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Journal of Computational Chemistry

Alvaro Muñoz-Castro, R Bruce King
Experimentally characterized endohedral metallofullerenes are of current interest in expanding the range of viable fullerenic structures and their applications. Smaller metallofullerenes, such as M@C28 , show that several d- and f-block elements can be efficiently confined in relatively small carbon cages. This article explores the potential capabilities of the smallest fullerene cage, that is, C20 , to encapsulate p-block elements from group 14, that is, E = Si, Ge, Sn, and Pb. Our interest relates to the bonding features and optical properties related to E@C20 ...
April 20, 2017: Journal of Computational Chemistry
Johannes M Dieterich, William C Witt, Emily A Carter
Kinetic energy density functionals (KEDFs) approximate the kinetic energy of a system of electrons directly from its electron density. They are used in electronic structure methods that lack direct access to orbitals, for example, orbital-free density functional theory (OFDFT) and certain embedding schemes. In this contribution, we introduce libKEDF, an accelerated library of modern KEDF implementations that emphasizes nonlocal KEDFs. We discuss implementation details and assess the performance of the KEDF implementations for large numbers of atoms...
April 20, 2017: Journal of Computational Chemistry
Shuai Wei, Charles L Brooks, Aaron T Frank
The rapid and accurate calculation of solvent accessible surface area (SASA) is extremely useful in the energetic analysis of biomolecules. For example, SASA models can be used to estimate the transfer free energy associated with biophysical processes, and when combined with coarse-grained simulations, can be particularly useful for accounting for solvation effects within the framework of implicit solvent models. In such cases, a fast and accurate, residue-wise SASA predictor is highly desirable. Here, we develop a predictive model that estimates SASAs based on Cα-only protein structures...
April 16, 2017: Journal of Computational Chemistry
Cen Gao, Jeremy Desaphy, Michal Vieth
In this work, the ability of molecular dynamics simulations (MD) to prospectively predict regions of ligand binding sites that could undergo induced fit effects was investigated. Conventional MD was run on 39 apo structures (no ligand), and the resulting trajectories were compared to a set of 147 holo X-ray structures (ligand-bound). It was observed from the simulations, in the absence of the ligands, that structures exhibiting large residue conformational changes indicated higher likelihood of induced fit effects...
April 16, 2017: Journal of Computational Chemistry
Kuo Hao Lee, Jianhan Chen
Accurate treatment of solvent environment is critical for reliable simulations of protein conformational equilibria. Implicit treatment of solvation, such as using the generalized Born (GB) class of models arguably provides an optimal balance between computational efficiency and physical accuracy. Yet, GB models are frequently plagued by a tendency to generate overly compact structures. The physical origins of this drawback are relatively well understood, and the key to a balanced implicit solvent protein force field is careful optimization of physical parameters to achieve a sufficient level of cancellation of errors...
April 11, 2017: Journal of Computational Chemistry
Matthias Witte, Martin Rohrmüller, Uwe Gerstmann, Gerald Henkel, Wolf Gero Schmidt, Sonja Herres-Pawlis
The hexanuclear thioguanidine mixed-valent copper complex cation [Cu6 (NGuaS)6 ](+2) (NGuaS = o-SC6 H4 NC(NMe2 )2 ) and its oxidized/reduced states are theoretically analyzed by means of density functional theory (DFT) (TPSSh + D3BJ/def2-TZV (p)). A detailed bonding analysis using overlap populations is performed. We find that a delocalized Cu-based ring orbital serves as an acceptor for donated S p electrons. The formed fully delocalized orbitals give rise to a confined electron cloud within the Cu6 S6 cage which becomes larger on reduction...
April 10, 2017: Journal of Computational Chemistry
Juan Carlo Sancho-García, Ángel José Pérez-Jiménez, Marika Savarese, Éric Brémond, Juan Carlos Adamo
We study the orbital-dependence of three (parameter-free) double-hybrid density functionals, namely the PBE0-DH, the PBE-QIDH models, and the SOS1-PBE-QIDH spin-opposite-scaled variant of the latter. To do it, we feed all their energy terms with different sets of orbitals obtained previously from self-consistent density functional theory calculations using several exchange-correlation functionals (e.g., PBE, PBE0, PBEH&H), or directly with HF-PBE orbitals, to see their effect on selected datasets for atomization and reaction energies, the latter proned to marked self-interaction errors...
