text:
vophobic and electrostatic interactions have been shown to be inextricably linked. Moreover, the influence of electrostatic and solvophobic components on the selectivity of aromatic interactions has been demonstrated.",
	collection = "stacking",
	doi = "10.1016/S1367-5931(02)00359-9",
	localfile = "molecular stacking/2002 - Aromatic interactions in model systems.pdf",
	year = 2002
}

@Article{2003-Aikens-WBFSG,
	Author = "Christine M. Aikens and Simon P. Webb and Rob L. Bell and Graham D. Fletcher and Michael W. Schmidt and Mark S. Gordon",
	Title = "{A derivation of the frozen-orbital unrestricted open-shell and restricted closed-shell second-order perturbation theory analytic gradient expressions}",
	Journal = "Theor. Chem. Acc.",
	Volume = "110",
	Pages = "233–253",
	abstract = "Abstract. A detailed derivation of the frozen-orbital second-order perturbation theory (MP2) analytic gradient in the spin-orbital basis is presented. The summation ranges and modiﬁcation of the MP2 gradient terms that result from the frozen-orbital approximation are clearly identiﬁed. The frozen-orbital analytic gradients for unrestricted MP2 and closed-shell MP2 are determined from the spin-orbital derivation. A discussion of useful implementation procedures is included. Timings from full and frozen-orbital MP2 gradient calculations on the molecule silicocene (the silicon analog of the sandwich compound ferrocene) are also presented.",
	collection = "quantum chemistry",
	doi = "10.1007/s00214-003-0453-3",
	localfile = "quantum chemistry/2003 - A derivation of the frozen-orbital unrestricted open-shell and restricted closed-shell second-order perturbation theory analytic gradient expressions.pdf",
	year = 2003
}

@Article{2003-Bader,
	Author = "Richard F. W. Bader",
	Title = "{Letter to the editor: Quantum mechanics, or orbitals?}",
	Journal = "Int. J. Quant. Chem.",
	Volume = "94",
	Number = "3",
	Pages = "173–177",
	abstract = "(Excerpt) Frenking recently reviewed the book From Lewis to Electron Densities, by Gillespie and Popelier. The book presents an interpretation of chemical bonding and molecular geometry using properties of the electron density, coupled with the theory of atoms in molecules. The review serves as the focal point for a dialogue on the use of orbital representations of the wavefunction in the interpretation of chemistry, as opposed to the use of quantum mechanical observables and their governing theorems, an approach enabling the prediction as well as the interpretation of chemical observations. Frenking is adamant in his criticism of the approach based on the density because it “is based on a physically observable property of the molecule” rather than on the mathematical wavefunction, a result of being “too abstract and too elusive” for chemists to grasp.",
	collection = "philosophy",
	doi = "10.1002/qua.10627",
	localfile = "philosophy/2003 - Letter to the editor: Quantum mechanics, or orbitals?.pdf",
	shorttitle = "Letter to the editor",
	year = 2003
}

@Article{2003-Bedrov-SS,
	Author = "Dmitry Bedrov and Grant D. Smith and James S. Smith",
	Title = "{Matrix-induced nanoparticle interactions in a polymer melt: a molecular dynamics simulations study}",
	Journal = "J. Chem. Phys.",
	Volume = "119",
	Number = "19",
	Pages = "10438",
	abstract = "A molecular dynamics simulation study of the inﬂuence of a polymer melt matrix consisting of bead-necklace polymers on the effective interaction between two spherical nanoparticles was performed. The potential of mean force POMF between the two nanoparticles as well as entropy and energy contributions to the POMF was determined as a function of nanoparticle separation. The role of energy on the POMF was investigated by varying the strength of the polymer–nanoparticle interaction and comparing structure and POMF with those obtained for an athermal model. All features of the POMF as a function of nanoparticle separation were found to be strongly correlated with the polymer matrix density, the structure of the polymer at the nanoparticle interface, and the structure of the polymer in the interparticle region. The POMF was not found to correlate with polymer chain dimensions e.g., radius of gyration in contrast to colloidal suspensions in dilute and semidilute solutions. Both energy and entropy effects were found to make important contributions to the POMF. For the athermal system, where all matrix-induced interactions are entropic in nature, the nanoparticle POMF was found to exhibit qualitatively different behavior from that of the energetic systems.",
	collection = "polymer nanocomposites",
	doi = "10.1063/1.1615965",
	localfile = "polymer nanocomposites/2003 - Matrix-induced nanoparticle interactions in a polymer melt: a molecular dynamics simulations study.pdf",
	year = 2003
}

@Article{2003-Bockstaller-LMT,
	Author = "Michael R. Bockstaller and Yonit Lapetnikov and Shlomo Margel and Edwin L. Thomas",
	Title = "{Size-selective organization of enthalpic compatabilized nanocrystals in ternary block copolymer/particle mixtures}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "125",
	Pages = "5276–5277",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ja034523t",
	keywords = "block copolymers; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2003 - Size-selective organization of enthalpic compatibilized nanocrystals in ternary block copolymer-particle mixtures.pdf",
	methods = "absorbance, DLS, TEM",
	systems = "Au@PS-PEP, silica@PS-PEP",
	year = 2003
}

@Article{2003-Bockstaller-Thomas,
	Author = "Michael R. Bockstaller and Edwin L. Thomas",
	Title = "{Optical properties of polymer-based photonic nanocomposite materials}",
	Journal = "J. Phys. Chem. B",
	Volume = "107",
	Pages = "10017–10024",
	abstract = "Designing metallodielectric nanocomposite materials for photonic applications implies the ability to reliably model and predict the effect of metallic inclusions on the optical properties of a microstructured composite material. We present a detailed analysis of the optical properties of block copolymer based, multilayered metallodielectric Bragg reflectors and discuss the implications of nanosize-specific effects on the design of composite materials for photonic applications. A series of lamellar poly(styrene-b-ethylene/propylene) copolymer thin films with varying filling fraction of gold nanocrystals preferentially but randomly distributed within the poly(styrene) domains have been studied by reflectometry. The reflective properties are compared to model calculations based on effective medium concepts taking into account confinement effects on the dielectric function of the nanocrystals. The particle size causes strong alterations in the dielectric function of the metal inclusions that have relevance for the attainable dielectric contrast within periodic nanocomposites.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/jp035286j",
	keywords = "block copolymers; nanoparticle distribution; nanospheres; optical properties; polymer architecture; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2003 - Optical properties of polymer-based photonic nanocomposite materials.pdf",
	methods = "profilometry, reflectance, absorbance, ellipsometry, SAXS, TEM",
	systems = "Au-PS@PS-PEP",
	year = 2003
}

@Article{2003-Boker-EHKLZZSUAMK,
	Author = "Alexander Böker and H. Elbs and Helmut Hansel and A. Knoll and Sabine Ludwigs and Heiko Zettl and Andrei V. Zvelindovsky and G. J. Agur Sevink and Volker Urban and Volker Abetz and A. H. E. Muller and Georg Krausch",
	Title = "{Electric Field Induced Alignment of Concentrated Block Copolymer Solutions}",
	Journal = "Macromolecules",
	Volume = "36",
	Number = "21",
	Pages = "8078–8087",
	abstract = "We investigate the microdomain orientation kinetics of concentrated block copolymer solutions exposed to a dc electric field by time-resolved synchrotron small-angle X-ray scattering. As a model system, we use a lamellar polystyrene-b-polyisoprene block copolymer dissolved in toluene. Our results indicate two different microscopic mechanisms, i.e., nucleation and growth of domains and grain rotation. The former dominates close to the orderdisorder transition, while the latter prevails under more strongly segregated conditions. This conclusion is corroborated by computer simulations based on dynamic density functional theory. The orientation kinetics follows a single-exponential behavior with characteristic time constants varying from a few seconds to some minutes depending on polymer concentration, temperature, and electric field strength. From the experimental results we deduce optimum conditions for the preparation of highly anisotropic bulk polymer samples via solvent casting in the presence of an electric field.",
	collection = "block copolymers",
	doi = "10.1021/ma021347k",
	keywords = "block copolymers; electric fields; mesophase transitions",
	localfile = "block copolymers/2003 - Electric field induced alignment of concentrated block copolymer solutions.pdf",
	year = 2003
}

@Article{2003-Bolhuis-ML,
	Author = "Peter G. Bolhuis and Evert Jan Meijer and Ard A. Louis",
	Title = "{Colloid–polymer mixtures in the protein limit}",
	Journal = "Phys. Rev. Lett.",
	Volume = "90",
	Number = "6",
	Pages = "068304",
	abstract = "We computed the phase-separation behavior and effective interactions of colloid-polymer mixtures in the ‘‘protein limit,’’ where the polymer radius of gyration is much larger than the colloid radius. For ideal polymers, the critical colloidal packing fraction tends to zero, whereas for interacting polymers in a good solvent the behavior is governed by a universal binodal, implying a constant critical colloid packing fraction. In both systems the depletion interaction is not well described by effective pair potentials but requires the incorporation of many-body contributions.",
	collection = "polymers",
	doi = "10.1103/PhysRevLett.90.068304",
	localfile = "polymers/2003 - Colloid-polymer mixtures in the protein limit.pdf",
	year = 2003
}

@Article{2003-Brown-MMA,
	Author = "D. Brown and P. Mele and S. Marceau and N. D. Alberola",
	Title = "{A molecular dynamics study of a model nanoparticle embedded in a polymer matrix}",
	Journal = "Macromolecules",
	Volume = "36",
	Pages = "1395–1406",
	abstract = "Molecular dynamics (MD) simulations have been used to examine the structure and dynamics of a system containing an inorganic nanoparticle embedded in a polymer matrix. This paper represents a preliminary investigation into the feasibility of examining such relatively large systems using atomistic modeling techniques. No attempt is made here to model any specific system. A generic linear polymer “united-atom” model is first created in an amorphous phase before the insertion of an atomistically detailed silica nanoparticle of diameter 4.4 nm. A novel method to insert a nanoparticle into a polymer matrix is given. The entire system is contained in a standard periodic simulation cell of side length ∼10 nm. The volume fraction of silica corresponded to 4.5\%. The composite system was subsequently relaxed at 300 K and at two different pressures using standard MD techniques, the gmq suite of programs being used for this purpose. Results are presented regarding the variation of the structure and dynamics of the system with respect to the distance from the polymer-nanoparticle interface and as a function of pressure. A clear structuring of the polymer chains around the nanoparticle is seen with prominent first and second peaks in the radial density function and a concurrent development of preferred chain orientation. The probability of trans conformers is also higher close to the interface and shows a distinct gradient. In contrast, evidence for chain immobilization is less obvious overall although dynamic properties are more sensitive to changes in the pressure. Comparisons are also made between the bulk moduli of the pure polymer and composite systems.",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma020951s",
	keywords = "nanospheres; polymer nanocomposites",
	localfile = "polymer nanocomposites/2003 - A molecular dynamics study of a model nanoparticle embedded in a polymer matrix.pdf",
	year = 2003
}

@Article{2003-Buxton-Balazs,
	Author = "Gavin A. Buxton and Anna C. Balazs",
	Title = "{Simulating the morphology and mechanical properties of filled diblock copolymers}",
	Journal = "Phys. Rev. E",
	Volume = "67",
	Pages = "031802",
	collection = "block copolymer nanocomposites",
	doi = "10.1103/PhysRevE.67.031802",
	keywords = "block copolymers; mechanical properties; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2003 - Simulating the morphology and mechanical properties of filled diblock copolymers.pdf",
	methods = "CDS/BD",
	year = 2003
}

@Article{2003-Buxton-LB,
	Author = "Gavin A. Buxton and Jae Youn Lee and Anna C. Balazs",
	Title = "{Computer simulation of morphologies and optical properties of filled diblock copolymers}",
	Journal = "Macromolecules",
	Volume = "36",
	Pages = "9631–9637",
	Note = "Besides describing SCFT/DFT, has some sensible observations. Page 9632: If the particle radius is beyond the root-mean-squared end-to-end distance of the chain, it may be more appropriate to view a particle as a substrate (...). If the particle is on the smae size scale as a monomer, then it may be sufficient to treat the particle as a solvent molecule. Ref.20: There is a fundamental reason why the polymer-particle interactions should be treated differently than the particle-particle interactions. (...) In real systems, the nanoparticles are solids and impenetrable to each other.",
	abstract = "We integrate two computational techniques in order to determine the optical properties of self-assembled mixtures of diblock copolymers and nanoparticles. To determine the morphology of the system, we first use an approach that combines a self-consistent-field theory (SCFT) for the diblocks with a density functional theory (DFT) for the particles. Using this SCF/DFT model, we focus on the lamellar phase of AB diblocks and calculate volume fraction profiles for systems containing selective or nonselective nanoparticles. We use the volume fraction profiles from the SCF/DFT and assign typical dielectric constants for the different polymer domains and the particles to characterize the dielectric properties of the composite. A finite difference time domain (FDTD) technique is then used to simulate the propagation of light through this heterogeneous material. The results of this study allow us to determine how the polymer-particle interactions affect the spatial distribution of fillers within the polymer matrix and how this distribution in turn affects the optical properties of the nanocomposite. The findings can provide guidelines for facilitating the design of photonic band gap materials.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma034322",
	keywords = "block copolymers; nanoparticle distribution; nanospheres; optical properties; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2003 - Computer simulation of morphologies and optical properties of filled diblock copolymers.pdf",
	methods = "SCFT/DFT, finite elements",
	year = 2003
}

@Article{2003-Chen-HB,
	Author = "Ting Chen and Glenn Hefter and Richard Buchner",
	Title = "{Dielectric spectroscopy of squeous solutions of KCl and CsCl}",
	Journal = "J. Phys. Chem. A",
	Volume = "107",
	Pages = "4025–4031",
	cited = "39 (2003-04-29)",
	collection = "molecular sovlation",
	doi = "10.1021/jp026429p",
	localfile = "molecular solvation/2003 - Dielectric spectroscopy of aqueous solutions of KCl and CsCl.pdf",
	year = 2003
}

