text:
B3LYP and time-dependent Hartree-Fock . Typically, FMO2-TDDFT reproduced the full TDDFT excitation energies within 0.1 eV, and for one excited state the error was about 0.2 eV. Beside the accurate reproduction of the TDDFT excitation energies, we also automatically get an excitation energy decomposition analysis, which provides the contributions of individual fragments. Finally, the efﬁciency of our approach was exempliﬁed on the LC-BLYP/ 6-31G* calculation of the lowest singlet excitation of the photoactive yellow protein which consists of 1931 atoms, and the obtained value of 3.1 eV is in agreement with the experimental value of 2.8 eV.",
	collection = "molecular fragmentation",
	doi = "10.1063/1.2772850",
	localfile = "molecular fragmentation/2007 - Time-dependent density functional theory based upon the fragment molecular orbital method.pdf",
	methods = "FMO, TDDFT",
	year = 2007
}

@Article{2007-Chiu-KBKP,
	Author = "Julia J. Chiu and Bumjoon J. Kim and Gi-Ra Yi and Joona Bang and Edward J. Kramer and David J. Pine",
	Title = "{Distribution of nanoparticles in lamellar domains of block copolymers}",
	Journal = "Macromolecules",
	Volume = "40",
	Pages = "3361–3365",
	Note = "Studies distribution of PS-coated particles inside PS-b-P2VP lammellae.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma061503d",
	keywords = "block copolymers; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2007 - Distribution of nanoparticles in lamellar domains of block copolymers.pdf",
	methods = "TEM",
	systems = "Au-PS@PS-P2VP",
	year = 2007
}

@Article{2007-Choi-SSL,
	Author = "H. D. Choi and P. J. Seo and B. W. Son and U. Lee",
	Title = "{5-iodo-3-methylsulfinyl-2-phenyl-1-benzofuran}",
	Journal = "Acta Cryst. E",
	Volume = "63",
	Pages = "O3745 – U2447",
	collection = "halogen bonding",
	doi = "10.1107/S1600536807038822",
	localfile = "halogen bonding/2007 - 5-iodo-3-methylsulfinyl-2-phenyl-1-benzofuran.pdf",
	size = "10 p.",
	year = 2007
}

@Article{2007-Clark-HMP,
	Author = "Timothy Clark and M. Hennemann and Jane S. Murray and Peter Politzer",
	Title = "{Halogen bonding: the sigma-hole}",
	Journal = "J. Mol. Model.",
	Volume = "13",
	Number = "2",
	Pages = "291 – 296",
	abstract = "Halogen bonding refers to the non-covalent interactions of halogen atoms X in some molecules, RX, with negative sites on others. It can be explained by the presence of a region of positive electrostatic potential, the sigma-hole, on the outermost portion of the halogen's surface, centered on the R-X axis. We have carried out a natural bond order B3LYP analysis of the molecules CF3X, with X = F, Cl, Br and I. It shows that the Cl, Br and I atoms in these molecules closely approximate the s(2)p(x)(2)p(y)(2)p(z)(1) configuration, where the z-axis is along the R-X bond. The three unshared pairs of electrons produce a belt of negative electrostatic potential around the central part of X, leaving the outermost region positive, the sigma-hole. This is not found in the case of fluorine, for which the combination of its high electronegativity plus significant sp-hybridization causes an influx of electronic charge that neutralizes the sigma-hole. These factors become progressively less important in proceeding to Cl, Br and I, and their effects are also counteracted by the presence of electron-withdrawing substituents in the remainder of the molecule. Thus a sigma-hole is observed for the Cl in CF3Cl, but not in CH3Cl.",
	collection = "halogen bonding",
	localfile = "halogen bonding/2007 - Halogen bonding: the sigma-hole.pdf",
	year = 2007
}

@Article{2007-Cockroft-PZASLVLUH,
	Author = "Scott L. Cockroft and Julie Perkins and Cristiano Zonta and Harry Adams and Sharon E. Spey and Caroline M. R. Low and Jeremy G. Vinter and Kevin R. Lawson and Christopher J. Urch and Christopher A. Hunter",
	Title = "{Substituent effects on aromatic stacking interactions}",
	Journal = "Org. Biomol. Chem.",
	Volume = "5",
	Number = "7",
	Pages = "1062",
	abstract = "Synthetic supramolecular zipper complexes have been used to quantify substituent effects on the free energies of aromatic stacking interactions. The conformational properties of the complexes have been characterised using NMR spectroscopy in CDCl3, and by comparison with the solid state structures of model compounds. The structural similarity of the complexes makes it possible to apply the double mutant cycle method to evaluate the magnitudes of 24 different aromatic stacking interactions. The major trends in the interaction energy can be rationalised using a simple model based on electrostatic interactions between the pi-faces of the two aromatic rings. However, electrostatic interactions between the substituents of one ring and the pi-face of the other make an additional contribution, due to the slight offset in the stacking geometry. This property makes aromatic stacking interactions particularly sensitive to changes in orientation as well as the nature and location of substituents.",
	collection = "stacking",
	doi = "10.1039/b617576g",
	localfile = "molecular stacking/2007 - Substituent effects on aromatic stacking interactions.pdf",
	year = 2007
}

@Article{2007-Costanzo-Beyer,
	Author = "Philip J. Costanzo and Frederick L. Beyer",
	Title = "{Thermally driven assembly of nanoparticles in polymer matrices}",
	Journal = "Macromolecules",
	Volume = "40",
	Pages = "3996–4001",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma070447t",
	keywords = "block copolymers; nanomigration; nanoparticle distribution; nanoparticle grafts; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2007 - Thermally driven assembly of nanoparticles in polymer matrices.pdf",
	methods = "TEM, SAXS",
	systems = "Au-PS-PEG@PS-PMMA",
	year = 2007
}

@Article{2007-Cybulski-Lytle,
	Author = "Sławomir M. Cybulski and Marion L. Lytle",
	Title = "{The origin of deficiency of the supermolecule second-order Møller-Plesset approach for evaluating interaction energies}",
	Journal = "J. Chem. Phys.",
	Volume = "127",
	Pages = "141102",
	abstract = "Calculations for the complex of thymine and adenine are used to show that the supermolecule second-order Møller-Plesset perturbation theory (MP2) approach for evaluating interaction energies fails in certain cases because of the behavior of one of its components: the uncoupled Hartree-Fock dispersion energy. A simple approach for correcting the MP2 supermolecule interaction energies is proposed. It focuses on correcting a relatively small difference between the MP2 and coupled cluster interaction energies, which is a very appealing feature of the new approach considering a benchmark role played by coupled cluster results.",
	collection = "molecular interactions",
	doi = "10.1063/1.2795693",
	localfile = "molecular interactions/2007 - The origin of deficiency of the supermolecular second-order Moller-Plesset approach for evaluating interaction energies.pdf",
	year = 2007
}

@Article{2007-Dai-PACJY,
	Author = "Jixun Dai and Chandanamali Punchihewa and Attila Ambrus and Ding Chen and Roger A. Jones and Danzhou Yang",
	Title = "{Structure of the intramolecular human telomeric G-quadruplex in potassium solution: a novel adenine triple formation}",
	Journal = "Nucl. Acids Res.",
	Volume = "35",
	Number = "7",
	Pages = "2440–2450",
	abstract = "We report the {NMR} solution structure of the intramolecular G-quadruplex formed in human telomeric {DNA} in K+. The hybrid-type telomeric G-quadruplex consists of three G-tetrads linked with mixed parallel-antiparallel G-strands, with the bottom two G-tetrads having the same G-arrangement (anti:anti:syn:anti) and the top G-tetrad having the reversed G-arrangement (syn:syn:anti:syn). The three {TTA} loop segments adopt different conformations, with the first {TTA} assuming a double-chain-reversal loop conformation, and the second and third {TTA} assuming lateral loop conformations. The {NMR} structure is very well defined, including the three {TTA} loops and the two flanking sequences at 5'- and 3'-ends. Our study indicates that the three loop regions interact with the core G-tetrads in a specific way that defines and stabilizes the unique human telomeric G-quadruplex structure in K+. Significantly, a novel adenine triple platform is formed with three naturally occurring adenine residues, A21, A3 and A9, capping the top tetrad of the hybrid-type telomeric G-quadruplex. This adenine triple is likely to play an important role in the formation of a stable human telomeric G-quadruplex structure in K+. The unique human telomeric G-quadruplex structure formed in K+ suggests that it can be specifically targeted for anticancer drug design.",
	collection = "nucleic acids",
	doi = "10.1093/nar",
	localfile = "nucleic acids/2007 - Structure of the intramolecular human telomeric G-quadruplex in potassium solution: a novel adenine triple formation.pdf",
	shorttitle = "Structure of the intramolecular human telomeric G-quadruplex in potassium solution",
	year = 2007
}

@Article{2007-Darling,
	Author = "S. B. Darling",
	Title = "{Directing the self-assembly of block copolymers}",
	Journal = "Prog. Polym. Sci.",
	Volume = "32",
	Pages = "1152–1204",
	abstract = "Recently, a new spotlight has been focused on block copolymers, thoroughly studied for nearly half a century, because of their potential use in numerous nanotechnologies. This renewed interest is a consequence of the self-assembled microdomains characteristic of these materials. The size, shape, and arrangement of these nanoscopic structures are all tunable through synthetic chemistry of the constituent molecules. Capturing the vast technological potential of block copolymers will, in many cases, require precise control over the orientation and alignment of the microdomains. This review summarizes extant applications and alignment techniques and provides an outlook toward the future. In an effort to provide a practical resource for researchers, the article is structured to identify the reported alignment approaches for a given polymer morphology rather than sorting by alignment technique. Speciﬁc materials have also been deemphasized because the alignment methods, with few exceptions, are general to a speciﬁc morphology or set of morphologies. In addition to a detailed summary of traditional methodologies, some very recent results such as optical alignment of liquid crystalline block copolymers, lithographic chemical patterning, and alignment in pores are highlighted.",
	collection = "block copolymers",
	doi = "10.1016/j.progpolymsci.2007.05.004",
	keywords = "block copolymers",
	localfile = "block copolymers/2007 - Directing the self-assembly of block copolymers.pdf",
	type = "Review",
	year = 2007
}

@Article{2007-Deshmukh-BCC,
	Author = "Ranjan D. Deshmukh and Gavin A. Buxton and Nigel Clarke and Russell J. Composto",
	Title = "{Nanoscale block copolymer templates decorated by nanoparticle arrays}",
	Journal = "Macromolecules",
	Volume = "40",
	Pages = "6316–6324",
	Note = "Shows SFM/TEM images and CDS results for a perpendicular->parallel transition in NP-loaded BCP lammellae at a surface.",
	abstract = "We present a novel one-step assembly process that encompasses in-situ formation of silver nanoparticles (NP), directed assembly of block copolymers into a perpendicular lamellar morphology, and NP organization into patterned arrays. This process utilizes organometallic precursors that thermally decompose and form spatially organized NP arrays on the free surface of the block copolymer. As NP concentration increases, the conversion of perpendicular to parallel lamellar morphology at the free surface slows down. A cell dynamical system (CDS) simulation captures the dynamics of this reorganization. The final structure is attractive for producing nanodevices because the surface is decorated by NP that are arranged in parallel arrays with tunable NP separation.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma0707943",
	keywords = "block copolymers; nanogrowth; nanoparticle aggregation; nanospheres; polymer nanocomposites; thin films",
	localfile = "block copolymer nanocomposites/2007 - Nanoscale block copolymer templates decorated by nanopartiicle arrays.pdf",
	methods = "AFM, TEM, CDS/BD",
	systems = "Ag@PS-PMMA",
	year = 2007
}

@Article{2007-Deshmukh-Composto,
	Author = "Ranjan D. Deshmukh and Russell J. Composto",
	Title = "{Direct observation of nanoparticle embedding into the surface of a polymer melt}",
	Journal = "Langmuir",
	Volume = "23",
	Pages = "13169–13173",
	abstract = "Direct embedding of metal nanoparticles (NPs) into the surface of a polymer melt is observed by TEM and a new embedding mechanism proposed. Upon annealing above the glass transition temperature of polystyrene (PS), NPs (20 nm gold) are rapidly covered by a thin PS wetting layer, h* 1.3-1.8 nm (i.e., about two or three monomers). Because it creates capillary pressure on a NP, this “universal” wetting layer is proposed to be responsible for NP embedding. The value of h* is independent of the molecular weight of PS and constant during the embedding process. The value of h* is found to be similar to the equilibrium wetting layer thickness of a polymer melt spreading on a metal substrate. Using a model that includes the spreading coefficient, long-range van der Waals interactions, and a chain-stretching penalty, h* is shown to be independent of the molecular weight of the polymer. Using this model and the measured value of h*, the interfacial energy between Au NP and PS is estimated to be 8.7 J/m2.",
	collection = "polymer nanocomposites",
	doi = "10.1021/la7025544",
	keywords = "nanomigration; nanoparticle distribution; polymer blends; polymer nanocomposites",
	localfile = "polymer nanocomposites/2007 - Direct observation of nanoparticle embedding into the surface of a polymer melt.pdf",
	year = 2007
}

@Article{2007-Deshmukh-LC,
	Author = "Ranjan D. Deshmukh and Yu Liu and Russell J. Composto",
	Title = "{Two-dimensional confinement of nanorods in block copolymer domains}",
	Journal = "Nano Lett.",
	Volume = "7",
	Number = "12",
	Pages = "3662–3668",
	Note = "Demonstrates orienting PEG-coated nanorods in a PS-b-PMMA diblock lammellar film.",
	abstract = "Gold nanorods (NRs) self-orient during the self-assembly of a symmetric poly(styrene-b-methyl methacrylate) (PS-b-PMMA) film. The NRs are selectively sequestered and confined in lamellar PMMA domains, which are narrower than the NR length. This confinement orients 71\% of NRs within ± 5° of the lamella plane. During solvent annealing, a gradient in the concentration of NRs is observed. This route to produce alternating layers containing conducting NRs separated by dielectric domains has the potential for fabricating self-assembled nanodevices.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/nl071908r",
	keywords = "alignment; block copolymers; nanorods; polymer nanocomposites; thin films",
	localfile = "block copolymer nanocomposites/2007 - Two-dimensional confinement of nanorods in block copolymer domains.pdf",
	methods = "backscattering, absorbance, TEM",
	systems = "Au(rods)-PS@PS-PMMA",
	year = 2007
}

