text:
the nanoparticle dispersion, however, the morphology of these materials is many times uncontrolled, yielding isotropic nanofilled systems, not necessarily spatially “engineered, designed and tailored” materials. To impact high-technology applications requiring unique electrical, thermal, and optical properties, manufacturing techniques enabling control of the nanoparticle arrangement and distribution must be developed. This paper will examine the status of approaches for directing the hierarchical morphology of nanoparticle dispersions in three dimensions, and beyond uniaxial alignment, using examples from the literature to highlight the potential and issues. Ultimately, two general approaches to this challenge are emerging, namely, external-in (directed patterning of nanoparticle dispersions) and internal-out (mesophase assembly of nanoparticles).",
	collection = "polymer nanocomposites",
	doi = "10.1021/cm062693",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2007 - Polymer nanocomposites with prescribed morphology: going beyond nanoparticle-filled polymers.pdf",
	type = "Review",
	year = 2007
}

@Article{2007-Wu-Li,
	Author = "Jianzhong Wu and Zhidong Li",
	Title = "{Density-functional theory for complex fluids}",
	Journal = "Annu. Rev. Phys. Chem.",
	Volume = "58",
	Pages = "85–112",
	Note = "A thoughtful review packed with valuable references.",
	abstract = "Density-functional theory (DFT) and its variations provide a fruitful approach to the computational modeling of the microscopic structures and phase behavior of soft-condensed matter. The methodology takes deep root in quantum mechanics but shares a mathematical similarity with a number of classical approaches in statistical mechanics. This review discusses different strategies commonly used to formulate the free-energy functional of complex ﬂuids for either phenomena-oriented applications or as a generic description of the thermodynamic nonideality owing to various components of intermolecular forces. We emphasize the connections among different schemes of DFT approximations, their underlying assumptions, and inherent limitations. We also address extensions of equilibrium DFT to phenomenological theories for the dynamic properties of complex ﬂuids and for the kinetics of phase transitions. In addition, we highlight the recent literature concerning applications of DFT to diverse static and time-dependent phenomena in complex ﬂuids.",
	collection = "statistical mechanics",
	doi = "10.1146/annurev.physchem.58.032806.104650",
	localfile = "statistical mechanics/2007 - Density-functional theory for complex fluids.pdf",
	rating = "3",
	read = "2011-03-17",
	type = "Review",
	year = 2007
}

@Article{2007-Wu-ZWC,
	Author = "J. Y. Wu and J. C. Zhang and Z. X. Wang and W. L. Cao",
	Title = "{Theoretical study on intermolecular interactions in {B}r{F}/{H}n{X} adducts}",
	Journal = "Chem. Phys.",
	Volume = "338",
	Number = "1",
	Pages = "69 – 74",
	abstract = "Equilibrium geometries, interaction energies, and charge transfer for the intermolecular interactions between BrF and HnX (HF, H2O, and NH3) were studied at the MP2/6-311++G(3d,3p) level. The halogen-bonded geometry and hydrogen-bonded geometry are observed in these interactions. The calculated interaction energies show that the halogen-bonded structures are more stable than the corresponding hydrogen-bonded structures. To study the nature of the intermolecular interactions, symmetry-adapted perturbation theory (SAPT) calculations were carried out and the results indicate that the halogen bonding interactions are dominantly inductive energy in nature, while electrostatic energy governs the hydrogen bonding interactions. (C) 2007 Elsevier B.V. All rights reserved.",
	collection = "halogen bonding",
	doi = "10.1016/j.chemphys.2007.07.043",
	localfile = "halogen bonding/2007 - Theoretical study on intermolecular interactions in BrF-HnX adducts.pdf",
	year = 2007
}

@Article{2007-Zhang-LL,
	Author = "Liangshun Zhang and Jiaping Lin and Shaoliang Lin",
	Title = "{Self-assembly behavior of amphiphilic block copolymer-nanoparticle mixture in dilute solution studied by self-consistent-field theory and density functional theory}",
	Journal = "Macromolecules",
	Volume = "40",
	Pages = "5582–5592",
	Note = "Shows association and encapsulation of NPs in dilute solutions.",
	abstract = "A theoretical approach combining self-consistent-field theory (SCFT) for fluids and density functional theory (DFT) for particles was applied to investigate the self-assembly behavior of amphiphilic diblock copolymer/nanoparticle mixture in dilute solution. Two kinds of hydrophobic nanoparticles are studied: one is that the particles are selective to hydrophobic blocks but are incompatible with hydrophilic blocks, and the other is that the particles are nonselective to hydrophobic and hydrophilic blocks. For both cases, the self-association of amphiphilic block copolymer/nanoparticle mixture is observed, and the nanoparticles are spatially organized in the clusters. The aggregate morphologies can be tuned by the particle radius and particle volume fraction. For the selective particles, the aggregate morphologies of amphiphilic block copolymer/nanoparticle mixture can experience a transition from vesicles to mixture of circlelike and rod micelles as the particle radius and/or particle volume fraction increase. For the nonselective nanoparticles, the large compound micelles are produced instead of the vesicles. The large compound micelles transform to the mixture of large compound micelles and circle-like micelles with an increase in particle volume fraction and/or radius. The distribution of nanoparticles in the clusters is also affected by the particle radius and volume fraction. For both cases, when the values of nanoparticle radius and/or volume fraction are small, the nanoparticles are almost uniformly distributed in the cores of micelles. However, the particles tend to localize near the interfaces between the core and shell with increasing particle volume fraction and/or radius.",
	collection = "polymers",
	doi = "10.1021/ma070986y",
	keywords = "block copolymers; nanospheres; polymer mixtures",
	localfile = "polymers/2007 - Self-assembly behavior of amphiphilic block copolymer-nanoparticle mixture in dilute solution studied by self-consistent-field theory and density functional theory.pdf",
	year = 2007
}

@Article{2007-Zou-HEW,
	Author = "Shan Zou and Rui Hong and Todd Emrick and Gilbert C. Walker",
	Title = "{Ordered CdSe nanoparticles within self-assembled block copolymer domains on surfaces}",
	Journal = "Langmuir",
	Volume = "23",
	Pages = "1612–1614",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/la0629274",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2007 - Ordered CdSe nanoparticles within self-assembled block copolymer domains on surfaces.pdf",
	methods = "AFM, SEM",
	rating = "2",
	read = "2012-03-21",
	systems = "CdSe-PEO@PS-P2VP, CdSe-TOPO@PS",
	year = 2007
}

@Article{2008-Allegra-RV,
	Author = "Giuseppe Allegra and Guido Raos and Michele Vacatello",
	Title = "{Theories and simulations of polymer-based nanocomposites: from chain statistics to reinforcement}",
	Journal = "Prog. Polym. Sci.",
	Volume = "33",
	Pages = "683–731",
	abstract = "A survey of the present understanding of particle-ﬁlled polymers is presented, as obtained from either theoretical or computational approaches. We concentrate on composites in which the nanoparticles are either spherical or statistically isotropic aggregates, and the matrix is a homopolymer melt or a cross-linked elastomer. Recent progress has been prompted by the preparation and careful characterization of well-deﬁned model systems, as well as by theoretical developments and the application of computer simulation to increasingly realistic models. After an introduction providing the main motivations (Section 1), an overview of the basic phenomenology and recent experimental results is presented (Section 2), with special emphasis on the Payne effect and related aspects. In Section 3, we discuss results of equilibrium molecular dynamics and Monte Carlo simulations of polymer chains in the presence of nanoparticles. After a concise theoretical description, these are compared with those obtained from integral equation and density functional approaches (Section 4). The molecular origins of the inter-particle-depletion interaction are discussed, as well as the phase-separation diagram of the nanoparticle/polymer system. The related issue of polymer chains and networks compressed between planar surfaces is also dealt with. In Section 5 simulations and theories of polymer dynamics at the interface are discussed, with special emphasis on the effects of surface roughness and on the vicinity of the glass transition. In Section 6 the overall viscoelastic response of polymer nanocomposites is considered, both from the point of view of molecular-level simulations and of continuum mechanics approaches. The concluding remarks (Section 7) discuss some of the open challenges in the ﬁeld.",
	collection = "polymer nanocomposites",
	doi = "10.1016/j.progpolymsci.2008.02.003",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2008 - Theories and simulations of polymer-based nanocomposites: from chain statistics to reinforcement.pdf",
	type = "Review",
	year = 2008
}

@Article{2008-Antypov-Elliott,
	Author = "Dmytro Antypov and James A. Elliott",
	Title = "{Wang-Landau simulation of polymer-nanoparticle mixtures}",
	Journal = "Macromolecules",
	Volume = "41",
	Pages = "7243–7250",
	abstract = "The behavior of a coarse-grained polymer chain in the solution containing two types of interacting species is studied using a face-centered cubic lattice model. The majority component in our model represents the solvent, while the active low volume fraction component is regarded as reversibly adsorbing nanoparticles. Using a novel density-biased method, we calculate the complete phase diagram, which demonstrates the effect of addition of freely moving interactive centers on the equilibrium properties of a polymer chain immersed in either good or poor solvent. Three distinct collapsed and one extended phase are found, each phase comprising two regions with different polymeric degrees of freedom.",
	collection = "polymers",
	doi = "10.1021/ma8012652",
	keywords = "polymer mixtures; lattice model",
	localfile = "polymers/2008 - Wang-Landau simulation of polymer-nanoparticle mixtures.pdf",
	year = 2008
}

@Article{2008-Asturiol-DS,
	Author = "David Asturiol and Miquel Duran and Pedro Salvador",
	Title = "{Intramolecular basis set superposition error effects on the planarity of benzene and other aromatic molecules: A solution to the problem}",
	Journal = "J. Chem. Phys.",
	Volume = "128",
	Pages = "",
	abstract = "Recently, the surprising result that ab initio calculations on benzene and other planar arenes at correlated MP2, MP3, configuration interaction with singles and doubles (CISD), and coupled cluster with singles and doubles levels of theory using standard Pople's basis sets yield nonplanar minima has been reported. 'the planar optimized structures turn out to be transition states presenting one or more large imaginary frequencies, whereas single-determinant-based methods lead to the expected planar minima and no imaginary frequencies. It has been suggested that such anomalous behavior can be originated by two-electron basis set incompleteness error. In this work, we show that the reported pitfalls can be interpreted in terms of intramolecular basis set superposition error (BSSE) effects, mostly between the C-H moieties constituting the arenes. We have carried out counterpoise-corrected optimizations and frequency calculations at the Hartree-Fock, B3LYP, MP2, and CISD levels of theory With several basis sets for a number of arenes. In all cases, correcting for intramolecular BSSE fixes the anomalous behavior of the correlated methods, whereas no significant differences are observed in the single-determinant case. Consequently, all systems studied are planar at all levels of theory. The effect of different intramolecular fragment definitions and the particular case of charged species, namely, cyclopentadienyl and indenyl anions, respectively, are also discussed. (c) 2008 American Institute of Physics. C1 [Asturiol, David; Duran, Miquel; Salvador, Pedro] Univ Girona, Inst Quim Computac, Girona 17071, Spain. [Duran, Miquel; Salvador, Pedro] Univ Girona, Dept Quim, Girona 17071, Spain.",
	collection = "basis set superposition",
	doi = "10.1063/1.2902974",
	localfile = "basis set superposition/2008 - Intramolecular basis set superposition error effects on the planarity of benzene and other aromatic molecules: a solution to the problem.pdf",
	year = 2008
}

@Article{2008-Bader,
	Author = "Richard F. W. Bader",
	Title = "{Nearsightedness of electronic matter as seen by a physicist and a chemist}",
	Journal = "J. Phys. Chem. A",
	Volume = "112",
	Number = "51",
	Pages = "13717–13728",
	collection = "quantum chemistry",
	doi = "10.1021/jp806282j",
	localfile = "quantum chemistry/2008 - Nearsightedness of electronic matter as seen by a physicist and a chemist.pdf",
	methods = "AIM",
	year = 2008
}

@Article{2008-Barone-GGSLAB,
	Author = "Giampaolo Barone and Célia Fonseca Guerra and Noemi Gambino and Arturo Silvestri and Antonino Lauria and Anna Maria Almerico and F. Matthias Bickelhaupt",
	Title = "{Intercalation of daunomycin into stacked {DNA} base pairs. DFT study of an anticancer drug}",
	Journal = "J. Biomol. Struct. Dyn.",
	Volume = "26",
	Pages = "115–129",
	abstract = "We have computationally studied the intercalation of the antitumor drug daunomycin into six stacks of Watson-Crick DNA base pairs (i.e., AT-AT, AT-TA, GC-AT, CG-TA, GC-GC, GC-CG) using density functional theory (DFT). The proton affinity of the DNA intercalator daunomycin in water was computed to be 159.2 kcal/mol at BP86/TZ2P, which is in line with the experimental observation that daunomycin is protonated under physiological conditions. The intercalation interaction of protonated daunomycin with two stacked DNA base pairs was studied through a hybrid approach in which intercalation is treated at LDA/TZP while the molecular structure of daunomycin and hydrogen-bonded Watson-Crick pairs is computed at BP86/TZ2P. We find that the affinity of the drug for the six considered base pair dimers decreases in the order AT-AT > AT-TA > GC-AT > GC-TA > GC-CG > GC-GC, in excellent agreement with experimental data on the thermodynamics of the interaction between daunomycin and synthetic polynucleotides in aqueous solution. Our analyses show that the overall stability of the intercalation complexes comes mainly from π–π stacking but an important contribution to the computed and experimentally observed sequence specificity comes from hydrogen bonding between daunomycin and hetero atoms in the minor groove of AT base pairs.",
	collection = "nucleic acid intercalation",
	keywords = "intercalation; stacking",
	localfile = "nucleic acid intercalation/2008 - Intercalation of daunomycin into stacked DNA base pairs. DFT study of an anticancer drug.pdf",
	year = 2008
}

@Article{2008-Berg-Arean,
	Author = "{A. W. C. van den} Berg and C. O. Arean",
	Title = "{Materials for hydrogen storage: current research trends and perspectives}",
	Journal = "Chem. Commun.",
	Number = "6",
	Pages = "668",
	collection = "hydrogen sorption",
	doi = "10.1039/b712576n",
	localfile = "hydrogen sorption/2007 - Materials for hydrogen storage: current research trends and perspectives.pdf",
	shorttitle = "Materials for hydrogen storage",
	year = 2008
}

