A new measurement method of Hansen solubility parameter on fine particles using capillary penetration Chem. Phys. (IF 1.707) Pub Date : 2019-01-18 Shinichi Tsutsumi, Kenji Kondo, Yuki Kato, Nobuyuki Fujiwara, Hideki Yamamoto
Replacing salt correction factors with optimized RNA nearest-neighbour enthalpy and entropy parameters Chem. Phys. (IF 1.707) Pub Date : 2019-01-17 Izabela Ferreira, Elizabeth A. Jolley, Brent M. Znosko, Gerald Weber
From Biomass-derived Wastes (Bagasse, Wheat Straw and Shavings) to Activated Carbon with Three-dimensional Connected Architecture and Porous Structure for Li-ion Batteries Chem. Phys. (IF 1.707) Pub Date : 2019-01-17 Hongri Wan, Xiaofang Hu
Enhancement of monolayer SnSe light absorption by strain engineering: A DFT calculation Chem. Phys. (IF 1.707) Pub Date : 2019-01-17 Tuan V. Vu, Hien D. Tong, Truong Khang Nguyen, Chuong V. Nguyen, A.A. Lavrentyev, O.Y. Khyzhun, B.V. Gabrelian, Hai L. Luong, Khang D. Pham, Phuc Toan Dang, Dat D. Vo
Strain effects on the electronic and optical properties of monolayer SnSe is studied by APW + lo method in DFT framework. The applied strains cause direct-indirect transition of SnSe band gap which is mainly constructed by s / p hybridization. The armchair ε ac and zigzag ε zz reduce the unstrained band gap of 1.05 eV down to 0 eV at 12 % compression, but at 12 % tension, the band gap decreases to 0.726–0.804 eV. The band gap always increases under biaxial strain ε b at at 12 % compression to 12 % tension. We observe an enhancement of real ε 1 ( ω ) and imaginary ε 2 ( ω ) parts of dielectric function by 14 % - 30 % of magnitude, wider peak distribution to infrared and ultra-violet regions, and appearance of new peaks in the ε 1 ( ω ) and ε 2 ( ω ) spectrums. As a consequence, the light absorption α ( ω ) is significantly enhanced in the ultra-violet region and the absorption even starts at lower energy at infrared region.
Graphene role in improved solar photocatalytic performance of TiO2-RGO nanocomposite Chem. Phys. (IF 1.707) Pub Date : 2019-01-17 Horacio Edgardo Garrafa-Gálvez, Clemente Guadalupe Alvarado-Beltrán, Jorge Luis Almaral-Sánchez, Abel Hurtado-Macías, Angélica María Garzon-Fontecha, Priscy Alfredo Luque, Andrés Castro-Beltrán
Efficient visible-light-responsive photocatalyst: hybrid TiO2-Ag3PO4 nanorods Chem. Phys. (IF 1.707) Pub Date : 2019-01-16 Yulong Jia, Ying Ma, Lili Zhu, Jun Dong, Yinhe Lin
Uniformity ansatz for inverse dielectric function of spatially restricted nonlocal polar medium as a novel approach for calculation of electric characteristics of ion-solvent system Chem. Phys. (IF 1.707) Pub Date : 2019-01-11 Mikhail A. Vorotyntsev, Andrey A. Rubashkin
Till now, calculation of the electrostatic potential distribution and other electric properties of a nonlocal polar medium occupying a restricted spatial region has been carried out within the framework of two different approaches. One of them (which may be called “unrestricted medium approximation”, UMA) disregards the existence of “external region” (where dielectric properties are different from those of the medium), i.e. it assumes that the medium occupies the whole space so that its nonlocal dielectric properties are everywhere identical to those of the bulk medium while the charges (sources of the electric field) are considered as immersed inside the medium, without creating cavities or modifying its dielectric properties. Another approach (usually called “dielectric approximation”, DA) takes into account the difference of dielectric properties between the region occupied by the medium, V, and an “external” region; as for the nonlocal dielectric function inside region V it is assumed to be identical to that of the bulk medium, even for its spatial points near the boundary of the region. The actual study has proposed a novel general procedure (called IDA) for solving the same problem. Similar to the DA one, it also takes into account the difference of dielectric properties in region V and external region(s). However, a different background relation (“uniformity ansatz”) is assumed for dielectric properties of the spatially restricted polar medium: its correlation function of polarization fluctuations has the same form (identical to that for the unrestricted medium) in all points inside spatial region V, even in the vicinity of its boundary. The same property is automatically fulfilled for the inverse dielectric function of the medium inside region V. For several important geometries of the system (e.g. half-space, spherical or cylindrical cavity, etc.) thus defined “the inverse dielectric approach” (IDA) results in simple analytical expressions for the potential and electric field distributions for any nonlocal dielectric function of the bulk polar medium as well as for any distribution of “external charges” (satisfying to the corresponding symmetry conditions). As the first application, the IDA approach has been used for analysis of the electric field and potential distributions for the spherically symmetrical system where a cavity (imitating a “solute ion”) is surrounded by a nonlocal dielectric medium (“polar solvent”). Analytical expressions for these characteristics as well as for the electrostatic contribution to the solvation energy have been derived for any spherically symmetrical distribution of the ionic charge (which may be located in the general case both inside the cavity and outside this region) and for any dielectric responses both inside the cavity and of the polar medium outside the cavity. These results are in perfect agreement with the general principles that both the potential distribution outside the cavity and the ion solvation energy are determined only by the total ionic charge inside the cavity while they are independent of the particular charge distribution in this region. Effects due to the ionic charge penetration into the polar medium are also analyzed. Results for the potential distribution and solvation energy are compared for the novel IDA approach with those for the UMA and for the DA procedures. Conclusion on substantial advantages of the IDA method has been made.
Nonadiabatic conical nodes are near but not at an elliptical conical intersection Chem. Phys. (IF 1.707) Pub Date : 2019-01-10 Peter W. Foster, David M. Jonas
The Competitive Formation Mechanism of N-nitrosodimethylamine and Formaldehyde Dimethylhydrazone from 1,1-Dimethylhydrazine during Ozonation in Air: A Combined Theoretical and Experimental Study Chem. Phys. (IF 1.707) Pub Date : 2019-01-10 Dan Huang, Xiangxuan Liu, Chunshan Zuo, Xuanjun Wang, Zheng Xie, Xin Gao
Large π-π Separation Energies of Some Energetic Compounds Chem. Phys. (IF 1.707) Pub Date : 2019-01-10 Bisheng Tan, Hongzhen Li, Hui Huang, Yong Han, Jingming Li, Ming Li, Xinping Long
Some energetic compounds are formed by linking several energetic aromatic rings directly or through bridging groups or spiro or fused structures. To describe the interactions between these aromatic rings, large π-π separation energy was proposed, and a computational approach based on isodesmic reaction equations was also developed. This novel energy can indicate the stability of these energetic compounds, and it is closely related to their sensitivities. The large π-π separation energy was derived for energetic compounds, it can be applied to other other directly linked, atom-bridged (or group-bridged), spiro and fused aromatic structures, including some dimetallic coordination compounds.
A four-dimensional Numerov approach and its application to the vibrational eigenstates of linear triatomic molecules – the interplay between anharmonicity and inter-mode coupling Chem. Phys. (IF 1.707) Pub Date : 2019-01-09 Ulrich Kuenzer, Thomas S. Hofer
An adapted formulation of the grid-based Numerov approach to solve Schrödinger’s equation has been extended to four dimensional systems and applied to problems in vibrational spectroscopy. The advantage of this novel implementation is that no approximations or assumptions with respect to the wavefunctions are required and the achieved accuracy at a given stencil size is only limited by the selected grid-spacing. To validate this approach the vibrational eigenstates and the corresponding wavenumbers of the linear molecules CO 2 , BeH 2 and HCN were investigated. Based on a potential energy grid at CCSD(T)/cc-pVnZ (n=T, Q) level all fundamental wavenumbers could be reproduced with deviations of less than 1% of the experimental values. Furthermore, the hierarchical application of a one- to four-dimensional Numerov treatment provides detailed information about the increasing influence of inter-mode coupling in addition to the inherent account for anharmonic contributions. The associated vibrational states are eigenfunctions of the Numerov matrix eigenvalue problem. Since no vibrational basis functions have to be applied in this approach, the respective eigenstates are characterized using isosurfaces of the wavefunctions in the hyperplane x 4 = 0 . This enables the direct examination of the individual wavefunctions via suitable visualization tools and the assignment of the respective vibrational quantum numbers.
