautomeric forms of nucleic acid bases (cytosine, thymine, guanine and adenine) and their derivatives methylated at the Nl (pyrimidines) or N9 (purines) positions. At the HF/6-31G(d,p) geometries, the dipole moments, electronic densities and molecular electrostatic potentials (MEPs) were computed using the HF/6-31G(d,p), MP2(fc)/6-31G(d,p), DlT(B3-LYP)/6-31G(d,p), DlT(B3-LYP)/6-31++G(d,p) methods and DFT with inclusion of Becke nonlocal, gradient-corrected exchange energy terms (DFT(NLE) method) with the numerical DNP basis set. The same properties were also computed using the DFT(B3-LYP)/6-31G(d,p) method for the corresponding optimized geometries of the molecules. The charges that reproduce the MEP maps from the ab initio (HF, MP2) and DFT calculations were fitted and compared. The ground state molecular parameters (rotational constants, dipole moments) of the methylated bases are compared with the molecular parameters calculated at the same level for the nonmethylated DNA bases and with available experimental data. The results show that the DFT calculations reproduce well the MP2 results for the MEPs, the ESP charges and the dipole moments of the DNA bases and their N-methylated derivatives.",
	collection = "nucleic acid bases",
	doi = "10.1016/0301-0104(95)00413-0",
	localfile = "nucleic acid bases/1996 - Molecular and electrostatic properties of the N-methylated nucleic acid bases by density functional theory.pdf",
	year = 1996
}

@Article{1996-Bloomfield,
	Author = "Victor A. Bloomfield",
	Title = "{DNA condensation}",
	Journal = "Curr. Op. Struct. Biol",
	Volume = "6",
	Pages = "334–341",
	collection = "nucleic acids",
	doi = "10.1016/S0959-440X(96)80052-2",
	issue = "3",
	localfile = "nucleic acids/1996 - DNA condensation.pdf",
	read = "2012-11-10",
	year = 1996
}

@Article{1996-Bone-Bader,
	Author = "Richard G. A. Bone and Richard F. W. Bader",
	Title = "{Identifying and Analyzing Intermolecular Bonding Interactions in van der Waals Molecules†}",
	Journal = "J. Phys. Chem.",
	Volume = "100",
	Number = "26",
	Pages = "10892–10911",
	abstract = "Atomic interaction lines and (3,1) critical points were located in the intermoleclar regions of a total of 36 configurations of 11 van der Waals dimers and a trimer, none of which contain a hydrogen bond. The complexes comprised combinations of five moieties: argon atoms and the molecules {C2H2,} {CO2,} {OCS,} and {SO2.} Atomic interaction lines in the intermolecular region denote the dominant atomatom interactions underlying the weak interactions. The set of complexes allows us to draw conclusions about the role of the intermolecular charge density in binding. We find that the values of the charge density and its principal axes of curvature at intermolecular critical points in these systems are an order of magnitude less than those found in hydrogen-bonded systems and that the (3,-1) critical points display the hallmarks of closed-shell interactions. The strong correlation between the value of rho at a bond critical point and the binding energy of the complex that has been found previously for hydrogen-bonded systems is harder to expose with the van der Waals molecules presented here. For example, comparison must be restricted to structures in which the same pairs of atoms are interacting. We find that conflict structures may be associated with both equilibrium and transition state conformations but that significant nonrigidity is usually a consequence. We are able to make some predictions concerning the likely occurrence of intermolecular critical points in systems larger than those described here.",
	collection = "molecular interactions",
	doi = "10.1021/jp953512m",
	localfile = "molecular interactions/1996 - Identifying and analyzing intermolecular bonding interactions in van der Waals molecules.pdf",
	year = 1996
}

@Article{1996-Bukowski-JS,
	Author = "Robert Bukowski and Bogumił Jeziorski and Krzysztof Szalewicz",
	Title = "{Basis set superposition problem in interaction energy calcualtions with explicitly correlated bases: saturated second- and third-order energies for He2}",
	Journal = "J. Chem. Phys.",
	Volume = "104",
	Number = "9",
	Pages = "3306–3319",
	abstract = "Explicitly correlated basis set of Gaussian-type geminals has been employed in supermolecular calculations of the interaction energy of two helium atoms using the second- and third-order of the many-body perturbation theory and the Møller–Plesset partitioning of the Hamiltonian. A geminal extension of the counterpoise procedure of Boys and Bernardi has been proposed to correct for the basis set superposition error. Performance of the proposed correction scheme has been analyzed at the second-order level using a sequence of geminal bases varying in the degree of completeness in representing the intra- and intermonomer correlation effects. The nonlinear parameters of these bases were optimized by minimizing the second-order energy of the helium atom and the second-order dispersion energy of the He dimer. The best upper bounds to date have been obtained for both quantities. The numerical results show that the counterpoise procedure should be used at all levels of basis set completeness. By employing the union of the largest of the obtained bases and reoptimizing some of the nonlinear parameters using the complete second-order energy functional for the dimer, the best estimates to date of the second- and third-order supermolecular interaction energies for He2 have been computed. At the minimum interatomic separation these energies are estimated to be accurate to 0.01 K or better. Adding higher-order terms computed using orbital bases, leads to a helium dimer interaction potential with the depth of 11.00 K, somewhat larger than current experimental results.",
	collection = "molecular interactions",
	doi = "10.1063/1.471093",
	localfile = "molecular interactions/1996 - Basis set superposition problem in interaction energy calculations with explicitly correlated bases: saturated second- and third-order energies for He2.pdf",
	year = 1996
}

@Article{1996-Chaires-SSFPP,
	Author = "Jonathan B. Chaires and S. Satyanarayana and D. Suh and Izabela Fokt and T. Przewloka and Waldemar Priebe",
	Title = "{Parsing the free energy of anthracycline antibiotic binding to {DNA}}",
	Journal = "Biochemistry",
	Volume = "35",
	Number = "7",
	Pages = "2047–2053",
	abstract = "The DNA binding free energy of eight anthracycline antibiotics was determined as a function of NaCl concentration, Compounds were chosen for study that differed from the parent compounds, doxorubicin or daunorubicin, at a single chemical substituent. Determination of the salt concentration dependence of the binding constant allowed us to dissect the DNA binding free energy of each compound into its component nonelectrostatic and polyelectrolyte contributions. Comparison of the nonelectrostatic free energy contribution allowed us to evaluate the net energetic contribution of specific functional groups to DNA binding. These quantitative data revealed a surprisingly large and favorable energetic contribution (2 kcal mol(-1)) of the groove-binding daunosamine moiety and a substantial energetic penalty for alteration of its stereochemistry, The energetic cost of removal of hydroxyl groups at the C-9 and C-14 positions (which structural studies indicate may participate in hydrogen-bonding interactions with the DNA) was approximately 1 kcal mol(-1). Replacement of the 3'-amino group with a hydroxyl group led to a loss of 0.7 kcal mol(-1) in binding free energy, above and beyond the energetic penalty resulting from the removal of its positive charge from the antibiotic. The results and analysis presented here provide a rigorous and detailed description of structure-DNA affinity relationships among anthracycline antibiotics. The results are of general interest in understanding how total ligand binding free energies are partitioned among substituents and will be useful in the formulation of rules for the rational design of novel DNA binding agents.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/bi952812r",
	localfile = "nucleic acid intercalation/1996 - Parsing the free energy of anthracycline antibiotic binding to DNA.pdf",
	year = 1996
}

@Article{1996-Chebrou-BAG,
	Author = "Herve Chebrou and Frederic Bigey and Alain Arnaud and Pierre Galzy",
	Title = "{Study of the amidase signature group}",
	Journal = "Biochim. Biophys. Acta",
	Volume = "1298",
	Pages = "285–293",
	abstract = "Computer methods for database search, multiple alignment and cluster analysis indicated significant homology between amino-acid sequences of 21 amidases or amidohydrolases (EC 3.5). All of them were found to be involved in the reduction of organic nitrogen compounds and ammonia production. A conserved motif was found which may be important in amide binding and in catalytic mechanisms. Homology studies between these amidases and some ureases, nitrilases and acyl-transferases or enzymes with unknown functions provided new insight into the evolution of these proteins. Dissemination of these genes seemed to be facilitated by transfer of genetic elements such as transposons and plasmids.",
	collection = "enzymes",
	doi = "10.1016/S0167-4838(96)00145-8",
	localfile = "enzymes/1996 - Study of the amidase signature group.pdf",
	year = 1996
}

@Article{1996-Chen-Gordon,
	Author = "Wei Chen and Mark S. Gordon",
	Title = "{Energy Decomposition Analyses for {Many-Body} Interaction and Applications to Water Complexes}",
	Journal = "J. Phys. Chem.",
	Volume = "100",
	Number = "34",
	Pages = "14316–14328",
	abstract = "Two algorithms for many-body interaction energy decomposition within the {HartreeFock} approximation are presented. These two schemes, which are extensions of the two-body {KitauraMorokuma} {(KM)} analysis and the reduced variational space self-consistent-field {(RVS} {SCF)} method, decompose the interaction energy into electrostatic, exchange, polarization, and charge transfer components. The {Hartree-Fock} interaction energies for the optimum water dimer, trimer, and tetramer were analyzed in terms of two-, three-, and four-body terms of these individual components. Counterpoise calculations of the exchange and charge transfer components proposed by Tomasi were performed to estimate the basis set superposition errors. The results show that the three-body nonadditive terms of water trimer and tetramer are dominated by the polarization and charge transfer components at their optimized structures with various basis sets and that the four-body term of water tetramer is very small. The {RVS} {SCF} energy components, whose corresponding wave functions obey the Pauli exclusion principle, are better behaved than their counterparts in the {KM} analysis when the orbital interactions are strong.",
	collection = "molecular interactions",
	doi = "10.1021/jp960694r",
	keywords = "algorithms",
	localfile = "molecular interactions/1996 - Energy decomposition analyses for many-body interaction and applications to water complexes.pdf",
	year = 1996
}

@Article{1996-Cioslowski-Stefanov,
	Author = "Jerzy Cioslowski and Boris B. Stefanov",
	Title = "{Analytical derivatives of atomic zero-flux surfaces and properties of atoms in molecules with respect to external perturbations}",
	Journal = "J. Chem. Phys.",
	Volume = "105",
	Number = "19",
	Pages = "8741–8747",
	abstract = "A complete theory of the response of the atomic zero-ﬂux surfaces to external perturbations is presented. The resulting expressions for the analytical derivatives of the properties of atoms in molecules AIMs are implemented in an efﬁcient computer code. Several test calculations demonstrate the clear advantages of the new approach over methods based upon numerical differentiation. The present development opens an avenue to routine calculations of the second-order response properties of AIMs.",
	collection = "molecular fragmentation",
	doi = "10.1063/1.472653",
	localfile = "molecular fragmentation/1996 - Analytical derivatives of atomic zero-flux surfaces and properties of atoms in molecules with respect to external perturbations.pdf",
	year = 1996
}

@Article{1996-Cravatt-GMBLG,
	Author = "Benjamin F. Cravatt and Dan K. Giang and Stephen P. Mayfield and Dale L. Boger and Richard A. Lerner and Norton B. Gilula",
	Title = "{Molecular characterization of an enzyme that degrades neuromodulatory fatty-acid amides}",
	Journal = "Nature",
	Volume = "384",
	Pages = "83–87",
	collection = "enzymes",
	doi = "10.1038/384083a0",
	keywords = "hydrolysis",
	localfile = "enzymes/1996 - Molecular characterization of an enzyme that degrades neuromodulatory fatty-acid amides.pdf",
	year = 1996
}

