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Journal of Computational Chemistry

Dario Ghersi, Abhishek Parakh, Mihaly Mezei
Four pseudorandom number generators were compared with a physical, quantum-based random number generator using the NIST suite of statistical tests, which only the quantum-based random number generator could successfully pass. We then measured the effect of the five random number generators on various calculated properties in different Markov-chain Monte Carlo simulations. Two types of systems were tested: conformational sampling of a small molecule in aqueous solution and liquid methanol under constant temperature and pressure...
September 18, 2017: Journal of Computational Chemistry
Filip Šebesta, Mateusz Z Brela, Silvia Diaz, Sebastian Miranda, Jane S Murray, Soledad Gutiérrez-Oliva, Alejandro Toro-Labbé, Artur Michalak, Jaroslav V Burda
This study involves the intramolecular proton transfer (PT) process on a thymine nucleobase between N3 and O2 atoms. We explore a mechanism for the PT assisted by hexacoordinated divalent metals cations, namely Mg(2+) , Zn(2+) , and Hg(2+) . Our results point out that this reaction corresponds to a two-stage process. The first involves the PT from one of the aqua ligands toward O2. The implications of this stage are the formation of a hydroxo anion bound to the metal center and a positively charged thymine...
September 18, 2017: Journal of Computational Chemistry
Tymofii Yu Nikolaienko, Eugene S Kryachko, Grygoriy A Dolgonos
Twenty years have already been passed since the endohedral fullerene's void ceaselessly attracts attention of both, experimentalists and theoreticians, computational chemists and physicists in particular, who direct their efforts on computer simulations of encapsulating atoms and molecules into fullerene void and on unraveling the arising bonding patterns. We review recent developments on the endohedral He2 @C60 fullerene, on its experimental observation and on related computational works. The two latter are the main concerns in the present work: on the one hand, there experimentally exists the He dimer embedded into C60 void...
September 6, 2017: Journal of Computational Chemistry
Peter Politzer, Jane S Murray
σ-Holes and π-holes are regions of molecules with electronic densities lower than their surroundings. There are often positive electrostatic potentials associated with them. Through these potentials, the molecule can interact attractively with negative sites, such as lone pairs, π electrons, and anions. Such noncovalent interactions, "σ-hole bonding" and "π-hole bonding," are increasingly recognized as being important in a number of different areas. In this article, we discuss and compare the natures and characteristics of σ-holes and π-holes, and factors that influence the strengths and locations of the resulting electrostatic potentials...
September 6, 2017: Journal of Computational Chemistry
Jeremy P Coe, Nuno M S Almeida, Martin J Paterson
We investigate if a range of challenging spin systems can be described sufficiently well using Monte Carlo configuration interaction (MCCI) and the density matrix renormalization group (DMRG) in a way that heads toward a more "black box" approach. Experimental results and other computational methods are used for comparison. The gap between the lowest doublet and quartet state of methylidyne (CH) is first considered. We then look at a range of first-row transition metal monocarbonyls: MCO when M is titanium, vanadium, chromium, or manganese...
September 2, 2017: Journal of Computational Chemistry
Andreas J Achazi, Dirk Andrae, Hans-Ulrich Reissig, Beate Paulus
A detailed model for the reaction mechanism of the samarium diiodide (SmI2 ) mediated reductive coupling of N-oxoalkyl-substituted methyl indole-3-carboxylates is developed in this study by determining the Gibbs energies for the intermediates of possible reaction pathways. The Gibbs energies at ambient temperature are calculated with dispersion corrected density functional theory in combination with implicit (D-COSMO-RS) and explicit solvent description. Temperature dependent ro-vibrational contributions are considered with the help of statistical thermodynamics...
September 2, 2017: Journal of Computational Chemistry
Yasuhiro Imada, Haruki Nakamura, Yu Takano
Heme is involved in various biochemical roles in hemoproteins. In the present study, the effect of heme distortion on the redox potential was systematically investigated with density functional calculations. We focused on the ruffled and saddled distortions of heme, which correspond to the two lowest-frequency normal modes. Our computations demonstrated that the ruffled distortion tended to reduce the redox potential of heme and that the transition of the electronic configuration occurred from (dxz , dyz )(3) (dxy )(2) to (dxz , dyz )(4) (dxy )(1) ...
