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density functional theory

Sheila López-Rosa, Moyocoyani Molina-Espíritu, Rodolfo O Esquivel, Catalina Soriano-Correa, Jésus S Dehesa
The relative structural location of a selected group of 27 sulfonamide-like molecules in a chemical space defined by three information theory quantities (Shannon entropy, Fisher information, and disequilibrium) is discussed. This group is composed of 15 active bacteriostatic molecules, 11 theoretically designed ones, and para-aminobenzoic acid. This endeavor allows molecules that share common chemical properties through the molecular backbone, but with significant differences in the identity of the chemical substituents, which might result in bacteriostatic activity, to be structurally classified and characterized...
December 5, 2016: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Li-Kun Yang, Xia-Guang Zhang, Fang-Zu Yang, De-Yin Wu, Zhong-Qun Tian, Xiang-Yang Liu
Density functional theory calculations have been used to elucidate the mechanism of the addition reaction of acetaldehyde to the positively charged hydrogenated silicene (H-silicene). We find that the positively charged H-silicene plane could be partially restructured to form a vacant Si site, enabling a further nucleophilic addition reaction. After acetaldehyde molecule attached to the H-silicene plane, two competing pathways are involved in hydrogen abstraction process: a random reaction mechanism and a chain reaction mechanism...
December 6, 2016: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Denisa Geffertová, Syed Tahir Ali, Veronika Šolínová, Marcela Krečmerová, Antonín Holý, Zdeněk Havlas, Václav Kašička
Capillary electrophoresis (CE) and quantum mechanical density functional theory (DFT) were applied to the investigation of the acid-base and electromigration properties of important compounds: newly synthesized derivatives of 5-azacytosine - analogs of efficient antiviral drug cidofovir. These compounds exhibit a strong antiviral activity and they are considered as potential new antiviral agents. For their characterization and application, it is necessary to know their acid-base properties, particularly the acidity constants (pKa) of their ionogenic groups (the basic N(3) atom of the triazine ring and the acidic phosphonic acid group in the alkyl chain)...
November 29, 2016: Journal of Chromatography. A
Feili Lai, Dingyu Yong, Xueliang Ning, Bicai Pan, Yue-E Miao, Tianxi Liu
Molybdenum diselenide (MoSe2 ) has emerged as a promising electrocatalyst for hydrogen evolution reaction (HER). However, its properties are still confined due to the limited active sites and poor conductivity. Thus, it remains a great challenge to synergistically achieve structural and electronic modulations for MoSe2 -based HER catalysts because of the contradictory relationship between these two characteristics. Herein, bacterial cellulose-derived carbon nanofibers are used to assist the uniform growth of few-layered MoSe2 nanosheets, which effectively increase the active sites of MoSe2 for hydrogen atom adsorption...
December 5, 2016: Small
Matias R Fagiani, Xiaowei Song, Petko Petkov, Sreekanta Debnath, Sandy Gewinner, Wieland Schöllkopf, Thomas Heine, André Fielicke, Knut R Asmis
We use cryogenic ion vibrational spectroscopy to characterize the structure and fluxionality of the magic number boron cluster B13(+) . The infrared photodissociation (IRPD) spectrum of the D2 -tagged all-(11) B isotopologue of B13(+) is reported in the spectral range from 435 to 1790 cm(-1) and unambiguously assigned to a planar boron double wheel structure based on a comparison to simulated IR spectra of low energy isomers from density-functional-theory (DFT) computations. Born-Oppenheimer DFT molecular dynamics simulations show that B13(+) exhibits internal quasi-rotation already at 100 K...
December 5, 2016: Angewandte Chemie
Evgen V Govor, Karrar Al-Ameed, Indranil Chakraborty, Carla S Coste, Olena Govor, Yiannis Sanakis, John E McGrady, Raphael G Raptis
One-electron reduction of a pyrazolate-bridged triangular Fe3 (μ3 -O) core induces a cascade wherein all three metal centers switch from high-spin Fe(3+) to low-spin Fe(2.66+) . This hypothesis is supported by spectroscopic data ((1) H-NMR, UV-vis-NIR, infra-red, (57) Fe-Mössbauer, EPR), X-ray crystallographic characterization of the cluster in both oxidation states and also density functional theory. The reduction induces substantial contraction in all bond lengths around the metal centers, along with diagnostic shifts in the spectroscopic parameters...
December 5, 2016: Angewandte Chemie
Priyanka Tavhare, Amol Deshmukh, Ajay Chaudhari
We have performed an ab initio and density functional theory study of the hydrogen adsorption on a lithium (Li)-decorated pentalene (C8H6Li2) complex. The C8H6Li2 complex can interact with a maximum of two hydrogen molecules with a H2 uptake capacity of 3.36 wt%. The effect of the number and position of boron atom substitution in the C8H6Li2 complex on the H2 uptake capacity is also studied. Two and four carbon atoms are substituted by boron atoms in the C8H6Li2 complex. Two different structures are considered for each of the two and four boron atom substitutions...
