Read by QxMD icon Read

Journal of Computational Chemistry

Rebekka Haack, Stephan Schulz, Georg Jansen
Triggered by the observation of a short Bi⋯Bi distance and a BiTeBi bond angle of only 86.6° in the crystal structure of bis(diethylbismuthanyl)tellurane quantum chemical computations on interactions between neighboring Bi atoms in Te(BiR2 )2 molecules (R = H, Me, Et) and in (BiH3 )2 were undertaken. Bi⋯Bi distances atoms were found to significantly shorten upon inclusion of the d shells of the heavy metal atoms into the electron correlation treatment, and it was confirmed that interaction energies from spin component-scaled second-order Møller-Plesset theory (SCS-MP2) agree well with coupled-cluster singles and doubles theory including perturbative triples (CCSD(T))...
March 13, 2018: Journal of Computational Chemistry
Daniel J Mermelstein, Charles Lin, Gard Nelson, Rachael Kretsch, J Andrew McCammon, Ross C Walker
Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of biological processes and accelerating the design and optimization of therapeutics for numerous diseases. Computing power and theory have, however, long been insufficient to enable AFE calculations to be routinely applied in early stage drug discovery. One of the major difficulties in performing AFE calculations is the length of time required for calculations to converge to an ensemble average...
March 12, 2018: Journal of Computational Chemistry
Łukasz Szeleszczuk, Dariusz Maciej Pisklak, Monika Zielińska-Pisklak
The aim of this study was to determine whether the periodic density functional theory (DFT) calculations can be used for accurate prediction of the influence of the increased pressure on crystal structure and stability of molecular solids. To achieve this goal a series of geometry optimization and thermodynamic parameters calculations were performed for γ-glycine and δ-glycine structures at different pressure values using CASTEP program. In order to perform most accurate geometry optimization various exchange-correlation functionals defined within generalized gradient approximation (GGA): PBE, PW91, RPBE, WC, PBESOL as well as defined within local density approximation (LDA), i...
March 12, 2018: Journal of Computational Chemistry
Domenico Ninno, Giovanni Cantele, Fabio Trani
We show that the central finite difference formula for the first and the second derivative of a function can be derived, in the context of quantum mechanics, as matrix elements of the momentum and kinetic energy operators on discrete coordinate eigenkets |xn〉 defined on a uniform grid. Starting from the discretization of integrals involving canonical commutations, simple closed-form expressions of the matrix elements are obtained. A detailed analysis of the convergence toward the continuum limit with respect to both the grid spacing and the derivative approximation order is presented...
March 8, 2018: Journal of Computational Chemistry
Toshiyuki Takayanagi, Taiki Nakatomi
Many catalytic and biomolecular reactions containing transition metals involve changes in the electronic spin state. These processes are referred to as "spin-forbidden" reactions within nonrelativistic quantum mechanics framework. To understand detailed reaction mechanisms of spin-forbidden reactions, one must characterize reaction pathways on potential energy surfaces with different spin states and then identify crossing points. Here we propose a practical computational scheme, where only the lowest mixed-spin eigenstate obtained from the diagonalization of the spin-coupled Hamiltonian matrix is used in reaction path search calculations...
March 5, 2018: Journal of Computational Chemistry
Jacek Koput
The accurate ground-state potential energy surface of germanium dicarbide, GeC2 , has been determined from ab initio calculations using the coupled-cluster approach. The core-electron correlation, higher-order valence-electron correlation, and scalar relativistic effects were taken into account. The potential energy surface of GeC2 was shown to be extraordinarily flat near the T-shaped equilibrium configuration. The potential energy barrier to the linear CCGe configuration was predicted to be 1218 cm-1 . The vibration-rotation energy levels of some GeC2 isotopologues were calculated using a variational method...
March 5, 2018: Journal of Computational Chemistry
Peiwen Zhao, Yuxiang Bu
We computationally design a series of azobenzene (AB)-bridged double radicalized nucleobases, a novel kind of diradical Janus-type nucleobases, and explore their spin coupling characteristics. Calculations prove that such diradical Janus-bases not only normally match with their complementary bases, but also exhibit well-defined diradical character with photo-convertible intramolecular magnetic couplings (antiferromagnetic vs. ferromagnetic). Combination of four radical nucleobases (rG, rA, rC, rT) and photoswitch AB can yield 10 diradical Janus-bases with different magnetic characteristics in which AB functions a bridge to mediate the spin coupling between two radical bases...
