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Journal of Computational Chemistry

Roberto Cammi, Bo Chen, Martin Rahm
We show that the pressure acting on atoms and molecular systems within the compression cavity of the eXtreme-Pressure Polarizable Continuum method can be expressed in terms of the electron density of the systems and of the Pauli-repulsion confining potential. The analytical expression holds for spherical cavities as well as for cavities constructed from van der Waals spheres of the constituting atoms of the molecular systems. © 2018 Wiley Periodicals, Inc.
September 22, 2018: Journal of Computational Chemistry
Manfred Speldrich, Jan van Leusen, Paul Kögerler
An update to the computational framework CONDON, introducing the ability to model and predict the magnetic and electronic properties of polynuclear exchanged-coupled actinide systems, such as homonuclear and heteronuclear coordination clusters of 5f ions, is presented. The program can intuitively fit experimental magnetic and spectroscopic data from multiple sources simultaneously, under consideration of a "full model" ligand field theory Hamiltonian. CONDON accounts simultaneously for all aspects relevant to the magnetic characteristics: interelectronic repulsion, ligand field potential, spin-orbit coupling, interatomic exchange interactions, and applied magnetic field...
September 22, 2018: Journal of Computational Chemistry
M W Li, P M Zimmerman
The computational cost of quantum chemical methods grows rapidly with increasing level of theory and basis set size. At increasing costs, higher accuracies can be reached, forcing a compromise between cost and accuracy for most molecular systems. Heats of reaction, however, are mostly determined by a subset of atoms that experience significant bonding and/or electronic changes. To exploit this fact, the Stepwise Basis Builder (SBB) algorithm selectively adds basis functions to reactive atoms and maintains small basis sets on spectator atoms...
September 21, 2018: Journal of Computational Chemistry
Min Qian, Bowen Qin, Haiyan Yuan, Wenliang Li, Jingping Zhang
The mechanism of N-Bromosuccinimide (NBS) promoted synthesis of imidazo[1,2-a]pyridine in water as well as the effective activation modes of NBS was investigated by Density Functional Theory (DFT) calculations. Two main mechanisms that differ in the reaction sequence of substrate were explored: styrene with NBS then followed by 2-aminopyridine (M1) or simultaneously with NBS and 2-aminopyridine (M2), and water-assisted M2 is the more favored one. We found that the adding sequence of 2-aminopyridine affects profoundly on the title reaction...
September 20, 2018: Journal of Computational Chemistry
Marisa E Smith, N J B Green, S M Pimblott
A computational Monte Carlo simulation approach for modeling the thermalization of low-energy electrons is presented. The simulation methods rely on, and use, experimentally based cross sections for elastic and inelastic collisions. To demonstrate the different simulation options, average numbers of interactions and the range of low-energy electrons with initial energies ranging from 1 to 20 eV are calculated for density normalized gaseous water. Experimental gas-phase cross sections for (subexcitation) electrons of energies in the range of 1-20 eV were taken from the compilation of Hayashi...
September 20, 2018: Journal of Computational Chemistry
Vindi M Jayasinghe-Arachchige, Qiaoyu Hu, Gaurav Sharma, Thomas J Paul, Marcus Lundberg, David Quinonero, Tatjana N Parac-Vogt, Rajeev Prabhakar
In this study, mechanisms of hydrolysis of all four chemically diverse cleavage sites of human serum albumin (HSA) by [Zr(OH)(PW11 O39 )]4- (ZrK) have been investigated using the hybrid two-layer QM/MM (ONIOM) method. These reactions have been proposed to occur through the following two mechanisms: internal attack (IA) and water assisted (WA). In both mechanisms, the cleavage of the peptide bond in the Cys392-Glu393 site of HSA is predicted to occur in the rate-limiting step of the mechanism. With the barrier of 27...
September 20, 2018: Journal of Computational Chemistry
Masao Hayami, Junji Seino, Yuya Nakajima, Masahiko Nakano, Yasuhiro Ikabata, Takeshi Yoshikawa, Takuro Oyama, Kenta Hiraga, So Hirata, Hiromi Nakai
The Relativistic And Quantum Electronic Theory (RAQET) program is a new software package, which is designed for large-scale two-component relativistic quantum chemical (QC) calculations. The package includes several efficient schemes and algorithms for calculations involving large molecules which contain heavy elements in accurate relativistic formalisms. These calculations can be carried out in terms of the two-component relativistic Hamiltonian, wavefunction theory, density functional theory, core potential scheme, and evaluation of electron repulsion integrals...
