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Journal of Computational Chemistry

Duc D Nguyen, Bao Wang, Guo-Wei Wei
Poisson-Boltzmann (PB) model is one of the most popular implicit solvent models in biophysical modeling and computation. The ability of providing accurate and reliable PB estimation of electrostatic solvation free energy, ΔGel, and binding free energy, ΔΔGel, is important to computational biophysics and biochemistry. In this work, we investigate the grid dependence of our PB solver (MIBPB) with solvent excluded surfaces for estimating both electrostatic solvation free energies and electrostatic binding free energies...
February 16, 2017: Journal of Computational Chemistry
Renato Pereira Orenha, Régis Tadeu Santiago, Roberto Luiz Andrade Haiduke, Sérgio Emanuel Galembeck
Two treatments of relativistic effects, namely effective core potentials (ECP) and all-electron scalar relativistic effects (DKH2), are used to obtain geometries and chemical reaction energies for a series of ruthenium complexes in B3LYP/def2-TZVP calculations. Specifically, the reaction energies of reduction (A-F), isomerization (G-I), and Cl(-) negative trans influence in relation to NH3 (J-L) are considered. The ECP and DKH2 approaches provided geometric parameters close to experimental data and the same ordering for energy changes of reactions A-L...
February 16, 2017: Journal of Computational Chemistry
Greg Starek, J Alfredo Freites, Simon Bernèche, Douglas J Tobias
We used targeted molecular dynamics, informed by experimentally determined inter-atomic distances defining the pore region of open and closed states of the KvAP voltage-gated potassium channel, to generate a gating pathway of the pore domain in the absence of the voltage-sensing domains. We then performed umbrella sampling simulations along this pathway to calculate a potential of mean force that describes the free energy landscape connecting the closed and open conformations of the pore domain. The resulting energetic landscape displays three minima, corresponding to stable open, closed, and intermediate conformations with roughly similar stabilities...
February 16, 2017: Journal of Computational Chemistry
Anton Raskovalov
The molecular dynamics is one of the most widely used methods for the simulation of the properties corresponding to ionic motion. Unfortunately, classical molecular dynamics cannot be applied for electron transfer simulation. Suggested modification of the molecular dynamics allows performing the electron transfer from one particle to another during simulation runtime. All additional data structure and the corresponding algorithms are presented in this article. The method can be applied to the systems with pair Van der Waals and Coulomb interactions...
February 16, 2017: Journal of Computational Chemistry
Evelio Francisco, Daniel Menéndez Crespo, Aurora Costales, Ángel Martín Pendás
Interatomic exchange-correlation energies correspond to the covalent energetic contributions to an interatomic interaction in real space theories of the chemical bond, but their widespread use is severely limited due to their computationally intensive character. In the same way as the multipolar (mp) expansion is customary used in biomolecular modeling to approximate the classical Coulomb interaction between two charge densities ρA(r) and ρB(r), we examine in this work the mp approach to approximate the interatomic exchange-correlation (xc) energies of the Interacting Quantum Atoms method...
February 16, 2017: Journal of Computational Chemistry
Yaowarat Surakhot, Viktor Laszlo, Chirawat Chitpakdee, Vinich Promarak, Taweesak Sudyoadsuk, Nawee Kungwan, Tim Kowalczyk, Stephan Irle, Siriporn Jungsuttiwong
The search for greater efficiency in organic dye-sensitized solar cells (DSCs) and in their perovskite cousins is greatly aided by a more complete understanding of the spectral and morphological properties of the photoactive layer. This investigation resolves a discrepancy in the observed photoconversion efficiency (PCE) of two closely related DSCs based on carbazole-containing D-π-A organic sensitizers. Detailed theoretical characterization of the absorption spectra, dye adsorption on TiO2 , and electronic couplings for charge separation and recombination permit a systematic determination of the origin of the difference in PCE...
February 13, 2017: Journal of Computational Chemistry
Ryuhei Harada, Yu Takano, Yasuteru Shigeta
The folding processes of mini-proteins (FSD-EY/FBPWW28 domain) were computationally investigated by an enhanced conformational sampling method. Through the analyses of trajectories, these mini-proteins had multiple folding pathways different from a simple two-state folding, and the multiple folding processes were initiated by partial formations of secondary structures. These findings can be used to understand the folding of large proteins, that is, which secondary structures are partially folded in the early process, and how the remaining parts are sequentially folded...
