text:
enzymes that selectively remove a wide variety of alkylated nucleobases over the natural bases.",
	collection = "nucleic acid bases",
	doi = "10.1039/b718621e",
	localfile = "nucleic acid bases/2008 - Computational comparison of the stacking inteactions betweenthe aromatic amino acids and teh natural or (cationic) methylated nucleobases.pdf",
	year = 2008
}

@Article{2008-Rutledge-Wetmore,
	Author = "Lesley R. Rutledge and Stacey D. Wetmore",
	Title = "{Remarkably Strong {T-Shaped} Interactions between Aromatic Amino Acids and Adenine: Their Increase upon Nucleobase Methylation and a Comparison to Stacking}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "4",
	Number = "10",
	Pages = "1768–1780",
	abstract = "T-shaped geometries and interaction energies between select {DNA} nucleobases (adenine or 3-methyladenine) and all aromatic amino acids (histidine, phenylalanine, tyrosine, or tryptophan) were examined using {BSSE-corrected} {MP2/6−31G*(0.25)} potential energy surface scans, which determined the preferred nucleobase (face)–amino acid (edge) and nucleobase (edge)–amino acid (face) interactions. The energies of dimers with the strongest interactions were further studied at the {CCSD(T)/CBS} level of theory, which suggests that the T-shaped interactions in adenine dimers are very strong (up to −35 {kJ} mol−1). Nucleobase methylation to form a cationic damaged base (3-methyladenine) plays a large role in the relative monomer orientations and magnitude of the interactions, which increase by 17−125\%. Most importantly, this study is the first to compare the stacking and T-shaped interactions between all aromatic amino acids and select (natural and damaged) {DNA} nucleobases where the differences between stacking and T-shaped interactions at the {CCSD(T)/CBS} level are small. Therefore, our results indicate that T-shaped interactions cannot be ignored when studying biological processes, and this manuscript discusses the importance of these interactions in the context of {DNA} repair.",
	collection = "nucleic acid bases",
	doi = "10.1021/ct8002332",
	localfile = "nucleic acid bases/2008 - Remarkably strong t-shaped interactions between aromatic amino acids and adenine: their increase upon nucleobase methylation and a comparison to stacking.pdf",
	shorttitle = "Remarkably Strong {T-Shaped} Interactions between Aromatic Amino Acids and Adenine",
	year = 2008
}

@Article{2008-Schmidt-SRZHWUKB,
	Author = "Kristin Schmidt and Heiko G. Schoberth and Markus Ruppel and Heiko Zettl and Helmut Hansel and Thomas M. Weiss and Volker Urban and Georg Krausch and Alexander Böker",
	Title = "{Reversible tuning of a block-copolymer nanostructure via electric fields}",
	Journal = "Nature Mat.",
	Volume = "7",
	Pages = "142–145",
	abstract = "Block copolymers consisting of incompatible components self-assemble into microphase-separated domains yielding highly regular structures with characteristic length scales of the order of several tens of nanometres. Therefore, in the past decades, block copolymers have gained considerable potential for nanotechnological applications, such as in nanostructured networks and membranes, nanoparticle templates and high-density data storage media. However, the characteristic size of the resulting structures is usually determined by molecular parameters of the constituent polymer molecules and cannot easily be adjusted on demand. Here, we show that electric d.c. ﬁelds can be used to tune the characteristic spacing of a block-copolymer nanostructure with high accuracy by as much as 6\% in a fully reversible way on a timescale in the range of several milliseconds. We discuss the inﬂuence of various physical parameters on the tuning process and study the time response of the nanostructure to the applied ﬁeld. A tentative explanation of the observed eﬀect is given on the basis of anisotropic polarizabilities and permanent dipole moments of the monomeric constituents. This electric-ﬁeld-induced effect further enhances the high technological potential of block-copolymer-based soft-lithography applications.",
	collection = "block copolymers",
	localfile = "block copolymers/2008 - Reversible tuning of a block-copolymer nanostructure via electric fields.pdf",
	year = 2008
}

@Article{2008-Service,
	Author = "Robert F. Service",
	Title = "{Problem solved (sort of)}",
	Journal = "Science",
	Volume = "321",
	Pages = "784–786",
	Note = "Nice snapshot of the current state-of-the-art of protein folding, although frames the folding problem in mostly engineering terms. Quote from Peter Wolynes: 'What was called the protein folding problem 20 years ago is solved.'",
	collection = "protein structure",
	doi = "10.1126/science.321.5890.784",
	keywords = "protein folding",
	localfile = "protein structure/2008 - Problem solved (sort of).pdf",
	rating = "3",
	read = "2012-10-04",
	type = "News",
	year = 2008
}

@Article{2008-Sevink-Zvelindovsky,
	Author = "G. J. Agur Sevink and Andrei V. Zvelindovsky",
	Title = "{Block copolymers confined in a nanopore: Pathfinding in a curving and frustrating flatland}",
	Journal = "J. Chem. Phys.",
	Volume = "128",
	Number = "8",
	Pages = "084901",
	abstract = "We have studied structure formation in a conﬁned block copolymer melt by means of dynamic density functional theory. The conﬁnement is two dimensional, and the conﬁned geometry is that of a cylindrical nanopore. Although the results of this study are general, our coarse-grained molecular model is inspired by an experimental lamella-forming polysterene-polybutadiene diblock copolymer system K. Shin et al., Science 306, 76 2004 , in which an exotic toroidal structure was observed upon conﬁnement in alumina nanopores. Our computational study shows that a zoo of exotic structures can be formed, although the majority, including the catenoid, helix, and double helix that were also found in Monte Carlo nanopore studies, are metastable states. We introduce a general classiﬁcation scheme and consider the role of kinetics and elongational pressure on stability and formation pathway of both equilibrium and metastable structures in detail. We ﬁnd that helicity and threefold connections mediate structural transitions on a larger scale. Moreover, by matching the remaining parameter in our mesoscopic method, the Flory-Huggins parameter , to the experimental system, we obtain a structure that resembles the experimental toroidal structure in great detail. Here, the most important factor seems to be the roughness of the pore, i.e., small variations of the pore radius on a scale that is larger than the characteristic size in the system.",
	archiveprefix = "arXiv",
	collection = "block copolymers",
	doi = "10.1063/1.2829406",
	eprint = "0712.1415v2",
	keywords = "block copolymers; nanoconfinement",
	localfile = "block copolymers/2008 - Block copolymers confined in a nanopore: pathfinding in a curving and frustrating flatland.pdf",
	methods = "DDFT",
	primaryclass = "cond-mat.soft",
	shorttitle = "Block copolymers confined in a nanopore",
	year = 2008
}

@Article{2008-Sknepnek-ALST,
	Author = "Rastko Sknepnek and Joshua A. Anderson and Monica H. Lamm and Jörg Schmalian and Alex Travesset",
	Title = "{Nanoparticle ordering via functionalized block copolymers in solution}",
	Journal = "ACS Nano",
	Volume = "2",
	Number = "6",
	Pages = "1259–1265",
	abstract = "We consider nanoparticles and functionalized copolymers, block copolymers with attached end groups possessing a speciﬁc afﬁnity for nanoparticles, in solution. Using molecular dynamics, we show that nanoparticles are able to direct the self-assembly of the polymer/nanoparticle composite. We perform a detailed study for a wide range of nanoparticle sizes and concentrations. We show that the nanoparticles order in a number of distinct phases: simple cubic, layered hexagonal, hexagonal columnar, gyroid, and a novel square columnar. Our results show that nanoparticles ordered with functionalized block copolymers can provide a simple and efﬁcient tool for assembling novel materials with nanometer scale resolution.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/nn8001449",
	keywords = "block copolymers; mesophase transitions; nanopinning; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2008 - Nanoparticle ordering via functionalized block copolymer in solution.pdf",
	methods = "CG MD",
	year = 2008
}

@Article{2008-Skwara-KGB,
	Author = "Bartłomiej Skwara and Anna Kaczmarek and Robert W. Góra and Wojciech Bartkowiak",
	Title = "{On decomposition of itneraction-induced electric properties of HF dimer}",
	Journal = "Chem. Phys. Lett.",
	Volume = "461",
	Pages = "203–206",
	abstract = "Interaction energy in the linear HF dimer is calculated by means of the variational–perturbational scheme. Interaction-induced electric properties: dipole moment, polarizability and ﬁrst-order hyperpolarizability are decomposed into the terms of physical meaning as the corresponding derivatives of the interaction energy components. The distance dependence of the particular contributions to the interaction energy as well as to the electric properties is reported.",
	collection = "hydrogen bonding",
	doi = "10.1016/j.cplett.2008.07.019",
	localfile = "hydrogen bonding/2008 - On decomposition of interaction-induced electric properties of HF dimer.pdf",
	systems = "HF dimer",
	year = 2008
}

@Article{2008-Soderhjelm-Ryde,
	Author = "Pär Söderhjelm and Ulf Ryde",
	Title = "{Conformational dependence of charges in protein simulations}",
	Journal = "J. Comp. Chem.",
	Volume = "30",
	Number = "5",
	Pages = "750–760",
	collection = "proteins",
	doi = "10.1002/jcc.21097",
	localfile = "proteins/2008 - Conformational dependence of charges in protein simulations.pdf",
	year = 2008
}

@Article{2008-Song-JSA,
	Author = "Kai-Xu Song and Yu-Xi Jia and Zhao-Yan Sun and Li-Jia An",
	Title = "{Lattice Boltzmann study of hydrodynamic effects in lamellar ordering process of two-dimensional quenched block copolymers}",
	Journal = "J. Chem. Phys.",
	Volume = "129",
	Pages = "144901",
	collection = "block copolymers",
	doi = "10.1063/1.2981804",
	keywords = "block copolymers; hydrodynamics",
	localfile = "block copolymers/2008 - Lattice Boltzmann study of hydrodynamic effects in lamellar ordering process of two-dimensional quenched block copolymers.pdf",
	methods = "LB",
	year = 2008
}

@Article{2008-Sponer-RH,
	Author = "Jiří Šponer and Kevin E. Riley and Pavel Hobza",
	Title = "{Nature and magnitude of aromatic stacking of nucleic acid bases}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "10",
	Number = "19",
	Pages = "2595",
	abstract = "This review summarises recent advances in quantum chemical calculations of base-stacking forces in nucleic acids. We explain in detail the very complex relationship between the gas-phase base-stacking energies, as revealed by quantum chemical (QM) calculations, and the highly variable roles of these interactions in nucleic acids. This issue is rarely discussed in quantum chemical and physical chemistry literature. We further extensively discuss methods that are available for base-stacking studies, complexity of comparison of stacking calculations with gas phase experiments, balance of forces in stacked complexes of nucleic acid bases, and the relation between QM and force field descriptions. We also review all recent calculations on base- stacking systems, including details analysis of the B-DNA stacking. Specific attention is paid to the highest accuracy QM calculations, to the decomposition of the interactions, and development of dispersion-balanced DFT methods. Future prospects of computational studies of base stacking are discussed.",
	collection = "stacking",
	doi = "10.1039/b719370j",
	localfile = "molecular stacking/2008 - Nature and magnitude of aromatic stacking of nucleic acid bases.pdf",
	year = 2008
}

@Article{2008-Stojkovic-Piantanida,
	Author = "Marijana Radić Stojković and Ivo Piantanida",
	Title = "{Tuning urea–phenanthridinium conjugates for {DNA/RNA} and base pair recognition}",
	Journal = "Tetrahedron",
	Volume = "64",
	Number = "33",
	Pages = "7807–7814",
	collection = "nucleic acid intercalation",
	doi = "10.1016/j.tet.2008.05.142",
	localfile = "nucleic acid intercalation/2008 - Tuning urea-phenanthridinium conjugates for DNA-RNA and base pair recognition.pdf",
	year = 2008
}

@Article{2008-Stone,
	Author = "Anthony J. Stone",
	Title = "{Intermolecular Potentials}",
	Journal = "Science",
	Pages = "787–789",
	collection = "molecular interactions",
	doi = "10.1126/science.1158006",
	localfile = "molecular interactions/2008 - Intermolecular potentials.pdf",
	rating = "2",
	read = "2012-06-07",
	type = "Perspective",
	year = 2008
}

@Article{2008-Szarek-DTS,
	Author = "Paweł Szarek and Edyta Dyguda-Kazimierowicz and Akitomo Tachibana and W. Andrzej Sokalski",
	Title = "{Physical nature of intermolecular interactions within cAMP-dependent protein kinase active site: differential transition state stabilization in phosphoryl transfer reaction}",
	Journal = "J. Phys. Chem. B",
	Volume = "112",
	Pages = "11819–11826",
	abstract = "The origin of enzyme catalytic activity may be effectively explored within the nonempirical theory of intermolecular interactions. The knowledge of electrostatic, exchange, delocalization, and correlation components of the transition state and substrates stabilization energy arising from each enzyme active site residue allows to examine the most essential physical effects involved in enzymatic catalysis. Consequently, one can build approximate models of the catalytic activity in a systematic and legitimate manner. Whenever the dominant role of electrostatic interactions is recognized or assumed, the properties of an optimal catalytic environment could be simply generalized and visualized by means of catalytic ﬁelds that, in turn, aids the design of new catalysts. Differential transition state stabilization (DTSS) methodology has been applied herein to the phosphoryl transfer reaction catalyzed by cAMP-dependent protein kinase (PKA). The MP2 results correlate well with the available experimental data and theoretical ﬁndings indicating that Lys72, Asp166, and the two magnesium ions contribute -22.7, -13.3, -32.4, and -15.2 kcal/mol to differential transition state stabilization, respectively. Although all interaction energy components except that of electron correlation contribution are meaningful, the ﬁrst-order electrostatic term correlates perfectly with MP2 catalytic activity. Catalytic ﬁeld technique was also employed to visualize crucial electrostatic features of an ideal catalyst and to compare the latter with the environment provided by PKA active site. The map of regional electronic chemical potential was used to analyze the unfavorable catalytic effect of Lys168. It was found that locally induced polarization of TS atoms thermodynamically destabilizes electrons, pulling them to regions displaying higher electronic chemical potential.",
	collection = "enzymes",
	doi = "10.1021/jp8040633",
	localfile = "enzymes/2008 - Physical nature of intermolecular interactions within cMAP-dependent protein kinase active site: differential transition state stabiliation in phosphoryl transfer reaction.pdf",
	year = 2008
}