@Article{2007-Donchev,
	Author = "A. G. Donchev",
	Title = "{Ab initio study of the effects of orientation and corrugation for H[sub 2] adsorbed on polycyclic aromatic hydrocarbons}",
	Journal = "J. Chem. Phys.",
	Volume = "126",
	Number = "12",
	Pages = "124706",
	collection = "hydrogen sorption",
	doi = "10.1063/1.2717174",
	localfile = "hydrogen sorption/2007 - Ab initio study of the effects of orientation and corrugation for H2 adsorbed on polycyclic aromatic hydrocarbons.pdf",
	year = 2007
}

@Article{2007-Dyguda-Kazimierowicz-SL,
	Author = "Edyta Dyguda-Kazimierowicz and W. Andrzej Sokalski and Jerzy Leszczyński",
	Title = "{Non-empirical study of the phosphorylzation reaction catalyzed by 4-methyl-5-beta-hydroxyethylthiazole kinase: relevance of the theory of intermolecular interactions}",
	Journal = "J. Mol. Model.",
	Volume = "13",
	Pages = "839–849",
	collection = "molecular reactions",
	doi = "10.1007/s00894-007-0192-9",
	localfile = "molecular reactions/2007 - Non-empirical study of the phosphorylation reaction catalyzed by 4-methyl-4-beta-hydroxyethylthiazole kinase: relevance of the theory of intermolecular interactions.pdf",
	year = 2007
}

@Article{2007-Fedorov-IIKPN,
	Author = "Dmitri G. Fedorov and Kazuya Ishimura and T. Ishida and Kazuo Kitaura and Peter Pulay and S. Nagase",
	Title = "{Accuracy of the three-body fragment molecular orbital method applied to {M}oller-{P}lesset perturbation theory}",
	Journal = "J. Comp. Chem.",
	Volume = "28",
	Number = "9",
	Pages = "1476 – 1484",
	abstract = "The three-body energy expansion in the fragment molecular orbital method (FMO) was applied to the 2nd order Møller–Plesset theory (MP2). The accuracy of both the two and three-body expansions was determined for water clusters, alanine n-mers (alpha-helices and beta-strands) and one synthetic protein, using the 6-31G* and 6-311G* basis sets. At the best level of theory (three-body, two molecules/residues per fragment), the absolute errors in energy relative to ab initio MP2 were at most 1.2 and 5.0 mhartree, for the 6-31G* and 6-311G* basis sets, respectively. The relative accuracy was at worst 99.996\% and 99.96\%, for 6-31G* and 6-311G*, respectively. A three-body approximation was introduced and the optimum threshold value was determined. The protein calculation (6-31G*) at the production level (FMO2/2) took 3 h on 36 3.2-GHz Pentium 4 nodes and had the absolute error in the MP2 correlation energy of only 2 kcal/mol.",
	collection = "molecular fragmentation",
	doi = "10.1002/jcc.20645",
	keywords = "electronic structure",
	localfile = "molecular fragmentation/2007 - Accuracy of the three-body fragment molecular orbital method applied to Moller-Plesset perturbation theory.pdf",
	methods = "MP2, FMO",
	systems = "water clusters, alanine oligomers, synthetic protein",
	year = 2007
}

@Article{2007-Fedorov-IUK,
	Author = "Dmitri G. Fedorov and T. Ishida and Masami Uebayasi and Kazuo Kitaura",
	Title = "{The fragment molecular orbital method for geometry optimizations of polypeptides and proteins}",
	Journal = "J. Phys. Chem. A",
	Volume = "111",
	Number = "14",
	Pages = "2722 – 2732",
	abstract = "The fragment molecular orbital method (FMO) has been used with a large number of wave functions for single-point calculations, and its high accuracy in comparison to ab initio methods has been well established. We have developed the analytic derivative of the electrostatic interaction between far separated fragments and performed a number of restricted Hartree-Fock (RHF) geometry optimizations using FMO and ab initio methods. In particular, the alpha-helix, beta-turn, and extended conformers of a 10-residue polyalanine were studied and the good FMO accuracy was established (the rms deviations for the former two forms were about 0.2 A and for the latter structure about 0.001 A). Met-enkephalin dimer was used as a model for the polypeptide binding and computed at the 3-21G and 6-31G* levels with a similar accuracy achieved; the error in the binding energy predictions (FMO vs ab initio) was 1-3 kcal/mol. Chignolin (PDB: 1uao) and an agonist polypeptide of the erythropoietin receptor protein (emp1) were optimized at the 3-21(+)G level, with the rms deviation from ab initio of about 0.2 A, or 0.5 degrees in terms of bond angles. The effect of solvation on the structure optimization was studied in chignolin and the Trp-cage miniprotein construct (PDB:1l2y), by describing water with TIP3P. The computed structures in gas phase and solution are compared to each other and experiment.",
	collection = "protein structure",
	doi = "10.1021/jp0671042",
	localfile = "protein structure/2007 - The fragment molecular orbital method for geometry optimizations of polypeptides and proteins.pdf",
	methods = "FMO",
	year = 2007
}

@Article{2007-Fedorov-Kitaura,
	Author = "Dmitri G. Fedorov and Kazuo Kitaura",
	Title = "{Extending the power of quantum chemistry to large systems with the fragment molecular orbital method}",
	Journal = "J. Phys. Chem. A",
	Volume = "111",
	Number = "30",
	Pages = "6904 – 6914",
	abstract = "Following the brief review of the modern fragment-based methods and other approaches to perform quantum-mechanical calculations of large systems, the theoretical development of the fragment molecular orbital method (FMO) is covered in detail, with the emphasis on the physical properties, which can be computed with FMO. The FMO-based polarizable continuum model (PCM) for treating the solvent effects in large systems and the pair interaction energy decomposition analysis (PIEDA) are described in some detail, and a range of applications of FMO to biological studies is introduced. The factors determining the relative stability of polypeptide conformers (alpha-helix, beta-turn, and extended form) are elucidated using FMO/PCM and PIEDA, and the interactions in the Trp-cage miniprotein construct (PDB: 1L2Y) are analyzed using PIEDA.",
	collection = "molecular fragmentation",
	doi = "10.1021/jp0716740",
	localfile = "molecular fragmentation/2007 - Extending the power of quantum chemistry to large systems with the fragment molecular orbital method.pdf",
	methods = "FMO",
	year = 2007
}

@Article{2007-Fedorov-Kitaura-1,
	Author = "Dmitri G. Fedorov and Kazuo Kitaura",
	Title = "{Pair interaction energy decomposition analysis}",
	Journal = "J. Comp. Chem.",
	Volume = "28",
	Number = "1",
	Pages = "222–237",
	abstract = "The energy decomposition analysis {(EDA)} by Kitaura and Morokuma was redeveloped in the framework of the fragment molecular orbital method {(FMO).} The proposed pair interaction energy decomposition analysis {(PIEDA)} can treat large molecular clusters and the systems in which fragments are connected by covalent bonds, such as proteins. The interaction energy in {PIEDA} is divided into the same contributions as in {EDA:} the electrostatic, exchange-repulsion, and charge transfer energies, to which the correlation (dispersion) term was added. The careful comparison to the ab initio {EDA} interaction energies for water clusters with 2-16 molecules revealed that {PIEDA} has the error of at most 1.2 kcal/mol (or about 1\%). The analysis was applied to {(H2O)1024,} the alpha helix, beta turn, and beta strand of polyalanine {(ALA)10,} as well as to the synthetic protein {(PDB} code {1L2Y)} with 20 residues. The comparative aspects of the polypeptide isomer stability are discussed in detail.",
	collection = "molecular interactions",
	doi = "10.1002/jcc.20496",
	localfile = "molecular interactions/2007 - Pair interaction energy decomposition analysis.pdf",
	methods = "PIEDA",
	year = 2007
}

@Article{2007-Ferguson-Denny,
	Author = "Lynnette R. Ferguson and William A. Denny",
	Title = "{Genotoxicity of non-covalent interactions: {DNA} intercalators}",
	Journal = "Mutation Research",
	Volume = "623",
	Pages = "14–23",
	collection = "nucleic acid intercalation",
	doi = "10.1016/j.mrfmmm.2007.03.014",
	localfile = "nucleic acid intercalation/2007 - Genotoxicity of non-covalent interactions: DNA intercalators.pdf",
	year = 2007
}

@Article{2007-Fredrickson,
	Author = "Glenn H. Fredrickson",
	Title = "{Computational field theory of polymers: opportunities and challenges}",
	Journal = "Soft Matter",
	Volume = "3",
	Pages = "1329–1334",
	abstract = "This article highlights my group’s recent progress in developing a new class of computer simulation tools for studying the equilibrium self-assembly and thermodynamic properties of complex polymeric fluids. Our approach utilizes well known formal methods for converting ‘‘particle-based’’ statistical mechanical models of fluids into field theories, but builds on the formalism to develop practical strategies for conducting numerical simulations. This field-theoretic simulation (FTS) approach has the advantage of being efficient in treating polymeric fluids at high density and high molecular weight, unlike conventional simulation methods. I report on recent advances in the methodology and emerging applications, as well as challenges for the future.",
	collection = "polymers",
	doi = "10.1039/b710604a",
	keywords = "polymers",
	localfile = "polymers/2007 - Computational field theory of polymers: opportunities and challenges.pdf",
	year = 2007
}

@Article{2007-Ginzburg-Balijepali,
	Author = "Valeriy V. Ginzburg and Sudhakar Balijepali",
	Title = "{Modeling the thermodynamics of the interaction of nanoparticles with cell membranes}",
	Journal = "Nano Lett.",
	Volume = "7",
	Number = "12",
	Pages = "3716–3722",
	abstract = "Interactions between nanoparticles and cell membranes may play a crucial role in determining the cytotoxicity of nanoparticles as well as their potential application as drug delivery vehicles or therapeutic agents. It has been shown that such interactions are often determined not by biochemical but by physicochemical factors (e.g., nanoparticle size, hydrophobicity, and surface charge density). Here, we propose a mesoscale thermodynamic model describing the transitions in membrane morphology observed after exposure to various types of nanoparticles. Our simulations demonstrate under which conditions (determined by particle size and hydrophilic/hydrophobic interactions) the particles can adsorb into the membrane or compromise the membrane integrity to result in the formation of nanosized holes. The model could be refined to include a more accurate description of various phospholipid membranes, and its results could be applied in the design of specific nanoparticles for various biomedical applications.",
	collection = "nanoparticles",
	doi = "10.1021/nl072053l",
	keywords = "biological nanocomposites; nanospheres; cell membranes; receptors; thin films",
	localfile = "nanoparticles/2007 - Modeling the thermodynamics of the interaction of nanoparticles with cell membranes.pdf",
	year = 2007
}

@Article{2007-Grzywa-DSFSO,
	Author = "Renata Grzywa and Edyta Dyguda-Kazimierowicz and Marcin Sieńczyk and Mikołaj Feliks and W. Andrzej Sokalski and Józef Oleksyszyn",
	Title = "{The molecular basis of urokinase inhibition: from the nonempirical analysis of intermolecular interactions to the prediction of binding affinity}",
	Journal = "J. Mol. Model.",
	Volume = "{13}",
	Number = "{6-7}",
	Pages = "{677–683}",
	abstract = "{Urokinase-type plasminogen activator (uPA) is a trypsin-like serine protease that plays a crucial role in angiogenesis process. In addition to its physiological role in healthy organisms, angiogenesis is extremely important in cancer growth and metastasis, resulting in numerous attempts to understand its control and to develop new approaches to anticancer therapy. The alpha-aminoalkylphosphonate diphenyl esters are well known as highly efficient serine protease inhibitors. However, their mode of binding has not been verified experimentally in details. For a group of average and potent phosphonic inhibitors of urokinase, flexible docking calculations were performed to gain an insight into the active site interactions responsible for observed enzyme inhibition. The docking results are consistent with the previously suggested mode of inhibitors binding. Subsequently, rigorous ab initio study of binding energy was carried out, followed by its decomposition according to the variation-perturbation procedure to reveal stabilization energy constituents with clear physical meaning. Availability of the experimental inhibitory activities and comparison with theoretical binding energy allows for the validation of theoretical models of inhibition, as well as estimation of the possible potential for binding affinity prediction. Since the docking results accompanied by molecular mechanics optimization suggested that several crucial active site contacts were too short, the optimal distances corresponding to the minimum ab initio interaction energy were also evaluated. Despite the deficiencies of force field-optimized enzyme-inhibitor structures, satisfactory agreement with experimental inhibitory activity was obtained for the electrostatic interaction energy, suggesting its possible application in the binding affinity prediction.}",
	collection = "enzymes",
	doi = "10.1007/s00894-007-0193-8",
	localfile = "enzymes/2007 - The molecular basis of urokinase inhibition: from the nonempirical analysis of intermolecular interactions to the prediction of binding affinity.pdf",
	year = 2007
}

@Article{2007-Gunkel-STT,
	Author = "I. Gunkel and S. Stepanow and T. Thurn-Albrecht and S. Trimper",
	Title = "{Fluctuation effects in the theory of microphase separation of diblock copolymers in the presence of an electric field}",
	Journal = "Macromolecules",
	Volume = "40",
	Pages = "2186–2191",
	abstract = "We generalize the Fredrickson-Helfand theory of the microphase separation in symmetric diblock copolymer melts by taking into account the influence of a time-independent homogeneous electric field on the composition fluctuations within the self-consistent Hartree approximation. We predict that electric fields suppress composition fluctuations, and consequently weaken the first-order transition. In the presence of an electric field the critical temperature of the order-disorder transition is shifted toward its mean-field value. The collective structure factor in the disordered phase becomes anisotropic in the presence of the electric field. Fluctuational modulations of the order parameter along the field direction are strongest suppressed. The latter is in accordance with the parallel orientation of the lamellae in the ordered state.",
	collection = "block copolymers",
	doi = "10.1021/ma0623993",
	keywords = "block copolymers; electric fields",
	localfile = "block copolymers/2007 - Fluctuation effects in the theory of microphase separation of diblock copolymers in the presence of an electric field.pdf",
	year = 2007
}