Fate of protected HBT based chemodosimeters after undergoing deprotection: restoration of ESIPT or generation of emissive phenoxide? Chem. Phys. (IF 1.707) Pub Date : 2019-01-07 Arghyadeep Bhattacharyya, Subhash Chandra Makhal, Nikhil Guchhait
OH protected 2-(hydroxyphenyl) benzothiazole (HBT) based ratiometric chemodosimeters have previously been reported to undergo regeneration of excited state intramolecular proton transfer (ESIPT) process upon deprotection. In the current work it is demonstrated for the first time that generation of anion of HBT leads to the optical changes in these types of chemodosimeters rather than regeneration of HBT by using a Hydrazine specific chemodosimeter based on substituted HBT.
Germanium-Isotope-Driven Distortion and Disorder in Clathrate Framework Chem. Phys. (IF 1.707) Pub Date : 2019-01-07 Zhengshang Wang, Longqing Chen, Wenbin Qiu, Xiaoman Shi, Huan He, Yixiang Sun, Liuwei Zhao, Xiangjun Wei, Lin Gu, Jun Tang
We report a definitive evidence that germanium isotope effect triggers a noticeable cage distortion in n-type Ba8Ga16Ge30 (BGG) with complete substitution of isotope Ge-76. Further extended X-ray absorption fine structure technique reflects a large disorder in the cages of the sample, although no accompanying obvious changing in distance of Ge-Ga/Ge is demonstrated. Hence, we suggest that the cumulative cage distortion originates from the variation of bond angle instead of bond length. Moreover, the intensive electron-phonon scattering is dominated by the isotope effect. These findings highlight atomic isotope engineering for modifying crystal structure and possibly even thermoelectric performance.
Bandgap Tuning of C3N monolayer: A First-Principles Study Chem. Phys. (IF 1.707) Pub Date : 2019-01-07 Liyan Xie, Li Yang, Wanying Ge, Xijun Wang, Jun Jiang
The newly found graphene-like material C3N exhibits great potential in a variety of important applications, due to its unique topological and electronic structures. To extend the utilization, a crucial challenge is to make its intrinsic bandgap (1.03 eV) tunable. Here we performed first-principles calculations to investigate the band structure variations of C3N monolayer under various surface modification treatments, including defect engineering, surface decoration and substitutional doping. Results show that those treatments can induce impurity states, orbital rehybridization, and n- or p-type doping simultaneously, and therefore enable effective band structure adjustment. Importantly, some linear relationships between the bandgap and doping concentration are revealed, paving the way for precise control of C3N bandgap.
Linear and Nonlinear Herzberg−Teller Vibronic Coupling Effects. I: Electronic Photon Echo Spectroscopy Chem. Phys. (IF 1.707) Pub Date : 2019-01-08 Mohamad Toutounji
The dependence of the transition dipole moment on nuclear coordinates gives rise to non-Condon interaction, signaling that the adiabatic Herzberg-Teller vibronic coupling should be considered. This coupling manifests itself in linear spectroscopy through the breakdown of the mirror image symmetry between the absorption and emission spectra. The stronger the non-Condon interaction, the more pronounced is the absorption-emission asymmetry. A nuclear exponential function is used as a simple model to represent the electronic transition dipole moment, the purpose of which is to avoid the use of eigenstate- approach, convergence issues, and finally be able to extend its applicability to nonlinear spectroscopy inexpensively while accounting for linear and nonlinear non-Condon effects (Herzberg-Teller vibronic coupling). The non-Condon effects on linear and nonlinear spectroscopic signals (e.g. 2-pulse photon echo) are examined. Closed-form expressions of the non-Condon electronic transition dipole moment time correlation functions, accounting for Herzberg-Teller vibronic coupling effects, are derived. It is shown that nonlinear optical signals in time domain such as 2-pulse photon echo signal, conspicuously reflects the degree of the non-Condon interaction (mostly constructive interference in this work) despite the inhomogeneous broadening disguising the homogeneous structural aspects of the molecular system of interest. As such, this study should be useful in relation to extracting structural and dynamical information of condensed molecular systems. Model calculations of absorption and emission spectra and 2-pulse photon echo signals of Herzberg-Teller vibronically coupled systems are presented. The method presented here seems to more efficient computationally, fast and stable compared to the methods which involve perturbation theory and eigenstate expansion.
Dual frequency-comb spectroscopy of chromophores in condensed phases Chem. Phys. (IF 1.707) Pub Date : 2019-01-03 JunWoo Kim, Jonggu Jeon, Tai Hyun Yoon, Minhaeng Cho
Femtosecond time-resolved spectroscopy and frequency-comb spectroscopy have been individually developed to achieve better time and frequency resolutions, respectively. The two spectroscopic techniques have been developed for different systems, even though they use mode-locked laser in common. Recently, there was an interesting merge of the two techniques into a dual frequency-comb (DFC) spectroscopy, resulting in a new femtosecond spectroscopy with simple instrumentation and high data acquisition speed compared to conventional femtosecond spectroscopic techniques. By slightly detuning the repetition rates of two phase-locked frequency-comb lasers, both automatic time-delay scanning and parallel data recording with single point detectors are possible. Thus, we anticipate that the DFC spectroscopy would allow one to expand the application limits of the conventional femtosecond spectroscopic methods. In this Perspective article, we provide reviews of linear and nonlinear DFC spectroscopy theory and applications with a perspective on the development of coherent multidimensional frequency-comb spectroscopy.
Machine Learning of Two-Dimensional Spectroscopic Data Chem. Phys. (IF 1.707) Pub Date : 2019-01-04 Mirta Rodríguez, Tobias Kramer
Two-dimensional electronic spectroscopy has become one of the main experimental tools for analyzing the dynamics of excitonic energy transfer in large molecular complexes. Simplified theoretical models are usually employed to extract model parameters from the experimental spectral data. Here we show that computationally expensive but exact theoretical methods encoded into a neural network can be used to extract model parameters and infer structural information such as dipole orientation from two dimensional electronic spectra (2DES) or reversely, to produce 2DES from model parameters. We propose to use machine learning as a tool to predict unknown parameters in the models underlying recorded spectra and as a way to encode computationally expensive numerical methods into efficient prediction tools. We showcase the use of a trained neural network to efficiently compute disordered averaged spectra and demonstrate that disorder averaging has non-trivial effects for polarization controlled 2DES.
Thermodynamic stability of diatomic dications of the families of alkaline earth oxides and hydrides: the cases of BaO2+ and BaH2+ Chem. Phys. (IF 1.707) Pub Date : 2019-01-04 Levi Gonçalves dos Santos, Fernando R. Ornellas
The low-lying electronic states of the diatomic dications BaO2+ and BaH2+ are investigated at a high level of theory. The potential energy curves constructed and the associated spectroscopic parameters provide a global and reliable characterization of these species attesting for their thermodynamic stability. The ground state (X3Σ-) of BaO2+ is bound (De) by 13.11 kcal mol-1, with an equilibrium distance of 5.526 a0, and the harmonic constant (ωe) equal to 175.1 cm-1. The first excited state (A 3Π), lying higher by 3216 cm-1, is also thermodynamic stable (De = 4.04 kcal mol-1,ωe = 123.7 cm-1). Einstein spontaneous emission coefficients (Av́v́́) were evaluated for all band systems, and lifetimes estimated. For the dication BaH2+, only the ground state (X2Σ+) is thermodynamic stable with De = 5.50 kcal mol-1, Re = 5.444 a0, and ωe = 409.4 cm-1. New experimental results for the mass spectra of BaO2+ are also provided.
