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Journal of Computational Chemistry

Axel Wuttke, Ricardo A Mata
The interpretation of chemical properties/phenomena can often be aided through the use of imagery. The mapping of molecular electrostatic potentials is a prime example, serving as a guideline in the design of novel compounds or understanding transition state stabilization effects. It is today a common tool for theoreticians and experimentalists alike. With the emergence of concepts such as dispersion energy donors, and the overall importance of dispersion in chemical systems, representations targeting such a class of interactions are warranted...
October 20, 2016: Journal of Computational Chemistry
Asanga Bandara, Afra Panahi, George A Pantelopulos, John E Straub
For 40 years, the existence and possible functional importance of cholesterol dimer formation has been discussed. Due to challenges associated with structural studies of membrane lipids, there has as yet been no direct experimental verification of the existence and relevance of the cholesterol dimer. Building on recent advances in lipid force fields for molecular simulation, in this work the structure and stability of the cholesterol dimer is characterized in POPC bilayers in absence and presence of sphingomyelin...
October 20, 2016: Journal of Computational Chemistry
Noor Asidah Mohamed, Richard T Bradshaw, Jonathan W Essex
The effects of electronic polarization in biomolecular interactions will differ depending on the local dielectric constant of the environment, such as in solvent, DNA, proteins, and membranes. Here the performance of the AMOEBA polarizable force field is evaluated under nonaqueous conditions by calculating the solvation free energies of small molecules in four common organic solvents. Results are compared with experimental data and equivalent simulations performed with the GAFF pairwise-additive force field...
October 19, 2016: Journal of Computational Chemistry
Sadegh Salehzadeh, Farahnaz Maleki
In this work, a new equation consist of A⋅⋅⋅B, B⋅⋅⋅C, A⋅⋅⋅BC, and AB⋅⋅⋅C interactions is proposed for calculating the total interaction energy of noncyclic ABC triads. New equations are also proposed for calculating the changes in values of A⋅⋅⋅B and B⋅⋅⋅C interactions on the formation of triad from the corresponding dyads. The advantages of equations proposed here in comparison with many-body interaction energy approach are discussed. All proposed equations were tested in F3 MLi⋅⋅⋅NCH⋅⋅⋅HLH and F3 MLi⋅⋅⋅HLH⋅⋅⋅HCN (M = C, Si; L = Be, Mg) as well as H3 N⋅⋅⋅XY⋅⋅⋅HF (X, Y = F, Cl, Br) noncyclic A⋅⋅⋅B⋅⋅⋅C triads...
October 18, 2016: Journal of Computational Chemistry
Shinji Iida, Tadaaki Mashimo, Takashi Kurosawa, Hironobu Hojo, Hiroya Muta, Yuji Goto, Yoshifumi Fukunishi, Haruki Nakamura, Junichi Higo
The C-terminal domain (CTD) of tumor suppressor protein p53 is an intrinsically disordered region that binds to various partner proteins, where lysine of CTD is acetylated/nonacetylated and histidine neutralized/non-neutralized. Because of the flexibility of the unbound CTD, a free-energy landscape (FEL) is a useful quantity for determining its statistical properties. We conducted enhanced conformational sampling of CTD in the unbound state via virtual system coupled multicanonical molecular dynamics, in which the lysine was acetylated or nonacetylated and histidine was charged or neutralized...
October 13, 2016: Journal of Computational Chemistry
Ignacy Cukrowski, Filip Sagan, Mariusz Paweł Mitoraj
In the present account, the real space fragment attributed molecular system energy change (FAMSEC) approach, interacting quantum atoms energy decomposition scheme as well as molecular orbitals based the extended transition state scheme coupled with natural orbitals for chemical valence (ETS-NOCV) have been, for the first time, successfully used to delineate factors of importance for stability of the 2-butene conformers (cis-eq, cis-TS, trans-eq, trans-TS). Our results demonstrate that atoms of the controversial H-H contact in cis-eq (i) are involved in attractive interaction dominated by the exchange-correlation term, (ii) are weekly stabilized, (iii) show trends in several descriptors found in other typical H-bonds, and (iv) are part of most stabilized CH-HC fragment (loc-FAMSEC = -3...
