Ab Initio Surface Research Articles

Strikingly Different Effects of Hydrogen Bonding on the Photodynamics of Individual Nucleobases in DNA: Comparison of Guanine and Cytosine

Ab initio surface hopping dynamics calculations were performed to study the photophysical behavior of cytosine and guanine embedded in DNA using a quantum mechanical/molecular mechanics (QM/MM) approach. It was found that the decay rates of photo excited cytosine and guanine were affected in a completely different way by the hydrogen bonding to the DNA environment. In case of cytosine, the geometrical restrictions exerted by the hydrogen bonds did not influence the relaxation time of cytosine significantly due to the generally small cytosine ring puckering required to access the crossing region between excited and ground state. On the contrary, the presence of hydrogen bonds significantly altered the photodynamics of guanine. The analysis of the dynamics indicates that the major contribution to the lifetime changes comes from the interstrand hydrogen bonds. These bonds considerably restricted the out-of-plane motions of the NH(2) group of guanine which are necessary for the ultrafast decay to the ground state. As a result, only a negligible amount of trajectories decayed into the ground state for guanine embedded in DNA within the simulation time of 0.5 ps, while for comparison, the isolated guanine relaxed to the ground state with a lifetime of about 0.22 ps. These examples show that, in addition to phenomena related to electronic interactions between nucleobases, there also exist relatively simple mechanisms in DNA by which the lifetime of a nucleobase is significantly enhanced as compared to the gas phase.

Ab initio calculation of the rotational spectrum of methane vibrational ground state

In a previous article we have introduced an alternative perturbation scheme to the traditional one starting from the harmonic oscillator, rigid rotator Hamiltonian, to find approximate solutions of the spectral problem for rotation-vibration molecular Hamiltonians. The convergence of our method for the methane vibrational ground state rotational energy levels was quicker than that of the traditional method, as expected, and our predictions were quantitative. In this second article, we study the convergence of the ab initio calculation of effective dipole moments for methane within the same theoretical frame. The first order of perturbation when applied to the electric dipole moment operator of a spherical top gives the expression used in previous spectroscopic studies. Higher orders of perturbation give corrections corresponding to higher centrifugal distortion contributions and are calculated accurately for the first time. Two potential energy surfaces of the literature have been used for solving the anharmonic vibrational problem by means of the vibrational mean field configuration interaction approach. Two corresponding dipole moment surfaces were calculated in this work at a high level of theory. The predicted intensities agree better with recent experimental values than their empirical fit. This suggests that our ab initio dipole moment surface and effective dipole moment operator are both highly accurate.

Theoretical simulations of the vibrational predissociation spectra of H 5 + and D 5 + clusters

In the present study, the effect of the potential energy surface representation on the infrared spectra features of the H+ 5 and D+ 5 clusters is investigated. For the spectral simulations, we adopted a recently proposed (Sanz-Sanz et al. in Phys Rev A 84:060502-1–4, 2011) two-dimensional adiabatic quantum model to describe the proton-transfer motion between the two H2 or D2 units. The reported calculations make use of a reliable “on the fly” DFT-based potential surface and the corresponding new dipole moment surface. The results of the vibrational predissociation dynamics are compared with earlier and recent experimental data available from mass-selected photodissociation spectroscopy, as well as with previous theoretical calculations based on an analytical ab initio parameterized surfaces. The role of the potential topology on the spectral features is studied, and general trends are discussed.

An isotopic-independent highly accurate potential energy surface for CO2 isotopologues and an initial 12C16O2 infrared line list