@Article{2007-Hall-LFB,
	Author = "David M. Hall and Turab Lookman and Glenn H. Fredrickson and Sanjoy Banerjee",
	Title = "{Numerical method for hydrodynamic transport of inhomogeneous polymer melts}",
	Journal = "J. Comp. Phys.",
	Volume = "224",
	Pages = "681–698",
	abstract = "We introduce a mesoscale method for simulating hydrodynamic transport and self-assembly of inhomogeneous polymer melts in pressure driven and drag induced ﬂows. This method extends dynamic self-consistent ﬁeld theory (DSCFT) into the hydrodynamic regime where bulk material transport and viscoelastic eﬀects play a signiﬁcant role. The method combines four distinct components as a single coupled system, including (1) non-equilibrium self-consistent ﬁeld theory describing block copolymer self-assembly, (2) multi-ﬂuid Navier–Stokes type hydrodynamics for tracking material transport, (3) constitutive equations modeling viscoelastic phase separation, and (4) rigid wall ﬁelds which represent moving channel boundaries, machine components, and nano-particulate ﬁllers. We also present an eﬃcient, pseudo-spectral implementation for this set of coupled equations which enables practical application of the model in periodic domains. We validate the model by reproducing well known phenomena including equilibrium diblock meso-phases, analytic Stokes ﬂows, and viscoelastic phase separation of glassy/elastic polymer melts. We also demonstrate the stability and accuracy of the numerical implementation by examining its convergence under grid-size reﬁnement.",
	archiveprefix = "arXiv",
	collection = "block copolymers",
	doi = "10.1016/j.jcp.2006.10.027",
	eprint = "cond-mat/0603774v2",
	keywords = "block copolymers; hydrodynamics",
	localfile = "block copolymers/2007 - Numerical method for hydrodynamic transport of inhomogeneous polymer melts.pdf",
	methods = "HSCFT",
	primaryclass = "cond-mat.soft",
	rating = "3",
	read = "2011-11-26",
	year = 2007
}

@Article{2007-Hartung-GB,
	Author = "J. Hartung and A. Gross and U. Bergstrasser",
	Title = "{5-(4-chlorophenyl)-3-hydroxy-4-methylthiazole-2(3{H})-thione:
an instance of bifurcated hydrogen bonding}",
	Journal = "Acta Cryst. E",
	Volume = "63",
	Pages = "O2743 – O2745",
	collection = "halogen bonding",
	doi = "10.1107/S1600536807018016",
	localfile = "halogen bonding/2007 - 5-(4-Chlorophenyl)-3-hydroxy-4-methylthiazole-2(3H)-thione: an instance of bifurcated hydrogen bonding.pdf",
	year = 2007
}

@Article{2007-He-TERBLW,
	Author = "Jinbo He and Ravisubhash Tangirala and Todd Emrick and Thomas P. Russell and Alexander Böker and Xuefa Li",
	Title = "{Self-assembly of nanoparticle-copolymer mixtures: a kinetic point of view}",
	Journal = "Adv. Mater.",
	Volume = "19",
	Pages = "381–385",
	collection = "block copolymer nanocomposites",
	doi = "10.1002/adma.200602094",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2007 - Self-assembly of nanoparticle-copolymer mixtures: a kinetic point of view.pdf",
	methods = "SAXS, SEM, SFM",
	rating = "2",
	read = "2012-03-21",
	systems = "CdSe-TOPO@PS-P2VP",
	year = 2007
}

@Article{2007-Hendry-MBE,
	Author = "Lawrence B. Hendry and Virendra B. Mahesh and Edwin D. Bransome Jr. and Douglas E. Ewing",
	Title = "{Small molecule intercalation with double stranded DNA: implications for normal gene regulation and for predicting the biological efficacy and genotoxicity of drugs and other chemicals}",
	Journal = "Mutation Research",
	Volume = "623",
	Pages = "53–71",
	abstract = "The binding of small molecules to double stranded DNA including intercalation between base pairs has been a topic of research for over 40 years. For the most part, however, intercalation has been of marginal interest given the prevailing notion that binding of small molecules to protein receptors is largely responsible for governing biological function. This picture is now changing with the discovery of nuclear enzymes, e.g. topoisomerases that modulate intercalation of various compounds including certain antitumor drugs and genotoxins. While intercalators are classically ﬂat, aromatic structures that can easily insert between base pairs, our laboratories reported in 1977 that a number of biologically active compounds with greater molecular thickness, e.g. steroid hormones, could ﬁt stereospeciﬁcally between base pairs. The hypothesis was advanced that intercalation was a salient feature of the action of gene regulatory molecules. Two parallel lines of research were pursued: (1) development of technology to employ intercalation in the design of safe and effective chemicals, e.g. pharmaceuticals, nutraceuticals, agricultural chemicals; (2) exploration of intercalation in the mode of action of nuclear receptor proteins. Computer modeling demonstrated that degree of ﬁt of certain small molecules into DNA intercalation sites correlated with degree of biological activity but not with strength of receptor binding. These ﬁndings led to computational tools including pharmacophores and search engines to design new drug candidates by predicting desirable and undesirable activities. The speciﬁc sequences in DNA into which ligands best intercalated were later found in the consensus sequences of genes activated by nuclear receptors implying intercalation was central to their mode of action. Recently, the orientation of ligands bound to nuclear receptors was found to match closely the spatial locations of ligands derived from intercalation into unwound gene sequences suggesting that nuclear receptors may be guiding ligands to DNA with remarkable precision. Based upon multiple lines of experimental evidence, we suggest that intercalation in double stranded DNA is a ubiquitous, natural process and a salient feature of the regulation of genes. If double stranded DNA is proven to be the ultimate target of genomic drug action, intercalation will emerge as a cornerstone of the future discovery of safe and effective pharmaceuticals.",
	collection = "nucleic acid intercalation",
	doi = "10.1016/j.mrfmmm.2007.03.009",
	localfile = "nucleic acid intercalation/2007 - Small molecule intercalation with double stranded DNA: implications for normal gene regulation and for predicting the biological efficacy and genotoxicity of drugs and other chemicals.pdf",
	year = 2007
}

@Article{2007-Hernandez-Trujillo-CFB,
	Author = "Jesús Hernández-Trujillo and Fernando {Cortés-Guzmán} and {De-Chai} Fang and Richard F. W. Bader",
	Title = "{Forces in molecules}",
	Journal = "Faraday Discuss.",
	Volume = "135",
	Pages = "79–95",
	abstract = "Chemistry is determined by the electrostatic forces acting within a collection of nuclei and electrons. The attraction of the nuclei for the electrons is the only attractive force in a molecule and is the force responsible for the bonding between atoms. This is the attractive force acting on the electrons in the Ehrenfest force and on the nuclei in the Feynman force, one that is countered by the repulsion between the electrons in the former and by the repulsion between the nuclei in the latter. The virial theorem relates these forces to the energy changes resulting from interactions between atoms. All bonding, as signified by the presence of a bond path, has a common origin in terms of the mechanics determined by the Ehrenfest, Feynman and virial theorems. This paper is concerned in particular with the mechanics of interaction encountered in what are classically described as 'nonbonded interactions'-are atoms that 'touch' bonded or repelling one another?",
	collection = "molecular structure",
	doi = "10.1039/b604996f",
	localfile = "molecular structure/2007 - Forces in molecules.pdf",
	year = 2007
}

@Article{2007-Hooper-Schweizer,
	Author = "Justin B. Hooper and Kenneth S. Schweizer",
	Title = "{Real space structure and scattering patterns of model polymer nanocomposites}",
	Journal = "Macromolecules",
	Volume = "40",
	Pages = "6998–7008",
	abstract = "Microscopic polymer liquid state theory is employed to study the real space pair correlation functions and collective scattering structure factors of melt polymer nanocomposites composed of hard spheres and adsorbing homopolymers over length scales ranging from monomeric to macroscopic. Increasing filler volume fraction has a profound effect on the polymer matrix, inducing oscillatory reorganization on a length scale commensurate with the nanoparticle diameter. The near contact interfacial monomer-filler pair correlations are suppressed by nanoparticle addition, but on larger scales power law correlations emerge with filler imprinted oscillatory features. Increased nanoparticle volume fraction also substantially changes interfiller packing, inducing a transition from a highly bridged or sterically stabilized type of organization in the infinite dilution limit to more diffuse liquidlike packing characterized by many-particle clustering. Distinctive modifications of the collective polymer structure factor include an increase in the osmotic compressibility, the emergence of a large bound layer or microphase-separation-like scattering peak on a length scale controlled by filler size indicative of distinct bound polymer layers, and a local rarefaction and suppression of the coherence of the monomer cage scale packing. All the real and Fourier space correlations depend in distinctive manners on the physical and chemical variables (filler size, volume fraction, strength and spatial range of the interfacial cohesion) and proximity to the contact aggregation and bridging phase separation boundaries. The bulk modulus of the nanocomposite generically softens with the addition of fillers corresponding to enhanced total density fluctuations.",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma071147e",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2007 - Real space structure and scattering patterns of model polymer nanocomposites.pdf",
	year = 2007
}

@Article{2007-Hopkins-ET,
	Author = "Brian W. Hopkins and Adel M. {ElSohly} and Gregory S. Tschumper",
	Title = "{Reliable structures and energetics for two new delocalized pi-pi prototypes: cyanogen dimer and diacetylene dimer}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "9",
	Number = "13",
	Pages = "1550",
	abstract = "Two new prototype delocalized pi...pi complexes are introduced: the dimers of cyanogen, (N C-C N)(2), and diacetylene, (HC C-C CH)(2). These dimers have properties similar to larger delocalized pi...pi systems such as benzene dimer but are small enough that they can be probed in far greater detail with high accuracy electronic structure methods. Parallel-slipped and T-shaped structures of both cyanogen dimer and diacetylene dimer have been optimized with 15 different procedures. The effects of basis set size, theoretical method, counterpoise correction, and the rigid monomer approximation on the structure and energetics of each dimer have been examined. MP2 and CCSD( T) optimized geometries for all four dimer structures are reported, as well as estimates of the CCSD( T) complete basis set (CBS) interaction energy for every optimized geometry. The data reported here suggest that future optimizations of delocalized pi...pi clusters should be carried out with basis sets of triple-zeta quality. Larger basis sets and the expensive counterpoise correction to the molecular geometry are not necessary. The rigid monomer approximation has very little effect on structure and energetics of these dimers and may be used without consequence. Due to a consistent cancellation of errors, optimization with the MP2 method leads to CCSD(T)/CBS interaction energies that are within 0.2 kcal mol(-1) of those for structures optimized with the CCSD( T) method. Future studies that aim to resolve structures separated by a few tenths of a kcal mol(-1) should consider the effects of optimization with the CCSD(T) method.",
	collection = "stacking",
	doi = "10.1039/b616878g",
	localfile = "molecular stacking/2007 - Reliable structures and energetics for two new delocalized pi-pi prototypes: cyanogen dimer and diacetylene dimer.pdf",
	shorttitle = "Reliable structures and energetics for two new delocalized ?",
	year = 2007
}

@Article{2007-Houlding-LP,
	Author = "S. Houlding and S. Y. Liem and Paul L. A. Popelier",
	Title = "{A polarizable high-rank quantum topological electrostatic potential developed using neural networks: Molecular dynamics simulations on the hydrogen fluoride dimer}",
	Journal = "Int. J. Quant. Chem.",
	Volume = "107",
	Number = "14",
	Pages = "2817–2827",
	abstract = "The {HF} molecule is a simple polar system that serves as a prototype for developing new potentials. Here we build on earlier work {[Liem} and Popelier, J Chem Phys 2003, 119, 4560] in which a high-rank multipolar potential was used to simulate liquid {HF.} That work was the first example of high-rank multipole moments (up to hexadecapole) being employed in conjunction with multipolar Ewald summation in a molecular dynamics simulation. This potential is now extended with polarization, which is delivered by artificial neural networks. The neural nets predict how atomic multipole moments change as the position of neighboring molecules vary. This novel approach is successfully tested on the {HF} dimer in vacuum. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007",
	collection = "molecular electrostatics",
	doi = "10.1002/qua.21507",
	localfile = "molecular electrostatics/2007 - A polarizable high-rank quantum topological electrostatic potential developed using neural networks: molecular dynamics simulations on the hydrogen fluoride dimer.pdf",
	shorttitle = "A polarizable high-rank quantum topological electrostatic potential developed using neural networks",
	year = 2007
}

@Article{2007-Huang-WJL,
	Author = "Ching-Mao Huang and Kung-Hwa Wei and U-Ser Jeng and Keng S. Liang",
	Title = "{Structural evolution of poly(styrene-b-4-vinylpyridine) diblock copolymer-gold nanoparticle mixtures from solution to solid state}",
	Journal = "Macromolecules",
	Volume = "40",
	Pages = "5067–5074",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma0704764",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2007 - Structural evolution of poly(styrene-b-4-vinylpyridine) diblock copolymer and gold nanoparticle mixtures from solution to solid state.pdf",
	methods = "TEM, SAXS, TGA, XPS",
	rating = "2",
	read = "2012-03-21",
	systems = "Au-phenylethanethiol@PS-P4VP",
	year = 2007
}

@Article{2007-Hubner-Klopper,
	Author = "Olaf Hubner and Wim Klopper",
	Title = "{Interaction of Dihydrogen with Small and Light Molecules}",
	Journal = "J. Phys. Chem. A",
	Volume = "111",
	Number = "12",
	Pages = "2426–2433",
	collection = "hydrogen sorption",
	doi = "10.1021/jp0677647",
	localfile = "hydrogen sorption/2007 - Interaction of dihydrogen with small and light molecules.pdf",
	systems = "digydrogen near small molecules",
	year = 2007
}

