Journal of Computational Chemistry

Li, Shuyan; Xi, Lili; Li, Jiazhong; Wang, Chengqi; Lei, Beilei; Shen, Yulin; Liu, Huanxiang; Yao, Xiaojun; Li, Biao

doi: 10.1002/jcc.21701pmid: 21425278

Molecular cause of human disease retains as one of the most attractive scientific research targets for decades. An effective approach toward this topic is analysis and identification of disease‐related amino acid polymorphisms. In this work, we developed a concise and promising deleterious amino acid polymorphism identification method SeqSubPred based on 44 features solely extracted from protein sequence. SeqSubPred achieved surprisingly good predictive ability with accuracy (0.88) and area under receiver operating characteristic (0.94) without resorting to homology or evolution information, which is frequently used in similar methods and usually more complex and time‐consuming. SeqSubPred also identified several critical sequence features obtained from random forests model, and these features brought some interesting insights into the factors affecting human disease‐related amino acid substitutions. The online version of SeqSubPred method is available at montana.informatics.indiana.edu/cgi‐bin/seqmut/seqsubpred.cgi © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011

Aquino, Adélia J. A.; Nachtigallova, Dana; Hobza, Pavel; Truhlar, Donald G.; Hättig, Christof; Lischka, Hans

doi: 10.1002/jcc.21702pmid: 21425279

Electronic singlet excitations of stacked adenine–thymine (AT) and guanine–cytosine (GC) complexes have been investigated with respect to local excitation and charge‐transfer (CT) characters. Potential energy curves for rigid displacement of the nucleobases have been computed to establish the distance dependence of the CT states. The second‐order algebraic diagrammatic construction (ADC(2)) method served as reference approach for comparison to a selected set of density functionals used within the time‐dependent density functional theory (TD‐DFT). Particular attention was dedicated to the performance of the recently developed family of M06 functionals. The calculations for the stacked complexes show that at the ADC(2) level, the lowest CT state is S6 for the AT and as S4 for the GC pair. At the reference geometry, the actual charge transferred is found to be 0.73 e for AT. In case of GC, this amount is much smaller (0.17 e). With increasing separation of the two nucleobases, the CT state is strongly destabilized. The M06‐2X version provides a relatively good reproduction of the ADC(2) results. It avoids the serious overstabilization and overcrowding of the spectrum found with the B3LYP functional. On the other hand, M06‐HF destabilizes the CT state too strongly. TD‐DFT/M06‐2X calculations in solution (heptane, isoquinoline, and water) using the polarizable continuum model show a stabilization of the CT state and an increase in CT character with increasing polarity of the solvent. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011

Terakawa, Tsuyoshi; Kameda, Tomoshi; Takada, Shoji

doi: 10.1002/jcc.21703pmid: 21425280

To reduce the number of replicas required in the conventional replica exchange method for huge systems, recently the replica exchange with solute tempering (REST) method was proposed. Here we showed that a variant of REST realized by rescaling the force‐field parameters can be performed with GROMACS 4 without changing the code. We tested the variant REST for alanine dipeptide and an N‐terminal peptide from p53 confirming its performance nearly equal to the original REST. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011

Li, Hongping; Lv, Shuhui; Liu, Xiaojuan; Meng, Jian

doi: 10.1002/jcc.21704pmid: 21425281

First‐principles calculations using the augmented plane wave plus local orbitals method, as implemented in the WIEN2K code, have been carried out to study the A‐B intersite charge transfer and the correlated electrical and magnetic properties of the perovskite BiCu3Fe4O12, especially as regards the charge transfer. The results indicate that the charge transfer between A‐site Cu and B‐site Fe is by way of O 2p orbitals, and during this process orbital hybridization plays an important role. More importantly, the charge transfer is of 3d9 + 4d5L0.75→3d9L + 4d5 type (here L denotes an oxygen hole or a ligand hole). During this process, the magnetic interaction experiences a transition from Cu‐Fe ferrimagnetic coupling to G‐type antiferromagnetic coupling within B‐site Fe with paramagnetic Cu3+. As to electrical property, it undergoes a metal to insulator transition. All our calculated results are consistent with the available experimental results. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011

Karagiannis, Efstathios E.; Kefalidis, Christos E.; Petrakopoulou, Ioanna; Tsipis, Constantinos A.

doi: 10.1002/jcc.21705pmid: 21425282

The structural, electronic, bonding, magnetic, and optical properties of bimetallic (CunRum)+/0/− (n + m ≤ 3; n, m = 0–3) clusters were computed in the framework of the density functional theory (DFT) and time‐dependent DFT (TD‐DFT) using the full‐range PBE0 nonlocal hybrid GGA functional combined with the Def2‐QZVPP basis sets. Several low‐lying states have been investigated and the stability of the ground state spinomers was estimated with respect to all possible fragmentation schemes. Molecular orbital and population analysis schemes along with computed electronic parameters illustrated the details of the bonding mechanisms in the (CunRum)+/0/− clusters. The TD‐DFT computed UV–visible absorption spectra of the bimetallic clusters have been fully analyzed and assignments of all principal electronic transitions were made and interpreted in terms of contribution from specific molecular orbital excitations. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011

