text:
",
	systems = "HF dimer",
	year = 1984
}

@Article{1984-Jain-Sobell,
	Author = "S. C. Jain and H. M. Sobell",
	Title = "{Visualization of Drug-Nucleic Acid Interactions at Atomic Resolution. VIII. Structures of Two Ethidiumdinucleoside Monophosphate Crystalline Complexes Containing Ethidium: Cytidylyl(3'-5')Guanosine}",
	Journal = "J. Biomol. Struct. Dyn.",
	Volume = "1",
	Number = "5",
	Pages = "1179–1194",
	collection = "nucleic acid intercalation",
	localfile = {},
	year = 1984
}

@Article{1984-Jain-Sobell-1,
	Author = "S. C. Jain and H. M. Sobell",
	Title = "{Visualization of drug-nucleic acid interactions at atomic resolution .7. structure of an ethidium dinucleoside monophosphate crystalline complex, ethidium - uridylyl(3'-5')adenosine}",
	Journal = "J. Biomol. Struct. Dyn.",
	Volume = "1",
	Number = "5",
	Pages = "1161–1177",
	collection = "nucleic acid intercalation",
	localfile = {},
	year = 1984
}

@Article{1984-Latajka-Scheiner,
	Author = "Zdzisław Latajka and Steve Scheiner",
	Title = "{Effects of basis set and electron correlation on the calculated properties of the ammonia dimer}",
	Journal = "J. Chem. Phys.",
	Volume = "81",
	Number = "1",
	Pages = "407–409",
	collection = "basis set dependence",
	doi = "10.1063/1.447319",
	localfile = "basis set dependence/1984 - Effects of basis set and electron correlation on the calculated properties of the ammonia dimer.pdf",
	year = 1984
}

@Article{1984-LeFeber-NRHLKBKW,
	Author = "W. P. LeFeber and D. A. Norris and S. R. Ryan and J. C. Huff and L. A. Lee and M. Kubo and S. T. Boyce and B. L. Kotzin and W. L. Weston",
	Title = "{Ultraviolet light induces binding of antibodies to selected nuclear antigens on cultured human keratinocytes}",
	Journal = "J. Clin. Invest.",
	Volume = "74",
	Number = "4",
	Pages = "1545–1551",
	collection = "cells",
	localfile = "cells/1984 - Ultraviolet light induces binding of antibodies to selected nuclear antigens on cultured human keratinocytes.pdf",
	year = 1984
}

@Article{1984-Singh-Kollman,
	Author = "U. C. Singh and P. A. Kollman",
	Title = "{An approach to computing electrostatic charges for molecules}",
	Journal = "J. Comput. Chem.",
	Volume = "5",
	Pages = "129–45",
	collection = "molecular electrostatics",
	doi = "10.1002/jcc.540050204",
	localfile = {},
	year = 1984
}

@Article{1984-Stone-Tough,
	Author = "Anthony J. Stone and R. J. A. Tough",
	Title = "{Spherical tensor theory of long-range intermolecular forces}",
	Journal = "Chem. Phys. Lett.",
	Volume = "110",
	Number = "2",
	abstract = "General expresions are given for the electrostatic, induction and dispersion energies of a pair of interacting molecules in terms of spherical tensor components of the molecular multipole moments and polarizabilities. The orientation dependence is given in terms of the scalar expansion functions.",
	collection = "molecular interactions",
	doi = "10.1016/0009-2614(84)80160-8",
	localfile = "molecular interactions/1984 - Spherical tensor theory of long-range intermolecular forces.pdf",
	year = 1984
}

@Article{1984-Tang-Toennies,
	Author = "Kwong-Tin Tang and J. Peter Toennies",
	Title = "{An improved simple model for the van der Waals potential based on universal damping functions for the dispersion coefficients}",
	Journal = "J. Chem. Phys.",
	Volume = "80",
	Number = "8",
	Pages = "3726–3741",
	collection = "molecular interactions",
	doi = "10.1063/1.447150",
	localfile = "molecular interactions/1984 - An improved simple model for the van der Waals potential based on universal damping functions for the dispersion coefficients.pdf",
	year = 1984
}

@Article{1985-Amos-HKRS,
	Author = "R. D. Amos and N. C. Handy and P. J. Knowles and J.E. Rice and Anthony J. Stone",
	Title = "{Ab-initio prediction of properties of CO2, NH3, and CO2...NH3}",
	Journal = "J. Phys. Chem.",
	Volume = "89",
	Pages = "2186–2192",
	abstract = "The recent experiments by Klemperer et al. on small van der Waals molecules have demonstrated the need for a full understanding of the properties of these systems. In this paper, the results of large basis set calculations at the SCF level of accuracy are reported. The properties calculated include electric multipole moments through tenth rank, some second-order properties such as polarizabilities and magnetizabilities,and frequency-dependent second-order properties. From these, properties which describe the long-range interaction of these molecules may be calculated, such as C, and C8coefficients. A distributed multipole analysis of the charge distributions is given. The Buckingham-Fowler model to describe the interaction of CO,and NH3 is investigated and compared with SCF calculations on the complex. Both predict the T shape structure found by Klemperer.",
	collection = "molecular electrostatics",
	doi = "10.1021/j100257a010",
	localfile = "molecular electrostatics/1985 - Ab-initio prediction of properties of CO2, NH3, and CO2...NH3.pdf",
	year = 1985
}

@Article{1985-Brown-Altermatt,
	Author = "I. D. Brown and D. Altermatt",
	Title = "{Bond-valence parameters obtained from a systematic analysis of the inorganic crystal structure database}",
	Journal = "Acta Cryst. B",
	Volume = "41",
	Pages = "244–247",
	collection = "crystallography",
	doi = "10.1107/S0108768185002063",
	keywords = "bond valence",
	localfile = "crystallography/1985 - Bond-valence parameters obtained from a systematic analysis of the inorganic crystal structure database.pdf",
	methods = "bond valence method",
	rating = "3",
	read = "2014-02-01",
	year = 1984
}

@Article{1985-Buckingham-Fowler,
	Author = "A. David Buckingham and P. W. Fowler",
	Title = "{A model for the geometries of van der Waals complexes}",
	Journal = "Can. J. Chem.",
	Volume = "63",
	Pages = "2018–2025",
	collection = "molecular electrostatics",
	doi = "10.1139/v85-334",
	localfile = "molecular electrostatics/1985 - A model for the geomtries of van der Waals complexes.pdf",
	year = 1985
}

@Article{1985-Cammi-BT,
	Author = "R. Cammi and R. Bonaccorsi and Jacopo Tomasi",
	Title = "{Counterpoise corrections to the interaction energy components in bimolecular complexes}",
	Journal = "Theor. Chim. Acta",
	Volume = "68",
	Number = "4",
	Pages = "271–283",
	abstract = "A new definition of counterpoise corrections {(CP)} to the components of {?E} evaluated with the Kitaura and Morokuma method is presented and tested on the {(H2O)2} and {(NH3·HF)} molecular systems with two different basis sets. The {CP} corrections are further decomposed into subsystems contributions, facilitating their interpretation and the elaboration of computationally simplified procedures.",
	collection = "basis set superposition",
	doi = "10.1007/BF00527535",
	keywords = "counterpoise correction",
	localfile = "basis set superposition/1985 - Counterpoise corrections to the interaction energy components in bimolecular complexes.pdf",
	year = 1985
}

@Article{1985-Car-Parinello,
	Author = "M. Car and M. Parrinello",
	Title = "{Unified approach for molecular dynamics and density functional theory}",
	Journal = "Phys. Rev. Lett.",
	Volume = "55",
	Number = "22",
	Pages = "2471–2474",
	collection = "molecular dynamics",
	doi = "10.1103/PhysRevLett.55.2471",
	localfile = "molecular dynamics/1985 - Unified approach for molecular dynamics and density functional theory.pdf",
	rating = "3",
	year = 1985
}

@Article{1985-Pommier-MSZK,
	Author = "Yves Pommier and Jon K. Minford and Ronald E. Schwartz and Leonard A. Zwelling and Kurt W. Kohn",
	Title = "{Effects of the {DNA} intercalators 4'-(9-acridinylamino)methanesulfon-m-anisidide and 2-methyl-9-hydroxyellipticinium on topoisomerase {II} mediated {DNA} strand cleavage and strand passage}",
	Journal = "Biochemistry",
	Volume = "24",
	Number = "23",
	Pages = "6410–6416",
	collection = "nucleic acid drugs",
	doi = "10.1021/bi00344a015",
	keywords = "nucleic acid intercalation",
	localfile = "nucleic acid drugs/1985 - Effects of the DNA intercalators 4'-(9-acridinylamino)methanesulfon-m-anisidide and 2-methyl-9-hydroxyellipticinium o ntopoisomerase II mediated DNA strand cleavage and strand passage.pdf",
	year = 1985
}

@Article{1985-Schwenke-Truhlar,
	Author = "David W. Schwenke and Donald G. Truhlar",
	Title = "{Systematic study of basis set superposition errors in the calculated interaction energy of two {HF} molecules}",
	Journal = "J. Chem. Phys.",
	Volume = "82",
	Number = "5",
	Pages = "2418–2426",
	cited = "394 (2005-05-29)",
	collection = "basis set superposition",
	doi = "10.1063/1.448335",
	localfile = "basis set superposition/1985 - Systematic study of basis set superposition errors in the calculated interaction energy of two HF molecules.pdf",
	year = 1985
}

@Article{1985-Sokalski,
	Author = "W. Andrzej Sokalski",
	Title = "{The physical nature of catalytic activity due to the molecular environment in terms of intermolecular interaction theory: derivation of simplified models}",
	Journal = "J. Mol. Catal.",
	Volume = "30",
	Pages = "395–410",
	abstract = "The catalytic or inhibitory activity of a molecular environment has been quantitatively represented as the difference between the interaction energies of the transition complex and the substrate complex with catalyst, and it has been further decomposed into the electrostatic multipole, electrostatic penetration, exchange, induction and dispersion contributions defined within exchange perturbation theory. A sample analysis of catalytic activity of the first hydration shell has been performed for the reaction CO2 + H20 -> H2CO3 within the LCAO MO SCF ab initio approach. Results indicate a significant contribution of the electrostatic multipole term in the overall catalytic activity. However, the remaining electrostatic penetration, exchange, induction and dispersion interactions seem to be non-negligible but cancelling each other to a great extent, justifying some intuitively assumed electrostatic hypotheses on’the nature of catalytic activity. More approximate models of gradually increasing simplicity have been briefly outlined based on cumulative atomic multipole expansion and nonempirical short range atom-atom potentials, making it possible to deal with much larger molecular systems and to predict the sites of the most effective solvation or the charge distribution of the optimal catalyst for a given reaction.",
	collection = "molecular catalysis",
	doi = "10.1016/0304-5102(85)85049-5",
	localfile = "molecular catalysis/1985 - The physical anture of catalytic activity due to the molecular environment in terms of intermolecular interaction theory: derivation of simplified models.pdf",
	year = 1985
}

@Article{1985-Stone-Alderton,
	Author = "Anthony J. Stone and M. Alderton",
	Title = "{Distributed multipole analysis. Methods and applications}",
	Journal = "Mol. Phys.",
	Volume = "56",
	Number = "5",
	Pages = "1047–1064",
	collection = "molecular electrostatics",
	doi = "10.1080/00268978500102891",
	keywords = "multipole moments",
	localfile = "molecular electrostatics/2002 - Distributed multipole analysis: methods and applications.pdf",
	methods = "DMA",
	year = 1985
}

@Article{1986-Breslauer-FBM,
	Author = "Kenneth J. Breslauer and Ronald Frank and Helmut Blöcker and Luis A. Marky",
	Title = "{Predicting {DNA} duplex stability from the base sequence}",
	Journal = "Proc. Natl. Acad. Sci.",
	Volume = "83",
	Number = "11",
	Pages = "3746–3750",
	abstract = "We report the complete thermodynamic library of all 10 {Watson-Crick} {DNA} nearest-neighbor interactions. We obtained the relevant thermodynamic data from calorimetric studies on 19 {DNA} oligomers and 9 {DNA} polymers. We show how these thermodynamic data can be used to calculate the stability and predict the temperature-dependent behavior of any {DNA} duplex structure from knowledge of its base sequence. We illustrate our method of calculation by using the nearest-neighbor data to predict transition enthalpies and free energies for a series of {DNA} oligomers. These predicted values are in excellent agreement with the corresponding values determined experimentally. This agreement demonstrates that a {DNA} duplex structure thermodynamically can be considered to be the sum of its nearest-neighbor interactions. Armed with this knowledge and the nearest-neighbor thermodynamic data reported here, scientists now will be able to predict the stability (delta G degree) and the melting behavior (delta H degree) of any {DNA} duplex structure from inspection of its primary sequence. This capability should prove valuable in numerous applications, such as predicting the stability of a probe-gene complex; selecting optimal conditions for a hybridization experiment; deciding on the minimum length of a probe; predicting the influence of a specific transversion or transition on the stability of an affected {DNA} region; and predicting the relative stabilities of local domains within a {DNA} duplex.",
	collection = "nucleic acids",
	doi = "10.1073/pnas.83.11.3746",
	keywords = "nucleic acid stability",
	localfile = "nucleic acids/1986 - Predicting DNA duplex stability from the base sequence.pdf",
	year = 1986
}

@Article{1986-Buckingham-FS,
	Author = "A. David Buckingham and P. W. Fowler and Anthony J. Stone",
	Title = "{Electrostatic predictions of shapes and properties of Van der Waals molecules}",
	Journal = "Int. Rev. Phys. Chem.",
	Volume = "5",
	Pages = "107–114",
	abstract = "The application of long-range models to shapes and dipole moments of Van der Waals complexes is reviewed. A simple model incorporating electrostatic interactions through distributed point multipoles, and short-range repulsion through hard spheres, has wide predictive power for the shapes of hydrogen-bonded and other complexes. Successes and limitations of the model are discussed. Inclusion of a distributed polarizability allows semiquantitative prediction of dipole moments of complexes.",
	collection = "molecular electrostatics",
	doi = "10.1080/01442358609353370",
	localfile = "molecular electrostatics/1986 - Electrostatic predictions of shapes and properties of Van der Waals molecules.pdf",
	methods = "DMA",
	year = 1986
}