@Article{2007-Itahara-Imaizumi,
	Author = "Toshio Itahara and Kozo Imaizumi",
	Title = "{Role of Nitrogen Atom in Aromatic Stacking}",
	Journal = "J. Phys. Chem. B",
	Volume = "111",
	Number = "8",
	Pages = "2025–2032",
	abstract = "Aromatic stacking of 9,9`-(alpha,omega-alkanediyl)bis[adenine] (1), 1,1`-(alpha,omega-alkanediyl)bis[benzimidazole] (2), and 9-[omega-(benzimidazol-1-yl)alkyl]adenine (3) were studied at low concentrations of these compounds by means of {UV} and {NMR} spectroscopies. The {UV} hypochromic effect at T {oC} was determined as the ratio of the integration strength B at T {oC} {(T} = 27, 40, and 50) to that at 60 {oC.} The {UV} hypochromic effects of 1 and 3 were remarkable in water, suggesting a formation of intramolecular aromatic stacking, while the {UV} data of 2 did not present unambiguous evidence supporting aromatic stacking. A difference of chemical shift of each aromatic ring proton between 27 and 80 {oC,} that is Deltadelta = delta(80 {oC)} delta(27 {oC),} was given as an indication of the aromatic stacking in the {NMR} study. On the basis the data of Deltadelta, 1 and 3 were stabilized by a stacking interaction in the buffer solution at {pD} 7.0 but not in the organic solvents. On the other hand, the {NMR} data did not indicate the formation of aromatic stacking of 2 either in the organic solvents or in the aqueous solution. The thermodynamic parameters of the intramolecular aromatic stacking of 3 were determined by means of {NMR} spectroscopy.",
	collection = "stacking",
	doi = "10.1021/jp0664521",
	localfile = "molecular stacking/2007 - Role of nitrogen atom in aromatic stacking.pdf",
	year = 2007
}

@Article{2007-Ito-FMNT,
	Author = "Mika Ito and Kaori Fukuzawa and Yuji Mochizuki and Tatsuya Nakano and Shigenori Tanaka",
	Title = "{Ab initio fragment molecular orbital study of molecular interactions between liganded retinoid {X} receptor and its coactivator: {R}oles of helix 12 in the coactivator binding mechanism}",
	Journal = "J. Phys. Chem. B",
	Volume = "111",
	Number = "13",
	Pages = "3525 – 3533",
	collection = "proteins",
	doi = "10.1021/jp070054w",
	localfile = "proteins/2007 - Ab initio fragment molecular orbital study of molecular interactions between liganded retinoid X receptor and its coactivator.pdf",
	year = 2007
}

@Article{2007-Jacobson-MA,
	Author = "Ken Jacobson and Ole G. Mouritsen and Richard G. W. Anderson",
	Title = "{Lipid rafts: at a crossroad between cell biology and physics}",
	Journal = "Nature Cell Biol.",
	Volume = "9",
	Number = "1",
	Pages = "7–14",
	abstract = "Membrane lateral heterogeneity is accepted as a requirement for the function of biological membranes and the notion of lipid rafts gives specificity to this broad concept. However, the lipid raft field is now at a technical impasse because the physical tools to study biological membranes as a liquid that is ordered in space and time are still being developed. This has lead to a disconnection between the concept of lipid rafts as derived from biochemical and biophysical assays and their existence in the cell. Here, we compare the concept of lipid rafts as it has emerged from the study of synthetic membranes with the reality of lateral heterogeneity in biological membranes. Further application of existing tools and the development of new tools are needed to understand the dynamic heterogeneity of biological membranes.",
	collection = "cells",
	doi = "10.1038/ncb0107-7",
	keywords = "cell membranes",
	localfile = "cells/2007 - Lipid rafts: at a crossroad between cell biology and physics.pdf",
	shorttitle = "Lipid rafts",
	year = 2007
}

@Article{2007-Jadzinsky-CABK,
	Author = "Pablo D. Jadzinsky and Guillermo Calero and Christopher J. Ackerson and David A. Bushnell and Roger D. Kornberg",
	Title = "{Structure of a thiol monolayer-protected gold nanoparticle at 1.1A resolution}",
	Journal = "Science",
	Volume = "318",
	Pages = "430–433",
	abstract = "Structural information on nanometer-sized gold particles has been limited, due in part to the problem of preparing homogeneous material. Here we report the crystallization and x-ray structure determination of a p-mercaptobenzoic acid (p-MBA)–protected gold nanoparticle, which comprises 102 gold atoms and 44 p-MBAs. The central gold atoms are packed in a Marks decahedron, surrounded by additional layers of gold atoms in unanticipated geometries. The p-MBAs interact not only with the gold but also with one another, forming a rigid surface layer. The particles are chiral, with the two enantiomers alternating in the crystal lattice. The discrete nature of the particle may be explained by the closing of a 58-electron shell.",
	collection = "nanoparticles",
	doi = "10.1126/science.1148624",
	keywords = "nanoparticle structure; nanospheres",
	localfile = "nanoparticles/2007 - Structure of a thiol monolayer-protected gold nanoparticle at 1.1A resolution.pdf",
	rating = "2",
	year = 2007
}

@Article{2007-Janovec-SKPKUMBPI,
	Author = "Ladislav Janovec and Danica Sabolová and Mária Kožurková and Helena Paulíková and Pavol Kristian and Ján Ungvarský and Erika Moravčiková and Mária Bajdichová and Dusan Podhradský and Ján Imrich",
	Title = "{Synthesis, {DNA} Interaction, and Cytotoxic Activity of a Novel {Proflavine−Dithiazolidinone} Pharmacophore}",
	Journal = "Bioconjugate Chem.",
	Volume = "18",
	Number = "1",
	Pages = "93–100",
	abstract = "Five novel proflavinedithiazolidinone derivatives 4a4e have been designed and synthesized by the reaction of dialkyl acridin-3,6-diyl dithioureas 3a3e with methyl bromoacetate. The binding affinity of dithiazolidinone hydrochlorides 5a5e with calf thymus {DNA} and plasmid {(pUC19)} {DNA} was investigated by a variety of spectroscopic techniques including {UVvis,} fluorescence, and {CD} spectroscopy. The effects of 5a5e on the thermal denaturation profiles of calf thymus {DNA} were also studied. From spectrophotometric and spectrofluorimetric titrations, the binding constants for the {pUC19} {DNAdrug} complexes were determined {(K} = 6.22.2 104 M-1). In vitro cytotoxic activities of compounds 5a5e toward murine leukemia cell line L1210 and human uterus carcinoma {HeLa} cells were also examined. 2`,2` {`-[(Acridin-3,6-diyl)diimino]-3`,3`} `-dipropyl-1,3-dithiazolidin-4-one hydrochloride (5b) showed the highest activity against these cells with {IC50} values of 6.3 {muM} and 12.9 {muM} over the course of 72 h.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/bc060168v",
	localfile = "nucleic acid intercalation/2007 - Synthesis, DNA intercalation, and cytotoxic activity of a novel proflavine-dithiazolidinone pharmacophore.pdf",
	year = 2007
}

@Article{2007-Janowski-FP,
	Author = "Tomasz Janowski and Alan R. Ford and Peter Pulay",
	Title = "{Parallel calculation of coupled cluster singles and doubles wave functions using array files}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "3",
	Pages = "1368–1377",
	abstract = "A new parallel implementation of the Coupled Cluster Singles and Doubles (CCSD) and related wave functions (e.g Quadratic Configuration Interaction, QCI, and Coupled Electron Pair, CEPA) is described, based on the Array Files middleware. The program can handle large basis sets, even without utilizing symmetry, on modest distributed memory workstation clusters. High computational efficiency is achieved by formulating all major operations in terms of matrix multiplications. Timings are provided for systems with 50-228 valence electrons and up to 1144 basis functions, with little or no symmetry. Our largest calculation (QCISD/aug-cc-pVQZ for the parallel displaced benzene dimer) uses 1512 basis functions. Calculations on the benzene dimer show that the usual procedure of estimating the effect of basis set enlargement from second-order Møller-Plesset (MP2) calculations is less reliable than previously assumed. Replacing the weak pair amplitudes in CCSD/QCISD calculations by MP2 amplitudes affects the calculated energy only slightly.",
	collection = "cheminformatics",
	doi = "10.1021/ct700048u",
	localfile = "cheminformatics/2007 - Parallel calculation of coupled cluster singles and doubles wave functions using array files.pdf",
	year = 2007
}

@Article{2007-Janowski-Pulay,
	Author = "Tomasz Janowski and Peter Pulay",
	Title = "{High accuracy benchmark calculations on the benzene dimer potential energy surface}",
	Journal = "Chem. Phys. Lett.",
	Volume = "447",
	Number = "1-3",
	Pages = "27–32",
	abstract = "Using our new parallel {CCSD(T)/QCISD(T)} program, we have optimized the geometries of the main conformations and performed potential scans on the benzene dimer at the {QCISD(T)/aug-cc-pVTZ} level. For each optimized geometry, single point energies were evaluated at the {QCISD(T)/aug-cc-pVxZ} level, where x = {D,T,Q.} The largest calculation, {QCISD(T)/aug-cc-pVQZ} involves 30 correlated orbitals and 1512 basis functions and is thus among the largest coupled cluster type calculations performed to date. The results allow a critical evaluation of {MP2-based} basis set extrapolation procedures.",
	collection = "stacking",
	doi = "10.1016/j.cplett.2007.09.003",
	localfile = "molecular stacking/2007 - High accuracy benchmark calculations on the benzene dimer potential energy surface.pdf",
	year = 2007
}

@Article{2007-Jurecka-CHS,
	Author = "Petr Jurečka and Jiří Černý and Pavel Hobza and Dennis R. Salahub",
	Title = "{Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations}",
	Journal = "J. Comp. Chem.",
	Volume = "28",
	Pages = "555–569",
	collection = "molecular interactions",
	doi = "10.1002/jcc.20570",
	localfile = "molecular interactions/2007 - Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calcualtions.pdf",
	methods = "CCSD(T), MP2",
	systems = "S22",
	year = 2007
}

@Article{2007-Khaliullin-CLBH,
	Author = "Rustam Z. Khaliullin and Erika A. Cobar and Rohini C. Lochan and Alexis T. Bell and Martin Head-Gordon",
	Title = "{Unravelling the Origin of Intermolecular Interactions Using Absolutely Localized Molecular Orbitals}",
	Journal = "J. Phys. Chem. A",
	Volume = "111",
	Number = "36",
	Pages = "8753–8765",
	abstract = "An energy decomposition analysis {(EDA)} method is proposed to isolate physically relevant components of the total intermolecular interaction energies such as the contribution from interacting frozen monomer densities, the energy lowering due to polarization of the densities, and the further energy lowering due to charge-transfer effects. This method is conceptually similar to existing {EDA} methods such as Morokuma analysis but includes several important new features. The first is a fully self-consistent treatment of the energy lowering due to polarization, which is evaluated by a self-consistent field calculation in which the molecular orbital coefficients are constrained to be block-diagonal (absolutely localized) in the interacting molecules to prohibit charge transfer. The second new feature is the ability to separate forward and back-donation in the charge-transfer energy term using a perturbative approximation starting from the optimized block-diagonal reference. The newly proposed {EDA} method is used to understand the fundamental aspects of intermolecular interactions such as the degree of covalency in the hydrogen bonding in water and the contributions of forward and back-donation in synergic bonding in metal complexes. Additionally, it is demonstrated that this method can be used to identify the factors controlling the interaction of the molecular hydrogen with open metal centers in potential hydrogen storage materials and the interaction of methane with rhenium complexes.",
	collection = "molecular interactions",
	doi = "10.1021/jp073685z",
	localfile = "molecular interactions/2007 - Unravelling the origin of intermolecular interactions using absolutely localized molecular orbitals.pdf",
	year = 2007
}

@Article{2007-Kim-BHCPJYK,
	Author = "Bumjoon J. Kim and Joona Bang and Craig J. Hawker and Julia J. Chiu and David J. Pine and Se Gyu Jang and Seung-Man Yang and Edward J. Kramer",
	Title = "{Creating surfactant nanoparticles for block copolymer composites through surface chemistry}",
	Journal = "Langmuir",
	Volume = "23",
	Pages = "12693–12703",
	Note = "This article is a reference point for 2009-Kim-Matsen and other computations of functionalized nanoparticles. The PS-SH ligand used had a MW of 1.5 or 3.4 kg/mol, which correspond to 15 and 33 styrene monomers. The P2VP-SH lignds of 1.5 and 3 kg/mol correspond to 15 and 29 monomers. The 196 kg/mol BCP contains around 1900 monomers per chain.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/la701906n",
	keywords = "block copolymers; nanoparticle distribution; nanoparticle grafts; nanospheres; optical properties; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2007 - Creating surfactant nanoparticles for block copolymer composites through surface chemistry.pdf",
	methods = "TEM",
	systems = "Au-PS@PS-P2VP, Au-P2VP@PS-P2VP",
	year = 2007
}

@Article{2007-Kim-FHK,
	Author = "Bumjoon J. Kim and Glenn H. Fredrickson and Craig J. Hawker and Edward J. Kramer",
	Title = "{Nanoparticle surfactants as a route to bicontinuous block copolymer morphologies}",
	Journal = "Langmuir",
	Volume = "23",
	Pages = "7804–7809",
	Note = "This article preceeds 2007-Kim-BHCPJYK, which is important for 2009-Kim-Matsen and other theoretical reports. The main finding is a critical areal chain density, below which NPs go to the interface to form a bicontinuous morphology.",
	abstract = "The surface chemistry of nanoparticles can be modified so that these particles behave like surfactants and localize at interfaces between two fluids. We demonstrate that small volume fractions φP of such surfactant nanoparticles added to lamellar diblock copolymers lead initially to a decrease in lamellar thickness with φP, a consequence of decreasing interfacial tension, up to a critical value of φP, beyond which the block copolymer adopts a bicontinuous morphology. These bicontinuous morphologies have stable domain spacings below 100 nm that further decrease with increasing φP and offer new routes to nanoscopically engineered polymer films with potential photovoltaic, fuel cell, and battery applications.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/la700507j",
	keywords = "block copolymers; mesophase transitions; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2007 - Nanoparticle surfactants as a route to bicontineuous block copolymer morphologies.pdf",
	methods = "TEM",
	systems = "Au-PS(2.38 chains/nm2)@PS-b-P2VP(196 kg/mol)",
	year = 2007
}