April 10, 2017: Journal of Computational Chemistry
Anand Kumar, Miquel Duran, Miquel Solà
The bonding patterns in coronene are complicated and controversial as denoted by the lack of consensus of how its electronic structure should be described. Among the different proposed descriptions, the two most representative are those generated by Clar's aromatic π-sextet and adaptative natural density partitioning (AdNDP) models. Quantum-chemical calculations at the density functional theory level are performed to evaluate the model that gives a better representation of coronene. To this end, we analyse the molecular structure of coronene, we estimate the aromaticity of its inner and outer rings using various local aromaticity descriptors, and we assess its chemical reactivity from the study of the Diels-Alder reaction with cyclopentadiene...
April 10, 2017: Journal of Computational Chemistry
George Opletal, Timothy C Petersen, Amanda S Barnard, Salvy P Russo
Reverse Monte Carlo (RMC) simulations were performed to investigate the effectiveness of any combination of five experimentally motivated constraints on the reproduction of a test case, a ternary ab initio model. It was found that low energy structures fitting a variety of constraints commonly used in the RMC methodology could still provide an incorrect description of the chemical structural unit populations in multi-elemental systems. It is shown that the use of an elemental bond type constraint is an effective way to avoid this...
April 10, 2017: Journal of Computational Chemistry
Zhifeng Lin, Tian Lu, Xun-Lei Ding
In this work, we designed a series of superalkali-doped Si12 C12 nanocage M3 O@Si12 C12 (M = Li, Na, K) with donor-acceptor framework. Density functional theory calculations demonstrated that the HOMO-LUMO gap of the complexes conspicuously narrowed with increase of atomic number of the alkali metal, the value decreased from 5.452 eV of pure Si12 C12 nanocage to 3.750, 2.984, and 2.634 eV of Li3 O@Si12 C12 , Na3 O@Si12 C12 , and K3 O@Si12 C12 , respectively. This finding shows that the pristine Si12 C12 cluster could be transformed to n-type semiconductor by introduction of the superalkali M3 O...
April 5, 2017: Journal of Computational Chemistry
Christopher R Ellis, Cheng-Chieh Tsai, Fang-Yu Lin, Jana Shen
BACE1 is a major therapeutic target for prevention and treatment of Alzheimer's disease. Developing inhibitors that can selectively target BACE1 in favor of other proteases, especially cathepsin D (CatD), has presented significant challenges. Here, we investigate the conformational dynamics and protonation states of BACE1 and CatD using continuous constant pH molecular dynamics with pH replica-exchange sampling protocol. Despite similar structure, BACE1 and CatD exhibit markedly different active site dynamics...
April 2, 2017: Journal of Computational Chemistry
Osamu Miyashita, Chigusa Kobayashi, Takaharu Mori, Yuji Sugita, Florence Tama
Flexible fitting is a computational algorithm to derive a new conformational model that conforms to low-resolution experimental data by transforming a known structure. A common application is against data from cryo-electron microscopy to obtain conformational models in new functional states. The conventional flexible fitting algorithms cannot derive correct structures in some cases due to the complexity of conformational transitions. In this study, we show the importance of conformational ensemble in the refinement process by performing multiple fittings trials using a variety of different force constants...
April 1, 2017: Journal of Computational Chemistry
Christian J Suess, Jonathan D Hirst, Nicholas A Besley
The development of optical multidimensional spectroscopic techniques has opened up new possibilities for the study of biological processes. Recently, ultrafast two-dimensional ultraviolet spectroscopy experiments have determined the rates of tryptophan → heme electron transfer and excitation energy transfer for the two tryptophan residues in myoglobin (Consani et al., Science, 2013, 339, 1586). Here, we show that accurate prediction of these rates can be achieved using Marcus theory in conjunction with time-dependent density functional theory...
April 1, 2017: Journal of Computational Chemistry
Chong Yang, Andreas Dreuw
The applicability and limitations of the restricted virtual space (RVS) approximation within the algebraic-diagrammatic construction (ADC) scheme for the polarization propagator up to third order is evaluated. In RVS-ADC, not only the core but also a substantial amount of energetically high-lying virtual orbitals is restricted in excitation energy calculations of low-lying excited electronic states. Using octatetraene, indole, and pyridine as representative examples and different standard basis sets of triple-zeta quality, RVS-ADC(2) turns out to be highly useful and to have negligible effects on ππ* excited states...
