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Journal of Physical Chemistry. A

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https://www.readbyqxmd.com/read/27809534/dynamic-conversion-between-se-n-covalent-and-noncovalent-interactions
#1
Meng Xie, Lili Wang, Fang Liu, Dongju Zhang, Jun Gao
Se-N dynamic covalent bond is a new dynamic covalent bond which has applications in the fabrication of stimuli responsive and self-healing functional materials. Although recent advances have been achieved in the experimental aspect, little is known about the formation mechanism of Se-N dynamic covalent bond. Here the structures and nature of Se-N dynamic covalent bond between three kinds of pyridine derivatives R-C5H4N, [pyridine (R = H), 4-methylpyridine (R = CH3), 4-dimethylamino-pyridine (R = N(CH3)2)] and phenylselenyl bromine (PhSeBr) have been analyzed using density functional theory...
November 3, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27809530/an-ab-initio-investigation-of-the-ground-states-of-f2p-s-n-f2pns-and-f2psn
#2
Jiwon Moon, Heehyun Baek, Joonghan Kim
A recent spectroscopic experiment identified difluorothiophosphoryl nitrene (F2P(S)N) and found that it showed rich photochemistry. However, a discrepancy between the experimental results and the quantum chemical calculations was reported. Thus, high-level ab initio calculations using the coupled-cluster singles and doubles with perturbative triples and second-order multiconfigurational perturbation theory were performed to elucidate this inconsistency. The discrepancy arose due to the failure to consider the triplet state of difluoro(thionitroso)phosphine (F2PNS)...
November 3, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27809528/structural-characterization-of-sulfur-containing-water-clusters-using-a-density-functional-based-tight-binding-approach
#3
Kseniia A Korchagina, Aude Simon, Mathias Rapacioli, Fernand Spiegelman, Jérôme Cuny
A global optimization search of low-energy isomers is carried out to investigate the structural and stability properties of sulfur-containing water clusters, including both (H2O)nSO4(2-) and (H2O)nH2SO4 aggregates. The systematic optimization algorithm involves a combination of parallel-tempering molecular dynamics and periodic gradient-driven quenches with energy and energy-gradient calculations performed using the Self-Consistent-Charge Density-Functional based Tight-Binding (SCC-DFTB) scheme. Comparisons with new MP2 and DFT calculations on the smallest systems and previous ab initio investigations of the literature show that the SCC-DFTB approach provides a fairly accurate description of both neutral and ionic species, comparable to that of DFT...
November 3, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27809523/similarities-and-differences-between-rna-and-dna-double-helical-structures-in-circular-dichroism-spectroscopy-a-sac-ci-study
#4
Tomoo Miyahara, Hiroshi Nakatsuji, Hiroshi Sugiyama
The helical structures of DNA and RNA are investigated experimentally using circular dichroism (CD) spectroscopy. The signs and the shapes of the CD spectra are much different between the right- and left-handed structures as well as between DNA and RNA. The main difference lies in the sign at around 295 nm of the CD spectra: it is positive for the right-handed B-DNA and the left-handed Z-RNA but is negative for the left-handed Z-DNA and the right-handed A-RNA. We calculated the SAC-CI CD spectra of DNA and RNA using the tetramer models, which include both hydrogen-bonding and stacking interactions that are important in both DNA and RNA...
November 3, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27805406/organometallic-chalcones-functioning-as-radical-traps-observations-on-the-solvated-electron-reduction-and-the-c-%C3%A2-h2oh-and-c-%C3%A2-h2cl-addition-processes-a-time-resolved-mechanistic-study
#5
Tamara Maldonado, Guillermo J Ferraudi, Alexander Graham Lappin, Fernando Godoy
The pulse radiolysis method was used to investigate reactions between organometallic chalcones derived from ferrocene, cyrhetrene and cymantrene substituted with a phenyl (R1) or a 4'-Benzo-15-Crown-5 (B1) moiety and the solvated electron, e(-)sol, and two radicals. The principal spectroscopic transformations resolved with the e(-)sol reactions reveal that the chalcone compounds react under the diffusion controlled regime with little difference due to the organic substituent. The principal reaction product is the radical anion chalcone, centered in the -C(=O)CH=CH- moiety...
