Semiempirical Potential Energy Surface Research Articles

Temperature effects on the branching dynamics in the model ambimodal (6 + 4)/(4 + 2) intramolecular cycloaddition reaction.

C14H20 (tetradecapentaene) is a simple model system exhibiting post transition-state behavior, wherein both the (6 + 4) and (4 + 2) cycloaddition products are formed from one ambimocal transition state structure. We studied the bifurcation dynamics starting from the two ambimodal transition state structures, the chair-form and boat-form, using the quasi-classical trajectory, classical molecular dynamics, and ring-polymer molecular dynamics methods on the parameter-optimized semiempirical GFN2-xTB potential energy surface. It was found that the calculated branching fractions differ between the chair-form and boat-form due to the different nature in the IRC pathways. We also investigated the effects of temperature on bifurcation dynamics and found that, at higher temperatures, trajectories stay longer in the intermediate region of the potential energy surface.

Simulation of interlayer coupling for electroactive covalent organic framework design.

Porous, stacked two-dimensional covalent organic frameworks (2D COFs) bearing semiconducting linkers can support directional charge transfer across adjacent layers of the COF. To better inform the current and possible future design rules for enhancing electron and hole transport in such materials, an understanding of how linker selection and functionalization affects interlayer electronic couplings is essential. We report electronic structure simulation and analysis of electronic couplings across adjacent linker units and to encapsulated species in functionalized electroactive 2D COFs. The detailed dependence of these electronic couplings on interlayer interactions is examined through scans along key interlayer degrees of freedom and through configurational sampling from equilibrium molecular dynamics on semiempirical potential energy surfaces. Beyond affirming the sensitivity of the electronic coupling to interlayer distance and orientation, these studies offer guidance toward linker functionalization strategies for enhancing charge carrier transport in electroactive 2D COFs.

Direct chemical dynamics simulations of CN- + CH3I bimolecular nucleophilic substitution reaction.

Bimolecular nucleophilic substitution reactions have been studied for more than a century. Experimental and theoretical investigations of these reactions are extensively going on due to their wide applicability and the discovery of new features of these reactions. The CN- + CH3I nucleophilic substitution reaction can result in two isomeric products (NCCH3/CNCH3 + I-) because the incoming nucleophile has two reactive centers. Velocity map imaging experiments of this reaction have been reported and dominant direct rebound dynamics and high internal energy excitation of the reaction products were found in the experiments. However, it was not possible to directly obtain the isomer branching ratios from the experimental data and statistical ratios were predicted based on a numerical simulation. In the present work, direct chemical dynamics simulations of this reaction were performed using density functional theory and semi-empirical potential energy surfaces. Reactivity was low at all collision energies and direct rebound dynamics was observed in a major fraction of trajectories in agreement with experiments. However, the branching ratios computed from the trajectories were different from the previously reported estimates. Product energy distributions and scattering angles were computed and detailed atomic level reaction mechanisms are presented.

Statistical dynamics of bimolecular recombination of alkali and halide ions

By means of quasiclassical trajectory simulation on semiempirical diabatic potential energy surfaces proposed earlier, we have studied the dynamics of the bimolecular recombination reactions RCs+ + X– → CsX + R for X– = F–, I– and R = Ar, Xe. The results obtained include the excitation functions of the reactions in the range of collision energies \(E_{{{\text{col}}}}\) from 0.1 to 2.5 eV as well as the distributions of the energy of the flying apart of the products, the opacity functions, and the distributions of the vibrational and rotational energies of the CsX molecule at \(E_{{{\text{col}}}} = 0.1\), 0.2, and 0.3 eV. For each of the four systems considered, the cross section of bimolecular recombination drops as the collision energy grows. In all the cases, the distributions of the vibrational energy of the product molecule are strongly non-equilibrium, whereas the distributions of the rotational energy are relatively close to equilibrium ones. On the whole, the behavior of the statistical dynamical characteristics of bimolecular recombination turns out to depend on the halide ion X– to a much greater extent than on the neutral atom R.Graphical abstract

Synthesis of ab initio and effective Hamiltonian line lists for ozone

A synthetic line list for the ozone molecule is presented. Variational calculation using the semi-empirical potential energy surface (PES) and ab initio dipole moment surface (DMS) produce very accurate values of line intensities, but give line positions far away from their experimental values. Furthermore assignment of approximate rotational and vibrational quantum numbers are missing from variationally calculated line list. Effective Hamiltonian calculations are complimentary to ab initio line lists in these properties giving excellent value of line positions, close to experimental ones, and a full set of quantum numbers assignment. The synthesis of both these qualities in one line list is highly desirable. Here a synthetic line list for 16O3 is presented. The method of corrections of distorted intensities in variational linelist with ab initio DMS due to the artificial intensity stealing is developed and applied. Comparison of the synthetic line list with all major published line lists and available experimental data is given. The calculated line intensities agree to within experimental error for most bands for which accurate measurements are available.

