Unphysical divergences in response theory
Transition densities between excited states are key for nonlineartheoretical spectroscopy and multi-state non-adiabatic molecular dynamics (NAMD) simulations. In the framework of responsetheory, these transition densities are accessible from poles of the quadratic response function. It was shown recently that the thus obtained transition densities within time-dependent Hartree-Fock (TDHF) and adiabatictime-dependent density functional theory (TDDFT) exhibit unphysical divergences when the difference inexcitation energy of the two states of interest matches anotherexcitation energy. This unphysical behavior is a consequence...
Source: Journal of Chemical Physics - October 4, 2016 Category: Physics Authors: Shane M. Parker, Saswata Roy and Filipp Furche Source Type: research
Explicitly correlated coupled-cluster theory for static polarizabilities
A method of calculation of staticpolarizabilities withwavefunctions, corresponding to linearly approximated explicitly correlatedcoupled-cluster singles and doubles [CCSD(F12)] model, has been formulated and implemented. For the proper description of the response of system on appliedelectric field, modified ansatz is introduced for geminal part of cluster operators. Such extension of CCSD(F12) model provides balanced description of both perturbed and unperturbedwave functions, what leads to the increase of the accuracy of targetpolarizabilities. As a part of algorithm, explicitly correlated version of coupled-perturbed CCS...
Source: Journal of Chemical Physics - October 4, 2016 Category: Physics Authors: Denis Bokhan, Dmitrii N. Trubnikov, Ajith Perera and Rodney J. Bartlett Source Type: research
Recoupling the singlet- and triplet-pairing channels in single-reference coupled cluster theory
It is well known that single-referencecoupled clustertheory truncated to low orders ofexcitations gives the right answer for the right reason when systems are dominated by dynamical or weak correlation. Static or strong correlation is more problematic, causing often catastrophic breakdown of restrictedcoupled cluster. This failure can be remedied, e.g., by allowing symmetry breaking in the reference or taking a multi-reference approach, but poses an interesting theoretical problem, especially since many groups have found that simplifying theT2 operator or the doubles amplitudeequations gives better results. In singlet-pair...
Source: Journal of Chemical Physics - October 4, 2016 Category: Physics Authors: John A. Gomez, Thomas M. Henderson and Gustavo E. Scuseria Source Type: research
Polyaspartic acid facilitates oxolation within iron(iii) oxide pre-nucleation clusters and drives the formation of organic-inorganic composites
The interplay betweenpolymers and inorganic minerals during the formation of solids is crucial for biomineralization and bio-inspiredmaterials, and advancedmaterial properties can be achieved with organic-inorganiccomposites. By studying the reaction mechanisms, basic questions on organic-inorganic interactions and their role duringmaterial formation can be answered, enabling more target-oriented strategies in future synthetic approaches. Here, we present a comprehensive study on the hydrolysis ofiron(iii) in the presence of polyasparticacid. For the basic investigation of the formation mechanism, a titration assay was use...
Source: Journal of Chemical Physics - October 3, 2016 Category: Physics Authors: J. Scheck, M. Drechsler, X. Ma, M. T. St öckl, J. Konsek, J. B. Schwaderer, S. M. Stadler, J. J. De Yoreo and D. Gebauer Source Type: research
Asymmetry in structural response of inner and outer transmembrane segments of CorA protein by a coarse-grain model
Structure of CorAprotein and its inner (i.corA) and outer (o.corA) transmembrane (TM) components are investigated as a function oftemperature by a coarse-grainedMonte Carlo simulation. Thermal response of i.corA is found to differ considerably from that of the outer component, o.corA. Analysis of the radius of gyration reveals that the inner TM component undergoes a continuous transition from a globular conformation to a random coilstructure on raising thetemperature. In contrast, the outer transmembrane component exhibits an abrupt (nearly discontinuous) thermal response in a narrow range oftemperature. Scaling of thestru...
