text:
of study such as biochemistry and chemical biology lie? This seemingly straightforward question continues to inspire vigorous debate from both sides of the aisle these days.",
	collection = "philosophy",
	doi = "10.1021/cb9003095",
	localfile = "philosophy/2009 - Chemistry or biology. The debate continues.pdf",
	year = 2009
}

@Article{2009-Makowski-KGA,
	Author = "Marcin Makowski and Jacek Korchowiec and Feng Long Gu and Yuriko Aoki",
	Title = "{Describing electron correlation effects in the framework of the elongation method - elongation-MP2: formalism, implementation and efficiency}",
	Journal = "J. Comp. Chem.",
	abstract = "The extension of the elongation method into description of electron correlation effects at ab intio level is presented. The formalism and implementation of the elongation-MP2 methodology is discussed. The results of calculations for model systems are presented to illustrate efﬁciency and accuracy of the method. Directions of the further development are highlighted.",
	collection = "quantum chemistry",
	doi = "10.1002/jcc.21462",
	localfile = "quantum chemistry/2009 - Describing electron correlation effects in the framework of the elongation method - elongation-MP2: formalism, implementation and efficiency.pdf",
	year = 2009
}

@Article{2009-Martens,
	Author = "Eric Martens",
	Title = "{A Nobel misses the mark?}",
	Journal = "ACS Chem. Biol.",
	Volume = "4",
	Number = "11",
	Pages = "885",
	abstract = "Last month, when the Royal Swedish Academy of Sciences awarded the Nobel Prize in Chemistry to Venkatraman Ramakrishnan of the MRC Laboratory, Thomas A. Steitz of Yale University, and Ada E. Yonath of the Weizmann Institute, not everyone was pleased.",
	collection = "philosophy",
	doi = "10.1021/cb900281p",
	localfile = "philosophy/2009 - A Nobel misses the mark.pdf",
	year = 2009
}

@Article{2009-Mermin,
	Author = "N. David Mermin",
	Title = "{What's bat about this habit}",
	Journal = "Physics Today",
	Volume = "62",
	Number = "5",
	Pages = "8–9",
	collection = "philosophy",
	localfile = "philosophy/2009 - What's bad about this habit.pdf",
	year = 2009
}

@Article{2009-Mermin-1,
	Author = "N. David Mermin and Phillip Pearle and Sabine Hossenfelder and Alexey Burov and Joseph Isler and Fletcher J. Goldin and Mark Alford and Amin Dharamsi and Leonardo Colletti and Rodney Brooks and Fred Kuttner and Bruce Rosenblum and Derek Walton and Michael Nauenberg",
	Title = "{Mermin habitually answers opinions, real and abstract}",
	Journal = "Physics Today",
	Volume = "62",
	Number = "9",
	Pages = "10–15",
	collection = "philosophy",
	doi = "10.1063/1.3226701",
	localfile = "philosophy/2009 - Mermin habitually answers opinions, real and abstract.pdf",
	year = 2009
}

@Article{2009-Mezzenga-Roukolainen,
	Author = "Raffaele Mezzenga and Janne Ruokolainen",
	Title = "{Nanoparticles in the right place}",
	Journal = "Nature Mat.",
	Volume = "8",
	Pages = "926–928",
	abstract = "Hybrid materials based on block copolymers and nanoparticles are a promising class of nanocomposites. Tailoring the block copolymer properties by using supramolecular chemistry allows control of the particle spatial organization and resulting composite properties.",
	collection = "block copolymer nanocomposites",
	keywords = "block copolymers; hydrogen bonding; nanomigration; nanoparticle distribution; nanopinning; nanospheres; polymer nanocomposites; surfactants",
	localfile = "block copolymer nanocomposites/2009 - Nanoparticles in the right place.pdf",
	type = "Editorial",
	year = 2009
}

@Article{2009-Milano-Kawakatsu,
	Author = "Giuseppe Milano and Toshihiro Kawakatsu",
	Title = "{Hybrid particle-field molecular dynamics simulations for dense polymer systems}",
	Journal = "J. Chem. Phys.",
	Volume = "130",
	Pages = "214106",
	abstract = "We propose a theoretical scheme for a hybrid simulation technique where self-consistent ﬁeld theory and molecular dynamics simulation are combined (MD-SCF). We describe the detail of the main implementation issues on the evaluation of a smooth three-dimensional spatial density distribution and its special gradient based on the positions of particles. The treatments of our multiscale model system on an atomic scale or on a speciﬁc coarse-grained scale are carefully discussed. We perform a series of test simulations on this hybrid model system and compare the structural correlations on the atomic scale with those of classical MD simulations. The results are very encouraging and open a way to an efﬁcient strategy that possess the main advantages common to the SCF and the atomistic approaches, while avoiding the disadvantages of each of the treatments.",
	collection = "block copolymers",
	doi = "10.1063/1.3142103",
	keywords = "block copolymers; coarse graining",
	localfile = "block copolymers/2009 - Hybrid particle-field molecular dynamics simulatiosn for dense polymer systems.pdf",
	methods = "MD with mean field interactions",
	rating = "2",
	year = 2009
}

@Article{2009-Mistark-PYLYTRA,
	Author = "Peter A. Mistark and Soojin Park and Sibel Ebru Yalcin and Dong Hyun Lee and Ozgur Yavuzcetin and Mark T. Tuominen and Thomas P. Russell and Marc Achermann",
	Title = "{Block-copolymer-based plasmonic nanostructures}",
	Journal = "ACS Nano",
	Volume = "3",
	Number = "12",
	Pages = "3987–3992",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/nn901245w",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2009 - Block-copolymer-based plasmonic nanostructures.pdf",
	methods = "SFM",
	rating = "2",
	read = "2012-03-21",
	systems = "Au@PS-P4VP, Au@PS-PEO",
	year = 2009
}

@Article{2009-Mitoraj-MZ,
	Author = "Mariusz P. Mitoraj and Artur Michalak and Tom Ziegler",
	Title = "{A Combined Charge and Energy Decomposition Scheme for Bond Analysis}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "5",
	Number = "4",
	Pages = "962–975",
	abstract = "In the present study we have introduced a new scheme for chemical bond analysis by combining the Extended Transition State {(ETS)} method [ Theor. Chim. Acta 1977, 46, 1 ] with the Natural Orbitals for Chemical Valence {(NOCV)} theory [ J. Phys. Chem. A 2008, 112, 1933 ; J. Mol. Model. 2007, 13, 347 ]. The {ETS-NOCV} charge and energy decomposition scheme based on the {Kohn−Sham} approach makes it not only possible to decompose the deformation density, Δρ, into the different components (such as σ, π, δ, etc.) of the chemical bond, but it also provides the corresponding energy contributions to the total bond energy. Thus, the {ETS-NOCV} scheme offers a compact, qualitative, and quantitative picture of the chemical bond formation within one common theoretical framework. Although, the {ETS-NOCV} approach contains a certain arbitrariness in the definition of the molecular subsystems that constitute the whole molecule, it can be widely used for the description of different types of chemical bonds. The applicability of the {ETS-NOCV} scheme is demonstrated for single {(H3X−XH3,} for X = C, Si, Ge, Sn) and multiple {(H2XXH2,} {H3CXXCH3,} for X = C, Ge) covalent bonds between main group elements, for sextuple and quadruple bonds between metal centers {(Cr2,} Mo2, W2, {[Cl4CrCrCl4]4-),} and for double bonds between a metal and a main group element {((CO)5CrXH2,} for X = C, Si, Ge, Sn). We include finally two applications involving hydrogen bonding. The first covers the adenine-thymine base pair and the second the interaction between {C−H} bonds and the metal center in the alkyl complex.",
	collection = "molecular fragmentation",
	doi = "10.1021/ct800503d",
	localfile = "molecular interactions/2009 - A combined charge and energy decomposition scheme for bond analysis.pdf",
	year = 2009
}

@Article{2009-Molnar-HWM,
	Author = "Laszlo {Fusti Molnar} and Xiao He and Bing Wang and Kenneth M. Jr. Merz",
	Title = "{Further analysis and comparative study of intermolecular interactions using dimers from the S22 database}",
	Journal = "J. Chem. Phys.",
	Volume = "131",
	Pages = "065102",
	abstract = "Accurate MP2 and CCSD T complete basis set CBS interaction energy curves 14 points for each curve have been obtained for 20 of the dimers reported in the S22 set and analytical Morse curves have been ﬁtted that can be used in developing updated density functional theory DFT and force ﬁeld models. The magnitude and the effect of the basis set superposition error BSSE were carefully investigated. We found that going up to aug-cc-pVDZ and aug-cc-pVTZ basis sets is enough to obtain accurate CBS MP2 energies when BSSE corrected values are used but aug-cc-pVTZ and aug-cc-pVQZ basis sets are needed when the BSSE uncorrected total energies are used in CBS extrapolations. MP2 interaction energies with smaller basis sets such as 6-31G are found to have very little dispersion energy and that the true source of dispersion attributed attractive interactions is almost entirely due to BSSE. MP2 and CCSD T CBS interaction energies are found to be very close to one another if aromatic systems are not involved. Comparative analyses have been performed with semiempirical and ab initio methods utilizing the moderate in size but affordable 6-31G basis set both of which can be readily applied to macromolecular systems. The new M06-2X and M06-L DFT functionals were found to be more accurate than all methods tested herein. Interaction energy curves using the SG1 grid showed discontinuities for several of the dimer systems but this problem disappeared when ﬁner DFT numerical grids were used.",
	collection = "molecular interactions",
	doi = "10.1063/1.3173809",
	localfile = "molecular interactions/2009 - Further analysis and comparitive study of intermolecular interactions using dimer from the S22 database.pdf",
	year = 2009
}

@Article{2009-Monticelli-SKV,
	Author = "Luca Monticelli and Emppu Salonen and Pu Chun Ke and Ilpo Vattulainen",
	Title = "{Effects of carbon nanoparticles on lipid membranes: a molecular simulation perspective}",
	Journal = "Soft Matter",
	Volume = "5",
	Pages = "4433–4445",
	abstract = "We review recent simulation studies of carbon nanoparticles interacting with lipid membranes. We first consider the state-of-the-art methodology associated with atomistic as well as coarse-grained models of carbon nanoparticles and lipid systems, and then discuss recent simulation studies of fullerenes, carbon nanotubes and other carbon-based nanoparticles interacting with biological lipid interfaces. We close this article with a brief consideration of the future challenges guided by experiments.",
	collection = "lipid bilayers",
	keywords = "biological nanocomposites; fullerenes; lipid bilayers",
	localfile = "lipid bilayers/2009 - Effects of carbon nanoparticles on lipid membranes: a molecular simulations perspective.pdf",
	type = "Review",
	year = 2009
}

@Article{2009-Morgado-JSHS,
	Author = "C. A. Morgado and Petr Jurečka and Daniel Svozil and Pavel Hobza and Jiří Šponer",
	Title = "{Balance of Attraction and Repulsion in {Nucleic-Acid} Base Stacking: {CCSD(T)/Complete-Basis-Set-Limit} Calculations on Uracil Dimer and a Comparison with the {Force-Field} Description}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "5",
	Number = "6",
	Pages = "1524–1544",
	abstract = "We have carried out reference quantum-chemical calculations for about 100 geometries of the uracil dimer in stacked conformations. The calculations have been specifically aimed at geometries with unoptimized distances between the monomers including geometries with mutually tilted monomers. Such geometries are characterized by a delicate balance between local steric clashes and local unstacking and had until now not been investigated using reference quantum-mechanics (QM) methods. Nonparallel stacking geometries often occur in nucleic acids and are of decisive importance, for example, for local conformational variations in B-DNA. Errors in the short-range repulsion region would have a major impact on potential energy scans which were often used in the past to investigate local geometry variations in DNA. An incorrect description of such geometries may also partially affect molecular dynamics (MD) simulations in applications when quantitative accuracy is required. The reference OM calculations have been carried out using the MP2 method extrapolated to the complete basis-set limit and corrected for higher-order electron-correlation contributions using CCSD(T) calculations with a medium-sized basis set. These reference calculations have been used as benchmark data to test the performance of the DFT-D, SCS(MI)-MP2, and DFT-SAPT QM methods and of the AMBER molecular-mechanics (MM) force field. The QM methods show close to quantitative agreement with the reference data, albeit the DFT-D method tends to modestly exaggerate the repulsion of steric clashes. The force field in general also provides a good description of base stacking for the systems studied here. However, for geometries with close interatomic contacts and clashes, the repulsion effects are rather severely exaggerated. The discrepancy reported here should not affect the overall stability of MD simulations and qualitative applications of the force field. However, it may affect the description of subtle quantitative effects such as the local conformational variations in B-DNA. Preliminary calculations for two H-bonded uracil base pairs, including one with a C-H center dot center dot center dot OH-bond, indicate excellent performance of the tested QM methods for all intermonomer distances. The force field, on the other hand, is less satisfactory, especially in the repulsive regions.",
	collection = "stacking",
	doi = "10.1021/ct9000125",
	localfile = "molecular stacking/2009 - Balance of attraction and repulsion in nucleic-acid base stacking: CCSD(T) complete basis set limit calculations on uracil dimer and a comparison with the force field description.pdf",
	shorttitle = "Balance of Attraction and Repulsion in {Nucleic-Acid} Base Stacking",
	year = 2009
}

@Article{2009-Mourik,
	Author = "{Tanja van} Mourik",
	Title = "{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 = "206–208",
	abstract = "A Letter by Gu et al. [J. Gu, Jing Wang, Jerzy Leszczynski, Y. Xie, H.F. Schaefer III, Chem. Phys. Lett. 459 (2008) 164] presented MP2/6-31+G(d) and MP2/TZVPP stacking energies for the uracil and thymine dimers, with the aim to assess the performance of the new M06-2X density functional. However, the stacking energies were not corrected for the basis set superposition error (BSSE). Here we show that correction for this error dramatically changes the results. BSSE correction severely reduces the stacking energy of the thymine dimer, whereas the stacked uracil dimer structure considered by Gu et al. is not even a minimum on the MP2/6-31+G(d) potential energy surface. (C) 2009 Elsevier B.V. All rights reserved. C1 Univ St Andrews, Sch Chem, St Andrews KY16 9ST, Fife, Scotland.",
	collection = "basis set superposition",
	doi = "10.1016/j.cplett.2009.03.050",
	localfile = "basis set superposition/2009 - Comment on 'To stack or not to stack'.pdf",
	year = 2009
}

