text:
iao-Wei Yeh and Kung-Hwa Wei and Ya-Sen Sun and U-Ser Jeng and Keng S. Liang",
	Title = "{CdS nanoparticles induce a morphological transformation of poly(styryne-b-4-vinylpyridine) from hexagonally packed cylinders to a lamellar structure}",
	Journal = "Macromolecules",
	Volume = "38",
	Pages = "6559–6565",
	Note = "Demonstrates hexagonal-to-lamellar transition of P4VP domains in S4CP copolymer loaded with CdS nanoparticles.",
	abstract = "Mercaptoacetic acid-modified CdS nanoparticles disperse selectively in the poly(4-vinylpyridine) domains of poly(styrene-b-4-vinylpyridine) (S4VP) block copolymer as a result of the formation of hydrogen bonds. This process in turn induces the morphological transformation of S4VP from a hexagonally packed cylinder structure into a lamellar structure, as evidenced from transmission electron microscopy, atomic force microscopy, and small-angle X-ray scattering studies. This transformation is consistent with that suggested by a theoretical prediction of the phase diagram of the mixed diblock copolymer/nanoparticle system.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma047653a",
	keywords = "block copolymers; mesophase transitions; nanospheres; polymer nanocomposites; thin films",
	localfile = "block copolymer nanocomposites/2005 - CdS nanoparticles induce a morphological transformation of poly(styrene-b-4-vinylpyridine) from hyxagonally packed cylinders to a lamellar structure.pdf",
	methods = "DSC, NMR, SAXS, AFM, TEM",
	systems = "CdS@PS-P4VP",
	year = 2005
}

@Article{2005-Yildirim-Turner,
	Author = "Ilyas Yildirim and Douglas H. Turner",
	Title = "{{RNA} Challenges for Computational Chemists}",
	Journal = "Biochemistry",
	Volume = "44",
	Number = "40",
	Pages = "13225–13234",
	abstract = "Some experimental results for the thermodynamics of {RNA} folding cannot be explained by simple pairwise hydrogen-bonding models. Such effects include the stabilities of isoguanosineisocytidine {(iGiC)} base pairs and of various 2 2 nucleotide internal loops. Presumably, these results can be explained by base stacking effects, which can be partitioned into Coulombic and overlap effects. We review experimental measurements that provide benchmarks for testing the approximations and theories used for modeling nucleic acids. Quantitative agreement between experiment and theory will indicate understanding of the interactions determining {RNA} stability and structure.",
	collection = "nucleic acids",
	doi = "10.1021/bi051236o",
	localfile = "nucleic acids/2005 - RNA challanges for comptuational chemists.pdf",
	year = 2005
}

@Article{2005-Zhang-XBMRER,
	Author = "Qingling Zhang and Ting Xu and David Butterfield and Matthew J. Misner and Du Yoel Ryu and Todd Emrick and Thomas P. Russell",
	Title = "{Controlled placement of CdSe nanoparticles in diblock copolymer templates by electrophoretic deposition}",
	Journal = "Nano Lett.",
	Volume = "5",
	Number = "2",
	Pages = "357–361",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/nl048103t",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2005 - Controlled placement of CdSe nanoparticles in diblock copolymer templates by electrophoretic deposition.pdf",
	methods = "TEM, photoluminescence",
	rating = "2",
	read = "2012-03-21",
	systems = "CdSe-{theocarboxylic acid}@PS-PMMA",
	year = 2005
}

@Article{2006-Alonso-ACCRM,
	Author = "Angel Alonso and María Jesús Almendral and Y. Curto and Julio J. Criado and Emilio Rodríguez and Juan Luis Manzano",
	Title = "{Determination of the {DNA}-binding characteristics of ethidium bromide, proflavine, and cisplatin by flow injection analysis: Usefulness in studies on antitumor drugs}",
	Journal = "Anal. Biochem.",
	Volume = "355",
	Number = "2",
	Pages = "157–164",
	collection = "nucleic acid intercalation",
	doi = "10.1016/j.ab.2006.06.004",
	keywords = "nucleic acid intercalation",
	localfile = "nucleic acid intercalation/2006 - Determination of the DNA-binding characteristics of ethidium bromide, proflavine and cisplatin by flow injection analysis: usefulness in studies on antitumor drugs.pdf",
	year = 2006
}

@Article{2006-Amari-AZFMINCN,
	Author = "Shinji Amari and M. Aizawa and J. W. Zhang and Kaori Fukuzawa and Yuji Mochizuki and Y. Iwasawa and Kotoko Nakata and H. Chuman and Tatsuya Nakano",
	Title = "{V{ISCANA}: {V}isualized cluster analysis of protein-ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening}",
	Journal = "J. Chem. Inf. Model.",
	Volume = "46",
	Number = "1",
	Pages = "221 – 230",
	abstract = "We have developed a visualized cluster analysis of protein-ligand interaction (VISCANA) that analyzes the pattern of the interaction of the receptor and ligand on the basis of quantum theory for virtual ligand screening. Kitaura et al. (Chem. Phys. Lett. 1999, 312, 319-324.) have proposed an ab initio fragment molecular orbital (FMO) method by which large molecules such as proteins can be easily treated with chemical accuracy. In the FMO method, a total energy of the molecule is evaluated by summation of fragment energies and interfragment interaction energies (IFIEs). In this paper, we have proposed a cluster analysis using the dissimilarity that is defined as the squared Euclidean distance between IFIEs of two ligands. Although the result of an ordered table by clustering is still a massive collection of numbers, we combine a clustering method with a graphical representation of the IFIEs by representing each data point with colors that quantitatively and qualitatively reflect the IFIEs. We applied VISCANA to a docking study of pharmacophores of the human estrogen receptor alpha ligand-binding domain (57 amino acid residues). By using VISCANA, we could classify even structurally different ligands into functionally similar clusters according to the interaction pattern of a ligand and amino acid residues of the receptor protein. In addition, VISCANA could estimate the correct docking conformation by analyzing patterns of the receptor-ligand interactions of some conformations through the docking calculation.",
	collection = "cheminformatics",
	localfile = "cheminformatics/2006 - VISCANA: Visualized cluster analysis of protein-ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening.pdf",
	year = 2006
}

@Article{2006-Antony-Grimme,
	Author = "Jens Antony and Stefan Grimme",
	Title = "{Density functional theory including dispersion corrections for intermolecular interactions in a large benchmark set of biologically relevant molecules}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "8",
	Pages = "5287–5293",
	collection = "molecular interactions",
	doi = "10.1039/b612585a",
	localfile = "molecular interactions/2006 - Density functional theory including dispersion corrections for itnermolecular interactions n a large benchmark set of biologically relevant molecules.pdf",
	year = 2006
}

@Article{2006-Arkhipov-FS,
	Author = "Anton S. Arkhipov and Peter L. Freddolino and Klaus Schulten",
	Title = "{Stability and dynamics of virus capsids described by coarse-grained modeling}",
	Journal = "Structure",
	Volume = "14",
	Pages = "1767–1777",
	abstract = "We report a study of the structural dynamics of viral capsids, simulated on a microsecond timescale, by employing a coarse-graining molecular dynamics method. The method was calibrated against an all-atom simulation of one complete virus. Among the studied capsids, some collapsed rapidly, while others were found to be stable. Interlocking between coat proteins is found to be a key factor determining the stability of the capsids.",
	collection = "viruses",
	doi = "10.1016/j.str.2006.10.003",
	localfile = "viruses/2006 - Stability and dynamics of virus capsids described by coars-grained modeling.pdf",
	year = 2006
}

@Article{2006-Aslanoglu,
	Author = "Mehmet Aslanoglu",
	Title = "{Electrochemical and spectroscopic studies of the interaction of proflavine with {DNA}}",
	Journal = "Anal. Sci.",
	Volume = "22",
	Pages = "439–443",
	abstract = "The interaction of proflavine with herring sperm DNA has been investigated by cyclic voltammetry and UV-Vis spectroscopy as well as viscosity measurements. Shifts in the peak potentials in cyclic voltammetry, spectral changes in UV absorption titration, an increase in viscosity of DNA and the results of the effect of ionic strength on the binding constant strongly support the intercalation of proflavine into the DNA double helix. The binding constant for the interaction between proflavine and DNA was K = 2.32 (±0.41) × 104 M–1 and the binding site size was 2.07 (±0.1) base pairs, estimated in voltammetric measurements. The value of the binding site size was determined to be closer to that expected for a planar intercalating agent. The standard Gibbs free-energy change is ca. –24.90 kJ/mol at 25˚C, indicating the spontaneity of the binding interaction. The binding constant determined by UV absorption measurements was K = 2.20 (±0.48) × 104 M–1, which is very close to the value determined by cyclic voltammetry assuming that the binding equilibrium is static.",
	collection = "nucleic acid intercalation",
	doi = "10.2116/analsci.22.439",
	localfile = "nucleic acid intercalation/2006 - Electrochemical and spectroscopic studies of the itneraction of proflavine with DNA.pdf",
	year = 2006
}

@Article{2006-Babin-BDS,
	Author = "Volodymyr Babin and Jason Baucom and Thomas A. Darden and Celeste Sagui",
	Title = "{Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure}",
	Journal = "J. Phys. Chem. B",
	Volume = "110",
	Pages = "11571–11581",
	abstract = "We have investigated to what extent molecular dynamics (MD) simulations can reproduce DNA sequence-specific features, given different electrostatic descriptions and different cell environments. For this purpose, we have carried out multiple unrestrained MD simulations of the DNA duplex d(CCAACGTTGG)$\_2$. With respect to the electrostatic descriptions, two different force fields are studied: a traditional description based on atomic point charges and a polarizable force field. With respect to the cell environment, the difference between crystal and solution environments is emphasized, as well as the structural importance of divalent ions. By imposing the correct experimental unit cell environment, an initial configuration with two ideal B-DNA duplexes in the unit cell is shown to converge to the crystallographic structure. This convergence is measured by the appearance of sequence-dependent features that very closely resemble the crystallographic ones as well as by the decay of the all-atom root-mean-squared coordinates deviations (RMSD) with respect to the crystallographic structure. Given the appropriate crystallographic constraints, this is the first example of multiple nanosecond molecular dynamics trajectory that shows an ideal B-DNA model converging to an experimental structure, with a significant decay of RMSD.",
	collection = "nucleic acids",
	doi = "10.1021/jp061421r",
	localfile = "nucleic acids/2006 - Molecular dynamics simulations of DNA with polarizable force fields.pdf",
	year = 2006
}

@Article{2006-Bader,
	Author = "Richard F. W. Bader",
	Title = "{Pauli Repulsions Exist Only in the Eye of the Beholder}",
	Journal = "Chem. Eur. J.",
	Volume = "12",
	Number = "10",
	Pages = "2896–2901",
	abstract = "This paper presents a rebuttal to the preceding paper in this issue entitled {Hydrogen-Hydrogen} Bonding in Planar Biphenyl, Predicted by {Atoms-In-Molecules} Theory, Does Not Existr. The arguments presented therein are based on an arbitrary partitioning of the energy into contributions from physically unrealizable states of the system. The response given here is presented in terms of the Feynman, Ehrenfest, and virial theorems of quantum mechanics and the observable properties of a system. A reader is thus free to choose between subjectivity or physics.",
	collection = "molecular interactions",
	doi = "10.1002/chem.200501589",
	localfile = "molecular interactions/2006 - Pauli repulsions exist only in the eye of the beholder.pdf",
	year = 2006
}

@Article{2006-Balaban-Klein,
	Author = "A.T. Balaban and D.J. Klein",
	Title = "{Is chemistry 'The Central Science'? How are different sciences related? Co-citation, reductionism, emergence, and posets}",
	Journal = "Scientometrics",
	Volume = "69",
	Number = "3",
	Pages = "615–637",
	abstract = "According to a widely used introductory chemistry text by T. E. Brown et al.,1 chemistry is ‘The Central Science’. But scientometric co-citation analyses indicate that biochemistry seems presently to be more interconnected to other sciences. On the other hand, mathematics is considered by many to permeate all sciences and hence might compete as the choice for centrality. A critical commentary and argument leads to a proposal for an alternative partially ordered hierarchical “framework” map of sciences. This argument is supplemented by a scientometric approach based on university course requirements for different curricula, so as to support our partially ordered map. This alternative “framework” mapping then is seen to indicate a special position for chemistry, as where significant branching begins.",
	collection = "philosophy",
	doi = "10.1007/s11192-006-0173-2",
	localfile = "philosophy/2006 - Is chemistry 'The Central Science'. How are different sciences related. Co-citation, reductionaism, emergence, and posets.pdf",
	year = 2006
}

@Article{2006-Balazs-ER,
	Author = "Anna C. Balazs and Todd Emrick and Thomas P. Russell",
	Title = "{Nanoparticle Polymer Composites: Where Two Small Worlds Meet}",
	Journal = "Science",
	Volume = "314",
	Number = "5802",
	Pages = "1107–1110",
	abstract = "The mixing of polymers and nanoparticles is opening pathways for engineering flexible composites that exhibit advantageous electrical, optical, or mechanical properties. Recent advances reveal routes to exploit both enthalpic and entropic interactions so as to direct the spatial distribution of nanoparticles and thereby control the macroscopic performance of the material. For example, by tailoring the particle coating and size, researchers have created self-healing materials for improved sustainability and self-corralling rods for photovoltaic applications. A challenge for future studies is to create hierarchically structured composites in which each sublayer contributes a distinct function to yield a mechanically integrated, multifunctional material.",
	collection = "polymer nanocomposites",
	doi = "10.1126/science.1130557",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2006 - Nanoparticle polymer composites: where two small worlds meet.pdf",
	rating = "2",
	shorttitle = "Nanoparticle Polymer Composites",
	type = "Review",
	year = 2006
}

