Two-dimensional Potential Energy Surface Research Articles

Collisional excitation of C2H(X2Σ+) by para-H2(j = 0): Fine-structure resolved transitions

We report theoretical cross sections and rate coefficients for the collisional excitation of C2H(X2Σ+) by para-H2(j=0). The two molecules are treated as rigid rotors. The intermolecular interaction is described by a two-dimensional potential energy surface (PES) averaged over H2 orientations and based on RCCSD(T) calculations with aug-cc-pVTZ basis sets plus bond functions. Close-coupling calculations of collisional excitation cross sections for the first 25 fine-structure levels of C2H yielded rate coefficients up to 100K. The results show marked differences with recent excitation rate coefficients determined for C2H with He as the collision partner.

Infrared and Raman spectra, theoretical calculations, conformations, and two-dimensional potential energy surface of 2-cyclopenten-1-one ethylene ketal.

The infrared and Raman spectra of the bicyclic spiro molecule 2-cyclopenten-1-one ethylene ketal (CEK) have been recorded. Density functional theory (DFT) calculations were used to compute the theoretical spectra, and these agree well with the experimental spectra. The structures and conformational energies for the two pairs of conformational minima, which can be defined in terms of ring-bending (x) and ring-twisting (τ) vibrational coordinates, have also been calculated. Utilizing the results from ab initio MP2/cc-PVTZ computations, a two-dimensional potential energy surface (PES) was calculated. The energy levels and wave functions for this PES were then calculated, and the characteristics of these were analyzed. At lower energies, all of the quantum states are doubly degenerate and correspond to either the lower-energy conformation L or to conformation H, which is 154 cm(-1) higher in energy. At energies above the barrier to interconversion of 264 cm(-1), the wave functions show that the quantum levels have significant probabilities for both conformations.

Spatial structure of 2-(2´-hydroxyphenyl)-4-methylchromanes and some specific features of intramolecular hydrogen bond

The B3LYP/6-311++G(2d,2p) method was used to study spatial structures in the gas phase of 2S*,4S*- and 2S*,4R*-2-(2´-hydroxyphenyl)-4-methylchromanes (1 and 2), which are the products of thermal dimerization of o-vinylphenol. A two-dimensional potential energy surface of the internal rotation of the cyclic fragments of the molecule around the C(2)—C(1´) bond and the OH group around the C(2´)—O(2´) bond was built for chromane 1. The appearance of the stretching vibration absorption band for free OH groups in the IR spectra of solutions of chromanes 1 and 2 in low polar solvents allowed us to draw a conclusion that, despite the presence of a "classic" strong enough intramolecular hydrogen bond (IMHB) O—H...O between the OH group and the O atom of heterocycle, some molecules 1 and 2 exist in solutions as rotamers with the free OH group. Theoretical evaluation shows that the amount of such rotamers in the gas phase is ~8%, while in solution, according to the IR spectroscopy data, it is ~12%. Theoretical evaluation of the IMHB enthalpy for o-phenylchromanes 1 and 2 gives the value of 1.9 kcal mol−1.

Hydrogen bond coupling in sodium dihydrogen triacetate.

The coupling of hydrogen bonds is central to structures and functions of biological systems. Hydrogen bond coupling in sodium dihydrogen triacetate (SDHTA) is investigated as a model for the hydrogen bonded systems of the type O-H…O. The two-dimensional potential energy surface is derived from the full-dimensional one by selecting the relevant vibrational modes of the hydrogen bonds. The potential energy surfaces in terms of normal modes describing the anharmonic motion in the vicinity of the equilibrium geometry of SDHTA are calculated for the different species, namely, HH, HD, DH, and DD isotopomers. The ground state wave functions and their relation to the hydrogen bond structural parameters are discussed. It has been found that the hydrogen bonds in SDHTA are uncoupled, that is elongation of the deuterated hydrogen bond does not affect the non-deuterated one.

A fast relaxation of electronically-excited inclusion complexes of a styryl dye with cucurbit[7]uril

The relaxation of electronically-excited states of styryl dye (1) and its complexes with cucurbit[7]uril (CB[7]) in aqueous solution was studied by fluorescence steady-state and upconversion techniques. The decay of fluorescence, a 5-fold enhancement of which was observed upon addition of CB[7], was fitted to three exponential functions with time constants of 274, 43 and 1.8ps in the presence of CB[7], and 100, 30, and 1.9ps without it. In the framework of a simple model, based on the two-dimensional potential energy surface, the obtained results indicate that upon complexation the fluorescence rate constant of dye 1 increases by 3.8 times.

