text:
Number = "1-3",
	Pages = "191–199",
	abstract = "Calculations on the structure of {m-AMSA} using the semiempirical {MNDO,} {AM1} and {PM3} and density {functional-B3LYP/6-31G(d)} methods are reported. To assess the accuracy of these methods in predicting the structure of {m-AMSA-base} and {m-AMSA-cation,} the resulting geometrical parameters are compared with available crystallographic data. Structural and electronic properties of {m-AMSA} and its inactive {isomer–o-AMSA} calculated using the above mentioned methods are also described and differences between these two compounds are tried to be found. A marked difference in the biological activity observed between the two molecules can be attributed to geometric factors and also differences in their electronic properties.",
	collection = "nucleic acid drugs",
	doi = "10.1016/j.theochem.2004.04.029",
	localfile = "nucleic acid drugs/2004 - The semiempirical and DFT methods in studies on geometry and energetics of AMSA isomers: comparison of m-AMSA and o-AMSA properties.pdf",
	shorttitle = "The semiempirical and {DFT} methods in studies on geometry and energetics of {AMSA} isomers",
	year = 2004
}

@Article{2004-Reister-Fredrickson,
	Author = "Ellen Reister and Glenn H. Fredrickson",
	Title = "{Nanoparticles in a diblock copolymer background: the potential of mean force}",
	Journal = "Macromolecules",
	Volume = "37",
	Pages = "4718–4730",
	Note = "Studies the PMF between two bare, selective particles in a diblock above and under ODT.",
	abstract = "We have investigated the potential of mean force between two nanoparticles that are surrounded by a symmetric diblock copolymer matrix. The hard nanoparticles are modeled as attractive to one kind of polymer. Using self-consistent-field theory (SCFT), we analyze the energy change of the system when the distance between the particles is changed and subsequently derive the potential of mean force between the particles. Above the order-disorder transition (ODT) the attractive potential of the particles for one kind of monomers leads to a lamellar structure around the particles. These density waves interfere with each other when the distance between the particles is changed, leading to separations with alternating attraction and repulsion between the particles. We further derive analytic results for the potential of mean force in the limit of a weak influence of the particles on the system using the random phase approximation for a diblock copolymer melt. These analytical results are compared with SCFT results. Below the ODT, we insert the particles in such a way that the axis connecting them is either perpendicular or parallel to the lamellar polymer structure. Using SCFT, we study the energy and structural change of the system when the particle distance is changed for these two cases.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma035849p",
	keywords = "block copolymers; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2004 - Nanoparticles in a diblock copolymer background: the potential of mean force.pdf",
	methods = "SCFT",
	year = 2004
}

@Article{2004-Rinaldi-BRD,
	Author = "Daniel Rinaldi and Alain Bouchy and Jean-Louis Rivail and Valerie Dillet",
	Title = "{A self-consistent reaction field model of solvation using distributed multipoles. {I}. {E}nergy and energy derivatives}",
	Journal = "J. Chem. Phys.",
	Volume = "120",
	Number = "5",
	Pages = "2343–2350",
	abstract = "The self-consistent reaction field model developed previously by the authors in the case of single center multipole expansion of the electronic structure of the solute has been extended to the case of a distributed multipole expansion. Three different expansions have been tested and two of them have proved to be rapidly convergent. The performances of the code are illustrated by the density functional theory treatment of few test systems: guanine, cytosine, and cytosine hydrated with one and three water molecules. A robust fast computer code has been tested to get the electronic structure, the electrostatic contribution to the solute-solvent free energy of interaction, and the optimized molecular geometry in solution. (C) 2004 American Institute of Physics.",
	cited = "3 (2005-05-05)",
	collection = "molecular solvation",
	doi = "10.1063/1.1635355",
	localfile = "molecular solvation/2004 - A self-consistent reaction field model of solvation using distributed multipole. I. Energy and energy derivatives.pdf",
	year = 2004
}

@Article{2004-Sagui-PDR,
	Author = "Celeste Sagui and Pawel Pomorski and Thomas A. Darden and Christopher Roland",
	Title = "{Ab initio calculation of electrostatic multipole with Wannier functions for large-scale biomolecular simulations}",
	Journal = "J. Chem. Phys.",
	Volume = "120",
	Number = "9",
	Pages = "4530–4544",
	abstract = "It has long been known that accurate electrostatics is a key issue for improving current force ﬁelds for large-scale biomolecular simulations. Typically, this calls for an improved and more accurate description of the molecular electrostatic potential, which eliminates the artifacts associated with current point charge-based descriptions. In turn, this involves the partitioning of the extended molecular charge distribution, so that charges and multipole moments can be assigned to different atoms. As an alternate to current approaches, we have investigated a charge partitioning scheme that is based on the maximally localized Wannier functions. This has the advantage of partitioning the charge, and placing it around the molecule in a chemically meaningful manner. Moreover, higher order multipoles may all be calculated without any undue numerical difﬁculties. Tests on isolated molecules and water dimers, show that the molecular electrostatic potentials generated by such a Wannier-function based approach are in excellent agreement with the density functional-based calculations.",
	collection = "molecular electrostatics",
	doi = "10.1063/1.1644800",
	localfile = "molecular electrostatics/2004 - Ab initio calculation of electrostatic multipoles with Wannier functions for large-scale biomolecular simulations.pdf",
	year = 2004
}

@Article{2004-Sato-Buchner,
	Author = "Takaaki Sato and Richard Buchner",
	Title = "{Dielectric relaxation processes in ethanol/water mixtures}",
	Journal = "J. Phys. Chem. A",
	Volume = "108",
	Pages = "5007–5015",
	cited = "49 (2013-04-29)",
	collection = "molecular solvation",
	doi = "10.1021/jp035255o",
	localfile = "molecular solvation/2004 - Dielectric relaxation processes in ethanol-water mixtures.pdf",
	year = 2004
}

@Article{2004-Sheng-BPRAC,
	Author = "N. Sheng and M. C. Boyce and D. M. Parks and G. C. Rutledge and J. I. Abes and R. E. Cohen",
	Title = "{Multiscale micromechanical modeling of polymer/clay nanocomposites and the effective clay particle}",
	Journal = "Polymer",
	Volume = "45",
	Pages = "487–506",
	collection = "polymer nanocomposites",
	doi = "10.1016/j.polymer.2003.10.100",
	keywords = "mechanical properties; polymer nanocomposites",
	localfile = "polymer nanocomposites/2004 - Multiscale micromechanical modeling of polymer-clay nanocomposites and the effective clay particle.pdf",
	year = 2004
}

@Article{2004-Simonsen-HK,
	Author = "Adam C. Simonsen and Per L. Hansen and Beate Klosgen",
	Title = "{Nanobuibbles give evidence of incomplete wetting at a hydrophobic interface}",
	Journal = "J. Colloid Interface Sci.",
	Volume = "204",
	Pages = "291–299",
	cited = "91 (2013-04-29)",
	collection = "interfaces",
	doi = "10.1016/j.jcis.2003.12.035",
	localfile = "interfaces/2004 - Nanobubbles give evidence of incomplete wetting at a hydrophobic interface.pdf",
	year = 2004
}

@Article{2004-Szefczyk-MRS,
	Author = "Borys Szefczyk and Adrian J. Mulholland and Kara E. Ranaghan and W. Andrzej Sokalski",
	Title = "{Differential transition-state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "126",
	Pages = "16148–16159",
	abstract = "Chorismate mutase is a key model system in the development of theories of enzyme catalysis. To analyze the physical nature of catalytic interactions within the enzyme active site and to estimate the stabilization of the transition state (TS) relative to the substrate (differential transition state stabilization, DTSS), we have carried out nonempirical variation-perturbation analysis of the electrostatic, exchange, delocalization, and correlation interactions of the enzyme-bound substrate and transition-state structures derived from ab initio QM/MM modeling of Bacillus subtilis chorismate mutase. Significant TS stabilization by approximately -23 kcal/mol [MP2/6-31G(d)] relative to the bound substrate is in agreement with that of previous QM/MM modeling and contrasts with suggestions that catalysis by this enzyme arises purely from conformational selection effects. The most important contributions to DTSS come from the residues, Arg90, Arg7, Glu78, a crystallographic water molecule, Arg116, and Arg63, and are dominated by electrostatic effects. Analysis of the differential electrostatic potential of the TS and substrate allows calculation of the catalytic field, predicting the optimal location of charged groups to achieve maximal DTSS. Comparison with the active site of the enzyme from those of several species shows that the positions of charged active site residues correspond closely to the optimal catalytic field, showing that the enzyme has evolved specifically to stabilize the TS relative to the substrate.",
	collection = "enzymes",
	doi = "10.1021/ja049376t",
	localfile = "enzymes/2004 - Differential transition-state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field.pdf",
	year = 2004
}

@Article{2004-Thompson-RL,
	Author = "Russell B. Thompson and Kim O. Rasmussen and Turab Lookman",
	Title = "{Origins of elastic properties in ordered block copolymer-nanoparticle composites}",
	Journal = "Nano Lett.",
	Volume = "4",
	Number = "12",
	Pages = "2455–2459",
	Note = "Predicts a diblock copolymer lamellar phase (Nχ=25) to be weaker (lower tensile modulus) when loaded (15\%) with spherical 0.725Rg NPs.",
	abstract = "We predict a diblock copolymer melt in the lamellar phase with added spherical nanoparticles that have an affinity for one block to have a lower tensile modulus than a pure diblock copolymer system. This weakening is due to the swelling of the lamellar domain by nanoparticles and the displacement of polymer by elastically inert fillers. Despite the overall decrease in the tensile modulus of a polydomain sample, the shear modulus for a single domain is unaffected by fillers.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/nl048407f",
	keywords = "block copolymers; mechanical properties; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2004 - Origins of elastic properties in ordered block copolymer-nanoparticle composites.pdf",
	methods = "SCFT",
	year = 2004
}

@Article{2004-Trieb-RWWL,
	Author = "Michael Trieb and Christine Rauch and Fajar R. Wibowo and Bernd Wellenzohn and Klaus R. Liedl",
	Title = "{Cooperative effects on the formation of intercalation sites}",
	Journal = "Nucl. Acids Res.",
	Volume = "32",
	Number = "15",
	Pages = "4696–4703",
	abstract = "Daunomycin is one of the most important agents used in anticancer chemotherapy. It interacts with {DNA} through intercalation of its planar chromophore between successive base pairs. The effect of intercalation on structure, dynamics and energetics is the topic of a wealth of scientific studies. In the present study, we report a computational examination of the energetics of the intercalation process. In detail, we concentrate on the energetic penalty that intercalation of daunomycin introduces into {DNA} by disturbing it from its unbound conformation. For these means, we are analyzing already published molecular dynamics simulations of {daunomycin-DNA} complexes and present novel simulations of a {bisdaunomycin-DNA} and a {9-dehydroxydaunomycin-DNA} intercalated complex using the {MM-GBSA} module implemented in the {AMBER} suite of programs. Using this molecular dynamics based, continuum solvent method we were able to calculate the energy required to form an intercalation site. Consequently, we compare the free energy of the duplex {d(CGCGCGATCGCGCG)2} in the B-form conformation with the respective conformations when intercalated with daunomycin and a bisintercalating analog. Our results show that the introduction of one single intercalation site costs [{\textasciitilde}]32 kcal/mol. For double intercalation, or intercalation of the bisintercalator, the respective value for one intercalation site decreases to 27 and 24 kcal/mol, respectively, at a theoretical salt concentration of 0.15 M. This proposes that at least in these cases, a synergistic effect takes place. Although it is well known that intercalation leads to substantial disturbance of the {DNA} conformation, already performed investigations suggest a lower energetic penalty. Nevertheless to the best of our knowledge the calculations presented here are the most complete ones and consider hydration effects for the first time. The interaction energy between the ligand and the {DNA} certainly over-compensates this penalty for introducing the intercalation site and thus favors complexation. Such analyses are helpful for the description of allosteric effects in protein ligand binding.",
	collection = "nucleic acid intercalation",
	doi = "10.1093/nar",
	localfile = "nucleic acid intercalation/2004 - Cooperative effects on teh formation of itnercalation sites.pdf",
	year = 2004
}

@Article{2004-Tsuzuki-HUM,
	Author = "Seiji Tsuzuki and Kazumasa Honda and Tadafumi Uchimaru and Masuhiro Mikami",
	Title = "{High-level ab initio computations of structures and interaction energies of naphthalene dimers: Origin of attraction and its directionality}",
	Journal = "J. Chem. Phys.",
	Volume = "120",
	Number = "2",
	Pages = "647",
	abstract = "The intermolecular interaction energies of naphthalene dimers have been calculated by using an aromatic intermolecular interaction model (a model chemistry for the evaluation of intermolecular interactions between aromatic molecules). The CCSD(T) (coupled cluster calculations with single and double substitutions with noniterative triple excitations) interaction energy at the basis set limit has been estimated from the second-order Møller–Plesset perturbation interaction energy near saturation and the CCSD(T) correction term obtained using a medium-size basis set. The estimated interaction energies of the set of geometries explored in this work show that two structures emerge as being the lowest energy, and may effectively be considered as isoenergetic on the basis of the errors inherent in out extrapolation procedure. These structures are the slipped-parallel (C-i) structure (-5.73 kcal/mol) and the cross (D-2d) structure (-5.28 kcal/mol). The T-shaped (C-2v) and sandwich (D-2h) dimers are substantially less stable (-4.34 and -3.78 kcal/mol, respectively). The dispersion interaction is found to be the major source of attraction in the naphthalene dimer. The electrostatic interaction is substantially smaller than the dispersion interaction. The large dispersion interaction is the cause of the large binding energies of the cross and slipped-parallel dimers.",
	collection = "stacking",
	doi = "10.1063/1.1630953",
	localfile = "molecular stacking/2004 - High-level ab initio computations of structures and interaction energies of naphthalene dimers: origin of attraction and its directionality.pdf",
	shorttitle = "High-level ab initio computations of structures and interaction energies of naphthalene dimers",
	year = 2004
}

