High-quality Ab Initio Research Articles

Room temperature line lists for deuterated water

Line lists are presented for six deuterated isotopologues of water vapor namely HD16O, HD17O, HD18O, D216O, D217O and D218O. These line lists are prepared using empirically-determined energy levels, where available, to provide transition frequencies and high-quality ab initio dipole moment surfaces to provide transition intensities. The reliability of the predicted intensities is tested by computing multiple line lists and analyzing the stability of the results. The resulting intensities are expected to be accurate to a few percent for well-behaved, stable transitions. Complete T=296 K line lists are provided for each species.

A new potential energy surface of LiHCl system and dynamic studies for the Li(2S) + HCl(X1Σ+) → LiCl(X1Σ+) + H(2S) reaction.

A new global potential energy surface (PES) is constructed for the ground state of LiHCl system based on high-quality ab initio energy points calculated using multi-reference configuration interaction calculations with the Davidson correction. The AVQZ and WCVQZ basis sets are employed for H and Li atoms, respectively. To compensate the relativistic effects of heavy element, the AWCVQZ-DK basis set is employed for Cl atom. The neural network method is used for fitting the PES, and the root mean square error is small (1.36 × 10-2 eV). The spectroscopic constants of the diatoms obtained from the new PES agree well with experimental data. The geometric characteristics of the transition state and the complex are examined and compared with the previous theoretical values. To study the reaction dynamics of the Li(2S) + HCl(X1Σ+) → LiCl(X1Σ+) + H(2S) reaction, quantum reactive scattering dynamics calculations using collection reactant-coordinate-based wave packet method are conducted based on the new PES. The results of the reaction probabilities indicate that a small barrier exists along the reaction path as observed from the PES. The integral cross section curves reveal that the product molecule LiCl is easily excited. In addition, the reaction is dominated by forward scattering, and similar pattern is observed from Becker's experiment.

Rate coefficients and kinetic isotope effects of the abstraction reaction of H atoms from methylsilane

ABSTRACTThermal rate constants for chemical reactions using improved canonical variational transition state theory (ICVT) with small-curvature tunnelling (SCT) contributions in a temperature range 180–2000 K are reported. The general procedure is used with high-quality ab initio computations and semi-classical reaction probabilities along the minimum energy path (MEP). The approach is based on a vibrational adiabatic reaction path and is applied to the multiple-channel hydrogen abstraction reaction H + SiH3CH3 → products and its isotopically substituted variants. All the degrees of freedom are optimised and harmonic vibrational frequencies and zero-point energies are calculated at the MP2 level with the cc-pVTZ basis set. Single-point energies are calculated at a higher level of theory; CCSD(T)-F12a/VTZ-F12. ICVT/SCT rate constants show that the quantum tunnelling contributions at low temperatures are relatively important and the H-abstraction channel from SiH3 group of SiH3CH3 is the major pathway. The total rate constants are given by the following expression: ktot(ICVT/SCT) = 2.29 10−18 T2.42 exp(−350.9/T) cm3 molec−1 s−1. These calculated rates are in agreement with the available experiments. The ICVT/SCT method is further exploited to predict primary and secondary kinetic isotope effects, respectively).

Assessment of Empirical Models versus High-Accuracy Ab Initio Methods for Nucleobase Stacking: Evaluating the Importance of Charge Penetration.

Molecular mechanics (MM) force field models have been demonstrated to have difficulty reproducing certain potential energy surfaces of π-stacked complexes. Here, we examine the performance of the AMBER and CHARMM models relative to high-quality ab initio data across systematic helical parameter scans and typical B-DNA geometries for π-stacking energies of nucleobase dimers. These force fields perform best for typical B-DNA geometries (mean absolute error < 1 kcal mol(-1)), whereas errors typically approach ∼2 kcal mol(-1) for broader potential scans, with maximum errors > 10 kcal mol(-1) relative to high-quality ab initio reference interaction energies. The adequate performance of MM models near minimum energy structures is accomplished through cancellation of errors in various energy terms, whereas large errors at short intermolecular distances are caused by large MM electrostatics errors due to a lack of explicit terms modeling charge penetration effects.

