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A. Laref: Tight-binding molecular dynamics simulation of ZnSe liquid within the local environment dependence.1-10
Chengqi Wang, Lili Xi, Shuyan Li, Huanxiang Liu, Xiaojun Yao: A sequence-based computational model for the prediction of the solvent accessible surface area for α-helix and β-barrel transmembrane residues.11-17
Xiang Po Du, Veng Cheong Lo, Yuan Xu Wang: The effect of structure and phase transformation on the mechanical properties of Re2N and the stability of Mn2N.18-24
Yusuke Ootani, Tetsuya Taketsugu: Ab initio molecular dynamics approach to tunneling splitting in polyatomic molecules.60-65
Li Wang, Yanjie Li, Hong-Qing He, Jinglai Zhang: Hydrogen abstraction reactions of OH radicals with CH3CH2CH2Cl and CH3CHClCH3: A mechanistic and kinetic study.66-75
Pedro Gonnet: Pairwise verlet lists: Combining cell lists and verlet lists to improve memory locality and parallelism.76-81
Yu Li Yan, Yuan Xu Wang: Electronic structure and low temperature thermoelectric properties of In24 M8 O48 (M = Ge4+, Sn4+, Ti4+, and Zr4+).88-92
Xu-Geng Guo, Jing-Lai Zhang, Yuan Zhao: Ab initio characterization of size dependence of electronic spectra for linear anionic carbon clusters Cn- (n = 4-17).93-102
Chi-Shiun Wu, Ming-Der Su: Theoretical investigations of the reactivities of four-membered N-heterocyclic carbene analogues of the group 13 elements.103-111
Wolf-Dietrich Ihlenfeldt: Comment on the paper "indexing molecules with chemical graph Identifiers" by Elisabeth Gregori-Puigjané, Rut Garriga-Sust, and Jordi Mestres.237
Eshel Faraggi, Tuo Zhang, Yuedong Yang, Lukasz A. Kurgan, Yaoqi Zhou: SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles.259-267
Steven Lettieri, Daniel M. Zuckerman: Accelerating molecular monte carlo simulations using distance and orientation-dependent energy tables: Tuning from atomistic accuracy to smoothed "coarse-grained" models.268-275
Shantanu Kadam, Kumar Vanka: A new approximate method for the stochastic simulation of chemical systems: The representative reaction approach.276-285
Takaharu Mori, Fumiko Ogushi, Yuji Sugita: Analysis of lipid surface area in protein-membrane systems combining voronoi tessellation and monte carlo integration methods.286-293
Cui Liu, Dong-Xia Zhao, Zhong-Zhi Yang: Direct evaluation of individual hydrogen bond energy in situ in intra- and intermolecular multiple hydrogen bonds system.379-390
Andrew J. Logsdail, Z. Y. Li, Roy L. Johnston: Development and optimization of a novel genetic algorithm for identifying nanoclusters from scanning transmission electron microscopy images.391-400
Feng Yu: Ab Initio direct classical trajectory investigation on the SN2 reaction of F- with NH2F: Nonstatistical central barrier recrossing dynamics.401-405
Marcus Lundberg: Understanding cross-boundary events in ONIOM QM: QM' calculations.406-415
Jorge M. C. Marques, A. A. C. C. Pais, P. E. Abreu: On the use of big-bang method to generate low-energy structures of atomic clusters modeled with pair potentials of different ranges.442-452
Fangqiang Zhu, Gerhard Hummer: Convergence and error estimation in free energy calculations using the weighted histogram analysis method.453-465
Wei-Quan Tian: Modeling nonlinear optics of nanosystems with sum-over-states model.466-470
Bu-Tong Li, Lu-Lin Li, Hai-Shun Wu: Theoretical calculation about the valence and rydberg excited states of hydrogen cyanide.484-489
Wenming Sun, Yuxiang Bu, Yixuan Wang: Interaction and protection mechanism between li@C60 and nucleic acid bases (NABs): Performance of PM6-DH2 on noncovalent interaction of NABs-Li@C60.490-501
Fabrice Avaltroni, Clemence Corminboeuf: Identifying clusters as low-lying mimina - efficiency of stochastic and genetic algorithms using inexpensive electronic structure levels.502-508
Shuming Zhang: A reliable and efficient first principles-based method for predicting pKa values. III. Adding explicit water molecules: Can the theoretical slope be reproduced and pKa values predicted more accurately?517-526
Weiwei Xue, Huanxiang Liu, Xiaojun Yao: Molecular mechanism of HIV-1 integrase-vDNA interactions and strand transfer inhibitor action: A molecular modeling perspective.527-536