Landscapes of four-enantiomer conical intersections for photoisomerization of stilbene: CASSCF calculation.

The photoisomerization of cis- and trans-stilbene through conical intersections (CI) is mainly governed by four dihedral angles around central C═C double bonds. The two of them are C-C═C-C and H-C═C-H dihedral angles that are found to form a mirror rotation coordinate, and the mirror plane appears at the two dihedral angles equal to zeros with which the middle state is defined through partial optimization. There exist the first-type of hula-twist-CI enantiomers, the second-type of hula-twist-CI enantiomers, the first-type of one-bond-flip-CI enantiomers, and the second type of one-bond-flip-CI enantiomers as well as cis-enantiomers and trans-enantiomers with respect to this mirror plane. The complete active space self-consistent field method is employed to calculate minimum potential energy profile along the mirror rotation coordinate for each enantiomers, and it is found that the left-hand manifold and the right-hand manifold of potential energy surfaces can be energetically transferred via photoisomerization. Furthermore, two-dimensional potential energy surfaces in terms of the branching plane g-h coordinates are constructed at vicinity of each conical intersection, and the landscapes of conical intersections show distinct feature, and in excited-state four potential wells separated in different section of g-h plane related to different conical intersections which indicate different photoisomerization pathways.

Mechanism and kinetics of electrochemical reduction of tert-butyl bromide molecule - improvement of theoretical model

In the present article the earlier formulated theoretical model of the adiabatic electrochemical reduction of the tert-butyl bromide molecule [1] is improved. The potential energy profiles describing dissociation of the C-Br bond in the neutral molecule and in the anion, which in the previous work were based on quantum calculations performed in vacuo, are replaced with new ones, derived from similar calculations, but taking into account solvent (dimethyl sulfoxide) effects. The modified two-dimensional potential energy surfaces were introduced into the simulation program and the rate constants were re-examined for three different values of the solvent reorganization energies λ: 0.624, 1.0 and 1.41324eV. The results are found to differ significantly from those reported previously, exhibiting now better agreement with experimental estimates for the activation energy and the transfer coefficient α. New values of α calculated in the interval of overpotentials η=1.3-1.45V are found to decrease with η from 0.262 to 0.237 when λ=0.624eV, from 0.305 to 0.273 when λ=1eV, and from 0.332 to 0.308 when λ=1.41324eV (the latter obtained approximately). The transfer coefficient is shown to decrease also with the temperature, but this effect is much weaker than reported in our previous study [2]. Some trends found in our results are explained by the saddle point avoidance phenomenon.

Atmospheric reaction of Cl + methacrolein: a theoretical study on the mechanism, and pressure- and temperature-dependent rate constants.

Methacrolein is a major degradation product of isoprene, the reaction of methacrolein with Cl atoms may play some roles in the degradation of isoprene where these species are relatively abundant. However, the energetics and kinetics of this reaction, which govern the reaction branching, are still not well understood so far. In the present study, two-dimensional potential energy surfaces were constructed to analyze the minimum energy path of the barrierless addition process between Cl and the C═C double bond of methacrolein, which reveals that the terminal addition intermediate is directly formed from the addition reaction. The terminal addition intermediate can further yield different products among which the reaction paths abstracting the aldehyde hydrogen atom and the methyl hydrogen atom are dominant reaction exits. The minimum reaction path for the direct aldehydic hydrogen atom abstraction is also obtained. The reaction kinetics was calculated by the variational transition state theory in conjunction with the master equation method. From the theoretical model we predicted that the overall rate constant of the Cl + methacrolein reaction at 297 K and atmospheric pressure is koverall = 2.3× 10(-10) cm(3) molecule(-1) s(-1), and the branching ratio of the aldehydic hydrogen abstraction is about 12%. The reaction is pressure dependent at P < 10 Torr with the high pressure limit at about 100 Torr. The calculated results could well account for the experimental observations.

Theoretical calculations and vibrational potential energy surface of 4-silaspiro(3,3)heptane

Theoretical computations have been carried out on 4-silaspiro(3,3)heptane (SSH) in order to calculate its molecular structure and conformational energies. The molecule has two puckered four-membered rings with dihedral angles of 34.2° and a tilt angle of 9.4° between the two rings. Energy calculations were carried out for different conformations of SSH. These results allowed the generation of a two-dimensional ring-puckering potential energy surface (PES) of the form V = a(x1 (4) + x2 (4)) - b(x1 (2) + x2 (2)) + cx1 (2)x2 (2), where x1 and x2 are the ring-puckering coordinates for the two rings. The presence of sufficiently high potential energy barriers prevents the molecule from undergoing pseudorotation. The quantum states, wave functions, and predicted spectra resulting from the PESs were calculated.