Source: Journal of Chemical Physics - October 3, 2016 Category: Physics Authors: Sunan Kitjaruwankul, Channarong Khrutto, Pornthep Sompornpisut, B. L. Farmer and R. B. Pandey Source Type: research
Growth kinetics of racemic heptahelicene-2-carboxylic acid nanowires on calcite (104)
Molecularself-assembly of racemic heptahelicene-2-carboxylic acid on a dielectric substrate at room temperature can be used to generate wire-like organic nanostructures consisting of single and double molecular rows. By means of non-contact atomic force microscopy, we investigate the growth of the wire-like pattern after deposition by experimental andtheoretical means. From analyzing the time dependence of the mean row length, two distinct regimes were found. At the early post-deposition stage, the mean length grows in time. Subsequently, a crossover to a second regime is observed, where the mean row length remains nearly ...
Source: Journal of Chemical Physics - October 3, 2016 Category: Physics Authors: Mario Einax, Tobias Richter, Markus Nimmrich, Philipp Rahe, Irena G. Star á, Ivo Starý, Angelika Kühnle and Philipp Maass Source Type: research
Insight into the mechanism for the methanol synthesis via the hydrogenation of CO2 over a Co-modified Cu(100) surface: A DFT study
A comprehensive density functional theory calculation was employed to investigate thereaction mechanism of methanol synthesis on a Co-modified Cu(100) surface via CO2 hydrogenation. The Cu(100) surface with embedded small Co clusters prepared experimentally was employed as a model system to explore the effects of Co dopant on the catalytic performance of Cu(100) surface towards CH3OH synthesis. Theactivation energy barriers and thereactionenergies of 16 elementarysurface reactions were determined. Our calculated results show that the most favorablereaction pathway for the hydrogenation of CO2 to CH3OH follows the sequence ...
Source: Journal of Chemical Physics - October 3, 2016 Category: Physics Authors: Mei Qiu, Huilin Tao, Rong Li, Yi Li, Xin Huang, Wenkai Chen, Wenyue Su and Yongfan Zhang Source Type: research
Markov state model of the two-state behaviour of water
With the help of a Markov StateModel (MSM), two-state behaviour is resolved for two computermodels of water in a temperature range from 255 K to room temperature (295 K). The method is first validated for ST2 water, for which the so far strongest evidence for aliquid-liquid phase transition exists. In that case, the results from the MSM can be cross-checked against the radialdistribution functiong5(r) of the 5th-closest water molecule around a given reference water molecule. The latter is a commonly used local order parameter, which exhibits a bimodal distribution just above the liquid-liquidcritical point that represents ...
Source: Journal of Chemical Physics - October 3, 2016 Category: Physics Authors: Peter Hamm Source Type: research
Characterization of the primary hydration shell of the hydroxide ion with H2 tagging vibrational spectroscopy of the OH − ⋅ (H2O)n=2,3 and OD− ⋅ (D2O)n=2,3 clusters
We report the isotope-dependent vibrationalpredissociationspectra of the H2-tagged OH−⋅ (H2O)n=2,3 clusters, from which we determine the strongly coordination-dependent energies of the fundamentals due to the OH groups bound to theion and the intramolecular bending modes of thewater molecules. The HOH bending fundamental is completely missing in the delocalized OH−⋅ (H2O) binary complex but is recovered upon adding the secondwater molecule, thereby establishing that the dihydrate behaves as a hydroxideion solvated by two essentially intactwater molecules. The energies of the observed OH stretches are in good agreem...
Source: Journal of Chemical Physics - October 3, 2016 Category: Physics Authors: Olga Gorlova, Joseph W. DePalma, Conrad T. Wolke, Antonio Brathwaite, Tuguldur T. Odbadrakh, Kenneth D. Jordan, Anne B. McCoy and Mark A. Johnson Source Type: research
Mode-specific multi-channel dynamics of the F − + CHD2Cl reaction on a global ab initio potential energy surface
We report a detailedquasiclassical trajectory study for the dynamics of theground-state and CH/CD stretching-excited F− + CHD2Cl(vCH/CD = 0, 1) → Cl− + CHD2F, HF + CD2Cl−, and DF + CHDCl− SN2, proton-, and deuteron-abstractionreactions using a full-dimensional globalab initio analytical potential energy surface. The simulations show that (a) CHD2Cl(vCH/CD = 1), especially forvCH = 1, maintains its mode-specific excited character prior to interaction, (b) the SN2reaction is vibrationally mode-specific, (c) double inversion can occur and is enhanced upon CH/CD stretching excitations, (d) in the abstractionreactions...
