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Journal of Physical Chemistry. A

Minhua Zhang, Lihang Chen, Huaming Yang, Jing Ma
Combining molecular dynamics (MD) and quantum chemistry (QM) simulation, the association mechanism of acetic acid systems were examined. DFT method was proposed to compare the hydrogen-bonding energy of variable acetic acid dimers, and definitely provided the stable dimers configuration. Geometry parameters of dimers were also obtained by QM calculations, which were taken as the characteristic criteria for further MD analysis. Proportion of different acetic acid dimers in gas phase was obtained by Radial distribution function (RDF) analysis, and cyclic dimer with two O=c-Hoacid hydrogen bonds was demonstrated as the most stable structure...
May 26, 2017: Journal of Physical Chemistry. A
Dorota Wileńska, Piotr Skurski, Iwona Anusiewicz
The isomeric structures formed by the aluminum fluoride (AlF3) system and surrounding water molecules were theoretically examined by employing MP2 and CCSD(T) methods and the aug-cc-pVDZ basis set together with the polarized continuum solvation model within a self-consistent reaction field treatment. The calculations performed for the AlF3·n(H2O) systems (n = 1-6) revealed that facial and meridional octahedral structures correspond to the lowest energy isomers for the AlF3·4H2O, AlF3·5H2O, and AlF3·6H2O systems, whereas the isomers containing the H3O(+) and AlF3OH(-) fragments were predicted to be less stable by only 5-7 kcal/mol, which indicates the possible formation of the hydronium cations in such systems even at room temperature...
May 26, 2017: Journal of Physical Chemistry. A
Akira Matsugi, Hiroumi Shiina
The thermal decomposition of gaseous nitromethane and the subsequent bimolecular reaction between CH3 and NO2 have been experimentally studied using time-resolved cavity-enhanced absorption spectroscopy behind reflected shock waves in the temperature range 1336-1827 K and at a pressure of 100 kPa. Temporal evolution of NO2 was observed following the pyrolysis of nitromethane (diluted to 80-140 ppm in argon) by monitoring the absorption around 400 nm. The primary objectives of the current work were to evaluate the rate constant for the CH3 + NO2 reaction (k2) and to examine the contribution of the roaming isomerization pathway in nitromethane decomposition...
May 26, 2017: Journal of Physical Chemistry. A
Tao Yang, Ryoichi Fukuda, Roberto Cammi, Masahiro Ehara
High-pressure Diels-Alder cycloaddition reaction of fullerenes is an important synthetic method for the thermally stable cycloadducts. The effects of high pressure on the potential energy surfaces of Diels-Alder cycloaddition of cyclopentadiene and C60 were studied with a recently developed approach, the polarizable continuum model for extreme pressure (XP-PCM). It is revealed that the high pressure reduces the activation energies and increases reaction energies drastically, making the DA reaction more favorable...
May 26, 2017: Journal of Physical Chemistry. A
Junlin Jiang, Amani A Alsam, Shanshan Wang, Shawkat M Aly, Zhenxing Pan, Omar F Mohammed, Kirk S Schanze
A series of -conjugated oligomer-acceptor dyads were synthesized that feature oligo(phenylene ethynylene) (OPE) conjugated backbones end-capped with a naphthalene diimide (NDI) acceptor. The OPE segments vary in length from 4 to 8 phenylene ethynene units (PEn-NDI, where n = 4, 6 and 8). Fluorescence and transient absorption spectroscopy reveals that intramolecular OPE NDI charge transfer dominates the deactivation of excited states of the PEn-NDI oligomers. Both charge separation (CS) and charge recombination (CR) are strongly exothermic (G0CS ~ -1...
May 25, 2017: Journal of Physical Chemistry. A
Tumpa Sadhukhan, Dharitri Das, Pratik Kalekar, Vidya Avasare, Sourav Pal
Triose sugar, 1,3-Dihydroxy acetone (DHA) on treatment with Fenton's reagent releases CO under physiological conditions. The release of CO has been demonstrated by myoglobin assay and quantum chemical studies. The mechanistic study has been carried out using B3LYP/6-311++G(d,p), M06-2X/6-311++G(d,p) and CCSD(T)//M06-2X/6-311++G(d,p) level of theories in aqueous medium with dielectric constant of 78.39 by employing polarized continuum model (PCM). The theoretical investigation shows that DHA breaks down completely into two equivalents of CO, one equivalent of CO2 and six equivalents of H2O without formation of toxic metabolites...
