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ORCIDJournal of Computational Chemistry, Volume 29
Volume 29, Number 1, January 2008
- Tanja Van Mourik:
Comment on "Aromatic-Backbone Interactions in Model alpha-Helical Peptides" [Palermo et al., J Comput Chem 2007, 28, 1208]. 1-3 - József Csontos, Nicholas Y. Palermo, Richard F. Murphy, Sándor Lovas:
Reply to "Comment on Aromatic-Backbone Interactions in Model alpha-Helical Peptides". 4-7 - Michael T. Feldmann, Julian C. Cummings, David R. Kent IV, Richard P. Muller, William A. Goddard III:
Manager-worker-based model for the parallelization of quantum Monte Carlo on heterogeneous and homogeneous networks. 8-16 - Kun Song, Viktor Hornak, Carlos De Los Santos, Arthur P. Grollman, Carlos Simmerling:
Molecular mechanics parameters for the FapydG DNA lesion. 17-23 - Lula Rosso, Ian R. Gould
:
Structure and dynamics of phospholipid bilayers using recently developed general all-atom force fields. 24-37 - Katrin Spiegel, Alessandra Magistrato, Patrick Maurer, Paolo Ruggerone, Ursula Rothlisberger, Paolo Carloni, Jan Reedijk, Michael L. Klein:
Parameterization of azole-bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure. 38-49 - R. James Milgram, Guanfeng Liu, Jean-Claude Latombe:
On the structure of the inverse kinematics map of a fragment of protein backbone. 50-68 - Francisco Rodríguez-Ropero, Jordi Casanovas, Carlos Alemán:
Ab initio calculations on pi-stacked thiophene dimer, trimer, and tetramer: Structure, interaction energy, cooperative effects, and intermolecular electronic parameters. 69-78 - Evgenii V. Kovalyov, Vladimir Elokhin, Aleksandr V. Myshlyavtsev:
Stochastic simulation of physicochemical processes performance over supported metal nanoparticles. 79-86 - Yongcheng Zhou, Michael Feig, Guo-Wei Wei:
Highly accurate biomolecular electrostatics in continuum dielectric environments. 87-97 - N. R. Jena, P. S. Kushwaha, P. C. Mishra:
Reaction of hypochlorous acid with imidazole: Formation of 2-chloro- and 2-oxoimidazoles. 98-107 - Ewgenij Proschak, Matthias Rupp, Swetlana Derksen, Gisbert Schneider:
Shapelets: Possibilities and limitations of shape-based virtual screening. 108-114 - Chinapong Kritayakornupong:
The Jahn-Teller effect of the Cr2+ ion in aqueous solution: Ab initio QM/MM molecular dynamics simulations. 115-121 - Matej Praprotnik, Stanko Hocevar, Milan Hodoscek, Matej Penca, Dusanka Janezic:
New all-atom force field for molecular dynamics simulation of an AlPO4-34 molecular sieve. 122-129 - Alexander V. Larin, D. N. Trubnikov, Daniel P. Vercauteren:
Electric field convergence versus atomic basis sets in all-siliceous zeolites. 130-138 - Ignacio Fdez. Galván, Martin J. Field:
Improving the efficiency of the NEB reaction path finding algorithm. 139-143
- Josep M. Porta, Lluís Ros, Federico Thomas, Francesc Corcho, Josep Cantó, Juan Jesús Pérez:
Complete maps of molecular-loop conformational spaces. 144-155
Volume 29, Number 2, January 2008
- Markus Christen, Wilfred F. van Gunsteren:
On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review. 157-166 - Florian Weigend:
Hartree-Fock exchange fitting basis sets for H to Rn. 167-175 - Weihua Zhu, Heming Xiao:
Ab initio study of electronic structure and optical properties of heavy-metal azides: TlN3, AgN3, and CuN3. 176-184 - Nathan E. Schultz, Yan Zhao, Donald G. Truhlar:
Benchmarking approximate density functional theory for s/d excitation energies in 3d transition metal cations. 185-189 - Mark Pinsky, David Casanova, Pere Alemany, Santiago Alvarez, David Avnir, Chaim Dryzun, Ziv Kizner, Alexander Sterkin:
Symmetry operation measures. 190-197 - Jian-Yi Ma, Jing-Bo Wang, Xiang-Yuan Li, Yao Huang, Quan Zhu, Ke-Xiang Fu:
A study on orientation and absorption spectrum of interfacial molecules by using continuum model. 198-210 - Qishi Du, Ri-Bo Huang, Yu-Tuo Wei, Li-Qin Du, Kuo-Chen Chou:
Multiple field three dimensional quantitative structure-activity relationship (MF-3D-QSAR). 211-219 - Dmitry N. Tarasov, R. P. Tiger:
Numerical computations of molecular reactions in associated systems caused by the formation of fractal structures. 220-224 - Yasuji Inada, Hideo Orita:
Efficiency of numerical basis sets for predicting the binding energies of hydrogen bonded complexes: Evidence of small basis set superposition error compared to Gaussian basis sets. 225-232 - Milan Oncák, Martin Srnec:
Electronic structure and physical properties of MiXi clusters (M = B, Al; X = N, P; i = 1, 2, 3): Ab initio study. 233-246 - Jing Yang, Qian Shu Li, Shaowen Zhang:
Direct dynamics study on the reaction of acetaldehyde with ozone. 247-255 - Kun Liu, Wensheng Bian:
Extensive theoretical study on the low-lying electronic states of silicon monofluoride cation including spin-orbit coupling. 256-265 - Bahram Hemmateenejad, Afshan Mohajeri:
Application of quantum topological molecular similarity descriptors in QSPR study of the O-methylation of substituted phenols. 266-274 - Yun Ding, Ye Mei, John Z. H. Zhang, Fu-Ming Tao:
Efficient bond function basis set for pi-pi interaction energies. 275-279 - Miguel A. Zamora, Fernando D. Suvire, Ricardo D. Enriz:
Ring inversion in 1, 4, 7 cyclononatriene and analogues: Ab initio and DFT calculations and topological analysis. 280-290 - Yin Wei, T. Singer, H. Mayr, G. Narahari Sastry, Hendrik Zipse:
Assessment of theoretical methods for the calculation of methyl cation affinities. 291-297 - Sean A. C. McDowell:
A comparative study of some red- and blue-shifted linear H-bonded complexes of N2. 298-305
- Mohamed Zerara:
pyVib, a computer program for the analysis of infrared and Raman optical activity. 306-311 - Willem-Jan Van Zeist, Célia Fonseca Guerra, Friedrich Matthias Bickelhaupt:
PyFrag - Streamlining your reaction path analysis. 312-315
Volume 29, Number 3, February 2008
- Yoanna María Alvarez-Ginarte, Yovani Marrero-Ponce, José Alberto Ruiz-García, Luis Alberto Montero-Cabrera, José Manuel García de la Vega, Pedro Noheda Marin, Rachel Crespo-Otero, Francisco Torrens Zaragoza, Ramón García-Domenech:
Applying pattern recognition methods plus quantum and physico-chemical molecular descriptors to analyze the anabolic activity of structurally diverse steroids. 317-333 - Koji Yasuda:
Two-electron integral evaluation on the graphics processor unit. 334-342 - Arvids Stashans, Gaston Chamba, Henry Pinto:
Electronic structure, chemical bonding, and geometry of pure and Sr-doped CaCO3. 343-349 - Ruibo Wu, Zexing Cao:
QM/MM study of catalytic methyl transfer by the N5-glutamine SAM-dependent methyltransferase and its inhibition by the nitrogen analogue of coenzyme. 350-357 - Stijn Fias, Sofie Van Damme, Patrick Bultinck:
Multidimensionality of delocalization indices and nucleus independent chemical shifts in polycyclic aromatic hydrocarbons. 358-366 - Norberto Castillo, Katherine N. Robertson, S. C. Choi, Russell J. Boyd, Osvald Knop:
Bond length and the electron density at the bond critical point: X-X, Z-Z, and C-Z bonds (X = Li-F, Z = Na-Cl). 367-379 - Peter W. Bates, Guo-Wei Wei, Shan Zhao:
Minimal molecular surfaces and their applications. 380-391 - Daniel Norberg, Nessima Salhi-Benachenhou:
McLafferty rearrangement of the radical cations of butanal and 3-fluorobutanal: A theoretical investigation of the concerted and stepwise mechanisms. 392-406 - Sebastian Schlund, Robert Müller, Carsten Graßmann, Bernd Engels:
Conformational analysis of arginine in gas phase - A strategy for scanning the potential energy surface effectively. 407-415 - Gilles Frison, Gilles Ohanessian:
A comparative study of semiempirical, ab initio, and DFT methods in evaluating metal-ligand bond strength, proton affinity, and interactions between first and second shell ligands in Zn-biomimetic complexes. 416-433 - Bin Gao, Jun Jiang, Kai Liu, Ziyu Wu, Wei Lu, Yi Luo:
An efficient first-principle approach for electronic structures calculations of nanomaterials. 434-444 - Richard J. Wheatley:
Time-dependent coupled-cluster calculations of polarizabilities and dispersion energy coefficients. 445-450 - Manuel Piacenza, Fabio Della Sala, Eduardo Fabiano, T. Maiolo, Giuseppe Gigli:
Torsional effects on excitation energies of thiophene derivatives induced by beta-substituents: Comparison between time-dependent density functional theory and approximated coupled cluster approaches. 451-457 - Toshiaki Matsubara, Michel Dupuis, Misako Aida:
An insight into the environmental effects of the pocket of the active site of the enzyme. Ab initio ONIOM-molecular dynamics (MD) study on cytosine deaminase. 458-465 - Chao Deng, Qiang-Gen Li, Yi Ren, Ning-Bew Wong, San-Yan Chu, Hua-Jie Zhu:
A comprehensive theoretical study on the hydrolysis of carbonyl sulfide in the neutral water. 466-480 - Bryan M. Wong, Maria M. Fadri, Sumathy Raman:
Thermodynamic calculations for molecules with asymmetric internal rotors. II. Application to the 1, 2-dihaloethanes. 481-487
- V. Ganesh, Ritwik Kavathekar, Anuja P. Rahalkar, Shridhar R. Gadre:
WebProp: Web interface for ab initio calculation of molecular one-electron properties. 488-495
Volume 29, Number 4, March 2007
- John Cullen:
An approximate diatomics in molecules formulation of generalized valence bond theory. 497-504 - Xiao-Wei Fan, Xue-Hai Ju:
Theoretical studies on four-membered ring compounds with NF2, ONO2, N3, and NO2 groups. 505-513 - Jiali Gao, Kin-Yiu Wong, Dan Thomas Major:
Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water. 514-522 - José-Vicente Pitarch Ruiz, José Sánchez-Marín, A. M. Velasco:
Full configuration interaction calculation of the low lying valence and Rydberg states of BeH. 523-532 - Maykel Cruz-Monteagudo, M. Natália Dias Soeiro Cordeiro, Fernanda Borges:
Computational chemistry approach for the early detection of drug-induced idiosyncratic liver toxicity. 533-549 - Lei Yang, Jing-Yao Liu, Li Wang, Hong-Qing He, Ying Wang, Ze-Sheng Li:
Theoretical study of the reactions CF3CH2OCHF2 + OH/Cl and its product radicals and parent ether(CH3CH2OCH3) with OH. 550-561 - Joseph P. Kenny, Curtis L. Janssen, Edward F. Valeev, Theresa L. Windus:
Components for integral evaluation in quantum chemistry. 562-577 - Flavio Forti, Xavier Barril, F. Javier Luque, Modesto Orozco:
Extension of the MST continuum solvation model to the RM1 semiempirical hamiltonian. 578-587 - M. Leonor Contreras, José Alvarez, D. Guajardo, Roberto Rozas:
Understanding topological symmetry: A heuristic approach to its determination. 588-600 - Aibing Liu, Steven J. Stuart:
Empirical bond-order potential for hydrocarbons: Adaptive treatment of van der Waals interactions. 601-611 - Yasushi Honda, Atsushi Kurihara, Masahiko Hada, Hiroshi Nakatsuji:
Excitation and circular dichroism spectra of (-)-(3aS, 7aS)-2-chalcogena-trans-hydrindans(Ch = S, Se, Te): SAC and SAC-CI calculations. 612-621 - Karl Nicholas Kirschner, Austin B. Yongye, Sarah M. Tschampel, Jorge González-Outeiriño, Charlisa R. Daniels, Bethany Lachele Foley, Robert J. Woods:
GLYCAM06: A generalizable biomolecular force field. Carbohydrates. 622-655 - Humberto González Díaz, Francisco J. Prado-Prado:
Unified QSAR and network-based computational chemistry approach to antimicrobials, part 1: Multispecies activity models for antifungals. 656-667 - Wei Yang, Hugh Nymeyer, Huan-Xiang Zhou, Bernd A. Berg, Rafael Brüschweiler:
Quantitative computer simulations of biomolecules: A snapshot. 668-672
Volume 29, Number 5, 15 April 2008
- Kitiyaporn Wittayanarakul, Supot Hannongbua, Michael Feig:
Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors. 673-685 - Cai-Yun Geng, Ji-Lai Li, Xu-Ri Huang, Hui-Ling Liu, Zhuo Li, Chia-Chung Sun:
Theoretical elucidation of the rhodium-catalyzed [4 + 2] annulation reactions. 686-693 - Alex Robertson, Edgar Luttmann, Vijay S. Pande:
Effects of long-range electrostatic forces on simulated protein folding kinetics. 694-700 - Urs Haberthür, Amedeo Caflisch:
FACTS: Fast analytical continuum treatment of solvation. 701-715 - R. C. Binning Jr., Daniel E. Bacelo:
High-spin versus broken symmetry - Effect of DFT spin density representation on the geometries of three diiron (III) model compounds. 716-723 - Marcel Swart, Friedrich Matthias Bickelhaupt:
QUILD: QUantum-regions interconnected by local descriptions. 724-734 - Yutaka Imamura, Hiroyoshi Kiryu, Hiromi Nakai:
Colle-Salvetti-type correction for electron-nucleus correlation in the nuclear orbital plus molecular orbital theory. 735-740 - Robert M. Whitnell, Dow P. Hurst, Patricia H. Reggio, Frank Guarnieri:
Conformational memories with variable bond angles. 741-752 - Mikael P. Johansson, Ville R. I. Kaila, Liisa Laakkonen:
Charge parameterization of the metal centers in cytochrome c oxidase. 753-767 - Svetlana Stepanenko, Bernd Engels:
New Tabu Search based global optimization methods outline of algorithms and study of efficiency. 768-780 - Zhen Zhou, Jijun Zhao, Paul von Ragué Schleyer, Zhongfang Chen:
Insertion of C50 into single-walled carbon nanotubes: Selectivity in interwall spacing and C50 isomers. 781-787 - Emilio Gallicchio, Ronald M. Levy, Manish Parashar:
Asynchronous replica exchange for molecular simulations. 788-794 - Matteo Masetti, Andrea Cavalli, Maurizio Recanatini:
Modeling the hERG potassium channel in a phospholipid bilayer: Molecular dynamics and drug docking studies. 795-808 - Yue-meng Ji, Xiao-lei Zhao, Jing-Yao Liu, Ying Wang, Ze-Sheng Li:
Theoretical dynamic studies on the reactions of CH3C(O)CH3-nCln (n = 0-3) with the chlorine atom. 809-819 - Mark A. Olson, Michael Feig, Charles L. Brooks III:
Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions. 820-831 - Mahmoud Mirzaei, Nasser L. Hadipour:
A computational NQR study on the hydrogen-bonded lattice of cytosine-5-acetic acid. 832-838
- Noel M. O'Boyle, Adam L. Tenderholt, Karol M. Langner:
cclib: A library for package-independent computational chemistry algorithms. 839-845
Volume 29, Number 6, 30 April 2008
- Rainer Grohmann, Torsten Schindler:
Toward robust QSPR models: Synergistic utilization of robust regression and variable elimination. 847-860 - Haydée Valdés, Vojtech Klusák, Michal Pitonák, Otto Exner, Ivo Starý, Pavel Hobza, Lubomír Rulísek:
Evaluation of the intramolecular basis set superposition error in the calculations of larger molecules: [n]helicenes and Phe-Gly-Phe tripeptide. 861-870 - Tatsuhiko Miyata, Fumio Hirata:
Combination of molecular dynamics method and 3D-RISM theory for conformational sampling of large flexible molecules in solution. 871-882 - Huancong Shi, David C. Roettger, Allan L. L. East:
Photochemistry studied with ab initio orbital-correlation and state-correlation plots: Classic cyclobutene ring opening, and the reaction of N2 with photoexcited O2. 883-891 - Fabienne Bessac, Feliu Maseras:
DFT modeling of reactivity in an ionic liquid: How many ion pairs? 892-899 - Kalju Kahn, Iiris Kahn:
Improved efficiency of focal point conformational analysis with truncated correlation consistent basis sets. 900-911 - Sandro Chiodo, Nino Russo:
Determination of spin-orbit coupling contributions in the framework of density functional theory. 912-920 - Denis Jacquemin, Eric A. Perpète, Ilaria Ciofini, Carlo Adamo:
Revisiting the relationship between the bond length alternation and the first hyperpolarizability with range-separated hybrid functionals. 921-925 - C. H. Mak:
RNA conformational sampling. I. Single-nucleotide loop closure. 926-933 - Stefan Duret, Ahmed Bouferguene, Hassan Safouhi:
Strategies for an efficient implementation of the Gauss-Bessel quadrature for the evaluation of multicenter integral over STFs. 934-944 - Lívia B. Pártay, György Hantal, Pál Jedlovszky, Árpád Vincze, George Horvai:
A new method for determining the interfacial molecules and characterizing the surface roughness in computer simulations. Application to the liquid-vapor interface of water. 945-956 - Fabrizio Santoro, Vincenzo Barone, Roberto Improta:
Can TD-DFT calculations accurately describe the excited states behavior of stacked nucleobases? The cytosine dimer as a test case. 957-964 - Deepak Bandyopadhyay, Dimitris K. Agrafiotis:
A self-organizing algorithm for molecular alignment and pharmacophore development. 965-982 - Alicia M. Davis, Gary Joanis, Lorena Tribe:
Molecular modeling of polymer-clay nanocomposite precursors: Lysine in montmorillonite interlayers. 983-987 - Grzegorz Mazur:
An improved SCPF scheme for polarization energy calculations. 988-993 - Núria Queralt, David Taratiel, Coen de Graaf, Rosa Caballol, Renzo Cimiraglia, Celestino Angeli:
On the applicability of multireference second-order perturbation theory to study weak magnetic coupling in molecular complexes. 994-1003 - Sabine Schweizer, Jörg Kussmann, Bernd Doser, Christian Ochsenfeld:
Linear-scaling Cholesky decomposition. 1004-1010 - Christoph R. Jacob, Johannes Neugebauer, Lucas Visscher:
A flexible implementation of frozen-density embedding for use in multilevel simulations. 1011-1018
Volume 29, Number 7, May 2008
- Ross C. Walker, Michael F. Crowley, David A. Case:
The implementation of a fast and accurate QM/MM potential method in Amber. 1019-1031 - Sunil Patil, R. C. Aiyer, K. C. Sharma:
Globally convergent computation of chemical equilibrium composition. 1032-1036 - Mette Alstrup Lie, Birgit Schiøtt:
A DFT study of solvation effects on the tautomeric equilibrium and catalytic ylide generation of thiamin models. 1037-1047 - Sven Lammers, Stephan Lutz, Markus Meuwly:
Reactive force fields for proton transfer dynamics. 1048-1063 - Miquel Torrent-Sucarrat, Pedro Salvador, Miquel Solà, Paul Geerlings:
The hardness kernel as the basis for global and local reactivity indices. 1064-1072 - Woo Youn Kim, Kwang S. Kim:
Carbon nanotube, graphene, nanowire, and molecule-based electron and spin transport phenomena using the nonequilibrium Green's function method at the level of first principles theory. 1073-1083 - Asbjørn Holt, Gunnar Karlström:
An intramolecular induction correction model of the molecular dipole moment. 1084-1091 - Marcel Schmidt am Busch, Anne Lopes, David Mignon, Thomas Simonson:
Computational protein design: Software implementation, parameter optimization, and performance of a simple model. 1092-1102 - Udo Schnupf, Julious L. Willett, Wayne B. Bosma, Frank A. Momany:
DFT conformational studies of alpha-maltotriose. 1103-1112 - Ninad V. Prabhu, Manoranjan Panda, Qingyi Yang, Kim A. Sharp:
Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules. 1113-1130 - Anthony D. Hill, Peter J. Reilly:
A Gibbs free energy correlation for automated docking of carbohydrates. 1131-1141 - Yang Zhong, G. Lee Warren, Sandeep Patel:
Thermodynamic and structural properties of methanol-water solutions using nonadditive interaction models. 1142-1152 - Christina L. Vizcarra, Naigong Zhang, Shannon A. Marshall, Ned S. Wingreen, Chen Zeng, Stephen L. Mayo:
An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design. 1153-1162 - Elad Project, Esther Nachliel, Menachem Gutman:
Parameterization of Ca+2-protein interactions for molecular dynamics simulations. 1163-1169 - Hui Zhang, Guiling Zhang, Jing-Yao Liu, Bo Liu, Xiaoyang Yu, Ze-Sheng Li:
Theoretical study on the OH + CH3NHC(O)OCH3 reaction. 1170-1176 - Oliver J. Clarke, Martin J. Parker:
Time-averaged predictions of folded and misfolded peptides using a reduced physicochemical model. 1177-1185
Volume 29, Number 8, June 2008
- Seiken Tokura, Takeshi Sato, Takao Tsuneda, Takahito Nakajima, Kimihiko Hirao:
A dual-level state-specific time-dependent density-functional theory. 1187-1197 - Viktor Bezugly, Pawel Wielgus, Frank R. Wagner, Miroslav Kohout, Yuri Grin:
Electron localizability indicators ELI and ELIA: The case of highly correlated wavefunctions for the argon atom. 1198-1207 - Seung Kyu Min, Eun Cheol Lee, Han Myoung Lee, Dong Young Kim, Dongwook Kim, Kwang S. Kim:
Complete basis set limit of Ab initio binding energies and geometrical parameters for various typical types of complexes. 1208-1221 - Yong Wu, Lu Jin, Ying Xue, Daiqian Xie, Chan Kyung Kim, Yong Guo, Guosen Yan:
Theoretical study on the hydrolysis mechanism of N, N-dimethyl-N'-(2-oxo-1, 2-dihydro-pyrimidinyl)formamidine: Water-assisted mechanism and cluster-continuum model. 1222-1232 - Francisco Rodríguez-Ropero, David Zanuy, Carlos Alemán:
Molecular dynamics of a calix[4]arene-containing polymer in dichloromethane solution: Ability of the solvent molecules to fill the cavity of the macrocycle. 1233-1241 - Alexander G. Donchev, Nikolay G. Galkin, Alexey A. Illarionov, Oleg V. Khoruzhii, Michael A. Olevanov, Vladimir D. Ozrin, Leonid B. Pereyaslavets, Vladimir I. Tarasov:
Assessment of performance of the general purpose polarizable force field QMPFF3 in condensed phase. 1242-1249 - Yong Wu, Ying Xue, Chan Kyung Kim:
Computational studies on the dimers and the thermal dimerization of norbornadiene. 1250-1258 - Ying Xiong, Hai-Ting Lu, Chang-Guo Zhan:
Dynamic structures of phosphodiesterase-5 active site by combined molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations. 1259-1267 - Chen Levi, Jan M. L. Martin, Ilana Bar:
Fundamental vibrational frequencies and dominant resonances in methylamine isotopologues by ab initio and density functional theory methods. 1268-1276 - Maciej Haranczyk, John D. Holliday, Peter Willett, Maciej Gutowski:
Structure and singly occupied molecular orbital analysis of anionic tautomers of guanine. 1277-1291 - Qi Dai, Tian-Ming Wang:
Use of statistical measures for analyzing RNA secondary structures. 1292-1305 - Wai-Leung Yim, Thorsten Klüner:
Atoms-in-molecules analysis for planewave DFT calculations - A numerical approach on a successively interpolated charge density grid. 1306-1315 - Ryangguk Kim, Jeffrey Skolnick:
Assessment of programs for ligand binding affinity prediction. 1316-1331 - Olexander Yakovenko, Alexander A. Oliferenko, Volodymyr G. Bdzhola, Vladimir A. Palyulin, Nikolai S. Zefirov:
Kirchhoff atomic charges fitted to multipole moments: Implementation for a virtual screening system. 1332-1343 - József Csontos, Nicholas Y. Palermo, Richard F. Murphy, Sándor Lovas:
Calculation of weakly polar interaction energies in polypeptides using density functional and local Møller-Plesset perturbation theory. 1344-1352
Volume 29, Number 9, 15 July 2008
- Sophie Barbe, Marc Le Bret:
Ab initio determination of the flexibility of 2'-aminoribonucleosides and 2'-aminoarabinonucleosides inserted in duplexes. 1353-1363 - Yi-Yuan Chiu, Jenn-Kang Hwang, Jinn-Moon Yang:
Soft energy function and generic evolutionary method for discriminating native from nonnative protein conformations. 1364-1373 - Villö K. Pálfi, András Perczel:
How stable is a collagen triple helix? An ab initio study on various collagen and beta-sheet forming sequences. 1374-1386 - Robert Ponec, György Lendvay, Joaquin Chaves:
Structure and bonding in binuclear metal carbonyls from the analysis of domain averaged Fermi holes. I. Fe2(CO)9 and Co2(CO)8. 1387-1398 - Hajime Hirao:
A reactive bond orbital investigation of the Diels-Alder reaction between 1, 3-butadiene and ethylene: Energy decomposition, state correlation diagram, and electron density analyses. 1399-1407 - Pablo Echenique, José Luis Alonso:
Efficient model chemistries for peptides. I. General framework and a study of the heterolevel approximation in RHF and MP2 with Pople split-valence basis sets. 1408-1422 - Xueye Wang, Hengliang Wang, Yuanqiang Tan:
DFT study of the cryptand and benzocryptand and their complexes with alkali metal cations: Li+, Na+, K+. 1423-1428 - Karine Voltz, Joanna Trylska, Valentina Tozzini, Vandana Kurkal-Siebert, Jörg Langowski, Jeremy C. Smith:
Coarse-grained force field for the nucleosome from self-consistent multiscaling. 1429-1439 - Julien Pilmé, Jean-Philip Piquemal:
Advancing beyond charge analysis using the electronic localization function: Chemically intuitive distribution of electrostatic moments. 1440-1449 - Mauro Ferrero, Michel Rérat, Roberto Orlando, Roberto Dovesi:
The calculation of static polarizabilities of 1-3D periodic compounds. the implementation in the crystal code. 1450-1459 - Piotr Rotkiewicz, Jeffrey Skolnick:
Fast procedure for reconstruction of full-atom protein models from reduced representations. 1460-1465 - József Csontos, Péter Kálmán, Gyula Tasi, Miklós Kálmán, Richard F. Murphy, Sándor Lovas:
The effect of electron correlation on the conformational space of melatonin. 1466-1471 - Laurence Leherte, Daniel P. Vercauteren:
Collective motions of rigid fragments in protein structures from smoothed electron density distributions. 1472-1489 - Asit K. Chandra, Salma Parveen, Subojit Das, Thérèse Zeegers-Huyskens:
Blue shifts of the C-H stretching vibrations in hydrogen-bonded and protonated trimethylamine. Effect of hyperconjugation on bond properties. 1490-1496 - Matthew A. Addicoat, Mark A. Buntine, Brian F. Yates, Gregory F. Metha:
Associative versus dissociative binding of CO to 4d transition metal trimers: A density functional study. 1497-1506 - Riccardo Chelli, Victor V. Volkov, Roberto Righini:
Retrieval of spectral and dynamic properties from two-dimensional infrared pump-probe experiments. 1507-1516 - Qi Liu, Victor Olman, Huiqing Liu, Xiuzi Ye, Shilun Qiu, Ying Xu:
RNACluster: An integrated tool for RNA secondary structure comparison and clustering. 1517-1526
Volume 29, Number 10, 30 July 2008
- Ivelin Georgiev, Ryan H. Lilien, Bruce Randall Donald:
The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles. 1527-1542 - Ferran Feixas, Eduard Matito, Jordi Poater, Miquel Solà:
On the performance of some aromaticity indices: A critical assessment using a test set. 1543-1554 - Yutaka Imamura, Hiromi Nakai:
Energy density analysis for second-order Møller-Plesset perturbation theory and coupled-cluster theory with singles and doubles: Application to C2H4-CH4 complexes. 1555-1563 - Juan Torras, Gustavo de M. Seabra, Erik Deumens, Samuel B. Trickey, Adrian E. Roitberg:
A versatile AMBER-Gaussian QM/MM interface through PUPIL. 1564-1573 - Michal Brylinski, Jeffrey Skolnick:
Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. 1574-1588 - Linda Angela Zotti, Gilberto Teobaldi, Krisztian Palotás, Wei Ji, Hongjun Gao, Werner A. Hofer:
Adsorption of benzene, fluorobenzene and meta-di-fluorobenzene on Cu(110): A computational study. 1589-1595 - Ke Chen, Lukasz A. Kurgan, Jishou Ruan:
Prediction of protein structural class using novel evolutionary collocation-based sequence representation. 1596-1604 - Vladimir Hnizdo, Jun Tan, Benjamin J. Killian, Michael K. Gilson:
Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods. 1605-1614 - Pawel Szabelski:
Spontaneous segregation on a hybrid chiral surface. 1615-1625 - Jong Chan Kim, Kyoung Hoon Kim, Jaehoon Jung, Young-Kyu Han:
Reaction mechanisms of dissociative chemisorption of HI, I2, and CH3I on a magic cluster Al-13. 1626-1631 - Yu-Hua Yao, Qi Dai, Xu-Ying Nan, Ping-An He, Zuo-Ming Nie, Song-Ping Zhou, Yao-Zhou Zhang:
Analysis of similarity/dissimilarity of DNA sequences based on a class of 2D graphical representation. 1632-1639 - Thenmalarchelvi Rathinavelan, Wonpil Im:
A novel strategy to determine protein structures using exclusively residual dipolar coupling. 1640-1649 - Qingxu Li, Yuanping Yi, Zhigang Shuai:
Local approach to coupled cluster evaluation of polarizabilities for long conjugated molecules. 1650-1655 - Federico Iori, Stefano Corni:
Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces. 1656-1666 - Xiao-Jing Liu, Chuan-Lu Yang, Xiang Zhang, Ke-Li Han, Zichao Tang:
Theoretical study on the structure and formation mechanism of [C6H5Mm]- (M-Ag, Au; m = 1-3). 1667-1674 - Liang-Tsung Huang, M. Michael Gromiha:
Analysis and prediction of protein folding rates using quadratic response surface models. 1675-1683 - David de Sancho, Antonio Rey:
Energy minimizations with a combination of two knowledge-based potentials for protein folding. 1684-1692 - Paul Labute:
The generalized Born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area. 1693-1698
Volume 29, Number 11, August 2008
- Nitin S. Sapre, Nilanjana Pancholi, Swagata Gupta, Neelima Sapre:
Computational modeling of tetrahydroimidazo-[4, 5, 1-jk][1, 4]-benzodiazepinone derivatives: An atomistic drug design approach using Kier-Hall electrotopological state (E-state) indices. 1699-1706 - Michel Masella, Daniel Borgis, Philippe Cuniasse:
Combining a polarizable force-field and a coarse-grained polarizable solvent model: Application to long dynamics simulations of bovine pancreatic trypsin inhibitor. 1707-1724 - Laban Bondesson, Elias Rudberg, Yi Luo, Pawel Salek:
Basis set dependence of solute-solvent interaction energy of benzene in water: A HF/DFT study. 1725-1732 - Alexander G. Donchev:
Nonadditive effects in ternary H2-cation-PAH systems. 1733-1739 - Luca Monticelli, Eric J. Sorin, D. Peter Tieleman, Vijay S. Pande, Giorgio Colombo:
Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories. 1740-1752 - Max W. Chang, Richard K. Belew, Kate S. Carroll, Arthur J. Olson, David S. Goodsell:
Empirical entropic contributions in computational docking: Evaluation in APS reductase complexes. 1753-1761 - Naigong Zhang, Chen Zeng:
Reference energy extremal optimization: A stochastic search algorithm applied to computational protein design. 1762-1771 - Xueguang Shao, Xiaoli Yang, Wensheng Cai:
A dynamic lattice searching method with interior operation for unbiased optimization of large Lennard-Jones clusters. 1772-1779 - Tian Zhang, Haoping Zheng, Shu Yan:
The equivalent potential of water for electronic structure of aspartic acid. 1780-1787 - Siamkhanthang Neihsial, Richard H. Duncan Lyngdoh:
Novel H-bonded base dimers as repeat units for information-bearing self-associative duplexes: A B3LYP/6-31G* search. 1788-1797 - Ying Zhang, Xin Xu, Yijing Yan:
Systematic investigation on the geometric dependence of the calculated nuclear magnetic shielding constants. 1798-1807 - K. Periya Vijayalakshmi, Cherumuttathu H. Suresh:
Theoretical studies on the carcinogenicity of polycyclic aromatic hydrocarbons. 1808-1817 - Chan Kyung Kim, Soo Gyeong Cho, Chang Kon Kim, Hyung-Yeon Park, Hui Zhang, Hai Whang Lee:
Prediction of densities for solid energetic molecules with molecular surface electrostatic potentials. 1818-1824 - M. Y. Wang, Lin Cheng, Zhijian Wu:
Density functional study on the reaction mechanism of palladium-catalyzed addition of cyanoboranes to alkynes. 1825-1839 - Cherumuttathu H. Suresh, Aswathy Mary Vargheese, K. Periya Vijayalakshmi, Neetha Mohan, Nobuaki Koga:
Role of structural water molecule in HIV protease-inhibitor complexes: A QM/MM study. 1840-1849 - Ning He, Hong-Bin Xie, Yi-Hong Ding:
Structures and stability of lithium monosilicide clusters SiLin (n = 4-16): What is the maximum number, magic number, and core number for lithium coordination to silicon? 1850-1858 - Sunhwan Jo, Taehoon Kim, Vidyashankara G. Iyer, Wonpil Im:
CHARMM-GUI: A web-based graphical user interface for CHARMM. 1859-1865
Volume 29, Number 12, September 2008
- Xiuzhen Hu, Qianzhong Li:
Using support vector machine to predict beta- and gamma-turns in proteins. 1867-1875 - Witold Dyrka, Andy T. Augousti, Malgorzata Kotulska:
Ion flux through membrane channels - An enhanced algorithm for the Poisson-Nernst-Planck model. 1876-1888 - Fahrettin Gogtas:
Time-dependent quantum study of the kinetics of the H(2S) + FO(2II) -> OH(2II) + F(2P) reaction. 1889-1894 - Timothy J. Giese, Darrin M. York:
Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities. 1895-1904 - Asbjørn Holt, Gunnar Karlström:
Induction correction model for rotation of two or three dihedral angles. 1905-1911 - Keiko Shinoda, Wataru Shinoda, Masuhiro Mikami:
Efficient free energy calculation of water across lipid membranes. 1912-1918 - Rong-Zhen Liao, Wan-Jian Ding, Jian-Guo Yu, Wei-Hai Fang, Ruo-Zhuang Liu:
Theoretical studies on pyridoxal 5'-phosphate-dependent transamination of alpha-amino acids. 1919-1929 - Daisuke Katagiri, Hideyoshi Fuji, Saburo Neya, Tyuji Hoshino:
Ab initio protein structure prediction with force field parameters derived from water-phase quantum chemical calculation. 1930-1944 - Pankaj R. Daga, Robert J. Doerksen:
Stereoelectronic properties of spiroquinazolinones in differential PDE7 inhibitory activity. 1945-1954 - Anna Marabotti, Francesca Spyrakis, Angelo M. Facchiano, Pietro Cozzini, Saverio Alberti, Glen E. Kellogg, Andrea Mozzarelli:
Energy-based prediction of amino acid-nucleotide base recognition. 1955-1969 - Magdalena Gruziel, Pawel Grochowski, Joanna Trylska:
The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff. 1970-1981 - Inés Corral, Leticia González:
Theoretical investigation of anthracene-9, 10-endoperoxide vertical singlet and triplet excitation spectra. 1982-1991 - Amit Mor, Guy Ziv, Yaakov Levy:
Simulations of proteins with inhomogeneous degrees of freedom: The effect of thermostats. 1992-1998 - István Komáromi, Michael C. Owen, Richard F. Murphy, Sándor Lovas:
Development of glycyl radical parameters for the OPLS-AA/L force field. 1999-2009 - Guang-Jiu Zhao, Ke-Li Han:
Time-dependent density functional theory study on hydrogen-bonded intramolecular charge-transfer excited state of 4-dimethylamino-benzonitrile in methanol. 2010-2017 - Xuan Xiao, Wei-Zhong Lin, Kuo-Chen Chou:
Using grey dynamic modeling and pseudo amino acid composition to predict protein structural classes. 2018-2024 - Hujun Xie, Ruibo Wu, Fei Xia, Zexing Cao:
Effects of electron attachment on C5'-O5' and C1'-N1 bond cleavages of pyrimidine nucleotides: A theoretical study. 2025-2032 - Asbjørn Holt, Gunnar Karlström:
Inclusion of the quadrupole moment when describing polarization. The effect of the dipole-quadrupole polarizability. 2033-2038
Volume 29, Number 13, October 2008
- Richard Dronskowski, Gernot Frenking:
Foreword. 2039-2043 - Jürgen Hafner:
Ab-initio simulations of materials using VASP: Density-functional theory and beyond. 2044-2078 - Robert A. Evarestov, Andrei V. Bandura, M. V. Losev, E. A. Kotomin, Yu. F. Zhukovskii, Dmitry Bocharov:
A first-principles DFT study of UN bulk and (001) surface: Comparative LCAO and PW calculations. 2079-2087 - Torsten Kerber, Marek Sierka, Joachim Sauer:
Application of semiempirical long-range dispersion corrections to periodic systems in density functional theory. 2088-2097 - Michael J. Gillan, Dario Alfè, Stefano de Gironcoli, Frederick R. Manby:
High-precision calculation of Hartree-Fock energy of crystals. 2098-2106 - Elena Voloshina, Beate Paulus:
Cohesive properties of CeN and LaN from first principles. 2107-2112 - Cesare Pisani, Lorenzo Maschio, Silvia Casassa, Migen Halo, Martin Schütz, Denis Usvyat:
Periodic local MP2 method for the study of electronic correlation in crystals: Theory and preliminary applications. 2113-2124 - Sheng-Qing Xia, Svilen Bobev:
Are Ba11Cd6Sb12 and Sr11Cd6Sb12 Zintl phases or not? A density-functional theory study. 2125-2133 - Jianxiao Xu, Holger Kleinke:
Unusual Sb-Sb bonding in high temperature thermoelectric materials. 2134-2143 - Pere Alemany, Miquel Llunell, Enric Canadell:
Roles of cations, electronegativity difference, and anionic interlayer interactions in the metallic versus nonmetallic character of Zintl phases related to arsenic. 2144-2153 - Changhoon Lee, Myung-Hwan Whangbo, Jürgen Köhler:
Analysis of electronic structures and chemical bonding of metal-rich compounds. I. Density functional study of Pt metal, LiPt2, LiPt, and Li2Pt. 2154-2160 - Alexey I. Baranov, Miroslav Kohout:
Electron localizability for hexagonal element structures. 2161-2171 - Dong-Kyun Seo, Sang-Hwan Kim:
Nature of Stoner condition for metallic ferromagnetism. 2172-2176 - German D. Samolyuk, Gordon J. Miller:
Relation between chemical bonding and exchange coupling approaches to the description of ordering in itinerant magnets. 2177-2186 - Dadi Dai, Hongjun Xiang, Myung-Hwan Whangbo:
Effects of spin-orbit coupling on magnetic properties of discrete and extended magnetic systems. 2187-2209 - Daniel Fritsch, Klaus Koepernik, Manuel Richter, Helmut Eschrig:
Transition metal dimers as potential molecular magnets: A challenge to computational chemistry. 2210-2219 - Andreì L. Tchougréeff, Richard Dronskowski:
A computational study of the crystal and electronic structure of the room temperature organometallic ferromagnet V(TCNE)2. 2220-2233 - C. Richard A. Catlow, Samuel A. French, Alexey A. Sokol, Abdullah A. Al-Sunaidi, Scott M. Woodley:
Zinc oxide: A case study in contemporary computational solid state chemistry. 2234-2249 - Karl Jug, Viatcheslav A. Tikhomirov:
Influence of intrinsic defects on the properties of zinc oxide. 2250-2254 - Atsushi Togo, Peter Kroll:
First-principles lattice dynamics calculations of the phase boundary between beta-Si3N4 and gamma-Si3N4 at elevated temperatures and pressures. 2255-2259 - Holger Wolff, Richard Dronskowski:
First-principles and molecular-dynamics study of structure and bonding in perovskite-type oxynitrides ABO2N (A = Ca, Sr, Ba; B = Ta, Nb). 2260-2267 - Claudio Marcelo Zicovich-Wilson, Fernando Javier Torres, Fabien Pascale, Loredana Valenzano, Roberto Orlando, Roberto Dovesi:
Ab initio simulation of the IR spectra of pyrope, grossular, and andradite. 2268-2278 - Jerome Cuny, Sabri Messaoudi, Veronique Alonzo, Eric Furet, Jean-François Halet, Eric Le Fur, Sharon E. Ashbrook, Chris J. Pickard, Regis Gautier, Laurent Le Polles:
DFT calculations of quadrupolar solid-state NMR properties: Some examples in solid-state inorganic chemistry. 2279-2287 - Lindsay E. Roy, Tomasz Durakiewicz, Richard L. Martin, Juan E. Peralta, Gustavo E. Scuseria, Cliff G. Olson, John J. Joyce, Ela Guziewicz:
Dispersion in the Mott insulator UO2: A comparison of photoemission spectroscopy and screened hybrid density functional theory. 2288-2294 - Florian Janetzko, Thomas Bredow, Gerald Geudtner, Andreas M. Köster:
Boron-doped diamond: Investigation of the stability of surface-doping versus bulk-doping using cyclic cluster model calculations. 2295-2301 - Ilka Hegemann, Andreas Schwaebe, Karin Fink:
Adsorption of single Cu atoms at differently stabilized polar ZnO surfaces: An ab initio study. 2302-2310
Volume 29, Number 14, 15 November 2008
- Takashi Tsuchimochi, Masato Kobayashi, Ayako Nakata, Yutaka Imamura, Hiromi Nakai:
Application of the Sakurai-Sugiura projection method to core-excited-state calculation by time-dependent density functional theory. 2311-2316 - Masato Morita, Satoshi Yabushita:
Photoionization cross sections with optimized orbital exponents within the complex basis function method. 2317-2329 - Andreas B. Pribil, Thomas S. Hofer, Bernhard R. Randolf, Bernd M. Rode:
Structure and dynamics of phosphate ion in aqueous solution: An ab initio QMCF MD study. 2330-2334 - Daniel R. Fisher, David R. Kent IV, Michael T. Feldmann, William A. Goddard III:
An optimized initialization algorithm to ensure accuracy in quantum Monte Carlo calculations. 2335-2343 - Alexander V. Larin, I. K. Sakodynskaya, D. N. Trubnikov:
Convergence of electric field and electric field gradient versus atomic basis sets in all-siliceous and Mg substituted phillipsites. 2344-2358 - Carl-Johan Högberg, Alexei M. Nikitin, Alexander Lyubartsev:
Modification of the CHARMM force field for DMPC lipid bilayer. 2359-2369 - Zdenek Chval, Miroslav Sip, Jaroslav V. Burda:
The trans effect in square-planar platinum(II) complexes - A density functional study. 2370-2381 - Paraskevas A. Karipidis, Constantinos A. Tsipis:
The dramatic effect of NH3 co-ligation on the FE+-assisted activation of carbon dioxide in the gas phase: From bare metal ions to complexes. 2382-2396 - Lula Rosso, Antony D. Gee, Ian R. Gould:
Ab initio computational study of positron emission tomography ligands interacting with lipid molecule for the prediction of nonspecific binding. 2397-2405 - Gennady N. Chuev, Maxim V. Fedorov, Sandro Chiodo, Nino Russo, Emilia Sicilia:
Hydration of ionic species studied by the reference interaction site model with a repulsive bridge correction. 2406-2415 - Jens Krüger, Wolfgang B. Fischer:
Exploring the conformational space of Vpu from HIV-1: A versatile adaptable protein. 2416-2424 - Karmen Condic-Jurkic, V. Tamara Perchyonok, Hendrik Zipse, David M. Smith:
On the modeling of arginine-bound carboxylates: A case study with Pyruvate Formate-Lyase. 2425-2433 - G. G. Camiletti, S. F. Machado, F. E. Jorge:
Gaussian basis set of double zeta quality for atoms K through Kr: Application in DFT calculations of molecular properties. 2434-2444 - Maykel Cruz-Monteagudo, Fernanda Borges, M. Natália Dias Soeiro Cordeiro:
Desirability-based multiobjective optimization for global QSAR studies: Application to the design of novel NSAIDs with improved analgesic, antiinflammatory, and ulcerogenic profiles. 2445-2459 - Carmen Herrmann, Johannes Neugebauer, Markus Reiher:
QM/MM vibrational mode tracking. 2460-2470 - Masato Morita, Satoshi Yabushita:
Photoionization cross sections of H2+ and H2 with complex Gaussian-type basis functions optimized for the frequency-dependent polarizabilities. 2471-2478 - Jinwoo Lee, Keehyoung Joo, Seung-Yeon Kim, Jooyoung Lee:
Re-examination of structure optimization of off-lattice protein AB models by conformational space annealing. 2479-2484
- Asbjørn Holt, Gunnar Karlström:
Inclusion of the quadrupole moment when describing polarization. The effect of the dipole-quadrupole polarizability. 2485-2486
Volume 29, Number 15, 30 November 2008
- Chin-Hung Lai, Ming-Der Su:
Theoretical characterizations of HAsXH (X = N, P, As, Sb, and Bi) isomers in the singlet and triplet states. 2487-2499 - Juan A. Castillo-Garit, Yovani Marrero-Ponce, Francisco Torrens, Ramón García-Domenech, Vicente Romero-Zaldivar:
Bond-based 3D-chiral linear indices: Theory and QSAR applications to central chirality codification. 2500-2512 - Yajun Liu, Hongyan Xiao, Mengtao Sun, Weihai Fang:
Spin-orbit Ab initio investigation of the photodissociation of dibromomethane in the gas and solution phases. 2513-2519 - Wei Shi, Edward J. Maginn:
Improvement in molecule exchange efficiency in Gibbs ensemble Monte Carlo: Development and implementation of the continuous fractional component move. 2520-2530 - Hirotaka Ode, Yuri Matsuo, Saburo Neya, Tyuji Hoshino:
Force field parameters for rotation around chi torsion axis in nucleic acids. 2531-2542 - Olgun Guvench, Shannon N. Greene, Ganesh Kamath, John W. Brady, Richard M. Venable, Richard W. Pastor, Alexander D. MacKerell Jr.:
Additive empirical force field for hexopyranose monosaccharides. 2543-2564 - Natércia F. Brás, Sara A. Moura-Tamames, Pedro Alexandrino Fernandes, Maria João Ramos:
Mechanistic studies on the formation of glycosidase-substrate and glycosidase-inhibitor covalent intermediates. 2565-2574 - Gernot Kieseritzky, Ernst-Walter Knapp:
Improved pKa prediction: Combining empirical and semimicroscopic methods. 2575-2581 - Pierre Poulain, Adrien Saladin, Brigitte Hartmann, Chantal Prévost:
Insights on protein-DNA recognition by coarse grain modelling. 2582-2592 - Giovanni Grazioso, Andrea Cavalli, Marco De Amici, Maurizio Recanatini, Carlo De Micheli:
Alpha7 nicotinic acetylcholine receptor agonists: Prediction of their binding affinity through a molecular mechanics Poisson-Boltzmann surface area approach. 2593-2602 - Jakob Schluttig, Michael Bachmann, Wolfhard Janke:
Comparative molecular dynamics and Monte Carlo study of statistical properties for coarse-grained heteropolymers. 2603-2612
Volume 29, Number 16, December 2008
- Santiago Vilar, Humberto González Díaz, Lourdes Santana, Eugenio Uriarte:
QSAR model for alignment-free prediction of human breast cancer biomarkers based on electrostatic potentials of protein pseudofolding HP-lattice networks. 2613-2622 - Yan-Hong Cui, Wei-Quan Tian, Ji-Kang Feng, De-Li Chen:
Structures, stabilities, electronic, and optical properties of C64 fullerene isomers, anions (C642- and C644-), metallofullerene Sc2@C64, and Sc2C2@C64. 2623-2630 - Lili Sun, Shuwei Tang, Yingfei Chang, Zhanliang Wang, Rongshun Wang:
Searching for stable hept-C62X2 (X = F, Cl, and Br): Structures and stabilities of heptagon-containing C62 halogenated derivatives. 2631-2635 - Jiazhong Li, Beilei Lei, Huanxiang Liu, Shuyan Li, Xiaojun Yao, Mancang Liu, Paola Gramatica:
QSAR study of malonyl-CoA decarboxylase inhibitors using GA-MLR and a new strategy of consensus modeling. 2636-2647 - Guoming Liang, Xiaoguang Bao, Jiande Gu:
The possibility of the decomposition of 2'-deoxyribose moiety of thymidine induced by the low energy electron attachment. 2648-2655 - Tomonaga Ozawa, Kosuke Okazaki:
CH/pi hydrogen bonds determine the selectivity of the Src homology 2 domain to tyrosine phosphotyrosyl peptides: An ab initio fragment molecular orbital study. 2656-2666 - Mahito Chiba, Dmitri G. Fedorov, Kazuo Kitaura:
Polarizable continuum model with the fragment molecular orbital-based time-dependent density functional theory. 2667-2676 - Karolina Kisowska, Slawomir Berski, Zdzislaw Latajka:
The structure and chemical bonding in the N2-CuX and N2***XCu (X = F, Cl, Br) systems studied by means of the molecular orbital and Quantum Chemical Topology methods. 2677-2692 - Valery Andrushchenko, Petr Bour:
Circular dichroism enhancement in large DNA aggregates simulated by a generalized oscillator model. 2693-2703 - María Suárez, Pablo Tortosa, Javier Carrera, Alfonso Jaramillo:
Pareto optimization in computational protein design with multiple objectives. 2704-2711 - Mark Pinsky, Chaim Dryzun, David Casanova, Pere Alemany, David Avnir:
Analytical methods for calculating Continuous Symmetry Measures and the Chirality Measure. 2712-2721 - Norbert Flocke, Victor Lotrich:
Efficient electronic integrals and their generalized derivatives for object oriented implementations of electronic structure calculations. 2722-2736
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