September 2, 2017: Journal of Computational Chemistry
Philipp Pracht, Christoph Alexander Bauer, Stefan Grimme
We present an automated quantum chemical protocol for the determination of preferred protonation sites in organic and organometallic molecules containing up to a few hundred atoms. It is based on the Foster-Boys orbital localization method, whereby we automatically identify lone pairs and π orbitals as possible protonation sites. The method becomes efficient in conjunction with the robust and fast GFN-xTB semiempirical method proposed recently (Grimme et al., J. Chem. Theory Comput. 2017, 13, 1989). The protonated isomers that are found within a few seconds to minutes of computational wall-time on a standard desktop computer are then energetically refined using density functional theory (DFT), where we use a high-level double-hybrid reference method to benchmark GFN-xTB and low-cost DFT approaches...
August 31, 2017: Journal of Computational Chemistry
Ryuhei Harada, Yasuteru Shigeta
Parallel cascade selection molecular dynamics (PaCS-MD) is an enhanced conformational sampling method for searching structural transition pathways from a given reactant to a product. Recently, a temperature-aided PaCS-MD (Vinod et al., Eur. Biophys. J. 2016, 45, 463) has been proposed as its extension, in which the temperatures were introduced as additional parameters in conformational resampling, whereas the temperature is fixed in the original PaCS-MD. In the present study, temperature-shuffled PaCS-MD is proposed as a further extension of temperature-aided PaCS-MD in which the temperatures are shuffled among different replicas at the beginning of each cycle of conformational resampling...
August 31, 2017: Journal of Computational Chemistry
Sławomir J Grabowski
The N⋅⋅⋅B triel bonds in complexes of boron trihalides, BX3 (X = F, Cl, Br, and I), with species acting as Lewis bases through the nitrogen center, NH3 , N2 , and HCN, are analyzed theoretically (MP2/aug-cc-pVTZ calculations). It is confirmed that stronger Lewis acid properties of the boron center are observed for the BCl3 moiety than for the BF3 one in complexes with the strong Lewis base (NH3 ); while the opposite order is observed for complexes with the weak Lewis base (N2 ). The BX3 NCH complexes (for X = Cl, Br, and I) are characterized by two tautomeric forms and by two corresponding N⋅⋅⋅B distances, the shorter one possesses characteristics of the covalent bond...
August 31, 2017: Journal of Computational Chemistry
Matthew J L Mills, Kenneth L Sale, Blake A Simmons, Paul L A Popelier
Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter-free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available...
August 31, 2017: Journal of Computational Chemistry
Rahul Chakraborty, Samik Bose, Debashree Ghosh
Ionization of nucleobases is affected by their biological environment, which includes both the effect of adjacent nucleotides as well as the presence of water around it. Guanine and its nucleotide have the lowest ionization potentials among the various DNA bases. Therefore, the threshold of ionization is dependent on that of guanine and its characterization is crucial to the prediction of interaction of light with DNA. We investigate the effect of solvation on the vertical ionization energies (VIEs) of guanine and its nucleotide...
August 30, 2017: Journal of Computational Chemistry
Francesco Caruso, Sarah Paumier, Miriam Rossi
Embelin is a phytochemical component of tropical plants that have a long history of being used in ethnic pharmacology in various parts of the world, including Ayurdvedic and Chinese medicinal texts. Many modern studies confirm its promise as a medicinal compound. The X-ray crystal structure determination of embelin shows a remarkably ordered alkyl chain and particularly strong pi-pi interactions for a nonaromatic system. The molecule has a torsion angle of 67° between the ring and the alkyl chain of the molecule and differs markedly from that seen when embelin is embedded in the plasminogen activator inhibitor-1 (PAI-1) binding site (almost planar-with about 10° torsion angle)...
August 28, 2017: Journal of Computational Chemistry
Suliman Adam, Michaela Knapp-Mohammady, Jun Yi, Ana-Nicoleta Bondar
Photosystem II is a complex protein-cofactor machinery that splits water molecules into molecular oxygen, protons, and electrons. All-atom molecular dynamics simulations have the potential to contribute to our general understanding of how photosystem II works. To perform reliable all-atom simulations, we need accurate force field parameters for the cofactor molecules. We present here CHARMM bonded and non-bonded parameters for the iron-containing cofactors of photosystem II that include a six-coordinated heme moiety coordinated by two histidine groups, and a non-heme iron complex coordinated by bicarbonate and four histidines...