@Article{1986-Hurst-FSB,
	Author = "G. J. B. Hurst and P. W. Fowler and Anthony J. Stone and A. David Buckingham",
	Title = "{Intermolecular forces in van der Waals dimers}",
	Journal = "Int. J. Quant. Chem.",
	Volume = "29",
	Pages = "1223–1239",
	collection = "molecular interactions",
	doi = "10.1002/qua.560290520",
	localfile = "molecular interactions/1986 - Intermolecular forces in van der Waals dimers.pdf",
	year = 1986
}

@Article{1986-Jackson,
    Author = "Frank Jackson",
    Title = "{What Mary didn't know}",
    Journal = "The Journal of Philosophy",
    Volume = "83",
    Number = "5",
    Pages = "291-295",
    collection = "philosophy",
    doi = "10.2307/2026143",
    localfile = "philosphy/What Mary didn'y know.pdf",
    year = 1986
}

@Article{1986-Minford-PFKKMMSZ,
	Author = "Jon K. Minford and Yves Pommier and Jan Filipski and Kurt W. Kohn and Donna Kerrigan and Michael Mattern and Steven Michaels and Ronald E. Schwartz and Leonard A. Zwelling",
	Title = "{Isolation of intercalator-dependent protein-linked {DNA} strand cleavage activity from cell nuclei and identification as topoisomerase {II}}",
	Journal = "Biochemistry",
	Volume = "25",
	Number = "1",
	Pages = "9–16",
	collection = "nucleic acid drugs",
	doi = "10.1021/bi00349a002",
	localfile = "nucleic acid drugs/1986 - Isolation of intercalator-dependent protein-linked DNA strand cleavage activity from cell nuclei and identification as topoisomerase II.pdf",
	year = 1986
}

@Article{1986-Spackman,
	Author = "Mark A. Spackman",
	Title = "{A simple quantitative model of hydrogen bonding}",
	Journal = "J. Chem. Phys.",
	Volume = "85",
	Number = "11",
	Pages = "6587–6601",
	abstract = "A simple model for the computation of intermolecular interactions is described. It consists of atom-atom potentials for the representation of repulsion and dispersion energies, adn an evaluation of the electrostatic energy in terms of partitioned multipole moments of the monomer electron distributions. Applications are given in detail for hydrogen-bonded dimers of the molecules HF, HCL, CO, N$\_2$, Cl$\_2$, HCN, CO$\_2$, N$\_2$O, OCS, HCCH, NCCN, and HCCCN, and the results compared with {\it ab initio} and experimental resutls. Hydrogen bond energies are obtained to better than 4 kJ mol$\_{-1}$, intermolecular separations to typically better than 0.15 ${\AA}$, and intermolecular angles within 5$^o$, all compared with experiment. Force constants and vibrational frequencies are also well reproduced.",
	collection = "hydrogen bonding",
	doi = "10.1063/1.451441",
	localfile = "hydrogen bonding/1986 - A simple quantitative model of hydrogen bonding.pdf",
	year = 1986
}

@Article{1986-Szczesniak-Scheiner,
	Author = "Małgorzata M. Szczęśniak and Steve Scheiner",
	Title = "{Correction of the basis set superposition error in {SCF} and {MP2} interaction energies. The water dimer}",
	Journal = "J. Chem. Phys.",
	Volume = "84",
	Number = "11",
	Pages = "6328 – 6335",
	collection = "basis set superposition",
	doi = "10.1063/1.450725",
	localfile = "basis set superposition/1986 - Correction of the basis set superposition error in SCF and MP2 interaction energies. The water dimer.pdf",
	methods = "MP2",
	systems = "water dimer",
	year = 1986
}

@Article{1987-Bader-CCC,
	Author = "Richard F. W. Bader and Marshall T. Carroll and James R. Cheeseman and Cheng Chang",
	Title = "{Properties of atoms in molecules: atomic volumes}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "109",
	Number = "26",
	Pages = "7968–7979",
	abstract = "The theory of atoms in molecules defines an atom and the average values of its properties. The intersection of an atomic surface, as defined by a property of the charge density, with a particular envelope of the charge density defines the volume of an atom in a molecule. The value of the density envelope used to bound the “open” portion of an atomic region can be chosen on the basis of comparison with measured properties. The nature of the results are, in any event, independent of the choice for envelopes which contain over 96\% of the total electronic charge and lie within the usual range of van der Waals contact distances. It is shown that the volumes of methyl and methylene groups in normal hydrocarbons are transferable properties, as are their charge distributions, populations, and energies. The volume of a carbon atom subject to steric crowding is found to decrease as its stability and electron population increase. This behavior is opposite to that found for a carbon atom in a system with geometric strain as found in cyclic and bicyclic molecules. The stability, population, and volume of a carbon atom all undergo parallel increases as the atom is subjected to an increasing degree of geometric strain. The volumes of the bridgehead carbon atoms in bicyclo[ l.l.O]butane and [ l.l.l]propellane are 1.2 and 1.5 times, respectively, the volume of a methyl carbon atom. As anticipated on the basis of the orbital model, an increase in geometric strain is correlated with an increase in s character and thus one finds the electron population, stability, and volume of a carbon atom to undergo the same parallel increases in value through the series ethane, ethylene, acetylene. As a first step in the investigation of how atoms fit together, the changes in the atomic volumes accompanying the formation of a hydrogen bond are determined. The changes in volume are correlated with the changes in the atomic populations and energies for the formation of homo and hetero dimers of water and ammonia and their protonated species.",
	collection = "molecular fragmentation",
	doi = "10.1021/ja00260a006",
	localfile = "molecular fragmentation/1987 - Properties of atoms in molecules: atomic volumes.pdf",
	shorttitle = "Properties of atoms in molecules",
	year = 1987
}

@Article{1987-Bader-LGCMW,
	Author = "Richard F. W. Bader and A. Larouche and Carlo Gatti and Marshall T. Carroll and Preston J. {MacDougall} and K. B. Wiberg",
	Title = "{Properties of atoms in molecules: Dipole moments and transferability of properties}",
	Journal = "J. Chem. Phys.",
	Volume = "87",
	Number = "2",
	Pages = "1142–1152",
	abstract = "This paper uses the theory of atoms in molecules to investigate the origin of molecular dipole moments. The dipole moment is given by a sum over the net charge and first moment of every atom in a molecule. The first term leads to a charge transfer cotnribution $\mu\_c$, the second to an atomic polarization contribution $\mu\_a$. It is shown that both terms are, in general, of equal importnace in determining both the static molecular dipole moments and the moment induced by a nuclear dispalcement. Models which imploy only point charges and corresponding bond moments which follow rigidly the nuclear framework, i.e., models which approximate $\mu\_c$ and ignore $\mu\_a$, are shown to lead to results that are incompatible with the cahnges that are found to occur in a molecualr charge dusturbution during a nuclear vibration. The dipole moment is shown to be another group property that is transferable between molecules in the normal hydrocarbons. This property, along with the net charge, the energy, the correlation energy (expressed as a functional fo the charge density), and the atomic volumes are transferable for methyl and methylene groups because of a corresponding transferability of the distribution of charge over the basins of the atoms in these groups up to their surfaces of zero flux in the gradient vector of the charge density. Trnassferability of group properties is not a result of the trnasferability of individual orbitals or geminals, which necessarily have tails lying outside of the group in question. Atoms have not tails and their energy, as is known from experiment, can in certain instances be transferred between systems with changes of less thatn 1 kcal/mol. The properties of atoms in molecules can be determined experimentally and quantum mechanics predicts these properties, just as it predicts the properties of a total system.",
	collection = "molecular fragmentation",
	doi = "10.1063/1.453294",
	localfile = "molecular fragmentation/1987 - Properties of atoms in molecules: dipole moments and transferability of properties.pdf",
	shorttitle = "Properties of atoms in molecules",
	year = 1987
}

@Article{1987-Breslauer-RCFCZSM,
	Author = "Kenneth J. Breslauer and David P. Remeta and Wan-Yin Chou and Robert Ferrante and James Curry and Denise Zaunczkowski and James G. Snyder and Luis A. Marky",
	Title = "{Enthalpy-entropy compensations in drug-{DNA} binding studies}",
	Journal = "Proc. Natl. Acad. Sci.",
	Volume = "84",
	Number = "24",
	Pages = "8922–8926",
	cited = "146 (2005-05-14)",
	collection = "nucleic acid intercalation",
	localfile = "nucleic acid intercalation/1987 - Enthalpy-entropy compensations in drug-DNA binding studies.pdf",
	year = 1987
}

@Article{1987-Fredrickson-Helfand,
	Author = "Glenn H. Fredrickson and Eugene Helfand",
	Title = "{Fluctuation effects in the theory of microphase separation in block copolymers}",
	Journal = "J. Chem. Phys.",
	Volume = "87",
	Number = "1",
	Pages = "697–705",
	abstract = "The effect of composition fluctuations on the microphase separation transition in diblock copolymers is investigated. Such fluctuation corrections, which were neglected in the mean field treatment of Leibler, are found to be significant for the molecular weights usually encountered. The analysis is facilitated by reducing the block copolymer Hamiltonian to a form previously studied by Brazovskii. Our principal results are the following: (i) A symmetric diblock copolymer is predicted to undergo a first order phase transition at a larger value ofXN than the second order transition found by Leibler. The Flory interaction parameter is denoted X and N is the number of statistical segments per chain. The location of the transition is predicted to be at (XN)t = 10.495 + 41.022 N -1/3, where the peak in the scattering function attains its maximum value of 0.12328 N 1/3 • (ii) We find windows in composition, with finite width, through which it is possible to pass from the disordered phase to each ofthe ordered microphases (lamellar, hexagonal, and body-centered-cubic) by changing temperature. (iii) All the results of Leibler are recovered in the limit of block copolymers with infinite molecular weight.",
	collection = "polymers",
	doi = "10.1063/1.453566",
	localfile = "polymers/1987 - Fluctuation effects in teh theory of micrphase separation in block copolymers.pdf",
	year = 1987
}

@Article{1987-Gutowski-DCP,
	Author = "Maciej Gutowski and {Frans B. van} {Duijneveldt} and Grzegorz Chałasiński and Lucjan Piela",
	Title = "{Proper correction for the basis set superposition error in SCF calculations of intermolecular interactions}",
	Journal = "Mol. Phys.",
	Volume = "61",
	Pages = "233",
	abstract = "The effects of basis set extension to the space of the partner monomer in supermolecular SCF and perturbation calcualtions have been analysed for the model He2 and HeLi+ systems. In contrast to the suggestions of many authors it is demonstrated that the correction for the basis set superposition error should be calcualted with the full basis set of the dimer without removing the occupied orbitals of the partner monomer. In fact, the enlargement of the monomer basis set by the partner occupied orbitals effectively imprived the first-order exchange interaction energy. For the first-order electrostatic interaction energy any enlargement of a poor or medium size basis set of the monomer by the partner orbitals worsens its value.",
	collection = "basis set superposition",
	doi = "10.1080/00268978700101101",
	localfile = "basis set superposition/1987 - Proper correction for the basis set superposition error in SCF calculations of intermolecular interactions.pdf",
	year = 1987
}

@Article{1987-Hinton-Nowlan,
	Author = "Geoffrey E. Hinton and Steven J. Nowlan",
	Title = "{How learning can guide evolution}",
	Journal = "Complex Systems",
	Volume = "1",
	Number = "3",
	Pages = "495–502",
	collection = "evolution",
	keywords = "neural network; Baldwin effect",
	localfile = "evolution/1987 - How learning can guide evolution.pdf",
	rating = "3",
	read = "2015-01-31",
	year = 1987
}

@Article{1987-Hwang-Warshel,
	Author = "J.-K. Hwang and Arieh Warshel",
	Title = "{Semiquantitative calculations of catalytic free energies in genetically modified enzymes}",
	Journal = "Biochemistry",
	Volume = "26",
	Pages = "2669–2673",
	collection = "enzymes",
	localfile = "enzymes/1987 - Semiquantitative calculations of catalytic free energies in genetically modified enzymes.pdf",
	year = 1987
}

@Article{1987-Pommier-CKMMK,
	Author = "Yves Pommier and Joseph Covey and Donna Kerrigan and William Mattes and Judith Markovits and Kurt W. Kohn",
	Title = "{Role of {DNA} intercalation in the inhibition of purified mouse leukemia {(L1210)} {DNA} topoisomerase {II} by 9-aminoacridines}",
	Journal = "Biochem. Pharmacol.",
	Volume = "36",
	Number = "20",
	Pages = "3477–3486",
	abstract = "An attempt was made to analyze the mechanism by which 4'-(9-acridinylamino)methanesulfon-m-anisidide {(m-AMSA)} inhibits mammalian {DNA} topoisomerase {II.} The effects of various 9-aininoacridine derivatives differing by their {DNA} affinities and {DNA} sequence selectivity of binding were compared in the presence of purified mouse leukemia L1210 {DNA} topoisomerase {II.} No correlation was found between {DNA} unwinding and topoisomerase {II} inhibition. {9-Aminoacridine} was inactive as a topoisomerase {II} inhibitor and {o-AMSA} was only weakly active. The location of L1210 topoisomerase {II} mediated {DNA} breaks produced in the absence or presence of 9-aminoacridines were studied in {[32P]-} end-labeled {pBR} 322 {DNA.} All 9-aminoacridines, even those differing by their {DNA} sequence selectivity of binding, produced similar {DNA} cleavage patterns. Most drug-induced topoisomerase {II} mediated {DNA} breaks appeared at sites that were already cleaved by the enzyme in the absence of drug. The present results suggest that 9-aminoacridines inhibit L1210 {DNA} topoisomerase {II} by interacting at or near {enzyme-DNA} complexes by some unknown {DNA} effect or by direct protein interaction.",
	collection = "nucleic acid drugs",
	doi = "10.1016/0006-2952(87)90329-7",
	localfile = "nucleic acid drugs/1987 - Role of DNA intercalation in the inhibition of purified mouse leukemia (L1210) DNA topoisomerase II by 9-aminoacridines.pdf",
	year = 1987
}