Hua Dong, Bo-Zhen Chen, Ming-Bao Huang, Roland Lindh: The bergman cyclizations of the enediyne and its N-substituted analogs using multiconfigurational second-order perturbation theory.537-549
Stefano Costanzi, Santiago Vilar: In Silico screening for agonists and blockers of the β2 adrenergic receptor: Implications of inactive and activated state structures.561-572
Jun-Xi Liang, Zhi-Yuan Geng, Yong-Cheng Wang: Density functional study of SN2 substitution reactions for CH3Cl + CX1X2•- (X1X2 = HH, HF, HCl, HBr, HI, FF, ClCl, BrBr, and II).595-606
Florent Barbault, François Maurel: Is inhibition process better described with MD(QM/MM) simulations? The case of urokinase type plasminogen activator inhibitors.607-616
Milind M. Deshmukh, Shigeyoshi Sakaki: Two-step evaluation of binding energy and potential energy surface of van der Waals complexes.617-628
Soumya Ganguly Neogi, Pinaki Chaudhury: Structure and spectroscopy of water-fluoride microclusters: A combined genetic algorithm and DFT-based study.629-639
M. Kaukonen, A. Gulans, P. Havu, Esko I. Kauppinen: Lennard-Jones parameters for small diameter carbon nanotubes and water for molecular mechanics simulations from van der Waals density functional calculations.652-658
A. Laref, S. Laref, S. Bin-Omran: Electronic structure, X-ray absorption, and optical spectroscopy of LaCoO3 in the ground-state and excited-states.673-684
Jan Rezác, Kevin E. Riley, Pavel Hobza: Evaluation of the performance of post-Hartree-Fock methods in terms of intermolecular distance in noncovalent complexes.691-694
Katrin Tonigold, Axel Groß: Dispersive interactions in water bilayers at metallic surfaces: A comparison of the PBE and RPBE functional including semiempirical dispersion corrections.695-701
Milan Randic: Very efficient search for protein alignment - VESPA.702-707
Wenjing Zhang, Yanyan Zhu, Donghui Wei, Mingsheng Tang: Mechanisms of the cascade synthesis of substituted 4-amino-1, 2, 4-triazol-3-one from huisgen zwitterion and aldehyde hydrazone: A DFT study.715-722
Juan Andrés, Slawomir Berski, Luis R. Domingo, Patricio González-Navarrete: Nature of the ring-closure process along the rearrangement of octa-1, 3, 5, 7-tetraene to cycloocta-1, 3, 5-triene from the perspective of the electron localization function and catastrophe theory.748-756
Sampath Koppole, Michael Schaefer: A discriminative Ramachandran potential of mean force aimed at minimizing secondary structure bias.791-799
Truong Ba Tai, Minh Tho Nguyen: Electronic structure and thermochemical properties of silicon-doped lithium clusters LinSi0/+, n = 1-8: New insights on their stability.800-809
Software News and Updates
Philipp Plessow, Florian Weigend: Seminumerical calculation of the Hartree-Fock exchange matrix: Application to two-component procedures and efficient evaluation of local hybrid density functionals.810-816
Alessandro Erba, Cesare Pisani: Evaluation of the electron momentum density of crystalline systems from ab initio linear combination of atomic orbitals calculations.822-831
Yury N. Vorobjev: Potential of mean force of water-proton bath and molecular dynamic simulation of proteins at constant pH.832-842
Joop H. van Lenthe, H. B. Broer-Braam, Zahid Rashid: On the efficiency of VBSCF algorithms, a comment on "An efficient algorithm for energy gradients and orbital optimization in valence bond theory".911-913
Wei Wu, Yirong Mo: Reply to comment on the paper "An efficient Algorithm for Energy Gradients and Orbital Optimization in Valence Bond Theory".914-915
Gustavo L. C. Moura, Alfredo Mayall Simas: Quantum molecular mechanics - a noniterative procedure for the fast Ab Initio calculation of closed shell systems.958-969
K. V. Turcheniuk, A. B. Rozhenko: (σ3, λ5)-phosphoranes versus (σ3, λ3)-thiaphosphiranes: Quantum chemical investigation of products of phosphaalkene sulfurization.1023-1028
Antonio Ricci, Andrea Brancale: Density functional theory calculation of cyclic carboxylic phosphorus mixed anhydrides as possible intermediates in biochemical reactions: Implications for the Pro-Tide approach.1029-1037
Qi Cao, Jing Wang, Zhao-Shuo Tian, Zai-Feng Xie, Fu-Quan Bai: Theoretical investigation on the photophysical properties of N-heterocyclic carbene iridium (III) complexes (fpmb)xIr(bptz)3-x (x = 1-2).1038-1046