August 28, 2017: Journal of Computational Chemistry
Peter I Maxwell, Paul L A Popelier
Accurate description of the intrinsic preferences of amino acids is important to consider when developing a biomolecular force field. In this study, we use a modern energy partitioning approach called Interacting Quantum Atoms to inspect the cause of the φ and ψ torsional preferences of three dipeptides (Gly, Val, and Ile). Repeating energy trends at each of the molecular, functional group, and atomic levels are observed across both (1) the three amino acids and (2) the φ/ψ scans in Ramachandran plots. At the molecular level, it is surprisingly electrostatic destabilization that causes the high-energy regions in the Ramachandran plot, not molecular steric hindrance (related to the intra-atomic energy)...
August 25, 2017: Journal of Computational Chemistry
Kuo Hao Lee, Jianhan Chen
Recasting temperature replica exchange (T-RE) as a special case of Gibbs sampling has led to a simple and efficient scheme for enhanced mixing (Chodera and Shirts, J. Chem. Phys., 2011, 135, 194110). To critically examine if T-RE with independence sampling (T-REis) improves conformational sampling, we performed T-RE and T-REis simulations of ordered and disordered proteins using coarse-grained and atomistic models. The results demonstrate that T-REis effectively increase the replica mobility in temperatures space with minimal computational overhead, especially for folded proteins...
August 25, 2017: Journal of Computational Chemistry
Jayangika N Dahanayake, Chandana Kasireddy, Jonathan M Ellis, Derek Hildebrandt, Olivia A Hull, Joseph P Karnes, Dylan Morlan, Katie R Mitchell-Koch
The ability of electronic structure methods (11 density functionals, HF, and MP2 calculations; two basis sets and two solvation models) to accurately calculate the (19) F chemical shifts of 31 structures of fluorinated amino acids and analogues with known experimental (19) F NMR spectra has been evaluated. For this task, BHandHLYP, ωB97X, and Hartree-Fock with scaling factors (provided within) are most accurate. Additionally, the accuracy of methods to calculate relative changes in fluorine shielding across 23 sets of structural variants, such as zwitterionic amino acids versus side chains only, was also determined...
August 21, 2017: Journal of Computational Chemistry
Robert A Evarestov, Andrei V Bandura, Vitaly V Porsev, Alexey V Kovalenko
Hybrid density functional theory calculations are performed for the first time on the phonon dispersion and thermodynamic properties of WS2 -based single-wall nanotubes. Symmetry analysis is presented for phonon modes in nanotubes using the standard (crystallographic) factorization for line groups. Symmetry and the number of infra-red and Raman active modes in achiral WS2 nanotubes are given for armchair and zigzag chiralities. It is demonstrated that a number of infrared and Raman active modes is independent on the nanotube diameter...
August 21, 2017: Journal of Computational Chemistry
Ma Del Refugio Cuevas-Flores, Marco Antonio Garcia-Revilla, Massimiliano Bartolomei
Cisplatin (CP) has been widely used as an anticancer drug for more than 30 years despite severe side effects due to its low bioavailability and poor specificity. For this reason, it is paramount to study and design novel nanomaterials to be used as vectors capable to effectively deliver the drug to the biological target. The CP square-planar geometry, together with its low water solubility, suggests that it could be possibly easily adsorbed on 2D graphene nanostructures through the interaction with the related highly conjugated π-electron system...
August 21, 2017: Journal of Computational Chemistry
Sean McConnell, Johannes Kästner
Canonical instanton theory is known to overestimate the rate constant close to a system-dependent crossover temperature and is inapplicable above that temperature. We compare the accuracy of the reaction rate constants calculated using recent semi-classical rate expressions to those from canonical instanton theory. We show that rate constants calculated purely from solving the stability matrix for the action in degrees of freedom orthogonal to the instanton path is not applicable at arbitrarily low temperatures and use two methods to overcome this...
August 19, 2017: Journal of Computational Chemistry
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