February 13, 2017: Journal of Computational Chemistry
Álvaro Vega-Vega, Carmen Barrientos, Antonio Largo
A theoretical study of monoboronyls of different metals has been carried out. We have chosen Mg as representative of s-block elements, Al for the p-block, and Group 11 metals (Cu, Ag, and Au) for the d-block. Different behaviors are observed: bonding through the oxygen atom is preferred in the case of Al, for all Group 11 monoboronyls bonding through the boron atom prevails and both interactions give rise to almost isoenergetic compounds in the case of Mg. Predictions for the spectroscopic parameters relevant for rotational and vibrational spectroscopy of the different competitive species are provided...
February 12, 2017: Journal of Computational Chemistry
Hossein Mohammadiarani, Harish Vashisth
Insulin plays a crucial physiological role in glucose control by initiating a number of signaling events on binding and activating its cell surface receptor. Insulin mimics have, therefore, become promising agents for treating diabetes and to probe the mechanism of interaction of insulin with its receptor. Specifically, many insulin-mimetic peptide sequences have been discovered and found to selectively function as agonists and antagonists, but their structures and the mechanistic details of their interactions with the receptor remain challenging to characterize...
February 12, 2017: Journal of Computational Chemistry
Kun Yuan, Rui-Sheng Zhao, Jia-Jia Zheng, Hong Zheng, Shigeru Nagase, Sheng-Dun Zhao, Yan-Zhi Liu, Xiang Zhao
Noncovalent interactions involving aromatic rings, such as π···π stacking, CH···π are very essential for supramolecular carbon nanostructures. Graphite is a typical homogenous carbon matter based on π···π stacking of graphene sheets. Even in systems not involving aromatic groups, the stability of diamondoid dimer and layer-layer graphane dimer originates from C - H···H - C noncovalent interaction. In this article, the structures and properties of novel heterogeneous layer-layer carbon-nanostructures involving π···H-C-C-H···π···H-C-C-H stacking based on [n]-graphane and [n]-graphene and their derivatives are theoretically investigated for n = 16-54 using dispersion corrected density functional theory B3LYP-D3 method...
February 6, 2017: Journal of Computational Chemistry
Jingyuan Gao, Wenliang Li, Jingping Zhang
To explore the adsorption and separation properties of CO2 in a novel material consisting of a series of polyoxometalates (POMs) impregnated within supramolecular porous catenane (shorted as SPC), grand canonical Monte Carlo (GCMC) simulations and ab initio calculations were used. GCMC simulations showed this impregnation can enhance CO2 /CH4 (or CO2 /N2 ) selectivity almost 30 times compared to the bare SPC due to the strong interaction of CO2 with the nPOMs@SPC structures. And, the loading of CO2 inhibits the adsorption of CH4 (or N2 ) as CO2 occupying the preferred adsorption sites...
February 6, 2017: Journal of Computational Chemistry
Francesc Viñes, Oriol Lamiel-García, Kyoung Chul Ko, Jin Yong Lee, Francesc Illas
The effect of the amount of Hartree-Fock mixing parameter (α) and of the screening parameter (w) defining the range separated HSE type hybrid functional is systematically studied for a series of seven metal oxides: TiO2 , ZrO2 , CuO2 , ZnO, MgO, SnO2 , and SrTiO3 . First, reliable band gap values were determined by comparing the optimal α reproducing the experiment with the inverse of the experimental dielectric constant. Then, the effect of the w in the HSE functional on the calculated band gap was explored in detail...
February 4, 2017: Journal of Computational Chemistry
Baofeng Zhang, Denise Kilburg, Peter Eastman, Vijay S Pande, Emilio Gallicchio
We present an algorithm to efficiently compute accurate volumes and surface areas of macromolecules on graphical processing unit (GPU) devices using an analytic model which represents atomic volumes by continuous Gaussian densities. The volume of the molecule is expressed by means of the inclusion-exclusion formula, which is based on the summation of overlap integrals among multiple atomic densities. The surface area of the molecule is obtained by differentiation of the molecular volume with respect to atomic radii...
