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computational chemistry

David L Davies, Stuart A Macgregor, Claire L McMullin
Computational studies on carboxylate-assisted C-H activation and functionalization at group 8-10 transition metal centers are reviewed. This Review is organized by metal and will cover work published from late 2009 until mid-2016. A brief overview of computational work prior to 2010 is also provided, and this outlines the understanding of carboxylate-assisted C-H activation in terms of the "ambiphilic metal-ligand assistance" (AMLA) and "concerted metalation deprotonation" (CMD) concepts. Computational studies are then surveyed in terms of the nature of the C-H bond being activated (C(sp(2))-H or C(sp(3))-H), the nature of the process involved (intramolecular with a directing group or intermolecular), and the context (stoichiometric C-H activation or within a variety of catalytic processes)...
May 22, 2017: Chemical Reviews
Shivaraj R Maidur, Parutagouda Shankaragouda Patil, Anusha Ekbote, Tze Shyang Chia, Ching Kheng Quah
In the present work, the title chalcone, (2E)-3-(4-fluorophenyl)-1-(4-{[(1E)-(4-fluorophenyl) methylene]amino}phenyl)prop-2-en-1-one (abbreviated as FAMFC), was synthesized and structurally characterized by single-crystal X-ray diffraction. The compound is crystallized in the monoclinic system with non-centrosymmetric space group P21 and hence it satisfies the essential condition for materials to exhibit second-order nonlinear optical properties. The molecular structure was further confirmed by using FT-IR and (1)H NMR spectroscopic techniques...
May 9, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Caitlyn Makins, Douglas A Whitelaw, Michael McGregor, Alix Petit, Robert G Mothersole, Kathleen E Prosser, Kirsten R Wolthers
Ornithine 4,5-aminomutase (OAM) from Clostridium sticklandii is an adenosylcobalamin (AdoCbl) and pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes a 1,2-amino shift, interconverting D-ornithine and 2S, 4R-diaminopentanoate. The reaction occurs via a radical-based mechanism whereby a PLP-bound substrate radical undergoes intramolecular isomerization via an azacyclopropylcarbinyl radical intermediate. Herein, we investigated the catalytic role of active site residues that form non-covalent interactions with PLP and/or substrate, D-ornithine...
May 17, 2017: Biochimica et Biophysica Acta
Teruko Matsuo, Hiroshi Tsugawa, Hiromi Miyagawa, Eiichiro Fukusaki
Compound identification using unknown electron ionization (EI) mass spectra in gas chromatography coupled with mass spectrometry (GC-MS) is challenging in untargeted metabolomics, natural product chemistry, or exposome research. While the total count of EI-MS records included in publicly or commercially available databases is over 900,000, efficient use of this huge database has not been achieved in metabolomics. Therefore, we proposed a 'four-step' strategy for the identification of biologically significant metabolites using an integrated cheminformatics approach: (i) Quality control calibration curve to reduce background noise, (ii) variable selection by hypothesis testing in principal component analysis for the efficient selection of target peaks, (iii) searching the EI-MS spectral database, and (iv) retention index (RI) filtering in combination with RI predictions...
May 18, 2017: Analytical Chemistry
Jörg Behler
Modern simulation techniques have reached a level of maturity, which allows addressing a wide range of problems in chemistry and materials science. Unfortunately, the application of first principles methods with predictive power is still limited to rather small systems, and in spite of the rapid evolution of computer hardware no fundamental change of this situation can be expected. Consequently, to reach an atomic level understanding of complex systems, the development of more efficient but equally reliable atomistic potentials has received considerable attention in recent years...
May 18, 2017: Angewandte Chemie
Sylwia Huber, Fabio Casagrande, Melanie N Hug, Lisha Wang, Philipp Heine, Lutz Kummer, Andreas Plückthun, Michael Hennig
The neurotensin receptor 1 represents an important drug target involved in various diseases of the central nervous system. So far, the full exploitation of potential therapeutic activities has been compromised by the lack of compounds with favorable physicochemical and pharmacokinetic properties which efficiently penetrate the blood-brain barrier. Recent progress in the generation of stabilized variants of solubilized neurotensin receptor 1 and its subsequent purification and successful structure determination presents a solid starting point to apply the approach of fragment-based screening to extend the chemical space of known neurotensin receptor 1 ligands...