@Article{2006-Buda-Dunietz,
	Author = "Corneliu Buda and Barry D. Dunietz",
	Title = "{Hydrogen Physisorption on the Organic Linker in Metal Organic Frameworks: Ab Initio Computational Study}",
	Journal = "J. Phys. Chem. B",
	Volume = "110",
	Number = "21",
	Pages = "10479–10484",
	abstract = "Research for materials offering efficient hydrogen storage and transport has recently received increased attention. Metal organic frameworks (MOFs) provide one promising group of materials where several recent advances were reported in this direction. In this computational study ab initio methods are employed to study the physisorption of hydrogen on conjugated systems. These systems are used as models for the organic linker within MOFs. Here, we focus on the adsorption sites related to the organic linker with special attention to the edge site, which was only recently reported to exist as the weakest adsorbing site in MOFs. We also investigate chemically modified models of the organic connector that result in enforcing this adsorption site. This may be crucial for improving the uptake properties of these materials to the goal defined by DOE for efficient hydrogen transport materials.",
	collection = "hydrogen sorption",
	doi = "10.1021/jp061249r",
	localfile = "hydrogen sorption/2006 - Hydrogen physisorption on the organic linker in metal organic frameworks: ab initio computational study.pdf",
	shorttitle = "Hydrogen Physisorption on the Organic Linker in Metal Organic Frameworks",
	year = 2006
}

@Article{2006-Burge-PHTN,
	Author = "Sarah Burge and Gary N. Parkinson and Pascale Hazel and Alan K. Todd and Stephen Neidle",
	Title = "{Quadruplex {DNA:} sequence, topology and structure}",
	Journal = "Nucl. Acids Res.",
	Volume = "34",
	Number = "19",
	Pages = "5402–5415",
	abstract = "G-quadruplexes are higher-order {DNA} and {RNA} structures formed from G-rich sequences that are built around tetrads of hydrogen-bonded guanine bases. Potential quadruplex sequences have been identified in G-rich eukaryotic telomeres, and more recently in non-telomeric genomic {DNA,} e.g. in nuclease-hypersensitive promoter regions. The natural role and biological validation of these structures is starting to be explored, and there is particular interest in them as targets for therapeutic intervention. This survey focuses on the folding and structural features on quadruplexes formed from telomeric and non-telomeric {DNA} sequences, and examines fundamental aspects of topology and the emerging relationships with sequence. Emphasis is placed on information from the high-resolution methods of X-ray crystallography and {NMR,} and their scope and current limitations are discussed. Such information, together with biological insights, will be important for the discovery of drugs targeting quadruplexes from particular genes.",
	collection = "nucleic acids",
	doi = "10.1093/nar",
	localfile = "nucleic acids/2006 - Quadruplex DNA: sequence, topology and structure.pdf",
	shorttitle = "Quadruplex {DNA}",
	year = 2006
}

@Article{2006-Chaires,
	Author = "Jonathan B. Chaires",
	Title = "{A thermodynamic signature for drug-DNA binding mode}",
	Journal = "Arch. Biochem. Biophys.",
	Volume = "453",
	Number = "1",
	Pages = "26–31",
	collection = "nucleic acid drugs",
	doi = "10.1016/j.abb.2006.03.027",
	localfile = "nucleic acid drugs/2006 - A thermodynamic signature for drug-DNA bindingmode.pdf",
	year = 2006
}

@Article{2006-Chan-HG,
	Author = "Elaine R. Chan and Lin C. Ho and Sharon C. Glotzer",
	Title = "{Computer simulations of block copolymer tethered nanoparticle self-assembly}",
	Journal = "J. Chem. Phys.",
	Volume = "125",
	Number = "6",
	Pages = "064905",
	Note = "Demonstrates various structures of diblock-tethered NPs for different A/B block fractions.",
	abstract = "We perform molecular simulations to study the self-assembly of block copolymer tethered cubic nanoparticles. Minimal models of the tethered nanoscale building blocks {(NBBs)} are utilized to explore the structures arising from self-assembly. We demonstrate that attaching a rigid nanocube to a diblock copolymer affects the typical equilibrium morphologies exhibited by the pure copolymer. Lamellar and cylindrical phases are observed in both systems but not at the corresponding relative copolymer tether block fractions. The effect of nanoparticle geometry on phase behavior is investigated by comparing the self-assembled structures formed by the tethered {NBBs} with those of their linear {ABC} triblock copolymer counterparts. The tethered nanocubes exhibit the conventional triblock copolymer lamellar and cylindrical phases when the repulsive interactions between different blocks are symmetric. The rigid and bulky nature of the cube induces interfacial curvature in the tethered {NBB} phases compared to their linear {ABC} triblock copolymer counterparts. We compare our results with those structures obtained from {ABC} diblock copolymer tethered nanospheres to further elucidate the role of cubic nanoparticle geometry on self-assembly.",
	collection = "nanoparticles",
	doi = "10.1063/1.2241151",
	keywords = "nanoparticle grafts",
	localfile = "nanoparticles/2006 - Computer simulations of block copolymer tethered nanoparticle self-assembly.pdf",
	year = 2006
}

@Article{2006-Condon,
	Author = "Anne Condon",
	Title = "{Designed {DNA} molecules: principles and applications of molecular nanotechnology}",
	Journal = "Nat. Rev. Genetics",
	Volume = "7",
	Number = "7",
	Pages = "565–575",
	abstract = "Long admired for its informational role in the cell, {DNA} is now emerging as an ideal molecule for molecular nanotechnology. Biologists and biochemists have discovered {DNA} sequences and structures with new functional properties, which are able to prevent the expression of harmful genes or detect macromolecules at low concentrations. Physical and computational scientists can design rigid {DNA} structures that serve as scaffolds for the organization of matter at the molecular scale, and can build simple {DNA-computing} devices, diagnostic machines and {DNA} motors. The integration of biological and engineering advances offers great potential for therapeutic and diagnostic applications, and for nanoscale electronic engineering.",
	collection = "nucleic acids",
	doi = "10.1038/nrg1892",
	localfile = "nucleic acids/2006 - Designed DNA molecules: principles and applications of molecular nanotechnology.pdf",
	shorttitle = "Designed {DNA} molecules",
	year = 2006
}

@Article{2006-Daoulas-MPNS,
	Author = "Kostas Ch. Daoulas and Marcus Müller and Juan J. {de Pablo} and Paul F. Nealey and Grant D. Smith",
	Title = "{Morphologies of multi-component polymer systems: single chain in mean field simulation studies}",
	Journal = "Soft Matter",
	Volume = "2",
	Pages = "573–583",
	Note = "methods: MC with mean fields",
	abstract = "Recent work exploring phase separation and self-asembly in multicomponent polymer fluids using a particle-base self-consistent field simulation method is reviewed. The computational method is placed in the context of classical molecular dynamics and Monte Carlo simulations as well as field-theoretic approaches. Its potential is illustrated by applications ranging from spinodal decomposition in symmetric polymer blends and the ordering of diblock copolymers in the bulk to more complex phenomena such as solvent evaporation from thin polymer films and the fabrication of three-dimensional bicontinuous diblock copolymer morphologies via reconstruction on patterned substrates.",
	collection = "block copolymers",
	doi = "10.1039/b602610a",
	keywords = "block copolymers",
	localfile = "block copolymers/2006 - Morphology of multi-component polymer systems: single chain in mean field simulation studies.pdf",
	methods = "SCMF",
	rating = "2",
	read = "2011-05-02",
	year = 2006
}

@Article{2006-Daoulas-Muller,
	Author = "Kostas Ch. Daoulas and Marcus Müller",
	Title = "{Single chain in mean field simulations: quasi-instantaneous field approximation and quantitative comparison with Monte Carlo simulations}",
	Journal = "J. Chem. Phys.",
	Volume = "125",
	Pages = "184904",
	Note = "methods: MC with mean fields",
	collection = "block copolymers",
	doi = "10.1063/1.2364506",
	keywords = "block copolymers",
	localfile = "block copolymers/2006 - Single chain in mean field simulations: quasi-instantaneous field approximation and quantitative comparison with Monte Carlo simulations.pdf",
	year = 2006
}

@Article{2006-Dickman,
	Author = "Mark J. Dickman",
	Title = "{Post column nucleic acid intercalation for the fluorescent detection of nucleic acids using ion pair reverse phase high-performance liquid chromatography}",
	Journal = "Anal. Biochem.",
	Volume = "360",
	Pages = "282–287",
	abstract = "Here we report a simple and eVective procedure enabling the Xuorescent detection of nucleic acids following the rapid, high-resolution separation using ion pair reverse phase chromatography. This approach uses postcolumn nucleic acid intercalation of Xuorescent dyes with subsequent Xuorescent detection, demonstrating more than a 1000-fold increase in sensitivity in the detection of nucleic acids when compared with traditional UV detection. Moreover, a wide range of intercalating dyes can be incorporated, including those known to disrupt the structure of the nucleic acids, thereby enabling the sensitive detection of DNA and RNA with no adverse eVect on resolution of the nucleic acids during ion pair reverse phase chromatography. In addition, such approaches allow one to readily distinguish single-stranded DNA from double-stranded DNA following their separation using ion pair reverse phase high-performance liquid chromatography.",
	collection = "nucleic acid intercalation",
	doi = "10.1016/j.ab.2006.09.034",
	localfile = "nucleic acid intercalation/2007 - Post column nucleic acid intercalation for the flourescent detection of nucleic acids using ion pair reverse phase high-performance liquid chromatography.pdf",
	year = 2007
}

@Article{2006-Fedorov-Kitaura,
	Author = "Dmitri G. Fedorov and Kazuo Kitaura",
	Title = "{The three-body fragment molecular orbital method for accurate calculations of large systems}",
	Journal = "Chem. Phys. Lett.",
	Volume = "433",
	Number = "1-3",
	Pages = "182 – 187",
	abstract = "The approximations used in the context of the fragment molecular orbital method were critically revised, the origin of the approximation error determined and an improvement proposed. The three-body method which has been so far very expensive, was reformulated to be used with the approximations, and its efficacy both in terms of accuracy and computational timings carefully established on a set of representative systems. Timings and accuracy are reported for the two and three-body methods, including their application to two proteins 1L2Y and 1IO5 (PDB codes) and (H2O)(1024) (at the RHF/6-31G* level).",
	collection = "molecular fragmentation",
	doi = "10.1016/j.cplett.2006.10.052",
	localfile = "molecular fragmentation/2006 - The three-body fragment molecular orbital method for accurate calculations of large systems.pdf",
	methods = "FMO",
	year = 2006
}

@Article{2006-Feldkamp-Niemeyer,
	Author = "Udo Feldkamp and Christof M. Niemeyer",
	Title = "{Rational Design of {DNA} Nanoarchitectures}",
	Journal = "Angew. Chem. Int. Ed.",
	Volume = "45",
	Number = "12",
	Pages = "1856–1876",
	abstract = "{DNA} has many physical and chemical properties that make it a powerful material for molecular constructions at the nanometer length scale. In particular, its ability to form duplexes and other secondary structures through predictable nucleotide-sequence-directed hybridization allows for the design of programmable structural motifs which can self-assemble to form large supramolecular arrays, scaffolds, and even mechanical and logical nanodevices. Despite the large variety of structural motifs used as building blocks in the programmed assembly of supramolecular {DNA} nanoarchitectures, the various modules share underlying principles in terms of the design of their hierarchical configuration and the implemented nucleotide sequences. This Review is intended to provide an overview of this fascinating and rapidly growing field of research from the structural design point of view.",
	collection = "nucleic acids",
	doi = "10.1002/anie.200502358",
	localfile = "nucleic acids/2006 - Rational design of DNA nanoarchitectures.pdf",
	year = 2006
}

@Article{2006-Freddolino-ALMS,
	Author = "Peter L. Freddolino and Anton S. Arkhipov and Steven B. Larson and Alexander McPherson and Klaus Schulten",
	Title = "{Molecular dynamics simulations of the complete satellite tobacco mosaic virus}",
	Journal = "Structure",
	Volume = "14",
	Pages = "437–449",
	abstract = "This work presents an all-atom molecular dynamics simulation of a complete virus, the satellite tobacco mosaic virus. Simulations with up to 1 million atoms for over 50 ns demonstrate the stability of the entire virion and of the RNA core alone, while the capsid without RNA exhibits a pronounced instability. Physical properties of the simulated virus particle including electrostatic potential, radial distribution of viral components, and patterns of correlated motion are analyzed, and the implications for the assembly and infection mechanism of the virus are discussed.",
	collection = "viruses",
	doi = "10.1016/j.str.2005.11.014",
	localfile = "viruses/2006 - Molecular dynamics simulations of the complete satellite tobacco mosaic virus.pdf",
	year = 2006
}

@Article{2006-Fukuzawa-KMKNT,
	Author = "Kaori Fukuzawa and Y. Komeiji and Yuji Mochizuki and A. Kato and Tatsuya Nakano and Shigenori Tanaka",
	Title = "{Intra- and intermolecular interactions between cyclic-{AMP} receptor protein and {DNA}: {A}b initio fragment molecular orbital study}",
	Journal = "J. Comp. Chem.",
	Volume = "27",
	Number = "8",
	Pages = "948 – 960",
	abstract = "The ab initio fragment molecular orbital (FMO) calculations were performed for the cAMP receptor protein (CRP) complexed with a cAMP and DNA duplex to elucidate their sequence-specific binding and the stability of the DNA duplex, as determined by analysis of their inter- and intramolecular interactions. Calculations were performed with the AMBER94 force field and at the HF and MP2 levels with several basis sets. The interfragment interaction energies (IFIEs) were analyzed for interactions of CRP-cAMP with each base pair, DNA duplex with each amino acid residue, and each base pair with each residue. In addition, base-base interactions were analyzed including hydrogen bonding and stacking of DNA. In the interaction between DNA and CRP-cAMP, there was a significant charge transfer (CT) from the DNA to CRP. and this CT interaction played an important role as well as the electrostatic interactions. It is necessary to apply a quantum mechanical approach beyond the “classical” force-field approach to describe the sequence specificity. In the DNA intramolecular interaction, the dispersion interactions dominated the stabilization of the base-pair stacking interactions. Strong, attractive 1,2-stacking interactions and weak, repulsive 1,3-stacking interactions were observed. Comparison of the intramolecular interactions of free and complexed DNA revealed that the base-pairing interactions were stronger, and the stacking interactions were weaker, in the complexed structure. Therefore, the DNA duplex stability appears to change due to both the electrostatic and the CT interactions that take place under conditions of DNA-CRP binding. (c) 2006 Wiley Periodicals, Inc.",
	collection = "proteins",
	doi = "10.1002/jcc.20399",
	localfile = "proteins/2006 - Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA.pdf",
	year = 2006
}