September 20, 2018: Journal of Computational Chemistry
Izaac Mitchell, Bálint Aradi, Alister J Page
The timescale problem-in which high barriers on the free energy surface trap molecular dynamics simulations in local energy wells-is a key limitation of current reactive MD simulations based on the density functional tight binding (DFTB) potential. Here, we report a new interface between the DFTB+ software package and the PLUMED library for performing DFTB-based free energy calculations. We demonstrate the performance of this interface for 3 archetypal rare-event chemical reactions, (i) intramolecular proton transfer in malonaldehyde, (ii) bowl inversion in corannulene, and (iii) oxygen diffusion on graphene...
September 20, 2018: Journal of Computational Chemistry
Helen Nathalia Thompson, Claudia Elizabeth Thompson, Rafael Andrade Caceres, Laurent Emmanuel Dardenne, Paulo Augusto Netz, Hubert Stassen
Prions are proteins that cause a group of invariably fatal neurodegenerative diseases, one of the most known being bovine spongiform encephalopathy. The three-dimensional structure of PrPSc , the altered isoform of the prion protein, has not been fully elucidated yet, and studies on prion conversion mechanisms must rely on hypothetical β-rich structures. Experimental and computational studies indicate that the use of low pH is capable to produce a gain of β-structure content in the otherwise unstructured N-terminal region...
September 20, 2018: Journal of Computational Chemistry
Michel Dupuis, Meghana Nallapu
We describe a new way to decompose one-electron orbitals of a molecule into atom-centered or fragment-centered orbitals by an approach that we call "maximal orbital analysis" (MOA). The MOA analysis is based on the corresponding orbital transformation (COT) that has the unique mathematical property of maximizing any sub-trace of the overlap matrix, in Hilbert metric sense, between two sets of nonorthogonal orbitals. Here, one set comprises the molecule orbitals (Hartree-Fock, Kohn-Sham, complete-active-space, or any set of orthonormal molecular orbitals), the other set comprises the basis functions associated with an atom or a group of atoms...
September 18, 2018: Journal of Computational Chemistry
James Dix, Leo Lue, Paola Carbone
Experiments of nanoconfined water between graphene sheets at high pressure suggest that it forms a square ice structure (Algara-Siller et al., Nature, 2015, 519, 443). Molecular dynamics (MD) simulations have been used to attempt to recreate this structure, but there have been discrepancies in the structure formed by the confined water depending on the simulation set-up that was employed and particularly on the choice of water model. Here, using classical molecular dynamics simulations, we have systematically investigated the effect that three different water models (SPC/E, TIP4P/2005 and TIP5P) have on the structure of water confined between two rigid graphene sheets with a 0...
September 18, 2018: Journal of Computational Chemistry
Masayoshi Nakano, Takanori Nagami, Takayoshi Tonami, Kenji Okada, Soichi Ito, Ryohei Kishi, Yasutaka Kitagawa, Takashi Kubo
The singlet fission (SF) dynamics of pentacene linear aggregate models are investigated using the quantum master equation method by focusing on the Frenkel excitonic (FE) coupling effects on the SF rate and double triplet (TT) yield as well as on their aggregate size dependences. It is found that for the dimer model, unrealistically large FE couplings are needed to provide significant effects on the SF dynamics, while for the larger aggregate models a realistic FE coupling causes significant variations in the SF dynamics: as increasing the aggregate size, the SF rate rapidly increases, attains the maximum at 8-mer (~3 times enhancement as compared to the non-FE-coupling case) and then decreases, approaching a stationary value after 12-mer, although the stationary TT yield at 20-mer remains slightly smaller than that in the non-FE-coupling case...
September 18, 2018: Journal of Computational Chemistry
Taras Dauzhenka, Petras J Kundrotas, Ilya A Vakser
Protein-protein docking procedures typically perform the global scan of the proteins relative positions, followed by the local refinement of the putative matches. Because of the size of the search space, the global scan is usually implemented as rigid-body search, using computationally inexpensive intermolecular energy approximations. An adequate refinement has to take into account structural flexibility. Since the refinement performs conformational search of the interacting proteins, it is extremely computationally challenging, given the enormous amount of the internal degrees of freedom...