@Article{2004-Tyagi-LBB,
	Author = "Sandeep Tyagi and Jae Youn Lee and Gavin A. Buxton and Anna C. Balazs",
	Title = "{Using nanocomposite coatings to heal surface defects}",
	Journal = "Macromolecules",
	Volume = "37",
	Pages = "9160–9168",
	abstract = "Using computer simulations, we investigate the benefits of coating substrates that contain nanoscale defects with nanoparticle-filled polymer films. In particular, we focus on surfaces that contain a nanoscopic notch and use molecular dynamics (MD) simulations to determine the particle and polymer distribution on the damaged surface. The calculations reveal that a high volume fraction of relatively large particles are localized in the notch. Here, the polymer melt induces a depletion attraction between the particles and surface and thereby drives the nanoparticles into the defect. The time required for these relatively large particles to migrate to the notch is comparable to the time needed for the chains to move by approximately four radius of gyrations. The morphology obtained from the MD simulation serves as the input to the lattice spring model (LSM), which allows us to determine the mechanical properties of the nanocomposite-coated surface. The results show that the stress concentration at the notch tip is significantly reduced due to the presence of the nanoparticles. The application of such nanocomposite coatings could potentially yield defect-free surfaces that exhibit enhanced mechanical properties.",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma048773l",
	localfile = "polymer nanocomposites/2004 - Using nanocomposite coating to heal surface defects.pdf",
	year = 2004
}

@Article{2004-Varnai-Zakrzewska,
	Author = "Peter Varnai and Krystyna Zakrzewska",
	Title = "{{DNA} and its counterions: a molecular dynamics study}",
	Journal = "Nucl. Acids Res.",
	Volume = "32",
	Number = "14",
	Pages = "4269–4280",
	abstract = "The behaviour of mobile counterions, Na+ and K+, was analysed around a {B-DNA} double helix with the sequence {CCATGCGCTGAC} in aqueous solution during two 50 ns long molecular dynamics trajectories. The movement of both monovalent ions remains diffusive in the presence of {DNA.} Ions sample the complete space available during the simulation time, although individual ions sample only about one-third of the simulation box. Ions preferentially sample electronegative sites around {DNA,} but direct binding to {DNA} bases remains a rather rare event, with highest site occupancy values of {\textless}13\%. The location of direct binding sites depends greatly on the nature of the counterion. While Na+ binding in both grooves is strongly sequence-dependent with the preferred binding site in the minor groove, K+ mainly visits the major groove and binds close to the centre of the oligomer. The electrostatic potential of an average {DNA} structure therefore cannot account for the ability of a site to bind a given cation; other factors must also play a role. An extensive analysis of the influence of counterions on {DNA} conformation showed no evidence of minor groove narrowing upon ion binding. A significant difference between the conformations of the double helix in the different simulations can be attributed to extensive {alpha}/{gamma} transitions in the phosphate backbone during the simulation with Na+. These transitions, with lifetimes over tens of nanoseconds, however, appear to be correlated with ion binding to phosphates. The ion-specific conformational properties of {DNA,} hitherto largely overlooked, may play an important role in {DNA} recognition and binding.",
	collection = "nucleic acids",
	doi = "10.1093/nar",
	localfile = "nucleic acids/2004 - DNA and its counterions: a molecular dynamics study.pdf",
	shorttitle = "{DNA} and its counterions",
	year = 2004
}

@Article{2004-Volkov-Coppens,
	Author = "Anatoliy Volkov and Phillip Coppens",
	Title = "{Calculation of Electrostatic Interaction Energies in Molecular Dimers From Atomic Multipole Moments Obtained By Different Methods of Electron Density Partitioning}",
	Journal = "J. Comp. Chem.",
	Volume = "25",
	Number = "7",
	Pages = "921–934",
	abstract = "Accurate and fast evaluation of electrostatic interactions in molecular systems is still one of the most challenging tasks in the rapidly advancing field of macromolecular chemistry, including molecular recognition, protein modeling and drug design. One of the most convenient and accurate approaches is based on a Buckingham-type approximation that uses the multipole moment expansion of molecular/atomic charge distributions. In the mid-1980s it was shown that the pseudoatom model commonly used in experimental X-ray charge density studies can be easily combined with the Buckingham-type approach for calculation of electrostatic interactions, plus atom-atom potentials for evaluation of the total interaction energies in molecular systems. While many such studies have been reported, little attention has been paid to the accuracy of evaluation of the purely electrostatic interactions as errors may be absorbed in the semiempirical atom-atom potentials that have to be used to account for exchange repulsion and dispersion forces. This study is aimed at the evaluation of the accuracy of the calculation of electrostatic interaction energies with the Buckingham approach. To eliminate experimental uncertainties, the atomic moments are based on theoretical single-molecule electron densities calculated at various levels of theory. The electrostatic interaction energies for a total of I I dimers of a-glycine, N-acetylglycine and L-(+)-lactic acid structures calculated according to Buckingham with pseudoatom, stockholder and atoms-in-molecules moments are compared with those evaluated with the Morokuma-Ziegler energy decomposition scheme. For a-glycine a comparison with direct “pixel-by-pixel” integration method, recently developed Gavezzotti, is also made. It is found that the theoretical pseudoatom moments combined with the Buckingham model do predict the correct relative electrostatic interactions energies, although the absolute interaction energies are underestimated in some cases. The good agreement between electrostatic interaction energies computed with Morokuma-Ziegler partitioning, Gavezzotti's method, and the Buckingham approach with atoms-in-molecules moments demonstrates that reliable and accurate evaluation of electrostatic interactions in molecular systems of considerable complexity is now feasible.",
	cited = "6 (2005-04-13)",
	collection = "molecular electrostatics",
	doi = "10.1002/jcc.20023",
	localfile = "molecular electrostatics/2004 - Calculation of electrostatic interaction energies in molecular dimers from atomic multipole moments obtained by different methods of electron density partitioning.pdf",
	year = 2004
}

@Article{2004-Wengel,
	Author = "Jesper Wengel",
	Title = "{Nucleic acid nanotechnology-towards Angstrom-scale engineering}",
	Journal = "Org. Biomol. Chem.",
	Volume = "2",
	Number = "3",
	Pages = "277–280",
	abstract = "Nucleic acids and analogues are suitable building blocks for reliable self-assembly of nanometer-sized two- or three-dimensional materials. In order to mimic or approach nature with respect to size and function, Angstrom-scale chemical engineering is emerging as pivotal for future developments. Efforts within nucleic acid nanotechnology will be focussed on generating rigid and stable low nanometer-sized structures carrying functionalities with predictable spatial positioning allowing, by encoded self-assembly, functional nucleic acid architectures to be built towards applications within the biological and material sciences.",
	collection = "nucleic acids",
	doi = "10.1039/b313986g",
	localfile = "nucleic acids/2004 - Nucleic acid nanotechnology - towards angstrom-scale engineering.pdf",
	year = 2004
}

@Article{2004-Xu-ZSGOZGR,
	Author = "Ting Xu and Andrei V. Zvelindovsky and G. J. Agur Sevink and Oleg Gang and Ben Ocko and Yuqing Zhu and Samuel P. Gido and Thomas P. Russell",
	Title = "{Electric Field Induced {Sphere-to-Cylinder} Transition in Diblock Copolymer Thin Films}",
	Journal = "Macromolecules",
	Volume = "37",
	Number = "18",
	Pages = "6980–6984",
	abstract = "An electric field induced sphere-to-cylinder transition in thin films of asymmetric polystyrene-b-poly(methyl methacrylate) diblock copolymers was observed. In the absence of an applied electric field, thin films of the asymmetric diblock copolymer consisted of layers of spherical microdomains with poor in-plane long-range ordering. Under a {40V/mum} applied electric field, hexagonally packed cylindrical microdomains normal to the surface were found. Cross-sectional transmission electron microscopy images of the intermediate stages of the alignment indicated that, under an electric field, the asymmetric diblock copolymer formed spherical microdomains that were deformed into ellipsoids and, with time, interconnected into cylindrical microdomains oriented in the direction of the applied electric field. Simulations suggest that improved long-range order of the cylindrical microdomains could be achieved by cycling the electrical field.",
	collection = "block copolymers",
	doi = "10.1021/ma049235b",
	keywords = "block copolymers; electric fields; mesophase transitions",
	localfile = "block copolymers/2004 - Electric field induced sphere-to-cylinder transition in diblock copolymer thin films.pdf",
	year = 2004
}

@Article{2004-Yan,
	Author = "Hao Yan",
	Title = "{Materials Science: Nucleic Acid Nanotechnology}",
	Journal = "Science",
	Volume = "306",
	Number = "5704",
	Pages = "2048–2049",
	abstract = "(Excerpt) Nucleic acids are best known as the carriers of genetic information, but they are also a versatile material for designing nanometer-scale structures, because nucleic acid sequences can be designed such that the strands fold into well-defined secondary structures. In 1982, Seeman (1) first proposed using branched DNA building blocks to construct ordered arrays. In recent years, DNA has been shown to be an ideal molecule for building micrometer-scale arrays (2, 3) with nanometer-scale features. DNA can also be used to make nanometer-scale materials with moving parts, such as nanotweezers.",
	collection = "nucleic acids",
	doi = "10.1126/science.1106754",
	localfile = "nucleic acids/2004 - Materials Science: Nucleic acid nanotechnology.pdf",
	shorttitle = "{MATERIALS} {SCIENCE}",
	year = 2004
}

@Article{2005-Alexander-Cravatt,
	Author = "Jessica P. Alexander and Benjamin F. Cravatt",
	Title = "{mechanism of carbamate inactivation of FAAH: implications for the design of covalent inhibitors and in vivo functional probes for enzymes}",
	Journal = "Chem. Biol.",
	Volume = "12",
	Pages = "1179–1187",
	abstract = "Fatty acid amide hydrolase (FAAH) regulates a large class of signaling lipids, including the endocannabinoid anandamide. Carbamate inhibitors of FAAH display analgesic and anxiolytic properties in rodents. However, the mechanism by which carbamates inhibit FAAH remains obscure. Here, we provide biochemical evidence that carbamates covalently modify the active site of FAAH by adopting an orientation opposite of that originally predicted from modeling. Based on these results, a series of carbamates was designed that display enhanced potency. One agent was converted into a ‘‘click chemistry’’ probe to comprehensively evaluate the proteome reactivity of FAAH-directed carbamates in vivo. These inhibitors were selective for FAAH in the nervous system, but they reacted with several enzymes in peripheral tissues. The experimental strategy described herein can be used to create in vivo probes for any enzyme susceptible to covalent inhibition.",
	collection = "enzymes",
	doi = "10.1016/j.chembiol.2005.08.011",
	localfile = "enzymes/2005 - Mechanism of carbamate inactivation of FAAH: implications for the design of covalent inhibitors and in vivo functional probes for enzymes.pdf",
	year = 2005
}

@Article{2005-Bader,
	Author = "Richard F. W. Bader",
	Title = "{The Quantum Mechanical Basis of Conceptual Chemistry}",
	Journal = "Monatshefte für Chemie",
	Volume = "136",
	Number = "6",
	Pages = "819–854",
	abstract = "An experimentalist approaching theory for an understanding of conceptual chemistry that can be related to measurable properties, focuses on the electron density distribution. One finds in the topology of the electron density the definition of an atom, of the bonding between atoms, and of the boundary condition for the extension of quantum mechanics to an open system – to an atom in a molecule. This paper describes this approach, as it evolved from the failure of existing models to a study of molecular charge distributions and of how these studies resulted in the extension of quantum mechanics to an open system using the action principle.",
	collection = "philosophy",
	doi = "10.1007/s00706-005-0307-x",
	localfile = "philosophy/2005 - The quantum mechanical basis of conceptual chemistry.pdf",
	year = 2005
}

@Article{2005-Bader-Fang,
	Author = "Richard F. W. Bader and {De-Chai} Fang",
	Title = "{Properties of atoms in molecules: caged atoms and the Ehrenfest force}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "1",
	Pages = "403–414",
	abstract = "This paper uses the properties of atom X enclosed within an adamantane cage, denoted by X@C10H16, as a vehicle to introduce the Ehrenfest force into the discussion of bonding, the properties being determined by the physics of an open system. This is the force acting on an atom in a molecule and determining the potential energy appearing in Slater’s molecular virial theorem. The Ehrenfest force acting across the interatomic surface of a bonded pair of atoms linked by a bond paths is attractive, each atom being drawn toward the other, and the associated surface virial that measures the contribution to the energy arising from the formation of the surface is stabilizing. It is the Ehrenfest force that determines the adhesive properties of surfaces. The endothermicity of formation for X ) He or Ne is not a result of instabilities incurred in the interaction of X with the four methine carbons to which it is bonded, interactions that are stabilizing both in terms of the changes in the atomic energies and in the surface virials. The exothermicity for X = Be2+, B3+, and Al3+ is a consequence of the transfer of electron density from the hydrogen atoms to the carbon and X atoms, the exothermicity increasing with charge transfer despite an increase in the contained volume of X.",
	collection = "quantum chemistry",
	doi = "10.1021/ct049839l",
	localfile = "quantum chemistry/2005 - Properties of atoms in molecules: caged atoms and the Ehrenfest force.pdf",
	year = 2005
}

@Article{2005-Bansal-YLCBKS,
	Author = "Amitabh Bansal and Hoichang Yang and Chunzhao Li and Kilwon Cho and Brian C. Benicewicz and Sanat K. Kumar and Linda S. Schadler",
	Title = "{Quantitative equivalence between polymer nanocomposites and thin polymer films}",
	Journal = "Nature Mat.",
	Volume = "4",
	Pages = "693–698",
	collection = "polymer nanocomposites",
	doi = "10.1038/nmat1447",
	keywords = "polymer nanocomposites; thin films",
	localfile = "block copolymer nanocomposites/2005 - Quantitative equivalece between polymer nanocomposites and thin polymer films.pdf",
	year = 2005
}