Ab Initio Investigation of the Abstraction Reactions by H and D from Tetramethylsilane and Its Deuterated Substitutions

Thermal rate constants for chemical reactions using the corrections of zero curvature tunneling (ZCT) and of small curvature tunneling (SCT) methods are reported. The general procedure is implemented and used with high-quality ab initio computations and semiclassical reaction probabilities along the minimum energy path (MEP). The approach is based on a vibrational adiabatic reaction path and is applied to the H + Si(CH3)4 → H2 + Si(CH3)3CH2 reaction and its isotopically substituted variants. All of the degrees of freedom are optimized, and harmonic vibrational frequencies and zero-point energies are calculated at the MP2(full) level with the cc-pVTZ basis set. Single-point energies are calculated at a higher level of theory with the same basis set, namely, CCSD(T,full). The influence of the basis set superposition error (BSSE) on the energetics is tested. The method is further exploited to predict primary and secondary kinetic isotope effects (KIEs and SKIEs, respectively). Rate constants computed with the ZCT and SCT methods over a wide temperature range (180-2000 K) show important quantum tunneling effects at low temperatures when compared to rates obtained from the purely classical transition-state theory (TST) and from the canonical variational transition state theory (CVT). For the H + Si(CH3)4 reaction, they are given by the following expressions: k(TST/ZCT) = 9.47 × 10(-19) × T(2.65) exp(-2455.7/T) and k(CVT/SCT) = 7.81 × 10(-19) × T(2.61) exp[(2704.2/T) (in cm(3) molecule(-1) s(-1)). These calculated rates are in very good agreement with those from available experiments.

Unravelling the Structure of Protic Ionic Liquids with Theoretical and Experimental Methods: Ethyl-, Propyl- and Butylammonium Nitrate Explored by Raman Spectroscopy and DFT Calculations

We present an analysis of gas-phase structures of small clusters of n-alkylammonium nitrates (ethyl, propyl, and butyl) together with vibrational Raman spectroscopy of their respective liquid phases. The assignment and interpretation of the resonant frequencies have been performed by comparison with high-quality ab initio (DFT) computations. The theoretical spectra are in excellent agreement with the measured ones and allow the interpretation and assignment of almost all the spectral features. A careful analysis of the vibrational frequencies and of the electronic structure of the compounds has provided additional information on various structural features and on the rather complex hydrogen bonding network that exists in such compounds. A geometric structure of the short-range local arrangement in the bulk phases is also proposed.

Enthalpy difference between conformations of normal alkanes: effects of basis set and chain length on intramolecular basis set superposition error

The quantum chemistry of conformation equilibrium is a field where great accuracy (better than 100 cal mol−1) is needed because the energy difference between molecular conformers rarely exceeds 1000–3000 cal mol−1. The conformation equilibrium of straight-chain (normal) alkanes is of particular interest and importance for modern chemistry. In this paper, an extra error source for high-quality ab initio (first principles) and DFT calculations of the conformation equilibrium of normal alkanes, namely the intramolecular basis set superposition error (BSSE), is discussed. In contrast to out-of-plane vibrations in benzene molecules, diffuse functions on carbon and hydrogen atoms were found to greatly reduce the relative BSSE of n-alkanes. The corrections due to the intramolecular BSSE were found to be almost identical for the MP2, MP4, and CCSD(T) levels of theory. Their cancelation is expected when CCSD(T)/CBS (CBS, complete basis set) energies are evaluated by addition schemes. For larger normal alkanes (N > 12), the magnitude of the BSSE correction was found to be up to three times larger than the relative stability of the conformer; in this case, the basis set superposition error led to a two orders of magnitude difference in conformer abundance. No error cancelation due to the basis set superposition was found. A comparison with amino acid, peptide, and protein data was provided.