Dynamics of third order direct three-body recombination of heavy ions.

The direct three-body recombination reactions Cs+ + X- + R → CsX + R (X = F, I and R = Ar, Xe) are studied within the quasiclassical trajectory method using diabatic semiempirical potential energy surfaces, the encounters of the ions being non-central. The collision energies range between 1 and 10 eV (values typical for low temperature plasma), while the so-called delay parameter, which characterizes the delay in the arrival of the neutral atom R in relation to the time instant when the distance between the ions attains its minimum, is equal to 0 or 20%. The calculation results include the recombination excitation functions, the opacity functions, and the vibrational and rotational energy distributions of the recombination products. All the four reactions considered exhibit similar overall statistical dynamics, but each process has its own features. On the whole, for both the recombining pairs Cs+ + F- and Cs+ + I-, xenon is more effective than argon as an acceptor of excess energy from the ion pair. The rotational energy distributions of the salt molecules CsF and CsI are almost equilibrium, whereas the vibrational energy distributions are strongly non-equilibrium.

A semi-empirical potential energy surface and line list for H<sub>2</sub><sup>16</sup>O extending into the near-ultraviolet

Abstract. Accurate reference spectroscopic information for the water molecule from the microwave to the near-ultraviolet is of paramount importance in atmospheric research. A semi-empirical potential energy surface for the ground electronic state of H216O has been created by refining almost 4000 experimentally determined energy levels. These states extend into regions with large values of rotational and vibrational excitation. For all states considered in our refinement procedure, which extend to 37 000 cm−1 and J=20 (total angular momentum), the average root-mean-square deviation is approximately 0.05 cm−1. This potential energy surface offers significant improvements when compared to recent models by accurately predicting states possessing high values of J. This feature will offer significant improvements in calculated line positions for high-temperature spectra where transitions between high J states become more prominent. Combining this potential with the latest dipole moment surface for water vapour, a line list has been calculated which extends reliably to 37 000 cm−1. Obtaining reliable results in the ultraviolet is of special importance as it is a challenging spectral region for the water molecule both experimentally and theoretically. Comparisons are made against several experimental sources of cross sections in the near-ultraviolet and discrepancies are observed. In the near-ultraviolet our calculations are in agreement with recent atmospheric retrievals and the upper limit obtained using broadband spectroscopy by Wilson et al. (2016, p. 194), but they do not support recent suggestions of very strong absorption in this region.

Calculated line lists for H216O and H218O with extensive comparisons to theoretical and experimental sources including the HITRAN2016 database

New line lists are presented for the two most abundant water isotopologues; H216O and H218O. The H216O line list extends to 25710 cm−1 with intensity stabilities provided via ratios of calculated intensities obtained from two different semi-empirical potential energy surfaces. The line list for H218O extends to 20000 cm−1. The minimum intensity considered for all is 10−30 cm molecule−1 at 296 K, assuming 100% abundance for each isotopologue. Fluctuation of calculated intensities caused by changes in the underlying potential energy are found to be significant, particularly for weak transitions. Direct comparisons are made against eighteen different sources of line intensities, both experimental and theoretical, many of which are used within the HITRAN2016 database. With some exceptions, there is excellent agreement between our line lists and the experimental intensities in HITRAN2016. In the infrared region, many H216O bands which exhibit intensity differences of 5–10% between to the most recent ’POKAZATEL’ line list (Polyansky et al., [Mon. Not. Roy. Astron. Soc. 480, 2597 (2018)] and observation, are now generally predicted to within 1%. For H218O, there are systematic differences in the strongest intensities calculated in this work versus those obtained from semi-empirical calculations. In the visible, computed cross sections show smaller residuals between our work and both HITRAN2016 and HITEMP2010 than POKAZATEL. While our line list accurately reproduces HITEMP2010 cross sections in the observed region, residuals produced from this comparison do however highlight the need to update line positions in the visible spectrum of HITEMP2010. These line lists will be used to update many transition intensities and line positions in the HITRAN2016 database.