@Article{2009-Murtola-BVDK,
	Author = "Teemu Murtola and Alex Bunker and Ilpo Vattulainen and Markus Deserno and Mikko Karttunen",
	Title = "{Multiscale modeling of emergent materials: biological and soft matter}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "11",
	Pages = "1869–1892",
	abstract = "In this review, we focus on four current related issues in multiscale modeling of soft and biological matter. First, we discuss how to use structural information from detailed models (or experiments) to construct coarse-grained ones in a hierarchical and systematic way. This is discussed in the context of the so-called Henderson theorem and the inverse Monte Carlo method of Lyubartsev and Laaksonen. In the second part, we take a different look at coarse graining by analyzing conformations of molecules. This is done by the application of self-organizing maps, i.e., a neural network type approach. Such an approach can be used to guide the selection of the relevant degrees of freedom. Then, we discuss technical issues related to the popular dissipative particle dynamics (DPD) method. Importantly, the potentials derived using the inverse Monte Carlo method can be used together with the DPD thermostat. In the final part we focus on solvent-free modeling which offers a different route to coarse graining by integrating out the degrees of freedom associated with solvent.",
	collection = "coarse graining",
	doi = "10.1039/b818051b",
	keywords = "coarse graining",
	localfile = "coarse graining/2009 - Multiscale modeling of emergent materials: biological and soft matter.pdf",
	type = "Perspective",
	year = 2009
}

@Article{2009-Nasertayoob-Shahbazian,
	Author = "Payam Nasertayoob and Shant Shahbazian",
	Title = "{Revisiting the foundations of the quantum theory of atoms in molecules: Toward a rigorous definition of topological atoms}",
	Journal = "Int. J. Quant. Chem.",
	Volume = "109",
	Number = "4",
	Pages = "726–732",
	abstract = "An explicit classification of consistent variational constraints within the context of the ldquoquantum theory of proper open subsystemsrdquo as well as the ldquoquantum theory of atoms in moleculesrdquo {(QTAIM)} it presented. It is demonstrated that the general variational procedure is not sensitive enough to discriminate between different mathematically consistent variational conditions. The uniqueness of the regional kinetic energy is employed to derive the net zero-flux condition and the regions satisfying this condition are named as quantum divided basins. A modified form of the local zero-flux is proposed in order to define topological atoms within the context of the orthodox {QTAIM.} © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009",
	collection = "molecular fragmentation",
	doi = "10.1002/qua.21864",
	localfile = "molecular fragmentation/2009 - Revisiting the foundations of the quantum theory of atoms in molecules: toward a rigorous definition of topological atoms.pdf",
	shorttitle = "Revisiting the foundations of the quantum theory of atoms in molecules",
	year = 2009
}

@Article{2009-Neto-Lapis,
	Author = "Brenno A. D. Neto and Alexandre A. M. Lapis",
	Title = "{Recent Developments in the Chemistry of Deoxyribonucleic Acid {(DNA)} Intercalators: Principles, Design, Synthesis, Applications and Trends}",
	Journal = "Molecules",
	Volume = "14",
	Number = "5",
	Pages = "1725–1746",
	collection = "nucleic acid intercalation",
	doi = "10.3390/molecules14051725",
	localfile = "nucleic acid intercalation/2009 - Recent developments in the chemistry of DNA intercalators: principles, design, synthesis, applications and trends.pdf",
	shorttitle = "Recent Developments in the Chemistry of Deoxyribonucleic Acid {(DNA)} Intercalators",
	year = 2009
}

@Article{2009-Noguera-RRSOBS,
	Author = "M. Noguera and R. {Ríos-Font} and L. {Rodríguez-Santiago} and X. {Solans-Monfort} and A. Oliva and Joan Bertran and M. Sodupe",
	Title = "{Influence of π-stacking on the N7 and O6 proton affinity of guanine}",
	Journal = "Theor. Chem. Acc.",
	Volume = "123",
	Number = "1-2",
	Pages = "105–111",
	abstract = "The influence of pi-stacking interactions between guanine (G) and the side chain of tyrosine (Tyr) on the N7 and O6 proton affinities of guanine and on the capability of these sites to act as hydrogen bond acceptors is analyzed at the B3LYP-D, M05-2X and MP2 levels of theory. With all methods, results from full geometry optimizations indicate that stacking interactions increase the N7 and O6 proton affinities by about 5-6 kcal mol(-1), the increase being slightly larger for N7. Consistently with these results, hydrogen bond distances between guanine and one water molecule decrease in the stacked system. Moreover, interaction energy between H2O and (G-Tyr) is found to be 2-3 kcal mol(-1) larger than in G center dot center dot center dot H2O. This strengthening arises from the additional Tyr-H2O stabilizing interactions and from a cooperative interplay between stacking and hydrogen bond forces.",
	collection = "nucleic acid bases",
	doi = "10.1007/s00214-009-0542-z",
	localfile = "nucleic acid bases/2009 - Influence of pi stacking on the N7 and O6 proton affinity of guanine.pdf",
	year = 2009
}

@Article{2009-Nowicka-ZKMS,
	Author = "Anna M. Nowicka and Ewelina Zabost and Barbara Klim and Zofia Mazerska and Zbigniew Stojek",
	Title = "{Interactions of Dissolved {dsDNA} with Intercalating Drug by Anodic Voltammetry and Spectroscopy. Influence of {pH}}",
	Journal = "Electroanalysis",
	Volume = "21",
	Number = "1",
	Pages = "52–60",
	abstract = "The interactions of C-1305 {(5-dimethylaminopropylamino-8-hydroxy-6H-v-triazolo[4,5,1-de]acridin-6-one)} with {DNA} were studied using differential pulse voltammetry and {UV-vis} spectroscopy. C-1305 interacts with {dsDNA} in two ways: by intercalation and by binding to the minor-groove. For the intercalation at physiological {pH} (7.4) the values of the binding constant, K1, and the binding-site size, n1, equal 3.36×105 M-1 and 2.5, respectively. For the weak interactions the K2 and n2 parameters equal 0.18×105 M-1 and 4. In the presence of excess {NaCl} the weak interactions do not vanish, therefore they are assigned to the minor groove binding. Substantial and complex is the influence of {pH.}",
	collection = "nucleic acid intercalation",
	doi = "10.1002/elan.200804464",
	localfile = "nucleic acid intercalation/2008 - Interactions of dissolved dsDNA with intercalating drug by anodic voltammetry and spectroscopy. Influence of pH.pdf",
	year = 2009
}

@Article{2009-Oh-Green,
	Author = "Hyunjoon Oh and Peter F. Green",
	Title = "{Polymer chain dynamics and glass transition in athermal polymer/nanoparticle mixtures}",
	Journal = "Nature Mat.",
	Volume = "8",
	Pages = "139–143",
	collection = "polymer nanocomposites",
	doi = "10.1038/NMAT2354",
	keywords = "nanospheres; polymer nanocomposites",
	localfile = "polymer nanocomposites/2009 - Polymer chain dynamics and glass transition in athermal polymer-nanoparticle mixtures.pdf",
	year = 2009
}

@Article{2009-Olszowka-HKSTB,
	Author = "Violetta Olszowka and Markus Hund and Volker Kuntermann and Sabine Scherdel and Larisa Tsarkova and Alexander Böker",
	Title = "{Electric field alignment of a block copolymer nanopattern: direct observation of the microscopic mechanism}",
	Journal = "ACS Nano",
	Volume = "3",
	Number = "5",
	Pages = "1091–1096",
	abstract = "Using quasi-in-situ scanning force microscopy we study the details of nanopattern alignment in ABC terblock copolymer thin ﬁlms in the presence of an in-plane electric ﬁeld. Because of the surface interactions and electric ﬁeld the lamellae are oriented both perpendicular to the plane of the ﬁlm and parallel to the electric ﬁeld. We identiﬁed two distinct defect types which govern the orientation mechanism. Ring-like (tori) and open-end defects dominate at the early stage of the orientation process, while mainly classic topological defects (disclinations and dislocations) are involved in long-range ordering at the late stages. Comparison of the time evolution of the defect density with the evolution of the orientational order parameter suggests that tori-defects are essential for the effective reorientation. Further, the quasi-in-situ SFM imaging allowed us to elucidate the inﬂuence of the electric ﬁeld strength on the propagation velocity of the topological defects.",
	collection = "block copolymers",
	doi = "10.1021/nn900081u",
	localfile = "block copolymers/2009 - Electric field alignment of a block copolymer nanopattern: direct observation of the microscopic mechanism.pdf",
	year = 2009
}

@Article{2009-Park-Lu,
	Author = "Jonghyun Park and Wei Lu",
	Title = "{Interaction of nanoparticles with lipid bilayers}",
	Journal = "Phys. Rev. E",
	Volume = "80",
	Pages = "021607",
	collection = "lipid bilayers",
	doi = "10.1103/PhysRevE.80.021607",
	keywords = "biological nanocomposites; lipid bilayers; nanospheres",
	localfile = "lipid bilayers/2009 - Interaction of nanoparticles with lipid layers.pdf",
	year = 2009
}

@Article{2009-Paton-Goodman,
	Author = "Robert S. Paton and Jonathan M. Goodman",
	Title = "{Hydrogen bonding and π-stacking: how reliable are force fields? A critical evaluation of force field descriptions of nonbonded interactions}",
	Journal = "J. Chem. Inf. Model.",
	Volume = "49",
	Pages = "944–955",
	abstract = "We have evaluated the performance of a set of widely used force ﬁelds by calculating the geometries and stabilization energies for a large collection of intermolecular complexes. These complexes are representative of a range of chemical and biological systems for which hydrogen bonding, electrostatic, and van der Waals interactions play important roles. Benchmark energies are taken from the high-level ab initio values in the JSCH-2005 and S22 data sets. All of the force ﬁelds underestimate stabilization resulting from hydrogen bonding, but the energetics of electrostatic and van der Waals interactions are described more accurately. OPLSAA gave a mean unsigned error of 2 kcal mol-1 for all 165 complexes studied, and outperforms DFT calculations employing very large basis sets for the S22 complexes. The magnitude of hydrogen bonding interactions are severely underestimated by all of the force ﬁelds tested, which contributes signiﬁcantly to the overall mean error; if complexes which are predominantly bound by hydrogen bonding interactions are discounted, the mean unsigned error of OPLSAA is reduced to 1 kcal mol-1. For added clarity, web-based interactive displays of the results have been developed which allow comparisons of force ﬁeld and ab initio geometries to be performed and the structures viewed and rotated in three dimensions.",
	collection = "molecular interactions",
	doi = "10.1021/ci900009f",
	localfile = "molecular interactions/2009 - Hydrogen bonding and pi-stacking: how reliable are force fields. A critical evaluation of force field descriptions of nonbonded interactions.pdf",
	year = 2009
}

@Article{2009-Perlovsky,
	Author = "Leonid Perlovsky",
	Title = "{Language and cognition}",
	Journal = "Neural Networks",
	Volume = "22",
	Pages = "247–257",
	collection = "neuroscience",
	doi = "10.1016/j.neunet.2009.03.007",
	keywords = "language; cognition",
	localfile = "neuroscience/2009 - Language and cognition.pdf",
	rating = "2",
	read = "2013-07-12",
	year = 2009
}

@Article{2009-Pinna-SZ,
	Author = "Marco Pinna and Ludwig Schreier and Andrei V. Zvelindovsky",
	Title = "{Mechanisms of electric-field-induced alignment of block copolymer lamellae}",
	Journal = "Soft Matter",
	Volume = "5",
	Pages = "970–973",
	abstract = "We demonstrate that two mechanisms of lamellae reorientation observed experimentally under applied electric ﬁeld [A. Boker H. Elbs, H. Hansel, A. Knoll, S. Ludwigs, H. Zettl, V. Urban, V. Abetz, A. H. E. Muller and G. Krausch, Phys. Rev. Lett., 2002, 89, 135502] which have been previously described within dynamic self consistent ﬁeld theory [A. V. Zvelindovsky and G. J. A. Sevink, Phys. Rev. Lett., 2003, 90, 049601] can be fully explained within a much more simple model using the Ginzburg–Landau Hamiltonian. A third alignment mechanism has been identiﬁed which was not previously reported. A more complete picture of reorientation under electric ﬁeld emerges that clariﬁes the crucial role of structural defects.",
	collection = "block copolymers",
	doi = "10.1039/b814969k",
	keywords = "block copolymers; electric fields",
	localfile = "block copolymers/2009 - Mechanisms of electric-field-inuced alignment of block copolymer lamellae.pdf",
	year = 2009
}

@Article{2009-Pitonak-JNPH,
	Author = "Michal Pitoňák and Tomasz Janowski and P. Neogrády and Peter Pulay and Pavel Hobza",
	Title = "{Convergence of the {CCSD(T)} Correction Term for the Stacked Complex Methyl {Adenine−Methyl} Thymine: Comparison with {Lower-Cost} Alternatives}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "5",
	Number = "7",
	Pages = "1761–1766",
	abstract = "We have performed large-scale calculations for the interaction energy of the stacked methyl adenine-methyl thymine complex at the CCSD(T)/aug-ccpVXZ (X ) D,T) levels. The results can serve as benchmarks for the evaluation of two methods, MP2.5, introduced recently, and the widely used ∆CCSD(T) correction deﬁned as the difference between the CCSD(T) and MP2 energies. Our results conﬁrm that the ∆CCSD(T) correction converges much faster toward the complete basis set (CBS) limit than toward the MP2 or CCSD(T) energies. This justiﬁes approximating the CBS energy by adding the ∆CCSD(T) correction calculated with a modest basis set to a large basis MP2 energy. The fast convergence of the ∆CCSD(T) correction is not obvious, as the individual CCSD and (T) contributions converge less rapidly than their sum. The MP2.5 method performs very well for this system, with results very close to CCSD(T). It is conjectured that using a ∆MP2.5 correction, deﬁned analogously to ∆CCSD(T), with large basis sets may yield more reliable nonbonded interaction energies than using ∆CCSD(T) with a smaller basis set. This would result in important computational savings as the MP3 scales computationally much less steep than CCSD(T), although higher than SCS-MP2, a similar approximation.",
	collection = "stacking",
	doi = "10.1021/ct900126q",
	localfile = "molecular stacking/2009 - Convergence of the CCSD(T) correction term for the stacked complex methyl adenine-methyl thymine: comparison with lower-cost alternatives.pdf",
	shorttitle = "Convergence of the {CCSD(T)} Correction Term for the Stacked Complex Methyl {Adenine−Methyl} Thymine",
	year = 2009
}