Magnetizabilities at Self-Interaction-Corrected Density Functional Theory Level.

Using a recent high-quality ab initio coupled cluster benchmark set for magnetizabilities, we assess the performance of a set of density functionals, representing different levels of complexity, from the local density approximation (LDA), via generalized gradient approximations (GGA's) to kinetic energy density including meta-GGA's. The effect of self-interaction correction (SIC) is remarkable and, in most cases, leads to a significant error reduction, revealing the sensitivity of magnetizability toward a physically sound exchange-correlation potential.

Theoretical treatment of the electronic excited states of the DMSO molecule: A challenge for current theoretical methods

We present here a computational study of the vertical excitation energies of the dimethylsulfoxide (DMSO) molecule. This molecule is the simplest among the sulfoxides and it is here used as a model for testing the performance of current high quality ab initio computations and to asses the possibility of studying larger molecules containing the sulfoxide group. We shall present a detailed comparison of the results obtained by different methodologies with recent experimental data.

A theoretical study of alanine dipeptide and analogs

We present a preliminary report on the conformational and energetic analysis of the molecule (S)-2-acetylamino-N-methylpropanamide (alanine dipeptide) and an analog molecule, (S)-α-formylamino-propanamide, using high-quality ab initio methods. Alanine dipeptide and its analogs are of interest since they incorporate many of the structural features found in proteins, such as intramolecular hydrogen bonds, conformational flexibility, and a variety of chemical functionality. One purpose of this study is to provide a useful benchmark calculation, MP2/6-31 + G**//HF/6-31 + G*, for a number of conformations of the alanine system. Based on the comparison of these benchmark calculations with lower-level basis sets, HF/3-21G was chosen to generate a fully relaxed φ, ψ dihedral map. These calculations are the first of their kind on systems of this size. Features of the φ, ψ alanine dipeptide map that are discussed include the energetically accessible conformations and possible pathways for their intercon-version. In addition, we illustrate the importance of fully optimized geometries and the proper evaluation of correlation energies.

Accurate calculations in drug discovery research: the biological roles of magnesium and calcium ions

The use of computational chemistry in drug discovery has in the past been largely restricted to the use of empirical potential functions or semi-empirical quantum mechanics. Computer power is now offering the opportunity to employ high quality ab initio methods of the sort pioneered by Fritz Schaefer. Here the general scene of computational drug discovery is set and a specific problem where accurate methods are essential is introduced. This problem is the contrasting roles of Mg2+ and Ca2+ in biology, the understanding of which requires very accurate calculation of binding free energies between the cations and organic anions as well as with proteins.

Mechanistic Insights into the Bazarov Synthesis of Urea from NH3 and CO2 Using Electronic Structure Calculation Methods

The mechanism of the noncatalyzed and reagent-catalyzed Bazarov synthesis of urea has extensively been investigated in the gas phase by means of density functional (B3LYP/6-31G(d,p)) and high quality ab initio (CBS-QB3) computational techniques. It was found that the first step of urea formation from NH3(g) and CO2(g) corresponds to a simple addition reaction leading to the carbamic acid intermediate, a process being slightly endothermic. Among the three possible reaction mechanisms considered, the addition-elimination-addition (AEA) and the double addition-elimination (DAE) mechanisms are almost equally favored, while the concerted (C) one was predicted kinetically forbidden. The second step involves the formation of loose adducts between NH3 and carbamic acid corresponding to an ammonium carbamate intermediate, which subsequently dehydrates to urea. The formation of "ammonium carbamate" corresponds to an almost thermoneutral process, whereas its dehydration, which is the rate-determining step, is highly endothermic. The Bazarov synthesis of urea is strongly assisted by the active participation of extra NH3 or H2O molecules (autocatalysis). For all reaction pathways studied the entire geometric and energetic profiles were computed and thoroughly analyzed. The reaction scheme described herein can be related with the formation of both isocyanic acid, H-N=C=O, and carbamic acid, H2N-COOH, as key intermediates in the initial formation of organic molecules, such as urea, under prebiotic conditions.

