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Journal of Physical Chemistry. A

David J Masiello, William Parker Reinhardt
Macroscopic, many-body self-trapped and quantum superposition states of the gaseous double-well Bose-Einstein condensate (BEC) are investigated within the context of a multiconfigurational bosonic self-consistent field theory based upon underlying spatially symmetry-broken one-body wave functions. To aid in the interpretation of our results, an approximate model is constructed in the extreme Fock state limit, in which self-trapped and superposition states emerge in the many-body spectrum, striking a delicate balance between the degree of symmetry breaking, the effects of the condensate's mean field, and that of atomic correlation...
February 20, 2019: Journal of Physical Chemistry. A
Gabriel Frederico Martins, Benedito J Costa Cabral
The electron binding energies for the trans and cis conformers of azobenzene (AB), a prototypical photo-switch, were investigated by electron propagator theory (EPT). The EPT results are compared with data from photoelectron and electron transmission spectroscopies and complemented by the calculation of the differences between vertical and adiabatic ionization energies and electron affinities of the AB conformers. These differences are discussed in terms of the geometry changes associated with the processes of ionization and electron attachment...
February 19, 2019: Journal of Physical Chemistry. A
Thais Scott, Reed Nieman, Adam Luxon, Boyi Zhang, Hans Lischka, Laura Gagliardi, Carol A Parish
Three diradical pyrazine isomers were characterized using highly correlated, multi-reference methods. The lowest lying singlet and triplet state geometries of 2,3-didehydropyrazine (ortho), 2,5-didehydropyrazine (para) and 2,6-didehydropyrazine (meta) were determined. Two active reference spaces were utilized. The complete active space (CAS) (8o,8e) includes the σ and σ* orbitals on the dehydrocarbon atoms as well as the valence π and π* orbitals. The CAS (12o,10e) reference space includes two additional orbitals corresponding to the in-phase and out-of-phase nitrogen lone pair orbitals...
February 19, 2019: Journal of Physical Chemistry. A
Sijia S Dong, Kevin Benchen Huang, Laura Gagliardi, Donald G Truhlar
Mixed-valence compounds with strong couplings between electronic states constitute one of the most challenging types of multireference systems for electronic structure theory. Previous work on a model mixed-valence compound, the 2,2´,6,6´-tetrahydro-4H,4´H-5,5´-spirobi[cyclopenta[c]pyrrole] cation, showed that multireference perturbation theory (MRPT) can give a physical energy surface for the mixed-valence compound only by going to the third order or by using a scheme involving averaging orbital energies in a way specific to mixed-valence systems...
February 19, 2019: Journal of Physical Chemistry. A
Nour-Eddine Ghermani
In this paper, the molecular electrostatic potential energy V is first estimated from the electric field generated by an experimental electron density. Once the high resolution X-ray diffraction data are fitted against the Hansen-Coppens multipole model, the electric field E is analytically computed on every point inside and around the molecule by using our own software FIELD. The potential energy is then obtained by a numerical and robust integration of E2/2. The topological analysis of the electric field is carried out to reveal the specific contribution of atoms in a molecule...
February 18, 2019: Journal of Physical Chemistry. A
Donglian Huang, Shanfeng Chen, Jingzhi Pu, Xuecai Tan, Yan Zhou
Cyclobutane pyrimidine dimer (CPD) is a major photoproduct of deoxyribonucleic acid (DNA) that is damaged by ultraviolet light. This DNA lesion can be repaired by DNA photolyase with the aid of UV light and two cofactors. To understand the repair mechanism of CPD and whether protonation of CPD participates in the DNA repair process, the cycloreversion reactions of four CPD models and proton transfers between the adjacent residue Glu283 and CPD models were explored through quantum mechanical method. Two-dimensional maps of potential energy surface in vacuum and in implicit water solution were calculated at the ωB97XD/6-311++G(2df,2pd) level...
February 18, 2019: Journal of Physical Chemistry. A
Engelbert Reusch, Dustin Kaiser, Domenik Schleier, Rachel Buschmann, Anke Krüger, Thomas Hermann, Bernd Engels, Ingo Fischer, Patrick Hemberger
Mass-selective threshold photoelectron spectroscopy in the gas phase was employed to characterize the dialkynyl triplet carbenes pentadiynylidene (HC5H), methylpentadiynylidene (MeC5H) and dimethylpentadiynylidene (MeC5Me). Diazo compounds were employed as precursors to generate the carbenes by flash pyrolysis. The R1-C5-R2 carbon chains were photoionized by vacuum ultraviolet (VUV) synchrotron radiation in photoelectron photoion coincidence (PEPICO) experiments. High-level ab initio computations were carried out to support the interpretation of the experiments...
