Read by QxMD icon Read

Journal of Computational Chemistry

Maja Gruden, Ljubica Andjeklović, Akkarapattiakal Kuriappan Jissy, Stepan Stepanović, Matija Zlatar, Qiang Cui, Marcus Elstner
Density Functional Tight Binding (DFTB) models are two to three orders of magnitude faster than ab initio and Density Functional Theory (DFT) methods and therefore are particularly attractive in applications to large molecules and condensed phase systems. To establish the applicability of DFTB models to general chemical reactions, we conduct benchmark calculations for barrier heights and reaction energetics of organic molecules using existing databases and several new ones compiled in this study. Structures for the transition states and stable species have been fully optimized at the DFTB level, making it possible to characterize the reliability of DFTB models in a more thorough fashion compared to conducting single point energy calculations as done in previous benchmark studies...
July 24, 2017: Journal of Computational Chemistry
Jing-Shuang Dang, Wei-Wei Wang, Jia-Jia Zheng, Shigeru Nagase, Xiang Zhao
Although the existence of Stone-Wales (5-7) defect at graphene edge has been clarified experimentally, theoretical study on the formation mechanism is still imperfect. In particular, the regioselectivity of multistep reactions at edge (self-reconstruction and growth with foreign carbon feedstock) is essential to understand the kinetic behavior of reactive boundaries but investigations are still lacking. Herein, by using finite-sized models, multistep reconstructions and carbon dimer additions of a bared zigzag edge are introduced using density functional theory calculations...
July 18, 2017: Journal of Computational Chemistry
Ryosuke Ishizuka, Nobuyuki Matubayasi
A self-consistent scheme combining the molecular dynamics (MD) simulation and density functional theory (DFT) was recently proposed to incorporate the effects of the charge transfer and polarization of ions into non-poralizable force fields of ionic liquids for improved description of energetics and dynamics. The purpose of the present work is to analyze the detailed setups of the MD/DFT scheme by focusing on how the basis set, exchange-correlation (XC) functional, charge-fitting method or force field for the intramolecular and Lennard-Jones interactions affects the MD/DFT results of 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl) imide ( [C1mim][NTf2]) and 1-ethyl-3-methylimidazolium glycinate ( [C2mim][Gly])...
July 18, 2017: Journal of Computational Chemistry
Changjun Chen
Complete free energy surface in the collective variable space provides important information of the reaction mechanisms of the molecules. But, sufficient sampling in the collective variable space is not easy. The space expands quickly with the number of the collective variables. To solve the problem, many methods utilize artificial biasing potentials to flatten out the original free energy surface of the molecule in the simulation. Their performances are sensitive to the definitions of the biasing potentials...
July 18, 2017: Journal of Computational Chemistry
Haiyan Yuan, Pin Xiao, Yiying Zheng, Jingping Zhang
Silver-mediated hydroazidation of unactivated alkynes has been developed as a new method for the synthesis of vinyl azides. Density functional theory calculations toward this reaction reveal that terminal alkynes with TMS-N3 participated hydroazidation proceed through HN3 formation, deprotonation and silver acetylides formation, nucleophilic addition, and protonation of terminal carbon by AgHCO3 . It is also found that water molecules and activation modes of Ag (I) have a significant influence on the title reaction mechanism...
July 18, 2017: Journal of Computational Chemistry
Andreas Lücke, Uwe Gerstmann, Thomas D Kühne, Wolf G Schmidt
A numerically efficient yet highly accurate implementation of the crystal orbital Hamilton population (COHP) scheme for plane-wave calculations is presented. It is based on the projector-augmented wave (PAW) formalism in combination with norm-conserving pseudopotentials and allows to extract chemical interactions between atoms from band-structure calculations even for large and complex systems. The potential of the present COHP implementation is demonstrated by an in-depth analysis of the intensively investigated metal-insulator transition in atomic-scale indium wires self-assembled on the Si(111) surface...
July 18, 2017: Journal of Computational Chemistry
Bun Chan, Yukio Kawashima, Kimihiko Hirao
In the present study, we have explored several prospects for the further development of screened-exchange density functional theory (SX-DFT) procedures. Using the performance of HSE06 as our measure, we find that the use of alternative correlation functionals (as oppose to PBEc in HSE06) also yields adequate results for a diverse set of thermochemical properties. We have further examined the performance of new SX-DFT procedures (termed HSEB-type methods) that comprise the HSEx exchange and a (near-optimal) reparametrized B97c (cOS,0  = cSS,0  = 1, cOS,1  = -1...