@Article{1987-Pople-HR,
	Author = "John A. Pople and Martin Head-Gordon and Krishnan Raghavachari",
	Title = "{Quadratic configuration interaction. A general technique for determining electron correlation energies}",
	Journal = "J. Chem. Phys.",
	Volume = "87",
	Number = "10",
	Pages = "5968–5975",
	abstract = "A general procedure is introduced for calculation of the electron correlation energy, starting from a single Hartree-Fock determinant. The normal equations of (linear) configuration interaction theory are modified by introducing new terms which are quadratic in the configuration coefficients and which ensure size consistency in the resulting total energy. When used in the truncated configuration space of single and double substitutions, the method, termed QCISD, leads to a tractable set of quadratic equations. The relation of this method to coupled-cluster (CCSD) theory is discussed. A simplified method of adding corrections for triple substitutions is outlined, leading to a method termed QCISD(T). Both of these new procedures are tested (and compared with other procedures) by application to some small systems for which full configuration interaction results are available.",
	collection = "quantum chemistry",
	doi = "10.1063/1.453520",
	localfile = "quantum chemistry/1987 - Quadratic configuration interaction. A general technique of determining electron correlation energies.pdf",
	year = 1987
}

@Article{1987-Price-Stone,
	Author = "Sarah L. Price and Anthony J. Stone",
	Title = "{The electrostatic interactions in van der {W}aals complexes involving aromatic molecules}",
	Journal = "J. Chem. Phys.",
	Volume = "86",
	Number = "5",
	Pages = "2859–2868",
	abstract = "The minima in the electrostatic energy, for accessible orientation, have been located for the s-tetrazine and benzene dimers and the 1:1 complexes of s-tetrazine with hydrogen chloride, water, acetylene, and benzene, and of benzene with acetylene, anthracene, and perylene. The minima give reasonably successful predictions of the structures of these van der Waals molecules, demonstrating the importance of the electostatic interactions in these systems. The electrostatic energy was calcualted using sets of distributed multipole obtained from ab initio wave functions of the monomers. This method is contrasted with empirical point charge and central multipole models for the electrostatic energy. It is shown that the simple models for the electrostatic interactions can give qualitatively misleading results for aromatic systems.",
	collection = "stacking",
	doi = "10.1063/1.452037",
	localfile = "molecular stacking/1986 - The electrostatic interactions in van der Waals complexes involving aromatic molecules.pdf",
	year = 1987
}

@Article{1987-Schweizer-Curro,
	Author = "Kenneth S. Schweizer and John G. Curro",
	Title = "{Integral-equation theory of the structure of polymer melts}",
	Journal = "Phys. Rev. Lett.",
	Volume = "58",
	Number = "3",
	Pages = "246–249",
	collection = "polymers",
	doi = "10.1103/PhysRevLett.58.246",
	localfile = "polymers/1987 - Integral-equation theory of the structure of polymer melts.pdf",
	year = 1987
}

@Article{1987-Sokalski-Sawaryn,
	Author = "W. Andrzej Sokalski and Andrzej Sawaryn",
	Title = "{Correlated molecular and cumulative atomic multipole moments}",
	Journal = "J. Chem. Phys.",
	Volume = "87",
	Number = "1",
	Pages = "526–534",
	cited = "76 (2005-05-05)",
	collection = "molecular electrostatics",
	doi = "10.1063/1.453600",
	localfile = "molecular electrostatics/1987 - Correlated molecular and cumulative atomic multipole moments.pdf",
	year = 1987
}

@Article{1987-Spackman,
	Author = "Mark A. Spackman",
	Title = "{A simple quantitative model of hydrogen bonding. Application to more complex systems}",
	Journal = "J. Phys. Chem.",
	Volume = "91",
	Pages = "3179–3186",
	abstract = "The simple model of hydrogen bonding described previously is applied to a large number of dimers comprised of HF, HCl, H$\_2$0 , H$\_2$S, H$\_2$C$\_0$,NH,, and PH$\_3$. Equilibrium geometries and energies are generally in good agreement with ab initio or experimental results. A notable failure of the model occurs for NH,-HF, and reasons for this are explored. The neglect of the proton-acceptor repulsive term in the model appears to amount to implicit inclusion of a composite charge-transfer/polarization term of opposite sign.",
	collection = "hydrogen bonding",
	doi = "10.1021/j100296a015",
	localfile = "hydrogen bonding/1987 - A simple quantitative model of hydrogen bonding. Application to more complex systems.pdf",
	year = 1987
}

@Article{1987-Stevens-Fink,
	Author = "Walter J. Stevens and William H. Fink",
	Title = "{Frozen fragment reduced variational space analysis of hydrogen bonding interactions. Application to the water dimer}",
	Journal = "Chem. Phys. Lett.",
	Volume = "139",
	Number = "1",
	Pages = "15–22",
	abstract = "A reduced variational space method is presented for analyzing hydrogen bonding interactions in terms of Coulomb and exchange, polarizability, and charge-transfer components. The method relies on the use of {SCF} optimized monomer orbitais in dimer calculations in which the wavefunction of one monomer is held frozen while the other is optimized with a basis set including selected subsets of the unoccupied monomer orbitals. Freezing the monomer wavefunctions allows the polarizability and charge-transfer interactions to be ascribed to specific monomers. Applications are presented for the interaction energy and dipole moment of the water dimer.",
	collection = "molecular interactions",
	doi = "10.1016/0009-2614(87)80143-4",
	localfile = "molecular interactions/1987 - Frozen fragment reduced variational space analysis of hydrogen bonding interactions. Application to the water dimer.pdf",
	year = 1987
}

@Article{1988-Bauschlicher-Langhoff,
	Author = "Charles W. Bauschlicher and Stephen R. Langhoff",
	Title = "{Full configuration-interaction study of the ionic–neutral curve crossing in {LiF}}",
	Journal = "J. Chem. Phys.",
	Volume = "89",
	Number = "7",
	Pages = "4246",
	collection = "molecular reactions",
	doi = "10.1063/1.455702",
	localfile = "molecular reactions/1988 - Full configuration-interaction study of the ionic-neutral curve crossing in LiF.pdf",
	year = 1988
}

@Article{1988-Ben-Chetrit-CST,
	Author = "Eldad Ben-Chetrit and Edward K. L. Chan and Kevin F. Sullivan and Eng M. Tan",
	Title = "{A 52-kD protein is a novel component of the SS-A/Ro antigenic particle}",
	Journal = "J. Exp. Med.",
	Volume = "167",
	Pages = "1560–1571",
	collection = "cells",
	localfile = "cells/1988 - A 52-kD protein is a novel component of the SS-A-Ro antigenic particle.pdf",
	year = 1988
}

@Article{1988-Buckingham-FH,
	Author = "A. David Buckingham and P. W. Fowler and Jeremy M. Hutson",
	Title = "{Theoretical studies of van der Waals molecules and intermolecular forces}",
	Journal = "Chem. Rev.",
	Volume = "88",
	Pages = "963–988",
	abstract = "(Excerpt) Over the past 10 years, there have been major advances in experimental methods for observing van der Waals complexes, mostly by spectroscopic means. The resulting spectra contain a great deal of detailed information on intermolecular forces and have stimulated corresponding advances in the theoretical methods used for calculating intermolecular potential energy surfaces and for handling the dynamics of the complexes themselves. The purpose of this review is to describe the theoretical advances that have been made in the study of van der Waals complexes and the resulting advances in our understanding of intermolecular forces.",
	collection = "molecular interactions",
	doi = "10.1021/cr00088a008",
	localfile = "molecular interactions/1988 - Theoretical studies of van der Waals molecules and intermolecular forces.pdf",
	year = 1988
}

@Article{1988-Chalasinski-Gutowski,
	Author = "Grzegorz Chałasiński and Maciej Gutowski",
	Title = "{Weak interactions between small systems. Models for studying the nature of intermolecular forces and challenging problems for ab initio calculations}",
	Journal = "Chem. Rev.",
	Volume = "88",
	Pages = "943–962",
	abstract = "(Excerpt) The study of intermolecular forces is important for applications in many different branches of science. Crystallography, molecular biology, surface and colloid chemistry, molecular spectroscopy, molecular beam scattering, thermodynamics, and polymer science all benefit from knowledge as to the nature of intermolecular forces.",
	collection = "molecular interactions",
	doi = "10.1021/cr00088a007",
	localfile = "molecular interactions/1988 - Weak interactions between small systems. Models for studying the nature of intermolecular forces and challanging problems for ab initio calculations.pdf",
	year = 1988
}

@Article{1988-Gatti-MB,
	Author = "Carlo Gatti and Preston J. {MacDougall} and Richard F. W. Bader",
	Title = "{Effect of electron correlation on the topological properties of molecular charge distributions}",
	Journal = "J. Chem. Phys.",
	Volume = "88",
	Number = "6",
	Pages = "3792–3804",
	abstract = "This paper reports on the effect of electron correlation on the topological properties of the charge density and its associated gradient vector and Laplacian fields. The properties of these fields define the atoms, their reactivity, and the structure of a molecular system withing the theory of atoms in molecules. The singlet and triplet states of CH$\_2$, CF$\_2$, and SiH$\_2$ are investigated using a configuration interaction methods which includes all single and double excitations with respect to suitable zero-order reference wave functions, together with a number of hydrocarbon molecules including unsaturated and geometrically strained systems for which the correlation is introduced via the generalized valence bond approach. It is found that the correlated charge distributions possess the same number and kind of critical poitns in both the $\rho(r)$ and Laplacian fields as are found for SCF charge distirbutions. Thus the topology of a charge dsitribution and the structure it defines are unaffected by the addition of Coulomb correlation. The quantitative changes in the properties of the charge density at the critical points in both $\rho(r)$ and the Laplacian induced by correlation are found to be small in magnitude and to be more pronounced for shared or covalent atomic interactions than for systems with pronounced charge transfer between the atoms. The properties of the atoms in these molecules also axhibit correspondingly small changes in value.",
	collection = "quantum chemistry",
	doi = "10.1063/1.453879",
	localfile = "quantum chemistry/1988 - Effect of electron correlation on the topological properties of molecular charge distributions.pdf",
	year = 1988
}

@Article{1988-Hobza-Zahradnik,
	Author = "Pavel Hobza and Rudolf Zahradnik",
	Title = "{Intermolecular interactions between medium-sized systems. Nonempirical and empirical calculations of interaction energies: successes and failures}",
	Journal = "Chem. Rev.",
	Volume = "88",
	Pages = "871–897",
	abstract = "(Excerpt) Four types of interactions are distinguished in physics: strong, electromagnetic, weak, and gravitational. Strong interactions between protons and neutrons result in the formation of atomic nuclei. Much weaker interactions between nuclei and electrons (called electromagnetic) lead to formation of atoms.",
	collection = "molecular interactions",
	doi = "10.1021/cr00088a004",
	localfile = "molecular interactions/1988 - Intermolecular interactions between medium-sized systems. Nonempirical and empirical calculations of interaction energies: successes and failures.pdf",
	year = 1988
}

@Article{1988-Latajka-Scheiner,
	Author = "Zdzisław Latajka and Steve Scheiner",
	Title = "{Structure, energetics and vibrational spectra of H-bonded systems. Dimers and trimers of HF and HCL}",
	Journal = "Chem. Phys.",
	Volume = "122",
	Pages = "413–430",
	abstract = "The title complexes are studied by ab initio methods using double-c basis sets augmented by diffuse sp and two sets of polarization functions. The binding energies decrease in the order (HF),> HF...HCI> (HCI)?, all ofwhich form pseudolinear H bonds. While not important for (HF),, correlation plays an increasingly larger role as each HF is replaced by HCI, contributing 2/3 of the total binding energy of (HCI)*. (HF), and (HCI)3 are both Cghcyclic and exhibit cooperativity, particularly (HF)3; correlation appears to be negligible in the three-body nonadditive interaction energies. The red shift of the HF stretch in ( HF)3 is nearly twice as great as in the dimer while little enhancement is observed in the HCI analogues. The other two observable bands in the trimers are of fairly high intensity and correspond to an out-of-plane and in-plane bend. The intermolecular stretching modes in the dimers and trimers are of very low intensity. A clear relationship is noted between the intermolecular frequencies and the strength of the interaction.",
	collection = "hydrogen bonding",
	doi = "10.1016/0301-0104(88)80023-5",
	keywords = "hydrogen bonding",
	localfile = "hydrogen bonding/1988 - Structure, energetics and vibrational spectra of H-bonded systems. Dimers and trimers of HF and HCL.pdf",
	year = 1988
}

@Article{1988-Sokalski-RP,
	Author = "W. Andrzej Sokalski and Szczepan Roszak and Krzysztof Pecul",
	Title = "{An efficient procedure for decomposition of the {SCF} interaction energy into components with reduced basis set dependence}",
	Journal = "Chem. Phys. Lett.",
	Volume = "153",
	Number = "2-3",
	Pages = "153–159",
	cited = "61 (2005-05-05)",
	collection = "molecular interactions",
	doi = "10.1016/0009-2614(88)85203-5",
	localfile = "molecular interactions/1988 - An efficient procedure for decomposition of the SCF interaction energy into components with reduced basis set dependence.pdf",
	year = 1988
}

@Article{1988-Szalewicz-CKB,
	Author = "Krzysztof Szalewicz and S. J. Cole and Włodzimierz Kołos and R. J. Bertlett",
	Title = "{A theoretical study of the water dimer interaction}",
	Journal = "J. Chem. Phys.",
	Volume = "89",
	Number = "6",
	Pages = "3662 – 3673",
	collection = "hydrogen bonding",
	doi = "10.1063/1.454886",
	localfile = "hydrogen bonding/1988 - A theoretical study of the water dimer interaction.pdf",
	year = 1988
}