October 12, 2016: Journal of Computational Chemistry
Sergei F Vyboishchikov
We report correlation energies, electron densities, and exchange-correlation potentials obtained from configuration interaction and density functional calculations on spherically confined He, Be, Be(2+) , and Ne atoms. The variation of the correlation energy with the confinement radius Rc is relatively small for the He, Be(2+) , and Ne systems. Curiously, the Lee-Yang-Parr (LYP) functional works well for weak confinements but fails completely for small Rc . However, in the neutral beryllium atom the CI correlation energy increases markedly with decreasing Rc ...
October 12, 2016: Journal of Computational Chemistry
Duc D Nguyen, Guo-Wei Wei
This article explores the impact of surface area, volume, curvature, and Lennard-Jones (LJ) potential on solvation free energy predictions. Rigidity surfaces are utilized to generate robust analytical expressions for maximum, minimum, mean, and Gaussian curvatures of solvent-solute interfaces, and define a generalized Poisson-Boltzmann (GPB) equation with a smooth dielectric profile. Extensive correlation analysis is performed to examine the linear dependence of surface area, surface enclosed volume, maximum curvature, minimum curvature, mean curvature, and Gaussian curvature for solvation modeling...
October 8, 2016: Journal of Computational Chemistry
Hiroaki Nishizawa, Hisashi Okumura
A quantum mechanical/molecular mechanical (QM/MM) approach based on the density-functional tight-binding (DFTB) theory is a useful tool for analyzing chemical reaction systems in detail. In this study, an efficient QM/MM method is developed by the combination of the DFTB/MM and particle mesh Ewald (PME) methods. Because the Fock matrix, which is required in the DFTB calculation, is analytically obtained by the PME method, the Coulomb energy is accurately and rapidly computed. For assessing the performance of this method, DFTB/MM calculations and molecular dynamics simulation are conducted for a system consisting of two amyloid-β(1-16) peptides and a zinc ion in explicit water under periodic boundary conditions...
October 8, 2016: Journal of Computational Chemistry
Youhan Lee, Roberta Poloni, Jihan Kim
We propose a novel biased Widom insertion method that can efficiently compute the Henry coefficient, KH , of gas molecules inside porous materials exhibiting strong adsorption sites by employing purely DFT calculations. This is achieved by partitioning the simulation volume into strongly and weakly adsorbing regions and selectively biasing the Widom insertion moves into the former region. We show that only few thousands of single point energy calculations are necessary to achieve accurate statistics compared to many hundreds of thousands or millions of such calculations in conventional random insertions...
October 8, 2016: Journal of Computational Chemistry
Jaewoon Jung, Yuji Sugita
Parallelization of molecular dynamics (MD) simulation is essential for investigating conformational dynamics of large biological systems, such as ribosomes, viruses, and multiple proteins in cellular environments. To improve efficiency in the parallel computation, we have to reduce the amount of data transfer between processors by introducing domain decomposition schemes. Also, it is important to optimize the computational balance between real-space non-bonded interactions and reciprocal-space interactions for long-range electrostatic interactions...
October 6, 2016: Journal of Computational Chemistry
Huan Guo, Alejandro Morales-Bayuelo, Tianlv Xu, Roya Momen, Lingling Wang, Ping Yang, Steven R Kirk, Samantha Jenkins
Currently the theories to explain and predict the classification of the electronic reorganization due to the torquoselectivity of a ring-opening reaction cannot accommodate the directional character of the reaction pathway; the torquoselectivity is a type of stereoselectivity and therefore is dependent on the pathway. Therefore, in this investigation we introduced new measures from quantum theory of atoms in molecules and the stress tensor to clearly distinguish and quantify the transition states of the inward (TSIC) and outward (TSOC) conrotations of competitive ring-opening reactions of 3-(trifluoromethyl)cyclobut-1-ene and 1-cyano-1-methylcyclobutene...
October 6, 2016: Journal of Computational Chemistry
Son Tung Ngo, Huynh Minh Hung, Minh Tho Nguyen
The fast pulling ligand (FPL) out of binding cavity using non-equilibrium molecular dynamics (MD) simulations was demonstrated to be a rapid, accurate and low CPU demand method for the determination of the relative binding affinities of a large number of HIV-1 protease (PR) inhibitors. In this approach, the ligand is pulled out of the binding cavity of the protein using external harmonic forces, and the work of pulling force corresponds to the relative binding affinity of HIV-1 PR inhibitor. The correlation coefficient between the pulling work and the experimental binding free energy of R=-0...