A Crossed Molecular Beams Investigation of the Reactions of Atomic Silicon (Si(3P)) with C4H6 Isomers (1,3-Butadiene, 1,2-Butadiene, and 1-Butyne) Chem. Phys. (IF 1.707) Pub Date : 2019-01-02 Aaron M. Thomas, Beni B. Dangi, Tao Yang, Ralf I. Kaiser, Bing-Jian Sun, Tzu-Jung Chou, Agnes H.H. Chang
The bimolecular gas phase reactions of ground state silicon (Si(3P)) with the C4H6 isomers 1,3-butadiene, 1,2-butadiene, and 1-butyne were investigated under single collision conditions in a crossed molecular beams machine at collision energies of about 15 kJ mol−1. Our data suggest each reaction proceeds indirectly via SiC4H6 intermediates that decompose by elimination of molecular hydrogen through tight exit transition states. In the Si(3P) plus 1,3-butadiene system, multiple product channels are open as evidenced by the observation of molecular hydrogen, hydrogen deuteride, and molecular deuterium losses in experiments utilizing isotopologues of 1,3-butadiene. Non-adiabatic reaction dynamics likely dominate the reaction mechanism in each Si(3P)-hydrocarbon system via intersystem crossing from the triplet to the singlet manifold. These systems are unique in that the reactions proceed at relatively low collision energies and yield products in overall exoergic reactions, unlike the reactions of Si(3P) with the C1-C3 hydrocarbon which have highly endoergic product channels.
Isotopic evidences of the preferential coordination between 12CO2 and urease enzyme Chem. Phys. (IF 1.707) Pub Date : 2018-12-26 Sanchi Maithani, Abhijit Maity, Mithun Pal, Sayoni Bhattacharya, Gourab Dutta Banik, Chiranjit Ghosh, Sujit Chaudhuri, Manik Pradhan
The active Ni(II) centre of metalloenzyme urease forms a coordination with substrate urea prior to the hydrolysis of urea. The present study provided the direct experimental evidences of isotope preferential coordination between Ni(II) metal centre of urease enzyme and substrate urea, which eventually alters the product yield. Furthermore, in-vitro experiments revealed that the specific 12CO2 isotopic species bridges between heavier isotope of substrate urea [13CO(NH2)2] and Ni(II) centre of urease for more effective coordination, which ultimately enhances the yield of the reaction. Finally, the in-vitro observations have been validated under in-vivo physiological conditions exploiting the urease activity of the gastric pathogen Helicobacter pylori present in human stomach. Hence, the present study paves the way for better understanding of the isotope-selective catalytic activity of urease enzyme and exemplifies the link between 12CO2 and urease enzyme.
Physical and Chemical Insights into Molecular Adsorption of Copolymer’s Monomers on Rutile Surface Chem. Phys. (IF 1.707) Pub Date : 2018-12-27 D.T. Ta, A.K. Tieu, H. Zhu, M.H. Le, T.T.H. Ta, V.N. Tran, S. Wan
The adsorption of triblock copolymer’s moieties such as DME, 1,2-DME, and 1,2-DMP on a Rutile surface has been studied by DFT. The insights into their adsorption mechanism have been investigated by analyzing various physical and chemical properties such as the adsorption energies, the structural properties, difference of charge density, density of state, bond overlap population, and the atomic partial charge. Dispersion interaction plays a major role on the absorption energy in 1,2–DME, and the upward bridging oxygen configurations of DME and 1,2–DMP; whilst electrostatic and polarization energies are insignificant. A new Ob-Ti bond has been formed from the overlap of lone-pair electrons between orbital O 2p and Ti 3d in downward bridging oxygen configurations of DME and 1,2–DMP, which results in a significantly larger adsorption energies compared with other configurations. The molecular torsion is considered as a barrier that prevent Ob-down of 1,2–DME to create the bond with Ti.
Empirical assignment of absorbing electronic state contributions to OCS photodissociation product state populations from 214 to 248 nm Chem. Phys. (IF 1.707) Pub Date : 2018-12-23 Colin J. Wallace, Carolyn E. Gunthardt, George C. McBane, Simon W. North
The photodissociation dynamics of OCS near 214 nm for the S( 1 D 2 ) channel were studied using velocity map ion imaging. Earlier studies at this wavelength were extended with new measurements of vector correlations and reanalysis of the rotational distributions in the υ= 0 and υ= 1 CO products. The results were employed to identify the contributions of the 21 A ′ (A) and 1 1 A ′ ′ (B) electronic state absorptions in OCS to the population of each CO final state. The contributions of the 1 1 A ′ ′ (B) state to the CO (υ= 1) population was found to be ∼ 2.5 times smaller ( f B = 0.14 ± 0.04 ) than previous theoretical estimates, and that to the CO (υ= 0) distribution ∼ 1.7 times smaller ( f B = 0.20 ± 0.04 ). A similar analysis was applied to experimental rotational distributions from the literature at photolysis wavelengths of 223 nm, 230 nm, and 248 nm.
On Matching The Magnetic Torque Exerted By A Rotating Magnetic Field To The Torsional Stiffness Of Braided DNA Molecules For Torque Estimations Chem. Phys. (IF 1.707) Pub Date : 2018-12-17 Carlos J. Martínez-Santiago, Edwin Quiñones
We present a force spectroscopic method to quantify the torque exerted by braided DNA molecules. It involved a rotating magnetic field, with torsional stiffness comparable to the torque exerted by braided DNA molecules, to manipulate the macromolecules. During the initial stages of the braiding process, the probe rotated synchronously with the external field. However, when enough torsional free energy was accumulated in the molecules, the probe started oscillating. We exploited this oscillatory behavior for developing a procedure to estimate the torque exerted by the molecules. The procedure entailed modelling the system as a non-linear oscillator, which considered the dynamics of the angular orientation of the magnetic field vector with respect to the magnetic moment of the probe.
Reaction Mechanism, Rate Constants, and Product Yields for the Oxidation of Embedded Five-Member Ring Radicals with Atomic Oxygen Chem. Phys. (IF 1.707) Pub Date : 2018-12-17 G.R. Galimova, V.N. Azyazov, D.P. Porfiriev, A.M. Mebel
Oxidation mechanism of an embedded five-member ring on a surface of a carbonaceous particle with atomic oxygen has been studied employing G3(MP2,CC)//B3LYP/6-311G* potential energy surface calculations for C15H9 + O reactions. Temperature- and pressure-dependent reaction rate constants have been evaluated using the RRKM – Master Equation approach. The mechanism involves barrierless oxygen atom addition to a carbon atom on a free edge of a five-member ring followed by migration of the H atom from the attacked C atom to an ortho position followed by the five-member ring opening and elimination of the CO group, with the five-member ring being fully destroyed. When the embedded ring has three common sides with surrounding six-member rings and one free-edge carbon atom, the only product is the 4-phenanthrenyl radical. When the embedded ring has two common sides with the six-member rings and two free-edge C atoms, two different decarbonylation products possessing a phenalene core can be formed depending on the direction of the 1,2-H shift.
Characterization of the coherent dynamics of bacteriochlorophyll a in solution Chem. Phys. (IF 1.707) Pub Date : 2018-12-17 Elena Meneghin, Danilo Pedron, Elisabetta Collini
Disclosing the physical origin of quantum beatings in the early dynamics of biological light-harvesting pigment-protein complexes is one of the major challenges in the ultrafast spectroscopy community. 2D electronic spectroscopy (2DES) is a powerful tool for this purpose, but the complexity of the beating behavior in multichromophoric systems complicates the interpretation. For this reason, the availability of control datasets providing a full characterization of the response of isolated chromophores is highly desirable to untangle the features of intermolecular interactions from the properties of individual pigments. Here, a thorough 2DES characterization of the frequencies and dephasing times of intramolecular vibrational coherences of bacteriochlorophyll a in solution is provided. Several beating modes in the ground and excited state have been found and their dephasing times have been determined. The obtained results represent an essential interpretation key of the beating dynamics of pigment-protein complexes binding bacteriochlorophyll a.
The Interaction between Chitosan and Tannic acid Calculated Based on the Density Functional Theory Chem. Phys. (IF 1.707) Pub Date : 2018-12-18 Xiaojiao An, Yong Kang, Guishui Li
This paper presented the study of the interaction between tannic acid and chitosan in flocculation process on molecular level. Gallic acid (GA) was selected as tannic monomer and dimer chitosan was selected as the chitosan for simulation based on the density functional theory. Molecular electrostatic potential analysis was conducted to clear the active interaction site, and the possible atoms formed hydrogen bond. A series of analysis were performed to reveal non-covalent interaction between GA and chitosan, including calculation of statistic thermodynamic properties under solvent effect, reduced density gradient (RDG) analysis, independent gradient model (IGM) analysis and symmetry adapted perturbation theory (SAPT) energy decomposition analysis. It was concluded that electrostatic interactions was the main driving energy in the tannic acid flocculation process, and its contribution is about 55.5% in total attractive energies, respectively.