THEORETICAL STUDIES OF $\tilde{A}{}^1 A^{\prime\prime}\to\tilde{X}{}^1 A^\prime$ RESONANCE EMISSION SPECTRA OF HCN/DCN USING SINGLE LANCZOS PROPAGATION METHOD

Using an efficient single Lanczos propagation method, we report the [Formula: see text] resonance emission spectra of HCN and DCN from a number of low-lying vibrational levels of the Ã-state manifold. Our calculations represent the first such undertaking in which a high-quality ab initio based potential energy surface of the excited (Ã1 A″) state and a [Formula: see text] transition dipole surface were used. The results show a significant improvement over previous theoretical work in reproducing experimental stimulated emission pumping spectra of HCN. The improved theory-experiment agreement is attributed to the accurate Ã-state potential energy surface, while the impact of the transition dipole function was found to be relatively minor.

The ionization energy and ΔHf (0 K) of CP, PCP and PCCP

By employing high-quality ab initio methods [RCCSD(T)/cc-pV5Z//UQCISD/6-311G(2d)], the adiabatic ionization energies of CP, PCP and PCCP are calculated, yielding values of 10.92±0.05, 8.78±0.05, and 9.43±0.05 eV. In addition, ΔH f (0 K) for CP, PCP and PCCP are derived, giving values of 124±2, 96±2 and 103±4 kcal mol −1 , respectively. Some notable discrepancies with literature values are highlighted. The ground state of CP + is confirmed to be the X 3Π state arising from a ⋯π 3σ 1 configuration, with the ⋯ π 4 σ 0( 1Σ +) state lying 0.75 eV higher in energy.

Are cumulenones kinked? A systematic high-level ab initio study of H2CCCO, H2CCCCO and H2CCCCCO

The cumulenones, propadienone (H2CCCO), butatrienone (H2CCCCO) and pentatetraenone (H2CCCCCO) have been systematically investigated with high-quality ab initio methods. At our highest levels of theory, the equilibrium structures of all three cumulenones show significant bending in the heavy-atom chain. Although the barrier to linearity of the carbon chain is significant for propadienone (approximately 5kJmol−1), the calculated barriers for butatrienone and pentatetraenone are very small (less than 0.5kJmol−1). Calculated spectroscopic properties of the cumulenones are in good agreement with available experimental data.

Quantum scattering on coupled ab initio potential energy surfaces for the Cl(2P)+HCl→ClH+Cl(2P) reaction

We present the results of accurate quantum dynamical calculations for the Cl(2P)+HCl→ClH+Cl(2P) reaction using a coupled channel reactive scattering method based on hyperspherical coordinates. The calculations include the three potential energy surfaces (12A′, 22A′ and 12A″) that correlate to the ground states of the reactants and products, as well as electrostatic, Coriolis and spin–orbit couplings. The electrostatic surfaces and couplings are taken from the high quality ab initio computations of A. J. Dobbyn, J. N. L. Connor, N.A. Besley, P. J. Knowles and G. C. Schatz [Phys. Chem. Chem. Phys., 1999, 1, 957], with the barrier heights scaled so that thermal rate coefficients derived from the scattering calculations agree with experimental data. Only the total angular momentum quantum number J = ½ partial wave is calculated; state selected and thermal rate coefficients are obtained using a J-shifting approximation. We study basis set convergence and compare single and multiple surface results, with emphasis on state selected and total cumulative reaction probabilities and thermal rate coefficients, including branching between ground and excited spin–orbit states. The contribution of resonances to the scattering is discussed and analysed. We also compare with scattering results using an earlier, more approximate, set of potential surfaces and couplings due to C. S. Maierle, G. C. Schatz, M. S. Gordon, P. McCabe and J. N. L. Connor [J. Chem. Soc., Faraday Trans., 1997, 93, 709].