March 27, 2017: Journal of Computational Chemistry
Shigeru Yamaguchi, Takahiro Nishimura, Yuta Hibe, Masaki Nagai, Hirofumi Sato, Ian Johnston
In organic chemistry, Comparative Molecular Field Analysis (CoMFA) can be defined as a regression analysis between reaction outcomes and molecular fields, wherein we can extract and visualize important structural information from the coefficients of the constructed regression models. In CoMFA, partial least-squares (PLS) regression, which determines all coefficients in the model, is used for fitting the regression models. However, in organic reactions, steric effects are observed only near the reactive site, indicating that a large number of regression coefficients in the CoMFA of organic reactions should be assigned as 0...
March 27, 2017: Journal of Computational Chemistry
Christopher G Myers, B Montgomery Pettitt
Packing of double-stranded DNA in phages must overcome both electrostatic repulsions and the problem of persistence length. We consider coarse-grained models with the ability to kink and with randomly generated disorder. We show that the introduction of kinking into configurations of the DNA polymer packaged within spherical confinement results in significant reductions of the overall energies and pressures. We use a kink model which has the ability to deform every 24 bp, close to the average length predicted from phage sequence...
March 27, 2017: Journal of Computational Chemistry
Kenji Hirano, Hiroshi Nakano, Yoshihide Nakao, Hirofumi Sato, Shigeyoshi Sakaki
Photo absorption properties of p-coumaric acid, the chromophore of photoactive yellow protein, in aqueous solution were investigated by means of reference interaction site model self-consistent field with spatial electron density distribution (RISM-SCF-SEDD) method. RISM-SCF-SEDD is a combination methodology of electronic structure theory and statistical mechanics for molecular liquids. Here, time-dependent density functional theory was coupled with RISM equation to study the electronic structure of p-coumaric acid in aqueous system...
March 27, 2017: Journal of Computational Chemistry
Gaëtan Rubez, Jean-Matthieu Etancelin, Xavier Vigouroux, Michael Krajecki, Jean-Charles Boisson, Eric Hénon
The NCI approach is a modern tool to reveal chemical noncovalent interactions. It is particularly attractive to describe ligand-protein binding. A custom implementation for NCI using promolecular density is presented. It is designed to leverage the computational power of NVIDIA graphics processing unit (GPU) accelerators through the CUDA programming model. The code performances of three versions are examined on a test set of 144 systems. NCI calculations are particularly well suited to the GPU architecture, which reduces drastically the computational time...
March 25, 2017: Journal of Computational Chemistry
Changhao Wang, Li Xiao, Ray Luo
Continuum solvent models, particularly those based on the Poisson-Boltzmann equation (PBE), are widely used in the studies of biomolecular structures and functions. Existing PBE developments have been mainly focused on how to obtain more accurate and/or more efficient numerical potentials and energies. However to adopt the PBE models for molecular dynamics simulations, a difficulty is how to interpret dielectric boundary forces accurately and efficiently for robust dynamics simulations. This study documents the implementation and analysis of a range of standard fitting schemes, including both one-sided and two-sided methods with both first-order and second-order Taylor expansions, to calculate molecular surface electric fields to facilitate the numerical calculation of dielectric boundary forces...
March 20, 2017: Journal of Computational Chemistry
Jihène Jerbi, Michael Springborg
The aim of the present study is to provide computational insight using dispersion-corrected density-functional calculations into the reactivity properties of modified cytosine in the gas phase and in aqueous solution, whereby special emphasis is put on systems that are obtained through demethylation and methylation. Since this field is relatively incipient, our goal is to identify relationships between reactivity and stability for the modified compounds to understand their biological functionalities. Our results show that addition of a methyl, hydroxylmethyl, formyl, or carboxyl group reduces the length of the nearest hydrogen bond between the cytosine-guanine (CG) base pair and increases the length of the longest hydrogen bond of the DNA base pair...
March 20, 2017: Journal of Computational Chemistry
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