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computational chemistry

Jon Zubeltzu, Emilio Artacho
Water confined to nanoscale widths in two dimensions between ideal planar walls has been the subject of ample study, aiming at understanding the intrinsic response of water to confinement, avoiding the consideration of the chemistry of actual confining materials. In this work, we study the response of such nanoconfined water to the imposition of a periodicity in the confinement by means of computer simulations, both using empirical potentials and from first-principles. For that we propose a periodic confining potential emulating the atomistic oscillation of the confining walls, which allows varying the lattice parameter and amplitude of the oscillation...
November 21, 2017: Journal of Chemical Physics
M T C Martins-Costa, J M Anglada, J S Francisco, Manuel F Ruiz-López
Understanding the difference between observed and modeled concentrations of HOx radicals in the troposphere is a current major issue in atmospheric chemistry. It is widely believed that existing atmospheric models miss a source of such radicals and several potential new sources have been proposed. In recent years, interest has increased on the role played by cloud droplets and organic aerosols. Computer modeling of ozone photolysis, for instance, has shown that atmospheric aqueous interfaces accelerate the associated OH production rate by as much as 3-4 orders of magnitude...
November 22, 2017: Physical Chemistry Chemical Physics: PCCP
Zhongling Lang, Peng Yang, Zhengguo Lin, Likai Yan, Ming-Xing Li, Jorge J Carbó, Ulrich Kortz, Josep M Poblet
The development of rational synthetic procedures with desired nuclearity and high selectivity is a critical issue in inorganic chemistry. Here we demonstrate a comprehensive understanding of the template effect induced by metal cations in the formation mechanism of the class of polyoxopalladates ({MPd12L8} nanocube and {MPd15L10} nanostar) by combining computational and experimental techniques. The capture of a M (n+) guest ion by a peripheral palladium(ii)-oxo shell leads to a competition between the parent Pd(2+) addenda ion and the respective guest metal ion...
November 1, 2017: Chemical Science
Yun-Fang Yang, Peiyuan Yu, Kendall N Houk
The mechanisms of Diels-Alder reactions between 1,2,3-triazines and enamines have been explored with density functional theory computations. The focus of this work is on the origins of the different reactivities and mechanisms induced by substituents and by hexafluoroisopropanol (HFIP) solvent. These inverse electron-demand Diels-Alder reactions of triazines have wide applications in bioorthogonal chemistry and natural product synthesis. Both concerted and stepwise cycloadditions are predicted, depending on the nature of substituents and solvents...
November 21, 2017: Journal of the American Chemical Society
Anne Kathrine R Junker, Thomas Just Sørensen
The influence of an electron donating substituent on the photophysical properties of 1-azathioxanthone dyes has been investigated using optical spectroscopy and theoretical models. The motivation behind the study is based on the fact that thioxanthones are efficient triplet sensitizers, and thus promising sensitizers for lanthanide centered emission. By adding an aza group to one of the phenyl ring systems, direct coordination to a lanthanide center becomes possible, which makes azathoixanthones great candidates as antenna chromophores in lanthanide(III) based dyes...
November 21, 2017: Methods and Applications in Fluorescence
Bing Yang, Shixue Liu, Zijing Lin
Quantum chemistry calculations play a fundamental role in revealing the molecular structures observed in gas-phase spectroscopic measurements. The supersonic jet cooling widely used in single molecular spectroscopy experiment is a non-equilibrium process and often causes confusion on the theoretical and experimental comparison. A computational approach is proposed here to account for the effect of the non-equilibrium cooling on the experimental spectra and applied to the cases of tyrosin-glycine (YG), tryptophane-glycine (WG) and glycine-tryptophane (GW)...
November 20, 2017: Scientific Reports
Dillon P Cogan, Graham A Hudson, Zhengan Zhang, Taras V Pogorelov, Wilfred A van der Donk, Douglas A Mitchell, Satish K Nair
The [4+2] cycloaddition reaction is an enabling transformation in modern synthetic organic chemistry, but there are only limited examples of dedicated natural enzymes that can catalyze this transformation. Thiopeptides (or more formally thiazolyl peptides) are a class of thiazole-containing, highly modified, macrocyclic secondary metabolites made from ribosomally synthesized precursor peptides. The characteristic feature of these natural products is a six-membered nitrogenous heterocycle that is assembled via a formal [4+2] cycloaddition between two dehydroalanine (Dha) residues...
