Journal 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
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• Frank Eckert, Andreas Klamt:
  Accurate prediction of basicity in aqueous solution with COSMO-RS. 11-19
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• Tamás Beke, Csaba Somlai, András Perczel:
  Toward a rational design of -peptide structures. 20-38
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• Jing Ma, Shuhua Li, Wei Li:
  A multireference configuration interaction method based on the separated electron pair wave functions. 39-47
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• 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
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• Kaori Ueno-Noto, Miki Hara-Yokoyama, Keiko Takano:
  Recognition of tandem sialic acid residues by CD38: A theoretical study. 53-60
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• 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
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• 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
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• Yasemin Kurtulus, Michael Gilleßen, Richard Dronskowski:
  Electronic structure, chemical bonding, and finite-temperature magnetic properties of full Heusler alloys. 90-102
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• Brent A. Gregersen, Darrin M. York:
  A charge-scaling implementation of the variational electrostatic projection method. 103-115
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• 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
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Volume 27, Number 2, January 2006

• Hairong Ma, Martin Gruebele:
  Low barrier kinetics: Dependence on observables and free energy surface. 125-134
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• Christoph Van Wüllen:
  Numerical instabilities in the computation of pseudopotential matrix elements. 135-141
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• 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
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• Anne Milet, Yves Gimbert, Andrew E. Greene:
  Reaction of nitrones with silyl ketene acetals: A DFT study. 157-162
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• 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
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• Ivan Rivalta, Nino Russo, Emilia Sicilia:
  Methane activation by chromium oxide cations in the gas phase: A theoretical study. 174-187
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• 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
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• Jie Hu, Ao Ma, Aaron R. Dinner:
  Monte Carlo simulations of biomolecules: The MC module in CHARMM. 203-216
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• 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
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• 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
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• José Luis Alonso, Pablo Echenique:
  A physically meaningful method for the comparison of potential energy functions. 238-252
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• J. A. L. Rabone, N. H. De Leeuw:
  Interatomic potential models for natural apatite crystals: Incorporating strontium and the lanthanides. 253-266
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Volume 27, Number 3, February 2006

• Zhijian Wu:
  Electronic structures of 3d-metal mononitrides. 267-276
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• Kaushalya S. Ekanayake, Pierre R. Lebreton:
  Activation barriers for DNA alkylation by carcinogenic methane diazonium ions. 277-286
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• Andrzej Bil, Zdzislaw Latajka:
  The hydroperoxy radical as a hydrogen bond acceptor. HOO-HCl complexes - Ab initio study. 287-295
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• Andrei M. Tokmachev, Richard Dronskowski:
  Electron group functions for the analysis of the electronic structures of molecules. 296-308
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• 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
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• Tsjerk A. Wassenaar, Alan E. Mark:
  The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions. 316-325
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• Eirik Fossgård, Kenneth Ruud:
  Superlinear scaling in master-slave quantum chemical calculations using in-core storage of two-electron integrals. 326-333
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• Prasad V. Bharatam, Pansy Iqbal:
  Theoretical studies on electron delocalization in diaminoguanidine. 334-343
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• 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
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• Timothy J. Dudley, Ryan M. Olson, Michael W. Schmidt, Mark S. Gordon:
  Parallel coupled perturbed CASSCF equations and analytic CASSCF second derivatives. 352-362
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• Jian Wang, Yi-Hong Ding, Gong-Bing Wu, Chia-Chung Sun:
  Gaseous reaction mechanism of C2F radical with water. 363-367
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• 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
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• Geoffrey K. Hom, Stephen L. Mayo:
  A search algorithm for fixed-composition protein design. 375-378
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• Hisashi Okumura, Yuko Okamoto:
  Multibaric-multithermal ensemble molecular dynamics simulations. 379-395
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• Radka Svobodová Vareková, Jaroslav Koca:
  Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method. 396-405
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Volume 27, Number 4, March 2006