Preconditioners for the geometry optimisation and saddle point search of molecular systems

A class of preconditioners is introduced to enhance geometry optimisation and transition state search of molecular systems. We start from the Hessian of molecular mechanical terms, decompose it and retain only its positive definite part to construct a sparse preconditioner matrix. The construction requires only the computation of the gradient of the corresponding molecular mechanical terms that are already available in popular force field software packages. For molecular crystals, the preconditioner can be combined straightforwardly with the exponential preconditioner recently introduced for periodic systems. The efficiency is demonstrated on several systems using empirical, semiempirical and ab initio potential energy surfaces.

Analysis of the red and green optical absorption spectrum of gas phase ammonia

Room temperature NH3 absorption spectra recorded at the Kitt Peak National Solar Observatory in 1980 are analyzed. The spectra cover two regions in the visible: 15,200 – 15,700 cm−1 and 17,950 – 18,250 cm−1. These high overtone rotation-vibration spectra are analyzed using both combination differences and variational line lists. Two variational line lists were computed using the TROVE nuclear motion program: one is based on an ab initio potential energy surface (PES) while the other used a semi-empirical PES. Ab initio dipole moment surfaces are used in both cases. 95 energy levels with J=1−7 are determined from analysis of the experimental spectrum in the 5νNH (red) region and 46 for 6νNH (green) region. These levels span four vibrational bands in each of the two regions, associated with stretching overtones.

Investigation of adsorption mechanism of Fe, Cu, and Zn ions in extraction and preconcentration process on synthesized graphene oxide using an indole derivative

3-(chloro(2-methyl-1H-indol-3-yl)methyl)-2-methyl-1H-indole (MIMI) was chosen for separation and preconcentration of iron (III), copper (II), and zinc by solid-phase extraction (SPE). Ion–MIMI chelates are adsorbed onto synthesized graphene oxide (GO) as adsorbent, eluted with HNO3 and determined by flame atomic absorption spectrometry (FAAS). The adsorption mechanism of titled metal complexes on GO was investigated by using computational chemistry approach based on PM7 semi-empirical potential energy surface. The influences of analytical parameters were investigated. The interference effect of common cations tested did not interfere with the recovery of understudied ions. The preconcentration factor of 312.5 and the detection limits of 0.62, 0.28, and 0.05 ng mL−1 for iron (III), copper (II), and zinc, respectively, were obtained. The developed SPE method was successfully utilized for the determination of trace metal ions in different certified reference materials and real samples (including water, cheese, honey, tomato, leaves of spinach, and milk) by FAAS.

Closer versus Long Range Interaction Effects on the Non-Arrhenius Behavior of Quasi-Resonant O2 + N2 Collisions.

We report in this paper an investigation on energy transfer processes from vibration to vibration and/or translation in thermal and subthermal regimes for the O2 + N2 system performed using quantum-classical calculations on different empirical, semiempirical, and ab initio potential energy surfaces. In particular, the paper focuses on the rationalization of the non-Arrhenius behavior (inversion of the temperature dependence) of the quasi-resonant vibration-to-vibration energy transfer transition rate coefficients at threshold. To better understand the microscopic nature of the involved processes, we pushed the calculations to the detail of the related cross sections and analyzed the impact of the medium and long-range components of the interaction on them. Furthermore, the variation with temperature of the dependence of the quasi-resonant rate coefficient on the vibrational energy gap between initial and final vibrational states and the effectiveness of quantum-classical calculations to overcome the limitations of the purely classical treatments were also investigated. These treatments, handled in an open molecular science fashion by chaining data and competencies of the various laboratories using a grid empowered molecular simulator, have allowed a rationalization of the dependence of the computed rate coefficients in terms of the distortion of the O2-N2 configuration during the diatom-diatom collisions. A way of relating such distortions to a smooth and continuous progress variable, allowing a proper evolution from both long to closer range formulation of the interaction and from its entrance to exit channel (through the strong interaction region) relaxed graphical representations, is also discussed in the paper.