@Article{2003-Dziekonski-SPL,
	Author = "Paweł Dziekoński and W. Andrzej Sokalski and Yevgeniy Podolyan and Jerzy Leszczyński",
	Title = "{Nonempirical analysis of the catalytic activity of the molecular environment: optimal static and dynamic catalytic fields for double proton transfer in formamide-formamidine complex}",
	Journal = "Chem. Phys. Lett.",
	Volume = "367",
	Pages = "367–375",
	collection = "molecular solvation",
	doi = "10.1016/S0009-2614(02)01712-8",
	localfile = "molecular solvation/2003 - Nonempirical analysis of the catalytic activity of the molecular environment: optimal static and dynamic catalytic fields for double proton transfer in formamide-formamidine ocmplex.pdf",
	year = 2003
}

@Article{2003-Eckel-RRWSA,
	Author = "Rainer Eckel and Robert Ros and Alexandra Ros and Sven David Wilking and Norbert Sewald and Dario Anselmetti",
	Title = "{Identification of Binding Mechanisms in Single {Molecule-DNA} Complexes}",
	Journal = "Biophys. J.",
	Volume = "85",
	Number = "3",
	Pages = "1968–1973",
	abstract = "Changes in the elastic properties of single deoxyribonucleic acid {(DNA)} molecules in the presence of different {DNA-binding} agents are identified using atomic force microscope single molecule force spectroscopy. We investigated the binding of {poly(dG-dC)} {dsDNA} with the minor groove binder distamycin A, two supposed major groove binders, an [alpha]-helical and a 310-helical peptide, the intercalants daunomycin, ethidium bromide and {YO,} and the bis-intercalant {YOYO.} Characteristic mechanical fingerprints in the overstretching behavior of the studied single {DNA-ligand} complexes were observed allowing the distinction between different binding modes. Docking of ligands to the minor or major groove of {DNA} has the effect that the intramolecular {B-S} transition remains visible as a distinct plateau in the force-extension trace. By contrast, intercalation of small molecules into the double helix is characterized by the vanishing of the {B-S} plateau. These findings lead to the conclusion that atomic force microscope force spectroscopy can be regarded as a single molecule biosensor and is a potent tool for the characterization of binding motives of small ligands to {DNA.}",
	collection = "nucleic acid drugs",
	doi = "10.1016/S0006-3495(03)74624-4",
	localfile = "nucleic acid intercalation/2003 - Identification of binding mechanisms in single molecule-DNA complexes.pdf",
	year = 2003
}

@Article{2003-Fraaije-Sevink,
	Author = "Johannes G. E. M. Fraaije and G. J. Agur Sevink",
	Title = "{Model for pattern formation in polymer surfactant nanodroplets}",
	Journal = "Macromolecules",
	Volume = "36",
	Number = "21",
	Pages = "7891–7893",
	abstract = "(Excerpt) Through self-consistent-field simulation we discovered remarkable bicontinuous structures in dispersed droplets of polymer surfactant (Figures 1 and 2). The nanodroplet structures are soft and fragile: the molecular bonding energy is weak, derived from self-assembly of polymer molecules.",
	collection = "block copolymers",
	doi = "10.1021/ma025559t",
	keywords = "block copolymers; nanoconfinement",
	localfile = "block copolymers/2003 - Model for pattern formation in polymer surfactant nanodroplets.pdf",
	year = 2003
}

@Article{2003-Frenking,
	Author = "Gernot Frenking",
	Title = "{Book Review: Chemical Bonding and Molecular Geometry From Lewis to Electron Densities. By Ronald J. Gillespie and Paul L. A. Popelier}",
	Journal = "Angew. Chem. Int. Ed.",
	Volume = "42",
	Number = "2",
	Pages = "143–147",
	abstract = "(Excerpt) The explanation of molecular geometries in terms of theoretical models is one of the most fundamental concepts in chemistry. Nearly every chemistry textbook devotes an introductory chapter to the question of how the geometrical arrangement of the atoms in a molecule can be rationalized by means of an ordering scheme, the rules of which should be as simple and comprehensive as possible.",
	collection = "philosophy",
	doi = "10.1002/anie.200390069",
	localfile = "philosophy/2003 - Book review: Chemical Bonding and Molecular Geometry.pdf",
	year = 2003
}

@Article{2003-George-Sastry,
	Author = "John George and Nandhibatla V. Sastry",
	Title = "{Densities, dynamic viscosities, speeds of sound, and relative permittivities for water + alkanediols (propane-1,2- and -1,3-diol and butane-1,2-, -1,3-, -1,4-, and -2,3-diol) at different demperatures}",
	Journal = "J. Chem. Eng. Data",
	Volume = "48",
	Pages = "1529–1539",
	cited = "57 (2013-04-29)",
	collection = "molecular dovlation",
	doi = "10.1021/je0340755",
	localfile = "molecular solvation/2003 - Densitiesm dynamics viscosities, speeds of sound, and relative permittivities for water + alkanediols (propane-1,2- and -1.3-diol and butane-1.2-, -1.3-, -1.4-, and -2.3-diol) at different temperatures.pdf",
	year = 2003
}

@InProceedings{2003-Ghemawat-GL,
	Author = "Sanjay Ghemawat and Howard Gobioff and Shun-Tak Leung",
	Title = "{The Google File System}",
	BookTitle = "{Proceedings of the 19th ACM Symposium on Operating Systems Principles}",
	Pages = "20–43",
	Publisher = "ACM",
	collection = "infromatics",
	keywords = "big data",
	localfile = "informatics/2003 - The Google file system.pdf",
	rating = "2",
	read = "2013-06-15",
	year = 2003
}

@Article{2003-Guillot-MALH,
	Author = "Benoit Guillot and Nicolas Muzet and Emilio Artacho and Claude Lecomte and Christan Helsch",
	Title = "{Experimental and theoretical electron density studies in large molecules: {NAD+}, beta-nicotinamide adenine dinucleotide}",
	Journal = "J. Phys. Chem. B",
	Volume = "107",
	Pages = "9109–9121",
	abstract = "NAD+ is the oxidized form of the coenzyme redox pair NAD+/NADH and plays a main role in catalysis of biological processes. Accurate X-ray diffraction data have been collected at 100 K from a crystal of the free acid form of the coenzyme NAD+ with a CCD area detector up to 0.55 Å resolution. A multipole refinement was carried out, and the electron density of the molecule has been analyzed in order to further model its interaction with enzymes. The electron density of NAD+ has also been computed by a DFT (density functional theory) approach. The charge density and electrostatic potential obtained from experiment and theory compare well. There is a very good agreement between the theoretical and experimental charge densities for all the C-C and C-N type connections of the NAD+ molecule; this is less the case for the pyrophosphate region. The experimental electron density lone pairs of the pyrophosphate lateral oxygen atoms are distorted by hydrogen bonds effects. The electrostatic potential has large spatial extensions with highly positive and negative regions, suggesting that NAD+ is likely to interact with proteins mostly by electrostatic interactions.",
	collection = "molecular crystals",
	doi = "10.1021/jp034478b",
	localfile = "molecular crystals/2003 - Experimental and theoretical electron density studies in large molecules: NAD+, beta-nicotinamide adenine dinucleotide.pdf",
	year = 2003
}

@Article{2003-Hesselmann-Jansen,
	Author = "Andreas Heßelmann and Georg Jansen",
	Title = "{Intermolecular dispersion energies from time-dependent density functional theory}",
	Journal = "Chem. Phys. Lett.",
	Volume = "367",
	Pages = "778–784",
	collection = "molecular interactions",
	doi = "10.1016/S0009-2614(02)01796-7",
	localfile = "molecular interactions/2003 - Intermolecular dispersion energies from time-dependent density functional theory.pdf",
	systems = "He2, Ne2, Ar2, NeAr, NeHF, ArHF, dihydrogen dimer, HF dimer, water dimer",
	year = 2003
}

@Article{2003-Hill-FHLSL,
	Author = "Glake Hill and G. Forde and N. Hill and William A. Lester and W. Andrzej Sokalski and Jerzy Leszczyński",
	Title = "{Interaction energies in stacked {DNA} bases? how important are electrostatics?}",
	Journal = "Chem. Phys. Lett.",
	Volume = "381",
	Number = "5-6",
	Pages = "729–732",
	abstract = "For the first time, the physical nature of intermolecular interactions between 10 DNA stacked bases has been examined by an interaction energy decomposition method based on the variation-perturbation theory. The dominant correlation term including dispersion interactions is found to be cancelled to a considerable extent by exchange and delocalization contributions leaving the relatively smaller long range electrostatic contribution as the most important factor determining relative stacking interaction energies. The electrostatic multipole component closely mimics the trend of total interaction energy in all considered systems.",
	collection = "stacking",
	doi = "10.1016/j.cplett.2003.09.076",
	localfile = "molecular stacking/2003 - Interaction energies in stacked DNA bases. How important are electrostatics.pdf",
	year = 2003
}

@Article{2003-Huetz-RG,
	Author = "Philippe Huetz and Christophe Ramseyer and Claude Girardet",
	Title = "{Ab initio study of the influence of conformation on partial charge distribution of dioctadecylamine}",
	Journal = "Chem. Phys. Lett.",
	Volume = "380",
	Number = "3-4",
	Pages = "424–434",
	abstract = "The lipid dioctadecylamine {(DODA)} has been shown to self-organize in plate-like structures in aqueous solution. While in a previous model, we investigated by simulations its mesoscopic collective behaviour, here, we considered atomic partial charge distribution as determined by ab initio quantum chemical computations, and its relationship with different conformations of the {DODA} molecule. After comparison of the charges obtained at different levels of theory on the stretched form of {DODA,} we show that gas phase charges are sufficient to represent what appears to be an intrinsic property of the lipid, independently from the solvent. As the molecule becomes distorted, significant partial charge fluctuations appear along the aliphatic chains.",
	collection = "molecular fragmentation",
	doi = "10.1016/j.cplett.2003.09.059",
	localfile = "molecular fragmentation/2003 - Ab initio study of the influence of conformation on partial charge distribution of dioctadecylamine.pdf",
	year = 2003
}

@Article{2003-Jensen-JRBPKB,
	Author = "Torben R. Jensen and Morten Ø. Jensen and Niels Reitzel and Konstantin Balashev and Gunther H. Peters and KRistian Kjaer and Thomas Bjørnholm",
	Title = "{Water in contact with extended hydrophobic surfaces: direct evidence of weak dewetting}",
	Journal = "Phys. Rev. Lett.",
	Volume = "90",
	Number = "8",
	Pages = "086101",
	cited = "85 (2013-04-29)",
	collection = "interfaces",
	doi = "10.1103/PhysRevLett.90.086101",
	localfile = "interfaces/2003 - Water in contact with extended hydrophobic surfaces: direct evidence of weak dewetting.pdf",
	year = 2003
}

@Article{2003-Jesus-RLR,
	Author = "A. J. Lopes Jesus and Mario T. S. Rosado and M. Luisa P. Leitao and Jose S. Redinha",
	Title = "{Molecular structure of butanediol isomers in gas and liquid states: combination of DFT calculations and infrared spectroscopy studies}",
	Journal = "J. Phys. Chem. A",
	Volume = "107",
	Pages = "391–3897",
	cited = "23 (2013-04-29)",
	collection = "molecular structure",
	doi = "10.1021/jp027123l",
	localfile = "molecular structure/2003 - Molecualr structure of butanediol isomers in gas and liquid states: combination of DFT calculations and infrared spectroscopy studies.pdf",
	year = 2003
}

@Article{2003-Jonscher-JW,
	Author = "Andrew J. Jonscher and Agnieszka Jurlewicz and Karina Weron",
	Title = "{Stochastic schemes of dielectric relaxation in correlated-cluster systems}",
	Journal = "Contemporary Physics",
	Volume = "44",
	Number = "4",
	Pages = "329–339",
	cited = "30 (2013-04-29)",
	collection = "statistics",
	doi = "10.1080/0010751031000077369",
	localfile = "statistics/2003 - Stochastic schemes of dielectric relaxation in correlated-cluster systems.pdf",
	year = 2003
}

@Article{2003-Jurecka-Hobza,
	Author = "Petr Jurečka and Pavel Hobza",
	Title = "{True Stabilization Energies for the Optimal Planar {Hydrogen-Bonded} and Stacked Structures of {Guanine···Cytosine,} {Adenine···Thymine,} and Their 9- and {1-Methyl} Derivatives: Complete Basis Set Calculations at the {MP2} and {CCSD(T)} Levels and Comparison with Experiment}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "125",
	Number = "50",
	Pages = "15608–15613",
	abstract = "Planar H-bonded and stacked structures of guanine(...)cytosine (G(...)C), adenine(...)thymine (A(...)T), 9-methylguanine(...)1-methylcytosine (mG(...)mC), and 9-methyladenine(...)1-methylthymine (mA(...)mT) were optimized at the RI-MP2 level using the TZVPP ([5s3p2d1f/3s2p1d]) basis set. Planar H-bonded structures of G(...)C, mG(...)mC, and A(...)T correspond to the Watson-Crick (WC) arrangement, in contrast to mA(...)mT for which the Hoogsteen (H) structure is found. Stabilization energies for all structures were determined as the sum of the complete basis set limit of MP2 energies and a (DeltaE(CCSD(T)) - DeltaE(MP2)) correction term evaluated with the cc-pVDZ(0.25,0.15) basis set. The complete basis set limit of MP2 energies was determined by two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T and X = T and Q. This procedure is required since the convergency of the MP2 interaction energy for the present complexes is rather slow, and it is thus important to include the extrapolation to the complete basis set limit. For the MP2/aug-cc-pVQZ level of theory, stabilization energies for all complexes studied are already very close to the complete basis set limit. The much cheaper D–>T extrapolation provided a complete basis set limit close (by less than 0.7 kcal/mol) to the more accurate T–>Q term, and the D–>T extrapolation can be recommended for evaluation of complete basis set limits of more extended complexes (e.g. larger motifs of DNA). The convergency of the (DeltaE(CCSD(T)) - DeltaE(MP2)) term is known to be faster than that of the MP2 or CCSD(T) correlation energy itself, and the cc-pVDZ(0.25,0.15) basis set provides reasonable values for planar H-bonded as well as stacked structures. Inclusion of the CCSD(T) correction is essential for obtaining reliable relative values for planar H-bonding and stacking interactions; neglecting the CCSD(T) correction results in very considerable errors between 2.5 and 3.4 kcal/mol. Final stabilization energies (kcal/mol) for the base pairs studied are very substantial (A(...)T WC, 15.4; mA(...)mT H, 16.3; A(...)T stacked, 11.6; mA(...)mT stacked, 13.1; G(...)C WC, 28.8; mG(...)mC WC, 28.5; G(...)C stacked, 16.9; mG(...)mC stacked, 18.0), much larger than published previously. On the basis of comparison with experimental data, we conclude that our values represent the lower boundary of the true stabilization energies. On the basis of error analysis, we expect the present H-bonding energies to be fairly close to the true values, while stacked energies are still expected to be about 10\% too low. The stacking energy for the mG(...)mC pair is considerably lower than the respective H-bonding energy, but it is larger than the mA(...)mT H-bonding energy. This conclusion could significantly change the present view on the importance of specific H-bonding interactions and nonspecific stacking interactions in nature, for instance, in DNA. Present stabilization energies for H-bonding and stacking energies represent the most accurate and reliable values and can be considered as new reference data.",
	collection = "stacking",
	doi = "10.1021/ja036611j",
	localfile = "molecular stacking/2003 - True stabilization energies for the optimal planar hydrogen-bonded and stacked structures: complete basis set calcualtions aat teh MP2 and CCSD(T) levels and comparison with experiment.pdf",
	shorttitle = "True Stabilization Energies for the Optimal Planar {Hydrogen-Bonded} and Stacked Structures of {Guanine···Cytosine,} {Adenine···Thymine,} and Their 9- and {1-Methyl} Derivatives",
	year = 2003
}