@Article{2006-Fukuzawa-MTKN,
	Author = "Kaori Fukuzawa and Yuji Mochizuki and Shigenori Tanaka and Kazuo Kitaura and Tatsuya Nakano",
	Title = "{Molecular interactions between estrogen receptor and its ligand studied by the ab initio fragment molecular orbital method}",
	Journal = "J. Phys. Chem. B",
	Volume = "110",
	Number = "32",
	Pages = "16102 – 16110",
	abstract = "The ab initio fragment molecular orbital calculations were performed for molecular interactions of the whole estrogen receptor (ER) ligand-binding domain with a natural ligand, 17 ss-estradiol (EST). The interaction energies of the ligand at the residue level were calculated using HF and MP2 methods with several basis sets. The charge-transfer (CT) interactions were also analyzed based on configuration analysis for fragment interaction. Strong electrostatic interactions were observed between the EST and surrounding charged/polarized residues, Glu353, Arg394, His524, and Thr347. Weak electrostatic and significant van der Waals dispersion interactions were observed between the EST and the many surrounding hydrophobic residues. Together with the experimental interpretations, both interactions equally contributed to the total binding energies, and it was found that the inclusion of electron correlation was essential to obtain an appropriate picture of the interaction. The strongest interaction energy was observed between Glu353 and the EST, and the CT interactions from the lone- pair orbital of the carbonyl oxygen of Glu353 to the alpha*(OH) orbital of the hydroxyl group of EST were found to be important. The CT interactions from the lone- pair orbital of EST to the alpha*(NH) of Arg394 and from the lone- pair orbital of EST to the alpha*(NH) of His524 were also observed. These CT interactions occurred through the hydrogen-bond networks between the ER and EST. Therefore, electron donations from the ER to the EST and electron back-donations from EST to the ER were characteristic of ER-ligand binding. Our approach provides a powerful tool to understanding detailed molecular interactions at the quantum mechanical level.",
	collection = "molecular signaling",
	localfile = "molecular signaling/2006 - Molecular interactions between estrogen receptor and its ligand.pdf",
	year = 2006
}

@Article{2006-Galano-Alvarez-Idaboy,
	Author = "Annia Galano and J. Raúl Alvarez-Idaboy",
	Title = "{A new approach to counterpoise correction to {BSSE}}",
	Journal = "J. Comp. Chem.",
	Volume = "27",
	Number = "11",
	Pages = "1203 – 1210",
	abstract = "In the present work the intermolecular BSSE, associated to the A-B interaction, is obtained by subtracting the intramolecular BSSE of the fragments from the intramolecular BSSE of the supermolecule, and considering every atom as a fragment in the calculation of each intramolecular BSSE. This atom by atom scheme (CPaa) is based on the consideration that the proximity of the fragments may affect the intramolecular BSSE of every involved species, and artificially influences the value of the BSSE associated to the supermolecule formation. It drastically decreases the reported counterpoise overcorrection of the A-B interaction, even though it does not deal with all the overcorrection because it includes all the orbitals, and not only the unoccupied ones. This new approach has been tested on the water dimer, some hydrogen fluoride weakly bonded complexes, the conformational analysis of 1,2-dichloroethane, and the reaction profile of formaldehyde + OH reaction. (c) 2006 Wiley Periodicals, Inc.",
	collection = "basis set superposition",
	doi = "10.1002/jcc.20438",
	keywords = "counterpoise correction",
	localfile = "basis set superposition/2006 - A new approach to counterpoise correction to BSSE.pdf",
	year = 2006
}

@Article{2006-Ganesan-PSN,
	Author = "Venkat Ganesan and Victor Pryamitsyn and Megha Surve and Bharadwaj Narayanan",
	Title = "{Noncontinuum effects in nanoparticle dynamics in polymers}",
	Journal = "J. Chem. Phys.",
	Volume = "124",
	Pages = "221102",
	abstract = "We propose a continuum model for the dynamics of particles in polymer matrices which encompasses arbitrary size ratios of the polymer and particle. We present analytical and computer simulation results for the mobility of the particles and the viscosity of the suspension for the case of unentangled polymer melts. Our results indicate strong dependencies of the particle mobility upon the polymer-particle size ratios and much reduced intrinsic viscosities for the suspensions. These predictions rationalize some recent experimental observations on the dynamics of nanoparticles in polymer melts.",
	collection = "polymer nanocomposites",
	doi = "10.1063/1.2209241",
	localfile = "polymer nanocomposites/2006 - Noncontinuum effects in nanoparticle dynamics in polymers.pdf",
	year = 2006
}

@Article{2006-Garden-LK,
	Author = "Anna L. Garden and Joseph R. Lane and Henrik G. Kjaergaard",
	Title = "{Counterpoise corrected geometries of hydrated complexes}",
	Journal = "J. Chem. Phys.",
	Volume = "125",
	Number = "14",
	Pages = "144317–7",
	abstract = "We have calculated the equilibrium geometries of the hydrated complexes, H2O·CO2, H2O·CS2,H2O·OCS, H2O·SO2, and H2O·SO3, in the electronic ground state. We have used the coupled cluster with singles, doubles, and perturbative triples ab initio method with a correlation consistent augmented triple-zeta basis set. We find that a counterpoise corrected optimization scheme is important for an accurate description of the geometries. These high level ab initio calculated geometries are of comparable quality to those obtained experimentally.",
	collection = "basis set superposition",
	doi = "10.1063/1.2357932",
	localfile = "basis set superposition/2006 - Counterpoise corrected geometries of hydrated complexes.pdf",
	year = 2006
}

@Article{2006-Guha-HHMRSWW,
	Author = "Rajarshi Guha and Michael T. Howard and Geoffrey R. Hutchison and Peter {Murray-Rust} and Henry Rzepa and Christoph Steinbeck and Jörg Wegner and Egon L. Willighagen",
	Title = "{The Blue {Obelisk–Interoperability} in Chemical Informatics}",
	Journal = "J. Chem. Inf. Model.",
	Volume = "46",
	Number = "3",
	Pages = "991–998",
	collection = "cheminformatics",
	doi = "10.1021/ci050400b",
	localfile = "cheminformatics/2006 - The Blue Obelisk - interoperability in chemical informatics.pdf",
	rating = "2",
	read = "2011-01-20",
	year = 2006
}

@Article{2006-Gupta-ZEBR,
	Author = "Suresh Gupta and Qingling Zhang and Todd Emrick and Anna C. Balazs and Thomas P. Russell",
	Title = "{Entropy-driven segregation of nanoparticles to cracks in multilayered composite polymer structures}",
	Journal = "Nature Mat.",
	Volume = "5",
	Pages = "229–234",
	abstract = "Multilayer composites, which combine ductile polymers with brittle ﬁlms, constitute vital components for optical communications, microelectronics and bio-engineering applications. However, crack formation is a critical problem in these materials; thus, designing layered systems that can respond to environmental changes and undergo self-healing is particularly important for a range of technologies. Here, nanoparticles dispersed in a polymer matrix were found to migrate to a crack generated at the interface between the polymer and a glassy layer. Segregation of the nanoparticles to the crack depended on both the enthalpic and entropic interactions between the polymer and nanoparticles. In particular, poly(ethylene oxide)-covered 5.2-nm spherical nanoparticles in a poly(methyl methacrylate) matrix diffused to cracks in the adjoining silicon oxide layer, whereas tri-n-octylphosphine oxide-covered nanoparticles did not. These results point to a simple means of fabricating systems that can self-heal, improving the durability of multilayered systems, or form the basis for auto-responsive materials.",
	collection = "polymer nanocomposites",
	keywords = "healing; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "polymer nanocomposites/2006 - Entropy-driven segregation of nanoparticles to cracks in multilayered composite polymer structures.pdf",
	year = 2006
}

@Article{2006-Hall-LFB,
	Author = "David M. Hall and Turab Lookman and Glenn H. Fredrickson and Sanjoy Banerjee",
	Title = "{Hydrodynamic self-consistent field theory for inhomogeneous polymer melts}",
	Journal = "Phys. Rev. Lett.",
	Volume = "97",
	Pages = "114501",
	abstract = "We introduce a mesoscale technique for simulating the structure and rheology of block-copolymer melts and blends in hydrodynamic ﬂows. The technique couples dynamic self-consistent ﬁeld theory with continuum hydrodynamics and ﬂow penalization to simulate polymeric ﬂuid ﬂows in channels of arbitrary geometry. We demonstrate the method by studying phase separation of an ABC triblock copolymer melt in a submicron channel with neutral wall wetting conditions. We ﬁnd that surface wetting effects and shear effects compete, producing wall-perpendicular lamellae in the absence of ﬂow and wall-parallel lamellae in cases where the shear rate exceeds some critical Weissenberg number.",
	archiveprefix = "arXiv",
	collection = "block copolymers",
	doi = "10.1103/PhysRevLett.97.114501",
	eprint = "cond-mat/0603769v2",
	keywords = "block copolymers; hydrodynamics; polymer blends; rheology",
	localfile = "block copolymers/2006 - Hydrodynamic self-consistent field theory for inhomogeneous polymer melts.pdf",
	methods = "HSCFT",
	primaryclass = "cond-mat.soft",
	rating = "2",
	year = 2006
}

@Article{2006-Haryono-Binder,
	Author = "Agus Haryono and Wolfgang H. Binder",
	Title = "{{Controlled arrangement of nanoparticle arrays in block-copolymer domains}tech}",
	Journal = "Small",
	Volume = "2",
	Number = "5",
	Pages = "600–611",
	Note = "Contains opinion that the technological application of BCP nanocomposites are in their infancy (quoted in my 2012 Soft Matter review).",
	abstract = "This review describes recent results on the precise spatial distribution control of metal and semiconductor nanoparticles into domains of microphase-separated block copolymers. Specific focus is directed towards selective incorporation into a specific microphase of a block copolymer. Details on theoretical aspects concerning nanoparticle incorporation as well as practical examples are given. Furthermore, examples on applications and technological aspects of the resulting nanoparticle/polymer nanocomposites are provided.",
	collection = "block copolymer nanocomposites",
	doi = "10.1002/smll.200500474",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2006 - Controlled arrangement of nanoparticle arrays in block-copolymer domains.pdf",
	rating = "2",
	type = "Review",
	year = 2006
}

@Article{2006-Hesselmann-JS,
	Author = "Andreas Heßelmann and Georg Jansen and Martin Schütz",
	Title = "{{Interaction energy contributions of {H}-bonded and stacked structures of the {AT} and {GC} {DNA} base pairs} from the combined density functional theory and intermolecular perturbation theory approach}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "128",
	Pages = "11730–11731",
	abstract = "In the past decade, we have seen a strong increase in the number of quantum chemical studies of the interaction between the purine and pyrimidine constituents of DNA.1-5 One of the goals of these studies is to provide as accurate as possible interaction energies for which, with a notable exception,6 there is hardly any experimental information available. Another important goal is to provide insight into the nature of the interactions between the nucleobases.",
	collection = "nucleic acid bases",
	doi = "10.1021/ja0633363",
	keywords = "hydrogen bonding; aromatic stacking",
	localfile = "nucleic acid bases/2006 - Interaction energy contributions of H-bonded and stacked structures of the AT and GC base pairs from the combined density functional theory and intermolecular perturbation theory approach.pdf",
	year = 2006
}

@Article{2006-Hill-PW,
	Author = "J. Grant Hill and James A. Platts and {Hans-Joachim} Werner",
	Title = "{Calculation of intermolecular interactions in the benzene dimer using coupled-cluster and local electron correlation methods}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "8",
	Number = "35",
	Pages = "4072",
	abstract = "Potential energy curves for the parallel-displaced, T-shaped and sandwich structures of the benzene dimer are computed with density fitted local second-order Møller–Plesset perturbation theory (DF-LMP2) as well as with the spin-component scaled (SCS) variant of DF-LMP2. While DF-LMP2 strongly overestimates the dispersion interaction, in common with canonical MP2, the DF-SCS-LMP2 interaction energies are in excellent agreement with the best available literature values along the entire potential energy curves. The DF-SCS-LMP2 dissociation energies for the three structures are also compared with new complete basis set estimates of the interaction energies obtained from accurate coupled cluster (CCSD(T)) and DF-SCS-MP2 calculations. Since LMP2 is essentially free of basis set superposition errors, counterpoise corrections are not required. As a result, DF-SCS-LMP2 is computationally inexpensive and represents an attractive method for the study of larger pi-stacked systems such as truncated sections of DNA.",
	collection = "stacking",
	doi = "10.1039/b608623c",
	localfile = "molecular stacking/2006 - Calculation of intermolecular interactions in the benzene dimer using coupled-cluster and local electron correlation methods.pdf",
	year = 2006
}

@Article{2006-Hobza-ZM,
	Author = "Pavel Hobza and Rudolf Zahradnik and Klaus {Muller-Dethlefs}",
	Title = "{The World of {Non-Covalent} Interactions: 2006}",
	Journal = "Coll. Czech. Chem. Comm.",
	Volume = "71",
	Number = "4",
	Pages = "443–531",
	abstract = "The review focusses on the fundamental importance of non-covalent interactions in nature by illustrating specific examples from chemistry, physics and the biosciences. Laser spectroscopic methods and both ab initio and molecular modelling procedures used for the study of non-covalent interactions in molecular clusters are briefly outlined. The role of structure and geometry, stabilization energy, potential and free energy surfaces for molecular clusters is extensively discussed in the light of the most advanced ab initio computational results for the CCSD(T) method, extrapolated to the CBS limit. The most important types of non-covalent complexes are classified and several small and medium size non-covalent systems, including H-bonded and improper H-bonded complexes, nucleic acid base pairs, and peptides and proteins are discussed with some detail. Finally, we evaluate the interpretation of experimental results in comparison with state of the art theoretical models: this is illustrated for phenol...Ar, the benzene dimer and nucleic acid base pairs. A review with 270 references.",
	collection = "molecular interactions",
	doi = "10.1135/cccc20060443",
	localfile = "molecular interactions/2006 - The world of non-covalent interactions: 2006.pdf",
	shorttitle = "The World of {Non-Covalent} Interactions",
	year = 2006
}