• Kazuya Ishimura, Peter Pulay, Shigeru Nagase:
  A new parallel algorithm of MP2 energy calculations. 407-413
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• Arnaldo Rapallo:
  An algorithm for the uniform sampling of iso-energy surfaces and for the calculation of microcanonical averages. 414-425
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• Hiroyuki Nakashima, Jun-Ya Hasegawa, Hiroshi Nakatsuji:
  On the reversible O2 binding of the Fe-porphyrin complex. 426-433
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• Pekka Manninen, Juha Vaara:
  Systematic Gaussian basis-set limit using completeness-optimized primitive sets. A case for magnetic properties. 434-445
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• Franci Merzel, Milan Hodoscek, Dusanka Janezic, Alain Sanson:
  New force field for calcium binding sites in annexin-membrane complexes. 446-452
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• Norio Yoshida, Fumio Hirata:
  A new method to determine electrostatic potential around a macromolecule in solution from molecular wave functions. 453-462
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• Masahiro Sekiya, Takeshi Noro, Eisaku Miyoshi, You Osanai, Toshikatsu Koga:
  Relativistic correlating basis sets for lanthanide atoms from Ce to Lu. 463-470
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• Hideaki Nakamura, Masaru Aniya:
  Thermodynamic properties of Ag2OB2O3 glasses by a modified scale-transformed energy space sampling Monte Carlo method. 471-477
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• 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
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• Gerald Geudtner, Florian Janetzko, Andreas M. Köster, Alberto Vela, Patrizia Calaminici:
  Parallelization of the deMon2k code. 483-490
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• 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
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• Qiang Wang, Yi-Hong Ding, Hong-Bin Xie, Chia-Chung Sun:
  Theoretical study on structures and stabilities of [H, Ge, C, N]. 505-514
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• Arianna Fornili, Yohann Moreau, Maurizio Sironi, Xavier Assfeld:
  On the suitability of strictly localized orbitals for hybrid QM/MM calculations. 515-523
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• 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
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Volume 27, Number 5, April 2006

• Min Hsien Liu, Cheng Chen:
  Modified calculations of hydrocarbon thermodynamic properties. 537-544
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• Hong-Bin Xie, Yi-Hong Ding, Chia-Chung Sun:
  Ylidic radical-molecule reactions. 545-551
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• 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
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• Stanislav Böhm, Otto Exner:
  Are calculated enthalpies of formation sometimes more reliable than experimental? A test on alkyl substituted benzoic acids. 571-577
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• Li-Ming Yang, Yi-Hong Ding, Qiang Wang, Chia-Chung Sun:
  Monosilicon-substituted cyanoacetylene: A computational study. 578-595
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• Diego R. Alcoba, Luis Lain, Alícia Torre, Roberto C. Bochicchio:
  An orbital localization criterion based on the theory of fuzzy atoms. 596-608
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• 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
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• Giulio Gianese, Stefano Pascarella:
  A consensus procedure improving solvent accessibility prediction. 621-626
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• P. Cassam-Chenaï, J. Liévin:
  The VMFCI method: A flexible tool for solving the molecular vibration problem. 627-640
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• Hong-Bin Xie, Yi-Hong Ding, Chia-Chung Sun:
  Radical reaction C3H+NO: A mechanistic study. 641-660
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• 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
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• Håkan W. Hugosson, Alessandro Laio, Patrick Maurer, Ursula Rothlisberger:
  A comparative theoretical study of dipeptide solvation in water. 672-684
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Volume 27, Number 6, April 2006

