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Journal of Physical Chemistry. A

Laszlo Krotos, Gabor Czako
We report a chemically accurate global ab initio full-dimensional potential energy surface (PES) for the Cl(2P3/2) + CH4 reaction improving the high-energy region of our previous PES [Czakó, G.; Bowman, J. M. Science 2011, 334, 343-346]. Besides the abstraction (HCl + CH3) and the Walden-inversion substitution (H + CH3Cl) channels, the new PES accurately describes novel substitution pathways via retention of configuration. Quasiclassical trajectory simulation on this PES reveals that the substitution channel opens around 40 kcal/mol collision energy via Walden inversion and the retention cross sections raise from ∼50 kcal/mol...
November 21, 2017: Journal of Physical Chemistry. A
Brigitte Stucki-Buchli, Philip J M Johnson, Olga Bozovic, Claudio Zanobini, Klemens L Koziol, Peter Hamm, Adnan Gulzar, Steffen Wolf, Sebastian Buchenberg, Gerhard Stock
We explore the capability of the non-natural amino acid azidohomoalanine (AHA) as an IR label to sense relatively small structural changes in proteins with the help of 2D IR difference spectroscopy. To that end, we AHA-labelled an allosteric protein (the PDZ2 domain from human tyrosine-phosphatase 1E) and furthermore covalently linked it to an azobenzene-derived photoswitch as to mimic its conformational transition upon ligand binding. To determine the strengths and limitations of the AHA label, in total six mutants have been investigated with the label at sites with varying properties...
November 21, 2017: Journal of Physical Chemistry. A
Manoj Kumar, Joseph S Francisco
Using theoretical calculations and Born Oppenheimer molecular dynamics simulations, it is shown here that Criegee intermediate, which is principally produced in the olefin ozonolysis, can activate H-X (X = H, CH3, CH2F, CHF2, CF3, and SiH3) under mild conditions, a reaction that has long been known for transition metals. The zwitter ionic electronic structure of Criegee intermediate makes it an interesting metal-free system for activating enthalpically strong small molecules such as H2, methane, silanes, and boranes...
November 21, 2017: Journal of Physical Chemistry. A
Jasper D Cook, Thomas J Carey, Dylan H Arias, Justin C Johnson, Niels H Damrauer
A detailed photophysical picture is elaborated for a structurally well-defined and symmetrical bis-tetracene dimer in solution. The molecule was designed for interrogation of the initial photophysical steps (S1 → (1)TT) in intramolecular singlet fission (SF). (Triisopropylsilyl)acetylene substituents on the dimer TIPS-BT1 as well as a monomer model TIPS-Tc enable a comparison of photophysical properties, including transient absorption dynamics, as solvent polarity is varied. In nonpolar toluene solutions, TIPS-BT1 decays via radiative and nonradiative pathways to the ground state with no evidence for dynamics related to the initial stages of SF...
November 21, 2017: Journal of Physical Chemistry. A
James A Phillips, Samuel J Danforth, Nicholas J Hora, John R Lanska, Anna W Waller
The FCH2CN-BCl3 and ClCH2CN-BCl3 complexes were investigated by quantum-chemical computations and low-temperature, matrix-isolation-IR spectroscopy. Theory predicts two stable equilibrium structures, with distinctly different B-N distances, for both complexes. One set of structures, which correspond to the global energy minima, exhibit B-N distances of 1.610 and 1.604 Å for FCH2CN-BCl3 and ClCH2CN-BCl3, respectively (via M06-2X/aug-cc-pVTZ). The corresponding binding energies are 5.3 and 6.3 kcal/mol. For the metastable structures, the B-N distances are 2...
November 21, 2017: Journal of Physical Chemistry. A
S Pelloni, P F Provasi, G I Pagola, M B Ferraro, P Lazzeretti
The trace of tensors that account for chiroptical response of the H2O2 molecule is a function of the HO-OH dihedral angle. It vanishes at 0° and 180°, due to the presence of molecular symmetry planes, but also for values in the range 90-100° of this angle, in which the molecule is unquestionably chiral. Such an atypical effect is caused by counterbalancing contributions of diagonal tensor components with nearly maximal magnitude but opposite sign, determined by electron flow in open or closed helical paths, and associated with induced electric and magnetic dipole moments and anapole moments...