@Article{1996-Elcock-RR,
	Author = "Adrian H. Elcock and Alison Rodger and W. Graham Richards",
	Title = "{Theoretical studies of the intercalation of 9-hydroxyellipticine in {DNA}}",
	Journal = "Biopolymers",
	Volume = "39",
	Number = "3",
	Pages = "309–326",
	abstract = "Extensive molecular dynamics {(MD)} simulations have been used to investigate the intercalative binding of 9-hydroxyellipticine to the {DNA} oligonucleotide {d(ATATATATATAT)2.} Four independent simulations differing in the initial orientation of the drug at the intercalation site were carried out, and compared both with each other and a control simulation of the free {DNA} sequence. The structure of the latter was compared with structures obtained from x-ray crystallography and nmr spectroscopy, as well as the theoretically derived ldquoalternating {B-DNArdquo} model {[A.} Klug et al. (1979), Journal of Molecular Biology, Vol. 131, p. 669]. The alternation of twist angles observed in experimental structures was reproduced in the simulation. All four independent simulations of the {drug-DNA} intercalation complex converged in placing the pyridine ring of the ellipticine chromophore in the major groove; in one case this involved a 180° rotation of the drug at the intercalation site. At a more detailed level, the drug is seen to be capable of adopting several distinct orientations, each stable over a period of hundreds of picoseconds. Despite the presence of several polar groups in the drug, however, no direct hydrogen bonding to the {DNA} occurs; instead, interactions between the methyl groups of the drug and the thymine bases at the intercalation site appear important in determining the orientational preferences of the drug. Comparison of the intercalation complexes with the free {DNA} sequence shows a degree of unwinding resulting from intercalation, in good agreement with experimental results, but spread over the three central base-pair steps, not confined to the intercalation site itself. Measurements of torsional rigidity indicate only a slight stiffening of the {DNA} restricted to the immediate site of intercalation. The structures obtained from the {MD} simulations were used to calculate theoretical {CD} spectra, with separate simulations giving very different results. This appears to indicate that given an accurate assignment of the main electronic transition dipole moment of the ellipticine chromophore, discrimination of the more realistic binding geometries may be possible. The relative merits of the various drug orientations observed in the simulations are discussed and a perpendicular orientation of the drug at the intercalation site is considered to be the most consistent with experimental data. While the simulations themselves represent a total of over 2 ns, however, the differences apparent between independent runs indicate that longer simulation times will be required before a complete, unequivocal view of {DNA} intercalation is obtained. © 1996 John Wiley \& Sons, Inc.",
	collection = "nucleic acid intercalation",
	doi = "10.1002/(SICI)1097-0282(199609)39:3",
	localfile = "nucleic acid intercalation/1996 - Theoretical studies of the intercalation of 9-hydroxyellipticine in DNA.pdf",
	year = 1996
}

@Article{1996-Giannelis,
	Author = "Emmanuel P. Giannelis",
	Title = "{Polymer layered silicate nanocomposites}",
	Journal = "Adv. Mater.",
	Volume = "8",
	Number = "1",
	Pages = "29–35",
	abstract = "Polymer nanocomposites with layered silicates as the inorganic phase (reinforcement) are discussed. The materials design and synthesis rely on the ability of layered silicates to intercalate in the galleries between their layers a wide range of monomers and polymers. Special emphasis i placed on a new, versatile and environmentally benign synthesis approach by polymer melt intercalation. I0contrast to in-situ polymerization and solution intercalation, melt intercalation involves mixing the layered silicate with the polymer and heating the mixture above the softening point of the polymer. Compatibility with various polymers is accomplished by derivatizing the silicates with alkyl ammonium cations via an ion exchange reaction. By hetuning the surface characteristics nanodispersion (i.e. intercalation or delamination) can be accomplished. The resulting polymer layered silicate (PLS) nanocomposites exhibit properties dramatically different from their more conventional counterparts. For example, PLS nanocomposites can attain a particular degree of stiffoesr, strength and barrier properties with far less inorganic content than comparable glass- or mineral reinforced polymers and, therefore, they are far lighter i weight. In addition, PLS nanocomposites exhibit significant increase in thermal stability as well as self-extinguishing characteristics. The combination of improved properties, convenient processing and low cost has already led to a few commercial applications with more currently under development.",
	collection = "polymer nanocomposites",
	doi = "10.1002/adma.19960080104",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/1996 - Polymer layered silicate nanocomposites.pdf",
	year = 1996
}

@Article{1996-Grineva-Zhuraviev,
	Author = "Olga V. Grineva and Vladimir I. Zhuraviev",
	Title = "{Densities and dielectric properties of three butanediols and their solutiosn with 10 mol \% water}",
	Journal = "J. Chem. Eng. Data",
	Volume = "41",
	Pages = "604–607",
	cited = "18 (2013-04-29)",
	collection = "molecular solvation",
	doi = "10.1021/je950313n",
	localfile = {molecular solvation/1996 - Densities and dielectric properties of three butanediols and their solutions with 10 mol \% water.pdf},
	year = 1996
}

@Article{1996-Guckian-SRSPTK,
	Author = "Kevin M. Guckian and Barbara A. Schweitzer and Rex X.-F. Ren and Charles J. Sheils and Pamela L. Paris and Deborah C. Tahmassebi and Eric T. Kool",
	Title = "{Experimental measurement of aromatic stacking affinities in the context of duplex {DNA}}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "118",
	Number = "34",
	Pages = "8182–8183",
	abstract = "(Excerpt) Noncovalent interactions between aromatic molecules are widely believed to be important contributing factors in the stabilization of organized structure in biological macromolecules. Among the most significant aromatic-aromatic interactions are those found in helical nucleic acid structures. Since the identity of the nearest neighbors to a given base pair is the best single predictor of thermodynamics in DNA duplexes, it is clear that aromatic π-π interactions are crucial to the stabilization of these structures.",
	cited = "129 (2005-05-23)",
	collection = "stacking",
	doi = "10.1021/ja961733f",
	keywrods = "stacking",
	localfile = "molecular stacking/1996 - Experimental measurement of aromatic stacking affinities.pdf",
	year = 1996
}

@Article{1996-Humphrey-DS,
	Author = "William Humphrey and Andrew Dalke and Klaus Schulten",
	Title = "{{VMD} – {V}isual {M}olecular {D}ynamics}",
	Journal = "J. Mol. Graph.",
	Volume = 14,
	Pages = "33–38",
	collection = "cheminformatics",
	localfile = {},
	tbreference = "222",
	tbstatus = "Published.",
	techrep = "",
	url = "http://www.ks.uiuc.edu/Research/vmd",
	year = 1996
}

@Article{1996-Jensen,
	Author = "Frank Jensen",
	Title = "{The magnitude of intramolecular basis set superposition error}",
	Journal = "Chem. Phys. Lett.",
	Volume = "261",
	Pages = "633–636",
	abstract = "It is shown that part of what normally is considered a basis set effect on relative energies, more properly may be interpreted as intramolecular basis set superposition error.",
	collection = "basis set superposition",
	doi = "10.1016/0009-2614(96)01033-0",
	keywords = "basis set superposition error",
	localfile = "basis set superposition/1996 - The magnitude of intramolecular basis set superposition error.pdf",
	year = 1996
}

@Article{1996-Karelson-LK,
	Author = "Mati Karelson and Victor S. Lobanov and Alan R. Katritzky",
	Title = "{Quantum-chemical descriptors in QSAR/QSPR studies}",
	Journal = "Chem. Rev.",
	Volume = "96",
	Pages = "1027–1043",
	abstract = "(Excerpt) The present article reviews applications of quantum chemical descriptors in the development of QSAR/QSPR dealing with the chemical, physical, biochemical, and pharmacological properties of compounds.",
	collection = "quantum chemistry",
	doi = "10.1021/cr950202r",
	localfile = "molecular structure/1996 - Quantum-chemical decsriptors in QSAR and QSPR studies.pdf",
	year = 1996
}

@Article{1996-Kellogg-WMLRGS,
	Author = "G. J. Kellogg and D. G. Walton and Anne M. Mayes and P. Lambooy and Thomas P. Russell and P. D. Gallagher and S. K. Satija",
	Title = "{Observed surface energy effects in confined diblock copolymers}",
	Journal = "Phys. Rev. Lett.",
	Volume = "76",
	Number = "14",
	Pages = "2503–2506",
	abstract = "By using thin layers of random copolymer, we have varied the specificity of block-wall interactions for films of diblock copolymer confined between parallel walls. For highly specific interactions (bare walls), one block component segregates to both interfaces, and the frustration due to incommensuration between film thickness and the diblock’s bulk period is accommodated by the formation of layers parallel to the walls with perturbed period. In contrast, reduced specific interactions (random-copolymer-coated walls) allow the frustration to be accommodated by perpendicular ordering of the diblock, such that both block components are present at the walls.",
	collection = "block copolymers",
	doi = "10.1103/PhysRevLett.76.2503",
	keywords = "block copolymers; thin films",
	localfile = "block copolymers/1996 - Observed surface energy effects in confined diblock copolymers.pdf",
	rating = "3",
	year = 1996
}

@Article{1996-Klopper-QS,
	Author = "Wim Klopper and Martin Quack and Martin A. Suhm",
	Title = "{A new ab initio based six-dimensional semi-empirical pair interaction potential for HF}",
	Journal = "Chem. Phys. Lett.",
	Volume = "261",
	Pages = "35–44",
	abstract = "We present an analytical pair potential for hydrogen fluoride based on 3284 ab initio points at counterpoise-corrected MP2-R12 and lower levels using a large basis set. Empirical refinements are applied though comparison of experimental data with solutions of the multidimensional nuclear Schrodinger equation and appropriate mixing and scaling of the ab initio data. The new potentials are compared to previous dimer potential hypersurfaces and spectroscopic data, yielding best estimates of 19.1(2) kJ/mol for the dimer dissociation energy $D\_e$ and 4.2(2) kJ/mol for the electronic hydrogen bond tunneling barrier.",
	collection = "hydrogen bonding",
	doi = "10.1016/0009-2614(96)00901-3",
	keywords = "hydrogen bonding; semi-empirical methods",
	localfile = "hydrogen bonding/1996 - A new ab initio based six-dimensional semi-empirical pair interaction potential for HF.pdf",
	methods = "MP2",
	systems = "HF dimer",
	year = 1996
}

@Article{1996-Klosgen-RKK,
	Author = "Beate Klosgen and Christoph Reichle and Stephan Kohlsmann and Klaus D. Kramer",
	Title = "{Dielectric spectroscopy as a sensor of membrane headgroup mobility and hydration}",
	Journal = "Biophys. J.",
	Volume = "71",
	Pages = "3251–3260",
	cited = "45 (2013-04-29)",
	collection = "lipid bilayers",
	doi = "10.1016/S0006-3495(96)79518-8",
	localfile = "lipid bilayers/1996 - Dielectric spectroscopy as a sensor of membrane headgroup mobility and hydration.pdf",
	year = 1996
}

@Article{1996-Koch-Stone,
	Author = "Uwe Koch and Anthony J. Stone",
	Title = "{Conformational dependence of the molecular charge distribution and its influence on intermolecular interactions}",
	Journal = "J. Chem. Soc., Faraday Trans.",
	Volume = "92",
	Number = "10",
	Pages = "1701–1708",
	abstract = "The conformational dependence of the intermolecular electrostatic interaction energy has been studied for three model compounds interacting with water molecules. The variation in the molecular charge distribution with conformation can have an important influence on intermolecular hydrogen-bond energies. Rotational barriers of hydrated molecules are substantially affected when this variation is taken into account. The significance of this effect has been evaluated for N-methylacetamide, ethanol and {N,N-dimethylacetamide.} It is shown that the conformational dependence of the molecular charge distribution can be described with high accuracy by expressing the atomic multipole moments as a short Fourier series in the dihedral angle.",
	collection = "molecular electrostatics",
	doi = "10.1039/FT9969201701",
	keywords = "molecular structure",
	localfile = "molecular electrostatics/1996 - Conformational dependence of the molecular charge distirbution and its influence on intermolecular interactions.pdf",
	year = 1996
}