@Article{2003-Lee-SB,
	Author = "Jae Youn Lee and Zhenyu Shou and Anna C. Balazs",
	Title = "{Predicting the morphologies of confined copolymer-nanoparticle mixtures}",
	Journal = "Macromolecules",
	Volume = "36",
	Pages = "7730–7739",
	abstract = "To isolate the factors that control the structure of nanocomposite thin films, we develop a computational model and scaling theory to investigate the behavior of diblock/nanoparticle mixtures that are confined between two hard walls. We find that in such restricted geometries a polymer-induced depletion attraction drives the particles to these walls. If the particles are chemically distinct from the walls, they will effectively modify the chemical nature of these substrates. This change in chemistry, in turn, affects the polymer-wall interactions and consequently the structure of the film. We illustrate this point by considering mixtures of particles and symmetric diblocks and show that the confining walls can be exploited to promote the self-assembly of the system into particle nanowires that extend throughout the films and are separated by nanoscale stripes of polymer domains. Such films constitute vital components in the fabrication of nanoscale devices. Furthermore, the results point to a novel technique for modifying the chemical nature of coatings and films entirely through self-assembly. Since this technique relies on entropic effects, it constitutes a fairly robust method that can be applied more generally than approaches that rely primarily on chemistry-specific enthalpic effects.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma034765d",
	keywords = "alignment; block copolymers; nanoparticle distribution; nanospheres; polymer nanocomposites; thin films",
	localfile = "block copolymer nanocomposites/2003 - Predicting morphologies of confined copolymer-nanoparticle mixtures.pdf",
	methods = "SCFT/DFT",
	year = 2003
}

@Article{2003-Lee-SB-1,
	Author = "Jae Youn Lee and Zhenyu Shou and Anna C. Balazs",
	Title = "{Modeling the self-assembly of copolymer-nanoparticle mixtures confined between solid surfaces}",
	Journal = "Phys. Rev. Lett.",
	Volume = "91",
	Number = "3",
	Pages = "136103",
	Note = "Demonstrates BCP lamellae between two hard walls with nonselective cubic particles at interfaces.",
	abstract = "Using numerical calculations, we undertake the ﬁrst morphological studies of mixtures of AB diblocks and nanoparticles that are conﬁned between two hard walls. A complex interplay of entropic and enthalpic interactions drives the nonselective particles to localize at the hard walls and A=B interfaces, causing the mixture to spontaneously self-assemble into particle-decorated lamellae that are oriented perpendicular to the surfaces. The ﬁlm reveals a periodic array of particle ‘‘nanowires’’ that are separated by the nanoscale polymer domains, yielding a vital material for nanodevice fabrication.",
	collection = "block copolymer nanocomposites",
	doi = "10.1103/PhysRevLett.91.136103",
	keywords = "alignment; block copolymers; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2003 - Modeling the self-assembly of copolymer-nanoparticle mixtures confined between solid surfaces.pdf",
	methods = "SCFT/DFT",
	year = 2003
}

@Article{2003-Legeza-RH,
	Author = "Ö. Legeza and J. Röder and B. A. Hess",
	Title = "{{QC-DMRG} - study of the ionic–neutral curve crossing of {LiF}}",
	Journal = "Mol. Phys.",
	Volume = "101",
	Number = "13",
	Pages = "2019",
	collection = "molecular reactions",
	doi = "10.1080/0026897031000155625",
	keywords = "reactions",
	localfile = "molecular reactions/2003 - QC-DMRG study of the ionic-neutral curve crossing of LiF.pdf",
	methods = "QC-DMRG",
	systems = "LiF",
	year = 2003
}

@Article{2003-Liem-Popelier,
	Author = "S. Y. Liem and Paul L. A. Popelier",
	Title = "{High-rank quantum topological electrostatic potential: Molecular dynamics simulation of liquid hydrogen fluoride}",
	Journal = "J. Chem. Phys.",
	Volume = "119",
	Number = "8",
	Pages = "4560–4566",
	collection = "molecular electrostatics",
	doi = "10.1063/1.1593012",
	localfile = "molecular electrostatics/2003 - High-rank quantum topological electrostatic potential: molecular dynamics simulation of liquid hydrogen fluoride.pdf",
	shorttitle = "High-rank quantum topological electrostatic potential",
	year = 2003
}

@Article{2003-Matta,
	Author = "Chérif F. Matta",
	Title = "{Application of the quantum theory of atoms in molecules to selected physico-chemical and biophysical problems: Focus on correlation with experiment}",
	Journal = "J. Comp. Chem.",
	Volume = "24",
	Number = "4",
	Pages = "453–463",
	abstract = "This article reviews how the quantum theory of atoms in molecules {(QTAIM)} can be used to predict experimental physico-chemical properties of molecules of biologic interest: the amino acids, the polycyclic aromatic hydrocarbons {(PAH),} and the opiates, for example, morphine and {PEO.} The predicted experimental properties are as diverse as the partial molar volumes, the free energies of hydration, the second code-letter in the genetic code, the resonance energies, and the proton spin-spin coupling constants. Recent examples of the utilization of {QTAIM} to construct excellent statistical models (with squared correlation coefficients (r2) \> 0.9) correlating properties of the electron density and of the pair density to experiment are reviewed. Some new results on the solvent effects on electron delocalization are also presented.",
	collection = "protein amino acids",
	doi = "10.1002/jcc.10208",
	localfile = "protein amino acids/2003 - Application of the quantum theory of atoms in molecules to selected physico-chemical and biophysical problems: focus on correlation with experiment.pdf",
	methods = "QTAIM",
	year = 2003
}

@Article{2003-Matta-Bader,
	Author = "Chérif F. Matta and Richard F. W. Bader",
	Title = "{{Atoms-in-molecules study of the genetically encoded amino acids. {III.} Bond and atomic properties and their correlations with experiment including mutation-induced changes in protein stability and genetic coding}34 (}",
	Journal = "Proteins",
	Volume = "52",
	Number = "3",
	Pages = "360–399",
	abstract = "This article presents a study of the molecular charge distributions of the genetically encoded amino acids {(AA),} one that builds on the previous determination of their equilibrium geometries and the demonstrated transferability of their common geometrical parameters. The properties of the charge distributions are characterized and given quantitative expression in terms of the bond and atomic properties determined within the quantum theory of atoms-in-molecules {(QTAIM)} that defines atoms and bonds in terms of the observable charge density. The properties so defined are demonstrated to be remarkably transferable, a reflection of the underlying transferability of the charge distributions of the main chain and other groups common to the {AA.} The use of the atomic properties in obtaining an understanding of the biological functions of the {AA,} whether free or bound in a polypeptide, is demonstrated by the excellent statistical correlations they yield with experimental physicochemical properties. A property of the {AA} side chains of particular importance is the charge separation index {(CSI),} a quantity previously defined as the sum of the magnitudes of the atomic charges and which measures the degree of separation of positive and negative charges in the side chain of interest. The {CSI} values provide a correlation with the measured free energies of transfer of capped side chain analogues, from the vapor phase to aqueous solution, yielding a linear regression equation with r2 = 0.94. The atomic volume is defined by the van der Waals isodensity surface and it, together with the {CSI,} which accounts for the electrostriction of the solvent, yield a linear regression (r2 = 0.98) with the measured partial molar volumes of the {AAs.} The changes in free energies of transfer from octanol to water upon interchanging 153 pairs of {AAs} and from cyclohexane to water upon interchanging 190 pairs of {AAs,} were modeled using only three calculated parameters (representing electrostatic and volume contributions) yielding linear regressions with r2 values of 0.78 and 0.89, respectively. These results are a prelude to the single-site mutation-induced changes in the stabilities of two typical proteins: ubiquitin and staphylococcal nuclease. Strong quadratic correlations (r2 sim 0.9) were obtained between {DeltaCSI} upon mutation and each of the two terms {DeltaDeltaH} and {TDeltaDeltaS} taken from recent and accurate differential scanning calorimetry experiments on ubiquitin. When the two terms are summed to yield {DeltaDeltaG,} the quadratic terms nearly cancel, and the result is a simple linear fit between {DeltaDeltaG} and {DeltaCSI} with r2 = 0.88. As another example, the change in the stability of staphylococcal nuclease upon mutation has been fitted linearly (r2 = 0.83) to the sum of a {DeltaCSI} term and a term representing the change in the van der Waals volume of the side chains upon mutation. The suggested correlation of the polarity of the side chain with the second letter of the {AA} triplet genetic codon is given concrete expression in a classification of the side chains in terms of their {CSI} values and their group dipole moments. For example, all amino acids with a pyrimidine base as their second letter in {mRNA} possess side-chain {CSI} le 2.8 (with the exception of Cys), whereas all those with {CSI} \> 2.8 possess an purine base. The article concludes with two proposals for measuring and predicting molecular complementarity: van der Waals complementarity expressed in terms of the van der Waals isodensity surface and Lewis complementarity expressed in terms of the local charge concentrations and depletions defined by the topology of the Laplacian of the electron density. A display of the experimentally accessible Laplacian distribution for a folded protein would offer a clear picture of the operation of the ldquostereochemical coderdquo proposed as the determinant in the folding process.",
	collection = "protein amino acids",
	doi = "10.1002/prot.10414",
	localfile = "protein amino acids/2003 - AIM study of the genetically encoded amino acids. III. Bond and atomic properties and their correlations with experiment including mutation-induced changes in protein stability and genetic coding.pdf",
	year = 2003
}

@Article{2003-McCauliffe-Wozniacka,
	Author = "Daniel P. MacCauliffe and Anna Woźniacka",
	Title = "{52 kD Ro/SS-A localizes to punctuate structures in the cytoplasm of epithelial cells}",
	Journal = "Cell. Mol. Biol. Lett.",
	Volume = "8",
	Pages = "133–140",
	collection = "cells",
	localfile = "cells/2003 - 52 kD Ro-SS-A localizes to punctuate structures in the cytoplasm of epithelial cells.pdf",
	year = 2003
}

@Article{2003-McDowell,
	Author = "Sean A. C. McDowell",
	Title = "{A computational study of the LiH dimer}",
	Journal = "J. Comp. Chem.",
	Volume = "24",
	Pages = "1201–1207",
	abstract = "A theoretical study of the properties of the linear LiH dimer was undertaken. In this dimer, an unusual type of hydrogen bonding (termed “inverse” hydrogen bonding by some authors), which involves the hydrogen bonded molecule acting as an electron donor (rather than as a proton donor), is exhibited. The optimized geometry, dipole moment, interaction energy, atomic charges, harmonic vibrational frequencies, and frequency shifts for the dimer are computed at the SCF, MP2, and QCISD levels of theory using mainly a 6-31 G(d,p) basis set. We also examined the relative stability of the mono-deuterated isotopomers of linear (LiH)2, i.e., Li—H . . . Li—D and Li—D . . . Li—H. Analysis of the normal vibrational modes, changes in the partial atomic charges, and changes in the vibrational frequencies of LiH on complexation were used to gain insight into the bonding and properties of the linear LiH dimer and its isotopomers.",
	collection = "hydrogen bonding",
	doi = "10.1002/jcc.10281",
	localfile = "hydrogen bonding/2003 - A computational study of the LiH dimer.pdf",
	year = 2003
}

@Article{2003-McKinney-Cravatt,
	Author = "Michele K. McKinney and Benjamin F. Cravatt",
	Title = "{Evidence for distinct roles in catalysis for residues of the serine-serine-lysine catalytic triad of fatty acid amide hydrolase}",
	Journal = "J. Biol. Chem.",
	Volume = "278",
	Number = "39",
	Pages = "37393–37399",
	abstract = "Fatty acid amide hydrolase {(FAAH)} is a mammalian amidase signature enzyme that inactivates neuromodulatory fatty acid amides, including the endogenous cannabinoid anandamide and the sleep-inducing substance oleamide. The recent determination of the three-dimensional structures of {FAAH} and two distantly related bacterial amidase signature enzymes indicates that these enzymes employ an unusual serine-serine-lysine triad for catalysis {(Ser-241/Ser-217/Lys-142} in {FAAH).} Mutagenesis of each of the triad residues in {FAAH} has been shown to severely reduce amidase activity; however, how these residues contribute, both individually and in cooperation, to catalysis remains unclear. Here, through a combination of site-directed mutagenesis, enzyme kinetics, and chemical labeling experiments, we provide evidence that each {FAAH} triad residue plays a distinct role in catalysis. In particular, the mutation of Lys-142 to alanine indicates that this residue functions as both a base involved in the activation of the Ser-241 nucleophile and an acid that participates in the protonation of the substrate leaving group. This latter property appears to support the unusual ability of {FAAH} to hydrolyze amides and esters at equivalent rates. Interestingly, although structural evidence indicates that the impact of Lys-142 on catalysis probably occurs through the bridging Ser-217, the mutation of this latter residue to alanine impaired catalytic activity but left the amide/ester hydrolysis ratios of {FAAH} intact. Collectively, these findings suggest that {FAAH} possesses a specialized active site structure dedicated to a mechanism for competitive amide and ester hydrolysis where nucleophile attack and leaving group protonation occur in a coordinated manner dependent on Lys-142.",
	collection = "enzymes",
	doi = "10.1074/jbc.M303922200",
	keywords = "active site",
	localfile = "enzymes/2003 - Evidence for distinct roles in catalysis for residues of the serine-serine-lysine catalytic triad of fatty acid amide hydrolase.pdf",
	year = 2003
}