An isotopic-independent, highly accurate potential energy surface (PES) has been determined for CO(2) by refining a purely ab initio PES with selected, purely experimentally determined rovibrational energy levels. The purely ab initio PES is denoted Ames-0, while the refined PES is denoted Ames-1. Detailed tests are performed to demonstrate the spectroscopic accuracy of the Ames-1 PES. It is shown that Ames-1 yields σ(rms) (root-mean-squares error) = 0.0156 cm(-1) for 6873 J = 0-117 (12)C(16)O(2) experimental energy levels, even though less than 500 (12)C(16)O(2) energy levels were included in the refinement procedure. It is also demonstrated that, without any additional refinement, Ames-1 yields very good agreement for isotopologues. Specifically, for the (12)C(16)O(2) and (13)C(16)O(2) isotopologues, spectroscopic constants G(v) computed from Ames-1 are within ±0.01 and 0.02 cm(-1) of reliable experimentally derived values, while for the (16)O(12)C(18)O, (16)O(12)C(17)O, (16)O(13)C(18)O, (16)O(13)C(17)O, (12)C(18)O(2), (17)O(12)C(18)O, (12)C(17)O(2), (13)C(18)O(2), (13)C(17)O(2), (17)O(13)C(18)O, and (14)C(16)O(2) isotopologues, the differences are between ±0.10 and 0.15 cm(-1). To our knowledge, this is the first time a polyatomic PES has been refined using such high J values, and this has led to new challenges in the refinement procedure. An initial high quality, purely ab initio dipole moment surface (DMS) is constructed and used to generate a 296 K line list. For most bands, experimental IR intensities are well reproduced for (12)C(16)O(2) using Ames-1 and the DMS. For more than 80% of the bands, the experimental intensities are reproduced with σ(rms)(ΔI) < 20% or σ(rms)(ΔI∕δ(obs)) < 5. A few exceptions are analyzed and discussed. Directions for future improvements are discussed, though it is concluded that the current Ames-1 and the DMS should be useful in analyzing and assigning high-resolution laboratory or astronomical spectra.

Line lists for H218O and H217O based on empirical line positions and ab initio intensities

New line lists for isotopically substituted water are presented. Most line positions were calculated from experimentally determined energy levels, while all line intensities were computed using an ab initio dipole moment surface. Transitions for which experimental energy levels are unavailable use calculated line positions. These line lists cover the range 0.05–20000cm−1 and are significantly more complete and potentially more accurate than the line lists available via standard databases. All lines with intensities (scaled by isotopologue abundance) greater than 10−29cm/molecule at 296K are included, augmented by weaker lines originating from pure rotational transitions. The final line lists contain 39918 lines for H218O and 27546 for H217O and are presented in standard HITRAN format. The number of experimentally determined H218O and H217O line positions is, respectively, 32970 (83% of the total) and 17073 (62%) and in both cases the average estimated uncertainty is 2×10−4cm−1. The number of ab initio line intensities with an estimated uncertainty of 1% is 16621 (42%) for H218O and 13159 (48%) for H217O.

Long-range three-body atom–diatom potential for doublet Li3

An accurate long-range ab initio potential energy surface has been calculated for the ground state X2A′ lithium trimer in the frozen diatom approximation using all electron RCCSD (T). The ab initio energies are corrected for basis set superposition error and extrapolated to the complete basis limit. Molecular van der Waals dispersion coefficients and three-body dispersion damping terms for the atom–diatomic dissociation limit are presented from a linear least squares fit and shown to be an essentially exact representation of the ab initio surface at long range.

Three-state surface hopping calculations of acetaldehyde photodissociation to CH3 + HCO on ab initio potential surfaces

We report Trajectory Surface Hopping (TSH) calculations of CH3CHO photodissociation involving three electronic states, S1, T1, and S0, with a focus on the radical products CH3 + HCO, which can be formed from both T0 and S0. We use previously reported potential energy surfaces and spin-orbit couplings for T1 and S0 and report a new potential and spin-orbit coupling for S1 here. Roughly 32 000 trajectories are performed at energies corresponding to seven photolysis wavelengths between 372 and 230 nm. Motivated by recent experiments, we examine the branching ratio of the T1 to S0 pathways as a function of photolysis energy. We also present the relative translational energy and CH3 vibrational energy distributions from these pathways at a photolysis energy of 100 kcal mol(-1), formed from both the T1 and S0 potentials. As with standard quasiclassical trajectory calculations, violation of zero-point energy for products also occurs in TSH calculations. This is shown to be a serious issue for this branching ratio and one of several methods considered to deal with this issue is shown to give satisfactory results.

