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computational chemistry

Ctirad Červinka, Michal Fulem
A computational methodology for calculation of sublimation enthalpies of molecular crystals from first principles is developed and validated by comparison to critically evaluated literature experimental data. Temperature dependent sublimation enthalpies for a set of selected 22 molecular crystals in their low-temperature phases are calculated. The computational methodology consists in several building blocks based on high level electronic structure methods of quantum chemistry and statistical thermodynamics...
April 24, 2017: Journal of Chemical Theory and Computation
Vincent Pohl, Gunter Hermann, Jean Christophe Tremblay
The aim of the present contribution is to provide a framework for analyzing and visualizing the correlated many-electron dynamics of molecular systems, where an explicitly time-dependent electronic wave packet is represented as a linear combination of N-electron wave functions. The central quantity of interest is the electronic flux density, which contains all information about the transient electronic density, the associated phase, and their temporal evolution. It is computed from the associated one-electron operator by reducing the multideterminantal, many-electron wave packet using the Slater-Condon rules...
April 24, 2017: Journal of Computational Chemistry
Enis Nadia Md Yusof, Mohamed I M Tahir, Thahira B S A Ravoof, Sang Loon Tan, Edward R T Tiekink
The title di-thio-carbazate ester (I), C18H18N2S2 [systematic name: (E)-4-methyl-benzyl 2-[(E)-3-phenyl-allyl-idene]hydrazinecarbodi-thio-ate, comprises an almost planar central CN2S2 residue [r.m.s. deviation = 0.0131 Å]. The methyl-ene(tolyl-4) group forms a dihedral angle of 72.25 (4)° with the best plane through the remaining non-hydrogen atoms [r.m.s. deviation = 0.0586 Å] so the mol-ecule approximates mirror symmetry with the 4-tolyl group bis-ected by the plane. The configuration about both double bonds in the N-N=C-C=C chain is E; the chain has an all trans conformation...
April 1, 2017: Acta Crystallographica. Section E, Crystallographic Communications
Kevin M Tangen, Roxanne Leval, Ankit I Mehta, Andreas A Linninger
BACKGROUND: Intrathecal drug delivery is an attractive option to circumvent the blood-brain barrier for pain management through its increased efficacy of pain relief, reduction in adverse side effects, and cost-effectiveness. Unfortunately, there are limited guidelines for physicians to choose infusion or drug pump settings to administer therapeutic doses to specific regions of the spine or the brain. Although empiric trialing of intrathecal drugs is critical to determine the sustained side effects, currently there is no inexpensive in vitro method to guide the selection of spinal drug delivery parameters...
May 2017: Anesthesia and Analgesia
Shaobin Tang, Weihua Wu, Liangxian Liu, Zexing Cao, Xiaoxuan Wei, Zhongfang Chen
Graphene oxides (GOs) or reduced GOs (rGOs) may offer extraordinary potential for chemical functionalization of graphene due to their unique electronic and structural properties. By means of dispersion-corrected density functional theory computations, we systematically investigated the Diels-Alder (DA) chemistry of GOs. Our computations showed that the dual nature of GOs as both a diene and a dienophile is stronger than that of pristine graphene. Interestingly, the interior bonds of a graphene surface modified by oxygen-containing groups could be functionalized by maleic anhydride (MA) and 2,3-dimethoxybutadiene (DMBD) through cycloaddition reactions, and the cycloaddition products of MA and DMBD are more favorable than the non-covalent complexes between these reagents and the GO surface...
April 20, 2017: Physical Chemistry Chemical Physics: PCCP
Helen Moylan, Joseph McDouall
The theory and computation of EPR parameters from first principles has seen a great deal of development over the past two decades. In particular, various techniques for the computation of the electronic g tensor have been implemented in many quantum chemistry packages. These methods have been successfully applied to paramagnetic organic species and transition metal systems. The situation is less well-understood and established in the case of actinide containing molecules and there is a dearth of experimental data available for validation of computations...
April 19, 2017: Chemistry: a European Journal
Xiao-Yun Zhao, Qiang Chen, Hai-Ru Li, Yue-Wen Mu, Hai-Gang Lu, Si-Dian Li
The recently observed cage-like borospherenes D2d B40(-/0) and C3/C2 B39(-) have attracted considerable attention in chemistry and materials science. Based on extensive global minimum searches and first-principles theory calculations, we present herein the possibility of cage-like Cs B39(+) (1) and Cs B39(+) (2) which possess five hexagonal and heptagonal faces and one filled hexagon and follow the bonding pattern of σ + π double delocalization with 12 delocalized π bonds over a σ-skeleton, adding two new members to the borospherene family...