@Article{2008-Bludsky-RS,
	Author = "Ota Bludský and Miroslav Rubeš and Pavel Soldán",
	Title = "{Ab initio investigation of intermolecular interactions in solid benzene}",
	Journal = "Phys. Rev. B",
	Volume = "77",
	Number = "9",
	Pages = "092103",
	abstract = "A computational strategy for the evaluation of the crystal lattice constants and cohesive energy of the weakly bound molecular solids is proposed. The strategy is based on the high level ab initio coupled-cluster determination of the pairwise additive contribution to the interaction energy. The zero-point-energy correction and nonadditive contributions to the interaction energy are treated using density functional methods. The experimental crystal lattice constants of the solid benzene are reproduced, and the value of 480 meV/molecule is calculated for its cohesive energy.",
	collection = "stacking",
	doi = "10.1103/PhysRevB.77.092103",
	localfile = "molecular stacking/2008 - Ab initio investigation of intermolecular interactions in solid benzene.pdf",
	year = 2008
}

@Article{2008-Bludsky-RSN,
	Author = "Ota Bludský and Miroslav Rubeš and Pavel Soldán and Petr Nachtigall",
	Title = "{Investigation of the benzene-dimer potential energy surface: {DFT/CCSD(T)} correction scheme}",
	Journal = "J. Chem. Phys.",
	Volume = "128",
	Number = "11",
	Pages = "114102",
	abstract = "A novel method, designated as the density functional theory/coupled-cluster with single and double and perturbative triple excitation [DFT/CCSD(T)] correction scheme, was developed for precise calculations of weakly interacting sp(2) hydrocarbon molecules and applied to the benzene dimer. The DFT/CCSD(T) interaction energies are in excellent agreement with the estimated CCSD(T)/complete basis set interaction energies. The tilted T-shaped structure having C-s symmetry was determined to be a global minimum on the benzene-dimer potential energy surface (PES), approximately 0.1 kcal/mol more stable than the parallel-displaced structure. A fully optimized set of ten stationary points on the benzene-dimer PES is proposed for the evaluation of the reliability of methods for the description of weakly interacting systems.",
	collection = "stacking",
	doi = "10.1063/1.2890968",
	localfile = "molecular stacking/2008 - Investigation of the benzene dimer potential energy surface: DFT-CCSD(T) correction scheme.pdf",
	methods = "CCSD(T)",
	shorttitle = "Investigation of the benzene-dimer potential energy surface",
	year = 2008
}

@Article{2008-Brown-MMA,
	Author = "D. Brown and V. Marcadon and P. Mele and N. D. Alberola",
	Title = "{Effect of filler particle size on the properties of model nanocomposites}",
	Journal = "Macromolecules",
	Volume = "41",
	Pages = "1499–1511",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma701940j",
	keywords = "nanospheres; polymer nanocomposites",
	localfile = "polymer nanocomposites/2008 - Effect of filler particle size on the properties of model nanocomposites.pdf",
	year = 2008
}

@Article{2008-Cabria-LA,
	Author = "I. Cabria and M. J. Lopez and J. A. Alonso",
	Title = "{Hydrogen storage capacities of nanoporous carbon calculated by density functional and {Møller–Plesset} methods}",
	Journal = "Phys. Rev. B",
	Volume = "78",
	Number = "7",
	Pages = "075415–9",
	collection = "hydrogen sorption",
	doi = "10.1103/PhysRevB.78.075415",
	localfile = "hydrogen sorption/2008 - Hydrogen storage capacities of nanporous carbon calculated by density functional and Moller-Plesset methods.pdf",
	year = 2008
}

@Article{2008-Cates-Clegg,
	Author = "Michael E. Cates and Paul S. Clegg",
	Title = "{Bijels: a new lcass of soft materials}",
	Journal = "Soft Matter",
	Volume = "4",
	Pages = "2132–2138",
	collection = "jamming",
	doi = "10.1039/b807312k",
	keywords = "jamming; suspensions",
	localfile = "jamming/2008 - Bijels: a new class of soft materials.pdf",
	type = "Highlight",
	year = 2008
}

@Article{2008-Chai-Buriak,
	Author = "Jinan Chai and Jilian M. Buriak",
	Title = "{Using cylindrical domains of block copolymers to self-assemble and align metallic nanowires}",
	Journal = "ACS Nano",
	Volume = "2",
	Number = "3",
	Pages = "489–501",
	abstract = "Block copolymer thin ﬁlms can be used as soft templates for a wide range of surfaces where large area patterns of nanoscale features are desired. The cylindrical domains of acid-sensitive, self-assembled monolayers of polystyrene poly(2-vinylpyridine) block copolymers on silicon surfaces were utilized as structural elements for the production of parallel metal nanowires. Metal ion loading of the P2VP block with simple aqueous solutions of anionic metal complexes is accomplished via protonation of this basic block, rendering it cationic; electrostatic attraction leads to a high local concentration of metal complexes within the protonated P2VP domain. A subsequent brief plasma treatment simultaneously removes the polymer and produces metallic nanowires. The morphology of the patterns can modulated by controlling solution concentration, deposition time, and molecular weight of the block copolymers, as well as other factors. Horizontal metallic nanoarrays can be aligned on e-beam lithographically deﬁned silicon substrates within different shapes, via graphoepitaxy. This method is highly versatile as the procedures to manipulate nanowire composition, dimension, spacing, and orientation are straightforward and based upon efﬁcient aqueous inorganic chemistry.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/nn700341s",
	keywords = "alignment; block copolymers; nanowires; thin films",
	localfile = "block copolymer nanocomposites/2008 - Using cylindrical domains of block copolymers to self-assemble and align metallic nanowires.pdf",
	methods = "XPS, AFM, SEM, Auger",
	systems = "Pt(wires)@PS-P2VP",
	year = 2008
}

@Article{2008-Cian-LDTTRM,
	Author = "Anne De Cian and Laurent Lacroix and Céline Douarre and Nassima {Temime-Smaali} and Chantal Trentesaux and {Jean-François} Riou and {Jean-Louis} Mergny",
	Title = "{Targeting telomeres and telomerase}",
	Journal = "Biochimie",
	Volume = "90",
	Number = "1",
	Pages = "131–155",
	abstract = "Telomeres and telomerase represent, at least in theory, an extremely attractive target for cancer therapy. The objective of this review is to present the latest view on the mechanism(s) of action of telomerase inhibitors, with an emphasis on a specific class of telomere ligands called G-quadruplex ligands, and to discuss their potential use in oncology.",
	collection = "nucleic acid drugs",
	doi = "10.1016/j.biochi.2007.07.011",
	localfile = "nucleic acid drugs/2008 - Targeting telomeres and telomerase.pdf",
	year = 2008
}

@Article{2008-Cooper-TPSLL,
	Author = "Valentino R. Cooper and Timo Thonhauser and Aaron Puzder and Elsebeth Schröder and Bengt I. Lundqvist and David C. Langreth",
	Title = "{Stacking Interactions and the twist of {DNA}}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "130",
	Number = "4",
	Pages = "1304–1308",
	abstract = "The importance of stacking interactions for the Twist and stability of DNA is investigated using the fully ab initio van der Waals density functional (vdW-DF).(1,2) Our results highlight the role that binary interactions between adjacent sets of base pairs play in defining the sequence-dependent Twists observed in high-resolution experiments. Furthermore, they demonstrate that additional stability gained by the presence of thymine is due to methyl interactions with neighboring bases, thus adding to our understanding of the mechanisms that contribute to the relative stability of DNA and RNA. Our mapping of the energy required to twist each of the 10 unique base pair steps should provide valuable information for future studies of nucleic acid stability and dynamics. The method introduced will enable the nonempirical theoretical study of significantly larger pieces of DNA or DNA/amino acid complexes than previously possible.",
	collection = "stacking",
	doi = "10.1021/ja0761941",
	localfile = "molecular stacking/2008 - Stacking interactions and the twist of DNA.pdf",
	year = 2008
}

@Article{2008-Copeland-AFCT,
	Author = "Kari L. Copeland and Julie A. Anderson and Adam R. Farley and James R. Cox and Gregory S. Tschumper",
	Title = "{Probing {Phenylalanine/Adenine} {π-Stacking} Interactions in Protein Complexes with Explicitly Correlated and {CCSD(T)} Computations}",
	Journal = "J. Phys. Chem. B",
	Volume = "112",
	Number = "45",
	Pages = "14291–14295",
	abstract = "To examine the effects of pi-stacking interactions between aromatic amino acid side chains and adenine bearing ligands in crystalline protein structures, 26 toluene/(N9-methyl)adenine model configurations have been constructed from protein/ligand crystal structures. Full geometry optimizations with the MP2 method cause the 26 crystal structures to collapse to six unique structures. The complete basis set (CBS) limit of the CCSD(T) interaction energies has been determined for all 32 structures by combining explicitly correlated MP2-R12 computations with a correction for higher-order correlation effects from CCSD(T) calculations. The CCSD(T) CBS limit interaction energies of the 26 crystal structures range from -3.19 to -6.77 kcal mol(-1) and average -5.01 kcal mol(-1). The CCSD(T) CBS limit interaction energies of the optimized complexes increase by roughly 1.5 kcal mol(-1) on average to -6.54 kcal mol(-1) (ranging from -5.93 to -7.05 kcal mol(-1)). Corrections for higher-order correlation effects are extremely important for both sets of structures and are responsible for the modest increase in the interaction energy after optimization. The MP2 method overbinds the crystal structures by 2.31 kcal mol(-1) on average compared to 4.50 kcal mol(-1) for the optimized structures.",
	collection = "stacking",
	doi = "10.1021/jp805528v",
	keywords = "aromatic stacking",
	localfile = "molecular stacking/2008 - Probing phenylalanine-adenine stacking interactions in protein complexes with explicitly correlated and CCSD(T) computations.pdf",
	year = 2008
}

@Article{2008-Cysewski-CZC,
	Author = "Piotr Cysewski and Żaneta Czyżnikowska and Robert Zaleśny and Przemyslaw Czeleń",
	Title = "{The {post-SCF} quantum chemistry characteristics of the guanine–guanine stacking {B-DNA}}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "10",
	Number = "19",
	Pages = "2665",
	abstract = "The stacking interactions of two guanine molecules were analyzed detail at the DF-MP2/aug-ccpVDZ level of theory for conformations appearing B-DNA. The dependence of intermolecular interaction energies on the pairs of step parameters (shift, slide, rise, tilt, roll and twist) was determined. The values of these parameters were chosen to cover the whole range of variability appearing crystallographic data. The scanning procedure was performed by subsequent changes of two variables with fixed values of the remaining base-pair and base-step BDNA parameters. Additionally, the hybrid variational-perturbational scheme was applied for the decomposition of the interaction energy into physically meaningful contributions at the MP2 level of theory. The significant impact of the mutual orientations of guanine bases was observed not only on the total intermolecular energy but also on its components. The second-order dispersion interaction is the most significant contribution to stabilization energy and is about eight times larger compared to the first-order electrostatic term with relaxation effects, which is also of stabilizing character. The dispersion interactions may vary up to 9.6 kcal mol(-1) between different guanine-guanine conformations. The parameters de. ning the mutual orientation of stacked guanine molecules have a different impact on the stabilization of the investigated complex. The following base-step parameters have only a minor impact on the stabilization energies: shift-slide, shift-roll, shift-twist, slide-twist and roll-twist. On the other hand, parameters such as rise and tilt significantly influence intermolecular interactions, i.e. strong attraction occurs only for a limited range of their values.",
	collection = "stacking",
	doi = "10.1039/b718635e",
	localfile = "molecular stacking/2008 - The post-SCF quantum chemistry characteristics of the guanine-guanine stacking in B-DNA.pdf",
	year = 2008
}

@Article{2008-Darley-HP,
	Author = "Michael G. Darley and Chris M. Handley and Paul L. A. Popelier",
	Title = "{Beyond Point Charges: Dynamic Polarization from Neural Net Predicted Multipole Moments}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "4",
	Number = "9",
	Pages = "1435–1448",
	collection = "molecular electrostatics",
	doi = "10.1021/ct800166r",
	localfile = "molecular electrostatics/2008 - Beyond point charges: dynamic polarization from neural net predicted multipole moments.pdf",
	shorttitle = "Beyond Point Charges",
	year = 2008
}

@Article{2008-Dean-Ghemawat,
	Author = "Jeffrey Dean and Sanjay Ghemawat",
	Title = "{MapReduce: simplified data processing on large clusters}",
	Journal = "Commun. ACM",
	Volume = "51",
	Number = "1",
	Pages = "107–113",
	collection = "informatics",
	doi = "10.1145/1327452.1327492",
	keywords = "big data",
	localfile = "informatics/2008 - MapReduce: simplified data processing on large clusters.pdf",
	rating = "2",
	read = "2013-07-05",
	year = 2008
}

@Article{2008-Detcheverry-KDMNP,
	Author = "François A. Detcheverry and Huiman Kang and Kostas Ch. Daoulas and Marcus Müller and Paul F. Nealey and Juan J. {de Pablo}",
	Title = "{Monte Carlo Simulations of a Coarse Grain Model for Block Copolymers and Nanocomposites}",
	Journal = "Macromolecules",
	Volume = "41",
	Number = "13",
	Pages = "4989–5001",
	Note = "Demonstrates MC for a field-based polymer model and explicitely-interacting particles.",
	abstract = "A coarse grain model and a Monte Carlo sampling formalism are proposed for simulations of self-assembly in block copolymer melts and nanoparticle−copolymer composites. Our approach relies on a particle-based representation of the system, it does not invoke a saddle point approximation, and it permits treatment of large three-dimensional systems. We provide a detailed description of the model and methods and discuss their relationship to results from self-consistent-field theory and single chain in mean field simulations. The validity of the proposed approach is addressed by applying it to study systems whose description within existing approaches would be demanding. In particular, we use it to examine the directed assembly of copolymer blends and nanoparticles on nanopatterned substrates. We show that results from simulations are in good agreement with experiment, and we use our theoretical findings to help explain the experimental observations.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma702514v",
	keywords = "alignment; block copolymers; nanospheres; patterned substrates; polymer nanocomposites; thin films",
	localfile = "block copolymers/2008 - Monte Carlo simulations of a coarse grain model for block copolymers and nanocomposites.pdf",
	methods = "SEM, MC with mean fields",
	systems = "CdSe-TDPA@PS-PMMA",
	year = 2008
}