@Article{2005-Benevides-Thomas,
	Author = "James M. Benevides and George J. Thomas",
	Title = "{Local Conformational Changes Induced in {B-DNA} by Ethidium Intercalation}",
	Journal = "Biochemistry",
	Volume = "44",
	Number = "8",
	Pages = "2993–2999",
	abstract = "Structural effects of binding the intercalating drug ethidium bromide {(EtBr)} to 160 base pair (bp) fragments of nucleosomal calf thymus {DNA} have been probed by the method of Raman difference spectroscopy. With the use of a near-infrared {(NIR)} laser source to excite the Raman spectrum at 752 nm, vibrational signatures of both the {EtBr} intercalant and {DNA} target have been identified in spectra of the {drugDNA} complexes. Analysis of the results obtained on complexes consisting of 1 {EtBr} bound/10 bp leads to the following conclusions: (i) Raman markers diagnostic of {DNA} phosphodiester conformation are converted from the B type to the A type with {EtBr} binding, commensurate with the proportion of ethidium-bound nucleotides in the complex. (ii) Ethidium binding converts deoxynucleoside sugar puckers from the C2`-endo to the C3`-endo conformation, also consistent with binding stoichiometry. Both pyrimidine and purine deoxynucleoside sugar puckers are perturbed by the phenanthridinium ring intercalation. (iii) Phenanthridinium insertion between bases is accomplished with no apparent change in hypochromicities of purine or pyrimidine Raman markers, indicating that basephenanthridinium interactions provide compensatory hypochromic effects. (iv) Novel Raman markers of helix unwinding have been identified and assigned primarily to methylene deformation modes of the deoxyribosyl {C2`H2} and {C5`H2} groups. The present study provides new insights into {drugDNA} recognition in solution and demonstrates the feasibility of {NIRRaman} spectroscopy for structural studies of highly chromophoric {DNA} complexes.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/bi048651l",
	localfile = "nucleic acid intercalation/2005 - Local conformational changes induced in B-DNA by ethidium intercalation.pdf",
	year = 2005
}

@Article{2005-Binder-KSF,
	Author = "Wolfgang H. Binder and Christian Kluger and Christoph J. Straif and Gernot Freidbacher",
	Title = "{Directed nanoparticle binding onto microphase-separated block copolymer thin films}",
	Journal = "Macromolecules",
	Volume = "38",
	Pages = "9405–9410",
	Note = "Demonstrates the binding of NPs to specific regions of a lamellar BCP melt via hydrogen bonds.",
	abstract = "(Excerpt) The binding of nanoparticles (NPs) onto polymeric surfaces is an important step in generating ordered particle arrays. Usually, self-assembly processes are required to direct nanocrystals with sizes from 1 nm up to tens of nanometers onto functional surfaces. Critical for this binding and deposition process is (a) the control of the chemical nature of the surface onto which the NPs are bound, (b) the structure of the surface of the nanoparticles, in particular the chemical moieties bound, and (c) the tuning of the supramolecular interaction acting between the NP surface and the polymeric surface in terms of binding strength, binding multiplicity, and binding kinetics. In the past, several NP/surface systems relying on self-assembled monolayers (SAM’s) have been reported.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma0518252",
	keywords = "block copolymers; nanopinning; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2005 - Directed nanoparticle binding onto microphase-separated block copolymer thin films.pdf",
	methods = "GPC, NMR, AFM",
	systems = "Au@PS-PVP",
	year = 2005
}

@Article{2005-Bockstaller-MT,
	Author = "Michael R. Bockstaller and Rafal A. Mickiewicz and Edwin L. Thomas",
	Title = "{Block copolymer nanocomposites: perspectives for tailored functional materials}",
	Journal = "Adv. Mater.",
	Volume = "17",
	Pages = "1331–1349",
	abstract = "Heterogeneous materials in which the characteristic length scale of the filler material is in the nanometer range-i.e., nanocomposites-is currently one of the fastest growing areas of materials research. Polymer nanocomposites have expanded beyond the original scope of polymer-nanocrystal dispersions for refractive-index tuning or clay-filled homopolymers primarily pursued for mechanical reinforcement, to include a wide range of applications. This article highlights recent research efforts in the field of structure formation in block copolymer-based nanocomposite materials, and points out opportunities for novel materials based on inclusion of different types of nanoparticles. The use of block copolymers instead of homopolymers as the matrix is shown to afford opportunities for controlling the spatial and orientational distribution of the nanoelements. This, in turn, allows much more sophisticated tailoring of the overall properties of the composite material.",
	collection = "block copolymer nanocomposites",
	doi = "10.1002/adma.200500167",
	keywords = "block copolymers; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2005 - Block copolymer nanocomposites: perspecitves for tailored functional materials.pdf",
	rating = "2",
	type = "Review",
	year = 2005
}

@Article{2005-Bordiga-VRRCZABHL,
	Author = "Silvia Bordiga and Jenny G. Vitillo and Gabriele Ricchiardi and Laura Regli and Donato Cocina and Adriano Zecchina and Bjørnar Arstad and Morten Bjørgen and Jasmina Hafizovic and Karl Petter Lillerud",
	Title = "{Interaction of Hydrogen with {MOF-5}}",
	Journal = "J. Phys. Chem. B",
	Volume = "109",
	Number = "39",
	Pages = "18237–18242",
	collection = "hydrogen sorption",
	doi = "10.1021/jp052611p",
	localfile = "hydrogen sorption/2005 - Interaction of hydrogen with MOF-5.pdf",
	year = 2005
}

@Article{2005-Bryk,
	Author = "Paweł Bryk",
	Title = "{Wetting in mixtures of colloids and excluded-volume polymers from density-functional theory}",
	Journal = "J. Chem. Phys.",
	Volume = "123",
	Pages = "234907",
	collection = "polymers",
	doi = "10.1063/1.2129261",
	localfile = "polymers/2005 - Wetting in mixtures of colloids and excluded-volume polymers from density-functional theory.pdf",
	year = 2005
}

@Article{2005-Cao-Wu,
	Author = "Dapeng Cao and Jianzhong Wu",
	Title = "{Microstructure of block copolymers near selective surfaces: theoretical predictions and configurational-bias Monte Carlo simulation}",
	Journal = "Macromolecules",
	Volume = "38",
	Pages = "971–978",
	abstract = "We report a new density functional theory (DFT) for block copolymers and its performance for representing the microscopic structure has been tested with the configurational-bias Monte Carlo simulation. The segmental density profiles are calculated for systems containing short block copolymers, represented by tangent-sphere square-well chains of sequences “AABB”, “AAAABBBB”, “ABBBBA”, “ABBBBBBA”, “BBAABB”, and “BBBBAABBBB” confined in slit pores where the planar surfaces attract “A” segments but repel “B” segments. The detailed segmental density profiles are calculated for block copolymers confined in slit pores where the planar surfaces attract “A” segments but repel “B” segments. For all conditions considered, the microscopic structures predicted by the DFT are in excellent agreement with the simulation results. Interesting loop and tail conformations of the block copolymers are observed near the selective surfaces. The effects of surface energy, chain length, and copolymer backbone structures on the microscopic segregation of “AB” segments are also investigated.",
	collection = "block copolymers",
	doi = "10.1021/ma048394s",
	keywords = "block copolymers",
	localfile = "block copolymers/2005 - Microstructure of block copolymers near selective surfaces: theoretical predictions and configurational-bias Monte Carlo simulation.pdf",
	year = 2005
}

@Article{2005-Cencek-KPS,
	Author = "Wojciech Cencek and Jacek Komasa and Krzysztof Pachucki and Krzysztof Szalewicz",
	Title = "{Relativistic correction to the helium dimer interaction energy}",
	Journal = "Phys. Rev. Lett.",
	Volume = "95",
	Number = "23",
	abstract = "The lowest-order relativistic correction to the helium-helium interaction energy has been calculated for the first time, using two independent methods based on expansions in explicitly correlated Gaussian functions. At the equilibrium interatomic distance of 5.6 bohr, this correction amounts to +15.4 +/- 0.6 mK. As a by-product, a new upper bound of -10.9985 K for the nonrelativistic Born-Oppenheimer interaction energy has been obtained.",
	collection = "molecular interactions",
	doi = "10.1103/PhysRevLett.95.233004",
	localfile = "molecular interactions/2005 - Relativistic correction to the helium dimer interaction energy.pdf",
	year = 2005
}

@Article{2005-Chan-ZLNG,
	Author = "Elaine R. Chan and Xi Zhang and Cheng-Ying Lee and Matthew Neurock and Sharon C. Glotzer",
	Title = "{Simulations of tetra-tethered organic-inorganic nanocube–polymer assemblies}",
	Journal = "Macromolecules",
	Volume = "38",
	Pages = "6168–6180",
	abstract = "We perform molecular simulations to study the self-assembly of tetratethered nanoparticles with a cubic geometry. We develop a minimal model of the tethered nanoscale building block (NBB) to represent a polyhedral oligomeric silsesquioxane (POSS) molecule with polymeric functionalities based on information about the molecular structure and interactions obtained from ab initio density functional theory calculations. Using this model, we explore the rich nanostructures formed from self-assembly of the NBBs and make analogies with the morphologies observed in block copolymer, surfactant, and liquid crystalline systems. On the basis of the assembled structures produced and determination of the location and nature of the order-disorder transitions in the system, we propose phase diagrams to describe the behavior of these molecules. We find that qualitative similarities exist between the phase diagrams for the tetratethered NBBs and those for block copolymer and surfactant systems.",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma047722l",
	keywords = "self-assembly; nanoparticle grafts; nanospheres",
	localfile = "polymer nanocomposites/2005 - Simulations of tetra-tethered organic-inorganic nanocube-polymer assemblies.pdf",
	year = 2005
}

@Article{2005-Chang-YHCH,
	Author = "Ta-Chau Chang and Yih-Pey Yang and Kai-Hsiang Huang and Cheng-Chung Chang and Christoph Hecht",
	Title = "{Investigation of {Thionin–DNA} Interaction by Satellite Hole Spectroscopy}",
	Journal = "Optics \& Spectroscopy",
	Volume = "98",
	Number = "5",
	Pages = "655–660",
	abstract = "The interactions of the two tautomers of thionin dye with {DNA} have been investigated by using satellite hole burning spectroscopy. Similar features in the absorption and satellite hole spectra of thionin in the presence of calf thymus {(CT)} {DNA} and polynucleotides {[d(GC)6]2} {(GC)} suggested that thionin preferentially binds to {GC} rather than polynucleotides {[d(AT)6]2} {(AT).} Different binding effects of the two tautomers to {DNA} could be observed. While the imino form fully intercalates into the {DNA} base pairs, the amino form is only partially intercalated. In addition, a broad hole associated with an antihole appeared in the presence of {DNA,} particularly in {GC} base pairs. The coincidence of the antihole with the absorption band of the amino form showed that the amino form is the photoproduct of the imino form. An increase in intensity of the broad hole and its antihole and the loss of nonresonant hole intensity upon interaction with {CT} {DNA} could be described by rapid ground state recovery resulting from fast charge transfer between the intercalated thionin and a guanine base quenching the internal conversion. © 2005 Pleiades Publishing, Inc. {[ABSTRACT} {FROM} {AUTHOR]}",
	collection = "nucleic acid intercalation",
	doi = "10.1134/1.1929049",
	localfile = "nucleic acid intercalation/2005 - Investigation of thionin-DNA interaction by satellite hole spectroscopy.pdf",
	year = 2005
}

@Article{2005-Chen-HH,
	Author = "Yung-Lung Chen and Chun-Huei Huang and Wei-Ping Hu",
	Title = "{Theoretical study on the small clusters of LiH, NaH, BeH$\_2$, and MgH$\_2$}",
	Journal = "J. Phys. Chem. A",
	Volume = "109",
	Pages = "9627–9636",
	abstract = "High-level ab initio molecular orbital theory is used to calculate the geometries, vibrational frequencies, atomic charges, and binding energies of the small clusters (LiH)n, (NaH)n, (BeH2)n, and (MgH2)n (n ) 1-4). For (LiH)n and (NaH)n, there are planar cyclic structures when n ) 2, 3. We have found the cubic structure Td in addition to the planar cyclic D4h when n ) 4. The D4h is less stable than the Td geometry. For (BeH2)n and (MgH2)n, when n ) 3, there are three kinds of structures: chain C2V, planar cyclic D3h, and hat-like C2V. The C2V geometry is more stable than the others. When n ) 4, there are four kinds of structures: chain D2h, cubic Td, string-like C2, and cubic transformation C1. The most stable compounds in the families of (LiH)n, (NaH)n, (BeH2)n, and (MgH2)n are cubic Td, cubic Td, chain D2h, and string-like C2 geometries, respectively, when n ) 4. Calculated binding energies range from -24 to -37 kcal/mol for (LiH)n and -19 to -30 kcal/mol for (NaH)n, (BeH2)n, and (MgH2)n. The hydrogen atoms in hydride clusters always have negative charges. The atomic charges of planar cyclic structures are weaker than those of cubic structures, and there is a tendency of reducing along with the increase of the cluster size. The vibrational frequencies of planar cyclic structures have consistent tendency, too. It indicates that the bond distance increases with the ionic character of the bond.",
	collection = "hydrogen bonding",
	doi = "10.1021/jp051978r",
	localfile = "hydrogen bonding/2005 - Theoretical study on the small clusters of LiH, NaH, BeH2, and MgH2.pdf",
	year = 2005
}

@Article{2005-Cheng-CPKPS,
	Author = "Hansong Cheng and Alan C. Cooper and Guido P. Pez and Milen K. Kostov and Pamela Piotrowski and Steven J. Stuart",
	Title = "{Molecular Dynamics Simulations on the Effects of Diameter and Chirality on Hydrogen Adsorption in Single Walled Carbon Nanotubes}",
	Journal = "J. Phys. Chem. B",
	Volume = "109",
	Number = "9",
	Pages = "3780–3786",
	abstract = "We present systematic molecular dynamics simulation studies of hydrogen storage in single walled carbon nanotubes of various diameters and chiralities using a recently developed curvature-dependent force field. Our main objective is to address the following fundamental issues: 1. For a given H2 loading and nanotube type, what is the H2 distribution in the nanotube bundle? 2. For a given nanotube type, what is the maximal loading (H2 coverage)? 3. What is the diameter range and chirality for which H2 adsorption is most energetically favorable? Our simulation results suggest strong dependence of H2 adsorption energies on the nanotube diameter but less dependence on the chirality. Substantial lattice expansion upon H2 adsorption was found. The average adsorption energy increases with the lowering of nanotube diameter (higher curvature) and decreases with higher H2 loading. The calculated H2 vibrational power spectra and radial distribution functions indicate a strong attractive interaction between H2 and nanotube walls. The calculated diffusion coefficients are much higher than what has been reported for H2 in microporous materials such as zeolites, indicating that diffusivity does not present a problem for hydrogen storage in carbon nanotubes.",
	collection = "hydrogen sorption",
	doi = "10.1021/jp045358m",
	keywords = "fullerenes; hydrogen adsorption",
	localfile = "hydrogen sorption/2005 - Molecular dynamics simulations on the effects of diameter and chirality on hydrogen adsorption in single walled carbon nanotubes.pdf",
	year = 2005
}