@Article{1988-Vigne-Maeder-Claverie,
	Author = "Fabienne Vigne-Maeder and Pierre Claverie",
	Title = "{The exact multicenter multipolar part of a molecular charge dsitribution and its simplified representations}",
	Journal = "J. Chem. Phys.",
	Volume = "88",
	Number = "8",
	Pages = "4934–4948",
	collection = "molecular electrostatics",
	doi = "10.1063/1.454705",
	localfile = "molecular electrostatics/1988 - The exact multicenter multipolar part of a molecular charge distribution and its simplified representations.pdf",
	year = 1988
}

@Article{1989-Bader,
	Author = "Richard F. W. Bader",
	Title = "{Atoms in molecules in external fields}",
	Journal = "J. Chem. Phys.",
	Volume = "91",
	Number = "11",
	Pages = "6989–7001",
	abstract = "The theory of atoms in molecules is extended to the case where the molecules is in the presence of an electromagnetic field. This theory is based upon a generalization of quantum mechanics to an open system, as obtained through a corresponding extension of Schinger's principle of stationary action. The extension of this principle is possible only if the open system satisfies a particular boundary condition, one which is expressed as a constraint on the variation of the action integral. This is the condition that it be nouded by a surface of zero flux in the gradient vector field of the charge density, the definition of an atom in a molecule. It is shown that this boundary constraint again suffices to define an atom as a quantum subsystem when the molecule is in the presence of an electromagnetic field. The mechanics of an open system and its properties are determined by the fluxes in corresponding vector current densities through its surface. As in the fieldfree case, the obtainment of these currents from the variation of the action integral is a direct result of the variation of the atomic durface and of the imposition of the variational constraint on its boundary. The currents in this case consist o a paramgnetic and a diamagnetic contribution, currents whose presence are a necessary requirement for the description of the properties of a system in the presence of extternal fields. The variational statement of the Heisenberg equation of motion obtained from the principle of stationary action is used to derive the Ehrenfest force and virial theorems for an atom in a molecule in teh presence of external electric and magnetic fields. In this case, the are forces acting on the interior of the atom which arise from the magnetic presures acting on its surface. it is shown that the molecular electric polarizability and magnetic susceptibility, like other properties, are rigurously expressible as a sum of atomic contributions.",
	collection = "quantum chemistry",
	doi = "10.1063/1.457315",
	localfile = "quantum chemistry/1989 - Atoms in molecules in external fields.pdf",
	year = 1989
}

@Article{1989-Haser-Ahlrichs,
	Author = "Marco Haser and Reinhart Ahlrichs",
	Title = "{Improvements on the direct SCF method}",
	Journal = "J. Comp. Chem.",
	Volume = "10",
	Number = "1",
	Pages = "104–111",
	collection = "cheminformatics",
	doi = "10.1002/jcc.540100111",
	localfile = "cheminformatics/1989 - Improvements on the direct SCF method.pdf",
	year = 1989
}

@Article{1989-Matouschek-KSF,
	Author = "Andreas Matouschek and James T. {Kellis Jr.} and Luis Serrano and Alan R. Fersht",
	Title = "{Mapping the transition state and pathway of protein folding by protein engineering}",
	Journal = "Nature",
	Volume = "340",
	Pages = "122–126",
	collection = "protein structure",
	doi = "10.1038/340122a0",
	keywords = "protein folding",
	localfile = "protein structure/1989 - Mapping the transition state and apthway of protein folding by protein engineering.pdf",
	rating = "3",
	read = "2012-11-25",
	year = 1989
}

@Article{1989-Russell-CDM,
	Author = "Thomas P. Russell and G. Coulon and V. R. Deline and D. C. Miller",
	Title = "{Characteristics of the surface-induced orientation for symmetric diblock PS/PMMA copolymers}",
	Journal = "Macromolecules",
	Volume = "22",
	Pages = "4600–4606",
	collection = "block copolymers",
	doi = "10.1021/ma00202a036",
	keywords = "block copolymers; thin films",
	localfile = "block copolymers/1989 - Characteristics of the surface-induced orientation for symmetric diblock PS-PMMA copolymers.pdf",
	rating = "2",
	year = 1989
}

@Article{1989-Rybak-SJ,
	Author = "S. Rybak and Krzysztof Szalewicz and Bogumił Jeziorski",
	Title = "{An accurate calculation of the 1st-order interaction energy for the helium dimer}",
	Journal = "J. Chem. Phys.",
	Volume = "91",
	Number = "8",
	Pages = "4779 – 4784",
	collection = "molecular interactions",
	doi = "10.1063/1.456767",
	localfile = "molecular interactions/1989 - An accurate calculation of the first-order interaction energy for the helium dimer.pdf",
	year = 1989
}

@Article{1989-Sawaryn-Sokalski,
	Author = "Andrzej Sawaryn and W. Andrzej Sokalski",
	Title = "{Cumulative atomic multipole moments and point-charge models describing molecular charge-distribution}",
	Journal = "Comput. Phys. Commun.",
	Volume = "52",
	Number = "3",
	Pages = "397–408",
	cited = "14 (2005-05-05)",
	collection = "molecular electrostatics",
	doi = "10.1016/0010-4655(89)90114-8",
	localfile = "molecular electrostatics/1989 - Cumulative atomic multipole moments and point charge models describing molecular charge distirbution.pdf",
	methods = "CAMM",
	year = 1989
}

@Article{1989-Snyder-HDKRB,
	Author = "James G. Snyder and Neil G. Hartman and Beatrice Langlois {D'Estantoit} and Olga Kennard and David P. Remeta and Kenneth J. Breslauer",
	Title = "{Binding of actinomycin D to {DNA:} evidence for a nonclassical high-affinity binding mode that does not require {GpC} sites.}",
	Journal = "Proc. Natl. Acad. Sci.",
	Volume = "86",
	Number = "11",
	Pages = "3968–3972",
	collection = "nucleic acid intercalation",
	doi = "10.1073/pnas.86.11.3968",
	localfile = "nucleic acid intercalation/1989 - Binding of actinomycin D to DNA: evidence for a nonclassical high-affinity binding mode that does not require GpC sites.pdf",
	shorttitle = "Binding of actinomycin D to {DNA}",
	year = 1989
}

@Article{1989-Weissman-WH,
	Author = "Haim Weissman and George H .Weiss and Shlomo Havlin",
	Title = "{Transport properties of the continuous-time random walk with a long-tailed waiting-time density}",
	Journal = "J. Stat. Phys.",
	Volume = "57",
	Number = "1-2",
	Pages = "301–318",
	cited = "47 (2013-04-29)",
	collection = "statistics",
	doi = "10.1007/BF01023645",
	localfile = "statistics/1989 - Transport properties of the continuous-time random walk with a long-tailed waiting-time density.pdf",
	year = 1989
}

@Article{1990-Altschul-GMML,
	Author = "Stephen F. Altschul and Warren Gish and Webb Miller and Eugene W. Myers and David J. Lipman",
	Title = "{Basic local alignment search tool}",
	Journal = "J. Mol. Biol.",
	Volume = "215",
	Pages = "403–410",
	collection = "cheminformatics",
	doi = "10.1016/S0022-2836(05)80360-2",
	localfile = "cheminformatics/1990 - Basic local alignment search tool.pdf",
	year = 1990
}

@Article{1990-Barthel-BBH,
	Author = "J. Barthel and K. Bachhuber and R. Buchner and H. Hetzenauer",
	Title = "{Dielectric spectra of some common solvent in the microwave region. Water and lower alcohols}",
	Journal = "Chem. Phys. Lett.",
	Volume = "165",
	Number = "4",
	Pages = "369–373",
	cited = "336 (2013-04-29)",
	collection = "molecular solvation",
	doi = "10.1016/0009-2614(90)87204-5",
	localfile = "molecular solvation/1990 - Deielectric spectra of some common solvents in the microwave region. Water and lower alcohols.pdf",
	year = 1990
}

@Article{1990-Frisch-HP,
	Author = "Michael J. Frisch and Martin Head-Gordon and John A. Pople",
	Title = "{A direct MP2 gradient method}",
	Journal = "Chem. Phys. Lett.",
	Volume = "166",
	Pages = "275–280",
	abstract = "We present a direct method for evaluating the gradient of the second-order Møller–Plesset (MP2) energy without storing any quartic quantities, such as two-electron repulsion integrals (ERIs), double substitution amplitudes or the two-particle density matrix. For an N-basis-function calculation, N3 memory is required, and the ERIs and their tint derivatives are computed up to 0 (number of occupied orbitals) times, plus additional ERI evaluations to obtain the Hartree-Fock (HF) orbitals and solve the coupled perturbed HF equation. Larger amounts of memory are used to reduce the 0 evaluations in the MP2 step. The floating point operation count is still proportional to ON 4, as in conventional MP2 gradient codes since ERI evaluation is just an N 4 step. Illustrative calculations are reported to assess the performance of the algorithm.",
	collection = "cheminformatics",
	doi = "10.1016/0009-2614(90)80029-D",
	keywords = "algorithms",
	localfile = "cheminformatics/1990 - A direct MP2 gradient method.pdf",
	year = 1990
}

@Article{1990-Furukawa-KLN,
	Author = "Fukumi Furukawa and Mari Kashihara-Sawami and Martin B. Lyons and David A. Norris",
	Title = "{Binding antibodies to the extractable nuclear antigens SS-A/Ro and SS-B/La is induced on the surface of human keratinocytes by ultraviolet light (UVL): implications for the pathogenesis of photosensitive cutaneous lupus}",
	Journal = "J. Invest. Dermatol.",
	Volume = "94",
	Number = "1",
	Pages = "77–85",
	collection = "cells",
	localfile = "cells/1990 - Binding antibodies to the extractable nuclear antigens SS-A-Ro and SS-B-La is induced on the surface of human keratinocytes by ultraviolet light: implication for the pathogenesis of photosensitive cutaneous lupus.pdf",
	year = 1990
}

@Article{1990-Laidig-Bader,
	Author = "Keith E. Laidig and Richard F. W. Bader",
	Title = "{Properties of atoms in molecules: Atomic polarizabilities}",
	Journal = "J. Chem. Phys.",
	Volume = "93",
	Number = "10",
	Pages = "7213–7224",
	abstract = "The theory of atoms in molecules is applied to the determination of the atomic and group contributions to the molecular polariability in diatomic and polyatomic systems, covering a wide range of atomic interactions. The calculations are performed through the use of coupled-perturbed Hartree-Fock theory. An applied field polarized the atomic charge distirbutions and induces a transfer of charge between them. The resulting changes in the dipole moment per unit applied field determine the corresponding contributions to the polarizability. In general, the component of the polarizability along the internuclear axis in a linear molecuels or in the direction of a chain of bonds in a nonlinear polyatomic molecule, exceeds the perpendicular component because of the transfer of electronic charge between the two ends of the molecules, between the methyl groups in ethane, and between the methylene groups in ethene, for example. Atoms shielded from an applied field, carbon in methane for example, polarize in a direction counter to that of the applied field, responding instead to the opposing field created by the transfer of charge between the exterior atoms. The same behavior is found in vibrationally induced polarizations of a molecualr charge distribution. The extent of atomic polarization and of interatomic charge transfer caused by an external field are readily related to known properties of the atomic charge distributions and the corresponding contributions to the polarizability may be understood and predicted. The mean molecular polarizability and its group contributions are found to be lienarly proprtional to the corresponding sum of atomic volumes, making possible the preditction of molecular polarizabilities from tabulated atomic volumes as determined by the theory of atoms in molecules.",
	collection = "molecular fragmentation",
	doi = "10.1063/1.459444",
	localfile = "molecular fragmentation/1990 - Properties of atoms in molecules: atomic polarizabilities.pdf",
	shorttitle = "Properties of atoms in molecules",
	year = 1990
}

@Article{1990-Lee-Rendell-Taylor,
	Author = "T. J. Lee and A. P. Rendell and P. R. Taylor",
	Title = "{Comparison of the quadratic configuration-interaction and coupled-cluster approaches to electron correlation including the effect of triple excitations}",
	Journal = "J. Phys. Chem.",
	Volume = "94",
	Number = "14",
	Pages = "5463–5468",
	collection = "quantum chemistry",
	doi = "10.1021/j100377a008",
	localfile = "quantum chemistry/1990 - Comparison of the quadratic configuration interaction and coupled-cluster approaches to electorn correlation including the effect of triple excitations.pdf",
	year = 1990
}

@Article{1990-Thijsse-Sietsma,
	Author = "Barend J. Thijsse and Jilt Sietsma",
	Title = "{A critical look at the RDFs of 11 different amorphous alloys}",
	Journal = "J. Non-Cryst. Solids",
	Volume = "177-188",
	Number = "1",
	Pages = "176–179",
	collection = "statistical mechanics",
	doi = "10.1016/0022-3093(90)90907-4",
	keywords = "metallic glasses; radial distribution function",
	localfile = "statistical mechanics/1990 - A critical look at the RDFs of 11 different amorphous alloys.pdf",
	rating = "2",
	read = "2012-09-01",
	year = 1990
}

@Article{1991-Bader,
	Author = "Richard F. W. Bader",
	Title = "{A quantum theory of molecular structure and its applications}",
	Journal = "Chem. Rev.",
	Volume = "91",
	Number = "5",
	Pages = "893–928",
	abstract = "The role of physics in chemistry is to predict what can be observed and to provide an understanding of these observations. The dominant operational concept of chemistry is that of an atom in a molecule with a determinable and characteristic set of properties. Thus the physics of chemistry is necessarily the physics of an atom in a molecule, that is of an open system, one which is free to exchange charge and momentum with neighboring atoms. To extend the predictions of physics to the domain of chemistry it is therefore, necessary to generalize quantum mechanics to a subsystem of a total system. Such a generalization is indeed possible, but only if the open system satisfies a particular boundary condition. When this condition is met, one obtains a definition of an atom in a molecule and a prediction of its properties. Inseparable from the quantum definition of an atom in a molecule is the definition of the bonds which link the atoms to yield a molecular structure. In essence, the quantum description of an open system recovers the molecular structure hypothesis-that a molecule is a collection of atoms each with a characteristic set of properties, that are linked by a network of bonds. The emergence of this hypothesis from 19th century experimental chemistry is thus seen as having been an inevitable consequence of physics.",
	collection = "quantum chemistry",
	doi = "10.1021/cr00005a013",
	localfile = "quantum chemistry/1991 - A quantum theory of molecular structure and its applications.pdf",
	year = 1991
}