@Article{2008-Dryza-PB,
	Author = "V. Dryza and B. L. J. Poad and E. J. Bieske",
	Title = "{Attachment of molecular hydrogen to an isolated boron cation: an infrared and ab initio study}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "130",
	Pages = "12986–12991",
	abstract = "Abstract: Structural properties of the B+-H2 electrostatic complex are investigated through its rotationally resolved infrared spectrum in the H-H stretch region (3905-3975 cm-1). The spectrum, which was obtained by monitoring B+ photofragments while the IR wavelength was scanned, is consistent with the complex having a T-shaped structure and a vibrationally averaged intermolecular separation of 2.26 Å, which decreases by 0.04 Å when the H2 subunit is vibrationally excited. The H-H stretch transition of B+-H2 is red-shifted by 220.6 ( 1.5 cm-1 from that of the free H2 molecule, much more than for other dihydrogen complexes with comparable binding energies. Properties of B+-H2 and the related Li+-H2, Na+-H2, and Al+-H2 complexes are explored through ab initio calculations at the MP2/aug-cc-pVTZ level. The unusually large red-shift for B+-H2 is explained as due to electron donation from the H2 σg bonding orbital to the unoccupied 2pz orbital on the B+ ion.",
	collection = "hydrogen sorption",
	doi = "10.1021/ja8018302",
	localfile = "hydrogen sorption/2009 - Attachment of molecular hydrogen to an isolated boron cation: an infrared and ab initio study.pdf",
	year = 2008
}

@Article{2008-Dyguda-Kazimierowicz-SL,
	Author = "Edyta Dyguda-Kazimierowicz and W. Andrzej Sokalski and Jerzy Leszczyński",
	Title = "{Gas-phase mechanisms of degradation of hazardous organophosphorous compounds: do they follow a common pattern of alkaline hydrolysis reaction as in phosphotriesterase?}",
	Journal = "J. Phys. Chem. B",
	Volume = "112",
	Pages = "9982–9991",
	abstract = "A comprehensive ab initio analysis of the gas-phase mechanisms of alkaline hydrolysis for a number of phosphotriesterase substrates;O,O-diisopropyl phosphoroﬂuoridate (DFP), O-isopropyl methyl phosphonoﬂuoridate, O,O-diethyl p-nitrophenyl phosphate (paraoxon), O,O-diethyl p-nitrophenyl thiophosphate (parathion), N-acetyl phosphoramidothioate (acephate), O,O-diethyl S-2-ethylthioethyl phosphorothioate (demeton-S) and O-ethyl N,N-dimethyl phosphoramidocyanidate;has been presented herein. The results indicate that, although an associative mechanism of alkaline hydrolysis is followed by all these compounds, P-F and P-CN bonds are cleaved according to the multistep addition-elimination scheme, whereas the breakage of P-O and P-S bonds appears to be consistent with the one-step direct-displacement mechanism. Of the two alternative reaction pathways present in all those cases (except of acephate), the most probable one involves the proton from a nucleophilic hydroxide experiencing an additional stabilization by the phosphoryl oxygen atom.",
	collection = "molecular reactions",
	doi = "10.1021/jp800386f",
	localfile = "molecular reactions/2008 - Gas-phase mechanisms of degradation of hazardous organophosphorous compounds: do they follow a common pattern of alkaline hydrolysis reaction as in phosphotriesterase.pdf",
	year = 2008
}

@Article{2008-Escudero-FQD,
	Author = "Daniel Escudero and Antonio Frontera and David Quiñonero and Pere M. Deya",
	Title = "{On the importance of the inclusion of the basis set superposition error counterpoise correction during optimization of ion-pi complexes}",
	Journal = "Chem. Phys. Lett.",
	Volume = "455",
	Pages = "325–330",
	abstract = "Several complexes of hexafluorobenzene and trifluorobenzene with halide anions have been optimized using the HF, B3LYP and MP2 methods and either the 6-31++G** or 6-311++G** basis sets. The BSSE ( basis set superposition error) counterpoise correction (CP) was included during the geometry optimization for all complexes at the six levels of theory. The results were compared with cation-pi complexes of benzene and trifluorobenzene. The effect of inclusion of BSSE-CP correction during the optimization is very important in some anion-pi complexes. (c) 2008 Elsevier B. V. All rights reserved. C1 [Escudero, Daniel; Frontera, Antonio; Quinonero, David; Deya, Pere M.] Univ Illes Balears, Dept Quim, Palma de Mallorca 07122, Spain.",
	collection = "basis set superposition",
	doi = "10.1016/j.cplett.2008.02.074",
	keywords = "basis set superposition error; counterpoise correction",
	localfile = "basis set superposition/2008 - On the importance of the inclusion of the basis set superposition error counterpoise correction during optimization of ion-pi complexes.pdf",
	year = 2008
}

@Article{2008-Fiethen-JHS,
	Author = "Annamaria Fiethen and Georg Jansen and Andreas Heßelmann and Martin Schütz",
	Title = "{Stacking energies for average B-DNA structures form the combined density functional theory and symmetry-adapted perturbation theory approach}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "130",
	Pages = "1802–1803",
	abstract = "The π-stacking energy between parallel layers of hydrogen-bonded base pairs is one of the important factors stabilizing the structure of DNA.",
	collection = "stacking",
	doi = "10.1021/ja076781m",
	localfile = "molecular stacking/2008 - Stacking energies for average B-DNA structures from the combined density fucntional theory and symmetry-adapted perturbation theory approach.pdf",
	year = 2008
}

@Article{2008-Gaines-SSBTRS,
	Author = "Michelle K. Gaines and Steven D. Smith and Jon Samseth and Michael R. Bockstaller and Russell B. Thompson and Kim O. Rasmussen and Richard J. Spontak",
	Title = "{Nanoparticle-regulated phase behavior of ordered block coplymers}",
	Journal = "Soft Matter",
	Volume = "4",
	Pages = "1609–1612",
	Note = "Shows experimental verification for predicted increased ODT in diblock nanocomposites.",
	abstract = "Although block copolymer motifs have received considerable attention as supramolecular templates for inorganic nanoparticles, experimental observations of a nanostructured diblock copolymer containing inorganic nanoparticles—supported by theoretical trends predicted from a hybrid self-consistent ﬁeld/density functional theory—conﬁrm that nanoparticle size and selectivity can likewise stabilize the copolymer nanostructure by increasing its order–disorder transition temperature.",
	collection = "block copolymer nanocomposites",
	doi = "10.1039/b805540h",
	keywords = "block copolymers; mesophase transitions; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2008 - Nanoparticle-regulated phase behavior of ordered block copolymers.pdf",
	methods = "rheometry, GPC, NMR, SCFT/DFT",
	systems = "silica-OH@PS-PMMA, silica-MMA@PS-PMMA, silica-octyl@PS-PMMA, silica-PS@PS-PMMA",
	year = 2008
}

@Article{2008-Ganesan,
	Author = "Venkat Ganesan",
	Title = "{Some issues in polymer nanocomposites: theoretical and modeling opportunities for polymer phsyics}",
	Journal = "J. Polym. Sci. Pt. B-Polym. Phys.",
	Volume = "46",
	Pages = "2666–2671",
	abstract = "Addition of ﬁllers to polymers has long been used as a strategy to enhance the properties of polymers. In the last two decades, however, a class of materials termed as “polymer nanocomposites” (PNC) has evolved to refer to blends of polymers and inorganic ﬁllers in which the inorganic component has one or more dimensions below 100 nm. Examples of such materials include mixtures of a variety of homopolymers and multicomponent polymers blended with ﬁllers such as clays, nanotubes, Fullerenes, polyhedral oligomeric silsesquioxanes (POSS), nanoscopic silica particles, and so forth.",
	collection = "polymer nanocomposites",
	doi = "10.1002/polb.21587",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2008 - Some issues in polymer nanocomposites: theoretical and modeling opportunities for polymer physics.pdf",
	type = "Viewpoint",
	year = 2008
}

@Article{2008-Gao-SZ,
	Author = "Yi Gao and Nan Shao and Xiao Cheng Zeng",
	Title = "{Ab initio study of thiolate-protected Au102 nanocluster}",
	Journal = "ACS Nano",
	Volume = "2",
	Number = "7",
	Pages = "1497–1503",
	collection = "nanoparticles",
	doi = "10.1021/nn800268w",
	keywords = "nanoparticle structure",
	localfile = "nanoparticles/2008 - Ab initio study of thiolate-protected Au102 nanocluster.pdf",
	year = 2008
}

@Article{2008-Gkionis-PH,
	Author = "Konstantinos Gkionis and James A. Platts and J. Grant Hill",
	Title = "{Insights into {DNA} Binding of Ruthenium Arene Complexes: Role of Hydrogen Bonding and π Stacking}",
	Journal = "Inorg. Chem.",
	Volume = "47",
	Number = "9",
	Pages = "3893–3902",
	abstract = "Density functional theory (DFT) methods are used to investigate the binding of ruthenium arene complexes, proposed as promising anticancer drugs, to isolated nucleobases. This shows a clear preference for binding at guanine over any other base and an approximately 100 kJ mol-1 difference in binding between guanine and adenine in the gas phase, while binding to cytosine and inosine are intermediate in energy between these extremes. Solvation reduces binding energies and the discrimination between bases but maintains the overall pattern of binding. DFT and ab initio data on arene-base interactions in the absence of ruthenium show that stacking and hydrogen-bonding interactions play a signiﬁcant role but cannot account for all of the energy difference between bases observed. Atoms-in-molecules analysis allows further decomposition of binding energies into contributions from covalent-binding, hydrogen-bonding, and π-stacking interactions. Larger arenes undergo stabilizing stacking interactions, whereas N-H · · · X hydrogen bonding is independent of arene. Pairing of guanine to cytosine is affected by ruthenium complexation, with individual hydrogen-bonding energies being altered but the overall pairing energy remaining almost constant.",
	collection = "nucleic acid bases",
	doi = "10.1021/ic702459h",
	keywords = "hydrogen bonding; aromatic stacking",
	localfile = "nucleic acid bases/2008 - Insights into DNA binding of ruthenium arene complexes: role of hydrogen bonding and stacking.pdf",
	shorttitle = "Insights into {DNA} Binding of Ruthenium Arene Complexes",
	year = 2008
}

@Article{2008-Gramada-Bourne,
	Author = "Apostol Gramada and Philip E. Bourne",
	Title = "{Resolving a distribution of charge into intrinsic multipole moments: a rankwise distirbuted multipole analysis}",
	Journal = "Phys. Rev. E",
	Volume = "78",
	Pages = "066601",
	collection = "molecular electrostatics",
	doi = "10.1103/PhysRevE.78.066601",
	localfile = "molecular electrostatics/2008 - Resolving a distribution of charge into intrinsic multipole moments: a rankwise distributed multipole analysis.pdf",
	year = 2008
}

@Article{2008-Grimme,
	Author = "Stefan Grimme",
	Title = "{Do Special Noncovalent π–π Stacking Interactions Really Exist?}",
	Journal = "Angew. Chem. Int. Ed.",
	Volume = "47",
	Number = "18",
	Pages = "3430–3434",
	abstract = "(Excerpt) Noncovalent interactions play an increasingly important role in modern chemical research, and are nowadays considered as cornerstones in supramolecular chemistry, materials science, and even biochemistry. When unsaturated organic groups are involved in noncovalent interactions, the terms “π–π stacking”, or more generally “π–π interactions” are often used. As noted recently, this classification has a quite mysterious flavor. For larger structures, π–π stacking is a phenomenon that is theoretically not well understood, although some progress has been made.",
	collection = "stacking",
	doi = "10.1002/anie.200705157",
	localfile = "molecular stacking/2008 - Do special noncovalent stacking interactions really exist?.pdf",
	year = 2008
}

@Article{2008-Hamilton-BSM,
	Author = "Charles W. Hamilton and R. Tom Baker and Anne Staubitz and Ian Manners",
	Title = "{B-N compounds for chemical hydrogen storage}",
	Journal = "Chem. Soc. Rev.",
	Volume = "38",
	Pages = "279–293",
	abstract = "Hydrogen storage for transportation applications requires high volumetric and gravimetric storage capacity. B–N compounds are well suited as storage materials due to their light weight and propensity for bearing multiple protic (N–H) and hydridic (B–H) hydrogens. This critical review brieﬂy covers the various methods of hydrogen storage, and then concentrates on chemical hydrogen storage using B–N compounds. The simplest B–N compound, ammonia borane (H3NBH3), which has a potential 19.6 wt\% hydrogen storage capacity, will be emphasised (127 references).",
	collection = "hydrogen sorption",
	doi = "10.1039/b800312m",
	localfile = "hydrogen sorption/2009 - B-N compounds for chemical hydrogen storage.pdf",
	year = 2009
}

@Article{2008-He-ZL,
	Author = "Linli He and Linxi Zhang and Haojun Liang",
	Title = "{The effects of nanoparticles on the lamellar phase separation of diblock copolymers}",
	Journal = "J. Phys. Chem. B",
	Volume = "112",
	Pages = "4194–4203",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/jp0757412",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2008 - The effects of nanoparticles on the lamellar phase separation of diblock copolymers.pdf",
	methods = "DPD",
	rating = "2",
	read = "2012-03-21",
	year = 2008
}