A theoretical study on electronic predissociation in the NeBr2 van der Waals molecule

We present the first comprehensive ab initio study of the Ne–Br2 potential energy surfaces and the non-adiabatic couplings between the valence excited electronic states. These ab initio results are used to obtain 3-D approximate potentials for each electronic state, and these potentials are used in a wave packet calculation of the competing electronic predissociation and vibrational predissociation dynamics. The results of this calculation are in excellent agreement with both experimental results and a previous empirical fit to the experiments. The calculations allow us to observe not only the competition between vibrational and electronic dynamics for the dimer, but also the competition between two different electronic channels. Coupling to the 2g state dominates for the levels studied here, but coupling to the C state is progressively more important for low vibrational levels, and may dominate at levels below which the current results pertain. The ability of ab initio surfaces and couplings to so accurately reproduce experimental data raises the hope of a complete understanding of the VP and EP dynamics for other Rg-halogen dimers. Success in the case presented here is largely due to the fact that the VP dynamics for the vibrational levels in this study are in the simple, direct regime. Understanding the simple case so thoroughly provides new hope that the more complicated examples, such as ArI2 and NeCl2, for which experiment and theory are not currently in accord, may yet yield to analysis.

Intermolecular potential and rovibrational states of the H2O–D2 complex

A five-dimensional intermolecular potential for H2O–D2 was obtained from the full nine-dimensional ab initio potential surface of Valiron et al. [P. Valiron, M. Wernli, A. Faure, L. Wiesenfeld, C. Rist, S. Kedžuch, J. Noga, J. Chem. Phys. 129 (2008) 134306] by averaging over the ground state vibrational wave functions of H2O and D2. On this five-dimensional potential with a well depth De of 232.12cm−1 we calculated the bound rovibrational levels of H2O–D2 for total angular momentum J=0–3. The method used to compute the rovibrational levels is similar to a scattering approach—it involves a basis of coupled free rotor wave functions for the hindered internal rotations and the overall rotation of the dimer—while it uses a discrete variable representation of the intermolecular distance coordinate R. The basis was adapted to the permutation symmetry associated with the para/ortho (p/o) nature of both H2O and D2, as well as to inversion symmetry. As expected, the H2O–D2 dimer is more strongly bound than its H2O–H2 isotopologue [cf. A. van der Avoird, D.J. Nesbitt, J. Chem. Phys. 134 (2011) 044314], with dissociation energies D0 of 46.10, 50.59, 67.43, and 73.53cm−1 for pH2O–oD2, oH2O–oD2, pH2O–pD2, and oH2O–pD2. A rotationally resolved infrared spectrum of H2O–D2 was measured in the frequency region of the H2O bend mode. The ab initio calculated values of the rotational and distortion constants agree well with the values extracted from this spectrum.

A variationally computed line list for hot NH3

We present 'BYTe', a comprehensive 'hot' line list for the ro-vibrational transitions of ammonia, 14NH3, in its ground electronic state. This line list has been computed variationally using the program suite TROVE, a new spectroscopically-determined potential energy surface and an ab initio dipole moment surface. BYTe, is designed to be used at all temperatures up to 1500K. It comprises 1137650964 transitions in the frequency range from 0 to 12000 cm-1, constructed from 1366519 energy levels below 18000 cm-1 having J values below 36. Comparisons with laboratory data confirm the accuracy of the line list which is suitable for modelling a variety of astrophysical problems including the atmospheres of extrasolar planets and brown dwarfs.

Towards efficient refinement of molecular potential energy surfaces: Ammonia as a case study

In order to approach experimental accuracy in ro-vibrational calculations for polyatomic molecules one needs to empirically refine even a high accuracy ab initio potential energy surface (PES). This is most efficiently done through a least-squares fitting of theoretical energies to the available experimental data by varying potential parameters in a given analytical representation. The PES resulting from such a fitting is then referred to as a ‘spectroscopic’ PES. In the present work we report a new approach to the construction of ‘spectroscopic’ PESs of polyatomic molecules. We represent the refinement as a perturbation to the initial PES, which is diagonalized in a basis of eigenfunctions of the unperturbed Hamiltonian. We apply this method to construct a new ‘spectroscopic’ PES for 14NH 3 using literature values for observed spectroscopic data for J ⩽ 8 and covering the energy range below 10 300 cm −1. We impose the constraint that the resulting PES remain close to the ab initio surface. The new ‘spectroscopic’ PES of NH 3 (called NH3-Y2010) reproduces the selected experimental term values with a root-mean-square deviation of 0.2 cm −1.