@Article{1991-Brese-OKeeffe,
	Author = "N. E. Brese and M. O'Keeffe",
	Title = "{Bond-valence parameters for solids}",
	Journal = "Acta Cryst. B",
	Volume = "47",
	Pages = "192–197",
	collection = "crystallography",
	doi = "10.1107/S0108768190011041",
	keywords = "bond valence",
	localfile = "crystallography/1991 - Bond-valence parameters for solids.pdf",
	rating = "2",
	read = "2013-02-02",
	year = 1991
}

@Article{1991-Guttman-Cooke,
	Author = "Andras Guttman and Nelson Cooke",
	Title = "{Capillary gel affinity electrophoresis of {DNA} fragments}",
	Journal = "Anal. Chem.",
	Volume = "63",
	Number = "18",
	Pages = "2038–2042",
	abstract = "The incorporation of an affinity band wlthln a polyacrylamide gel provides a general means of manipulating the seiectivlty of capillary gel electrophoresis separations. As an example of the approach, high resolution o DNA restriction fragments by capliary gel affinity electrophoresis has been achieved by addlng a soluble intercalating agent, ethidium bromlde, to the gel-buffer system. A migration model has been developed that can be used for selectlvlty optimization. Various parameters, such as llgand concentration and applied electric field, have been examined in terms of their influence on retention and Selectivity of different-size DNA molecules. From this study, high-resolutlon separations have been developed with efficiencies as high as $10^7$ theoretical plates per meter.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/ac00018a027",
	localfile = "nucleic acids/1991 - Capillary gel affinity electrophoresis of DNA fragments.pdf",
	year = 1991
}

@Article{1991-Jorgensen-IMBZ,
	Author = "Kent Jørgensen and John Hjort Ipsen and Ole G. Mouritsen and Donald Bennett and Martin J. Zuckermann",
	Title = "{A general model for the interaction of foreign molecules with lipid membranes: drugs and anaesthetics}",
	Journal = "Biochim. Biophys. Acta",
	Volume = "1062",
	Pages = "227–238",
	abstract = "A general microscopic interaction model is proposed to describe the changes in the physical properties of phospholipid bilayer membranes due to foreign molecules which, to different degrees, partition between the membrane phases and the aqueous environment. The model is a multi-state lattice model for the main phase transition of lipid bilayers and the foreign molecules are assumed to intercalate as interstitials in the lattice. By varying the model parameters, the diversity in the thermodynamic properties of the model is explored using computer-simulation techniques which faithfully take account of the thermal fluctuations. The calculations are performed in both the canonical and the grand canonical ensembles corresponding to the cases where the concentration of foreign molecules in the membrane is either fixed or varies as the external conditions are changed. A classification of the diverse thermal behaviour, specifically with regard to the phase diagram, the specific heat, the density fluctuations, and the partition coefficient, is suggested with a view to rationalizing a large body of experimental measurements of the effects of different foreign molecules on membrane properties. The range of foreign molecules considered includes compounds as diverse as volatile general anaesthetics like halothane, cocaine-derived local anaesthetics like procaine, calcium-channel blocking drugs like verapamil, antidepressants like chlorpromazine, and anti-cancer agents like adriamycin.",
	collection = "lipids",
	doi = "10.1016/0005-2736(91)90397-Q",
	keywords = "lattice model",
	localfile = "lipid bilayers/1992 - A general model for the interaction of foreign molecules with lipid membranes: drugs and anaesthetics.pdf",
	year = 1991
}

@Article{1991-Prusiner,
	Author = "Stanley B. Prusiner",
	Title = "{Molecular Biology of Prion Diseases}",
	Journal = "Science",
	Volume = "252",
	Pages = "1515–1522",
	abstract = "Prions cause transmissible and genetic neurodegenerative diseases, including scrapie and bovine spongiform encephalopathy of animals and Creutzfeldt-Jakob and Gerstmann-Straussler-Scheinker diseases of humans. Infectious prion particles are composed largely, if not entirely, of an abnormal isoform of the prion protein, which is encoded by a chromosomal gene. A posttranslational process, as yet unidentified, converts the cellular prion protein into an abnormal isoform. Scrapie incubation times, neuropathology, and prion synthesis in transgenic mice are controlled by the prion protein gene. Point mutations in the prion protein genes of animals and humans are genetically linked to development of neurodegeneration. Transgenic mice expressing mutant prion proteins spontaneously develop neurologic dysfunction and spongiform neuropathology. Understanding prion diseases may advance investigations ofother neurodegenerative disorders and of the processes by which neurons differentiate, function for decades, and then grow senescent.",
	collection = "proteins",
	doi = "10.1126/science.1675487",
	localfile = "proteins/1991 - Molecular biology of prion diseases.pdf",
	year = 1991
}

@Article{1991-Rappe-Goddard,
	Author = "Anthony K. Rappe and William {A. III} Goddard",
	Title = "{Charge equilibrium for molecular dynamics simulations}",
	Journal = "J. Phys. Chem.",
	Volume = "95",
	Pages = "3358–3363",
	collection = "molecular dynamics",
	doi = "10.1021/j100161a070",
	localfile = "molecular dynamics/1991 - Charge equilibration for molecular dynamics simulations.pdf",
	rating = "3",
	read = "2012-02-01",
	year = 1991
}

@Article{1991-Sokalski-LLSSOR,
	Author = "W. Andrzej Sokalski and Jack Lai and Ning Luo and S. Sun and M. Shibata and Rick L. Ornstein and Rein Rein",
	Title = "{Ab initio study of the electrostatic multipole nature of torsional potentials}",
	Journal = "Int. J. Quant. Chem.",
	Pages = "61–71",
	collection = "molecular electrostatics",
	doi = "10.1002/qua.560400711",
	localfile = "molecular electrostatics/1991 - Ab initio study of the electrostatic multipole nature of torsional potentials.pdf",
	year = 1991
}

@Article{1991-Sokalski-Roszak,
	Author = "W. Andrzej Sokalski and Szczepan Roszak",
	Title = "{Efficient techniques for the decomposition of intermolecular interaction energy at SCF level and beyond}",
	Journal = "J. Mol. Struct.: {THEOCHEM}",
	Volume = "234",
	Pages = "387–400",
	abstract = "Some techniques for the decomposition of SCF mteraction energy have been reviewed with particular emphasis on their basis set dependency, computational economy and simplicity. The consequences of using more approximate SCF procedures based on ZDO approximation have been also analyzed. Efficient methods for estimating intra- and inter-molecular correlation components of interaction energy are discussed.",
	collection = "molecular interactions",
	doi = "10.1016/0166-1280(91)89025-V",
	localfile = "molecular interactions/1991 - Efficient techniques for the decomposition of intermolecular interaction energy at SCF level and beyond.pdf",
	year = 1991
}

@Article{1991-Wadkins-Graves,
	Author = "Randy M. Wadkins and David E. Graves",
	Title = "{Interactions of anilinoacridines with nucleic acids: effects of substituent modifications on {DNA-binding} properties}",
	Journal = "Biochemistry",
	Volume = "30",
	Number = "17",
	Pages = "4277–4283",
	abstract = "Spectroscopic methods are used to probe the interactions of several anilinoacridine analogues with calf thymus D N A over a wide range of temperatures and sodium chloride concentrations. The structurally similar compounds m-AMSA, AMSA (both active as antitumor agents), and o-AMSA (inactive as an antitumor agent) have been widely studied in their abilities to bind D N A in an intercalative manner. Recent studies from this laboratory reveal distinct differences in the thermodynamic binding mechanisms between m-AMSA and o-AMSA (Wadkins \& Graves, 1989), with the m-AMSA-DNA interaction being an enthalpy-driven process while the binding of o-AMSA to D N A is characterized by more positive entropy values. T o further examine the physical chemical properties associated with these compounds and their correlation with antitumor activities, an in-depth investigation into the thermodynamic parameters of these compounds and structurally related anilinoacridine analogues was performed. These studies demonstrate that substituent type and position on the aniline ring of the anilinoacridines greatly influences both the affinities of these drugs in binding to D N A and dictates whether the D N A binding is an enthalpy- or entropy-driven process. The differences in thermodynamic mechanisms of binding between the two isomers along with molecular modeling studies reveal the electronic and/or steric factors resulting from the positioning of the methoxy substituent group on the anilino ring directs the DNA-binding properties through orientation of the methanesulfonamido group a t the 1’ position of the aniline ring. The orientation of this substituent group may result in favorable contacts through hydrogen bonding with neighboring base pairs and ultimately influence the biological effectiveness as an antitumor agent.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/bi00231a025",
	localfile = "nucleic acid intercalation/1991 - Interactions of anilinoacridines with nucleic acids: effects of substituent modifications on DNA-binding properties.pdf",
	shorttitle = "Interactions of anilinoacridines with nucleic acids",
	year = 1991
}

@Article{1992-Jones,
	Author = "S. K. Jones",
	Title = "{Ultraviolet radiation (UVR) induces cell-surface Ro/SSA antigen expression by human keratinocytes in vitro: a possible mechanism for the UVR induction of cutaneous lupus lesions}",
	Journal = "Br. J. Dermatol.",
	Volume = "126",
	Number = "6",
	Pages = "546–553",
	collection = "cells",
	localfile = "cells/1992 - Ultraviolet radiation (UVR) induces cell-surface Ro-SSA antigen expression by human keratinocytes in vitro: a possible mechanism for the UVR induction of cutaneous lupus lesions.pdf",
	year = 1992
}

@Article{1992-Lai-Herr,
	Author = "Jiann-Shiun Lai and Winship Herr",
	Title = "{Ethidium-bromide provides a simple tool for identifying genuine {DNA}-independent protein associations}",
	Journal = "Proc. Natl. Acad. Sci.",
	Volume = "89",
	Number = "15",
	Pages = "6958–6962",
	abstract = "DNA-dependent and DNA-independent associations of DNA-binding proteins are important in transcriptional regulation. The analysis of DNA-independent associations frequently relies on assaying protein interaction in the absence of target DNA sequences. We have found that contaminating DNA in protein preparations can stabilize DNA-dependent associations that may appear DNA-independent. Three cellular proteins of 70, 85, and 110 kDa coimmunoprecipitated with the octamer motif-binding protein Oct-2 because of the presence of contaminating DNA in the cell extracts. In addition, heterodimer formation between Oct-1 (or Oct-2) and Pit-1 during protein-affinity chromatography was stabilized by the contaminating DNA. In both instances, these DNA-dependent protein associations were selectively inhibited by ethidium bromide in the precipitation reaction without any evident effect on DNA-independent protein associations. Thus, ethidium bromide may serve as a simple and general indicator of DNA-dependent and DNA-independent protein associations.",
	cited = "262 (2005-04-13)",
	collection = "nucleic acid intercalation",
	doi = "10.1073/pnas.89.15.6958",
	localfile = "nucleic acid intercalation/1992 - Ethidium bromide provides a simple tool for identifying genuine DNA-independent protein associations.pdf",
	year = 1992
}

@Article{1992-Rappe-CCGS,
	Author = "A. K. Rappe and C. J. Casewit and K. S. Colwell and William {A. III} Goddard and W. M. Skiff",
	Title = "{UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "114",
	Pages = "10024–10035",
	abstract = "A new molecular mechanics force field, the Universal force field (UFF), is described wherein the force field parameters are estimated using general rules based only on the element, its hybridization, and its connectivity. The force field functional forms, parameters, and generating formulas for the full periodic table are presented.",
	collection = "cheminformatics",
	doi = "10.1021/ja00051a040",
	localfile = "cheminformatics/1992 - UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations.pdf",
	year = 1992
}

@Article{1992-Sokalski-SRO,
	Author = "W. Andrzej Sokalski and M. Shibata and Rein Rein and Rick L. Ornstein",
	Title = "{Cumulative atomic multipole moments complement any atomic charge model to obtain more accurate electrostatic properties}",
	Journal = "J. Comp. Chem.",
	Volume = "13",
	Number = "7",
	Pages = "883–887",
	abstract = "The quality of several atomic charge models based on different definitions has been analyzed using cumulative atomic multipole moments {(CAMM).} This formalism can generate higher atomic moments starting from any atomic charges, while preserving the corresponding molecular moments. The atomic-charge contribution to the higher molecular moments, as well as to the electrostatic potentials, has been examined for {CO} and {HCN} molecules at several different levels of theory. The results clearly show that the electrostatic potential obtained from {CAMM} expansion is convergent up to the R-5 term for all atomic charge models used. This illustrates that higher atomic moments can be used to supplement any atomic charge model to obtain more accurate description of electrostatic properties.",
	collection = "molecular electrostatics",
	doi = "10.1002/jcc.540130713",
	localfile = "molecular electrostatics/1982 - Cumulative atomic multipole moments complement any atomic charge model to obtain more accurate electrostatic properties.pdf",
	year = 1992
}