@Article{2008-Trewin-DC,
	Author = "Abbie Trewin and George R. Darling and Andrew I. Cooper",
	Title = "{{“Naked”} fluoride binding sites for physisorptive hydrogen storage}",
	Journal = "New J. Chem.",
	Volume = "32",
	Number = "1",
	Pages = "17–20",
	abstract = "Charge separated ammonium fluorides are calculated to have enhanced binding affinities with molecular hydrogen; a model is proposed for a hypothetical porous polymer where “naked” fluoride moieties are site isolated and available for H2 physisorption.",
	collection = "hydrogen sorption",
	doi = "10.1039/b714593d",
	localfile = "hydrogen sorption/2007 - Naked fluoride binding sites for physisorptive hydrogen storage.pdf",
	year = 2008
}

@Article{2008-Tuteja-DM,
	Author = "Anish Tuteja and Phillip Duxbury and Michael E. Mackay",
	Title = "{Polymer chain swelling induced by dispersed nanoparticles}",
	Journal = "Phys. Rev. Lett.",
	Volume = "100",
	Pages = "077801",
	abstract = "The dimensions of individual deuterated polystyrene (d-PS) chains in a well-dispersed mixture of protonated polystyrene and chemically identical nanoparticles was determined by neutron scattering. A 10\%–20\% increase in the radius of gyration of d-PS was found when the nanoparticles are homogeneously dispersed in the polymer, an effect that occurs only when the radius of gyration of the polymer is larger than the nanoparticle radius. These results are reconciled with the existing literature.",
	collection = "polymer nanocomposites",
	doi = "10.1103/PhysRevLett.100.077801",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2008 - Polymer chain swelling induced by dispersed nanoparticles.pdf",
	year = 2008
}

@Article{2008-Valdes-KPESHR,
	Author = "Haydée Valdés and Vojtéch Klusák and Michal Pitoňák and Otto Exner and Ivo Starý and Pavel Hobza and Lubomir Rulišék",
	Title = "{Evaluation of the intramolecular basis set superposition error in the calculations of larger molecules: [n]Helicenes and Phe-Gly-Phe tripeptide}",
	Journal = "J. Comp. Chem.",
	Volume = "29",
	Pages = "861–870",
	abstract = "Correlated ab initio calculations on large systems, such as the popular MP2 (or RI-MP2) method, suffer from the intramolecular basis set superposition error (BSSE). This error is typically manifested in molecules with folded structures, characterized by intramolecular dispersion interactions. It can dramatically affect the energy differences between various conformers as well as intramolecular stabilities, and it can even impair the accuracy of the predictions of the equilibrium molecular structures. In this study, we will present two extreme cases of intramolecular BSSE, the internal stability of [n]helicene molecules and the relative energies of various conformers of phenylalanyl-glycyl-phenylalanine tripeptide (Phe-Gly-Phe), and compare the calculated data with benchmark values (experimental or high-level theoretical data). As a practical and cheap solution to the accurate treatment of the systems with large anticipated value of intramolecular BSSE, the recently developed density functional method augmented with an empirical dispersion term (DFT-D) is proposed and shown to provide very good results in both of the above described representative cases. (c) 2007 Wiley Periodicals, Inc. C1 Acad Sci Czech Republic, Inst Organ Chem \& Biochem, Gilead Sci Res Ctr, Prague 166 10 6, Czech Republic. IOCB, Prague 166 10 6, Czech Republic. Ctr Complex Mol Syst \& Biomol, Prague 166 10 6, Czech Republic.",
	collection = "basis set superposition",
	doi = "10.1002/jcc.20841",
	localfile = "/home/kml/data/library/basis set superposition/2008 - Evaluation of the intramolecular basis set superposition error in the calculations of larger molecules: [n]helicenes and Phe-Gly-Phe tripeptide.pdf",
	year = 2008
}

@Article{2008-Varandas,
	Author = "A. J. C. Varandas",
	Title = "{Can extrapolation to the basis set limit be an alternative to the counterpoise correction? A study on the helium dimer}",
	Journal = "Theor. Chem. Acc.",
	Volume = "119",
	Pages = "511–521",
	abstract = "Configuration interaction and coupled cluster calculations are reported for He-2 using various orbital basis sets of the d-aug-AVXZ type, with the results being extrapolated to the one electron basis set limit both with counterpoise and without counterpoise correction. A generalized uniform singletand triplet-pair extrapolation scheme has been utilized for such a purpose. Using appropriate corrections to mimic full configuration interaction, the energies were predicted in excellent agreement with the best available estimates. The results also suggest that extrapolation to the complete basis set limit may be a general alternative to the counterpoise correction that yields a more accurate potential energy while being more economical. C1 Univ Coimbra, Dept Quim, P-3004 Coimbra, Portugal.",
	collection = "basis set superposition",
	doi = "10.1007/s00214-008-0419-6",
	keywords = "basis set extrapolation; basis set superposition error",
	localfile = {basis set superposition/2008 - Can extrapolation to the basis set limit be an alternative to the counterpoise correction? A study on the helium dimer.pdf},
	year = 2008
}

@Article{2008-Wang-CR,
	Author = "Jia-Yu Wang and Wei Chen and Thomas P. Russell",
	Title = "{Influence of interfacial energy on electric-field-induced sphere-to-cylinder transition in block copolymer thin films}",
	Journal = "Macromolecules",
	Volume = "41",
	Pages = "7227–7231",
	abstract = "The effect of the interfacial energy on the electric-ﬁeld-induced sphere-to-cylinder (S-to-C) transition in polystyrene-b-poly(methyl methacrylate) (PS-b-PMMA) copolymer thin ﬁlms was studied as a function of the difference in the interfacial interactions of the PS and PMMA blocks with the substrate, δ. It was found that the interfacial energies altered both the critical electric ﬁeld strength and the time scales of kinetics. A very strong preferential interfacial interaction suppressed the electric-ﬁeld-induced S-to-C transition even though such a transition occurred on a neutralized surface where the interfacial interactions were balanced. For a moderate interfacial interaction, the S-to-C transition can be induced by an applied electric ﬁeld, but the time scale of the morphology change is much longer. Furthermore, the formation of ionic complexes in the BCP was found to enhance the electric-ﬁeld-induced S-to-C transition even on a native Si substrate without any surface modiﬁcation, providing a simple route to generate ordered arrays of high-aspect-ratio cylinders oriented normal to a ﬁlm surface.",
	collection = "block copolymers",
	doi = "10.1021/ma800717v",
	keywords = "block copolymers",
	localfile = "block copolymers/2008 - Influence of interfacial energy on electric-field-induced sphere-to-cylinder transition in block copolymer thin films.pdf",
	year = 2008
}

@Article{2008-Warren-MSKZGDW,
	Author = "Scott C. Warren and Lauren C. Messina and Liane S. Slaughter and Marleen Kamperman and Qim Zhou and Sol M. Gruner and Francis J. DiSalvo and Ulrich Wiesner",
	Title = "{Ordered mesoporous materials from metal nanoparticle-block copolymer self-assembly}",
	Journal = "Science",
	Volume = "320",
	Pages = "1748–1752",
	abstract = "The synthesis of ordered mesoporous metal composites and ordered mesoporous metals is a challenge because metals have high surface energies that favor low surface areas. We present results from the self-assembly of block copolymers with ligand-stabilized platinum nanoparticles, leading to lamellar CCM-Pt-4 and inverse hexagonal (CCM-Pt-6) hybrid mesostructures with high nanoparticle loadings. Pyrolysis of the CCM-Pt-6 hybrid produces an ordered mesoporous platinum-carbon nanocomposite with open and large pores (≥10 nanometers). Removal of the carbon leads to ordered porous platinum mesostructures. The platinum-carbon nanocomposite has very high electrical conductivity (400 siemens per centimeter) for an ordered mesoporous material fabricated from block copolymer self-assembly.",
	collection = "block copolymer nanocomposites",
	doi = "10.1126/science.1159950",
	keywords = "block copolymers; nanospheres; porosity; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2008 - Ordered mesoporous materials from metal nanoparticle-block copolymer self-assembly.pdf",
	methods = "NMR, SAXS, powder XRD, TEM",
	systems = "Pt-ligand@PI-PDMAEMAcite",
	year = 2008
}

@Article{2008-Williams-DW,
	Author = "T. Gavin Williams and Nathan J. {DeYonker} and Angela K. Wilson",
	Title = "{{Hartree-Fock} complete basis set limit properties for transition metal diatomics}",
	Journal = "J. Chem. Phys.",
	Volume = "128",
	Number = "4",
	Pages = "044101–9",
	abstract = "Numerical Hartree-Fock HF energies accurate to at least 1 hartree are reported for 27 diatomic transition-metal-containing species. The convergence of HF energies toward this numerical limit upon increasing the basis set size has been investigated, where standard nonrelativistic all-electron correlation consistent basis sets and augmented basis sets, developed by Balabanov and Peterson J. Chem. Phys. 123, 064107 2005 , were employed. Several schemes which enable the complete basis set CBS limit to be determined have been investigated, and the resulting energies have been compared to the numerical Hartree-Fock energies. When comparing basis set extrapolation schemes, those in the form of exponential functions perform well for our test set, with mean absolute deviations from numerical HF energies of 234 and 153 Eh, when the CBS limit has been determined using a two-point ﬁt as proposed by Halkier et al. Chem. Phys. Lett. 302, 437 1999 on calculations of triple- and quadruple- basis set qualities and calculations of quadruple- and quintuple- basis set qualities, respectively. Overall, extrapolation schemes in the form of a power series are not recommended for the extrapolation of transition metal HF energies. The impact of basis set superposition error has also been examined.",
	collection = "basis set dependence",
	doi = "10.1063/1.2822907",
	localfile = "basis set dependence/2008 - Hartree-Fock complete basis set limit properties for transition metal diatomics.pdf",
	year = 2008
}

@Article{2008-Xu-OLC,
	Author = "Chen Xu and Kohji Ohno and Vincent Ladmiral and Russell J. Composto",
	Title = "{Dispersion of polymer-grafted magnetic nanoparticles in homopolymers and block copolymers}",
	Journal = "Polymer",
	Volume = "49",
	Pages = "3568–3577",
	collection = "block copolymer nanocomposites",
	doi = "10.1016/j.polymer.2008.05.040",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2008 - Dispersion of polymer-grafted magnetic nanoparticles in homopolymers and block copolymers.pdf",
	methods = "AFM, TEM",
	rating = "2",
	read = "2012-03-21",
	systems = "magnetite-PMMA@PMMA, magnetite-PMMA@PS-PMMA",
	year = 2008
}

@Article{2008-Zeng-YL,
	Author = "Q. H. Zeng and A. B. Yu and G. Q. Lu",
	Title = "{Multiscale modeling and simulation of polymer nanocomposites}",
	Journal = "Prog. Polym. Sci.",
	Volume = "33",
	Pages = "191–269",
	abstract = "Polymer nanocomposites offer a wide range of promising applications because of their much enhanced properties arising from the reinforcement of nanoparticles. However, further development of such nanomaterials depends on the fundamental understanding of their hierarchical structures and behaviors which requires multiscale modeling and simulation strategies to provide seamless coupling among various length and time scales. In this review, we ﬁrst introduce some computational methods that have been applied to polymer nanocomposites, covering from molecular scale (e.g., molecular dynamics, Monte Carlo), microscale (e.g., Brownian dynamics, dissipative particle dynamics, lattice Boltzmann, time-dependent Ginzburg–Landau method, dynamic density functional theory method) to mesoscale and macroscale (e.g., micromechanics, equivalent-continuum and self-similar approaches, ﬁnite element method). Then, we discuss in some detail their applications to various aspects of polymer nanocomposites, including the thermodynamics and kinetics of formation, molecular structure and dynamics, morphology, processing behaviors, and mechanical properties. Finally, we address the importance of multiscale simulation strategies in the understanding and predictive capabilities of polymer nanocomposites in which few studies have been reported. The present review aims to summarize the recent advances in the fundamental understanding of polymer nanocomposites reinforced by nanoﬁllers (e.g., spherical nanoparticles, nanotubes, clay platelets) and stimulate further research in this area.",
	collection = "polymer nanocomposites",
	doi = "10.1016/j.progpolymsci.2007.09.002",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2008 - Multiscale modeling and simulation of polymer nanocomposites.pdf",
	type = "Review",
	year = 2008
}

@Article{2008-Zhao-YZ,
	Author = "Dan Zhao and Daqiang Yuan and {Hong-Cai} Zhou",
	Title = "{The current status of hydrogen storage in metal-organic frameworks}",
	Journal = "Energy Environ. Sci.",
	Volume = "1",
	Number = "2",
	Pages = "222–235",
	abstract = "The theoretical and experimental hydrogen storage studies on metal-organic frameworks {(MOFs)} have been reviewed. Seven distinct factors influencing hydrogen uptake capacity in {MOFs} have been classified and discussed. Based on existing studies, some possible future developments have been proposed.",
	collection = "hydrogen sorption",
	localfile = "hydrogen sorption/2008 - The current status of hydrogen storage in metal-organic frameworks.pdf",
	year = 2008
}

@Article{2009-Acevedo-Jorgensen,
	Author = "Orlando Acevedo and William L. Jorgensen",
	Title = "{Advances in Quantum and Molecular Mechanical {(QM/MM)} Simulations for Organic and Enzymatic Reactions}",
	Journal = "Acc. Chem. Res.",
	Volume = "43",
	Number = "1",
	Pages = "142–151",
	abstract = "Application of combined quantum and molecular mechanical {(QM/MM)} methods focuses on predicting activation barriers and the structures of stationary points for organic and enzymatic reactions. Characterization of the factors that stabilize transition structures in solution and in enzyme active sites provides a basis for design and optimization of catalysts. Continued technological advances allowed for expansion from prototypical cases to mechanistic studies featuring detailed enzyme and condensed-phase environments with full integration of the {QM} calculations and configurational sampling. This required improved algorithms featuring fast {QM} methods, advances in computing changes in free energies including free-energy perturbation {(FEP)} calculations, and enhanced configurational sampling. In particular, the present Account highlights development of the {PDDG/PM3} semi-empirical {QM} method, computation of multi-dimensional potentials of mean force {(PMF),} incorporation of on-the-fly {QM} in Monte Carlo {(MC)} simulations, and a polynomial quadrature method for efficient modeling of proton-transfer reactions. The utility of this {QM/MM/MC/FEP} methodology is illustrated for a variety of organic reactions including substitution, decarboxylation, elimination, and pericyclic reactions. A comparison to experimental kinetic results on medium effects has verified the accuracy of the {QM/MM} approach in the full range of solvents from hydrocarbons to water to ionic liquids. Corresponding results from ab initio and density functional theory {(DFT)} methods with continuum-based treatments of solvation reveal deficiencies, particularly for protic solvents. Also summarized in this Account are three specific {QM/MM} applications to biomolecular systems: (1) a recent study that clarified the mechanism for the reaction of 2-pyrone derivatives catalyzed by macrophomate synthase as a tandem Michael−aldol sequence rather than a {Diels−Alder} reaction, (2) elucidation of the mechanism of action of fatty acid amide hydrolase {(FAAH),} an unusual {Ser-Ser-Lys} proteolytic enzyme, and (3) the construction of enzymes for Kemp elimination of 5-nitrobenzisoxazole that highlights the utility of {QM/MM} in the design of artificial enzymes.",
	collection = "quantum chemistry",
	doi = "10.1021/ar900171c",
	localfile = "quantum chemistry/2009 - Advances in quantum and molecular mechanics simulations for organic and enzymatic reactions.pdf",
	year = 2009
}