February 18, 2019: Journal of Physical Chemistry. A
Mark Fedkin, Yun Kyung Shin, Nabankur Dasgupta, Jejoon Yeon, Weiwei Zhang, Diana van Duin, Adri C T van Duin, Kento Mori, Atsushi Fujiwara, Masahiko Machida, Hiroki Nakamura, Masahiko Okumura
A new ReaxFF reactive force field has been developed for water-electrolyte systems including cations Li+, Na+, K+ and Cs+, and anions F-, Cl- and I-. The reactive force field parameters have been trained against quantum mechanical (QM) calculations related to water binding energies, hydration energies and energies of proton transfer. The new force field has been validated by applying it to molecular dynamics (MD) simulations of the ionization of different electrolytes in water and comparison of the results with experimental observations and thermodynamics...
February 18, 2019: Journal of Physical Chemistry. A
Vasilii M Khanin, Ivan I Vrubel, Roman G Polozkov, Ivan A Shelykh, Ivan D Venevtsev, Piotr A Rodnyi, Herfried Wieczorek, Jack Boerekamp, Sandra Spoor, Andries Meijerink, Cees R Ronda
Afterglow is an important phenomenon in luminescent materials and can be desired (e.g. persistent phosphors) or undesired (e.g. scintillators). Understanding and predicting afterglow is often based on analysis of thermally stimulated luminescence (TSL) glow curves assuming the presence of one or more discrete trap states. Here we present a new approach for the description of the time-dependent afterglow from TSL glow curves using a model with a distribution of trap depths. The method is based on the deconvolution of the energy dependent density of occupied traps derived from TSL glow curves using Tikhonov regularization...
February 18, 2019: Journal of Physical Chemistry. A
Fethi Khaled, Binod Raj Giri, Dapeng Liu, Emmanuel Assaf, Christa Fittschen, Aamir Farooq
Hydroxyl radicals and olefins are quite important from combustion and atmospheric chemistry standpoint. Large amounts of olefinic compounds are emitted into the earth's atmosphere from both biogenic and anthropogenic sources. Olefins make a significant share in the tranportation fuels (e.g., up to 20% by volume in gasoline), and they appear as important intermediates during hydrocarbon oxidation. As olefins inhibit low-temperature heat release, they have caught some attention for their applicability in future advanced combustion engine technology...
February 15, 2019: Journal of Physical Chemistry. A
Volker Beutner, Liam M Duffy, Henning Meyer
We investigate the potential for sensitively detecting mm-wave absorption through multi-photon ionization using the lowest rotational transition in CO (X$^1\Sigma$, J=1 $\leftarrow$ J=0) at 115~GHz as a diagnostic tool. This transition represents an almost perfect realization of a quantum mechanical 2-level system. In the experiment, the output of a powerful continuous mm-wave source with sub-kHz resolution propagates counter to a pulsed molecular beam causing Doppler shifted resonances. Absorption is detected by monitoring the involved rotational levels through resonance enhanced multi-photon ionization (REMPI)...
February 15, 2019: Journal of Physical Chemistry. A
Federico J Hernandez, Franco P Bonafé, Bálint Aradi, Thomas Frauenheim, Cristian G Sanchez
In the present work we have applied a fully atomistic electron-nuclear real-time propagation protocol to compute the impulsive vibrational spectroscopy of the five DNA/RNA nucleobases in order to study the very first steps (sub-picosecond) of their energy distribution after UV excitation. We have observed that after the pump pulse absorption, the system is prepared in a coherent superposition of the ground and the pumped electronic excited states in the equilibrium geometry of the ground state. Furthermore, for relatively low fluency values of the pump pulse, the dominant contribution to the electronic wavefunction of the coherent state is of the ground state and the mean potential energy surface within the Ehrenfest approximation is similar to that of the ground state...
February 15, 2019: Journal of Physical Chemistry. A
Chen Zhou, Laura Gagliardi, Donald G Truhlar
The energetic order of four states of iron porphyrin, FeP, is studied by the multi-configuration pair-density functional method (MC-PDFT). Five active space prescriptions, namely CAS(8, 6), CAS(8, 11), CAS(16, 15), RAS(34,2,2;13,6,16), and DMRG(34, 35), are used to obtain the kinetic energy, density, and on-top density. Although the ground spin state of FeP depends on the selection of the active space when one uses second-order perturbation theory, all five active spaces correctly lead to a triplet ground state by PDFT...