@Article{2005-Chiu-KKP,
	Author = "Julia J. Chiu and Bumjoon J. Kim and Edward J. Kramer and David J. Pine",
	Title = "{Control of nanoparticle location in block copolymers}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "127",
	Pages = "5036–5037",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ja050376i",
	keywords = "block copolymers; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2005 - Control of nanoparticle location in block copolymers.pdf",
	methods = "TEM",
	systems = "Au-PS@PS-PVP, Au-PVP@PS-PVP, Au-PS-PVP@PS-PVP",
	year = 2005
}

@Article{2005-Cockroft-HLPU,
	Author = "Scott L. Cockroft and Christopher A. Hunter and Kevin R. Lawson and Julie Perkins and Christopher J. Urch",
	Title = "{Electrostatic Control of Aromatic Stacking Interactions}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "127",
	Number = "24",
	Pages = "8594–8595",
	abstract = "A supramolecular approach has been used to investigate the free energies of intermolecular aromatic stacking interactions. Chemical double mutant cycles have been used to measure the effect of a range of substituents on face-to-face stacking interactions with phenyl and pentafluorophenyl rings. Electrostatic effects dominate the trends in interaction energy.",
	collection = "stacking",
	doi = "10.1021/ja050880n",
	localfile = "molecular stacking/2005 - Electrostatic control of aromatic stacking interactions.pdf",
	year = 2005
}

@Article{2005-Cortes-Guzman-Bader,
	Author = "Fernando {Cortés-Guzmán} and Richard F. W. Bader",
	Title = "{Complementarity of {QTAIM} and {MO} theory in the study of bonding in donor-acceptor complexes}",
	Journal = "Coord. Chem. Rev.",
	Volume = "249",
	Number = "5-6",
	Pages = "633–662",
	collection = "quantum chemistry",
	doi = "10.1016/j.ccr.2004.08.022",
	localfile = "quantum chemistry/2005 - Complementarity of QTAIM and MO theory in the study of bonding in donor-acceptor complexes.pdf",
	year = 2005
}

@Article{2005-Cysewski-C,
	Author = "Piotr Cysewski and Żaneta Czyżnikowska-Balcerak",
	Title = "{The MP2 quantum chemistry study on the local minima of guanine stacked with all four nucleic acid bases in conformations corresponding to mean B-DNA}",
	Journal = "J. Mol. Struct.: THEOCHEM",
	Volume = "757",
	Pages = "29–36",
	collection = "nucleic acid bases",
	keywords = "guanine; aromatic stacking",
	localfile = "nucleic acid bases/2005 - The MP2 quantum chemistry study on the local minima of huanine stacked with all four nucleic acid bases in conformations corresponding to mean B-DNA.pdf",
	methods = "MP2/6-31G*",
	systems = "guanine/guanine, guanine/cytosine, guanine/adenine, guanine/uracil",
	year = 2005
}

@Article{2005-Dabkowska-JH,
	Author = "Iwona Dąbkowska and Petr Jurečka and Pavel Hobza",
	Title = "{On geometries of stacked and H-bonded nucleic acid base pairs determined at various {DFT,} {MP2,} and {CCSD(T)} levels up to the {CCSD(T)/complete} basis set limit level}",
	Journal = "J. Chem. Phys.",
	Volume = "122",
	Number = "20",
	Pages = "204322",
	abstract = "The geometries and interaction energies of stacked and hydrogen-bonded uracil dimers and a stacked adenine¯thymine pair were studied by means of high-level quantum chemical calculations. Speciﬁcally, standard as well as counterpoise-corrected optimizations were performed at second-order Møller–Plesset MP2 and coupled cluster level of theory with single, double, and perturbative triple excitations CCSD T levels with various basis sets up to the complete basis set limit. The results can be summarized as follows: i standard geometry optimization with small basis set e.g., 6-31G* provides fairly reasonable intermolecular separation; ii geometry optimization with extended basis sets at the MP2 level underestimates the intermolecular distances compared to the reference CCSD T results, whereas the MP2/cc-pVTZ counterpoise-corrected optimization agrees well with the reference geometries and, therefore, is recommended as a next step for improving MP2/cc-pVTZ geometries; iii the stabilization energy of stacked nucleic acids base pairs depends considerably on the method used for geometry optimization, so the use of reliable geometries, such as counterpoise-corrected MP2/cc-pVTZ ones, is recommended; iv the density functional theory methods fail completely in locating the energy minima for stacked structures and when the geometries from MP2 calculations are used, the resulting stabilization energies are strongly underestimated; v the self-consistent charges–density functional tight binding method, with inclusion of the empirical dispersion energy, accurately reproduces interaction energies and geometries of dispersion-bonded stacked complexes; this method can thus be recommended for prescanning the potential energy surfaces of van der Waals complexes.",
	collection = "nucleic acid bases",
	doi = "10.1063/1.1906205",
	localfile = "nucleic acid bases/2005 - On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels.pdf",
	year = 2005
}

@Article{2005-Dabkowska-VJH,
	Author = "Iwona Dąbkowska and Haydée Valdés Gonzalez and Petr Jurečka and Pavel Hobza",
	Title = "{Stabilization Energies of the Hydrogen-Bonded and Stacked Structures of Nucleic Acid Base Pairs in the Crystal Geometries of CG, AT, and AC DNA Steps and in the NMR Geometry of the 5'-d(GCGAAGC)-3' Hairpin: Complete Basis Set Calculations at the MP2 and CCSD(T) Levels}",
	Journal = "J. Phys. Chem. A",
	Volume = "109",
	Pages = "1131–1136",
	abstract = "Stabilization energies of the H-bonded and stacked structures of a DNA base pair were studied in the crystal structures of adenine-thymine, cytosine-guanine, and adenine-cytosine steps as well as in the 5′-d(GCGAAGC)-3′ hairpin (utilizing the NMR geometry). Stabilization energies were determined as the sum of the complete basis set (CBS) limit of MP2 stabilization energies and the ∆ECCSD(T) - ∆EMP2 correction term evaluated with the 6-31G*(0.25) basis set. The CBS limit was determined by a two-point extrapolation using the aug-cc-pVXZ basis sets for X ) D and T. While the H-bonding energies are comparable to those of base pairs in a crystal and a vacuum, the stacking energies are considerably smaller in a crystal. Despite this, the stacking is still important and accounts for a significant part of the overall stabilization. It contributes equally to the stability of DNA as does H-bonding for AT-rich DNAs, while in the case of GC-rich DNAs it forms about one-third of the total stabilization. Interstrand stacking reaches surprisingly large values, well comparable to the intrastrand ones, and thus contributes significantly to the overall stabilization. The hairpin structure is characterized by significant stacking, and both guanine‚‚‚cytosine pairs possess stacking energies larger than 11.5 kcal/mol. A high portion of stabilization in the studied hairpin comes from stacking (similar to that found for AT-rich DNAs) despite the fact that it contains two GC Watson-Crick pairs having very large H-bonding stabilization. The DFT/B3LYP/6-31G** method yields satisfactory values of interaction energies for H-bonded structures, while it fails completely for stacking.",
	collection = "nucleic acid bases",
	doi = "10.1021/jp046738a",
	localfile = "nucleic acid bases/2005 - Stabilization energies of the hydrogen-bonded and stacked strucutres of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5'-d(GCGAAGC)-3' hairpin: complete basis set calculations.pdf",
	year = 2005
}

@Article{2005-Dyguda-GSL,
	Author = "Edyta Dyguda and Jolanta Grembecka and W. Andrzej Sokalski and Jerzy Leszczyński",
	Title = "{Origins of the activity of {PAL} and {LAP} enzyme inhibitors: Toward ab initio binding affinity prediction}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "127",
	Number = "6",
	Pages = "1658–1659",
	abstract = "(Excerpt) Molecular recognition involving noncovalent interactions between receptor and ligand molecules determines a great variety of chemical and biological phenomena, including the catalytic and inhibitory effects of enzymes.",
	cited = "0 (2005-04-13)",
	collection = "enzymes",
	doi = "10.1021/ja042691v",
	localfile = "enzymes/2005 - Origins of the activity of PAL and LAP enzyme inhibitors: Toward ab initio binding affinity prediction.pdf",
	year = 2005
}

@Article{2005-Fantacci-ASMR,
	Author = "Simona Fantacci and Filippo De Angelis and Antonio Sgamellotti and Alessandro Marrone and Nazzareno Re",
	Title = "{Photophysical Properties of {[Ru(phen)2(dppz)]2+} Intercalated into {DNA:} An Integrated {Car−Parrinello} and {TDDFT} Study}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "127",
	Number = "41",
	Pages = "14144–14145",
	abstract = "Combined {CarParrinello} and time-dependent {DFT} calculations performed on {[Ru(phen)2dppz]2+} intercalated into an adeninethymine tetramer reveal a remarkable influence of the base pairs in determining the electronic structure and the character of the excited states involved in the absorption and emission processes.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/ja054368d",
	localfile = {nucleic acid intercalation/2005 - Photophysical properties of [Ru(phen)2(dppz)]2+ intercalated into DNA; an integrated Car-Parrinello and TDDFT study.pdf},
	shorttitle = "Photophysical Properties of {[Ru(phen)2(dppz)]2+} Intercalated into {DNA}",
	year = 2005
}

@Article{2005-Fedorov-Kitaura,
	Author = "Dmitri G. Fedorov and Kazuo Kitaura",
	Title = "{Coupled-cluster theory based upon the fragment molecular-orbital method}",
	Journal = "J. Chem. Phys.",
	Volume = "123",
	Number = "13",
	abstract = "The fragment molecular-orbital (FMO) method was combined with the single-reference coupled-cluster (CC) theory. The developed method (FMO-CC) was applied at the CCSD and CCSD(T) levels of theory, for the cc-pVnZ family of basis sets (n=D,T,Q) to water clusters and glycine oligomers (up to 32 molecules/residues using as large basis sets as possible for the given system). The two- and three-body FMO-CC results are discussed at length, with emphasis on the basis-set dependence and three-body effects. Two- and three-body approximations based on interfragment distances were developed and the values appropriate for their accurate application carefully determined. The error in recovering the correlation energy was several millihartree for the two-body FMO-CC method and in the submillihartree range for the three-body FMO-CC method. In the largest calculations, we were able to perform the CCSD(T) calculations of (H2O)(32) with the cc-pVQZ basis set (3680 basis functions) and (GLY)(32) with the cc-VDZ basis set (712 correlated electrons). FMO-CC was parallelized using the upper level of the two-layer parallelization scheme. The computational scaling of the two-body FMO-CC method was demonstrated to be nearly linear. As an example of timings, CCSD(T) calculations of (H2O)(32) with cc-pVDZ took 13 min on an eight node 3.2-GHz Pentium4 cluster.",
	collection = "molecular fragmentation",
	localfile = "molecular fragmentation/2005 - Coupled-cluster theory based upon the fragment molecular-orbital method.pdf",
	methods = "FMO, CCSD, CCSD(T)",
	year = 2005
}

@Article{2005-Fukuzawa-KUNKN,
	Author = "Kaori Fukuzawa and Kazuo Kitaura and Masami Uebayasi and Kotoko Nakata and Tsuguchika Kaminuma and Tatsuya Nakano",
	Title = "{Ab initio quantum mechanical study of the binding energies of human estrogen receptor alpha with its ligands: an application of fragment molecular orbital method}",
	Journal = "J. Comp. Chem.",
	Volume = "26",
	Pages = "1–10",
	abstract = "We have theoretically examined the relative binding afﬁnities (RBA) of typical ligands, 17 -estradiol (EST), 17 -estradiol (ESTA), genistein (GEN), raloxifene (RAL), 4-hydroxytamoxifen (OHT), tamoxifen (TAM), clomifene (CLO), 4-hydroxyclomifene (OHC), diethylstilbestrol (DES), bisphenol A (BISA), and bisphenol F (BISF), to the -subtype of the human estrogen receptor ligand-binding domain (hER LBD), by calculating their binding energies. The ab initio fragment molecular orbital (FMO) method, which we have recently proposed for the calculations of macromolecules such as proteins, was applied at the HF/STO-3G level. The receptor protein was primarily modeled by 50 amino acid residues surrounding the ligand. The number of atoms in these model complexes is about 850, including hydrogen atoms. For the complexes with EST, RAL, OHT, and DES, the binding energies were calculated again with the entire ER LBD consisting of 241 residues or about 4000 atoms. No signiﬁcant difference was found in the calculated binding energies between the model and the real protein complexes. This indicates that the binding between the protein and its ligands is well characterized by the model protein with the 50 residues. The calculated binding energies relative to EST were very well correlated with the experimental RBA (the correlation coefﬁcient r 0.837) for the ligands studied in this work. We also found that the charge transfer between ER and ligands is signiﬁcant on ER–ligand binding. To our knowledge, this is the ﬁrst achievement of ab initio quantum mechanical calculations of large molecules such as the entire ER LBD protein.",
	collection = "molecular signaling",
	localfile = "molecular signaling/2005 - Ab initio quantum mechanical study of the binding energies of human estrogen receptor alpha with its ligands: an application of fragment molecule orbital method.pdf",
	year = 2005
}

@Article{2005-Ginzburg,
	Author = "Valeriy V. Ginzburg",
	Title = "{Influence of nanoparticles on miscibility of polymer blends. A simple theory}",
	Journal = "Macromolecules",
	Volume = "38",
	Pages = "2362–2367",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma0482821",
	localfile = "polymer nanocomposites/2005 - Influence of nanoparticles on miscibility of polymer blends. A simplr theory.pdf",
	year = 2005
}

@Article{2005-Gora-GL,
	Author = "Robert W. Góra and Sławomir J. Grabowski and Jerzy Leszczyński",
	Title = "{Dimers of formic acid, acetic acid, formamide and pyrrole-2-carboxylic acid: an ab initio study}",
	Journal = "J. Phys. Chem. A",
	Volume = "109",
	Pages = "6397–6405",
	abstract = "The intermolecular hydrogen bonds in dimers of formic acid, acetic acid, and formamide were investigated. Additionally, three configurations of the pyrrole-2-carboxylic acid (PCA) dimer were studied to analyze how the pyrrole π-electron system influences the carboxylic groups connected by double O-H‚‚‚O hydrogen bonds. The ab initio calculations for the systems investigated were performed at MP2/6-311++G(d,p), MP2/aug-cc-pVDZ, and MP2/aug-cc-pVTZ//MP2/aug-cc-pVDZ levels of theory. The “atoms in molecules” theory of Bader was used and the analysis of the critical points was performed to study the nature of hydrogen bonds. The decomposition of the total interaction energy applied here reveals that the delocalization energy term is a particularly important attractive contribution in these systems, more important in the case of systems forming homonuclear O-H‚‚‚O double hydrogen bonds than in the case of those connected through heteronuclear N-H‚‚‚O bonds. Because the systems analyzed may be formally classified as the resonance-assisted hydrogen bonds (RAHBs), it seems that the dominant contribution from the delocalization interaction energy term is a distinguished feature of such interactions.",
	collection = "hydrogen bonding",
	doi = "10.1021/jp044072e",
	localfile = "hydrogen bonding/2005 - Dimers of formic acid, acetic acid, formamide and pyrrole-2-carboxylic acid: an ab initio study.pdf",
	year = 2005
}