@Article{2008-Hesselman,
	Author = "Andreas Heßelmann",
	Title = "{Improved supermolecular second order Møller–Plesset intermolecular interaction energies using time-dependent density functional response theory}",
	Journal = "J. Chem. Phys.",
	Volume = "128",
	Pages = "144112",
	abstract = "The supermolecular second order Møller-Plesset (MP2) intermolecular interaction energy is corrected by employing time-dependent density functional (TDDFT) response theory. This is done by replacing the uncoupled second order dispersion contribution contained in the supermolecular MP2 energy with the coupled dispersion energy obtained from the TDDFT approach. Preliminary results for the rare gas dimers He2, Ne2, and Ar2 and a few structures of the (HF)2 and (H2O)2 dimers show that the conventional MP2 interaction energies are considerably improved by this procedure if compared to coupled cluster singles doubles with perturbative triples [CCSD(T)] interaction energies. However, the quality of the interaction energies obtained in this way strongly depends on the exchange-correlation potential employed in the monomer calculations: It is shown that an exact exchange-only potential surprisingly often performs better than an asymptotically corrected hybrid exchange-correlation potential. Therefore the method proposed in this work is similar to the method by Cybulski and Lytle [J. Chem. Phys., 127, 141102 (2007)] which corrects the supermolecular MP2 energies with a scaled dispersion energy from time-dependent Hartree–Fock. The results in this work are also compared to the combination of density functional theory and intermolecular perturbation theory.",
	collection = "molecular interactions",
	doi = "10.1063/1.2905808",
	localfile = "molecular interactions/2008 - Improved supermolecular second order Moller-Plesset intermolecular interaction energies using time-dependent density functional response theory.pdf",
	year = 2008
}

@Article{2008-Honda-Kawakatsu,
	Author = "Takashi Honda and Toshihiro Kawakatsu",
	Title = "{Hydrodynamic effects on the disorder-to-order transitions of diblock copolymer melts}",
	Journal = "J. Chem. Phys.",
	Volume = "129",
	Pages = "114904",
	abstract = "Dynamic self-consistent ﬁeld theory and Navier–Stokes equation are coupled to study hydrodynamic effects on the disorder-to-order transition of diblock copolymer melts. Simulations are performed for different values of the viscosity and the results are compared with those without the hydrodynamic effects. The lower the viscosity is, the faster the free energy density decays. Starting from uniformly mixed initial states, body-centered-cubic spheres, hexagonally packed cylinders, and lamellar structures are obtained in the presence of the hydrodynamic effects. On the contrary, the bicontinuous double gyroid structure cannot be obtained even with the hydrodynamic effects. The scattering intensities of the domain structures are calculated to conﬁrm these properties of the ordering of the structures",
	collection = "block copolymers",
	doi = "10.1063/1.2977742",
	keywords = "block copolymers; hydrodynamics",
	localfile = "block copolymers/2008 - Hydrodynamic effects on the disorder-to-ordre transistions of diblock copolymer melts.pdf",
	year = 2008
}

@Article{2008-Huppert,
	Author = "Julian Leon Huppert",
	Title = "{Four-stranded nucleic acids: structure, function and targeting of G-quadruplexes}",
	Journal = "Chem. Soc. Rev.",
	Volume = "37",
	Number = "7",
	Pages = "1375–1384",
	abstract = "There are many structures that can be adopted by nucleic acids other than the famous {Watson-Crick} duplex form. This tutorial review describes the guanine rich G-quadruplex structure, highlighting the chemical interactions governing its formation, and the topological variants that exist. The methods that are used to study G-quadruplex structures are described, with examples of the information that may be derived from these different methods. Next, the proposed biological functions of G-quadruplexes are discussed, highlighting especially their presence in telomeric regions and gene promoters. G-quadruplex structures are the subject of considerable interest for the development of small-molecule ligands, and are also the targets of a wide variety of natural proteins.",
	collection = "nucleic acid drugs",
	doi = "10.1039/b702491f",
	localfile = "nucleic acid drugs/2008 - Four-stranded nucleic acids: structure, function and targeting of G-qudruplexes.pdf",
	shorttitle = "Four-stranded nucleic acids",
	year = 2008
}

@Article{2008-Improta,
	Author = "Roberto Improta",
	Title = "{The excited states of pi-stacked 9-methyladenine oligomers: a TD-DFT study in aqueous solution}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "10",
	Pages = "2656–2664",
	abstract = "An extensive PCM/TD-DFT study of the excited states of p-stacked 9-methyladenine oligomers (from the dimer up to the pentamer), adopting the B-DNA conformation, is reported. Linear response PCM/TD-PBE0 calculations provide a reliable description of the stacking eﬀect on the bright excited states but PBE0, when compared to CAM-B3LYP, LC-oPBE and M052X functionals, overestimates the stability of the electronic states with inter-monomer charge transfer (CT) character. On the other hand, state speciﬁc PCM/TD-DFT calculations conﬁrm that the lowest energy excited state of the dimer corresponds to a dark excimer produced by inter-monomer CT between two stacked bases. Conﬁrming the experimental indications, the spectroscopic states of the oligomers are delocalized over multiple bases.",
	collection = "stacking",
	doi = "10.1039/b718562f",
	localfile = "molecular stacking/2008 - The excited states of pi-stacked 9-methyladenine oligomers: a TD-DFT study in aqueous solution.pdf",
	year = 2008
}

@Article{2008-Iwata-FNAMWT,
	Author = "T. Iwata and Kaori Fukuzawa and K. Nakajima and S. Aida-Hyugaji and Yuji Mochizuki and Hirofumi Watanabe and Shigenori Tanaka",
	Title = "{Theoretical analysis of binding specificity of influenza viral hemagglutinin to avian and human receptors based on the fragment molecular orbital method}",
	Journal = "Comput. Biol. Chem.",
	Volume = "32",
	Number = "3",
	Pages = "198 – 211",
	abstract = "The hemagglutinin (HA) protein of the influenza virus binds to the host cell receptor in the early stage of viral infection. A change in binding specificity from avian alpha 2-3 to human alpha 2-6 receptor is essential for optimal human-to-human transmission and pandemics. Therefore, it is important to reveal the key factors governing the binding affinity of HA-receptor complex at the molecular level for the understanding and prediction of influenza pandemics. In this work, on the basis of ab initio fragment molecular orbital (FMO) method, we have carried out the interaction energy analysis of HA-receptor complexes to quantitatively elucidate the binding specificity of HAs to avian and human receptors. To discuss the binding property of influenza HA comprehensively, a number of HAs from human H1, swine H1, avian H3 and avian H5 viruses were analyzed. We performed detailed investigations about the interaction patterns of complexes of various HAs and receptor analogues, and revealed that intra-molecular interactions between conserved residues in HA play an important role for HA-receptor binding. These results may provide a hint to understand the role of conserved acidic residues at the receptor binding site which are destabilized by the electrostatic repulsion with sialic acid. The calculated binding energies and interaction patterns between receptor and HAs are consistent with the binding specificities of each HA and thus explain the receptor binding mechanism. The calculated results in the present analysis have provided a number of viewpoints regarding the models for the HA-receptor binding specificity associated with mutated residues. Examples include the role of Glu190 and Gln226 for the binding specificity of H5 HA. Since H5 HA has not yet been adapted to human receptor and the mechanism of the specificity change is unknown, this result is helpful for the prediction of the change in receptor specificity associated with forthcoming possible pandemics.",
	collection = "viruses",
	localfile = "viruses/2008 - Theoretical analysis of binding specificity of influenza viral hemagglutinin.pdf",
	year = 2008
}

@Article{2008-Janowski-Pulay,
	Author = "Tomasz Janowski and Peter Pulay",
	Title = "{Efficient parallel implementation of the CCSD external exchange operator and the perturbative triples (T) energy calculation}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "4",
	Pages = "1585–1592",
	abstract = "A new, efﬁcient parallel algorithm is presented for the most expensive step in coupled cluster singles and doubles (CCSD) energy calculations, the external exchange operator (EEO). The new implementation requires much less input/output than our previous algorithm and takes better advantage of integral screening. It is formulated as a series of matrix multiplications. Both the atomic orbital integrals and the corresponding CC coefﬁcients are broken up into smaller blocks to diminish the memory requirement. Integrals are presorted to make their sparsity pattern more regular. This allows the simultaneous use of two normally conﬂicting techniques for speeding up the CCSD procedure: the use of highly efﬁcient dense matrix multiplication routines and the efﬁcient utilization of sparsity. We also describe an efﬁcient parallel implementation of the perturbative triples correction to CCSD and related methods. Using the Array Files tool for distributed ﬁlesystems, parallelization is straightforward and does not compromise efﬁciency. Representative timings are shown for calculations with 282-1528 atomic orbitals, 68-228 correlated electrons, and various symmetries, C1 to C2h.",
	collection = "cheminformatics",
	doi = "10.1021/ct800142f",
	keywords = "algorithms",
	localfile = "cheminformatics/2008 - Efficient parallel implementation of the CCSD external exchange operator and the perturbative triples (T) energy calculation.pdf",
	year = 2008
}

@Article{2008-Jayaraman-Schweizer,
	Author = "Arthi Jayaraman and Kenneth S. Schweizer",
	Title = "{Effect of the number and placement of polymer tethers on the structure of concenctrated solutions and melts of hybrid nanoparticles}",
	Journal = "Langmuir",
	Volume = "24",
	Pages = "11119–11130",
	collection = "polymer nanocomposites",
	doi = "10.1021/la801432b",
	keywords = "self-assembly; nanoparticle grafts; nanospheres",
	localfile = "polymer nanocomposites/2008 - Effect of the number and placement of polymer tethers on the structure of concentrated solutions and melts of hybrid nanoparticles.pdf",
	year = 2008
}

@Article{2008-Jayaraman-Schweizer-1,
	Author = "Arthi Jayaraman and Kenneth S. Schweizer",
	Title = "{Effective interactions, structure, and phase behavior of lightly tethered nanoparticles in polymer melts}",
	Journal = "Macromolecules",
	Volume = "41",
	Pages = "9430–9438",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma801722m",
	keywords = "self-assembly; nanoparticle grafts; nanospheres; polymer nanocomposites",
	localfile = "polymer nanocomposites/2008 - Effective interactions, structure, and phase behavior of lightly tethered nanoparticles in polymer melts.pdf",
	year = 2008
}

@Article{2008-Jayaraman-Schweizer-2,
	Author = "Arthi Jayaraman and Kenneth S. Schweizer",
	Title = "{Structure and assembly of dense solutions and melts of single tethered nanoparticles}",
	Journal = "J. Chem. Phys.",
	Volume = "128",
	Pages = "164904",
	collection = "polymer nanocomposites",
	doi = "10.1063/1.2907717",
	keywords = "self-assembly; nanoparticle grafts; nanospheres",
	localfile = "polymer nanocomposites/2008 - Structure and assembly of dense solutions and melts of single tethered nanoparticles.pdf",
	year = 2008
}

@Article{2008-Jeziorska-CPJS,
	Author = "Małgorzata Jeziorska and Wojciech Cencek and Konrad Patkowski and Bogumił Jeziorski and Krzysztof Szalewicz",
	Title = "{Complete basis set extrapolations of dispersion, exchange, and coupled-clusters contributions to the interaction energy: a helium dimer study}",
	Journal = "Int. J. Quant. Chem.",
	Volume = "108",
	Number = "12",
	Pages = "2053–2075",
	abstract = "Effectiveness of various extrapolation schemes in predicting complete basis set (CBS) values of interaction energies has been investigated for the helium dimer as a function of interatomic separation R. The investigations were performed separately for the leading dispersion and exchange contributions to the interaction energy and for the interaction energy computed using the coupled cluster method with single and double excitations (CCSD). For all these contributions, practically exact reference values were obtained from Gaussian-type geminal calculations. Sequences of orbital basis sets augmented with diffuse and bond functions or augmented with two sets of diffuse functions have been employed, with the cardinal numbers up to X = 7. The functional form EX = ECBS + A(X − k)−α was applied for the extrapolations, where EX is the contribution to the interaction energy computed with a basis set of cardinal number X. The main conclusion of this work is that CBS extrapolations of an appropriate functional form generally improve the accuracy of the interaction energies at a very small additional computational cost (of the order of 10\%) and should be recommended in calculations of interatomic and intermolecular potentials. The effectiveness of the extrapolations signiﬁcantly depends, however, on the interatomic separation R and on the composition of the basis set. Basis sets with midbond functions, well known to provide at a given size much more accurate nonextrapolated results than bases lacking such functions, have been found to perform best also in extrapolations. The X −1 extrapolations of dispersion energies computed with midbond function turned out to be very efﬁcient (except at large R), reducing the errors by an order of magnitude for small X and a factor of two for large X (where the errors of nonextrapolated results are already very small). If midbond functions are not used, the X −3 formula is most appropriate for the dispersion energies. For the exchange component of the interaction energy, the best results are obtained—in both types of basis sets—with the X −4 extrapolation, which leads (in both cases) to almost an order of magnitude reduction of the error. The X −3 and (X − 1)−3 extrapolations work also well, but give smaller improvements. The correlation component of the CCSD interaction energy extrapolates best with α between 2 and 3 for bases with midbond functions and between 3 and 4 for bases without such functions.",
	collection = "basis set dependence",
	doi = "10.1002/qua.21722",
	localfile = "basis set dependence/2008 - Complete basis set extrapolations of dispersion, exchange and coupled-clusters contributions to the interaction energy: a helium dimer study.pdf",
	shorttitle = "Complete basis set extrapolations of dispersion, exchange, and coupled-clusters contributions to the interaction energy",
	year = 2008
}

@Article{2008-Jin-Wu,
	Author = "Jiezhu Jin and Jianzhong Wu",
	Title = "{A theoretical study for nanoparticle partitioning in the lamellae of diblock copolymers}",
	Journal = "J. Chem. Phys.",
	Volume = "128",
	Pages = "074901",
	abstract = "Morphology control is important for practical applications of composite materials that consist of functional polymers and nanoparticles. Toward that end, block copolymers provide useful templates to arrange nanoparticles in the scaffold of self-organized polymer microdomains. This paper reports theoretical predictions for the distribution of nanoparticles in the lamellar structures of symmetric diblock copolymers on the basis of a polymer density functional theory DFT and the potential distribution theorem PDT . The DFT predicts periodic spacing of lamellar structures in good agreement with molecular dynamics simulations. With the polymer structure from DFT as the input, the PDT is used to examine the effects of particle size, surface energy, polymer chain length, and compressibility on the distribution of nanoparticles in the limit of low particle density. It is found that the nanoparticle distribution depends not only on the particle size and surface energy but also in the local structure of the microdomain interface, polymer chain length, and compressibility. The theoretical predictions are compared well with experiments and simulations.",
	collection = "block copolymer nanocomposites",
	doi = "10.1063/1.2827470",
	keywords = "block copolymers; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2008 - A theoretical study for nanoparticle partitioning in the lamellae of diblock copolymers.pdf",
	methods = "DFT",
	year = 2008
}