@Article{2009-Plattner-Meuwly,
	Author = "Nuria Plattner and Markus Meuwly",
	Title = "{Higher order multipole moments for molecular dynamics simulations}",
	Journal = "J. Mol. Model.",
	Volume = "15",
	Number = "6",
	Pages = "687–694",
	collection = "molecular electrostatics",
	doi = "10.1007/s00894-009-0465-6",
	localfile = "molecular electrostatics/2009 - Higher order multipole moments for molecular dynamics simulations.pdf",
	year = 2009
}

@Article{2009-Podeszwa-RS,
	Author = "Rafał Podeszwa and Betsy M. Rice and Krzysztof Szalewicz",
	Title = "{Crystal structure prediction for cyclotrimethylene trinitramine {(RDX)} from first principles}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "11",
	Number = "26",
	Pages = "5512–5518",
	abstract = "Crystal structure prediction and molecular dynamics methods were applied to the cyclotrimethylene trinitramine {(RDX)} crystal to explore the stability rankings of various polymorphs using a recently developed nonempirical potential energy function that describes the {RDX} dimer interactions. The energies of 500 high-density structures resulting from molecular packing were minimized and the 14 lowest-energy structures were subjected to isothermal-isostress molecular dynamics {(NsT-MD)} simulations. For both crystal structure prediction methods and molecular dynamics simulations, the lowest-energy polymorph corresponded to the experimental structure; furthermore, the lattice energy of this polymorph was lower than that of the other polymorphs by at least 1.1 kcal mol-1. Crystal parameters and densities of the low-energy crystal produced by the {NsT-MD} simulations matched those of the experimental crystal to within 1\% of density and cell edge lengths and 0.01[degree] of the cell angle. The arrangement of the molecules within the time-averaged unit cell were in equally outstanding agreement with experiment, with the largest deviation of the location of the molecular mass centers being less than 0.07 {[Angstrom]} and the largest deviation in molecular orientation being less than 2.8[degree]. {NsT-MD} simulations were also used to calculate crystallographic parameters as functions of temperature and pressure and the results were in a reasonable agreement with experiment.",
	collection = "molecular crystals",
	doi = "10.1039/b902015b",
	localfile = "molecular crystals/2009 - Crystal structure prediction for cyclotrimethylene trinitramine (RDX) from first principles.pdf",
	year = 2009
}

@Article{2009-Price,
	Author = "Sarah L. Price",
	Title = "{Computed Crystal Energy Landscapes for Understanding and Predicting Organic Crystal Structures and Polymorphism}",
	Journal = "Acc. Chem. Res.",
	Volume = "42",
	Number = "1",
	Pages = "117–126",
	abstract = "The phenomenon of polymorphism, the ability of a molecule to adopt more than one crystal structure, is a well-established property of crystalline solids. The possible variations in physical properties between polymorphs make the reliable reproduction of a crystalline form essential for all research using organic materials, as well as quality control in manufacture. Thus, the last two decades have seen both an increase in interest in polymorphism and the availability of the computer power needed to make the computational prediction of organic crystal structures a practical possibility. In the past decade, researchers have made considerable improvements in the theoretical basis for calculating the sets of structures that are within the energy range of possible polymorphism, called crystal energy landscapes. It is common to ﬁnd that a molecule has a wide variety of ways of packing with lattice energy within a few kilojoules per mole of the most stable structure. However, as we develop methods to search for and characterize “all” solid forms, it is also now usual for polymorphs and solvates to be found. Thus, the computed crystal energy landscape reﬂects and to an increasing extent “predicts” the emerging complexity of the solid state observed for many organic molecules. This Account will discuss the ways in which the calculation of the crystal energy landscape of a molecule can be used as a complementary technique to solid form screening for polymorphs. Current methods can predict the known crystal structure, even under “blind test” conditions, but such successes are generally restricted to those structures that are the most stable over a wide range of thermodynamic conditions. The other low-energy structures can be alternative polymorphs, which have sometimes been found in later experimental studies. Examining the computed structures reveals the various compromises between close packing, hydrogen bonding, and π-π stacking that can result in energetically feasible structures. Indeed, we have observed that systems with many almost equi-energetic structures that contain a common interchangeable motif correlate with a tendency to disorder and problems with control of the crystallization product. Thus, contrasting the computed crystal energy landscape with the known crystal structures of a given molecule provides a valuable complement to solid form screening, and the examination of the low-energy structures often leads to a rationalization of the forms found.",
	collection = "molecular crystals",
	doi = "10.1021/ar800147t",
	localfile = "molecular crystals/2009 - Computed crystal energy landscapes for understanding and predicting organic crystal structures and polymorphism.pdf",
	year = 2009
}

@Article{2009-Ricci-Netz,
	Author = "Clarisse G. Ricci and Paulo A. Netz",
	Title = "{Docking Studies on {DNA-Ligand} Interactions: Building and Application of a Protocol To Identify the Binding Mode}",
	Journal = "J. Chem. Inf. Model.",
	Volume = "49",
	Pages = "1925–1935",
	abstract = "Despite {DNA} being an important target for several drugs, most of the docking programs are validated only for proteins and their ligands. In this paper, we used {AutoDock} 4.0 to perform self-dockings and cross dockings between two {DNA} ligands (a minor groove binder and an intercalator) and four distinct receptors: 1) crystallographic {DNA} without intercalation gap; 2) crystallographic {DNA} with intercalation gap; 3) canonical {B-DNA;} and 4) modified {B-DNA} with intercalation gap. Besides being efficient in self-dockings, {AutoDock} is capable of correctly identifying two of the main {DNA} binding modes with the condition that the target possesses an artificial intercalation gap. Therefore, we suggest a default protocol to identify {DNA} binding modes which uses a modified canonical {DNA} (with gap) as receptor. This protocol was applied to dock two different Tröger bases to {DNA} and the predicted binding modes agree with those suggested, yet not established, by experimental data. We also applied the protocol to dock aflatoxin B1 exo-8,9-epoxide, and the results are in complete agreement with experimental data from the literature. We propose that this approach can be used to investigate other ligands whose binding mode to {DNA} remains unknown, yielding a suitable starting point for further theoretical studies such as molecular dynamics simulations.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/ci9001537",
	localfile = "nucleic acid intercalation/2009 - Docking studies on DNA-ligand interactions: building and application of a protocol to identify the binding mode.pdf",
	shorttitle = "Docking Studies on {DNA-Ligand} Interactions",
	year = 2009
}

@Article{2009-Riley-MPCH,
	Author = "Kevin E. Riley and Jane S. Murray and Peter Politzer and Monica C. Concha and Pavel Hobza",
	Title = "{{Br···O} Complexes as Probes of Factors Affecting Halogen Bonding: Interactions of Bromobenzenes and Bromopyrimidines with Acetone}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "5",
	Number = "1",
	Pages = "155–163",
	abstract = "Halogen bonding is a unique type of noncovalent binding phenomenon in which a halogen atom interacts attractively with an electronegative atom such as oxygen or nitrogen. These types of interactions have been the subject of many recent investigations because of their potential in the development of new materials and pharmaceutical compounds. Recently, it was observed that most halogen bonding interactions in biological contexts involve close contacts between a halogen bound to an aromatic ring and a carbonyl oxygen on a protein’s backbone structure. In this work we investigate interactions of substituted bromobenzenes and bromopyrimidines with acetone to ascertain the effects of various substituents upon the strengths of these interactions. It was found that replacement of ring hydrogens in these systems has dramatic effects upon the interaction strengths of the resulting complexes, which have interaction energies between −1.80 and −7.11 kcal/mol. Examination of the electrostatic potentials of the substituted bromobenzene and bromopyrimidine monomers indicates that the addition of substituents has a large influence upon the most positive electrostatic potential on the surface of the interacting bromine and thus modulates these halogen bonding interactions. Results obtained using the symmetry-adapted perturbation theory {(SAPT)} interaction energy decomposition procedure also indicate that electrostatic interactions play the key role in these halogen bonding interactions. These results have important implications in drug design and crystal engineering. Halogen bonds have been a subject of great interest in these fields because of their unique noncovalent bonding characteristics.",
	collection = "halogen bonding",
	doi = "10.1021/ct8004134",
	localfile = "halogen bonding/2009 - Br...O complexes as probes of factors affecting halogen bonding: interactions of bromobenzenes and bromopyrimidines with acetone.pdf",
	shorttitle = "{Br···O} Complexes as Probes of Factors Affecting Halogen Bonding",
	year = 2009
}

@Article{2009-Rocha,
	Author = "M.S. Rocha",
	Title = "{Modeling the entropic structural transition of DNA complexes formed with intercalating drugs}",
	Journal = "Phys. Biol.",
	Volume = "6",
	Pages = "036013",
	abstract = "A ﬁrst approach is presented to explain the entropic structural transition observed in the persistence length of DNA complexes formed with intercalating drug molecules. The proposed model is based on calculating the effective persistence length of two entropic springs associated in series, one intercalated with drug molecules and the other without drugs. As the total drug concentration in the sample increases, the lengths of the two entropic springs vary, modifying the effective persistence length. The theoretical predictions of this model are then compared to experimental results, and a good accordance was obtained.",
	collection = "nucleic acid intercalation",
	doi = "10.1088/1478-3975",
	keywords = "nucleic acid intercalation",
	localfile = "nucleic acid intercalation/2009 - Modeling the entropic structural transition of DNA complexes formed with intercalating drugs.pdf",
	year = 2009
}

@Article{2009-Rodriguez-BAMGB,
	Author = "Juan I. Rodriguez and Richard F. W. Bader and Paul W. Ayers and Carine Michel and Andreas W. Götz and Carles Bo",
	Title = "{A high performance grid-based algorithm for computing {QTAIM} properties}",
	Journal = "Chem. Phys. Lett.",
	Volume = "472",
	Number = "1-3",
	Pages = "149–152",
	abstract = "An improved version of our method for computing {QTAIM} {[J.I.} Rodríguez, {A.M.} Köster, {P.W.} Ayers, A. {Santos-Valle,} A. Vela, G. Merino, J. Comp. Chem. (2009), in press, doi:10.1002/jcc.21134] is presented. Vectorization and parallelization of the previous algorithm, together with molecular symmetry, make the present algorithm as much as two orders of magnitude faster than our original method. The present method scales linearly with both system size and the number of processors. The performance of the method is demonstrated by computing the {QTAIM} atomic properties of a series of carbon nanotubes. Our results show that the {CPU} time for a {QTAIM} property calculation is comparable to that of a {SCF-single} point calculation. The accuracy of the original method is also improved.",
	collection = "cheminformatics",
	doi = "10.1016/j.cplett.2009.02.081",
	keywords = "algorithms",
	localfile = "cheminformatics/2009 - A high performance grid-based algorithm for computing QTAIM properties.pdf",
	methods = "QTAIM",
	year = 2009
}

@Article{2009-Ruiz-GRSB,
	Author = "Rebeca Ruiz and Begona Garcia and Guiseppe Ruisi and Arturo Silvestri and Giampaolo Barone",
	Title = "{Computational study of the interaction of proflavine with d(ATATATATAT)2 and d(GCGCGCGCGC)2}",
	Journal = "J. Mol. Struct.: {THEOCHEM}",
	Volume = "915",
	Pages = "86–92",
	abstract = "The interaction of proﬂavine (PR) with two B-DNA decamers of alternating AT and GC sequence, called [deca(dG-dC)]2 and [deca(dA-dT)]2, respectively, was computationally investigated by the ONIOM method, exploiting a three-layer QM/QM/MM hybrid approach. The highest level QM method was applied to the model system, which comprises the intercalation site (5th and 6th base pairs) and the inserted PR molecule. The connecting sugar phosphate backbone was added in the medium layer region. Both higher and medium level layers, differing in the size of the basis set used, were treated by the DFT MPWB1K functional. The full system in the lower layer was described by the empirical AMBER force ﬁeld. The calculated values of the interaction energy of PR with [deca(dG-dC)]2 and [deca(dA-dT)]2, as well as with the dinucleotides d(GpC)2, and d(ApT)2, the latter considered either in vacuo and in the mimicked water solvent, support for a static higher afﬁnity toward G-C compared to the A-T DNA base sequences, in agreement with structural results from crystallographic studies. Furthermore, the different structural characteristics of the [deca(dG-dC)]2/PR complex compared to those of the [deca(dA-dT)]2/PR, furnish a possible interpretation of apparently controversial experimental thermodynamic data, explained in terms of two possible modes of non-covalent binding of ligands with DNA, namely intercalation and external binding, respectively.",
	collection = "nucleic acid intercalation",
	doi = "10.1016/j.theochem.2009.08.022",
	localfile = "nucleic acid intercalation/2009 - Computational study of the interaction of proflavine with d(ATATATATAT)2 and d(GCGCGCGCGC)2.pdf",
	year = 2009
}

@Article{2009-Ruscio-KBH,
	Author = "Jory Z. Ruscio and Jonathan E. Kohn and K. Aurelia Ball and Teresa Head-Gordon",
	Title = "{The influence of protein dynamics on the success of computational enzyme design}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "131",
	Pages = "14111–14115",
	abstract = "Abstract: We characterize the molecular dynamics of a previously described computational de novo designed enzyme optimized to perform a multistep retrol-aldol reaction when engineered into a TIM barrel protein scaffold. The molecular dynamics simulations show that the protein dynamics under physiological conditions of temperature and aqueous environment distorts the designed geometric factors of the substrate-enzyme reaction intermediates, such that catalysis is limited by the primary retrol-aldol step of proton abstraction from the covalently bound substrate and its interactions with a histidine-aspartate dyad. These results emphasize that computational enzyme designs will beneﬁt from considerations of dynamical ﬂuctuations when optimizing active site geometries.",
	collection = "enzymes",
	doi = "10.1021/ja905396s",
	localfile = "enzymes/2009 - The influence of protein dynamics on the success of computational enzyme design.pdf",
	year = 2009
}