Atom-centered symmetry functions for constructing high-dimensional neural network potentials

Neural networks offer an unbiased and numerically very accurate approach to represent high-dimensional ab initio potential-energy surfaces. Once constructed, neural network potentials can provide the energies and forces many orders of magnitude faster than electronic structure calculations, and thus enable molecular dynamics simulations of large systems. However, Cartesian coordinates are not a good choice to represent the atomic positions, and a transformation to symmetry functions is required. Using simple benchmark systems, the properties of several types of symmetry functions suitable for the construction of high-dimensional neural network potential-energy surfaces are discussed in detail. The symmetry functions are general and can be applied to all types of systems such as molecules, crystalline and amorphous solids, and liquids.

Quasiparticle interference in antiferromagnetic parent compounds of iron-based superconductors

Recently reported quasiparticle interference imaging in underdoped Ca(Fe${}_{1\ensuremath{-}x}$Co${}_{x}$)${}_{2}$As${}_{2}$ shows pronounced $C$${}_{2}$ asymmetry, which is interpreted as an indication of an electronic nematic phase with a unidirectional electron band, dispersive predominantly along the $b$ axis of this orthorhombic material. On the other hand, even more recent transport measurements on untwinned samples show near isotropy of the resistivity in the $\mathit{ab}$ plane, with slightly larger conductivity along $a$ (and not $b$). We show that, in fact, both sets of data are consistent with the calculated ab initio Fermi surfaces, which have a decisively broken $C$${}_{4}$ and yet similar Fermi velocity in both directions. This reconciles completely the apparent contradiction between the conclusions of the scanning tunneling microscopy and the transport experiments.

Quantitative vibronic coupling calculations: the formyloxyl radical

The performance of different choices of parametrization for the quasidiabatic Hamiltonian approach of Koppel et al. (Adv Chem Phys 57:59, 1984) is studied for the \({\tilde X}^2A_1\) and \({\tilde A}^2B_2\) states of the formyloxyl radical, \(\hbox{HCO}_2\). Two basic classes of parametrization are analyzed. In the first (vertical), the model Hamiltonian is constructed in such a way that it reproduces an ab initio surface near the geometry of the absorbing state in a spectroscopic transition; the second scheme (adiabatic) is designed to provide a faithful representation of the ab initio surface near the final state structures. The latter is better suited to treat energy level spacings, especially at relatively low energies, while the former may offer advantages in some cases where it may provide a more balanced description of the final states and/or features such as seams of conical intersections. For \(\hbox{HCO}_2\), the most interesting and prominent feature of the vibronic coupling scheme is a strong coordinate dependence of the coupling between the two electronic states. This effect renders effectively useless parametrization approaches in which the linear coupling strength is assumed constant. Moreover, through selective softening of the 2A1 state potential and corresponding reduction in its zero-point energy, this seemingly arcane property of the vibronic coupling in \(\hbox{HCO}_2\) is principally responsible for the ground state of this molecule being 2A1 instead of 2B2, as the adiabatic potential energy surface minimum of the latter is some 500 \(\hbox{cm}^{-1}\) lower.

Optimized semiempirical potential energy surface for H2 16O up to 26000 cm−1

A semiempirical potential energy surface is obtained for the major isotopologue of the water molecule H216O that allows the vibration-rotation energy levels in the range of 0–26000 cm−1 to be calculated with an accuracy almost equal to the average experimental accuracy of measurements in the infrared and visible ranges. Variational calculations using this potential energy surface reproduce the experimental energy values of more than 1500 vibration-rotation levels of H216O with the total angular momentum quantum number J = 0, 2, and 5 in the indicated range with a standard deviation of 0.022 cm−1. The potential was obtained by optimizing a starting ab initio surface using a combination of two approaches, i.e., (1) the multiplication of the starting ab initio surface by a morphing function whose parameters were optimized and (2) the optimization of parameters of the ab initio surface using both the experimental values of energy levels and the results of quantum-chemical electronic structure calculations.

