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computational chemistry

Ganna Gryn'ova, Leesa M Smith, Michelle L Coote
In the present work we use accurate quantum chemistry to evaluate several known and novel nitroxides bearing acid-base groups as pH-switchable control agents for room temperature NMP. Based on G3(MP2,CC)(+)//M06-2X/6-31+G(d) calculations with UAKS-CPCM/M06-2X/6-31+G(d) solvation corrections, a number of novel nitroxides are predicted to be suitable for controlled polymerization of bulk styrene at room temperature when deprotonated (i.e. negatively charged), while remaining inert when neutral. These include an α-ethyl analogue of 3-carboxy-PROXYL and novel derivatives of 2,2,5-trimethyl-4-phenyl-3-azahexane-3-nitroxide (TIPNO) that have been modified to include acidic groups...
August 16, 2017: Physical Chemistry Chemical Physics: PCCP
Kasper P Kepp
Inspection of heme protein structures in the protein data bank reveals four isomers of heme characterized by different relative orientations of the vinyl side chains; remarkably, all these have been reported in multiple protein structures. Density functional theory computations explain this as due to similar energy of the isomers but with a sizable (25 kJ mol(-1)) barrier to interconversion arising from restricted rotation around the conjugated bonds. The four isomers, EE, EZ, ZE, and ZZ, were then investigated as 4-coordinate hemes, as 5-coordinate deoxyhemes, in 6-coordinate O2-adducts of globins and as compound I intermediates typical of heme peroxidases...
August 14, 2017: Physical Chemistry Chemical Physics: PCCP
Peng Dai, Jonathan K Williams, Chi Zhang, Matthew Welborn, James J Shepherd, Tianyu Zhu, Troy Van Voorhis, Mei Hong, Bradley L Pentelute
Natural enzymes use local environments to tune the reactivity of amino acid side chains. In searching for small peptides with similar properties, we discovered a four-residue π-clamp motif (Phe-Cys-Pro-Phe) for regio- and chemoselective arylation of cysteine in ribosomally produced proteins. Here we report mutational, computational, and structural findings directed toward elucidating the molecular factors that drive π-clamp-mediated arylation. We show the significance of a trans conformation prolyl amide bond for the π-clamp reactivity...
August 11, 2017: Scientific Reports
Jingxiang Zhao, Zhongfang Chen
The production of ammonia (NH3) from molecular dinitrogen (N2) under mild conditions is one of the most attractive and challenging process in chemistry. Here by means of density functional theory (DFT) computations, we systemically investigated the potential of single transition metal atoms (Sc to Zn, Mo, Ru, Rh, Pd, and Ag) supported on the experimentally available defective boron nitride (TM-BN) monolayer with a boron monovacancy, as a N2 fixation electrocatalyst. Our computations revealed that the single Mo atom supported by defective BN nanosheet exhibits the highest catalytic activity for N2 fixation at room temperature through an enzymatic mechanism with a quite low overpotential of 0...
August 11, 2017: Journal of the American Chemical Society
Qi Yu, Pan Wang, Fangfang Ma, Hong-Bin Xie, Ning He, Jingwen Chen
Quantum chemistry calculations and kinetic modeling were performed to investigate the nitrosation mechanism and kinetics of diamine piperazine (PZ), an alternative solvent for widely used monoethanolamine in postcombustion CO2 capture (PCCC), by two typical nitrosating agents, NO2(-) and N2O3, in the presence of CO2. Various PZ species and nitrosating agents formed by the reactions of PZ, NO2(-), and N2O3 with CO2 were considered. The results indicated that the reactions of PZ species having NH group with N2O3 contribute the most to the formation of nitrosamines in the absorber unit of PCCC and follow a novel three-step nitrosation mechanism, which is initiated by the formation of a charge-transfer complex...
August 4, 2017: Chemosphere
Max Pillong, Jan A Hiss, Petra Schneider, Yen-Chu Lin, Gernot Posselt, Bernhard Pfeiffer, Markus Blatter, Alex T Müller, Simon Bachler, Claudia S Neuhaus, Petra S Dittrich, Karl-Heinz Altmann, Silja Wessler, Gisbert Schneider
Specific interactions of peptides with lipid membranes are essential for cellular communication and constitute a central aspect of the innate host defense against pathogens. A computational method for generating innovative membrane-pore-forming peptides inspired by natural templates is presented. Peptide representation in terms of sequence- and topology-dependent hydrophobic moments is introduced. This design concept proves to be appropriate for the de novo generation of first-in-class membrane-active peptides with the anticipated mode of action...