@Article{2009-Rutledge-DW,
	Author = "Lesley R. Rutledge and Holly F. Durst and Stacey D. Wetmore",
	Title = "{Evidence for Stabilization of {DNA/RNA−Protein} Complexes Arising from {Nucleobase−Amino} Acid Stacking and {T-Shaped} Interactions}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "5",
	Number = "5",
	Pages = "1400–1410",
	abstract = "The stacking and T-shaped interactions between the natural DNA or RNA nucleobases (adenine, cytosine, guanine, thymine, uracil) and all aromatic amino acids (histidine, phenylalanine, tyrosine, tryptophan) were investigated using ab initio quantum mechanical calculations. We characterized the potential energy surface of nucleobase−amino acid dimers using the MP2/6-31G*(0.25) method. The stabilization energies in dimers with the strongest interactions were further examined at the CCSD(T)/CBS level of theory. Results at the highest level of theory possible for these systems indicate that both stacking and T-shaped interactions are very close in magnitude to biologically relevant hydrogen bonds. Additionally, T-shaped interactions are as strong, if not stronger, than the corresponding stacking interactions. Our systematic consideration of the interaction energies in 485 possible combinations of monomers shows that a variety of these contacts are essential when considering the role of aromatic amino acids in the binding of proteins to DNA or RNA. This work also illustrates how our calculated binding strengths can be used by biochemists to estimate the magnitude of these noncovalent interactions in a variety of DNA/RNA−protein active sites.",
	collection = "nucleic acid bases",
	doi = "10.1021/ct800567q",
	localfile = "nucleic acid bases/2009 - Evidence for stabilization of DNA an RNA-protein complexes arising from nucleobase-amino acid stacking an T-shaped interactions.pdf",
	year = 2009
}

@Article{2009-Salvador-FD,
	Author = "Pedro Salvador and Xavier Fradera and Miquel Duran",
	Title = "{Quantitative Assessment of the Effect of Basis Set Superposition Error on the Electron Density of Molecular Complexes by Means of Quantum Molecular Similarity Measures}",
	Journal = "Int. J. Quant. Chem.",
	Volume = "109",
	Pages = "2572–2580",
	abstract = "The Chemical Hamiltonian Approach (CHA) method is applied to obtain Basis Set Superposition Error (BSSE)-free molecular orbitals at the Hartree-Fock (HF) and Density Functional Theory (DFT) levels of theory. To assess qualitatively the effect of the BSSE on the first-order electron density, we had previously applied Bader's analysis of the intermolecular critical points located on the electron density, as well as density difference maps for several hydrogen bonded complexes. In this work, Quantum Molecular Similarity Measures are probed as an alternative avenue to properly quantify the electronic relaxation due to the BSSE removal by means of distance indices between the uncorrected and corrected charge densities. It is shown that BSSE contamination is more important at the DFT level of theory, and in some cases, changes on the topology of the electron density are observed upon BSSE correction. Inclusion of diffuse functions have been found to dramatically decrease the BSSE effect in both geometry and electron density. The CHA method represents a good compromise to obtain accurate results with small basis sets. (C) 2009 Wiley Periodicals, Inc. Int J Quantum Chem 109: 2572-2580, 2009 C1 [Duran, Miquel] Univ Girona, Inst Computat Chem, Girona 17071, Spain. Univ Girona, Dept Chem, Girona 17071, Spain.",
	collection = "basis set superposition",
	doi = "10.1002/qua.22039",
	localfile = "basis set superposition/2009 - Quantitative assessment of the effect of basis set superposition error on the electorn density of molecular complexes by means of quantum molecular similarity measures.pdf",
	year = 2009
}

@Article{2009-Schneider,
	Author = "Hans-Jörg Schneider",
	Title = "{Binding Mechanisms in Supramolecular Complexes}",
	Journal = "Angew. Chem. Int. Ed.",
	Volume = "48",
	Number = "22",
	Pages = "3924–3977",
	abstract = "Forces to reckon with: Supramolecular complexes, such as the one shown, are normally based on a combination of different interactions such as ion pairing, hydrogen bonds, and stacking interactions. The not always simple characterization of the nature and strength of intermolecular forces provides assistance to the understanding of biomimetic systems, as well as for the design of synthetic receptors, drugs, and intelligent {materials.Supramolecular} chemistry has expanded dramatically in recent years both in terms of potential applications and in its relevance to analogous biological systems. The formation and function of supramolecular complexes occur through a multiplicity of often difficult to differentiate noncovalent forces. The aim of this Review is to describe the crucial interaction mechanisms in context, and thus classify the entire subject. In most cases, organic host-guest complexes have been selected as examples, but biologically relevant problems are also considered. An understanding and quantification of intermolecular interactions is of importance both for the rational planning of new supramolecular systems, including intelligent materials, as well as for developing new biologically active agents.",
	collection = "molecular interactions",
	doi = "10.1002/anie.200802947",
	localfile = "molecular interactions/2009 - Binding mechanisms in supramolecular complexes.pdf",
	year = 2009
}

@Article{2009-Schwabe-Grimme,
	Author = "Tobias Schwabe and Stefan Grimme",
	Title = "{Benzenium-Ethene Complex: A Fundamental Problem for Standard Second-Order Møller–Plesset Theory}",
	Journal = "J. Phys. Chem. A",
	Volume = "113",
	Pages = "3005–3008",
	abstract = "Recently, Kolboe and Svelle pointed out that second-order Møller–Plesset perturbation theory (MP2) incorrectly predicts a barrierless reaction of the benzenium-ethene complex to the ethyl-1H-benzene cation in contrast to other considered quantum chemical methods [J. Phys. Chem. A 2008, 112, 6399]. In a subsequent Letter in this Journal, van Mourik related this behavior to the basis set superposition error [J. Phys. Chem. A 2008, 112, 11017]. Here we call show that this is not the case but that the failure is due to an intrinsic (overcorrelation) problem of MP2. Improved perturbation methods (SCS-MP2 and B2PLYP double-hybrid functionals) provide correct results. C1 [Schwabe, Tobias; Grimme, Stefan] Univ Munster, Inst Organ Chem, D-48149 Munster, Germany.",
	collection = "basis set superposition",
	doi = "10.1021/jp9003938",
	localfile = "basis set superposition/2009 - Benzenium-ethene complex: a fundamental problem for standard second-order Moller-Plesset theory.pdf",
	year = 2009
}

@Article{2009-Scocchi-PHFFP,
	Author = "Giulio Scocchi and Paola Posocco and Jan-Willem Handgraaf and Johannes G. E. M. Fraaije and Maurizio Fermeglia and Sabrina Pricl",
	Title = "{A complete multiscale modelling approach for polymer-clay nanocomposites}",
	Journal = "Chem. Eur. J.",
	Volume = "15",
	Pages = "7586–7592",
	abstract = "We present an innovative, multiscale computational approach to probe the behaviour of polymer–clay nanocomposites (PCNs). Our modeling recipe is based on 1) quantum/force-field-based atomistic simulation to derive interaction energies among all system components; 2) mapping of these values onto mesoscopic bead-field (MBF) hybrid-method parameters; 3) mesoscopic simulations to determine system density distributions and morphologies (i.e., intercalated versus exfoliated); and 4) simulations at finite-element levels to calculate the relative macroscopic properties. The entire computational procedure has been applied to two well-known PCN systems, namely Nylon 6/Cloisite 20A and Nylon 6/Cloisite 30B, as test materials, and their mechanical properties were predicted in excellent agreement with the available experimental data. Importantly, our methodology is a truly bottom-up approach, and no “learning from experiment” was needed in any step of the entire procedure.",
	collection = "polymer nanocomposites",
	doi = "10.1002/chem.200900995",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2009 - A complete multiscale modelling approach for polymer-clay nanocomposites.pdf",
	year = 2009
}

@Article{2009-Sherrill-TH,
	Author = "C. David Sherrill and Tait Takatani and Edward G. Hohenstein",
	Title = "{An Assessment of Theoretical Methods for Nonbonded Interactions: Comparison to Complete Basis Set Limit {Coupled-Cluster} Potential Energy Curves for the Benzene Dimer, the Methane Dimer, {Benzene−Methane,} and {Benzene−H2S†}}",
	Journal = "J. Phys. Chem. A",
	Volume = "113",
	Number = "38",
	Pages = "10146–10159",
	abstract = "Large, correlation-consistent basis sets have been used to very closely approximate the coupled-cluster singles, doubles, and perturbative triples {[CCSD(T)]} complete basis set potential energy curves of several prototype nonbonded complexes, the sandwich, T-shaped, and parallel-displaced benzene dimers, the methane−benzene complex, the {H2S−benzene} complex, and the methane dimer. These benchmark potential energy curves are used to assess the performance of several methods for nonbonded interactions, including various spin-component-scaled second-order perturbation theory {(SCS-MP2)} methods, the spin-componet-scaled coupled-cluster singles and doubles method {(SCS-CCSD),} density functional theory empirically corrected for dispersion {(DFT-D),} and the meta-generalized-gradient approximation functionals {M05-2X} and {M06-2X.} These approaches generally provide good results for the test set, with the {SCS} methods being somewhat more robust. {M05-2X} underbinds for the test cases considered, while the performances of {DFT-D} and {M06-2X} are similar. Density fitting, dual basis, and local correlation approximations all introduce only small errors in the interaction energies but can speed up the computations significantly, particulary when used in combination.",
	collection = "molecular interactions",
	doi = "10.1021/jp9034375",
	localfile = "molecular interactions/2009 - An assessment of theoretical methods for nonbonded interactions.pdf",
	shorttitle = "An Assessment of Theoretical Methods for Nonbonded Interactions",
	year = 2009
}

@Article{2009-Sillar-HS,
	Author = "Kaido Sillar and Alexander Hofmann and Joachim Sauer",
	Title = "{Ab Initio Study of Hydrogen Adsorption in {MOF-5}}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "131",
	Number = "11",
	Pages = "4143–4150",
	abstract = "Metal-organic frameworks (MOFs) are promising adsorbents for hydrogen storage. Density functional theory and second-order Møller-Plesset perturbation theory (MP2) are used to calculate the interaction energies between H2 and individual structural elements of the MOF-5 framework. The strongest interaction, ∆H77 ) -7.1 kJ/mol, is found for the R-site of the OZn4(O2Ph)6 nodes. We show that dispersion interactions and zero-point vibrational energies must be taken into account. Comparison of calculations done under periodic boundary conditions for the complete structure with those done for ﬁnite models cut from the MOF-5 framework shows that the interactions with H2 originate mainly from the local environment around the adsorption site. When used within a Multi-Langmuir model, the MP2 results reproduce measured adsorption isotherms (the predicted amount is 6 wt \% at 77 K and 40 bar) if we assume that the H2 molecules preserve their rotational degrees of freedom in the adsorbed state. This allows to discriminate between different isotherms measured for different MOF-5 samples and to reliably predict isotherms for new MOF structures.",
	collection = "hydrogen sorption",
	doi = "10.1021/ja8099079",
	localfile = "hydrogen sorption/2009 - Ab initio study of hydrogen adsorption in MOF-5.pdf",
	year = 2009
}

@Article{2009-Singh-MKK,
	Author = "N. Jiten Singh and Seung Kyu Min and Dong Young Kim and Kwang S. Kim",
	Title = "{Comprehensive energy analysis for various types of π-interaction}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "5",
	Pages = "515–529",
	abstract = "We have investigated various types of π-interactions, where one of the interacting π-systems is represented by an aromatic benzene molecule. The system includes Rg-π, CH-π, π-π(D), π-π(T), H-π(T), π+-π(D), π+-π(T), H+-π(T), π+2-π(D), M+-π, and M+2-π complexes, where Rg denotes a rare gas or noble atom, M denotes a metal, and D/T indicates displaced-stacked/T-shaped structure. The microsolvation effect is also considered. We note that the interaction between a cationic π system and a neutral π system (πcation-π interaction) is so far ambiguously considered as either π-π or cation-π interaction. In terms of total binding energy, the πcation-π interaction is weaker than the cation-π interaction, but much stronger than the π-π interaction. When the hydrophilic (N-H)+ or (C-H)+ group in a singly charged π+ system (as in protonated histidine, arginine, pyridine, or dimethyl imidazolium) interacts with a π-system, the complex favors a T-shaped form [π+-π(T) complex]. However, in the presence of polar solvating molecules or counteranions, these species interact with the (N-H)+/(C-H)+ group, while the π+ system interacts with the neutral aromatic ring. Then, the displaced-stacked form [π+-π(D) complex] is favored or otherwise nearly isoenergetic to the π+-π(T) form. The π+-π systems are stabilized mainly by both dispersion and electrostatic energies. Ternary diagrams using either attractive energy components or both attractive and repulsive energy components show that the π+-π(D) complexes have more contribution from dispersion energy but less contribution from induction energy than the π+-π(T) complexes, while both complexes have similar percentage contributions from electrostatic and exchange energy components. In particular, the π+-π(D) complexes are found to be distinctly different from the π-π complexes and the non-π organic or metallic cation-π complexes.",
	collection = "stacking",
	doi = "10.1021/ct800471b",
	localfile = "molecular stacking/2009 - Comprehensive energy analysis for various types of pi-interaction.pdf",
	year = 2009
}

@Article{2009-Skwara-BS,
	Author = "Bartłomiej Skwara and Wojciech Bartkowiak and Daniel Luiz {Da Silva}",
	Title = "{On the basis set superposition error in supermolecular calculations of interaction-induced electric properties: many-body components}",
	Journal = "Theor. Chem. Acc.",
	Volume = "122",
	Pages = "127–136",
	abstract = "In the present paper we analyze basis set superposition error (BSSE) removal methods from many-body components of interaction-induced electric properties. The Valiron-Mayer function counterpoise (VMFC), site-site function counterpoise (SSFC) and TB methods have been employed in order to obtain the incremental optical components of linear hydrogen fluoride clusters (HF)n, where n = {3,4}. Following Mierzwicki and Latajka, who have performed similar calculations for the interaction energy, we compare those three methods of eliminating BSSE using several Dunning's correlation consistent basis sets. C1 [Skwara, Bartlomiej; Bartkowiak, Wojciech; Da Silva, Daniel Luiz] Wroclaw Univ Technol, Inst Phys \& Theoret Chem, PL-50370 Wroclaw, Poland.",
	collection = "basis set superposition",
	doi = "10.1007/s00214-008-0492-x",
	localfile = "basis set superposition/2009 - On the basis set superposition error in supermolecular calculations of interaction-induced electric properties: many-body components.pdf",
	year = 2009
}

