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computational chemistry

Courtney E Elwell, Nicole L Gagnon, Benjamin D Neisen, Debanjan Dhar, Andrew D Spaeth, Gereon M Yee, William B Tolman
A longstanding research goal has been to understand the nature and role of copper-oxygen intermediates within copper-containing enzymes and abiological catalysts. Synthetic chemistry has played a pivotal role in highlighting the viability of proposed intermediates and expanding the library of known copper-oxygen cores. In addition to the number of new complexes that have been synthesized since the previous reviews on this topic in this journal (Mirica, L. M.; Ottenwaelder, X.; Stack, T. D. P. Chem. Rev. 2004, 104, 1013-1046 and Lewis, E...
January 19, 2017: Chemical Reviews
Jing Yang, Mostafa Youssef, Bilge Yildiz
We present a multi-scale approach to predict equilibrium defect concentrations across oxide/oxide hetero-interfaces. There are three factors that need to be taken into account simultaneously for computing defect redistribution around the hetero-interfaces: the variation of local bonding environment at the interface as epitomized in defect segregation energies, the band offset at the interface, and the equilibration of the chemical potentials of species and electrons via ionic and electronic drift-diffusion fluxes...
January 19, 2017: Physical Chemistry Chemical Physics: PCCP
You Xu, Alessandra Villa, Lennart Nilsson
Locked nucleic acid (LNA), a modified nucleoside which contains a bridging group across the ribose ring, improves the stability of DNA/RNA duplexes significantly, and therefore is of interest in biotechnology and gene therapy applications. In this study, we investigate the free energy change between LNA and DNA nucleosides. The transformation requires the breaking of the bridging group across the ribose ring, a problematic transformation in free energy calculations. To address this, we have developed a 3-step (easy to implement) and a 1-step protocol (more efficient, but more complicated to setup), for single and dual topologies in classical molecular dynamics simulations, using the Bennett Acceptance Ratio method to calculate the free energy...
January 19, 2017: Journal of Computational Chemistry
Hilary M Chase, Junming Ho, Mary Alice Upshur, Regan J Thomson, Victor S Batista, Franz M Geiger
Hilary M. Chase1#, Junming Ho2#, Mary Alice Upshur1, Regan J. Thomson1, Victor S. Batista3, Franz M. Geiger1* 1Department of Chemistry, Northwestern University, Evanston, IL. 60208, United States; 2 Agency for Science, Technology and Research, Institute of High Performance Computing, 1 Fusionopolis Way #16-16 Connexis North, Singapore 138632; 3Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT. 06520, United States # These authors contributed equally to this work. *corresponding author: geigerf@chem...
January 19, 2017: Journal of Physical Chemistry. A
Salim Ok, David W Hoyt, Amity Andersen, Julie Sheets, Susan A Welch, David R Cole, Karl Todd Mueller, Nancy M Washton
Characterization and modeling of the molecular-level behavior of simple hydrocarbon gases, such as methane, in the presence of both nonporous and nano-porous mineral matrices allows for predictive understanding of important processes in engineered and natural systems. In this study, changes in local electromagnetic environments of the carbon atoms in methane under conditions of high pressure (up to 130 bar) and moderate temperature (up to 346 K) were observed with 13C magic-angle spinning (MAS) NMR spectroscopy while the methane gas was mixed with two model solid substrates: a fumed non-porous, 12 nm particle size silica and a mesoporous silica with 200 nm particle size and 4 nm average pore diameter...
January 18, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Mohammad-Reza Rashidi, Somaieh Soltani
Given the rising trend in medicinal chemistry strategy to reduce cytochrome P450-dependent metabolism, aldehyde oxidase (AOX) has recently gained increased attention in drug discovery programs and the number of drug candidates that are metabolized by AOX is steadily growing. Areas covered: Despite the emerging importance of AOX in drug discovery, there are certain major recognized problems associated with AOX-mediated metabolism of drugs. Intra- and inter-species variations in AOX activity, the lack of reliable and predictive animal models using the common experimental animals, and failure in the predictions of in vivo metabolic activity of AOX using traditional in vitro methods are among these issues that are covered in this article...