@Article{2009-Addicoat-Collins,
	Author = "Matthew A. Addicoat and Michael A. Collins",
	Title = "{Accurate treatment of nonbonded interactions within systematic molecular fragmentation}",
	Journal = "J. Chem. Phys.",
	Volume = "131",
	Pages = "104103",
	abstract = "The accuracy of the systematic fragment approach to the estimation of molecular electronic energies is enhanced by a signiﬁcantly improved treatment of nonbonded interactions between molecular fragments. Distributed electrostatic interactions, pairwise dispersion interactions, and many-body induction are evaluated from ab initio calculations of small molecular fragments. The accuracy of the complete approach is reported for a large sample of typical neutral organic molecules.",
	collection = "molecular fragmentation",
	doi = "10.1063/1.3222639",
	localfile = "molecular fragmentation/2009 - Accurate treatment of nonbonded interactions within systematic molecular fragmentation.pdf",
	year = 2009
}

@Article{2009-Akcora-LKMLBSAPPGITCD,
	Author = "Pinar Akcora and Hongjun Liu and Sanat K. Kumar and Joseph Moll and Yu Li and Brian C. Benicewicz and Linda S. Schadler and Devrim Acehan and Athanassios Z. Panagiotopoulos and Victor Pryamitsyn and Venkat Ganesan and Jan Ilavsky and Pappanan Thiyagarajan and Ralph H. Colby and Jack F. Douglas",
	Title = "{Anisotropic self-assembly of spherical polymer-grafted nanoparticles}",
	Journal = "Nature Mat.",
	Volume = "8",
	Pages = "354–359",
	abstract = "It is easy to understand the self-assembly of particles with anisotropic shapes or interactions (for example, cobalt nanoparticles or proteins) into highly extended structures. However, there is no experimentally established strategy for creating a range of anisotropic structures from common spherical nanoparticles. We demonstrate that spherical nanoparticles uniformly grafted with macromolecules (‘nanoparticle amphiphiles’) robustly self-assemble into a variety of anisotropic superstructures when they are dispersed in the corresponding homopolymer matrix. Theory and simulations suggest that this self-assembly reﬂects a balance between the energy gain when particle cores approach and the entropy of distorting the grafted polymers. The effectively directional nature of the particle interactions is thus a many-body emergent property. Our experiments demonstrate that this approach to nanoparticle self-assembly enables considerable control for the creation of polymer nanocomposites with enhanced mechanical properties. Grafted nanoparticles are thus versatile building blocks for creating tunable and functional particle superstructures with signiﬁcant practical applications.",
	collection = "polymer nanocomposites",
	doi = "10.1038/NMAT2404",
	keywords = "self-assembly; nanoparticle grafts; nanospheres; polymer nanocomposites",
	localfile = "polymer nanocomposites/2009 - Anisotropic self-assembly of spherical polymer-grafted nanoparticles.pdf",
	year = 2009
}

@Article{2009-Arkhipov-RWS,
	Author = "Anton S. Arkhipov and Wouter H. Roos and Gijs J. L. Wuite and Klaus Schulten",
	Title = "{Elucidating the mechanism behind irreversible deformation of viral capsids}",
	Journal = "Biophys. J.",
	Volume = "97",
	Pages = "2061–2069",
	abstract = "Atomic force microscopy has recently provided highly precise measurements of mechanical properties of various viruses. However, molecular details underlying viral mechanics remain unresolved. Here we report atomic force microscopy nanoindentation experiments on T=4 hepatitis B virus (HBV) capsids combined with coarse-grained molecular dynamics simulations, which permit interpretation of experimental results at the molecular level. The force response of the indented capsid recorded in simulations agrees with experimental observations. In both experiment and simulation, irreversible capsid deformation is observed for deep indentations. Simulations show the irreversibility to be due to local bending and shifting of capsid proteins, rather than their global rearrangement. These results emphasize the viability of large capsid deformations without significant changes of the mutual positions of HBV capsid proteins, in contrast to the stiffer capsids of other viruses, which exhibit more extensive contacts between their capsid proteins than seen in the case of HBV.",
	collection = "viruses",
	doi = "10.1016/j.bpj.2009.07.039",
	localfile = "viruses/2009 - Elucidating the mechanism behind irreversible deformation of viral capsids.pdf",
	year = 2009
}

@Article{2009-Asturiol-DS,
	Author = "David Asturiol and Miquel Duran and Pedro Salvador",
	Title = "{Intramolecular Basis Set Superposition Error Effects on the Planarity of DNA and RNA Nucleobases}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "5",
	Pages = "2574–2581",
	abstract = "Molecules of utmost importance like DNA and RNA nucleobases are predicted to be nonplanar by a typical ab initio method, such as second order Møller–Plesset perturbation theory (MP2) combined with standard Pople's basis sets. Similarly to the case of other planar aromatic systems, these pitfalls can be explained in terms of intramolecular basis set superposition error (BSSE) effects, induced by local basis set deficiencies. We demonstrate that conventional BSSE correction techniques such as the Counterpoise method can account for this wrong behavior and provide proper correction whenever spurious results occur, mainly in case of thymine, uracil and guanine but also to lower extent for adenine and cytosine. We also show that special care must be taken when assessing the BSSE by means of ghost-orbital calculations for strongly overlapping fragments. Often molecular orbitals in the isolated fragment calculation have a different orientation as in the ghost-orbital calculation. This can lead to bogus derivatives of the CP-correction term, essential to account for geometry and vibrational BSSE effects. C1 [Duran, Miquel; Salvador, Pedro] Univ Girona, Inst Quim Computac, Girona 17071, Spain. [Duran, Miquel; Salvador, Pedro] Univ Girona, Dept Quim, Girona 17071, Spain. [Asturiol, David] Univ Girona, Inst Quim Computac Parc Cient \& Tecnol, Girona 17003, Spain.",
	collection = "basis set superposition",
	doi = "10.1021/ct900056u",
	localfile = "basis set superposition/2009 - Intramolecular basis set supertposition error effects on the planarity of DNA and RNA nulceobases.pdf",
	year = 2009
}

@Article{2009-Balabin-L,
	Author = "Roman M. Balabin and Ekaterina I. Lomakina",
	Title = "{Neural network approach to quantum-chemistry data: accurate prediction of density function theory energies}",
	Journal = "J. Chem. Phys.",
	Volume = "131",
	Pages = "074104",
	collection = "quantum chemistry",
	doi = "10.1063/1.3206326",
	keywords = "neural network; density functional theory",
	localfile = "quantum chemistry/2009 - Neural network approach to quantum-chemistry data: accurate prediuction of density functional theory energies.pdf",
	rating = "2",
	read = "2015-02-05",
	year = 2009
}

@Article{2009-Banas-JWSO,
	Author = "Pavel Banas and Petr Jurečka and Nils G. Walter and Jiří Šponer and Michal Otyepka",
	Title = "{Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM}",
	Journal = "Methods",
	Volume = "49",
	Pages = "202–216",
	abstract = "Hybrid QM/MM methods combine the rigor of quantum mechanical (QM) calculations with the low computational cost of empirical molecular mechanical (MM) treatment allowing to capture dynamic properties to probe critical atomistic details of enzyme reactions. Catalysis by RNA enzymes (ribozymes) has only recently begun to be addressed with QM/MM approaches and is thus still a ﬁeld under development. This review surveys methodology as well as recent advances in QM/MM applications to RNA mechanisms, including those of the HDV, hairpin, and hammerhead ribozymes, as well as the ribosome. We compare and correlate QM/MM results with those from QM and/or molecular dynamics (MD) simulations, and discuss scope and limitations with a critical eye on current shortcomings in available methodologies and computer resources. We thus hope to foster mutual appreciation and facilitate collaboration between experimentalists and theorists to jointly advance our understanding of RNA catalysis at an atomistic level.",
	collection = "molecular catalysis",
	doi = "10.1016/j.ymeth.2009.04.007",
	localfile = "molecular catalysis/2009 - Theoretical studies of RNA catalysis: hybrid QMMM methods and their comparison with MD and QM.pdf",
	year = 2009
}

@Article{2009-Bernal-Uruchurtu-HJ,
	Author = "Margarita I. {Bernal-Uruchurtu} and Ramón {Hernández-Lamoneda} and Kenneth C. Janda",
	Title = "{On the unusual properties of halogen bonds: a detailed ab Initio study of {X2−(H2O)1−5} clusters {(X} = Cl and Br)}",
	Journal = "J. Phys. Chem. A",
	Volume = "113",
	Number = "19",
	Pages = "5496–5505",
	abstract = "Halogen bonds have received a great deal of attention in recent years. Their properties, sometimes paralleled with those of hydrogen bonds, have not yet been fully understood. In this work, we investigate the nature of the intermolecular interactions between Cl2 and Br2 with water. Our analysis of several features of {MP2/aug-cc-pVDZ-optimized} stable clusters with different number and arrangement of water molecules shows that two different kinds of halogen−water coordination patterns are involved in the stability and properties found for these systems: halogen bonds {(X−X···O)} and halogen−hydrogen interactions, {(X−X···H−O−H).} Both types of interactions result in a large polarization of the halogen molecule, which leads to important cooperative effects on these structures. Although the general structural aspects of these clusters can be understood in terms of dipole−quadrupole forces at long range, where it is the dominant term, the {SAPT} analysis shows that factors such as polarization of π densities and dispersion become increasingly important close to equilibrium. In particular, we show that the halogen−hydrogen interactions are weaker than halogen−oxygen interactions mainly due to the electrostatic and dispersion forces. We also calculate vibrational and electronic shifts that should be helpful for the interpretation of experimental results and for investigating the microsolvation phenomena for halogens in an aqueous environment.",
	collection = "halogen bonding",
	doi = "10.1021/jp900490p",
	localfile = "halogen bonding/2009 - On the unusual properties of halogen bonds: a detailed ab initio study.pdf",
	shorttitle = "On the Unusual Properties of Halogen Bonds",
	year = 2009
}

@Article{2009-Biver-VJJS,
	Author = "Tarita Biver and Marcella Venturini and Elizabeth A. {Jares-Erijman} and Thomas M. Jovin and Fernando Secco",
	Title = "{{7-Aminoactinomycin} Binding to {DNA} Sequences Lacking {GpC} Sites: A Thermodynamic and Kinetic Study}",
	Journal = "Biochemistry",
	Volume = "48",
	Number = "1",
	Pages = "173–179",
	abstract = "The interaction of 7-aminoactinomycin {(7AAMD)} with selected {DNA} sequences {(TAGTTA,} R5, {HP5,} and {HP1)} of different lengths and secondary structures, all containing a {5′-TAGT-3′} block, was studied at an ionic strength of 0.02 M and {pH} 7.7 by means of fluorescence equilibrium and kinetic (stopped-flow) measurements. Both approaches indicated that the antibiotic binds strongly to both the single-stranded and hairpin {(HP1)} structures, although the sequences lacked the canonical {GpC} sites favored by actinomycin. Binding isotherms and initial rate analyses revealed that the binding stoichiometry was 1:1 in all cases. While the single-stranded sequences displayed a simple monoexponential kinetic behavior, the binding of {7AAMD} to {HP1} at {\textless}30 {°C} was biphasic and could be rationalized in terms of a sequential formation of two isomeric bound forms or alternatively in terms of an {ssHP1−hpHP1} equilibrium, with both {HP1} forms reacting with {7AAMD.} The rates of complex dissociation induced by the detergent {SDS} were also measured. After correction of the kinetic traces for spurious effects that can be attributed to the {SDS,} monoexponential traces were obtained, with relaxation times in agreement with the kinetics of complex formation.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/bi801671c",
	localfile = "nucleic acid intercalation/2009 - 7-aminoactinomycin binding to DNA sequences alcking GpC sites: a thermodynamic and kinetic study.pdf",
	year = 2009
}

@Article{2009-Blum-Reymond,
	Author = "Lorenz C. Blum and {Jean-Louis} Reymond",
	Title = "{970 Million Druglike Small Molecules for Virtual Screening in the Chemical Universe Database {GDB-13}}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "131",
	Number = "25",
	Pages = "8732–8733",
	abstract = "(Excerpt) One of the most important chemical issues in drug discovery is innovation, in particular at the level of small organic fragments that can provide new lead structures. The search for novel molecules can be assisted by in silico methods such as enumeration of chemical space, breeding of molecules by genetic algorithms, and analysis of molecular scaffolds. We recently proposed an exhaustive enumeration approach for small organic molecules by assembling the chemical universe database GDB-11, which describes the 26.4 million structures containing up to 11 atoms of C, N, O, and F that satisfy simple chemical stability and synthetic feasibility rules. We now report GDB-13, which enumerates in a similar manner small organic molecules containing up to 13 atoms of C, N, O, S, and Cl. With 977 468 314 structures, GDB-13 is thelargest freely available small molecule database to date.",
	collection = "cheminformatics",
	doi = "10.1021/ja902302h",
	keywords = "big data; drug discovery",
	localfile = "cheminformatics/2009 - 970 million druglike molecules for virtual screening in the chemical universe database GDB-13.pdf",
	year = 2009
}