@Article{2009-Srivastava-KBMLNS,
	Author = "S. Srivastava and A. K. Kandar and J. K. Basu and M. K. Mukhopadhyay and L. B. Lurio and S. Narayanan and S. K. Sinha",
	Title = "{Complex dynamics in polymer nanocomposites}",
	Journal = "Phys. Rev. E",
	Volume = "79",
	Pages = "021408",
	abstract = "Polymer nanocomposites offer the potential to create a new type of hybrid material with unique thermal, optical, or electrical properties. Understanding their structure, phase behavior, and dynamics is crucial for realizing such potentials. In this work we provide an experimental insight into the dynamics of such composites in terms of the temperature, wave vector, and volume fraction of nanoparticles, using multispeckle synchrotron x-ray photon correlation spectroscopy measurements on gold nanoparticles embedded in polymethylmethacrylate. Detailed analysis of the intermediate scattering functions reveals possible existence of an intrinsic length scale for dynamic heterogeneity in polymer nanocomposites similar to that seen in other soft materials like colloidal gels and glasses.",
	collection = "polymer nanocomposites",
	doi = "10.1103/PhysRevE.79.021408",
	localfile = "polymer nanocomposites/2009 - Complex dynamics in polymer nanocomposites.pdf",
	year = 2009
}

@Article{2009-Stone-Misquitta,
	Author = "Anthony J. Stone and Alston J. Misquitta",
	Title = "{Charge-transfer in symmetry-adapted perturbation theory}",
	Journal = "Chem. Phys. Lett.",
	Volume = "473",
	Pages = "201–205",
	collection = "molecular interactions",
	doi = "10.1016/j.cplett.2009.03.073",
	localfile = "molecular interactions/2009 - Charge-transfer in symmetry-adapted perturbation theory.pdf",
	year = 2009
}

@Article{2009-Su-Li,
	Author = "Peifeng Su and Hui Li",
	Title = "{Energy decomposition analysis of covalent bonds and intermolecular interactions}",
	Journal = "J. Chem. Phys.",
	Volume = "131",
	Number = "1",
	Pages = "014102–15",
	collection = "molecular interactions",
	doi = "10.1063/1.3159673",
	localfile = "molecular interactions/2009 - Energy decomposition analysis of covalent bonds and intermolecular interactions.pdf",
	year = 2009
}

@Article{2009-Sukumar,
	Author = "Nagamani Sukumar",
	Title = "{The chemist's concept of molecular structure}",
	Journal = "Found. Chem.",
	Volume = "11",
	Number = "1",
	Pages = "7–20",
	abstract = "Abstract The concept of molecular structure is fundamental to the practice and understanding of chemistry, but the meaning of this term has evolved and is still evolving. The {Born–Oppenheimer} separation of electronic and nuclear motions lies at the heart of most modern quantum chemical models of molecular structure. While this separation introduces a great computational and practical simplification, it is neither essential to the conceptual formulation of molecular structure nor universally valid. Going beyond the {Born–Oppenheimer} approximation introduces new paradigms, bringing fresh insight into the chemistry of fluxional molecules, proteins, superconductors and macroscopic dielectrics, thus opening up new avenues for exploration. But it requires that our ideas of molecular structure need to evolve beyond simple ball-and-stick-type models.",
	collection = "molecular structure",
	doi = "10.1007/s10698-008-9060-7",
	localfile = "molecular structure/2009 - The chemists concept of molecular structure.pdf",
	year = 2009
}

@Article{2009-Tang-Ma,
	Author = "Qi-yun Tang and Yu-quang Ma",
	Title = "{Self-assembly of rod-shaped particles in diblock-copolymer templates}",
	Journal = "J. Phys. Chem. B",
	Volume = "113",
	Pages = "10117–10120",
	Note = "Looks at the effect of nanorod shape on a BCP phase diagram.",
	abstract = "We investigate the self-assembly of hard rod-shaped particles with an afﬁnity for A block in diblock AB copolymer templates. The results are consistent with a series of recent experimental ﬁndings. Furthermore, we construct the phase diagrams of the mixture with different aspect ratios of particles by changing the particle concentration φp and the volume fraction f of the A block. The variation of the aspect ratio in different particle concentrations will signiﬁcantly inﬂuence the effective volume of the A component and consequent phase behavior of nanoparticle/copolymer hybrid systems, which may account for the emergence of some unexpected phenomena of morphological transitions. The present study provides insightful guidance to control the nanometer-length-scale structures of shaped particles for potential applications as functional devices.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/jp901170x",
	keywords = "block copolymers; mesophase transitions; nanorods; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2009 - Self-assembly of rod-shaped particles in diblock0copolymer templates.pdf",
	methods = "SCFT/BD",
	year = 2009
}

@Article{2009-Termonia,
	Author = "Yves Termonia",
	Title = "{Monte-Carlo modeling of dense polymer melts near nanoparticles}",
	Journal = "Polymer",
	Volume = "50",
	Pages = "1062–1066",
	abstract = "Using Monte-Carlo techniques, we study polymer chain conformations near nanoparticles for dense melts of high molecular weight. Our results indicate the presence of a thin interfacial region (1–2 nm in thickness) within which polymer segments orient tangentially to the particle surface causing a stretching and widening of the chain ellipsoid. That region is also characterized by an accumulation of chain ends and a decrease in polymer density. Nanoparticles also affect polymer properties far away into the bulk. Thus, at small particle radius, we observe an overall swelling of the polymer chains when the distance between the centers of mass of nearest-neighbor particles becomes smaller than the radius of gyration of the chains.",
	collection = "polymer nanocomposites",
	doi = "10.1016/j.polymer.2008.12.032",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2009 - Monte-Carlo modeling of dense polymer melts near nanoparticles.pdf",
	year = 2009
}

@Article{2009-Toth-VHFFPP,
	Author = "Radovan Toth and Dirk-Jan Voorn and Jan-Willem Handgraaf and Johannes G. E. M. Fraaije and Maurizio Fermeglia and Sabrina Pricl and Paola Posocco",
	Title = "{Multiscale computer simulation studies of water-based montmorillonite-poly(ethylene oxide) nanocomposites}",
	Journal = "Macromolecules",
	Volume = "42",
	Pages = "8260–8270",
	abstract = "This work presents a multiscale computational approach to probe the behavior of polymer/clay nanocomposites based on poly(ethylene oxide) (PEO)/montmorillonite (MMT) as obtained from water intercalation. In details, our modeling recipe is based on four sequential steps: (a) atomistic molecular dynamics simulations to derive interaction energy values among all system components; (b) mapping of these values onto mesoscale dissipative particle dynamics parameters; (c) mesoscopic simulations to determine system density distributions and morphologies (i.e., intercalated vs exfoliated); (d) simulations at finite-element levels to calculate the relative macroscopic properties. The entire computational procedure has been applied to four PEO/MMT systems with PEO chains of different molecular weight (750, 1100, 2000, and 5000), and thermal and electrical characteristics were predicted in excellent agreement with the available experimental data. Importantly, our methodology constitutes a truly integrated multiscale modeling approach, in which no “learning against experiment” has been performed in any step of the computational recipe.",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma901584w",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2009 - Multiscale computer simulation studies of water-based montmorillonite-poly(ethylene oxide) nanocomposites.pdf",
	year = 2009
}

@Article{2009-Wang-Hill,
	Author = "Mu Wang and Reghan J. Hill",
	Title = "{Anomalous bulk viscosity of polymer-nanocomposite melts}",
	Journal = "Soft Matter",
	Volume = "5",
	Pages = "3940–3953",
	collection = "polymer nanocomposites",
	doi = "10.1039/b905686f",
	localfile = "polymer nanocomposites/2009 - Anomalous bulk viscosity of polymer-nanocomposite melts.pdf",
	year = 2009
}

@Article{2009-Wang-JZ,
	Author = "Weizhou Wang and Baoming Ji and Yu Zhang",
	Title = "{Chalcogen Bond: A Sister Noncovalent Bond to Halogen Bond}",
	Journal = "J. Phys. Chem. A",
	Volume = "113",
	Number = "28",
	Pages = "8132–8135",
	abstract = "A sister noncovalent bond to halogen bond, termed chalcogen bond, is defined in this article. By selecting the complexes {H2CS···Cl−,} {F2CS···Cl−,} {OCS···Cl−,} and {SCS···Cl−} as models, the bond-length change, interaction energy, topological property of the electron charge density and its Laplacian, and the charge transfer of the chalcogen bond have been investigated in detail theoretically. It was found that the similar misshaped electron clouds of the chalcogen atom and the halogen atom result in the similar properties of the chalcogen bond and the halogen bond. Experimental results are in good agreement with the theoretical predictions.",
	collection = "halogen bonding",
	doi = "10.1021/jp904128b",
	localfile = "halogen bonding/2009 - Chalcogen bond: a sister noncovalent bond to halogen bond.pdf",
	year = 2009
}

@Article{2009-Wang-Liebau,
	Author = "Xiqu Wang and Friedrich Liebau",
	Title = "{On the optimization of bond-valence parameters: artifacts conceal chemical effects}",
	Journal = "Acta Cryst. B",
	Volume = "65",
	Pages = "96–98",
	Note = "Page 96: If the large observed deviations between the values of BVS and the stoichiometric valence of the lone-pair cations are caused by incorrectly calculated bond valences for thier bonds, the corresponding deviations should also be seen in the VBS values of the anions bonded to them.",
	collection = "crystallography",
	doi = "10.1107/S010876810804086X",
	localfile = "crystallography/2009 - On the optimization of bond-valence parameters: artifacts conceal chemical effects.pdf",
	rating = "3",
	read = "2014-02-20",
	year = 2009
}

@Article{2009-Wang-XZYY,
	Author = "Juan Wang and Xiaowen Xu and Zhanxia Zhang and Fan Yang and Xiurong Yang",
	Title = "{{Real-Time} Study of Genomic {DNA} Structural Changes upon Interaction with Small Molecules Using {Dual-Polarization} Interferometry}",
	Journal = "Anal. Chem.",
	Volume = "81",
	Number = "12",
	Pages = "4914–4921",
	abstract = "The structural changes of genomic {DNA} upon interaction with small molecules have been studied in real time using dual-polarization interferometry {(DPI).} Native or thermally denatured {DNA} was immobilized on the silicon oxynitride surface via a preadsorbed poly(ethylenimine) {(PEI)} layer. The mass loading was similar for both types of {DNA;} however, native {DNA} formed a looser and thicker layer due to its rigidity, unlike the more flexible denatured {DNA,} which mixed with {PEI} to form a denser and thinner layer. Ethidium bromide {(EtBr),} a classical intercalator, induced the large thickness decrease and density increase of native {DNA} (double-stranded), but a slight increase in both the thickness and density of denatured {DNA} (partial single-stranded). Spermine that electrostatically binds {DNA} induced the increase in layer thickness and decrease in the density of both native and denatured {DNA.} However, the looser structure of native {DNA} made it more accessible to spermine, leading to a higher binding amount and larger thickness increase. For native {DNA,} {EtBr} induced a slow and less reversible contraction of {DNA} owing to intercalation, while spermine induced a fast and reversible expansion of {DNA} owing to electrostatic interaction. {DPI} offers an effective means for real-time study of {DNA} structural changes during the interactions.",
	collection = "nucleic acid drugs",
	doi = "10.1021/ac900591k",
	localfile = "nucleic acid drugs/2009 - Real-time study of genomic DNA structural changes upon interaction with small molecules using dual-polarization interferometry.pdf",
	year = 2009
}

@Article{2009-Wei-JZHL,
	Author = "Chunying Wei and Guoqing Jia and Jun Zhou and Gaoyi Han and Can Li",
	Title = "{Evidence for the binding mode of porphyrins to G-quadruplex {DNA}}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "11",
	Number = "20",
	Pages = "4025–4032",
	abstract = "Interactions of porphyrin derivatives {5,10,15,20-tetrakis(N-methylpyridinium-4-yl)-21H,23H-porphyrin} {(TMPyP4)} and {5,10,15,20-tetrakis(N-propylpyridinium-4-yl)-21H,23H-porphyrin} {(TPrPyP4)} with human telomeric {AG3(T2AG3)3} G-quadruplex {DNAs} in 150 {mM} K+-containing buffer in the presence or absence of 40\% molecular crowding agent poly(ethylene glycol) {(PEG} 200) were studied by absorption titration fitting and time-resolved fluorescence spectroscopy. The results show that two {TMPyP4} (or {TPrPyP4)} molecules bind to antiparallel/parallel hybrid structure of {AG3(T2AG3)3} G-quadruplex by end-stacking and outside groove binding modes in the absence of {PEG.} Interestingly, in the presence of {PEG} one porphyrin molecule is stacked between two parallel {AG3(T2AG3)3} G- quadruplexes to form a sandwich structure, another porphyrin molecule is bound to the groove of the G-quadruplex. The interactions of {TMPyP4} with different structures of {AG3(T2AG3)3} G-quadruplex are non cooperative, the binding constants of two independent binding sites are 1.07 [times] 106 and 4.42 [times] 108 M-1 for an antiparallel/parallel hybrid structure of {AG3(T2AG3)3,} 8.67 [times] 105 and 2.26 [times] 108 M-1 for parallel-stranded {AG3(T2AG3)3} G-quadruplex. Conversely, the two binding sites are cooperative for {TPrPyP4,} the apparent association constants are 5.58 [times] 106 and 1.24 [times] 107 M-1 for parallel-stranded and antiparallel/parallel hybrid structures of {AG3(T2AG3)3} G-quadruplex, respectively.",
	collection = "nucleic acid drugs",
	doi = "10.1039/b901027k",
	localfile = "nucleic acid drugs/2009 - Evidence for the binding mode of porphyrins to G-quadruplex DNA.pdf",
	year = 2009
}

@Article{2009-Wu-AZ,
	Author = "Qin Wu and Paul W. Ayers and Yingkai Zhang",
	Title = "{Density-based energy decomposition analysis for intermolecular interactions with variationally determined intermediate state energies}",
	Journal = "J. Chem. Phys.",
	Volume = "131",
	Number = "16",
	Pages = "164112–8",
	collection = "molecular interactions",
	doi = "10.1063/1.3253797",
	localfile = "molecular interactions/2009 - Density-based energy decomposition analysis for intermolecular interactions with variatioanlly determined intermediate state energies.pdf",
	year = 2009
}