@Article{2007-Krishnamoorti-Vaia,
	Author = "Ramanan Krishnamoorti and Richard A. Vaia",
	Title = "{Polymer nanocomposites}",
	Journal = "J. Polym. Sci. Pt. B-Polym. Phys.",
	Volume = "45",
	Number = "24",
	Pages = "3252–3256",
	abstract = "Polymer nanocomposites are distinguished by the convergence of length scales corresponding to the radius of gyration of the polymer chains, a dimension of the nanoparticle and the mean distance between the nanoparticles. The consequences of this convergence on the physics of the polymer chains are considered, and some of the outstanding issues and their potential consequences on structure—property relations for polymer nanocomposites are highlighted.",
	collection = "polymer nanocomposites",
	doi = "10.1002/polb.21319",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2007 - Polymer nanocomposites.pdf",
	type = "Viewpoint",
	year = 2007
}

@Article{2007-Kurisaki-FKMNICRWT,
	Author = "I. Kurisaki and Kaori Fukuzawa and Y. Komeiji and Yuji Mochizuki and Tatsuya Nakano and J. Imada and A. Chmielewski and S. M. Rothstein and Hirofumi Watanabe and Shigenori Tanaka",
	Title = "{Visualization analysis of inter-fragment interaction energies of {CRP}-c{AMP}-{DNA} complex based on the fragment molecular orbital method}",
	Journal = "Biophys. Chem.",
	Volume = "130",
	Number = "1-2",
	Pages = "1 – 9",
	abstract = "A visualization method for inter-fragment interaction energies (IFIEs) of biopolymers is presented on the basis of the fragment molecular orbital (FMO) method. The IFIEs appropriately illustrate the information about the interaction energies between the fragments consisting of amino acids, nucleotides and other molecules. The IFTEs are usually analyzed in a matrix form called an IFTE matrix. Analyzing the IFIE matrix, we detect important fragments for the function of biomolecular systems and quantify the strength of interaction energies based on quantum chemistry, including the effects of charge transfer, electronic polarization and dispersion force. In this study, by analyzing a protein-DNA complex, we report a visual representation of the IFTE matrix, a so-called IFTE map. We comprehensively examine what information the THE map contains concerning structures and stabilities of the protein-DNA complex.",
	collection = "proteins",
	localfile = "proteins/2007 - Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex.pdf",
	methods = "FMO",
	year = 2007
}

@Article{2007-Labar-Michaux,
	Author = "Geoffray Labar and Catherine Michaux",
	Title = "{Fatty acid amide hydrolase: from characterization to therapeutics}",
	Journal = "Chem. Biodivers.",
	Number = "4",
	Pages = "1882–1902",
	abstract = "Fatty acid amide hydrolase (FAAH) is an integral membrane enzyme within the amidase-signature family that terminates the action of several endogenous lipid messengers, including oleamide and the endocannabinoid anandamide. The hydrolysis of such messengers leads to molecules devoid of biological activity, and, therefore, modulates a number of neurobehavioral processes in mammals, including pain, sleep, feeding, and locomotor activity. Investigations into the structure and function of FAAH, its biological and therapeutic implications, as well as a description of different families of FAAH inhibitors are the topic of this review.",
	collection = "enzymes",
	localfile = "enzymes/2007 - Fatty acid hydrolase: from characterization to therapeutics.pdf",
	year = 2007
}

@Article{2007-Laicer-MT,
	Author = "Castro S. T. Laicer and Randy A. Mrozek and T. Andrew Taton",
	Title = "{Domain nucleation dictates overall nanostructure in composites of block copolymers and model nanorods}",
	Journal = "Polymer",
	Volume = "48",
	Pages = "1316–1328",
	Note = "Demonstrates BCP domain alignment using long nanoparticle seeds; the accompanying DDFT simulations seem problematic.",
	abstract = "The detailed nanostructure of composites formed from block copolymers and nanoparticles is known to depend sensitively on the preferred morphology of the block copolymer, on the shapes of the particles, and on interactions between the two components. But it can also depend on the kinetics of self-assembly in the polymer, and there are circumstances under which the kinetics of morphologically selective domain nucleation and growth determine the overall nanostructure of the composite. To study the mechanism of morphological seeding in block-copolymer nanocomposites, we have combined cylinder phases of polystyrene-block-polyisoprene diblock (as a solution in dibutylphthalate) and poly(styrene-block-isoprene-block-styrene) triblock (as a blend with homopolystyrene) copolymers with gold nanorods of different diameters and surface treatments. Polarized optical microscopy and transmission electron microscopy on these composites demonstrate that the nanorods selectively nucleate coaxial domains of copolymer cylinders (i.e., domains of cylinders aligned along the same axis as the nanorod). These single nucleation events occur regardless of nanorod diameter and surface character, and determine the order of most of the surrounding polymer. Mesoscale modeling of the nucleation process, performed with nanorods of different diameters and with different polymeresurface interactions, illustrates the mechanism by which copolymer-dispersed nanorods with different sizes and surface chemistry can template the organization of cylindrical copolymer domains.",
	collection = "block copolymer nanocomposites",
	doi = "10.1016/j.polymer.2006.12.056",
	keywords = "block copolymers; nanorods; mesophase nucleation; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2007 - Domain nucleation dictates overall nanostructure in composites of block copolymers and model nanorods.pdf",
	methods = "SAXS, AFM, TEM, SEM, DDFT",
	systems = "Au(rods)@PS-PI",
	year = 2007
}

@Article{2007-Lan-FB,
	Author = "Qiang Lan and Lorraine F. Francis and Frank S. Bates",
	Title = "{Silica nanoparticle dispersions in homopolymer versus block copolymer}",
	Journal = "J. Polym. Sci. Pt. B-Polym. Phys.",
	Volume = "45",
	Pages = "2284–2299",
	abstract = "Silica nanoparticles (17 pm 4 nm in diameter) were modified by grafting polystyrene chains to the surfaces using atom transfer radical polymerization (ATRP). The molecular weight of the grafted chains ranged from 8 to 48 kDa. These modified nanoparticles were mixed in solution with poly(styrene) homopolymer (18-120 kDa) and symmetric poly(styrene-b-butadiene) (PS-PB) diblock copolymer (34-465 kDa) and the states of dispersion in the dried composites were characterized by TEM. In the so-called wet brush limit, when the graft molecualr weight equals or exceeds the matrix value, the silica particles form a uniform random dispersion in poly(styrene). Increasing the hompolymer matrix molecular weight above the graft value results in particle clustering and macroscopic-phase separation. Mixtures of the lamellar formaing block copolymer and nanoparticles exhibit a very different trend, with particle clustering at the lower PS-PB molecular weights and dispersion at the highest value. This latter finding is rationalized on the basis of packing constraints associated with lamnellar order and the effective particle dimensions, and the degree of solvation at ordering, both of which favor higher molecualr weight block copolymers.",
	collection = "block copolymer nanocomposites",
	doi = "10.1002/polb.21251",
	keywords = "block copolymers; nanoparticle aggregation; nanoparticle distribution; nanoparticle grafts; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2007 - Silica nanoparticle dispersions in homopolymer versus block copolymer.pdf",
	methods = "TGA, GPC, DLS, SAXS, TEM",
	systems = "silica-PS@PS-PB",
	year = 2007
}

@Article{2007-Larkin-BBCMMVWWLTGH,
	Author = "M. A. Larkin and G. Blackshields and N. P. Brown and R. Chenna and P. A. McGettigan and H. McWilliam and F. Valentin and I. M. Wallace and A. Wilm and R. Lopez and J. D. Thompson and T. J. Gibson and D. G. Higgins",
	Title = "{Clustal W and Clustal X version 2.0}",
	Journal = "Bioinformatics",
	Volume = "23",
	Number = "21",
	Pages = "2947–2948",
	abstract = "Summary: The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in Cþþ. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. Availability: The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/ clustalw2/\ Contact: clustalw@ucd.ie",
	collection = "cheminformatics",
	doi = "10.1093/bioinformatics",
	keywords = "software",
	localfile = "cheminformatics/2007 - Clustal W and Clustal X version 2.0.pdf",
	year = 2007
}

@Article{2007-Lee-LSRWT,
	Author = "Byeongdu Lee and Chieh-Tsung Lo and Soenke Seifert and Nancy L. Dietz Rago and Randall E. Winans and Pappanan Thiyagarajan",
	Title = "{Anomalous small-angle X-ray scattering characterization of bulk block copolymer-nanoparticle composites}",
	Journal = "Macromolecules",
	Volume = "40",
	Pages = "4235–4243",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma062916h",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2007 - Anomalous small-angle X-ray scattering characterization of bulk block copolymer-nanoparticle composites.pdf",
	methods = "SAXS, TEM",
	rating = "2",
	read = "2012-03-21",
	systems = "Au-PS@PS-P2VP",
	year = 2007
}

@Article{2007-Lee-RO,
	Author = "David Lee and Oliver Redfern and Christine Orengo",
	Title = "{Predicting protein function from sequence and structure}",
	Journal = "Nat. Rev. Mol. Cell Biol.",
	Volume = "8",
	Pages = "995–1005",
	collection = "proteins",
	doi = "10.1038/nrm2281",
	keywords = "protein function; homology",
	localfile = "proteins/2007 - Predicting protein function from sequence and structure.pdf",
	ratings = "2",
	read = "2012-08-02",
	year = 2007
}

@Article{2007-Lo-LPRSWT,
	Author = "Chieh-Tsung Lo and Byeongdu Lee and Vilas G. Pol and Nancy L. Dietz Rago and Soenke Seifert and Randall E. Winans and Pappanan Thiyagarajan",
	Title = "{Effect of molecular properties of block copolymers and nanoparticles on the morphology of self-assembled bulk nanocomposites}",
	Journal = "Macromolecules",
	Volume = "40",
	Pages = "8302–8310",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma070835v",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2007 - Effect of molecular properties of block copolymers and nanoparticles on the morphology of self-assembled bulk nanocomposites.pdf",
	methods = "SAXS, TEM",
	rating = "2",
	read = "2012-03-21",
	systems = "Au-PS@PS-P2VP",
	year = 2007
}

@Article{2007-Lo-LRWT,
	Author = "Chieh-Tsung Lo and Byeongdu Lee and Nancy L. Dietz Rago and Randall E. Winans and Pappanan Thiyagarajan",
	Title = "{Strategy for better ordering in diblock copolymer based nanocomposites}",
	Journal = "Macromol. Rapid Commun.",
	Volume = "28",
	Pages = "1607–1612",
	Note = "The idea presented here is simple and general, and could be used for other systems.",
	collection = "block copolymer nanocomposites",
	doi = "10.1002/marc.200700412",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2007 - Strategy for better ordering in diblock copolymer based nanocomposites.pdf",
	methods = "SAXS, TEM",
	rating = "2",
	read = "2012-03-21",
	systems = "Au-PS@PS-P2VP",
	year = 2007
}

@Article{2007-Lo-LWT,
	Author = "Chieh-Tsung Lo and Byeongdu Lee and Randall E. Winans and Pappanan Thiyagarajan",
	Title = "{Phase behavior of nanoparticle-diblock copolymer complex in a selective solvent}",
	Journal = "Macromolecules",
	Volume = "40",
	Pages = "641–647",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma061950t",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2007 - Phase behavior of nanoparticle-diblock copolymer complex in a selective solvent.pdf",
	methods = "SANS",
	rating = "2",
	read = "2012-03-21",
	systems = "Au-PS@PS-P2VP",
	year = 2007
}

@Article{2007-Lodola-MZTPHM,
	Author = "Alessio Lodola and Marco Mor and Jolanta Żurek and Giorgio Tarzia and Daniele Piomelli and Jeremy N. Harvey and Adrian J. Mulholland",
	Title = "{Conformational Effects in Enzyme Catalysis: Reaction via a High Energy Conformation in Fatty Acid Amide Hydrolase}",
	Journal = "Biophys. J.",
	Volume = "92",
	Number = "2",
	Pages = "L20–L22",
	abstract = "Quantum mechanics/molecular mechanics and molecular dynamics simulations of fatty acid amide hydrolase show that reaction (amide hydrolysis) occurs via a distinct, high energy conformation. This unusual ﬁnding has important implications for fatty acid amide hydrolase, a key enzyme in the endocannabinoid system. These results demonstrate the importance of structural ﬂuctuations and the need to include them in the modeling of enzyme reactions. They also show that approaches based simply on studying enzyme-substrate complexes can be misleading for understanding biochemical reactivity.",
	collection = "enzymes",
	doi = "10.1529/biophysj.106.098434",
	keywords = "hydrolysis",
	localfile = {enzymes/2007 - Conformational effects in enzyme catalysis; reaction via a high energy conformation in fatty acid amide hydrolase.pdf},
	methods = "MD, QM/MM",
	shorttitle = "Conformational Effects in Enzyme Catalysis",
	systems = "fatty acid amide hydrolase",
	year = 2007
}

@Article{2007-McGarrity-FFM,
	Author = "Erin S. McGarrity and Amalie L. Frischknecht and L. J. D. Frink and Michael E. Mackay",
	Title = "{Surface-induced first-order transition in athermal polymer-nanoparticle blends}",
	Journal = "Phys. Rev. Lett.",
	Volume = "99",
	Pages = "238302",
	abstract = "We investigate the phase behavior of athermal polymer-nanoparticle blends near a substrate. We apply a recent ﬂuids density functional theory of Tripathi and Chapman to a simple model of the blend as a mixture of hard spheres and freely jointed hard chains, near a hard wall. We ﬁnd that there is a ﬁrst-order phase transition in which the nanoparticles expel the polymer from the surface to form a monolayer. The nanoparticle transition density depends on the length of the polymer and the overall bulk density of the system. The effect is due both to packing entropy effects related to size asymmetry between the components and to the polymer conﬁgurational entropy. The simplicity of the system allows us to understand the so-called ‘‘entropic-push’’ observed in experiments.",
	collection = "polymer nanocomposites",
	doi = "10.1103/PhysRevLett.99.238302",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2007 - Surface-induced first-order transition in athermal polymer-nanoparticle blends.pdf",
	year = 2007
}