February 14, 2019: Journal of Physical Chemistry. A
Lynn Ferres, Jenny Cheung, Wolfgang Stahl, Ha Vinh Lam Nguyen
The microwave spectrum of 3,4-dimethylanisole, a molecule containing three methyl groups allowing for internal rotation, was recorded using a pulsed molecular jet Fourier transform microwave spectrometer operating in the frequency range from 2.0 to 26.5 GHz. Quantum chemical calculations yielded two conformers with a trans and a cis configuration of the methoxy group, both of which were assigned in the experimental spectrum. Torsional splittings due to the internal rotations of two methyl groups attached to the aromatic ring were resolved and analysed...
February 14, 2019: Journal of Physical Chemistry. A
Tomoo Miyahara, Hiroshi Nakatsuji
Bacteriorhodopsin (BR) and Halorhodopsin (HR) are well-known light-driven ion-pumping rhodopsins. BR transfers a proton from the intracellular medium to the extracellular medium. HR takes in chloride-ion from the extracellular medium. A new light-driven sodium-ion-pumping rhodopsin was discovered in 2013 by Inoue, Kandori and co-workers (Nat. Commun. 2013, 4, 1678). The purpose of this article is to elucidate the proton, sodium-ion and chloride-ion transfer mechanisms and the geometrical changes of the intermediates...
February 14, 2019: Journal of Physical Chemistry. A
Manish Sharma, Daniel Sethio, Latévi Max Lawson Daku, Hans Hagemann
The closoborane and their derivatives have attracted high interest owing to their superionic conductivity. Very recently, high ionic conductivities have been reported for compounds containing the closoborane ion B12 H12 2- . In this work, we address halogen substituted ions B12 Hn X12-n 2- (n = 0-3, 6, 9-12 and X = F, Cl, Br) using DFT calculations to probe the structures, the chemical stability and the electrochemical stability as well as spectroscopic properties in view of potential future applications. Considering the theoretical reaction n/12 B12 H12 2- + (12-n)/12 B12 X12 2- --> B12 Hn X12-n 2- , it appears that for X = Cl and Br the compounds with n=6 are stabilized by about 100kJ/mol...
February 13, 2019: Journal of Physical Chemistry. A
Wesley B Cardoso, Ardiley T Avelar, Norton Gomes de Almeida, Guilherme Colherinhas
In this work, we propose and investigate numerically the electronic transitions of a new system useful for quantum information tasks composed by a graphene quantum dot (GQD) interacting with two Li+ ions in opposed facing directions. By changing the distance of the Li+ ions we find a region in which only electronic transitions of GQD → Li+ are allowed. Notably, into this region emerges the possibility of controlled electronic transitions for both ions in the symmetric case via appropriate external electric fields...
February 13, 2019: Journal of Physical Chemistry. A
Mikkel Bregnhøj, Kris Strunge, Rasmus Juhl Sørensen, Markus Stroebele, Thorsten Hummel, Hans-Juergen Meyer, Frank Jensen, Peter R Ogilby
The photophysics of selected tungsten iodide clusters was examined with respect to their role as a photosensitizer for the production of singlet oxygen, O2(a1Δg). We examined all-iodo octahedral clusters, [W6I8(I6)]2-, and ligand-substituted octahedral clusters, [W6I8(L6)] 2-, in which the ligand, L, occupies the outer apical positions surrounding the cluster core. We also examined a square pyramidal cluster, [W5I8(I5)]-, in which the tungsten core was presumably more accessible to diffusional encounter with ground state oxygen, O2(X3Σg-)...
February 13, 2019: Journal of Physical Chemistry. A
Yi-Pei Li, Kehang Han, Colin A Grambow, William H Green
Because collecting precise and accurate chemistry data is often challenging, chemistry datasets usually only span a small region of chemical space, which limits the performance and the scope of applicability of data-driven models. To address this issue, we integrated an active learning machine with automatic ab initio calculations to form a self-evolving model that can continuously adapt to new species appointed by the users. In the present work, we demonstrate the self-evolving concept by modeling the formation enthalpies of stable closed-shell polycyclic species calculated at the B3LYP/6-31G(2df,p) level of theory...
February 13, 2019: Journal of Physical Chemistry. A
Alexander N Morozov, Alexander Moiseevich Mebel
Potential energy surfaces for the allyl + phenyl and benzyl + vinyl barrierless radical association reactions have been studied at the CCSD(T)-F12/cc-pVTZ-f12//B3LYP/6-311G** level of theory. Variable reaction coordinate transition state theory (VRC-TST) has been employed to evaluate high-pressure limit rate constants for the barrierless channels. Then, Rice-Ramsperger-Kassel-Marcus Master Equation (RRKM-ME) calculations have been performed to assess phenomenological rate constants and product branching ratios of various reaction channels at different temperatures and pressures...
February 13, 2019: Journal of Physical Chemistry. A
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