@Article{2009-Xu-OLMKC,
	Author = "Chen Xu and Kohji Ohno and Vincent Ladmiral and Daniel E. Milkie and James M. Kikkawa and Russell J. Composto",
	Title = "{Simultaneous block copolymer and magnetic nanoparticle assembly in nanocomposite films}",
	Journal = "Macromolecules",
	Volume = "42",
	Pages = "1219–1228",
	abstract = "We investigate self-assembly of nanocomposite ﬁlms composed of lamellar-forming poly(styrene-b-methyl methacrylate) (PS-b-PMMA) and PMMA-grafted magnetite (Fe3O4) nanoparticles (NPs). The Fe3O4 NPs are grafted with PMMA brushes with molecular weights ranging from 2700 to 35 700 g/mol. For the NP with the lowest molecular weight brush, the morphology of the nanocomposite ﬁlm depends on the NP concentration (φNP). At low φNP, the block copolymer self-assembles into mixed morphology of perpendicular lamellae (perpendicular Lam) and parallel lamellae (|Lam), and the ⊥Lam are stabilized by individual NPs or small NP aggregates. The NPs can also retard the dynamics of self-assembly of block copolymer ﬁlms. At high φNP, NPs form small aggregates which inhibit the formation of a lamellar structure. As the molecular weight of the PMMA brush increases to 13 300 or 35 700 g/mol, the Fe3O4 NPs form aggregates in the as-cast nanocomposite ﬁlms, and this behavior is attributed to aggregation of NPs in the solution state. Since the size of NP aggregates is larger than the copolymer domain size, the block copolymer has to self-assemble around these aggregates. The magnetic properties of these nanocomposite ﬁlms are characterized, and typical superparamagnetic behavior is observed.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma8022266",
	keywords = "block copolymers; mesophase transitions; nanoparticle aggregation; nanospheres; polymer nanocomposites; thin films",
	localfile = "block copolymer nanocomposites/2009 - Simultaneous block copolymer and magnetic nanoparticle assembly in nanocomposite films.pdf",
	methods = "AFM, TEM, SQUID",
	systems = "magnetite-PMMA@PS-PMMA",
	year = 2009
}

@Article{2009-Yan-SB,
	Author = "Li-Tang Yan and Heiko G. Schoberth and Alexander Böker",
	Title = "{Large-scale oriented assembly of nanoparticles in diblock copolymer templates under electric fields}",
	Journal = "Macromol. Chem. Phys.",
	Volume = "210",
	Pages = "1003–1010",
	collection = "block copolymer nanocomposites",
	doi = "10.1002/macp.200900040",
	keywords = "block copolymers; electric fields; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2009 - Large-scale oriented assembly of nanoparticles in diblock copolymer templates under electric fields.pdf",
	methods = "CDS",
	read = "2012-03-21",
	year = 2009
}

@Article{2009-Yang-LTZ,
	Author = "Qinhua Yang and Ming Li and Chaohui Tong and Yuejin Zhu",
	Title = "{Phase behaviors of diblock copolymer-nanoparticle films under nanopore confinement}",
	Journal = "J. Chem. Phys.",
	Volume = "130",
	Pages = "094903",
	abstract = "We employ self-consistent-ﬁeld and density-functional theories to simulate the phase behaviors of diblock copolymer-nanoparticle mixtures conﬁned in a two-dimensional circular pore. By varying the block ratio, the size of the pore, and the particle concentration, rich phase structures are discovered. It is shown that the structural frustration, the loss of conformational entropy of the polymer chains under conﬁnement, the curvature of the pore, and the steric packing effect of the particles play important roles in determining the morphologies of the nanocomposites under circular conﬁnement. It is found that the increase in the particle concentration can promote the transformation of concentric lamellas to the cylindrical domains. Our results suggest effective ways to stabilize the phase orderings of diblock copolymer-nanoparticle mixtures under two-dimensional circular conﬁnement.",
	collection = "block copolymer nanocomposites",
	doi = "10.1063/1.3055601",
	keywords = "block copolymers; mesophase transitions; nanoconfinement; nanospheres; polymer nanocomposites; thin films",
	localfile = "block copolymer nanocomposites/2009 - Phase behaviors of diblock copolymer-nanoparticle films under nanopore confinement.pdf",
	methods = "SCFT/DFT",
	year = 2009
}

@Article{2009-Yoon-CS,
	Author = "Chang Won Yoon and Patrick J. Carroll and Larry G. Sneddon",
	Title = "{Ammonia Triborane: A New Synthesis, Structural Determinations, and Hydrolytic {Hydrogen-Release} Properties}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "131",
	Number = "2",
	Pages = "855–864",
	abstract = "Iodine oxidation of {B3H8−} in glyme solution to produce {(glyme)B3H7,} followed by displacement of the coordinated glyme by reaction with anhydrous ammonia provides a safe and convenient preparation of ammonia triborane, {NH3B3H7} (1). X-ray crystallographic determinations and {DFT} computational studies of both {NH3B3H7} and the {NH3B3H7·18-crown-6} adduct demonstrate that while computations predict a symmetric single bridging-hydrogen conformation, {NH3B3H7} has a highly asymmetric structure in the solid-state that results from intermolecular {N−H+···H−−B} dihydrogen bonding interactions. Studies of its hydrolytic reactions have shown that upon the addition of acid or an appropriate transition metal catalyst, aqueous solutions of 1 rapidly release hydrogen, with 6.1 materials wt \% H2-release being achieved from a 22.7 wt \% aqueous solution of 1 at room temperature in the presence of 5 wt \% {Rh/Al2O3} (1.1 mol\% Rh). The rate of H2-release was controlled by both the catalyst loadings and temperature.",
	collection = "hydrogen sorption",
	doi = "10.1021/ja808045p",
	localfile = "hydrogen sorption/2008 - Ammonia triborane: a new synthesis, structural determinations, and hydrolytic hydrogen-release properties.pdf",
	shorttitle = "Ammonia Triborane",
	year = 2009
}

@Article{2009-Zhang-Lin,
	Author = "Liangshun Zhang and Jiaping Lin",
	Title = "{Hierarchically ordered nanocomposites self-assembled from linear-alternating block copolymer-nanoparticle mixture}",
	Journal = "Macromolecules",
	Volume = "42",
	Pages = "1410–1414",
	abstract = "Using self-consistent ﬁeld and density functional theories, we undertake a ﬁrst investigation on the hierarchically ordered structures self-assembled from linear-alternating block copolymer/nanoparticle mixture. The linear-alternating block copolymers self-assemble into the lamellar structure with two length scales, providing a template to direct the nanoparticle distribution. The spontaneously hierarchical organization of nanoparticles within the ordered copolymer structures was found to be dependent on the particle concentration and particle radius. Furthermore, the presence of the nanoparticles can also induce the hierarchical structure change due to the entropic effects. We envisage that this approach opens a gateway to construct hierarchically ordered nanocomposites with different length scales.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma802539q",
	keywords = "block copolymers; mesophase transitions; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2009 - Hierarchically ordered nanocomposites self-assembled from linear-alternating block copolymer-nanoparticle mixture.pdf",
	methods = "SCFT/DFT",
	year = 2009
}

@Article{2009-Zhao-TMSLRMJWPFAX,
	Author = "Yue Zhao and Kari Thorkelsson and Alexander J. Mastroianni and Thomas Schilling and Joseph M. Luther and Benjamin J. Rancatore and Kazuyuki Matsunaga and Hiroshi Jinnai and Yue Wu and Daniel Poulsen and Jean M. J. Frechet and A. Pail Alivisatos and Ting Xu",
	Title = "{Small-molecule-directed nanoparticle assembly towards stimuli-responsive nanocomposites}",
	Journal = "Nature Mat.",
	Volume = "8",
	Pages = "979–985",
	abstract = "Precise control of the spatial organization of nanoscopic building blocks, such as nanoparticles, over multiple length scales is a bottleneck in the ‘bottom-up’ generation of technologically important materials. Only a few approaches have been shown to achieve nanoparticle assemblies without surface modiﬁcation. We demonstrate a simple yet versatile approach to produce stimuli-responsive hierarchical assemblies of readily available nanoparticles by combining small molecules and block copolymers. Organization of nanoparticles into one-, two- and three-dimensional arrays with controlled inter-particle separation and ordering is achieved without chemical modiﬁcation of either the nanoparticles or block copolymers. Nanocomposites responsive to heat and light are demonstrated, where the spatial distribution of the nanoparticles can be varied by exposure to heat or light or changing the local environment. The approach described is applicable to a wide range of nanoparticles and compatible with existing fabrication processes, thereby enabling a non-disruptive approach for the generation of functional devices.",
	collection = "block copolymer nanocomposites",
	doi = "10.1038/NMAT2565",
	keywords = "block copolymers; hydrogen bonding; nanomigration; nanoparticle distribution; nanopinning; nanospheres; polymer nanocomposites; surfactants; thin films",
	localfile = "block copolymer nanocomposites/2009 - Small-molecule-directed nanoparticle assembly towards stimuli-responsive nanocomposites.pdf",
	methods = "SAXS, TEM",
	systems = "CdS@PS-P4VP, Pb@PS-P4VP",
	year = 2009
}

@Article{2009-Zhou-CLS,
	Author = "Weizheng Zhou and Jian Cao and Weichang Liu and Simeon Stoyanov",
	Title = "{How rigid rods self-assemble at curved surfaces}",
	Journal = "Angew. Chem. Int. Ed.",
	Volume = "48",
	Pages = "378–381",
	collection = "interfaces",
	doi = "10.1002/anie.200804194",
	keywords = "bubbles",
	localfile = "interfaces/2009 - How rigid rods self-assemble at curved surfaces.pdf",
	methods = "SEM",
	rating = "3",
	read = "2010-12-10",
	year = 2009
}

@Article{2009-Zhou-Gilson,
	Author = "{Huan-Xiang} Zhou and Michael K. Gilson",
	Title = "{Theory of Free Energy and Entropy in Noncovalent Binding}",
	Journal = "Chem. Rev.",
	collection = "molecular interactions",
	doi = "10.1021/cr800551w",
	localfile = "molecular interactions/2009 - Theory of free energy and entropy in noncovalent binding.pdf",
	year = 2009
}

@Article{2009-Zoelen-Brinke,
	Author = "{Wendy van} Zoelen and Gerrit {ten Brinke}",
	Title = "{Thin films of complexed block copolymers}",
	Journal = "Soft Matter",
	Volume = "5",
	Pages = "1568–1582",
	abstract = "(Excerpt) Since the emergence of the earliest computers, which could easily ﬁll an entire room, vast improvements in lithographic techniques have made hardware sizes continuously smaller, at the same time resulting in higher speeds and less energy consumed per computing function. Current lithographic techniques have already reached a periodicity of less than 100 nm, however, as these techniques will eventually reach their limit with respect to costs and resolution, new methods to produce nanopatterns with a sub 100 nm periodicity are pursued in order to continue the downscaling trend.",
	collection = "block copolymers",
	doi = "10.1039/b817093b",
	keywords = "block copolymers; thin films",
	localfile = "block copolymers/2009 - Thin films of complexed block copolymers.pdf",
	type = "Review",
	year = 2009
}

@Article{2010-Agarwal-QA,
	Author = "Praveen Agarwal and Haibo Qi and Lynden A. Archer",
	Title = "{The ages in a self-suspended nanoparticle liquid}",
	Journal = "Nano Lett.",
	Volume = "10",
	Pages = "111–115",
	abstract = "Telomers ionically tethered to nanometer-sized particles yield self-suspended nanoparticle-laden liquids with unusual dynamical features. By subjecting these suspensions to controlled, modest shear strains, we find that their flow behaviors observed using experiments performed on time scales of tens of seconds can be projected to obtain maps of their dynamic response on geological scales. That such extraordinary slow dynamic processes can be uncovered from real-time measurements by simply stretching a system provides a simple but powerful tool for interrogating extremely slow motions in other jammed physical states.",
	collection = "nanoparticles",
	doi = "10.1021/nl9029847",
	keywords = "jamming; nanoparticle grafts; nanospheres; polymer mixtures; suspensions",
	localfile = "nanoparticles/2010 - The ages in a self-suspended nanoparticle liquid.pdf",
	methods = "TEM, TGA, rheometry",
	systems = "silica@PEG",
	year = 2010
}

@Article{2010-Akcora-KSBS,
	Author = "Pinar Akcora and Sanat K. Kumar and Victoria G. Sakai and Yu Li and Brian C. Benicewicz and Linda S. Schadler",
	Title = "{Segmental dynamics in PMMA-grafted nanoparticle composites}",
	Journal = "Macromolecules",
	Volume = "43",
	Pages = "8275–8281",
	abstract = "We have recently shown that silica nanoparticles grafted with polystyrene chains behave akin to block copolymers due to the “dislike” between the nanoparticles and the grafts. These decorated nanoparticles, thus, self-assemble into various morphologies, from well-dispersed nanoparticles to anisotropic superstructures, when they are placed in homopolystyrene matrices of different molecular masses. Here, we consider a slightly different case, where the grafted chains and the matrix (both PMMA) are strongly attracted to the silica nanoparticle surface. We then conjecture that these systems show phase mixing or demixing depending on the miscibility between the brush and matrix chains (“autophobic dewetting”). At 15 mass \% particle loading, composites created using the same grafted nanoparticle, but with two different matrices, yield well dispersed nanoparticles or nanoparticle “agglomerates”, respectively. Rheology experiments show that the composites display solid-like behavior only when the particles are aggregated. As deduced in previous work, this difference in behavior is attributed to the presence of percolating particle clusters in the agglomerated samples which allows for stress propagation through the system. Going further, we compare the local mobility of matrix and grafted segments of both composites using quasi-elastic neutron scattering experiments. For the liquid-like system, the mean square displacements of the grafted chains and matrix chains, the particle structuring and mechanical response are all unaffected by annealing time. In contrast, in the reinforced case, only the local matrix motion is unaffected by time. Since the particle clustering and solid-like mechanical reinforcement increase with increasing time, we conclude that mechanical reinforcement in polymer nanocomposites is purely based on the nanoparticles, with essentially no “interference” from the matrix. In conjunction with other results in the literature, we then surmise that mechanical reinforcement is caused by the bridging of particles by the grafted polymer layers and not due to the formation of “glassy” polymer layers on the nanoparticles.",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma101240j",
	localfile = "polymer nanocomposites/2010 - Segmental dynamics in PMMA-grafted nanoparticle composites.pdf",
	year = 2010
}