@Article{1993-Bader-Keith,
	Author = "Richard F. W. Bader and Todd A. Keith",
	Title = "{Properties of atoms in molecules: Magnetic susceptibilities}",
	Journal = "J. Chem. Phys.",
	Volume = "99",
	Number = "5",
	Pages = "3683–3693",
	abstract = "The molecular magnetic susceptibility tensor x is expressible as a sum of atomic or group contributions. An atomic contribution consists of a basin and a surface component; the former is given by the integral of a magnetization density over the basin of the atom, and the latter, by the integral of the flux in the position weighted current density through the interatomic surfaces that the atom shares with its bonded neighbors. The surface component is obtained as a consequenceof the.atomic hypervirial theorem defining the average of the velocity operator. Magnetic properties are determined by the observableelectron current density, and the atomic behavior of this field has been correlated with corresponding behavior of the electron density. Thus the importance of the magnetization within an atomic basin relative to the flux in current through its interatomic surfaces parallels the extent to which the electron density is localized within the individual atomic basins. For example, 77\% of the pronounced anisotropy in benzene arises from the flux in current through the interatomic surfaces of the ring atoms induced by a field applied perpendicular to the ring surface. The methyl and methylene group contributions to $\bar{\chi}$ are found to be transferable in the homologous seriesof hydrocarbons and to equal Pascal’s group increments within experimental error.",
	collection = "molecular fragmentation",
	doi = "10.1063/1.466166",
	localfile = "molecular fragmentation/1993 - Properties of atoms in molecules: magnetic susceptibilities.pdf",
	shorttitle = "Properties of atoms in molecules",
	year = 1993
}

@Article{1993-Bayly-CCK,
	Author = "Christopher I. Bayly and Piotr Cieplak and Wendy D. Cornell and Peter A. Kollman",
	Title = "{A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model}",
	Journal = "J. Phys. Chem.",
	Volume = "97",
	Pages = "10269–10280",
	abstract = "W e present a new approach to generating electrostatic potential (ESP) derived charges for molecules. The major strength of electrostatic potential derived charges is that they optimally reproduce the intermolecular interaction properties of molecules with a simple two-body additive potential, provided, of course, that a suitably accurate level of quantum mechanical calculation is used to derive the E S P around the molecule. Previously, the major weaknesses of these charges have been that they were not easily transferable between common functional groups in related molecules, they have often been conformationally dependent, and the large charges that frequently occur can be problematic for simulating intramolecular interactions. Introducing restraints in the form of a penalty function into the fitting process considerably reduces the above problems, with only a minor decrease in the quality of the fit to the quantum mechanical ESP. Several other refinements in addition to the restrained electrostatic potential (RESP) fit yield a general and algorithmic charge fitting procedure for generating atom-centered point charges. This approach can thus be recommended for general use in molecular mechanics, molecular dynamics, and free energy calculations for any organic or bioorganic system.",
	collection = "molecular electrostatics",
	localfile = "molecular electrostatics/1993 - A well-behaved electrostatic potential based method using charge restraints for deriving atomic charge: the RESP model.pdf",
	year = 1993
}

@Article{1993-Ben-Chetrit,
	Author = "Eldad Ben-Chetrit",
	Title = "{The molecular basis of the SSA/Ro antigens and the clinical significance of their autoantibodies}",
	Journal = "Br. J. Rheumatol.",
	Volume = "32",
	Pages = "396–402",
	collection = "cells",
	localfile = "cells/1993 - The molecular basis of the SSA-Ro antigens and the clinical significance of their autoantibodies.pdf",
	year = 1993
}

@Article{1993-Chaires-PGB,
	Author = "Jonathan B. Chaires and Waldemar Priebe and David E. Graves and T. G. Burke",
	Title = "{Dissection of the free energy of anthracycline antibiotic binding to {DNA:} electrostatic contributions}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "115",
	Number = "13",
	Pages = "5360–5364",
	abstract = "Fluorescence titration methods and equilibrium dialysis were used to study the thermodynamics of the interaction of doxorubicin, the @ anomer of doxorubicin, daunorubicin, and hydroxyrubicin with DNA. All of these except hydroxyrubicin carry a net charge of +1 a t neutral pH, arising from the protonation of the daunosamine moiety. Hydroxyrubicin is a synthetic anthracycline antibiotic in which the amine moiety has been replaced by a hydroxyl group, whicfi is uncharged but polar at neutral pH. The comparative binding studies we describe offer a unique opportunity to evaluate the electrostatic contributions to the D N A binding free energy of these anthracycline antibiotics and to test specific predictions arising from current polyelectrolyte theory as applied to ligand-DNA interactions. We find that the quantity (6 log K/6 log [M+]) changes from a value of -0.95 for doxorubicin to -0.18 for hydroxyrubicin. The latter value is in excellent agreement with the value of -0.24 predicted by the theory of Friedman and Manning for the interaction of an uncharged intercalating ligand with DNA. The D N A binding free energy decreases from -8.8 kcal mol-' for doxorubicin to -7.2 kcal mol-' for hydroxyrubicin under solution conditions of 200 mM Na+, p H 7.0, 20 OC. The results we obtain allow us to dissect the D N A binding free energy into its electrostatic and nonelectrostatic components. Knowledge of these values helps to clarify the precise role of the amine group in doxorubicin binding to DNA. In addition, comparison of the D N A binding of doxorubicin with the /3 anomer of doxorubicin provides a striking example of stereoselective antibiotic binding to DNA.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/ja00066a002",
	localfile = "nucleic acid intercalation/1992 - Dissection of the free energy of anthracycyline antibiotic binding to DNA: electrostatic contributions.pdf",
	shorttitle = "Dissection of the free energy of anthracycline antibiotic binding to {DNA}",
	year = 1993
}

@Article{1993-Cozzi-CAS,
	Author = "Franco Cozzi and Mauro Cinquini and Rita Annuziata and Jay S. Siegel",
	Title = "{Dominance of polar/pi over charge-transfer effects in stacked phenyl interactions}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "115",
	Pages = "5330–5331",
	abstract = "(Excerpt) Molecular recognition, the keystone of supramolecular chemistry, depends on a variety of noncovalent interactions. Among these, arene-arene interactions play a fundamental role in the selective complexation of a-neutral guests inside cyclophane cavities and molecular clefts. The interactions between simple arenes comprise pi-acid/base (charge-transfer), van der Waals (dispersive), and polar electrostatic (Coulombic) component. Rational design of molecular receptors requires a substantial understanding of the component basis for these arene-arene interactions.",
	collection = "stacking",
	doi = "10.1021/ja00065a069",
	localfile = "molecular stacking/1993 - Dominance of polar-pi over charge-transfer effects in stacked phenyl interactions.pdf",
	year = 1993
}

@Article{1993-Dykstra,
	Author = "Clifford E. Dykstra",
	Title = "{Electrostatic interaction potentials in molecular force fields}",
	Journal = "Chem. Rev.",
	Volume = "93",
	Pages = "2339–2353",
	abstract = "(Excerpt) Electrostatics refers to the interaction of charges and charge distributions in the absence of time-dependent variations. For instance, polarization of a charge distribution by a uniform field is a problem of electrostatics so long as the field is static or not varying in time. Electrostatic analysis and electrostaticmodeling have become major elements in efforta to achieve accurate molecular and intermolecular force fields and potentials. Their use represents an attempt to invoke classical physics over quantum mechanics in order to have computationally workable potentials.",
	collection = "molecular electrostatics",
	doi = "10.1021/cr00023a001",
	localfile = "molecular electrostatics/1993 - Electrostatic interaction potentials in molecular force fields.pdf",
	year = 1993
}

@Article{1993-Fraaije,
	Author = "Johannes G. E. M. Fraaije",
	Title = "{Dynamic density functional theory for microphase separation kinetics of block copolymer melts}",
	Journal = "J. Chem. Phys.",
	Volume = "99",
	Number = "11",
	Pages = "9202–9212",
	abstract = "In this paper, we describe a numerical method for the calculation of collective diffusion relaxation mechanisms in quenched block copolymer melts. The method entails the repeated calculation of two opposing fields-an external potential field U, conjugate to the density field p, and an energetic interaction field E. The external field is calculated by numerical inversion of the density functionals and the energetic interaction field is calculated directly by integratlon over the density field. When the two fields are balanced U=E, we recover the self-consistent field solutions' when the two fields are off balance, the spatial gradient of E-U is the thermodynami force which drives the collective diffusion. We introduce a simple local coupling approximation for the Onsager kinetic coefficients of short freely jointed chains in weakly ordered systems. Fluctuations are added by incorporation of a random Langevin force in the diffusion equation. Numerical results of decomposition in symmetric and asymmetric diblock copolymer melts indicate that the method is capable of describing extremely slow defect annihilation relaxation modes. We find that in the nonlinear regime, the density patterns evolve to metastable states, in which isolated defects separate relatively well-ordered crystalline microdomains. These final states are typical for many industrial applications of incompletely relaxed copolymer melts.",
	collection = "block copolymers",
	doi = "10.1063/1.465536",
	keywords = "block copolymers; microdomains",
	localfile = "block copolymers/1993 - Dynamic density functional theory for microphase separation kinetics of block copolymer melts.pdf",
	methods = "DDFT",
	year = 1993
}

@Article{1993-Gutowski-RL,
	Author = "Maciej Gutowski and {Jeanne G. C. M. van} {Duijneveldt-van de Rijdt} and {Joop H. van} {Lenthe}",
	Title = "{Accuracy of the Boys and Bernardi function counterpoise method}",
	Journal = "J. Chem. Phys.",
	Volume = "98",
	Number = "6",
	Pages = "4728–4727",
	collection = "basis set superposition",
	doi = "10.1063/1.465106",
	localfile = "basis set superposition/1993 - Accuracy of the Boys and Bernardi function counterpoise method.pdf",
	year = 1993
}

@Article{1993-Kojima-UKOFKK,
	Author = "Y. Kojima and A. Usuki and M. Kawasumi and A. Okada and Y. Fukushima and T. Kurauchi and O. Kamigaito",
	Title = "{Michanical properties of nylon 6-clay hybrid}",
	Journal = "J. Mater. Res.",
	Volume = "8",
	Number = "5",
	Pages = "1185–1189",
	Note = "First clay-enforced nylon materials.",
	abstract = "Various nylon 6-clay hybrids, such as molecular composites of nylon 6 and silicate layers of montmorillonite and saponite, NCH's and NCHP's, respectively, have been synthesized. To estimate the mechanical properties of these hybrids, tensile, flexural, impact, and heat distortion tests were carried out. NCH was found superior in strength and modulus and comparable in impact strength to nylon 6. The heat distortion temperature (HDT) of NCH (montmorillonite: 4.7 wt. \%) was 152-degrees-C, which was 87-degrees-C higher than that of nylon 6. In NCHP, saponite had a smaller effect on the increase of these mechanical properties. The modulus and HDT of NCH and NCHP increased with an increase in the amount of clay minerals. It was found that these properties were well described by the contribution of the constrained region calculated from the storage and loss modulus at the glass transition temperature. According to the mixing law on elastic modulus, the following expression was obtained between the modulus E at 120-degrees-C and the fraction of the constrained region C, E(n) = E(c)n . C, where the values of n and E(c) (modulus of the constrained region) were 0.685 and 1.02 GPa, respectively.",
	collection = "polymer nanocomposites",
	doi = "10.1557/JMR.1993.1185",
	keywords = "mechanical properties; polymer nanocomposites",
	localfile = "polymer nanocomposites/1993 - Mechanical properties of nylon 6-clay hybrid.pdf",
	rating = "3",
	year = 1993
}

@Article{1993-Koster-KJ,
	Author = "Andreas M. Koster and Christian Kolle and Karl Jug",
	Title = "{Approximation of molecular electrostatic potentials}",
	Journal = "J. Chem. Phys.",
	Volume = "99",
	Number = "2",
	Pages = "1224–1229",
	collection = "molecular electrostatics",
	doi = "10.1063/1.465366",
	localfile = "molecular electrostatics/1993 - Approximation of molecular electrostatic potentials.pdf",
	year = 1993
}

@Article{1993-Liang-ESH,
	Author = "Congxin Liang and Carl S. Ewig and Terry R. Stouch and Arnold T. Hagler",
	Title = "{Ab initio studies of lipid model species. 1. Dimethyl phosphate and methyl propyl phosphate anions}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "115",
	Pages = "1537–1545",
	abstract = "With the aim of developing force fields for lipid/membrane simulations, extensive ab initio calculations have been carried out on lipid model compounds. This contribution reports results from searching the potential energy surfaces of two simple model species, the dimethyl phosphate and methyl propyl phosphate anions. It is shown that most of the critical structural features of phospholipids found experimentally in crystals, in the gel and liquid crystal phases, and in solution are also seen from quantum mechanical calculations on these simple systems in the gas phase. Thus, a gauche-gauche conformation about phosphate is favored for the dimethyl phosphate anion, as is also seen experimentally for phospholipids (and nucleotides). Also, the CCOP torsional angle in the methyl propyl phosphate anion tends to be anti-periplanar or trans, as is the case in most of the structures of phospholipids in crystals and in solution. The vibrational spectra of various conformers of these species have been analyzed in detail. The results reveal some diagnostic frequencies for experimental determination of conformational preferences in structurally related phosphates.",
	collection = "lipids",
	doi = "10.1021/ja00057a046",
	keywords = "lipids",
	localfile = "lipid molecules/1993 - Ab initio studies of lipid model species. 1. Dimethyl phosphate and methyl propyl phosphate anions.pdf",
	year = 1993
}

@Article{1993-Meyer-Almes-Porschke,
	Author = "Franz Josef Meyer-Almes and Dietmar Porschke",
	Title = "{Mechanism of intercalation into the DNA double helix by ethidium}",
	Journal = "Biochemistry",
	Volume = "32",
	Pages = "4246–4253",
	abstract = "The mechanism of intercalation into DNA double helices by ethidium has been analyzed by temperature-jump relaxation and stopped-flow measurements using fluorescence detection. Artifacts due to field- or flow-induced alignment have been eliminated by measurements under magic angle conditions; the theoretical basis for suppression of orientation effects resulting from external forces is given for the case of fluorescence measurements. Excluded site effects have been avoided by restriction to low degrees of binding. The temperature-jump relaxation observed for ethidium binding to DNA could be described by single exponentials under most conditions. The reciprocal time constants increased linearly with the DNA concentration, leading to association rate constants of 2.7 X lo6 M-l s-1 a t 12 OC. These rate constants are virtually independent of the DNA chain length for samples with 200,500,4228, and 30 000 base pairs, showing that the rate is controlled by reaction and not by a diffusive process. At high DNA concentrations around 200 pM, an additional relaxation effect with an amplitude opposite to the main one is observed which is probably due to some conformational change of the DNA-ethidium complex. The results obtained by stopped-flow measurements are consistent with those from T-jump measurements, but owing to higher amplitudes and better signal to noise ratios, the stopped-flow data clearly require two exponentials for satisfactory representation. The reciprocal time constants for both processes increase linearly with the DNA concentration. The simplest mechanism consistent with this result involves parallel formation of two different complexes with a direct transfer of ethidium between the binding sites. The experimental data for a synthetic D N A with one type of base pairs, poly[d(A-T)], are very similar to those for natural DNA; thus, the relatively complex reaction mechanism of intercalation is not due to base-pair heterogeneity. Apparently the two complexes are formed by intercalation of ethidium between the base pairs from the directions of the major and the minor grooves of the double helix. Our results demonstrate that the Joule temperature-jump technique does not introduce artifacts due to field-induced processes, when this technique is used with appropriate care.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/bi00067a012",
	localfile = "nucleic acid intercalation/1993 - mechanism of intercalation into the DNA double helix by ethidium.pdf",
	year = 1993
}