November 21, 2017: Journal of Physical Chemistry. A
Yavuz S Ceylan, Thomas R Cundari
A computational analysis of model transition-metal terminal boride [MB(PNP(R))] complexes is reported. A combination of density functional theory methods, natural bond orbital analysis, and multiconfiguration self-consistent field calculations were employed to investigate the structure and bonding of terminal boride complexes, in particular, the extent of metal dπ-boron pπ bonding. Comparison of metal-boride, -borylene, and-boryl bond lengths confirms the presence of metal-boron π bonds, albeit the modest shortening (∼3%) of the metal-boron bond suggests that the π-bonding is very weak in terminal borides...
November 21, 2017: Journal of Physical Chemistry. A
Darin J Ulness, Daniel B Turner
Two-quantum two-dimensional electronic spectroscopy (2Q 2D ES) may provide a measure of electron-correlation energies in molecules. Attempts to obtain this profound but elusive signal have relied on experimental implementations using femtosecond laser pulses, which induce an overwhelming background signal of nonresonant response. Here we explore theoretically the signatures of electron correlation in coherent 2Q 2D ES measurements that use spectrally incoherent light, I((4)) 2Q 2D ES. One can use such fields to suppress nonresonant response, and therefore this method may better isolate the desired signature of electron correlation...
November 21, 2017: Journal of Physical Chemistry. A
Vladislav S Krasnoukhov, Denis P Porfiriev, Igor P Zavershinskiy, Valeriy N Azyazov, Alexander M Mebel
Formation of fulvene and benzene through the reaction of cyclopentadienyl (C5H5) with methyl radical (CH3) and consequent dissociation of its primary C6H7 products has been studied using ab initio and theoretical kinetics calculations. The potential energies and geometries of all involved species have been computed at the CCSD(T)-F12/cc-pVTZ-f12//B2PLYPD3/aug-cc-pVDZ level theory. Multichannel/multiwell RRKM-Master Equation calculations have been utilized to produce phenomenological pressure- and temperature-dependent absolute and individual-channel rate constants for various reactions at the C6H8 and C6H7 potential energy surfaces...
November 21, 2017: Journal of Physical Chemistry. A
Xi Chen, C Franklin Goldsmith
A detailed analysis of the reaction of CH3CCH2 and CH3CHCH with molecular oxygen is presented. The C3H5O2 potential energy surface was characterized using a combination of electronic structure methods. The majority of the stationary points on the PES was determined at the CCSD(T)-F12a/cc-pVTZ-F12//B2PLYPD3/cc-pVTZ level of theory, with the remaining transition states computed using multireference methods. Microcanonical rate theory and the master equation are used to determine the temperature- and pressure-dependent rate coefficients for each reaction channel...
November 21, 2017: Journal of Physical Chemistry. A
Tapta Kanchan Roy, Natalia S Nagornova, Oleg V Boyarkin, R Benny Gerber
The intrinsic structures of biomolecules in the gas phase may not reflect their native solution geometries. Microsolvation of the molecules bridges the two environments, enabling a tracking of molecular structural changes upon hydration at the atomistic level. We employ density functional calculations to compute a large pool of structures and vibrational spectra for a gas-phase complex, in which a doubly protonated decapeptide, gramicidin S, is solvated by two water molecules. Though most vibrations of this large complex are treated in a harmonic approximation, the water molecules and the vibrations of the host ion coupled to them are locally described by a quantum mechanical vibrational self-consistent field theory with second-order perturbation correction (VSCF-PT2)...
November 21, 2017: Journal of Physical Chemistry. A
Anthony W Schlimgen, David A Mazziotti
Metal dithiolates have a wide range of applications from catalysis to molecular conductors with the ligands being the source of electrons during electrochemical oxidation in an effect known as ligand noninnocence. Recent large-scale variational two-electron reduced-density matrix (2-RDM) calculations of the vanadium oxo complex and manganese superoxide dismutase show that quantum entanglement stabilizes the addition of an electron to the ligands, providing a quantum mechanical explanation for ligand noninnocence...
November 20, 2017: Journal of Physical Chemistry. A
Vytor Pinheiro Oliveira, Elfi Kraka
The noncovalent interactions of 32 complexes involving pnicogens, chalcogens and halogens atoms were investigated at the CCSD(T)/aug-cc-pVTZ level of theory. Two different types of complexes could be distinguished based on geometric parameters, electron difference densities, and the charge transfer mechanisms associated with each type. In the type I conformation, the monomers adopt a skewed orientation allowing charge to be transfer between both monomers, whereas in the type II conformation the monomers adopt a linear arrangement, maximizing charge transfer in only one direction...