@Article{2007-Murray-LCP,
	Author = "Jane S. Murray and Pat Lane and Timothy Clark and Peter Politzer",
	Title = "{Sigma-hole bonding: molecules containing group {VI} atoms}",
	Journal = "J. Mol. Model.",
	Volume = "13",
	Number = "10",
	Pages = "1033 – 1038",
	collection = "halogen bonding",
	doi = "10.1007/s00894-007-0225-4",
	localfile = "halogen bonding/2007 - Sigma-hole bonding: molecules containing group VI atoms.pdf",
	size = "6 p.",
	year = 2007
}

@Article{2007-Murray-LP,
	Author = "Jane S. Murray and Pat Lane and Peter Politzer",
	Title = "{A predicted new type of directional noncovalent interaction}",
	Journal = "Int. J. Quant. Chem.",
	Volume = "107",
	Number = "12",
	Pages = "2286 – 2292",
	abstract = "The electrostatic potentials computed on the surfaces of a series of molecules RX, where X is a Group V atom, show that some of these atoms have regions of positive potential on their outer surfaces, approximately on the extensions of the R-X bonds. This suggests the likelihood of weak, directional noncovalent interactions between such atoms and nucleophiles, paralleling what has already been established for Groups VI and VII. The origins and relative strengths of the positive regions are explained in terms of the sigma-hole concept, supported by natural bond orbital analyses. MP2/6-311++G(3df,2p) calculations confirm the formation of stable complexes between five such Group V molecules and the model nucleophile HCN. (c) 2007 Wiley Periodicals, Inc.",
	collection = "halogen bonding",
	doi = "10.1002/qua.21352",
	localfile = "halogen bonding/2007 - A predicted new type of directional noncovalent interaction.pdf",
	year = 2007
}

@Article{2007-Mutch-vDE,
	Author = "Kevin J. Mutch and Jeroen S. {van Duijneveldt} and Julian Eastoe",
	Title = "{Colloid–polymer mixtures in the protein limit}",
	Journal = "Soft Matter",
	Volume = "3",
	Pages = "155–167",
	collection = "polymers",
	doi = "10.1039/b611137h",
	keywords = "polymer nanocomposites",
	localfile = "polymers/2007 - Colloid-polymer mixtures in the protein limit.pdf",
	type = "Review",
	year = 2007
}

@Article{2007-Nakayama-FKSSKASSMI,
	Author = "T. Nakayama and H. Fukuda and T. Kamikawa and Y. Sakamoto and A. Sugita and M. Kawasaki and T. Amano and H. Sato and S. Sakaki and I. Morino and G. Inoue",
	Title = "{Effective interaction energy of water dimer at room temperature: {A}n experimental and theoretical study}",
	Journal = "J. Chem. Phys.",
	Volume = "127",
	Number = "13",
	abstract = "Buffer-gas pressure broadening for the nu(1)+nu(3) band of H2O at 1.34-1.44 mu m 2007 American Institute of Physics.for a variety of buffer gases was investigated at room temperature using continuous-wave cavity ring-down spectroscopy. The effective interaction energy of water dimer under room temperature conditions was evaluated from the pressure broadening coefficients for rare gases using Permenter-Seaver's relation. Monte Carlo simulations were performed using ab initio molecular orbital calculations to evaluate the interaction energies for the water dimer at 300 K. In this theoretical calculation, the orientations of the two water molecules were statistically treated.",
	collection = "hydrogen bonding",
	doi = "10.1063/1.2773726",
	keywords = "hydrogen bonding; water",
	localfile = "hydrogen bonding/2007 - Effective interaction energy of water dimer at room temperature: An experimental and theoretical study.pdf",
	systems = "water dimer",
	year = 2007
}

@Article{2007-Negri-Saendig,
	Author = "Fabrizia Negri and Nadja Saendig",
	Title = "{Tuning the physisorption of molecular hydrogen: binding to aromatic, hetero-aromatic and metal-organic framework materials}",
	Journal = "Theor. Chem. Acc.",
	Volume = "118",
	Number = "1",
	Pages = "149–163",
	collection = "hydrogen sorption",
	doi = "10.1007/s00214-007-0254-1",
	localfile = "hydrogen sorption/2007 - Tuning the physisorption of molecular hydrogen: binding to aromatic, hetero-aromatic and metal-organic framework materials.pdf",
	shorttitle = "Tuning the physisorption of molecular hydrogen",
	year = 2007
}

@Article{2007-Nelson-FD,
	Author = "Stephanie M. Nelson and Lynnette R. Ferguson and William A. Denny",
	Title = "{Non-covalent ligand/DNA interactions: minor groove binding agents}",
	Journal = "Mutation Research",
	Volume = "623",
	Pages = "24–40",
	abstract = "An understanding of the mechanism by which minor groove binding agents interact with DNA has led to the design of agents that can reversibly bind with high selectivity to extended DNA target sequences. Simple compounds, such as the polypyrroles and the bis-benzimidazoles, have been used as carriers for alkylating agents effectively directing alkylation to speciﬁc DNA sequences. The spectrum of DNA alkylation and mutation by classical alkylators, such as nitrogen mustards, has been profoundly modiﬁed by such attachment. The observed “side-by-side” binding of small polypyrrole antibiotics has led to the design of synthetic hairpin polyamides with programmable DNA sequence selectivity. These compounds are able to compete with natural substrates, such as speciﬁc transcription factors, and alter gene expression. They are being developed as artiﬁcial transcription factors, able to deliver activating peptides to speciﬁc recognition sequences, and as potential protein–DNA dimerization agents. Hairpin polyamides are also being used as carriers for the delivery of alkylators to deﬁned DNA sites. The degree of control of gene expression thus offered by the hairpin polyamides suggests enormous promise for their clinical utility. Recent developments with other minor groove binding small molecules and technological advances are also discussed.",
	collection = "nucleic acid drugs",
	doi = "10.1016/j.mrfmmm.2007.03.012",
	localfile = "nucleic acid drugs/2007 - Non-covalent ligand-DNA interactions: minor groove binding agents.pdf",
	year = 2007
}

@Article{2007-Oganesian-Bryan,
	Author = "Liana Oganesian and Tracy M. Bryan",
	Title = "{Physiological relevance of telomeric G-quadruplex formation: a potential drug target}",
	Journal = "BioEssays",
	Volume = "29",
	Number = "2",
	Pages = "155–165",
	abstract = "The concept of a G-quartet, a unique structural arrangement intrinsic to guanine-rich DNA, was first introduced by Gellert and colleagues((1)) over 40 years ago. For decades, it has been uncertain whether the G-quartet and the structure that it gives rise to, the G-quadruplex, are purely in vitro phenomena. Nevertheless, the presence of signature G-rich motifs in the eukaryotic genome, and the plethora of proteins that bind to, modify or resolve this nucleic acid structure in vitro have provided circumstantial evidence for its physiological relevance. More recently, direct visualisation of G-quadruplex DNA at native telomeres was achieved, bolstering the evidence for its existence in the cell. Furthermore, G-quadruplex folded telomeric DNA has been found to perturb telomere function and to impede the action of telomerase, an enzyme overexpressed in > 85\% of human cancers, hence opening up a novel avenue for cancer therapy in the form of G-quadruplex stabilising agents.",
	collection = "nucleic acids",
	doi = "10.1002/bies.20523",
	localfile = "nucleic acids/2007 - Physiological relevance of telomeric G-quadruplex formation: a potential drug target.pdf",
	shorttitle = "Physiological relevance of telomeric G-quadruplex formation",
	year = 2007
}

@Article{2007-Okiyama-WFNMITE,
	Author = "Y. Okiyama and Hirofumi Watanabe and Kaori Fukuzawa and Tatsuya Nakano and Yuji Mochizuki and Takeshi Ishikawa and Shigenori Tanaka and K. Ebina",
	Title = "{Application of the fragment molecular orbital method for determination of atomic charges on polypeptides}",
	Journal = "Chem. Phys. Lett.",
	Volume = "449",
	Number = "4-6",
	Pages = "329 – 335",
	abstract = "The electrostatic potential fitting methods for the determination of atomic charges are applied to polypeptides on the basis of the fragment molecular orbital (FMO) method. We show that the charges determined in the pair-approximation stage agree with those determined from the conventional molecular orbital method within an error of 1\%. Analyzing the dependency of charges on the structural variation of glycine trimer and the reproducibility of electrostatic potential on the surface of the ligand-binding pocket of estrogen receptor, we also show the applicability of the FMO method for atomic charge determination using the electrostatic potential fitting.",
	collection = "protein structure",
	localfile = "protein structure/2007 - Application of the fragment molecular orbital method for determination of atomic charges on polypeptides.pdf",
	year = 2007
}

@Article{2007-Oliphant,
	Author = "Travis E. Oliphant",
	Title = "{Python for Scientific Computing}",
	Journal = "Comput. Sci. Eng.",
	Volume = "9",
	Number = "3",
	Pages = "10–20",
	abstract = "Python is an excellent “steering” language for scientific codes written in other languages. However, with additional basic tools, Python transforms into a high-level language suited for scientific and engineering code that's often fast enough to be immediately useful but also flexible enough to be sped up with additional extensions.",
	collection = "informatics",
	localfile = "informatics/2007 - Python for scientific computing.pdf",
	year = 2007
}

@Article{2007-Park-KHKBH,
	Author = "Sung Chan Park and Bumjoon J. Kim and Craig J. Hawker and Edward J. Kramer and Joona Bang and Jeong Sook Ha",
	Title = "{Controlled ordering of block copolymer thin films by the addition of hydrophilic nanoparticles}",
	Journal = "Macromolecules",
	Volume = "40",
	Pages = "8119–8124",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma071442z",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2007 - Controlled ordering of block copolymer thin films by the addition of hydrophilic nanoparticles.pdf",
	methods = "SFM, SEM, TEM",
	rating = "2",
	read = "2012-03-21",
	systems = "Au-PEO@PS-PMMA",
	year = 2007
}

@Article{2007-Parkinson-GN,
	Author = "Gary N. Parkinson and Ragini Ghosh and Stephen Neidle",
	Title = "{Structural Basis for Binding of Porphyrin to Human Telomeres†,‡}",
	Journal = "Biochemistry",
	Volume = "46",
	Number = "9",
	Pages = "2390–2397",
	abstract = "Maintenance of telomere integrity is a hallmark of human cancer, and the single-stranded 3` ends of telomeric {DNA} are targets for small-molecule anticancer therapies. We report here the crystal structure of a bimolecular human telomeric quadruplex, of the sequence {d(TAGGGTTAGGG),} in a complex with the quadruplex-binding ligand {5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin} {(TMPyP4)} to a resolution of 2.09 A. The {DNA} quadruplex topology is parallel-stranded with external double-chain-reversal propeller loops, consistent with previous structural determinations. The porphyrin molecules bind by stacking onto the {TTA} nucleotides, either as part of the external loop structure or at the 5` region of the stacked quadruplex. This involves stacked on hydrogen-bonded base pairs, formed from those nucleotides not involved in the formation of G-tetrads, and there are thus no direct ligand interactions with G-tetrads. This is in accord with the relative nonselectivity by {TMPyP4} for quadruplex {DNAs} compared to duplex {DNA.} Porphyrin binding is achieved by remodeling of loops compared to the ligand-free structures. Implications for the design of quadruplex-binding ligands are discussed, together with a model for the formation of anaphase bridges, which are observed following cellular treatment with {TMPyP4.}",
	collection = "nucleic acid drugs",
	doi = "10.1021/bi062244n",
	localfile = "nucleic acid drugs/2007 - Structural basis for binding of porphyrin to human telomeres.pdf",
	year = 2007
}

@Article{2007-Patel-PK,
	Author = "Dinshaw J. Patel and Anh Tuan Phan and Vitaly Kuryavyi",
	Title = "{Human telomere, oncogenic promoter and {5'-UTR} G-quadruplexes: diverse higher order {DNA} and {RNA} targets for cancer therapeutics}",
	Journal = "Nucl. Acids Res.",
	Volume = "35",
	Number = "22",
	Pages = "7429–7455",
	abstract = "Guanine-rich {DNA} sequences can form G-quadruplexes stabilized by stacked {G-G-G-G} tetrads in monovalent cation-containing solution. The length and number of individual G-tracts and the length and sequence context of linker residues define the diverse topologies adopted by G-quadruplexes. The review highlights recent solution {NMR-based} G-quadruplex structures formed by the four-repeat human telomere in K+ solution and the guanine-rich strands of c-myc, c-kit and variant bcl-2 oncogenic promoters, as well as a bimolecular G-quadruplex that targets {HIV-1} integrase. Such structure determinations have helped to identify unanticipated scaffolds such as interlocked G-quadruplexes, as well as novel topologies represented by double-chain-reversal and V-shaped loops, triads, mixed tetrads, adenine-mediated pentads and hexads and snap-back G-tetrad alignments. The review also highlights the recent identification of guanine-rich sequences positioned adjacent to translation start sites in 5'-untranslated regions {(5'-UTRs)} of {RNA} oncogenic sequences. The activity of the enzyme telomerase, which maintains telomere length, can be negatively regulated through G-quadruplex formation at telomeric ends. The review evaluates progress related to ongoing efforts to identify small molecule drugs that bind and stabilize distinct G-quadruplex scaffolds associated with telomeric and oncogenic sequences, and outlines progress towards identifying recognition principles based on several X-ray-based structures of {ligand-G-quadruplex} complexes.",
	collection = "nucleic acids",
	doi = "10.1093/nar",
	localfile = "nucleic acids/2007 - Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics.pdf",
	shorttitle = "Human telomere, oncogenic promoter and {5'-UTR} G-quadruplexes",
	year = 2007
}