@Article{2009-Brown,
	Author = "Ian D. Brown",
	Title = "{Recent developments in the methods and applications of the bond valence model}",
	Journal = "Chem. Rev.",
	Volume = "109",
	Pages = "6858–6919",
	collection = "crystallography",
	doi = "10.1021/cr900053k",
	keywords = "bond valence",
	localfile = "crystallography/2009 - Recent developments in the methods and applications of the bond valence model.pdf",
	rating = "3",
	read = "2014-02-10",
	year = 2009
}

@Article{2009-Bushmarinov-LA,
	Author = "I. S. Bushmarinov and Konstantin A Lyssenko and Mikhail Yu Antipin",
	Title = "{Atomic energy in the {'Atoms} in Molecules' theory and its use for solving chemical problems}",
	Journal = "Russian Chem. Rev.",
	Volume = "78",
	Number = "4",
	Pages = "283–302",
	abstract = "The theoretical and practical aspects of the use of atomic energy in R Bader's theory `Atoms in Molecules' for solving problems of physical and structural chemistry are considered. The bibliography includes 148 references.",
	collection = "molecular fragmentation",
	doi = "10.1070/RC2009v078n04ABEH004017",
	localfile = "molecular fragmentation/2009 - Atomic energy in the atoms in molecules theory and its use for solving chemical problems.pdf",
	year = 2009
}

@Article{2009-Ceniceros-FM,
	Author = "Hector D. Ceniceros and Glenn H. Fredrickson and George O. Mohler",
	Title = "{Coupled flow-polymer dynamics via statistical field theory: modeling and computation}",
	Journal = "J. Comp. Phys.",
	Volume = "228",
	Pages = "1624–1638",
	abstract = "Field-theoretic models, which replace interactions between polymers with interactions between polymers and one or more conjugate ﬁelds, offer a systematic framework for coarse-graining of complex ﬂuids systems. While this approach has been used successfully to investigate a wide range of polymer formulations at equilibrium, ﬁeld-theoretic models often fail to accurately capture the non-equilibrium behavior of polymers, especially in the early stages of phase separation. Here the ‘‘two-ﬂuid” approach serves as a useful alternative, treating the motions of ﬂuid components separately in order to incorporate asymmetries between polymer molecules. In this work we focus on the connection of these two theories, drawing upon the strengths of each of the approaches in order to couple polymer microstructure with the dynamics of the ﬂow in a systematic way. For illustrative purposes we work with an inhomogeneous melt of elastic dumbbell polymers, though our methodology will apply more generally to a wide variety of inhomogeneous systems. First we derive the model, incorporating thermodynamic forces into a two-ﬂuid model for the ﬂow through the introduction of conjugate chemical potential and elastic strain ﬁelds for the polymer density and stress. The resulting equations are composed of a system of fourth order PDEs coupled with a non-linear, non-local optimization problem to determine the conjugate ﬁelds. The coupled system is severely stiff and with a high degree of computational complexity. Next, we overcome the formidable numerical challenges posed by the model by designing a robust semi-implicit method based on linear asymptotic behavior of the leading order terms at small scales, by exploiting the exponential structure of global (integral) operators, and by parallelizing the non-linear optimization problem. The semi-implicit method effectively removes the fourth order stability constraint associated with explicit methods and we observe only a ﬁrst order time-step restriction. The algorithm for solving the non-linear optimization problem, which takes advantage of the form of the operators being optimized, reduces the overall simulation time by several orders of magnitude. We illustrate the methodology with several examples of phase separation in an initially quiescent ﬂow.",
	collection = "polymers",
	doi = "10.1016/j.jcp.2008.11.009",
	localfile = "polymers/2009 - Coupled flow-polymer dynamics via statistical field theory: Modeling and computations.pdf",
	year = 2009
}

@Article{2009-Chen-Ruckenstein,
	Author = "Houyang Chen and Eli Ruckenstein",
	Title = "{Nanoparticle aggregation in the presence of a block copolymer}",
	Journal = "J. Chem. Phys.",
	Volume = "131",
	Pages = "244904",
	Note = "Advocates critical values for NP-NP and NP-BCP interactions for NP aggregation.",
	abstract = "By employing dissipative particle dynamics simulations, we investigated the cooperative phase behavior of composites containing diblock copolymer molecules and nanoparticles. The nanoparticles and their aggregates are located either in the domains generated by each of the two kinds of segments of the block copolymer and/or at their interface. Various conditions, such as the interactions between nanoparticles, the interactions between them and the segments of the block copolymer, the interactions between the segments of the block copolymer, and the volume ratio of nanoparticles to block copolymer, have been changed to gather information about nanoparticle aggregation and block copolymer/nanoparticles morphology building. The dynamics of nanoparticles aggregation and the evolution of the morphology of the block copolymer have been followed. Our ﬁndings have identiﬁed two critical repulsive interactions regarding nanoparticle aggregation, one between nanoparticles and the other between the segments of the block copolymer and nanoparticles. Aggregates have been generated for repulsive interactions larger than the former critical value or smaller than the latter one.",
	collection = "block copolymer nanocomposites",
	doi = "10.1063/1.3280064",
	keywords = "block copolymers; nanoparticle aggregation; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2009 - Nanoparticle aggregation in the presence of a block copolymer.pdf",
	methods = "DPD",
	year = 2009
}

@Article{2009-Churchill-NRW,
	Author = "Cassandra D. M. Churchill and Lex Navarro-Whyte and Lesley R. Rutledge and Stacey D. Wetmore",
	Title = "{Effects of the biological backbone on DNA-protein stacking interactions}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "11",
	Pages = "10657–10670",
	abstract = "The p–p stacking (face-to-face) interactions between the ﬁve natural DNA or RNA nucleobases and the four aromatic amino acids were compared using three different types of dimers: (1) a truncated nucleoside (nucleobase) stacked with a truncated amino acid; (2) a truncated nucleoside (nucleobase) stacked with an extended amino acid; and (3) a nucleoside (extended nucleobase) stacked with a truncated amino acid. Systematic (MP2/6-31G*(0.25)) potential energy surface scans reveal important information about the eﬀects of the deoxyribose sugar and protein backbone on the structure and binding energy between truncated nucleobase and amino acid models that are typically implemented in the literature. Most notably, electrostatic and steric interactions arising from the bulkiness of the biological backbones can change the preferred relative orientations of DNA and protein p-systems. More importantly, the protein backbone can strengthen the stacking energy (by up to 10 kJ molÀ1), while the deoxyribose moiety can strengthen or weaken the stacking interaction depending on the positioning of the amino acid relative to the sugar residue. These eﬀects are likely due to additional interactions between the amino acid or nucleobase ring and the backbone in the extended monomer rather than signiﬁcant changes in the properties of the biological p-systems upon model extension. Since the present work reveals that all calculated DNA–protein stacking interactions are signiﬁcant and approach the strength of other noncovalent interactions between biomolecules, both p–p and backbone–p interactions must be considered when attempting to gain a complete picture of DNA–protein binding.",
	collection = "stacking",
	localfile = "molecular stacking/2009 - Effects of biological backbone on DNA-protein stacking interactions.pdf",
	year = 2009
}

@Article{2009-Churchill-Wetmore,
	Author = "Cassandra D. M. Churchill and Stacey D. Wetmore",
	Title = "{Noncovalent interactions involving histidine: the effect of charge on pi-pi stacking and T-shaped interactions with the DNA nucleobases}",
	Journal = "J. Phys. Chem. B",
	Volume = "113",
	Pages = "16046–16058",
	collection = "nucleic acid bases",
	doi = "10.1021/jp907887y",
	localfile = "nucleic acid bases/2009 - Noncovalent interactions involving histidine: the effect of charge on pi-pi stcaking and T-shaped interactions with the DNA nucleobases.pdf",
	year = 2009
}

@Article{2009-Cock-ACCCDFHKWH,
	Author = "Peter J. A. Cock and Tiago Antao and Jeffrey T. Chang and Brad A. Chapman and Cymon J. Cox and Andrew Dalke and Iddo Friedberg and Thomas Hamelryck and Frank Kauff and Bartek Wilczyński and {Michiel J. L. de} Hoon",
	Title = "{Biopython: freely available Python tools for computational molecular biology and bioinformatics}",
	Journal = "Bioinformatics",
	Volume = "25",
	Number = "11",
	Pages = "1422–1423",
	abstract = "Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/\_Mailing\_listspeter.cock@scri.ac.uk.",
	collection = "cheminformatics",
	doi = "10.1093/bioinformatics",
	eprint = "http://bioinformatics.oxfordjournals.org/cgi/reprint/25/11/1422.pdf",
	localfile = "cheminformatics/2009 - Biopython: freely available Python tools for computational molecular biology and bioinformatics.pdf",
	year = 2009
}

@Article{2009-Cysewski,
	Author = "Piotr Cysewski",
	Title = "{Intra-strand stacking interactions in {B-DNA} crystals characterized by {post-SCF} quantum chemistry computations}",
	Journal = "New J. Chem.",
	Volume = "33",
	Number = "9",
	Pages = "1909–1917",
	abstract = "The distributions of intermolecular interaction energies {(IIE)} of all possible 5[prime or {minute]-X/Y-3[prime} or minute] {(X,} Y = A, G, T, C) stacked pairs in conformations exactly matching to intra-strand orientations occurring in crystallographic {B-DNA} double strands were characterized by quantum chemistry calculations on {MP2/aug-cc-pvDZ} level. The essential feature of this approach is sampling over meaningful conformations and getting statistically significant data on the energetics of stacking interactions in {B-DNA} crystals. Based on the most frequently occurring {IIE} values (in kcal mol-1) the following order of the intra-strand stacking interactions in {B-DNA} solids is concluded: {G/A} -10.2 +/- 1.1 {\textgreater} {A/G} -9.2 +/- 1.0 [approximate] {G/C} -8.7 +/- 1.2 {\textgreater} {A/A} -8.3 +/- 1.0 {\textgreater} {A/T} -7.7 +/- 0.9 {\textgreater} {C/G} -7.2 +/- 0.9 {\textgreater} {T/G} -6.5 +/- 1.3 [approximate] {A/C} -6.2 +/- 0.8 [approximate] {G/T} -6.2 +/- 1.3 {\textgreater} {T/A} -5.6 +/- 0.9 {\textgreater} {G/G} -5.1 +/- 1.1 {\textgreater} {T/C} -4.9 +/- 0.7 {\textgreater} {C/T} -4.8 +/- 1.1 {\textgreater} {T/T} -4.7 +/- 0.5 {\textgreater} {C/A} -3.8 +/- 0.8 {\textgreater} {C/C} -1.0 +/- 1.0 (standard deviations are provided in parenthesis). Sequence-related structural diversities and {SCF} and correlation contributions to the stacking interactions are also discussed. The most representative structures of stacked dimers were found based on a clustering protocol.",
	collection = "stacking",
	doi = "10.1039/b909327c",
	keywords = "aromatic stacking",
	localfile = "molecular stacking/2009 - Intra-strand stacking interactions in B-DNA crystals characterized by post-SCF quantum chemistry computations.pdf",
	methods = "MP2/aug-cc-pvDZ",
	year = 2009
}

@Article{2009-Czyznikowska,
	Author = "Żaneta Czyżnikowska",
	Title = "{On the importance of electrostatics in stabilization of stacked guanine–adenine complexes appearing in {B-DNA} crystals}",
	Journal = "J. Mol. Struct.: {THEOCHEM}",
	Volume = "895",
	Number = "1-3",
	Pages = "161–167",
	abstract = "In this paper, the importance of the first-order electrostatic energy in stabilization of stacked guanine-adenine complexes is discussed for conformations of the complexes appearing in B-DNA crystals. The interaction energy components were calculated at the SCF level of theory using variational-perturbational scheme and compared with the total MP2 intermolecular interaction energy. It is demonstrated that electrostatic energy plays an important role in the stabilization of analyzed structures. Moreover, the results of calculations show that the electrostatic component is much more dependent on the conformations of guanine-adenine complexes than the total MP2 interaction energy. (C) 2008 Elsevier B.V. All rights reserved.",
	collection = "stacking",
	doi = "10.1016/j.theochem.2008.10.040",
	localfile = "molecular stacking/2009 - On the importance of electrostatics in stabilization of stacked guanine-adenine complexes appearing in B-DNA crystals.pdf",
	year = 2009
}

@Article{2009-Czyznikowska-1,
	Author = "Żaneta Czyżnikowska",
	Title = "{How does modification of adenine by hydroxyl radical influence the stability and the nature of stacking interactions in adenine-cytosine complex?}",
	Journal = "J. Mol. Model.",
	Volume = "15",
	Number = "6",
	Pages = "615–622",
	abstract = "This study reports on ab initio calculations of adenine - cytosine complexes in two different context alignments appearing in B-DNA. The influence of adenine modification by hydroxyl radical on the stability of the complexes is also discussed. The analysis was performed on over 40 crystallographic structures for each of the sequence contexts. In most cases, modification of adenine by hydroxyl radical leads to less negative intermolecular interaction energies. The issue of the influence of alteration of structural base step parameters on the stability of modified and unmodified adenine - cytosine complexes is also addressed. Analysis of the dependence of intermolecular interaction energy on base step parameters reveals that for twist and shift modification of adenine by hydroxyl radical leads to quite different interaction energy profiles in comparison with unmodified complexes. In order to elucidate the physical origins of this phenomenon, i.e. to analyze how the modification of adenine by hydroxyl radical is reflected in the change of intermolecular interaction energy components, a variational-perturbational decomposition scheme was applied at the MP2/aug-cc-pVDZ level of theory.",
	collection = "stacking",
	doi = "10.1007/s00894-008-0447-0",
	localfile = "molecular stacking/2009 - How does modification of adenine by hydroxyl radical influence the stability and the nature of stacking itneractions in adenine-cytosine complex?.pdf",
	year = 2009
}