November 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
Santiago Rodríguez-Jiménez, Mingrui Yang, Ian Stewart, Anna L Garden, Sally Brooker
A simple method, using density functional theory (DFT), of predicting spin state in advance of synthesis is reported. Specifically, an excellent correlation is observed between the switching temperatures (T1/2) in CDCl3 solution of five spin crossover (SCO)-active [FeII(Lazine)2(NCBH3)2] complex-es and the DFT calculated (and the observed) 15N NMR chemical shift (δNA) of the five different azine-substituted 1,2,4-triazole ligands employed, Lazine = 4-(4-methylphenyl)-3-phenyl-5-(azine)-1,2,4-triazole, where azine = pyridine, pyridazine, 4-pyrimidine, pyrazine and 2-pyrimidine...
November 21, 2017: Journal of the American Chemical Society
Hyun Uk Kim, Kai Blin, Sang Yup Lee, Tilmann Weber
Understanding a complex working mechanism of biosynthetic gene clusters (BGCs) encoding secondary metabolites is a key to discovery of new antibiotics. Computational resources continue to be developed in order to better process increasing volumes of genome and chemistry data, and thereby better understand BGCs. In this context, this review highlights recent advances in computational resources for secondary metabolites with emphasis on genome mining, compound identification and dereplication as well as databases...
November 16, 2017: Current Opinion in Microbiology
Maximilian Dürr, Johannes Klein, Axel Kahnt, Sabine Becker, Ralph Puchta, Biprajit Sarkar, Ivana Ivanović-Burmazović
A dinuclear ruthenium complex bridged by 2,3,5,6-pyrazinetetracarboxylic acid (μ-LH2(2-)) was synthesized and characterized by X-ray crystallography, cyclic voltammetry under ambient and elevated pressures, electron paramagnetic resonance (EPR) and UV/vis-NIR (NIR = near-infrared) spectroelectrochemistry, pulse radiolysis, and computational methods. We probed for the first time in the field of mixed-valency the use of high-pressure electrochemical methods. The investigations were directed toward the influence of the protonation state of the bridging ligand on the electronic communication between the ruthenium ions, since such behavior is interesting in terms of modulating redox chemistry by pH...
November 20, 2017: Inorganic Chemistry
Sven M J Rogge, Michel Waroquier, Veronique Van Speybroeck
Over the past two decades, metal-organic frameworks (MOFs) have matured from interesting academic peculiarities toward a continuously expanding class of hybrid, nanoporous materials tuned for targeted technological applications such as gas storage and heterogeneous catalysis. These oft-times crystalline materials, composed of inorganic moieties interconnected by organic ligands, can be endowed with desired structural and chemical features by judiciously functionalizing or substituting these building blocks...
November 20, 2017: Accounts of Chemical Research
Takuya Maeyama
Fricke gel dosimeters are based on the aqueous ferrous sulfate solution that has been used as a reliable chemical dosimeter for more than 90 years. The amount of radiation-induced oxidation of ferrous ions to ferric ions could be evaluated three-dimensionally via optical computed tomography (OCT) or magnetic resonance imaging (MRI). Three-dimensional dosimetry is expected to be a useful tool, in particular, for the verification of complex radiation dose planning in advanced radiation cancer therapy. Compared with other 3D gel dosimeters, there are several problems such as retention of dose distribution or dose sensitivity; however, they can easily be prepared in a chemistry laboratory...
2017: Japanese Journal of Medical Physics
Mohamad Mohebifar, Erin R Johnson, Christopher N Rowley
London dispersion interactions play an integral role in materials science and biophysics. Force fields for atomistic molecular simulations typically represent dispersion interactions by the 12-6 Lennard-Jones potential, using empirically-determined parameters. These parameters are generally underdetermined and there is no straightforward way to test if they are physically realistic. Alternatively, the exchange-hole dipole moment (XDM) model from density-functional theory predicts atomic and molecular London dispersion coefficients from first principles, providing an innovative strategy to validate the dispersion terms of molecular-mechanical force fields...
November 17, 2017: Journal of Chemical Theory and Computation
Feng Zhu, Jacob Rodriguez, Tianyi Yang, Ilia Kevlishvili, Eric Miller, Duk Yi, Sloane O'Neill, Michael Rourke, Peng Liu, Maciej A Walczak
Stereoselective manipulations at the C1 anomeric position of saccharides are one of the central goals of preparative carbohydrate chemistry. Historically, the majority of reactions forming a bond with anomeric carbon has focused on reactions of nucleophiles with saccharide donors equipped with a leaving group. Here, we describe a novel approach to stereoselective synthesis of C-aryl glycosides capitalizing on the highly stereospecific reaction of anomeric nucleophiles. First, methods for the preparation of anomeric stannanes have been developed and optimized to afford both anomers of common saccharides in high anomeric selectivities...