@Article{2006-Hooper-Schweizer,
	Author = "Justin B. Hooper and Kenneth S. Schweizer",
	Title = "{Theory of phase separation in polymer nanocomposites}",
	Journal = "Macromolecules",
	Volume = "39",
	Pages = "5133–5142",
	abstract = "The microscopic polymer reference interaction site model theory of polymer nanocomposites composed of flexible chains and spherical nanoparticles has been employed to study second virial coefficients and spinodal demixing over a wide range of interfacial chemistry, chain length, and particle size conditions. For hard fillers, two distinct phase separation behaviors, separated by a miscibility window, are generically predicted. One demixing curve occurs at relatively low monomer-particle attraction strength and corresponds to a very abrupt transition from an entropic depletion attraction-induced phase separated state to an enthalpically stabilized miscible fluid. The homogeneous mixture arises via a steric stabilization mechanism associated with the formation of thin, thermodynamically stable bound polymer layers around fillers. The second demixing transition occurs at relatively high monomer-particle adsorption energy and is inferred to involve the formation of an equilibrium physical network phase with local bridging of particles by polymers. This spinodal is sensitive to both particle-monomer diameter ratio and the spatial range of the interfacial attraction. The miscibility window narrows, and can ultimately disappear, with increasing polymer chain length, direct van der Waals attractions between fillers, and/or particle-monomer size asymmetry ratio. The implications of our results for the design of well-dispersed thermodynamically stable polymer nanocomposites, and the formation of nonequilibrium gels, are discussed.",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma060577m",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2006 - Theory of phase separation in polymer nanocomposites.pdf",
	year = 2006
}

@Article{2006-Horowitz-Hud,
	Author = "Eric D. Horowitz and Nicholas V. Hud",
	Title = "{Ethidium and Proflavine Binding to a {2‘,5‘-Linked} {RNA} Duplex}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "128",
	Number = "48",
	Pages = "15380–15381",
	abstract = "Despite over 40 years of physical investigations, fundamental questions persist regarding the energetics of {RNA} and {DNA} intercalation. The dramatic unwinding of a nucleic acid duplex upon intercalation immediately suggests that the nucleic acid backbone should play a significant role in dictating the free energy of intercalation. However, the contribution of the backbone to intercalation free energy is difficult to appreciate given the intertwined energetics associated with intercalation (e.g., pipi stacking and solvent effects). Fluorescence titrations were used to determine the association constants of two known intercalators, proflavine and ethidium, for duplex 2`,5`-linked {RNA.} Proflavine was found to bind 2`,5` {RNA} with an association constant 25-fold greater than that measured for standard, 3`,5`-linked {RNA.} In contrast, ethidium binds 2`,5` {RNA} less favorably than standard {RNA.}",
	collection = "nucleic acid intercalation",
	doi = "10.1021/ja065339l",
	localfile = "nucleic acid intercalation/2006 - Ethidium and proflavine binding to a 2',5'-linked RNA duplex.pdf",
	year = 2006
}

@Article{2006-Huang-BB,
	Author = "X. C. Huang and B. J. Braams and J. M. Bowman",
	Title = "{Ab initio potential energy and dipole moment surfaces of ({H}2{O})(2)}",
	Journal = "J. Phys. Chem. A",
	Volume = "110",
	Number = "2",
	Pages = "445 – 451",
	abstract = "A full-dimensional ab initio potential energy surface (PES) and dipole moment surface (DMS) are reported for the water dimer, (H2O)(2). The CCSD(T)-PES is a very precise fit to 19 805 ab initio energies obtained with the coupled-cluster (CCSD(T)) method, using an aug-cc-pVTZ basis. The standard Counterpoise correction was applied to approximately eliminate basis set superposition errors. The fit is based on an approach that incorporates the permutational symmetry of identical atoms [Huang, X.: Braams, B.; Bowman, J. M. J. Chem. Phys. 2005, 122, 044308]. The DMS is a fit to the dipole moment obtained with Møller–Plesset (MP2) theory, using an aug-cc-pVTZ basis. The PES has an RMS fitting error of 31 cm(-1) for energies below 20 000 cm-1, relative to the global minimum. This surface can describe various internal floppy motions, including various monomer inversions, and isomerization pathways. Ten characteristic stationary points have been located on the surface, four of which are transition structures and the rest are higher order saddle points. Their geometrical and vibrational properties are presented and compared with available previous theoretical work. The CCSD(T)-PES and MP2-DMS dissociate correctly (and symmetrically) to two H2O monomers, with D-e 1665.7 cm(-1) (19.93 kJ/mol). Accurate quantum calculations of the zero-point energy of the dimer (using diffusion Monte Carlo) and the monomers (using, a vibrational configuration interaction approach) are reported, and these together with D-e give a value of D-0 of 1042 cm(-1) (12.44 kJ/mol). A best estimated value is 1130 cm(-1) (13.5 kJ/mol).",
	collection = "hydrogen bonding",
	doi = "10.1021/jp053583d",
	localfile = "hydrogen bonding/2006 - Ab initio potential energy and dipole moment surfaces of (H2O)(2).pdf",
	year = 2006
}

@Article{2006-Ishikawa-MNAMHFTTKFTM,
	Author = "Takeshi Ishikawa and Yuji Mochizuki and Tatsuya Nakano and Shinji Amari and H. Mori and H. Honda and T. Fujita and H. Tokiwa and Shigenori Tanaka and Y. Komeiji and Kaori Fukuzawa and K. Tanaka and E. Miyoshi",
	Title = "{Fragment molecular orbital calculations on large scale systems containing heavy metal atom}",
	Journal = "Chem. Phys. Lett.",
	Volume = "427",
	Number = "1-3",
	Pages = "159 – 165",
	abstract = "We have realized a fully quantum mechanical treatment of large scale systems containing heavy metal atom, by introducing the model core potential (MCP) technique into the fragment molecular orbital (FMO) scheme. The scalar relativistic effects are incorporated by the use of MCP. This FMO/MCP method was applied to the divalent mercury ion hydrated, with 256 water molecules at the second-order Møller–Plesset (MP2) perturbation level. The complex between cisplatin and DNA was also calculated with MP2, where about a thousand of water molecules and dozens of sodium ions were employed for the explicit treatment of hydration. (c) 2006 Elsevier B.V. All rights reserved.",
	collection = "nucleic acid drugs",
	localfile = "nucleic acid drugs/2006 - Fragment molecular orbital calculations on large scale systems containing heavy metal atom.pdf",
	year = 2006
}

@Article{2006-Ishimura-PN,
	Author = "Kazuya Ishimura and Peter Pulay and Shigeru Nagase",
	Title = "{A new parallel algorithm of {MP2} energy calculations}",
	Journal = "J. Comp. Chem.",
	Volume = "27",
	Number = "4",
	Pages = "407–413",
	abstract = "A new parallel algorithm has been developed for second-order {Møller-Plesset} perturbation theory {(MP2)} energy calculations. Its main projected applications are for large molecules, for instance, for the calculation of dispersion interaction. Tests on a moderate number of processors (2-16) show that the program has high {CPU} and parallel efficiency. Timings are presented for two relatively large molecules, taxol {(C47H51NO14)} and luciferin {(C11H8N2O3S2),} the former with the {6-31G*} and {6-311G**} basis sets (1032 and 1484 basis functions, 164 correlated orbitals), and the latter with the {aug-cc-pVDZ} and {aug-cc-pVTZ} basis sets (530 and 1198 basis functions, 46 correlated orbitals). An {MP2} energy calculation on {C130H10} (1970 basis functions, 265 correlated orbitals) completed in less than 2 h on 128 processors.",
	collection = "quantum chemistry",
	doi = "10.1002/jcc.20348",
	keywords = "algorithms",
	localfile = "cheminformatics/2006 - A new parallel algorithm of MP2 energy calculations.pdf",
	methods = "MP2",
	year = 2006
}

@Article{2006-Jurecka-SCH,
	Author = "Petr Jurečka and Jiří Šponer and Jiří Černý and Pavel Hobza",
	Title = "{Benchmark database of accurate {(MP2} and {CCSD(T)} complete basis set limit) interaction energies of small model complexes, {DNA} base pairs, and amino acid pairs}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "8",
	Number = "17",
	Pages = "1985",
	abstract = "MP2 and CCSD(T) complete basis set (CBS) limit interaction energies and geometries for more than 100 DNA base pairs, amino acid pairs and model complexes are for the ﬁrst time presented together. Extrapolation to the CBS limit is done by using two-point extrapolation methods and diﬀerent basis sets (aug-cc-pVDZ – aug-cc-pVTZ, aug-cc-pVTZ – aug-cc-pVQZ, cc-pVTZ – cc-pVQZ) are utilized. The CCSD(T) correction term, determined as a diﬀerence between CCSD(T) and MP2 interaction energies, is evaluated with smaller basis sets (6-31G** and cc-pVDZ). Two sets of complex geometries were used, optimized or experimental ones. The JSCH-2005 benchmark set, which is now available to the chemical community, can be used for testing lower-level computational methods. For the ﬁrst screening the smaller training set (S22) containing 22 model complexes can be recommended. In this case larger basis sets were used for extrapolation to the CBS limit and also CCSD(T) and counterpoise-corrected MP2 optimized geometries were sometimes adopted.",
	collection = "molecular interactions",
	doi = "10.1039/b600027d",
	localfile = "molecular interactions/2006 - Benchmark database of accurate interaction energies of small model complexes, DNA base pairs, and amino acid pairs.pdf",
	year = 2006
}

@Article{2006-Kim-BHK,
	Author = "Bumjoon J. Kim and Joona Bang and Craig J. Hawker and Edward J. Kramer",
	Title = "{Effect of areal chain density on the location of polymer-modified gold nanoparticles in a block copolymer template}",
	Journal = "Macromolecules",
	Volume = "39",
	Pages = "4108–4114",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma060308w",
	keywords = "block copolymers; nanoparticle distribution; nanoparticle grafts; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2006 - Effect of areal chain density on the location of polymer-modified gold nanoparticles in a block copolymer template.pdf",
	methods = "TEM, gravimetry",
	rating = "2",
	read = "2012-03-21",
	systems = "Au-PS@PS-P2VP",
	year = 2006
}

@Article{2006-Kubar-HRH,
	Author = "Tomáš Kubař and Michal Hanus and Filip Ryjáček and Pavel Hobza",
	Title = "{Binding of cationic and neutral phenanthridine intercalators to a {DNA} oligomer is controlled by dispersion energy: quantum chemical calculations and molecular mechanics simulations}",
	Journal = "Chem. Eur. J.",
	Volume = "12",
	Number = "1",
	Pages = "280–290",
	abstract = "Correlated ab initio as well as semiempirical quantum chemical calculations and molecular dynamics simulations were used to study the intercalation of cationic ethidium, cationic 5-ethyl-6-phenylphenanthridinium and uncharged 3,8-diamino-6-phenyl-phenanthridine to DNA. The stabilization energy of the cationic intercalators is considerably larger than that of the uncharged one. The dominant energy contribution with all intercalators is represented by dispersion energy. In the case of the cationic intercalators, the electrostatic and charge-transfer terms are also important. The DG of ethidium intercalation to DNA was estimated at À4.5 kcal molÀ1 and this value agrees well with the experimental result. Of six contributions to the final free energy, the interaction energy value is crucial. The intercalation process is governed by the non-covalent stacking (including charge-transfer) interaction while the hydrogen bonding between the ethidium amino groups and the DNA backbone is less important. This is confirmed by the evaluation of the interaction energy as well as by the calculation of the free energy change. The intercalation affects the macroscopic properties of DNA in terms of its flexibility. This explains the easier entry of another intercalator molecule in the vicinity of an existing intercalation site.",
	collection = "nucleic acid intercalation",
	doi = "10.1002/chem.200500725",
	localfile = "nucleic acid intercalation/2006 - Binding of cationic and neutral phenanthridine intercalators to a DNA oligomer is controlled by dispersion energy: quantum chemical calculations and molecular mechanics simulations.pdf",
	shorttitle = "Binding of Cationic and Neutral Phenanthridine Intercalators to a {DNA} Oligomer Is Controlled by Dispersion Energy",
	year = 2006
}

@Article{2006-Lin-Schick,
	Author = "Chin-Yet Lin and M. Schick",
	Title = "{Self-consistent field study of the alignment by an electric field of a cylindrical phase of block copolymer}",
	Journal = "J. Chem. Phys.",
	Volume = "125",
	Pages = "034902",
	abstract = "Self-consistent ﬁeld theory is applied to a ﬁlm of cylindrical-forming block copolymer subject to a surface ﬁeld which tends to align the cylinders parallel to electrical plates, and to an external electric ﬁeld tending to align them perpendicular to the plates. The Maxwell equations and self-consistent ﬁeld equations are solved exactly, numerically, in real space. By comparing the free energies of different conﬁgurations, we show that for weak surface ﬁelds, the phase of cylinders parallel to the plates makes a direct transition to a phase in which the cylinders are aligned with the ﬁeld throughout the sample. For stronger surface ﬁelds, there is an intermediate phase in which cylinders in the interior of the ﬁlm, aligned with the ﬁeld, terminate near the plates. For surface ﬁelds which favor the minority block, there is a boundary layer of hexagonal symmetry at the plates in which the monomers favored by the surface ﬁeld occupy a larger area than they would if the cylinders extended to the surface.",
	collection = "block copolymers",
	doi = "10.1063/1.2214718",
	keywords = "block copolymers; electric fields",
	localfile = "block copolymers/2006 - Self-consitent field study of the alignment by an electric field of a cylindrical phase of block copolymer.pdf",
	methods = "SCFT",
	year = 2006
}