Szalay, Zsófia; Rohonczy, János

doi: 10.1002/jcc.21706pmid: 21425283

During the past few years, general‐purpose graphics processing units (GPGPUs) have become rather popular in the high performance computing community. In this study, we present an implementation of the simulation of dynamic nuclear magnetic resonance (DNMR) spectra. The algorithm is based on the kinetic Monte Carlo method and therefore can benefit from the multithreaded architecture of the GPGPU. By careful optimization of the algorithm a 30–100‐fold speed increase could be achieved. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011

Zhao, Li‐Zhen; Su, Wan‐Sheng; Lu, Wen‐Cai; Wang, C. Z.; Ho, K. M.

doi: 10.1002/jcc.21708pmid: 21425284

We performed first‐principles calculations to study the structure and stability of Si70 cluster. The results from the density functional theory calculation with the Becke–Lee–Yang–Parr and B3LYP exchange‐correlation functionals suggest that a diamond‐like Si70 isomer is the most stable structure, in contrast to endohedral fullerenes of Si70. On the other hand, an endohedral fullerene of Si16@Si54 was found to be slightly lower in energy than the diamond‐like Si70 if the Predew–Burke–Ernzerhof functional is used. Our calculation results suggest that around n = 70, the endohedral fullerene and diamond‐like isomer are expected to be competitive. The calculated IR vibration spectra, ionization potential, and inverse mobilities were also calculated and discussed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011

Liu, Yang; Sun, Huai

doi: 10.1002/jcc.21709pmid: 21425285

DFT calculations were carried out to study heme complexes with diatomic ligand (CO, NO, or O2) and trans‐imidazole ligand. The optimized electronic ground states of CO, NO, and O2 adducts are singlet, doublet, and open‐shell singlet, respectively. For O2 adduct, the open‐shell singlet is slightly lower in energy than the close‐shell singlet. However, important differences are found in optimized structures and vibrational frequencies. Particularly, the trans‐imidazole‐induced frequency up‐shift of the FeO(O) stretching mode can be predicted only with the open‐shell singlet as ground state. An analysis of normal modes confirms that the up‐shifts in the bent (NO and O2) adducts are mainly due to mixing of FeX(O) stretching mode with FeXO bending coordinate. Our study of binding mechanism indicates that a secondary source of the upshifts is the diminished weakening of the FeX(O) bonds. The FeX(O) bond strengths are modulated by σ competition mechanism, which weakens the FeX(O) bond and σ–π cooperation mechanism, which only exists in the bent adducts and enforce the FeX(O) bond. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011

Ikebe, Jinzen; Umezawa, Koji; Kamiya, Narutoshi; Sugihara, Takanori; Yonezawa, Yasushige; Takano, Yu; Nakamura, Haruki; Higo, Junichi

doi: 10.1002/jcc.21710pmid: 21425286

Trivial trajectory parallelization of multicanonical molecular dynamics (TTP‐McMD) explores the conformational space of a biological system with multiple short runs of McMD starting from various initial structures. This method simply connects (i.e., trivially parallelizes) the short trajectories and generates a long trajectory. First, we theoretically prove that the simple trajectory connection satisfies a detailed balance automatically. Thus, the resultant long trajectory is regarded as a single multicanonical trajectory. Second, we applied TTP‐McMD to an alanine decapeptide with an all‐atom model in explicit water to compute a free‐energy landscape. The theory imposes two requirements on the multiple trajectories. We have demonstrated that TTP‐McMD naturally satisfies the requirements. The TTP‐McMD produces the free‐energy landscape considerably faster than a single‐run McMD does. We quantitatively showed that the accuracy of the computed landscape increases with increasing the number of multiple runs. Generally, the free‐energy landscape of a large biological system is unknown a priori. The current method is suitable for conformational sampling of such a large system to reduce the waiting time to obtain a canonical ensemble statistically reliable. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011

Han, Chong; Yan, Shi‐Shen; Lin, Xue‐Ling; Hu, Shu‐Jun; Zhao, Ming‐Wen; Yao, Xin‐Xin; Chen, Yan‐Xue; Liu, Guo‐Lei; Mei, Liang‐Mo

doi: 10.1002/jcc.21711pmid: 21425287

First‐principles calculations of undoped HfO2 and cobalt‐doped HfO2 have been carried out to study the magnetic properties of the dielectric material. In contrast to previous reports, it was found that the native defects in HfO2 could not induce strong ferromagnetism. However, the cobalt substituting hafnium is the most stable defect under oxidation condition, and the ferromagnetic (FM) coupling between the cobalt substitutions is favorable in various configurations. We found that the FM coupling is mediated by the threefold‐coordinated oxygen atoms in monoclinic HfO2 and could be further enhanced in electron‐rich condition. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011