Ab initio calculation of H + He+^+ charge transfer cross sections for plasma physics

The charge transfer in low energy (0.25 to 150 eV/amu) H($nl$) + He$^+(1s)$ collisions is investigated using a quasi-molecular approach for the $n=2,3$ as well as the first two $n=4$ singlet states. The diabatic potential energy curves of the HeH$^+$ molecular ion are obtained from the adiabatic potential energy curves and the non-adiabatic radial coupling matrix elements using a two-by-two diabatization method, and a time-dependent wave-packet approach is used to calculate the state-to-state cross sections. We find a strong dependence of the charge transfer cross section in the principal and orbital quantum numbers $n$ and $l$ of the initial or final state. We estimate the effect of the non-adiabatic rotational couplings, which is found to be important even at energies below 1 eV/amu. However, the effect is small on the total cross sections at energies below 10 eV/amu. We observe that to calculate charge transfer cross sections in a $n$ manifold, it is only necessary to include states with $n^{\prime}\leq n$, and we discuss the limitations of our approach as the number of states increases.Comment: 14 pages, 10 figure

Attosecond electronic and nuclear quantum photodynamics of ozone: time-dependent Dyson orbitals and dipole

A nonadiabatic scheme for the description of the coupled electron and nuclear motions in the ozone molecule was proposed recently. An initial coherent nonstationary state was prepared as a superposition of the ground state and the excited Hartley band. In this situation neither the electrons nor the nuclei are in a stationary state. The multiconfiguration time dependent Hartree method was used to solve the coupled nuclear quantum dynamics in the framework of the adiabatic separation of the time-dependent Schr\"odinger equation. The resulting wave packet shows an oscillation of the electron density between the two chemical bonds. As a first step for probing the electronic motion we computed the time-dependent molecular dipole and the Dyson orbitals. The latter play an important role in the explanation of the photoelectron angular distribution. Calculations of the Dyson orbitals are presented both for the time-independent as well as the time-dependent situations. We limited our description of the electronic motion to the Franck-Condon region only due to the localization of the nuclear wave packets around this point during the first 5-6 fs

H2, HD, and D2 in the small cage of structure II clathrate hydrate: vibrational frequency shifts from fully coupled quantum six-dimensional calculations of the vibration-translation-rotation eigenstates

We report the first fully coupled quantum six-dimensional (6D) bound-state calculations of the vibration-translation-rotation eigenstates of a flexible H2, HD, and D2 molecule confined inside the small cage of the structure II clathrate hydrate embedded in larger hydrate domains with up to 76 H2O molecules, treated as rigid. Our calculations use a pairwise-additive 6D intermolecular potential energy surface for H2 in the hydrate domain, based on an ab initio 6D H2–H2O pair potential for flexible H2 and rigid H2O. They extend to the first excited (v = 1) vibrational state of H2, along with two isotopologues, providing a direct computation of vibrational frequency shifts. We show that obtaining a converged v = 1 vibrational state of the caged molecule does not require converging the very large number of intermolecular translation-rotation states belonging to the v = 0 manifold up to the energy of the intramolecular stretch fundamental (≈4100 cm−1 for H2). Only a relatively modest-size basis for the intermolecular degrees of freedom is needed to accurately describe the vibrational averaging over the delocalized wave function of the quantum ground state of the system. For the caged H2, our computed fundamental translational excitations, rotational j = 0 → 1 transitions, and frequency shifts of the stretch fundamental are in excellent agreement with recent quantum 5D (rigid H2) results [A. Powers et al., J. Chem. Phys. 148, 144304 (2018)]. Our computed frequency shift of −43 cm−1 for H2 is only 14% away from the experimental value at 20 K

The effect of the condensed-phase environment on the vibrational frequency shift of a hydrogen molecule inside clathrate hydrates