@Article{2010-Anderson-ST,
	Author = "Joshua A. Anderson and Rastko Sknepnek and Alex Travesset",
	Title = "{Design of polymer nanocomposites in solution by polymer functionalization}",
	Journal = "Phys. Rev. E",
	Volume = "82",
	Pages = "021803",
	abstract = "Polymer nanocomposites, materials combining polymers and inorganic components such as nanosized crystallites or nanoparticles have attracted significant attention in recent years. A successful strategy for designing polymer nanocomposites is polymer functionalization via attaching functional groups with specific affinity for the inorganic component. In this paper, a systematic investigation by molecular dynamics of polymer functionalization for design of composites combining nanosize crystallites with multiblock polymers in solution is presented. It is shown that functionalization is an example of active self-assembly, where the resulting polymer nanocomposite exhibits a different type of order than the original pure polymer system ͑without inorganic components͒. Optimal polymer architectures and concentrations are identified appropriate for different applications, alongside an in-depth analysis on the origin and stability of the resulting phases as well as its experimental implications.",
	collection = "block copolymer nanocomposites",
	doi = "10.1103/PhysRevE.82.021803",
	keywords = "block copolymers; mesophase transitions; nanoparticle distribution; nanopinning; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2010 - Design of polymer nanocomposites in solution by polymer functionalization.pdf",
	methods = "CG MD",
	year = 2010
}

@Article{2010-Balabin,
	Author = "Roman M. Balabin",
	Title = "{Communications: is quantum chemical treatment of biopolymers accurate? Intramolecular basis set superposition error (BSSE)}",
	Journal = "J. Chem. Phys.",
	Volume = "132",
	Pages = "231101",
	collection = "basis set superposition",
	doi = "10.1063/1.3442466",
	localfile = "basis set superposition/2010 - Communicaions: is quantum chemical treatment of biopolymers accurate. Intramolecular basis set superposition error (BSSE).pdf",
	year = 2010
}

@Article{2010-Bockstaller-ROC,
	Author = "Michael R. Bockstaller and Hyung Ju Ryu and Satyajeet Ohja and Jihoon Choi",
	Title = "{1D periodic bimetallic superstructures by co-assembly of ternary block copolymer-nanoparticle blends}",
	Journal = "J. Mater. Chem.",
	Volume = "20",
	Pages = "9339–9341",
	Note = "Composite with two nanoparticle types of different size, going separately to the interface and tp domain centers.",
	collection = "block copolymer nanocomposites",
	doi = "10.1039/c0jm01810d",
	keywords = "block copolymers; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2010 - 1D periodic bimetallic superstructures by co-assembly of ternary block copolymer-nanoparticle blends.pdf",
	methods = "SEM, STEM",
	rating = "2",
	read = "2012-03-21",
	systems = "(Au-dodecyl,Co-TOPO)@PS-PEP",
	year = 2010
}

@Article{2010-Bois-CDBDGPS,
	Author = "Laurence Bois and Fernand Chassegneux and Cédric Desroches and Yann Battie and Nathalie Destouches and Nicole Gilon and Stéphane Parola and Olivier Stéphan",
	Title = "{Electroless growth of silver nanoparticles into mesostructured silica block copolymer films}",
	Journal = "Langmuir",
	Volume = "26",
	Number = "11",
	Pages = "8729–8736",
	Note = "Shows how to form Ag NPs inside a BCP film, aggregating them into nanowires.",
	abstract = "Silver nanoparticles and silver nanowires have been grown inside mesostructured silica films obtained from block copolymers using two successive reduction steps: the first one involves a sodium borohydride reduction or a photoreduction of silver nitrate contained in the film, and the second one consists of a silver deposit on the primary nanoparticles, carried out by silver ion solution reduction with hydroxylamine chloride. We have demonstrated that the F127 block copolymer ((PEO)106(PPO)70(PEO)106), “F type”, mesostructured silica film is a suitable “soft” template for the fabrication of spherical silver nanoparticles arrays. Silver spheres grow from 7 to 11 nm upon the second reduction step. As a consequence, a red shift of the surface plasmon resonance associated with metallic silver has been observed and attributed to plasmonic coupling between particles. Using a P123 block copolymer ((PEO)$\_{20}$(PPO)$\_{70}$(PEO)$\_{20}$), “P type”, mesostructured silica film, we have obtained silver nanowires with typical dimension of 10 nm Â 100 nm. The corresponding surface plasmon resonance is blue-shifted. The hydroxylamine chloride treatment appears to be efficient only when a previous chemical reduction is performed, assuming that the first sodium borohydride reduction induces a high concentration of silver nuclei in the first layer of the porous silica (film/air interface), which explains their reactivity for further growth.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/la904491v",
	keywords = "block copolymers; nanogrowth; nanospheres; nanowires; polymer nanocomposites; thin films",
	localfile = "block copolymer nanocomposites/2010 - Electroless growth of silver nanoparticles into mesostructured silica block copolymer films.pdf",
	methods = "absorbance spectroscopy, ICP-OES, powder XRD, TEM",
	systems = "Ag@PEO-PPO-PEO",
	year = 2010
}

@Article{2010-Chen-Ruckenstein,
	Author = "Houyang Chen and Eli Ruckenstein",
	Title = "{Structure and particle aggregation in block copolymer-binary nanoparticle composites}",
	Journal = "Polymer",
	Volume = "51",
	Pages = "5869–5882",
	collection = "block copolymer nanocomposites",
	doi = "10.1016/j.polymer.2010.10.011",
	keywords = "block copolymers; nanoparticle aggregation; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2010 - Structure and particle aggregation in block copolymer-binary nanoparticle composites.pdf",
	year = 2010
}

@Article{2010-Crossland-LHS,
	Author = "Edward J. W. Crossland and Sabine Ludwigs and Marc A. Hillmyer and Ulrich Steiner",
	Title = "{Control of gyroid forming block copolymer templates: effects of an electric field and surface topography}",
	Journal = "Soft Matter",
	Volume = "6",
	Pages = "670–676",
	abstract = "The control over 10 nm scale porosity derived from self-assembly of copolymers is an extremely promising method for the synthesis of organic–inorganic hybrid materials applied, for example, in solar cells. Here, we report the thin ﬁlm behaviour of a poly(4-ﬂuorostyrene)-b-poly(D,L-lactide) PFS-b-PLA block copolymer which adopts the bicontinuous gyroid phase in the bulk and may be used to form a porous template suitable for patterning functional materials by selective degradation of the minority PLA domains. The response of the copolymer morphology to DC electric ﬁelds is probed at temperatures where the bulk copolymer adopts either the gyroid or the cylindrical phase. At 150C electric ﬁeld alignment results in vertical arrays of cylinders, lamellae, and perforated lamellae while at 180 C the gyroid phase coexists with a standing perforated lamellar phase. We show that both polymer–substrate interactions and substrate topography are critical factors determining substrate reconstruction of the gyroid phase. Spontaneous cross-ﬁlm percolation of the minority network phase on a given substrate, a prerequisite for electrochemical replication, is dependent on surface topology at the scale of the gyroid unit cell. Importantly, under suitable processing conditions all these complex copolymer morphologies can be electrochemically replicated to produce highly ordered freestanding nanostructured arrays over large areas.",
	collection = "block copolymers",
	doi = "10.1039/b914421h",
	keywords = "block copolymers; electric fields",
	localfile = "block copolymers/2010 - Control of gyroid forming block copolymer templates: effects of an electric field and surface topography.pdf",
	year = 2010
}

@Article{2010-Dickinson,
	Author = "Eric Dickinson",
	Title = "{Food emulsions and foams: stabilization by particles}",
	Journal = "Curr. Op. Coll. Int. Sci.",
	Volume = "15",
	Pages = "40–49",
	collection = "interfaces",
	doi = "10.1016/j.cocis.2009.11.001",
	keywords = "emulsions; foams",
	localfile = "interfaces/2010 - Food emulsions and foams: stabilization by particles.pdf",
	read = "2010-06-12",
	year = 2010
}

@Article{2010-Frischknecht-MM,
	Author = "Amalie L. Frischknecht and Erin S. McGarrity and Michael E. Mackay",
	Title = "{Expanded chain dimensions in polymer melts with nanoparticle fillers}",
	Journal = "J. Chem. Phys.",
	Volume = "132",
	Pages = "204901",
	abstract = "We apply the self-consistent polymer reference interaction site model SC/PRISM to liquid state calculations of the chain dimensions in polymer melts with added nanoparticle ﬁllers. The nanoparticles are assumed to be smaller than the polymer radius of gyration and are attracted to the polymer so that they are miscible. We ﬁnd that the nanoparticles perturb the chain dimensions, causing an increase in the radius of gyration with increasing nanoparticle volume fractions, assuming reasonable interaction energies between the various components. The magnitude of the expansion is in qualitative agreement with recent neutron scattering results and suggests that the SC/PRISM approach is reasonable when dealing with these apparent nonlinear phenomena present in nanocomposites in the protein limit.",
	collection = "polymer nanocomposites",
	doi = "10.1063/1.3428760",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2010 - Expanded chain dimensions in polymer melts with nanoparticle fillers.pdf",
	year = 2010
}

@Article{2010-Galatsis-WOOHCMCNB,
	Author = "Kosmas Galatsis and Kang L. Wang and Mihri Ozkan and Cengiz S. Ozkan and Yu Huang and Jane P. Chang and Harold G. Monbouquette and Yong Chen and Paul F. Nealey and Youssry Botros",
	Title = "{Patterning and templating for nanoelectronics}",
	Journal = "Adv. Mater.",
	Volume = "22",
	Pages = "769–778",
	abstract = "The semiconductor industry will soon be launching 32 nm complementary metal oxide semiconductor (CMOS) technology node using 193 nm lithography patterning technology to fabricate microprocessors with more than 2 billion transistors. To ensure the survival of Moore’s law, alternative patterning techniques that offer advantages beyond conventional top-down patterning are aggressively being explored. It is evident that most alternative patterning techniques may not offer compelling advantages to succeed conventional top-down lithography for silicon integrated circuits, but alternative approaches may well indeed offer functional advantages in realising next-generation information processing nanoarchitectures such as those based on cellular, bioinsipired, magnetic dot logic, and crossbar schemes. This paper highlights and evaluates some patterning methods from the Center on Functional Engineered Nano Architectonics in Los Angeles and discusses key benchmarking criteria with respect to CMOS scaling.",
	collection = "nanotechnology",
	doi = "10.1002/adma.200901689",
	localfile = "nanotechnology/2010 - Patterning and templating for nanoelectronics.pdf",
	type = "Viewpoint",
	year = 2010
}

@Article{2010-Ganesan-EP,
	Author = "Venkat Ganesan and Christopher J. Ellison and Victor Pryamitsyn",
	Title = "{Mean-field models of structure and dispersion of polymer-nanoparticle mixtures}",
	Journal = "Soft Matter",
	Volume = "6",
	Pages = "4010–4025",
	abstract = "We review some recent research developments in coarse-grained modeling based on mean-ﬁeld approaches of the equilibrium dispersion and structure of polymer nanoparticle composites. We focus on three issues: (i) dispersion and phase behavior of particles in homopolymer matrices; (ii) dispersion in mixtures of homopolymers with grafted nanoparticles; (iii) self-assembly and organization of nanoparticles in block copolymer matrices. In each of these topics, we highlight that the dispersability and the resulting structure of the nanoparticle suspension may exhibit far more complexities than one may deduce using simple miscibility criterion involving the energetic interactions between the polymer matrix and the particle. In each case, we review our own research contributions accompanied by a brief discussion of related theoretical studies and some possible future directions.",
	collection = "polymer nanocomposites",
	doi = "10.1039/b926992d",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2010 - Mean-field models of structure and dispersion of polymer-nanoparticle mixtures.pdf",
	type = "Review",
	year = 2010
}

@Article{2010-Ghosh-KVWHGSSK,
	Author = "Debashree Ghosh and Gmytro Kosenkov and Vitalii Vanovschi and Christopher F. Williams and John M. Herbert and Mark S. Gordon and Michael W. Schmidt and Lyudmila V. Slipchenko and Anna I. Krylov",
	Title = "{Noncovalent interactions in extended systems described by the effective fragment potential method: theory and application to nucleobase oligomers}",
	Journal = "J. Phys. Chem. A",
	Volume = "114",
	Pages = "12739–12754",
	abstract = "The implementation of the effective fragment potential (EFP) method within the Q-CHEM electronic structure package is presented. The EFP method is used to study noncovalent π-π and hydrogen-bonding interactions in DNA strands. Since EFP is a computationally inexpensive alternative to high-level ab initio calculations, it is possible to go beyond the dimers of nucleic acid bases and to investigate the asymptotic behavior of different components of the total interaction energy. The calculations demonstrated that the dispersion energy is a leading component in π-stacked oligomers of all sizes. Exchange-repulsion energy also plays an important role. The contribution of polarization is small in these systems, whereas the magnitude of electrostatics varies. Pairwise fragment interactions (i.e., the sum of dimer binding energies) were found to be a good approximation for the oligomer energy.",
	collection = "stacking",
	doi = "10.1021/jp107557p",
	localfile = "molecular stacking/2010 - Noncovalent interactions in extended systems described by the effective fragment potential method: theory and application to nucleobase oligomers.pdf",
	year = 2010
}