July 18, 2017: Journal of Computational Chemistry
Chigusa Kobayashi, Jaewoon Jung, Yasuhiro Matsunaga, Takaharu Mori, Tadashi Ando, Koichi Tamura, Motoshi Kamiya, Yuji Sugita
GENeralized-Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessible time scale by adopting highly parallelized schemes and enhanced conformational sampling algorithms. In this new version, GENESIS 1.1, new functions and advanced algorithms have been added. The all-atom and coarse-grained potential energy functions used in AMBER and GROMACS packages now become available in addition to CHARMM energy functions...
July 18, 2017: Journal of Computational Chemistry
Manash Protim Borpuzari, Rahul Kar
System-dependent nonempirical tuning of range-separated functional provides a way to minimize the delocalization error of the system. However, existing nonempirical tuning method requires the computation of several ΔSCF calculations to determine the optimal μ value. In this article, we have defined a scheme to evaluate the optimal μ value with single self-consistent field calculation. Our method is based on the evaluation of the spherically symmetric average Electron localization function (ELF) region. According to this scheme, the radius of the spherically symmetric average ELF region gives is a measure of the distance at which the long-range part of the range-separated functional becomes dominant...
July 18, 2017: Journal of Computational Chemistry
Silvia Díaz, Mateusz Z Brela, Soledad Gutiérrez-Oliva, Alejandro Toro-Labbé, Artur Michalak
The partitioning of the reaction force based on the extended-transition-state natural orbital for chemical valence (ETS-NOCV) scheme has been proposed. This approach, together with the analysis of reaction electronic flux (REF), has been applied in a description of the changes in the electronic structure along the IRC pathway for the HCN/CNH isomerization reaction assisted by water. Two complementary ways of partitioning the system into molecular fragments have been considered ("reactant perspective" and "product perspective")...
July 18, 2017: Journal of Computational Chemistry
Stefano Corni
We have considered the system investigated by Steinmann et al. by means of the image charge model originally proposed in Iori and Corni, J. Comput. Chem. 2008, 29, 1656. Qualitatively correct results are obtained, that compare favorably with the relevant analytical benchmarks. We show that the effect of the asymmetry of the rod model can be controlled, when needed, as originally suggested, that is, by shorter rods. This strategy does not increase neither the complexity of the model nor its computational cost...
July 11, 2017: Journal of Computational Chemistry
Shanshan Cao, Haiyan Yuan, Yang Yang, Mang Wang, Xiaoying Zhang, Jingping Zhang
The mechanism of the HBr-catalyzed Friedel-Crafts-type reaction between β-naphthol and HCHO was investigated by DFT to improve this reaction. The HBr-H2 O co-catalyzed the preferential pathway undergoes the concerted nucleophilic addition and hydrogen shift, stepwise followed by H2 O elimination and the CC bond formation. The origin of the high catalytic activity of HBr is ascribed to CH···Br(-) and OH···Br(-) interactions, which suggest that the active species is Br(-) . Moreover, water molecules efficiently assist in improving the activity of Br(-) ...
July 11, 2017: Journal of Computational Chemistry
Lakshmanan Sandhiya, Hendrik Zipse
OO bond homolysis in hydrogen peroxide (H2 O2 ) has been studied using theoretical methods of four conceptually different types: hybrid DFT (B3LYP, M06-2X), double-hybrid DFT (B2-PLYP), coupled-cluster (CCSD(T)), and multiconfigurational (CASPT2). In addition, the effects of basis set size have also been analyzed. For all of these methods, the OO bond homolysis in hydrogen peroxide has been found to proceed through hydrogen bonded radical pair complexes. Reaction barriers for collapse of the radical pairs to hydrogen peroxide are minute, leading to an overall very flat potential energy surface...