May 25, 2017: Journal of Physical Chemistry. A
Christa Fittschen, Emmanuel Assaf, Luc Vereecken
The possible formation of HO2 and NO2 as products from the reaction of OH and NO under atmospheric conditions, in competition to the formation of HONO, has been investigated experimentally and theoretically. Experiments have been carried out by directly measuring the formation of HO2 radicals using laser photolysis coupled to cw-CRDS. OH radicals have been generated from the reaction of F-atoms with H2O, and absolute HO2 and OH profiles have been recorded at different NO concentrations. The potential energy surface has been calculated and the rate constant has been obtained from RRKM master equation modeling...
May 25, 2017: Journal of Physical Chemistry. A
Kaiqiang Zhang, Stefan T Thynell
The dimerization of HNO and subsequent yield of N2O in aqueous solution are studied based on the theoretical calculations and kinetic simulations. The initial dimerization reactions were computed at various levels of theory and large divergence was observed in the predictions of the gas-phase free energies. The T1 diagnostics at CCSD(T)/aug-cc-pVTZ suggests multireference characteristics of the HNO dimers and the transition states. The solution-phase free energies were obtained using the wB97XD method and the SMD solvation model...
May 24, 2017: Journal of Physical Chemistry. A
Yogeshwaran Krishnan, Nishant Sharma, Upakarasamy Lourderaj, Manikandan Paranjothy
Gas phase decomposition of protonated amino acids are of great interest due to their role in understanding protein and peptide chemistry. Several experimental and theoretical studies have been reported in the literature on this subject. In the present work, decomposition of the aromatic amino acid protonated tryptophan was studied by on-the-fly classical chemical dynamics simulations using density functional theory. Mass spectrometry and electronic structure theory studies have shown multiple dissociation pathways for this biologically relevant molecule...
May 24, 2017: Journal of Physical Chemistry. A
Toshihiko Maeyama, Takuto Shimamori, Asuka Fujii
Excess-electron binding to dimers and trimers of secondary amide molecules was studied by a combination of photoelectron spectroscopy and theoretical calculations. Vertical detachment energies (VDEs) of the cluster anions were measured in the range of a few hundred meV. We found a tendency for VDE to decline with extension of alkyl side-chains. It was fairly reproduced by results of quantum chemical calculations based on density functional theory. For the optimized structures of the cluster anions, the excess electron is located diffusively around the dangling NH group of the hydrogen-bond acceptor molecule...
May 24, 2017: Journal of Physical Chemistry. A
Jennifer A Ciezak-Jenkins, G M Borstad, I G Batyrev
The high-pressure behavior of 3,4-bis(4-nitro-1,2,5-oxadiazol-3-yl)-1,2,5-oxadiazole (LLM-172) has been studied to 36 GPa by Raman spectroscopy and 50 GPa by X-ray diffraction. The Raman spectra and calculated unit-cell volumes at select pressures show reasonable qualitative agreement with first-principles density functional theory calculations. Raman peaks exhibit a gradual broadening and loss of intensity upon compression to near 20 GPa. Above 20 GPa, most Raman features disappear with the exception of modes associated with the skeletal ring modes...
May 24, 2017: Journal of Physical Chemistry. A
Laura Moroni, Marco Pagliai, Riccardo Chelli, Giangaetano Pietraperzia, Pier Remigio Salvi, Cristina Gellini
1,6-methano[10]annulene solutions into cyclohexane have been subjected to continuous and pulsed UV irradiation. Photolysis occurs in both cases, giving naphthalene as a minor and major product, respectively. The wavelength dependence of the reaction in solution indicates that the photochemical process occurs exciting 1,6-methano[10]annulene in the second and third singlet electronic excited states. The reaction kinetics has been determined under pulsed irradiation. From the time dependence of concentrations, along with the support of density functional theory calculations and early published data, two mechanisms are proposed for naphthalene production...
May 23, 2017: Journal of Physical Chemistry. A
A C F Santos, M A MacDonald, A B Rocha, N Appathurai, M M Sant'Anna, W Holetz, R Wehlitz, L Zuin
The dynamics of the photofragmentation pathways of tetrachloroethylene with photon energies from 15 up to 250 eV encompassing the Cl 2p edge is presented. In order to distinguish the fragmentation channels, the ionic fragments were separated according to their mass-to-charge ratio, measured in coincidence with the photoelectrons, and collected as a function of the incident photon energy. Distinct minima or maxima are found in the partial ion yield in the region between 40 and 50 eV. These features are believed to be associated with the Cooper minimum which results from a molecular orbital with a strong atomic 3p subshell character...