@Article{1996-Kohn-BP,
	Author = "W. Kohn and A. D. Becke and R. G. Parr",
	Title = "{Density functional theory of electronic structure}",
	Journal = "J. Phys. Chem.",
	Volume = "100",
	Pages = "12974–12980",
	abstract = "Density functional theory (DFT) is a (in principle exact) theory of electronic structure, based on the electron density distribution n(r), instead of the many-electron wave function Ψ(r1,r2,r3,...). Having been widely used for over 30 years by physicists working on the electronic structure of solids, surfaces, defects, etc., it has more recently also become popular with theoretical and computational chemists. The present article is directed at the chemical community. It aims to convey the basic concepts and breadth of applications: the current status and trends of approximation methods (local density and generalized gradient approximations, hybrid methods) and the new light which DFT has been shedding on important concepts like electronegativity, hardness, and chemical reactivity index.",
	collection = "quantum chemistry",
	doi = "10.1021/jp960669l",
	localfile = "quantum chemistry/1996 - Density functional theory of electronic structure.pdf",
	year = 1996
}

@Article{1996-Matsen-Bates,
	Author = "Mark W. Matsen and F. S. Bates",
	Title = "{Unifying weak- and strong-segregation block copolymer theories}",
	Journal = "Macromolecules",
	Volume = "29",
	Number = "4",
	Pages = "1091–1098",
	collection = "block copolymers",
	doi = "10.1021/ma951138i",
	keywords = "block copolymers",
	localfile = "block copolymers/1996 - Unifying weak- and strong-segregation block copolymer theories.pdf",
	year = 1996
}

@Article{1996-Maurits-AEF,
	Author = "N. M. Maurits and P. Altevogt and O. A. Evers and J. G. E. M. Fraaije",
	Title = "{Simple numerical quadrature rules for Gaussian chain polymer density functional calcualtions in 3D and implementation on parallel platforms}",
	Journal = "Comp. Theor. Pol. Sci.",
	Volume = "6",
	Number = "1-2",
	Pages = "1–8",
	collection = "informatics",
	keywords = "quadrature",
	localfile = {informatics/1996 - Simple numerical quadrature rules for Gaussian chain polymer density functional calcualtions in 3D and implementation on parallel platforms.ps},
	read = "2011-10-10",
	year = 1996
}

@Article{1996-Mecozzi-WD,
	Author = "Sandro Mecozzi and Anthony P. {West Jr.} and Dennis A. Dougherty",
	Title = "{Cation-π interactions in aromatics of biological and medicinal interest: electrostatic potential surfaces as a useful qualitative guide}",
	Journal = "Proc. Natl. Acad. Sci.",
	Volume = "93",
	Number = "20",
	Pages = "10566–10571",
	abstract = "The cation-pi interaction is an important, general force for molecular recognition in biological receptors. Through the sidechains of aromatic amino acids, novel binding sites for cationic ligands such as acetylcholine can be constructed. We report here a number of calculations on prototypical cation-pi systems, emphasizing structures of relevance to biological receptors and prototypical heterocycles of the type often of importance in medicinal chemistry. Trends in the data can be rationalized using a relatively simple model that emphasizes the electrostatic component of the cation-pi interaction. In particular, plots of the electrostatic potential surfaces of the relevant aromatics provide useful guidelines for predicting cation-pi interactions in new systems.",
	collection = "molecular electrostatics",
	doi = "10.1073/pnas.93.20.10566",
	localfile = "molecular electrostatics/1996 - Cation-pi interactions in aromatics of biological and medicinal interest: electrostatic potential surfaces as a useful qualitative guide.pdf",
	shorttitle = "Cation-pi interactions in aromatics of biological and medicinal interest",
	year = 1996
}

@Article{1996-Mecozzi-WD-1,
	Author = "Sandro Mecozzi and Anthony P. {West Jr.} and Dennis A. Dougherty",
	Title = "{Cation−π Interactions in Simple Aromatics: Electrostatics Provide a Predictive Tool}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "118",
	Number = "9",
	Pages = "2307–2308",
	abstract = "(Excerpt) In recent years, the cation-π interaction has come to be appreciated as an important noncovalent binding force. Studies in the gas phase,2 in aqueous media using synthetic receptors, and in a biological context with a number of protein systems have established the broad scope and significance of this interaction. A complete, quantitative description of the cation-π interaction would involve a number of intermolecular forces, such as charge-quadrupole, charge-dipole, charge-induced dipole, charge transfer, dispersion forces, and, in some cases, a hydrophobic component. However, we have argued that, to first order, the major aspect of the cation-π interaction is electrostatic in nature, involving the interaction of the cation with the large, permanent quadrupole moment of the aromatic. In the present work we describe an evaluation of the extent to which the electrostatic model can rationalize Variations in cation binding abilities among various aromatic systems. We find that, indeed, the electrostatic model provides a quantitative understanding of the trend seen across a series of prototypical aromatic systems.",
	collection = "molecular electrostatics",
	doi = "10.1021/ja9539608",
	localfile = "molecular electrostatics/1996 - Cation-pi interactions in simple aromatics: electrostatics provide a predictive tool.pdf",
	shorttitle = "Cation−π Interactions in Simple Aromatics",
	year = 1996
}

@Article{1996-Moszynski-HJ,
	Author = "Robert Moszyński and Tino G. A. Heijmen and Bogumił Jeziorski",
	Title = "{Symmetry-adapted perturbation theory for the calculation of Hartree-Fock interaction energies }",
	Journal = "Mol. Phys.",
	Volume = "88",
	Number = "3",
	Pages = "741–758",
	abstract = "A symmetry-adapted perturbation theory is formulated for the calculation of Hartree-Fock interaction energies of closed-shell dimers. The proposed schem e leads to a basis-set-independent interpretation of the Hartree- Fock interaction energy in terms of basic concepts of the theory of intermolecular forces : electrostatics, exchange and induction. Numerical results for different geom etries of He2 , Ne2 , He-C2H2 , He-CO, Ar-HF, (HF)2 and (H2O)2 complexes show that in the region of the van der Waals minimum the proposed perturbation theory reproduces accurately the Hartree-Fock interaction energy. This fast convergence and relatively small computational cost of the proposed perturbation scheme suggest that this method is a practical alternative for the standard superm olecular approach.",
	collection = "molecular interactions",
	doi = "10.1080/00268979609482451",
	localfile = "molecular interactions/1996 - Symmetry-adapted perturbation theory for the calculation of Hartree-Fock interaction energies.pdf",
	year = 1996
}

@Article{1996-Oberholzer-OCB,
	Author = "Martin Oberholzer and Marc Östreicher and Heinz Christen and Marcel Brühlmann",
	Title = "{Methods in quantitative image analysis}",
	Journal = "Histochem. Cell. Biol.",
	Volume = "105",
	Pages = "333–355",
	collection = "informatics",
	keywords = "image analysis",
	localfile = "informatics/1996 - Methods in quantitative image analysis.pdf",
	year = 1996
}

@Article{1996-Popelier,
	Author = "Paul L. A. Popelier",
	Title = "{Integration of atoms in molecules: a critical examination}",
	Journal = "Mol. Phys.",
	Volume = "87",
	Number = "5",
	Pages = "1169–1187",
	abstract = "The theory of atoms in molecules rigorously defines reliable, accurate, consistent and stable average atomic properties. Obtaining these properties poses a complicated integration which is revisited in this paper and critically examined ab ovo. An integration algorithm using an analytical representation of the interatomic surface is proposed. This new technique is implemented in the program MORPHY 2.0, allowing automatic integration of all atoms in one input deck without external topological information. The present algorithm is illustrated via a few selected molecules with emphasis on the accuracy of(high) atomic electrostatic moments. It is shown that the theory of 'atoms in molecules' yields sufficiently accurate moments to reproduce the exact ab initio electrostatic potential.",
	collection = "cheminformatics",
	doi = "10.1080/00268979650027072",
	keywords = "multipole expansion",
	localfile = "cheminformatics/1996 - Integration of atoms in molecules: a critical examination.pdf",
	year = 1996
}

@Article{1996-Resat-Mezei,
	Author = "H. Resat and Mihaly Mezei",
	Title = "{Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate}",
	Journal = "Biophys. J.",
	Volume = "71",
	Number = "3",
	Pages = "1179–1190",
	abstract = "The grand canonical ensemble Monte Carlo molecular simulation method is used to investigate hydration patterns in the crystal hydrate structure of the dCpG/proflavine intercalated complex. The objective of this study is to show by example that the recently advocated grand canonical ensemble simulation is a computationally efficient method for determining the positions of the hydrating water molecules in protein and nucleic acid structures. A detailed molecular simulation convergence analysis and an analogous comparison of the theoretical results with experiments clearly show that the grand ensemble simulations can be far more advantageous than the comparable canonical ensemble simulations.",
	collection = "nucleic acid intercalation",
	doi = "10.1016/S0006-3495(96)79322-0",
	localfile = "nucleic acid intercalation/1996 - Grand canonical ensemble Monte Carlo simulation of the dCpG-proflavine crystal hydrate.pdf",
	year = 1996
}

@Article{1996-Simon-DD,
	Author = "Silvia Simon and Miquel Duran and Joseph J. Dannenberg",
	Title = "{How does basis set superposition error change the potential surfaces for hydrogen-bonded dimers?}",
	Journal = "J. Chem. Phys.",
	Volume = "105",
	Number = "24",
	Pages = "11024–11031",
	abstract = "We describe a simple method to automate the geometric optimization of molecular orbital calculations of supermolecules on potential surfaces that are corrected for basis set superposition error using the counterpoise CP method. This method is applied to the H-bonding complexes HF/HCN, HF/H2O, and HCCH/H2O using the 6-31G d,p and D95d,p basis sets at both the Hartree–Fock and second-order Møller–Plesset levels. We report the interaction energies, geometries, and vibrational frequencies of these complexes on the CP-optimized surfaces; and compare them with similar values calculated using traditional methods, including the more traditional single point CP correction. Upon optimization on the CP-corrected surface, the interaction energies become more negative before vibrational corrections and the H-bonding stretching vibrations decrease in all cases. The extent of the effects vary from extremely small to quite large depending on the complex and the calculational method. The relative magnitudes of the vibrational corrections cannot be predicted from the H-bond stretching frequencies alone.",
	collection = "basis set superposition",
	doi = "10.1063/1.472902",
	localfile = "basis set superposition/1996 - How does basis set superposition error change the potential surfaces for hydrogen-bonded dimers.pdf",
	year = 1996
}

@Article{1996-Soga-ZG,
	Author = "K. Geoffrey Soga and Martin J. Zuckermann and Hong Guo",
	Title = "{Binary polymer brush in a solvent}",
	Journal = "Macromolecules",
	Volume = "29",
	Pages = "1998–2005",
	collection = "polymer brushes",
	doi = "10.1021/ma951102q",
	keywrods = "polymer brushes",
	localfile = "polymer brushes/1996 - Binary polymer brush in a solvent.pdf",
	year = 1996
}