@Article{2010-Goswami-Sumpter,
	Author = "Monojoy Goswami and Bobby G. Stumpter",
	Title = "{Anomalous chain diffusion in polymer nanocomposites for carying polymer-filler interactions strengths}",
	Journal = "Phys. Rev. E",
	Volume = "81",
	Pages = "041801",
	abstract = "Anomalous diffusion of polymer chains in a polymer nanocomposite melt is investigated for different polymer-nanoparticle interaction strengths using stochastic molecular dynamics simulations. For spherical nanoparticles dispersed in a polymer matrix the results indicate that the chain motion exhibits three distinct regions of diffusion, the Rouse-like motion, an intermediate subdiffusive regime followed by a normal Fickian diffusion. The motion of the chain end monomers shows a scaling that can be attributed to the formation of strong “networklike” structures, which have been seen in a variety of polymer nanocomposite systems. Irrespective of the polymer-particle interaction strengths, these three regimes seem to be present with small deviations. Further investigation on dynamic structure factor shows that the deviations simply exist due to the presence of strong enthalpic interactions between the monomers with the nanoparticles, albeit preserving the anomaly in the chain diffusion. The time-temperature superposition principle is also tested for this system and shows a striking resemblance with systems near glass transition and biological systems with molecular crowding. The universality class of the problem can be enormously important in understanding materials with strong afﬁnity to form either a glass, a gel or networklike structures.",
	collection = "polymer nanocomposites",
	doi = "10.1103/PhysRevE.81.041801",
	keywords = "nanospheres; polymer nanocomposites",
	localfile = "polymer nanocomposites/2010 - Anomalous chain diffusion in polymer nanocomposites for varying polymer-filler interaction strengths.pdf",
	year = 2010
}

@Article{2010-Grafova-PRH,
	Author = "Lucie Gráfová and Michal Pitoňák and Jan Řezáč and Pavel Hobza",
	Title = "{Comparative study of selected wave function and density functional methods for noncovalent interaction energy calculations using the extended S22 data set}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "6",
	Pages = "2365–2376",
	collection = "molecular interactions",
	doi = "10.1021/ct1002253",
	localfile = "molecular interactions/2010 - Comparative study of selected wave function and density functional methods for noncovalent interactions energy calculations using the extended S22 data set.pdf",
	year = 2010
}

@Article{2010-Groot-Stoyanov,
	Author = "Robert D. Groot and Simeon D. Stoyanov",
	Title = "{CLose apcking density and fracture strength of adsorbed polydisperse particle layers}",
	Journal = "Soft Matter",
	Volume = "7",
	Pages = "4750",
	collection = "jamming",
	doi = "10.1039/c0sm00859a",
	localfile = "jamming/2011 - Close packing density and fracture strength of adsorbed polydisperse particle layers.pdf",
	rating = "2",
	read = "2011-09-05",
	year = 2010
}

@Article{2010-Grzelczak-VFL,
	Author = "Marek Grzelczak and Jan Vermant and Eric M. Furst and Luis M. Liz-Marzan",
	Title = "{Directed self-assembly of nanoparticles}",
	Journal = "ACS Nano",
	Volume = "4",
	Number = "7",
	Pages = "3591–3605",
	abstract = "Within the ﬁeld of nanotechnology, nanoparticles are one of the most prominent and promising candidates for technological applications. Self-assembly of nanoparticles has been identiﬁed as an important process where the building blocks spontaneously organize into ordered structures by thermodynamic and other constraints. However, in order to successfully exploit nanoparticle self-assembly in technological applications and to ensure efﬁcient scale-up, a high level of direction and control is required. The present review critically investigates to what extent self-assembly can be directed, enhanced, or controlled by either changing the energy or entropy landscapes, using templates or applying external ﬁelds.",
	collection = "nanoparticles",
	doi = "10.1021/nn100869j",
	keywords = "self-assembly",
	localfile = "block copolymer nanocomposites/2010 - Directed self-assembly of nanoparticles.pdf",
	type = "Review",
	year = 2010
}

@Article{2010-Hall-JS,
	Author = "Lisa M. Hall and Arthi Jayaraman and Kenneth S. Schweizer",
	Title = "{Molecular theories of polymer nanocomposites}",
	Journal = "Curr. Op. Solid State Mat. Sci.",
	Volume = "14",
	Pages = "38–48",
	abstract = "Signiﬁcant progress towards the development of microscopic predictive theories of the equilibrium structure, polymer-mediated interactions, and phase behavior of polymer nanocomposites has been made recently based on liquid state integral equation, density functional, and self-consistent mean ﬁeld approaches. The basics of these three theoretical frameworks are summarized, and selected highlights of their recent applications discussed for spherical, nonspherical, and polymer-grafted nanoparticles dissolved in athermal and adsorbing concentrated solutions and homopolymer melts. The role of nanoparticle size, volume fraction, and interfacial cohesive interactions is emphasized, especially with regards to their inﬂuence on ﬁller dispersion and spatial ordering via entropic depletion attraction, polymer adsorption-mediated steric stabilization, and local bridging of nanoparticles. Some of the many remaining theoretical challenges and open fundamental questions are summarized.",
	collection = "polymer nanocomposites",
	doi = "10.1016/j.cossms.2009.08.004",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2010 - Molecular theories of polymer nanocomposites.pdf",
	type = "Review",
	year = 2010
}

@Article{2010-Hall-Schweizer,
	Author = "Lisa M. Hall and Kenneth S. Schweizer",
	Title = "{Structure, scattering patterns and phase behavior of polymer nanocomposites with nonspherical fillers}",
	Journal = "Soft Matter",
	Volume = "6",
	Pages = "1015–1025",
	collection = "polymer nanocomposites",
	doi = "10.1039/b919160g",
	keywords = "nanoplates; nanorods; polymer nanocomposites",
	localfile = "polymer nanocomposites/2010 - Structure, scattering patterns and phase behavior of polymer nanocomposites with nonspherical fillers.pdf",
	year = 2010
}

@Article{2010-Hammond-DPS,
	Author = "Matthew R. Hammond and Herve Dietsch and Olivier Pravaz and Peter Schurtenberger",
	Title = "{Mutual alignment of block copolymer-magnetic nanoparticle composites in a magnetic field}",
	Journal = "Macromolecules",
	Volume = "43",
	Pages = "8340–8343",
	Note = "Demonstrates the alignment of diblock copolymer lamellae along with needle-like NPs in a magnetic field, and associated problems.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma1012896",
	keywords = "alignment; block copolymers; magnetic fields; mesophase coexistence; nanorods; polymer nanocomposites; thin films",
	localfile = "block copolymer nanocomposites/2010 - Mutual alignment of block copolymer-magnetic nanoparticle composites in a magnetic field.pdf",
	methods = "SAXS, TEM",
	systems = "hematite(needles)-P2VP-PS@PS-P2VP",
	year = 2010
}

@Article{2010-Han-KJC,
	Author = "Young-Kyu Han and Hyemi Kim and Jaehoon Jung and Young Cheol Choi",
	Title = "{Understanding the magic nature of ligand-protected gold nanoparticle Au102(MBA)44}",
	Journal = "J. Phys. Chem. C",
	Volume = "114",
	Pages = "7548–7552",
	abstract = "A recent landmark achievement (Jadzinsky et al. Science 2007, 318, 430) reported the successful crystallization and X-ray measurements of para-mercaptobenzoic acid (p-MBA)-protected gold nanoparticles containing 102 gold atoms and 44 p-MBAs. To gain more insight into the Au102(SR)44 nanoclusters, we have performed density functional calculations for Au102(SMe)44 and its neighboring systems. The exceptional stability of Au102(SR)44 can be attributed to three coexisting factors: effective staple-motif formation, high stability against dissociation, and a large HOMO-LUMO gap.",
	collection = "nanoparticles",
	doi = "10.1021/jp907435s",
	keywords = "nanoparticle structure",
	localfile = "nanoparticles/2010 - Understanding the magic nature of ligand-protected gold nanoparticle Au102(MBA)44.pdf",
	year = 2010
}

@Article{2010-Hargis-SHW,
	Author = "Jacqueline C. Hargis and {Henry F. III} Schaefer and K. N. Houk and Steven E. Wheeler",
	Title = "{Noncovalent interactions of a benzo[a]pyrene diol epoxide with DNA base pairs: insight into the formation of adducts of (+)-BaP DE-2 with DNA}",
	Journal = "J. Phys. Chem. A",
	Volume = "114",
	Pages = "2038–2044",
	abstract = "Noncovalent complexes of a tumorigenic benzo[a]pyrene diol epoxide with the guanine-cytosine (GC) and adenine-thymine (AT) base pairs have been examined computationally. (+)-BaP DE-2 forms covalent adducts with DNA via nucleophilic attack on the (+)-BaP DE-2 epoxide. Computational results predict ﬁve thermodynamically accessible complexes of AT with (+)-BaP DE-2 that are compatible with intact DNA. Among these, two are expected to lead to adenine adducts. In the lowest energy AT · · · (+)-BaP DE-2 complex, which has a gas-phase interaction energy of -20.9 kcal mol-1, the exocyclic NH2 of adenine is positioned for backside epoxide attack and formation of a trans adduct. The most energetically favorable complex leading to formation of a cis ring-opened adduct lies only 0.6 kcal mol-1 higher in energy. For GC · · · (+)-BaP DE-2, there are only two thermodynamically accessible complexes. The higher-lying complex, bound in the gas phase by 24.4 kcal mol-1 relative to separated GC and (+)-BaP DE-2, would lead to a trans ring-opened N2-guanine adduct. In the global minimum energy GC · · · (+)-BaP DE-2 complex, bound by 27.3 kcal mol-1, the exocyclic NH2 group of cytosine is positioned for cis epoxide addition. However, adducts of (+)-BaP DE-2 with cytosine are rarely observed experimentally. The paucity of cytosine adducts, despite the predicted thermodynamic stability of this GC · · · (+)-BaP DE-2 complex, is attributed to the electrostatic destabilization of the benzylic cation intermediate thought to precede cis addition.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/jp911376p",
	localfile = "nucleic acid intercalation/2010 - Noncovalent interactions of a benzo[a]pyrene diol epoxide with DNA base pairs: insight into the formation of adducts of (+)-BaP DE-2 with DNA.pdf",
	year = 2010
}

@Article{2010-Harton-KYKHLMLVG,
	Author = "Shane E. Harton and Sanat K. Kumar and Hoichang Yang and Tadanori Koga and Kyle Hicks and HyungKi Lee and Jovan Mijovic and Ming Liu and Richard S. Vallery and David W. Gidley",
	Title = "{Immobilized polymer layers on spherical nanoparicles}",
	Journal = "Macromolecules",
	Volume = "43",
	Pages = "3415–3421",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma902484d",
	keywords = "polymer nanocomposites",
	localfile = "nanoparticles/2010 - Immobilized polymer layers on spherical nanoparticles.pdf",
	year = 2010
}

@Article{2010-He-ZL,
	Author = "Linli He and Linxi Zhang and Haojun Liang",
	Title = "{Mono- or bidisperse nanorods mixtures in diblock copolymers}",
	Journal = "Polymer",
	Volume = "51",
	Pages = "3303–3314",
	abstract = "Mixtures of diblock copolymers (DBCPs) and mono- or bidisperse nanorods (NRs), are systematically investigated via dissipative particle dynamics simulations. For the mixtures of DBCPs and monodisperse NRs, we investigate the effects of the nanorod (NR) volume fraction, NR length, and interaction strength between blocks and NRs on the self-assembly of the composites. For the mixtures of DBCPs and bidisperse NRs in which the NRs are different in length, the binary NRs with varied compositions can induce various morphological transitions, as well as present the uniform orientations and discriminative distributions. The inherent mechanism for driving such rich phase behaviors can be further exploited on he basis of considering the enthalpic and entropic effects. The results provide some guidelines for engineering nanocomposites with the desired morphologies and functions.",
	collection = "block copolymer nanocomposites",
	doi = "10.1016/j.polymer.2010.05.026",
	keywords = "block copolymers; mesophase transitions; nanorods; polydispersity; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2010 - Mono- and bidisperse nanorods mixtures in diblock copolymers.pdf",
	methods = "DPD",
	year = 2010
}

@Article{2010-Hohenstein-Sherrill,
	Author = "Edward G. Hohenstein and C. David Sherrill",
	Title = "{Density fitting of intramonomer correlation effects in symmetry-adapted perturbation theory}",
	Journal = "J. Chem. Phys.",
	Volume = "133",
	Pages = "014101",
	abstract = "Symmetry-adapted perturbation theory SAPT offers insight into the nature of intermolecular interactions. In addition, accurate energies can be obtained from the wave function-based variant of SAPT provided that intramonomer electron correlation effects are included. We apply density-ﬁtting DF approximations to the intramonomer correlation corrections in SAPT. The introduction of this approximation leads to an improvement in the computational cost of SAPT by reducing the scaling of certain SAPT terms, reducing the amount of disk I/O, and avoiding the explicit computation of certain types of MO integrals. We have implemented all the intramonomer correlation corrections to SAPT through second-order under the DF approximation. Additionally, leading third-order terms are also implemented. The accuracy of this truncation of SAPT is tested against the S22 test set of Hobza and co-workers Phys. Chem. Chem. Phys. 8, 1985 2006 . When the intramonomer corrections to dispersion are included in SAPT, a mean absolute deviation of 0.3– 0.4 kcal mol−1 is observed for the S22 test set when using an aug-cc-pVDZ basis. The computations on the adenine-thymine complexes in the S22 test set with an aug-cc-pVDZ basis represent the largest SAPT computations to date that include this degree of intramonomer correlation. Computations of this size can now be performed routinely with our newly developed DF-SAPT program.",
	collection = "molecular interactions",
	doi = "10.1063/1.3451077",
	localfile = "molecular interactions/2010 - Density fitting of intramonomer correlation effects in symmetry-adapted perturbation theory.pdf",
	year = 2010
}

@Article{2010-Hohenstein-Sherrill-1,
	Author = "Edward G. Hohenstein and C. David Sherrill",
	Title = "{Density fitting and Cholesky decomposition approximations in symmetry-adapted perturbation theory: implementation and application to probe the nature of pi-pi interactions in linear acenes}",
	Journal = "J. Chem. Phys.",
	Volume = "132",
	Pages = "184111",
	abstract = "Density ﬁtting (DF) approximations have been used to increase the efﬁciency of several quantum mechanical methods. In this work, we apply DF and a related approach, Cholesky decomposition (CD) , to wave function-based symmetry-adapted perturbation theory (SAPT). We also test the one-center approximation to the Cholesky decomposition. The DF and CD approximations lead to a dramatic improvement in the overall computational cost of SAPT, while introducing negligible errors. For typical target accuracies, the Cholesky basis needed is noticeably smaller than the DF basis although the cost of constructing the Cholesky vectors is slightly greater than that of constructing the three-index DF integrals . The SAPT program developed in this work is applied to the interactions between acenes previously studied by Grimme Angew. Chem., Int. Ed. 4

license: MIT

license_type: permissive

extension: bib