@Article{2003-Metropoulos-PM,
	Author = "Aristophanes Metropoulos and Aristotle Papakondylis and Aristides Mavridis",
	Title = "{Ab initio investigation of the ground state properties of {PO,} {PO[sup} +], and {PO[sup} -]}",
	Journal = "J. Chem. Phys.",
	Volume = "119",
	Number = "12",
	Pages = "5981–5987",
	collection = "molecular reactions",
	doi = "10.1063/1.1599341",
	localfile = "molecular reactions/2003 - Ab initio investigation of the ground state properties of PO, PO+, and PO-.pdf",
	year = 2003
}

@Article{2003-Meyer-CD,
	Author = "Emmanuel A. Meyer and Ronald K. Castellano and François Diederich",
	Title = "{Interactions with Aromatic Rings in Chemical and Biological Recognition}",
	Journal = "Angew. Chem. Int. Ed.",
	Volume = "42",
	Number = "11",
	Pages = "1210–1250",
	abstract = "Intermolecular interactions involving aromatic rings are key processes in both chemical and biological recognition. Their understanding is essential for rational drug design and lead optimization in medicinal chemistry. Different approaches - biological studies, molecular recognition studies with artificial receptors, crystallographic database mining, gas-phase studies, and theoretical calculations - are pursued to generate a profound understanding of the structural and energetic parameters of individual recognition modes involving aromatic rings. This review attempts to combine and summarize the knowledge gained from these investigations. The review focuses mainly on examples with biological relevance since one of its aims it to enhance the knowledge of molecular recognition forces that is essential for drug development.",
	collection = "stacking",
	doi = "10.1002/anie.200390319",
	localfile = "molecular stacking/2003 - Interactions with aromatic rings in chemical and biological recognition.pdf",
	year = 2003
}

@Article{2003-Mierzwicki-Latajka,
	Author = "Krzysztof Mierzwicki and Zdzisław Latajka",
	Title = "{Basis set superposition error in N-body clusters}",
	Journal = "Chem. Phys. Lett.",
	Volume = "380",
	Pages = "654–664",
	abstract = "We present a new scheme for calculating the basis set superposition error (BSSE) in N-body clusters. It is based on the assumption that each n-body term can be expressed as a sum of only two-body contributions. The conventional Boys-Bernardi method can be used thus for calculating BSSE-corrected energy terms. The scheme is illustrated by some calculations on the hydrogen fluoride trimers and tetramers. The results are compared to the ones obtained with the site-site function counterpoise (SSFC), the hierarchical (Valiron-Mayer) function counterpoise (VMFC), the pairwise additive function counterpoise (PAFC), and the successive reaction counterpoise (SRCP) schemes. (C) 2003 Published by Elsevier B.V. C1 Univ Wroclaw, Fac Chem, PL-50383 Wroclaw, Poland.",
	collection = "basis set superposition",
	doi = "10.1016/j.cplett.2003.09.038",
	keywords = "basis set superposition error",
	localfile = "basis set superposition/2003 - Basis set superposition error in N-nody clusters.pdf",
	year = 2003
}

@Article{2003-Misquitta-JS,
	Author = "Alston J. Misquitta and Bogumił Jeziorski and Krzysztof Szalewicz",
	Title = "{Dispersion energy from density-functional theory description of monomers}",
	Journal = "Phys. Rev. Lett.",
	Volume = "91",
	Number = "3",
	Pages = "033201",
	collection = "molecular interactions",
	doi = "10.1103/PhysRevLett.91.033201",
	localfile = "molecular interactions/2003 - Dispersion energy from density-functional theory description of monomers.pdf",
	year = 2003
}

@Article{2003-Nakatani-HMHS,
	Author = "Kazuhiko Nakatani and Souta Horie and Tadashi Murase and Shinya Hagihara and Isao Saito",
	Title = "{Assessment of the sequence dependency for the binding of 2-aminonaphthyridine to the guanine bulge}",
	Journal = "Bioorg. Med. Chem.",
	Volume = "11",
	Number = "10",
	Pages = "2347–2353",
	abstract = "We have studied the sequence dependent binding of 2-amino-1,8-naphthyridine derivative 1 to a single guanine bulge. The free energy changes for the binding to a guanine bulge with different sequence contexts {(5'X\_Y3'/3'X'GY'5')} were determined by a curve fitting of the thermal denaturation profile of {DNA} in the presence and absence of 1. The data showed that (i) the binding of 1 to a guanine bulge is stronger for those flanking the {G-C} base pair than {A-T} base pair, (ii) the guanine 3' side to 1 in the complex is especially effective for the complex stabilization, and (iii) the increase of Tm in the presence of 1 is not a good estimate for the sequence dependent binding. The most efficient 1-binding was observed for the sequence of {G\_G/CGC.} Molecular modeling simulations suggested that stacking interaction between the 3' side guanine and 1 is the molecular basis for the strong binding to {G\_G/CGC.}",
	collection = "nucleic acid intercalation",
	doi = "10.1016/S0968-0896(03)00026-9",
	localfile = "nucleic acid intercalation/2003 - Assessment of the sequence dependency for the binding of 2-aminonapththyridine to the guanine bulge.pdf",
	year = 2003
}

@Article{2003-Perez-Casas-HC,
	Author = "Silvia Pérez-Casas and Jesús Hernández-Trujillo and Miguel Costas",
	Title = "{Experimental and theoretical study of aromatic-aromatic interactions. {A}ssociation enthalpies and central and distributed multipole electric moments analysis}",
	Journal = "J. Phys. Chem. B",
	Volume = "107",
	Number = "17",
	Pages = "4167–4174",
	abstract = "Aromatic-aromatic interactions are studied experimentally through heat capacity measurements that, with the aid of an association model, provide an estimate of the association enthalpy of the aromatic-aromatic complexes formed in solution. These enthalpies are empirically correlated with the product of the quadrupole moments of the molecules involved. The compounds used in this work are hexafluorobenzene (HFB), pentafluorobenzene (PFB), triflourobenzene (TFB), flourobenzene, (FB), benzene (BEN), toluene (TOL), naphthalene (NAP), and 1-methylnaphthalene (MEN). The 10 pairs studied are HFB-MEN, HFB-BEN, HFB-TOL, NAP-HFB, PFB-MEN, PFB-BEN, HFB-FB, BEN-MEN, FB-MEN, and TFB-MEN. The electrostatic interaction between the molecules forming the 10 aromatic-aromatic pairs is calculated expressing their charge distributions in terms of both central and distributed multipole electric moments. It is concluded that the changes in association enthalpies of aromatic-aromatic complexes can be explained by the electrostatic contribution to the interaction energy.",
	collection = "stacking",
	doi = "10.1021/jp0225828",
	localfile = "molecular stacking/2003 - Experimental and theoretical study of aromatic-aromatic interactions. Association enthalpies and central and distributed multipole electric moments analysis.pdf",
	year = 2003
}

@Article{2003-Piomelli,
	Author = "Daniele Piomelli",
	Title = "{The molecular logic of endocannabinoid singalling}",
	Journal = "Nature Reviews",
	Volume = "4",
	Pages = "873",
	abstract = "The endocannabinoids are a family of lipid messengers that engage the cell surface receptors that are targeted by ∆9-tetrahydrocannabinol, the active principle in marijuana (Cannabis). They are made on demand through cleavage of membrane precursors and are involved in various short-range signalling processes. In the brain, they combine with CB1 cannabinoid receptors on axon terminals to regulate ion channel activity and neurotransmitter release. Their ability to modulate synaptic efficacy has a wide range of functional consequences and provides unique therapeutic possibilities.",
	collection = "molecular signaling",
	localfile = "molecular signaling/2003 - The molecular logic of endocannabinoid signaling.pdf",
	year = 2003
}

@Article{2003-Popelier-Rafat,
	Author = "Paul L. A. Popelier and Michel Rafat",
	Title = "{The electrostatic potential generated by topological atoms: a continuous multipole method leading to larger convergence regions}",
	Journal = "Chem. Phys. Lett.",
	Volume = "376",
	Number = "1-2",
	Pages = "148–153",
	abstract = "The electrostatic potential generated by an atom in a molecule can be conveniently expressed by traditional multipole expansions. The disadvantage of such expansions is that they introduce a divergence sphere within which the expansion diverges. Because of their finite size, atoms defined according to quantum chemical topology (QCT) yield a small divergence sphere. However the introduction of an alternative continuous multipole expansion reduces the divergence region even further. The new method allows the electrostatic potential to be evaluated accurately at shortrange, which is illustrated for a pair of simple molecules.",
	cited = "1 (2005-05-24)",
	collection = "molecular electrostatics",
	doi = "10.1016/S0009-2614(03)00957-6",
	localfile = "molecular electrostatics/2003 - The electrostatic potential generated by topological atoms: a continuous multipole method leading to larger convergence regions.pdf",
	year = 2003
}

@Article{2003-Ramirez-TCS,
	Author = "F. Javier Ramirez and Inaki Tunon and Juan A. Collado and Estanislao Silla",
	Title = "{Structural and vibrational study of the tautomerism of histamine free-base in solution}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "125",
	Pages = "2328–2340",
	abstract = "Infrared and Raman spectroscopy in H2O and D2O and quantum Density Functional calculations were used to determine the structure of histamine free-base in aqueous solution. A quantum mechanical study of the tautomeric equilibrium of histamine free-base in solution was performed at the 6-311G** level. Electronic correlation energies were included by using the hybrid functional B3LYP. The solvent was simulated as a continuum characterized by a dielectric constant, and the quantum system (solute) was placed in an ellipsoidal cavity. Solute-solvent electrostatic interaction was calculated by means a multipolar moment expansion introduced in the Hamiltonian. Four relevant histamine conformations were optimized by allowing all the geometrical parameters to vary independently, which involved both the gauche-trans and the N3H-N1H tautomerisms. The calculated free energies predicted N3H-gauche as the most stable one of histamine free-base in solution. The order of stability is here completely altered with respect to previous results in gas phase, which presented the N1H-gauche conformer as the most stable structure. Our results also differ from previous Monte Carlo simulations, which obtained the N3H-trans conformer as the most stable in solution, although in this case, the histamine structures were kept frozen to the gas-phase geometry. Vibrational spectroscopy results support theoretical ones. Quadratic force fields for the four histamine conformers were achieved under the same calculation methodology. Previously, a general assignment of the infrared and Raman spectra of histamine free-base was proposed for solutions in both natural and heavy water. This allowed us to compare the experimental set of both wavenumbers and infrared intensities with the calculated ones. The lowest quadratic mean wavenumber deviation was obtained for the N3H-gauche conformer, in agreement with the free-energy calculations. Calculated infrared intensities were also compared to the experimental intensities, supporting this conformer as the relevant structure of histamine free-base in solution. It was then selected for a complete vibrational dynamics calculation, starting with a low-level scaling procedure to fit the set of calculated wavenumbers to the experimental values. The results were presented in terms of quadratic force constants, potential energy distribution, and normal modes.",
	collection = "molecular signaling",
	doi = "10.1021/ja027103x",
	localfile = "molecular signaling/2003 - Structural and vibrational study of the tautomerism of histamine free-base in solution.pdf",
	year = 2003
}

@Article{2003-Ray-Okamoto,
	Author = "Suprakas Sinha Ray and Masami Okamoto",
	Title = "{Polymer/layered silicate nanocomposites: a review from preparation to processing}",
	Journal = "Prog. Polym. Sci.",
	Volume = "28",
	Pages = "1539–1641",
	abstract = "A review is given of the academic and industrial aspects of the preparation, characterization, materials properties, crystallization behavior, melt rheology, and processing of polymer/layered silicate nanocomposites. These materials are ttracting considerable interest in polymer science research. Hectorite and montmorillonite are among the most commonly used smectite-type layered silicates for the preparation of nanocomposites. Smectites are a valuable mineral class for industrial applications because of their high cation exchange capacities, surface area, surface reactivity, adsorptive properties, and, in the case of hectorite, high viscosity and transparency in solution. In their pristine form they are hydrophilic in nature, and this property makes them very difﬁcult to disperse into a polymer matrix. The most common way to remove this difﬁculty is to replace interlayer cations with quarternized ammonium or phosphonium cations, preferably with long alkyl chains.",
	collection = "polymer nanocomposites",
	doi = "10.1016/j.progpolymsci.2003.08.002",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2003 - Polymer layered silicate nanocomposites: a review from preparation to processing.pdf",
	type = "Review",
	year = 2003
}

@Article{2003-Rosu-PGALMRM,
	Author = "Frederic Rosu and Edwin De Pauw and Lionel Guittat and Patrizia Alberti and Laurent Lacroix and Patrick Mailliet and {Jean-François} Riou and {Jean-Louis} Mergny",
	Title = "{Selective Interaction of Ethidium Derivatives with Quadruplexes: An Equilibrium Dialysis and Electrospray Ionization Mass Spectrometry Analysis†}",
	Journal = "Biochemistry",
	Volume = "42",
	Number = "35",
	Pages = "10361–10371",
	abstract = "The telomeric G-rich single-stranded {DNA} can adopt in vitro an intramolecular quadruplex structure, which has been shown to directly inhibit telomerase activity. The reactivation of this enzyme in immortalized and most cancer cells suggests that telomerase is a relevant target in oncology, and telomerase inhibitors have been proposed as new potential anticancer agents. In this paper, we have analyzed the selectivity of four ethidium derivatives and ethidium itself toward different G-quadruplex species, with electrospray mass spectrometry and competitive equilibrium dialysis and evaluated their inhibitory properties against telomerase. A selectivity profile may be obtained through electrospray ionization mass spectrometry {(ESI-MS),} which is in fair agreement with competitive equilibrium dialysis data. It also provides unambiguous data on the number of binding sites per nucleic acid (maximal number of two ethidium derivatives per quadruplex, in agreement with external stacking). Our experiments also demonstrate that one compound (4) is the most active and selective G-quadruplex ligand within this series and the most selective telomerase inhibitor in a modified {TRAP-G4} assay.",
	collection = "nucleic acid drugs",
	doi = "10.1021/bi034531m",
	localfile = "nucleic acid drugs/2003 - Selective interaction of ethidium derivatives with quadruplexes: an equilibrium dialysis and electrospray ionization mass spectrometry analysis.pdf",
	shorttitle = "Selective Interaction of Ethidium Derivatives with Quadruplexes",
	year = 2003
}