• Qishi Du, Da-Peng Li, Wen-Zhang He, Kuo-Chen Chou:
  Heuristic molecular lipophilicity potential (HMLP): Lipophilicity and hydrophilicity of amino acid side chains. 685-692
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• 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
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• Yasunobu Seno:
  Allostery of the two-state model of hemoglobin studied by ECEPP energy minimization. 701-710
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• Chunsheng Shi, Masahiko Morinaga:
  Doping effects on proton incorporation and conduction in SrZrO3. 711-718
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• 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
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• Siu-Hung Chien, Peter M. W. Gill:
  SG-0: A small standard grid for DFT quadrature on large systems. 730-739
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• Tomasz Borowski, Ewa Broclawik, Christopher J. Schofield, Per E. M. Siegbahn:
  Epimerization and desaturation by carbapenem synthase (CarC). A hybrid DFT study. 740-748
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• 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
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• Fabio E. Penotti:
  Orbital-orthogonality constraints and basis-set optimization. 762-772
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• 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
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• 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
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• Primoz Pristovsek, Lorella Franzoni:
  Stereospecific assignments of protein NMR resonances based on the tertiary structure and 2D/3D NOE data. 791-797
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• 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
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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
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• 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
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• 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
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• 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
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• Lionello Pogliani:
  The hydrogen perturbation in molecular connectivity computations. 868-882
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• Lin Jin, Yi-Hong Ding, Jian Wang, Chia-Chung Sun:
  Reaction mechanism of the CCN radical with nitric oxide. 883-893
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• Jia-Xu Zhang, Ze-Sheng Li, Jing-Yao Liu, Chia-Chung Sun:
  Theoretical study on the mechanism of the CH2F + NO2 reaction. 894-905
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• Kazuki Ohno, Minoru Sakurai:
  Linear-scaling molecular orbital calculations for the pKa values of ionizable residues in proteins. 906-916
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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
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• J. H. Van Lenthe, R. Zwaans, Huub J. J. Van Dam, M. F. Guest:
  Starting SCF calculations by superposition of atomic densities. 926-932
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• 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
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• Shiqi Zhou:
  Rapidly convergent procedure to solve the density profile equation in the classical density functional theory. 941-947
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• 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
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• K. Darowicki, W. Felisiak:
  On the joint time-frequency characteristics of chemical oscillations. 961-965
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• 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
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• 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
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• 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
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• 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
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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
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• Roberto Flores-Moreno, Rodrigo J. Alvarez-Mendez, Alberto Vela, Andreas M. Köster:
  Half-numerical evaluation of pseudopotential integrals. 1009-1019
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• 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
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• 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
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• 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
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Volume 27, Number 10, July 2006

• Patrick Musch, Bernd Engels:
  DIESEL-MP2: A new program to perform large-scale multireference-MP2 computations. 1055-1062
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• Andrew E. Whitten, Joshua J. McKinnon, Mark A. Spackman:
  Electric field-derived point charges to mimic the electrostatics in molecular crystals. 1063-1070
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• Benjamin D. Allen, Stephen L. Mayo:
  Dramatic performance enhancements for the FASTER optimization algorithm. 1071-1075
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• Pablo Echenique, José Luis Alonso:
  Definition of Systematic, Approximately Separable, and Modular Internal Coordinates (SASMIC) for macromolecular simulation. 1076-1087
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• Karl Jug, Viatcheslav A. Tikhomirov:
  Anion substitution in zinc chalcogenides. 1088-1092
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• 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
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• 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
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• Genyuan Li, Herschel Rabitz:
  Ratio control variate method for efficiently determining high-dimensional model representations. 1112-1118
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Volume 27, Number 11, August 2006

• Liwei Liu, Tianming Wang:
  2D representation of protein secondary structure sequences and its applications. 1119-1124
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• 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
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• Hyunbum Jang, Thomas B. Woolf:
  Multiple pathways in conformational transitions of the alanine dipeptide: An application of dynamic importance sampling. 1136-1141
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• Flavia P. Agostini, Diogo De O. Soares-Pinto, Marcelo A. Moret, Carla Osthoff, Pedro G. Pascutti:
  Generalized simulated annealing applied to protein folding studies. 1142-1155
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• 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
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• 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
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• Dusan P. Djurdjevic, Mark J. Biggs:
  Ab initio protein fold prediction using evolutionary algorithms: Influence of design and control parameters on performance. 1177-1195
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• Bo Liao, Xuyu Xiang, Wen Zhu:
  Coronavirus phylogeny based on 2D graphical representation of DNA sequence. 1196-1202
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• Annia Galano, J. Raúl Alvarez-Idaboy:
  A new approach to counterpoise correction to BSSE. 1203-1210
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• E. S. Ferrari, R. C. Burton, R. J. Davey, A. Gavezzotti:
  Simulation of phase separation in alcohol/water mixtures using two-body force field and standard molecular dynamics. 1211-1219
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Volume 27, Number 12, September 2006

