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Journal of Computational Chemistry, Volume 28
Volume 28, Number 1, January 2007
- Gernot Frenking, Sason Shaik:
Foreword. 1-3
- R. F. W. Bader, Jesús Hernández-Trujillo
, Fernando Cortés-Guzmán
Chemical bonding: From Lewis to atoms in molecules. 4-14 - Gernot Frenking, Andreas Krapp:
Unicorns in the world of chemical bonding models. 15-24 - Werner Kutzelnigg:
What I like about Hückel theory. 25-34 - Jean-Paul Malrieu, Nathalie Guihéry, Carmen Jiménez Calzado
Bond electron pair: Its relevance and analysis from the quantum chemistry point of view. 35-50 - Sason Shaik:
The Lewis legacy: The chemical bond - A territory and heartland of chemistry. 51-61 - Ana Simões
In between worlds: G.N. Lewis, the shared pair bond and its multifarious contexts. 62-72 - Donald G. Truhlar
Valence bond theory for chemical dynamics. 73-86 - Ronald J. Gillespie, Edward A. Robinson:
Gilbert N. Lewis and the chemical bond: The electron pair and the octet rule from 1916 to the present day. 87-97 - Mary Jo Nye:
Working tools for theoretical chemistry: Polanyi, eyring, and debates over the "semiempirical method". 98-108
- Robert Ponec, Joaquin Chaves:
Electron pairing and chemical bonds: Pair localization in ELF domains from the analysis of domain averaged Fermi holes. 109-116 - Gernot Frenking, Christoph Loschen, Andreas Krapp, Stefan Fau, Steven H. Strauss:
Electronic structure of CO - An exercise in modern chemical bonding theory. 117-126 - Marcos Mandado
QTAIM n-center delocalization indices as descriptors of aromaticity in mono and poly heterocycles. 127-136 - Philippe C. Hiberty, Sason Shaik:
A survey of recent developments in ab initio valence bond theory. 137-151 - Patrick Bultinck
Aromaticity in linear polyacenes: Generalized population analysis and molecular quantum similarity approach. 152-160 - Ángel Martín Pendás
Chemical fragments in real space: Definitions, properties, and energetic decompositions. 161-184 - Peifeng Su, Lingchun Song, Wei Wu, Philippe C. Hiberty, Sason Shaik:
A valence bond study of the dioxygen molecule. 185-197 - Clark R. Landis, Frank Weinhold
Valence and extra-valence orbitals in main group and transition metal bonding. 198-203 - I. Mayer:
Bond order and valence indices: A personal account. 204-221 - Dmitri G. Fedorov, Kazuo Kitaura:
Pair interaction energy decomposition analysis. 222-237 - Friedrich Matthias Bickelhaupt
Covalent versus ionic bonding in alkalimetal fluoride oligomers. 238-250 - Dmitry Yu. Zubarev, Alexander I. Boldyrev:
Comprehensive analysis of chemical bonding in boron clusters. 251-268 - Lionel Goodman, Ronald R. Sauers:
Diffuse functions in natural bond orbital analysis. 269-275 - Lyudmila V. Slipchenko
Electrostatic energy in the effective fragment potential method: Theory and application to benzene dimer. 276-291 - Michel Rafat, Paul L. A. Popelier:
Atom-atom partitioning of total (super)molecular energy: The hidden terms of classical force fields. 292-301 - Thomas Heine
sigma and pi contributions to the induced magnetic field: Indicators for the mobility of electrons in molecules. 302-309 - Dandamudi Usha Rani, Dasari L. V. K. Prasad, John F. Nixon, Eluvathingal D. Jemmis
Electronic structure and bonding studies on triple-decker sandwich complexes with a P6 middle ring. 310-319 - Martin Kaupp:
The role of radial nodes of atomic orbitals for chemical bonding and the periodic table. 320-325 - Iñigo García-Yoldi, Fernando Mota, Juan J. Novoa
The origin of the two-electron/four-centers C-C bond in pi-TCNE22- dimers: Electrostatic or dispersion? 326-334 - B. Sateesh, A. Srinivas Reddy, G. Narahari Sastry:
Towards design of the smallest planar tetracoordinate carbon and boron systems. 335-343 - Chaitanya S. Wannere, Ankan Paul, Rainer Herges, Kendall N. Houk, Henry F. Schaefer III, Paul von Ragué Schleyer:
The existence of secondary orbital interactions. 344-361 - Gabriel Merino, Miguel A. Méndez-Rojas
Recent advances in planar tetracoordinate carbon chemistry. 362-372 - Igor V. Alabugin
Rehybridization as a general mechanism for maximizing chemical and supramolecular bonding and a driving force for chemical reactions. 373-390 - Klaus Ruedenberg, Michael W. Schmidt:
Why does electron sharing lead to covalent bonding? A variational analysis. 391-410 - Dmitry V. Khoroshun, Djamaladdin G. Musaev, Keiji Morokuma:
Electronic reorganization: Origin of sigma trans promotion effect. 423-441 - Anthony Scemama
Maximum probability domains from Quantum Monte Carlo calculations. 442-454 - John Frederick Beck, Yirong Mo:
How resonance assists hydrogen bonding interactions: An energy decomposition analysis. 455-466
Volume 28, Number 2, January 2007
- Zi-Zhang Wei, Bu-Tong Li, Hong-Xing Zhang, Chia-Chung Sun, Ke-Li Han:
A theoretical investigation of the excited states of OCLO radical, cation, and anion using the CASSCF/CASPT2 method. 467-477 - Ross C. Walker, Ian P. Mercer, Ian R. Gould
Comparison of basis set effects and the performance of ab initio and DFT methods for probing equilibrium fluctuations. 478-490 - M. Rami Reddy, U. C. Singh, Mark D. Erion:
Ab initio quantum mechanics-based free energy perturbation method for calculating relative solvation free energies. 491-494 - Evelyn Mayaan, Adam Moser, Alexander D. MacKerell Jr., Darrin M. York
CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes. 495-507 - Chun Li, Ai-hua Wang, Lili Xing:
Similarity of RNA secondary structures. 508-512 - Sheng-Yong Yang, Ming-Li Xiang, Li-Juan Chen, Guo-Bin Xie, Bing Shi, Yu-Quan Wei
Free energy profiles for monomer capture in Grubbs- and SHOP-type olefin polymerization catalysts: A constraint ab initio molecular dynamics study. 513-518 - Wei-Qi Lin, Jian-Hui Jiang, Yan-Ping Zhou, Hai-Long Wu, Guo-Li Shen, Ru-Qin Yu:
Support vector machine based training of multilayer feedforward neural networks as optimized by particle swarm algorithm: Application in QSAR studies of bioactivity of organic compounds. 519-527 - S. A. De Marothy, Margareta R. A. Blomberg, Per E. M. Siegbahn:
Elucidating the mechanism for the reduction of nitrite by copper nitrite reductase - A contribution from quantum chemical studies. 528-539 - Jose Manuel Hermida-Ramón
Blue-shifting hydrogen bond in the benzene-benzene and benzene-naphthalene complexes. 540-546 - Kalju Kahn, Alex A. Granovsky, Jozef Noga
Convergence of third order correlation energy in atoms and molecules. 547-554 - Petr Jurecka, Jirí Cerný
Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations. 555-569 - Pedro Gonnet
A simple algorithm to accelerate the computation of non-bonded interactions in cell-based molecular dynamics simulations. 570-573 - Miquel Torrent-Sucarrat
On the quality of the hardness kernel and the Fukui function to evaluate the global hardness. 574-583 - Riccardo Conte
Direct evaluation via forced oscillation method of the electronic state density of sizable clusters. 584-593 - Hong Seok Kang:
A theoretical study of fullerene-ferrocene hybrids. 594-600 - Svetlana Stepanenko, Bernd Engels:
Gradient tabu search. 601-611 - Hung-Ming Chen, Bo-Fu Liu, Hui-Ling Huang, Shiow-Fen Hwang, Shinn-Ying Ho
SODOCK: Swarm optimization for highly flexible protein-ligand docking. 612-623
Volume 28, Number 3, February 2007
- Chang Kon Kim, Dong J. Kim, Y. Hsieh, Hai Whang Lee, Bon-Su Lee, Chan Kyung Kim:
Effects of entropy on the gas-phase pyrolysis of ethyl N, N-dimethylcarbamate. 625-631 - Benoît Bories, Daniel Maynau, Marie-Laure Bonnet:
Selected excitation for CAS-SDCI calculations. 632-643 - Irina S. Moreira
Computational alanine scanning mutagenesis - An improved methodological approach. 644-654 - Vladimir Hnizdo, Eva Darian, Adam Fedorowicz, Eugene Demchuk, Shengqiao Li, Harshinder Singh:
Nearest-neighbor nonparametric method for estimating the configurational entropy of complex molecules. 655-668 - Jinhyuk Lee, Wonpil Im:
Implementation and application of helix-helix distance and crossing angle restraint potentials. 669-680 - Tomasz Panczyk
Collisions of ideal gas molecules with a rough/fractal surface. A computational study. 681-688 - Zhitao Xu, Harry H. Luo, D. Peter Tieleman:
Modifying the OPLS-AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off-plane charge model for aromatic residues. 689-697 - Dimitri N. Laikov
Neglect of four- and approximation of one-, two-, and three-center two-electron integrals in a symmetrically orthogonalized basis. 698-702 - Zhijian Wu, M. Y. Wang, Zhong-Min Su:
Electronic structures and chemical bonding in diatomic ScX to ZnX (X = S, Se, Te). 703-714 - Ruben Ghulghazaryan, Shura Hayryan, Chin-Kun Hu
Efficient combination of Wang-Landau and transition matrix Monte Carlo methods for protein simulations. 715-726
Volume 28, Number 4, March 2007
- Yoong-Kee Choe
Theoretical study of the electronic spectra of oxidized and reduced states of lumiflavin and its derivative. 727-739 - Terutaka Yoshizawa, Masahiko Hada:
Calculations of frequency-dependent molecular magnetizabilities with quasi-relativistic time-dependent generalized unrestricted Hartree-Fock method. 740-747 - Jaime Fernández Rico, Rafael López, Ignacio Ema, Guillermo Ramírez
Generation of basis sets with high degree of fulfillment of the Hellmann-Feynman theorem. 748-758 - Bryan M. Wong
Thermodynamic calculations for molecules with asymmetric internal rotors - application to 1, 3-butadiene. 759-766 - Ernesto Estrada
Point scattering: A new geometric invariant with applications from (Nano)clusters to biomolecules. 767-777 - Vladimir I. Bolshakov, Vladimir V. Rossikhin, Eugene O. Voronkov
