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Journal of Physical Chemistry. A

Yu Ran Lee, Chung Bin Park, Jiye Hwang, Bongjune Sung, Hong Lae Kim, Chan Ho Kwon
We have measured the high-resolution vibrational spectra of a thietane (trimethylene sulfide) cation in the gas phase by employing the vacuum ultraviolet mass-analyzed threshold ionization (VUV-MATI) spectroscopic technique. Peaks in the low frequency region of the observed MATI spectrum of thietane originate from a progression of the ring puckering vibrational mode (typical in small heterocyclic molecules), which is successfully reproduced by quantum chemical calculations with one-dimensional (1D) symmetric double-well potentials along the ring puckering coordinates on both the S0 and D0 states, the ground electronic states of neutral and cation of thietane, respectively...
January 13, 2017: Journal of Physical Chemistry. A
Akinori Shimizu, Yoshihisa Inoue, Tadashi Mori
The circular dichroisms (CDs) of planar chiral [2.2]- and [3.3]-pyridinophanes were investigated experimentally and theoretically. Strong multi-signate Cotton effects (CEs), typical for cyclophane derivatives, were observed. The CD spectra of [2.2]- and [3.3]-paracyclophanes closely resembled in pattern to each other, despite the much greater conformational variations in the latter. Upon protonation, both of the cyclophanes suffered dramatic CD spectral changes with accompanying complete sign inversion, which was attributed to the reversal of diploe moment of pyridinium versus pyridine moiety...
January 13, 2017: Journal of Physical Chemistry. A
Huyen Thi Nguyen, Tran Dieu Hang, Minh Tho Nguyen
(Abstract) High accuracy calculations were carried out to study the mechanisms of the reactions between the diatomic silicon monoxide (SiO) with NH3 and CH4. These reactions are relevant to the SiO-related astrochemistry and atmospheric chemistry as well as the activation of the N-H and C-H bonds by the SiO triple bond. Energetic data used in the construction of potential energy surfaces describing the SiO + NH3/CH4 reactions were obtained at the coupled-cluster theory with extrapolation to the complete basis set limit (CCSD(T)/CBS) using DFT/B3LYP/aug-cc-pVTZ optimized geometries...
January 13, 2017: Journal of Physical Chemistry. A
Carolyne B Braga, Roberto Rittner
The conformational preferences of amino acids and their derivatives have been the subject of many investigations, because protein folding pathways that determine three-dimensional geometries are primarily restricted by the conformational space of each amino acid residue. Here we systematically describe the conformational behavior of l-histidine methyl ester (His-OMe) and its N-acetylated derivative (Ac-His-OMe) in the isolated phase and in solution. To this end, we employed spectroscopic techniques ((1)H NMR and IR), supported by quantum chemical calculations...
January 13, 2017: Journal of Physical Chemistry. A
Jialin Wen, Tianbao Ma, Weiwei Zhang, Adri C T van Duin, Xinchun Lu
In this work, we use ReaxFF molecular dynamics simulations to investigate the interaction between water molecules and silicon surfaces with different orientations under ambient temperatures of 300 and 500 K. We studied the water adsorption and dissociation processes as well as the silicon oxidation process on the Si (100), (110), and (111) surfaces. The simulation results indicate that water can adsorb on the Si surfaces in the forms of molecular adsorption and dissociative adsorption, making the surfaces terminated by H2O, OH, and H species...
January 13, 2017: Journal of Physical Chemistry. A
Jinfei Ling, Xunlei Ding, Zhenyu Li, Jinlong Yang
Molecular clusters formed by m nitric acid molecules and n ammonia molecules are studied with density functional theory. For smaller clusters with m, n ≤ 4, all possible combinations of m and n are considered, while for larger clusters in the 5 ≤ m, n ≤ 8 range we only consider the possibilities with |m - n| ≤ 1. Hydrogen bond network formation is an important stabilization mechanism in these clusters. At the same time, proton transfer is generally preferred except in the smallest clusters. Nitric acid and ammonia evaporation rates of these clusters are calculated with both collision activation barriers and reaction thermodynamics explicitly considered...
January 13, 2017: Journal of Physical Chemistry. A
I G Batyrev
The formation of nitrogen-hydrogen networked compounds is a promising approach for obtaining high energy density materials. Multiple experimental reports indicate that the synthesis pressure and temperature of high-energy nitrogen networked compounds significantly decrease when adding hydrogen to nitrogen. One- and two-dimensional structures of nitrogen-hydrogen mixtures are reported to form during synthesis and have also been observed with simulations; however, the structures are not thoroughly established or well understood...