@Article{2008-Kalra-LLLMWJ,
	Author = "Vibha Kalra and Jinwoo Lee and Hun Lee and Seung Goo Lee and Manuel Marquez and Ulrich Wiesner and Yong Lak Joo",
	Title = "{Controlling nanoparticle location via confined assembly in electrospun block copolymer nanofibers}",
	Journal = "Small",
	Volume = "4",
	Number = "11",
	Pages = "2067–1073",
	Note = "Demonstrates selective incorporation of magnetite NPs in electrospun PS-b-PI nanofibers.",
	abstract = "Coaxial nanoﬁbers with poly(styrene-block-isoprene) (PS-b-PI)/magnetite nanoparticles as core and silica as shell are fabricated using electrospinning. Thermally stable silica helps to anneal the ﬁbers above the glass transition temperature of PS-b-PI and form ordered nanocomposite morphologies. Monodisperse magnetite nanoparticles (NPs; 4 nm) are synthesized and surface coated with oleic acid to provide marginal selectivity towards an isoprene domain. When 4 wt\% nanoparticles are added to symmetric PS-b-PI, transmission electron microscopy (TEM) images of microtomed electrospun ﬁbers reveal that NPs are uniformly dispersed only in the PI domain, and that the conﬁned lamellar assembly in the form of alternate concentric rings of PS and PI is preserved. For 10 wt\% NPs, a morphology transition is seen from concentric rings to a co-continuous phase with NPs again uniformly dispersed in the PI domains. No aggregates or loss of PI selectivity is found in spite of interparticle attraction. Magnetic properties are measured using a superconducting quantum interference device (SQUID) magnetometer and all nanocomposite ﬁber samples exhibit superparamagnetic behavior.",
	collection = "block copolymer nanocomposites",
	keywords = "block copolymers; thin fibers; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2008 - Controlling nanoparticle location via confined assembly in electrospun block copolymer nanofibers.pdf",
	methods = "physisorption, absorbance, Raman, SAXS, powder XRD, TEM, SEM, SQUID",
	systems = "magnetite-oleyl@PS-PI",
	year = 2008
}

@Article{2008-Kamp-Mulholland,
	Author = "{Marc W. van der} Kamp and Adrian J. Mulholland",
	Title = "{Computational enzymology: insight into biological catalysts from modelling}",
	Journal = "Nat. Prod. Rep.",
	Volume = "25",
	Pages = "1001–1014",
	abstract = "Molecular modelling and simulation can give atomic-level understanding of the fundamental mechanisms of enzyme catalysis. For example, modelling can identify likely enzyme reaction mechanisms, analyse catalytic interactions, and identify determinants of reactivity and speciﬁcity. Combined quantum mechanics/molecular mechanics (QM/MM) methods are an important technique in this maturing ﬁeld of computational enzymology. By coupling quantum chemical (electronic structure) calculations on the active site with a simpler, empirical ‘molecular mechanics’ treatment of the rest of the protein, QM/MM methods allow the modelling of reactions in enzymes. In this Highlight, QM/MM techniques are outlined and some recent applications are discussed. These applications illustrate how calculations of this type can be used to interpret and complement experiments, with important potential implications for practical developments such as drug and catalyst design.",
	collection = "enzymes",
	doi = "10.1039/b600517a",
	localfile = "enzymes/2008 - Computational enzymology: insight into biological catalysts from modelling.pdf",
	year = 2008
}

@Article{2008-Kang-DMSDHMPN,
	Author = "Huiman Kang and François A. Detcheverry and Andrew N. Mangham and Mark. P Stoykovich and Kostas Ch. Daoulas and Robert J. Hamers and Marcus Müller and Juan J. {de Pablo} and Paul F. Nealey",
	Title = "{Hierarchical assembly of nanoparticle superstructures from block copolymer-nanoparticle composites}",
	Journal = "Phys. Rev. Lett.",
	Volume = "100",
	Number = "14",
	Pages = "148303",
	Note = "Shows CdSe-TDPA/PS-b-PMMA film on a nanopatterned substrate, complemented by MC simulations.",
	abstract = "We investigate the assembly of block copolymer-nanoparticle composite films on chemically nanopatterned substrates and present fully three-dimensional simulations of a coarse grain model for these hybrid systems. The location and distribution of nanoparticles within the ordered block copolymer domains depends on the thermodynamic state of the composite in equilibrium with the surface. Hierarchical assembly of nanoparticles enables applications in which the ability to precisely control their locations within periodic and nonregular geometry patterns and arrays is required.",
	collection = "block copolymer nanocomposites",
	doi = "10.1103/PhysRevLett.100.148303",
	keywords = "alignment; block copolymers; nanospheres; patterned substrates; polymer nanocomposites; thin films",
	localfile = "block copolymer nanocomposites/2008 - Hierarchical assembly of nanoparticle superstructures from block copolymer-nanoparticle composites.pdf",
	methods = "SEM, MC with mean fields",
	systems = "CdSe-TDPA@PS-PMMA",
	year = 2008
}

@Article{2008-Kavanagh-JPO,
	Author = "K. L. Kavanagh and H. Jörnvall and B. Persson and U. Oppermann",
	Title = "{The SDR superfamily: functionl and stuctural diversity within a family of metabolic and regulatory enzymes}",
	Journal = "Cell. Mol. Life Sci.",
	Volume = "65",
	Pages = "3895–3906",
	Note = "Page 3896: The catalytic base in the majority of SDRs is a highly but not strictly conserved Tyr residue (..); Page 3897: (..) the only unifying criterion for SDRs is the Rossmann-fold scaffold and its ability to bind NAD(P) dinucleotides.",
	cited = "125 (2013-09-09)",
	collection = "proteins",
	doi = "10.1007/s00018-008-8588-y",
	localfile = "proteins/2008 - The SDR superfamily: functional and structural diversity within a family of metabolic and regulatory enzymes.pdf",
	rating = "2",
	read = "2013-09-09",
	systems = "SDR",
	year = 2008
}

@Article{2008-Kim-FK,
	Author = "Bumjoon J. Kim and Glenn H. Fredrickson and Edward J. Kramer",
	Title = "{Effect of polymer ligand molecular weight on polymer-coated nanoparticle location in block copolymers}",
	Journal = "Macromolecules",
	Volume = "41",
	Pages = "436–447",
	Note = "Reports observed distributions of PS-coated NPs in PS-b-P2VP lamellae as a function of coating density.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma701931z",
	keywords = "block copolymers; nanoparticle distribution; nanoparticle grafts; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2008 - Effect of polymer ligand molecular weight on polymer-coated nanoparticle location in block copolymers.pdf",
	methods = "TGA, TEM",
	systems = "Au-PS@PS-P2VP",
	year = 2008
}

@Article{2008-Kim-Matsen,
	Author = "Jaeup U. Kim and Mark W. Matsen",
	Title = "{Interaction between polymer-grafted particles}",
	Journal = "Macromolecules",
	Volume = "41",
	Pages = "4435–4443",
	collection = "nanoparticles",
	doi = "10.1021/ma8002856",
	keywords = "nanoparticle grafts; nanospheres",
	localfile = "nanoparticles/2008 - Interaction between polymer-grafted particles.pdf",
	year = 2008
}

@Article{2008-Klontzas-MTF,
	Author = "Emmanouel Klontzas and Andreas Mavrandonakis and Emmanuel Tylianakis and George E. Froudakis",
	Title = "{Improving Hydrogen Storage Capacity of {MOF} by Functionalization of the Organic Linker with Lithium Atoms}",
	Journal = "Nano Lett.",
	Volume = "8",
	Number = "6",
	Pages = "1572–1576",
	abstract = "A combination of quantum and classical calculations have been performed in order to investigate hydrogen storage in metal−organic frameworks {(MOFs)} modified by lithium alkoxide groups. Ab initio calculations showed that the interaction energies between the hydrogen molecules and this functional group are up to three times larger compared with unmodified {MOF.} This trend was verified by grand canonical Monte Carlo {(GCMC)} simulations in various thermodynamic conditions. The gravimetric capacity of the Li-modified {MOFs} reached the value of 10 wt \% at 77 K and 100 bar, while our results are very promising at room temperature, too, with 4.5 wt \%.",
	collection = "hydrogen sorption",
	doi = "10.1021/nl072941g",
	localfile = "hydrogen sorption/2008 - Improving hydrogen storage capacity of MOF by functionalization of the organic linker with lithium atoms.pdf",
	year = 2008
}

@Article{2008-Knorowski-AT,
	Author = "C. D. Knorowski and Joshua A. Anderson and Alex Travesset",
	Title = "{Self-assembled ordered polymer nanocomposites directed by attractive particles}",
	Journal = "J. Chem. Phys.",
	Volume = "128",
	Pages = "164903",
	abstract = "We theoretically investigate general conditions under which an inorganic phase can direct the self-assembly of an ordered polymer nanocomposite. For this purpose, we consider a solution of triblock copolymers forming a hexagonal phase of micelles and investigate the effect of adding attractive particles. We show that if the triblock is functionalized at its ends by attaching groups with speciﬁc afﬁnity for the particles, thus effectively becoming a pentablock, the particles direct the self-assembly of the system into phases where both the polymers and the particles exhibit mesoscopic order. Different lamellar and gyroid phases both with Ia3d and I4$\_1$32 space symmetries are presented in detail. Our results show that functionalization is a very powerful route for directing self-assembly of polymer nanocomposites. We brieﬂy discuss the connections with recent theoretical and experimental results in diblock melts with nanoparticles as well as for problems where polymers are used to template the growth of an inorganic phase in solution.",
	collection = "block copolymer nanocomposites",
	doi = "10.1063/1.2907744",
	keywords = "block copolymers; mesophase coexistence; mesophase transitions; nanopinning; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2008 - Self-assembled ordered polymer nanocomposites directed by attractive particles.pdf",
	methods = "CG MD",
	year = 2008
}

@Article{2008-Kosloff-Kolodny,
	Author = "Mickey Kosloff and Rachel Kolodny",
	Title = "{Sequence-similar, structure-dissimilar protein pairs in the PDB}",
	Journal = "Proteins",
	Volume = "71",
	Pages = "891–902",
	abstract = "It is often assumed that in the PDB, two proteins with similar sequences will aslo have similar structures. Accordingly, it has proved useful to develop subsets of the PDB from which 'redundant' structures have been removed, based on a sequence-based criterion for similarity. (...) Here, we show that this assumption is often not correct and that standard approaches to create subsets of the PDB can lead to the loss of structurally and functionally important information. (...) The source of the structural differences usually has a functional basis.",
	collection = "protein structure",
	doi = "10.1002/prot.21770",
	keywords = "homology",
	localfile = {},
	year = 2008
}

@Article{2008-Kostjukov-KDE,
	Author = "Viktor V. Kostjukov and N. M. Khomytova and D. B. Davies and M. P. Evstigneev",
	Title = "{Electrostatic contribution to the energy of binding of aromatic ligands with DNA}",
	Journal = "Biopolymers",
	Volume = "89",
	Number = "8",
	Pages = "680–690",
	abstract = "The method of solution of the nonlinear Poisson–Boltzmann equation was used to calculate electrostatic energy of binding of various aromatic ligands with DNA oligomers of different length. Analysis of the electrostatic contribution was made in terms of a two-step DNA binding process: formation of the intercalation cavity and insertion of the ligand. The total electrostatic energy was also partitioned into components: the energy of atom–atom coulombic interactions and the energy of interaction with surrounding water. The results indicate that electrostatic interactions are, as a whole, unfavorable to the intercalation process and that a correct analysis of structure-energy interrelation for Ligand-DNA interactions should only be accomplished at the level of the components rather than at the level of total electrostatic energy.",
	collection = "nucleic acid intercalation",
	doi = "10.1002/bip.20985",
	localfile = "nucleic acid intercalation/2008 - Electrostatic contribution to the energy of binding of aromatic ligands with DNA.pdf",
	year = 2008
}

@Article{2008-Kozurkova-SJMKUSFKI,
	Author = "Mária Kožurková and Danica Sabolová and Ladislav Janovec and Jaromir Mikeš and Ján Koval and Ján Ungvarský and Miroslava Štefanišinová and Peter Fedoročko and Pavol Kristian and Ján Imrich",
	Title = "{Cytotoxic activity of proflavine diureas: Synthesis, antitumor, evaluation and DNA binding properties of 1',1”-(acridin-3,6-diyl)-3',3”-dialkyldiureas}",
	Journal = "Bioorg. Med. Chem.",
	Volume = "16",
	Number = "7",
	Pages = "3976–3984",
	abstract = "The synthesis of novel 1',1”-(acridin-3,6-diyl)-3',3”-dialkyldiureas was reported. Their biological activity to inhibit cell proliferation was assessed by a MTT assay on two cell lines, HeLa and HCT-116, at micromolar concentration. 1',1”-(Acridin-3,6-diyl)-3',3”-dihexyldiurea hydrochloride was active on a HCT-116 cell line with an IC50 value of 3.1 mu M. The interaction of these compounds with calf thymus DNA was investigated by a variety of spectroscopic techniques including UV-vis, fluorescence and CD spectroscopy. From spectrofluorimetric titrations, binding constants for the DNA-drug complexes were determined (K = 0.9-4.2 x 10(5) M-1). Antiproliferative activity of synthesized derivatives might be related to their intercalation into DNA.",
	collection = "nucleic acid intercalation",
	doi = "10.1016/j.bmc.2008.01.026",
	localfile = {nucleic acid intercalation/2008 - Cytotoxic activity of proflavine diureas: synthesis, antitumor, evaluation and DNA binding properties of 1',1''-(acridin-3,6-diyl)-3',3''-dialkyldiureas.pdf},
	year = 2008
}