@Article{1993-Pal-Pal,
	Author = "Nikhil R. Pal and Sankar K. Pal",
	Title = "{A review on image segmentation techniques}",
	Journal = "Pattern Recognition",
	Volume = "26",
	Number = "9",
	Pages = "1277–1294",
	abstract = "Many image segmentation techniques are available in the literature. Some of these techniques use only the gray level histogram, some use spatial details while others use fuzzy set theoretic approaches. Most of these techniques are not suitable for noisy environments. Some works have been done using the Markov Random Field (MRF) model which is robust to noise, but is computationally involved. Neural network architectures which help to get the output in real time because of their parallel processing ability, have also been used for segmentation and they work fine even when the noise level is very high. The literature on color image segmentation is not that rich as it is for gray tone images. This paper critically reviews and summarizes some of these techniques. Attempts have been made to cover both fuzzy and non-fuzzy techniques including color image segmentation and neural network based approaches. Adequate attention is paid to segmentation of range images and magnetic resonance images. It also addresses the issue of quantitative evaluation of segmentation results.",
	collection = "informatics",
	doi = "10.1016/0031-3203(93)90135-J",
	keywords = "image analysis",
	localfile = "informatics/1993 - A review on image segmentation techniques.pdf",
	year = 1993
}

@Article{1993-Schmidt-BBEGJKMNSWDM,
	Author = "Michael W. Schmidt and Kim K. Baldridge and Jerry A. Boatz and Steven T. Elbert and Mark S. Gordon and Jan H. Jensen and Shiro Koseki and Nikita Matsunaga and Kiet A. Nguyen and Shujun J. Su and Theresa L. Windus and Michel Dupuis and John A. Montgomery",
	Title = "{General atomic and molecular electronic-structure system}",
	Journal = "J. Comp. Chem.",
	Volume = "14",
	Number = "11",
	Pages = "1347–1363",
	abstract = "A description of the ab initio quantum chemistry package GAMESS is presented. Chemical systems containing atoms through radon can be treated with wave functions ranging from the simplest closed-shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speedup results are given. Parallel calculations can be run on ordinary workstations as well as dedicated parallel machines. (C) 1993 by John Wiley \& Sons, Inc.",
	cited = "4365 (2005-05-05)",
	collection = "cheminformatics",
	localfile = "cheminformatics/1993 - General Atomic and Molecular Electronic Structure System.pdf",
	year = 1993
}

@Article{1993-Usuki-KKOFKK,
	Author = "A. Usuki and Y. Kojima and M. Kawasumi and A. Okada and Y. Fukushima and T. Kurauchi and O. Kamigaito",
	Title = "{Synthesis of nylon 6-clay hybrid}",
	Journal = "J. Mater. Res.",
	Volume = "8",
	Number = "5",
	Pages = "1179–1184",
	Note = "First clay-enforced nylon materials.",
	abstract = "It was found that montmorillonite cation exchanged for 12-aminolauric acid (12-montmorillonite) was swollen by epsilon-caprolactam to form a new intercalated compound. Caprolactam was polymerized in the interlayer of montmorillonite, a layer silicate, yielding a nylon 6-clay hybrid (NCH). The silicate layers of montmorillonite were uniformly dispersed in nylon 6. The carboxyl end groups of 12-aminolauric acid in 12-montmorillonite initiated polymerization of epsilon-caprolactam, and as 12-montmorillonite content became larger, the molecular weight of nylon was reduced. From the result of end-group analysis, carboxyl end groups were more than amino end groups. The difference between the carboxyl and the amino end groups was attributed to ammonium cations (-NH3+) of nylon molecules, because the difference agreed with the anion site concentration of the montmorillonite in NCH. It is suggested that the ammonium cations in nylon 6 interact with the anions in montmorillonite.",
	collection = "polymer nanocomposites",
	doi = "10.1557/JMR.1993.1179",
	keywords = "block copolymers; mechanical properties",
	localfile = "polymer nanocomposites/1993 - Synthesis of nylon 6-clay hybrid.pdf",
	rating = "2",
	year = 1993
}

@Article{1994-Amundson-HQHS,
	Author = "Karl Amundson and Eugene Helfand and Xina Quan and Steven D. Hudson and Steven D. Smith",
	Title = "{Alignment of lamellar block copolymer microstructure in an electric field. 2. Mechanisms of alignment}",
	Journal = "Macromolecules",
	Volume = "27",
	Pages = "6559–6570",
	abstract = "Alignment of lamellar block copolymer microstructurein an electric field was studied. Two mechanismsof alignment are considered selective electric-field-induceddisordering and alignment through movement of defects. The latter mechanism is supported by the findings that, in an aligned sample,defect structures exhibited a highly anisotropic arrangement and were spatially clumped. An analysis of field-induced forces on disclination lines and defect walls is presented. Also, defect interactions are considered. Through the interplay between these forces, the alignment process, the kinetics of alignment,and clumping of defects can be rationalized.",
	collection = "block copolymers",
	keywords = "alignment; block copolymers; electric fields",
	localfile = "block copolymers/1994 - Alignment of lamellar block copolymer microstructure in an electric field. 2. Mechanisms of alignment.pdf",
	year = 1994
}

@Article{1994-Bader,
	Author = "Richard F. W. Bader",
	Title = "{Principle of stationary action and the definition of a proper open system}",
	Journal = "Phys. Rev. B",
	Volume = "49",
	Number = "19",
	Pages = "13348",
	abstract = "The generalization of the variation of the action-integral operator introduced by Schwinger in the derivation of the principle of stationary action enables one to use this principle to obtain a description of the quantum mechanics of an open system. It is shown that augmenting the Lagrange-function operator by the divergence of the gradient of the density operator, a process which leaves the equations of motion unaltered, leads to a class of generators whose associated infinitesimal transformations yield variations of the action-integral operator for an open system, similar in form and content to those obtained for the total, isolated system. The augmented Lagrange-function operator and the associated action-integral operator are termed proper operators, since only their variation yields equations of motion for the observables of an open system, in agreement with the expressions obtained from the field equations. Modifying the generator in this manner is shown to be equivalent to requiring that the open system be bounded by a surface through which there is a local zero flux in the gradient vector field of the electron density. Only the observables of such properly defined open systems are described by the correct equations of motion. The physical significance of such proper open systems is discussed.",
	collection = "quantum chemistry",
	doi = "10.1103/PhysRevB.49.13348",
	localfile = "quantum chemistry/1994 - Principle of stationary action and the definition of a proper open system .pdf",
	year = 1994
}

@Article{1994-Bates-Fredrickson,
	Author = "Frank S. Bates and Glenn H. Fredrickson",
	Title = "{Conformational asymmetry and polymer-polymer thermodynamics}",
	Journal = "Macromolecules",
	Volume = "27",
	Pages = "1065–1067",
	abstract = "(Excerpt) The thermodynamics of mixing for high molecular weight amorphous polymers and low molecular weight liquids have much in common and several important differences.",
	collection = "polymers",
	doi = "10.1021/ma00082a030",
	localfile = "polymers/1994 - Conformational asymmetry and polymer-polymer thermodynamics.pdf",
	year = 1994
}

@Article{1994-Casciola-Rosen-AR,
	Author = "Livia A. Casciola-Rosen and Grant Anhalt and Antony Rosen",
	Title = "{Autoantigens targeted in systemic lupus erythematosus are clustered in two populations of surface structures on apoptotic keratinocytes}",
	Journal = "J. Exp. Med.",
	Volume = "179",
	Number = "4",
	Pages = "1317–1330",
	collection = "cells",
	localfile = "cells/1994 - Autoantigens targeted in systemic lupus erythematosus are clustered in two populations of surface structures on apoptotic keratinocytes.pdf",
	year = 1994
}

@Article{1994-Chalasinski-Szczesniak,
	Author = "Grzegorz Chałasiński and Małgorzata M. Szczęśniak",
	Title = "{Origins of structure and energetics of van der Waals clusters from ab initio calculations}",
	Journal = "Chem. Rev.",
	Volume = "94",
	Pages = "1723–1765",
	abstract = "(Excerpt) The concept of intermolecular forces has been central to the molecular theory of matter since the work of van der Waals. A great deal of effort has been expended in an attempt to establish a relationship between the properties of bulk matter and intermolecular forces. Historically, the studies in this area have proceeded in two directions. On one hand, the quantum and statistical mechanical apparatus has been developed which could translate the input from quantum mechanical treatment of intermolecular interactions into the properties of bulk materials. On the other hand, the inverse problem of molecular theory has also been addressed in an attempt to obtain the information on intermolecular forces from direct measurements of the macroscopic properties.",
	collection = "molecular interactions",
	doi = "10.1021/cr00031a001",
	localfile = "molecular interactions/1994 - Origins of structure and energetics of van der Waals clusters from ab initio calcualtions.pdf",
	year = 1994
}

@Article{1994-Duijneveldt-RL,
	Author = "{Frans B. van} {Duijneveldt} and {Jeanne G. C. M. van} {Duijneveldt-van de Rijdt} and {Joop H. van} {Lenthe}",
	Title = "{State of the Art in Counterpoise Theory}",
	Journal = "Chem. Rev.",
	Volume = "94",
	Number = "7",
	Pages = "1873–1885",
	abstract = "This review, covering the period 1987-1993, deals with quantum chemical studies that employ the supermolecular method with some form of counterpoise to calculate the interaction energies of molecular complexes. A theorem is provided showing that the standard counterpoise approach, in which, at a given geometry, energies are evaluated using the full basis set of the complex, yields a pure (i.e. BSSE-free) interaction energy. Artifacts resulting from secondary BSSE have been found to become negligible before the basis set limit of this interaction energy is attained. Alternative methods in which counterpoise is achieved by restricting the fragment description in the calculation of the full complex to the level used for the isolated fragment are formally nearly correct but have been found to give less satisfactory results, mainly because the relevant fragment properties converge only slowly to the basis set limit. Some practical aspects are considered as well, such as the ambiguities that arise in calculating the binding energy of a cluster of molecules.",
	collection = "basis set superposition",
	doi = "10.1021/cr00031a007",
	localfile = "basis set superposition/1994 - State of the art in counterpoise theory.pdf",
	year = 1994
}

@Article{1994-Elrod-Saykally,
	Author = "Matthew J. Elrod and Richard J. Saykally",
	Title = "{Many-body effects in intermolecular forces}",
	Journal = "Chem. Rev.",
	Volume = "94",
	Pages = "1975–1997",
	abstract = "(Excerpt) The investigation of many-body effects in intermolecular interactions has assumed increasing prominence as modern experimental and computational technology has progressed such that a detailed description of the condensed phases of matter is now possible through computer simulations. Indeed, these technologies have recently allowed great advances in the understanding of the binary interaction, such that many relevant pair potential energy surfaces are now obtainable by inversion of experimental data or by direct a b initio quantum chemical calculation. Paralleling these developments, many workers have attempted to extend this success to the construction of more general many-body potential energy surfaces, which are ultimately necessary to achieve the goal of describing macroscopic properties from a rigorous microscopic viewpoint.",
	collection = "molecular interactions",
	doi = "10.1021/cr00031a010",
	localfile = "molecular interactions/1994 - Many-body effects in intermolecular forces.pdf",
	year = 1994
}

@Article{1994-Fredrickson-LB,
	Author = "Glenn H. Fredrickson and Andrea J. Liu and Frank S. Bates",
	Title = "{Entropic corrections to the Flory–Huggins theory of polymer blends: architectural and conformational effects}",
	Journal = "Macromolecules",
	Volume = "27",
	Pages = "2503–2511",
	abstract = "We compute fluctuations corrections to the Flory–Huggins theory for athermal or nearly athermal polymer mixtures. These excess free energy contributions arise from architectural and flexibility differences between components, are quasi-universal, and are generally positive, favoring demixing. Specific cases considered are binary blends of linear hompolymers, homopolymer/block copolymer mixtures, and blends of branched and linear hompolymers. We identify invariant parameters and mixing rules for such systems that may help facilitate the design of miscible polyolefin blends.",
	collection = "polymers",
	doi = "10.1021/ma00087a019",
	localfile = "polymers/1994 - Entropic corrections to the Flory-Huggins theory of polymer blends: architectural and conformational effects.pdf",
	year = 1994
}