© 2018 Author(s). We report a theoretical study of the frequency shift (redshift) of the stretching fundamental transition of an H 2 molecule confined inside the small dodecahedral cage of the structure II clathrate hydrate and its dependence on the condensed-phase environment. In order to determine how much the hydrate water molecules beyond the confining small cage contribute to the vibrational frequency shift, quantum five-dimensional (5D) calculat ions of the coupled translation-rotation eigenstates are performed for H 2 in the v=0 and v=1 vibrational states inside spherical clathrate hydrate domains of increasing radius and a growing number of water molecules, ranging from 20 for the isolated small cage to over 1900. In these calculations, both H 2 and the water domains are treated as rigid. The 5D intermolecular potential energy surface (PES) of H 2 inside a hydrate domain is assumed to be pairwise additive. The H 2 -H 2 O pair interaction, represented by the 5D (rigid monomer) PES that depends on the vibrational state of H 2 , v=0 or v=1, is derived from the high-quality ab initio full-dimensional (9D) PES of the H 2 -H 2 O complex [P. Valiron et al., J. Chem. Phys. 129, 134306 (2008)]. The H 2 vibrational frequency shift calculated for the largest clathrate domain considered, which mimics the condensed-phase environment, is about 10% larger in magnitude than that obtained by taking into account only the small cage. The calculated splittings of the translational fundamental of H 2 change very little with the domain size, unlike the H 2 j = 1 rotational splittings that decrease significantly as the domain size increases. The changes in both the vibrational frequency shift and the j = 1 rotational splitting due to the condensed-phase effects arise predominantly from the H 2 O molecules in the first three complete hydration shells around H 2

Ab initio calculation of the 66 low lying electronic states of HeH+^+: adiabatic and diabatic representations

We present an ab initio study of the HeH$^+$ molecule. Using the quantum chemistry package MOLPRO and a large adapted basis set, we have calculated the adiabatic potential energy curves of the first 20 $^1 \Sigma^+$, 19 $^3\Sigma^+$, 12 $^1\Pi$, 9 $^3\Pi$, 4 $^1\Delta$ and 2 $^3\Delta$ electronic states of the ion in CASSCF and CI approaches. The results are compared with previous works. The radial and rotational non-adiabatic coupling matrix elements as well as the dipole moments are also calculated. The asymptotic behaviour of the potential energy curves and of the various couplings between the states is also studied. Using the radial couplings, the diabatic representation is defined and we present an example of our diabatization procedure on the $^1\Sigma^+$ states.Comment: v2. Minor text changes. 28 pages, 18 figures. accepted in J. Phys.

Peptide Bond Distortions from Planarity: New Insights from Quantum Mechanical Calculations and Peptide/Protein Crystal Structures

By combining quantum-mechanical analysis and statistical survey of peptide/protein structure databases we here report a thorough investigation of the conformational dependence of the geometry of peptide bond, the basic element of protein structures. Different peptide model systems have been studied by an integrated quantum mechanical approach, employing DFT, MP2 and CCSD(T) calculations, both in aqueous solution and in the gas phase. Also in absence of inter-residue interactions, small distortions from the planarity are more a rule than an exception, and they are mainly determined by the backbone ψ dihedral angle. These indications are fully corroborated by a statistical survey of accurate protein/peptide structures. Orbital analysis shows that orbital interactions between the σ system of Cα substituents and the π system of the amide bond are crucial for the modulation of peptide bond distortions. Our study thus indicates that, although long-range inter-molecular interactions can obviously affect the peptide planarity, their influence is statistically averaged. Therefore, the variability of peptide bond geometry in proteins is remarkably reproduced by extremely simplified systems since local factors are the main driving force of these observed trends. The implications of the present findings for protein structure determination, validation and prediction are also discussed

Explicitly correlated treatment of H2NSi and H2SiN radicals: Electronic structure calculations and rovibrational spectra