March 5, 2018: Journal of Computational Chemistry
Hannes Konrad Buchholz, Matthias Stein
Accurate lattice energies of organic crystals are important i.e. for the pharmaceutical industry. Periodic DFT calculations with atom-centered Gaussian basis functions with the Turbomole program are used to calculate lattice energies for several non-covalently bound organic molecular crystals. The accuracy and convergence of results with basis set size and k-space sampling from periodic calculations is evaluated for the two reference molecules benzoic acid and naphthalene. For the X23 benchmark set of small molecular crystals accurate lattice energies are obtained using the PBE-D3 functional...
March 5, 2018: Journal of Computational Chemistry
Chih-Kai Lin
As nitrogen-doped graphene has been widely applied in optoelectronic devices and catalytic reactions, in this work we have investigated where the nitrogen atoms tend to reside in the material and how they affect the electron density and spectroscopic properties from a theoretical point of view. DFT calculations on N-doped hexagonal and rectangular graphene nanoflakes (GNFs) showed that nitrogen atoms locating on zigzag edges are obviously more stable than those on armchair edges or inside flakes, and interestingly, the N-hydrogenated pyridine moiety could be preferable to pure pyridine moiety in large models...
March 5, 2018: Journal of Computational Chemistry
Chung F Wong
Drug-binding kinetics could play important roles in determining the efficacy of drugs and has caught the attention of more drug designers. Using the dissociation of 1H-pyrrolo[2,3-b]-pyridines from the focal adhesion kinase as an example, this work finds that steered molecular dynamics simulations could help screen compounds with long-residence times. It also reveals a two-step mechanism of ligand dissociation resembling the release of ADP from protein kinase A reported earlier. A phenyl group attaching to the pyrrole prolongs residence time by creating a large activation barrier for transition from the bound to the intermediate state when it becomes exposed to the solvent...
March 2, 2018: Journal of Computational Chemistry
Leandro Zanotto, Gabriel Heerdt, Paulo C T Souza, Guido Araujo, Munir S Skaf
Since the commercial introduction of Ion Mobility coupled with Mass Spectrometry (IM-MS) devices in 2003, a large number of research laboratories have embraced the technique. IM-MS is a fairly rapid experiment used as a molecular separation tool and to obtain structural information. The interpretation of IM-MS data is still challenging and relies heavily on theoretical calculations of the molecule's collision cross section (CCS) against a buffer gas. Here, a new software (HPCCS) is presented, which performs CCS calculations using high perfomance computing techniques...
March 2, 2018: Journal of Computational Chemistry
Alvaro J Lopez, Leandro Martínez
Fluorescence spectroscopy is an important method to study protein conformational dynamics and solvation structures. Tryptophan (Trp) residues are the most important and practical intrinsic probes for protein fluorescence due to the variability of their fluorescence wavelengths: Trp residues emit in wavelengths ranging from 308 to 360 nm depending on the local molecular environment. Fluorescence involves electronic transitions, thus its computational modeling is a challenging task. We show that it is possible to predict the wavelength of emission of a Trp residue from classical molecular dynamics simulations by computing the solvent-accessible surface area or the electrostatic interaction between the indole group and the rest of the system...
February 26, 2018: Journal of Computational Chemistry
Joachim Laun, Daniel Vilela Oliveira, Thomas Bredow
Consistent basis sets of double- and triple-zeta valence with polarization quality for the fifth period have been derived for periodic quantum-chemical solid-state calculations with the crystalline-orbital program CRYSTAL. They are an extension of the pob-TZVP basis sets, and are based on the full-relativistic effective core potentials (ECPs) of the Stuttgart/Cologne group and on the def2-SVP and def2-TZVP valence basis of the Ahlrichs group. We optimized orbital exponents and contraction coefficients to supply robust and stable self-consistent field (SCF) convergence for a wide range of different compounds...