January 13, 2017: Journal of Physical Chemistry. A
Nan-Nan Liu, Ying-Ying Xue, Yi-Hong Ding
[5]radialene, the missing link for synthesis of radialene family, has been finally obtained via the preparation and decomplexation of the [5]radialene-bis-Fe(CO)3 complex. The stability of [5]radialene complex benefits from the coordination with Fe(CO)3 by losing free 1,3-butadiene structures to avoid polymerization. In light of the similar coordination ability of half-sandwiches CpM(Cp = η5-C5H5; M = Fe, Co, Ni), there is a great possibility that the sandwiched complexes of [5]radialene with CpM are available...
January 12, 2017: Journal of Physical Chemistry. A
Jan H Jensen, Christopher J Swain, Lars Olsen
Rapid yet accurate pKa prediction for druglike molecules is a key challenge in computational chemistry. This study uses PM6-DH+/COSMO, PM6/COSMO, PM7/COSMO, PM3/COSMO, AM1/COSMO, PM3/SMD, AM1/SMD, and DFTB3/SMD to predict the pKa values of 53 amine groups in 48 druglike compounds. The approach uses an isodesmic reaction where the pKa value is computed relative to a chemically related reference compound for which the pKa value has been measured experimentally or estimated using a standard empirical approach...
January 12, 2017: Journal of Physical Chemistry. A
Peter A Eckert, Kevin J Kubarych
Hydrogenase enzymes enable organisms to use H2 as an energy source, having evolved extremely efficient biological catalysts for the reversible oxidation of molecular hydrogen. Small-molecule mimics of these enzymes provide both simplified models of the catalysis reactions and potential artificial catalysts that might be used to facilitate a hydrogen economy. We have studied two diiron hydrogenase mimics, μ-pdt-[Fe(CO)3]2 and μ-edt-[Fe(CO)3]2 (pdt = propanedithiolate, edt = ethanedithiolate), in a series of alkane solvents and have observed significant ultrafast spectral dynamics using two-dimensional infrared (2D-IR) spectroscopy...
January 12, 2017: Journal of Physical Chemistry. A
Pradeep Kumar Rao, Shridhar P Gejji
HFO-1345fz (CF3CF2CH═CH2 or 3,3,4,4,4-pentafluoro-1-butene) belongs to a class of hydrofluoro-olefins and represents a new generation of potential foam expansion agents. Its atmospheric impact and environmental acceptability can be estimated from the studies of kinetics and mechanism of its oxidative degradation. The molecular insights accompanying the reaction pathways in terms of the characterization of intermediates or products and radiative properties should prove useful for large-scale industrial applications...
January 12, 2017: Journal of Physical Chemistry. A
Yi Pan, Zhihong Luo, Yih-Chung Chang, Kai-Chung Lau, C Y Ng
The ionization energies (IEs) of TiO and TiO2 and the 0 K bond dissociation energies (D0) and the heats of formation at 0 K (ΔH°f0) and 298 K (ΔH°f298) for TiO/TiO(+) and TiO2/TiO2(+) are predicted by the wave-function-based CCSDTQ/CBS approach. The CCSDTQ/CBS calculations involve the approximation to the complete basis set (CBS) limit at the coupled cluster level up to full quadruple excitations along with the zero-point vibrational energy (ZPVE), high-order correlation (HOC), core-valence (CV) electronic, spin-orbit (SO) coupling, and scalar relativistic (SR) effect corrections...
January 11, 2017: Journal of Physical Chemistry. A
Rulin Feng, Monica Vasiliu, Kirk A Peterson, David A Dixon
Gas phase acidities and aqueous solution pKa's are predicted for MO2(OH)2 where center atom M is a main group 6, 16 and U atom using the Feller-Peterson-Dixon approach based on coupled cluster CCSD(T) calculations with additional corrections. The gas phase acidities of the MO2(OH)2 compounds are essentially the same for elements (M) of the same group, 304 - 310 kcal/mol at 298 K. All of the Group 6 compounds are 5 to 6 kcal/mol less acidic in the gas phase than H2SO4. The gas phase acidity of UO2(OH)2 is calculated to be up to 338...