The performance of the new 6-31G## basis set: Molecular structures and vibrational frequencies of transition metal carbonyls. 778-782 - Hsiu-Feng Lu, Feng-Yin Li, S. H. Lin:
Site specificity of alpha-H abstraction reaction among secondary structure motif - An ab initio study. 783-794 - Xingfa Gao
The way of stabilizing non-IPR fullerenes and structural elucidation of C54Cl8. 795-801 - Ying Wang, Jing-Yao Liu, Ze-Sheng Li, Li Wang, Chia-Chung Sun:
Theoretical study and rate constant calculation for reaction of CF3CH2OH with OH. 802-810 - M. Lawrence Ellzey Jr.:
Finite group theory for large systems. 3. Symmetry-generation of reduced matrix elements for icosahedral C20 and C60 molecules. 811-817 - Jeb Kegerreis, Nancy Makri:
Optimized Monte Carlo sampling in forward-backward semiclassical dynamics. 818-824 - Dorota Rutkowska-Zbik
Theoretical density functional theory studies on interactions of small biologically active molecules with isolated heme group. 825-831 - Michel Rafat, Paul L. A. Popelier:
Long range behavior of high-rank topological multipole moments. 832-838
Volume 28, Number 5, April 2007
- Robert A. Distasio Jr., Ryan P. Steele, Young Min Rhee
An improved algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Møller-Plesset perturbation theory: Application to alanine tetrapeptide conformational analysis. 839-856 - Victor Polo, Juan Andrés
New insights on the bridge carbon-carbon bond in propellanes: A theoretical study based on the analysis of the electron localization function. 857-864 - Jian Wang, Yi-Hong Ding, Shao-Wen Zhang, Chia-Chung Sun:
Theoretical study on the methyl radical with chlorinated methyl radicals CH3-nCln (n = 1, 2, 3) and CCl2. 865-876 - Martin R. Siegert, Matthias Heuchel
A generalized direct-particle-deletion scheme for the calculation of chemical potential and solubilities of small- and medium-sized molecules in amorphous polymers. 877-889 - Frits Daeyaert, Marc R. de Jonge
An ant algorithm for the conformational analysis of flexible molecules. 890-898 - Edward Sanville, Steven D. Kenny
Improved grid-based algorithm for Bader charge allocation. 899-908 - Alexander H. Boschitsch, Marcia O. Fenley:
A new outer boundary formulation and energy corrections for the nonlinear Poisson-Boltzmann equation. 909-921 - Hassan Sabzyan, Davood Farmanzadeh:
Electric field effects on the performance of a candidate multipole molecular switch: A quantum computational study. 922-931 - Ravichandra Mutyala, R. N. Reddy, M. Sumakanth, P. Reddanna, M. Rami Reddy:
Calculation of relative binding affinities of fructose 1, 6-bisphosphatase mutants with adenosine monophosphate using free energy perturbation method. 932-937 - Celine Roux, Nohad Gresh, Lalith E. Perera
Binding of 5-phospho-D-arabinonohydroxamate and 5-phospho-D-arabinonate inhibitors to zinc phosphomannose isomerase from Candida albicans studied by polarizable molecular mechanics and quantum mechanics. 938-957 - V. R. Ferro, Rafael López, Salama Omar, J. M. García de la Vega:
On the molecular electron structure of three phosphinine-containing macrocycles. 958-966 - W. J. Fan, R. Q. Zhang, Shubin Liu
Computation of large systems with an economic basis set: Structures and reactivity indices of nucleic acid base pairs from density functional theory. 967-974 - Yue-meng Ji, Xiao-lei Zhao, Ze-Sheng Li, Jing-Yao Liu:
Kinetic mechanism of the hydrogen abstraction reactions of the chlorine atoms with CH3CF2Cl and CH3CFCl2: A dual level direct dynamics study. 975-983 - Toru Inaba, Fumitoshi Sato:
Development of parallel density functional program using distributed matrix to calculate all-electron canonical wavefunction of large molecules. 984-995
Volume 28, Number 6, April 2007
- Ismael Tejero, Àngels González-Lafont
A PM3/d specific reaction parameterization for iron atom in the hydrogen abstraction catalyzed by soybean lipoxygenase-1. 997-1005 - Viwat Vchirawongkwin
Tl(I)-the strongest structure-breaking metal ion in water? A quantum mechanical/molecular mechanical simulation study. 1006-1016 - Arnau Cordomí
Effect of different treatments of long-range interactions and sampling conditions in molecular dynamic simulations of rhodopsin embedded in a dipalmitoyl phosphatidylcholine bilayer. 1017-1030 - Anna Marabotti
New computational strategy to analyze the interactions of ER alpha and ER beta with different ERE sequences. 1031-1041 - Humberto González Díaz
Computational chemistry approach to protein kinase recognition using 3D stochastic van der Waals spectral moments. 1042-1048 - Humberto González Díaz
2D-RNA-coupling numbers: A new computational chemistry approach to link secondary structure topology with biological function. 1049-1056 - Viwat Vchirawongkwin