@Article{2005-Gora-SLP,
	Author = "Robert W. Góra and W. Andrzej Sokalski and Jerzy Leszczyński and Virginia B. Pett",
	Title = "{The nature of interactions in the ionic crystal of 3-pentenenitrile, 2-nitro-5-oxo, ion(-1), sodium}",
	Journal = "J. Phys. Chem. B",
	Volume = "109",
	Number = "5",
	Pages = "2027–2033",
	abstract = "The hybrid variation-perturbation many-body interaction energy decomposition scheme has been applied to analyze the physical nature of interactions in the ionic 3-pentenenitrile, 2-nitro-5-oxo, ion(-1), sodium crystal, which can be regarded as a model for a large group of aromatic quaternary nitrogen salts. In the crystal structure the sodium ions and water molecules of adjacent unit cells form a positively charged “inorganic layer” with the sodium ions clustered together along the ab faces with the organic (negative) part in between. This puzzling crystal packing is due to a strong favorable interaction between the water molecule and the sodium ions and a substantial charge transfer from the carbanions that balances out the destabilizing sodium-sodium ion repulsion. Although the majority of cohesion energy of the crystal structure comes from the electrostatic interactions of ions, the resulting net stabilization also depends heavily on the nonadditive delocalization components, due to a counterbalance between the two-body delocalization and exchange effects. The estimated nonadditivity of interactions varies between 12\% and 22\%.",
	cited = "0 (2005-04-13)",
	collection = "molecular crystals",
	doi = "10.1021/jp046912v",
	localfile = "molecular crystals/2005 - The nature of interactions in the ionic crystal of 3-pentenenitrile, 2-nitro-5-oxo, ion(-1), sodium.pdf",
	year = 2005
}

@Article{2005-Hesselmann-JS,
	Author = "Andreas Heßelmann and Georg Jansen and Martin Schütz",
	Title = "{Density-functional theory-symmetry-adapted intermolecular perturbation theory with density fitting: A new efficient method to study intermolecular interaction energies}",
	Journal = "J. Chem. Phys.",
	Volume = "122",
	Number = "1",
	Pages = "014103",
	abstract = "The previously developed DFT-SAPT approach, which combines symmetry-adapted intermolecular perturbation theory SAPT with a density-functional theory DFT representation of the monomers, has been implemented by using density ﬁtting of two-electron objects. This approach, termed DF-DFT-SAPT, scales with the ﬁfth power of the molecular size and with the third power upon increase of the basis set size for a given dimer, thus drastically reducing the cost of the conventional DFT-SAPT method. The accuracy of the density ﬁtting approximation has been tested for the ethyne dimer. It has been found that the errors in the interaction energies due to density ﬁtting are below 10 3 kcal/mol with suitable auxiliary basis sets and thus one or two orders of magnitude smaller than the errors due to the use of a limited atomic orbital basis set. An investigation of three prominent structures of the benzene dimer, namely, the T shaped, parallel displaced, and sandwich geometries, employing basis sets of up to augmented quadruple- quality shows that DF-DFT-SAPT outperforms second-order Møller-Plesset theory MP2 and gives total interaction energies which are close to the best estimates infered from combining the results of MP2 and coupled-cluster theory with single, double, and perturbative triple excitations.",
	collection = "molecular interactions",
	doi = "10.1063/1.1824898",
	localfile = "molecular interactions/2005 - Density-functional theory-symmetry-adapted intermolecular perturbation theory with density fitting: a new efficient method to study intermolecular interactions energies.pdf",
	year = 2005
}

@Article{2005-Hooper-Schweizer,
	Author = "Justin B. Hooper and Kenneth S. Schweizer",
	Title = "{Contact aggregation, bridging, and steric stabilization in dense polymer-particle mixtures}",
	Journal = "Macromolecules",
	Volume = "38",
	Pages = "8858–8869",
	abstract = "A detailed computational study of the potential of mean force between a pair of spherical particles dissolved in a homopolymer melt has been performed using microscopic liquid state theory. The role of particle-to-monomer diameter ratio, degree of polymerization, strength and spatial range of monomer-particle attractions, and direct interfiller attractions has been established. Beyond the small particle regime, the potential of mean force scales linearly with the particle-to-monomer diameter ratio. This simple scaling allows the construction of master curves and the quantification of material specific aspects independent of the filler-to-monomer diameter ratio. For hard-sphere fillers, four general categories of polymer-mediated organization are found: contact aggregation due to depletion attraction, segment level tight particle bridging, steric stabilization due to thermodynamically stable “bound polymer layers”, and “tele-bridging” where distinct adsorbed layers coexist with longer range bridging. The conditions on the strength and spatial range of monomer-particle attractive interactions that define these different modes of organization have been established. Direct interparticle van der Waals attractions favor contact aggregation and thus compete with the rich polymer-mediated behavior. As the direct attractions increase in strength, the globally stable noncontact bridging configuration is gradually destabilized and replaced by contact aggregation as the most favored state of packing. However, bridging states often remain as metastable local minima. Steric stabilization systems are much less affected by direct interfiller attractions due to the thermodynamic stability of distinct bound polymer layers. This suggests design rules for achieving good particle dispersion. In addition, the interesting possibility is raised that sterically stabilized nanofillers may crystallize in a homopolymer matrix at relatively low volume fractions. Our results have implications for nonequilibrium phenomena such as gelation or filler network formation and kinetic stabilization via large repulsive barriers, which are qualitatively discussed.",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma051318k",
	keywords = "nanospheres; polymer nanocomposites",
	localfile = "polymer nanocomposites/2005 - Contact aggregation, bridging, and steric stabilization in dense polymer-particle mixtures.pdf",
	year = 2005
}

@Article{2005-Huang-BB,
	Author = "X. C. Huang and B. J. Braams and J. M. Bowman",
	Title = "{Ab initio potential energy and dipole moment surfaces for {H}5{O}2+}",
	Journal = "J. Chem. Phys.",
	Volume = "122",
	Number = "4",
	abstract = "Full-dimensional ab initio potential energy surface (PES) and dipole moment surface (DMS) are reported for H5O2+. Tens of thousands of coupled-cluster [CCSD(T)] and second-order Møller–Plesset (MP2) calculations of electronic energies, using aug-cc-pVTZ basis, were done. The energies were fit very precisely in terms of all the internuclear distances, using standard least-square procedures, however, with a fitting basis that satisfies permutational symmetry with respect to like atoms. The H5O2+ PES is a fit to 48 189 CCSD(T) energies, containing 7962 polynomial coefficients. The PES has a rms fitting error of 34.9 cm(-1) for the entire data set up to 110000 cm(-1). This surface can describe various internal floppy motions, including the H atom exchanges, monomer inversions, and monomer torsions. First- and higher-order saddle points have been located on the surface and compared with available previous theoretical work. In addition, the PES dissociates correctly (and symmetrically) to H2O + H3O+, with D-e = 11923.8 cm(-1). Geometrical and vibrational properties of the monomer fragments are presented. The corresponding global DMS fit (MP2 based) involves 3844 polynomial coefficients and also dissociates correctly. (C) 2005 American Institute of Physics.",
	collection = "hydrogen bonding",
	doi = "10.1063/1.1834500",
	localfile = "hydrogen bonding/2005 - Ab initio potential energy and dipole moment surfaces for H5O2+.pdf",
	year = 2005
}

@Article{2005-Huck,
	Author = "Wilhelm T. S. Huck",
	Title = "{Effects of nanoconfinement on the morphology and reactivity of organic materials}",
	Journal = "Chem. Commun.",
	Pages = "4143–4148",
	collection = "nanotechnology",
	doi = "10.1039/b502849n",
	keywords = "nanoconfinement",
	localfile = "nanotechnology/2005 - Effects of nanoconfinement on the morphology and reactivity of organic materials.pdf",
	rating = "3",
	read = "2012-01-14",
	type = "Review",
	year = 2005
}

@Article{2005-Hunter-RW,
	Author = "Ken C. Hunter and Lesley R. Rutledge and Stacey D. Wetmore",
	Title = "{The Hydrogen Bonding Properties of Cytosine: A Computational Study of Cytosine Complexed with Hydrogen Fluoride, Water, and Ammonia}",
	Journal = "J. Phys. Chem. A",
	Volume = "109",
	Number = "42",
	Pages = "9554–9562",
	abstract = "Density functional theory is used to study the hydrogen bonding pattern in cytosine, which does not contain alternating proton donor and acceptor sites and therefore is unique compared with the other pyrimidines. Complexes between various small molecules (HF, H2O, and NH3) and four main binding sites in (neutral and (N1) anionic) cytosine are considered. Two complexes (O2(N1) and N3(N4)) involve neighboring cytosine proton acceptor and donor sites, which leads to cooperative interactions and bidendate hydrogen bonds. The third (less stable) complex (N4) involves a single cytosine donor. The final (O2-N3) complex involves two cytosine proton acceptors, which leads to an anticooperative hydrogen bonding pattern for H2O and NH3. On the neutral surface, the anticooperative O2-N3 complex is less stable than those involving bidentate hydrogen bonds, and the H2O complex cannot be characterized when diffuse functions are included in the (6-31G(d,p)) basis set. On the contrary, the anionic O2-N3 structure is the most stable complex, while the HF and H2O N3(N4) complexes cannot be characterized with diffuse functions. B3LYP and MP2 potential energy surface scans are used to consider the relationship between the water N3(N4) and O2-N3 complexes. These calculations reveal that diffuse functions reduce the conversion barrier between the two complexes on both the neutral and anionic surfaces, where the reduction leads to a (O2-N3) energy plateau on the neutral surface and complete (N3(N4)) complex destabilization on the anionic surface. From these complexes, the effects of hydrogen bonds on the (N1) acidity of cytosine are determined, and it is found that the trends in the effects of hydrogen bonds on the (N1) acidity are similar for all pyrimidines.",
	collection = "nucleic acid bases",
	doi = "10.1021/jp0527709",
	localfile = "nucleic acid bases/2005 - The hydrogen bonding properties of cytosine: a computational study of cytosine complexed with hydrogen fluoride, water, and ammonia.pdf",
	shorttitle = "The Hydrogen Bonding Properties of Cytosine",
	year = 2005
}

@Article{2005-Kang-Taton,
	Author = "Youngjong Kang and T. Andrew Taton",
	Title = "{Controlling shell thickness in core-shell gold nanoparticles via surface-templated adsorption of block copolymer surfactants}",
	Journal = "Macromolecules",
	Volume = "38",
	Pages = "6115–6121",
	abstract = "When Au nanoparticles are encapsulated within shells of cross-linked, block copolymer amphiphiles, the structure of the shells is determined by the initial interaction between the amphiphile and the nanoparticle surface. In the case of small nanoparticles, for which particle size is comparable to the dimension of the block copolymer (FAu/Rg ≈ 1), particles act like solutes that are dissolved within polystyrene-block-poly(acrylic acid) (PS-b-PAA) micelle cores. In the case of larger nanoparticles (FAu/Rg > 1), PS-b-PAA adsorption is templated by the particle surface, and a concentric core-shell structure is formed. The thickness of this shell can be predicted from theoretical models of polymer adsorption onto highly curved surfaces and controlled by varying the ratio of polymer to available nanoparticle surface area. We anticipate that these rules will illustrate how cross-linked copolymer shells with predetermined thickness can be used to stabilize and functionalize a variety of nanoparticle materials.",
	collection = "nanoparticles",
	doi = "10.1021/ma050400c",
	keywords = "nanoparticle grafts",
	localfile = "nanoparticles/2005 - Controlling shell thickness in core-shell gold nanoparticles via surface-templated adsorption of block copolymer srfactants.pdf",
	year = 2005
}

@Article{2005-Kim-CYPK,
	Author = "Bumjoon J. Kim and Julia J. Chiu and Gi-Ra Yi and David J. Pine and Edward J. Kramer",
	Title = "{Nanoparticle-induced phase transitions in diblock-copolymer films}",
	Journal = "Adv. Mater.",
	Volume = "17",
	Pages = "2618–2622",
	Note = "Demonstrates order–order transition in PS-b-P2VP copolymer after loading the PS phase with grafted Au particles.",
	abstract = "(Excerpt) Incorporation of nanoparticles into self-assembled block copolymers has been explored as an efficient way for improving the mechanical strength, electrical conductivity, and optical properties of materials at the nanometer scale. Recent computer simulations predict that the cooperative self-organization of nanoparticles and block copolymers should yield a wide variety of structures with well-controlled particle arrangements. Such nanostructures may make it possible to fabricate novel functional materials, such as photonic bandgap materials, nanostructured solar cells, highly efficient catalysts, and high-density magnetic storage media. In particular, gold nanoparticles have attracted much interest for applications as catalysts as well as building blocks for electronic devices that operate at the single-electron level.",
	collection = "block copolymer nanocomposites",
	doi = "10.1002/adma.200500502",
	keywords = "block copolymers; mesophase transitions; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2005 - Nanoparticle-induced phase transitions in diblock-copolymer films.pdf",
	methods = "TEM, mass spectrometry",
	systems = "AU-PS@PS-P2VP",
	year = 2005
}

@Article{2005-Lenz-Schmid,
	Author = "Olaf Lenz and Friederike Schmid",
	Title = "{A simple computer model for liquid lipid bilayers}",
	Journal = "J. Mol. Liquids",
	Volume = "117",
	Pages = "147–152",
	abstract = "We present a simple coarse-grained bead-and-spring model for lipid bilayers. The system has been developed to reproduce the main (gel–liquid) transition of biological membranes on intermediate length scales of a couple of nanometres and is very efficient from a computational point of view. For the solvent environment, two different models are proposed. The first model forces the lipids to form bilayers by confining their heads in two parallel planes. In the second model, the bilayer is stabilised by a surrounding gas of bphantomQ solvent beads, which do not interact with each other. This model takes only slightly more computing time than the first one, while retaining the full membrane flexibility. We calculate the liquid–gel phase boundaries for both models and find that they are very similar.",
	collection = "lipids",
	localfile = "lipid bilayers/2005 - A simple computer model for liquid lipid bilayers.pdf",
	year = 2005
}