@Article{1996-Xantheas,
	Author = "Sotiris S. Xantheas",
	Title = "{On the importance of the fragment relaxation energy terms in the estimation of the basis set superposition error correction to the intermolecular interaction energy}",
	Journal = "J. Chem. Phys.",
	Volume = "104",
	Number = "21",
	Pages = "8821–8824",
	abstract = "The inclusion of the fragment relaxation energy terms in the estimation of the basis set superposition error BSSE correction to the interaction energy is necessary in order to ensure formal convergence to the uncorrected result at the complete basis set CBS limit. The problems associated with their omission are demonstrated for F H2O , Cl H2O , and H2O 2 especially when very large basis sets are used. The family of correlation consistent basis sets allows for a heuristic extrapolation of both uncorrected and BSSE-corrected electronic energy differences of the three complexes to the MP2 CBS limits of 27.1, 15.1, and 4.9 kcal/mol respectively.",
	collection = "basis set superposition",
	doi = "10.1063/1.471605",
	localfile = "basis set superposition/1996 - On the importance of the fragment relaxation energy terms in the estimation of the basis set superposition error correction to the intermolecular interaction energy.pdf",
	year = 1996
}

@Article{1996-Yell-WYM,
	Author = "Jannifer A. Yell and Lixiang Wang and Hongliang Yin and Daniel P. Mccauliffe",
	Title = "{Disparate locations of the 52- and 60-kDa Ro/SS-A antigens in cultured human keratinocytes}",
	Journal = "J. Invest. Dermatol.",
	Volume = "107",
	Number = "4",
	Pages = "622–626",
	collection = "cells",
	localfile = "cells/1996 - Disparate locations of the 52- and 60-kDa Ro-SS-A antigens in cultured human keratinocytes.pdf",
	year = 1996
}

@Article{1997-Babine-Bender,
	Author = "Robert E. Babine and Steven L. Bender",
	Title = "{Molecular recognition of protein-ligand complexes: applications to drug design}",
	Journal = "Chem. Rev.",
	Volume = "97",
	Pages = "1359–1472",
	abstract = "(Excerpt) Advances in molecular biology have had a dramatic impact on the drug discovery process. The ability to produce recombinant proteins of biological significance has greatly impacted the screening process.",
	collection = "enzymes",
	doi = "10.1021/cr960370z",
	keywords = "drug discovery",
	localfile = "enzymes/1997 - Molecular recognition of protein-ligand complexes: application to drug dedeign.pdf",
	year = 1997
}

@Article{1997-Bader-Austen,
	Author = "Richard F. W. Bader and Maggie A. Austen",
	Title = "{Properties of atoms in molecules: Atoms under pressure}",
	Journal = "J. Chem. Phys.",
	Volume = "107",
	Number = "11",
	Pages = "4271–4285",
	abstract = "The in situ pressure acting on the surface of an open system at the atomic level is deﬁned and determined by the virial theorem for a proper open system, one whose spatial boundary and equations of motion are determined by the principle of stationary action. The quantum pressure is determined by the virial of the force resulting from the electronic momentum ﬂux through the surface of the open system. A scaling procedure is used to demonstrate that the expectation value of the pressure–volume product of a proper open system is proportional to its surface virial. Previous work, in analogy with the classical virial theorem for a contained system, incorrectly relates the pressure to the external forces of constraint acting on a closed system. A neon vise consisting of a chain of three, four or ﬁve hydrogen molecules compressed between two neon atoms is used to introduce the quantum deﬁnition of pressure and study its effect on the mechanical properties of an atom and on the topology of the electron density. Pressures approaching 160 GPa have been calculated for the vise. The topology of the electron density and the homeomorphism it exhibits with the virial ﬁeld are found to be invariant to an increase in pressure, the electron density accumulating to an ever increasing extent between all pairs of nuclei which serve as the sole attractors. The virial of the Ehrenfest force acting on the surface of a compressed molecule provides a measure of the increase in the electronic kinetic energy resulting from the applied pressure. The effects of pressure on the intra- and intermolecular bonding are discussed in terms of pressure-induced changes in the electron density and in the mechanical properties of the atoms.",
	collection = "molecular fragmentation",
	doi = "10.1063/1.474769",
	localfile = "molecular fragmentation/1997 - Properties of atoms in molecules: atoms under pressure.pdf",
	shorttitle = "Properties of atoms in molecules",
	year = 1997
}

@Article{1997-Baginski-FB,
	Author = "Maciej Bagiński and Federico Fogolari and James M. Briggs",
	Title = "{Electrostatic and non-electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA}",
	Journal = "J. Mol. Biol.",
	Volume = "274",
	Pages = "253–267",
	collection = "nucleic acid intercalation",
	doi = "10.1006/jmbi.1997.1399",
	keywords = "nucleic acids; intercalation",
	localfile = "nucleic acid intercalation/1997 - Electrostatic and non-electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA.pdf",
	year = 1997
}

@Article{1997-Beck-CG,
	Author = "Bernd Beck and Timothy Clark and Robert C. Glen",
	Title = "{VESPA: a new, fast approach to electrostatic potential-derived atomic charges from semiempirical methods}",
	Journal = "J. Comp. Chem.",
	Volume = "18",
	Number = "6",
	Pages = "744–756",
	abstract = "An improved semiempirical method for computing electrostatic potential-derived atomic charges is described. It includes a very fast algorithm for the generation of the grid points around the molecule and the calculation of the electrostatic potential at these points. The dependency of the atomic point charges obtained on the number of grid points used in the fitting procedure is examined. For ‘‘buried’’ atoms a high density grid is necessary. It is possible to obtain 6-31G*-quality atom-centered point charges, even for phosphorus compounds, using AM1 or PM3. This approach can therefore be recommended for general use in QSAR or molecular mechanics for any organic and bioorganic system up to about 200 atoms.",
	collection = "molecular electrostatics",
	localfile = "molecular electrostatics/1997 - VESPA: a new, fast approach to electrostatic potential-derived atomic charges from semiempirical methods.pdf",
	year = 1997
}

@Article{1997-Beecroft-Ober,
	Author = "Laura L. Beecroft and Christopher K. Ober",
	Title = "{Nanocomposite materials for optical applications}",
	Journal = "Chem. Mater.",
	Volume = "9",
	Pages = "1302–1317",
	abstract = "A substantial amount of work has been carried out in the area of nanocomposite materials for optical applications. Composites are typically constructed by embedding an optically functional phase into a processable, transparent matrix material. By doing so, the optical properties can be utilized in more technologically important forms such as films and fibers. This review covers many areas of optical composite research to date. Composites with second-and third-order nonlinearities and laser amplification properties are discussed with examples from the recent literature. Other composites, including transparent magnets, may be made using similar structures. The principles used to construct these composites may have important technological applications soon and are therefore summarized in this review.",
	collection = "polymer nanocomposites",
	doi = "10.1021/cm960441a",
	keywords = "optical properties; polymer nanocomposites",
	localfile = "polymer nanocomposites/1997 - Nanocomposite materials for optical applications.pdf",
	type = "Review",
	year = 1997
}

@Article{1997-Bloomfield,
	Author = "Victor A. Bloomfield",
	Title = "{DNA condensation by multivalent cations}",
	Journal = "Biopolymers",
	Volume = "44",
	Pages = "269–282",
	collection = "nucleic acids",
	localfile = "nucleic acids/1997 - DNA condensation by multivalent cations.pdf",
	rating = "2",
	read = "2012-08-13",
	year = 1997
}

@Article{1997-Cioslowski-Liu,
	Author = "Jerzy Cioslowski and G. H. Liu",
	Title = "{Electrostatic interaction energies from a generalized {G}aussian quadrature}",
	Journal = "Chem. Phys. Lett.",
	Volume = "277",
	Number = "4",
	Pages = "299–305",
	abstract = "When used in conjunction with a properly chosen curvilinear coordinate system, a generalized Gaussian quadrature affords a new versatile approach to the computation of energies of electrostatic interaction between two non-overlapping, continuous charge distributions. Compared with the conventional discretization of distributions, this approach offers a vast reduction in computational effort without a concomitant loss of accuracy. Although potentially slower than the fast multipole method, the present formalism is more general and less prone to discretization errors due to finite grid sizes. Results of test calculations on the energies of classical electrostatic interaction between AIMs demonstrate the power of the new method.",
	cited = "4 (2005-05-22)",
	collection = "molecular electrostatics",
	doi = "10.1016/S0009-2614(97)00883-X",
	keywords = "quadrature",
	localfile = "molecular electrostatics/1997 - Electrostatic interaction energies from a generalized Gaussian quadrature.pdf",
	year = 1997
}

@Article{1997-Fraaije-VMPEHAG,
	Author = "Johannes G. E. M. Fraaije and {B. A. C. van} Vlimmeren and N. M. Maurits and M. Postma and O. A. Evers and C. Hoffman and P. Altevogt and G. Goldbeck-Wood",
	Title = "{The dynamic mean-field density functional method and its application to the mesoscopic dynamics of quenched block copolymer melts}",
	Journal = "J. Chem. Phys.",
	Volume = "106",
	Number = "10",
	Pages = "4260–4269",
	abstract = "In this paper we discuss a new generalized time-dependent Ginzburg-Landau theory for the numerical calculation of polymer phase separation kinetics in 3D. The thermodynamic forces are obtained by a mean-ﬁeld density functional method, using a Gaussian chain as a molecular model. The method is especially aimed at describing the formation kinetics of the irregular morphologies which are typical for many industrial systems. As proof of concept we present the formation of irregular morphologies in quenched symmetric and asymmetric block copolymer melts.",
	collection = "block copolymers",
	doi = "10.1063/1.473129",
	keywords = "block copolymers; microdomains",
	localfile = "block copolymers/1997 - The dynamic mean-field density functional method and its application to the mesoscopic dynamics of quenched block copolymer melts.pdf",
	methods = "DDFT",
	year = 1997
}

@Article{1997-Gunning-Raab,
	Author = "M. J. Gunning and R. E. Raab",
	Title = "{Physical implications of the use of primitive and traceless electric quadrupole moments}",
	Journal = "Mol. Phys.",
	Volume = "91",
	Number = "4",
	Pages = "589",
	collection = "molecular electrostatics",
	doi = "10.1080/002689797171085",
	localfile = "molecular electrostatics/1997 - Physical implications of the use of primitive and traceless electric quadrupole moments.pdf",
	year = 1997
}

@Article{1997-Hunter-Lu,
	Author = "Christopher A. Hunter and Xian-Jun Lu",
	Title = "{D{NA} base-stacking interactions: a comparison of theoretical calculations with oligonucleotide {X}-ray crystal structures}",
	Journal = "J. Mol. Biol.",
	Volume = "265",
	Number = "5",
	Pages = "603–619",
	abstract = "Experimental data on the conformational properties of dinucleotides taken from high-resolution X-ray crystal structures of oligonucleotides have been compared with theoretical energy calculations on the base-stacking interactions. The conformational properties of the dinucleotides determined by calculation agree well with the experimental data, which shows that the method used for computing the stacking interactions is reliable. In addition, the calculations provide insight into the origins of the major trends that are observed in the experimental data. The values of the step parameters roll, tilt and rise, are determined entirely by the van der Waals interactions, and this reflects the strong requirement that the bases remain stacked in close contact. Slide, shift and twist do not affect the vertical separation of the bases and are therefore less tightly constrained. Electrostatic interactions play an important role in determining the values of shift and slide, but the base-stacking interaction energy is essentially independent of the value of twist. Thus the experimental value of twist is most likely fixed by the constraints of the backbone, which are missing in these calculations. (C) 1997 Academic Press Limited.",
	cited = "54 (2005-04-27)",
	collection = "stacking",
	doi = "10.1006/jmbi.1996.0755",
	localfile = "molecular stacking/1997 - DNA base-stacking interactions: a comparison of theoretical calcualtions with oligonucleotide X-ray crystal structures.pdf",
	year = 1997
}