November 17, 2017: Journal of the American Chemical Society
Fabián G Cantú Reinhard, Prasenjit Barman, Gourab Mukherjee, Jitendra Kumar, Deep Kumar, Devesh Kumar, Chivukula V Sastri, Sam P de Visser
Oxygen atom transfer by high-valent enzymatic intermediates remains an enigma in chemical catalysis. In particular, manganese is an important first-row metal involved in key biochemical processes including the biosynthesis of mo-lecular oxygen (through the photosystem II complex) and biodegradation of toxic superoxide to hydrogen peroxide by superoxide dismutase. Biomimetic models of these biological systems have been developed to gain understanding on the structure and properties of short-lived intermediates but also with the aim to create environmentally benign oxidants...
November 17, 2017: Journal of the American Chemical Society
Michael Gastegger, Jörg Behler, Philipp Marquetand
Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects - typically neglected by conventional quantum chemistry approaches - we base our machine learning strategy on ab initio molecular dynamics simulations. While these simulations are usually extremely time consuming even for small molecules, we overcome these limitations by leveraging the power of a variety of machine learning techniques, not only accelerating simulations by several orders of magnitude, but also greatly extending the size of systems that can be treated...
October 1, 2017: Chemical Science
Heming Zhang, Xiaoxuan Wei, Xuedan Song, Shaheen Shah, Jingwen Chen, Jianhui Liu, Ce Hao, Zhongfang Chen
For organic pollutants, photodegradation, as a major abiotic elimination process and of great importance to the environmental fate and risk, involves rather complicated physical and chemical processes of excited molecules. Herein, we systematically studied the photophysical and photochemical processes of a widely used antibiotic, namely sulfapyridine. By means of density functional theory (DFT) computations, we examined the rate constants and the competition of both photophysical and photochemical processes, elucidated the photochemical reaction mechanism, calculated reaction quantum yield (Φ) based on both photophysical and photochemical processes, and subsequently estimated the photodegradation rate constant...
October 7, 2017: Chemosphere
Saptarshi Biswas, Shuwen Ma, Stefano Nuzzo, Brendan Twamley, Andrew T Russell, James A Platts, František Hartl, Robert J Baker
A series of complexes [Et4N][Ln(NCS)4(H2O)4] (Ln = Pr, Tb, Dy, Ho, Yb) have been structurally characterized, all showing the same structure, namely a distorted square antiprismatic coordination geometry, and the Ln-O and Ln-N bond lengths following the expected lanthanide contraction. When the counterion is Cs(+), a different structural motif is observed and the eight-coordinate complex Cs5[Nd(NCS)8] isolated. The thorium compounds [Me4N]4[Th(NCS)7(NO3)] and [Me4N]4[Th(NCS)6(NO3)2] have been characterized, and high coordination numbers are also observed...
November 16, 2017: Inorganic Chemistry
Konstantinos D Vogiatzis, Dongxia Ma, Jeppe Olsen, Laura Gagliardi, Wibe A de Jong
A new large-scale parallel multiconfigurational self-consistent field (MCSCF) implementation in the open-source NWChem computational chemistry code is presented. The generalized active space approach is used to partition large configuration interaction (CI) vectors and generate a sufficient number of batches that can be distributed to the available cores. Massively parallel CI calculations with large active spaces can be performed. The new parallel MCSCF implementation is tested for the chromium trimer and for an active space of 20 electrons in 20 orbitals, which can now routinely be performed...
November 14, 2017: Journal of Chemical Physics
U Divya Madhuri, T P Radhakrishnan
Fabrication of gold nanoclusters (GNCs) with tunable fluorescence characteristics inside polymer thin films is attractive from the device application perspective. In this study, GNCs are generated in situ in poly(methyl methacrylate) films exploiting their weak reducing capability with no additional reducing agent, and by short and mild thermal annealing; the chemistry involved is probed through control experiments. The nanoclusters formed with ∼0.5 weight percent of gold are very stable and show appreciable fluorescence emission with a small Stokes shift (∼40 nm); interestingly, blending polystyrene enhances the fluorescence...
November 14, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
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