May 23, 2017: Journal of Physical Chemistry. A
Noah E Horwitz, Brian T Phelan, Jordan N Nelson, Catherine M Mauck, Matthew D Krzyaniak, Michael R Wasielewski
Photoexcitation of electron donor-acceptor molecules frequently produces radical ion pairs with well-defined initial spin-polarized states that have attracted significant interest for spintronics. Transfer of this initial spin polarization to a stable radical is predicted to depend on the rates of the radical ion pair recombination reactions, but this prediction has not been tested experimentally. In this study, a stable radical/electron donor/chromophore/electron acceptor molecule, BDPA(•)-mPD-ANI-NDI, where BDPA(•) is α,γ-bisdiphenylene-β-phenylallyl, mPD is m-phenylenediamine, ANI is 4-aminonaphthalene-1,8-dicarboximide, and NDI is naphthalene-1,4:5,8-bis(dicarboximide), was synthesized...
May 22, 2017: Journal of Physical Chemistry. A
Adam Kell, Mahboobe Jassas, Khem Acharya, Kirsty Hacking, Richard J Cogdell, Ryszard J Jankowiak
This work discusses the protein conformational complexity of the B800-850 LH2 complexes from the purple sulfur bacterium Allochromatium vinosum, focusing on the spectral characteristics of the B850 chromophores. Low-temperature B850 absorption and the split B800 band shift blue and red, respectively, at elevated temperatures, revealing isosbestic points. The latter indicates the presence of two (unresolved) conformations of B850 bacteriochlorophylls (BChls), referred to as conformations 1 and 2, and two conformations of B800 BChls, denoted as B800R and B800B...
May 22, 2017: Journal of Physical Chemistry. A
Paul M Zimmerman
The method of increments is herein applied to produce accurate singlet-triplet gaps in a variety of challenging polyatomic systems involving main group elements. This strategy computes incremental Full Configuration Interaction (iFCI) energies for the two spin states in a size-extensive -body expansion. iFCI avoids exponential costs when is small, and thus is dependent on choice of reference function to maintain good accuracy at polynomial cost. The new algorithm presented in this article therefore employs a high-spin perfect pairing reference to capture the major qualities of the singlet and triplet wave functions at = 0...
May 22, 2017: Journal of Physical Chemistry. A
Shahin Hajilar, Behrouz Shafei, Tao Cheng, Andres Jaramillo-Botero
Understanding the structural, thermal, and mechanical properties of thaumasite is of great interest to the cement industry, mainly because it is the phase responsible for the aging and deterioration of civil infrastructures made of cementitious materials attacked by external sources of sulfate. Despite its importance, the effects of temperature and strain rate on the mechanical response of thaumasite have remained unexplored to date. In this study, the mechanical properties of thaumasite are fully characterized using the reactive molecular dynamics (RMD) method...
May 22, 2017: Journal of Physical Chemistry. A
Wei Sun, Zhaowu Wang, Tao Wang, Li Yang, Jun Jiang, Xing Yuan Zhang, Yi Luo, Guoqing Zhang
Room-temperature phosphorescence (RTP) from purely organic systems is of practical importance in biological imaging, oxygen sensing and displaying technologies. The key step to obtaining RTP from organic molecules is efficient intersystem crossing (ISC), which is usually low compared to inorganic materials. Here we show that protonation of a dye molecule, a thioflavin derivative, in strongly polar polyurethane can be used to effectively harness RTP. Prior to protonation, the predominant transition is π-π* for the polymer, which has nearly undetectable RTP due to the large singlet-triplet energy splitting (0...
May 22, 2017: Journal of Physical Chemistry. A
S Ausmeel, C Andersen, O J Nielsen, F F Østerstrøm, M S Johnson, E J K Nilsson
Lactones, cyclic esters of hydroxycarboxylic acids, are interesting biofuel candidates as they can be made from cellulosic biomass and have favorable physical and chemical properties for distribution and use. The reactions of γ-valerolactone (GVL), γ-crotonolactone (2(5H)-F), and α-methyl-γ-crotonolactone (3M-2(5H)-F) with Cl, OD, and O3 were investigated in a static chamber at 700 Torr and 298 ± 2 K. The relative rate method was used to determine kGVL+Cl = (4.56 ± 0.51) × 10(-11), kGVL+OD = (2.94 ± 0...
May 22, 2017: Journal of Physical Chemistry. A
Tianwen Bai, Jun Ling
The normal amine mechanism via proton transferring route (NAM-H) is widely accepted for synthesis of polypeptides with nonionic initiators. Besides proton, trimethylsilyl (TMS) group transferring process has been found in living/controlled polymerization initiated by N-TMS amine in experiments but the corresponding mechanism has never been proposed yet. In this work, we employed density functional theory (DFT) with solvation model to investigate the details of TMS-transfer mechanism, defined as NAM-TMS, for ring-opening polymerization of α-amino acid N-carboxyanhydride...
May 19, 2017: Journal of Physical Chemistry. A
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