Quantum mechanical/molecular mechanical simulations of the Tl(III) ion in water. 1057-1067 - Anna Jagielska, Harold A. Scheraga:
Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: All-atom molecular dynamics in implicit solvent. 1068-1082 - Pär Söderhjelm
Accuracy of distributed multipoles and polarizabilities: Comparison between the LoProp and MpProp models. 1083-1090 - Hitomi Yuki
Implementation of pi-pi interactions in molecular dynamics simulation. 1091-1099 - Kyoung Hoon Kim, Jaehoon Jung
Cyclic voltammetry modeling, geometries, and electronic properties for metallofullerene complexes with µ3-eta2: eta2: eta2-C60 bonding mode. 1100-1106 - Sang-Ho Lee, Kim Palmö, Samuel Krimm:
A comparative study of molecular dynamics in Cartesian and in internal coordinates: Dynamical instability in the latter caused by nonlinearity of the equations of motion. 1107-1118 - Stefano Alcaro
"Quasi flexible" automatic docking processing for studying stereoselective recognition mechanisms, part 2: Prediction of Delta Delta G of complexation and 1H-NMR NOE correlation. 1119-1128 - Minoru Saito, Isao Okazaki:
A 45-ns molecular dynamics simulation of hemoglobin in water by vectorizing and parallelizing COSMOS90 on the earth simulator: Dynamics of tertiary and quaternary structures. 1129-1136 - Takao Otsuka, Hiromi Nakai
Wavelet transform analysis of ab initio molecular dynamics simulation: Application to core-excitation dynamics of BF3. 1137-1144
- Ruth Huey, Garrett M. Morris
A semiempirical free energy force field with charge-based desolvation. 1145-1152
Volume 28, Number 7, May 2007
- Hui Zhang, Guiling Zhang, Li Wang, Bo Liu, Xiaoyang Yu, Ze-Sheng Li:
Theoretical study on the Br + CH3SCH3 reaction. 1153-1159 - Sérgio Filipe Sousa, Pedro Alexandrino Fernandes, Maria João Ramos
Theoretical studies on farnesyl transferase: Evidence for thioether product coordination to the active-site zinc sphere. 1160-1168 - Maxim Tafipolsky, Saeed Amirjalayer
Ab initio parametrized MM3 force field for the metal-organic framework MOF-5. 1169-1176 - Seth T. Call, Dmitry Yu. Zubarev, Alexander I. Boldyrev:
Global minimum structure searches via particle swarm optimization. 1177-1186 - David de Sancho
Evaluation of coarse grained models for hydrogen bonds in proteins. 1187-1199 - Adelio R. Matamala, Daniel E. Almonacid
A semiempirical approach to the intra-phycocyanin and inter-phycocyanin fluorescence resonance energy-transfer pathways in phycobilisomes. 1200-1207 - Nicholas Y. Palermo, József Csontos
Aromatic-backbone interactions in model alpha-helical peptides. 1208-1214 - Alan R. Ford, Tomasz Janowski
Array files for computational chemistry: MP2 energies. 1215-1220 - Yan-Li Zhao, Wei Kan, Hua Zhong, Haitao Yu, Hong-Gang Fu:
Combined DFT, QCISD(T), and G2 mechanism investigation for the reactions of carbon monophosphide CP with unsaturated hydrocarbons allene CH2CCH2 and methylacetylene CH3CCH. 1221-1233 - Fangqiang Zhu, Dimitris K. Agrafiotis
Self-organizing superimposition algorithm for conformational sampling. 1234-1239 - Evgueni B. Kadossov, Karen J. Gaskell
Effect of surrounding point charges on the density functional calculations of NixOx clusters (x = 4-12). 1240-1251 - Manuel Urbano-Cuadrado, Irene Luque Ruiz
QSAR models based on isomorphic and nonisomorphic data fusion for predicting the blood brain barrier permeability. 1252-1260 - Dennis M. Elking, Tom Darden, Robert J. Woods
Gaussian induced dipole polarization model. 1261-1274 - Chanin Nantasenamat
Prediction of GFP spectral properties using artificial neural network. 1275-1289
- Anthony K. Grafton:
Vibalizer: A free, web-based tool for rapid, quantitative comparison and analysis of calculated vibrational modes. 1290-1305
Volume 28, Number 8, June 2007
- David P. Tew
Electron correlation: The many-body problem at the heart of chemistry. 1307-1320 - N. R. Jena
Formation of 8-nitroguanine and 8-oxoguanine due to reactions of peroxynitrite with guanine. 1321-1335 - Andrew Leaver-Fay, Glenn L. Butterfoss, Jack Snoeyink
Maintaining solvent accessible surface area under rotamer substitution for protein design. 1336-1341 - Michael L. Mckee:
Modeling the nitrogenase FeMo cofactor with high-spin Fe8S9X+ (X=N, C) clusters. Is the first step for N2 reduction to NH3 a concerted dihydrogen transfer? 1342-1356 - Chin-Hung Lai
Can an OH radical form a strong hydrogen bond? A theoretical comparison with H2O. 1357-1363 - Anatoly M. Ruvinsky:
Role of binding entropy in the refinement of protein-ligand docking predictions: Analysis based on the use of 11 scoring functions. 1364-1372 - Veronika Kasalová, Wesley D. Allen, Henry F. Schaefer III, Eszter Czinki, Attila G. Császár
Molecular structures of the two most stable conformers of free glycine. 1373-1383 - Sönke Lorenz, Elmar Diederichs, Regina Telgmann, Christof Schütte:
Discrimination of dynamical system models for biological and chemical processes. 1384-1399 - Kilho Eom
Coarse-graining of protein structures for the normal mode studies. 1400-1410 - Carlos Silva López
Pseudopericyclic design drives antara-antara [1, 5] methylene sigmatropic shifts from a stepwise to a concerted mechanism. 1411-1416 - Jin Qiang Hou, Hong Seok Kang:
A DFT study on the dimerization of C62, H2-C62, and F2-C62. 1417-1426 - Xiaoli Yang, Wensheng Cai, Xueguang Shao
A dynamic lattice searching method with constructed core for optimization of large lennard-jones clusters. 1427-1433 - Qi Dai, Xiao-Qing Liu, Tian-Ming Wang, Damir Vukicevic:
Linear regression model of DNA sequences and its application. 1434-1445 - Qian Shu Li, Yu Xu:
A quantum chemistry study: A new kind of boron nitrides. 1446-1455 - Didier Bégué
Vibrational anharmonic calculations in solution: Performance of various DFT approaches. 1456-1462
Volume 28, Number 9, July 2007
- Hao Lin
Using pseudo amino acid composition to predict protein structural class: Approached by incorporating 400 dipeptide components. 1463-1466 - Wei-Qi Li, Wei-Quan Tian, Ji-Kang Feng, Zi-Zhong Liu, Ai-Min Ren, Chia-Chung Sun, Yuriko Aoki:
Electronic properties of tricoordinated phosphorus in hexagonal phosphininium compounds and molecular aromaticity. 1467-1475 - Dmitri G. Fedorov, Kazuya Ishimura
Accuracy of the three-body fragment molecular orbital method applied to Møller-Plesset perturbation theory. 1476-1484 - H. Lee Woodcock III, Milan Hodoscek, Andrew T. B. Gilbert, Peter M. W. Gill, Henry F. Schaefer III, Bernard R. Brooks:
Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations. 1485-1502 - Stephan Raub, Christel M. Marian
Quantum chemical investigation of hydrogen-bond strengths and partition into donor and acceptor contributions. 1503-1515 - Antonio Vila, Ricardo A. Mosquera
Atoms in molecules interpretation of the anomeric effect in the O-C-O unit. 1516-1530 - Mark P. Waller, Michael Bühl:
Vibrational corrections to geometries of transition metal complexes from density functional theory. 1531-1537 - Setsuko Nakagawa
Polarizable model potential function for nucleic acid bases. 1538-1550 - Marcel Swart
Energy landscapes of nucleophilic substitution reactions: A comparison of density functional theory and coupled cluster methods. 1551-1560 - Shinichi Yamabe, Noriko Tsuchida, Shoko Yamazaki:
Theoretical study of the role of solvent H2O in neopentyl and pinacol rearrangements. 1561-1571 - Matthew C. Zwier, Justin M. Shorb, Brent P. Krueger
Hybrid molecular dynamics-quantum mechanics simulations of solute spectral properties in the condensed phase: Evaluation of simulation parameters. 1572-1581 - Edmond P. F. Lee, John M. Dyke, Wan-Ki Chow
DFT and ab initio calculations on two reactions between hydrogen atoms and the fire suppressants 2-H heptafluoropropane and CF3Br. 1582-1592 - Dominik Gront
Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates. 1593-1597 - Olexandr Isayev
Theoretical calculations: Can Gibbs free energy for intermolecular complexes be predicted efficiently and accurately? 1598-1609
- T. Daniel Crawford, C. David Sherrill
PSI3: An open-source Ab Initio electronic structure package. 1610-1616
Volume 28, Number 10, July 2007
- Petr Danecek, Petr Bour:
Comparison of the numerical stability of methods for anharmonic calculations of vibrational molecular energies. 1617-1624 - Marcos Mandado
Chemical graph theory and n-center electron delocalization indices: A study on polycyclic aromatic hydrocarbons. 1625-1633 - José D. Faraldo-Gómez, Benoît Roux:
Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: Assessing entropic and environmental effects. 1634-1647 - Anna Jagielska, Jeffrey Skolnick:
Origin of intrinsic 310-helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field. 1648-1657 - Yongjian Li, Jian Wan, Xin Xu:
Theoretical study of the vertical excited states of benzene, pyrimidine, and pyrazine by the symmetry adapted cluster - Configuration interaction method. 1658-1667 - Dorota Latek
Protein structure prediction: Combining de novo modeling with sparse experimental data. 1668-1676 - Ying Li, Di Wu, Zhi-Ru Li, Chia-Chung Sun:
Structural and electronic properties of boron-doped lithium clusters: Ab initio and DFT studies. 1677-1684 - Yuri Alexeev
A parallel distributed data CPHF algorithm for analytic Hessians. 1685-1694 - Alexander V. Larin
Quick scheme for evaluation of atomic charges in arbitrary aluminophosphate sieves on the basis of electron densities calculated with DFT methods. 1695-1703 - M. Qaiser Fatmi, Thomas S. Hofer
Quantum mechanical charge field molecular dynamics simulation of the TiO2+ ion in aqueous solution. 1704-1710 - Pedro J. Ballester