• Gernot Frenking, Max C. Holthausen:
  Foreword. 1221-1222
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• Carmen Herrmann, Lian Yu, Markus Reiher:
  Spin states in polynuclear clusters: The [Fe2O2] core of the methane monooxygenase active site. 1223-1239
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• Guillermina Estiu, Dimas Suárez, Kenneth M. Merz Jr.:
  Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases. 1240-1262
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• Mihail Atanasov, Peter Comba, Bodo Martin, Vera Müller, Gopalan Rajaraman, Heidi Rohwer, Steffen Wunderlich:
  DFT models for copper(II) bispidine complexes: Structures, stabilities, isomerism, spin distribution, and spectroscopy. 1263-1277
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• Felix Studt, Felix Tuczek:
  Theoretical, spectroscopic, and mechanistic studies on transition-metal dinitrogen complexes: Implications to reactivity and relevance to the nitrogenase problem. 1278-1291
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• Wen-Ge Han, Tiqing Liu, Timothy Lovell, Louis Noodleman:
  DFT calculations of ⁵⁷Fe Mössbauer isomer shifts and quadrupole splittings for iron complexes in polar dielectric media: Applications to methane monooxygenase and ribonucleotide reductase. 1292-1306
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• Jonathan P. McNamara, Mahesh Sundararajan, Ian H. Hillier, Jun Ge, Andrew Campbell, Claudio Morgado:
  Can the semiempirical PM3 scheme describe iron-containing bioinorganic molecules? 1307-1323
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• Ahmet Altun, Sason Shaik, Walter Thiel:
  Systematic QM/MM investigation of factors that affect the cytochrome P450-catalyzed hydrogen abstraction of camphor. 1324-1337
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• Nicolai Lehnert, V. K. K. Praneeth, Florian Paulat:
  Electronic structure of iron(II)-porphyrin nitroxyl complexes: Molecular mechanism of fungal nitric oxide reductase (P450nor). 1338-1351
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• Jeremy N. Harvey, Christine M. Bathelt, Adrian J. Mulholland:
  QM/MM modeling of compound I active species in cytochrome P450, cytochrome C peroxidase, and ascorbate peroxidase. 1352-1362
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• Hiroyuki Nakashima, Jun-Ya Hasegawa, Hiroshi Nakatsuji:
  On the O2 binding of Fe-porphyrin, Fe-porphycene, and Fe-corrphycene complexes. 1363-1372
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• Margareta R. A. Blomberg, Per E. M. Siegbahn:
  Quantum chemistry applied to the mechanisms of transition metal containing enzymes - Cytochrome c oxidase, a particularly challenging case. 1373-1384
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• Robert K. Szilagyi, Mark A. Winslow:
  On the accuracy of density functional theory for iron - sulfur clusters. 1385-1397
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• Lubomír Rulísek, Kasper P. Jensen, Kristoffer Lundgren, Ulf Ryde:
  The reaction mechanism of iron and manganese superoxide dismutases studied by theoretical calculations. 1398-1414
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• Edward I. Solomon, Serge I. Gorelsky, Abhishek Dey:
  Metal-thiolate bonds in bioinorganic chemistry. 1415-1428
  Electronic Edition (link) BibTeX
• Jadwiga Kuta, Serguei Patchkovskii, Marek Z. Zgierski, Pawel M. Kozlowski:
  Performance of DFT in modeling electronic and structural properties of cobalamins. 1429-1437
  Electronic Edition (link) BibTeX
• Rajeev Prabhakar, Keiji Morokuma, Djamaladdin G. Musaev:
  A DFT study of the mechanism of Ni superoxide dismutase (NiSOD): Role of the active site cysteine-6 residue in the oxidative half-reaction. 1438-1445
  Electronic Edition (link) BibTeX
• Jean-Didier Maréchal, Feliu Maseras, Agustí Lledós, Liliane Mouawad, David Pérahia:
  A DFT study on the relative affinity for oxygen of the and subunits of hemoglobin. 1446-1453
  Electronic Edition (link) BibTeX
• Jesse W. Tye, Marcetta Y. Darensbourg, Michael B. Hall:
  Correlation between computed gas-phase and experimentally determined solution-phase infrared spectra: Models of the iron-iron hydrogenase enzyme active site. 1454-1462
  Electronic Edition (link) BibTeX
• Sebastian Sinnecker, Frank Neese:
  QM/MM calculations with DFT for taking into account protein effects on the EPR and optical spectra of metalloproteins. Plastocyanin as a case study. 1463-1475
  Electronic Edition (link) BibTeX