January 11, 2017: Journal of Physical Chemistry. A
Paul Avramov, Alexander A Kuzubov, Artem V Kuklin, Hyosun Lee, Evgenia A Kovaleva, Seiji Sakai, Shiro Entani, Hiroshi Naramoto, Pavel B Sorokin
The structure of the interfaces and the mechanisms of induced spin polarization of 1D infinite and finite narrow graphene- and h-BN zigzag nanoribbons placed on a SrO-terminated La1-xSrxMnO3 (LSMO) (001) surface were studied using density functional theory (DFT) electronic structure calculations. It was found that the π-conjugated nanofragments are bonded to the LSMO(001) surface by weak disperse interactions. The types of coordination of the fragments, the strength of bonding, and the rate of spin polarization depend upon the nature of the fragments...
January 11, 2017: Journal of Physical Chemistry. A
Ashutosh Kumar, T Daniel Crawford
The frozen-virtual natural-orbital (NO) approach, whereby the unoccupied-orbital space is constructed using a correlated density such as that from many-body perturbation theory, has proven to yield compact wave functions for determining ground-state correlation energies and associated properties, with corresponding occupation numbers providing a guide to the truncation of the virtual space. In this work this approach is tested for the first time for the calculation of higher-order response properties, particularly frequency-dependent dipole polarizabilities using coupled-cluster theory...
January 11, 2017: Journal of Physical Chemistry. A
Bethan Nichols, Erin N Sullivan, Mikhail Ryazanov, Daniel M Neumark
The photodissociation dynamics of the i-methylvinoxy (CH3COCH2) radical have been studied by means of fast beam coincidence translational spectroscopy. The radical was produced by photodetachment of the i-methylvinoxide anion at 700 nm, followed by dissociation at 225 nm (5.51 eV), 248 nm (5.00 eV), and 308 nm (4.03 eV). At all three dissociation energies, the major products were found to be CH3 + CH2CO, with a small amount of CO + C2H5 produced at the higher dissociation energies. Photofragment mass distributions and translational energy distributions were recorded for each wavelength...
January 11, 2017: Journal of Physical Chemistry. A
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
Alexander Moiseevich Mebel, Alexander Landera, Ralf I Kaiser
The article addresses the formation mechanisms of naphthalene and indene, which represent prototype polycyclic aromatic hydrocarbons (PAH) carrying two six-membered and one five plus a six-membered ring. Theoretical studies of the relevant chemical reactions are overviewed in terms of their potential energy surfaces, rate constants, and product branching ratios; these data are compared with experimental measurements in crossed molecular beams and the pyrolytic chemical reactor emulating the extreme conditions in the interstellar medium (ISM) and the combustion-like environment, respectively...
January 10, 2017: Journal of Physical Chemistry. A
Josue E Perez, Manoj Kumar, Joseph S Francisco, Amitabha Sinha
Atmospheric aerosols often contain a significant fraction of carbon-nitrogen functionality, which makes gas-phase aldehyde-amine chemistries an important source of nitrogen containing compounds in aerosols. Here we use high-level ab initio calculations to examine the key determinants of amine (ammonia, methylamine, and dimethylamine) addition onto three different aldehydes (acetaldehyde, glycolaldehyde, and 2-hydroperoxy acetaldehyde), with each reaction being catalyzed by a single water molecule. The model aldehydes reflect different degrees of oxygenation at a site adjacent to the carbonyl moiety, the α-site, and represent typical oxygenates that can arise from atmospheric oxidation especially under conditions where the concentration of NO is low...
January 10, 2017: Journal of Physical Chemistry. A
Di Zhang, Karl N Blodgett, Xiao Zhu, Timothy S Zwier
Suberoylanilide hydroxamic acid (C6H5NHCO(CH2)6CONHOH, SAHA) is a histone deacetylase inhibitor that causes growth arrest and differentiation of many tumor types and is an approved drug for the treatment of cancer. With a hydrogen-bonding amide group adjacent to its phenyl ring "head", and a hydroxamic acid group at the "tail" end of a C6 alkyl chain linker, SAHA possesses an interesting potential energy landscape to be probed by single-conformation methods. The alkyl chain's preference for extended structures is in competition with tail-to-head (T-H) or head-to-tail (H-T) hydrogen bonds between the amide and hydroxamic acid groups...
January 10, 2017: Journal of Physical Chemistry. A
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