Electronic properties of WS2 and WSe2 monolayers with biaxial strain: A first-principles study Chem. Phys. (IF 1.707) Pub Date : 2018-12-14 Do Muoi, Nguyen N. Hieu, Huong T. T. Phung, Huynh V. Phuc, B. Amin, Bui D. Hoi, Nguyen V. Hieu, Le C. Nhan, Chuong V. Nguyen, P.T.T. Le
In the present work, we consider electronic properties of WX2 (X = S, Se) monolayers under a biaxial strain ε b using the first principles study. Our calculations indicate that, at equilibrium, the WS2 and WSe2 monolayers are semiconductors with a direct band gap of respectively 1.800 eV and 1.566 eV while their bulk structures are indirect semiconductors. The electronic properties of the WX2 monolayers are very sensitive with the biaxial strain, especially compression strain. The biaxial strain ε b is the cause of the band gap of the WX2 monolayers and especially the semiconductor–metal phase transition has occurred in the WS2 monolayer at ε b = - 10 % . In addition, the direct–indirect band gap transition was observed in both WS2 and WSe2 monolayers at a certain elongation of biaxial strain ε b . The phase transitions in these monolayers can be very useful for their applications in nanoelectromechanical devices.
Exploring enhanced hydrogen adsorption on Ti doped Al nanoclusters: A DFT study Chem. Phys. (IF 1.707) Pub Date : 2018-04-27 Bishwajit Boruah, Bulumoni Kalita
The detailed mechanism of adsorption and dissociation of molecular hydrogen on bare and Ti doped Al6 clusters has been studied using Density Functional Theory (DFT). The study shows that the doping of Ti atom significantly changes the geometric and electronic structures of Al6 cluster. Noticeable electronic charge transfer takes place from Al to Ti atoms in TiAl5. The number of energy states near the Fermi level of bare Al6 cluster also increases upon Ti doping. Moreover, the weak molecular hydrogen physisorption on Al6 becomes relatively stronger in TiAl5 with binding energy value of −0.12 eV. Similarly, dissociative hydrogen chemisorption energy on TiAl5 (−2.80 eV) is higher than that on Al6 (−2.74 eV). The computed molecular hydrogen gravimetric content in TiAl5 cluster is 3.2 wt%. Further, dissociation of H2 in TiAl5 involves an activation barrier of 0.54 eV in contrast with barrier less dissociation in bare Al6 cluster.
Nuclear wavepackets along quantum paths in nonadiabatic electron wavepacket dynamics Chem. Phys. (IF 1.707) Pub Date : 2018-07-20 Kazuo Takatsuka
The path-branching theory as a nonadiabatic electron wavepacket theory (Yonehara et al., 2012), in which nonadiabatic electron wavepackets are propagated in time along branching nuclear paths, is extended so that Gaussian nuclear wavepackets are to be evolved in time along the variational quantum paths, which are determined consistently with the electron dynamics.
The π-conjugation length determines the fluorescence quenching mechanism of aromatic aldehydes in water Chem. Phys. (IF 1.707) Pub Date : 2018-07-20 Katharyn Fletcher, Maximilian Krämer, Uwe H.F. Bunz, Andreas Dreuw
Water-soluble distyrylbenzene-based aldehydes are excellent fluorescence turn-on indicators for amine detection, since they are themselves non-fluorescent in water. Here, the fluorescence quenching mechanisms of aldehydes with systematically increasing π-systems are investigated in an aqueous environment using quantum chemical methods. Although the aldehydes are structurally related, with each extension of the π-system the fluorescence quenching mechanism changes from excited-state hydrogen transfer to trans→cis isomerization and nπ∗ state-mediated intersystem crossing, until the aldehydes become fluorescent in water. For distyrylbenzene aldehyde, nπ∗ mediated ISC has been identified as major fluorescence quenching channel, which becomes closed upon reaction with an amine explaining its fluorescence turn-on sensitivity.
Excited state photodissociation dynamics of 2-, 3-, 4-hydroxyacetophenone: Theoretical study Chem. Phys. (IF 1.707) Pub Date : 2018-07-21 Yuri A. Dyakov, Stepas Toliautas, Leonid I. Trakhtenberg, Leonas Valkunas
Photodissociation of 2-, 3-, and 4-hydroxyacetophenone (2-, 3-, and 4-HAP) has been studied by analyzing excited-state potential energy surfaces (PES). For that, ab initio CASSCF(12,12)/6–31++G(d,p) calculations of low-lying excited states have been performed. Molecular beam study of photodissociation of 2-, 3-, and 4-HAP under laser excitation at 193 nm revealed that there are three possible dissociation channels of HAP: separation of H atom, CH3 and COCH3 fragments. In 2-HAP isomer the H separation channel is quenched. In this study we explain the quenching mechanism of the H separation channel and suggest a new model of CH3 and COCH3 fragment elimination reactions. Calculations of the excited-state PES reveal that the most of H, CH3 and COCH3 fragments arise after relaxation into the second, optically “dark” 2A″ state, while some of the reaction products result from the 1A″ state dissociation. Dissociation of 2-HAP through H separation in the 2A″ state is deemed impossible, which explains the absence of deprotonated fragments in the 2-HAP mass spectrum. Breaking of intramolecular hydrogen bond in 2-HAP needs much more energy than the CH3 detachment, which makes relaxation through the S1 − S0 conical intersection unfavorable.
Electronic states of dibenzo-p–dioxin. A synchrotron radiation linear dichroism Investigation Chem. Phys. (IF 1.707) Pub Date : 2018-12-08 Duy Duc Nguyen, Nykola C. Jones, Søren V. Hoffmann, Jens Spanget–Larsen
The UV absorbance bands of dibenzo-p-dioxin (dibenzo-1,4-dioxin, DD) are investigated by synchrotron radiation linear dichroism (SRLD) spectroscopy on molecular samples aligned in stretched polyethylene. The investigation covers the range 58000–30000 cm–1 (170–330 nm), thereby providing new information on the transitions of DD in the vacuum UV region. The observed polarization data enable experimental symmetry assignments of the observed transitions, leading to revision of previously published assignments by Ljubić and Sabljić (J. Phys. Chem. A 109 (2005) 8209-8217). In general, the experimental spectra are well predicted by the results of quantum chemical calculations using time-dependent density functional theory (TD–DFT). The observed absorbance in the region 58000–55000 cm–1 (170–180 nm) in the vacuum UV is almost entirely short-axis polarized, in pleasing agreement with the predicted spectrum.
Theoretical study of intramolecular singlet fission in xanthene-bonded pentacene dimers Chem. Phys. (IF 1.707) Pub Date : 2018-07-21 S. Rajagopala Reddy, Pedro B. Coto, Michael Thoss
Singlet fission is a spin-allowed process by which two non-interacting triplet excitons are generated from a singlet exciton. This type of multiexciton generation mechanism may have the potential to overcome the Shockley-Queisser limit and could enable the development of more efficient solar cells. In this contribution, we analyze intramolecular singlet fission in two modified pentacene dimers covalently bonded to a xanthene spacer employing density functional theory and multireference perturbation theory methods. The systems investigated differ in the electronic structure and bulkiness of the substituents used and in this work we analyze the impact that these aspects have in the relative contributions of the direct and mediated mechanisms to the intramolecular singlet fission.