Volume 27, Number 13, October 2006

• Myungshim Kang, Paul E. Smith:
  A Kirkwood-Buff derived force field for amides. 1477-1485
  Electronic Edition (link) BibTeX
• Marcel Swart, Ernst Rösler, F. Matthias Bickelhaupt:
  Proton affinities of maingroup-element hydrides and noble gases: Trends across the periodic table, structural effects, and DFT validation. 1486-1493
  Electronic Edition (link) BibTeX
• Haibo Yu, Daan P. Geerke, Haiyan Liu, Wilfred F. van Gunsteren:
  Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models. 1494-1504
  Electronic Edition (link) BibTeX
• P. Salvador, D. Asturiol, I. Mayer:
  A general efficient implementation of the BSSE-free SCF and MP2 methods based on the chemical Hamiltonian approach. 1505-1516
  Electronic Edition (link) BibTeX
• Alexey Aleksandrov, Thomas Simonson:
  The tetracycline: Mg2+ complex: A molecular mechanics force field. 1517-1533
  Electronic Edition (link) BibTeX
• Elena Herzog, Tomaso Frigato, Volkhard Helms, C. Roy D. Lancaster:
  Energy barriers of proton transfer reactions between amino acid side chain analogs and water from ab initio calculations. 1534-1547
  Electronic Edition (link) BibTeX
• Anders Irbäck, Sandipan Mohanty:
  PROFASI: A Monte Carlo simulation package for protein folding and aggregation. 1548-1555
  Electronic Edition (link) BibTeX
• Yi-Yu Ke, Yun-Chu Chen, Thy-Hou Lin:
  Structure of the virus capsid protein VP1 of enterovirus 71 predicted by some homology modeling and molecular docking studies. 1556-1570
  Electronic Edition (link) BibTeX
• Zhen Xi, Zhihong Yu, Congwei Niu, Shurong Ban, Guangfu Yang:
  Development of a general quantum-chemical descriptor for steric effects: Density functional theory based QSAR study of herbicidal sulfonylurea analogues. 1571-1576
  Electronic Edition (link) BibTeX
• Meng-Sheng Liao, John D. Watts, Ming-Ju Huang:
  Assessment of the performance of density-functional methods for calculations on iron porphyrins and related compounds. 1577-1592
  Electronic Edition (link) BibTeX
• Yuedong Yang, Haiyan Liu:
  Genetic algorithms for protein conformation sampling and optimization in a discrete backbone dihedral angle space. 1593-1602
  Electronic Edition (link) BibTeX
• Marcin Makowski, Jacek Korchowiec, Feng Long Gu, Yuriko Aoki:
  Efficiency and accuracy of the elongation method as applied to the electronic structures of large systems. 1603-1619
  Electronic Edition (link) BibTeX

• Matteo Ceccarelli, Piero Procacci, Massimo Marchi:
  Erratum - An ab initio force field for the cofactors of bacterial photosynthesis. 1620
  Electronic Edition (link) BibTeX
• Felix Studt, Felix Tuczek:
  Theoretical, spectroscopic, and mechanistic studies on transition-metal dinitrogen complexes: Implications to reactivity and relevance to the nitrogenase problem. 1621
  Electronic Edition (link) BibTeX