@Article{1997-Kaatze,
	Author = "Udo Kaatze",
	Title = "{The dielectric properties of water in its different states of interaction}",
	Journal = "J. Solution Chem.",
	Volume = "26",
	Number = "11",
	Pages = "1049–1112",
	cited = "76 (2013-04-29)",
	collection = "molecular solvation",
	doi = "10.1007/BF02768829",
	keywords = "water",
	localfile = "molecular solvation/1997 - The dielectric properties of water in its different states of interactions.pdf",
	year = 1997
}

@Article{1997-Korona-WBJS,
	Author = "Tatiana Korona and Hayes L. Williams and Robert Bukowski and Bogumił Jeziorski and Krzysztof Szalewicz",
	Title = "{Helium dimer potential from symmetry-adapted perturbation theory calculations using large {G}aussian geminal and orbital basis sets}",
	Journal = "J. Chem. Phys.",
	Volume = "106",
	Number = "12",
	Pages = "5109 – 5122",
	collection = "molecular interactions",
	doi = "10.1063/1.473556",
	localfile = "molecular interactions/1997 - Helium dimer potential from symmetry-adapted perturbation theory calcualtions using large Gaussian geminal and orbital basis sets.pdf",
	size = "14 p.",
	year = 1997
}

@Article{1997-Ma-Dougherty,
	Author = "Jennifer C. Ma and Dennis A. Dougherty",
	Title = "{The Cation−π Interaction}",
	Journal = "Chem. Rev.",
	Volume = "97",
	Pages = "1303–1324",
	abstract = "(Excerpt) Noncovalent interactions play a dominant role in many forefront areas of modern chemistry, from materials design to molecular biology. A detailed understanding of the physical origin and scope of such interactions has become a major goal of physical organic chemistry.",
	collection = "molecular interactions",
	doi = "10.1021/cr9603744",
	localfile = "molecular interactions/1997 - The cation-pi interaction.pdf",
	year = 1997
}

@Article{1997-Matsen,
	Author = "Mark W. Matsen",
	Title = "{Thin films of block copolymer}",
	Journal = "J. Chem. Phys.",
	Volume = "106",
	Pages = "7781–7791",
	abstract = "We develop a numerical method for examining complex morphologies in thin films of block copolymer using self-consistent field theory. Applying the method to confined films of symmetric diblock copolymer, we evaluate the stability of parallel, perpendicular, and mixed lamellar phases. In general, lamellar domains formed by the diblocks are oriented parallel to the film by surface fields. However, their orientation can flip to perpendicular when the natural period of the lamellae is incommensurate with the film thickness. Experiments and Monte Carlo simulations have indicated that mixed lamellar phases may also occur, but for symmetric diblocks, we find these phases to be slightly unstable relative to perpendicular lamellae. Nevertheless, just a small asymmetry in the molecule stabilizes a mixed lamellar phase. Although our work focuses on confined films, we do discuss the behavior that results when films are unconfined.",
	collection = "block copolymers",
	doi = "10.1063/1.473778",
	keywords = "block copolymers; thin films",
	localfile = "block copolymers/1997 - Thin films of block copolymer.pdf",
	methods = "SCFT",
	rating = "3",
	read = "2011-11-24",
	year = 1997
}

@Article{1997-Maurits-Fraaije,
	Author = "N. M. Maurits and Johannes G. E. M. Fraaije",
	Title = "{Mesoscopic dynamics of copolymer melts: from density dynamics to external potential dynamics using nonlocal kinetic coupling}",
	Journal = "J. Chem. Phys.",
	Volume = "107",
	Number = "15",
	Pages = "5879–5889",
	abstract = "In this paper we apply nonlocal kinetic coupling to the dynamic mean-ﬁeld density functional method, which is derived from generalized time-dependent Ginzburg–Landau theory. The method is applied to the mesoscopic dynamics of copolymer melts, which was previously simulated using a local coupling approximation. We discuss the general theory of time evolution of density variables with general kinetic coefﬁcients developed by Kawasaki and Sekimoto, and especially the limits of the theory that yield the local coupling approximation, the collective Rouse dynamics model, and the reptation dynamics model. We show how a simple approximation to the Rouse dynamics model leads to a feasible numerical model that includes the essential physical features of nonlocal kinetic coupling. This results in a dynamic equation for the external potential instead of the density which allows us to perform calculations of microphase separation in copolymer melts with increased relevance to experimental results. As may be expected from a numerical model that includes nonlocal kinetic coupling, the numerical results show an increased computational efﬁciency, less defects in the ﬁnal morphology, and a faster increase of the order parameter compared to local kinetic coupling.",
	collection = "block copolymers",
	doi = "10.1063/1.474313",
	keywords = "block copolymers; microdomains",
	localfile = "block copolymers/1997 - Mesoscopic dynamics of copolymer melts: from density dynamics to external potential dynamics using nonlocal kinetic coupling.pdf",
	methods = "DDFT",
	year = 1997
}

@Article{1997-McCauliffe,
	Author = "Daniel P. McCauliffe",
	Title = "{Cutaneous diseases in adults associated with Anti-Ro/SS-A autoantibody production}",
	Journal = "Lupus",
	Volume = "6",
	Pages = "158–166",
	collection = "cells",
	localfile = "cells/1997 - Cutaneous diseases in adults associated with Anti-Ro-SS-A autoantibody production.pdf",
	year = 1997
}

@Article{1997-McCauliffe-WSRS,
	Author = "Daniel P. McCauliffe and L. Wang and Minoru Satoh and W. H. Reeves and D. Small",
	Title = "{Recombinant 52 kDa Ro(SSA) ELISA detects autoantibodies in Sjögren's syndrome sera that go undetected by conventional serologic assays}",
	Journal = "J. Rheumatol.",
	Volume = "24",
	Pages = "860–866",
	collection = "cells",
	localfile = "cells/1997 - Recombinant 52 kDa Ro(SSA) ELISA detects autoantibodies in Sjogren's syndrome sera that go undetected by conventional serologic assays.pdf",
	year = 1997
}

@Article{1997-Neidle,
	Author = "Stephen Neidle",
	Title = "{Crystallographic insights into {DNA} minor groove recognition by drugs}",
	Journal = "Biopolymers",
	Volume = "44",
	Number = "1",
	Pages = "105 – 121",
	abstract = "This review surveys the crystal structures between minor groove drugs and oligonucleotides, of which over thirty have now been determined. The various factors that are involved in the observed A/T sequence selectivity of these drugs are examined in structural terms. The roles of; in particular, hydrogen-bond recognition and sequence-dependent groove width, are assessed, and as a consequence the minor groove drugs have been classified into two categories, dependent on the relative roles played by these two factors in sequence recognition. Implications for the recognition of non-A/T sequences are discussed.",
	collection = "nucleic acid drugs",
	localfile = "nucleic acid drugs/1997 - Crystallographic insights into DNA minor groove recognition by drugs.pdf",
	year = 1997
}

@Article{1997-Rozas,
	Author = "Isabel Rozas",
	Title = "{Atomic charges derived from different methods: A comparative study applied to {SO$\_2$} heterocycles}",
	Journal = "Int. J. Quant. Chem.",
	Volume = "62",
	Number = "5",
	Pages = "477–487",
	abstract = "Atomic charges were calculated at ab initio level using different methods of charge determination to compare them and estimate their utility in the electronic description of heterocycles containing the {SO2} moiety. Those procedures implemented on the Gaussian92 program were included {[Mulliken} population analysis, {Weinhold-Reed} natural population analysis {(NPA)} and {CHELPG].} The first two are based on the molecular orbitals while in the third one the charges are derived by fitting the electrostatic potential. Two sets of compounds were chosen to represent the different characteristics of the {SO2} heterocycles studied: simpler five-member heterocycles and {SO2} small derivatives. These molecules were optimized at the {HF/6-31G*} level and their energy evaluated by a punctual calculation {MP2/6-31G*//HF/6-31G*.} The dipole moments for these molecules were obtained by using all the methods previously mentioned and compared with the {SCF,} {MP2,} and experimental dipole moments. The influence on the charges of some atoms by changing the electronegativity of neighboring atoms has also been investigated for these compounds. The results obtained show that the best methods to describe the electronic distribution of the oxathiole studied are Mulliken and {CHELPG} at the {MP2} level of calculation. The charge distributions obtained with these two methods for these particular heterocycles are discussed. © 1997 John Wiley \& Sons, Inc. Int J Quant Chem 62: 477-487, 1997",
	collection = "molecular fragmentation",
	doi = "10.1002/(SICI)1097-461X(1997)62:5",
	localfile = "molecular fragmentation/1997 - Atomic charges derived from different methods: A comparative study applied to SO2 geterocycles.pdf",
	shorttitle = "Atomic charges derived from different methods",
	year = 1997
}

@Article{1997-Sanchez-Bajo-Cumbrera,
	Author = "F. Sanchez-Bajo and F. L. Cumbrera",
	Title = "{The use of the pseudo-Voigt function in the variance method of X-ray line-broadening analysis}",
	Journal = "J. Appl. Cryst.",
	Volume = "30",
	Pages = "427–430",
	collection = "crystallography",
	doi = "10.1107/S0021889896015464",
	localfile = "crystallography/1997 - The use of the pseudo-voigt function in the variance method of X-ray line0braodening analysis.pdf",
	rating = "2",
	read = "2012-09-20",
	year = 1997
}

@Article{1997-Sartorius-Schneider,
	Author = "Joachim Sartorius and Hans-Jörg Schneider",
	Title = "{Intercalation mechanisms with ds-{DNA}: binding modes and energy contributions with benzene, naphthalene, quinoline and indole derivatives including some antimalarials}",
	Journal = "J. Chem. Soc. Perkin Trans. 2",
	Number = "11",
	Pages = "2319–2327",
	abstract = "Intercalation mechanisms into double-stranded calf thymus DNA have been probed with 38 different ligands, largely based on naphthalene or quinoline systems, It is shown how NMR shift and line width changes of the ligand signals can be used to unequivocally differentiate intercalation from groove binding modes, and to obtain by curve fitting association constants K. These show acceptable agreement if derived from several independent NMR signals. Less reliable information is obtained from selected UV titrations, from DNA melting differences, from calorimetric measurements and from affinity comparison to polyamines, the latter being based on a fluorescence assay with ethidium bromide. In contrast to literature expectations the naphthalene-shaped ligands show similar affinities irrespective of the presence of nitrogen atoms, or even of charges within the aromatic system, Quinolinium and naphthalene derivatives only intercalate if they bear a positively charged side chain, and then with similar binding constants. Comparison of all systems as well as salt effects demonstrate that the binding can be quantified with additive contributions from salt bridges of the ammonium centres in the side chains, and from the stacking effects of the aromatic parts. There is no evidence for non-classical intercalation by partial insertion between the nucleobases, nor for any intercalation of phenyl units.",
	collection = "nucleic acid intercalation",
	localfile = "nucleic acid intercalation/1997 - Intercalation mechanisms with ds-DNA.pdf",
	year = 1997
}