@Article{2009-Czyznikowska-LGZC,
	Author = "Żaneta Czyżnikowska and Paweł Lipkowski and Robert W. Góra and Robert Zaleśny and A. C. Cheng",
	Title = "{On the Nature of Intermolecular Interactions in Nucleic Acid {Base−Amino} Acid {Side-Chain} Complexes}",
	Journal = "J. Phys. Chem. B",
	Volume = "113",
	Number = "33",
	Pages = "11511–11520",
	abstract = "Twenty hydrogen-bonded complexes composed of nucleic acid base and amino acid side chain have been analyzed using ab initio quantum chemistry methods with the aim of gaining insights into the nature of molecular interactions in these systems. The intermolecular interaction energies were estimated using the second-order {Møller−Plesset} perturbation theory and coupled clusters approach with single and double excitations, while their components have been determined by means of a hybrid variational−perturbational decomposition scheme. Additionally, the topological analysis of an electron density distribution of the studied complexes has been performed. In the case of all of the studied neutral complexes, the main source of stabilization is the delocalizaction energy associated with the electron density deformation upon the interaction which contributes almost half of the total interaction energy. Furthermore, analysis of the interaction induced difference density maps of complexes containing neutral amino acid side chains reveals that the delocalization component involves the electron density changes localized in the double-hydrogen-bonded ring structures. A relatively good correlation between the sum of densities at hydrogen-bond critical points and the {Hartree−Fock} intermolecular interaction energy components (electrostatic, delocalization, and exchange) has been observed for the two independently considered sets of complexes, containing positively charged and neutral amino acid side chains.",
	collection = "nucleic acid bases",
	doi = "10.1021/jp904146m",
	localfile = "nucleic acid bases/2009 - On the nature of intermolecule interactions in nucleic acid base-amino acid side-chain complexes.pdf",
	year = 2009
}

@Article{2009-Czyznikowska-Zalesny,
	Author = "Żaneta Czyżnikowska and Robert Zaleśny",
	Title = "{Theoretical insights into the nature of intermolecular interactions in cytosine dimer}",
	Journal = "Biophys. Chem.",
	Volume = "139",
	Number = "2-3",
	Pages = "137–143",
	abstract = "In this study we discuss stacking interactions in cytosine dimer in conformations appearing in B-DNA crystals. The variational-perturbational scheme was applied for decomposition of the intermolecular interaction energy at the MP2 level of theory. The significant influence of the mutual orientation of cytosine monomers was observed not only on the total intermolecular interaction energy but also on its components: Different components of intermolecular interaction energy depend in different manner on parameters describing mutual orientation of cytosine monomers.",
	collection = "stacking",
	doi = "10.1016/j.bpc.2008.11.001",
	localfile = "molecular stacking/2009 - Theoretical insights into the nature of intermolecular interactions in cytosine dmer.pdf",
	year = 2009
}

@Article{2009-Daoulas-CSM,
	Author = "Kostas Ch. Daoulas and Anna Cavallo and Roy Shenhar and Marcus Müller",
	Title = "{Phase behaviour of quasi-block copolymers: a DFT-based Monte Carlo study}",
	Journal = "Soft Matter",
	Volume = "5",
	Pages = "4499–4509",
	collection = "block copolymers",
	doi = "10.1039/b911364a",
	keywords = "block copolymers; mesophase transitions; nanogrowth; polymer blends",
	localfile = "block copolymers/2009 - Phase behaviour of quasi-block copolymers: a DFT-based Monte Carlo study.pdf",
	methods = "MC with mean fields",
	year = 2009
}

@Article{2009-Day-CCHABTVVJGDTEFBFHNLKPMKWSASSWS,
	Author = "Graeme M. Day and Timothy G. Cooper and Aurora J. {Cruz-Cabeza} and Katarzyna E. Hejczyk and Herman L. Ammon and Stephan X. M. Boerrigter and Jeffrey S. Tan and Raffaele G. Della Valle and Elisabetta Venuti and Jovan Jose and Shridhar R. Gadre and Gautam R. Desiraju and Tejender S. Thakur and {Bouke P. van} Eijck and Julio C. Facelli and Victor E. Bazterra and Marta B. Ferraro and Detlef W. M. Hofmann and Marcus A. Neumann and Frank J. J. Leusen and John Kendrick and Sarah L. Price and Alston J. Misquitta and Panagiotis G. Karamertzanis and Gareth W. A. Welch and Harold A. Scheraga and Yelena A. Arnautova and Martin U. Schmidt and {Jacco van de} Streek and Alexandra K. Wolf and Bernd Schweizer",
	Title = "{Significant progress in predicting the crystal structures of small organic molecules – a report on the fourth blind test}",
	Journal = "Acta Cryst. B",
	Volume = "65",
	Number = "2",
	Pages = "107–125",
	abstract = "We report on the organization and outcome of the fourth blind test of crystal structure prediction, an international collaborative project organized to evaluate the present state in computational methods of predicting the crystal structuresof small organic molecules. There were 14 research groups which took part, using a variety of methods to generate and rank the most likely crystal structures for four target systems: three single-component crystal structures and a 1:1 cocrystal. Participants were challenged to predict the crystal structures of the four systems, given only their molecular diagrams, while the recently determined but as-yet unpublished crystal structures were withheld by an independent referee. Three predictions were allowed for each system. The results demonstrate a dramatic improvement in rates of success over previous blind tests; in total, there were 13 successful predictions and, for each of the four targets, at least two groups correctly predicted the observed crystal structure. The successes include one participating group who correctly predicted all four crystal structures as their ﬁrst ranked choice, albeit at a considerable computational expense. The results reﬂect important improvements in modelling methods and suggest that, at least for the small and fairly rigid types of molecules included in this blind test, such calculations can be constructively applied to help understand crystallization and polymorphism of organic molecules.",
	collection = "molecular crystals",
	doi = "10.1107/S0108768109004066",
	localfile = "molecular crystals/2009 - Significant progress in predicting the crystal structures of small organic molecules - a report on the fourth blind test.pdf",
	year = 2009
}

@Article{2009-Dessailly-NJFKLFGRO,
	Author = "Benoir Dessailly and Rajesh Nair and Lukasz Jaroszewski and Eduardo Fajardo and Andrei Kouranov and David Lee and Andras Fiser and Adam Godzik and Burkhard Rost and Christine Orengo",
	Title = "{PSI-2: structural genomics to cover protein domain family space}",
	Journal = "Structure",
	Volume = "17",
	Pages = "869–881",
	collection = "genomics",
	doi = "10.1016/j.str.2009.03.015",
	keywords = "structural genomics",
	localfile = "genomics/2009 - PSI-2: structural genomics to cover protein domain family space.pdf",
	read = "2013-08-20",
	year = 2009
}

@Article{2009-Ebrahimi-HNG,
	Author = "Ali Ebrahimi and Mostafa Habibi and Razieh Sadat Neyband and Ali Reza Gholipour",
	Title = "{Cooperativity of π-stacking and hydrogen bonding interactions and substituent effects on X-ben||pyr...H–F complexes}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "11",
	Pages = "11424–11431",
	collection = "stacking",
	doi = "10.1039/b912419e",
	localfile = "molecular stacking/2009 - Cooperativity of pi-stacking and hydrogen bonding interactions adn substituent effects on X-ben pyr H-F complexes.pdf",
	year = 2009
}

@Article{2009-ElSohly-HCT,
	Author = "Adel M. {ElSohly} and Brian W. Hopkins and Kari L. Copeland and Gregory S. Tschumper",
	Title = "{Anchoring the potential energy surface of the diacetylene dimer}",
	Journal = "Mol. Phys.",
	Volume = "108",
	Number = "8-12",
	Pages = "923–928",
	abstract = "The diacetylene dimer, (H–C C–C C–H)2, serves as a useful prototype for delocalised -type interactions. It mimics many of the important characteristics of aromatic -stacking prototypes such as (C6H6)2 but is small enough that full geometry optimisations and vibrational frequency computations with analytic derivatives are feasible with sophisticated electronic structure techniques. Six stationary points on the potential energy surface (PES) of (H–C C–C C–H)2 have been identified and characterised with CCSD(T) computations. The relative energies of the stationary points on each PES have been anchored by combining explicitly correlated MP2-R12 computations with corrections for higher-order correlation effects as well as core correlation effects. These computations identify a Y-shaped global minimum with an electronic dissociation energy (De) of 1.84 kcal molÀ1 at the all-electron CCSD(T) complete basis set limit. Higher-order correlation corrections are necessary to correctly identify the global minimum while core correlation effects have almost no influence on the relative energies of the stationary points.",
	collection = "stacking",
	doi = "10.1080/00268970802695404",
	localfile = "molecular stacking/2009 - Anchoring the potential energy surface of the diacetylene dimer.pdf",
	year = 2009
}

@Article{2009-Gil-BBO,
	Author = "Adria Gil and Vicenc Branchadell and Joan Bertran and Antoni Oliva",
	Title = "{An Analysis of the Different Behavior of {DNA} and {RNA} through the Study of the Mutual Relationship between Stacking and Hydrogen Bonding}",
	Journal = "J. Phys. Chem. B",
	Volume = "113",
	Number = "14",
	Pages = "4907–4914",
	abstract = "The mutual relationship between stacking and hydrogen bonding and the possible inﬂuence of stacking in the different behavior of DNA and RNA base pairs have been studied through complete DFT optimization of different structures of A-U and A-T dimers (i.e., A-U/U-A and A-T/T-A), using some functionals developed by the group of Truhlar. The results obtained in this work clearly show that stacking and hydrogen bonding are deeply connected. The different behavior of DNA and RNA when replacing uracil by thymine can be interpreted through the formation of a stabilizing CH/π interaction between the methyl group of thymine and the ﬁve-member ring of adenine.",
	collection = "nucleic acid bases",
	doi = "10.1021/jp809737c",
	localfile = "nucleic acid bases/2009 - An analysis of the different behavior of DNA and RNA through the study of the mutual relationship between stacking adn hydrogen bonding.pdf",
	year = 2009
}

@Article{2009-Gordon-MPRSB,
	Author = "Mark S. Gordon and Jonathan M. Mullin and Spencer R. Pruit and Luke B. Roskop and Lyudmila V. Slipchenko and Jerry A. Boatz",
	Title = "{Accurate methods for large molecular systems}",
	Journal = "J. Phys. Chem. B",
	Volume = "113",
	Pages = "8646–9663",
	collection = "molecular fragmentation",
	doi = "10.1021/jp811519x",
	localfile = "molecular fragmentation/2009 - Accurate methods for large molecular systems.pdf",
	methods = "EFP2, FMO, SFM",
	rating = "3",
	read = "2012-08-06",
	type = "Review",
	year = 2009
}

@Article{2009-Gu-WLXS,
	Author = "Jiande D. Gu and Jing Wang and Jerzy Leszczyński and Yaoming Xie and {Henry F. III} Schaefer",
	Title = "{Reply to 'Comment on 'To stack or not to stack: Performance of a new density functional for the uracil and thymine dimers' [Chem. Phys. Lett. 459 (2008) 164]'}",
	Journal = "Chem. Phys. Lett.",
	Volume = "473",
	Pages = "209–210",
	abstract = "In this Letter, we want to address that the conclusions of the letter by Gu et al. have been misunderstood by Mourik in the comment. In our Letter (CPLETT-08-419R1), the good performance of the new functional M06-2X is concluded based on the comparison with the results based on the CCSD(T) studies. Also, we confirm here our previous assumption related to the nature of the stationary points on the MP2 potential energy surface. (C) 2009 Elsevier B.V. All rights reserved. C1 [Gu, Jiande; Wang, Jing; Leszczynski, Jerzy] Jackson State Univ, Dept Chem, Interdisciplinary Nanotox Ctr, Jackson, MS 39217 USA. [Gu, Jiande] CAS, Shanghai Inst Mat Med, Shanghai Inst Biol Sci,Drug Design \& Discovery Ct, State Key Lab Drug Res, Shanghai 201203, Peoples R China. [Gu, Jiande; Xie, Yaoming; Schaefer, Henry F., III] Univ Georgia, Ctr Computat Quantum Chem, Athens, GA 30602 USA.",
	collection = "basis set superposition",
	doi = "10.1016/j.cplett.2009.03.055",
	localfile = {},
	year = 2009
}

@Article{2009-Halevy-NP,
	Author = "Alon Halevy and Peter Norvig and Fernando Pereira",
	Title = "{The unreasonable effectiveness of data}",
	Journal = "IEEE Intelligent Systems",
	Volume = "24",
	Pages = "8–12",
	Note = "Page 12: Choose a representation that can use unsupervised learning on unlabeled data, which is so much more plentiful than labeled data.",
	collection = "philosphy",
	doi = "10.1109/MIS.2009.36",
	localfile = "philosophy/2009 - The unreasonable effectiveness of data.pdf",
	rating = "2",
	read = "2013-11-12",
	year = 2009
}

@Article{2009-Hall-LB,
	Author = "David M. Hall and Turab Lookman and Sanjoy Banerjee",
	Title = "{Non-equilibrium particle-field simulations of polymer-nanocomposite dynamics}",
	Journal = "Chem. Eng. Sci.",
	Volume = "64",
	Pages = "4754–4757",
	abstract = "We present a theoretical framework for simulating dynamic processes in polymeric fluids with embedded nanoparticles. The method couples an Eulerian, field-theoretic description of polymer hydrodynamics with a Lagrangian technique for tracking particles of arbitrary shape and size. Results are presented which reproduce nanoparticle localization in diblock nanosphere composites and interfacial jamming in homopolymer blend nanocomposites. Some of the method's unique capabilities are demonstrated by simulating systems containing non-spherical particles, particles of multiple sizes, and surface driven self-assembly.",
	collection = "block copolymer nanocomposites",
	doi = "10.1016/j.ces.2009.07.031",
	keywords = "block copolymers; hydrodynamics; nanorods; nanospheres; nanotriangles; polymer blends; polymer nanocomposites; rheology",
	localfile = "block copolymer nanocomposites/2009 - Non-equilibrium particle-field simulations of polymer-nanocomposite dynamics.pdf",
	methods = "HSCFT",
	rating = "2",
	year = 2009
}

@Article{2009-Han-MI,
	Author = "Sang Soo Han and Jose L. {Mendoza-Cortes} and William {A. III} Goddard",
	Title = "{Recent advances on simulation and theory of hydrogen storage in metal-organic frameworks and covalent organic frameworks}",
	Journal = "Chem. Soc. Rev.",
	Volume = "38",
	Number = "5",
	Pages = "1460–1476",
	abstract = "This critical review covers the application of computer simulations, including quantum calculations (ab initio and {DFT),} grand canonical {Monte-Carlo} simulations, and molecular dynamics simulations, to the burgeoning area of the hydrogen storage by metal-organic frameworks and covalent-organic frameworks. This review begins with an overview of the theoretical methods obtained from previous studies. Then strategies for the improvement of hydrogen storage in the porous materials are discussed in detail. The strategies include appropriate pore size, impregnation, catenation, open metal sites in metal oxide parts and within organic linker parts, doping of alkali elements onto organic linkers, substitution of metal oxide with lighter metals, functionalized organic linkers, and hydrogen spillover (186 references).",
	collection = "hydrogen sorption",
	doi = "10.1039/b802430h",
	localfile = "hydrogen sorption/2009 - Recent advances on simulation and theory of hydrogen storage in metal-organic frameworks and covalent organic frameworks.pdf",
	year = 2009
}