Source: Journal of Chemical Physics - October 3, 2016 Category: Physics Authors: Istv án Szabó and Gábor Czakó Source Type: research
Infrared absorption of 1-chloro-2-methyl-2-propyl [ ⋅C(CH3)2CH2Cl] and 2-chloro-2-methylpropyl [⋅CH2C(CH3)2Cl] radicals produced in the addition reactions of Cl with isobutene (i-C4H8) in solid para-hydrogen
The addition reactions of chlorine atom with isobutene (i-C4H8) insolidpara-hydrogen (p-H2) were investigated with infrared (IR)absorption spectra. When ap-H2 matrix containing Cl2 and isobutene was irradiated withultraviolet light at 365 nm, intense lines in a set at 534.5, 1001.0, 1212.9, 1366.0, 2961.6, and 2934.7 cm−1, and several weaker others due to the 1-chloro-2-methyl-2-propyl radical,⋅C(CH3)2CH2Cl, and those in a second set including intense ones at 642.7, 799.2, 1098.2, 1371.8, and 3027.3 cm−1 due to the 2-chloro-2-methylpropyl radical,⋅CH2C(CH3)2Cl, appeared; the ratio of⋅C(CH3)2CH2Cl to⋅CH2C(CH3)2C...
Source: Journal of Chemical Physics - October 3, 2016 Category: Physics Authors: Ching-Yin Chou and Yuan-Pern Lee Source Type: research
State-to-state differential cross sections for a four-atom reaction: H2 + OH → H2O + H in full dimensions
The time-dependent wave packet method has been employed to calculate state-to-state differential cross sections for the titlereaction in full dimensions. It is found that the majority of H2O is produced in the first stretching excited states, with a large fraction of available energy for thereaction ending up as product internal motion. The differential cross sections for collision energy up to 0.4 eV are all peaked in the backward direction, but the width of the angular distribution increases considerably as the increase of collision energy. The isotope effect was also examined by comparing the scattering angular distribu...
Source: Journal of Chemical Physics - October 3, 2016 Category: Physics Authors: Zhiqiang Zhao, Shu Liu and Dong H. Zhang Source Type: research
Dual binding mode in cohesin-dockerin complexes as assessed through stretching studies
A recent experimental study by Jobstet al. of stretching of a wild-type (WT) cohesin-dockerin complex has identified two kinds of the force-displacement patterns, with a single or double-peaked final rupture, which are termed “short” and “long” here. This duality has been interpreted as arising from the existence of two kinds of binding. Here, we analyze the separation of two cohesin-dockerin complexes ofC. thermocellum theoretically. We use a coarse-grainedstructure-based model and the values of the pulling speeds are nearly experimental. In their native states, the two systems differ in the mutual binding orienta...
Source: Journal of Chemical Physics - October 3, 2016 Category: Physics Authors: Micha ł Wojciechowski and Marek Cieplak Source Type: research
Tree based machine learning framework for predicting ground state energies of molecules
We present an application of the boosted regression tree algorithm for predictingground state energies of molecules made up of C, H, N, O, P, and S (CHNOPS). The PubChem chemical compounddatabase has been incorporated to construct a dataset of 16 242 molecules, whose electronicground state energies have been computed usingdensity functional theory. This dataset is used to train the boosted regression tree algorithm, which allows a computationally efficient and accurate prediction of molecularground state energies. Predictions from boosted regression trees are compared withneural network regression, a widely used method ...
Source: Journal of Chemical Physics - October 3, 2016 Category: Physics Authors: Burak Himmetoglu Source Type: research
Communication: Equivalence between symmetric and antisymmetric stretching modes of NH3 in promoting H + NH3 → H2 + NH2 reaction
We report here a state-of-the-art full-dimensional quantum dynamical study of the hydrogen abstractionreaction H + NH3→ H2 + NH2 on an accurateab initio based global potential energy surface. Thisreaction serves as an ideal candidate to study the relative efficacies of symmetric and degenerate antisymmetric stretching modes. Strong mode specificity, particularly for the NH3 stretching modes, is demonstrated. It is further shown that nearly identical efficacies of the symmetric and antisymmetric stretching modes of NH3 in promoting thereaction can be understood in terms of local-mode stretching vibrations of the reactant ...
Source: Journal of Chemical Physics - October 3, 2016 Category: Physics Authors: Hongwei Song, Minghui Yang and Hua Guo Source Type: research