@Article{1997-Schutz-BWLK,
	Author = "Martin Schütz and Steve Brdarski and Per-Olof Widmark and Roland Lindh and Gunnar Karlström",
	Title = "{The water dimer interaction energy: {C}onvergence to the basis set limit at the correlated level}",
	Journal = "J. Chem. Phys.",
	Volume = "107",
	Number = "12",
	Pages = "4597 – 4605",
	abstract = "The water dimer interaction energy and its convergence to the basis set limit was investigated, with electron correlation effects treated at the level of second order Møller–Plesset perturbation theory (MP2). ANO-type and large uncontracted basis sets were used, spreading over a wide range in size; the biggest set included 1046 functions with angular momentum up to (l=7). Core correlation effects were treated accurately by augmenting the original valence basis with extended sets of core polarization functions. The MP2 dimer interaction energy at the basis set limit was determined to -4.94+/-0.02 kcal/mol, with a contribution due to core correlation of -0.04 kcal/mol. Furthermore, based on some elementary considerations from intermolecular perturbation theory, a simple procedure was devised, which brings the counterpoise corrected interaction energies of moderate basis set calculations closer to the basis set limit. The interaction energies so obtained turned out be surprisingly stable with respect to extensions of the basis set. (C) 1997 American Institute of Physics.",
	collection = "basis set dependence",
	doi = "10.1063/1.474820",
	keywords = "water",
	localfile = "basis set dependence/1997 - The water dimer interaction energy: Convergence to the basis set limit at the correlated level.pdf",
	methods = "MP2",
	systems = "water dimer",
	year = 1997
}

@Article{1997-Szwajkajzer-Carey,
	Author = "Danuta Szwajkajzer and Jannette Carey",
	Title = "{Molecular and biological constraints on ligand-binding affinity and specificity}",
	Journal = "Biopolymers",
	Volume = "44",
	Pages = "181–198",
	abstract = "Abstract: Interactions between biological macromolecules have characteristic values of afﬁnity and speciﬁcity that are set according to the biological function that is served by the interaction in the organism. Here we examine the molecular mechanisms that are used to achieve the required values of afﬁnity and speciﬁcity in various biological systems.",
	collection = "molecular interactions",
	doi = "10.1002/(SICI)1097-0282(1997)44:2",
	localfile = "molecular interactions/1997 - Molecular and biological constraints on ligand-binding affinity and specificity.pdf",
	year = 1997
}

@Article{1997-Wang-PK,
	Author = "F. Wang and R. Pottel and U. Kaatze",
	Title = "{Dielectric properies of alkanediol/water mixtures}",
	Journal = "J. Phys. Chem. B",
	Volume = "101",
	Pages = "922–929",
	cited = "50 (2013-04-29)",
	collection = "molecular solvation",
	doi = "10.1021/jp963422x",
	localfile = "molecular solvation/1997 - Dielectric properties of alkanediol-water mixtures.pdf",
	year = 1997
}

@Article{1998-Arthanari-BKB,
	Author = "Haribabu Arthanari and Swarna Basu and Thomas L. Kawano and Philip H. Bolton",
	Title = "{Fluorescent dyes specific for quadruplex {DNA}}",
	Journal = "Nucl. Acids Res.",
	Volume = "26",
	Number = "16",
	Pages = "3724–3728",
	abstract = "Fluorescent dyes which are specific for duplex DNA have found a wide range of applications from staining gels to visualization of chromosomes. Porphyrin dyes have been found which are highly fluorescent in the presence of quadruplex but not duplex DNA, These dyes may offer a route to the specific detection of quadruplex DNA under biologically important conditions. There are three types of DNA quadruplex structures, and these may play important roles in telomere, centromere, triplet repeat, integration sites and other DNAs, and this first set of porphyrin dyes show some selectivity between the quadruplex types.",
	collection = "nucleic acid drugs",
	doi = "10.1093/nar",
	localfile = "nucleic acid drugs/1998 - Fluorescent dyes specific for quadruplex DNA.pdf",
	year = 1998
}

@Article{1998-Bader,
	Author = "Richard F. W. Bader",
	Title = "{A Bond Path: A Universal Indicator of Bonded Interactions}",
	Journal = "J. Phys. Chem. A",
	Volume = "102",
	Number = "37",
	Pages = "7314–7323",
	abstract = "The quantum mechanics of proper open systems yields the physics that governs the local behavior of the electron density, rho(r). The Ehrenfest force F(r) acting on an element of rho(r) and the virial field nu(r) that determine its potential energy are obtained from equations of motion for the electronic momentum and virial operators, respectively. Each is represented by a dressed density, a distribution in real space that results from replacing the property in question for a single electron with a corresponding density that describes its average interaction with all of the remaining particles in the system. All bond paths, lines of maximum density linking neighboring nuclei in a system in stable electrostatic equilibrium, have a common physical origin in terms of F(r) and nu(r), regardless of the nature of the interaction. Each is homeomorphically mirrored by a virial path, a line of maximally negative potential energy density linking the same nuclei. The presence of a bond path and its associated virial path provide a universal indicator of bonding between the atoms so linked. There is no net force acting on an element of rho(r) or on an atom in a molecule in a stationary state, and nu(r) is attractive everywhere. Thus, contrary to what has appeared in the literature, no repulsive forces act on atoms linked by a bond path, nor on their nuclei. All atomic interactions, including those described as nonbonded and responsible for binding in condensed states of matter, result from a local pairing of the densities of opposite spin electrons. This local pairing, which varies throughout space and with the strength of the interaction, should be distinguished from the notion of an electron pair, as embodied in the Lewis model.",
	collection = "molecular structure",
	doi = "10.1021/jp981794v",
	localfile = "molecular structure/1998 - Bond path: a universal indicator of bonded interactions.pdf",
	shorttitle = "A Bond Path",
	year = 1998
}

@Article{1998-Bader-Gatti,
	Author = "Richard F. W. Bader and Carlo Gatti",
	Title = "{A Green's function for the density}",
	Journal = "Chem. Phys. Lett.",
	Volume = "287",
	Number = "3-4",
	Pages = "233–238",
	abstract = "It is shown that the electron density at a point in space is determined by a Green's function, that is, the density at a point r is determined by contributions from a source function (r, r') at r'. This is done in two ways: through the use of the equation of motion for the generator (r-r')-1 for a proper open system, an atom, and by solving Poisson's equation for a potential given by the density [rho](r). The source function enables one to equate the value of the density at any point within a molecule to a sum of atomic contributions and to thus view properties of the density from a new perspective. For example, the observation of a characteristic bond path density, as in a terminal {H-C} group in a hydrocarbon chain, requires that the contribution to the density from atomic sources outside the group remain constant, regardless of the length of the chain.",
	collection = "quantum chemistry",
	doi = "10.1016/S0009-2614(97)01457-7",
	localfile = "quantum chemistry/1998 - A Green's function for the density.pdf",
	year = 1998
}

@Article{1998-Chaires,
	Author = "Jonathan B. Chaires",
	Title = "{Energetics of drug-{DNA} interactions}",
	Journal = "Biopolymers",
	Volume = "44",
	Number = "3",
	Pages = "201 – 215",
	abstract = "Understanding the thermodynamics of drug binding to DNA is of both practical and fundamental interest. The practical interest lies in the contribution that thermodynamics can make to the rational design process for the development of new DNA targeted drugs. Thermodynamics offer key insights into the molecular forces that drive complex formation that cannot be obtained by structural or computational studies alone. The fundamental interest in these interactions lies in what they can reveal about the general problems of parsing and predicting ligand binding free energies. For these problems, drug-DNA interactions offer several distinct advantages, among them being that the structures of many drug-DNA complexes are known at high resolution and that such structures reveal that in many cases the drug acts as a rigid body, with little conformational change upon binding. Complete thermodynamic profiles (Delta G, Delta H, Delta S, Delta C-p) for numerous drug-DNA interactions have been obtained with the help of high-sensitivity microcalorimetry. The purpose of this article is to offer a perspective on the interpretation of these thermodynamics parameters, and in particular how they might be correlated with known structural features. Obligatory conformational changes in the DNA to accommodate intercalators and the loss of translational and rotational freedom upon complex formation both present unfavorable free energy barriers for binding. Such barriers must be overcome by favorable free energy contributions from the hydrophobic transfer of ligand from solution into the binding site, polyelectrolyte contributions from coupled ion release, and molecular interactions (hydrogen and ionic bonds, van dei Waals interactions) that form within the binding site. Theoretical and semiempirical tools that allow estimates of these contributions to be made will be discussed, and their use in dissecting experimental data illustrated This process, even at the current level of approximation, can shed considerable light on the drug-DNA binding process. (C) 1998 John Wiley \& Sons, Inc.",
	collection = "nucleic acid drugs",
	doi = "10.1002/(SICI)1097-0282(1997)44:3",
	localfile = "nucleic acid drugs/1998 - Energetics of drug-DNA interactions.pdf",
	year = 1997
}

@Article{1998-Chaires-1,
	Author = "Jonathan B. Chaires",
	Title = "{Drug-{DNA} interactions}",
	Journal = "Curr. Op. Struct. Biol.",
	Volume = "8",
	Number = "3",
	Pages = "314 – 320",
	abstract = "Significant progress has been made over the past few years in studies of drug-DNA interactions. Structure-based design strategies have yielded new DNA-binding agents with clinical promise. The hairpin polyamides represent the result of a design strategy with outstanding potential. One specific molecule of this class has now been proven to inhibit the expression of a specific gene in vivo. A new bisintercalating anthracycline antibiotic binds with high affinity to DNA, and appears to overcome a specific form of multidrug resistance. Progress in fundamental studies of drug binding to DNA continues, with detailed thermodynamic studies providing new insights into the forces that drive complex formation. New tools have been developed in order to characterize both the binding mode and the sequence specificity of drug binding to DNA, tools that will enable the fundamental aspects of these biologically important reactions to be understood in more detail.",
	collection = "nucleic acid drugs",
	doi = "10.1016/S0959-440X(98)80064-X",
	localfile = "nucleic acid drugs/1997 - Drug-DNA interactions.pdf",
	year = 1998
}

@Article{1998-Chatterjee-Schweizer,
	Author = "Avik P. Chatterjee and Kenneth S. Schweizer",
	Title = "{Microscopic theory of polymer-mediated interactions between spherical particles}",
	Journal = "J. Chem. Phys.",
	Volume = "109",
	Number = "23",
	Pages = "10464–10476",
	collection = "polymer nanocomposites",
	doi = "10.1063/1.477729",
	keywords = "nanospheres; polymer nanocomposites",
	localfile = "polymer nanocomposites/1998 - Microscopic theory of polymer-mediated interactions between spherical particles.pdf",
	year = 1998
}

@Article{1998-Ciebien-CSC,
	Author = "J. F. Ciebien and R. T. Clay and B. H. Sohn and R. E. Cohen",
	Title = "{Brief review of metal nanoclusters in block copolymer films}",
	Journal = "New J. Chem.",
	Volume = "22",
	Pages = "685–691",
	collection = "block copolymer nanocomposites",
	doi = "10.1039/A709233D",
	keywords = "block copolymers; polymer nanocomposites; thin films",
	localfile = "block copolymer nanocomposites/1998 - Brief review of metal nanoclusters in block copolymer films.pdf",
	type = "Review",
	year = 1998
}

@Article{1998-Dziekonski-SKA,
	Author = "Paweł Dziekoński and W. Andrzej Sokalski and Emil Kassab and Marcel Allavena",
	Title = "{Electrostatic nature of catalytic effects resulting from Si>Al substitutions in ZMS-5 zeolite}",
	Journal = "Chem. Phys. Lett.",
	Volume = "288",
	Pages = "538–544",
	collection = "molecular catalysis",
	doi = "10.1016/S0009-2614(98)00330-3",
	localfile = "molecular catalysis/1998 - Electrostatic nature of catalytic effects resulting from Si>Al substitutions in ZMS-5 zeolite.pdf",
	year = 1998
}