@Article{2006-Listak-Bockstaller,
	Author = "Jessica Listak and Michael R. Bockstaller",
	Title = "{Stabilization of grain boundary morphologies in lamellar block copolymer-nanoparticle blends}",
	Journal = "Macromolecules",
	Volume = "39",
	Pages = "5820–5825",
	Note = "Shows evidence of swelling high elastic energy grain boundary regions by selective PS-coated NPs in a deformed PS-PEP BCP.",
	abstract = "Polymer-coated nanoparticle additives are shown to stabilize the formation of high-energy tilt and twist grain boundary structures in amorphous lamellar block copolymer/nanoparticle blends. The distribution of the particle additives within the grain boundary region depends on the level of perturbation of the equilibrium structure and presents analogies to previously described block copolymer/homopolymer blends. At small tilt angles (chevron grain boundary) the particle distribution is equal to the equilibrium distribution (here: center location of PS-coated gold particles within the PS domains of a PS-PEP block copolymer) whereas at larger tilt angles (omega or T-junction grain boundary structure) the particles are found to selectively swell the high elastic energy regions along the grain boundary, thereby stabilizing the formation of otherwise energetically unfavorable grain boundary structures presumably through the relaxation of chains in the grain boundary region. The direct visualization of the swelling process provides the first experimental evidence for the mechanism of stabilization of energetically unfavorable grain boundary structures by selective swelling and stress relief that was previously postulated for block copolymer/homopolymer blends and presents a model system for comparison with theoretical predictions.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma060778q",
	keywords = "block copolymers; healing; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2006 - Stabilization of grain boundary morphologies in lamellar block copolymer-nanoparticle blends.pdf",
	methods = "TGA, NMR, TEM",
	systems = "Au-PS@PS-PEP",
	year = 2006
}

@Article{2006-Lo-LWT,
	Author = "Chieh-Tsung Lo and Byeongdu Lee and Randall E. Winans and Pappanan Thiyagarajan",
	Title = "{Effect of dispersion of inorganic nanoparticles on the phase behavior of block copolymer in a selective solvent}",
	Journal = "Macromolecules",
	Volume = "39",
	Pages = "6318–6320",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma060879o",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2006 - Effect of dispersion of inorganic nanoparticles on the phase behavior of block copolymer in a selective solvent.pdf",
	methods = "SANS",
	rating = "2",
	read = "2012-03-21",
	systems = "Au-PS@PS-P2VP",
	year = 2006
}

@Article{2006-Lochan-Head-Gordon,
	Author = "Rohini C. Lochan and Martin Head-Gordon",
	Title = "{Computational studies of molecular hydrogen binding affinities: The role of dispersion forces, electrostatics, and orbital interactions}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "8",
	Number = "12",
	Pages = "1357",
	abstract = "Intermolecular interactions between H2 and ligands, metals, and metal–ligand complexes determine the binding aﬃnities of potential hydrogen storage materials (HSM), and thus their extent of potential for practical use. A brief survey of current activity on HSM is given. The key issue of binding strengths is examined from a basic perspective by surveying the distinct classes of interactions (dispersion, electrostatics, orbital interactions) in ﬁrst a general way, and then in the context of calculated binding aﬃnities for a range of model systems.",
	collection = "hydrogen sorption",
	doi = "10.1039/b515409j",
	localfile = "hydrogen sorption/2006 - Computational studies of molecular hydrogen binding affinitiesL the role of dispersion forces, electrostatics, and orbital interactions.pdf",
	shorttitle = "Computational studies of molecular hydrogen binding affinities",
	year = 2006
}

@Article{2006-Lyakhova-ZS,
	Author = "Kateryna S. Lyakhova and Andrei V. Zvelindovsky and G. J. Agur Sevink",
	Title = "{Kinetic Pathways of {Order-to-Order} Phase Transitions in Block Copolymer Films under an Electric Field}",
	Journal = "Macromolecules",
	Volume = "39",
	Number = "8",
	Pages = "3024–3037",
	abstract = "We study kinetic pathways of phase transitions in thin films of block copolymers subjected to an applied electric field by means of dynamic self-consistent-field calculations. We consider structures ranging from spheres to lamellae. We find that the kinetic pathway taken by a system near a phase transition is very different from the one far from a phase transition.",
	collection = "block copolymers",
	doi = "10.1021/ma060143r",
	keywords = "block copolymers; electric fields; mesophase transitions; thin films",
	localfile = "block copolymers/2006 - Kinetic pathways of order-to-order phase transitions in block copolymer films under an electric field.pdf",
	methods = "DDFT",
	year = 2006
}

@Article{2006-Matsen,
	Author = "Mark W. Matsen",
	Title = "{Undulation instability in block-copolymer lamellae subjected to a perpendicular electric field}",
	Journal = "Soft Matter",
	Volume = "2",
	Pages = "1048–1056",
	collection = "block copolymers",
	doi = "10.1039/b611064a",
	keywords = "block copolymers; electric fields",
	localfile = "block copolymers/2006 - Undulation instability in block-copolymer lamellae subjected to a perpendicular electric field.pdf",
	year = 2006
}

@Article{2006-Matta-Bader,
	Author = "Richard F. W. Bader and Chérif F. Matta",
	Title = "{An Experimentalist's Reply to 'What is an atom in a molecule?'}",
	Journal = "J. Phys. Chem. A",
	Volume = "110",
	Pages = "6365–6371",
	abstract = "Parr, Ayers and Nalewajski have opined in this Journal that the concept of an atom in a molecule “is an object knowable by the mind or intellect, not by the senses.” This view is countered by the two hundred years of experimental chemistry underlying the realization that the properties of some total system are the sum of its atomic contributions. This paper concludes that an experimentalist has no doubt but that he or she is measuring the properties of atoms when performing an experiment.",
	collection = "molecular fragmentation",
	doi = "10.1021/jp060761",
	localfile = "molecular fragmentation/2006 - An experimentalist's reply to 'What is an atom in a molecule?'.pdf",
	year = 2006
}

@Article{2006-Moniruzzaman-Winey,
	Author = "Mohammad Moniruzzaman and Karen I. Winey",
	Title = "{Polymer nanocomposites containing carbon nanotubes}",
	Journal = "Macromolecules",
	Volume = "39",
	Pages = "5194–5205",
	abstract = "We review the present state of polymer nanocomposites research in which the fillers are single-wall or multiwall carbon nanotubes. By way of background we provide a brief synopsis about carbon nanotube materials and their suspensions. We summarize and critique various nanotube/polymer composite fabrication methods including solution mixing, melt mixing, and in situ polymerization with a particular emphasis on evaluating the dispersion state of the nanotubes. We discuss mechanical, electrical, rheological, thermal, and flammability properties separately and how these physical properties depend on the size, aspect ratio, loading, dispersion state, and alignment of nanotubes within polymer nanocomposites. Finally, we summarize the current challenges to and opportunities for efficiently translating the extraordinary properties of carbon nanotubes to polymer matrices in hopes of facilitating progress in this emerging area.",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma060733p",
	keywords = "fullerenes; polymer nanocomposites",
	localfile = "polymer nanocomposites/2006 - Polymer nanocomposites containing carbon nanotubes.pdf",
	type = "Review",
	year = 2006
}

@Article{2006-Pachucki-Komasa,
	Author = "Krzysztof Pachucki and Jacek Komasa",
	Title = "{Radiative correction to the helium dimer interaction energy}",
	Journal = "J. Chem. Phys.",
	Volume = "124",
	Number = "6",
	collection = "molecular interactions",
	doi = "10.1063/1.2166017",
	localfile = "molecular interactions/2006 - Radiative correction to the helium dimer interaction energy.pdf",
	size = "4 p.",
	year = 2006
}

@Article{2006-Panek-WLL,
	Author = "Jarosław J. Panek and Piotr K. Wawrzyniak and Zdzisław Latajka and Jan Lundell",
	Title = "{Interaction energy decomposition analysis for formic acid complexes with argon and krypton atoms}",
	Journal = "Chem. Phys. Lett.",
	Volume = "417",
	Pages = "100–104",
	collection = "molecular interactions",
	doi = "10.1016/j.cplett.2005.09.129",
	localfile = "molecular interactions/2006 - Interaction energy decomposition analysis for formic acid complexes with argon and krypton atoms.pdf",
	year = 2006
}

@Article{2006-Park-CPH,
	Author = "Moon Jeung Park and Kookheon Char and Jongnam Park and Taeghwan Hyeon",
	Title = "{Effect of the casting solvent on the morphology of poly(styrene-b-isoprene) diblock copolymer-magnetic nanoparticle mixtures}",
	Journal = "Langmuir",
	Volume = "22",
	Number = "4",
	Pages = "1375–1378",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/la052218a",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2006 - Effect of the casting solvent on the morphology of poly(styrene-b-isoprene) diblock copolymer and magnetic nanoparticle mixtures.pdf",
	methods = "SAXS, TEM, DSC",
	rating = "2",
	read = "2012-03-21",
	year = 2006
}

@Article{2006-Perlovsky,
	Author = "Leonid I. Perlovsky",
	Title = "{Toward physics of the mind: concepts, emotions, consciousness, and symbols}",
	Journal = "Physics of Life Reviews",
	Volume = "3",
	Pages = "23–55",
	collection = "neuroscience",
	keywords = "creativity",
	localfile = "neuroscience/2006 - Toward physics of the mind: concepts, emotions, consciousness, and symbols.pdf",
	read = "2013-08-01",
	year = 2006
}

@Article{2006-Pinna-ZTG,
	Author = "Marco Pinna and Andrei V. Zvelindovsky and S. Todd and G. Goldbeck-Wood",
	Title = "{Cubic phases of block copolymers under shear and electric fields by cell dynamics simulation. I. Spherical phase}",
	Journal = "J. Chem. Phys.",
	Volume = "125",
	Pages = "154905",
	abstract = "Cell dynamics simulation is used to investigate pathways of sphere-to-cylinder transition in block copolymer melt under applied simple shear ﬂow and electric ﬁeld. Both ﬁelds can induce the transition when their strength is above some critical value. At weak ﬁelds the spherical phase is preserved, with spheres being deformed into ellipsoids. Weak shear ﬂow is found to improve order in the spherical phase. Observed sliding of layers of spheres under shear is very similar to the experimental ﬁnding by Hamley et al. J. Chem. Phys. 108, 6929 1998 . The kinetic pathways are sensitive to the degree of microphase separation in the system and hence affected by temperature. The details of the pathways are described by means of Minkowski functionals.",
	collection = "block copolymers",
	doi = "10.1063/1.2356468",
	localfile = "block copolymers/2006 - Cubic phases of block copolymers under shear and electric fields by cell dynamics simulations. I. Spherical phase.pdf",
	year = 2006
}

@Article{2006-Poater-SB,
	Author = "Jordi Poater and Miquel Sola and F. Matthias Bickelhaupt",
	Title = "{A model of the chemical bond must be rooted in quantum mechanics, provide insight, and possess predictive power}",
	Journal = "Chem. Eur. J.",
	Volume = "12",
	Pages = "2902–2905",
	abstract = "In this response to the preceding paper by Bader, we show that the core arguments and statements presented in the latter are flawed. We argue that it is insufficient for a model of the chemical bond to be rooted in quantum mechanics.",
	collection = "molecular structure",
	doi = "10.1002/chem.200600057",
	localfile = "molecular structure/2006 - A model of the chemical bond must be rooted in quantum mechanics, provide insight and possess predictive power.pdf",
	year = 2006
}

@Article{2006-Pryamitsyn-Ganesan,
	Author = "Victor Pryamitsyn and Venkat Ganesan",
	Title = "{Origins of linear viscoelastic behavior of polymer-nanoparticle composites}",
	Journal = "Macromolecules",
	Volume = "39",
	Pages = "844–856",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma051841z",
	localfile = "polymer nanocomposites/2006 - Origins of linear viscoelastic behavior of polymer-nanoparticle composites.pdf",
	year = 2006
}

@Article{2006-Pryamitsyn-Ganesan-1,
	Author = "Victor Pryamitsyn and Venkat Ganesan",
	Title = "{Strong segregation theory of block copolymer-nanoparticle composites}",
	Journal = "Macromolecules",
	Volume = "39",
	Pages = "8499–8510",
	Note = "Shows that lammellae contract for nonselective NPs in diblock lammellae.",
	abstract = "We present strong segregation approximation based analytical calculations and complementary computer simulation results on the ordering and structural characteristics of block copolymer-nanoparticle mixtures. We consider specifically the case of a symmetric block copolymer organized in a lamella phase, which is mixed with both selective and nonselective nanoparticles. We present results within the strong segregation approximation quantifying the density distribution of nanoparticles and the influence of the nanoparticles upon the lamella thickness and their elastic constants. The case of nonselective nanoparticles is treated in detail to account more accurately for both size effects and finite concentrations of nanoparticles. The latter results suggest the possibility of layer instabilities and morphological transitions resulting from the surfactant-like role of nonselective particles. Qualitative features of our model predictions are in agreement with our computer simulation results.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma0613382",
	keywords = "block copolymers; mechanical properties; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2006 - Strong segregation theory of block copolymer-nanoparticle composites.pdf",
	methods = "SST, DPD",
	year = 2006
}

@Article{2006-Qian-Krimm,
	Author = "Weili Qian and Samuel Krimm",
	Title = "{Charge density treatment of the molecule-charge interaction and its relation to the electrical component of hydrogen bonding: accuracy and distance dependence}",
	Journal = "J. Mol. Struct.",
	Volume = "766",
	Pages = "93–104",
	abstract = "In a previous paper [J. Phys. Chem. A 109 (2005) 5608], we developed a charge density treatment of the electrical interaction between a molecule and point charges, which was applied to the electrical component of the hydrogen-bond interaction in donor-molecule/acceptor-charge model systems. This approach has two important advantages: it is very accurate by avoiding the deﬁciencies of multipole treatments, and it provides a complete electrostatic, polarization, and hyperpolarization description of interaction forces as well as energies. In this paper, we present a more general treatment of the theory and an extended demonstration of the physical accuracy of this approach, and we explore the geometric dependence of the parameters of this treatment (charge density, linearly and non-linearly induced charge density, and their derivatives) for a series of ﬂuoromethane molecules interacting with a two-site FH. We ﬁnd that, for variation in linear separation along the C–H/F–H line, these parameters are very well represented by a arKb dependence, a and b being constants. For a large number of conﬁgurations, the relative rms between the predicted energies and atomic forces and the ab initio calculated values is w3–5\%. This study opens the way to a more complete description of the three-dimensional characterization of these parameters.",
	collection = "hydrogen bonding",
	doi = "10.1016/j.theochem.2006.03.044",
	localfile = "hydrogen bonding/2006 - Charge density treatment of the molecule-charge interaction and its realtion to the electrical component of hydrogen bonding: accuracy and distance dependence.pdf",
	year = 2006
}