Structural and spectroscopic characterization of E- and Z-isomers of azobenzene

Monomers of azobenzene were isolated in argon matrices at 15 K and characterized by infrared spectroscopy and theoretical calculations. When the equilibrium vapors existing over the azobenzene crystals at room temperature were trapped in the matrix, only the thermodynamically most stable E-azobenzene was detected. In an attempt to convert E-azobenzene into the Z isomer, the matrix-isolated E-monomers were irradiated either by broad-band or narrow-band UV-visible light of different wavelengths, in the 600-200 nm range. However, no E-to-Z transformation was observed under these conditions. In an alternative experiment, E-azobenzene was irradiated by UV-visible broad-band light in the gas phase prior to trapping in a matrix. In this case, the E-to-Z photoisomerization occurred, and both E- and Z-azobenzene monomers were detected in the matrix sample. Subsequent irradiation of the matrix with narrow-band tunable visible or UV light (λ < 550 nm) resulted in back conversion of Z-azobenzene into the E-form. The observed photoinduced E-to-Z isomerizations allowed for the reliable vibrational characterization of both azobenzene isomers. The two-dimensional potential energy surfaces of Z- and E-azobenzene were explored as functions of the torsional movement of the two phenyl rings. They exhibit large flat areas around the minima, for both isomers, allowing for large-amplitude zero-point torsional vibrations. For the Z-form, these vibrations were found to be responsible for significant changes in the equilibrium NN bond length (up to 0.3 pm). This also allowed to explain the experimentally observed frequency smearing of the N=N stretching vibration in this isomer.

Importance of a Nonlocal Description of Electron–Electron Interactions in Modeling the Dissociative Adsorption of H2 on Cu(100)

Describing the dissociation of molecules on metal surfaces is of major importance in understanding processes such as corrosion or heterogeneous catalysis. Because of its high efficiency and reasonable accuracy, density functional theory (DFT) is the method of choice in this field nowadays, but it can be expected that the semilocal treatment of the exchange-correlation introduces fundamental errors. To understand those errors, it is possible to reduce the complexity of the problem to, for example, describe the dissociation of H2 on Cu(100). In this work, we model this process for an embedded, metallic cluster comparing coupled cluster, configuration interaction, and semilocal DFT calculations. We calculate a two-dimensional potential energy surface (PES) and identify the minimum energy pathway (MEP) for dissociation, the transition state, and also the dissociation minimum. Compared to DFT calculations, the interactions between the molecule and the surface are far more long ranged in explicitly correlated m...

Catalytic Mechanism of Histone Acetyltransferase p300: From the Proton Transfer to Acetylation Reaction

The transcriptional coactivator and histone acetyltransferase (HAT) p300 acetylates the four core histones and other transcription factors to regulate a plethora of fundamental biological processes including cell growth, development, oncogenesis and apoptosis. Recent structural and biochemical studies on the p300 HAT domain revealed a Theorell-Chance, or "hit-and-run", catalytic mechanism. Nonetheless, the chemical mechanism of the entire reaction process including the proton transfer (PT) scheme and consequent acetylation reaction route remains unclear. In this study, a combined computational strategy consisting of molecular modeling, molecular dynamic (MD) simulation, and quantum mechanics/molecular mechanics (QM/MM) simulation was applied to elucidate these important issues. An initial p300/H3/Ac-CoA complex structure was modeled and optimized using a 100 ns MD simulation. Residues that play important roles in substrate binding and the acetylation reaction were comprehensively investigated. For the first time, these studies reveal a plausible PT scheme consisting of Y1394, D1507, and a conserved crystallographic water molecule, with all components of the scheme being stable during the MD simulation and the energy barrier low for PT to occur. The two-dimensional potential energy surface for the nucleophilic attack process was also calculated. The comparison of potential energies for two possible elimination half-reaction mechanisms revealed that Y1467 reprotonates the coenzyme-A leaving group to form product. This study provides new insights into the detailed catalytic mechanism of p300 and has important implications for the discovery of novel small molecule regulators for p300.