@Article{2008-Ladik-BB,
	Author = "Janos Ladik and Attila Bende and Ferenc Bogar",
	Title = "{The electronic structure of the four nucleotide bases in DNA, of their stacks, and of their homopolynucleotides in the absence and presence of water}",
	Journal = "J. Chem. Phys.",
	Volume = "128",
	Pages = "105101",
	collection = "nucleic acid bases",
	doi = "10.1063/1.2832860",
	localfile = "nucleic acid bases/2008 - The electronic structure of the four nucleotide bases in DNA, of their stacks, and their homopolynucleotides in the absence and presence of water.pdf",
	year = 2008
}

@Article{2008-Lane-CGT,
	Author = "Andrew N. Lane and Jonathan B. Chaires and Robert D. Gray and John O. Trent",
	Title = "{{Stability and kinetics of G-quadruplex structures}40 (20}",
	Journal = "Nucl. Acids Res.",
	Volume = "36",
	Number = "17",
	Pages = "5482–5515",
	abstract = "In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function. The unifying theme in this review is energetics. The thermodynamic stability of quadruplexes has not been studied in the same detail as {DNA} and {RNA} duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides. We provide an overview of the principles of stability and where available the experimental data that report on these principles. Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes. Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations. Quadruplex structures fold and unfold comparatively slowly, and {DNA} unwinding events associated with transcription and replication may be operating far from equilibrium. The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence.",
	collection = "nucleic acids",
	doi = "10.1093/nar",
	localfile = "nucleic acids/2008 - Stability and kinetics of G-quadruplex structures.pdf",
	year = 2008
}

@Article{2008-Li-HGLWER,
	Author = "Qifang Li and Jinbo He and Elizabeth Glogowski and Xuefa Li and Jin Wang and Todd Emrick and Thomas P. Russell",
	Title = "{Responsive assemblies: gold nanoparticles with mixed ligands in microphase separated block copolymers}",
	Journal = "Adv. Mater.",
	Volume = "20",
	Pages = "1462–1466",
	collection = "block copolymer nanocomposites",
	doi = "10.1002/adma.200702004",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2008 - Responsive assemblies: gold nanoparticles with mixed ligands in microphase spearated block copolymers.pdf",
	methods = "TEM, AFM, SFM, SAXS, TGA",
	rating = "2",
	read = "2012-03-21",
	systems = "Au{3nm}-(dodecanthiol,11-mercapto-1-undecanol)@PS-P2VP",
	year = 2008
}

@Article{2008-Liu-DN,
	Author = "{XiangDong} Liu and {HongYan} Diao and Norio Nishi",
	Title = "{Applied chemistry of natural {DNA}}",
	Journal = "Chem. Soc. Rev.",
	Volume = "37",
	Number = "12",
	Pages = "2745–2757",
	abstract = "Recently, natural {DNA} has emerged as an appealing biomacromolecule for functional materials. It is abundant and renewable, and possesses the well known double helix structure that promises many unique properties difficult to find in other polymers. Natural {DNA} has been applied in electronic, optical and biomaterials, as a catalyst for enantioselective reactions, and as a material for cleaning the environment. Most of the applications are based on combining {DNA} with other chemicals or nanoparticles by electrostatic binding, intercalation or groove binding. In this critical review article, recent developments in utilizing natural {DNA} are reviewed by focusing on three basic properties of {DNA:} the electrostatic property as a polyelectrolyte, selective affinity for small molecules, and biocompatibility (128 references).",
	collection = "nucleic acids",
	doi = "10.1039/b801433g",
	localfile = "nucleic acids/2008 - Applied chemistry of natural DNA.pdf",
	year = 2008
}

@Article{2008-Lodola-MRCTPM,
	Author = "Alessio Lodola and Marco Mor and Silvia Rivara and Christo Christov and Giorgio Tarzia and Daniele Piomelli and Adrian J. Mulholland",
	Title = "{Identification of productive inhibitor binding orientation in fatty acid amide hydrolase (FAAH) by QM/MM mechanistic modelling}",
	Journal = "Chem. Commun.",
	Volume = "2",
	Pages = "214–216",
	abstract = "Modelling of the mechanism of covalent adduct formation by the inhibitor O-arylcarbamate URB524 in FAAH shows that only one of the two possible inhibitor binding orientations is consistent with the experimentally observed irreversible carba-moylation of the nucleophile serine: this is a potentially crucial insight for designing new covalent inhibitors of this promising drug target.",
	collection = "enzymes",
	doi = "10.1039/b714136j",
	localfile = "enzymes/2008 - Identification of productive inhibitor binding orientation in fatty acid amide hydrolase (FAAH) by QMMM mechanistic modelling.pdf",
	year = 2008
}

@Article{2008-Marsili-CSP,
	Author = "Simone Marsili and Riccardo Chelli and Vincenzo Schettino and Piero Procacci",
	Title = "{Thermodynamics of stacking interactions in proteins}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "10",
	Number = "19",
	Pages = "2673",
	abstract = "Using a database of 6166 experimental structures taken from the Protein Data Bank, we have studied pair interactions between planar residues (Phe, Tyr, His, Arg, Glu and Asp) in proteins, known as pi-pi interactions. On the basis of appropriate coordinates de. ning the mutual arrangement of two residues, we have calculated 2-D potentials of mean force aimed at determining the stability of the most probable structures for aromatic-aromatic, aromatic-cation and aromatic-anion bound pairs. Our analysis reveals the thermodynamic relevance and the ubiquity of stacked complexes in proteins.",
	collection = "stacking",
	doi = "10.1039/b718519g",
	localfile = "molecular stacking/2008 - Thermodynamics of stacking interactions in proteins.pdf",
	year = 2008
}

@Article{2008-Matsen-Thompson,
	Author = "Mark W. Matsen and Russell B. Thompson",
	Title = "{Particle distributions in a block copolymer nanocomposite}",
	Journal = "Macromolecules",
	Volume = "41",
	Pages = "1853–1860",
	Note = "Discusses NP distribution in diblock lammellae in the dilute limit, as a function of size and selectivity.",
	abstract = "Self-consistent-field theory is used to predict the center-of-mass distribution of spherical nanoparticles embedded in the lamellar phase of a diblock copolymer melt. The calculation is performed in the dilute limit, where the particle-particle interactions have a negligible effect on the distribution. We investigate how the distribution is affected by particle radius R, surface affinity ΛN, diblock segregation χN, diblock composition f, and invariant polymerization index N. While the preferred location of the particles (i.e., interface or domain center) is primarily controlled by ΛN, the degree of particle localization depends on several factors. Larger values of R, χN, and N all tend to produce narrower particle distributions.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma7024545",
	keywords = "block copolymers; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2008 - Particle distributions in a block copolymer nanocomposite.pdf",
	methods = "SCFT/DFT",
	year = 2008
}

@Article{2008-Mavrandonakis-Klopper,
	Author = "Andreas Mavrandonakis and Wim Klopper",
	Title = "{{First-Principles} Study of Single and Multiple Dihydrogen Interaction with Lithium Containing Benzene Molecules}",
	Journal = "J. Phys. Chem. C",
	Volume = "112",
	Number = "30",
	Pages = "11580–11585",
	abstract = "The interactions of molecular hydrogen with Li containing benzene molecules were studied by means of density functional theory {(DFT),} second-order {Møller−Plesset} perturbation theory {(MP2),} and coupled-cluster theory including all single and double excitations in conjunction with a perturbative estimate of triple excitations {[CCSD(T)].} At the {DFT} and {MP2} levels the resolution of the identity {(RI)} approximation was invoked in the framework of the approaches {RI-DFT} and {RI-MP2.} The benzene derivatives studied in this work are lithium benzide {(C6H5Li),} lithium phenoxide {(C6H5OLi)} and lithium benzoate {(C6H5COOLi).} By extrapolating the {MP2} and {CCSD(T)} energies to the complete basis set limit, the interaction energy of dihydrogen with these benzene species is found to be 2.54, 2.66 and 2.57 kcal/mol respectively. In all cases, the H2 molecule takes a side-on position on the Li atom. The interactions are larger than typical van der Waals {(vdW)} forces and can be attributed to dipole···induced dipole electrostatic forces. Therefore, the organolithium structures studied can perhaps be used as building units for potential hydrogen storage materials.",
	collection = "hydrogen sorption",
	doi = "10.1021/jp8021369",
	localfile = "hydrogen sorption/2008 - First-principles study of single and multiple dihydrogen interactions with lithium containing benzene molecules.pdf",
	methods = "DFT, MP2, CSSD(T)",
	systems = "dihydrogen near aromatics",
	year = 2008
}

@Article{2008-McGarrity-FM,
	Author = "Erin S. McGarrity and Amalie L. Frischknecht and Michael E. Mackay",
	Title = "{Phase behavior of polymer-nanoparticle blends near a substrate}",
	Journal = "J. Chem. Phys.",
	Volume = "128",
	Pages = "154904",
	abstract = "We use the recent ﬂuids density functional theory of Tripathi and Chapman Phys. Rev. Lett. 94, 087801 2005 ; J. Chem. Phys. 122, 094506 2005 to investigate the phase behavior of athermal polymer/nanoparticle blends near a substrate. The blends are modeled as a mixture of hard spheres and freely jointed hard chains, near a hard wall. There is a ﬁrst order phase transition present in these blends in which the nanoparticles expel the polymer from the surface to form a monolayer at a certain nanoparticle concentration. The nanoparticle transition density depends on the length of the polymer, the nanoparticle diameter, and the overall bulk density of the system. The phase transition is due to both packing entropy effects related to size asymmetry between the components and to the polymer conﬁgurational entropy, justifying the so-called “entropic push” observed in experiments. In addition, a layered state is found at higher densities which resembles that in colloidal crystals, in which the polymer and nanoparticles form alternating discrete layers. We show that this laminar state has nearly the same free energy as the homogeneously mixed ﬂuid in the bulk and is nucleated by the surface.",
	collection = "polymer nanocomposites",
	doi = "10.1063/1.2899329",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2008 - Phase behavior of polymer-nanoparticle blends near a substrate.pdf",
	year = 2008
}

@Article{2008-Milchev-DB,
	Author = "A. Milchev and D. I. Dimitrov and K. Binder",
	Title = "{Excess free energy of nanoparticles in a polymer brush}",
	Journal = "Polymer",
	Volume = "49",
	Pages = "3611–3618",
	abstract = "We present an efﬁcient method for direct determination of the excess free energy DF of a nanoparticle inserted into a polymer brush. In contrast to Widom’s insertion method, the present approach can be efﬁciently implemented by Monte Carlo or Molecular Dynamics methods also in a dense environment. In the present investigation the method is used to determine the free energy penalty DF(R, D) for placing a spherical particle with an arbitrary radius R at different positions D between the grafting plane and the brush surface. Deep inside the brush, or for dense brushes, one ﬁnds DF f R3 whereas for shallow nanoclusions DF f R2, regardless of the particle interaction (attractive/repulsive) with the polymer. The pressure and density ﬁelds around spherical nanoinclusions in a polymer brush are also investigated. Extensive Monte Carlo simulations show that the force, exerted on the particle by the surrounding brush, depends essentially on the proximity of the nanocolloid particle to the brush surface not only in strength but also with respect to its angular distribution. For shallow nanoinclusions close to the brush surface this angular distribution is shown to result in a growing buoyant force while deep inside the brush this effect is negligible.",
	collection = "polymer brushes",
	doi = "10.1016/j.polymer.2008.04.032",
	localfile = "polymer brushes/2008 - Excess free energy of nanoparticles in a polymer brush.pdf",
	year = 2008
}

@Article{2008-Misquitta-WSP,
	Author = "Alston J. Misquitta and Gareth W. A. Welch and Anthony J. Stone and Sarah L. Price",
	Title = "{A first principles prediction of the crystal structure of {C6Br2ClFH2}}",
	Journal = "Chem. Phys. Lett.",
	Volume = "456",
	Number = "1-3",
	Pages = "105–109",
	abstract = "We have constructed an intermolecular potential for the 1,3-dibromo-2-chloro-5-ﬂuorobenzene molecule from ﬁrst principles using SAPT(DFT) interaction energy calculations and the Williams–Stone–Misquitta method for obtaining molecular properties in distributed form. This molecule was included in the fourth Blind Test of crystal structure prediction organised by the Cambridge Crystallographic Data Centre. Using our potential, we have predicted the crystal structure of C6 Br2 ClFH2 and found the lowest energy solution to be in excellent agreement with the experimentally observed crystal when it was subsequently revealed.",
	collection = "molecular crystals",
	doi = "10.1016/j.cplett.2008.02.113",
	localfile = "molecular crystals/2008 - A first principles prediction of the crystal structure of C6Br2ClFH2.pdf",
	year = 2008
}

@Article{2008-Mochizuki-YMNFTWT,
	Author = "Yuji Mochizuki and Katsumi Yamashita and Tadashi Murase and Tatsuya Nakano and Kaori Fukuzawa and Kazutomo Takematsu and Hirofumi Watanabe and Shigenori Tanaka",
	Title = "{Large scale {FMO}-{MP}2 calculations on a massively parallel-vector computer}",
	Journal = "Chem. Phys. Lett.",
	Volume = "457",
	Number = "4-6",
	Pages = "396 – 403",
	abstract = "The fragment molecular orbital (FMO) calculations have been successfully applied to a variety of realistic biochemical problems, by using our original ABINIT-MP program. In these applications, the inclusion of electron correlation through the second-order Møller–Plesset perturbation (MP2) was demonstrated to be essential to obtain qualitatively correct descriptions. Recently, the FMO calculations in ABINIT-MP were tuned for a massively parallel-vector processing. A series of FMO-MP2/6-31G calculations were performed on the Earth Simulator by which up to 4096 vector processors are available. The largest FMO-MP2 computation was carried out for an influenza hemagglutinin antigen-antibody system consisting of 921 residues, which was completed within one hour with 4096 processors.",
	collection = "cheminformatics",
	doi = "10.1016/j.cplett.2008.03.090",
	localfile = "cheminformatics/2008 - Large scale FMO-MP2 calculations on a massively parallel-vector computer.pdf",
	year = 2008
}