@Article{2006-Rafat-Popelier,
	Author = "Michel Rafat and Paul L. A. Popelier",
	Title = "{A convergent multipole expansion for 1,3 and 1,4 Coulomb interactions}",
	Journal = "J. Chem. Phys.",
	Volume = "124",
	Number = "14",
	Pages = "144102–7",
	collection = "molecular electrostatics",
	doi = "10.1063/1.2186993",
	keywords = "multipole expansion",
	localfile = "molecular electrostatics/2006 - A convergent multipole expansion for 1,3 and 1,4 Coulomb interactions.pdf",
	year = 2006
}

@Article{2006-Rafat-SP,
	Author = "Michel Rafat and Majeed Shaik and Paul L. A. Popelier",
	Title = "{Transferability of Quantum Topological Atoms in Terms of Electrostatic Interaction Energy}",
	Journal = "J. Phys. Chem. A",
	Volume = "110",
	Number = "50",
	Pages = "13578–13583",
	abstract = "Understanding atomic transferability is important to guide the design of a force field. Atoms in molecules are defined and computed according to the theory of quantum chemical topology {(QCT).} The electron density associated with such topological atoms is conveniently described by high-rank multipole moments. Here, we assess the transferability of atoms by means of their electrostatic interaction energy, using a convergent multipole expansion. The test systems are {(H2O)3} and {serine...(H2O)5.} The effect of a varying electron density cutoff (i.e., truncating the atoms) is discussed and the effect of polarization is quantified.",
	collection = "molecular fragmentation",
	doi = "10.1021/jp0652190",
	localfile = "molecular fragmentation/2006 - Transferability of quantum topological atoms in terms of electrostatic interaction energy.pdf",
	year = 2006
}

@Article{2006-Ren-Ma,
	Author = "Chun-lai Ren and Yu-quang Ma",
	Title = "{Phase behavior in thin films of confined colloid-polymer mixtures}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "128",
	Pages = "2733–2737",
	abstract = "Using self-consistent-field and density-functional theories, we first investigate colloidal self-assembly of colloid-polymer films confined between two soft surfaces grafted by polymers. With increasing colloidal concentrations, the film undergoes a series of transitions from disordered liquid –> sparse square –> hexagonal (or mixed square-hexagonal) –> dense square –> cylindrical structures in a plane, which results from the competition between the entropic elasticity of polymer brushes and the steric packing effect of colloidal particles. A phase diagram displays the stable regions of different in-layer ordering structures as the colloidal concentration is varied and layering transitions as the polymer-grafted density is decreased. Our results show a new control mechanism to stabilize the ordering of structures within the films.",
	collection = "polymer nanocomposites",
	doi = "10.1021/ja057569q",
	keywords = "thin films; polymer nanocomposites",
	localfile = "polymer nanocomposites/2006 - Phase behavior in thin films of confined colloid-polymer mixtures.pdf",
	year = 2006
}

@Article{2006-Rutledge-CHW,
	Author = "Lesley R. Rutledge and Lachlan S. {Campbell-Verduyn} and Ken C. Hunter and Stacey D. Wetmore",
	Title = "{Characterization of {Nucleobase−Amino} Acid Stacking Interactions Utilized by a {DNA} Repair Enzyme}",
	Journal = "J. Phys. Chem. B",
	Volume = "110",
	Number = "39",
	Pages = "19652–19663",
	abstract = "The present work characterizes the gas-phase stacking interactions between four aromatic amino acid residues (histidine, phenylalanine, tyrosine, and tryptophan) and adenine or 3-methyladenine due to the proposed utilization of these interactions by enzymes that repair {DNA} alkylation damage. The {MP2} potential energy surfaces of the stacked dimers are considered as a function of four variables (vertical displacement, angle of rotation, horizontal displacement, and tilt angle) using a variety of basis sets. It is found that the maximum stacking interaction energy decreases with the amino acid according to {TRP} {\textgreater} {TYR} {HIS} {\textgreater} {PHE} for both nucleobases. However, the magnitude of the stacking interaction significantly increases upon alkylation (by 50115\%). Comparison of the stacking energies calculated using our surface scans to those estimated from experimental crystal structures indicates that the stacking interactions within the active site of 3-methyladenine {DNA} glycosylase can account for 6575\% of the maximum possible stacking interaction between the relevant molecules. The decrease in stacking in the crystal structure arises due to significant differences in the relative orientations of the nucleobase and amino acid. Nevertheless, alkylation is found to significantly increase the stacking energy when the crystal structure geometries are considered. Our calculations provide computational support for suggestions that alkylation enhances the stacking interactions within the active site of {DNA} repair enzymes, and they give a measure of the magnitude of this enhancement. Our results suggest that alkylation likely plays a more important role in substrate identification and removal than the nature of the aromatic amino acid that interacts with the substrate via stacking interactions.",
	collection = "nucleic acid bases",
	doi = "10.1021/jp061939v",
	localfile = "nucleic acid bases/2006 - Characterization of nucleobase - amino acid stacking interactions utilized by a DNA repair enzyme.pdf",
	year = 2006
}

@Article{2006-Sides-KKF,
	Author = "Scott W. Sides and Bumjoon J. Kim and Edward J. Kramer and Glenn H. Fredrickson",
	Title = "{Hybrid particle-field simulations of polymer nanocomposites}",
	Journal = "Phys. Rev. Lett.",
	Volume = "96",
	Pages = "250601",
	Note = "Introduces the HPF method, and compares a 2D model to PS-b-P2VP with PS-coated Au nanoparticles.",
	abstract = "We present a theoretical framework and computer simulation methodology for investigating the equilibrium structure and properties of mesostructured polymeric ﬂuids with embedded colloids or nanoparticles. The method is based on a ﬁeld-theoretic description of the ﬂuid in which particle coordinates and chemical potential ﬁeld variables are simultaneously updated. The ﬂuid model can contain polymers of arbitrary chemical and architectural complexity, along with particles of all shapes, sizes, and surface treatments. Simulation results are compared with experiments conducted on polystyrene (PS)-functionalized Au nanoparticles in a PS-P2VP diblock copolymer melt.",
	collection = "block copolymer nanocomposites",
	doi = "10.1103/PhysRevLett.96.250601",
	keywords = "block copolymers; mesophase transitions; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2006 - Hybrid particle-field simulations of polymer nanocomposites.pdf",
	methods = "SCFT/BD",
	systems = "Au-PS@PS-P2VP",
	year = 2006
}

@Article{2006-Sinnokrot-Sherrill,
	Author = "Mutasem Omar Sinnokrot and C. David Sherrill",
	Title = "{High-accuracy quantum mechanical studies of π-π interactions in benzene dimers}",
	Journal = "J. Phys. Chem. A",
	Volume = "110",
	Pages = "10656–10668",
	collection = "molecular stacking",
	doi = "10.1021/jp0610416",
	keywords = "benzene",
	localfile = "molecular stacking/2006 - High-accuracy quantum mechanical studies of pi-pi interactions in benzene dimers.pdf",
	methods = "CCSD(T), MP2",
	systems = "benzene dimer",
	year = 2006
}

@Article{2006-Sponer-JMLOH,
	Author = "Jiří Šponer and Petr Jurečka and Ivan Marchan and F. Javier Luque and M. Orozco and Pavel Hobza",
	Title = "{Nature of base stacking: reference quantum-checmial stacking energies in ten unique {B-DNA} base pair steps}",
	Journal = "Chem. Eur. J.",
	Volume = "12",
	Pages = "2854–2865",
	collection = "stacking",
	doi = "10.1002/chem.200501239",
	localfile = "molecular stacking/2006 - Nature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps.pdf",
	year = 2006
}

@Article{2006-Spontak-SBKHSBR,
	Author = "Richard J. Spontak and Ravi Shankar and Michelle K. Bowman and Arjun S. Krishnan and Mark W. Hamersky and Jon Samseth and Michael R. Bockstaller and Kim O. Rasmussen",
	Title = "{Selectivity- and size-induced segregation of molecular and nanoscale species in microphase-ordered triblock copolymers}",
	Journal = "Nano Lett.",
	Volume = "6",
	Number = "9",
	Pages = "2115–2120",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/nl061205u",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2006 - Selectivity- and size-induced segregation of molecular and nanoscale species in microphase-ordered triblock copolymers.pdf",
	methods = "SCFT",
	rating = "2",
	read = "2012-03-21",
	year = 2006
}

@Article{2006-Sun-JLYW,
	Author = "Ya-Sen Sun and U-Ser Jeng and Keng S. Liang and Siao-Wei Yeh and Kung-Hwa Wei",
	Title = "{Transitions of domain ordering and domain size in a spherical-forming polystyrene-block-poly(ethylene oxide) copolymer and its composites with colloidal cadmium sulfide quantum dots}",
	Journal = "Polymer",
	Volume = "47",
	Pages = "1101–1107",
	Note = "Shows changes in PS-b-SE thermal stability and morphology at high temperatures after loading the PEO phase with CdS quantum dots.",
	abstract = "With speciﬁc annealing schemes applied to a neat polystyrene-block-poly(ethylene oxide) (SE) and its composites with cadmium sulﬁde quantum dots (CdS QD), we have observed microdomain structures and phase transitions in the system using temperature-resolved small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM). Both TEM images and SAXS results show clearly that incorporation of surfactant-tethered CdS QD preferentially into PEO blocks leads to increases in thermal stabilities of both bcc-packed lattice (referred as long-range order) and microdomains themselves in the sphere-forming SE/CdS composites. The bcc-packed lattice in the SE/CdS composites sustains better than that in the neat SE, during a temperature elevation to w160 8C, at which the bcc-packed SE/CdS spheres start to transform into micelles with a short-range liquid-like order. Quantitative model analysis shows that the PEO/CdS micelles can retain their size in the SE/CdS composites up to 200C, whereas the PEO micelles shrink after the softening of the PS matrix around 100 8C, and disassociate largely into the PS matrix of the neat SE at 160C.",
	collection = "block copolymer nanocomposites",
	doi = "10.1016/j.polymer.2005.12.055",
	keywords = "block copolymers; mesophase transitions; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2006 - Transition of domain ordering and domain size in a spherical-forming polystyrene-block-poly(ethylene oxide) copolymer and its composites with colloidal cadmium sulfide quantum dots.pdf",
	methods = "SAXS, TEM",
	systems = "CdS@PS-PEO",
	year = 2006
}

@Article{2006-Surve-PG,
	Author = "Megha Surve and Victor Pryamitsyn and Venkat Ganesan",
	Title = "{Nanoparticles in solutions of adsorbing polymers: pair interactions, percolation, and phase behavior}",
	Journal = "Langmuir",
	Volume = "22",
	Pages = "969–981",
	collection = "polymer nanocomposites",
	doi = "10.1021/la052422y",
	localfile = "polymer nanocomposites/2006 - Nanoparticles in solutions of adsorbing polymers: pair interactions, percolation, and phase behavior.pdf",
	year = 2006
}

@Article{2006-Swenson-JD,
	Author = "D Swenson and H Jaeger and C Dykstra",
	Title = "{Clustering of molecular hydrogen around benzene}",
	Journal = "Chem. Phys.",
	Volume = "326",
	Number = "2-3",
	Pages = "329–334",
	abstract = "Clustering of H2 molecules around benzene shows a number of interesting features that are important for understanding the interaction of hydrogen with certain materials. Clustering has been studied by ab initio calculations and by the development of a model potential. Ab initio calculations were carried out for several representative slices of the interaction potential surface for rigid H2 and benzene. A very concise functional form of the interaction potential surface was found, and this model potential was used to understand attachment patterns and predict energetics of clusters with up to 20 hydrogen molecules.",
	collection = "hydrogen sorption",
	doi = "10.1016/j.chemphys.2006.02.009",
	keywords = "benzene",
	localfile = "hydrogen sorption/2006 - Clustering of molecular hydrogen around benzene.pdf",
	year = 2006
}

@Article{2006-Tarzia-DGPTRLPMKP,
	Author = "Giorgio Tarzia and Andrea Duranti and Giuseppe Gatti and Giovanni Piersanti and Andrea Tontini and Silvia Rivara and Alessio Lodola and Pier Vencenzo Plazzi and Marco Mor and Satish Kathuria and Daniele Piomelli",
	Title = "{Synthesis and Structure–Activity Relationships of FAAH Inhibitors: Cyclohexylcarbamic Acid Biphenyl Esters with Chemical Modulation at the Proximal Phenyl Ring}",
	Journal = "ChemMedChem",
	Volume = "1",
	Pages = "130–139",
	abstract = "Fatty acid amide hydrolase (FAAH) is a serine hydrolase that catalyzes the intracellular hydrolysis of fatty acid ethanolamides such as anandamide and oleoylethanolamide. Targeting this enzyme may have important therapeutic potentials owing to the multiple physiological roles of these amides. Cyclohexylcarbamic acid biphenyl-3-yl ester (URB524) was one of the most promising FAAH inhibitors so far described. We report the modulation of the electronic and steric features of the proximal phenyl ring of this compound by introducing a series of substituents at the ortho and para positions. pIC50 values were found to correlate with molecular features thought to be involved in the recognition step such as steric hindrance and hydrogen-bonding ability. Derivatives with small polar groups at the para position of the proximal phenyl ring were slightly better FAAH inhibitors than the parent compound URB524.",
	collection = "enzymes",
	doi = "10.1002/cmdc.200500017",
	localfile = "enzymes/2006 - Synthesis and structure-activity relationships of FAAH inhibitors: cyclohyxelcarbamic acid biphenyl esters wth chemical modulation at the proximal pheny lring.pdf",
	systems = "FAAH",
	year = 2006
}

@Article{2006-Tsori-ALS,
	Author = "Yoav Tsori and David Andelman and Chin-Yet Lin and M. Schick",
	Title = "{Block copolymers in electric fields: a comparison of single-mode and self-consistent-field approximations}",
	Journal = "Macromolecules",
	Volume = "39",
	Pages = "289–293",
	collection = "block copolymers",
	doi = "10.1021/ma051715v",
	keywords = "block copolymers; electric fields",
	localfile = "block copolymers/2006 - Block copolymers in electric fields: a comparison of single-mode and self-consistent-field approximations.pdf",
	methods = "SCFT",
	rating = "2",
	read = "2012-01-25",
	year = 2006
}