Volume 27, Number 14, November 2006

• Azuma Matsuura, Hiroyuki Sato, Hirohiko Houjou, Shino Saito, Tomohiko Hayashi, Minoru Sakurai:
  Accurate evaluation of the absorption maxima of retinal proteins based on a hybrid QM/MM method. 1623-1630
  Electronic Edition (link) BibTeX
• Peter C. Anderson, Sandro Mecozzi:
  Minimum sequence requirements for selective RNA-ligand binding: A molecular mechanics algorithm using molecular dynamics and free-energy techniques. 1631-1640
  Electronic Edition (link) BibTeX
• Luis Fernández Pacios:
  Computational study of the process of hydrogen bond breaking: The case of the formamide-formic acid complex. 1641-1649
  Electronic Edition (link) BibTeX
• Luis Fernández Pacios, Pedro C. Gómez, Oscar Gálvez:
  Variation of atomic charges on proton transfer in strong hydrogen bonds: The case of anionic and neutral imidazole-acetate complexes. 1650-1661
  Electronic Edition (link) BibTeX
• Russell A. Brown, David A. Case:
  Second derivatives in generalized Born theory. 1662-1675
  Electronic Edition (link) BibTeX
• Nikolai N. Medvedev, V. P. Voloshin, V. A. Luchnikov, Marina L. Gavrilova:
  An algorithm for three-dimensional Voronoi S-network. 1676-1692
  Electronic Edition (link) BibTeX
• Oliver F. Lange, Lars V. Schäfer, Helmut Grubmüller:
  Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics. 1693-1702
  Electronic Edition (link) BibTeX
• S. Knippenberg, J.-P. François, M. S. Deleuze:
  Green's function study of the one-electron and shake-up ionization spectra of unsaturated hydrocarbon cage compounds. 1703-1722
  Electronic Edition (link) BibTeX
• Pathumwadee Intharathep, Anan Tongraar, Kritsana Sagarik:
  Ab initio QM/MM dynamics of H3O+ in water. 1723-1732
  Electronic Edition (link) BibTeX
• Pablo Echenique, Iván Calvo, José Luis Alonso:
  Quantum mechanical calculation of the effects of stiff and rigid constraints in the conformational equilibrium of the alanine dipeptide. 1733-1747
  Electronic Edition (link) BibTeX
• Pablo Echenique, Iván Calvo:
  Explicit factorization of external coordinates in constrained statistical mechanics models. 1748-1755
  Electronic Edition (link) BibTeX
• Jian Wang, Yi-Hong Ding, Chia-Chung Sun:
  Theoretical mechanistic study on the radical-molecule reactions of cyanomethylidyne with PH3, H2S, and HCl. 1756-1764
  Electronic Edition (link) BibTeX

• Nicholas M. Glykos:
  Software news and updates carma: A molecular dynamics analysis program. 1765-1768
  Electronic Edition (link) BibTeX