December 5, 2016: Physical Chemistry Chemical Physics: PCCP
Arthur V Cresce, Selena M Russell, Oleg Borodin, Joshua A Allen, Marshall A Schroeder, Michael Dai, Jing Peng, Mallory P Gobet, Steven G Greenbaum, Reginald E Rogers, Kang Xu
Sodium ion batteries are on the cusp of being a commercially available technology. Compared to lithium ion batteries, sodium ion batteries can potentially offer an attractive dollar-per-kilowatt-hour value, though at the penalty of reduced energy density. As a materials system, sodium ion batteries present a unique opportunity to apply lessons learned in the study of electrolytes for lithium ion batteries; specifically, the behavior of the sodium ion in an organic carbonate solution and the relationship of ion solvation with electrode surface passivation...
December 5, 2016: Physical Chemistry Chemical Physics: PCCP
Jeongjae Lee, Ieuan D Seymour, Andrew J Pell, Siân E Dutton, Clare P Grey
Rechargeable battery systems based on Mg-ion chemistries are generating significant interest as potential alternatives to Li-ion batteries. Despite the wealth of local structural information that could potentially be gained from Nuclear Magnetic Resonance (NMR) experiments of Mg-ion battery materials, systematic (25)Mg solid-state NMR studies have been scarce due to the low natural abundance, low gyromagnetic ratio, and significant quadrupole moment of (25)Mg (I = 5/2). This work reports a combined experimental (25)Mg NMR and first principles density functional theory (DFT) study of paramagnetic Mg transition metal oxide systems Mg6MnO8 and MgCr2O4 that serve as model systems for Mg-ion battery cathode materials...
December 5, 2016: Physical Chemistry Chemical Physics: PCCP
Javier D Fuhr, Maarten W van der Meijden, Lucila J Cristina, Luis M Rodríguez, Richard M Kellogg, J Esteban Gayone, Hugo Ascolani, Magalí Lingenfelder
The chiral expression of a molecule on a surface is driven from a random solid solution on Cu(100) to a racemic crystal on a Sn/Cu(100) alloy. Density functional theory simulations reveal how the growth of the racemate is influenced by the underlying surface.
December 5, 2016: Chemical Communications: Chem Comm
Andrea Zen, Loïc M Roch, Stephen J Cox, Xiao Liang Hu, Sandro Sorella, Dario Alfè, Angelos Michaelides
Clay minerals are ubiquitous in nature, and the manner in which they interact with their surroundings has important industrial and environmental implications. Consequently, a molecular-level understanding of the adsorption of molecules on clay surfaces is crucial. In this regard computer simulations play an important role, yet the accuracy of widely used empirical force fields (FF) and density functional theory (DFT) exchange-correlation functionals is often unclear in adsorption systems dominated by weak interactions...
November 23, 2016: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
Philipp Pedevilla, Stephen J Cox, Ben Slater, Angelos Michaelides
Feldspar minerals are the most common rock formers in Earth's crust. As such they play an important role in subjects ranging from geology to climate science. An atomistic understanding of the feldspar structure and its interaction with water is therefore desirable, not least because feldspar has been shown to dominate ice nucleation by mineral dusts in Earth's atmosphere. The complexity of the ice/feldspar interface arising from the numerous chemical motifs expressed on the surface makes it a challenging system...
March 31, 2016: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
Juan Frau, Francisco Muñoz, Daniel Glossman-Mitnik
The chemical reactivity of resveratrol isomers with the potential to play a role as inhibitors of the nonenzymatic glycation of amino acids and proteins, both acting as antioxidants and as chelating agents for metallic ions such as Cu, Al and Fe, have been studied by resorting to the latest family of Minnesota density functionals. The chemical reactivity descriptors have been calculated through Molecular Electron Density Theory encompassing Conceptual DFT. The active sites for nucleophilic and electrophilic attacks have been chosen by relating them to the Fukui function indices, the dual descriptor f ( 2 ) ( r ) and the electrophilic and nucleophilic Parr functions...
December 1, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
A Ehsani, M G Mahjani, M Hosseini, R Safari, R Moshrefi, H Mohammad Shiri
Inhibition performance of Thymus vulgaris plant leaves extract (thyme) as environmentally friendly (green) inhibitor for the corrosion protection of stainless steel (SS) type 304 in 1.0molL(-1) HCl solution was studied by potentiodynamic polarization, electrochemical impedance (EIS) and electrochemical noise measurements (EN) techniques. The EN data were analyzed with FFT technique to make the spectral power density plots. The calculations were performed by MATLAB 2014a software. Geometry optimization and calculation of the structural and electronic properties of the molecular system of inhibitor have been carried out using UB3LYP/6-311++G(∗∗) level...