@Article{2003-Sanishvili-YLSEDLTASJE,
	Author = "Ruslan Sanishvili and Alexander F. Yakunin and Roman A. Laskowski and Tatiana Skarina and Elena Evdokimova and Amanda Doherty-Kirby and Gilles A. Lajoie and Janet M. Thornton and Cheryl H. Arrowsmith and Alexei Savchenko and Andrzej Joachimiak and Aled M. Edwards",
	Title = "{Integrating structure, bioinformatics, and enzymology to discover function}",
	Journal = "J. Biol. Chem.",
	Volume = "278",
	Number = "28",
	Pages = "26039–26045",
	Note = "Applies an active site template search method in a function discovery pipeline.",
	collection = "enzymes",
	doi = "10.1074/jbc.M303867200",
	localfile = "enzymes/2003 - Integrating structure, bioinformatics, and enzymology to discover function.pdf",
	rating = "2",
	read = "2013-09-17",
	year = 2003
}

@Article{2003-Schmidt-Malwitz,
	Author = "Gudrun Schmidt and Matthew M. Malwitz",
	Title = "{Properties of polymer–nanoparticle composites}",
	Journal = "Curr. Op. Coll. Int. Sci.",
	Volume = "8",
	Pages = "103–108",
	abstract = "An overview of properties of polymer–nanoparticle composites in bulk and in solution is presented along with a review of work performed during the last 3 years. The review is particularly focused on organic–inorganic materials such as polymer–nanospheres, tubes, rods, fibers and nanoplatelets. Fundamental studies on flow-induced structures in polymer–particle composites are emphasized. This relatively new area demands sophisticated experiments to augment pragmatic knowledge necessary to support theoretical descriptions of composite structures and properties. The complexity of this area guarantees that this will remain an active field for some time to come.",
	collection = "polymer nanocomposites",
	doi = "10.1016/S1359-0294",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2003 - Properties of polymer-nanoparticle composites.pdf",
	type = "Review",
	year = 2003
}

@Article{2003-Starr-DG,
	Author = "Francis W. Starr and Jack F. Douglas and Sharon C. Glotzer",
	Title = "{Origin of particle clustering in a simulated polymer nanocomposite and its impact on rheology}",
	Journal = "J. Chem. Phys.",
	Volume = "119",
	Number = "3",
	Pages = "1777–1788",
	collection = "polymer nanocomposites",
	doi = "10.1063/1.1580099",
	localfile = "polymer nanocomposites/2003 - Origins of particle clustering in a simulated polymer nanocomposite and its impact on rheology.pdf",
	year = 2003
}

@Article{2003-Steitz-GHKKSSF,
	Author = "Roland Steitz and Thomas Gutberlet and Thomas Hauss and Beate Klosgen and Rumen Krastev and Sebastian Schemmel and Adam C. Simonsen and Gerhard H. Findenegg",
	Title = "{Nanobubbles and their precursor layer at the interface of water against a hydrophobic substrate}",
	Journal = "Langmuir",
	Volume = "19",
	Pages = "2409–2418",
	cited = "208 (2013-04-29)",
	collection = "interfaces",
	doi = "10.1021/la026731p",
	localfile = "interfaces/2003 - Nanobubbles and their precursor layer at the interface of water against a hydrophobic substrate.pdf",
	year = 2003
}

@Article{2003-Toczylowski-Cybulski,
	Author = "Rafał R. Toczyłowski and Sławomir M. Cybulski",
	Title = "{An Analysis of the Interactions between Nucleic Acid Bases: {Hydrogen-Bonded} Base Pairs}",
	Journal = "J. Phys. Chem. A",
	Volume = "107",
	Number = "3",
	Pages = "418–426",
	abstract = "Thirty-two nucleic acid hydrogen-bonded base pairs have been examined using second-order {Møller–Plesset} perturbation theory {(MP2)} and the {6-31G*(0.25)} and modified {aug-cc-pVDZ} basis sets. Complexes of Cs symmetry have been constructed from rigid monomers which allowed us to use a compact parametrization of their geometry based on the center of mass separation and Euler angles. The dependence of the interaction energy and its components on small geometrical modifications around the minima have been examined. The electrostatic and the exchange energies have been found to be the most important components of the overall interaction energy, although the dispersion and the induction energies also play important roles. The exchange energy, while typically not the largest in magnitude at the minima, is the most anisotropic component for rotations of the monomers in the plane of the complex. The analysis of the electron-correlated components reveals that the effect of the attractive dispersion energy is to a large degree canceled out by the repulsive correlation correction to the exchange energy.",
	collection = "nucleic acid bases",
	doi = "10.1021/jp021805r",
	localfile = "nucleic acid bases/2003 - An analysis of the interactions between nucleic acid bases: hydrogen-bonded base pairs.pdf",
	shorttitle = "An Analysis of the Interactions between Nucleic Acid Bases",
	year = 2003
}

@Article{2003-Vardevanyan-APDK,
	Author = "P. O. Vardevanyan and A. P. Antonyan and M. A. Parsadanyan and H. G. Davtyan and A. T. Karapetyan",
	Title = "{The binding of ethidium bromide with {DNA}:
interaction with single- and double-stranded
structures}",
	Journal = "Exp. Mol. Med.",
	Volume = "35",
	Number = "6",
	Pages = "527–533",
	abstract = "The pH-induced helix-coil transition of DNA and its complexes with EtBr is carried out at acidic pH in a wide interval of change of concentration ratio of EtBr/DNA. The binding isotherms of EtBr on double and single-stranded DNA at pH = 7.0 and pH = 3.0 (t = 25degreesC) are obtained by absorption and fluorimetric methods. Binding constants (K) and number of bases (n), corresponding to one binding site were determined. Non fluorescent “strong” complex with ds-DNA at pH = 7.0 and t = 25degreesC as well as “strong” and “weak” complexes with ss-DNA at pH = 3.0 and t = 25degreesC are revealed.",
	collection = "nucleic acid intercalation",
	localfile = "nucleic acid intercalation/2003 - The binding of ethidium bromide with DNA.pdf",
	year = 2003
}

@Article{2003-Wang-NP,
	Author = "Qiang Wang and Paul F. Nealey and Juan J. {de Pablo}",
	Title = "{Behavior of single nanoparticle/homopolymer chain in ordered structures of diblock copolymers}",
	Journal = "J. Chem. Phys.",
	Volume = "118",
	Number = "24",
	Pages = "11278–11285",
	Note = "Observes the positioning of a single particle and a single homopolymer chain in diclobk BCP structures.",
	abstract = "We have performed Monte Carlo simulations to study the behavior of a single nanoparticle and a single homopolymer chain in ordered structures of diblock copolymers. Our results show that the microphase-separated copolymers can be used to position nanoparticles or homopolymers according to their interactions with the two blocks. This is consistent with recent experimental observations. We also observe that, while short neutral homopolymers segregate at the A–B interfaces, longer neutral homopolymers exhibit an apparent preference for the cylinders over the matrix, mainly due to geometrical considerations associated with the curvature of A–B interfaces.",
	collection = "block copolymer nanocomposites",
	doi = "10.1063/1.1575207",
	keywords = "block copolymers; nanoparticle distribution; nanospheres; polymer blends; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2003 - Behavior of single nanoparticle or homopolymer chain in ordered structures of diblock copolymers.pdf",
	methods = "MC",
	year = 2003
}

@Article{2003-Whitehead-BSR,
	Author = "Christpoher E. Whitehead and Curt M. Breneman and Narayanasami Sukumar and M. D. Ryan",
	Title = "{Transferable atom equivalent multicentered multipole expansion method}",
	Journal = "J. Comp. Chem.",
	Volume = "24",
	Pages = "512–529",
	abstract = "The transferability of atomic and functional group properties is an implicit concept in chemistry. The work presented here describes the use of Transferable Atom Equivalents (TAE) to represent molecular electrostatic potential ﬁelds through the use of integrated atomic multipole moments that are associated with each TAE atom type used in the reconstruction. TAE molecular surface distributions of electrostatic potentials are compared with analytical ab initio and empirical (Gasteiger) partial charge reference models for several conformations of test peptides. Surface electrostatic potential distributions computed using TAE multipole representations were found to converge at the octopole level, with incremental improvement observed when hexadecapoles were included. Molecular electrostatic potential ﬁelds that were produced using the TAE method were observed to be responsive to conformational changes and to compare well with ab initio reference distributions. Generation of TAE atom types and their associated multipoles does not involve ﬁtting to sample electrostatic potential ﬁelds, but rather utilizes integrated AIM atomic electron density distributions within representative chemical environments. The RECON program was used for TAE reconstruction. RECON is capable of processing 5000 drug-sized molecules or 25 proteins per minute per 1.7 GHz P4 Linux processor.",
	collection = "molecular electrostatics",
	doi = "10.1002/jcc.10240",
	keywords = "multipole expansion",
	localfile = "molecular electrostatics/2003 - Transferable atom equivalent multicentered multipole expansion method.pdf",
	year = 2003
}

@Article{2003-Xu-HR,
	Author = "Ting Xu and Craig J. Hawker and Thomas P. Russell",
	Title = "{Interfacial energy effects on the electric field alignment of symmetric diblock copolymers}",
	Journal = "Macromolecules",
	Volume = "36",
	Pages = "6178–6182",
	abstract = "The alignment of diblock copolymer microdomains by an electric field depends on the segmental interaction between two blocks and the difference in the interfacial energies of each block with the substrate. Morphologies having mixed orientations are predicted when the difference in the interfacial energies of the two blocks is large. By modifying a surface with random copolymer brushes, interfacial energies were controlled and the influence of interfacial energy on the orientation of the copolymer microdomains by an electric field was examined. Complete alignment of the lamellar microdomains was achieved only when the interfacial interactions were balanced. In all other cases, lamellae adjacent to the substrate were oriented parallel to the substrate surface, whereas in the center of the sample the lamellae oriented in the direction of the applied field. These results can be ascribed to a pathway-dependent alignment and a high energetic barrier to achieve complete reorientation of the lamellae adjacent to the surface.",
	collection = "block copolymers",
	doi = "10.1021/ma034511s",
	keywords = "block copolymers; electric fields",
	localfile = "block copolymers/2003 - Interfacial energy effects on the electric field alignment of symmetric diblock copolymers.pdf",
	year = 2008
}

@Article{2003-Yeh-WSJL,
	Author = "Siao-Wei Yeh and Kung-Hwa Wei and Ya-Sen Sun and U-Ser Jeng and Keng S. Liang",
	Title = "{Morphological transformation of PS-b-PEO diblock copolymer by selectively dispersed colloidal CdS quantum dots}",
	Journal = "Macromolecules",
	Volume = "36",
	Pages = "7903–7907",
	Note = "Demonstrates morphology changes in PS-b-PEO copolymer upon adding PEO-selective CdS quantum dots.",
	abstract = "(Excerpt) Block copolymers are versatile platform materials because they can self-assemble into various nanostructures with period thicknesses between 10 and 100 nm under the appropriate compositions and conditions, owing to microphase separation between incompatible blocks.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma034800g",
	keywords = "block copolymers; mesophase transitions; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2003 - Morphological transformation of PS-b-PEO diblock copolymer by selectively dispersed coloidal CdS quantum dots.pdf",
	methods = "DSC, fluorescence, SAXS, WAXS, AFM, TEM",
	systems = "CdS@PS-PEO",
	year = 2003
}

@Article{2003-Zvelindovsky-Sevink,
	Author = "Andrei V. Zvelindovsky and G. J. Agur Sevink",
	Title = "{Comment on 'Microscopic mechanisms of electric-field-induced alignment of block copolymer microdomains'}",
	Journal = "Phys. Rev. Lett.",
	Volume = "90",
	Number = "4",
	Pages = "049601",
	abstract = "Boker et al. identiﬁed experimentally two distinct microscopic mechanisms of electric-ﬁeld-induced alignment of diblock copolymer microdomains. Close to order-disorder transition (ODT) the scattering peak from the lamellae parallel to the electrodes quickly disappears and a new peak from the perpendicular lamellae emerges. Further from ODT the peak merely rotates from the initial position towards the ﬁnal one. Using computer simulation, we are able to reproduce the observed scattering behavior. However, we suggest a microscopic picture different from the one put forward.",
	collection = "block copolymers",
	doi = "10.1103/PhysRevLett.90.049601",
	keywords = "alignment",
	localfile = "block copolymers/2003 - Comment on 'Microscopic mechanisms of electric-field-induced alignment of block copolymer microdomains'.pdf",
	year = 2003
}

@Article{2004-Aarts-DLBR,
	Author = "D. G. A. L. Aarts and R. P. A. Dullens and H. N. W. Lekkerkerker and D. Bonn and R. van Roij",
	Title = "{Interfacial tension and wetting in colloid–polymer mixtures}",
	Journal = "J. Chem. Phys.",
	Volume = "120",
	Number = "4",
	Pages = "1973–1980",
	abstract = "We calculate the interfacial tension and the wetting behavior in phase separated colloid–polymer mixtures both for ideal and excluded volume interacting polymers. Within the recently developed extension of the free volume theory to include polymer interactions ͓Aarts, Tuinier, and Lekkerkerker, J. Phys.: Condens. Matter 14, 7551 ͑2002͔͒ the interfacial tension of the free interface is calculated by adding a van der Waals squared gradient term. The wetting behavior at a hard wall is calculated following a Cahn–Fisher–Nakanishi approach taking the one- and two-body colloid-wall interactions into account. Comparing results for interacting polymers with those for ideal polymers we find that for interacting polymers the interfacial tension does not increase as steeply as a function of the gas–liquid colloid density difference. Furthermore, the wetting transition shifts to higher polymer concentrations, even to above the triple line. The predictions for both the interfacial tension and the wetting are compared to recent experiments.",
	collection = "polymers",
	doi = "10.1063/1.1635810",
	localfile = "polymers/2004 - Interfacial tension and wetting in colloid-polymer mixtures.pdf",
	year = 2004
}

