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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, 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, 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 - 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, 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. 1221-1233 - Fangqiang Zhu, Dimitris K. Agrafiotis:
Self-organizing superimposition algorithm for conformational sampling. 1234-1239 - Evgueni B. Kadossov, Karen J. Gaskell, Marjorie A. Langell:
Effect of surrounding point charges on the density functional calculations of NixOx clusters (x = 4-12). 1240-1251 - Manuel Urbano-Cuadrado, Irene Luque Ruiz, Miguel Ángel Gómez-Nieto:
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, Chartchalerm Isarankura-Na-Ayudhya, Natta Tansila, Thanakorn Naenna, Virapong Prachayasittikul:
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, Wim Klopper, Trygve Helgaker:
Electron correlation: The many-body problem at the heart of chemistry. 1307-1320 - N. R. Jena, P. C. Mishra:
Formation of 8-nitroguanine and 8-oxoguanine due to reactions of peroxynitrite with guanine. 1321-1335 - Andrew Leaver-Fay, Glenn L. Butterfoss, Jack Snoeyink, Brian Kuhlman:
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, Pi-Tai Chou:
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, Seung-Chul Baek, Jung-Hee Ahn, Sungsoo Na:
Coarse-graining of protein structures for the normal mode studies. 1400-1410 - Carlos Silva López, Olalla Nieto Faza, José A. Souto, Rosana Álvarez, Angel R. de Lera:
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, Claude Pouchan:
Vibrational anharmonic calculations in solution: Performance of various DFT approaches. 1456-1462
Volume 28, Number 9, July 2007
- Hao Lin, Qian-Zhong Li:
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, Toyokazu Ishida, Kazuo Kitaura, Peter Pulay, Shigeru Nagase:
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, Miquel Solà, Friedrich Matthias Bickelhaupt:
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, Foo-Tim Chau, Daniel K. W. Mok:
DFT and ab initio calculations on two reactions between hydrogen atoms and the fire suppressants 2-H heptafluoropropane and CF3Br. 1582-1592 - Dominik Gront, Sebastian Kmiecik, Andrzej Kolinski:
Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates. 1593-1597 - Olexandr Isayev, Leonid Gorb, Jerzy Leszczynski:
Theoretical calculations: Can Gibbs free energy for intermolecular complexes be predicted efficiently and accurately? 1598-1609
- T. Daniel Crawford, C. David Sherrill, Edward F. Valeev, Justin T. Fermann, Rollin A. King, Matthew L. Leininger, Shawn T. Brown, Curtis L. Janssen, Edward T. Seidl, Joseph P. Kenny, Wesley D. Allen:
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, María J. González-Moa, Ricardo A. Mosquera:
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, Dariusz Ekonomiuk, Andrzej Kolinski:
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, Michael W. Schmidt, Theresa L. Windus, Mark S. Gordon:
A parallel distributed data CPHF algorithm for analytic Hessians. 1685-1694 - Alexander V. Larin, W. J. Mortier, Daniel P. Vercauteren:
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, Bernhard R. Randolf, Bernd M. Rode:
Quantum mechanical charge field molecular dynamics simulation of the TiO2+ ion in aqueous solution. 1704-1710 - Pedro J. Ballester, W. Graham Richards:
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, Adélia J. A. Aquino, Peter Wolschann, Hans Lischka:
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, Toyokazu Ishida, Dmitri G. Fedorov, Kazuo Kitaura:
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, Martin Preuss, Karsten Hannewald, Friedhelm Bechstedt:
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, Robert A. Latour:
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, Humberto González Díaz, Guillermín Agüero-Chapín, Lourdes Santana, Fernanda Borges, Elena Rosa Domínguez, Gianni Podda, Eugenio Uriarte:
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, Yihan Shao, Martin Head-Gordon:
Fast evaluation of scaled opposite spin second-order Møller-Plesset correlation energies using auxiliary basis expansions and exploiting sparsity. 1953-1964 - Ian R. Gould, Hoda Abdel-Aal Bettley, Richard A. Bryce:
Correlated ab initio quantum chemical calculations of di- and trisaccharide conformations. 1965-1973 - Georgy Rychkov, Michael Petukhov:
Joint neighbors approximation of macromolecular solvent accessible surface area. 1974-1989 - Humberto González Díaz, Yunierkis Pérez-Castillo, Gianni Podda, Eugenio Uriarte:
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, Garth J. Simpson:
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, Z. Jamshidi, Hirotoshi Mori, Eisaku Miyoshi, Mariusz Klobukowski:
Electron affinities of heavier phosphoryl and thiophosphoryl halides APX3 (A = O, S and X = Br, I). 2027-2033 - Kazuya Ishimura, Peter Pulay, Shigeru Nagase:
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, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller:
Speeding up parallel GROMACS on high-latency networks. 2075-2084
Volume 28, Number 13, October 2007
- Francesco Ferrante, Gianfranco La Manna:
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, Julia M. Shifman:
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, Emine Cebe:
Odd-even effects in the homologous series of alkyl-cyanobiphenyl liquid crystals: A molecular dynamic study. 2140-2146 - Jingjing Zheng, Ahmet Altun, Walter Thiel:
Common system setup for the entire catalytic cycle of cytochrome P450cam in quantum mechanical/molecular mechanical studies. 2147-2158 - Riccardo Zanasi, Stefano Pelloni, Paolo Lazzeretti:
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, Daiqian Xie:
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, Lluís Ros, Federico Thomas, Francesc Corcho, Josep Cantó, Juan Jesús Pérez:
Complete maps of molecular-loop conformational spaces. 2170-2189 - Lin Cheng, M. Y. Wang, Zhijian Wu, Zhong-Min Su:
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, M. Carmen Villaverde, Fredy Sussman:
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, Yuto Komeiji, Yuji Mochizuki, Akifumi Kato, Tatsuya Nakano, Shigenori Tanaka:
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, I. Hyla-Kryspin, Stefan Grimme:
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, Dirk Leusser, Dietmar Stalke:
Chemical interpretation of molecular electron density distributions. 2317-2324 - Edda Kloppmann, G. Matthias Ullmann, Torsten Becker:
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, Melinda S. Hanes, Mark Voorhies, Navin Pokala, Tracy M. Handel:
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, Masaki Mine, Mariusz Klobukowski, Eisaku Miyoshi:
Revised model core potentials of s-block elements. 2424-2430 - Anan Wu, Ying Zhang, Xin Xu, Yijing Yan:
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, Ben Swerts, Tomoo Miyahara, Hiroshi Nakatsuji:
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, Sergio Giuffrida, Zs. Varga:
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, Yanjie Wei, Ulrich H. E. Hansmann, Siegfried Höfinger:
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, Srinivasa M. Gopal, Jung S. Oh, Kyu H. Lee, Wolfgang Wenzel:
All-atom de novo protein folding with a scalable evolutionary algorithm. 2552-2558 - Ángel J. Pérez-Jiménez, José M. Pérez-Jordá, Ibério de Pinho Ribeiro Moreira, Francesc Illas:
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, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, Klaus Schulten:
Accelerating molecular modeling applications with graphics processors. 2618-2640
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