Ultrafast nonradiative transition pathways in photo-excited pyrazine: Ab initio analysis of time-resolved vacuum ultraviolet photoelectron spectrum Chem. Phys. (IF 1.707) Pub Date : 2018-07-23 Benoît Mignolet, Manabu Kanno, Noriyuki Shimakura, Shiro Koseki, Françoise Remacle, Hirohiko Kono, Yuichi Fujimura
The internal conversion of photo-excited pyrazine, which occurs rapidly on a time scale of about 20 fs, has long been considered to proceed via a conical intersection between the optically bright S2 (1B2u, ππ∗) and dark S1 (1B3u, nπ∗) states. Since 2008, several theoretical studies have raised the possibility that other dark states S3 (1Au, nπ∗) and S4 (1B2g, nπ∗) may participate dominantly in the early stage of the nonradiative decay of S2. To clarify this issue, being motivated by the recent pump–probe experiment by Horio et al. [J. Chem. Phys. 145 (2016) 044306], we calculated vacuum ultraviolet photoelectron spectra for ionization from each of the four excited states. Comparison was made with the measured time-resolved photoelectron spectrum exhibiting a temporally varying multi-band structure. We confirmed no contribution of S3 or S4 and thus the validity of the conventional two-state (S2 → S1) picture for ultrafast nonradiative transition in pyrazine.
Strategy for creating rational fraction fits to stabilization graph data on metastable electronic states Chem. Phys. (IF 1.707) Pub Date : 2018-07-23 K. Gasperich, K.D. Jordan, J. Simons
An exactly soluble model of two diabatic electronic states interacting through a coupling of strength V is used to generate data for testing the rational fraction analytic continuation technique for determining the energies and widths of metastable states of anions. By making analytical connections between the coefficients in the rational fraction and the parameters of the model, we are able to suggest how to choose the orders of the polynomials and the range of the scaling parameter, Z, within which to compute the energies for a given precision. This analysis also allows us to specify the range of Z-values to use in constructing the rational fraction in a manner that allows determination of all parameters of the model for a given precision. The constraint on the Z-value ranges can be used as a guide for constructing rational fractions of data obtained in electronic structure calculations on actual resonance states.
Charge migration kinetics at a nanoscale ZnO/molecule interface structure: A stochastic Schrödinger equation approach Chem. Phys. (IF 1.707) Pub Date : 2018-07-24 Thomas Plehn, Volkhard May
Charge separation dynamics at a hybrid organic/inorganic interface is simulated. The intensively studied para-sexiphenyl/ZnO systems was taken as an example. By extending earlier computations, the work is focused on the hole motion in a cluster of 2553 molecules placed on a flat ZnO surface. A specific case of hole dynamics is studied where the electron injected into the ZnO lattice stays immobile close to the surface. To follow hole motion on a picosecond time-scale, relaxation processes due to intramolecular vibrations are included in the framework of a stochastic Schrödinger equation approach. Respective solutions are confronted with those of an ordinary time-dependent Schrödinger equation exclusively displaying coherent transfer. In the case of excluding dissipative effects, the created hole quickly overcomes the attractive Coulomb-interaction with respect to the immobile electron. However, the hole can escape only partly from the Coulomb well, when taking additional hole relaxation into account.
Phase-space wavepacket dynamics of internal conversion via conical intersection: Multi-state quantum Fokker-Planck equation approach Chem. Phys. (IF 1.707) Pub Date : 2018-07-26 Tatsushi Ikeda, Yoshitaka Tanimura
We theoretically investigate internal conversion processes of a photoexcited molecule in a condensed phase. The molecular system is described by two-dimensional adiabatic ground and excited potential energy surfaces that are coupled to heat baths. We quantify the role of conical intersection (CI) and avoided crossing (AC) in the PESs in dissipative environments by simulating the time evolution of wavepackets to compute the lifetime of the excited wavepacket, yield of the product, and adiabatic electronic coherence. For this purpose, we employ the multi-state quantum Fokker-Planck equation (MSQFPE) for a two-dimensional Wigner space utilizing the Wigner–Moyal expansion for the potential term and the Brinkman hierarchy expression for the momentum. We find that the calculated results are significantly different between the CI and AC cases due to the transition in the tuning mode and vibrational motion in the coupling mode.
Adjacent keto and enol groups in photochemistry of a cyclic molecule: Products, mechanisms and dynamics Chem. Phys. (IF 1.707) Pub Date : 2018-07-30 Dorit Shemesh, Ronnie Salomon, Stephanie Hyejin Kim, Geoffrey S. Tyndall, Sergey A. Nizkorodov, R. Benny Gerber
The photochemistry of carbonyl compounds is of considerable atmospheric importance, but the mechanisms and dynamics are often unknown. Here, we explore these topics for a system with adjacent keto and enol chromophoric groups. The photochemistry in the S1 and S2 states of the most stable tautomer of 1,2-cyclohexanedione, is studied theoretically using molecular dynamics simulations with a semi-empirical excited-state potential. Results are compared with experiments. The main results are: (1) Calculations provide an interpretation of the measured absorption spectrum. (2) There is good agreement between the predicted and experimental photoproducts. (3) Agreement with experiments on the products suggests the latter can be predicted without treating non-adiabatic transitions. (4) The mechanisms of formation of the products are predicted by the simulations. (5) The adjacent keto-enol system is found to be photochemically very different from the pure keto one.
Silicon rods as a negative electrode material for lithium-ion cells: quantum chemical modeling Chem. Phys. (IF 1.707) Pub Date : 2018-12-03 Yu.A. Dobrovolsky, E. Yu. Evschik, A.S. Zyubin, T.S. Zyubina, A.V. Shikhovtseva, V.M. Volokhov
Density functional theory including gradient correction and periodic boundary conditions was used for quantum-chemical modeling of the structural reorganization of silicon rods in processes of lithium insertion and extraction. The Li/Si ratios were considered over a concentration range from 3/1 to 1/8. It was found that after Li insertion, the regular structure of Si rods is distorted, and they become amorphous. At Li/Si ratio ∼ 1/1 and higher, after coating of rod surface by Li atoms or removing them from the surface layer of the rod and consequent annealing at moderate temperatures (400 - 600 K), a rapid (∼ 10 picoseconds) recovery of the uniform distribution of lithium atoms within silicon rod volume occurs. However, at low concentrations of lithium (Li/Si < 1/2), alignment does not occur. The results of this study clarify the limiting conditions for cycling without destruction of silicon rods, promising negative electrode materials for lithium-ion batteries.
Phenyl glycosides - Solid–State NMR, X-ray diffraction and conformational analysis using genetic algorithm Chem. Phys. (IF 1.707) Pub Date : 2018-12-03 Piotr Wałejko, Jarosław Bukowicki, Łukasz Dobrzycki, Katarzyna Paradowska
The X-ray structures of 2,6-dimethylphenyl and phenyl 2,3,4,6-tetra-O-acetyl β-glucosides (1 and 3) and phenyl α-mannoside (6) were obtained. The independent part of the unit cell of the glycosides 1 and 6 was formed by one molecule, and for the glucoside 3, two molecules in the crystal cell were observed. In deacetylated glycosides 4 and 6 the crystal structure was established by a hydrogen bond network formed between the sugar hydroxyls and solvent molecules. The 13C CPMAS NMR spectra of aryl glycosides 1-6 were analysed. In the spectrum of 3, doubling of the C4 aryl signal was observed which confirmed the presence of two independent molecules in the solid sample. The GAAGS (Genetic Algorithm-Assisted Grid Search) method was used to determine the low-energy conformers of α-mannosides and β-glucosides. The orientation of the aryl pendant group was calculated using Molecular Mechanics (MMFF94) as well as Quantum Mechanics theory (DFT, B3LYP/6-31+ G(d,p)).
Absorption and Raman scattering by molecule adsorbed on crystal surface: many particles approach Chem. Phys. (IF 1.707) Pub Date : 2018-12-01 A.M. Yaremko, V.V. Koroteev, V.O. Yukhymchuk, Yu.A. Romanyuk, O.M. Hreshchuk, A.J. Barnes, H. Ratajczak
The spectroscopy of an organic molecule adsorbed on the surface of a crystal is studied using the many particle approach. The interaction between electrons and vibrations of the molecule as well as the interaction of crystal electrons between each other and with the electrons of the molecule is taken into account. It is supposed that molecules adsorbed on the surface do not interact one with another directly but rather such interaction arises by the electrons of the crystal. All these interactions give rise to a very complicated dependence of the spectrum. Because all molecules are arbitrarily distributed on the crystal surface the symmetry of the system molecule-crystal surface is small, C1, and so all forbidden rules for absorption and Raman scattering (RS) processes are identical. Numerical simulation of the frequency dependence of absorption (or RS) coefficient, obtained in the framework of micro-approach using the Green function method, showed that at some relations between energy excitation of the molecule and the gap between the electron bands of the crystal film, and also the position of the Fermi level, can result in significant enhancement of absorption (or RS), relative to the free molecule, in the complex molecule-crystal film.