Room temperature linelists for CO2 asymmetric isotopologues with ab initio computed intensities

The present paper reports room temperature line lists for six asymmetric isotopologues of carbon dioxide: 16O12C18O (628), 16O12C17O (627), 16O13C18O (638),16O13C17O (637), 17O12C18O (728) and 17O13C18O (738), covering the range 0–8000cm−1. Variational rotation-vibration wavefunctions and energy levels are computed using the DVR3D software suite and a high quality semi-empirical potential energy surface (PES), followed by computation of intensities using an ab initio dipole moment surface (DMS). A theoretical procedure for quantifying sensitivity of line intensities to minor distortions of the PES/DMS renders our theoretical model as critically evaluated. Several recent high quality measurements and theoretical approaches are discussed to provide a benchmark of our results against the most accurate available data. Indeed, the thesis of transferability of accuracy among different isotopologues with the use of mass-independent PES is supported by several examples. Thereby, we conclude that the majority of line intensities for strong bands are predicted with sub-percent accuracy. Accurate line positions are generated using an effective Hamiltonian, constructed from the latest experiments. This study completes the list of relevant isotopologues of carbon dioxide; these line lists are available to remote sensing studies and inclusion in databases.

Room temperature line lists for CO2 symmetric isotopologues with ab initio computed intensities

Remote sensing experiments require high-accuracy, preferably sub-percent, line intensities and in response to this need we present computed room temperature line lists for six symmetric isotopologues of carbon dioxide: 13C16O2, 14C16O2, 12C17O2, 12C18O2, 13C17O2 and 13C18O2, covering the range 0–8000cm−1. Our calculation scheme is based on variational nuclear motion calculations and on a reliability analysis of the generated line intensities. Rotation–vibration wavefunctions and energy levels are computed using the DVR3D software suite and a high quality semi-empirical potential energy surface (PES), followed by computation of intensities using an ab initio dipole moment surface (DMS). Four line lists are computed for each isotopologue to quantify sensitivity to minor distortions of the PES/DMS. Reliable lines are benchmarked against recent state-of-the-art measurements and against the HITRAN2012 database, supporting the claim that the majority of line intensities for strong bands are predicted with sub-percent accuracy. Accurate line positions are generated using an effective Hamiltonian. We recommend the use of these line lists for future remote sensing studies and their inclusion in databases.

Improved Sugar Puckering Profiles for Nicotinamide Ribonucleoside for Hybrid QM/MM Simulations.

The coenzyme nicotinamide adenine dinucleotide (NAD+) and its reduced form (NADH) play ubiquitous roles as oxidizing and reducing agents in nature. The binding, and possibly the chemical redox step, of NAD+/NADH may be influenced by the cofactor conformational distribution and, in particular, by the ribose puckering of its nicotinamide-ribonucleoside (NR) moiety. In many hybrid quantum mechanics-molecular mechanics (QM/MM) studies of NAD+/NADH dependent enzymes, the QM region is treated by semiempirical (SE) methods. Recent work suggests that SE methods do not adequately describe the ring puckering in sugar molecules. In the present work we adopt an efficient and practical strategy to correct for this deficiency for NAD+/NADH. We have implemented a cost-effective correction to a SE Hamiltonian by adding a correction potential, which is defined as the difference between an accurate benchmark density functional theory (DFT) potential energy surface (PES) and the SE PES. In practice, this is implemented via a B-spline interpolation scheme for the grid-based potential energy difference surface. We find that the puckering population distributions obtained from free energy QM(SE)/MM simulations are in good agreement with DFT and in fair accord with experimental results. The corrected PES should facilitate a more accurate description of the ribose puckering in the NAD+/NADH cofactor in simulations of biological systems.

ExoMol line lists – XV. A new hot line list for hydrogen peroxide

A computed line list for hydrogen peroxide, H216O2, applicable to temperatures up to T = 1250 K is presented. A semi-empirical high-accuracy potential energy surface is constructed and used with an ab initio dipole moment surface as input trove to compute 7.5 million rotational-vibrational states and around 20 billion transitions with associated Einstein-A coefficients for rotational excitations up to J = 85. The resulting APTY line list is complete for wavenumbers below 6000 cm−1 (λ < 1.67 μm) and temperatures up to 1250 K. Room-temperature spectra are compared with laboratory measurements and data currently available in the HITRAN data base and literature. Our rms with line positions from the literature is 0.152 cm−1 and our absolute intensities agree better than 10 per cent. The full line list is available from the CDS data base as well as at www.exomol.com.

