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ORCIDJournal of Computational Chemistry, Volume 27
Volume 27, Number 1, January 2006
- Zhong-Zhi Yang, Qiang Zhang:
Study of peptide conformation in terms of the ABEEM/MM method. 1-10
- Frank Eckert, Andreas Klamt
:
Accurate prediction of basicity in aqueous solution with COSMO-RS. 11-19 - Tamás Beke, Csaba Somlai, András Perczel:
Toward a rational design of -peptide structures. 20-38 - Jing Ma, Shuhua Li, Wei Li:
A multireference configuration interaction method based on the separated electron pair wave functions. 39-47 - Yoshihiro Watanabe, Hiroshi Tatewaki, Toshikatsu Koga, Osamu Matsuoka:
Relativistic Gaussian basis sets for molecular calculations: Fully optimized single-family exponent basis sets for HHg. 48-52 - Kaori Ueno-Noto, Miki Hara-Yokoyama, Keiko Takano:
Recognition of tandem sialic acid residues by CD38: A theoretical study. 53-60 - Roberto L. A. Haiduke, Albérico B. F. da Silva:
Accurate relativistic adapted Gaussian basis sets for hydrogen through xenon without variational prolapse and to be used with both uniform sphere and Gaussian nucleus models. 61-71 - Zhiyun Yu, Matthew P. Jacobson, Richard A. Friesner:
What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules. 72-89 - Yasemin Kurtulus, Michael Gilleßen, Richard Dronskowski:
Electronic structure, chemical bonding, and finite-temperature magnetic properties of full Heusler alloys. 90-102 - Brent A. Gregersen, Darrin M. York:
A charge-scaling implementation of the variational electrostatic projection method. 103-115 - Carlos Silva López, Olalla Nieto Faza, Susana López Estévez, Angel R. de Lera:
Computation of vertical excitation energies of retinal and analogs: Scope and limitations. 116-123
Volume 27, Number 2, January 2006
- Hairong Ma, Martin Gruebele:
Low barrier kinetics: Dependence on observables and free energy surface. 125-134 - Christoph Van Wüllen:
Numerical instabilities in the computation of pseudopotential matrix elements. 135-141 - Christophe Gourlaouen, Jean-Philip Piquemal, Trond Saue, Olivier Parisel:
Revisiting the geometry of nd10 (n+1)s0 [M(H2O)]p+ complexes using four-component relativistic DFT calculations and scalar relativistic correlated CSOV energy decompositions (Mp+ = Cu+, Zn2+, Ag+, Cd2+, Au+, Hg2+). 142-156 - Anne Milet, Yves Gimbert, Andrew E. Greene:
Reaction of nitrones with silyl ketene acetals: A DFT study. 157-162 - Chantal T. Falzon, Delano P. Chong, Feng Wang:
Prediction of spectroscopic constants for diatomic molecules in the ground and excited states using time-dependent density functional theory. 163-173 - Ivan Rivalta, Nino Russo, Emilia Sicilia:
Methane activation by chromium oxide cations in the gas phase: A theoretical study. 174-187 - Fernando D. Suvire, Luis N. Santagata, José A. Bombasaro, Ricardo D. Enriz:
Dynamics of flexible cycloalkanes. Ab initio and DFT study of the conformational energy hypersurface of cyclononane. 188-202 - Jie Hu, Ao Ma, Aaron R. Dinner:
Monte Carlo simulations of biomolecules: The MC module in CHARMM. 203-216 - Marcelo Alves-Santos, Liliana Y. A. Dávila, Helena M. Petrilli, Rodrigo B. Capaz, Marília J. Caldas:
Application of standard DFT theory for nonbonded interactions in soft matter: Prototype study of poly-para-phenylene. 217-227 - Chultack Lim, Hee Soon Lee, Young-Woo Kwak, Cheol Ho Choi:
A theoretical study of thermal [1, 3]-sigmatropic rearrangements of 3-trimethylsilyl-1-pyrazoline: Concerted vs. stepwise mechanisms. 228-237 - José Luis Alonso, Pablo Echenique:
A physically meaningful method for the comparison of potential energy functions. 238-252 - Jeremy Andrew Lesl Rabone, N. H. De Leeuw:
Interatomic potential models for natural apatite crystals: Incorporating strontium and the lanthanides. 253-266
Volume 27, Number 3, February 2006
- Zhijian Wu:
Electronic structures of 3d-metal mononitrides. 267-276 - Kaushalya S. Ekanayake, Pierre R. Lebreton:
Activation barriers for DNA alkylation by carcinogenic methane diazonium ions. 277-286 - Andrzej Bil, Zdzislaw Latajka:
The hydroperoxy radical as a hydrogen bond acceptor. HOO-HCl complexes - Ab initio study. 287-295 - Andrei M. Tokmachev, Richard Dronskowski:
Electron group functions for the analysis of the electronic structures of molecules. 296-308 - Heinz Sklenar, Daniel Wüstner, Remo Rohs:
Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm and associated Jacobians. 309-315 - Tsjerk A. Wassenaar, Alan E. Mark:
The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions. 316-325 - Eirik Fossgård, Kenneth Ruud:
Superlinear scaling in master-slave quantum chemical calculations using in-core storage of two-electron integrals. 326-333 - Prasad V. Bharatam, Pansy Iqbal:
Theoretical studies on electron delocalization in diaminoguanidine. 334-343 - Inmaculada García Cuesta, Alfredo M. J. Sánchez De Merás, Paolo Lazzeretti:
Structure, magnetizability, and nuclear magnetic shielding tensors of bis-heteropentalenes. IV. Dihydrophospholophosphole isomers. 344-351 - Timothy J. Dudley, Ryan M. Olson, Michael W. Schmidt, Mark S. Gordon:
Parallel coupled perturbed CASSCF equations and analytic CASSCF second derivatives. 352-362 - Jian Wang, Yi-Hong Ding, Gong-Bing Wu, Chia-Chung Sun:
Gaseous reaction mechanism of C2F radical with water. 363-367 - Ke-Xiang Fu, Quan Zhu, Xiang-Yuan Li, Zhen Gong, Jian-Yi Ma, Rong-Xing He:
Continuous medium theory for nonequilibrium solvation: IV. Solvent reorganization energy of electron transfer based on conductor-like screening model. 368-374 - Geoffrey K. Hom, Stephen L. Mayo:
A search algorithm for fixed-composition protein design. 375-378 - Hisashi Okumura, Yuko Okamoto:
Multibaric-multithermal ensemble molecular dynamics simulations. 379-395 - Radka Svobodová Vareková, Jaroslav Koca:
Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method. 396-405
Volume 27, Number 4, March 2006
- Kazuya Ishimura, Peter Pulay, Shigeru Nagase:
A new parallel algorithm of MP2 energy calculations. 407-413 - Arnaldo Rapallo:
An algorithm for the uniform sampling of iso-energy surfaces and for the calculation of microcanonical averages. 414-425 - Hiroyuki Nakashima, Jun-Ya Hasegawa, Hiroshi Nakatsuji:
On the reversible O2 binding of the Fe-porphyrin complex. 426-433 - Pekka Manninen, Juha Vaara:
Systematic Gaussian basis-set limit using completeness-optimized primitive sets. A case for magnetic properties. 434-445 - Franci Merzel, Milan Hodoscek, Dusanka Janezic, Alain Sanson:
New force field for calcium binding sites in annexin-membrane complexes. 446-452 - Norio Yoshida, Fumio Hirata:
A new method to determine electrostatic potential around a macromolecule in solution from molecular wave functions. 453-462 - Masahiro Sekiya, Takeshi Noro, Eisaku Miyoshi, You Osanai, Toshikatsu Koga:
Relativistic correlating basis sets for lanthanide atoms from Ce to Lu. 463-470 - Hideaki Nakamura, Masaru Aniya:
Thermodynamic properties of Ag2OB2O3 glasses by a modified scale-transformed energy space sampling Monte Carlo method. 471-477 - Xuan Xiao, Shihuang Shao, Zheng-De Huang, Kuo-Chen Chou:
Using pseudo amino acid composition to predict protein structural classes: Approached with complexity measure factor. 478-482 - Gerald Geudtner, Florian Janetzko, Andreas M. Köster, Alberto Vela, Patrizia Calaminici:
Parallelization of the deMon2k code. 483-490 - Mark P. Waller, Arturo Robertazzi, James A. Platts, David E. Hibbs, Peter A. Williams:
Hybrid density functional theory for -stacking interactions: Application to benzenes, pyridines, and DNA bases. 491-504 - Qiang Wang, Yi-Hong Ding, Hong-Bin Xie, Chia-Chung Sun:
Theoretical study on structures and stabilities of [H, Ge, C, N]. 505-514 - Arianna Fornili, Yohann Moreau, Maurizio Sironi, Xavier Assfeld:
On the suitability of strictly localized orbitals for hybrid QM/MM calculations. 515-523 - Josep M. Oliva, Luis Serrano-Andrés:
A computational study of the lowest singlet and triplet states of neutral and dianionic 1, 2-substituted icosahedral and octahedral o-carboranes. 524-535
Volume 27, Number 5, April 2006
- Min Hsien Liu, Cheng Chen:
Modified calculations of hydrocarbon thermodynamic properties. 537-544 - Hong-Bin Xie, Yi-Hong Ding, Chia-Chung Sun:
Ylidic radical-molecule reactions. 545-551 - Mikhail V. Basilevsky, Igor V. Leontyev, Sofia V. Luschekina, Olga A. Kondakova, Vladimir B. Sulimov:
Computation of hydration free energies of organic solutes with an implicit water model. 552-570 - Stanislav Böhm, Otto Exner:
Are calculated enthalpies of formation sometimes more reliable than experimental? A test on alkyl substituted benzoic acids. 571-577 - Li-Ming Yang, Yi-Hong Ding, Qiang Wang, Chia-Chung Sun:
Monosilicon-substituted cyanoacetylene: A computational study. 578-595 - Diego R. Alcoba, Luis Lain, Alícia Torre, Roberto C. Bochicchio:
An orbital localization criterion based on the theory of fuzzy atoms. 596-608 - Anna Fiorentino, Deepangi Pandit, Kathleen M. Gilbert, Milind Misra, Rose Dios, Carol A. Venanzi:
Singular value decomposition of torsional angles of analogs of the dopamine reuptake inhibitor GBR 12909. 609-620 - Giulio Gianese, Stefano Pascarella:
A consensus procedure improving solvent accessibility prediction. 621-626 - P. Cassam-Chenaï, J. Liévin:
The VMFCI method: A flexible tool for solving the molecular vibration problem. 627-640 - Hong-Bin Xie, Yi-Hong Ding, Chia-Chung Sun:
Radical reaction C3H+NO: A mechanistic study. 641-660 - Jia-Xu Zhang, Ze-Sheng Li, Jing-Yao Liu, Chia-Chung Sun:
Theoretical mechanistic study on the radical-molecule reaction of CHCl2/CCl3 with NO2. 661-671 - Håkan W. Hugosson, Alessandro Laio, Patrick Maurer, Ursula Rothlisberger:
A comparative theoretical study of dipeptide solvation in water. 672-684
Volume 27, Number 6, April 2006
- Qishi Du, Dapeng Li, Wen-Zhang He, Kuo-Chen Chou:
Heuristic molecular lipophilicity potential (HMLP): Lipophilicity and hydrophilicity of amino acid side chains. 685-692 - Satyavani Vemparala, Ivaylo Ivanov, Vojislava Pophristic, Katrin Spiegel, Michael L. Klein:
Ab initio calculations of intramolecular parameters for a class of arylamide polymers. 693-700 - Yasunobu Seno:
Allostery of the two-state model of hemoglobin studied by ECEPP energy minimization. 701-710 - Chunsheng Shi, Masahiko Morinaga:
Doping effects on proton incorporation and conduction in SrZrO3. 711-718 - Jana Chocholousová, Michael Feig:
Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations. 719-729 - Siu-Hung Chien, Peter M. W. Gill:
SG-0: A small standard grid for DFT quadrature on large systems. 730-739 - Tomasz Borowski, Ewa Broclawik, Christopher J. Schofield, Per E. M. Siegbahn:
Epimerization and desaturation by carbapenem synthase (CarC). A hybrid DFT study. 740-748 - Guang-Tao Yu, Xu-Ri Huang, Yi-Hong Ding, Chia-Chung Sun, Au-Chin Tang:
Theoretical study on the [Si, C, N, O] potential energy surface. 749-761 - Fabio E. Penotti:
Orbital-orthogonality constraints and basis-set optimization. 762-772 - Ram Kinkar Roy, V. Usha, Bhisma K. Patel, Kimihiko Hirao:
Acetalization and thioacetalization of cabonyl compounds: A case study based on global and local electrophilicity descriptors. 773-780 - Zhi-Xiang Wang, Wei Zhang, Chun Wu, Hongxing Lei, Piotr Cieplak, Yong Duan:
Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides. 781-790 - Primoz Pristovsek, Lorella Franzoni:
Stereospecific assignments of protein NMR resonances based on the tertiary structure and 2D/3D NOE data. 791-797 - Li-Cheng Wu, Jorng-Tzong Horng, Shir-Ly Huang, Hsien-Da Huang, Baw-Jhiune Liu:
Detection of discriminative sequence motifs in proteins obtained from prokaryotes grown at various temperatures. 798-808
Volume 27, Number 7, May 2006
- Peng Bao, Zhong-Heng Yu:
Theoretical studies on the role of -electron delocalization in determining the conformation of N-benzylideneaniline with three types of LMO basis sets. 809-824 - Seongho Moon, David A. Case:
A comparison of quantum chemical models for calculating NMR shielding parameters in peptides: Mixed basis set and ONIOM methods combined with a complete basis set extrapolation. 825-836 - Jean-Francois Fuchs, Hristo Nedev, David Poger, Michel Ferrand, Valérie Brenner, Jean-Pierre Dognon, Serge Crouzy:
New model potentials for sulfur-copper(I) and sulfur-mercury(II) interactions in proteins: From ab initio to molecular dynamics. 837-856 - Yu Zhou, Chris Oostenbrink, Aldo Jongejan, Wilfred F. van Gunsteren, Wilfred R. Hagen, Simon W. De Leeuw, Jaap A. Jongejan:
Computational study of ground-state chiral induction in small peptides: Comparison of the relative stability of selected amino acid dimers and oligomers in homochiral and heterochiral combinations. 857-867 - Lionello Pogliani:
The hydrogen perturbation in molecular connectivity computations. 868-882 - Lin Jin, Yi-Hong Ding, Jian Wang, Chia-Chung Sun:
Reaction mechanism of the CCN radical with nitric oxide. 883-893 - Jia-Xu Zhang, Ze-Sheng Li, Jing-Yao Liu, Chia-Chung Sun:
Theoretical study on the mechanism of the CH2F + NO2 reaction. 894-905 - Kazuki Ohno, Minoru Sakurai:
Linear-scaling molecular orbital calculations for the pKa values of ionizable residues in proteins. 906-916
Volume 27, Number 8, June 2006
- Hiromi Nakai, Yasuaki Kikuchi:
Energy density analysis of cluster size dependence of surface-molecule interactions (II): Formate adsorption onto a Cu(111) surface. 917-925 - J. H. Van Lenthe, R. Zwaans, Huub J. J. Van Dam, M. F. Guest:
Starting SCF calculations by superposition of atomic densities. 926-932 - Ju Xie, Dacheng Feng, Shengyu Feng:
Theoretical study on the isomeric structures and the stability of silylenoid (Tsi)Cl2SiLi (Tsi = C(SiMe3)3). 933-940 - Shiqi Zhou:
Rapidly convergent procedure to solve the density profile equation in the classical density functional theory. 941-947 - 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. 948-960 - Kazimierz Darowicki, W. Felisiak:
On the joint time-frequency characteristics of chemical oscillations. 961-965 - Alexandra T. P. Carvalho, Pedro Alexandrino Fernandes, Maria João Ramos:
Determination of the pKa between the active site cysteines of thioredoxin and DsbA. 966-975 - Dmitri G. Fedorov, Kazuo Kitaura, Hui Li, Jan H. Jensen, Mark S. Gordon:
The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO). 976-985 - Zhi-Ru Li, Fang-Fang Wang, Di Wu, Ying Li, Wei Chen, Xiao-Ying Sun, Feng Long Gu, Yuriko Aoki:
Royal crown-shaped electride Li3-N3-Be containing two superatoms: New knowledge on aromaticity. 986-993