November 20, 2017: Journal of Physical Chemistry. A
Santanab Giri, Rakesh Parida, Madhurima Jana, Soledad Gutierrez-Oliva, Alejandro Toro-Labbé
The mechanism of ground and excited state double proton transfer reaction in formic acid dimer has been analyzed with the help of reaction force and the reaction electronic flux. The separation of reaction electronic flux in terms of electronic activity and reactivity, NBO, dual descriptor lends additional support for the mechanism. Interestingly we found that, the ground state double proton transfer mechanism is concerted synchronic, whereas the excited state double proton transfer is concerted asynchronic in nature...
November 20, 2017: Journal of Physical Chemistry. A
Farnaz Heidar-Zadeh, Paul Woodson Ayers, Toon Verstraelen, Ivan Vinogradov, Esteban Vöhringer-Martinez, Patrick Bultinck
Many population analysis methods are based on the precept that molecules should be built from fragments (typically atoms) that maximally resemble the isolated fragment. The resulting molecular building blocks are intuitive (because they maximally resemble well-understood systems) and transferable (because if two molecular fragments both resemble an isolated fragment, they necessarily resemble each other). Information theory is one way to measure the deviation between molecular fragments and their isolated counterparts, and one that lends itself to analysis...
November 17, 2017: Journal of Physical Chemistry. A
Eugene B Gordon, Alexander Vladimirovich Karabulin, Mikhail I Kulish, Vladimir Igorevich Matyushenko, Maxim E Stepanov
The thermal emission study in this work has shown that coagulation of metals in liquid helium is accompanied by enormous local overheating of several thousand degrees. Direct experiments demonstrated, for the first time, that condensation of metals in superfluid helium occurs via the specific mechanism which is substantially faster than that in normal liquid helium. It has been stated that coagulation of metals in superfluid helium indeed occurs in two stages - a "hot" one of nanoparticles coalescence with the formation of molten nanospheres and the subsequent stage of their sticking together into nanowires...
November 17, 2017: Journal of Physical Chemistry. A
Yi Yuan, Xiaocan Zhao, Sainan Wang, Liming Wang
Atmospheric oxidation mechanism of furan and methyl furans (MFs) initiated by OH radicals is studied using high-level quantum chemistry and kinetic calculations. The reaction starts mainly with OH addition to C2/C5-position, forming highly chemically activated adduct radical R2*/R5*, which would either be stabilized by collision or promptly isomerize to R2B*/R5B* by breaking the C2-O/C5-O bond and then isomerize to other conformers of R2B/R5B by internal rotations. Under the atmospheric conditions, the ring-retaining radical R2/R5 would recombine with O2 and be converted to a 5-hydroxy-2-furanone compound and a compound containing epoxide, ester, and carbonyl functional groups, while the ring-opening radicals R2B/R5B would react with O2 and form unsaturated 1,4-dicarbonyl compounds...
November 17, 2017: Journal of Physical Chemistry. A
Leonid L Rusevich, Guntars Zvejnieks, Alessandro Erba, Roberto Dovesi, Eugene E Kotomin
An enhancement of the piezoelectric properties of lead-free materials, which allow conversion of mechanical energy into electricity, is a task of great importance and interest. Results of first-principles calculations of piezoelectric/electromechanical properties of the Ba(1-x)SrxTiO3 (BSTO) ferroelectric solid solution with perovskite structure are presented and discussed. Calculations are performed within the linear combination of atomic orbitals (LCAO) approximation and periodic-boundary conditions, using advanced hybrid functionals of the density-functional-theory (DFT)...
November 17, 2017: Journal of Physical Chemistry. A
George Bajan Bacskay, Sture Nordholm
This work addresses the continuing disagreement between two schools of thought concerning the mechanism of covalent bonding. According to Hellmann, Ruedenberg and Kutzelnigg, covalent bonding is a quantum mechanical phenomenon whereby lowering of the kinetic energy associated with electron sharing, i.e. delocalization, is the key stabilization mechanism. The opposing view of Slater, Feynman and Bader has maintained that the source of stabilization is electrostatic potential energy lowering due to electron density redistribution to binding regions between nuclei...
November 17, 2017: Journal of Physical Chemistry. A
Diego A Cortes, Matthew J Elrod
Laboratory and field measurements have demonstrated that an isoprene-derived epoxide intermediate (IEPOX) is the origin of a wide range of chemical species found in ambient secondary organic aerosol (SOA). In order to explore the potential relevance of a similar mechanism for the formation of monoterpene-derived SOA, nuclear magnetic resonance techniques were used to study kinetics and reaction products of the aqueous phase reactions of several monoterpene epoxides: β-pinene oxide, limonene oxide, and limonene dioxide...
November 17, 2017: Journal of Physical Chemistry. A
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