@Article{2009-He-ZCL,
	Author = "Linli He and Linxi Zhang and Hongping Chen and Haojun Liang",
	Title = "{The phase behaviors of cylindrical diblock copolymers and rigid nanorods' mixtures}",
	Journal = "Polymer",
	Volume = "50",
	Pages = "3403–3410",
	abstract = "Mixtures of cylindrical forming diblock copolymers (DBCPs) and mobile nanorods (NRs) are systematically investigated via dissipative particle dynamics (DPD) simulations. Final morphology of such composites depends not only on the characteristics of the copolymers, but also on the physical or chemical features of NRs, such as NR number, length, and surface adsorption (neutral, A and B attractive). A consideration of enthalpic and entropic interactions is necessary when physically or chemically distinct NRs are introduced into the copolymer/nanorod composites. For the short NRs, the phase behavior is similar to that of spherical nanoparticles (NPs). For the long NRs, the self-assembly of NRs can inﬂuence both the orientation and morphology of diblock/nanorod mixtures. If more NRs are incorporated, under stronger conﬁnement from the host phase separated domains, the long NRs will aggregate and self-assemble into a certain spatial organization, inducing the morphological transitions of the composites from one phase to another. This behavior is not encountered for a similar system doped with spherical particles, emphasizing the role of particle shape in the interaction between doping particles and the host phase.",
	collection = "block copolymer nanocomposites",
	doi = "10.1016/j.polymer.2009.04.068",
	keywords = "block copolymers; mesophase transitions; nanorods; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2009 - The phase behaviors of cylindrical diblock copolymers and rigid nanorods' mixtures.pdf",
	methods = "DPD",
	year = 2009
}

@Article{2009-He-ZXL,
	Author = "Linli He and Linxi Zhang and Agen Xia and Haojun Liang",
	Title = "{Effect of nanorods on the mesophase structure of diblock copolymers}",
	Journal = "J. Chem. Phys.",
	Volume = "130",
	Pages = "144907",
	abstract = "Mixtures of symmetric diblock copolymers and rigid nanorods NRs that are preferentially wetted by one of the blocks A are systematically investigated via dissipative particle dynamics simulations. The morphology of such composites depends not only on the characteristics of the copolymers, but also on the physical or chemical features of the NRs, such as NR volume fraction, size, and polymer-NR interaction. We ﬁnd that the presence of NRs inﬂuences the phase behavior of copolymers and the phase-separated domains of copolymers in turn conﬁne the NRs spatial distribution and positional orientation. The morphologies and phase transitions of hybrids and the corresponding NRs distributed and oriented regularities can be rationalized on the basis of the relative enthalpic and entropic effects involving all of the species, A and B blocks, and NRs. These results suggest that by choosing appropriate parameters, our model systems may provide a prediction to control and design the high-performance composites.",
	collection = "block copolymer nanocomposites",
	doi = "10.1063/1.3089713",
	keywords = "block copolymers; mesophase transitions; nanorods; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2009 - Effect of nanorods on the mesophase structure of diblock copolymers.pdf",
	methods = "DPD",
	year = 2009
}

@Article{2009-Hill-Platts,
	Author = "J. Grant Hill and James A. Platts",
	Title = "{Local electron correlation descriptions of the intermolecular stacking interactiosn between aromatic intercalators and nucleic acids}",
	Journal = "Chem. Phys. Lett.",
	Volume = "479",
	Pages = "279–283",
	abstract = "Interaction energies for the binding of three intercalators to nucleic acid base pairs and base-pair steps are presented. Density ﬁtting (DF) and local (L) correlation methods are employed, allowing use of basis sets appropriate for description of non-covalent interactions. In common with previous studies of stacking interactions, DF-LMP2 overestimates binding by as much as 50\%. However, spin-component scaling (SCS) corrects for this effect, resulting in binding energies that support literature data obtained with small basis sets and/or density functional theory. The efﬁciency of this approach allows intercalators within base-pair steps to be studied, revealing substantial many body terms.",
	collection = "nucleic acid intercalation",
	doi = "10.1016/j.cplett.2009.08.021",
	localfile = "nucleic acid intercalation/2009 - Local electron correlation descriptions of the intermolecular stacking interactions between aromatic intercalators and nucleic acids.pdf",
	year = 2009
}

@Article{2009-Hirata,
	Author = "So Hirata",
	Title = "{Quantum chemistry of macromolecules and solids}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "11",
	Number = "38",
	Pages = "8397–8412",
	abstract = "Two classes of electronic structure methods for macromolecules and nonmetallic solids are reviewed, showcasing their applications to hydrocarbon polymers and organic molecular crystals. One is the crystalline orbital theory for periodic extended systems and the other is a localized-orbital, embedding-field approach for periodic or nonperiodic systems consisting of weakly-interacting subsystems. Both implement rigorous electron-correlation theories such as coupled-cluster and perturbation theories as well as density-functional approximations and can treat not just ground-state energies but also equilibrium structures, phonons (in the harmonic approximation and beyond), excitons, and quasiparticle energy bands (by the crystalline orbital theory only). Three key concepts underlying macromolecular and solid-state electronic structure theories-decay of effective inter-particle interactions, size extensivity, and periodicity-are identified and analyzed in the context of these two closely related approaches.",
	collection = "quantum chemistry",
	doi = "10.1039/b905812p",
	localfile = "quantum chemistry/2009 - Quantum chemistry of macromolecules and solids.pdf",
	year = 2009
}

@Article{2009-Horowitz-LHGH,
	Author = "Eric D. Horowitz and Seth Lilavivat and Benjamin W. Holladay and Markus W. Germann and Nicholas V. Hud",
	Title = "{Solution Structure and Thermodynamics of 2′,5′ {RNA} Intercalation}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "131",
	Number = "16",
	Pages = "5831–5838",
	abstract = "As a means to explore the influence of the nucleic acid backbone on the intercalative binding of ligands to {DNA} and {RNA,} we have determined the solution structure of a proflavine-bound 2′,5′-linked octamer duplex with the sequence {GCCGCGGC.} This structure represents the first {NMR} structure of an intercalated {RNA} duplex, of either backbone structural isomer. By comparison with X-ray crystal structures, we have identified similarities and differences between intercalated 3′,5′ and 2′,5′-linked {RNA} duplexes. First, the two forms of {RNA} have different sugar pucker geometries at the intercalated nucleotide steps, yet have the same interphosphate distances. Second, as in intercalated 3′,5′ {RNA,} the phosphate backbone angle ζ at the 2′,5′ {RNA} intercalation site prefers to be in the trans conformation, whereas unintercalated 2′,5′ and 3′,5′ {RNA} prefer the -gauche conformation. These observations provide new insights regarding the transitions required for intercalation of a phosphodiester-ribose backbone and suggest a possible contribution of the backbone to the origin of the nearest-neighbor exclusion principle. Thermodynamic studies presented for intercalation of both structural {RNA} isomers also reveal a surprising sensitivity of intercalator binding enthalpy and entropy to the details of {RNA} backbone structure.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/ja810068e",
	localfile = "nucleic acid intercalation/2009 - Solution structure and thermodynamics of 2',5' RNA intercalation.pdf",
	year = 2009
}

@Article{2009-Iacovella-Glotzer,
	Author = "Christopher R. Iacovella and Sharon C. Glotzer",
	Title = "{Phase behavior of ditethered nanospheres}",
	Journal = "Soft Matter",
	Volume = "5",
	Pages = "4492–4498",
	abstract = "We report the results from a computational study of the self-assembly of amphiphilic ditethered nanospheres using molecular simulation. We explore the phase behavior as a function of nanosphere diameter, interaction strength, and directionality of the tether–tether interactions. We predict the formation of seven distinct ordered phases. We compare these structures with those observed in linear and star triblock copolymer systems.",
	collection = "nanoparticles",
	doi = "10.1039/b909669h",
	keywords = "self-assembly; nanoparticle grafts; nanospheres",
	localfile = "nanoparticles/2009 - Phase behavior of ditethered nanospheres.pdf",
	year = 2009
}

@Article{2009-Issa-KWP,
	Author = "Nizar Issa and Panagiotis G. Karamertzanis and Gareth W. A. Welch and Sarah L. Price",
	Title = "{Can the Formation of Pharmaceutical Cocrystals Be Computationally Predicted? I. Comparison of Lattice Energies}",
	Journal = "Cryst. Growth Des.",
	Volume = "9",
	Number = "1",
	Pages = "442–453",
	abstract = "A cocrystal is only expected to form if it is thermodynamically more stable than the crystals of its components. To test whether this can be predicted with a current computational methodology, we compare the lattice energies of 12 cocrystals of 4-aminobenzoic acid, 8 of succinic acid and 6 of caffeine, with the sums of the lattice energies of their components. These three molecules were chosen for their potential use in pharmaceutical cocrystals and because they had sufﬁcient determinations of cocrystals and corresponding partner crystal structures in the Cambridge Structural Database. The lattice energies were evaluated using anisotropic intermolecular atom-atom potentials, with the electrostatic model and the intramolecular energy penalty for changes in speciﬁed torsion angles derived from ab initio calculations on the isolated molecules. The majority of the cocrystals are calculated to be more stable than their components, but the energy difference is only large in a few of the cases where the partner molecule cannot hydrogen bond to itself. More typically, the cocrystal stabilization is comparable to polymorphic energy differences and some of the speciﬁcally identiﬁed errors in the computational modeling. The cocrystals will be more stable relative to the observed disordered structures of caffeine and the kinetically preferred polymorph of 4-aminobenzoic acid, highlighting kinetic factors that may be involved in cocrystal formation. Overall, it appears that cocrystal formation should generally be predictable by comparing the relative stability of the most stable cocrystal and its pure components found on the computed crystal energy landscapes, but this is often very demanding of the accuracy of the method used to calculate the crystal energy.",
	collection = "molecular crystals",
	doi = "10.1021/cg800685z",
	localfile = {molecular crystals/2009 - Can the formation of pharmaceutical cocrystals be computationally predicted? I. Comparison of lattice energies.pdf},
	shorttitle = "Can the Formation of Pharmaceutical Cocrystals Be Computationally Predicted?",
	year = 2009
}

@Article{2009-Jayaraman-Schweizer,
	Author = "Arthi Jayaraman and Kenneth S. Schweizer",
	Title = "{Effective interactions and self-assembly of hybrid polymer grafted nanoparticles in a homopolymer matrix}",
	Journal = "Macromolecules",
	Volume = "42",
	Pages = "8423–8434",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma901631x",
	keywords = "self-assembly; nanoparticle grafts; nanospheres; polymer nanocomposites",
	localfile = "polymer nanocomposites/2009 - Effective interactions and self-assembly of hybrid polymer grafted nanoparticles in a homopolymer matrix.pdf",
	year = 2009
}

@Article{2009-Jayaraman-Schweizer-1,
	Author = "Arthi Jayaraman and Kenneth S. Schweizer",
	Title = "{Liquid state theory of the structure and phase behaviour of polymer-tethered nanoparticles in dense suspensions, melts and nanocomposites}",
	Journal = "Mol. Simul.",
	Volume = "35",
	Number = "10-11",
	Pages = "835–848",
	collection = "polymer nanocomposites",
	doi = "10.1080/08927020902744680",
	keywords = "self-assembly; nanoparticle grafts; nanospheres; polymer nanocomposites",
	localfile = "polymer nanocomposites/2009 - Liquid state theory of the structure and phase behaviour of polymer-tethered nanoparticles in dense suspensions, melts and nanocomposites.pdf",
	year = 2009
}

@Article{2009-Jin-WF,
	Author = "Jiezhu Jin and Jianzhong Wu and Amalie L. Frischknecht",
	Title = "{Modeling miscroscopic morphology and mechanical properties of block copolymer-nanoparticle composites}",
	Journal = "Macromolecules",
	Volume = "42",
	Pages = "7537–7544",
	abstract = "The morphology of block copolymer and nanoparticle composites depends not only on the copolymer architecture but also on the surface energy, geometry, and volume fraction of the embedding nanoparticles. Toward a quantitative description of the composite structure and associated thermo-mechanical properties from a molecular perspective, we examined the performance of a nonlocal density functional theory that accounts for the excluded-volume effects and intra- and inter-chain correlations self-consistently. It is predicted that, within the lamellar structures of symmetric block copolymers, neutral particles are localized at the microdomain interface, leading to a reduction of the lamellar thickness. Conversely, particles that are energetically biased to a particular microdomain expand the block copolymer lamellar structure. The dilation or shrinkage of the lamellar thickness also depends on the particle packing density. Both particle dispersion and particle-polymer interfacial structure are highly sensitive to the ratio of the particle diameter to the lamellar thickness. While small nanoparticles may either increase or reduce the extensional moduli of the composite material depending on the nanoparticle volume fraction and polymer-particle interactions, large particles always enhance the mechanical properties regardless of the polymer-particle interactions. The theoretical predictions are found to be in qualitative agreement with simulation results and experiments.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma9006686",
	keywords = "block copolymers; mechanical properties; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2009 - Modeling microscopic morphology and mechanical properties of block copolymer-nanoparticle composites.pdf",
	methods = "DFT",
	year = 2009
}

@Article{2009-Kalra-Joo,
	Author = "Vibha Kalra and Yong Lak Joo",
	Title = "{Coarse-grained molecular dynamics study of block copolymer/nanoparticle composites under elongational flow}",
	Journal = "J. Chem. Phys.",
	Volume = "131",
	Pages = "214904",
	abstract = "Symmetric diblock copolymer/nanoparticle NP systems under planar elongational ﬂow have been modeled and simulated using coarse-grained nonequilibrium molecular dynamics. The aim of our present study is to understand how the dispersion of NPs in a block copolymer system is inﬂuenced by elongational ﬂow and how the presence of NPs changes the rheology and ﬂow-induced morphology transition in block copolymers. We consider two different kinds of spherical NPs categorized with respect to their interaction potential with the polymeric blocks: 1 selective NPs that show a preference toward one of the blocks of a model diblock copolymer and 2 nonselective NPs that show equal attraction toward both blocks. For unrestricted simulation times during elongational ﬂow, spatially and temporally periodic boundary conditions devised by Kraynik and Reinelt Int. J. Multiphase Flow 18, 1045 1992 have been implemented. Our results show that the concentration peak of both selective NPs at the center of the preferred domain and nonselective NPs at the domain interface becomes broader with increasing elongation rate, suggesting that elongational ﬂow can be used as another parameter to control nanocomposite self-assembly. In addition, our results reveal that the onset of ﬂow-induced transition from lamellar to disordered morphology is greatly inﬂuenced by particle-particle and particle-polymer interactions.",
	collection = "block copolymer nanocomposites",
	doi = "10.1063/1.3266511",
	keywords = "block copolymers; rheology; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2009 - Coarse-grained molecular dynamics study of block copolymer-nanoaprticle composites under elongational flow.pdf",
	methods = "CG MD",
	year = 2009
}