Ultrafast shape recognition to search compound databases for similar molecular shapes. 1711-1723 - Scheila Furtado Braga, Douglas Soares Galvão
Molecular dynamics simulation of single wall carbon nanotubes polymerization under compression. 1724-1734 - Rungtiwa Chidthong, Supa Hannongbua
Excited state properties, fluorescence energies, and lifetime of a poly(fluorene-pyridine) copolymer, based on TD-DFT investigation. 1735-1742 - David Curcó, Carlos Alemán
Computational tool to model the packing of polycyclic chains: Structural analysis of amorphous polythiophene. 1743-1749 - Yuto Komeiji
Change in a protein's electronic structure induced by an explicit solvent: An ab initio fragment molecular orbital study of ubiquitin. 1750-1762 - Hossein Eslami, Florian Müller-Plathe:
Molecular dynamics simulation in the grand canonical ensemble. 1763-1773
Volume 28, Number 11, August 2007
- Charles L. Brooks III, Gernot Frenking, Shigeyoshi Sakaki:
Letter from the Editors. 1775 - Remmick So, Saman Alavi:
Vertical excitation energies for ribose and deoxyribose nucleosides. 1776-1782 - Stanislav Böhm, Otto Exner:
Inductive effects in radicals calculated from DFT energies; substituted bicyclo[2.2.2]octan-1-yloxy radicals. 1783-1789 - Jiande Gu, Jing Wang, Jerzy Leszczynski:
Iso-guanine quintet complexes coordinated by mono valent cations (Na+, K+, Rb+, and Cs+). 1790-1795 - Michael L. Mckee:
Modeling hydrogen evolution from the Fe4S4 and Fe8S9X (X = N, C) clusters. Can a Fe-S high-spin cluster serve as a surrogate for the FeMo cofactor? 1796-1808 - Yao-Yuan Chuang
Calculating rate constants with updated Hessians using variational transition state theory with multidimensional tunneling. 1809-1816 - R. Maul, Frank Ortmann
DFT studies using supercells and projector-augmented waves for structure, energetics, and dynamics of glycine, alanine, and cysteine. 1817-1833 - Wolfgang Quapp:
Finding the transition state without initial guess: The growing string method for Newton trajectory to isomerization and enantiomerization reaction of alanine dipeptide and poly(15)alanine. 1834-1847 - Tian Zhang, Haoping Zheng, Shu Yan:
Equivalent potential of water molecules for electronic structure of glutamic acid. 1848-1857 - Thenmalarchelvi Rathinavelan, Wonpil Im:
Explicit treatment of force contribution from alignment tensor using overdetermined linear equations and its application in NMR structure determination. 1858-1864 - V. A. Levashov, Simon J. L. Billinge, M. F. Thorpe:
Quantum correction to the pair distribution function. 1865-1882 - Yu Sun, Brian N. Dominy
Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface. 1883-1892 - Constantinos A. Tsipis, Ioannis G. Depastas, Christos E. Kefalidis
Growth format, electronic architecture, magnetic, and optical properties of aromatic cyclo-Cu3Au3 homotops. 1893-1908 - Maykel Cruz-Monteagudo
Computational chemistry development of a unified free energy Markov model for the distribution of 1300 chemicals to 38 different environmental or biological systems. 1909-1923
- Sofie Van Damme, Patrick Bultinck
A new computer program for QSAR-analysis: ARTE-QSAR. 1924-1928
Volume 28, Number 12, September 2007
- David Curcó, Carlos Alemán
Coarse-graining: A procedure to generate equilibrated and relaxed models of amorphous polymers. 1929-1935 - Imre Berente, Eszter Czinki, Gábor Náray-Szabó:
A combined electronegativity equalization and electrostatic potential fit method for the determination of atomic point charges. 1936-1942 - Gaurav Porwal, Swapnil Jain, S. Dhilly Babu, Deepak Singh, Hemant Nanavati, Santosh B. Noronha:
Protein structure prediction aided by geometrical and probabilistic constraints. 1943-1952 - Yousung Jung
Fast evaluation of scaled opposite spin second-order Møller-Plesset correlation energies using auxiliary basis expansions and exploiting sparsity. 1953-1964 - Ian R. Gould
Correlated ab initio quantum chemical calculations of di- and trisaccharide conformations. 1965-1973 - Georgy Rychkov
Joint neighbors approximation of macromolecular solvent accessible surface area. 1974-1989 - Humberto González Díaz
Computational chemistry comparison of stable/nonstable protein mutants classification models based on 3D and topological indices. 1990-1995 - Andrew J. Moad, Charles W. Moad, John M. Perry, Ronald D. Wampler, G. Scott Goeken, Nathan J. Begue, Tian Shen, Randy W. Heiland
NLOPredict: Visualization and data analysis software for nonlinear optics. 1996-2002 - Tomoko Akama, Masato Kobayashi, Hiromi Nakai
Implementation of divide-and-conquer method including Hartree-Fock exchange interaction. 2003-2012 - Vinzenz Bachler:
Orthogonal natural atomic orbitals form an appropriate one-electron basis for expanding CASSCF wave functions into localized bonding schemes and their weights. 2013-2019 - Alexei M. Nikitin, Alexander Lyubartsev