2017: PloS One
Balázs Olasz, István Szabó, Gábor Czakó
Bimolecular nucleophilic substitution (SN2) and proton transfer are fundamental processes in chemistry and F(-) + CH3I is an important prototype of these reactions. Here we develop the first full-dimensional ab initio analytical potential energy surface (PES) for the F(-) + CH3I system using a permutationally invariant fit of high-level composite energies obtained with the combination of the explicitly-correlated CCSD(T)-F12b method, the aug-cc-pVTZ basis, core electron correlation effects, and a relativistic effective core potential for iodine...
April 1, 2017: Chemical Science
Jean-Michel Carter, Shobbir Hussain
Background: The ability to obtain long read lengths during DNA sequencing has several potentially important practical applications. Especially long read lengths have been reported using the Nanopore sequencing method, currently commercially available from Oxford Nanopore Technologies (ONT). However, early reports have demonstrated only limited levels of combined throughput and sequence accuracy. Recently, ONT released a new CsgG pore sequencing system as well as a 250b/s translocation chemistry with potential for improvements...
April 6, 2017: Wellcome Open Research
A N Generalova, B N Chichkov, E V Khaydukov
Lanthanide-doped upconversion nanoparticles (UCNPs) have recently attracted great attention in theranostics due to their exceptional optical and physicochemical properties, which enable the design of a novel UCNP-based nanoplatform for luminescent imaging, temperature mapping, sensing, and therapy. In addition, UCNPs are considered to be ideal building blocks for development of multimodal probes for cells and whole body imaging, exploiting simple variation of host matrix, dopant ions, and surface chemistry...
May 4, 2017: Advances in Colloid and Interface Science
Panteleimon G Takis, Konstantinos D Papavasileiou, Loukas D Peristeras, Georgios C Boulougouris, Vasilios S Melissas, Anastassios N Troganis
Dimethyl sulfoxide (DMSO) has a significant, multi-faceted role in medicine, pharmacy, and biology as well as in biophysical chemistry and catalysis. Its physical properties and impact on biomolecular structures still attract major scientific interest, especially the interactions of DMSO with biomolecular functional groups. In the present study, we shed light on the "isolated" carboxylic (-COOH) and amide (-NH) interactions in neat DMSO via(1)H NMR studies along with extensive theoretical approaches, i.e. molecular dynamics (MD) simulations, density functional theory (DFT), and ab initio calculations, applied on model compounds (i...
May 12, 2017: Physical Chemistry Chemical Physics: PCCP
Thomas P Warelow, M Jake Pushie, Julien J H Cotelesage, Joanne M Santini, Graham N George
Arsenite oxidase is thought to be an ancient enzyme, originating before the divergence of the Archaea and the Bacteria. We have investigated the nature of the molybdenum active site of the arsenite oxidase from the Alphaproteobacterium Rhizobium sp. str. NT-26 using a combination of X-ray absorption spectroscopy and computational chemistry. Our analysis indicates an oxidized Mo(VI) active site with a structure that is far from equilibrium. We propose that this is an entatic state imposed by the protein on the active site through relative orientation of the two molybdopterin cofactors, in a variant of the Rây-Dutt twist of classical coordination chemistry, which we call the pterin twist hypothesis...
May 11, 2017: Scientific Reports
Nicola Carslaw, Louise Fletcher, Dwayne Heard, Trevor Ingham, Hannah Walker
We report measurements of hydroxyl (OH) and hydroperoxy (HO2 ) radicals made by laser-induced fluorescence spectroscopy in a computer classroom (i) in the absence of indoor activities (ii) during desk cleaning with a limonene-containing cleaner (iii) during operation of a commercially available 'air cleaning' device. In the unmanipulated environment, the one-minute averaged OH concentration remained close to or below the limit of detection (6.5 x 10(5) molecule cm(-3) ), whilst that of HO2 was 1.3 x 10(7) molecule cm(-3) ...
May 11, 2017: Indoor Air
Elena Kusevska, M Merced Montero-Campillo, Otilia Mó, Manuel Yáñez
Owing to its versatility in synthetic chemistry, TPB (tris[2-diisopropylphospino)phenyl]borane) is a very important frustrated Lewis Pair. The unusual stability of the neutral radical (TPB)Cu has been related to the presence of a one-electron B-Cu bond. Herein we show, through the use of different computational chemistry methods, that the existence and nature of this kind of A⋅⋅⋅M bond (A=donor atom, M=transition metal) depends on the surrounding chemical structure, and can be genuine one-electron sigma bonds only if appropriate metal ligands (Y), able to trap the charge in the desired region, are chosen...