August 11, 2017: Small
Stefan Clemens Meier, Albina Holz, Alexei Schmidt, Daniel Kratzert, Daniel Himmel, Ingo Krossing
The facile synthesis of a pentacarbonyl cobalt(I) salt without the need for a super acid as solvent is presented. This readily on a multigram scale accessible [Co(CO)₅]+[Al(ORF)₄]- {RF = C(CF₃)₃} salt undergoes substitution reactions with arenes yielding the hitherto unknown class of two-legged cobalt piano stool complexes [(arene)Co(CO)₂]+ with four different arene ligands. Such a substitution chemistry would have been impossible in super acid solution, as the arenes used would have been oxidized and / or protonated...
August 10, 2017: Chemistry: a European Journal
Miten Jain, John R Tyson, Matthew Loose, Camilla L C Ip, David A Eccles, Justin O'Grady, Sunir Malla, Richard M Leggett, Ola Wallerman, Hans J Jansen, Vadim Zalunin, Ewan Birney, Bonnie L Brown, Terrance P Snutch, Hugh E Olsen
BACKGROUND: Long-read sequencing is rapidly evolving and reshaping the suite of opportunities for genomic analysis. For the MinION in particular, as both the platform and chemistry develop, the user community requires reference data to set performance expectations and maximally exploit third-generation sequencing. We performed an analysis of MinION data derived from whole genome sequencing of Escherichiacoli K-12 using the R9.0 chemistry, comparing the results with the older R7.3 chemistry...
2017: F1000Research
Jakob Petersen, Eli Pollak
Attosecond ionization experiments have not resolved the question: ``What is the tunneling time?''. Different definitions of tunneling time lead to different results.Secondly, a zero tunneling time for a material particle suggests that the non-relativistic theory includes speeds greater than the speed of light. Chemical reactions, occurring via tunneling, should then not be considered in terms of a non-relativistic quantum theory calling into question quantum dynamics computations on tunneling reactions. To answer these questions, we define a new experimentally measurable paradigm - the tunneling flight time - and show that it vanishes for scattering through an Eckart or a square barrier, irrespective of barrier length or height, generalizing the Hartman effect...
August 9, 2017: Journal of Physical Chemistry Letters
Maggie Ng, Daniel K W Mok, Edmond P F Lee, John M Dyke
A theoretical study, involving the calculation of reaction enthalpies and activation energies, mechanisms and rate coefficients, has been made of the reaction of hydroxyl radicals with methyl nitrate, an important process for methyl nitrate removal in the earth's atmosphere. Four reaction channels were considered:- formation of H2O + CH2ONO2, CH3OOH + NO2, CH3OH + NO3, and CH3O + HNO3 . For all channels, geometry optimization and frequency calculations were carried out at the M06-2X/6-31+G** level, while relative energies were improved at the UCCSD(T*)-F12/CBS level...
August 9, 2017: Journal of Physical Chemistry. A
Kwang Suk Lee, Jee Soo Ha, Kyo Chul Koo
PURPOSE: Stone size and location are generally considered the most important factors associated with spontaneous ureter stone passage (SSP). Several parameters related to inflammatory changes have been identified as predictors associated with SSP. Our aim was to investigate the predictive role of neutrophil-to-lymphocyte ratio (NLR) for SSP. MATERIALS AND METHODS: A retrospective review was performed on 131 patients who were referred to the urology outpatient clinic and diagnosed with unilateral ureteral stones at our emergency department between July 2016 and December 2016...
September 2017: Yonsei Medical Journal
Kelli M Rutledge, Trevor Hamlin, Donna Baldisseri, Matthias Bickelhaupt, Mark Wayne Peczuh
The shapes adopted by large-ring, macrocyclic compounds play a role in their reactivity and their ability to be bound by biomolecules. We investigate the synthesis, conformational analysis, and properties of a specific family [13]-macrodilactones as models of natural product macrocycles. The features of our macrodilactones enable us to study the relationship between stereogenic centers and planar chirality through the modular synthesis of new members of this family of macrocycles. Here we report on insights gained from a new [13]-macrodilactone that is substituted at a position adjacent to the alkene in the molecule...
August 7, 2017: Chemistry, An Asian Journal
Kieran Griffiths, Athanassios C Tsipis, Prashant Kumar, Oliver P E Townrow, Alaa Abdul-Sada, Geoffrey R Akien, Amgalanbaatar Baldansuren, Alan C Spivey, George E Kostakis
Michael addition (MA) is one of the most well studied chemical transformation in synthetic chemistry. Here, we report the synthesis and crystal structures of a library of 3d/4f coordination clusters (CCs) formulated as [Zn(II)2Y(III)2L4(solv)X(Z)Y] and study their catalytic properties toward the MA of nitrostyrenes with barbituric acid derivatives. Each CC presents two borderline hard/soft Lewis acidic Zn(II) centers and two hard Lewis acidic Y(III) centers in a defect dicubane topology that brings the two different metals into a proximity of ∼3...