New six-site acetonitrile model for simulations of liquid acetonitrile and its aqueous mixtures. 2020-2026 - Tao Zeng
Electron affinities of heavier phosphoryl and thiophosphoryl halides APX3 (A = O, S and X = Br, I). 2027-2033 - Kazuya Ishimura
New parallel algorithm for MP2 energy gradient calculations. 2034-2042 - Qishi Du, Ri-Bo Huang, Yu-Tuo Wei, Cheng-Hua Wang, Kuo-Chen Chou:
Peptide reagent design based on physical and chemical properties of amino acid residues. 2043-2050 - Balázs Jójárt, Tamás A. Martinek:
Performance of the general amber force field in modeling aqueous POPC membrane bilayers. 2051-2058 - Liliana Wroblewska, Jeffrey Skolnick:
Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking. 2059-2066 - Yutaka Imamura, Takao Otsuka, Hiromi Nakai
Description of core excitations by time-dependent density functional theory with local density approximation, generalized gradient approximation, meta-generalized gradient approximation, and hybrid functionals. 2067-2074
- Carsten Kutzner, David van der Spoel
Speeding up parallel GROMACS on high-latency networks. 2075-2084
Volume 28, Number 13, October 2007
- Francesco Ferrante
Theoretical study of the interaction between sodium ion and a cyclopeptidic tubular structure. 2085-2090 - Run-Feng Chen, Chao Zheng, Qu-Li Fan, Wei Huang
Structural, electronic, and optical properties of 9-heterofluorenes: A quantum chemical study. 2091-2101 - Javier González, Xavier Giménez, Josep Maria Bofill:
Algorithm to evaluate rate constants for polyatomic chemical reactions. I. Theory and computational details. 2102-2110 - Javier González, Xavier Giménez, Josep Maria Bofill:
Algorithm to evaluate rate constants for polyatomic chemical reactions. II. Applications. 2111-2121 - Chen Yanover, Menachem Fromer
Dead-end elimination for multistate protein design. 2122-2129 - Bård Buttingsrud, Bjørn K. Alsberg, Per-Olof Åstrand
Validation of critical points in the electron density as descriptors by building quantitative structure-property relationships for the atomic polar tensor. 2130-2139 - Mine Ilk Capar
Odd-even effects in the homologous series of alkyl-cyanobiphenyl liquid crystals: A molecular dynamic study. 2140-2146 - Jingjing Zheng
Common system setup for the entire catalytic cycle of cytochrome P450cam in quantum mechanical/molecular mechanical studies. 2147-2158 - Riccardo Zanasi
Chiral discrimination via nuclear magnetic shielding polarisabilities from NMR spectroscopy: Theoretical study of (Ra)-1, 3-dimethylallene, (2R)-2-methyloxirane, and (2R)-N-methyloxaziridine. 2159-2163 - Yuanqiang Zhu, Yong Guo, Lidong Zhang
A computational investigation on the sequential rearrangement mechanism of 2-allyl-2, 4, 5-hexatrienaldehyde involving [1, 5]-hydrogen migration and 8pi-electrocyclization. 2164-2169 - Josep M. Porta
Complete maps of molecular-loop conformational spaces. 2170-2189 - Lin Cheng
Electronic structures and chemical bonding in 4d transition metal monohalides. 2190-2202 - Gabriele Milani, Federico Milani:
Genetic algorithm for the determination of binodal curves in ternary systems polymer-liquid(1)-liquid(2) and polymer(1)-polymer(2)-solvent. 2203-2215 - Santiago Vilar
Inhibitor docking screened by the modified SAFE_p scoring function: Application to cyclic urea HIV-1 PR inhibitors. 2216-2225 - Peter H. M. Budzelaar:
Geometry optimization using generalized, chemically meaningful constraints. 2226-2236 - Kaori Fukuzawa
Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study. 2237-2239
Volume 28, Number 14, November 2007
- Huynh-Hoa Bui, Alexandra J. Schiewe, Ian S. Haworth:
WATGEN: An algorithm for modeling water networks at protein-protein interfaces. 2241-2251 - Mikhail Pykavy, Christoph Van Wüllen
A systematic quantum chemical investigation of the C-H bond activation in methane by gas phase vanadium oxide cation VO+. 2252-2259 - Guiling Zhang, Hui Zhang, Miao Sun, Yanhong Liu, Xiaohong Pang, Xiaoyang Yu, Bo Liu, Ze-Sheng Li:
Substitution effect on the geometry and electronic structure of the ferrocene. 2260-2274 - Manuel Piacenza
A comparative quantum chemical study of the ruthenium catalyzed olefin metathesis. 2275-2285 - Wenli Zou, Wenjian Liu
Theoretical study on the low-lying electronic states of NiH and NiAt. 2286-2298 - Marko Schreiber, Leticia González
Structure and bonding of Ag(I)-DNA base complexes and Ag(I)-adenine-cytosine mispairs: An ab Initio study. 2299-2308 - David R. Kent IV, Richard P. Muller, Amos G. Anderson, William A. Goddard III, Michael T. Feldmann:
Efficient algorithm for "on-the-fly" error analysis of local or distributed serially correlated data. 2309-2316 - Julian Henn