@Article{2005-Lin-BHSXALWELWBR,
	Author = "Yao Lin and Alexander Böker and Jinbo He and Kevin Sill and Hongqi Xiang and Clarissa Abetz and Xuefa Li and Jin Wang and Todd Emrick and Su Long and Qiang Wang and Anna C. Balazs and Thomas P. Russell",
	Title = "{Self-directed self-assembly of nanoparticle/copolymer mixtures}",
	Journal = "Nature",
	Volume = "434",
	Pages = "55–59",
	Note = "Shows reorientation of cylinders in PS-b-P2VP films after adding TOPO-covered CdSe particles.",
	abstract = "(Excerpt) The organization of inorganic nanostructures within self-assembled organic or biological templates is receiving the attention of scientists interested in developing functional hybrid materials. Previous efforts have concentrated on using such scaffolds to spatially arrange nanoscopic elements as a strategy for tailoring the electrical, magnetic or photonic properties of the material. Recent theoretical arguments have suggested that synergistic interactions between self-organizing particles and a self-assembling matrix material can lead to hierarchically ordered structures. Here we show that mixtures of diblock copolymers and either cadmium selenide- or ferritin-based nanoparticles exhibit cooperative, coupled self-assembly on the nanoscale. In thin ﬁlms, the copolymers assemble into cylindrical domains, which dictate the spatial distribution of the nanoparticles; segregation of the particles to the interfaces mediates interfacial interactions and orients the copolymer domains normal to the surface, even when one of the blocks is strongly attracted to the substrate. Organization of both the polymeric and particulate entities is thus achieved without the use of external ﬁelds, opening a simple and general route for fabrication of nanostructured materials with hierarchical order.",
	collection = "block copolymer nanocomposites",
	doi = "10.1038/nature03310",
	keywords = "block copolymers; mesophase transitions; nanospheres; polymer nanocomposites; thin films",
	localfile = "block copolymer nanocomposites/2005 - Self-directed self-assembly of nanoparticle-copolymer mixtures.pdf",
	methods = "SAXS, AFM, optical microscopy, TEM, SEM",
	systems = "CdSe@PS-P2VP",
	year = 2005
}

@Article{2005-Lodola-MHTPM,
	Author = "Alessio Lodola and Marco Mor and Johannes C. Hermann and Giorgio Tarzia and Daniele Piomelli and Adrian J. Mulholland",
	Title = "{QM/MM modelling of oleamide hydrolysis in fatty acid amide hydrolase (FAAH) reveals a new mechanism of nucleophile activation}",
	Journal = "Chem. Commun.",
	Pages = "4399–4401",
	abstract = "Fatty acid amide hydrolase (FAAH), a promising target for the treatment of several central and peripheral nervous system disorders, such as anxiety, pain and hypertension, has an unusual catalytic site, and its mechanism has been uncertain; hybrid quantum mechanics/molecular mechanics (QM/MM) calculations reveal a new mechanism of nucleophile activation (involving a Lys–Ser–Ser catalytic triad), with potentially crucial insights for the design of potent and selective inhibitors.",
	collection = "enzymes",
	doi = "10.1039/b503887a",
	localfile = "enzymes/2005 - QMMM modelling of oleamide hydrolysis in fatty acid amide hydrolase (FAAH) reveals a new mechanism of nucleophile activation.pdf",
	year = 2005
}

@Article{2005-Luedtke-LT,
	Author = "Nathan W. Luedtke and Qi Liu and Yitzhak Tor",
	Title = "{On the Electronic Structure of Ethidium}",
	Journal = "Chem. Eur. J.",
	Volume = "11",
	Number = "2",
	Pages = "495–508",
	Note = "Generated π-electron density map based on various experimental results.",
	collection = "nucleic acid intercalation",
	doi = "10.1002/chem.200400559",
	localfile = "nucleic acid intercalation/2005 - On the electronic structure of ethidium.pdf",
	year = 2005
}

@Article{2005-Matsen,
	Author = "Mark W. Matsen",
	Title = "{Effect of chain tilt on the interaction between brush-coated colloids}",
	Journal = "Macromolecules",
	Volume = "38",
	Pages = "4525–4530",
	collection = "nanoparticles",
	doi = "10.1021/ma050362x",
	keywords = "nanoparticle grafts; nanospheres",
	localfile = "nanoparticles/2005 - Effect of chain tilt on the interaction between brush-coated colloids.pdf",
	year = 2005
}

@Article{2005-McKinney-Cravatt,
	Author = "Michele K. McKinney and Benjamin F. Cravatt",
	Title = "{Structure and function of fatty acid amide hydrolase}",
	Journal = "Ann. Rev. Biochem.",
	Volume = "74",
	Pages = "411–32",
	abstract = "Fatty acid amide hydrolase (FAAH) is a mammalian integral membrane enzyme that degrades the fatty acid amide family of endogenous signaling lipids, which includes the endogenous cannabinoid anandamide and the sleep-inducing substance oleamide. FAAH belongs to a large and diverse class of enzymes referred to as the amidase signature (AS) family. Investigations into the structure and function of FAAH, in combination with complementary studies of other AS enzymes, have engendered provocative molecular models to explain how this enzyme integrates into cell membranes and terminates fatty acid amide signaling in vivo. These studies, as well as their biological and therapeutic implications, are the subject of this review.",
	collection = "enzymes",
	doi = "10.1146/annurev.biochem.74.082803.133450",
	keywords = "hydrolysis",
	localfile = "enzymes/2005 - Structure and function of fatty acid amide hydrolase.pdf",
	systems = "fatty acid amide hydrolase",
	year = 2005
}

@Article{2005-Mignon-LG,
	Author = "Pierre Mignon and Stefan Loverix and Paul Geerlings",
	Title = "{Interplay between π-π interactions and the H-bonding ability of aromatic nitrogen bases}",
	Journal = "Chem. Phys. Lett.",
	Volume = "401",
	Pages = "40–46",
	abstract = "The inﬂuence of p–p interactions on the hydrogen bonding ability of pyrimidine and imidazole stacked with substituted benzenes in the T-shaped, parallel-displaced and parallel-sandwich arrangements is studied at the MP2 level of theory. While the dispersion is the major source of the stabilization of the complexes, it appears that the hydrogen bonding ability of the heterocycles is directly related to the electrostatic interaction between the cycles. The dispersion interaction can successfully be modeled by London's for-mula involving the polarizability. The reactivity descriptor local hardness, introduced in a conceptual DFT context, is found to be an excellent tool for the estimation of the interaction energy.",
	collection = "stacking",
	doi = "10.1016/j.cplett.2004.11.016",
	localfile = "molecular stacking/2005 - Interplay between pi-pi interactions and the H-bonding ability of aromatic nitrogen bases.pdf",
	year = 2005
}

@Article{2005-Mignon-LSG,
	Author = "Pierre Mignon and Stefan Loverix and Jan Steyaert and Paul Geerlings",
	Title = "{Influence of the π-π interaction on the hydrogen bonding capacity of stacked DNA/RNA bases}",
	Journal = "Nucl. Acids Res.",
	Volume = "33",
	Number = "6",
	Pages = "1779–1789",
	abstract = "The interplay between aromatic stacking and hydrogen bonding in nucleobases has been investigated via high-level quantum chemical calculations. The experimentally observed stacking arrangement between consecutive bases in DNA and RNA/DNA double helices is shown to enhance their hydrogen bonding ability as opposed to gas phase optimized complexes. This phenomenon results from more repulsive electrostatic interactions as is demonstrated in a model system of cytosine stacked offset-parallel with substituted benzenes. Therefore, the H-bonding capacity of the N3 and O2 atoms of cytosine increases linearly with the electrostatic repulsion between the stacked rings. The local hardness, a density functional theory-based reactivity descriptor, appears to be a key index associated with the molecular electrostatic potential (MEP) minima around H-bond accepting atoms, and is inversely proportional to the electrostatic interaction between stacked molecules. Finally, the MEP minima on surfaces around the bases in experimental structures of DNA and RNA–DNA double helices show that their hydrogen bonding capacity increases when taking more neighboring (intra-strand) stacking partners into account.",
	collection = "nucleic acid bases",
	doi = "10.1093/nar",
	localfile = "nucleic acid bases/2005 - Influence of the π-π interaction on the hydrogen bonding capacity of stacked DNA and RNA bases.pdf",
	year = 2005
}

@Article{2005-Misquitta-PJS,
	Author = "Alston J. Misquitta and Rafał Podeszwa and Bogumił Jeziorski and Krzysztof Szalewicz",
	Title = "{Intermolecular potentials based on symmetry-adapted perturbation theory with dispersion energies from time-dependent density-functional calculations}",
	Journal = "J. Chem. Phys.",
	Volume = "123",
	Number = "21",
	Pages = "214103",
	collection = "molecular interactions",
	doi = "10.1063/1.2135288",
	localfile = "molecular interactions/2005 - Intermolecular potentials based on symmetry-adapted perturbation theory with dispersion energies from time-dependent density-dunctional calcualtions.pdf",
	year = 2005
}

@Article{2005-Mochizuki-FKTKN,
	Author = "Yuji Mochizuki and Kaori Fukuzawa and A. Kato and Shigenori Tanaka and Kazuo Kitaura and Tatsuya Nakano",
	Title = "{A configuration analysis for fragment interaction}",
	Journal = "Chem. Phys. Lett.",
	Volume = "410",
	Number = "4-6",
	Pages = "247 – 253",
	abstract = "We propose a modified version of configuration analysis (CA) for the fragment interaction in conjunction with Kitaura's fragment molecular orbital (FMO) scheme. The proposal is abbreviated as CAFI. The MO sets of fragments are merged and then orthonormalized by the use of a weighted Lowdin orthonormalization. The energy calculation is performed with the concurrent electron relaxation functional (CERF). The relaxation energy is obtained in an orbital-wise fashion and is distinguished as the charge-transfer and the polarization. The utility of CAM is demonstrated through test calculations on hydrogen-bonding systems.",
	collection = "quantum chemistry",
	localfile = "molecular fragmentation/2005 - A configuration analysis for fragment interaction.pdf",
	year = 2005
}

@Article{2005-Mulder-DWK,
	Author = "F Mulder and T Dingemans and M Wagemaker and G Kearley",
	Title = "{Modelling of hydrogen adsorption in the metal organic framework {MOF5}}",
	Journal = "Chem. Phys.",
	Volume = "317",
	Number = "2-3",
	Pages = "113–118",
	collection = "hydrogen sorption",
	doi = "10.1016/j.chemphys.2005.06.003",
	localfile = "hydrogen sorption/2005 - Modelling of hydrogen adsorption in the metal organic framework MOF5.pdf",
	year = 2005
}

@Article{2005-Ozmusul-PSK,
	Author = "Murat S. Ozmusul and Catalin R. Picu and S. S. Sternstein and Sanat K. Kumar",
	Title = "{Lattice Monte Carlo simulations of chain conformations in polymer nanocomposites}",
	Journal = "Macromolecules",
	Volume = "38",
	Pages = "4495–4500",
	collection = "polymer nanocomposites",
	doi = "10.1021/ma0474731",
	keywords = "nanospheres; polymer conformations; polymer nanocomposites",
	localfile = "polymer nanocomposites/2005 - Lattice Monte Carlo simulations of chain conformations in polymer nanocomposites.pdf",
	year = 2005
}

@Article{2005-Parr-AN,
	Author = "Robert G. Parr and Paul W. Ayers and Roman F. Nalewajski",
	Title = "{What is an atom in a molecule?}",
	Journal = "J. Phys. Chem. A",
	Volume = "109",
	Pages = "3957–3959",
	abstract = "The derivation of the Hirshfeld atoms in molecules from information theory is clarified. The importance for chemistry of the concept of atoms in molecules (AIM) is stressed, and it is argued that this concept, while highly useful, constitutes a noumenon in the sense of Kant.",
	collection = "molecular fragmentation",
	doi = "10.1021/jp0404596",
	localfile = "molecular fragmentation/2005 - What is an atom in a molecule.pdf",
	year = 2005
}

@Article{2005-Patchkovskii,
	Author = "S. Patchkovskii",
	Title = "{From The Cover: Graphene nanostructures as tunable storage media for molecular hydrogen}",
	Journal = "Proc. Natl. Acad. Sci.",
	Volume = "102",
	Number = "30",
	Pages = "10439–10444",
	collection = "hydrogen sorption",
	doi = "10.1073/pnas.0501030102",
	localfile = "hydrogen sorption/2005 - Graphene nanostructures as tunable storage media for molecular hydrogen.pdf",
	shorttitle = "From The Cover",
	year = 2005
}

@Article{2005-Qian-Krimm,
	Author = "Weili Qian and Samuel Krimm",
	Title = "{Limitations of the molecular multipole expansion treatment of electrostatic interactions for C-H...O and O-H...O hydrogen bonds and application of a general charge denity approach}",
	Journal = "J. Phys. Chem. A",
	Volume = "109",
	Pages = "5608–5618",
	collection = "molecular electrostatics",
	doi = "10.1021/jp040683v",
	keywords = "multipole expansion",
	localfile = "molecular electrostatics/2005 - Limitations of the molecular multipole expansion treatment of electrostatic interactions for C-H...O and O-H...O hydrogen bonds and application of a general charge density approach.pdf",
	year = 2005
}

@Article{2005-Rafat-Popelier,
	Author = "Michel Rafat and Paul L. A. Popelier",
	Title = "{The electrostatic potential generated by topological atoms. {II}. {I}nverse multipole moments}",
	Journal = "J. Chem. Phys.",
	Volume = "123",
	Number = "20",
	abstract = "Quantum chemical topology defines finite atoms, whose bounded electron density generates a well-defined electrostatic potential. A multipole expansion based on spherical tensors provides a potential that is formally convergent outside the divergence sphere. Part I of this series [Paul L. A. Popelier and Michel Rafat, Chem. Phys. Lett.376, 148 (2003)] showed that a continuous multipole expansion expands the convergence region, thereby allowing the electrostatic potential to be evaluated at short range. Here, we propose a different method, based on “inverse” multipole moments, enabling an expansion that converges everywhere. These moments are defined by inverse (i.e., negative) powers of the magnitude of the position vector describing the electron density inside the atom. We illustrate this technique on nitrogen in N-2, oxygen in H2O, and oxygen in the phenolic group of the amino acid tyrosine. The proposed method constitutes a considerable advance over the method presented in Part I. (c) 2005 American Institute of Physics.",
	collection = "molecular electrostatics",
	doi = "10.1063/1.2126591",
	localfile = "molecular electrostatics/2005 - The electrostatic potential generated by topological atoms. II. Inverse mutlipole moments.pdf",
	year = 2005
}