Potential Energy Surface of the à State of NH2 and the Role of Excited States in the N(2D) + H2 Reaction

We present a global potential energy surface for the à state of NH2 (12A‘) based on application of the reproducing kernel Hilbert space (RKHS) interpolation method to high-quality ab initio (multireference configuration−interaction) results. This surface correlates adiabatically to the a1Δ state of NH, with a reaction endoergicity of about 8 kcal/mol, but it can also lead to formation of ground-state NH (exoergic by 29 kcal/mol) via nonadiabatic (Renner−Teller) interactions for linear HNH geometries that lie near the bottom of a 94 kcal/mol deep well that is accessible from N(2D) + H2 by insertion over a 3.4 kcal/mol barrier. This insertion barrier is about 1 kcal/mol higher in energy than the corresponding insertion barrier associated with the ground state of NH2(12A‘ ‘). As a result, the à state contributes measurably to both the thermal rate constant for N(2D) + H2 and the rate for NH(a1Δ) production. Extensive quasiclassical trajectory calculations are performed on the RKHS surface to study the N(2D) + H2 reaction dynamics, with the nonadiabatic rate constant estimated using a capture model. We find that the cross section for ground-state NH production is comparable to that obtained on the ground-state 1A‘ ‘ surface, except for a 1 kcal/mol shift upward in the effective threshold due to the different barrier height. The cross section for NH(a1Δ) production has a higher threshold energy and is about 15% of the ground-state cross section at energies well above threshold.

Monte Carlo simulation of F−(H2O)4 using an ab initio potential

We present results concerning the structure and energetics of the cluster F−(H2O)4 at 0 K, using high quality ab initio methods, and at a temperature of 300 K, using an ab initio Monte Carlo simulation. At 0 K, we find the global energy minimum corresponds to three waters solvating the fluoride ion and with the fourth water in an outer hydration shell, hydrogen bonding to the other water molecules. Structures involving four waters hydrogen bonding to the fluoride are, however, of only slightly higher energy. At 300 K, the simulation results indicate that the fluoride is mostly to be found within a tetrahedron of solvating water molecules. The cluster is mobile, however, and a wide variety of structures are sampled.

Reaction of H with highly vibrationally excited water: activated or not?

The dynamics of the collisions of H atoms with vibrationally excited H2O were studied using quasiclassical reactive and quantum mechanical non-reactive scattering calculations using the recently developed potential surface from Ochoa and Clary (OC). The trajectory calculations show that this endoergic reaction is activated for water in its vibrational ground state and with one quantum of OH stretch, but excitation by two or more OH stretch quanta results in diverging cross-sections at low translational energy. The reactive rate coefficients are very large for these states, being a significant fraction of the gas kinetic rate coefficient. This behavior is qualitatively different from what is obtained using the I5 surface of Isaacson, which shows activated behavior even for excitation as high as (04)-. To verify the accuracy of the OC surface, we have performed high quality abinitio calculations for H+H2O, considering geometries in the reagent region that correspond to high OH stretch excitation, and we find that the OC surface is qualitatively correct, but with too long a range in its attractive tail. Our quantum calculations of the total inelastic rate coefficients for collisions with water initially excited in OH stretch overtone states give values that are comparable in magnitude with the reactive rate coefficients for the same states. This suggests that in the recent measurements by Smith and coworkers of the rate coefficients for total loss of excited water, reaction and vibrational energy transfer are of comparable importance.

A study of the low-lying states of CaAr + and CaKr +

The spectroscopic constants of the ground 2Σ + states of CaAr + and CaKr + are determined using high quality ab initio methods. The computed binding energies are 789 and 1252 cm −1, respectively, in good agreement with the experimental determination of Pullins, Scurlock, Reddic and Duncan (J. Chem. Phys. 104 (1996) 7518). The much smaller CaKr + binding energy determined by Buthelezi, Bellert, Lewis and Brucat (Chem. Phys. Lett. 246 (1995) 145) is shown to be due to deficiencies in the method used to approximate the binding energy of the excited state.