November 2, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27805402/computational-study-of-ways-by-which-exo-silatranes-might-be-prepared
#6
Carolynn Hoeksema, Marc Jordan Adler, Thomas Marlowe Gilbert
Exo-silatranes involve cage structures where the nitrogen lone pair points away from the cage rather than into it. This distinguishes them from the well-established endo-silatranes. Exo-silatranes have not been observed experimentally, consistent with a significant benefit to silicon-nitrogen interactions inside the cages as suggested for endo-silatranes. Identifying examples of exo-silatranes would prove useful in understanding Si-N interactions, as they would represent the "no interaction" extreme of the spectrum...
November 2, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27805397/electronic-structure-and-potential-reactivity-of-silaaromatic-molecules
#7
Yang Yang, Martin A Mosquera, Kwan Skinner, Andres E Becerra, Vasgen A Shamamian, George C Schatz, Mark A Ratner, Tobin J Marks
Silicon-based materials are crucial for conventional electronics. The fascinating properties of the new two-dimensional material silicene, the silicon analogue of graphene (one atom- thick silicon sheets), offer a potential bridge between conventional and molecular electronics. The ground-state configuration of silicene is buckled, which compromises optimal constructive overlap of p orbitals. Because silicene is not planar like graphene, it has a lower, intrinsic, electron/hole mobility than graphene. This motivates a search for improved, alternative, planar ma- terials...
November 2, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27802385/two-photon-excited-fluorescence-encoded-infrared-spectroscopy
#8
Joseph Nathanael Mastron, Andrei Tokmakoff
We report on a method for performing ultrafast infrared (IR) vibrational spectroscopy using fluorescence detection. Vibrational dynamics on the ground electronic state driven by femtosecond mid-infrared pulses are detected by changes in fluorescence amplitude resulting from modulation of a two-photon visible transition by nuclear motion. We examine a series of coumarin dyes and study the signals as a function of solvent and excitation pulse parameters. The measured signal characterizes the relaxation of vibrational populations and coherences, but yields different information than conventional IR transient absorption measurements...
November 1, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27802382/locating-the-proton-in-nicotinamide-protomers-via-low-resolution-uv-action-spectroscopy-of-electrosprayed-solutions
#9
Edward Matthews, Caroline E H Dessent
Even in relatively simple molecules, the sites of protonation or deprotonation formed upon electrospray ionization can be controversial. This situation means that it is important to develop new approaches for identifying "protomers" and "deprotomers". In this study, we demonstrate that routine, low-resolution UV laser photodissociation spectroscopy in an adapted commercial mass spectrometer can be applied to identify the gaseous protomers of nicotinamide formed upon electrospray. Nicotinamide is an important biological molecule that posesses multiple protonation sites associated with its pyridine and amide groups...
November 1, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27802060/halogen-%C3%AF-interactions-between-benzene-and-x2-cx4-x-cl-br-assessment-of-various-density-functionals-with-respect-to-ccsd-t
#10
Il-Seung Youn, Dong Yeon Kim, Woo Jong Cho, Jenica Marie L Madridejos, Han Myoung Lee, Maciej Kolaski, Joonho Lee, Chunggi Baig, Seung Koo Shin, Michael Filatov, Kwang S Kim
Various types of interactions between halogen (X) and π moiety (X-π interaction) including halogen bonding play important roles in forming the structures of biological, supramolecular, and nanomaterial systems containing halogens and aromatic rings. Furthermore, halogen molecules such as X2 and CX4 (X = Cl/Br) can be intercalated in graphite and bilayer graphene for doping and graphene functionalization/modification. Due to the X-π interactions, though recently highly studied, their structures are still hardly predictable...