April 19, 2017: Physical Chemistry Chemical Physics: PCCP
Upinder Singh Bhalla
Sequences of events are ubiquitous in sensory, motor, and cognitive function. Key computational operations, including pattern recognition, event prediction, and plasticity, involve neural discrimination of spatio-temporal sequences. Here we show that synaptically-driven reaction-diffusion pathways on dendrites can perform sequence discrimination on behaviorally relevant time-scales. We used abstract signaling models to show that selectivity arises when inputs at successive locations are aligned with, and amplified by, propagating chemical waves triggered by previous inputs...
April 19, 2017: ELife
Zewen Xiao, Ke-Zhao Du, Weiwei Meng, Jianbo Wang, David B Mitzi, Yanfa Yan
Recently, there has been substantial interest in developing double-B-cation halide perovskites, which hold the potential to overcome the toxicity and instability issues inherent within emerging lead halide-based solar absorber materials. Among all double perovskites investigated, In(I)-based Cs2InBiCl6 and Cs2InSbCl6 have been proposed as promising thin-film photovoltaic absorber candidates, with computational examination predicting suitable materials properties, including direct bandgap and small effective masses for both electrons and holes...
April 24, 2017: Journal of the American Chemical Society
Thiago Cardoso Vale, Flávia Cristina de Lima Pinto, José Luiz Pedroso, Marília Alves Dos Reis, Ilza Rosa Batista, Rodrigo Affonseca Bressan, René Leandro Magalhães Rivero, Renato Adam Mendonça, Orlando G Barsottini
History A 43-year-old right-handed man presented with a history of progressive mild left-sided weakness and slowness of movements. Symptoms began 4 years earlier, and the patient noticed a progressive decline in his daily routine due to gait difficulties in the past year. There was no history of head trauma, surgery, drug therapy, smoking, or alcohol abuse, nor was there any relevant family history. Examination revealed normal cognition (29 of 30 points on the Mini-Mental State Examination and 27 of 30 points on the Montreal Cognitive Assessment) and normal cerebellar, sensory, cranial nerve, and autonomic function...
May 2017: Radiology
Felipe T Lee-Montiel, Subin M George, Albert H Gough, Anup D Sharma, Juanfang Wu, Richard DeBiasio, Lawrence A Vernetti, D Lansing Taylor
This article describes our next generation human Liver Acinus MicroPhysiology System (LAMPS). The key demonstration of this study was that Zone 1 and Zone 3 microenvironments can be established by controlling the oxygen tension in individual devices over the range of ca. 3 to 13%. The oxygen tension was computationally modeled using input on the microfluidic device dimensions, numbers of cells, oxygen consumption rates of hepatocytes, the diffusion coefficients of oxygen in different materials and the flow rate of media in the MicroPhysiology System (MPS)...
January 1, 2017: Experimental Biology and Medicine
Davide Presti, Alfonso Pedone, Daniele Licari, Vincenzo Barone
We present the implementation of the solid state (SoS)NMR module for the simulation of several 1D and 2D NMR spectra of all the elements in the periodic table in the virtual multifrequency spectrometer (VMS). This module is fully integrated with the graphical user interface of VMS (VMS-Draw) [Licari et al., J. Comput. Chem. 36, 2015, 321-334], a freeware tool which allows a user-friendly handling of structures and analyses of advanced spectroscopical properties of chemical compounds-from model systems to real-world applications...
April 20, 2017: Journal of Chemical Theory and Computation
Xue-Rui You, Lin-Yan Feng, Rui Li, Hua-Jin Zhai
We report a computational study on the structures and bonding of a charged molecular alloy D 2h [Pd2As14](4-) (1), as well as a model D 2h [Au2Sb14](4-) (2) cluster. Our effort makes use of an array of quantum chemistry tools: canonical molecular orbital analysis, adaptive natural density partitioning, natural bond orbital analysis, orbital composition analysis, and nucleus independent chemical shift calculations. Both clusters consist of two X7 (X = As, Sb) cages, which are interconnected via a M2 (M = Pd, Au) dumbbell, featuring two distorted square-planar MX4 units...