@Article{2007-Pendas-FB,
	Author = "A. Martin Pendas and E. Francisco and M. A. Blanco",
	Title = "{Charge transfer, chemical potentials, and the nature of functional groups: answers from quantum chemical topology}",
	Journal = "Faraday Discuss.",
	Volume = "135",
	Pages = "423–438",
	abstract = "We analyze the response of a quantum group within a molecule to charge transfer by using the interacting quantum atoms approach {(IQA),} an energy partitioning scheme within the quantum theory of atoms in molecules {(QTAM).} It is shown that this response lies at the core of the concept of the functional group. The manipulation of fractional electron populations is carried out by using distribution functions for the electron number within the quantum basins. Several test systems are studied to show that similar chemical potential groups are characterized by similar energetic behavior upon interaction with other groups. The origin of the empirical additivity rules for group energies in simple hydrocarbons is also investigated. It turns out to rest on the independent saturation of both the self-energies and the interaction energies of the groups as the size of the chain increases. We also show that our results are compatible with the standard group energies of the {QTAM.}",
	collection = "molecular fragmentation",
	doi = "10.1039/b604983d",
	localfile = "molecular fragmentation/2007 - Charge transfer, chemical potentials, and the nature of functional groups: answers from quantum chemical topology.pdf",
	shorttitle = "Charge transfer, chemical potentials, and the nature of functional groups",
	year = 2007
}

@Article{2007-Phan-KBNP,
	Author = "Anh Tuan Phan and Vitaly Kuryavyi and Sarah Burge and Stephen Neidle and Dinshaw J. Patel",
	Title = "{{Structure of an Unprecedented {G-Quadruplex} Scaffold in the Human c-kit Promoter}53 (}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "129",
	Number = "14",
	Pages = "4386–4392",
	abstract = "The c-kit oncogene is an important target in the treatment of gastrointestinal tumors. A potential approach to inhibition of the expression of this gene involves selective stabilization of G-quadruplex structures that may be induced to form in the c-kit promoter region. Here we report on the structure of an unprecedented intramolecular G-quadruplex formed by a G-rich sequence in the c-kit promoter in K+ solution. The structure represents a new folding topology with several unique features. Most strikingly, an isolated guanine is involved in G-tetrad core formation, despite the presence of four three-guanine tracts. There are four loops: two single-residue double-chain-reversal loops, a two-residue loop, and a five-residue stem-loop, which contain base-pairing alignments. This unique structural scaffold provides a highly specific platform for the future design of ligands specifically targeted to the promoter {DNA} of c-kit.",
	collection = "nucleic acids",
	doi = "10.1021/ja068739h",
	localfile = "nucleic acids/2007 - Structure of an unprecedented G-quadruplex scaffold in the human c-kit promoter.pdf",
	year = 2007
}

@Article{2007-Phan-KLP,
	Author = "Anh Tuan Phan and Vitaly Kuryavyi and Kim Ngoc Luu and Dinshaw J. Patel",
	Title = "{Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution}",
	Journal = "Nucl. Acids Res.",
	Volume = "35",
	Number = "19",
	Pages = "6517–6525",
	abstract = "Intramolecular G-quadruplexes formed by human telomere sequences are attractive anticancer targets. Recently, four-repeat human telomere sequences have been shown to form two different intramolecular (3 + 1) G-quadruplexes in K+ solution {(Form} 1 and Form 2). Here we report on the solution structures of both Form 1 and Form 2 adopted by natural human telomere sequences. Both structures contain the (3 + 1) G-tetrad core with one double-chain-reversal and two edgewise loops, but differ in the successive order of loop arrangements within the G-quadruplex scaffold. Our results provide the structural details at the two ends of the G-tetrad core in the context of natural sequences and information on different loop conformations. This structural information might be important for our understanding of telomere G-quadruplex structures and for anticancer drug design targeted to such scaffolds.",
	collection = "nucleic acids",
	doi = "10.1093/nar",
	localfile = "nucleic acids/2007 - Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution.pdf",
	year = 2007
}

@Article{2007-Pileni,
	Author = "M.-P. Pileni",
	Title = "{Self-assembly of inorganic nanocrystals: fabrication and collective intrinsic properties}",
	Journal = "Acc. Chem. Res.",
	Volume = "40",
	Pages = "685–693",
	collection = "nanotechnology",
	doi = "10.1021/ar6000582",
	localfile = "nanotechnology/2007 - Self-assembly of inorganic nanocrystals: fabrication and collective intrinsic properties.pdf",
	year = 2007
}

@Article{2007-Politzer-LCMM,
	Author = "Peter Politzer and Pat Lane and Monica C. Concha and Yuguang Ma and Jane S. Murray",
	Title = "{An overview of halogen bonding}",
	Journal = "J. Mol. Model.",
	Volume = "13",
	Number = "2",
	Pages = "305 – 311",
	collection = "halogen bonding",
	doi = "10.1007/s00894-006-0154-7",
	keywords = "halogen bonding",
	localfile = "halogen bonding/2007 - An overview of halogen bonding.pdf",
	size = "7 p.",
	year = 2007
}

@Article{2007-Politzer-MC,
	Author = "Peter Politzer and Jane S. Murray and Monica C. Concha",
	Title = "{Halogen bonding and the design of new materials: organic bromides, chlorides and perhaps even fluorides as donors}",
	Journal = "J. Mol. Model.",
	Volume = "13",
	Number = "6-7",
	Pages = "643 – 650",
	collection = "halogen bonding",
	doi = "10.1007/s00894-007-0176-9",
	localfile = "halogen bonding/2007 - Halogen bonding and the design of new materials: organic bromides, chlorides and perhaps even fluorides as donors.pdf",
	year = 2007
}

@Article{2007-Rafat-Popelier,
	Author = "Michel Rafat and Paul L. A. Popelier",
	Title = "{Long range behavior of high-rank topological multipole moments}",
	Journal = "J. Comp. Chem.",
	Volume = "28",
	Number = "4",
	Pages = "832–838",
	abstract = "The construction of a high-rank multipolar force field (for peptides) is a complex task, leading to several intermediate questions in need of a clear answer. Here we focus on the convergence of the (electrostatic) multipolar expansion at medium and long range. Using molecular electron densities, quantum chemical topology {(QCT)} defines the atoms as finite volumes, each endowed with multipole moments. The terms in the multipole expansion are grouped according to powers of the internuclear distance, {R-L.} Given two atom types at a given distance, we determine which rank {(L)} is necessary for the electrostatic energy to converge to the exact interaction energy within a certain error. With this information, the rank of the expansion for each interaction can be adapted to the required accuracy and the available computing power. © 2007 Wiley Periodicals, Inc. J Comput Chem 28: 832-838, 2007",
	collection = "molecular electrostatics",
	doi = "10.1002/jcc.20610",
	keywords = "multipole expansion",
	localfile = "molecular electrostatics/2007 - Longe range behavior of high rank topological multipole moments.pdf",
	year = 2007
}

@Article{2007-Reynwar-IHMKD,
	Author = "Benedict J. Reynwar and Gregoria Illya and Vagelis A. Harmandaris and Martin M. Müller and Kurt Kremer and Markus Deserno",
	Title = "{Aggregation and vesiculation of membrane proteins by cruvature-mediated interactions}",
	Journal = "Nature",
	Volume = "447",
	Pages = "461–464",
	abstract = "Membrane remodelling plays an important role in cellular tasks such as endocytosis, vesiculation and protein sorting, and in the biogenesis of organelles such as the endoplasmic reticulum or the Golgi apparatus. It is well established that the remodelling process is aided by specialized proteins that can sense as well as create membrane curvature, and trigger tubulation when added to synthetic liposomes. (...)",
	collection = "lipid bilayers",
	doi = "10.1038/nature05840",
	keywords = "biological nanocomposites; cell membranes; lipid bilayers; nanospheres",
	localfile = "lipid bilayers/2007 - Aggregation and vesiculation of membrane proteins by curvature-mediated interactions.pdf",
	methods = "CG MD",
	type = "Letter",
	year = 2007
}

@Article{2007-Rob-PS,
	Author = "Fazle Rob and Rafał Podeszwa and Krzysztof Szalewicz",
	Title = "{Electrostatic interaction energies with overlap effects from a localized approach}",
	Journal = "Chem. Phys. Lett.",
	Volume = "445",
	Number = "4-5",
	Pages = "315–320",
	abstract = "An ab initio method is proposed for calculations of intermolecular forces which should be applicable to interactions of monomers containing several hundreds atoms and scale linearly with system size. This approach unifies asymptotic approximation to intermolecular forces with symmetry-adapted perturbation theory (SAPT) treatment. Inexpensive asymptotic formulas are applied to interactions of fragments of monomers which are far apart, whereas fairly expensive SAPT formulas are applied to fragments which are near each other, where overlap effects cannot be neglected. This Letter implements the method for the electrostatic interactions. The electrostatic energies are reproduced to 1\% with about dozen or so atoms in near-range regions.",
	collection = "molecular electrostatics",
	doi = "10.1016/j.cplett.2007.07.065",
	localfile = "molecular electrostatics/2007 - Electrostatic interactions energies with overlap effects from a localized approach.pdf",
	year = 2007
}

@Article{2007-Rutledge-WW,
	Author = "Lesley R. Rutledge and Craig A. Wheaton and Stacey D. Wetmore",
	Title = "{A computational characterization of the hydrogen-bonding and stacking interactions of hypoxanthine}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "9",
	Number = "4",
	Pages = "497",
	abstract = "The hydrogen-bonding and stacking interactions of hypoxanthine, a potential universal nucleobase, were calculated using a variety of methodologies (CCSD(T), MP2, B3LYP, PWB6K, AMBER). All methods predict that the hydrogen-bonding interaction in the hypoxanthine–cytosine pair is approximately 25 kJ molÀ1 stronger than that in the other dimers. Although the calculations support suggestions from experiments that hypoxanthine preferentially binds with cytosine, the trend in the calculated hydrogen-bond strengths for the remaining natural nucleobases do not show a strong correlation with the experimentally predicted binding preferences. However, our calculations suggest that the stacking interactions of hypoxanthine are similar in magnitude to the hydrogen-bonding interactions at all levels of theory (with the exception of B3LYP, which incorrectly predicts stacked dimers to be unstable). Therefore, stacking interactions should also be considered when analyzing the stability of DNA helices containing hypoxanthine and the use of larger models that account for both hydrogen-bonding and stacking within DNA duplexes will likely result in better agreement with experimental observations. For the majority of the dimers, PWB6K and AMBER provide reasonable binding strengths at reduced computational costs, and therefore will be useful techniques for considering larger models.",
	collection = "nucleic acid bases",
	doi = "10.1039/b606388h",
	localfile = "nucleic acid bases/2007 - A computational characterization of the hydrogen-bonding and stacking interactions of hypoxanthine.pdf",
	year = 2007
}

@Article{2007-Schmidt-SSHFWSZBK,
	Author = "Kristin Schmidt and Heiko G. Schoberth and Frank Schubert and Helmut Hansel and Franz Fischer and Thomas M. Weiss and G. J. Agur Sevink and Andrei V. Zvelindovsky and Alexander Böker and Georg Krausch",
	Title = "{Scaling behavior of the reorientation kinetics of block copolymers exposed to electric fields}",
	Journal = "Soft Matter",
	Volume = "3",
	Number = "4",
	Pages = "448–453",
	abstract = "We have followed the reorientation kinetics of various block copolymer solutions exposed to an external electric {DC} field. The characteristic time constants follow a power law indicating that the reorientation is driven by a decrease in electrostatic energy. Moreover, the observed exponent suggests an activated process in line with the expectations for a nucleation and growth process. When properly scaled, the data collapse onto a single master curve spanning several orders of magnitude both in reduced time and in reduced energy. The power law dependence of the rate of reorientation derived from computer simulations based on dynamic density functional theory agrees well with the experimental observations. First experiments in {AC} electric fields at sufficiently high frequencies confirm the notion that the reorientation process is dominated by differences in the dielectric constants rather than by mobile ions.",
	collection = "block copolymers",
	doi = "10.1039/b614143a",
	localfile = "block copolymers/2007 - Scaling behavior of the reorientation kinetics of block copolymers exposed to electric fields.pdf",
	year = 2007
}

@Article{2007-Schuchardt-DESGCLW,
	Author = "Karen L. Schuchardt and Brett T. Didier and Todd Elsethagen and Lisong Sun and Vidhya Gurumoorthi and Jared Chase and Jun Li and Theresa L. Windus",
	Title = "{Basis set exchange: a community database for computational sciences}",
	Journal = "J. Chem. Inf. Model.",
	Volume = "47",
	Pages = "1045–1052",
	collection = "cheminformatics",
	doi = "10.1021/ci600510j",
	localfile = "cheminformatics/2007 - Basis set exchange: a community database for computational sciences.pdf",
	url = "http://bse.pnl.gov",
	year = 2007
}

@Article{2007-Sen-XKYBHHHS,
	Author = "Sudeepto Sen and Yuping Xie and Sanat K. Kumar and Hoichang Yang and Amitabh Bansal and Derek L. Ho and Lisa M. Hall and Justin B. Hooper and Kenneth S. Schweizer",
	Title = "{Chain conformations and bound-layer correlations in polymer nanocomposites}",
	Journal = "Phys. Rev. Lett.",
	Volume = "98",
	Pages = "128302",
	abstract = "Small angle neutron scattering studies on polystyrene loaded with spherical silica nanoparticles under contrast-matched conditions unequivocally show that chain conformations follow unperturbed Gaussian statistics independent of chain molecular weight and ﬁller composition. Liquid state theory calculations are consistent with this conclusion and also predict ﬁller-induced modiﬁcation of interchain polymer correlations which have a distinctive scattering signature that is in nearly quantitative agreement with our observations.",
	collection = "polymer nanocomposites",
	doi = "10.1103/PhysRevLett.98.128302",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2007 - Chain conformations and bound-layer correlations in polymer nanocomposites.pdf",
	year = 2007
}