@Article{1994-Glendening-Streitwieser,
	Author = "Eric D. Glendening and Andrew Streitwieser",
	Title = "{Natural energy decomposition analysis: An energy partitioning procedure for molecular interactions with application to weak hydrogen bonding, strong ionic, and moderate donor–acceptor interactions}",
	Journal = "J. Chem. Phys.",
	Volume = "100",
	Number = "4",
	Pages = "2900–2909",
	abstract = "We present a procedure for partitioning the Hartre-Fock self-consistent-field (SCF) interaction energy into electrostatic, charge transfer, and deformation components. The natural bond orbital (NBO) approach of Weinhold and co-workers is employed to construct intermediate supermolecule and fragment wave functions that satisfy the Pauli exclusion principle, thereby avoiding the principal deficiency of the popular Kitaura-Morokuma energy decomposition scheme. The function counterpoise method of Boys and Bernardi enters the procedure naturally, providing an estimate of basis set superposition error (BSSE) . We lind that the energy components exhibit little basis set dependence when BSSE is small. Applications are presented for several representative molecular and ion complexes: the weak hydrogen bond of the water dimer, the strong ionic interaction of the alkali metal hydrides, and the moderate donor-acceptor interactions of BH3NH3 and BH,C!O. Electrostatic interaction dominates the long-range region of the potential energy surface and charge transfer is strongly stabilizing for fragments within van der Waals contact. The repulsive interaction in the short range region of the potential arises from deformation as the fragment wave functions distort to avoid significant interpenetration.",
	collection = "molecular interactions",
	doi = "10.1063/1.466432",
	localfile = "molecular interactions/1994 - Natural energy decomposition analysis: an energy partitioning procedure for molecular interactions with application to weak hydrogen bonding, strong ionic, and moderate donor-acceptor interactions.pdf",
	shorttitle = "Natural energy decomposition analysis",
	year = 1994
}

@Article{1994-Gurovich,
	Author = "Eugene Gurovich",
	Title = "{Copolymers under a monomer orienting field}",
	Journal = "Macromolecules",
	Volume = "27",
	Pages = "7063–7066",
	collection = "block copolymers",
	doi = "10.1021/ma00102a009",
	keywords = "block copolymers; electric fields",
	localfile = "block copolymers/1994 - Copolymers under a monomer orienting field.pdf",
	year = 1994
}

@Article{1994-Gurovich-1,
	Author = "Eugene Gurovich",
	Title = "{On microphase separation of block copolymers in an electric field: four universal classes}",
	Journal = "Macromolecules",
	Volume = "27",
	Pages = "7339–7362",
	collection = "block copolymers",
	doi = "10.1021/ma00103a015",
	localfile = "block copolymers/1994 - On microphase separation of block copolymers in an electric field: four universal classes.pdf",
	year = 1994
}

@Article{1994-Jeziorski-MS,
	Author = "Bogumił Jeziorski and Robert Moszyński and Krzysztof Szalewicz",
	Title = "{Perturbation Theory Approach to Intermolecular Potential Energy Surfaces of van der {W}aals Complexes}",
	Journal = "Chem. Rev.",
	Volume = "94",
	Pages = "1887–1930",
	collection = "molecular interactions",
	doi = "10.1021/cr00031a008",
	localfile = "molecular interactions/1994 - Perturbation theory approach to intermolecular potential enery surfaces of van der Waals complexes.pdf",
	year = 1994
}

@Article{1994-Kawashima-ZLS,
	Author = "T. Kawashima and E. G. Zappi and T.-S. Lieu and R. D. Sontheimer",
	Title = "{Impact of ultraviolet radiation on the cellular expression of Ro/SS-A-autoantigenic polypeptides}",
	Journal = "Dermatology",
	Volume = "189 suppl 1",
	Pages = "6–10",
	collection = "cells",
	localfile = "cells/1994 - Impact of ultraviolet radiation on the cellular expression of Ro-SS-A-autoantigenic polypeptides.pdf",
	year = 1994
}

@Article{1994-Kelekar-SK,
	Author = "Ameeta Kelekar and Michael R. Saitta and Jack D. Keene",
	Title = "{Molecular composition of Ro small ribonucleoprotein complexes in human cells}",
	Journal = "J. Clin. Invest.",
	Volume = "93",
	Pages = "1637–1644",
	collection = "cells",
	localfile = "cells/1994 - Molecular composition of Ro small ribonucleoprotein complexes in human cells.pdf",
	year = 1994
}

@Article{1994-Klafter-Zumofen,
	Author = "J. Klafter and G. Zumofen",
	Title = "{Probability distributions for continuous-time random walks with long tails}",
	Journal = "J. Phys. Chem.",
	Volume = "98",
	Pages = "7366–7370",
	cited = "43 (2013-04-29)",
	collection = "statistics",
	localfile = "statistics/1994 - Probability distributions for continuous-time random walks with long tails.pdf",
	year = 1994
}

@Article{1994-Krugh,
	Author = "Thomas R. Krugh",
	Title = "{Drug-{DNA} interactions}",
	Journal = "Curr. Op. Struct. Biol.",
	Volume = "4",
	Number = "3",
	Pages = "351 – 364",
	abstract = "Structures of drug-DNA oligomer complexes provide a molecular basis for the interpretation of sequence-selective binding as measured by DNA footprinting. Thermodynamic data, obtained from calorimetry, thermal denaturation, and equilibrium measurements are also an important aspect of drug-DNA complex formation. Although many ligand-DNA complexes exhibit a single conformation in solution, there are examples of systems undergoing exchange between two or more conformations in solution. A 2-aminofluorene-DNA oligomer duplex adopts two conformations, one exhibiting Watson-Crick pairing at the modified guanine, and a second conformation in which base pairing is disrupted and the fluorene moiety is stacked within the duplex. NMR-derived structures of oligonucleotides with actinomycin D, nogalomycin, bisintercalartors, lexitropsins and triplex binding ligands highlight recent advances in this area. The development of (pyridine-2-carboxamide-neotropsin)(2)-C-6, a synthetic dimer that binds in the minor groove, is but one example of the synergistic interaction of NMR structural analysis, molecular modeling, and chemical synthesis.",
	collection = "nucleic acid drugs",
	doi = "10.1016/S0959-440X(94)90103-1",
	localfile = "nucleic acid drugs/1994 - Drug-DNA interactions.pdf",
	year = 1994
}

@Article{1994-Lambooy-RKMGS,
	Author = "P. Lambooy and Thomas P. Russell and G. J. Kellogg and Anne M. Mayes and P. D. Gallagher and S. K. Satija",
	Title = "{Observed frustration in confined block copolymers}",
	Journal = "Phys. Rev. Lett.",
	Volume = "72",
	Number = "18",
	Pages = "2899–2902",
	collection = "block copolymers",
	doi = "10.1103/PhysRevLett.72.2899",
	keywords = "block copolymers; nanoconfinement; thin films",
	localfile = "block copolymers/1994 - Observed frustration in confined block copolymers.pdf",
	rating = "2",
	year = 1994
}

@Article{1994-Laradji-GZ,
	Author = "Mohamed Laradji and Hong Guo and Martin J. Zuckermann",
	Title = "{Off-lattice Monte Carlo simulation of polymer brushes in good solvents}",
	Journal = "Phys. Rev. E",
	Volume = "49",
	Number = "4",
	Pages = "3199–3206",
	collection = "polymer brushes",
	doi = "10.1103/PhysRevE.49.3199",
	keywords = "polymer brushes",
	localfile = "polymer brushes/1994 - Off-lattice Monte Carlo simulation of polymer brushes in good solvents.pdf",
	methods = "MC",
	year = 1994
}

@Article{1994-Latajka-Bouteiller,
	Author = "Zdzisław Latajka and Yves Bouteiller",
	Title = "{Application of density functional methods for the study of hydrogen-bonded systems: the hydrogen fluoride dimer}",
	Journal = "J. Chem. Phys.",
	Volume = "101",
	Number = "11",
	Pages = "9793–9799",
	abstract = "Systematic studies of the ability of a broad family of density functional methods applied to hydrogen-bonded complexes have been carried out on the hydrogen fiuoride dimer. Specifically, calculations have been performed using basis sets of triple-zeta quality with diffuse functions and multiple sets of polarization functions. Various local and nonlocal exchange-correlation functionals have been applied in order to study the structure, energetics, and vibrational properties of the hydrogen fluoride dimer. The comparison with the experimental data, and also with results coming from ab initio methods (Hartree-Fock, Møller–Plesset second order, and quadratic configuration interaction with the single and double excitations) shows good performance of nonlocal density functional methods for the description of hydrogen-bonded systems. The calculated binding energy, with nonlocal Becke exchange and Lee-Yang-Parr correlation functionals and a 6-311++G(3df,3pd) basis set, is 4.48 kcal/mol and is in good agreement with experimental value and prior calculations.",
	collection = "hydrogen bonding",
	doi = "10.1063/1.467944",
	keywords = "hydrogen bonding",
	localfile = "hydrogen bonding/1994 - Application of density functional methods for the study of hydrogen-bonded systems: the hydrogen fluoride dimer.pdf",
	year = 1994
}

@Article{1994-Liang-ESH,
	Author = "Congxin Liang and Carl S. Ewig and Terry R. Stouch and Arnold T. Hagler",
	Title = "{Ab initio studies of lipid model species. 2. Conformational analysis of inositols}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "116",
	Pages = "3904–3911",
	abstract = "Molecular species containing inositol are among the most ubiquitous naturally occurring compounds. For example they are commonly found in biomembranes as one of the few head groups of phospholipids. To help characterize their structural properties we have studied the conformational preferences of inositol. It has long been held that among the eight possible cis-trans isomers of inositols shown in Figure 1, the all-equatorial (6e) scyllo-inositol is intrinsically the most stable. However we report here ab initio calculations using Hartree-Fock and second-order Møller–Plesset perturbation methods and also calculations based on density-functional methods, all of which show that this long held view on conformational analysis of isolated inositol molecules is questionable. We have found that the naturally much more abundant myo-inositol, with five equatorial and one axial hydroxyl groups (5e/1a), and the nonnaturally occurring neo-inositol with four equatorial and two axial hydroxyls (4e/2a), tend to be slightly lower in energy than scyllo-inositol. In terms of the free energy, contributions from nuclear motions also favor myo-inositol over scyllo-inositol, making the former consistently more stable. Although an axial hydroxyl group introduces strain energy primarily due to 1,4 O-axial...O and O-axial...C repulsions, it can form more favorable intramolecular hydrogen bonds, which appear to be dominant. The O-axial...H-axial...C interaction also favors the axial hydroxyl orientation. On the other hand, when all intramolecular hydrogen bonds in scyllo- and myo-inositols are removed by properly orienting OH groups, as may occur in aqueous solution or crystals, scyllo becomes lower in energy than myo. Calculations were also carried out on phosphoryl inositols, and the results indicate that axial phosphate substitution may be favored as well. These effects were analyzed in terms of the cyclohexane ring structures and compared with experimental results.",
	collection = "lipids",
	doi = "10.1021/ja00088a029",
	keywords = "lipids",
	localfile = "lipid molecules/1994 - Ab initio studies of lipid model species. 2. Conformational analysis of inositols.pdf",
	year = 1994
}

@Article{1994-Matsen-Schick,
	Author = "Mark W. Matsen and M. Schick",
	Title = "{Stable and unstable phases of a diblock copolymer melt}",
	Journal = "Phys. Rev. Lett.",
	Volume = "72",
	Number = "16",
	Pages = "2660–2669",
	collection = "block copolymers",
	doi = "10.1103/PhysRevLett.72.2660",
	keywords = "block copolymers",
	localfile = "block copolymers/1994 - Stable and unstable phases of a diblock copolymer melt.pdf",
	year = 1994
}

@Article{1994-Meister-Schwarz,
	Author = "J. Meister and W. H. E. Schwarz",
	Title = "{Principal components of ionicity}",
	Journal = "J. Phys. Chem.",
	Volume = "98",
	Pages = "8245–8252",
	Note = "One principal component for ionicity arises in an analysis of over 20 different deifnitions of partial charge, presumably demonstrating atomic charges do reflect an underlying physical observable.",
	collection = "molecular electrostatics",
	doi = "10.1021/j100084a048",
	localfile = {},
	rating = "2",
	read = "2015-05-05",
	year = 1994
}

@Article{1994-Moy-FG,
	Author = "Vincent T. Moy and Ernst-Ludwig Florin and Hermann E. Gaub",
	Title = "{Intermolecular forces and energies between ligands and receptors}",
	Journal = "Science",
	Volume = "266",
	Pages = "257–259",
	Note = "Page 257: In experiments where the interaction was limited to a few molecules, the force required to rupture contact between ligand and receptor-functionalized surfaces ocurred in integer multiples. (...) the process must be adiabatic (...) Dissipative and entropy driven processes occur beyond the rupture point and are thus irrelevant to the unbinding force, although they may dominate the free energy of the system. Page 258: (...) our model predicts that the equilibrium constant of the complex, but not its unbinding force, will depend on the conditions of the buffer. (...) These differences in the characteristics of the pair potentials are reflected in the nature of the molecular recognition and the functions of the two systems.",
	collection = "molecular interactions",
	doi = "10.1126/science.7939660",
	localfile = "molecular interactions/1994 - Intermolecular forces and energies between ligands and receptors.pdf",
	rating = 3,
	read = "2013-10-08",
	year = 1994
}

@Article{1994-Neusser-Krause,
	Author = "H. J. Neusser and H. Krause",
	Title = "{Binding energy and structure of van der Waals complexes of benzene}",
	Journal = "Chem. Rev.",
	Volume = "94",
	Pages = "1829–1843",
	abstract = "(Excerpt) The microscopic understanding of intermolecular interaction leading to van der Waals molecules requires the spectroscopic investigation of well-defined finite isolated complexes. A basic physical property to be investigated is the nature and strength of the two-body interaction between the two constituents in a dimer, being the simplest and smallest van der Waals molecule. Among these, dimers of benzene with itself, noble gases, and other molecules are prototype systems for weakly bound van der Waals clusters between nonpolar constituents. Due to the highly symmetric planar structure of the benzene molecule they represent an ideal system for these studies.",
	collection = "molecular interactions",
	doi = "10.1021/cr00031a005",
	localfile = "molecular interactions/1994 - Binding energy and structure of van der Waals complexes of benzene.pdf",
	year = 1994
}

@Article{1994-Newcomb-Gellman,
	Author = "Lisa F. Newcomb and Samuel H. Gellman",
	Title = "{Aromatic stacking interactions in aqueous solution - evidence that neither classical hydrophobic effects nor dispersion forces are important}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "116",
	Number = "11",
	Pages = "4993–4994",
	abstract = "(Excerpt) The association of aromatic surfaces with one another is believed to play a significant role in the folding and complexation behavior of biopolymers. The forces that drive

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