February 4, 2017: Journal of Computational Chemistry
Bercem Dutagaci, Maryam Sayadi, Michael Feig
The heterogeneous dielectric generalized Born (HDGB) implicit membrane formalism is extended by the addition of a van der Waals dispersion term to better describe the nonpolar components of the free energy of solvation. The new model, termed HDGBvdW, improves the energy estimates in the hydrophobic interior of the membrane, where polar and charged species are rarely found and nonpolar interactions become significant. The implicit van der Waals term for the membrane environment extends the model from Gallicchio et al...
February 4, 2017: Journal of Computational Chemistry
Sarah Witzke, Nanna Holmgaard List, Jógvan Magnus Haugaard Olsen, Casper Steinmann, Michael Petersen, Maarten T P Beerepoot, Jacob Kongsted
A set of average atom-centered charges and polarizabilities has been developed for three types of phospholipids for use in polarizable embedding calculations. The lipids investigated are 1,2-dimyristoyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, and 1-palmitoyl-2-oleoyl-sn-glycerol-3-phospho-L-serine given their common use both in experimental and computational studies. The charges, and to a lesser extent the polarizabilities, are found to depend strongly on the molecular conformation of the lipids...
February 3, 2017: Journal of Computational Chemistry
Sirous Yourdkhani, Mirosław Jabłoński
The physical nature of charge-inverted hydrogen bonds in H3 XH ⋯YH3 (X = Si, Ge; Y = Al, Ga) dimer systems is studied by means of the SAPT(DFT)-based decomposition of interaction energies and supermolecular interaction energies based on MP2, SCS-MP2, MP2C, and CCSD(T) methods utilizing dimer-centered aug-cc-pCVnZ (n = D, T, Q) basis sets as well as an extrapolation to the complete basis set limit. It is revealed that charge-inverted hydrogen bonds are inductive in nature, although dispersion is also important...
January 31, 2017: Journal of Computational Chemistry
Leon A Sakkal, Kyle Z Rajkowski, Roger S Armen
Following insights from recent crystal structures of the muscarinic acetylcholine receptor, binding modes of Positive Allosteric Modulators (PAMs) were predicted under the assumption that PAMs should bind to the extracellular surface of the active state. A series of well-characterized PAMs for adenosine (A1 R, A2A R, A3 R) and muscarinic acetylcholine (M1 R, M5 R) receptors were modeled using both rigid and flexible receptor CHARMM-based molecular docking. Studies of adenosine receptors investigated the molecular basis of the probe-dependence of PAM activity by modeling in complex with specific agonist radioligands...
January 28, 2017: Journal of Computational Chemistry
Chao Wang, Yizhong Yuan, Xiaohui Tian
DFT method can severely overestimate the response properties for π-conjugation systems. The range-separated exchange and recently developed optimal IP-tuning process are evaluated on the prediction of static second hyperpolarizabilities of streptocyanines of increasing molecular length. The finite field results have shown that the exact exchange at midium and long distance can relieve only a part of the overshooting but still beyond satisfaction. The exact exchange at short distance has the oppsite effects showing the failure of converntional hGGA...
January 28, 2017: Journal of Computational Chemistry
Mark A Olson, Michael S Lee, In-Chul Yeh
This work presents replica-exchange molecular dynamics simulations of inserting a 16-residue Ebola virus fusion peptide into a membrane bilayer. A computational approach is applied for modeling the peptide at the explicit all-atom level and the membrane-aqueous bilayer by a generalized Born continuum model with a smoothed switching function (GBSW). We provide an assessment of the model calculations in terms of three metrics: (1) the ability to reproduce the NMR structure of the peptide determined in the presence of SDS micelles and comparable structural data on other fusion peptides; (2) determination of the effects of the mutation Trp-8 to Ala and sequence discrimination of the homologous Marburg virus; and (3) calculation of potentials of mean force for estimating the partitioning free energy and their comparison to predictions from the Wimley-White interfacial hydrophobicity scale...
January 28, 2017: Journal of Computational Chemistry
Mina Jafari, Paul M Zimmerman
The computational challenge of fast and reliable transition state and reaction path optimization requires new methodological strategies to maintain low cost, high accuracy, and systematic searching capabilities. The growing string method using internal coordinates has proven to be highly effective for the study of molecular, gas phase reactions, but difficulties in choosing a suitable coordinate system for periodic systems has prevented its use for surface chemistry. New developments are therefore needed, and presented herein, to handle surface reactions which include atoms with large coordination numbers that cannot be treated using standard internal coordinates...
January 28, 2017: Journal of Computational Chemistry
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