@Article{2004-Andrews-Weisenberger,
	Author = "R. Andrews and M. C. Weisenberger",
	Title = "{Carbon nanotube polymer composites}",
	Journal = "Curr. Op. Solid State Mat. Sci.",
	Volume = "8",
	Pages = "31–37",
	abstract = "The state of research into carbon nanotube/polymer–matrix composites for mechanical reinforcement is critically reviewed with emphasis on recent advances in CNT composite toughness. Particular interest is also given to interfacial bonding of carbon nanotubes to polymer matrices as it applies to stress transfer from the matrix to the CNT. Potential topics of oncoming focus are highlighted.",
	collection = "polymer nanocomposites",
	doi = "10.1016/j.cossms.2003.10.006",
	keywords = "fullerenes; polymer nanocomposites",
	localfile = "polymer nanocomposites/2004 - Carbon nanotube polymer composites.pdf",
	type = "Review",
	year = 2004
}

@Article{2004-Angelescu-WADCRC,
	Author = "Dan E. Angelescu and Judith H. Waller and Douglas H. Adamson and Paru Deshpande and Stephen Y. Chou and Richard A. Register and Paul M. Chaikin",
	Title = "{Macroscopic orientation of block copolymer cylinders in single-layer films by shearing}",
	Journal = "Adv. Mater.",
	Volume = "16",
	Number = "19",
	Pages = "1736–1740",
	collection = "block copolymers",
	doi = "10.1002/adma.200400643",
	keywords = "block copolymers",
	localfile = "block copolymers/2004 - Macroscopic orientation of block copolymer cylinders in single-layer films by shearing.pdf",
	year = 2004
}

@Article{2004-Bader-MC,
	Author = "Richard F. W. Bader and Chérif F. Matta and Fernando {Cortés-Guzmán}",
	Title = "{Where To Draw the Line in Defining a Molecular Structure}",
	Journal = "Organometallics",
	Volume = "23",
	Number = "26",
	Pages = "6253–6263",
	abstract = "Shown is an envelope of the Laplacian of the electron density for the {CpMn(CO)3} complex illustrating its recovery of the donoracceptor interactions of a metal complex in terms of the alignment of the charge concentrations on the ligands with the regions of charge depletions or holes on the metal atom. The theory of atoms in molecules is shown to complement ligand field, frontier orbital, and dpippi* back-bonding models.",
	collection = "molecular structure",
	doi = "10.1021/om049450g",
	localfile = "molecular structure/2004 - Where to draw the line in defining a molecular structure.pdf",
	year = 2004
}

@Article{2004-Bader-Matta,
	Author = "Richard F. W. Bader and Chérif F. Matta",
	Title = "{Atomic Charges Are Measurable Quantum Expectation Values: A Rebuttal of Criticisms of {QTAIM} Charges}",
	Journal = "J. Phys. Chem. A",
	Volume = "108",
	Number = "40",
	Pages = "8385–8394",
	abstract = "The charge on an atom in a molecule is defined by the quantum theory of atoms in molecules (QTAIM) as the expectation value of the number operator, a Dirac observable. An atomic charge is measurable and it, together with its change, contributes to numerous measurable properties: to all molecular moments, to molecular polarizability, to intensities of electronic, infrared, and Raman absorption intensities, and to the polarization of a dielectric. The properties resulting from an applied magnetic field parallel those induced by an electric field, with the induced atomic charge being replaced by the atomic current. The phenomena of polarization and magnetization, permanent or induced, have a common physical basis when described in terms of the physics of an open system, all expressions exhibiting a single underlying structure in terms of their atomic contributions. The paper points out that this physics and the appeal the experiment it affords are lost when one employs other definitions of an atomic charge.",
	collection = "molecular fragmentation",
	doi = "10.1021/jp0482666",
	localfile = "molecular fragmentation/2004 - Atomic charges are measurable quantum expectation values: a rebuttal of criticisms of QTAIM charges.pdf",
	year = 2004
}

@Article{2004-Baucom-TFKDS,
	Author = "Jason Baucom and Thomas Transue and Miguel Fuentes-Cabrera and J. M. Krahn and Thomas A. Darden and Celeste Sagui",
	Title = "{Molecular dynamics simulations of the d(CCAACGTTGG)2 decamer in crystal environment: comparison of atomic point-charge, extra-point, and polarizable force fields}",
	Journal = "J. Chem. Phys.",
	Volume = "121",
	Number = "14",
	Pages = "6998–7008",
	abstract = "Molecular dynamics simulations of the DNA duplex d(CCAACGTTGG)$\_2$ were used to study the relationship between DNA sequence and structure in a crystal environment. Three different force ﬁelds were used: a traditional description based on atomic point charges, a polarizable force ﬁeld, and an ‘‘extra-point’’ force ﬁeld with additional charges on extranuclear sites . It is found that all the force ﬁelds reproduce fairly well the sequence-dependent features of the experimental structure. The polarizable force ﬁeld, however, provides the most accurate representation of the crystal structure and the sequence-dependent effects observed in the experiment. These results point out to the need of the inclusion of polarization for accurate descriptions of DNA.",
	collection = "nucleic acids",
	doi = "10.1063/1.1788631",
	localfile = "nucleic acids/2004 - Molecular dynamics of the d(CCAACGTTGG)2 decamer in crystal environment: comparison of atomic point-charge, extra-point, and polarizable force fields.pdf",
	year = 2005
}

@Article{2004-Bockstaller-Thomas,
	Author = "Michael R. Bockstaller and Edwin L. Thomas",
	Title = "{Proximity effects in self-organized binary particle–block copolymer blends}",
	Journal = "Phys. Rev. Lett.",
	Volume = "93",
	Number = "16",
	Pages = "166106",
	abstract = "Dependent on the surface chemistry of gold nanocrystals of equal metal core size, two morphological types of self-organized block copolymer–particle blends are observed: (1) the segregation of the nanocrystals to the interfacial areas or (2) the preferential uniform distribution within one of the respective polymer domains. The confinement of the nanocrystals to the narrow interfacial regions of the microstructure in type one blends results in high local particle filling fractions and gives rise to electromagnetic coupling upon light irradiation, accompanied by a pronounced increase in absorbance.",
	collection = "block copolymer nanocomposites",
	doi = "10.1103/PhysRevLett.93.166106",
	keywords = "block copolymers; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2004 - Proximity effects in self-organized binary particle-block copolymer blends.pdf",
	methods = "absorbance, TEM",
	systems = "Au-dodcyl@PS-PEP, Au-PS@PS-PEP",
	year = 2004
}

@Article{2004-Burnecki-Weron,
	Author = "Krzysztof Burnecki and Aleksander Weron",
	Title = "{Lévy stable processes. From stationary to self-similar dynamics and back. An application to finance}",
	Journal = "Acta Phys. Pol. B",
	Volume = "35",
	Number = "4",
	Pages = "1343–1359",
	collection = "statistics",
	localfile = "statistics/2004 - Levy stable processes. From sationary to self-similar dynamics and back. An application to finance.pdf",
	year = 2004
}

@Article{2004-Carmichael-CD,
	Author = "Matthew Carmichael and Kimberly Chenoweth and Clifford E. Dykstra",
	Title = "{Hydrogen Molecule Clusters}",
	Journal = "J. Phys. Chem. A",
	Volume = "108",
	Number = "15",
	Pages = "3143–3152",
	abstract = "Ab initio calculations at the MP2 and coupled cluster levels have been performed for small clusters of hydrogen molecules. A concise model interaction potential was constructed on the basis of ab initio potential surface points for the dimer and on comparison with ab initio results for the trimer and tetramer. The model was used to investigate key features of cluster growth, starting with the aggregation energies for clusters with up to 10 molecules. Fully anharmonic zero-point vibrational energies were evaluated for these clusters and were found to be a sizable fraction of the well depth for small clusters. Calculations on larger clusters were used to follow the approach to regular structures in large aggregations, the energetics of cluster growth, and the internal rotation potential for hydrogen molecules embedded in a large cluster. It was found that the essentially free rotation involves concerted reorientation of hydrogen molecules in the first surrounding shell.",
	collection = "hydrogen sorption",
	doi = "10.1021/jp037209u",
	localfile = "hydrogen sorption/2004 - Hydrogen molecule clusters.pdf",
	year = 2004
}

@Article{2004-Cashman-Kellogg,
	Author = "Derek J. Cashman and Glen E. Kellogg",
	Title = "{A computational model for anthracycline binding to {DNA}: tuning groove-binding intercalators for specific sequences}",
	Journal = "J. Med. Chem.",
	Volume = "47",
	Number = "6",
	Pages = "1360–1374",
	abstract = "Anthracycline antibiotics such as doxorubicin and its analogues have been in common use as anticancer drugs for almost half a century. There has been intense interest in the DNA binding sequence specificity of these compounds in recent years, with the hope that a compound could be identified that could possibly modulate gene expression or exhibit reduced toxicity. To computationally analyze this phenomenon, we have constructed molecular models of 65 doxorubicin analogues and their complexes with eight distinct DNA octamer sequences. The HINT (Hydropathic INTeractions) program was utilized to describe binding, including differences in the functional group contributions as well as sequence selectivity. Of these 65 compounds, two compounds were calculated to have a selectivity (the calculated DeltaDeltaG(sel) between the sequence with the strongest binding and the second strongest binding sequence) greater than -0.75 kcal mol(-1) for one sequence over all others, 10 compounds were specific between -0.50 and -0.74 kcal mol(-1), 18 compounds were specific between -0.25 and -0.49 kcal mol(-1), and 35 compounds were virtually nonspecific with a DeltaDeltaG below -0.24 kcal mol(-1). Several compounds have been identified from this study that include features which may enhance sequence selectivity, including several with a halogen in lieu of the 4'-OH in the daunosamine sugar, one compound with a nonaromatic six-membered ring (pirarubicin) in place of the 4'OH, and a compound with an aromatic ring in the vicinity of the C-14 region (zorubicin). Removal of the methoxy group at the C-4 position on the aglycone portion also appears to add potency and selectivity (idarubicin). Overall, efficient computational methods are presented that can be utilized to analyze the free energy of binding and sequence selectivity of both known and designed analogues of doxorubicin to identify future lead compounds for further experimental research.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/jm030529h",
	localfile = "nucleic acid intercalation/2004 - A computational model for anthracycline binding to DNA.pdf",
	year = 2004
}

@Article{2004-Cencek-JBJJS,
	Author = "Wojciech Cencek and Małgorzata Jeziorska and Robert Bukowski and Michał Jaszuński and Bogumił Jeziorski and Krzysztof Szalewicz",
	Title = "{Helium dimer interaction energies from {G}aussian geminal and orbital calculations}",
	Journal = "J. Phys. Chem. A",
	Volume = "108",
	Number = "15",
	Pages = "3211 – 3224",
	collection = "molecular interactions",
	doi = "10.1021/jp037544i",
	localfile = "molecular interactions/2004 - Helium dimer interaction energies from gaussian geminal and orbital calculations.pdf",
	size = "14 p.",
	year = 2004
}

@Article{2004-Chaudhari-SAM,
	Author = "Ajay Chaudhari and A. G. Shankarwar and B. R. Arbad and S. C. Mehrotra",
	Title = "{Dielectric relaxation in glycine-water and glycine-ethanol-water solutions using time domain reflectometry}",
	Journal = "J. Solution Chem.",
	Volume = "33",
	Number = "3",
	Pages = "313–323",
	collection = "molecular solvation",
	doi = "10.1023/B:JOSL.0000035363.49294.d1",
	localfile = "molecular solvation/2004 - Dielectric relaxation in glycine-water and glycine-ethanol-water solutions using time domain reflectometry.pdf",
	year = 2004
}

@Article{2004-Cortes-Guzman-Bader,
	Author = "Fernando {Cortés-Guzmán} and Richard F. W. Bader",
	Title = "{Role of functional groups in linear regression analysis of molecular properties}",
	Journal = "J. Phys. Org. Chem.",
	Volume = "17",
	Number = "2",
	Pages = "95–99",
	abstract = "This paper contrasts the use of functional groups, coupled with the quantum theory of atoms in molecules {(QTAIM),} in expressing the results of linear fittings of molecular properties, as opposed to expressing the linearity in terms of the total number of electrons. The use of {QTAIM} brings to the fore the additivity and transferability of group properties.",
	collection = "molecular fragmentation",
	doi = "10.1002/poc.702",
	localfile = "molecular fragmentation/2004 - Role of functional groups in linear regression analysis of molecular properties.pdf",
	year = 2004
}

@Article{2004-Davis,
	Author = "Jeffery T. Davis",
	Title = "{{G-Quartets} 40 Years Later: From {5prime-GMP} to Molecular Biology and Supramolecular Chemistry}",
	Journal = "Angew. Chem. Int. Ed.",
	Volume = "43",
	Number = "6",
	Pages = "668–698",
	abstract = "Molecular self-assembly is central to many processes in both biology and supramolecular chemistry. The G-quartet, a hydrogen-bonded macrocycle formed by cation-templated assembly of guanosine, was first identified in 1962 as the basis for the aggregation of 5prime-guanosine monophosphate. We now know that many nucleosides, oligonucleotides, and synthetic derivatives form a rich array of functional G-quartets. The G-quartet surfaces in areas ranging from structural biology and medicinal chemistry to supramolecular chemistry and nanotechnology. This Review integrates and summarizes knowledge gained from these different areas, with emphasis on G-quartet structure, function, and molecular recognition.",
	collection = "nucleic acids",
	doi = "10.1002/anie.200300589",
	localfile = "nucleic acids/2004 - G-quartets 40 years later: from 5'-GMP to molecular biology and supramolecular chemistry.pdf",
	shorttitle = "{G-Quartets} 40 Years Later",
	year = 2004
}