@Article{2005-Rauf-GAGRAK,
	Author = "S. Rauf and J. J. Gooding and Kalsoom Akhtar and M. Afzal Ghauri and M. Rahman and Munir A. Anwar and A. M. Khalid",
	Title = "{Electrochemical approach of anticancer drugs - {DNA} interaction}",
	Journal = "J. Pharm. Biomed. Analysis",
	Volume = "37",
	Number = "2",
	Pages = "205 – 217",
	abstract = "The interaction of drugs with DNA is among the most important aspects of biological studies in drug discovery and pharmaceutical development processes. In recent years there has been a growing interest in the electrochemical investigation of interaction between anticancer drugs and DNA. Observing the pre and post electrochemical signals of DNA or drug interaction provides good evidence for the interaction mechanism to be elucidated. Also this interaction could be used for the quantification of these drugs and for the determination of new drugs targeting DNA. Electrochemical approach can provide new insight into rational drug design and would lead to further understanding of the interaction mechanism between anticancer drugs and DNA.",
	collection = "nucleic acid drugs",
	doi = "10.1016/j.jpba.2004.10.037",
	keywords = "drug discovery",
	localfile = "nucleic acid drugs/2005 - Electrochemical approach of anticancer drugs - DNA interaction.pdf",
	year = 2005
}

@Article{2005-Reister-Fredrickson,
	Author = "Ellen Reister and Glenn H. Fredrickson",
	Title = "{Phase behavior of a blend of polymer-tethered nanoparticles with diblock copolymers}",
	Journal = "J. Chem. Phys.",
	Volume = "123",
	Pages = "214903",
	Note = "Studies effect of A-grafted NPs on AB diblock copolymer phase separation (lamellar and disordered phases in 2D).",
	abstract = "Using the self-consistent ﬁeld theory SCFT, we investigate the phase behavior of a mixture of diblock copolymers and nanoparticles with monodisperse polymer chains tethered to their surfaces. We assume the size of the nanoparticles to be much smaller than that of the attached polymer chains and therefore model the particles with their grafted polymer “shell” as star polymers. The polymer chains attached to the particles are of the same species as one of the blocks of the symmetric diblock copolymer. Of primary interest is how to tune the shell of the particle by changing both the length and number of tethered polymers in order to achieve higher loading of nanoparticles within an ordered structure without macrophase separation occurring. We ﬁnd that the phase behavior of the system is very sensitive to the size of the particle including its tethered shell. The region of microphase separation is increased upon decreasing the star polymer size, which may be achieved by shortening and/or removing tethered polymer chains. To explore the possible structures in these systems we employ SCFT simulations that provide insight into the arrangement of the different species in these complex composites.",
	collection = "block copolymer nanocomposites",
	doi = "10.1063/1.2117008",
	keywords = "block copolymers; mesophase transitions; nanoparticle distribution; nanoparticle grafts; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2005 - Phase behavior of a blend of polymer-tethered nanoparticles with diblock copolymers.pdf",
	methods = "SCFT",
	year = 2005
}

@Article{2005-Rowsell-Yaghi,
	Author = "Jesse L. C. Rowsell and Omar M. Yaghi",
	Title = "{Strategies for Hydrogen Storage in {Metal-Organic} Frameworks}",
	Journal = "Angew. Chem. Int. Ed.",
	Volume = "44",
	Number = "30",
	Pages = "4670–4679",
	collection = "hydrogen sorption",
	doi = "10.1002/anie.200462786",
	localfile = "hydrogen sorption/2005 - Stretegies for hydrogen storage in emtal-organic frameworks.pdf",
	year = 2005
}

@Article{2005-Schmidt-BZSHFWAZSK,
	Author = "Kristin Schmidt and Alexander Böker and Heiko Zettl and Frank Schubert and Helmut Hansel and Franz Fischer and Thomas M. Weiss and Volker Abetz and Andrei V. Zvelindovsky and G. J. Agur Sevink and Georg Krausch",
	Title = "{Influence of Initial Order on the Microscopic Mechanism of Electric Field Induced Alignment of Block Copolymer Microdomains}",
	Journal = "Langmuir",
	Volume = "21",
	Number = "25",
	Pages = "11974–11980",
	abstract = "We investigate the mechanism of microdomain orientation in concentrated block copolymer solutions exposed to a dc electric field by in situ synchrotron small-angle X-ray scattering {(SAXS).} As a model system, we use concentrated solutions of a lamellar polystyrene-b-polyisoprene block copolymer in toluene. We find that both the microscopic mechanism of reorientation and the kinetics of the process strongly depend on the initial degree of order in the system. In a highly ordered lamellar system with the lamellae being aligned perpendicular to the electric field vector, only nucleation and growth of domains is possible as a pathway to reorientation and the process proceeds rather slowly. In less ordered samples, grain rotation becomes possible as an alternative pathway, and the process proceeds considerably faster. The interpretation of our finding is strongly corroborated by dynamic self-consistent field simulations.",
	collection = "block copolymers",
	doi = "10.1021/la051346w",
	keywords = "block copolymers; electric fields",
	localfile = "block copolymers/2005 - Influence of initial order on the microscopic mechanism of electric field induced alignment of block copolymer microdomains.pdf",
	year = 2005
}

@Article{2005-Schultz-HG,
	Author = "Andrew J. Schultz and Carol K. Hall and Jan Genzer",
	Title = "{Computer Simulation of Block {Copolymer/Nanoparticle} Composites}",
	Journal = "Macromolecules",
	Volume = "38",
	Number = "7",
	Pages = "3007–3016",
	Note = "Shows phase diagrams as a function of coplymer block interation and NP volume fraction.",
	abstract = "Discontinuous molecular dynamics simulation is used to study the phase behavior of diblock copolymer/nanoparticle composites. The copolymers are modeled as chains of tangent hard-spheres with square shoulder repulsions between unlike species, while the nanoparticles are modeled as hard-spheres with a square shoulder repulsion with one of the copolymer blocks. The resulting phase diagrams are presented for composites containing nanoparticles of various sizes and interaction strengths and include lamellae, perforated lamellae, cylinders, and disordered phases. Composites containing large nanoparticles also exhibit two-phase coexistence between different copolymer phases or between a copolymer phase and a nanoparticle phase, depending on the nanoparticle interaction strength. We also present concentration profiles perpendicular to the lamellar interface for nanoparticles of different sizes and interaction strengths. Neutral nanoparticles concentrate at the interface between copolymer domains, while interacting nanoparticles concentrate within the favorable domain. The larger nanoparticles are more easily localized but have less impact on the copolymer concentration profiles. The lamellar spacing increases with nanoparticle volume fraction for interacting nanoparticles but decreases with nanoparticle size. The locations of the phase transitions are in qualitative agreement with theoretical predictions, but the concentration profiles are inconsistent with theoretical predictions. The variation of the spacing with nanoparticle volume fraction is consistent with experimental data.",
	collection = "block copolymer nanocomposites",
	doi = "10.1021/ma0496910",
	keywords = "block copolymers; mesophase transitions; nanoparticle distribution; nanospheres; polymer nanocomposites",
	localfile = "block copolymer nanocomposites/2005 - Computer simulation of block copolymer and nanoparticle composites.pdf",
	methods = "CG MD",
	year = 2005
}

@Article{2005-Seio-USS,
	Author = "Kohji Seio and Hisashi Ukawa and Koh-ichiro Shohda and Mitsuo Sekine",
	Title = "{Computational evaluation of intermolecular interactions of a universal base 3-nitropyrrole in stacked dimers and DNA duplexes}",
	Journal = "J. Biomol. Struct. Dyn.",
	Volume = "22",
	Number = "6",
	Pages = "735–746",
	Note = "The end result was a force field parametrization of 3NP based on quantum chemical calculations for stacks with canonical bases.",
	collection = "molecular stacking",
	doi = "10.1080/07391102.2005.10507040",
	keywords = "force fields",
	localfile = "molecular stacking/2005 - Computational evaluation of intermolecular interactions of a universal base 3-nitropyrrole in stacked dimers and DNA duplexes.pdf",
	methods = "MP2/6-31G*, CHELPG, AMBER",
	rating = "2",
	read = "2013-05-10",
	systems = "3-nitropyrrole, 3NP, 3NP/guanine, 3NP/adenine, 3NP/cytosine, 3NP/uracil",
	year = 2005
}

@Article{2005-Shenhar-NR,
	Author = "Roy Shenhar and Tyler B. Norsten and Vincent M. Rotello",
	Title = "{Polymer-mediated nanoparticle assembly: structural control and applications}",
	Journal = "Adv. Mater.",
	Volume = "17",
	Number = "6",
	Pages = "657–669",
	collection = "polymer nanocomposites",
	doi = "10.1002/adma.200401291",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2005 - Polymer-mediated nanoparticle assembly: structural control and applications.pdf",
	type = "Review",
	year = 2005
}

@Article{2005-Sobczyk-GK,
	Author = "Lucjan Sobczyk and Sławomir J. Grabowski and Tadeusz M. Krygowski",
	Title = "{Interrelation between H-bond an pi-electron delocalization}",
	Journal = "Chem. Rev.",
	Volume = "105",
	Pages = "33513–3560",
	abstract = "(Excerpt) Among many various kinds of molecular interactions, the H-bond has a special position. The term is ubiquitous in the world that surrounds us, but also it is often applied in different ways. The H-bond is of great importance in natural sciences. This relates particularly to biological aspects, such as molecular recognition that could be a basis for the creation of life,1-4 formation of higher order structures of peptides and nucleic acids,5 and biochemical processes, particularly the enzymes catalyzed.6,7 One can say that the H-bond plays a double role in biological systems: on one hand, as a relatively strong directional interaction, it leads to relatively stable supramolecular structures, and on the other hand, because of dynamic features of the proton, it is an active site for initiation of chemical reactions.",
	collection = "hydrogen bonding",
	doi = "10.1021/cr030083c",
	localfile = "hydrogen bonding/2005 - Interrelation between H-bond and pi-electron delocalization.pdf",
	year = 2005
}

@Article{2005-Starcevic-KPZSK,
	Author = "Kristina Starčevic and Grace Karminski-Zamola and Ivo Piantanida and Mldaen Žinić and Lidija Šuman and Marijeta Kralji",
	Title = "{Photoinduced switch of a {DNA}/{RNA} inactive molecule into a classical intercalator}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "127",
	Number = "4",
	Pages = "1074–1075",
	abstract = "(Excerpt) The intercalation of planar aromatic or heteroaromatic molecules into the the DNA/RNA is considered to be important for the therapeutic action of many antitumor agents.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/ja0438866",
	localfile = "nucleic acid intercalation/2005 - Photoinduced switch of a DNA inactive molecule into a classical intercalator.pdf",
	year = 2005
}

@Article{2005-Stone,
	Author = "Anthony J. Stone",
	Title = "{Distributed Multipole Analysis: Stability for Large Basis Sets}",
	Journal = "J. Chem. Theory Comp.",
	Volume = "1",
	Number = "6",
	Pages = "1128–1132",
	abstract = "The distributed multipole analysis procedure, for describing a molecular charge distribution in terms of multipole moments on the individual atoms (or other sites) of the molecule, is not stable with respect to a change of basis set, and indeed, the calculated moments change substantially and unpredictably when the basis set is improved, even though the resulting electrostatic potential changes very little. A revised procedure is proposed, which uses grid-based quadrature for partitioning the contributions to the charge density from diffuse basis functions. The resulting procedure is very stable, and the calculated multipole moments converge rapidly to stable values as the size of the basis is increased.",
	collection = "molecular electrostatics",
	doi = "10.1021/ct050190",
	localfile = "molecular electrostatics/2005 - Distirbuted multipole analysis: stability for large basis sets.pdf",
	shorttitle = "Distributed Multipole Analysis",
	year = 2005
}

@Article{2005-Stratford-APD,
	Author = "K. Stratford and R. Adhikari and Ignacio Pagonabarraga and J.-C. Desplat",
	Title = "{Lattice Boltzmann for binary fluids with suspended colloids}",
	Journal = "J .Stat. Phys.",
	Volume = "121",
	Pages = "163–178",
	collection = "interfaces",
	doi = "10.1007/s10955-005-8411-1",
	keywords = "binary fluids; suspensions",
	localfile = "interfaces/2005 - Lattice Boltzmann for binary fluids with suspended colloids.pdf",
	methods = "LB",
	year = 2005
}

@Article{2005-Stratford-APDC,
	Author = "K. Stratford and R. Adhikari and Ignacio Pagonabarraga and J.-C. Desplat and M. E. Cates",
	Title = "{Colloidal jamming at interfaces: a route to fluid-bicontinuous gels}",
	Journal = "Science",
	Volume = "309",
	Pages = "2198–2201",
	collection = "jamming",
	doi = "10.1126/science.1116589",
	keywords = "jamming; suspensions",
	localfile = "jamming/2005 - Colloidal jamming at interfaces: a route to fluid-bicontinuous gels.pdf",
	year = 2005
}

@Article{2005-Surve-PG,
	Author = "Megha Surve and Victor Pryamitsyn and Venkat Ganesan",
	Title = "{Depletion and pair interactions of proteins in polymer solutions}",
	Journal = "J. Chem. Phys.",
	Volume = "122",
	Pages = "154901",
	collection = "polymer nanocomposites",
	doi = "10.1063/1.187277",
	localfile = "polymer nanocomposites/2005 - Depletion and pair interactions of proteins in polymer solutions.pdf",
	year = 2005
}