January 17, 2017: Expert Opinion on Drug Discovery
Natália de Farias Silva, Raimundo Lopes da Silva, Kalene de Oliveira Almeida, Antônio Edilson Sousa do Nascimento-Júnior, Davi do Socorro Barros Brasil, José Otávio Carréra Silva-Júnior, Francisco Martins Teixeira, Roseane Maria Ribeiro-Costa
Chitosan has attracted much interest due to its special physical and chemical properties related to drug administration. Nanoparticles delivery systems from Vi Antigen are a promising approach in the struggle against typhoid fever. In this paper, we reported the obtainment and the characterization of Vi Antigen by Infrared spectroscopy as well as Molecular Modeling and Computational Chemistry studies of the Chitosan-Vi Antigen interaction through theoretical models. The results of the theoretical and experimental Infrared spectroscopy showed important bands related to N-Acetyl and O-Acetyl groups present in Vi Antigen...
December 31, 2016: Journal of Molecular Graphics & Modelling
Guoxi Xu, Zihan Huang, Pengyu Chen, Tianqi Cui, Xinghua Zhang, Bing Miao, Li-Tang Yan
Structurally dynamic polymers are recognized as a key potential to revolutionize technologies ranging from design of self-healing materials to numerous biomedical applications. Despite intense research in this area, optimizing reactivity and thereby improving self-healing ability at the most fundamental level pose urgent issue for wider applications of such emerging materials. Here, the authors report the first mechanistic investigation of the fundamental principle for the dependence of reactivity and self-healing capabilities on the properties inherent to dynamic polymers by combining large-scale computer simulation, theoretical analysis, and experimental discussion...
January 16, 2017: Small
Tristram Chivers, Risto S Laitinen
Cyclocondensation is a major preparative route for the generation of inorganic heterocycles especially in the case of ring systems involving a Group 15 or 16 element linked to nitrogen. This Perspective will consider recent experimental and computational studies involving the reactions of primary amines (or their synthetic equivalents) with pnictogen and chalcogen halides. The major focus will be a discussion of the identity and role of acyclic intermediates in the reaction pathways to ring formation, as well as the nature of the heterocycles so formed...
January 16, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
Arjen J de Haas, Jos Oomens, Jordy Bouwman
Energetic processing of gaseous polycyclic aromatic hydrocarbons (PAHs) plays a pivotal role in the chemistries of inter- and circumstellar environments, certain planetary atmospheres, and also in the chemistry of combustion and soot formation. Although the precursor PAH species have been extensively characterized, the products from these gaseous breakdown reactions have received far less attention. It has been particularly challenging to accurately determine their molecular structure in gas-phase experiments, where comparisons against theoretical modeling are best made...
January 12, 2017: Physical Chemistry Chemical Physics: PCCP
Chowdhury Ashraf, Adri C T van Duin
A detailed insight of key reactive events related to oxidation and pyrolysis of hydrocarbon fuels further enhances our understanding of combustion chemistry. Though comprehensive kinetic models are available for smaller hydrocarbons (typically C3 or lower), developing and validating reaction mechanisms for larger hydrocarbons is a daunting task, due to the complexity of their reaction networks. The ReaxFF method provides an attractive computational method to obtain reaction kinetics for complex fuel and fuel mixtures, providing an accuracy approaching ab-initio based methods, but with a significantly lower computational expense...
January 10, 2017: Journal of Physical Chemistry. A
Cameron M E Graham, Taylor E Pritchard, Paul D Boyle, Juuso Valjus, Heikki M Tuononen, Paul J Ragogna
Four-membered rings with a P2 Ch2 core (Ch=S, Se) and phosphorus in the +3 oxidation state have been synthesized. The utility of these rings as a source of monomeric phosphinidene chalcogenides was probed by the addition of an N-heterocyclic carbene, resulting in a base-stabilized phosphinidene sulfide. Similarly, persistence of the phosphinidene selenide in solution was shown through cycloaddition chemistry with 2,3-dimethylbutadiene at elevated temperatures. The observed reactivity was explained by detailed computational work that established the conditions upon which the P2 Ch2 rings can liberate phosphinidene chalcogenides...
January 10, 2017: Angewandte Chemie
Eric S Manas, Darren V S Green
The acronym "CADD" is often used interchangeably to refer to "Computer Aided Drug Discovery" and "Computer Aided Drug Design". While the former definition implies the use of a computer to impact one or more aspects of discovering a drug, in this paper we contend that computational chemists are most effective when they enable teams to apply true design principles as they strive to create medicines to treat human disease. We argue that teams must bring to bear multiple sub-disciplines of computational chemistry in an integrated manner in order to utilize these principles to address the multi-objective nature of the drug discovery problem...