@Article{2008-Monchaud-Teulade-Fichou,
	Author = "David Monchaud and {Marie-Paule} {Teulade-Fichou}",
	Title = "{A hitchhiker's guide to G-quadruplex ligands}",
	Journal = "Org. Biomol. Chem.",
	Volume = "6",
	Number = "4",
	Pages = "627–636",
	abstract = "Over the past decade, nucleic acid chemists have seen the spectacular emergence of molecules designed to interact efficiently and selectively with a peculiar {DNA} structure named G-quadruplex. Initially derived from classical {DNA} intercalators, these G-quadruplex ligands progressively became the focal point of new excitement since they appear to inhibit selectively the growth of cancer cells thereby opening interesting perspectives towards the development of novel anti-cancer drugs. The present article aims to help researchers enter this exciting research field, and to highlight recent advances in the design of G-quadruplex ligands.",
	collection = "nucleic acid drugs",
	doi = "10.1039/b714772b",
	localfile = "nucleic acid drugs/2008 - A hitchhiker's guide to G-quadruplex ligands.pdf",
	year = 2008
}

@Article{2008-Mor-LRVDTSPCKTP,
	Author = "Marco Mor and Alessio Lodola and Silvia Rivara and Federica Vacondio and Andrea Duranti and Andrea Tontini and Silvano Sanchini and Giovanni Piersanti and Jason R. Clapper and Alvin R. King and Giorgio Tarzia and Daniele Piomelli",
	Title = "{Synthesis and quantitative structure-activity relationship of fatty acid amide hydrolase inhibitors: modulation at the n-portion of biphenyl-3-yl alkylcarbamates}",
	Journal = "J. Med. Chem.",
	Volume = "51",
	Pages = "3487–3498",
	abstract = "Alkylcarbamic acid biphenyl-3-yl esters are a class of fatty acid amide hydrolase (FAAH) inhibitors that comprises cyclohexylcarbamic acid 3′-carbamoylbiphenyl-3-yl ester (URB597), a compound with analgesic, anxiolytic-like and antidepressant-like properties in rat and mouse models. Here, we extended the structure-activity relationships (SARs) for this class of compounds by replacing the cyclohexyl ring of the parent compound cyclohexylcarbamic acid biphenyl-3-yl ester (URB524) (FAAH IC50 ) 63 nM) with a selected set of substituents of different size, shape, ﬂexibility, and lipophilicity. Docking experiments and linear interaction energy (LIE) calculations indicated that the N-terminal group of O-arylcarbamates ﬁts within the lipophilic region of the substrate-binding site, mimicking the arachidonoyl chain of anandamide. Signiﬁcant potency improvements were observed for the β-naphthylmethyl derivative 4q (IC50 ) 5.3 nM) and its 3′-carbamoylbiphenyl-3-yl ester 4z (URB880, IC50 ) 0.63 nM), indicating that shape complementarity and hydrogen bonds are crucial to obtain highly potent inhibitors.",
	collection = "enzymes",
	doi = "10.1021/jm701631z",
	localfile = "enzymes/2008 - Synthesis and quantitative structure-activity relationship of fatty acid amide hydrolase inhibitors: modulation at the N-portion of biphenyl-3-yl alkylcarbamates.pdf",
	year = 2008
}

@Article{2008-Mourik,
	Author = "{Tanja van} Mourik",
	Title = "{Basis Set Superposition Error Effects Cause the Apparent Nonexistence of the Ethene/Benzenium Ion Complex on the MP2 Potential Energy Surface}",
	Journal = "J. Phys. Chem. A",
	Volume = "112",
	Pages = "11017–11020",
	abstract = "In a recent Letter (J. Phys. Chem. A 2008, 112, 6399) Kolboe and Svelle reported that the ethene/benzenium ion complex found by B3LYP transforms into an ethylbenzenium ion when MP2 with a large basis set is used. We find that the failure of MP2 to locate the ethene/benzenium ion complex is due to large basis set superposition errors. C1 Univ St Andrews, Sch Chem, St Andrews KY16 9ST, Fife, Scotland.",
	collection = "basis set superposition",
	doi = "10.1021/jp806986t",
	localfile = "basis set superposition/2008 - Basis set superposition error effects cause the apparent nonexistence of the ethene-benzenium ion complex on the MP2 potential energy surface.pdf",
	year = 2008
}

@Article{2008-Mukherjee-LBH,
	Author = "Arnab Mukherjee and Richard Lavery and Biman Bagchi and James T. Hynes",
	Title = "{On the Molecular Mechanism of Drug Intercalation into {DNA:} A Simulation Study of the Intercalation Pathway, Free Energy, and {DNA} Structural Changes}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "130",
	Number = "30",
	Pages = "9747–9755",
	abstract = "Intercalation into {DNA} (insertion between a pair of base pairs) is a critical step in the function of many anticancer drugs. Despite its importance, a detailed mechanistic understanding of this process at the molecular level is lacking. We have constructed, using extensive atomistic computer simulations and umbrella sampling techniques, a free energy landscape for the intercalation of the anticancer drug daunomycin into a twelve base pair {B-DNA.} A similar free energy landscape has been constructed for a probable intermediate {DNA} minor groove-bound state. These allow a molecular level understanding of aspects of the thermodynamics, {DNA} structural changes, and kinetic pathways of the intercalation process. Key {DNA} structural changes involve opening the future intercalation site base pairs toward the minor groove (positive roll), followed by an increase in the rise, accompanied by hydrogen bonding changes of the minor groove waters. The calculated intercalation free energy change is −12.3 kcal/mol, in reasonable agreement with the experimental estimate −9.4 kcal/mol. The results point to a mechanism in which the drug first binds to the minor groove and then intercalates into the {DNA} in an activated process, which is found to be in general agreement with experimental kinetic results.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/ja8001666",
	localfile = "nucleic acid intercalation/2008 - On the molecular mechanism of drug intercalation into DNA: a simulation study of the intercalation pathway, free energy, and DNA structural changes.pdf",
	shorttitle = "On the Molecular Mechanism of Drug Intercalation into {DNA}",
	year = 2008
}

@Article{2008-Nasertayoob-Shahbazian,
	Author = "Payam Nasertayoob and Shant Shahbazian",
	Title = "{Revisiting the foundations of quantum theory of atoms in molecules {(QTAIM):} The variational procedure and the zero-flux conditions}",
	Journal = "Int. J. Quant. Chem.",
	Volume = "108",
	Number = "9",
	Pages = "1477–1484",
	abstract = "A rigorous mathematical procedure is proposed in order to employ the variational apparatus in “Quantum theory of atoms in molecules.” This mathematical procedure is free from the previously reported mathematical obstacles. Although it is possible to apply the Schrodinger’s variational procedure to derive the putative net zero-ﬂux condition, no claim has been made to derive the equation of motion (Schrodinger equation) from subsystem variational procedure. In this regard, the problem of admissible and general neighborhoods and their relevance to the subsystem variational procedure has been discussed thoroughly in this article. In the end, a brief discussion has been offered to emphasize the difference between the net and local zero-ﬂux conditions with particular emphasize on its logical consequences.",
	collection = "molecular fragmentation",
	doi = "10.1002/qua.21665",
	localfile = "molecular fragmentation/2008 - Revisiting the foundation of quantum theory of atoms in molecules: the variational procedure and the zero-flux conditions.pdf",
	year = 2008
}

@Article{2008-Neumann,
	Author = "Marcus A. Neumann",
	Title = "{{Tailor-Made} Force Fields for {Crystal-Structure} Prediction}",
	Journal = "J. Phys. Chem. B",
	Volume = "112",
	Number = "32",
	Pages = "9810–9829",
	abstract = "A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory {(DFT)} calculations with an empirical van der Waals correction. All {DFT} calculations are carried out with the {VASP} program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth {CCDC} blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.",
	collection = "molecular crystals",
	doi = "10.1021/jp710575h",
	keywords = "algorithms; force fields",
	localfile = "molecular crystals/2008 - Tailor-made force fields for crystal-structure prediction.pdf",
	year = 2008
}

@Article{2008-Nowak-Wysocki,
	Author = "Katarzyna Nowak and Stanislaw Wysocki",
	Title = "{An experimental and theoretical study of dipole moments of N-[4-(9-acridinylamino)-3-methoxyphenyl]methanesulfonamide}",
	Journal = "Spectroc. Acta Pt. A",
	Volume = "70",
	Number = "4",
	Pages = "805–810",
	abstract = "The excited state {(S1)} dipole moment of {m-AMSA} (1), an acridine derivative with antitumor activity, was determined from solvatochromic shifts of the lowest energy absorption band in several organic solvents. The effect of the solute shape and the values of polarizability on the determined change of dipole moment between ground and excited state was discussed. The dipole moments in S0 and S1 state were calculated in gas phase with semiempirical quantum-chemical and {DFT} and {CIS} methods and in solvents with {SM5.4A} solvation model and compared with values obtained experimentally. All the results show that the dipole moment of compound 1 in the excited state is higher than that in the ground state. These methods quite well predict the values of {[Delta][mu]} between two states of an investigated compound.",
	collection = "nucleic acid drugs",
	doi = "10.1016/j.saa.2007.09.038",
	localfile = "nucleic acid drugs/2008 - An experimental and theoretical study of dipole moments of N-[4-(9-acridinyloamino)-3-methoxyphenyl]methanesulfonamide.pdf",
	year = 2008
}

@Article{2008-Ou-LTHWG,
	Author = "{Tian-Miao} Ou and {Yu-Jing} Lu and {Jia-Heng} Tan and {Zhi-Shu} Huang and {Kwok-Yin} Wong and {Lian-Quan} Gu",
	Title = "{{G-Quadruplexes:} Targets in Anticancer Drug Design}",
	Journal = "ChemMedChem",
	Volume = "3",
	Number = "5",
	Pages = "690–713",
	abstract = "G-quadruplexes ore special secondary structures adopted in some guanine-rich DNA sequences. As guanine-rich sequences are present in important regions of the eukoryotic genome, such as telomeres and the regulatory regions of many genes, such structures may play important roles in the regulation of biological events in the body. G-quadruplexes have become valid targets for new anticancer drugs in the post few decades. Many leading compounds that target these structures have been reported, and a few of them hove entered preclinical or clinical trials. Nonetheless, the electivity of this kind of antitumor compound has yet to be improved in order to suppress the side effects caused by nonselective binding. As drug design targets, the topology and structural characteristics of quadruplexes, their possible biological roles, and the modes and sites of small-ligand binding to these structures should be understood clearly. Herein we provide a summary of published research that has set out to address the above problem to provide useful information on the design of small ligands that target G-quadruplexes. This review also covers research methodologies that have been developed to study the binding of ligands to G-quadruplexes.",
	collection = "nucleic acid drugs",
	doi = "10.1002/cmdc.200700300",
	localfile = "nucleic acid drugs/2008 - G-quadruplexes: targets in anticacncer drug design.pdf",
	shorttitle = "{G-Quadruplexes}",
	year = 2008
}

@Article{2008-Paul-Robeson,
	Author = "D. R. Paul and L. M. Robeson",
	Title = "{Polymer nanotechnology: nanocomposites}",
	Journal = "Polymer",
	Volume = "49",
	Pages = "3187–3204",
	Note = "Well written review, focused on clay nanocomposites.",
	abstract = "In the large field of nanotechnology, polymer matrix based nanocomposites have become a prominent area of current research and development. Exfoliated clay-based nanocomposites have dominated the polymer literature but there are a large number of other significant areas of current and emerging interest. This review will detail the technology involved with exfoliated clay-based nanocomposites and also include other important areas including barrier properties, flammability resistance, biomedical applications, electrical/electronic/optoelectronic applications and fuel cell interests. The important question of the ‘‘nano-effect’’ of nanoparticle or fiber inclusion relative to their larger scale counterparts is addressed relative to crystallization and glass transition behavior. Of course, other polymer (and composite)-based properties derive benefits from nanoscale filler or fiber addition and these are addressed",
	collection = "polymer nanocomposites",
	doi = "10.1016/j.polymer.2008.04.017",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2008 - Polymer nanotechnology: nanocomposites.pdf",
	rating = "2",
	read = "2011-11-10",
	type = "Review",
	year = 2008
}

@Article{2008-Pilme-Piquemal,
	Author = "Julien Pilme and {Jean-Philip} Piquemal",
	Title = "{Advancing beyond charge analysis using the electronic localization function: Chemically intuitive distribution of electrostatic moments}",
	Journal = "J. Comp. Chem.",
	Volume = "29",
	Number = "9",
	Pages = "1440–1449",
	abstract = "We propose here an evaluation of chemically intuitive distributed electrostatic moments using the topological analysis of the electron localization function {(ELF).} As this partition of the total charge density provides an accurate representation of the molecular dipole, the distributed electrostatic moments based on the {ELF} partition {(DEMEP)} allows computing of local moments located at non atomic centers such as lone pairs, sigma bonds and pi systems. As the local dipole contribution can be decomposed in polarization and charge transfer components, our results indicate that local dipolar polarization of the lone pairs and chemical reactivity are closely related whereas the charge transfer contribution is the key factor driving the local bond dipole. Results on relevant molecules show that local dipole contributions can be used to rationalize inductive polarization effects in alcohols derivatives and typical hydrogen bond interactions. Moreover, bond quadrupole polarization moments being related to a pi character enable to discuss bond multiplicities, and to sort families of molecules according to their bond order. That way, the nature of the {C\&bond;O} bond has been revisited for several typical systems by means of the {DEMEP} analysis which appears also helpful to discuss aromaticity. Special attention has been given to the carbon monoxide molecule, to the {CuCO} complex and to a weak intramolecular {N{\textbar}—CO} interaction involved in several biological systems. In this latter case, it is confirmed that the bond formation is mainly linked to the {CO} bond polarization. Transferability tests show that the approach is suitable for the design of advanced force fields. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008",
	collection = "molecular electrostatics",
	doi = "10.1002/jcc.20904",
	localfile = "molecular electrostatics/2008 - Advancing beyond charge analysis using the electronic localization function: chemically intuitive distribution of electrostatic moments.pdf",
	shorttitle = "Advancing beyond charge analysis using the electronic localization function",
	year = 2008
}