@Article{2006-Tubert-Brohman-AJ,
	Author = "Ivan {Tubert-Brohman} and Orlando Acevedo and William L. Jorgensen",
	Title = "{Elucidation of Hydrolysis Mechanisms for Fatty Acid Amide Hydrolase and Its {Lys142Ala} Variant via {QM/MM} Simulations}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "128",
	Number = "51",
	Pages = "16904–16913",
	abstract = "Fatty acid amide hydrolase {(FAAH)} is a serine hydrolase that degrades anandamide, an endocannabinoid, and oleamide, a sleep-inducing lipid, and has potential applications as a therapeutic target for neurological disorders. Remarkably, {FAAH} hydrolyzes amides and esters with similar rates; however, the normal preference for esters reemerges when Lys142 is mutated to alanine. To elucidate the hydrolysis mechanisms and the causes behind this variation of selectivity, mixed quantum and molecular mechanics {(QM/MM)} calculations were carried out to obtain free-energy profiles for alternative mechanisms for the enzymatic hydrolyses. The methodology features free-energy perturbation calculations in Monte Carlo simulations with {PDDG/PM3} as the {QM} method. For wild-type {FAAH,} the results support a mechanism, which features proton transfer from Ser217 to Lys142, simultaneous proton transfer from Ser241 to Ser217, and attack of Ser241 on the substrate's carbonyl carbon to yield a tetrahedral intermediate, which subsequently undergoes elimination with simultaneous protonation of the leaving group by a {Lys142-Ser217} proton shuttle. For the {Lys142Ala} mutant, a striking multistep sequence is proposed with simultaneous proton transfer from Ser241 to Ser217, attack of Ser241 on the carbonyl carbon of the substrate, and elimination of the leaving group and its protonation by Ser217. Support comes from the free-energy results, which well reproduce the observation that the {Lys142Ala} mutation in {FAAH} decreases the rate of hydrolysis for oleamide significantly more than for methyl oleate.",
	collection = "enzymes",
	doi = "10.1021/ja065863s",
	localfile = "enzymes/2006 - Elucidation of hydrolysis mechanisms for fatty acid amide hydrolase and its Lys142Ala variant via QMMM simulations.pdf",
	year = 2006
}

@Article{2006-Vanommerlaeghe-MLTG,
	Author = "K. Vanommeslaeghe and Pierre Mignon and Stefan Loverix and D. Tourwe and Paul Geerlings",
	Title = "{Influence of Stacking on the Hydrogen Bond Donating Potential of Nucleic Bases}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "2",
	Pages = "1444–1452",
	collection = "nucleic acid bases",
	doi = "10.1021/ct600150n",
	localfile = "nucleic acid bases/2006 - Influence of stacking on the hydrogen bond donating potential of nucleic bases.pdf",
	year = 2006
}

@Article{2006-Warshel-SKXLO,
	Author = "Arieh Warshel and Pankaz K. Sharma and Mitsunori Kato and Yun Xiang and Hanbin Liu and Mats H. M. Olsson",
	Title = "{Electrostatic basis for enzyme catalysis}",
	Journal = "Chem. Rev.",
	Volume = "106",
	Pages = "3210–3235",
	abstract = "(Excerpt) Enzymatic reactions play a fundamentally important role in controlling and performing most life processes. Thus, understanding how enzymes work has both fundamental and practical importance. In this respect it is crucial to understand what is the origin of the enormous catalytic power of enzymes, which remains one of the challenges of modern biophysics. Although many elements of this puzzle were elucidated by biochemical and structural studies, the source of the catalytic power of enzymes has not been widely understood and, clearly, has not been agreed upon by the scientific community. The current consensus is sometimes reduced to statements such as, “the enzyme binds the transition state stronger than the ground state” or “the catalytic groups are perfectly oriented”. However, such statements are not sufficient to explain this catalytic power since the real question is how this differential binding is accomplished and what are the actual catalytic groups.",
	collection = "enzymes",
	doi = "10.1021/cr0503106",
	localfile = "enzymes/2006 - Electrostatic basis for enzyme catalysis.pdf",
	year = 2006
}

@Article{2006-Wei-JYFL,
	Author = "Chunying Wei and Guoqing Jia and Jingli Yuan and Zhaochi Feng and Can Li",
	Title = "{A Spectroscopic Study on the Interactions of Porphyrin with {G-Quadruplex} {DNAs†}}",
	Journal = "Biochemistry",
	Volume = "45",
	Number = "21",
	Pages = "6681–6691",
	abstract = "Free-base porphyrin {(5,10,15,20-tetrakis(1-methyl-4-pyridyl)-21H,23H-porphine)} {(H2TMPyP4)} has been shown to be an effective telomerase inhibitor by an in vitro assay. Here, we examined the interactions of the {H2TMPyP4} with three distinct G-quadruplex {DNAs,} the parallel-stranded {(TG4T)4,} dimer-hairpin-folded {(G4T4G4)2,} and monomer-folded {AG3(T2AG3)3,} by ultraviolet resonance Raman spectroscopy {(UVRR),} {UVvis} absorption spectroscopy, fluorescence spectroscopy, and surface-enhanced Raman spectroscopy {(SERS).} The data obtained by the continuous variation titration method show that the binding stoichiometry of {H2TMPyP4/G-quadruplex} is 2:1 for {(TG4T)4} and 4:1 for {(G4T4G4)2} or {AG3(T2AG3)3.} The results of {SERS} spectra, {UVvis} absorption titration, and fluorescence emission spectra together with the binding stoichiometries reveal that two {H2TMPyP4} molecules are externally stacked at two ends of the parallel {(TG4T)4} G-quadruplex, whereas {H2TMPyP4} molecules can intercalate within their diagonal or lateral loop regions and intervals between two G-tetrads for {(G4T4G4)2} and {AG3(T2AG3)3} G-quadruplexes. The binding of {H2TMPyP4} to {(TG4T)4} G-quadruplex results in the hypochromicity of the {UV} Raman signal of {(TG4T)4,} indicating that the stacking effects between {H2TMPyP4} and {DNA} bases are significant. The Raman hyperchromicities and shifts are observed after the binding of {H2TMPyP4} to both {(G4T4G4)2} and {AG3(T2AG3)3} G-quadruplexes. This indicates that the intercalative {H2TMPyP4} can lengthen the vertical distance between adjacent G-tetrads of {(G4T4G4)2} and {AG3(T2AG3)3} and change their conformations. The present study provides new insights into the effect of {H2TMPyP4} binding on the structures of G-quadruplexes and also demonstrates that Raman spectroscopy is an ideal method for examining the interaction between drugs and G-quadruplexes.",
	collection = "nucleic acid drugs",
	doi = "10.1021/bi052356z",
	localfile = "nucleic acid drugs/2006 - A spectroscopic study on the interactions of porphyrin with G-quadruplex DNAs.pdf",
	year = 2006
}

@Article{2006-Wu,
	Author = "Jianzhong Wu",
	Title = "{Density functional theory for chemical engineering: from capillarity to soft materials}",
	Journal = "AIChE Journal",
	Volume = "52",
	Number = "3",
	Pages = "1169–1193",
	abstract = "Understanding the microscopic structure and macroscopic properties of condensed matter from a molecular perspective is important for both traditional and modern chemical engineering. A cornerstone of such understanding is provided by statistical mechanics, which bridges the gap between molecular events and the structural and physiochemical properties of macro- and mesoscopic systems. With ever-increasing computer power, molecular simulations and ab initio quantum mechanics are promising to provide a nearly exact route to accomplishing the full potential of statistical mechanics. However, in light of their versatility for solving problems involving multiple length and timescales that are yet unreachable by direct simulations, phenomenological and semiempirical methods remain relevant for chemical engineering applications in the foreseeable future. Classical density functional theory offers a compromise: on the one hand, it is able to retain the theoretical rigor of statistical mechanics and, on the other hand, similar to a phenomenological method, it demands only modest computational cost for modeling the properties of uniform and inhomogeneous systems. Recent advances are summarized of classical density functional theory with emphasis on applications to quantitative modeling of the phase and interfacial behavior of condensed ﬂuids and soft materials, including colloids, polymer solutions, nanocomposites, liquid crystals, and biological systems. Attention is also given to some potential applications of density functional theory to material fabrications and biomolecular engineering.",
	collection = "statistical mechanics",
	doi = "10.1002/aic.10713",
	localfile = "statistical mechanics/2006 - Density functional theory for chemical engineering: from capillarity to soft materials.pdf",
	type = "Review",
	year = 2006
}

@Article{2006-Xu-NS,
	Author = "Yan Xu and Yuki Noguchi and Hiroshi Sugiyama",
	Title = "{The new models of the human telomere {d[AGGG(TTAGGG)3]} in K+ solution}",
	Journal = "Bioorg. Med. Chem.",
	Volume = "14",
	Number = "16",
	Pages = "5584–5591",
	abstract = "The human telomeric sequence d[AGGG (TTAGGG)(3)] has been found to form different types of G-quadruplex structures. NMR revealed that in Na+ solution this 22 nucleotide (nt) sequence exhibits an antiparallel structure, whereas crystallographic studies in the presence of K+ showed a dramatically different parallel structure. The structure of this 22 nt sequence in the presence of K+ has drawn intense interest as the intracellular K+ concentration is greater than that of Na+. However, the question of the type of structure for the 22 nt telomeric sequence in K+ solution remains open. In this study, we substituted the Gs in the sequence with 8-bromoguanine and examined the resultant structures and thermal stabilities by circular dichroism (CD) spectroscopy. The results suggest that the 22 nt in K+ solution exists as a mixture of mixed-parallel/antiparallet and chair-type G-quadruplex. To date, the exact structure of human telomeric G-quadruplex in K+ solution is extremely controversial. The present study provides valuable information for understanding the discrepancies between the crystal and solution studies. We discuss the possible implications of the structure in understanding higher-order telomeric DNA structure and T-loop formation.",
	collection = "nucleic acids",
	doi = "10.1016/j.bmc.2006.04.033",
	localfile = "nucleic acids/2006 - The new models of the human telomere d[AGGG(TTAGGG)3] in K+ solution.pdf",
	year = 2006
}

@Article{2006-Yoon-Sneddon,
	Author = "Chang Won Yoon and Larry G. Sneddon",
	Title = "{Ammonia Triborane: A Promising New Candidate for {Amineborane-Based} Chemical Hydrogen Storage}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "128",
	Number = "43",
	Pages = "13992–13993",
	abstract = "(Excerpt) Because of their high hydrogen densities, boron based compounds, including especially sodium borohydride (NaBH4)1 and ammonia borane (NH3BH3),2 are now being intensely investigated as chemical hydrogen storage materials that can release hydrogen by hydrolytic processes.",
	collection = "hydrogen sorption",
	doi = "10.1021/ja064526g",
	localfile = "hydrogen sorption/2006 - Ammonia triborane: a promising new candidate for amineborane-based chemical hydrogen storage.pdf",
	shorttitle = "Ammonia Triborane",
	year = 2006
}

@Article{2007-Agapito-CS,
	Author = "Filipo Agapito and Benedito J. Costa Cabral and José A. Martinho Simoes",
	Title = "{A cost-efective basis-set extrapolation scheme: application to the energetics of homolytic bond dissociation}",
	Journal = "J. Mol. Struct.",
	Volume = "811",
	Pages = "361–372",
	abstract = "A composite procedure based on density functional theory (DFT) geometry optimizations and coupled cluster calculations with single and double excitations and perturbative treatment of triple excitations (CCSD(T)) is proposed for the evaluation of homolytic bond dissociation enthalpies (BDEs). The performance of several functionals for predicting the structure and vibrational frequencies of a selected set of closed- and open-shell species was investigated. By using the correlation consistent cc-pVTZ basis-set, it was found that B3LYP and VSXC geometries are in good agreement with experiment. B3LYP/cc-pVTZ geometries were then selected for CCSD(T) single-point energy calculations. The Hartree-Fock (HF) contribution to the total energy was estimated at the HF/cc-pV6Z level and also by using a (x = D(2),T(3),Q(4),5,6) ad hoc extrapolation. Complete basis-set values for CCSD(T) correlation energies were evaluated through dual (x, x + 1;x = 2) extrapolation schemes relying on calculations with the cc-pVxZ basis-set. The results illustrate the importance of the extrapolation schemes and show that (2, 3) extrapolated BDEs are more accurate than those calculated with the cc-pV6Z basis-set.",
	collection = "basis set dependence",
	doi = "10.1016/j.theochem.2006.12.050",
	keywords = "basis set extrapolation",
	localfile = "basis set dependence/2007 - A cost-effective basis-set extrapolation scheme: application to the energetics of homolytic bond sisociation.pdf",
	year = 2007
}

@Article{2007-Al-Shahib-BG,
	Author = "Ali Al-Shahib and Rainer Breitling and David R. Gilbert",
	Title = "{Predicting protein function by machine learning on amino acid sequences - a critical evaluation}",
	Journal = "BMC Genomics",
	Volume = "8",
	Pages = "78",
	collection = "proteins",
	doi = "10.1186/1471-2164-8-78",
	keywords = "enzyme function prediction; machine learning",
	localfile = "proteins/2007 - Predicting protein function by machine learning on amino acid sequences - a critical evaluation.pdf",
	rating = "2",
	read = "2013-09-09",
	year = 2007
}

@Article{2007-Alexander-Katz-Fredrickson,
	Author = "Alfredo Alexander-Katz and Glenn H. Fredrickson",
	Title = "{Diblock copolymer thin films: a field-theoretic simulation study}",
	Journal = "Macromolecules",
	Volume = "40",
	Pages = "4075–4087",
	collection = "block copolymers",
	doi = "10.1021/ma070005h",
	keywords = "block copolymers; thin films",
	localfile = "block copolymers/2007 - Diblock copolymer thin films: a field-theoretic simulation study.pdf",
	methods = "FTS",
	year = 2007
}