Optical transparency and electrical conductivity of intermediate filaments in Müller cells and single-wall carbon nanotubes Chem. Phys. (IF 1.707) Pub Date : 2018-11-29 Igor Khmelinskii, Vladimir Makarov
Presently we investigated the electrical conductivity and optical transparency of Müller cell intermediate filaments. For comparison, the same properties were also explored in the model system of single-wall carbon nanotubes. We report the method of separation and purification of porcine (Sus scrofa domestica) intermediate filaments, extracted from the retinal Müller cells. We also report experimental and theoretical methods of measurements and calculations of the resistivity and light transmission yield by the intermediate filaments and single wall carbon nanotubes. The measured resistivity values were (4.7±0.3)×10-4 and (2.8±0.2)×10-4 Ω⋅m-1⋅cm2 at 5°C (278 K), for the intermediate filaments and single wall carbon nanotubes, respectively, being quite close to those of typical metals. We report a method for measuring the light energy transmission by these nanostructures. We found that they efficiently transfer excitation energy along their axis, with the light reemitted at their other end. The measured yields of transferred light energy were 0.50±0.03 and 0.26±0.02 for intermediate filaments and single wall carbon nanotubes, respectively (λexc = 546.1 nm; T = 288 K). The reported results are novel, providing a direct confirmation of the earlier proposed quantum mechanism of light energy transport in the inverted retina of vertebrates. Our data also show that Müller cell intermediate filaments, in addition to their cytoskeletal function, are capable of providing for the light energy transfer within the inverted retina. The data obtained enable a significant progress in our understanding of the high-contrast vision of the vertebrate eyes. The most important conclusion of the current study is the discovery of light energy propagation along natural biological nanofibers (intermediate filaments). This result is completely novel and unique, being reported for the first time.
Photoisomerization of hemithioindigo compounds: Combining solvent- and substituent- effects into an advanced reaction model Chem. Phys. (IF 1.707) Pub Date : 2018-07-30 Franziska F. Graupner, Teja T. Herzog, Florian Rott, Sven Oesterling, Regina de Vivie-Riedle, Thorben Cordes, Wolfgang Zinth
Time resolved absorption and emission experiments are combined with quantum chemical calculations to obtain a quantitative understanding of the light-induced Z to E isomerization of the hemithioindigo photoswitch. Substitution and solvent polarity change the Z to E reaction time by three orders of magnitude from 9 ps for the para-methoxy substituted 5-methyl hemithioindigo in the unpolar cyclohexane to 9 ns for the para-cyano substituted molecule in di-chloromethane. A comparison with quantum chemical calculations reveals the role of the solvent polarity on the reaction speed for distinct substitution patterns of the stilbene moiety. The dipole moments of the different hemithioindigo photoswitches strongly vary on the excited state potential energy surface. Energetic stabilization of the minimum and simultaneous destabilization in the transition region increase the effective reaction barrier for polar solvents, thus strongly decelerating the reaction.
Redundant coordinates in quantum mechanics Chem. Phys. (IF 1.707) Pub Date : 2018-07-31 Eric Toombs, Tucker Carrington
We present a kinetic energy operator and inner product that can be used to solve the Schroedinger equation in redundant coordinates. The goal is to develop equations and a computational procedure that can be used with N coordinates for a system with M degrees of freedom, where N>M. In chemical physics, this might be useful for exploiting symmetry or exploiting certain representations of potentials. Calculations demonstrate that the ideas work.
The effect of hydrogen bonding on the nonadiabatic dynamics of a thymine-water cluster Chem. Phys. (IF 1.707) Pub Date : 2018-08-01 Hans Lischka, Mario Barbatti, Farhan Siddique, Anita Das, Adelia J.A. Aquino
Surface hopping photodynamics simulations have been performed on a cluster of thymine interacting with six water molecules (T(H2O)6). The second-order algebraic diagrammatic construction method (ADC(2)) has been used for calculating the required electronic energies and excited state gradients. Comparison with the previously performed photodynamics for the isolated thymine (Molecules 21 (2016) 1603) shows a similar global behavior and the central role of the S1(nπ∗) minimum for further long-term dynamics. The main difference comes from the destabilization of the nπ∗ state by hydrogen bonding, which leads to a significantly enhanced conversion rate from the bright S2(ππ∗) state to S1(nπ∗) for the T(H2O)6 cluster. On the other hand, the decay time to S0 and the trapping in S1 is significantly increased. Due to the localized character of the lone pair orbital involved in the nπ∗ transition at one oxygen atom, specific changes in the structure of the hydrogen bonded network are observed. Since the hydrogen bonding of the water molecules connected to that oxygen atom is specifically weakened, they show dissociations from thymine during the photodynamics, starting within 30 fs after electronic excitation of thymine.
Symmetry-induced kinetic isotope effects in the dissociation dynamics of CHCl3+ and CHCl4− Chem. Phys. (IF 1.707) Pub Date : 2018-08-01 Allan Christian Petersen, Theis I. Sølling, Max D.J. Waters
Loss of Cl from CHCl3+ with little excess energy is found to proceed via two distinct pathways, the reaction channel which is being followed is determined by a symmetry-induced kinetic isotope effect. Computational investigations suggest competition between a statistical adiabatic process and a process of electronic predissociation. For CHCl4− and CH2Cl3−, rotational predissociation contributes to the kinetic isotope effects for all isotopomers, whereas the particularly large effect observed for CH35Cl337Cl− also originates from symmetry-induced degeneracy of vibrational modes in the C3V point.
Substituent position effects on sunscreen photodynamics: A closer look at methyl anthranilate Chem. Phys. (IF 1.707) Pub Date : 2018-08-03 Natércia d.N. Rodrigues, Neil C. Cole-Filipiak, Matt A.P. Turner, Konstantina Krokidi, Georgia L. Thornton, Gareth W. Richings, Nicholas D.M. Hine, Vasilios G. Stavros
Towards the development of a bottom-up rationale for sunscreen design, the effects of substituent position on the ultrafast photodynamics of the sunscreen precursor methyl anthranilate (MA, an ortho compound) were evaluated by studying para- and meta-MA in vacuum. Time-resolved ion yield (TR-IY) measurements reveal a long-lived S1 excited state (≫1.2 ns) for para-MA, proposed to be the result of a weakly fluorescent, bound excited state. In the case of meta-MA, TR-IY transients reveal a much faster (∼2 ns) excited state relaxation, possibly due to multiple low-lying S1/S0 conical intersections of prefulvenic character. While meta-MA may not be an ideal sunscreen ingredient due to a low ultraviolet absorbance, its comparatively efficient relaxation mechanism may constitute an alternative to common sunscreen relaxation pathways. Thus, our results should prompt further studies of prefulvenic relaxation pathways in potential sunscreen agents.
On-the-fly ab initio three thawed Gaussians approximation: A semiclassical approach to Herzberg-Teller spectra Chem. Phys. (IF 1.707) Pub Date : 2018-08-03 Tomislav Begušić, Aurélien Patoz, Miroslav Šulc, Jiří Vaníček
Evaluation of symmetry-forbidden or weakly-allowed vibronic spectra requires treating the transition dipole moment beyond the Condon approximation. To include vibronic spectral features not captured in the global harmonic models, we have recently implemented an on-the-fly ab initio extended thawed Gaussian approximation, where the propagated wavepacket is a Gaussian multiplied by a linear polynomial. To include more anharmonic effects, here we represent the initial wavepacket by a superposition of three independent Gaussian wavepackets—one for the Condon term and two displaced Gaussians for the Herzberg–Teller part. Application of this ab initio “three thawed Gaussians approximation” to vibrationally resolved electronic spectra of the phenyl radical and benzene shows a clear improvement over the global harmonic and Condon approximations. The orientational averaging of spectra, the relation between the gradient of the transition dipole moment and nonadiabatic coupling vectors, and the details of the extended and three thawed Gaussians approximation are discussed.