Chemical interpretation of molecular electron density distributions. 2317-2324 - Edda Kloppmann, G. Matthias Ullmann
An extended dead-end elimination algorithm to determine gap-free lists of low energy states. 2325-2335 - Xinliang Yu, Bing Yi, Xueye Wang:
Prediction of refractive index of vinyl polymers by using density functional theory. 2336-2341 - Xizhen Zhang, Jiawei Luo, Li Yang:
New invariant of DNA sequence based on 3DD-curves and its application on phylogeny. 2342-2346
- Zengjian Hu, William M. Southerland:
Windock: Structure-based drug discovery on windows-based PCs. 2347-2351 - Kaushalya S. Ekanayake, Pierre R. Lebreton:
Model transition states for methane diazonium ion methylation of guanine runs in oligomeric DNA. 2352-2365 - Riccardo Nifosí, Pietro Amat, Valentina Tozzini
Variation of spectral, structural, and vibrational properties within the intrinsically fluorescent proteins family: A density functional study. 2366-2377 - Arnab B. Chowdry, Kimberly A. Reynolds
An object-oriented library for computational protein design. 2378-2388
- Klaus Ruedenberg, Michael W. Schmidt:
Why does electron sharing lead to covalent bonding? A variational analysis. 2389
Volume 28, Number 15, November 2007
- Kuo-Hsiang Chen, Jenn-Huei Lii, Yi Fan, Norman L. Allinger:
Molecular mechanics (MM4) study of amines. 2391-2412 - Congyi Zhou, Changming Nie, Shan Li, Zhonghai Li:
A novel semi-empirical topological descriptor Nt and the application to study on QSPR/QSAR. 2413-2423 - Hidenori Anjima, Shinya Tsukamoto, Hirotoshi Mori
Revised model core potentials of s-block elements. 2424-2430 - Anan Wu, Ying Zhang
Systematic studies on the computation of nuclear magnetic resonance shielding constants and chemical shifts: The density functional models. 2431-2442 - Jun-Ya Hasegawa, Kazuhiro Fujimoto
Excited states of GFP chromophore and active site studied by the SAC-CI method: Effect of protein-environment and mutations. 2443-2452 - Alexander Fischer, Sonja Waldhausen, Illia Horenko, Eike Meerbach, Christof Schütte:
Identification of biomolecular conformations from incomplete torsion angle observations by hidden markov models. 2453-2464 - A. Slepoy, M. D. Peters, A. P. Thompson:
Searching for globally optimal functional forms for interatomic potentials using genetic programming with parallel tempering. 2465-2471 - Wei Kan, Haitao Yu, Hong-Gang Fu, Yi-Qun Wu:
Theoretical investigation on the protonation reactions and products of the stable [N, C, C, S] isomers. 2472-2482 - Dario Duca, Giampaolo Barone
IDEA: Interface dynamics and energetics algorithm. 2483-2499 - Yan-Ling Liu, Ji-Kang Feng, Ai-Min Ren:
Structural, electronic, and optical properties of phosphole-containing pi-conjugated oligomers for light-emitting diodes. 2500-2509
- Nicholas Y. Palermo, József Csontos, Michael C. Owen, Richard F. Murphy, Sándor Lovas:
Aromatic-backbone interactions in model alpha-helical peptides. 2510
Volume 28, Number 16, December 2007
- Takeshi Noro, Masahiro Sekiya, You Osanai, Toshikatsu Koga, Hisashi Matsuyama:
Relativistic correlating basis sets for actinide atoms from 90Th to 103Lr. 2511-2516 - Ying Wang, Jing-Yao Liu, Ze-Sheng Li:
Ab initio direct dynamics studies on the reactions of chlorine atom with CH3-nFnCH2OH (n = 1-3). 2517-2530 - Emanuel H. Rubensson, Elias Rudberg, Pawel Salek:
A hierarchic sparse matrix data structure for large-scale Hartree-Fock/Kohn-Sham calculations. 2531-2537 - Parimal Kar
Systematic study of the boundary composition in Poisson Boltzmann calculations. 2538-2544 - Xiaoqing Liu, Zhilong Xiu, Xiaohui Li:
Numerical characterization of the conformation of cyclic peptides and its application. 2545-2551 - Abhinav Verma
All-atom de novo protein folding with a scalable evolutionary algorithm. 2552-2558 - Ángel J. Pérez-Jiménez
Merging multiconfigurational wavefunctions and correlation functionals to predict magnetic coupling constants. 2559-2568 - Pawel Salek, Andreas Hesselmann:
A self-contained and portable density functional theory library for use in Ab Initio quantum chemistry programs. 2569-2575 - Kay Hamacher:
Information theoretical measures to analyze trajectories in rational molecular design. 2576-2580 - Jon Baker, Krzysztof Wolinski, Peter Pulay:
Parallel DFT gradients using the Fourier Transform Coulomb method. 2581-2588 - D. Heringer, T. A. Niehaus, Marius Wanko, Thomas Frauenheim
Analytical excited state forces for the time-dependent density-functional tight-binding method. 2589-2601 - Michel Rafat, Paul L. A. Popelier:
Visualization and integration of quantum topological atoms by spatial discretization into finite elements. 2602-2617 - John E. Stone
Accelerating molecular modeling applications with graphics processors. 2618-2640
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