@Article{2004-DeRouchey-TR,
	Author = "J. DeRouchey and T. Thurn-Albrecht and Thomas P. Russell",
	Title = "{Block copolymer domain reorientation in an electric field: an in-situ small-angle X-ray scattering study}",
	Journal = "Macromolecules",
	Volume = "37",
	Pages = "2538–2543",
	abstract = "Using in-situ small-angle X-ray scattering, the electric field induced orientation of symmetric block copolymers of polystyrene and polyisoprene was investigated. Alignment of the lamellar microdomains parallel to the electric field was achieved within minutes to a high degree of orientation. Analysis of the scattering patterns indicated that, during alignment of the lamellar microdomains, the material goes through an intermediate state with substantially reduced long-range order. After orientation, the sample consists of many small grains with the lamellae being oriented parallel to the electric field and a random orientation in the plane perpendicular to the field.",
	collection = "block copolymers",
	doi = "10.1021/ma034739f",
	keywords = "electric fields",
	localfile = "block copolymers/2004 - Block copolymer domain reorientation in an electric field: an in-situ small-angle X-ray scattering study.pdf",
	year = 2004
}

@Article{2004-Dracinsky-Castano,
	Author = "Martin Dračinský and Obis Castaño",
	Title = "{Calculations of interaction energies of ellipticine derivatives with {DNA} base pairs}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "6",
	Number = "8",
	Pages = "1799–1805",
	abstract = "Properties of various derivatives of ellipticine and their stacking interactions with adenine-thymine and guanine-cytosine base pairs were investigated with an ab initio correlated method. The dependence of the interaction energy on the distance between an intercalator and a base-pair and on the twist angle between them was studied. The results were compared with three empirical potentials, two of which being based on the {AMBER} force field and the other one based on the {Lifson-Hagler} empirical potential. The global interaction energy minima geometries of three systems were searched. The performance of the empirical potentials is discussed.",
	collection = "nucleic acid intercalation",
	doi = "10.1039/b400471j",
	localfile = "nucleic acid intercalation/2004 - Calculations of interactions energies of ellipticine derivatives with DNA base pairs.pdf",
	year = 2004
}

@Article{2004-Fedorov-Kitaura,
	Author = "Dmitri G. Fedorov and Kazuo Kitaura",
	Title = "{The importance of three-body terms in the fragment molecular orbital method}",
	Journal = "J. Chem. Phys.",
	Volume = "120",
	Number = "15",
	Pages = "6832 – 6840",
	abstract = "A previously proposed two-body fragment molecular orbital method based on the restricted Hartree-Fock (RHF) method was extended to include explicit three-body terms. The accuracy of the method was tested on a set of representative molecules: (H2O)(n), n=16, 32, and 64, as well as alpha and beta n-mers of alanine, n=10, 20, and 40, using STO-3G, 3-21G, 6-31G, and 6-31++G** basis sets. Two- and three-body results are presented separately for assigning one and two molecules (or residues) per fragment. Total energies are found to differ from the regular RHF method by at most DeltaE(2/1)=0.06, DeltaE(2/2)=0.04, DeltaE(3/1)=0.02, and DeltaE(3/2)=0.003 (a.u.); rms energy gradients differ by at most DeltaG(2/1)=0.0015, DeltaG(2/2)=0.000 75, DeltaG(3/1)=0.000 20, and DeltaG(3/2)=0.000 10 (a.u./bohr), and rms dipole moments are reproduced with at most deltaD(2/1)=3.7, deltaD(2/2)=3.4, deltaD(3/1)=2.6, and deltaD(3/2)=3.1 (\%) relative error, where the subscript notation n/m refers to the n-body method based on m molecules (residues) per fragment. A few of the largest three-body calculations were performed with a separated trimer approximation, which presumably somewhat lowered the accuracy of mostly dipole moments which are very sensitive to slight variations in the density distribution. The proposed method is capable of providing sufficient chemical accuracy while providing detailed information on many-body interactions. (C) 2004 American Institute of Physics.",
	collection = "molecular fragmentation",
	doi = "10.1063/1.1687334",
	localfile = "molecular fragmentation/2004 - The importance of three-body terms in the fragment molecular orbital method.pdf",
	methods = "FMO, RHF",
	year = 2004
}

@Article{2004-Finkelstein-Galzitskaya,
	Author = "Aleksei V. Finkelstein and Oxana V. Galzitskaya",
	Title = "{Physics of protein folding}",
	Journal = "Physics of Life Reviews",
	Volume = "1",
	Pages = "23–56",
	Note = "Good discussion around the folding nucleus, rate and kinetics of small proteins",
	collection = "protein structure",
	keywords = "protein folding",
	localfile = "protein structure/2004 - Physics of protein folding.pdf",
	rating = "2",
	read = "2013-08-02",
	year = 2004
}

@Article{2004-Garcia-Viloca-GKT,
	Author = "Mireia Garcia-Volica and Jiali Gao and Martin Karplus and Donald G. Truhlar",
	Title = "{How enzymes work: analysis by modern rate theory and computer simulations}",
	Journal = "Science",
	Volume = "303",
	Pages = "186–195",
	abstract = "Advances in transition state theory and computer simulations are providing new insights into the sources of enzyme catalysis. Both lowering of the activation free energy and changes in the generalized transmission coefﬁcient (recrossing of the transition state, tunneling, and nonequilibrium contributions) can play a role. A framework for understanding these effects is presented, and the contributions of the different factors, as illustrated by speciﬁc enzymes, are identiﬁed and quantiﬁed by computer simulations. The resulting understanding of enzyme catalysis is used to comment on alternative proposals of how enzymes work.",
	collection = "enzymes",
	doi = "10.1126/science.1088172",
	localfile = "enzymes/2004 - How enzymes work: analysis by modern rate theory and computer simulations.pdf",
	year = 2004
}

@Article{2004-Gora-BRL,
	Author = "Robert W. Góra and Wojciech Bartkowiak and Szczepan Roszak and Jerzy Leszczyński",
	Title = "{Intermolecular interactions in solution: elucidating the influence of the solvent}",
	Journal = "J. Chem. Phys.",
	Volume = "120",
	Number = "6",
	Pages = "2802–2813",
	abstract = "A new approach for the analysis of intermolecular interactions in a solution is proposed. The changes in the interaction energy components due to the solvent effects are estimated on the basis of the interaction energy calculated in the presence of the electric ﬁeld induced in a polarizable medium, or in the ﬁeld of the effective fragment potentials. Obtained results indicate a signiﬁcant increase in stabilization resulting from electrostatic interactions as a result of the cooperative interactions between interacting subsystems and solvent molecules.",
	collection = "molecular solvation",
	doi = "10.1063/1.1636155",
	localfile = "molecular solvation/2004 - Intermolecular interactions in solution: elucidating the influence of the solvent.pdf",
	year = 2004
}

@Article{2004-Gresh-KTS,
	Author = "Nohad Gresh and Sherif A. Kafafi and Jean-François Truchon and Dennis R. Salahub",
	Title = "{Intramolecular interaction energies in model alanine and glycine tetrapeptides. {E}valuation of anisotropy, polarization, and correlation effects. a parallel ab initio {HF}/{MP}2, {DFT}, and polarizable molecular mechanics study}",
	Journal = "J. Comp. Chem.",
	Volume = "25",
	Number = "6",
	Pages = "823–834",
	abstract = "An extension of the SIBFA polarizable molecular mechanics procedure to flexible oligopeptides is reported. The procedure is evaluated by computing the relative conformational energies, deltaE(conf), of the alanine tetrapeptide in 10 representative conformations, which were originally derived by Beachy et al. (J Am Chem Soc 1997, 119, 5908) to benchmark molecular mechanics procedures with respect to ab initio computations. In the present study, a particular emphasis is on the separable nature of the components of the energy and the particular impact of the polarization energy component on deltaE(conf). We perform comparisons with respect to single-point HF, DFT, LMP2, and MP2 computations done at the SIBFA-derived energy minima. Such comparisons are made first for the 10 conformers derived from phi/psi torsional angle energy-minimization (the rigid rotor approach), and, in a second step, after allowing additional relaxation of the C-alpha centered valence angles. In both series of energy-minimization, the SIBFA deltaE(conf) compared best with the LMP2 results using the 6-311G** basis set, the rms being 1.3 kcal/mol. In the absence of the polarization component, the rms is 3.5 kcal/mol. In both series of minimizations, the magnitudes of deltaE(conf), computed as differences with respect to the most stable conformer taken as energy zero, decrease along the series: HF > DFT > LMP2 > SIBFA > MP2, indicative of increasing stabilization of the most highly folded conformers.",
	collection = "protein structure",
	doi = "10.1002/jcc.20012",
	localfile = "protein structure/2004 - Intramolecular interaction energies in model alanine and glycine tetrapeptides.pdf",
	year = 2004
}

@Article{2004-Hecht-FC,
	Author = "Christoph Hecht and Josef Friedrich and Ta-Chau Chang",
	Title = "{Interactions of Thionin with {DNA} Strands: Intercalation versus External Stacking}",
	Journal = "J. Phys. Chem. B",
	Volume = "108",
	Number = "29",
	Pages = "10241–10244",
	abstract = "We have investigated thionin in a glycerol/water glass bound to DNA quadruplexes and DNA duplexes with pressure-tuning hole-burning spectroscopy at 2 K. For free thionin as a reference we could identify the two tautomeric structures (imino and amino form) in the inhomogeneous absorption bands. The measurement of local compressibilities from the spectral hole shifts under pressure allowed the assignment of binding modes of thionin to the DNA strands. Thionin binds via external stacking to the dimeric hairpin quadruplex and binds to the monomeric quadruplex only by Coulombic interaction, whereas it intercalates into a linear GC-duplex structure. However, differences in the local compressibilities revealed that only the amino form is able to intercalate into the DNA duplex.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/jp0372993",
	localfile = "nucleic acid intercalation/2004 - Interactions of thionin with DNA strands: intercalation versus external stacking.pdf",
	shorttitle = "Interactions of Thionin with {DNA} Strands",
	year = 2004
}

@Article{2004-Hooper-SDKK,
	Author = "Justin B. Hooper and Kenneth S. Schweizer and T. G. Desai and R. Koshy and Pawl Keblinski",
	Title = "{Structure, surface excess and effective interactions in polymer nanocomposite melts and concentrated solutions}",
	Journal = "J. Chem. Phys.",
	Volume = "121",
	Number = "14",
	Pages = "6986–6997",
	abstract = "The Polymer Reference Interaction Site Model (PRISM) theory is employed to investigate structure, effective forces, and thermodynamics in dense polymer-particle mixtures in the one and two particle limit. The inﬂuence of particle size, degree of polymerization, and polymer reduced density is established. In the athermal limit, the surface excess is negative implying an entropic dewetting interface. Polymer induced depletion interactions are quantiﬁed via the particle-particle pair correlation function and potential of mean force. A transition from nearly monotonic decaying, attractive depletion interactions to much stronger repulsive-attractive oscillatory depletion forces occurs at roughly the semidilute-concentrated solution boundary. Under melt conditions, the depletion force is extremely large and attractive at contact, but is proceeded by a high repulsive barrier. For particle diameters larger than roughly ﬁve monomer diameters, division of the force by the particle radius results in a nearly universal collapse of the depletion force for all interparticle separations. Molecular dynamics simulations have been employed to determine the depletion force for nanoparticles of a diameter ﬁve times the monomer size over a wide range of polymer densities spanning the semidilute, concentrated, and melt regimes. PRISM calculations based on the spatially nonlocal hypernetted chain closure for particle-particle direct correlations capture all the rich features found in the simulations, with quantitative errors for the amplitude of the depletion forces at the level of a factor of 2 or less. The consequences of monomer-particle attractions are brieﬂy explored. Modiﬁcation of the polymer-particle pair correlations is relatively small, but much larger effects are found for the surface excess including an energetic driven transition to a wetting polymer-particle interface. The particle-particle potential of mean force exhibits multiple qualitatively different behaviors contact aggregation, steric stabilization, local bridging attraction depending on the strength and spatial range of the polymer-particle attraction.",
	collection = "polymer nanocomposites",
	doi = "10.1063/1.1790831",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2004 - Structure, surface excess and effective interafctions in polymer nanocomposite melts and concentrated solutions.pdf",
	year = 2004
}

@Article{2004-Hopkins-Tschumper,
	Author = "Brian W. Hopkins and Gregory S. Tschumper",
	Title = "{Ab Initio Studies of π···π Interactions: The Effects of Quadruple Excitations}",
	Journal = "J. Phys. Chem. A",
	Volume = "108",
	Number = "15",
	Pages = "2941–2948",
	abstract = "To examine the effects of including quadruple excitations in the electron correlation treatment when computing the binding energy of van der Waals dimers, we have calculated MP2, CCSD, CCSD(T), and CCSD(TQ) interaction energies for several van der Waals complexes ranging from helium dimer to furan dimer. Through comparison of CCSD(TQ) and CCSD(T) binding energies the first direct assessment of the effects of quadruple excitations on π‚‚‚π interactions is presented. The influence of triple excitations is assessed not only in the conventional manner that permeates the literature (comparison of CCSD(T) and MP2 interaction energies) but also via comparison of CCSD(T) and CCSD data. In systems exhibiting significant electron delocalization, it is well-known that triples contributions to binding energy are quite large (on the order of 1 kcal mol-1). In these cases, quadruple excitations are nonnegligible and tend to be an order of magnitude smaller than the correction to the binding energy from triple excitations (on the order of 0.1 kcal mol-1). The largest quadruples correction observed was +0.2 kcal mol-1 for the furan dimer.",
	collection = "stacking",
	doi = "10.1021/jp0369084",
	localfile = "molecular stacking/2004 - Ab initio studies of pi-pi Interactions: The Effects of Quadruple Excitations.pdf",
	shorttitle = "Ab Initio Studies of π···π Interactions",
	year = 2004
}