@Article{2009-Kan,
	Author = "{Yu-He} Kan",
	Title = "{Covalent or not? Energy decomposition analysis of metal-metal bonding in {alkaline-Earth} dimetallocene complexes}",
	Journal = "J. Mol. Struct.: {THEOCHEM}",
	Volume = "894",
	Number = "1-3",
	Pages = "88–92",
	abstract = "The geometries, metal-metal bond dissociation energies of Group 2 dimetallocene complexes {M2([eta]5-C5H5)2} {(M} = Be, Mg, Ca, Sr and Ba) have been calculated using density functional theory at the {BP86} level with {TZ2P} basis sets. The nature of metal-metal bonding has been analyzed with an energy decomposition method. The results revealed that the {M-M} binding interactions in these nonpolar bonding {alkaline-Earth} metal complexes have more ionic character than covalent character, rather than the sole covalent bond. Molecular orbital calculations indicate that, for the heavier {alkaline-Earth} metal {(Ca,} Sr and Ba) compounds, substantial (n - 1)d character is found in the [delta] bonding between metal and cyclopentadiene {(Cp)} ring, while there is few [delta] bonding interaction between {M-M} bond due to longer {M-M} bond distance.",
	collection = "molecular interactions",
	doi = "10.1016/j.theochem.2008.10.004",
	localfile = {molecular interactions/2009 - Covalent or not? Energy decomposition analysis of metal-metal bonding in alkaline-Earth dimetallocene complexes.pdf},
	shorttitle = "Covalent or not?",
	year = 2009
}

@Article{2009-Kandar-SBMSN,
	Author = "A. K. Kandar and S. Srivastava and J. K. Basu and M. K. Mukhopadhyay and S. Seifert and S. Narayanan",
	Title = "{Unusual dynamical arrest in polymer grafted nanoparticles}",
	Journal = "J. Chem. Phys.",
	Volume = "130",
	Pages = "121102",
	abstract = "We present results of temperature dependent measurements of dynamics of polymer grafted nanoparticles with high grafting density with star polymerlike morphology. We observed for the low grafting density and hence low functionality sample, a dynamically arrested state with lowering of temperature, similar to what was conjectured earlier. However the high grafting density sample shows liquidlike relaxation at all measured temperatures. Possible origin of dynamical arrest in the two grafting density sample is discussed",
	collection = "polymer nanocomposites",
	doi = "10.1063/1.3090484",
	localfile = "polymer nanocomposites/2009 - Unusual dynamical arrest in polymer grafted nanoparticles.pdf",
	year = 2009
}

@Article{2009-Kashem-PDWMGMCRPM,
	Author = "Mottakin M. Abul Kashem and Jan Perlich and Alexander Diethert and Weinan Wang and Mine Memesa and Jochen S. Gutmann and Eva Majkova and Ignac Cápek and Stephan V. Roth and Winfried Petry and Peter Möller-Buschbaum",
	Title = "{Array of magnetic nanoparticles via particle co-operated self-assembly in block copolymer thin film}",
	Journal = "Macromolecules",
	Volume = "42",
	Pages = "6202–6208",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma900942j",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2009 - Array of magnetic nanoparticles via particle co-operated self-assembly in block copolymer thin film.pdf",
	methods = "AFM, SEM, SAXS",
	rating = "2",
	read = "2012-03-21",
	systems = "magnetite@PS-PMMA",
	year = 2009
}

@Article{2009-Kenny,
	Author = "Peter W. Kenny",
	Title = "{Hydrogen bonding, electrostatic potential, and molecular design}",
	Journal = "J. Chem. Inf. Model.",
	Volume = "49",
	Pages = "1234–1244",
	abstract = "The VR(r) descriptor was introduced and shown to be an effective and useful predictor of hydrogen bond acidity. VR(r) is deﬁned as the electrostatic potential at a distance, r, from the donor hydrogen on an axis deﬁned by the nuclei of the hydrogen atom and the atom to which it is bonded. VR(r) is most predictive of hydrogen bond acidity for r ) 0.55 Å which is less than half the van der Waals radius of hydrogen. Calculated values of VR(r) and minimized electrostatic potential (Vmin) were used to show how molecular electrostatic potential can be used to provide insight into a number of hydrogen bonding phenomena, including lactam self-association, DNA base pairing, and bioisosterism. The effects of hydrogen bond formation on the strengths of other donors in the interacting molecules were explored and quantiﬁed. Implications of these results for modeling hydrogen bond acidity, derivation of atomic charges, and development of polarizable force ﬁelds were discussed.",
	collection = "hydrogen bonding",
	doi = "10.1021/ci9000234",
	localfile = "hydrogen bonding/2009 - Hydrogen bonding, electrostatic potential, and molecular design.pdf",
	year = 2009
}

@Article{2009-Khan-HABK,
	Author = "Jamil Khan and Shane E. Harton and Brian C. Benicewicz and Sanat K. Kumar",
	Title = "{Polymer crystallization in nanocomposites: spatial reorganization of nanoparticles}",
	Journal = "Macromolecules",
	Volume = "42",
	Pages = "5741–5744",
	abstract = "The crystal sizes and melting points of polyethyleneoxide, crystallized in the presence of silica nanoparticles, are only affected for particle loadings larger than 20 wt \%. X-ray scattering shows that the distribution of particle spacings in the semicrystalline state is always significantly broader than in the melt, even though the mean particle spacing is unchanged. We thus conclude that, at low loadings, the polymer “forces” the nanoparticle “defects” out of their way to crystallize in a minimally perturbed form. For higher loadings, the crystals become smaller in response to increased particle induced confinement. In contrast to currently held views that the particles control the crystallization process, e.g., by providing heterogeneous nucleation sites, we find that the crystalline lamellae dominate; i.e., they manipulate the nanoparticle dispersion, especially at low loadings.",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma900794t",
	keywords = "nanospheres; polymer nanocomposites",
	localfile = "polymer nanocomposites/2009 - Polymer crystallization in nanocomposites: spatial reorganization of nanoparticles.pdf",
	year = 2009
}

@Article{2009-Khounlavong-Ganesan,
	Author = "Landry Khounlavong and Venkat Ganesan",
	Title = "{Influence of interfacial layers upon the barrier properties of polymer nanocomposites}",
	Journal = "J. Chem. Phys.",
	Volume = "130",
	Pages = "104901",
	collection = "polymer nanocomposites",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2009 - Influence of interfacial layers upon the barrier properties of polymer nanocomposites.pdf",
	year = 2009
}

@Article{2009-Kim-FBHK,
	Author = "Bumjoon J. Kim and Glenn H. Fredrickson and Joona Bang and Craig J. Hawker and Edward J. Kramer",
	Title = "{Tailoring core-shell polymer-coated nanoparticles as block copolymer surfactants}",
	Journal = "Macromolecules",
	Volume = "42",
	Pages = "6193–6201",
	Note = "Studies morphology of PS-b-P2VP conatining Ps-coated Au NPs (2.85nm diameter) as a function of NP selectivity by varying areal coating density.",
	abstract = "The effect of core-shell polymer-coated nanoparticles on block copolymer morphology is investigated systematically by controlling particle positioning within a block copolymer template. Our approach of varying the areal chain density (Σ) of short thiol terminated polystyrene (PS-SH) brushes on the particles where the molecular weight (Mn) of the PS ligands (2.5 kg/mol) is used to control the fraction of the particles adsorbed to the interface of PS-b-P2VP diblock copolymer domains (Mn = 196 kg/mol). The change in Σ from 2.38 to 0.49 chains/nm2 brings systematic control over the fraction of Au particles bound to the PS/P2VP interface ( fi), this fraction ranging from 0 to 95\%. Particles with Σ of 2.38 chains/nm2 ( fi ∼ 0) were observed to localize within the PS domains and further produce a macroscopic particle aggregated phase separate from the PS-b-P2VP mesophase. In contrast, decreasing the Σ of PS chains provides for strong binding of Au nanoparticles to the PS/P2VP interfaces as a consequence of preferential wetting of one block of the copolymer (P2VP) to the Au substrate. Interestingly, the addition of low volume fractions (φP) of such nanoparticle surfactants (Σ < 1.1 chains/nm2) to lamellar diblock copolymers initially leads to a decrease in lamellar thickness, a consequence of decreasing interfacial tension, up to a critical value of φP beyond which the block copolymer adopts a bicontinuous morphology. The relationship between domain spacing and morphology of block copolymer with the level of nanoparticle surfactants will be discussed based on a strong-segregation model. In addition, the rational design of nanoparticle surfactants based on the nature and density of the grafted chains will be described.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma9009406",
	keywords = "block copolymers; mesophase transitions; nanoparticle distribution; nanoparticle grafts; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2009 - Tailoring core-shell polymer coated nanoparticles as block copolymer surfactants.pdf",
	methods = "TEM",
	systems = "Au-PS@PS-P2VP",
	year = 2009
}

@Article{2009-Kim-Matsen,
	Author = "Jaeup U. Kim and Mark W. Matsen",
	Title = "{Positioning Janus nanoparticles in block copolymer scaffolds}",
	Journal = "Phys. Rev. Lett.",
	Volume = "102",
	Number = "7",
	Pages = "078303",
	Note = "Identifies the formation of Janus particles from NPs with mixed coatings, as well as their distribution in a BCP lamellar phase.",
	abstract = "The periodic domains formed by block copolymer melts have been heralded as potential scaffolds for arranging nanoparticles in 3D space, provided we can control the positioning of the particles. Recent experiments have located particles at the domain interfaces by grafting mixed brushes to their surfaces. Here the underlying mechanism, which involves the transformation into Janus particles, is investigated with self-consistent ﬁeld theory using a new multi-coordinate-system algorithm.",
	collection = "block copolymer nanocomposites",
	doi = "10.1103/PhysRevLett.102.078303",
	keywords = "block copolymers; Janus particles; nanoparticle distribution; nanoparticle grafts; nanospheres",
	localfile = "block copolymer nanocomposites/2009 - Positioning nanoparticles in block copolymer scaffolds.pdf",
	methods = "SCFT",
	systems = "NP-{nA,nB}@NANB, NP-r{A,B}@NANB",
	year = 2009
}

@Article{2009-Kim-ZYWLK,
	Author = "Chang Kon Kim and Hui Zhang and Sung Hoon Yoon and Jongok Won and Myung-Jin Lee and Chan Kyung Kim",
	Title = "{Effects of Basis Set Superposition Error on Optimized Geometries and Complexation Energies of Organo-Alkali Metal Cation Complexes}",
	Journal = "J. Phys. Chem. A",
	Volume = "113",
	Pages = "513–519",
	abstract = "Theoretical studies were performed to study the binding of alkali metal cations, X+ (X = Li, Na, K), to poly(ethylene oxide) (PEO, I), poly(ethylene amine) (PEA, II), and poly(ethylene N-methylamine) (PEMA, III) by the Hartree-Fock (HF) and B3LYP methods using the 6-31 G(d) and 6-311 +G(d,p) basis sets. Two types of complex were considered in this study: a singly coordinated system (SCS) and a doubly coordinated system (DCS). Complexation energies were calculated both without and with basis set superposition error (BSSE). Because of the strong charge-dipole interactions, the complexation energies were largely negative and decreased in the order Li+ > Na+ > K+. Three possible counterpoise (CP) approaches were examined in detail. In the case of the function CP (fCP) correction, the complexation energies exhibited an unusual trend because of the deformation of the subunits. This problem was solved by including geometry relaxation in the CP-corrected (GCP) interaction energies. The effects on the structures and vibrational frequencies were small when the complexes were reoptimized on the CP-corrected potential energy surface-(PES). C1 [Kirn, Chang Kon; Zhang, Hui; Yoon, Sung Hoon; Kim, Chan Kyung] Inha Univ, Dept Chem, Inchon 402751, South Korea. [Won, Jongok] Sejong Univ, Dept Chem, Seoul 134747, South Korea. [Lee, Myung-Jin] Samsung Elect, Corp Technol Operat SAIT, Grp Emerging Ctr, Yongin 446712, Gyeonggi Do, South Korea.",
	collection = "basis set superposition",
	doi = "10.1021/jp802918b",
	localfile = "basis set superposition/2009 - Effects of basis set superposition error on optimized geometries adn complexation energies of organo-alkali metal cation complexes.pdf",
	year = 2009
}

@Article{2009-Kostjukov-KE,
	Author = "Viktor V. Kostjukov and N. M. Khomytova and M. P. Evstigneev",
	Title = "{Partition of thermodynamic energies of {drug-DNA} complexation}",
	Journal = "Biopolymers",
	Volume = "91",
	Number = "9",
	Pages = "773–790",
	collection = "nucleic acid intercalation",
	doi = "10.1002/bip.21227",
	localfile = "nucleic acid intercalation/2009 - Partition of thermodynamic energies of drug-DNA complexation.pdf",
	year = 2009
}

@Article{2009-Kostjukov-KSIDE,
	Author = "Viktor V. Kostjukov and N. M. Khomytova and A.A. Hernandez Santiago and R. Licona Ibarra and D. B. Davies and M.P. Evstigneev",
	Title = "{Calculation of the electrostatic charges and energies for intercalation of aromatic drug molecules with DNA}",
	Journal = "Int. J. Quant. Chem.",
	collection = "nucleic acid intercalation",
	doi = "10.1002/qua.22451",
	localfile = "nucleic acid intercalation/2009 - Calculation of the electrostatic charges and energies for intercalation of aromatic drug molcules with DNA.pdf",
	year = 2009
}