February 22, 2018: Journal of Computational Chemistry
Ruslan Shupanov, Alexander Chertovich, Pavel Kos
Nowadays, micellar polymerization is widely used in different fields of industry and research, including modern living polymerization technique. However, this process has many variables and there is no comprehensive model to describe all features. This research presents simulation methodology which describes key properties of such reactions to take a guide through a variety of their modifications. Dissipative particle dynamics is used in addition to Monte Carlo scheme to simulate initiation, propagation, and termination events...
February 21, 2018: Journal of Computational Chemistry
Ashley L Shoaf, Craig A Bayse
The identification of trigger bonds, bonds that break to initiate explosive decomposition, using computational methods could help direct the development of novel, "green" and efficient high energy density materials (HEDMs). Comparing bond densities in energetic materials to reference molecules using Wiberg bond indices (WBIs) provides a relative scale for bond activation (%ΔWBIs) to assign trigger bonds in a set of 63 nitroaromatic conventional energetic molecules. Intramolecular hydrogen bonding interactions enhance contributions of resonance structures that strengthen, or deactivate, the CNO2 trigger bonds and reduce the sensitivity of nitroaniline-based HEDMs...
February 21, 2018: Journal of Computational Chemistry
Tomonori Hayami, Kota Kasahara, Haruki Nakamura, Junichi Higo
An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent...
February 21, 2018: Journal of Computational Chemistry
Henrique S Fernandes, Maria J Ramos, Nuno M F S A Cerqueira
The notable advances obtained by computational (bio)chemistry provided its widespread use in many areas of science, in particular, in the study of reaction mechanisms. These studies involve a huge number of complex calculations, which are often carried out using the Gaussian suite of programs. The preparation of input files and the analysis of the output files are not easy tasks and often involve laborious and complex steps. Taking this into account, we developed molUP: a VMD plugin that offers a complete set of tools that enhance the preparation of QM and ONIOM (QM/MM, QM/QM, and QM/QM/MM) calculations...
February 21, 2018: Journal of Computational Chemistry
Quentin R Johnson, Richard J Lindsay, Tongye Shen
A computational method which extracts the dominant motions from an ensemble of biomolecular conformations via a correlation analysis of residue-residue contacts is presented. The algorithm first renders the structural information into contact matrices, then constructs the collective modes based on the correlated dynamics of a selected set of dynamic contacts. Associated programs can bridge the results for further visualization using graphics software. The aim of this method is to provide an analysis of conformations of biopolymers from the contact viewpoint...
February 21, 2018: Journal of Computational Chemistry
Julia Schacht, Johannes Horst Budau, Nicola Gaston, Beate Paulus
The introduction of the so called fluorolytic sol-gel synthesis in 2003 gave access to previously inaccessible aluminum oxo-fluorides, thus to nanoscopic materials and, more importantly, novel catalysts. The intermediate cluster structures synthesized and stabilized by Kemnitz and coworkers have mainly been protected by iso-propoxide groups. However, since catalytic reactions take place in a large variety of media, hydrophilic analogs of those clusters would be of interest. In this manuscript, we present a computational analysis for the fluorination reaction, which represents the second part of fluorolytic sol-gel synthesis, and a theoretical study of the synthesized Al4 F4 (μ4 -O)(μ-Oi Pr)5 [H(Oi Pr)2 ] nanostructure's conversion to its hydroxylated analog Al4 F4 (μ4 -O)(μ-OH)5 [H(OH)2 ] utilizing the nudged elastic band method...
February 21, 2018: Journal of Computational Chemistry
David D L Minh
A common strategy for speeding up molecular docking calculations is to precompute nonbonded interaction energies between a receptor molecule and a set of three-dimensional grids. The grids are then interpolated to compute energies for ligand atoms in many different binding poses. Here, I evaluate a smoothing strategy of taking a power transformation of grid point energies and inverse transformation of the result from trilinear interpolation. For molecular docking poses from 85 protein-ligand complexes, this smoothing procedure leads to significant accuracy improvements, including an approximately twofold reduction in the root mean square error at a grid spacing of 0...
February 18, 2018: 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"