July 11, 2017: Journal of Computational Chemistry
Amir Karton, Nitai Sylvetsky, Jan M L Martin
Atomization reactions are among the most challenging tests for electronic structure methods. We use the first-principles Weizmann-4 (W4) computational thermochemistry protocol to generate the W4-17 dataset of 200 total atomization energies (TAEs) with 3σ confidence intervals of 1 kJ mol(-1) . W4-17 is an extension of the earlier W4-11 dataset; it includes first- and second-row molecules and radicals with up to eight non-hydrogen atoms. These cover a broad spectrum of bonding situations and multireference character, and as such are an excellent benchmark for the parameterization and validation of highly accurate ab initio methods (e...
July 4, 2017: Journal of Computational Chemistry
I-Hsiang Lin, Yu-Huan Lu, Hsin-Tsung Chen
The O2 activation and CO oxidation on nitrogen-doped C59 N fullerene are investigated using first-principles calculations. The calculations indicate that the C59 N fullerene is able to activate O2 molecules resulting in the formation of superoxide species ( O2-) both kinetically and thermodynamically. The active superoxide can further react with CO to form CO2 via the Eley-Rideal mechanism by passing a stepwise reaction barrier of only 0.20 eV. Ab initio molecular dynamics (AIMD) simulation is carried out to evidence the feasibility of the Eley-Rideal mechanism...
July 4, 2017: Journal of Computational Chemistry
Stephan N Steinmann, Paul Fleurat-Lessard, Andreas W Götz, Carine Michel, Rodrigo Ferreira de Morais, Philippe Sautet
We re-investigate the image charge model of Iori and Corni (Iori and Corni, J. Comput. Chem. 2008, 29, 1656). We find that a simple symmetrization of their model allows to obtain quantitatively correct results for the electrostatic interaction of a water molecule with a metallic surface. This symmetrization reduces the magnitude of the electrostatic interaction to less than 10% of the total interaction energy. © 2017 Wiley Periodicals, Inc.
July 4, 2017: Journal of Computational Chemistry
Inaki Morao, Dmitri G Fedorov, Roger Robinson, Michelle Southey, Andrea Townsend-Nicholson, Mike J Bodkin, Alexander Heifetz
The reliable and precise evaluation of receptor-ligand interactions and pair-interaction energy is an essential element of rational drug design. While quantum mechanical (QM) methods have been a promising means by which to achieve this, traditional QM is not applicable for large biological systems due to its high computational cost. Here, the fragment molecular orbital (FMO) method has been used to accelerate QM calculations, and by combining FMO with the density-functional tight-binding (DFTB) method we are able to decrease computational cost 1000 times, achieving results in seconds, instead of hours...
July 4, 2017: Journal of Computational Chemistry
Per E M Siegbahn, Xichen Li
Density functional theory calculations have been made to investigate the stability of the energetics for the oxygen evolving complex of photosystem II. Results published elsewhere have given excellent agreement with experiments for both energetics and structures, where many of the experimental results were obtained several years after the calculations were done. The computational results were obtained after a careful extension from small models to a size of about 200 atoms, where stability of the results was demonstrated...
June 30, 2017: Journal of Computational Chemistry
Antonio Bauzá, Saikat Kumar Seth, Antonio Frontera
Using ab initio calculations, we analyze the interplay between π-hole interactions involving the nitro group of 1,4-dinitrobenzene and lone pair···π (lp···π), C-H···π or metal(M)···π noncovalent interactions. Moreover, we have also used 1,4-phenylenebis(phosphine dioxide) for comparison purposes. Interesting cooperativity effects are found when π-hole (F···N,P) and lp···π/C-H···π/M···π interactions coexist in the same supramolecular assembly. These effects are studied theoretically in terms of energetic and geometric features of the complexes, which are computed by ab initio methods (RI-MP2/def2-TZVP)...
June 30, 2017: Journal of Computational Chemistry
Sadanandam Namsani, Bhasker Gahtori, Sushil Auluck, Jayant K Singh
An interaction potential model has been developed, for the first time, for β-Cu2 Se using the ab initio derived data. The structure and elastic constants of β-Cu2 Se using the derived force-field are within a few percent of DFT derived structure and elastic constants and reported experimental structure. The derived force-field also shows remarkable ability to reproduce temperature dependent behavior of the specific heat and thermal expansion coefficient. The thermal structure evolution of the β-Cu2 Se is studied by performing the molecular dynamic simulations using the derived force-field...
June 30, 2017: Journal of Computational Chemistry
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"