@Article{2007-Shields-Mourik,
	Author = "Ashley E. Shields and {Tanja van} Mourik",
	Title = "{Comparison of ab initio and DFT electronic structure methods for peptides containing an aromatic ring: Effect of dispersion and BSSE}",
	Journal = "J. Phys. Chem. A",
	Volume = "111",
	Pages = "13272–13277",
	abstract = "We establish that routine B3LYP and MP2 methods give qualitatively wrong conformations for flexible organic systems containing pi systems and that recently developed methods can overcome the known inadequacies of these methods. This is illustrated for a molecule (a conformer of the Tyr-Gly dipeptide) for which B3LYP/6-31+G(d) and MP2/6-31+G(d) geometry optimizations yield strikingly different structures [Mol. Phys. 2006, 104, 559-570]: MP2 predicts a folded “closed-book” conformer with the glycine residue located above the tyrosine ring, whereas B3LYP predicts a more open conformation. By employing different levels of theory, including the local electron correlation methods LMP2 (local MP2) and LCCSD(T0) (local coupled cluster with single, double, and noniterative local triple excitations) and large basis sets (aug-cc-pVnZ, n = D, T, Q), it is shown that the folded MP2 minimum is an artifact caused by large intramolecular BSSE (basis set superposition error) effects in the MP2/6-31+G(d) calculations. The B3LYP functional gives the correct minimum, but the potential energy apparently rises too steeply when the glycine and tyrosine residues approach each other, presumably due to missing dispersion effects in the B3LYP calculations. The PWB6K and M052X functionals, designed to give good results for weak interactions, remedy this to some extent. The reduced BSSE in the LMP2 calculations leads to faster convergence with increasing basis set quality, and accurate results can be obtained with smaller basis sets as compared to canonical MP2. We propose LMP2 as a suitable method to study interactions with pi-electron clouds. C1 [Shields, Ashley E.; van Mourik, Tanja] Univ St Andrews, Sch Chem, St Andrews KY16 9ST, Fife, Scotland.",
	collection = "basis set superposition",
	doi = "10.1021/jp076496p",
	localfile = "basis set superposition/2007 - Comaprison of ab initio and DFT electronic structure methods for peptides containing an aromatic ring: effect of dispersion and BSSE.pdf",
	year = 2007
}

@Article{2007-Skwara-BZGL,
	Author = "Bartłomiej Skwara and Wojciech Bartkowiak and Agnieszka Zawada and Robert W. Góra and Jerzy Leszczyński",
	Title = "{On the cooperativity of the interaction-induced (hyper)polarizabilities of the selected hydrogen-bonded trimers}",
	Journal = "Chem. Phys. Lett.",
	Volume = "436",
	Pages = "116–123",
	abstract = "The intermolecular interaction eﬀects on the static electronic electric properties of three hydrogen-bonded systems (trimers of urea, ﬂuoroacetylene and diformamide) have been investigated. The two- and three-body components of interaction-induced dipole moment, polarizability and ﬁrst-order hyperpolarizability have been calculated and analyzed at the SCF and MP2 levels of theory. The cooperativity of the three-body eﬀects of the interaction-induced properties as well as the electron correlation eﬀects have been investigated. In addition to the study of interaction-induced properties, the performance of recently developed polarized Z3Pol basis set has been tested against the following systematically extended Dunning’s correlation consistent basis sets: aug-cc-pVDZ, aug-cc-pVTZ and d-aug-cc-pVDZ.",
	collection = "molecular interactions",
	doi = "10.1016/j.cplett.2007.01.032",
	localfile = "molecular interactions/2007 - On the cooperativity of the interaction-induced (hyper)polarizabilities of the selected hydrogen-bonded trimer.pdf",
	year = 2007
}

@Article{2007-Snyder,
	Author = "Ronald D. Snyder",
	Title = "{Assessment of atypical DNA intercalating agents in biological and in silico systems}",
	Journal = "Mutation Research",
	Volume = "623",
	Pages = "72–82",
	abstract = "Non-covalent genotoxic interaction between DNA and classical planar fused-ring intercalating agents, has been well understood for some time especially in the context of frameshift mutagenesis in bacterial systems. Recent evidence, however, suggests that a rather wide structural range of small non-fused ring molecules may also be capable of partial or complete DNA intercalation in mammalian cells. The present paper will review recent studies on the identiﬁcation and characterization of such atypically-structured molecules utilizing both cell-based and three-dimensional computational analyses focusing principally on prediction and detection of these atypical molecules. Mechanistic aspects of genotoxicity of such non-covalent binding molecules, with emphasis on marketed pharmaceuticals, will also be discussed. A review and presentation of new data using catalytic DNA topo II inhibitors, conﬁrms the notion that topoisomerase II poisoning arising via intercalation is the major mechanism of genotoxicity of these drugs.",
	collection = "nucleic acid intercalation",
	doi = "10.1016/j.mrfmmm.2007.03.006",
	localfile = "nucleic acid intercalation/2007 - Assessment of atypical DNA intercalating agents in biological and in silico systems.pdf",
	year = 2007
}

@Article{2007-Stephens-PB,
	Author = "Frances H. Stephens and Vincent Pons and R. Tom Baker",
	Title = "{Ammonia-borane: the hydrogen source par excellence?}",
	Journal = "Dalton Trans.",
	Number = "25",
	Pages = "2613",
	abstract = "Ammonia–borane, H3 NBH3 , is an intriguing molecule for chemical hydrogen storage applications. With both protic N–H and hydridic B–H bonds, three H atoms per main group element, and a low molecular weight, H3 NBH3 has the potential to meet the stringent gravimetric and volumetric hydrogen storage capacity targets needed for transportation applications. Furthermore, devising an energy-efﬁcient chemical process to regenerate H3 NBH3 from dehydrogenated BNHx material is an important step towards realization of a sustainable transportation fuel. In this perspective we discuss current progress in catalysis research to control the rate and extent of hydrogen release and preliminary efforts at regeneration of H3 NBH3.",
	collection = "hydrogen sorption",
	doi = "10.1039/b703053c",
	localfile = "hydrogen sorption/2007 - Ammonia-borane: the hydrogen source par excellence.pdf",
	shorttitle = "Ammonia?",
	year = 2007
}

@Article{2007-Stone-Misquitta,
	Author = "Anthony J. Stone and Alston J. Misquitta",
	Title = "{Atom-atom potentials from ab initio calculations}",
	Journal = "Int. Rev. Phys. Chem.",
	Volume = "26",
	Number = "1",
	Pages = "193–222",
	abstract = "Recent developments in ab initio intermolecular perturbation theory, using density functional theory, have made it possible to calculate intermolecular interactions between organic molecules of 30 or more atoms routinely and accurately. Related methods can provide accurate distributed properties of such molecules (multipoles and polarizabilities). These developments open up new possibilities for accurate ab initio atom–atom potentials, at a time when applications have raised new challenges, in that aspects of the interaction energy that were once ignored must now be accounted for. This review seeks to show how modern ab initio methods in intermolecular perturbation theory, and new methods for distributing molecular response properties, can be used to develop a new generation of atom–atom potentials.",
	collection = "molecular interactions",
	doi = "10.1080/01442350601081931",
	localfile = "molecular interactions/2007 - Atom-atom potentials from ab initio calcualtions.pdf",
	year = 2007
}

@Article{2007-Stoykovich-KDLLPMN,
	Author = "Mark P. Stoykovich and Huiman Kang and Kostas Ch. Daoulas and Guoliang Liu and Chi-Chun Liu and Juan J. de Pablo and Marcus Müller and Paul F. Nealey",
	Title = "{Directed self-assembly of block copolymers for nanolithography: fabrication of isolated features and essential integrated circuit geometries}",
	Journal = "ACS Nano",
	Volume = "1",
	Number = "3",
	Pages = "168–175",
	collection = "nanotechnology",
	doi = "10.1021/nn700164p",
	keywords = "block copolymers",
	localfile = "nanotechnology/2007 - Directed self-assembly of block copolymers for nanolithography: fabrication of isolated features and essential integrated circuit geometries.pdf",
	year = 2007
}

@Article{2007-Strekowski-Wilson,
	Author = "Lucjan Strekowski and Beth Wilson",
	Title = "{Noncovalent interactions with DNA: an overview}",
	Journal = "Mutation Research",
	Volume = "623",
	Pages = "3–13",
	abstract = "Over the last four decades, intense research has focused on the effects of small organic compounds that noncovalently bind to nucleic acids. These interactions have been shown to disrupt replication and/or transcription culminating in cellular death. Accordingly, DNA binding compounds have potential applications as anti-cancer and anti-viral agents. This report provides an overview of the different DNA-binding modes with an emphasis on DNA groove speciﬁcity for the groove-binding and intercalation modes. While most DNA-interacting agents selectively bind to DNA by either groove binding or intercalation, some compounds can exhibit both binding modes. The binding mode with the most favorable free energy for complex formation depends on the DNA sequence and structural features of the bound ligand.",
	collection = "nucleic acid drugs",
	doi = "10.1016/j.mrfmmm.2007.03.008",
	localfile = "nucleic acid drugs/2007 - Noncovalent interactions with DNA: an overview.pdf",
	year = 2007
}

@Article{2007-Swart-WGB,
	Author = "Marcel Swart and Tushar Wijst and Célia Fonseca Guerra and F. Matthias Bickelhaupt",
	Title = "{π-π stacking tackled with density functional theory}",
	Journal = "J. Mol. Model.",
	Volume = "13",
	Number = "12",
	Pages = "1245–1257",
	abstract = "Through comparison with ab initio reference data, we have evaluated the performance of various density functionals for describing π-π interactions as a function of the geometry between two stacked benzenes or benzene analogs, between two stacked DNA bases, and between two stacked Watson–Crick pairs. Our main purpose is to find a robust and computationally efficient density functional to be used specifically and only for describing π-π stacking interactions in DNA and other biological molecules in the framework of our recently developed QM/QM approach “QUILD”. In line with previous studies, most standard density functionals recover, at best, only part of the favorable stacking interactions. An exception is the new KT1 functional, which correctly yields bound π-stacked structures. Surprisingly, a similarly good performance is achieved with the computationally very robust and efficient local density approximation (LDA). Furthermore, we show that classical electrostatic interactions determine the shape and depth of the π-π stacking potential energy surface.",
	collection = "stacking",
	doi = "10.1007/s00894-007-0239-y",
	localfile = "molecular stacking/2007 - Pi-pi stacking tackled with density functional theory.pdf",
	year = 2007
}

@Article{2007-Thar-HK,
	Author = "Jens Thar and Rainer Hovorka and Barbara Kirchner",
	Title = "{Basis set superposition error along the free-energy surface of the water dimer}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "3",
	Pages = "1510–1517",
	abstract = "In this article we review the behavior of static plane wave basis set calculations in comparison to Gaussian basis set calculations. This was done in the framework of density functional theory for description of hydrogen bonds with the water dimer as an example. Furthermore we carried out molecular dynamics simulations enforcing the self-dissociation reaction of the water dimer to study the influence of the basis set onto the reaction. Not surprisingly, we find strongly varying results of the calculated forces for a chosen cutoff along the reaction coordinates. The basis set superposition errors of the dimer interaction energy are analyzed along the free-energy surface, i.e., along the trajectories. Based on the analysis along the trajectories a qualitative and quantitative estimate depending on the particular point of the free-energy surface can be provided. Namely, at the intermolecular O center dot center dot center dot H distance close to the equilibrium geometry the errors are smaller than at shorter O center dot center dot center dot H distances. However, the distribution at the equilibrium distance is more unsymmetrical than the distribution at short distances. It is wider, and the standard deviation is larger than at shorter distances where the basis set superposition error is larger. C1 Wilhelm Ostwald Inst Phys \& Theoret Chem, Lehrstuhl Theoret Chem, D-04103 Leipzig, Germany. Univ Bonn, Kekule Inst Organ Chem \& Biochem, D-53121 Bonn, Germany.",
	collection = "basis set superposition",
	doi = "10.1021/ct600259x",
	localfile = "basis set superposition/2007 - Basis set superposition error along the free-energy surface of the water dimer.pdf",
	systems = "water dimer",
	year = 2007
}

@Article{2007-Thomas-Hernenrother,
	Author = "Jason R. Thomas and Paul J. Hernenrother",
	Title = "{Targeting {RNA} with small molecules}",
	Journal = "Chem. Rev.",
	Volume = "108",
	Number = "4",
	Pages = "1171–1224",
	abstract = "The recently discovered functions of RNA dramatically expand the cellular roles for this macromolecule. RNA can no longer be viewed as a passive element, working simply as an intermediary between genomic information and the primary sequence of proteins. Rather, it is now recognized that RNA is essential for transcriptional regulation, trans- lational regulation, protein function, and catalysis, responsibilities that have classically been reserved for proteins. This recent explosion in RNA biology underscores the importance of RNA in normal and aberrant cellular functions and highlights the potential of targeting RNA for the treatment of a multitude of disease states.",
	collection = "nucleic acid drugs",
	doi = "10.1021/cr0681546",
	localfile = "nucleic acid drugs/2007 - Targeting RNA with small molecules.pdf",
	year = 2007
}

@Article{2007-Trogdon-MCP,
	Author = "G. Trogdon and Jane S. Murray and Monica C. Concha and Peter Politzer",
	Title = "{Molecular surface electrostatic potentials and anesthetic activity}",
	Journal = "J. Mol. Model.",
	Volume = "13",
	Number = "2",
	Pages = "313 – 318",
	collection = "halogen bonding",
	doi = "10.1007/s00894-006-0145-8",
	localfile = "halogen bonding/2007 - Molecular surface electrostatic potentials and anesthetic activity.pdf",
	year = 2007
}

@Article{2007-Vaia-Maguire,
	Author = "Richard A. Vaia and John F. Maguire",
	Title = "{Polymer nanocomposites with prescribed morphology: going beyond nanoparticle-filled polymers}",
	Journal = "Chem. Mater.",
	Volume = "19",
	Pages = "2736–2751",
	abstract = "Polymer nanocomposites (PNCs), i.e. nanoparticles (spheres, rods, and plates) dispersed in a polymer matrix, have garnered substantial academic and industrial interest since their inception, ca. 1990. With respect to the neat matrix, nanoparticle dispersion has been shown to enhance physical (e.g., barrier, erosion resistance, and reduced flammability), thermomechanical (e.g., heat distortion temperature, thermal expansion coefficient, and stiffness), and processing (e.g., surface finish and melt strength) characteristics. Beyond maximization of

repository: langner/library

repo_name: langner/library

branch_name: refs/heads/master