@Article{1998-Gellman,
	Author = "Samuel H. Gellman",
	Title = "{Foldamers: a manifesto}",
	Journal = "Acc. Chem. Res.",
	Volume = "31",
	Number = "4",
	Pages = "173–180",
	abstract = "I use the term “foldamer” to describe any polymer with a strong tendency to adopt a specific compact conformation. Among proteins, the term “compact” is associated with tertiary structure, and there is as yet no synthetic polymer that displays a specific tertiary structure. Protein tertiary structure arises from the assembly of elements of regular secondary structure (helices, sheets, and turns). The first step in foldamer design must therefore be to identify new backbones with well-defined secondary structural preferences. “Well-defined” in this case means that the conformational preference should be displayed in solution by oligomers of modest length, and I will designate as a foldamer any oligomer that meets this criterion. Within the past decade, a handful of research groups have described unnatural oligomers with interesting conformational propensities. The motivations behind such efforts are varied, but these studies suggest a collective, emerging realization that control over oligomer and polymer folding could lead to new types of molecules with useful properties. The purpose of this “manifesto” is to introduce a large audience to the broad research horizons offered by the concept of synthetic foldamers.",
	collection = "protein structure",
	doi = "10.1021/ar960298r",
	keywords = "protein folding",
	localfile = "protein structure/1998 - Foldamers: a manifesto.pdf",
	year = 1998
}

@Article{1998-Hodges-SL,
	Author = "Matthew P. Hodges and Anthony J. Stone and Enrique C. Lago",
	Title = "{Analytical potentials for HF dimer and larger HF clusters from ab initio calculations}",
	Journal = "J. Phys. Chem. A",
	Volume = "102",
	Pages = "2455–2465",
	abstract = "A new ab initio potential for hydrogen fluoride dimer is presented, constructed from properties calculated for the monomer and intermolecular perturbation theory calculations on the dimer. The potential is split into clearly defined contributions. The long-range electrostatic energy is represented by a distributed multipole model with multipoles up to hexadecapole. The induction energy is modelled by means of polarizabilities up to rank 2 at the center of mass. The repulsion energy is described by an anisotropic exponential site-site model. For the dispersion, two models have been used: a one-site anisotropic and a two-site isotropic model, both incorporating damping functions. The geometries, binding energies, and barrier height to tunneling motion are in good agreement with previous calculations. We also compare the classical and quantum corrected second virial coefficient with the limited data available. The potential is extended to larger clusters, the induction energy accounting for many-body contributions to the energy. For the trimer to the hexamer, we have characterized minima and transition states and decomposed the total interaction energy into its n-body components.",
	collection = "hydrogen bonding",
	doi = "10.1021/jp972148j",
	localfile = "hydrogen bonding/1998 - Analytical potentials for HF dimer and larger HF clusters from ab initio calcualtions.pdf",
	year = 1998
}

@Article{1998-Ismail-SFLWR,
	Author = "Matthew A. Ismail and Karen J. Sanders and Gareth C. Fennell and Harriet C. Latham and Paul Wormell and Alison Rodger",
	Title = "{Spectroscopic studies of 9-hydroxyellipticine binding to {DNA}}",
	Journal = "Biopolymers",
	Volume = "46",
	Number = "3",
	Pages = "127–143",
	abstract = "The binding of 9-hydroxyellipticine to calf thymus {DNA,} {poly[d(A-T)]2,} and {poly-[d(G-C)]2} has been studied in detail by means of {CD,} linear dichroism, resonance light scattering, and molecular dynamics. The transition moment polarizations of 9-hydroxyelliptiycine were determined in polyvinyl alcohol stretched film. Spectroscopic solution studies of the {DNA/drug} complex are combined with theoretical {CD} calculations using the final 50 ps of a series of molecular dynamics simulations as input. The spectroscopic data shows 9-hydroxyellipticine to adopt two main binding modes, one intercalative and the other a stacked binding mode involving the formation of drug oligomers in the {DNA} major groove. Analysis of the intercalated binding mode in {poly[d(A-T)]2} suggests the 9-hydroxyellipticine hydroxyl group lies in the minor groove and hydrogen bonds to water with the pyridine ring protruding into the major groove. The stacked binding mode was examined using resonance light scattering and it was concluded that the drug was forming small oligomer stacks rather than extended aggregates. Reduced linear dichroism measurements suggested a binding geometry that precluded a minor groove binding mode where the plane of the drug makes a 45° angle with the plane of the bases. Thus it was concluded that the drug stacks in the major groove. No obvious differences in the mode of binding of 9-hydroxyellipticine were observed between different {DNA} sequences; however, the stacked binding mode appeared to be more favorable for calf thymus {DNA} and {poly[d(G-C)]2} than for {poly[d(A-T)]2,} an observation that could be explained by the slightly greater steric hindrance of the {poly[d(A-T)]2} major groove. A strong concentration dependence was observed for the two binding modes where intercalation is favored at very low drug load, with stacking interactions becoming more prominent as the drug concentration is increased. Even at {DNA} : drug mixing ratios of 70:1 the stacked binding mode was still important for {GC-rich} {DNAs.} © 1998 John Wiley \& Sons, Inc. Biopoly 46: 127-143, 1998",
	collection = "nucleic acid intercalation",
	doi = "10.1002/(SICI)1097-0282(199809)46:3",
	localfile = "nucleic acid intercalation/1998 - Spectroscopic studies of 9-hydroxyellipticine binding to DNA.pdf",
	year = 1998
}

@Article{1998-Klopper-QS,
	Author = "Wim Klopper and Martin Quack and Martin A. Suhm",
	Title = "{HF dimer: Empirically refined analytical potential energy and dipole hypersurfaces from ab initio calcualtions}",
	Journal = "J. Chem. Phys.",
	Volume = "108",
	Number = "24",
	Pages = "10096–10115",
	abstract = "The interaction between two HF molecules as a function of all six internal coordinates is reported as calculated for 3284 selected points in conﬁguration space at counterpoise-corrected explicitly correlated levels and ﬁtted to an analytical expression, which is described in detail. The unweighted rms deviation for all 3284 points is 21 cm$^{-1}$. Empirical reﬁnements are applied through mixing and scaling of the ab initio data, guided by the comparison of multidimensional nuclear quantum energy levels with experimental data. The resulting semiempirical pair potentials labeled SC-2.9 and SO-3 contain 67 and 61 freely adjusted parameters and are combined with a four parameter monomer potential of generalized Poschl–Teller type. Various minimum energy paths and cuts are investigated. Major improvements over earlier HF dimer potentials are demonstrated via multidimensional solutions of the nuclear Schrodinger equation. Comparison with other high level ab initio calculations and with various experimental data reveals very good overall consistency. The new potential suggests strong Coriolis coupling in the librational degrees of freedom. Best estimates of stationary points, of the dimer dissociation energy ($D\_e$ 19.1$\pm$0.2 kJ/mol), of the electronic barrier to hydrogen bond exchange 4.2$\pm$0.2 kJ/mol , of the electronic barrier to linearity 3.9$\pm$0.2 kJ/mol , and of the electronic barrier to hydrogen exchange 175$\pm$10 kJ/mol are inferred. Based on accurate electric dipole functions for the monomer and distortion contributions calculated with a large basis at SCF level, a simple analytical six-dimensional electric dipole hypersurface is presented.",
	collection = "hydrogen bonding",
	doi = "10.1063/1.476470",
	keywords = "hydrogen bonding",
	localfile = "hydrogen bonding/1998 - HF dimer: empirically refined analytical potential energy and dipole hypersurfaces from ab initio calculations.pdf",
	systems = "HF dimer",
	year = 1998
}

@Article{1998-Lauter-Pasyuk-LAGCHK,
	Author = "V. Lauter-Pasyuk and H. J. Lauter and D. Ausserre and Y. Gallot and V. Cabuil and B. Hamdoun and E. I. Kornilov",
	Title = "{Neutron reflectivity studies of composite nanoparticle–copolymer thin films}",
	Journal = "Physica B",
	Volume = "248",
	Pages = "243–245",
	collection = "block copolymer nanocomposites",
	doi = "10.1016/S0921-4526(98)00241-5",
	keywords = "block copolymers; nanoparticle distribution; nanospheres; polymer nanocomposites; thin films",
	localfile = "block copolymer nanocomposites/1998 - Neutron reflectivity studies of composite nanoparticle-copolymer thin films.pdf",
	methods = "neutron diffraction",
	rating = "2",
	systems = "maghemite@PS-PBMA",
	year = 1998
}

@Article{1998-Lauter-Pasyuk-LAGCKH,
	Author = "V. Lauter-Pasyuk and H. J. Lauter and D. Ausserre and Y. Gallot and V. Cabuil and E. I. Kornilov and B. Hamdoun",
	Title = "{Effect of nanoparticle size on the internal structure of copolymer-nanoparticles composite thin films studied by neutron reflection}",
	Journal = "Physica B",
	Volume = "241-243",
	Pages = "1092–1094",
	collection = "block copolymer nanocomposites",
	doi = "10.1016/S0921-4526(97)00877-6",
	keywords = "block copolymers; polymer nanocomposites; thin films",
	localfile = "block copolymer nanocomposites/1998 - Effect of nanoparticle size on the internal structure of copolymer-nanoparticles composite thin films studied by neutron reflection.pdf",
	methods = "neutron diffraction",
	rating = "2",
	systems = "maghemite@PS-PBMA",
	year = 1998
}

@Article{1998-Lendvay-Mayer,
	Author = "G. Lendvay and Istvan Mayer",
	Title = "{Some difficulties in computing BSSE-corrected potential surfaces of chemical reactions}",
	Journal = "Chem. Phys. Lett.",
	Volume = "297",
	Pages = "365–373",
	abstract = "We performed a theoretical and numerical analysis of the different 'counterpoise correction' (CP) schemes potentially applicable to correct for the basis set superposition error (BSSE) in the neighborhood of transition structures of chemical reactions. The analysis proved that neither of them is satisfactory: all CP versions result in either discontinuous potential surfaces or yield different energies for the same species in different reactions. Standard CP correction is unavoidable and satisfactory when loosely bound preor post-reaction complexes are studied. For transition structures, however, doing no correction is better than any available CP method. (C) 1998 Elsevier Science B.V. All rights reserved. C1 Hungarian Acad Sci, Chem Res Ctr, Inst Chem, H-1525 Budapest, Hungary.",
	collection = "basis set superposition",
	doi = "10.1016/S0009-2614(98)01191-9",
	localfile = "basis set superposition/1998 - Some difficulties in computing BSSE-corrected potential surfaces of chemical reactions.pdf",
	year = 1998
}

@Article{1998-Mayer,
	Author = "Istvan Mayer",
	Title = "{The chemical Hamiltonian approach for treating the BSSE problem of intermolecular interactions}",
	Journal = "Int. J. Quant. Chem.",
	Volume = "70",
	Pages = "41–63",
	abstract = "The two alternative treatments of the BSSE problem of intermolecular interactions-the a posteriori counterpoise (CP) correction scheme of Boys and Bernardi (BB) and the a priori exclusion of the basic-set superposition error (BSSE) by using the “chemical Hamiltonian approach” (CHA)-are discussed. Alternative interpretations of the BB scheme are compared and some problems and paradoxes are described which can consistently be resolved by introducing a hierarchical scheme of N-body CP corrections. In CHA, one identifies those terms of the Hamiltonian (or Fockian) which cause the BSSE-the same terms cause the energy lowering in the “ghost orbitals” calculations; by omitting these terms from the Hamiltonian (Fockian), one can calculate BSSE-free wave functions, by use of which the BSSE-free values of the energy and of other physical quantities can be obtained in a conventional manner. CHA was successfully applied at the SCF and DET levels of theory, including systems containing three or more interacting subsystems or even infinite periodic chains. The pivot full CI calculations performed for small model systems showed the applicability of the approach for treating electron correlation as well. Mast recently, a CHA version of the MP2 theory and a second-order BSSE-free intermolecular PT have also been tested; they are also applicable for complexes of larger size. It was observed, at any level of theory, that the results given by the a posteriori BB and a priori CHA schemes converge to each other much faster than BSSE disappears from the uncorrected results. (C) 1998 John Wiley \& Sons, Inc. C1 Hungarian Acad Sci, Cent Res Inst Chem, H-1525 Budapest, Hungary.",
	collection = "basis set superposition",
	doi = "10.1002/(SICI)1097-461X(1998)70:1",
	localfile = "basis set superposition/1998 - The chemical Hamiltonian approach for treating the BSSE problem of intermolecular interactions.pdf",
	year = 1998
}