November 16, 2016: Journal of Colloid and Interface Science
Azita Khosravan, Safora Marani, Mohammad Sadegh Sadeghi Googheri
Drug fluorination has the potential to reproduce useful drugs with decreasing the side effect of them. Identifying the effect of this improvement on the chemical properties and biological interactions of drug symbolizes a meaningful progress in drug design. Here the fluorination of Donepezil as an anti-Alzheimer drug, including 7 fluorinated derivatives of it, was investigated computationally. In the first part of our calculations, the most important chemical properties of drug that affects the drug efficiency were investigated by applying the M06/6-31g (d, p) and M062X/6-31g (d, p) levels of theories...
November 25, 2016: Journal of Molecular Graphics & Modelling
Dinh Bao Nguyen, Thanh Danh Nguyen, Sangsoo Kim, Sang-Woo Joo
Spectral differences between cytosine (Cyt) and 5-methylcytosine (5MC) were investigated by means of Raman spectroscopy with a combination of density functional theory (DFT) calculations. Surface-enhanced Raman scattering (SERS) revealed discriminating peaks of 5MC from those of Cyt upon adsorption on gold nanoparticles (AuNPs). Among the notable features, the multiple bands between 850 and 700cm(-1) for the ring-breathing modes of 5MC and Cyt could be correlated well with the simulated spectra based on the DFT calculations of the adsorbates on the gold cluster atoms...
November 9, 2016: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Laura B Hoch, Paul Szymanski, Kulbir Kaur Ghuman, Le He, Kristine Liao, Qiao Qiao, Laura M Reyes, Yimei Zhu, Mostafa A El-Sayed, Chandra Veer Singh, Geoffrey A Ozin
In2O3-x(OH)y nanoparticles have been shown to function as an effective gas-phase photocatalyst for the reduction of CO2 to CO via the reverse water-gas shift reaction. Their photocatalytic activity is strongly correlated to the number of oxygen vacancy and hydroxide defects present in the system. To better understand how such defects interact with photogenerated electrons and holes in these materials, we have studied the relaxation dynamics of In2O3-x(OH)y nanoparticles with varying concentration of defects using two different excitation energies corresponding to above-band-gap (318-nm) and near-band-gap (405-nm) excitations...
November 28, 2016: Proceedings of the National Academy of Sciences of the United States of America
A C L Jones, H J Rutbeck-Goldman, T H Hisakado, A M Piñeiro, H W K Tom, A P Mills, B Barbiellini, J Kuriplach
The affinity A_{Ps} of positronium (Ps) atoms for a metal is the negative of the maximum kinetic energy with which Ps is emitted into vacuum when thermalized positrons in a metal encounter the surface. When this quantity is measured by ground state Ps time of flight (TOF), the precision is severely limited by the short triplet state lifetime of 142 ns. By quickly converting the emitted Ps atoms into long-lived Rydberg states, we are able to dramatically increase the TOF to allow precision measurements of A_{Ps}...
November 18, 2016: Physical Review Letters
Po-Jen Hsu, Kun-Lin Ho, Sheng-Hsien Lin, Jer-Lai Kuo
The potential energy surface (PES), structures and thermal properties of methanol clusters (MeOH)n with n = 8-15 were explored by replica-exchange molecular dynamics (REMD) simulations with an empirical model and refined using density functional theory (DFT) methods. For a given size, local minima structures were sampled from REMD trajectories and archived by a newly developed molecular database via a two-stage clustering algorithm (TSCA). Our TSCA utilizes both the topology of O-HO hydrogen bonding networks and the similarity of the shapes to filter out duplicates...
December 2, 2016: Physical Chemistry Chemical Physics: PCCP
Liming Wu, Hua Lin, Yu-Jun Zheng, Xiao-Ning Hu, Hong Chen, Ju-Song Yu
Two new non-centrosymmetric polar quaternary selenides, namely, RbZn4In5Se12 and CsZn4In5Se12, have been synthesized and structurally characterized. They exhibit 3D diamond-like framework (DLF) consisting of corner shared MSe4 (M = Zn/In) tetrahedra, in which the A+ ions are located. Both compounds are thermally stable up to 1300 K and exhibit large transmittance in the infrared region (0.65-25 μm) with measured optical band gaps of 2.06 eV for RbZn4In5Se12 and 2.11 eV for CsZn4In5Se12. Inspiringly, they exhibit good balance between strong second harmonic generation (SHG) efficiency (3...
December 1, 2016: Chemistry, An Asian Journal
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