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ORCIDJournal 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, Celestino Angeli:
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, María J. González-Moa, Ricardo A. Mosquera:
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, Robert Ponec, Ramon Carbó-Dorca:
Aromaticity in linear polyacenes: Generalized population analysis and molecular quantum similarity approach. 152-160 - Ángel Martín Pendás, M. A. Blanco, Evelio Francisco:
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, Miquel Solà, Célia Fonseca Guerra:
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, Mark S. Gordon:
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, Rafael Islas, Gabriel Merino:
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, K. N. Houk, Henry F. Schaefer III, Paul von Ragué Schleyer:
The existence of secondary orbital interactions. 344-361 - Gabriel Merino, Miguel A. Méndez-Rojas, Alberto Vela, Thomas Heine:
Recent advances in planar tetracoordinate carbon chemistry. 362-372 - Igor V. Alabugin, Mariappan Manoharan:
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, Michel Caffarel, Andreas Savin:
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, David R. Klug:
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, Tom Ziegler:
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, Ana M. Graña:
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, Pavel Hobza, Dennis R. Salahub:
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, Pedro Salvador, Paul Geerlings, Miquel Solà:
On the quality of the hardness kernel and the Fukui function to evaluate the global hardness. 574-583 - Riccardo Conte, G. P. Arrighini, C. Guidotti:
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, Pedro Alexandrino Fernandes, Maria João Ramos:
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 - Z. J. Wu, M. Y. Wang, Z. M. 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, Shigeru Nagase, Kichisuke Nishimoto:
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, Sumathy Raman:
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, Sergiy I. Okovytyy, Jerzy Leszczynski:
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, Yuliang Zhao:
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, Malgorzata Witko, Grazyna Stochel:
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, Yihan Shao, Martin Head-Gordon:
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, Bernard Silvi:
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, Dieter Hofmann:
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, Lucien M. H. Koymans, H. Maarten Vinkers:
An ant algorithm for the conformational analysis of flexible molecules. 890-898 - Edward Sanville, Steven D. Kenny, Roger Smith, Graeme Henkelman:
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, Jean-Philip Piquemal, Laurent Salmon:
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, José M. Lluch:
A PM3/d specific reaction parameterization for iron atom in the hydrogen abstraction catalyzed by soybean lipoxygenase-1. 997-1005 - Viwat Vchirawongkwin, Thomas S. Hofer, Bernhard R. Randolf, Bernd M. Rode:
Tl(I)-the strongest structure-breaking metal ion in water? A quantum mechanical/molecular mechanical simulation study. 1006-1016 - Arnau Cordomí, Olle Edholm, Juan Jesús Pérez:
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, Giovanni Colonna, Angelo M. Facchiano:
New computational strategy to analyze the interactions of ER alpha and ER beta with different ERE sequences. 1031-1041 - Humberto González Díaz, Liane Saíz-urra, Reinaldo Molina Ruiz, Yenny González-Díaz, Angeles Sánchez-González:
Computational chemistry approach to protein kinase recognition using 3D stochastic van der Waals spectral moments. 1042-1048 - Humberto González Díaz, Guillermín Agüero-Chapín, Javier Varona, Reinaldo Molina Ruiz, Giovanna Delogu, Lourdes Santana, Eugenio Uriarte, Gianni Podda:
2D-RNA-coupling numbers: A new computational chemistry approach to link secondary structure topology with biological function. 1049-1056 - Viwat Vchirawongkwin, Thomas S. Hofer, Bernhard R. Randolf, Bernd M. Rode:
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, J. W. Krogh, Gunnar Karlström, Ulf Ryde, Roland Lindh:
Accuracy of distributed multipoles and polarizabilities: Comparison between the LoProp and MpProp models. 1083-1090 - Hitomi Yuki, Yoshikazu Tanaka, Masayuki Hata, Hidenori Ishikawa, Saburo Neya, Tyuji Hoshino:
Implementation of pi-pi interactions in molecular dynamics simulation. 1091-1099 - Kyoung Hoon Kim, Jaehoon Jung, Bo Keun Park, Young-Kyu Han, Joon T. Park:
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, Francesco Gasparrini, O. Incani, L. Caglioti, Marco Pierini, Claudio Villani:
"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, Arthur J. Olson, David S. Goodsell:
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, Rochus Schmid:
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, Antonio Rey:
Evaluation of coarse grained models for hydrogen bonds in proteins. 1187-1199 - Adelio R. Matamala, Daniel E. Almonacid, Maximiliano F. Figueroa, José Martínez-Oyanedel, Marta C. Bunster:
A semiempirical approach to the intra-phycocyanin and inter-phycocyanin fluorescence resonance energy-transfer pathways in phycobilisomes. 1200-1207 - Nicholas Y. Palermo, József Csontos, Michael C. Owen, Richard F. Murphy, Sándor Lovas:
Aromatic-backbone interactions in model alpha-helical peptides. 1208-1214 - Alan R. Ford, Tomasz Janowski, Peter Pulay:
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.