Tetrazole acetic acid: Tautomers, conformers, and isomerization

Monomers of (tetrazol-5-yl)-acetic acid (TAA) were obtained by sublimation of the crystalline compound and the resulting vapors were isolated in cryogenic nitrogen matrices at 13 K. The conformational and tautomeric composition of TAA in the matrix was characterized by infrared spectroscopy and vibrational calculations carried out at the B3LYP/6-311++G(d,p) level. TAA may adopt two tautomeric modifications, 1H- and 2H-, depending on the position of the annular hydrogen atom. Two-dimensional potential energy surfaces (PESs) of TAA were theoretically calculated at the MP2/6-311++G(d,p) level, for each tautomer. Four and six symmetry-unique minima were located on these PESs, for 1H- and 2H-TAA, respectively. The energetics of the detected minima was subsequently refined by calculations at the QCISD level. Two 1H- and three 2H-conformers fall within the 0-8 kJ mol(-1) energy range and should be appreciably populated at the sublimation temperature (∼330 K). Observation of only one conformer for each tautomer (1ccc and 2pcc) is explained in terms of calculated barriers to conformational rearrangements. All conformers with the cis O=COH moiety are separated by low barriers (less than 10 kJ mol(-1)) and collapse to the most stable 1ccc (1H-) and 2pcc (2H-) forms during deposition of the matrix. On the trans O=COH surfaces, the relative energies are very high (between 12 and 27 kJ mol(-1)). The trans forms are not thermally populated at the sublimation conditions and were not detected in matrices. One high-energy form in each tautomer, 1cct (1H-) and 2pct (2H-), was found to differ from the most stable form only by rotation of the OH group and separated from other forms by high barriers. This opened a perspective for their stabilization in a matrix. 1cct and 2pct were generated in the matrices selectively by means of narrow-band near-infrared (NIR) irradiations of the samples at 6920 and 6937 cm(-1), where the first OH stretching overtone vibrations of 1ccc and 2pcc occur. The reverse transformations could be induced by irradiations at 7010 and 7030 cm(-1), transforming 1cct and 2pct back to 1ccc and 2pcc, also selectively. Besides the NIR-induced transformations, the photogenerated 1cct and 2pct forms also decay in N2 matrices back to 1ccc and 2pcc spontaneously, with characteristic decay times of hours (1H) and tens of minutes (2H). The decay mechanism is rationalized in terms of the proton tunneling. In crystals, TAA exists exclusively as 1H-tautomer. By contrast, the tautomeric composition of the matrix-isolated monomers was found to consist of both 1H- and 2H-tautomers, in comparable amounts. A mechanistic discussion of the tautomerization process occurring during sublimation, accounting also for the observed minor decomposition of TAA leading to CO2 and 5-methyl-tetrazole, is proposed.

Constraint Trajectory Surface-Hopping Molecular Dynamics Simulation of the Photoisomerization of Stilbene

Combining trajectory surface hopping (TSH) method with constraint molecular dynamics, we have extended TSH method from full to flexible dimensional potential energy surfaces. Classical trajectories are carried out in Cartesian coordinates with constraints in internal coordinates, while nonadiabatic switching probabilities are calculated separately in free internal coordinates by Landau-Zener and Zhu-Nakamura formulas along the seam. Two-dimensional potential energy surfaces of groundS0and excitedS1states are constructed analytically in terms of torsion angle and one dihedral angle around the central ethylenic C=C bond, and the other internal coordinates are all fixed at configuration of the conical intersection. At this conical intersection, the branching ratio from the present simulation is 48 : 52 (33 : 67) initially starting from trans(cis)-Stilbene in comparison with experimental value 50 : 50. Quantum yield for trans-to-cis isomerization is estimated as 49% in very good agreement with experimental value of 55%, while quantum yield for cis-to-trans isomerization is estimated as 47% in comparison with experimental value of 35%.

Theoretical study on reaction mechanism and kinetics of HNCS with CN

We presented a theoretical study on the detailed reaction mechanism and kinetics of the CN radical with the HNCS molecule. The barrierless minimum energy path and the most favorable entrance channel have been determined by constructing a two-dimensional potential energy surface of the C atom of CN attacking the HNCS molecule. The reaction of the C atom attacking the S atom was finally identified as the dominant entrance channel based on the rate constants' results calculated with the canonical variational transition state theory. The master equation method was employed to calculate the products' branching ratios, the overall rate constant, and the pressure dependence of the title reaction. The B3LYP∕6-311+G(2d,p) method was employed for all the geometrical optimizations and a multi-level extrapolation method based on the CCSD(T) and MP2(FC) energies was employed for further energy refinements.