Volume 27, Number 15, November 2006

• Carles Curutchet, Modesto Orozco, F. Javier Luque, Benedetta Mennucci, Jacopo Tomasi:
  Dispersion and repulsion contributions to the solvation free energy: Comparison of quantum mechanical and classical approaches in the polarizable continuum model. 1769-1780
  Electronic Edition (link) BibTeX
• Leticia González, Chantal Daniel:
  Photochemistry of CH3Mn(CO)5: A multiconfigurational ab initio study. 1781-1786
  Electronic Edition (link) BibTeX
• Stefan Grimme:
  Semiempirical GGA-type density functional constructed with a long-range dispersion correction. 1787-1799
  Electronic Edition (link) BibTeX
• Laurence Leherte:
  Similarity measures based on Gaussian-type promolecular electron density models: Alignment of small rigid molecules. 1800-1816
  Electronic Edition (link) BibTeX
• Jian Zhang, Mingyu Zhang, Yuanyuan Zhao, Baoguo Chen, Chia-Chung Sun:
  Ab initio studies on isomers of macropolyhedral borane ions [B20H18]n (n = 0, -2, -4). 1817-1821
  Electronic Edition (link) BibTeX
• Rogério Custodio, André Severo Pereira Gomes, Fabrício Ronil Sensato, Júlio Murilo dos Santos Trevas:
  Analysis of the segmented contraction of basis functions using density matrix theory. 1822-1829
  Electronic Edition (link) BibTeX
• Qi Dai, Xiao-Qing Liu, Tian-Ming Wang:
  Numerical characterization of DNA sequences based on the k-step Markov chain transition probability. 1830-1842
  Electronic Edition (link) BibTeX
• Vincent Zoete, Markus Meuwly:
  Importance of individual side chains for the stability of a protein fold: Computational alanine scanning of the insulin monomer. 1843-1857
  Electronic Edition (link) BibTeX
• Si-Dian Li, Chang-Qing Miao, Jin-Chang Guo, Guang-Ming Ren:
  Transition metal-boron complexes BnM: From bowls (n = 8-14) to tires (n = 14). 1858-1865
  Electronic Edition (link) BibTeX
• Sheng-You Huang, Xiaoqin Zou:
  An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials. 1866-1875
  Electronic Edition (link) BibTeX
• Sheng-You Huang, Xiaoqin Zou:
  An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function. 1876-1882
  Electronic Edition (link) BibTeX
• Padeleimon Karafiloglou:
  Control of delocalization and structural changes by means of an electric field. 1883-1891
  Electronic Edition (link) BibTeX
• Hugo R. R. Santos, Gregori Ujaque, Maria João Ramos, José A. N. F. Gomes:
  QM/QM study of the coverage effects on the adsorption of amino-cyclopentene at the Si(100) surface. 1892-1897
  Electronic Edition (link) BibTeX

Volume 27, Number 16, December 2006

• Sathesh Bhat, Traian Sulea, Enrico O. Purisima:
  Coupled atomic charge selectivity for optimal ligand-charge distributions at protein binding sites. 1899-1907
  Electronic Edition (link) BibTeX
• Yu Sun, Robert A. Latour:
  Comparison of implicit solvent models for the simulation of protein-surface interactions. 1908-1922
  Electronic Edition (link) BibTeX
• Mark S. Formaneck, Qiang Cui:
  The use of a generalized born model for the analysis of protein conformational transitions: A comparative study with explicit solvent simulations for chemotaxis Y protein (CheY). 1923-1943
  Electronic Edition (link) BibTeX
• Hannes H. Loeffler, Ahmed M. Mohammed, Yasuhiro Inada, Shigenobu Funahashi:
  Water exchange dynamics of manganese(II), cobalt(II), and nickel(II) ions in aqueous solution. 1944-1949
  Electronic Edition (link) BibTeX
• Benjamin F. Gherman, William B. Tolman, Christopher J. Cramer:
  Characterization of the structure and reactivity of monocopper-oxygen complexes supported by -diketiminate and anilido-imine ligands. 1950-1961
  Electronic Edition (link) BibTeX
• Sergei Izrailev, Fangqiang Zhu, Dimitris K. Agrafiotis:
  A distance geometry heuristic for expanding the range of geometries sampled during conformational search. 1962-1969
  Electronic Edition (link) BibTeX
• Roberto L. A. Haiduke, Albérico B. F. da Silva:
  Accurate relativistic adapted Gaussian basis sets for Cesium through Radon without variational prolapse and to be used with both uniform sphere and Gaussian nucleus models. 1970-1979
  Electronic Edition (link) BibTeX
• Inmaculada García Cuesta, Alfredo M. J. Sánchez De Merás, Paolo Lazzeretti:
  Diatropicity of tetraazanaphthalenes. 1980-1989
  Electronic Edition (link) BibTeX
• Christopher S. Page, Paul A. Bates:
  Can MM-PBSA calculations predict the specificities of protein kinase inhibitors? 1990-2007
  Electronic Edition (link) BibTeX