Adaptive time steps in trajectory surface hopping simulations

Trajectory surface hopping (TSH) simulations are often performed in combination with active-space multi-reference configuration interaction (MRCI) treatments. Technical problems may arise in such simulations if active and inactive orbitals strongly mix and switch in some particular regions. We propose to use adaptive time steps when such regions are encountered in TSH simulations. For this purpose, we present a computational protocol that is easy to implement and increases the computational effort only in the critical regions. We test this procedure through TSH simulations of a GFP chromophore model (OHBI) and a light-driven rotary molecular motor (F-NAIBP) on semiempirical MRCI potential energy surfaces, by comparing the results from simulations with adaptive time steps to analogous ones with constant time steps. For both test molecules, the number of successful trajectories without technical failures rises significantly, from 53% to 95% for OHBI and from 25% to 96% for F-NAIBP. The computed excited-state lifetime remains essentially the same for OHBI and increases somewhat for F-NAIBP, and there is almost no change in the computed quantum efficiency for internal rotation in F-NAIBP. We recommend the general use of adaptive time steps in TSH simulations with active-space CI methods because this will help to avoid technical problems, increase the overall efficiency and robustness of the simulations, and allow for a more complete sampling.

Effects of collision energy on stereodynamical information of the reaction F+HI→FI+H

The vector correlations between products and reactants for the reaction F+HI→FI+H are studied using quasi-classical trajectory (QCT) method. Employing a semiempirical LEPS potential energy surface constructed by Kornweitz and Persky, this work calculates the angular distributions of P(𝜃 r ), P(ϕ r ) and several PDDCSs in the center of mass frame. The effect of the collision energy on the product vector properties is also discussed.

Study on column SPE with synthesized graphene oxide and FAAS for determination of trace amount of Co(II) and Ni(II) ions in real samples.

A selective method for the preconcentration and separation of trace amounts of Co(II) and Ni(II) by column solid phase extraction has been developed. The method is based on the adsorption of metal ions as N-(5-methyl-2-hydroxyacetophenone)-N'-(2-hydroxyacetophenone) ethylene diamine (MHE) complex on synthesized graphene oxide. Computational modeling based on PM6 semi-empirical potential energy surface was utilized to investigate the interaction of metallic complexes with graphene oxide sheet. The adsorption was achieved quantitatively on graphene oxide at pH6.0 and then the retained analyte contents on the column were quantitatively eluted with 3.0 mol L(-1) HNO3. Experimental conditions for effective separation of trace levels of the analyte ions such as pH, flow rate, concentration of eluent, sample volume and interference ions were investigated. A preconcentration factor of 250 was achieved by passing 1250 mL of sample through the solid phase, while the limit of detection of Co(II) and Ni(II) ions were found to be 0.25 and 0.18 ng mL(-1), respectively. The method was applied to the determination of analyte ions in water, black tea and tomato samples.

Nuclear quantum effect and temperature dependency on the hydrogen-bonded structure of 7-azaindole dimer

The structure of 7-azaindole dimer (7AI2) as a model compound for DNA base pair has been studied by classical molecular dynamics (MD) and path integral molecular dynamics (PIMD) simulations on the semi-empirical PM6 potential energy surface at various temperatures, to investigate the nuclear quantum effect and temperature dependency on the hydrogen-bonded moiety of 7AI2. At 75 K, two H-bondings are maintained throughout a given simulation time in both classical and PIMD (quantum) simulations. At 150 K, these two H-bondings are maintained in only quantum simulation, while in classical simulation, the two H-bondings (or one H-bonding) are sometimes broken and reformed. For 225 K, these two H-bondings are broken in both classical and quantum simulations. We have also applied a principal component analysis to MD and PIMD simulations to analyze the intermolecular motions. We found that the ratio of the second lowest (dimer butterfly out-of-plane) vibrational mode from normal mode analysis which is the most dominant motion decreases with increasing temperature, whereas that of first lowest (dimer torsion out-of-plane) vibrational mode which is the second most dominant motion increases with increasing temperature from temperature 75 to 150 K and then decreases at 225 K due to the nuclear quantum effect. Moreover, the motions of two hydrogen-bonded structures are significantly different with increasing temperature. This difference is revealed by the principal component analysis which shows that the ratio of opening in-plane motion decreases and the ratio of stretching in-plane motion decreases.