Electron-proton transfer mechanism of excited-state hydrogen transfer in phenol−(NH3)n (n = 5) studied by delayed ionization detected femtosecond time-resolved NIR spectroscopy Chem. Phys. (IF 1.707) Pub Date : 2018-08-03 Mitsuhiko Miyazaki, Nozomi Washio, Masaaki Fujii
The reaction mechanism of a hydrogen transfer reaction has a fundamental importance in wide ranges of chemistry, such as redox reactions and enzymatic reactions. The excited-state hydrogen transfer (ESHT) of phenol–(NH3)n clusters is a benchmark system to study solvation effects on the ESHT reaction mechanism. Recently, we reported that the mechanism of the ESHT reaction changes to electron–proton decoupled transfer for phenol–(NH3)5, from a concerted hydrogen atom transfer for clusters with n < 5, based on observations of picosecond time-resolved NIR/IR spectroscopy (Miyazaki et al., 2018). However, the dynamics of the initial electron-transfer process has not been addressed because the rate is faster than the time-resolution of the picosecond time-resolved measurement. In this study, femtosecond time-resolved NIR spectroscopy was applied to the phenol–(NH3)5 to elucidate the initial electron-transfer process. Time evolutions probed in the range of 6000–9000 cm−1 detected two rise components that can be ascribed to electronic absorptions of the Franck-Condon region of the excitation and the transient charge-transfer complex, respectively. A kinetic analysis determined the time-scale of the initial charge-transfer process to be τCT = 370 ± 55 fs. The fast reaction time supports (almost) a barrier-less charge transfer process predicted by a theoretical calculation that shows solvation-induced strong mixing of ππ*-πσ* states.
Quantum dynamics of multi-dimensional rhodopsin photoisomerization models: Approximate versus accurate treatment of the secondary modes Chem. Phys. (IF 1.707) Pub Date : 2018-08-03 Matthieu Sala, Dassia Egorova
We numerically investigate the quantum dynamics of the high-dimensional rhodopsin photoisomerization models of Hahn and Stock using the multi-layer multi-configuration time-dependent Hartree (ML-MCTDH) method. The original two-state two-mode model is augmented with additional Raman-active modes observed experimentally and by a bath of low frequency modes that accounts in a generic fashion for the effect the protein and solvent environment. A previously used approximate method in which the two primary modes are treated using an accurate quantum dynamical method while the secondary modes are treated using the time-dependent Hartree (TDH) method is tested against ML-MCTDH calculations. It is shown that the former method does not capture the main effect of these modes on the electronic populations, on the coherent torsional dynamics and on the quantum yield of the photoisomerization reaction. Our ML-MCTDH calculations predict small photoisomerization quantum yields, in contradiction with the experiments, and call for a revision of the model.
The role of the charge-transfer states in the ultrafast excitonic dynamics of the DTDCTB dimers embedded in a crystal environment Chem. Phys. (IF 1.707) Pub Date : 2018-08-03 Shengshi Jiang, Yu Xie, Zhenggang Lan
Photoinduced excitonic dynamics plays an essential role in the solar energy conversion of organic solar cells. Following our previous work [J. Phys. Chem. C 121 (2017) 27263] on the energy transfer of the 2-[[7-(5-N,N-ditolylaminothiophen-2-yl)-2,1,3-benzothiadiazol-4-yl]methylene]malononitrile (DTDCTB) dimer, we try to understand the role of the intermolecular charge-transfer (CT) electronic states in the excitonic dynamics. When the CT states lie higher than local excited (LE) states and the LE/CT couplings are weak, the CT state plays a minor role. When the LE/CT couplings are strong enough, the CT states start to be unneglectable. When the CT states show lower energies than LE states, the CT states become important. In addition, the near-resonance condition may appear in the excitonic dynamics, resulting in the low-frequency oscillation pattern in the time-dependent electronic populations. This work provides the interesting insight on the role of the CT states in the excitonic dynamics of organic photovoltaic systems.
Intersystem crossing dynamics in singly substituted thiouracil studied by time-resolved photoelectron spectroscopy: Micro-environmental effects due to sulfur position Chem. Phys. (IF 1.707) Pub Date : 2018-08-09 Abed Mohamadzade, Shuming Bai, Mario Barbatti, Susanne Ullrich
The ultraviolet (UV) photophysics of the natural and modified nucleobases can be surprisingly different. In response to UV radiation, the natural pyrimidine nucleobases undergo ultrafast internal conversion back to the ground state, whereas their thiobase analogues, in which an oxygen has been replaced by sulfur, instead display efficient intersystem crossing to the triplet manifold. Here, the effect of the substituent position is investigated with time-resolved photoelectron spectroscopy on 4-thiouracil, which is contrasted to previous work on 2-thiouracil. Although the photophysical pathway of both structural isomers is similar, i.e., leading from the S2 (1ππ∗) state, via S1 (1nπ∗), to the triplet manifold and subsequently back to the ground state, the intersystem crossing dynamics are strongly influenced by the surrounding intramolecular environment of the sulfur atom.
Inelastic processes in low-energy iron-hydrogen collisions Chem. Phys. (IF 1.707) Pub Date : 2018-08-09 S.A. Yakovleva, A.K. Belyaev, W.P. Kraemer
The simplified model approach is applied to low-energy collisions of iron atoms and cations with hydrogen atoms and anions.Inelastic collisional processes for all transitions involving 97 low-lying covalent Fe + H states and two ionic Fe+ + H- molecular states are treated, and rate coefficients for excitation, de-excitation, ion-pair formation and neutralization processes are calculated within the Σ+6Π6,Δ6,Σ-4,Π4,Δ4 and 4Φ molecular symmetries.Rate coefficients with highest values correspond to the mutual neutralization processes Fe+(3d64s 6D) + H-→ Fe(3d6(3G)4s4p(3P°) w 5G°, v 5F°, y 5H°) + H(1s 2S) and Fe+(3d74F) + H-→ Fe(3d7(2G) 4p w 3F°, y 3H°, v 3G°) + H(1s 2S). The highest rate coefficients for excitation and de-excitation correspond to the Fe(3d6(3G)4s4p(3P°) v 5F°) + H(1s 2S)→ Fe(3d6(3G)4s4p(3P°) y 5H°) + H(1s 2S) process within the sextet molecular symmetries and the Fe(3d7(2D2)4p v 3F°) + H(1s 2S) → Fe(3d7(2G)4p v 3G°) + H(1s 2S) process within the quartet molecular symmetries.
On-the-fly molecular dynamics study of the excited-state branching reaction of α-methyl-cis-stilbene Chem. Phys. (IF 1.707) Pub Date : 2018-08-09 Takuro Tsutsumi, Yu Harabuchi, Rina Yamamoto, Satoshi Maeda, Tetsuya Taketsugu
The branching reaction of α-methyl-cis-stilbene (cis-mSB) into its trans-mSB and 4a,4b-dihydrophenanthrene (DHP) forms upon ππ∗ excitation was examined theoretically by exploring the excited-state potential energy surface and using on-the-fly molecular dynamics simulations at the spin-flip time-dependent density functional theory (SF-TDDFT) level of theory. The branching ratio of trajectories was calculated as DHP:twist = 11:29, where twist denotes a mid-region between the cis-form and trans-form, indicating that the trans-mSB is a dominant product. The branching mechanism was analyzed by comparison with the corresponding theoretical studies on stilbene (SB) and 1,1′-dimethyl-stilbene (dmSB). The present computations elucidate the origin of variations in the branching ratio in the photoreactions of cis-SB, cis-mSB, and cis-dmSB. We also found that, because of loss of the slow component of the decay to the ground state, cis-mSB shows a faster decay rate to the ground state than cis-SB and cis-dmSB.
Environmental effects on the dynamics in the light-harvesting complexes LH2 and LH3 based on molecular simulations Chem. Phys. (IF 1.707) Pub Date : 2018-08-10 Maria Ilaria Mallus, Yashoj Shakya, Jigneshkumar Dahyabhai Prajapati, Ulrich Kleinekathöfer
Although a multitude of theoretical studies exist on light-harvesting complex 2 (LH2), less is known about the light-harvesting complex 3 (LH3) of similar ring-like structure. In a comparative study of three system, i.e., the LH2 protein-pigment aggregate of the purple bacterium Rhodospirillum molischianum as well as for the LH2 and LH3 complexes of Rhodoblastus acidophilus the similarities and the differences in the excitonic system were analyzed. To this end, the systems have been studied in a multi-scale approach that combines molecular dynamics simulations with quantum chemistry calculations and quantum dynamics. Along the ground-state molecular dynamics trajectories, the excited energy gaps were determined in a quantum mechanics/molecular mechanics hybrid fashion. Based on the simulations, spectral densities, absorption spectra and exciton dynamics have been determined. After correcting for some shortcoming in the absorption spectra, the exciton dynamics within and between the ring systems have been determined and discussed.