November 1, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27802050/a-computational-mechanistic-study-of-redox-neutral-rh-iii-catalyzed-c-h-activation-reactions-of-arylnitrones-with-alkynes-role-of-noncovalent-interactions-in-controlling-selectivity
#11
Yang-Yang Xing, Jian-Biao Liu, Ying-Ying Tian, Chuan-Zhi Sun, Fang Huang, De-Zhan Chen
The mechanism of redox-neutral Rh(III)-catalyzed coupling reactions of arylnitrones with alkynes was investigated by density functional theory (DFT) calculations. The free energy profiles associated with the catalytic cycle, involving C(sp(2))-H activation, insertion of alkyne, transfer of O atom, cyclization and protodemetalation, are presented and analyzed. An overwhelming preference for alkyne insertion into Rh-C over Rh-O is observed among all pathways, and the most favorable route is determined. The pivalate-assisted C-H activation step is turnover-limiting, and the cyclization step determines the diastereoselectivity of the reaction, with the stereoselectivity arising mainly from the difference of noncovalent interactions in key transition states...
November 1, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27802038/photophysical-and-electrochemical-characterization-of-bodipy-containing-dyads-comparing-the-influence-of-an-a-d-a-versus-d-a-motif-on-excited-state-photophysics
#12
Samuel J Hendel, Ambata M Poe, Piyachai Khomein, Youngju Bae, S Thayumanavan, Elizabeth R Young
A complete photophysical characterization of organic molecules designed for use as molecular materials is critical in the design and construction of devices such as organic photovoltaics (OPV). The nature of a molecule's excited state will be altered in molecules employing the same chromophoric units but possessing different molecular architectures. For this reason, we examine the photophysical reactions of two BODIPY-based D-A and A-D-A molecules, where D is the donor and A is the acceptor. A BODIPY (4,4'-difluoro-4-bora-3a,4a-diaza-s-indacene) moiety serves as the A component and is connected through the meso position using a 3-hexylthiophene linker to a N-(2-ethylhexyl)dithieno[3,2-b:2',3'-d]pyrrole (DTP), which serves as the D component...
November 1, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27802030/temperature-dependence-of-hebr2-isomers-stability-through-rovibrational-mctdh-calculations
#13
Orlando Carrillo-Bohorquez, Alvaro Valdes, Rita Prosmiti
The multiconfiguration time-dependent Hartree (MCTDH) method using a six-dimensional Hamiltonian that includes all rotational and vibrational degrees of freedom and an ab initio potential energy surface was employed to calculate the rovibronic states of the HeBr2 van der Waals complex. All rotational states of energies within 7 cm -1 with respect to the energy of the linear ground state were calculated without restriction of the total angular momentum. In total, we obtained 500 and 320 rotationally excited states of the ground vibrational T-shaped and linear isomers of the HeBr2, respectively, and compared them with those predicted by the rigid rotor model...
November 1, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27801581/diabatization-for-time-dependent-density-functional-theory-exciton-transfers-and-related-conical-intersections
#14
Hiroyuki Tamura
Intermolecular exciton transfers and related conical intersections are analyzed by diabatization for time-dependent density functional theory. The diabatic states are expressed as a linear combination of the adiabatic states so as to emulate the well-defined reference states. The singlet exciton coupling calculated by the diabatization scheme includes contributions from the Coulomb (Förster) and electron exchange (Dexter) couplings. For triplet exciton transfers, the Dexter coupling, charge transfer integral, and diabatic potentials of stacked molecules are calculated for analyzing direct and superexchange pathways...
November 1, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27800689/ab-initio-modeling-of-friction-reducing-agents-shows-quantum-mechanical-interactions-can-have-macroscopic-manifestation
#15
Juan de Dios Hernández Velázquez, Joaquín Barroso-Flores, Armando Gama Goicochea
Two of the most commonly encountered friction reducing agents used in plastic sheet production are the amides known as erucamide and behenamide, which despite being almost identical chemically, lead to markedly different values of the friction coefficient. To understand the origin of this contrasting behavior, in this work we model brushes made of these two types of linear - chain molecules using quantum mechanical numerical simulations under the Density Functional Theory at the B97D/6-31G(d,p) level of theory...