ROTATIONAL ALIGNMENT OF PRODUCT MOLECULES FROM THE REACTION Ca + HCl→CaCl + H

The product rotational polarization in the Ca + HCl→CaCl + H reaction at collision energy of 20 kcal/mol has been studied via the quasiclassical trajectory method on a new ab initio potential surface. The P(θ r ) distribution of angle between k and j′, and the dihedral angular distribution P(Φ r ) characterizing k - k′ - j′ correlation are discussed, the angle distribution P(θ r , Φ r ) of product rotational vectors in the form of polar plot in θ r and Φ r are shown. Furthermore, four PDDCSs (2π/σ)(dσ00/dωt), (2π/σ)(dσ20/dωt), (2π/σ)(dσ22+/dωt) and (2π/σ)(dσ21-/dωt) are also presented. The present calculations reveal that the product rotational alignment is very strong. Finally, the state distributions of the product CaCl are investigated. The results showed that the CaCl product was formed with high vibrational and rotational excitation.

Incommensurate Magnetism in FeAs Strips: Neutron Scattering fromCaFe4As3

Magnetism in the orthorhombic metal CaFe(4)As(3) was examined through neutron diffraction for powder and single crystalline samples. Incommensurate [q(m) ≈ (0.37-0.39) × b*] and predominantly longitudinally (|| b) modulated order develops through a 2nd order phase transition at TN = 89.63(6) K with a 3D Heisenberg-like critical exponent β = 0.365(6). A 1st order transition at T2 = 25.6(9) K is associated with the development of a transverse component, locking q(m) to 0.375(2)b*, and increasing the moments from 2.1(1) to 2.2(3) μ B for Fe2+ and from 1.3(3) to 2.4(4) μB for Fe+. The ab initio Fermi surface is consistent with a nesting instability in cross-linked FeAs strips.

The decay mechanism of photoexcited guanine − A nonadiabatic dynamics study

Ab initio surface hopping dynamics calculations were performed for the biologically relevant tautomer of guanine in gas phase excited into the first ππ∗ state. The results show that the complete population of UV-excited molecules returns to the ground state following an exponential decay within ∼220 fs. This value is in good agreement with the experimentally obtained decay times of 148 and 360 fs. No fraction of the population remains trapped in the excited states. The internal conversion occurs in the ππ∗ state at two related types of conical intersections strongly puckered at the C2 atom. Only a small population of about 5% following an alternative pathway via a nπ∗ state was found in the dynamics.

Fast vibrational configuration interaction using generalized curvilinear coordinates and self-consistent basis

In this paper, we couple a numerical kinetic-energy operator approach to the direct-vibrational self-consistent field (VSCF)/vibrational configuration interaction (VCI) method for the calculation of vibrational anharmonic frequencies. By combining this with fast-VSCF, an efficient direct evaluation of the ab initio potential-energy surface (PES), we introduce a general formalism for the computation of vibrational bound states of molecular systems exhibiting large-amplitude motion such as methyl-group torsion. We validate our approach on an analytical two-dimensional model and apply it to the methanol molecule. We show that curvilinear coordinates lead to a significant improvement in the VSCF/VCI description of the torsional frequency in methanol, even for a simple two-mode coupling expansion of the PES. Moreover, we demonstrate that a curvilinear formulation of the fast-VSCF/VCI scheme improves its speed by a factor of two and its accuracy by a factor of 3.

Photodynamics of Azomethane: A Nonadiabatic Surface-Hopping Study†

The internal conversion and hot ground-state dynamics of trans- and cis-azomethane starting in the S(1) state have been investigated by nonadiabatic ab initio surface hopping dynamics using MCSCF-GVB-CAS and MRCISD methods and by determining energy minima and saddle points, minima on the crossing seam, and minimum energy pathways on the ground and first excited-state surfaces. The lifetimes and photoproducts from the dynamics simulations, geometric properties, excitation energies of selected stationary points and minimum energy pathways between them are reported. Our results favor a statistical model with trans-AZM moving to the ground-state minima before the first CN dissociation takes place. A detailed discussion in comparison to recent experimental and theoretical data is presented.