Comparative study of the photodynamics of malonaldehyde and acetylacetone Chem. Phys. (IF 1.707) Pub Date : 2018-08-10 Marin Sapunar, Tarek Ayari, Nađa Došlić
In this computational study we explore the photodynamics of malonaldehyde and compare it to that of the homologous acetylacetone. Upon photoexcitation to the bright S2(ππ∗) state malonaldehyde relaxes to the S1(nπ∗) state on an ultrashort time scale. Once in the S1(nπ∗) state the population of malonaldehyde splits. Part of the population undergoes internal conversion to the ground state by deplanarization of the H-chelate ring, while the other part crosses to the triplet manifold. The comparison with acetylacetone reveals a substantial increase of the internal conversion pathways, from less than 20% in acetylacetone to 40% in malonaldehyde. We show that the substitution of the aliphatic hydrogens by the methyl groups reduces the accessibility of the S1/S0 conical intersection seam in acetylacetone. The system then crosses to the triplet manifold and homolytic C–CH3 bond cleavage takes place.
The role of 1πσ∗ states in the formation of adenine radical-cations in DNA duplexes Chem. Phys. (IF 1.707) Pub Date : 2018-08-11 Tolga N.V. Karsili, Barbara Marchetti, Michael N.R. Ashfold
Photoinduced damage of DNA is a well-known but still far from fully understood phenomenon. Electronic structure methods are here employed to investigate potential roles of πσ∗ states in initiating photodamage, and ways in which πσ∗-state driven photochemistry might evolve with increasing molecular complexity. The study starts with the bare 9H-adenine molecule and progresses through to a model double-helix DNA duplex in aqueous solution. Relative to the gas phase, aqueous solvation is predicted to stabilize the 1πσ∗ states of these systems when exciting at the respective ground state equilibrium geometries, but to have relatively little effect on the asymptotic NH bond strengths. But the study also re-emphasises the potential importance of rival σ∗ ← π excitations, wherein a solute π electron is promoted to a σ∗ orbital localized on an OH bond of a complexing H2O molecule, as a route to forming parent radical cations – as have recently been observed following near UV photoexcitation of double-helix adenine-thymine duplexes in water (Banyasz et al., 2018). The subsequent deprotonation of such radical cations offers a rival low energy route to NH bond fission and radical formation in such duplexes.
Floque Hamiltonian for incorporating electronic excitation by a laser pulse into simulations of non-adiabatic dynamics Chem. Phys. (IF 1.707) Pub Date : 2018-08-11 Dmitry V. Makhov, Dmitrii V. Shalashilin
We present a simple way to incorporate a molecule-field interaction into non-adiabatic molecular dynamics. This makes possible integrated simulation of the photoexcitaion and the ensuing photodynamics, providing accurate initial conditions that are specific for the particular wave-length and duration of the laser pulse. The proposed approach is applied to simulate the dynamics of pyrrole photodissociation. The approach is particularly convenient for the use with ab initio Multiple Cloning approach, but the idea can be implemented in other quantum dynamics methods.
Ultrafast electronic deactivation of UV-excited adenine and its ribo- and deoxyribonucleosides and -nucleotides: A comparative study Chem. Phys. (IF 1.707) Pub Date : 2018-08-18 Uta C. Stange, Friedrich Temps
The high stability of the DNA bases after UV photoexcitation is generally ascribed to their intrinsic ability to dissipate the supplied electronic energy on ultrafast time scales. The sugar-phosphate backbone of the related nucleosides and nucleotides may modulate the efficiency of these relaxation processes by hydrogen bonding and/or intramolecular energy transfer. To elucidate these effects, we performed a comparative study of the excited-state lifetimes of 9H-adenine, its nucleosides adenosine and deoxyadenosine, and its nucleotides adenosine monophosphate and deoxyadenosine monophosphate by transient electronic absorption spectroscopy under otherwise constant experimental conditions. All five adenine derivatives were found to exhibit virtually identical spectro-temporal behavior with uniform excited-state lifetimes of τ1=0.19±0.03 ps and τ2=0.45±0.05 ps. The results support a common deactivation mechanism within the adenine unit that leaves the DNA sugar-phosphate backbone groups idle.
Multistate coupled quantum dynamics of photoexcited cytosine in gas-phase: Nonadiabatic absorption spectrum and ultrafast internal conversions Chem. Phys. (IF 1.707) Pub Date : 2018-08-18 Yanli Liu, Lara Martínez-Fernández, Javier Cerezo, Giacomo Prampolini, Roberto Improta, Fabrizio Santoro
Quantum dynamics simulations, with the Multiconfigurational Time Dependent Hartree method, are used to assign the very broad absorption spectrum of Cytosine in gas phase and study the relation between spectral features and the ultrafast internal conversions among its excited states. For each of the four populated tautomers of Cytosine we built a Linear Vibronic Coupling model, comprising all the low energy excited states up to ∼6.5 eV (7–9 states). We used Density Functional Theory and a general diabatization scheme based on the projection of the excited states on a set of reference ones. Vibronic progressions and inter-state couplings dominate the spectral shape, which is in nice agreement with experiment. Inter-state couplings contribute to the loss of vibronic resolution and to the spread of the absorption intensity along a large energy range. Their importance is different for each tautomer and is connected to the different decay times of the bright states.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
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- Asian J. Org. Chem.
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- Catal. Today
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- Combust. Flame
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- Crit. Rev. Solid State Mater. Sci.
- Cryst. Growth Des.
- Curr. Opin. Chem. Eng.
- Curr. Opin. Colloid Interface Sci.
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- Curr. Opin. Solid State Mater. Sci.
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- J. Acad. Nutr. Diet.
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- J. Alloys Compd.
- J. Am. Ceram. Soc.
- J. Am. Chem. Soc.
- J. Am. Soc. Mass Spectrom.
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- J. Anal. At. Spectrom.
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- J. Chem. Theory Comput.
- J. Chromatogr. A
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- J. CO2 UTIL.
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- J. Cryst. Growth
- J. Dairy Sci.
- J. Electroanal. Chem.
- J. Electrochem. Soc.
- J. Environ. Manage.
- J. Eur. Ceram. Soc.
- J. Fluorine Chem.
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- J. Food Sci.
- J. Funct. Foods
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- J. Heterocycl. Chem.
- J. Hydrol.
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- J. Mol. Catal. A Chem.
- J. Mol. Liq.
- J. Nat. Gas Sci. Eng.
- J. Nat. Prod.
- J. Nucl. Mater.
- J. Org. Chem.
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- J. Phys. Chem. C
- J. Phys. Chem. Lett.
- J. Polym. Sci. A Polym. Chem.
- J. Porphyr. Phthalocyanines
- J. Power Sources
- J. Solid State Chem.
- J. Taiwan Inst. Chem. E.
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- Mass Spectrom. Rev.
- Mater. Chem. Front.
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- Mater. Horiz.
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- Mater. Sci. Eng. R Rep.
- Mater. Today
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- Nat. Prod. Rep.
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- Natl. Sci. Rev.
- Neurochem. Int.
- New J. Chem.
- NPG Asia Mater.
- npj 2D Mater. Appl.
- npj Comput. Mater.
- npj Flex. Electron.
- npj Mater. Degrad.
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- Phys. Chem. Chem. Phys.
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- PLOS ONE
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- Polym. Degrad. Stabil.
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- Polym. Rev.
- Powder Technol.
- Proc. Combust. Inst.
- Prog. Cryst. Growth Ch. Mater.
- Prog. Energy Combust. Sci.
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- Prog. Solid State Chem.
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- Solar RRL
- Spectrochim. Acta. A Mol. Biomol. Spectrosc.
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