April 11, 2017: Scientific Reports
Hitesh Patel, Tobias Brinkjost, Oliver Koch
Motivation: Molecular docking is one of the successful approaches in structure based discovery and development of bioactive molecules in chemical biology and medicinal chemistry. Due to the huge amount of computational time that is still required, docking is often the last step in a virtual screening approach. Such screenings are set as workflows spanned over many steps, each aiming at different filtering task. These workflows can be automatized in large parts using python based toolkits except for docking using the docking software GOLD...
April 7, 2017: Bioinformatics
Kihyun Shin, Liang Zhang, Hyesung An, Hyunwoo Ha, Mi Yoo, Hyuck Mo Lee, Graeme Henkelman, Hyun You Kim
We use density functional theory calculations of Pt@Cu core@shell nanoparticles (NPs) to design bifunctional poison-free CO oxidation catalysts. By calculating the adsorption chemistry under CO oxidation conditions, we find that the Pt@Cu NPs will be active for CO oxidation with resistance to CO-poisoning. The CO oxidation pathway at the Pt-Cu interface is determined on the Pt NP covered with a full- and partial-shell of Cu. The exposed portion of the Pt core preferentially binds CO and the Cu shell binds O2, supplying oxygen for the reaction...
April 20, 2017: Nanoscale
Valentina Santolini, Marcin Miklitz, Enrico Berardo, Kim E Jelfs
We define a nomenclature for the classification of porous organic cage molecules, enumerating the 20 most probable topologies, 12 of which have been synthetically realised to date. We then discuss the computational challenges encountered when trying to predict the most likely topological outcomes from dynamic covalent chemistry (DCC) reactions of organic building blocks. This allows us to explore the extent to which comparing the internal energies of possible reaction outcomes is successful in predicting the topology for a series of 10 different building block combinations...
April 20, 2017: Nanoscale
Lucia Lisi, Michela Pizzoferrato, Fabiola Teresa Miscioscia, Alessandra Topai, Pierluigi Navarra
The neuro-pathogenic mechanism(s) underlying HIV-associated neurocognitive disorders are mostly unknown. HIV-infected macrophages and microglial cells play a crucial role and the metabolic fate of L-arginine may be highly relevant for microglia activation. In this context Arginase (ARG), which uses L-arginine as substrate, can be on the same time a target and source of oxidative stress and inflammation. In the present study, we investigated whether Integrase Strand Transfer Inhibitors (INSTIs) share with the other antiretroviral drugs the ability to inhibit ARG activity...
April 11, 2017: Journal of Neurochemistry
Yi-Yun Timothy Tsao, Karen L Wooley
A grand challenge that crosses synthetic chemistry and biology is the scalable production of functional analogues of biomacromolecules. We have focused our attention on the use of deoxynucleoside building blocks bearing non-natural bases to develop a synthetic methodology that allows for the construction of high molecular weight deoxynucleotide polymers. Our six-membered cyclic phosphoester ring-opening polymerization strategy is demonstrated, herein, by an initial preparation of novel polyphosphoesters, comprised of butenyl-functionalized deoxyribonucleoside repeat units, connected via 3',5'-backbone linkages...
April 10, 2017: Journal of the American Chemical Society
T J Penfold
Methods using a swarm of Gaussian basis functions to represent the nuclear wavefunction are a very appealing way to solve the time-dependent Schrödinger equation (TDSE) as they avoid the conventional scaling bottleneck of grid-based methods and provide a grid-free trajectory representation of the dynamics understudy. When coupled with direct (on-the-fly) dynamics, these methods offer the ability to simulate quantum dynamics of larger systems in full nuclear configuration space and avoid the requirement of a priori fitting of a potential energy surface...
April 10, 2017: Physical Chemistry Chemical Physics: PCCP
Hao Qiu, Erkai He
Metals are ubiquitous and normally co-occur as mixtures in soil, but there remains much to do regarding the development of appropriate models which incorporate mixture interactions and bioavailability to estimate their phytotoxicity and phytoaccumulation. Here, we developed a probability-based electrostatic toxicity model (ETM) and a Langmuir-type electrostatic uptake model (EUM) to predict and normalize toxicity and uptake of zinc-copper mixtures in Hordeum vulgare L. in different soils. For model development, the electrical potential (ψ0) and metal ion activities ({M(2+)}0) at the cell-membrane surface was computed based on plant physiological properties and soil solution chemistry...
April 5, 2017: Environmental Pollution
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