August 7, 2017: Inorganic Chemistry
Luca Liberale, Fabrizio Montecucco, Aldo Bonaventura, Ilaria Casetta, Silva Seraceni, Alessandro Trentini, Marina Padroni, Franco Dallegri, Enrico Fainardi, Federico Carbone
BACKGROUND: Acute ischemic stroke (AIS) triggers both systemic and neurovascular inflammation, influencing post-stroke recovery. In smokers with AIS inflammation might be further upregulated, increasing ischemia/reperfusion injury. Here, the predictive value of leukocyte and adhesion molecules levels on post-stroke outcomes was investigated. MATERIALS AND METHODS: 89 patients with AIS (n=30 smokers and n=59 non-smokers) were recruited and evaluated 1, 7 and 90 days after the onset to assess stroke severity by the National Institute of Health Stroke Scale (NIHSS) score as well as clinical recovery at 90 day by the modified Rankin Scale (mRS)...
August 7, 2017: European Journal of Clinical Investigation
Chad Priest, Bo Li, De-En Jiang
Exploring the structural interplay of ligands with uranyl can provide important knowledge for technology advances in uranium extraction from seawater. However, obtaining such chemical information is not an easy endeavor experimentally. From a plethora of computational methods, this work provides both microscopic insights and free-energy profiles of the binding between uranyl and deprotonated glutardiamidoxime (H2B) for which experimental structural information is not available, despite H2B being an important model ligand with an open-chain conformation for understanding aqueous uranium extraction chemistry...
August 7, 2017: Inorganic Chemistry
Christopher Mulligan, Joseph A Mindell
Transporters are crucial in a number of cellular functions, including nutrient uptake, cell signaling, and toxin removal. As such, transporters are important drug targets and their malfunction is related to several disease states. Treating transporter-related diseases and developing pharmaceuticals targeting transporters require an understanding of their mechanism. Achieving a detailed understanding of transporter mechanism depends on an integrative approach involving structural and computational approaches as well as biochemical and biophysical methodologies...
2017: Methods in Enzymology
Mitchell C Groenenboom, John Andrew Keith
Biomimetic hydride transfer catalysts are a promising route to efficiently convert CO2 into more useful products, but a lack of understanding about their atomic scale reaction mechanisms slows their development. To this end, we report a computational quantum chemistry study of how aqueous solvation influences CO2 reduction reactions facilitated by sodium borohydride (NaBH4) and a partially oxidized derivative (NaBH3OH). This work compares 0 K reaction barriers from nudged elastic band calculations to free energy barriers obtained at 300 K using potentials of mean force from umbrella sampling simulations...
August 2, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Gunter Hermann, Vincent Pohl, Jean Christophe Tremblay
In this contribution, we extend our framework for analyzing and visualizing correlated many-electron dynamics to non-variational, highly scalable electronic structure method. Specifically, an explicitly time-dependent electronic wave packet is written as a linear combination of N-electron wave functions at the configuration interaction singles (CIS) level, which are obtained from a reference time-dependent density functional theory (TDDFT) calculation. The procedure is implemented in the open-source Python program detCI@ORBKIT, which extends the capabilities of our recently published post-processing toolbox (Hermann et al...
August 1, 2017: Journal of Computational Chemistry
Neepa T Maitra
Charge transfer plays a crucial role in many processes of interest in physics, chemistry, and biochemistry. In many applications the size of the systems involved calls for time-dependent density functional theory (TDDFT) to be used in their computational modeling, due to its unprecedented balance between accuracy and efficiency. However, although exact in principle, in practise approximations must be made for the exchange-correlation functional in this theory, and the standard functional approximations perform poorly for excitations which have a long-range charge-transfer component...
August 2, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Dmitry G Khomyakov, Qadir K Timerghazin
Methyl thionitrite CH3SNO is an important model of S-nitrosated cysteine aminoacid residue (CysNO), a ubiquitous biological S-nitrosothiol (RSNO) involved in numerous physiological processes. As such, CH3SNO can provide insights into the intrinsic properties of the -SNO group in CysNO, in particular, its weak and labile S-N bond. Here, we report an ab initio computational investigation of the structure and properties of CH3SNO using a composite Feller-Peterson-Dixon scheme based on the explicitly correlated coupled cluster with single, double, and perturbative triple excitations calculations extrapolated to the complete basis set limit, CCSD(T)-F12/CBS, with a number of additive corrections for the effects of quadruple excitations, core-valence correlation, scalar-relativistic and spin-orbit effects, as well as harmonic zero-point vibrational energy with an anharmonicity correction...
July 28, 2017: Journal of Chemical Physics
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