@Article{2008-Pitonak-NRJUH,
	Author = "Michal Pitoňák and P. Neogrády and Jan Řezáč and Petr Jurečka and Miro Urban and Pavel Hobza",
	Title = "{Benzene Dimer: {High-Level} Wave Function and Density Functional Theory Calculations}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "4",
	Number = "11",
	Pages = "1829–1834",
	abstract = "High-level OVOS (optimized virtual orbital space) CCSD(T) interaction energy calculations (up to the aug-cc-pVQZ basis set) and various extrapolations toward the complete basis set (CBS) limit are presented for the most important structures on the benzene dimer potential energy surface. The geometries of these structures were obtained via an all-coordinate gradient geometry optimization using the DFT-D/BLYP method, covering the empirical dispersion correction fitted exclusively for this system. The fit was carried out against two estimated CCSD(T)/CBS potential energy curves corresponding to the distance variation between two benzene rings for the parallel-displaced (PD) and T-shaped (T) structures. The effect of the connected quadruple excitations on the interaction energy was estimated using the CCSD(TQ(f)) method in a 6-31 G*(0.25) basis set, destabilizing the T and T-shaped tilted (TT) structures by approximate to 0.02 kcal/mol and the PD structure by approximate to 0.04 kcal/mol. Our best CCSD(T)/CBS results show, within the error bars of the applied methodology, that the energetically lowest-lying structure is the TT structure, which is nearly 0.1 kcal/mol more stable than the almost isoenergetic PD and T structures. The specifically parametrized DFT-D/BLYP method leads to a correct energy ordering of the structures, with the errors being smaller by 0.2 kcal/mol with respect to the most accurate CCSD(T) values.",
	collection = "stacking",
	doi = "10.1021/ct800229h",
	localfile = "molecular stacking/2008 - Benzene dimer: high-level wave function and density functional theory calculations.pdf",
	shorttitle = "Benzene Dimer",
	year = 2008
}

@Article{2008-Plattner-Meuwly,
	Author = "Nuria Plattner and Markus Meuwly",
	Title = "{The role of higher {CO}-multipole moments in understanding the dynamics of photodissociated carbonmonoxide in myoglobin}",
	Journal = "Biophys. J.",
	Volume = "94",
	Number = "7",
	Pages = "2505–2515",
	abstract = "The inﬂuence of electrostatic multipole moments up to hexadecapole on the dynamics of photodissociated carbon monoxide (CO) in myoglobin is investigated. The CO electrostatic potential is expressed as an expansion into atomic multipole moments of increasing order up to octopole which are obtained from a distributed multipole analysis. Three models with increasingly accurate molecular multipoles (accurate quadrupole, octopole, and hexadecapole moments, respectively) are developed and used in molecular dynamics simulations. All models with a ﬂuctuating quadrupole moment correctly describe the location of the B-state whereas the sign of the octopole moment differentiates between the FeáááCO and FeáááOC orientation. For the infrared spectrum of photodissociated CO, considerable differences between the three electrostatic models are found. The most detailed electrostatic model correctly reproduces the splitting, shift, and width of the CO spectrum in the B-state. From an analysis of the trajectories, the spectroscopic B1 and B2 states are assigned to the FeáááCO and FeáááOC substates, respectively.",
	collection = "molecular electrostatics",
	doi = "10.1529/biophysj.107.120519",
	localfile = "molecular electrostatics/2008 - The role of higher CO multipole moments in understanding the dynamics of photodissociated carbon monoxide in myoglobin.pdf",
	systems = "carbon monoxide",
	year = 2008
}

@Article{2008-Plattner-Meuwly-1,
	Author = "Nuria Plattner and Markus Meuwly",
	Title = "{Atomistic simulations of {CO} vibrations in ices relevant to astrochemistry}",
	Journal = "ChemPhysChem",
	Volume = "9",
	Pages = "1271–1277",
	abstract = "The experimental absorption band of carbon monoxide (CO) in mixed ices has been extensively studied in the past. The astrophysical interest in this band is related to its characteristic shape, which appears to depend on the surrounding ice structure. Herein, molecular dynamics simulations are carried out to analyze the relationship between the structure of the ice and the infrared (IR) spectrum of embedded CO molecules at different concentrations. Instead of conventional force fields, anharmonic potentials are used for the bonded interactions. The electrostatic interactions are more accurately described by means of fluctuating atomic multipole moments (up to quadrupole). The experimentally observed splitting of the CO absorption band (gas phase: 2143 cmÀ1) into a blue- (2152 cmÀ1) and a red-shifted (2138 cmÀ1) signal is also found in the simulations. Complementary atomistic simulations allow us to relate the spectra with the structural features. The distinction between interstitial and substitutional CO molecules as the origin of this splitting is found to be qualitatively correct. However, at increasing CO concentrations, additional effects—such as mutual interactions between CO molecules—become important, and the simplistic picture needs to be revised.",
	collection = "molecular electrostatics",
	doi = "10.1002/cphc.200800030",
	localfile = "molecular electrostatics/2008 - Atomistic simulations of CO vibrations in ices relevant to astrochmistry.pdf",
	year = 2008
}

@Article{2008-Poad-WBBBKA,
	Author = "B. L. J. Poad and P. J. Wearne and E. J. Bieske and A. A. Buchachenko and D. I. G. Bennett and J. Klos and M. H. Alexander",
	Title = "{The Na$^{+}$–H$\_{2}$ cation complex: Rotationally resolved infrared spectrum, potential energy surface, and rovibrational calculations}",
	Journal = "J. Chem. Phys.",
	Volume = "129",
	Number = "18",
	Pages = "184306–8",
	collection = "hydrogen sorption",
	doi = "10.1063/1.3005785",
	localfile = "hydrogen sorption/2008 - The Na+-H2 cation complex: rotationally resolved infrared spectrum, potential energy surface, and rovibrational calcualtions.pdf",
	shorttitle = "The Na$^{+}$–H$\_{2}$ cation complex",
	year = 2008
}

@Article{2008-Price,
	Author = "Sarah L. Price",
	Title = "{Computational prediction of organic crystal structures and polymorphism}",
	Journal = "Int. Rev. Phys. Chem.",
	Volume = "27",
	Number = "3",
	Pages = "541",
	abstract = "The development of a robust manufacturing process for solid organic materials, such as pharmaceuticals, can be complicated when the molecules crystallize in different solid forms, including polymorphs. The diverse challenges to computational chemistry in computing the relative thermodynamic stability of different potential crystal structures for a range of organic molecules are outlined. Once the crystal structures which are thermodynamically feasible have been obtained, then comparison with the experimentally known polymorphs can provide interesting insights into crystallization behaviour. Although the computational prediction of polymorphism requires modelling the kinetic factors that can influence crystallization, the computational prediction of the crystal energy landscape is already a valuable complement to experimental searches for polymorphs.",
	collection = "molecular crystals",
	doi = "10.1080/01442350802102387",
	localfile = "molecular crystals/2008 - Computational prediction of organic crystal structures and polymorphism.pdf",
	year = 2008
}

@Article{2008-Price-1,
	Author = "Sarah L. Price",
	Title = "{From crystal structure prediction to polymorph prediction: interpreting the crystal energy landscape}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "10",
	Number = "15",
	Pages = "1996",
	abstract = "Many organic molecules are emerging as having many crystalline forms, including polymorphs and solvates, as more techniques are being used to generate and characterise the organic solid state. The fundamental scientiﬁc and industrial interest in controlling crystallisation is inspiring the development of computational methods of predicting which crystal structures are thermodynamically feasible. Sometimes, computing this crystal energy landscape will reveal that a molecule has one way of packing with itself that is suﬃciently more favourable than any other so only this crystal structure will be observed. More frequently, there will be many energy minima that are energetically feasible, showing approximately equi-energetic compromises between the various intermolecular interactions allowed by the conformational ﬂexibility. Such cases generally lead to multiple solid forms. At the moment, we usually calculate the lattice energy landscape, an approximation to the real crystal energy landscape at 0 K. Despite its limitations, many studies show that this is a valuable complement to solid form screening, which helps in discovering new structures as well as rationalising the solid forms that are found in experimental searches. The range of factors that can determine which of the thermodynamically feasible crystal structures are observed polymorphs, shows the many further challenges in developing crystal energy landscapes as a tool for control of the organic solid state.",
	collection = "molecular crystals",
	doi = "10.1039/b719351c",
	localfile = "molecular crystals/2008 - From crystal structure prediction t poylmorph prediction: Interpreting the crystal energy landscape.pdf",
	shorttitle = "From crystal structure prediction to polymorph prediction",
	year = 2008
}

@Article{2008-Reis,
	Author = "Fabio D. A. Aarao Reis",
	Title = "{Modeling self-assembly of diblock copolymer-nanoparticle composites}",
	Journal = "Macromolecules",
	Volume = "41",
	Pages = "8932–8937",
	Note = "Demonstrates the coexistence of different phases in NP/DBCP mixtures.",
	abstract = "A cell dynamics method for domain separation of diblock copolymers (DBCPs) interacting with nanoparticles (NPs) whose diffusion coefﬁcients depend on chain conﬁguration is proposed for self-assembly of DBCP/NP composites. Increasing NP concentration slows down domain separation, but matching NP diffusion lengths and lamellar size of DBCPs reduces this effect. The model also explains features of different nanocomposites, such as morphological transitions induced by NPs, the coexistence of lamellar and hexagonal patterns in a single sample, and peaked NP density proﬁles across the parallel domains.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma801592b",
	keywords = "block copolymers; mesophase coexistence; nanospheres; mesophase transitions; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2008 - Modeling self-assembly of diblock copolymer-nanoparticle composites.pdf",
	methods = "CDS/BD",
	year = 2008
}

@Article{2008-Rubes-BN,
	Author = "Miroslav Rubeš and Ota Bludský and Petr Nachtigall",
	Title = "{Investigation of the {Benzene-Naphthalene} and {Naphthalene-Naphthalene} Potential Energy Surfaces: {DFT/CCSD(T)} Correction Scheme}",
	Journal = "ChemPhysChem",
	Volume = "9",
	Number = "12",
	Pages = "1702–1708",
	abstract = "The potential energy surfaces of the naphthalene dimer and benzene-naphthalene complexes are investigated using the recently developed DFT/CCSD(T) correction scheme [J. Chem. Phys. 2008, 128, 114 102]. One and three minima are located on the PES of the benzene-naphthalene and the naphthalene dimer complexes, respectively, all of which are of the parallel-displaced type. The stabilities of benzene-naphthalene and the naphthalene dimer are -4.2 and -6.2 kcal mol(-1), respectively. Unlike the benzene dimer, where the T-shaped complex is the global minimum, the lowest-energy T-shaped structure is about 0.2 and 1.6 kcal mol(-1) above the global minimum on the benzene-naphthalene and the naphthalene dimer potential energy surfaces, respectively.",
	collection = "stacking",
	doi = "10.1002/cphc.200800274",
	localfile = "molecular stacking/2008 - Investigation of the benzene-naphthalene and naphthalene-naphthalene potential energy surfaces: DFT-CCSD(T) correction scheme.pdf",
	shorttitle = "Investigation of the {Benzene-Naphthalene} and {Naphthalene-Naphthalene} Potential Energy Surfaces",
	year = 2008
}

@Article{2008-Rubes-Bludsky,
	Author = "Miroslav Rubeš and Ota Bludský",
	Title = "{Intermolecular π–π interactions in solids}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "10",
	Number = "19",
	Pages = "2611",
	abstract = "A parameter-free DFT/CCSD(T) correction scheme is proposed for precise calculations (close to CCSD(T) accuracy) of weakly bound molecular solids. The correction scheme has been tested for solid benzene and graphite. The CCSD(T)/CBS correction to planewave DFT calculations reproduces the experimentally determined lattice constants for solid benzene. The calculated cohesive energy of benzene (457 meV per molecule) compares well with the experimental values of the heat of sublimation (460 - 560 meV per molecule). For graphite, the correction yields structural parameters (a = 2.46 angstrom, c = 6.60 angstrom) in good agreement with experiment (a = 2.46 A, c = 6.67 angstrom). The calculated exfoliation energy of 54 meV per atom agrees fairly well with the most recent experimental value of 52 +/- 5 meV per atom.",
	collection = "stacking",
	doi = "10.1039/b718701g",
	localfile = "molecular stacking/2008 - Intermolecular pi-pi interactions in solids.pdf",
	year = 2008
}

@Article{2008-Rutledge-DW,
	Author = "Lesley R. Rutledge and Holly F. Durst and Stacey D. Wetmore",
	Title = "{Computational comparison of the stacking interactions between the aromatic amino acids and the natural or (cationic) methylated nucleobases}",
	Journal = "Phys. Chem. Chem. Phys.",
	Volume = "10",
	Number = "19",
	Pages = "2801",
	abstract = "The maximum gas-phase MP2/6-31G*(0.25) stacking energies between the aromatic amino acids and the natural or methylated nucleobases were considered. The potential energy surfaces of dimers were searched as a function of the vertical separation, angle of rotation and horizontal displacement between monomers stacked according to their centers of mass. Our calculations reveal that the stacking interactions of adducts for a given nucleobase are dependent on the methylation site (by up to 20 kJ mol(-1)), where the relative magnitudes of the interactions are determined by the dipole moments of the adducts and the proton affinities of nucleobase methylation sites. Nevertheless, the differences in the (gas-phase) stacking of methylated adducts are small compared with the differences between the stacking of the corresponding natural and methylated nucleobases. Indeed, methylation increases the stacking energy by up to 40 kJ mol(-1) (or 135\%). Although immersing the dimers in different solvents decreases the gas-phase stacking energies with an increase in the polarity of the environment, base methylation still has a significant effect on the nucleobase stacking ability in solvents with large dipole moments, and, perhaps more importantly, environments that mimic enzyme active sites. Our results shed light on the workings of DNA repairs

license: MIT

license_type: permissive

extension: bib