@Article{2004-Hubner-GFK,
	Author = "Olaf Hubner and Andreas Gloss and Maximilian Fichtner and Wim Klopper",
	Title = "{On the interaction of dihydrogen with aromatic systems}",
	Journal = "J. Phys. Chem. A",
	Volume = "108",
	Number = "15",
	Pages = "3019–3023",
	abstract = "Second-order Møller-Plesset (MP2) calculations (using the approximate resolution of the identity, RI-MP2) in the TZVPP basis are performed to study the interaction of molecular hydrogen with the aromatic systems C6H5X (X ) H, F, OH, NH2, CH3, and CN), C10H8 (naphthalene and azulene), C14H10 (anthracene), C24H12 (coronene), p-C6H4(COOH)2 (terephthalic acid), and p-C6H4(COOLi)2 (dilithium terephthalate). Various adsorption positions are studied for C6H5F. The most favorable configuration places H2 above the aromatic plane with its axis pointing toward the middle of the ring. The electronic (van der Waals) interaction energy for the differently substituted benzenes correlates with the ability of the substituents to enrich the aromatic system electronically. The largest interaction energy (among the singly substituted benzenes) is found for aniline (4.5 kJ mol-1). Enlarging the aromatic system increases the interaction energy; the value for coronene amounts to 5.4 kJ mol-1. Extending the basis set and including terms linear in the interelectronic distances increases the interaction energy by about 1 kJ mol-1 relative to that of the TZVPP basis, whereas the inclusion of higher excitations by coupled-cluster calculations (including all single and double excitations with a perturbative estimate of triples, CCSD(T)) decreases the interaction energy by about the same amount.",
	collection = "hydrogen sorption",
	doi = "10.1021/jp031102p",
	keywords = "hydrogen adsorption",
	localfile = "hydrogen sorption/2004 - On the interaction of dihydrogen with aromatic systems.pdf",
	methods = "MP2, CCSD(T)",
	systems = "dihydrogen near aromatics",
	year = 2004
}

@Article{2004-Jankowski,
	Author = "Piotr Jankowski",
	Title = "{Approximate generation of full-dimensional ab initio van der Waals surfaces for high-resolution spectroscopy}",
	Journal = "J. Chem. Phys.",
	Volume = "121",
	Number = "4",
	Pages = "1655–1662",
	abstract = "A method for the generation of highly accurate, nearly-exact, full-dimensional interaction energy surfaces for weakly interacting subsystems is proposed. The method is based on the local expansion of the exact interaction energy surface in the Taylor series with respect to intramolecular coordinates. It is shown that without any signiﬁcant loss of accuracy this expansion can be limited to a few low-order terms. This leads to signiﬁcant savings in computations of the full-dimensional interaction energy surfaces. Also a method for the direct calculation of the interaction energy surface of reduced dimensionality, corresponding to averaging over the intramolecular vibrations, without explicit knowledge of the full-dimensional surface, is presented. The main ideas and computational features of the proposed scheme are comprehensively tested for the Ar-HF system.",
	collection = "molecular interactions",
	doi = "10.1063/1.1766293",
	localfile = "molecular interactions/2004 - Approximate generation of full-dimensional ab initio van der Waals surfaces for high-resolution spectroscopy.pdf",
	year = 2004
}

@Article{2004-Jeng-SLHL,
	Author = "U-Ser Jeng and Ya-Sen Sun and Hsin-Yi Lee and Chia-Hung Hsu and Keng S. Liang",
	Title = "{Binding effect of surface-modified cadmium sulfide on the microstructure of PS-b-PEO block copolymers}",
	Journal = "Macromolecules",
	Volume = "37",
	Pages = "4617–4622",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma049722r",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2004 - Binding effect of surface-modified cadmium sulfide on the microstructure of PS-b-PEO block copolymers.pdf",
	methods = "SAXS, TEM",
	rating = "2",
	read = "2012-03-21",
	systems = "CdS-ethanol@PS-PEO",
	year = 2004
}

@Article{2004-Jones-Thornton,
	Author = "Susan Jones and Janet M. Thornton",
	Title = "{Searching for functional sites in protein structures}",
	Journal = "Curr. Opin. Chem. Biol",
	Volume = "8",
	Pages = "3–7",
	Note = "Short snapshot of available methods in 2004, with several good references to follow up on.",
	cited = "113 (2013-08-28)",
	collection = "protein structures",
	doi = "10.1016/j.cbpa.2003.11.001",
	keywords = "active site",
	localfile = "protein structure/2004 - Searching for functional sites in protein structures.pdf",
	rating = "2",
	read = "2013-08-27",
	year = 2004
}

@Article{2004-Katz-Willner,
	Author = "Eugenii Katz and Itamar Willner",
	Title = "{Integrated {Nanoparticle-Biomolecule} Hybrid Systems: Synthesis, Properties, and Applications}",
	Journal = "Angew. Chem. Int. Ed.",
	Volume = "43",
	Number = "45",
	Pages = "6042–6108",
	abstract = "Nanomaterials, such as metal or semiconductor nanoparticles and nanorods, exhibit similar dimensions to those of biomolecules, such as proteins (enzymes, antigens, antibodies) or {DNA.} The integration of nanoparticles, which exhibit unique electronic, photonic, and catalytic properties, with biomaterials, which display unique recognition, catalytic, and inhibition properties, yields novel hybrid nanobiomaterials of synergetic properties and functions. This review describes recent advances in the synthesis of biomolecule-nanoparticle/nanorod hybrid systems and the application of such assemblies in the generation of {2D} and {3D} ordered structures in solutions and on surfaces. Particular emphasis is directed to the use of biomolecule-nanoparticle (metallic or semiconductive) assemblies for bioanalytical applications and for the fabrication of bioelectronic devices.",
	collection = "nanoparticles",
	doi = "10.1002/anie.200400651",
	localfile = "nanoparticles/2004 - Integrated nanoparticle-biomolecule hybrid systems: synthesis, properties, and applications.pdf",
	shorttitle = "Integrated {Nanoparticle-Biomolecule} Hybrid Systems",
	year = 2004
}

@Article{2004-Kedzierski-WSSL,
	Author = "Paweł Kędzierski and Paweł Wielgus and Adrian Sikora and W. Andrzej Sokalski and Jerzy Leszczyński",
	Title = "{Visualization of the differential transition state stabilziation within the active site environment}",
	Journal = "Int. J. Mol. Sci.",
	Volume = "5",
	Pages = "186–195",
	collection = "enzymes",
	doi = "10.3390/i5040186",
	keywords = "active site",
	localfile = "enzymes/2004 - Visualization of the differential transition state stabilization within the active site environment.pdf",
	methods = "DTSS",
	year = 2004
}

@Article{2004-Knoll-LHKSZM,
	Author = "A. Knoll and Kateryna S. Lyakhova and A. Horvat and Georg Krausch and G. J. Agur Sevink and Andrei V. Zvelindovsky and R. Magerle",
	Title = "{Direct imaging and mesoscale modelling of phase transitions in a nanostructured fluid}",
	Journal = "Nature Mat.",
	Volume = "3",
	Pages = "886–890",
	abstract = "(Excerpt) The kinetics of phase transitions is essential for understanding pattern formation in structured ﬂuids. These ﬂuids play a key role in the morphogenesis of biological cells, and they are very common in pharmaceutical products and plastic materials. Until now, it has not been possible to follow phase transitions in structured ﬂuids experimentally in real time and with high spatial resolution. Previous work has relied on static images and indirect experimental evidence from spatially averaging scattering experiments. Simulating the processes with computer models is a further challenge because of the multiple time and length scales involved.",
	collection = "block copolymers",
	doi = "10.1038/nmat1258",
	keywords = "block copolymers; mesophase transitions; thin films",
	localfile = "block copolymers/2004 - Direct imaging and mesoscale modelling of phase transitions in a nanostructured fluid.pdf",
	year = 2004
}

@Article{2004-Lee-BB,
	Author = "Jae Youn Lee and Gavin A. Buxton and Anna C. Balazs",
	Title = "{Using nanoparticles to create self-healing composites}",
	Journal = "J. Chem. Phys.",
	Volume = "121",
	Number = "11",
	Pages = "5531–5540",
	abstract = "The need for viable materials for optical communications, display technologies, and biomedical engineering is driving the creation of multilayer composites that combine brittle materials, such as glass, with moldable polymers. However, crack formation is a critical problem in composites where thin brittle ﬁlms lie in contact with deformable polymer layers. Using computer simulations, we show that adding nanoparticles to the polymers yields materials in which the particles become localized at nanoscale cracks and effectively form ‘‘patches’’ to repair the damaged regions. Through micromechanics simulations, we evaluate the properties of these systems in the undamaged, damaged, and healed states and determine optimal conditions for harnessing nanoparticles to act as responsive, self-assembled ‘‘band aids’’ for composite materials. The results reveal situations where the mechanical properties of the repaired composites can potentially be restored to 75\%–100\% of the undamaged material.",
	collection = "polymer nanocomposites",
	doi = "10.1063/1.1784432",
	keywords = "healing; nanoparticle aggregation; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "polymer nanocomposites/2004 - Using nanoparticles to create self-healing composites.pdf",
	year = 2004
}

@Article{2004-Liem-PL,
	Author = "S. Y. Liem and Paul L. A. Popelier and M. Leslie",
	Title = "{Simulation of liquid water using a high-rank quantum topological electrostatic potential}",
	Journal = "Int. J. Quant. Chem.",
	Volume = "99",
	Number = "5",
	Pages = "685–694",
	abstract = "For the first time a potential based on high-rank atomic multipole moments computed according to quantum chemical topology {(QCT)} has been used in molecular dynamics simulations. Completing earlier work on the performance of this {QCT} potential on small gas-phase van der Waals complexes we now focus on the liquid structure of water. Other than the parameter L, which keeps track of the rank of the electrostatic interaction, the current {QCT} potential contains only two adjustable parameters of the {Lennard-Jones} type. A system of 216 water molecules was simulated including long-range interactions represented by a high-rank multipolar Ewald summation. High-order multipolar interactions {(L} = 5) are essential to recover the typical features of a liquid-like structure. Liquid simulations at five different temperatures showed a maximum in the density and a temperature profile that agrees fairly well with experiment. The density of simulated water at 300 K and 1 atm is about 0.1\% off the experimental value, while the calculated potential energy of the liquid is within 3\% of the experimental result. The experimental value of the self-diffusion coefficient is underestimated by 35\%. The value of Cp is overestimated by 40\% and the thermal expansion coefficient alpha by 37\%. The calculated correlation coefficients between the calculated {QCT} profile and the experimental profile of {gOO(r),} {gOH(r),} and {gHH(r)} are 0.976, 0.970, and 0.972, respectively. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004",
	collection = "molecular electrostatics",
	doi = "10.1002/qua.20025",
	localfile = "molecular electrostatics/2004 - Simulation of liquid water using a high-rank quantum topological electorostatic potential.pdf",
	year = 2004
}

@Article{2004-Maroulis,
	Author = "George Maroulis",
	Title = "{A note on the electric multipole moments of carbon dioxide}",
	Journal = "Chem. Phys. Lett.",
	Volume = "396",
	Number = "1-3",
	Pages = "66–68",
	abstract = "We have obtained accurate values for the electric quadrupole {([Theta])} and hexadecapole moment {([Phi])} of carbon dioxide. A very large (19s14p8d6f1g) basis set consisting of 456 uncontracted Gaussian-type functions is thought to provide {near-Hartree-Fock} values for both properties, . At the {CCSD(T)} level of theory a [8s5p4d2f] basis set yields at the equilibrium bond length of Re = 2.192 a0. Our final estimate for the hexadecapole moment is .",
	collection = "molecular electrostatics",
	doi = "10.1016/j.cplett.2004.07.123",
	localfile = "molecular electrostatics/2004 - A note on the electric multipole moments of carbon dioxide.pdf",
	year = 2004
}

@Article{2004-Mochizuki-KNAK,
	Author = "Yuji Mochizuki and Shigeru Nagase and Tatsuya Nakano and Shinji Amari and Kazuo Kitaura",
	Title = "{Large scale MP2 calculations with fragment molecular orbital scheme}",
	Journal = "Chem. Phys. Lett.",
	Volume = "396",
	Pages = "473–479",
	abstract = "We have recently developed a parallelized integral-direct algorithm for the second-order Møller–Plesset perturbation theory (MP2) and implemented it into the ABINIT-MP program of the fragment molecular orbital (FMO) scheme. A ﬂexible parallelization is possible by combining the fragment indices (upper level) and the two-electron integral indices (lower level) on distributed computational resources, leading to an enhancement of in-core processings. In this Letter, we carry out a series of benchmark FMO–MP2 calculations of realistic proteins consisting of the tens of thousands of basis functions. The performance is shown to be high, indicating that the ABINIT-MP program is easily applicable to the realistic systems.",
	collection = "molecular fragmentation",
	doi = "10.1016/j.cplett.2004.08.082",
	localfile = "molecular fragmentation/2004 - Large-scale MP2 calculations with fragment molecular orbital scheme.pdf",
	year = 2004
}

@Article{2004-Mor-RLPTDTPKP,
	Author = "Marco Mor and Silvia Rivara and Alessio Lodola and Pier Vencenzo Plazzi and Giorgio Tarzia and Andrea Duranti and Andrea Tontini and Giovanni Piersanti and Satish Kathuria and Daniele Piomelli",
	Title = "{Cyclohexylcarbamic Acid 3′- or 4′-Substituted Biphenyl-3-yl Esters as Fatty Acid Amide Hydrolase Inhibitors: Synthesis, Quantitative Structure-Activity Relationships, and Molecular Modeling Studies}",
	Journal = "J. Med. Chem.",
	Volume = "47",
	Pages = "4998–5008",
	collection = "enzymes",
	doi = "10.1021/jm031140x",
	localfile = "enzymes/2004 - Caclyhexylcarbamic acid 3'- or 4'-substituted biphenyl-3-yl esters as fatty acid amide hydrolase inhibitors: synthesis, quantitative structure-activity relationships, and moleculae modeling studies.pdf",
	year = 2004
}

@Article{2004-Nowak-Wysocki,
	Author = "Katarzyna Nowak and Stanislaw Wysocki",
	Title = "{The semiempirical and {DFT} methods in studies on geometry and energetics of {AMSA} isomers: comparison of {m-AMSA} and {o-AMSA} properties}",
	Journal = "J. Mol. Struct.: {THEOCHEM}",
	Volume = "682",

license: MIT

license_type: permissive

extension: bib