- Zhi-Xiang Wang, Wei Zhang, Chun Wu, Hongxing Lei, Piotr Cieplak, Yong Duan:
Erratum - Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides. 994
Volume 27, Number 9, July 2006
- Antonio Cervellino, Cinzia Giannini, Antonietta Guagliardi:
On the efficient evaluation of Fourier patterns for nanoparticles and clusters. 995-1008 - Roberto Flores-Moreno, Rodrigo J. Alvarez-Mendez, Alberto Vela, Andreas M. Köster:
Half-numerical evaluation of pseudopotential integrals. 1009-1019 - Tzong-Yi Lee, Jorng-Tzong Horng, Hsueh-Fen Juan, Hsien-Da Huang, Li-Cheng Wu, Meng-Feng Tsai, Hsuan-Cheng Huang:
An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints. 1020-1032 - Aggeliki Kosmopoulou, Metaxia Vlassi, Athanassios Stavrakoudis, Constantinos Sakarellos, Maria Sakarellos-Daitsiotis:
T-cell epitopes of the La/SSB autoantigen: Prediction based on the homology modeling of HLA-DQ2/DQ7 with the insulin-B peptide/HLA-DQ8 complex. 1033-1044 - Hua Zhu, Yong Guo, Ying Xue, Daiqian Xie:
Ab initio potential energy surface and predicted microwave spectra for ArOCS dimer and structures of ArnOCS (n = 2-14) clusters. 1045-1053
Volume 27, Number 10, July 2006
- Patrick Musch, Bernd Engels:
DIESEL-MP2: A new program to perform large-scale multireference-MP2 computations. 1055-1062 - Andrew E. Whitten, Joshua J. McKinnon, Mark A. Spackman:
Electric field-derived point charges to mimic the electrostatics in molecular crystals. 1063-1070 - Benjamin D. Allen, Stephen L. Mayo:
Dramatic performance enhancements for the FASTER optimization algorithm. 1071-1075 - Pablo Echenique, José Luis Alonso:
Definition of Systematic, Approximately Separable, and Modular Internal Coordinates (SASMIC) for macromolecular simulation. 1076-1087 - Karl Jug, Viatcheslav A. Tikhomirov:
Anion substitution in zinc chalcogenides. 1088-1092 - T. S. Venkatesan, K. Deepika, S. Mahapatra:
The Jahn-Teller and pseudo-Jahn-Teller effects in the anion photoelectron spectroscopy of B3 cluster. 1093-1100 - Gerd Bruno Rocha, Ricardo Oliveira Freire, Alfredo Mayall Simas, James J. P. Stewart:
RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I. 1101-1111 - Genyuan Li, Herschel A. Rabitz:
Ratio control variate method for efficiently determining high-dimensional model representations. 1112-1118
Volume 27, Number 11, August 2006
- Liwei Liu, Tianming Wang:
2D representation of protein secondary structure sequences and its applications. 1119-1124 - Bahram Hemmateenejad, Ramin Miri, Mohammad A. Safarpour, Ahmad R. Mehdipour:
Accurate prediction of the blood-brain partitioning of a large set of solutes using ab initio calculations and genetic neural network modeling. 1125-1135 - Hyunbum Jang, Thomas B. Woolf:
Multiple pathways in conformational transitions of the alanine dipeptide: An application of dynamic importance sampling. 1136-1141 - Flavia P. Agostini, Diogo De O. Soares-Pinto, Marcelo A. Moret, Carla Osthoff, Pedro Geraldo Pascutti:
Generalized simulated annealing applied to protein folding studies. 1142-1155 - Ivan Infante, Bas van Stralen, Lucas Visscher:
A QM/MM study on the aqueous solvation of the tetrahydroxouranylate [UO2(OH)4]2- complex ion. 1156-1162 - Vincent Kräutler, Philippe H. Hünenberger:
A multiple time step algorithm compatible with a large number of distance classes and an arbitrary distance dependence of the time step size for the fast evaluation of nonbonded interactions in molecular simulations. 1163-1176 - Dusan P. Djurdjevic, Mark J. Biggs:
Ab initio protein fold prediction using evolutionary algorithms: Influence of design and control parameters on performance. 1177-1195