@Article{1998-Mayer-Valiron,
	Author = "Istvan Mayer and P. Valiron",
	Title = "{Second order Møller–Plesset perturbation theory without basis set superposition error }",
	Journal = "J. Chem. Phys.",
	Volume = "109",
	Number = "9",
	Pages = "3360–3373",
	abstract = "A second order Møller–Plesset perturbation theory which is free of the basis set superposition error BSSE is developed based on the ‘‘Chemical Hamiltonian Approach’’ CHA . The zeroth order Hamiltonian is built up on the BSSE-free but not orthogonal and not necessarily real canonic CHA–SCF orbitals and their orbital energies. As the exclusion of BSSE makes the problem nonHermitian, biorthogonal perturbation theory is used to obtain the ﬁrst order wave function. The second order energy is, however, calculated by using the conventional Hermitian Hamiltonian, in accord with the ‘‘CHA with conventional energy’’ recipe. For that reason we use a generalized Hylleraas functional introduced recently; this guarantees the second order energy to be real even in the case of complex CHA–SCF orbitals. The matrix elements entering the generalized Hylleraas functional are calculated by transforming all wave functions, creation and annihilation operators to an auxiliary orthonormalized basis. The new CHA-MP2 method has been tested on a number of van der Waals complexes and hydrogen bonded systems, by using a variety of different basis sets. In all cases a remarkable agreement has been found with the results given by the Boys and Bernardi’s counterpoise method CP ; this agreement is especially striking in the case of large and well-balanced basis sets. This indicates that the conceptually different CHA and CP schemes both take into account correctly the major BSSE effects.",
	collection = "basis set superposition",
	doi = "10.1063/1.476931",
	localfile = "basis set superposition/1998 - Second other Moller-Plesset perturbation theory without basis set superposition error.pdf",
	year = 1998
}

@Article{1998-Pourmand-BRP,
	Author = "Nader Pourmand and Irina Blange and Nils Ringertz and Ingvar Pettersson",
	Title = "{Intracellular localisation of the Ro 52 kD auto-antigen in HeLa cells visualised with green fluorescent protein chimeras}",
	Journal = "Autoimmunity",
	Volume = "28",
	Pages = "225–233",
	collection = "cells",
	localfile = "cells/1998 - Intracellular localisation of the Ro 52 kD auto-antigen in HeLa cells visualised with green fluorescent protein chimeras.pdf",
	year = 1998
}

@Article{1998-Prusiner,
	Author = "Stanley B. Prusiner",
	Title = "{Prions}",
	Journal = "Proc. Natl. Acad. Sci.",
	Volume = "95",
	Number = "23",
	Pages = "13363–13383",
	abstract = "Prions are unprecedented infectious pathogens that cause a group of invariably fatal neurodegenerative diseases by an entirely novel mechanism. Prion diseases may present as genetic, infectious, or sporadic disorders, all of which involve modification of the prion protein (PrP). Bovine spongiform encephalopathy (BSE), scrapie of sheep, and Creutzfeldt-Jakob disease (CJD) of humans are among the most notable prion diseases. Prions are transmissible particles that are devoid of nucleic acid and seem to be composed exclusively of a modified protein (PrPSc). The normal, cellular PrP (PrPC) is converted into PrPSc through a posttranslational process during which it acquires a high beta-sheet content. The species of a particular prion is encoded by the sequence of the chromosomal PrP gene of the mammals in which it last replicated, In contrast to pathogens carrying a nucleic acid genome, prions appear to encipher strain-specific properties in the tertiary structure of PrPSc. Transgenetic studies argue that PrPSc acts as a template upon which PrPC is refolded into a nascent PrPSc molecule through a process facilitated by another protein. Miniprions generated in transgenic mice expressing PrP, in which nearly half of the residues were deleted, exhibit unique biological properties and should facilitate structural studies of PrPSc. While knowledge about prions has profound implications for studies of the structural plasticity of proteins, investigations of prion diseases suggest that new strategies for the prevention and treatment of these disorders may also find application in the more common degenerative diseases.",
	collection = "proteins",
	doi = "10.1073/pnas.95.23.13363",
	localfile = "proteins/1998 - Prions.pdf",
	year = 1998
}

@Article{1998-Rayon-Sordo,
	Author = "Victor M. Rayon and Jóse A. Sordo",
	Title = "{On the validity of the counterpoise correction for the basis set superposition error including the fragment relaxation terms }",
	Journal = "Theor. Chem. Acc.",
	Volume = "99",
	Pages = "68–70",
	abstract = "Abstract. It is demonstrated that relatively large geometrical changes make Emsley et al.'s assumption (J Am Chem Soc (1978) 100:3303) on the counterpoise correction for the basis set superposition error including the fragment relaxation terms unacceptable.",
	collection = "basis set superposition",
	doi = "10.1007/s002140050305",
	keywords = "counterpoise correction",
	localfile = "basis set superposition/1998 - On the validity of the counterpoise correction for the basis set superposition error including fragment relaxation terms.pdf",
	year = 1998
}

@Article{1998-Sakamoto-Hashimoto,
	Author = "Naoki Sakamoto and Takeji Hashimoto",
	Title = "{Ordering dynamics of a symmetric polysterene-block-polyisoprene. 2. Real-space analysis on the formation of lamellar microdomain}",
	Journal = "Macromolecules",
	Volume = "31",
	Pages = "3815–3823",
	abstract = "We have investigated the morphology developed in the ordering process for a nearly symmetric polystyrene-block-polyisoprene diblock copolymer when the copolymer is rapidly brought from a disordered state to an ordered state. The ordering process was explored as a function of time and temperature primarily by transmission electron microscopy (TEM): the microdomain structures formed during the ordering process were observed on specimens frozen at particular times in the ordering process. Complementary small-angle X-ray scattering experiments on the specimens before and after freezing assured that the structures existed before freezing were really conserved in the frozen specimens. The TEM observations showed that the ordered grains of the lamellar microdomain were developed in the matrix of the disordered phase and that the grains grew at the expense of the disordered phase at all the temperatures covered in this study. The coexistence of the ordered and disordered phases suggests that this ordering is a nucleation and growth process. We found that the shape of the lamellar grains developed in the disordered phase were very anisotropic at all stages and temperatures covered in this study: the size along the lamellar normals was much larger than that parallel to the lamellar interfaces. Furthermore in the early stage of the ordering, the lamellae formed in the ordered grains were perforated but they eventually become solid lamellae.",
	collection = "block copolymers",
	keywords = "block copolymers; microdomains",
	localfile = "block copolymers/1998 - Ordering dynamics of a symmetric polysterene-block-polyisoprene. 2. Real-space analysis on the formation of lamellar microdomain.pdf",
	year = 1998
}

@Article{1998-Sibilia,
	Author = "Jean Sibilia",
	Title = "{Ro(SS-A) and anti-Ro(SS-A): An update}",
	Journal = "Rev. Rhum. Engl. Ed.",
	Volume = "65",
	Number = "1",
	Pages = "45–47",
	Note = "I don't have access to this article and have never read it.",
	abstract = "Anti-Ro/SSA antibodies are the antinuclear antibodies most commonly found in everyday clinical practice and are closely associated with Sjogren's syndrome, systemic lupus erythematosus and neonatal lupus. They play a pathogenic role in a variety of clinical manifestations, including skin lesions and neonatal lupus heart block. Autoantibodies to Ro(SS-A) recognize a ribonucleoprotein complex composed of small single-stranded RNAs (hYRNAs) and of one or more peptides. Four molecular forms of this complex have been differentiated based on the nature of the peptide: a lymphocyte and an erythrocyte Ro with a 60 kDa peptide, a lymphocyte Ro with a 52 kDa peptide and an erythrocyte Ro with a 54 kDa peptide. The Ro complex is found in most tissues and cells (erythrocytes, platelets), with differences in structure and quantity across tissues, species and embryonic development stages. Although its function remains unknown, its ability to bind nucleic acids and the fact that it shares homologies with gene regulation proteins suggest that it may participate in RNA transcription processes. A number of environmental factors (exposure to ultraviolet radiation, viral infections) may cause translocation of the Ro complex to nucleocytoplasmic and membrane sites where it is not normally found, thereby leading to the development of autoimmunity. The structure of the Ro(SS-A)-hYRNA complex and the development of autoimmunity are currently the focus of active research efforts that can be expected to improve our understanding of the clinical manifestations directly related to anti-Ro(SS-A) antibodies.",
	collection = "cells",
	localfile = {},
	year = 1998
}

@Article{1998-Szalewicz-Jeziorski,
	Author = "Krzysztof Szalewicz and Bogumił Jeziorski",
	Title = "{Comment on {“On} the importance of the fragment relaxation energy terms in the estimation of the basis set superposition error correction to the intermolecular interaction energy” {[J.} Chem. Phys. [bold 104], 8821 (1996)]}",
	Journal = "J. Chem. Phys.",
	Volume = "109",
	Number = "3",
	Pages = "1198–1200",
	collection = "basis set superposition",
	doi = "10.1063/1.476667",
	localfile = "basis set superposition/1998 - Comment on 'On the importance of the fragment relaxation energy terms in the estmation of the basis set superposition error correction to the intermolecular interactions energy'.pdf",
	year = 1998
}

@Article{1998-Truhlar,
	Author = "Donald G. Truhlar",
	Title = "{Basis-set extrapolation}",
	Journal = "Chem. Phys. Lett.",
	Volume = "294",
	Pages = "45–48",
	abstract = "A proposal for extrapolation of correlated electronic structure calculations based on correlation-consistent polarized double- and triple-zeta basis sets is evaluated. Optimum exponents are presented for separately extrapolating the Hartree–Fock and correlation energies, and the method is shown to yield energies that are more accurate than those from straight correlation-consistent polarized sextuple-zeta calculations at less than 1\% of the cost. For the test problems, the root-mean-square deviations from the complete basis limit are 1.3–2.4 kcalrmol for the extrapolated calculations and 3.0–4.4 kcalrmol for the polarized sextuple-zeta calculations.",
	collection = "basis set dependence",
	doi = "10.1016/S0009-2614(98)00866-5",
	localfile = "basis set dependence/1998 - Basis-set extrapolation.pdf",
	year = 1998
}

@Article{1999-Bader,
	Author = "Richard F. W. Bader",
	Title = "{Can there be more than a single definition of an atom in a molecule?}",
	Journal = "Can. J. Chem.",
	Volume = "77",
	Number = "1",
	Pages = "86–93",
	abstract = "Arguments are presented that the theoretical definition of an atom in a molecule or of a functional grouping of atoms that derive from experimental chemistry must be unique. Definitions based on the orbital model or, as recently proposed, in terms of domains defined by isovalued density envelopes fail for a number of reasons, among them being their failure to enable a quantum mechanical description of the atomic or group properties. Chemistry is concerned with the observation and measurement of properties. Definitions that do not predict the measurable, additive properties found for atoms in molecules fail to recover the essence of the atomic concept and can play no operational or predictive role in chemistry. Atoms exist in real space and their form determines their properties. There is but a single definition for an atom, free or bound, that meets this essential requirement.",
	collection = "molecular fragmentation",
	doi = "10

repository: langner/library

repo_name: langner/library

branch_name: refs/heads/master