October 6, 2016: Journal of Computational Chemistry
Shintaro Maekawa, Krzysztof Moorthi, Yasuteru Shigeta
Refractive indices of metal- and metalloid-containing compounds are systematically evaluated using the Lorentz-Lorenz equation with polarizabilities obtained via density functional theory (DFT). Among exchange-correlation functionals studied, the long-range corrected (LC) fuctionals yield the lowest errors for the polarizabilities of gaseous compounds and refractive indices of liquids. The LC-DFT predicts very well the wavelength dependence of refractive indices. A scheme for computing Abbe numbers of organometallic and organometaloid compounds is proposed and a refractive index - Abbe number plot for 80 compounds is constructed...
October 6, 2016: Journal of Computational Chemistry
Hiromi Nakai, Takeshi Yoshikawa, Yutaro Nonaka
This study presents an efficient algorithm to search for the poles of dynamic polarizability to obtain excited states of large systems with nonlocal excitation nature. The present algorithm adopts a homogeneous search with a constant frequency interval and a bisection search to achieve high accuracy. Furthermore, the subtraction process of the information about the detected poles from the total dynamic polarizability is used to extract the undetected pole contributions. Numerical assessments confirmed the accuracy and efficiency of the present algorithm in obtaining the excitation energies and oscillator strengths of all dipole-allowed excited states...
October 5, 2016: Journal of Computational Chemistry
Nohad Gresh, David Perahia, Benoit de Courcy, Johanna Foret, Céline Roux, Lea El-Khoury, Jean-Philip Piquemal, Laurent Salmon
Zn-metalloproteins are a major class of targets for drug design. They constitute a demanding testing ground for polarizable molecular mechanics/dynamics aimed at extending the realm of quantum chemistry (QC) to very long-duration molecular dynamics (MD). The reliability of such procedures needs to be demonstrated upon comparing the relative stabilities of competing candidate complexes of inhibitors with the recognition site stabilized in the course of MD. This could be necessary when no information is available regarding the experimental structure of the inhibitor-protein complex...
October 4, 2016: Journal of Computational Chemistry
Tianlv Xu, James Farrell, Yuning Xu, Roya Momen, Steven R Kirk, Samantha Jenkins, David J Wales
Using the quantum theory of atoms in molecules a near complete combined directed spanning quantum topology phase diagram (QTPD) was constructed from the nine (H2 O)5 reaction-pathways and five unique Poincaré-Hopf solutions that were found after an extensive search of the MP2 potential energy surface. Two new energy minima that were predicted from earlier work are found and include the first (H2 O)5 conformer with a 3-DQT quantum topology. The stress tensor Poincaré-Hopf relation indicated a preference for 2-DQT (H2 O)5 topologies as well as the presence of coupling between shared-shell OH BCPs to the hydrogen-bond BCPs that share an H NCP...
October 3, 2016: Journal of Computational Chemistry
Matteo Signorile, Alessandro Damin, Francesca Bonino, Valentina Crocellà, Carlo Lamberti, Silvia Bordiga
Ti-zeolites are interesting materials because of their key role in partial oxidation reactions, as well as under a fundamental point of view being regarded as single site catalysts. Both experimental and computational approaches have been widely applied to the characterization of their active sites, reaching a level of knowledge unmatchable by most other important catalysts. However, several questions are still open, being a proper energetic simulation of the adsorption process of simple molecules, fitting with the experimental outcomes, still missing...
November 15, 2016: Journal of Computational Chemistry
Carlos Silva Lopez, Olalla Nieto Faza, Frank De Proft, Antonios Kolocouris
The interactions of axial substituents in monosubstituted cyclohexane rings are studied in this work using an array of different computational techniques. Additionally, the anomalous axial preference for some bulky substituents is related to stabilizing dispersion interactions. We find that the C-Hax ···Yax contacts for various substituents with distances ranging from 2 to ∼5 Å may include attractive dispersion forces that can affect the conformational equilibrium; these forces co-exist with Pauli repulsive forces effected by Yax group due to van der Waals sphere penetration...
November 15, 2016: Journal of Computational Chemistry
Hong Liu, You-Liang Zhu, Zhong-Yuan Lu, Florian Müller-Plathe
We propose a kinetic chain growth algorithm for coarse-grained (CG) simulations in this work. By defining the reaction probability, it delivers a description of consecutive polymerization process. This algorithm is validated by modeling the process of individual styrene monomers polymerizing into polystyrene chains, which is proved to correctly reproduce the properties of polymers in experiments. By bridging the relationship between the generic chain growth process in CG simulations and the chemical details, the impediment to reaction can be reflected...
November 15, 2016: Journal of Computational Chemistry
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