January 9, 2017: Journal of Computer-aided Molecular Design
Han F van Dobben, Wim de Vries
We evaluated effects of atmospheric deposition of nitrogen on the composition of forest understorey vegetation both in space and time, using repeated data from the European wide monitoring program ICP-Forests, which focuses on normally managed forest. Our aim was to assess whether both spatial and temporal effects of deposition can be detected by a multiple regression approach using data from managed forests over a relatively short time interval, in which changes in the tree layer are limited. To characterize the vegetation, we used indicators derived from cover percentages per species using multivariate statistics and indicators derived from the presence/absence, that is, species numbers and Ellenberg's indicator values...
January 2017: Ecology and Evolution
Praveen Kumar, Bin Jiang, Hua Guo, Jacek Klos, Millard H Alexander, Bill Poirier
The high resolution spectroscopy of the SO 2 molecule is of great topical interest, in a wide variety of contexts ranging from origins of higher life, to astrophysics of the interstellar medium, to environmental chemistry. In particular, the C̃ 1 B 2 ← X̃ 1 A 1 UV photoabsorption spectrum has received considerable attention. This spectrum exhibits a highly regular progression of ∼ 20 or so strong peaks, spaced roughly 350 cm -1 apart, which is comparable to the C̃ 1 B 2 bending vibrational frequency...
January 9, 2017: Journal of Physical Chemistry. A
Markus Hoelscher, Walter Leitner
While industrial NH3 synthesis based on the Haber-Bosch-process was invented more than a century ago, there is still no molecular catalyst available which reduces N2 in the reaction system N2/H2 to NH3. As the many efforts of experimentally working research groups to develop a molecular catalyst for NH3 synthesis from N2/H2 have led to a variety of stoichiometric reductions it seems to be justified to undertake the attempt of systematizing the various approaches of how the N2 molecule might be reduced to NH3 with H2 at a transition metal complex...
January 9, 2017: Chemistry: a European Journal
Chang-Hong Chen, François P Gabbaï
Fluoride anion complexation impacts a number of areas ranging from sensing to nucleophilic fluorination chemistry. Described here is a new bidentate Lewis acid consisting of two stiborane units connected by a 1,8-triptycenediyl backbone. This neutral derivative captures fluoride with an unprecedented affinity for a neutral, water-compatible Lewis acid. Structural, spectroscopic and computational studies demonstrate that fluoride anion binding is assisted by the formation of a C-H⋅⋅⋅F hydrogen bond which involves a methine group of the 1,8-triptycenediyl backbone...
January 9, 2017: Angewandte Chemie
Aurélien Moncomble, Jean-Paul Cornard, Michel Meyer
The stereochemical activity of the lone pair on Pb(II) complexes is assessed using several theoretical methods, including structural analyses, computations of Fukui functions, natural bond orbitals, electron localization function, investigation of the electron density and of its laplacian. The attention is focused on four octadentate N-carbamoylmethyl-substituted tetraazamacrocycles of various ring sizes ranging from 8 to 14 atoms associated with the Pb(II) cation. The theoretical study illustrates the geometrical constraints imposed by the ring structure which limits the spatial development of the lone pair but without fully preventing it...
January 2017: Journal of Molecular Modeling
Carlos Marante, Markus Klinker, Inés Corral, Jesús González-Vázquez, Luca Argenti, Fernando Martín
The theoretical description of observables in attosecond pump-probe experiments requires a good representation of the system's ionization continuum. For polyelectronic molecules, however, this is still a challenge, due to the complicated short-range structure of correlated electronic wave functions. Whereas quantum chemistry packages (QCP) implementing sophisticated methods to compute bound electronic molecular states are well-established, comparable tools for the continuum are not widely available yet. To tackle this problem, we have developed a new approach that, by means of a hybrid Gaussian-B-spline basis, interfaces existing QCPs with close-coupling scattering methods...
January 6, 2017: Journal of Chemical Theory and Computation
Anatoly Mayburd, Ancha Baranova
PURPOSE: Novel, "outside of the box" approaches are needed for evaluating candidate molecules, especially in oncology. Throughout the years of 2000-2010, the efficiency of drug development fell to barely acceptable levels, and in the second decade of this century, levels have improved only marginally. This dismal condition continues despite unprecedented progress in the development of a variety of high-throughput tools, computational methods, aggregated databases, drug repurposing programs and innovative chemistries...
October 2016: Journal of Pharmacy & Pharmaceutical Sciences: a Publication of the Canadian Society for Pharmaceutical Sciences
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