@Article{2007-Bader,
	Author = "Richard F. W. Bader",
	Title = "{Everyman's Derivation of the Theory of Atoms in Molecules}",
	Journal = "J. Phys. Chem. A",
	Volume = "111",
	Number = "32",
	Pages = "7966–7972",
	abstract = "This paper demonstrates that it is straightforward to develop the theory of an atom in a moleculesthe extension of quantum mechanics to an open systemsby deriving the necessary equations of motion from Schrodinger’s equation, followed by a comparison of the predicted properties with experiment to determine the correct boundary condition. Although less fundamental than the variational derivation of the quantum theory of atoms in molecules, this heuristic approach makes the quantum mechanics of an atom in a molecule accessible to “everyman” possessing a knowledge of Schrodinger’s equation, aiding its general acceptance by experimental chemists.",
	collection = "quantum chemistry",
	doi = "10.1021/jp073213k",
	localfile = "quantum chemistry/2007 - Everyman's derivation of the theory of atoms in molecules.pdf",
	year = 2007
}

@Article{2007-Bader-HC,
	Author = "Richard F. W. Bader and Jesús Hernández-Trujillo and Fernando {Cortés-Guzmán}",
	Title = "{Chemical bonding: From Lewis to atoms in molecules}",
	Journal = "J. Comp. Chem.",
	Volume = "28",
	Number = "1",
	Pages = "4–14",
	abstract = "The Lewis electron pair concept and its role in bonding are recovered in the properties of the electron pair density and in the topology of the Laplacian of the electron density. These properties provide a bridge with the quantum mechanical description of bonding determined by the Feynman, Ehrenfest, and virial theorems, bonding being a consequence of the electrostatic forces acting within a molecular system.",
	collection = "quantum chemistry",
	doi = "10.1002/jcc.20528",
	localfile = "quantum chemistry/2007 - Chemical bonding: from Lewis to atoms in molecules.pdf",
	shorttitle = "Chemical bonding",
	year = 2007
}

@Article{2007-Bakowies,
	Author = "Dirk Bakowies",
	Title = "{Accurate extrapolation of electron correlation energies from small basis sets}",
	Journal = "J. Chem. Phys.",
	Volume = "127",
	Number = "16",
	Pages = "164109–12",
	abstract = "A new two-point scheme is proposed for the extrapolation of electron correlation energies obtained with small basis sets. Using the series of correlation-consistent polarized valence basis sets, cc-pVXZ, the basis set truncation error is expressed as EX X + i − . The angular momentum offset i captures differences in effective rates of convergence previously observed for ﬁrst-row molecules. It is based on simple electron counts and tends to values close to 0 for hydrogen-rich compounds and values closer to 1 for pure ﬁrst-row compounds containing several electronegative atoms. The formula is motivated theoretically by the structure of correlation-consistent basis sets which include basis functions up to angular momentum L = X − 1 for hydrogen and helium and up to L = X for ﬁrst-row atoms. It contains three parameters which are calibrated against a large set of 105 reference molecules H, C, N, O, F for extrapolations of MP2 and CCSD valence-shell correlation energies from double- and triple-zeta DT and triple- and quadruple-zeta TQ basis sets. The new model is shown to be three to ﬁve times more accurate than previous two-point schemes using a single parameter, and TQ extrapolations are found to reproduce a small set of available R12 reference data better than even 56 extrapolations using the conventional asymptotic limit formula EX X−3. Applications to a small selection of boron compounds and to neon show very satisfactory results as well. Limitations of the model are discussed.",
	collection = "basis set dependence",
	doi = "10.1063/1.2768359",
	localfile = "basis set dependence/2007 - Accurate extrapolation of electron correlation energies from small basis sets.pdf",
	year = 2007
}

@Article{2007-Bakowies-1,
	Author = "Dirk Bakowies",
	Title = "{Extrapolation of electron correlation energies to finite and complete basis set targets}",
	Journal = "J. Chem. Phys.",
	Volume = "127",
	Number = "8",
	Pages = "084105–23",
	abstract = "The electron correlation energy of two-electron atoms is known to converge asymptotically as L + 1 −3 to the complete basis set limit, where L is the maximum angular momentum quantum number included in the basis set. Numerical evidence has established a similar asymptotic convergence X−3 with the cardinal number X of correlation-consistent basis sets cc-pVXZ for coupled cluster singles and doubles CCSD and second order perturbation theory MP2 calculations of molecules. The main focus of this article is to probe for deviations from asymptotic convergence behavior for practical values of X by deﬁning a trial function X− that for an effective exponent = eff X , X + 1 , X + N provides the correct energy EX+N, when extrapolating from results for two smaller basis sets, EX and EX+1. This analysis is ﬁrst applied to “model” expansions available from analytical theory, and then to a large body of ﬁnite basis set results X = D , T , Q , 5 , 6 for 105 molecules containing H, C, N, O, and F, complemented by a smaller set of 14 molecules for which accurate complete basis set limits are available from MP2-R12 and CCSD-R12 calculations. eff is generally found to vary monotonically with the target of extrapolation, X + N, making results for large but ﬁnite basis sets a useful addition to the limited number of cases where complete basis set limits are available. Signiﬁcant differences in effective convergence behavior are observed between MP2 and CCSD valence correlation energies, between hydrogen-rich and hydrogen-free molecules, and, for He, between partial-wave expansions and correlation-consistent basis sets. Deviations from asymptotic convergence behavior tend to get smaller as X increases, but not always monotonically, and are still quite noticeable even for X = 5. Finally, correlation contributions to atomization energies rather than total energies exhibit a much larger variation of effective convergence behavior, and extrapolations from small basis sets are found to be particularly erratic for molecules containing several electronegative atoms. Observed effects are discussed in the light of results known from analytical theory. A carefully calibrated protocol for extrapolations to the complete basis set limit is presented, based on a single “optimal” exponent opt X , X + 1 , for the entire set of molecules, and compared to similar approaches reported in the literature.",
	collection = "basis set dependence",
	doi = "10.1063/1.2749516",
	localfile = "basis set dependence/2007 - Extrapolation of electron correlation energies to finite and complete basis set targets.pdf",
	year = 2007
}

@Article{2007-Barrientos-Sordo,
	Author = "C. Barrientos and Jóse A. Sordo",
	Title = "{On the application of the counterpoise correction for the basis set superposition error in geometry optimization calculations of molecular systems: some inconsistent results}",
	Journal = "Theor. Chem. Acc.",
	Volume = "118",
	Pages = "733–738",
	abstract = "It is shown that the conjecture that the total energy for a given molecular or supermolecular system is affected by basis set superposition error (BSSE) leads to inconsistent results. While the calculations of interaction energies, dissociation energies, or energy barriers depend on the fragments (reactants, products) involved in their definitions and, consequently, are affected by BSSE, the total energies of molecular or supermolecular systems do not depend on any virtual fragment partition and are, therefore, BSSE free. C1 Univ Valladolid, Fac Ciencias, Dept Quim Fis Inorgan, E-47005 Valladolid, Spain. Univ Oviedo, Fac Quim, Dept Quim Fis \& Analit, Lab Quim Computac, E-33006 Oviedo, Principado Astu, Spain.",
	collection = "basis set superposition",
	doi = "10.1007/s00214-007-0345-z",
	keywords = "basis set superposition error; counterpoise correction",
	localfile = "basis set superposition/2007 - On the application of the counterpoise correction for the basis set superposition error in geometry optimization calcualtions of molecular systems: some inconsistent results.pdf",
	year = 2007
}

@Article{2007-Bartlett-Musial,
	Author = "Rodney J. Bartlett and Monika Musiał",
	Title = "{Coupled-cluster theory in quantum chemistry}",
	Journal = "Rev. Mod. Phys.",
	Volume = "79",
	Number = "1",
	Pages = "291–352",
	abstract = "Today, coupled-cluster theory offers the most accurate results among the practical ab initio electronic-structure theories applicable to moderate-sized molecules. Though it was originally proposed for problems in physics, it has seen its greatest development in chemistry, enabling an extensive range of applications to molecular structure, excited states, properties, and all kinds of spectroscopy. In this review, the essential aspects of the theory are explained and illustrated with informative numerical results.",
	collection = "quantum chemistry",
	doi = "10.1103/RevModPhys.79.291",
	localfile = "quantum chemistry/2007 - Coupled-cluster theory in quantum chemistry.pdf",
	numpages = "61",
	year = 2007
}

@Article{2007-Baruss,
	Author = "Imants Baruss",
	Title = "{Franklin Wolff's mathematical resolution of existential issues}",
	Journal = "Journal of Scientific Exploration",
	Volume = "21",
	Number = "4",
	Pages = "751–756",
	abstract = "Just like anyone else, scientists can be troubled by existential questions such as “What is the purpose of life?” and “Why is there something instead of nothing?” One strategy for approaching such questions has been to suggest that a latent cognitive faculty needs to be activated in order to answer them. In effect, this means that a questioner needs to undergo a process of self-transformation leading to a transcendent state of consciousness in which such an ability is awakened. Franklin Wolff has proposed that there is a way of doing so, namely “mathematical yoga,” that is particularly suited for scientists. Such a spiritual practice consists of doing mathematics, while understanding what one is doing and maintaining a self-giving attitude. Although Wolff has attributed his own enlightenment to this mathematical path, it needs further empirical verification. Wolff s notions also suggest that, even without the occurrence of transcendent states of consciousness, abstract thinking could lead to states of consciousness characterized by greater than ordinary meaningfulness.",
	collection = "philosophy",
	localfile = "philosophy/2007 - Franklin Wolff's mathematical resolution of existential issues.pdf",
	year = 2007
}

@Article{2007-Borini-MRTABCEEMSS,
	Author = "S. Borini and A. Monari and E. Rossi and A. Tajti and C. Angeli and G.L. Bendazzoli and R. Cimiraglia and A. Emerson and S. Evangelisti and D. Maynau and J. Sanchez-Marin and P.G. Szalay",
	Title = "{FORTRAN Interface for Code Interoperability in Quantum Chemistry: The Q5Cost Library}",
	Journal = "J. Chem. Inf. Model.",
	Volume = "47",
	Pages = "1271–1277",
	collection = "cheminformatics",
	doi = "10.1021/ci7000567",
	localfile = "cheminformatics/2007 - FORTRAN interface for code interoperability in quantum chemistry.pdf",
	year = 2007
}

@Article{2007-Bukowski-SGA,
	Author = "Robert Bukowski and Krzysztof Szalewicz and Gerrit C. Groenenboom and Ad van der Avoird",
	Title = "{Predictions of the properties of water from first principles}",
	Journal = "Science",
	Volume = "315",
	Pages = "1249–1252",
	abstract = "A force field for water has been developed entirely from first principles, without any fitting to experimental data. it contains both pairwise and many-body interactions. This force field predicts the properties of the water dimer and of liquid water in excellent agreement with experiments, a previously elusive objective. Precise knowledge of the intermolecular interactions in water will facilitate a better understanding of this ubiquitous substance.",
	collection = "molecular interactions",
	keywords = "water; force fields; liquid state",
	localfile = "molecular interactions/2007 - Predictions of the properties of water from first principles.pdf",
	systems = "water dimer",
	year = 2007
}

@Article{2007-Cao-Wu,
	Author = "Dapeng Cao and Jianzhong Wu",
	Title = "{Density functional theory for a primitive model of nanoparticle-block copolymer mixtures}",
	Journal = "J. Chem. Phys.",
	Volume = "126",
	Number = "14",
	Pages = "144912",
	Note = "Description of density profiles of relatively short diblock BCPs containing relatively small NPs in a thin film.",
	abstract = "Amphiphilic block copolymers provide useful templates for fabrication of nanostructured materials that are appealing for a wide variety of applications. The preparation of polymer-particle hybrid materials requires a good understanding of the chemical nature and topology of the amphiphilic molecules as well as their interactions with the embedded nanoparticles. This article reports a density functional theory (DFT) for a coarse-grained model of block copolymer-nanoparticle mixtures that is able to account for the properties of particles and copolymers within a self-consistent framework. It predicts various well-organized structures that can be effectively controlled by adjusting the polymer chain length and polymer-particle interactions. Illustrative examples based on relatively short chains suggest that, in qualitative agreement with experiments, large particles tend to be excluded from a polymer brush near a solid substrate, whereas smaller particles may be dissolved. The DFT is able to capture the dispersion of large particles in the microdomain of block copolymer that is energetically favorable, but localization of smaller particles at the microdomain interfaces.",
	collection = "block copolymer nanocomposites",
	doi = "10.1063/1.2712442",
	keywords = "block copolymers; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2007 - Density functional theory for a primitive model of nanoparticle-block copolymer mixtures.pdf",
	methods = "DFT",
	year = 2007
}

@Article{2007-Chiba-FK,
	Author = "Mahito Chiba and Dmitri G. Fedorov and Kazuo Kitaura",
	Title = "{Time-dependent density functional theory with the multilayer fragment molecular orbital method}",
	Journal = "Chem. Phys. Lett.",
	Volume = "444",
	Number = "4-6",
	Pages = "346 – 350",
	abstract = "Time-dependent density functional theory (TDDFT) is combined with the multilayer fragment molecular orbital (FMO) method. The excitation energies of the system are estimated from those of its small active part, whereas the remaining part is described by its electron density distribution and the corresponding Coulomb field. The efficiency of this approach is illustrated on the lowest excitations of several solvated systems and phenylalanine-(alanine)(n). The full TDDFT excitation energies calculated are reproduced within 0.01 eV with LC-BLYP and the 6-31G* basis set.",
	collection = "molecular fragmentation",
	localfile = "molecular fragmentation/2007 - Time-dependent density functional theory with the multilayer fragment molecular orbital method.pdf",
	methods = "FMO, TDDFT",
	year = 2007
}

@Article{2007-Chiba-FK-1,
	Author = "Mahito Chiba and Dmitri G. Fedorov and Kazuo Kitaura",
	Title = "{Time-dependent density functional theory based upon the fragment molecular orbital method}",
	Journal = "J. Chem. Phys.",
	Volume = "127",
	Number = "10",
	Pages = "104108–11",
	abstract = "Time-dependent density functional theory TDDFT was combined with the two-body fragment molecular orbital method FMO2 . In this FMO2-TDDFT scheme, the system is divided into fragments, and the electron density for fragments is determined self-consistently. Consequently, only one main fragment of interest and several fragment pairs including it are calculated by TDDFT. To demonstrate the accuracy of FMO2-TDDFT, we computed several low-lying singlet and triplet excited states of solvated phenol and polyalanine using our method and the standard TDDFT for the full system. The BLYP functional with the long-range correction LC-BLYP was employed with the 6-31G* basis set some tests were also performed with 6-311G*, as well as with

license: MIT

license_type: permissive

extension: bib