A rotamer energy level study of sulfuric acid

It is a common approach in quantum chemical calculations for polyatomic molecules to rigidly constrain some of the degrees of freedom in order to make the calculations computationally feasible. However, the presence of the rigid constraints also affects the kinetic energy operator resulting in the frozen mode correction, originally derived by Pesonen [J. Chem. Phys. 139, 144310 (2013)]. In this study, we compare the effects of this correction to several different approximations to the kinetic energy operator used in the literature, in the specific case of the rotamer energy levels of sulfuric acid. The two stable conformers of sulfuric acid are connected by the rotations of the O-S-O-H dihedral angles and possess C2 and Cs symmetry in the order of increasing energy. Our results show that of the models tested, the largest differences with the frozen mode corrected values were obtained by simply omitting the passive degrees of freedom. For the lowest 17 excited states, this inappropriate treatment introduces an increase of 9.6 cm(-1) on average, with an increase of 8.7 cm(-1) in the zero-point energies. With our two-dimensional potential energy surface calculated at the CCSD(T)-F12a/VDZ-F12 level, we observe a radical shift in the density of states compared to the harmonic picture, combined with an increase in zero point energy. Thus, we conclude that the quantum mechanical inclusion of the different conformers of sulfuric acid have a significant effect on its vibrational partition function, suggesting that it will also have an impact on the computational values of the thermodynamic properties of any reactions where sulfuric acid plays a role. Finally, we also considered the effect of the anharmonicities for the other vibrational degrees of freedom with a VSCF-calculation at the DF-MP2-F12/VTZ-F12 level of theory but found that the inclusion of the other conformer had the more important effect on the vibrational partition function.

Multiple-pathways of carbon dioxide binding by a Lewis acid [B(C6F5)3] and a lewis base [P(tBu)3]: The energy landscape perspective

Using the reaction-relevant two-dimensional potential energy surface, an accurate reaction-pathway mapping and ab inito molecular dynamics, it is shown that CO2 capture by P(tBu)(3) and B(C6F5)(3) ...

Hydrogen transfer reactions in viscous media — Potential and free energy surfaces in solvent–solute coordinates and their kinetic implications

Two-dimensional potential energy and free energy surfaces are obtained using quantum mechanical and molecular dynamics calculations for four hydrogen transfer reactions in n-hexane solvent: the methyl–methane, n-propyl–n-propane, n-pentyl–n-pentane, and t-butyl–isobutane systems. The resultant surfaces have similar landscapes despite the fact the equilibrated solvent cavities for these systems are notably different in size and shape. The kinetic implications of these landscapes are discussed. The Arrhenius and tunneling kinetics of hydrogen transfer in nonpolar hydrocarbon solute–solvent systems are not expected to show any significant viscosity dependence.

Electrically dressed ultra-long-range polar Rydberg molecules

We investigate the impact of an electric field on the structure of ultralong-range polar diatomic Rydberg molecules. Both the s-wave and p-wave interactions of the Rydberg electron and the neutral ground state atom are taken into account. In the presence of the electric field the angular degree of freedom between the electric field and the internuclear axis acquires vibrational character and we encounter two-dimensional oscillatory adiabatic potential energy surfaces with an antiparallel equilibrium configuration. The electric field allows to shift the corresponding potential wells in such a manner that the importance of the p-wave interaction can be controlled and the individual wells are energetically lowered at different rates. As a consequence the equilibrium configuration and corresponding energetically lowest well move to larger internuclear distances for increasing field strength. For strong fields the admixture of non-polar molecular Rydberg states leads to the possibility of exciting the large angular momentum polar states via two-photon processes from the ground state of the atom. The resulting properties of the electric dipole moment and the vibrational spectra are analyzed with varying field strength.

A new six-dimensional potential energy surface for H2–N2O and its adiabatic-hindered-rotor treatment

A six-dimensional ab initio potential energy surface (PES) for H2-N2O which explicitly includes the symmetric and asymmetric vibrational coordinates Q1 and Q3 of N2O is calculated at the coupled-cluster singles and doubles with noniterative inclusion of connected triple level using an augmented correlation-consistent polarized-valence quadruple-zeta basis set together with midpoint bond functions. Four-dimensional intermolecular PESs are then obtained by fitting the vibrationally averaged interactions energies for υ3(N2O) = 0 and 1 to the Morse∕long-range analytical form. In the fits, fixing the long-range parameters at theoretical values smoothes over the numerical noise in the ab initio points in the long-range region of the potential. Using the adiabatic hindered-rotor approximation, two-dimensional PESs for hydrogen-N2O complexes with different isotopomers of hydrogen are generated by averaging the 4D PES over the rotation of the hydrogen molecule within the complex. The band-origin shifts for the hydrogen-N2O dimers calculated using both the 4D PESs and the angle-averaged 2D PESs are all in good agreement with each other and with the available experimental observations. The predicted infrared transition frequencies for para-H2-N2O and ortho-D2-N2O are also consistent with the observed spectra.