May 10, 2017: Angewandte Chemie
Valerie Vaissier, Troy Van Voorhis
The mechanism by which [NiFe] hydrogenase catalyses the oxidation of molecular hydrogen is a significant yet challenging topic in bioinorganic chemistry. With far-reaching applications in renewable energy and carbon mitigation, significant effort has been invested in the study of these complexes. In particular, computational approaches offer a unique perspective on how this enzyme functions at an electronic and atomistic level. In this article, we discuss state-of-the art quantum chemical methods and how they have helped deepen our comprehension of [NiFe] hydrogenase...
May 9, 2017: Essays in Biochemistry
Wen Zhu, Nigel G J Richards
Remarkably few enzymes are known to employ a mononuclear manganese ion that undergoes changes in redox state during catalysis. Many questions remain to be answered about the role of substrate binding and/or protein environment in modulating the redox properties of enzyme-bound Mn(II), the nature of the dioxygen species involved in the catalytic mechanism, and how these enzymes acquire Mn(II) given that many other metal ions in the cell form more stable protein complexes. Here, we summarize current knowledge concerning the structure and mechanism of five mononuclear manganese-dependent enzymes: superoxide dismutase, oxalate oxidase (OxOx), oxalate decarboxylase (OxDC), homoprotocatechuate 3,4-dioxygenase, and lipoxygenase (LOX)...
May 9, 2017: Essays in Biochemistry
Arshad Mehmood, Benjamin G Janesko
Atomic partial charges are widely used to predict reactivity. Partial charge alone is often insufficient: the carbons of benzene and cyclobutadiene, or those of diamond, graphene, and C60 , possess nearly identical partial charges and very different reactivities. Our atomic overlap distance complements computed partial charges by measuring the size of orbital lobes that best overlap with the wavefunction around an atom. Compact, chemically stable atoms tend to have overlap distances smaller than chemically soft, unstable atoms...
May 9, 2017: Angewandte Chemie
Thekla Cordes, Christian M Metallo
Metabolism coordinates the conversion of available nutrients toward energy, biosynthetic intermediates, and signaling molecules to mediate virtually all biological functions. Dysregulation of metabolic pathways contributes to many diseases, so a detailed understanding of human metabolism has significant therapeutic implications. Over the last decade major technological advances in the areas of analytical chemistry, computational estimation of intracellular fluxes, and biological engineering have improved our ability to observe and engineer metabolic pathways...
November 2016: Current Opinion in Chemical Engineering
Yajun Zheng, Colin M Tice, Suresh B Singh
In structure-based drug design, the basic goal is to design molecules that fit complementarily to a given binding pocket. Since such computationally modeled molecules may not adopt the intended bound conformation outside the binding pocket, one challenge is to ensure that the designed ligands adopt similar low energy conformations both inside and outside of the binding pocket. Computational chemistry methods and conformational preferences of small molecules from PDB and Cambridge Structural Database (CSD) can be used to predict the bound structures of the designed molecules...
April 27, 2017: Bioorganic & Medicinal Chemistry Letters
Pei Shi, Tao Wu, Panpan Li, Bingjie Guo, Gang Fang, Yafei Dong
Rapid developments have been made in synthetic biology within the past two decades, particularly in combination with chemistry, computer science, and other disciplines. Genetic components and internal features have been a main focus of research for synthetic biologists. Logic gates can be applied in various disciplines, but have not yet been used for plasmid design. GenoCAD is a computer-aided design software programme for synthetic biology that can be used to design complex structures. Thus, in this study, the authors analysed a large, commonly used data set containing over 70,000 feature sequences and eventually obtained comprehensive information for a complete data set without redundancy...
April 2017: IET Systems Biology
Virginie Raybaud, Sylvie Tambutté, Christine Ferrier-Pagès, Stéphanie Reynaud, Alexander A Venn, Éric Tambutté, Paul Nival, Denis Allemand
Critical to determining vulnerability or resilience of reef corals to Ocean Acidification (OA) is a clearer understanding of the extent to which corals can control carbonate chemistry in their Extracellular Calcifying Medium (ECM) where the CaCO3 skeleton is produced. Here, we employ a mathematical framework to calculate ECM aragonite saturation state (Ωarag.(ECM)) and carbonate system ion concentration using measurements of calcification rate, seawater characteristics (temperature, salinity and pH) and ECM pH (pH(ECM))...
May 3, 2017: Journal of Theoretical Biology
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