@Article{2005-Tauer-Sherrill,
	Author = "Tony P. Tauer and C. David Sherrill",
	Title = "{Beyond the Benzene Dimer: An Investigation of the Additivity of π-π Interactions}",
	Journal = "J. Phys. Chem. A",
	Volume = "109",
	Pages = "10475–10478",
	abstract = "The benzene dimer is the simplest prototype of π-π interactions and has been used to understand the fundamental physics of these interactions as they are observed in more complex systems. In biological systems, however, aromatic rings are rarely found in isolated pairs; thus, it is important to understand whether aromatic pairs remain a good model of π-π interactions in clusters. In this study, ab initio methods are used to compute the binding energies of several benzene trimers and tetramers, most of them in 1D stacked configurations. The two-body terms change only slightly relative to the dimer, and except for the cyclic trimer, the three-and four-body terms are negligible. This indicates that aromatic clusters do not feature any large nonadditive effects in their binding energies, and polarization effects in benzene clusters do not greatly change the binding that would be anticipated from unperturbed benzene-benzene interactions, at least for the 1D stacked systems considered. Three-body effects are larger for the cyclic trimer, but for all systems considered, the computed binding energies are within 10\% of what would be estimated from benzene dimer energies at the same geometries.",
	collection = "stacking",
	doi = "10.1021/jp0553479",
	localfile = "molecular stacking/2005 - Beyond the benzene dimer: an investigation of the additivity of pi-pi interactions.pdf",
	year = 2005
}

@Article{2005-Thostenson-LC,
	Author = "Erik T. Thostenson and Chunyu Li and Tsu-Wei Chou",
	Title = "{Nanocomposites in context}",
	Journal = "Compos. Sci. Technol.",
	Volume = "65",
	Pages = "491–516",
	abstract = "This paper provides an overview of recent advances in nanocomposites research. The key research opportunities and challenges in the development of structural and functional nanocomposites are addressed in the context of traditional ﬁber composites. The state of knowledge in processing, characterization, and analysis/modeling of nanocomposites is presented with a particular emphasis on identifying fundamental structure/property relationships. Critical issues in nanocomposites research as well as promising techniques for processing precursors for macroscopic nanocomposites are discussed.",
	collection = "polymer nanocomposites",
	doi = "10.1016/j.compscitech.2004.11.003",
	keywords = "polymer nanocomposites",
	localfile = "polymer nanocomposites/2005 - Nanocomposites in context.pdf",
	type = "Review",
	year = 2005
}

@Article{2005-Toczylowski-Cybulski,
	Author = "Rafał R. Toczyłowski and Sławomir M. Cybulski",
	Title = "{An analysis of the electrostatic interaction between nucleic acid bases}",
	Journal = "J. Chem. Phys.",
	Volume = "123",
	Number = "15",
	Pages = "154312–12",
	abstract = "Results from several commonly used approximate methods of evaluating electrostatic interactions have been compared to the rigorous, nonexpanded electrostatic energies at both uncorrelated and correlated levels of theory. We examined a number of energy proﬁles for both hydrogen bonded and stacked conﬁgurations of the nucleic acid base pairs. We found that the penetration effects play an extremely important role and the expanded electrostatic energies are signiﬁcantly underestimated with respect to the ab initio values. Apart from the inability to reproduce the magnitudes of the ab initio electrostatic energy, there are other problems with the available approximate electrostatic models. For example, the distributed multipole analysis, one of the most advanced methods, is extremely sensitive to the basis set and level of theory used to evaluate the multipole moments. Detailed ab initio results are provided that other researchers could use to test their approximate models.",
	collection = "nucleic acid bases",
	doi = "10.1063/1.2069887",
	localfile = "nucleic acid bases/2005 - An analysis of the electrostatic interaction between nucleic acid bases.pdf",
	year = 2005
}

@Article{2005-Tomasi-MC,
	Author = "Jacopo Tomasi and Benedetta Mennucci and Roberto Cammi",
	Title = "{Quantum mechanical continuum solvation models}",
	Journal = "Chem. Rev.",
	Volume = "105",
	Pages = "2999–3093",
	collection = "molecular solvation",
	doi = "10.1021/cr9904009",
	localfile = "molecular solvation/2005 - Quantum mechanical continuum solvation models.pdf",
	year = 2005
}

@Article{2005-Tripathi-Chapman,
	Author = "Sandeep Tripathi and Walter G. Chapman",
	Title = "{Microstructure and thermodynamics of inhomogeneous polymer blends and solutions}",
	Journal = "Phys. Rev. Lett.",
	Volume = "94",
	Pages = "087801",
	abstract = "A free energy density functional theory (DFT) for nonuniform polymeric mixtures is proposed based on ﬁrst order thermodynamic perturbation theory. The segment-density based free energy functional provides an accuracy comparable to the numerically intensive polymeric DFTs while preserving the computational simplicity of an atomic DFT. The presented applications for solutions and blends of branched and linear polymers demonstrate the capability of the theory to capture the entropic and enthalpic effects governing the microstructure.",
	collection = "polymers",
	doi = "10.1103/PhysRevLett.94.087801",
	localfile = "polymers/2005 - Microstructure and thermodynamics of inhomogeneous polymer blends and solutions.pdf",
	year = 2005
}

@Article{2005-Tripathi-Chapman-1,
	Author = "Sandeep Tripathi and Walter G. Chapman",
	Title = "{Microstructure of inhomogeneous polyatomic mixtures from a density functional formalism for atomic mixtures}",
	Journal = "J. Chem. Phys.",
	Volume = "122",
	Pages = "094506",
	abstract = "A free energy density functional theory DFT for inhomogeneous polymeric mixtures is developed by treating the polyatomic system as a strongly associating atomic ﬂuid mixture. The theory, derived in terms of segment density, retains the simple form of the DFTs for atomic ﬂuids. Invoking the complete bonding limit of a stoichiometric mixture in the association free energy functional yields a computationally simple and accurate functional for the polyatomic system. Comparisons of theory calculations with molecular simulations are presented for inhomogeneous solutions and blends of linear and branched chains, demonstrating the capability of the theory to accurately capture the entropic and enthalpic effects governing the microstructure.",
	collection = "polymers",
	doi = "10.1063/1.1853371",
	localfile = "polymers/2005 - Microstructure of inhomogeneous polyatomic mixtures fro ma density functional formalism for atomic mixtures.pdf",
	year = 2005
}

@Article{2005-Tuttle-KC,
	Author = "Tell Tuttle and Elfi Kraka and Dieter Cremer",
	Title = "{Docking, Triggering, and Biological Activity of Dynemicin A in {DNA:} A Computational Study}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "127",
	Number = "26",
	Pages = "9469–9484",
	abstract = "The triggering and biological activity of the naturally occurring enediyne dynemicin A (1) was investigated, both inside and outside the minor groove of the duplex 10-mer B-DNA sequence d(CTACTACTGG)‚d(CCAGTAGTAG), using density functional theory (B3LYP with the 3-21G and 6-31G(d) basis set), BD(T)/cc-pVDZ (Brueckner doubles with a perturbative treatment of triple excitations), and the ONIOM approach. Enediyne 1 is triggered by NADPH in a strongly exothermic reaction (-88 kcal/mol), which involves a number of intermediate steps. Untriggered 1 has a high barrier for the Bergman cyclization (52 kcal/mol) that is lowered after triggering to 16.7 kcal/mol due to an epoxide opening and the accompanying strain relief. The Bergman reaction of triggered 1 is slightly exothermic by 2.8 kcal/mol. The singlet biradical formed in this reaction is kinetically stable (activation enthalpies of 19.5 and 21.8 kcal/mol for retro-Bergman reactions) and is as reactive as para-benzyne. The activity-relevant docking mode is an edge-on insertion into the minor groove, whereas the intercalation between base pairs, although leading to larger binding energies, excludes a triggering of 1 and the development of its biological activity. Therefore, an insertion-intercalation model is developed, which can explain all known experimental observations made for 1. On the basis of the insertion-intercalation model it is explained why large intercalation energies suppress the biological activity of dynemicin and why double-strand scission can be achieved only in a two-step mechanism that involves two enediyne molecules, explaining thus the high ratio of single-strand to double-strand scission observed for 1.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/ja046251f",
	localfile = "nucleic acid intercalation/2005 - Docking, triggering, and biological activity of dynemicin A in DNA: a computational study.pdf",
	shorttitle = "Docking, Triggering, and Biological Activity of Dynemicin A in {DNA}",
	year = 2005
}

@Article{2005-Verberg-YB,
	Author = "Rolf Verberg and Julia M. Yeomans and Anna C. Balazs",
	Title = "{Modeling the flow of fluid/particle mixtures in microchannels: encapsulating nanoparticles within monodisperse droplets}",
	Journal = "J. Chem. Phys.",
	Volume = "123",
	Pages = "224706",
	collection = "interfaces",
	doi = "10.1063/1.2133733",
	keywords = "binary fluids; hydrodynamics; nanospheres; suspensions",
	localfile = "interfaces/2005 - Modeling the flow of fluid-particle mixtures in microchannels: encapsulating nanoparticles within monodisperse droplets.pdf",
	methods = "LB, BD",
	year = 2005
}

@Article{2005-Vladescu-MRW,
	Author = "Ioana D. Vladescu and Micah J. {McCauley} and Ioulia Rouzina and Mark C. Williams",
	Title = "{Mapping the Phase Diagram of Single {DNA} Molecule {Force-Induced} Melting in the Presence of Ethidium}",
	Journal = "Phys. Rev. Lett.",
	Volume = "95",
	Number = "15",
	Pages = "158102",
	abstract = "When a single {DNA} molecule is stretched beyond its normal contour length, a force-induced melting transition is observed. Ethidium binding increases the {DNA} contour length, decreases the elongation upon melting, and increases the {DNA} melting force in a manner that is consistent with the ethidium-induced changes in duplex {DNA} stability known from thermal melting studies. The {DNA} stretching curves map out a phase diagram and critical point in the force-extension-ethidium concentration space. Intercalation occurs between alternate base pairs at low forces and between every base pair at high forces.",
	collection = "nucleic acid intercalation",
	doi = "10.1103/PhysRevLett.95.158102",
	localfile = "nucleic acid intercalation/2005 - Mapping the phase diagram of single DNA molecule force-induced melting in the presence of ethidium.pdf",
	year = 2005
}

@Article{2005-Weck-Balakrishnan,
	Author = "P F Weck and N Balakrishnan",
	Title = "{Quantum dynamics of the Li + {HF} –> H + {LiF} reaction at ultralow temperatures}",
	Journal = "J. Chem. Phys.",
	Volume = "122",
	Number = "15",
	Pages = "154309",
	abstract = "Quantum-mechanical calculations are reported for the {Li+HF(v=0,1,j=0)->H+LiF(v',j')} bimolecular scattering process at low and ultralow temperatures. Calculations have been performed for zero total angular momentum using a recent high-accuracy potential-energy surface for the {X2A'} electronic ground state. For {Li+HF(v=0,j=0),} the reaction is dominated by resonances due to the decay of metastable states of the Li {cdots,...F-H} van der Waals complex. Assignment of these resonances has been carried out by calculating the eigenenergies of the quasibound states. We also find that while chemical reactivity is greatly enhanced by vibrational excitation, the resonances get mostly washed out in the reaction of vibrationally excited {HF} with Li atoms. In addition, we find that at low energies, the reaction is significantly suppressed due to the less-efficient tunneling of the relatively heavy fluorine atom.",
	collection = "molecular reactions",
	doi = "10.1063/1.1884115",
	localfile = "molecular reactions/2005 - Quantum dynamics of the Li+HF->H+LiF reaction at ultralow temperatures.pdf",
	year = 2005
}

@Article{2005-Xiao-Cushman,
	Author = "Xiangshu Xiao and Mark Cushman",
	Title = "{An Ab Initio Quantum Mechanics Calculation that Correlates with Ligand Orientation and {DNA} Cleavage Site Selectivity in {Camptothecin−DNA−Topoisomerase} I Ternary Cleavage Complexes}",
	Journal = "J. Am. Chem. Soc.",
	Volume = "127",
	Number = "28",
	Pages = "9960–9961",
	abstract = "(Excerpt) The discovery of the cytotoxic agent camptothecin (CPT, 1) (Chart 1) from the Chinese tree Camptotheca acuminata not only has provided a lead for the development of new anticancer drugs but also has led to the validation of topoisomerase I (top1) as a chemotherapeutic target. Top1 is a nuclear enzyme responsible for solving the topological problems associated with DNA replication and transcription by nicking and resealing one strand of DNA in a DNA duplex.",
	collection = "nucleic acid intercalation",
	doi = "10.1021/ja042485n",
	localfile = "nucleic acid intercalation/2005 - An ab initio quantum mechanics calculation that correlates with ligand orientation and DNA cleavage site selectivity in camptothecin-DNA-topoisomerase I ternary cleavage complexes.pdf",
	year = 2005
}

@Article{2005-Xu-ZSLJR,
	Author = "Ting Xu and Andrei V. Zvelindovsky and G. J. Agur Sevink and Kateryna S. Lyakhova and Hiroshi Jinnai and Thomas P. Russell",
	Title = "{Electric Field Alignment of Asymmetric Diblock Copolymer Thin Films}",
	Journal = "Macromolecules",
	Volume = "38",
	Number = "26",
	Pages = "10788–10798",
	abstract = "The electric field alignment of cylindrical microdomains in diblock copolymer thin films was studied using small-angle neutron scattering and transmission electron microscopy. The alignment process was followed with the block copolymer films in different initial states. Starting from a poorly ordered state, the cylindrical microdomain orientation was biased by the surface field that initially drove the cylindrical microdomains to be oriented parallel to the film surface. With further annealing, the cylinders were disrupted locally and formed ellipsoid-shaped microdomains that, with time, connected into cylindrical microdomains oriented in the field direction. Starting from an ordered state with cylinders parallel to the surface, the applied electric field enhanced fluctuations at the interfaces of the microdomains. The growth of the fluctuations continued until the cylindrical microdomains broke up into spherical microdomains, similar to that seen in the thermoreversible cylinder-to-sphere orderorder transition. With time, the spherical microdomains deformed into ellipsoidal domains that reconnected into cylindrical microdomains oriented at 45o with respect to the applied field direction. Further annealing aligned the tilted cylinders along the applied field direction. This reorientation process was much slower than from the poorly ordered state. The details of the realignment process are supported by computer simulations based on dynamic self-consistent-field theory.",
	collection = "block copolymers",
	doi = "10.1021/ma050521c",
	keywords = "block copolymers; electric fields; thin films",
	localfile = "block copolymers/2005 - Electric field alignment of asymmetric diblock copolymer thin films.pdf",
	year = 2005
}

@Article{2005-Yeh-WSJL,
	Author = "S

repository: langner/library

repo_name: langner/library

branch_name: refs/heads/master