November 1, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27798961/reactions-of-atomic-carbon-with-butene-isomers-implications-for-molecular-growth-in-carbon-rich-environments
#16
Jeremy Bourgalais, Michael Spencer, David L Osborn, Fabien Goulay, Sebastien D Le Picard
Product detection studies of C(3P) atom reactions with butene (C4H8) isomers (but-1-ene, cis-but-2-ene, trans-but-2-ene) are carried out in a flow tube reactor at 353 K and 4 Torr under multiple collision conditions. Ground state carbon atoms are generated by 248 nm laser photolysis of tetrabromomethane, CBr4, in a buffer of helium. Thermalized reaction products are detected using synchrotron tunable VUV photoionization and time of flight mass spectrometry. The temporal profiles of the detected ions are used to discriminate products from side or secondary reactions...
October 31, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27798960/reinvestigation-of-the-unimolecular-reactions-of-chf2chf2-identification-of-the-1-1-hf-elimination-component-from-addition-of-chf2cf-to-trans-2-butene
#17
Caleb A Smith, George L Heard, Donald W Setser, Bert E Holmes
The recombination of •CHF2 radicals in a room temperature bath gas was used to generate CHF2CHF2* molecules with 96 kcal mol-1 of vibrational energy. The CHF2CHF2* molecules decompose by four-centered 1,2-HF elimination and by three-centered 1,1-HF elimination reactions to give HF and either CHF=CF2 or :CFCHF2, respectively. The 1,1-HF component was identified by trapping the :CFCHF2 carbene with trans-2-butene that forms 1-fluoro-1-difluoromethyl-2,3-dimethylcyclopropane. The total rate constant for the decomposition of CHF2CHF2* was 6...
October 31, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27797521/accurate-determination-of-equilibrium-structure-of-3-aminophthalonitrile-by-gas-electron-diffraction-and-coupled-cluster-computations-structural-effects-due-to-intramolecular-charge-transfer
#18
Natalja Vogt, Denis S Savelyev, Nina I Giricheva, Mikhail K Islyaikin, Georgiy V Girichev
For the first time, the molecular structure of 3-aminophthalonitrile with unique electronic properties has been determined by the gas electron diffraction (GED) method supported by a mass spectrometric analysis of the gas phase. Moreover, it has been optimized at the high-level quantum-chemical coupled-cluster theory, CCSD(T), in conjunction with the triple-ζ basis set. The equilibrium structure has been determined from the GED data taking into account harmonic and anharmonic vibrational corrections estimated from the quantum-chemical force field (up to cubic terms)...
October 31, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27797519/symmetry-dependent-intramolecular-charge-transfer-dynamics-of-pyrene-derivatives-investigated-by-two-photon-excitation
#19
Sangsu Lee, Dongho Kim
Intramolecular charge transfer (ICT) processes in two-photon (TP) allowed states were investigated using three pyrene derivatives N1, N2C, and N2T, which have different molecular symmetry depending on the number and position of N,N-dimethylaniline donating substituents. Based on steady-state and non-degenerate two-photon absorption measurements, we investigated femtosecond transient absorption (TA) spectra by one- (OPE) and two-photon excitation (TPE). In the analysis of TA spectra, we discovered that the transfer rate from locally excited state to the ICT state by TPE is slower than that by OPE, indicating that the energy barrier between the TP and ICT states is higher than that between the one-photon (OP) allowed and ICT states...
October 31, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27797515/dependence-of-nonadiabatic-couplings-with-kohn-sham-orbitals-on-the-choice-of-density-functional-pure-vs-hybrid
#20
Yuhan Lin, Alexey V Akimov
Nonadiabatic molecular dynamics (NA-MD) is an extremely useful approach to model electron transfer dynamics in molecular and solid state systems. The performance of NA-MD simulations depends critically on the accuracy of the underlying electronic structure properties, such as state energies and nonadiabatic couplings (NAC). Practical NA-MD modeling relies extensively on computationally efficient pure density functionals, despite the known intrinsic problems of the latter. A reliable solution to the problems presented by the use of pure density functionals, is the use of hybrid functionals, however hybrid functionals are significantly more expensive...
October 31, 2016: Journal of Physical Chemistry. A
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