September 18, 2018: Journal of Computational Chemistry
Bun Chan, Yukio Kawashima, Kimihiko Hirao
In the present study, we have reparametrized the HISS exchange functional. The new "reHISS" exchange provides a balance between short- and mid-range Hartree-Fock exchange (HFX) and a large total HFX coverage, with a fast convergence to zero HFX in the long range. The five parameters in this functional (according to equations 3 and 4 in the main text) are cSR = 0.15, cMR = 2.5279, cLR = 0, ωSR = 0.27, and ωLR = 0.2192. The combination of reHISS exchange with a reparametrized B97c-type correlation functional (Chan et al...
September 18, 2018: Journal of Computational Chemistry
Van Tan Tran, Quoc Tri Tran
The geometrical structures, electron leading configurations, and relative energies of the low-lying states of VGe n -/0 (n = 5-7) clusters have been investigated with density functional theory and CASSCF/CASPT2 method. The pure GGA BP86 functional gave almost the same relative energy order for the low-lying states as the CASPT2 method. At the BP86 and CASPT2 levels, the ground states of VGe n -/0 (n = 5-7) clusters were proposed to be the 1 A1 and 2 A1 of A-VGe5 -/0 , 3 A″ and 2 A″, 2 A' (2 E2 ) of A-VGe6 -/0 , and 1 A' and 2 A' of A-VGe7 -/0 isomers...
September 12, 2018: Journal of Computational Chemistry
Jalal Z A Laloo, Nandini Savoo, Nassirah Laloo, Lydia Rhyman, Ponnadurai Ramasami
The distortion/interaction-activation strain model (D/I-ASM), a fragment analysis method, is applied to study the structure-reactivity relationship in reactions. The application of D/I-ASM involves the generation of input files for points along a reaction profile, submission of input files to a quantum software package, processing of parameters from the resulting output files and generation of graphical plots. The ExcelAutomat tool (Laloo et al., J. Comput. Aided Mol. Des. 2017, 31, 667) provides a framework and library in Visual Basic for Application programming language to process such files...
August 24, 2018: Journal of Computational Chemistry
László von Szentpály
The chemical potential is by definition constant in molecules, and electronic charge is in principle equilibrated by bonding. Does electronegativity offer the best scale to unify these principles? According to conceptual density functional theory (c-DFT), the electronegativity equalization (ENE) and chemical potential equalization (CPE) principles seem rigorous and identical. However, the operational formulations of CPE and ENE fail to validate this claim, and frequently dramatic deviations from equalization are reported...
August 24, 2018: Journal of Computational Chemistry
Takafumi Shiraogawa, G Candel, Ryoichi Fukuda, Ilaria Ciofini, Carlo Adamo, Akimitsu Okamoto, Masahiro Ehara
Recently, exciton-controlled hybridization-sensitive fluorescent oligonucleotide (ECHO) probe, which shows strong emission in the near-infrared region via hybridization to the target DNA and/or RNA strand, has been developed. In this work, photophysical properties of the chromophores of these probes and the fluorescent mechanism have been investigated by the SAC-CI and TD-DFT calculations. Three fluorescent cyanine chromophores whose excitation is challenging for TD-DFT methods, have been examined regarding the photo-absorption and emission spectra...
August 24, 2018: Journal of Computational Chemistry
Dirkie Myburgh, Stuart von Berg, Jan Dillen
Four energetic criteria, all rooted in the partitioning of a molecule into atomic basins based on the properties of the electron density, are compared and correlated with the presence of a bond path between two nonbonded atoms in a series of sterically crowded derivatives of the same tetracyclododecane molecule. It was found that there is no correlation between the selected energetic criteria and the existence of a bond path between the congested atoms, nor with the existence of Ehrenfest force, virial, or Coulomb potential paths between those atoms...
August 24, 2018: Journal of Computational Chemistry
Kyohei Kawashima, Takehiro Sato, Masamichi Ogasawara, Ken Kamikawa, Seiji Mori
Recently, planar-chiral phosphine-olefin ligands based on (η6 -arene)chromium(0) and (η5 -cyclopentadienyl)manganese(I), which are known as first- and second-generation, respectively, have been developed. These ligands were employed for Rh-catalyzed asymmetric 1,4-addition to enones. First-generation ligands involve high enantioselectivity for cyclic enones (>98% ee). Second-generation ligands involve high enantioselectivity for not only cyclic enones but also for acyclic enones (>98% ee). In this study, we have performed DFT calculations to investigate the origin of enantioselectivity...
August 24, 2018: Journal of Computational Chemistry
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