Various ab initio methods are used to compute the six dimensional potential energy surfaces (6D-PESs) of the ground states of the H2NSi and H2SiN radicals. They include standard coupled cluster (RCCSD(T)) techniques and the newly developed explicitly correlated RCCSD(T)-F12 methods. For H2NSi, the explicitly correlated techniques are viewed to provide data as accurate as the standard coupled cluster techniques, whereas small differences are noticed for H2SiN. These PESs are found to be very flat along the out-of-plane and some in-plane bending coordinates. Then, the analytic representations of these PESs are used to solve the nuclear motions by standard perturbation theory and variational calculations. For both isomers, a set of accurate spectroscopic parameters and the vibrational spectrum up to 4000 cm-1 are predicted. In particular, the analysis of our results shows the occurrence of anharmonic resonances for H2SiN even at low energies. © 2011 American Institute of Physics.L.J. thanks the Centre National de la Recherche Scientifique (CNRS, France) for financial support. M.L.S. acknowledges the MICINN (SPAIN) for the Grant No. AYA2008– 00446.Peer Reviewe

A harmonic adiabatic approximation to calculate vibrational states of ammonia

In the present work, we study the vibrational spectrum of ammonia in full dimensionality (6D), with special emphasis on the tunneling splitting. The inversion motion, i.e., the active mode v(2), is indeed relatively well decoupled from the other five inactive modes. Therefore, an adiabatic separation in an active wave function and an inactive one, approximated with a 5D-harmonic basis function, is certainly well adapted to describing this motion. This separation leads to several 1D-effective Hamiltonians for each 5D-harmonic basis function or adiabatic channel. Two models have been tested: the harmonic adiabatic approximation (HADA), when only one channel is used and the coupled HADA (cHADA), when several channels are coupled. In order to get reliable values for tunneling splitting, our calculations have shown that: (i) the calculation of the electronic potential has to be performed with a large atomic basis set (up to quintuple zeta) with a method including core-valence correlation; (ii) the cHADA is required since the HADA overestimates the energy levels. Furthermore, our values for the tunneling splitting are in good agreement with the experimental data of ammonia and several isotopomers. (C) 2004 Elsevier B.V. All rights reserved

Exact numerical computation of a kinetic energy operator in curvilinear coordinates

The conformation and dynamical behavior of molecular systems is very often advantageously described in terms of physically well-adapted curvilinear coordinates. It is rather easy to show that the numerous analytical expressions of the kinetic energy operator of a molecular system described in terms of n curvilinear coordinates can all be transformed into the following more usable expression: (T) over cap=Sigma(ij)f(2)(ij)(q)partial derivative(2)/partial derivativeq(i)partial derivativeq(j)+Sigma(i)f(1)(i)(q)partial derivative/partial derivativeq(i)+nu(q), where f(2)(ij)(q), f(1)(i)(q), and nu(q) are functions of the curvilinear coordinates q=(...,q(i),...). If the advantages of curvilinear coordinates are unquestionable, they do have a major drawback: the sometimes awful complexity of the analytical expression of the kinetic operator (T) over cap for molecular systems with more than five atoms. Therefore, we develop an algorithm for computing (T) over cap for a given value of the n curvilinear coordinates q. The calculation of the functions f(2)(ij)(q), f(1)(i)(q), and nu(q) only requires the knowledge of the Cartesian coordinates and their derivatives in terms of the n curvilinear coordinates. This coordinate transformation (curvilinear-->Cartesian) is very easy to perform and is widely used in quantum chemistry codes resorting to a Z-matrix to define the curvilinear coordinates. Thus, the functions f(2)(ij)(q), f(1)(i)(q), and nu(q) can be evaluated numerically and exactly for a given value of q, which makes it possible to propagate wavepackets or to simulate the spectra of rather complex systems (constrained Hamiltonian). The accuracy of this numerical procedure is tested by comparing two calculations of the bending spectrum of HCN: the first one, performed by using the present numerical kinetic operator procedure, the second one, obtained in previous studies, by using an analytical kinetic operator. Finally, the ab initio computation of the internal rotation spectrum and wave functions of 2-methylpropanal by means of dimensionality reduction, is given as an original application. (C) 2002 American Institute of Physics

Theoretical spectroscopy of trans-HNNH+ and isotopomers

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