@Article{2009-Kruger-Reauscher,
	Author = "Matthias Kruger and Markus Rauscher",
	Title = "{Diffusion of a sphere in a dilute solution of polymer coils}",
	Journal = "J. Chem. Phys.",
	Volume = "131",
	Pages = "094902",
	abstract = "We calculate the short time and the long time diffusion coefﬁcients of a spherical tracer particle in a polymer solution in the low density limit by solving the Smoluchowski equation for a two-particle system and applying a generalized Einstein relation ﬂuctuation dissipation theorem. The tracer particle as well as the polymer coils are idealized as hard spheres with a no-slip boundary condition for the solvent but the hydrodynamic radius of the polymer coils is allowed to be smaller than the direct-interaction radius. We take hydrodynamic interactions up to 11th order in the particle distance into account. For the limit of small polymers, the expected generalized Stokes–Einstein relation is found. The long time diffusion coefﬁcient also roughly obeys the generalized Stokes–Einstein relation for larger polymers whereas the short time coefﬁcient does not. We ﬁnd good qualitative and quantitative agreement to experiments.",
	collection = "polymer nanocomposites",
	doi = "10.1063/1.3216108",
	localfile = "polymer nanocomposites/2009 - Diffusion of a sphere in a dilute solution of polymer coils.pdf",
	year = 2009
}

@Article{2009-Kvamme-WC,
	Author = "Brandon Kvamme and Matthew C. F. Wander and Aurora E. Clark",
	Title = "{The role of basis set superposition error in water addition reactions to Ln(III) cations}",
	Journal = "Int. J. Quant. Chem.",
	Volume = "109",
	Pages = "2474–2481",
	abstract = "Our goal in this work was to characterize the importance of basis set superposition error (BSSE) in the reaction energetics of water addition to highly charged metal ions that exhibit strong ion-dipole interactions with water. The gas phase water addition reactions, M(H2O)3 N H2O 3 M(H2O)N 1 [M La(III), Lu(III); N 0 – 8] have been studied, with a particular emphasis on a posteriori methods for calculating BSSE and its constituent energetic components as a function of M(H2O)3 cluster size and water basis set. Because of accumulation of BSSE within the subclusters in the reaction series, the successive reaction counterpoise method for determining the BSSE correction interaction energies is advocated.",
	collection = "basis set superposition",
	doi = "10.1002/qua.22139",
	localfile = "basis set superposition/2009 - The role of basis set superposition error in water addition reactions to LN(III) cations.pdf",
	year = 2009
}

@Article{2009-Ladola-MSM,
	Author = "Alessio Lodola and Marco Mor and Jitnapa Sirirak and Adrian J. Mulholland",
	Title = "{Insight into the mechanism and inhibition of fatty acid amide hydrolase from quantum mechanics/molecular mechanics (QM/MM) modelling}",
	Journal = "Biochem. Soc. Trans.",
	Volume = "37",
	Pages = "363–367",
	abstract = "FAAH (fatty acid amide hydrolase) is a promising target for the treatment of several central nervous system and peripheral disorders. Combined QM/MM (quantum mechanics/molecular mechanics) calculations have elucidated the role of its unusual catalytic triad in the hydrolysis of oleamide and oleoylmethyl ester substrates, and have identiﬁed the productive inhibitor-binding orientation for the carbamoylating compound URB524. These are potentially crucial insights for designing new covalent inhibitors of this drug target.",
	collection = "enzymes",
	doi = "10.1042/BST0370363",
	localfile = "enzymes/2009 - Insights into the mechanism and inhibition of fatty acid amide hydrolase from quantum mechanics molecular mechanics (QMMM) modelling.pdf",
	year = 2009
}

@Article{2009-Li-CTLL,
	Author = "Shen Li and Valentino R. Cooper and Timo Thonhauser and Bengt I. Lundqvist and David C. Langreth",
	Title = "{Stacking Interactions and {DNA} Intercalation}",
	Journal = "J. Phys. Chem. B",
	Volume = "113",
	Number = "22",
	Pages = "11166–11172",
	abstract = "The relationship between stacking interactions and the intercalation of proflavine and ellipticine within {DNA} is investigated using a nonempirical van der Waals density functional for the correlation energy. Our results, employing a binary stack model, highlight fundamental, qualitative differences between base-pair−base-pair interactions and that of the stacked intercalator−base-pair system. The most notable result is the paucity of torque, which so distinctively defines the twist of {DNA.} Surprisingly, this model, when combined with a constraint on the twist of the surrounding base-pair steps to match the observed unwinding of the sugar−phosphate backbone, was sufficient for explaining the experimentally observed proflavine intercalator configuration. Our extensive mapping of the potential energy surface of base-pair−intercalator interactions can provide valuable information for future nonempirical studies of {DNA} intercalation dynamics.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/jp905765c",
	localfile = "nucleic acid intercalation/2009 - Stacking interactions and DNA intercalation.pdf",
	year = 2009
}

@Article{2009-Listak-HRRPMAB,
	Author = "Jessica Listak and Ilhem F. Hakem and Hyung Ju Ryu and Sofia Rangou and Nikolaos Politakos and Konstantinos Misichronis and Apostolos Avgeropoulos and Michael R. Bockstaller",
	Title = "{Effect of chain architecture on the compatibility of block copolymer-nanoparticle blends}",
	Journal = "Macromolecules",
	Volume = "42",
	Pages = "5766–5773",
	Note = "Aggregation of PS-grafted NPs in copolymers of various architectures.",
	abstract = "The effect of block copolymer chain connectivity on the structure formation in binary blends comprising block copolymer hosts and enthalpically neutralized particle fillers is investigated for linear diblock (AB) and triblock (ABA and BAB) as well as four-arm star copolymer architectures (AB3 and A3B). For particles with approximately constant effective size (defined here as the ratio of filler particle diameter to host polymer radius of gyration), miscibility was observed only within diblock copolymers and within the domains formed by the end blocks of triblock copolymers. The limitation of particle miscibility within the triblock mid-domain is interpreted as a consequence of the entropy loss associated with particle deposition due to the stretched configuration of bridged midblock chains. Particle aggregation was observed in both star copolymer samples irrespective of the architecture of the particle-loaded polymer domain. In the case of particle loading of the branched copolymer domain, this is rationalized as a consequence of the increased effective particle size, whereas the incompatibility of particle fillers in the linear block domain of miktoarm copolymer hosts is interpreted as a result of the coupling of dimensional changes within the microstructure along with the reduced axial compressibility of the particle-free branched domain. The sensitive dependence of the particle compatibility on the chain architecture of the polymer host illustrates a yet unexplored parameter space that will need to be taken into account if particle blends are to be designed with branched or multiblock host copolymer architectures.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma900600n",
	keywords = "block copolymers; nanospheres; polymer architecture; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2009 - Effect of chain architecture on the compatibility of block copolymer-nanoparticle blends.pdf",
	methods = "osmometry, SEC, NMR, TEM",
	systems = "Au-PS@PS-PI, Au-PS@PS-PI-PS, Au-PS@PI-PS-PI",
	year = 2009
}

@Article{2009-Liu-ZCW,
	Author = "Jun Liu and Liqun Zhang and Dapeng Cao and Wenchuan Wang",
	Title = "{Static, rheological and mechanical properties of polymer nanocomposites studied by computer modeling and simulation}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "11",
	Pages = "11365–11384",
	abstract = "Polymer nanocomposites (PNCs) often exhibit excellent mechanical, thermal, electrical and optical properties, because they combine the performances of both polymers and inorganic or organic nanoparticles. Recently, computer modeling and simulation are playing an important role in exploring the reinforcement mechanism of the PNCs and even the design of functional PNCs. This report provides an overview of the progress made in past decades in the investigation of the static, rheological and mechanical properties of polymer nanocomposites studied by computer modeling and simulation. Emphases are placed on exploring the mechanisms at the molecular level for the dispersion of nanoparticles in nanocomposites, the effects of nanoparticles on chain conformation and glass transition temperature (Tg), as well as viscoelastic and mechanical properties. Finally, some future challenges and opportunities in computer modeling and simulation of PNCs are addressed.",
	collection = "polymer nanocomposites",
	doi = "10.1039/b913511a",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2009 - Static, theological and mechanical properties of polymer nanocomposites studied by computer modeling and simulation.pdf",
	type = "Review",
	year = 2009
}

@Article{2009-Lo-Chao,
	Author = "Chieh-Tsung Lo and Chun-Jung Chao",
	Title = "{Synthesis and characterization of magnetic nanoparticle-block copolymer composites}",
	Journal = "Langmuir",
	Volume = "25",
	Number = "22",
	Pages = "12865–12869",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/la9032833",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2009 - Synthesis and characterization of magnetic nanoparticle-block copolymer composites.pdf",
	methods = "TEM, XPS, XRD",
	rating = "2",
	read = "2012-03-21",
	systems = "magnetite@PS-P2VP",
	year = 2009
}

@Article{2009-Lu-SWYYLJZ,
	Author = "{Yun-Xiang} Lu and Ting Shi and Yong Wang and Huaiyu Yang and Xiuhua Yan and Xiaoming Luo and Hualiang Jiang and Weiliang Zhu",
	Title = "{Halogen bonding: a novel interaction for rational drug design?}",
	Journal = "J. Med. Chem.",
	Volume = "52",
	Number = "9",
	Pages = "2854–2862",
	abstract = "Although recognized in small molecules for quite some time, the implications of halogen bonding in biomolecular systems are only now coming to light. In this study, several systems of proteins in complex with halogenated ligands have been investigated by using a two-layer QM/MM ONIOM methodology. In all cases, the halogen-oxygen distances are shown to be much less than the van der Waals radius sums. Single-point energy calculations unveil that the interaction becomes comparable in magnitude to classical hydrogen bonding. Furthermore, we found that the strength of the interactions attenuates in the order H ≈ I > Br > Cl. These results agree well with the characteristics discovered within small model halogen-bonded systems. A detailed analysis of the interactions reveals that halogen bonding interactions are responsible for the different conformation of the molecules in the active site. This study would help to establish such interaction as a potential and effective tool in the context of drug design.",
	collection = "halogen bonding",
	doi = "10.1021/jm9000133",
	localfile = "halogen bonding/2009 - Halogen bonding - an novel interaction for rational drug design?.pdf",
	year = 2009
}

@Article{2009-Lu-ZFZJY,
	Author = "{Yun-Xiang} Lu and {Jian-Wei} Zou and {Ji-Cai} Fan and {Wen-Na} Zhao and {Yong-Jun} Jiang and {Qing-Sen} Yu",
	Title = "{{Ab} initio calculations on halogen-bonded complexes and comparison with density functional methods}",
	Journal = "J. Comp. Chem.",
	Volume = "30",
	Number = "5",
	Pages = "725–732",
	abstract = "A systematic theoretical investigation on a series of dimeric complexes formed between some halocarbon molecules and electron donors has been carried out by employing both ab initio and density functional methods. Full geometry optimizations are performed at the {Møller–Plesset} second-order perturbation {(MP2)} level of theory with the Dunning's correlation-consistent basis set, {aug-cc-pVDZ.} Binding energies are extrapolated to the complete basis set {(CBS)} limit by means of two most commonly used extrapolation methods and the {aug-cc-pVXZ} {(X} = D, T, Q) basis sets series. The coupled cluster with single, double, and noniterative triple excitations {[CCSD(T)]} correction term, determined as a difference between {CCSD(T)} and {MP2} binding energies, is estimated with the {aug-cc-pVDZ} basis set. In general, the inclusion of higher-order electron correlation effects leads to a repulsive correction with respect to those predicted at the {MP2} level. The calculations described herein have shown that the {CCSD(T)} {CBS} limits yield binding energies with a range of -0.89 to -4.38 kcal/mol for the halogen-bonded complexes under study. The performance of several density functional theory {(DFT)} methods has been evaluated comparing the results with those obtained from {MP2} and {CCSD(T).} It is shown that {PBEKCIS,} B97-1, and {MPWLYP} functionals provide accuracies close to the computationally very expensive ab initio methods. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009",
	collection = "halogen bonding",
	doi = "10.1002/jcc.21094",
	localfile = "halogen bonding/2009 - Ab initio calculations on halogen-bonded complexes and comparison with density functional methods.pdf",
	year = 2009
}

@Article{2009-Luzuriaga-GP,
	Author = "{Alaitz Ruiz de} Luzuriaga and Hans J. Grande and José A. Pomposo",
	Title = "{Phase diagrams in compressible weakly interacting all-polymer nanocomposites}",
	Journal = "J. Chem. Phys.",
	Volume = "130",
	Pages = "084905",
	abstract = "A compressible regular solution free energy model for describing the phase behavior of weakly interacting binary blends comprising nonrigid polymer nanoparticles and linear-polymer chains i.e., all-polymer nanocomposites has been developed by incorporating speciﬁc nanoparticle-nanoparticle and nanoparticle-polymer contributions into the original free volume theory for binary polymer blends of Ruzette et al. J. Chem. Phys. 114, 8205 2001 . The extended model allows predicting phase behavior for weakly interacting polymer-nanoparticle/linear-polymer nanocomposites using only pure component properties nanoparticle and polymer sizes, mass densities, coefﬁcients of thermal expansion, and solubility parameters . The effect of polymer and nanoparticle size, as well as those arising from nanoparticle rigidity, exchange interaction energy and composition on the phase behavior of all-polymer nanocomposites have been systematically investigated. A rich variety of phase diagrams including upper critical solution temperature-type, lower critical solution temperature-type, and hour-glass shape are illustrated. Predicted phase diagrams for nonrigid poly styrene -nanoparticle PS-np /linear-poly styrene l-PS , and branched poly ethylene -nanoparticle PE-np /l-PS nanocomposites were in excellent agreement with available experimental data.",
	collection = "polymer nanocomposites",
	doi = "10.1063/1.3078248",
	keywords = "polymer blends; polymer nanocomposites",
	localfile = "polymer nanocomposites/2009 - Phase diagrams in compressible weakly interacting all-polymer nanocomposites.pdf",
	year = 2009
}

@Article{2009-Mahapatra,
	Author = "Anirban Mahapatra",
	Title = "{Chemistry or biology? The debate continues...}",
	Journal = "ACS Chem. Biol.",
	Volume = "4",
	Number = "12",
	Pages = "969–970",
	abstract = "Where exactly on the continuum between absolute biology and pure chemistry do areas

repository: langner/library

repo_name: langner/library

branch_name: refs/heads/master