Ab initio thermochemistry of some halogenated cyclopropanes

The standard enthalpies of formation for a series of chloro- and fluoro-substituted cyclopropanes have been calculated by using high-level ab initio G3/B3LYP methods. The relative stabilities of isomers and the influence of substituents on thermochemistry in several classes of substituted derivatives are discussed.     

Ab initio spectroscopy and thermochemistry of the BN molecule

The lowest¹Σ⁺ and³Π states of the BN molecule have been studied using the quadratic configuration interaction method and (spdf) basis sets. The lowest¹Σ⁺ and³Π states lie extremely closely (T _e≈100 cm^?1) together; it is not clear which is the ground state. The very small separation should form a useful benchmark for basis sets and electron correlation methods. The dissociation energyD ₀ is computed to be 103.9±2 kcal/mol. A self-consistent set of spectroscopic constants is derived from a combination of ab initio and experimental data. JANAF-style thermodynamic functions in the range 100–6000 K, including anharmonic, rovibrational coupling, centrifugal stretching, and spin-orbit coupling effects are computed using direct numerical summation over the 25 lowest electronic states. A modified procedure for the latter is outlined that reduces computer time by one or two orders of magnitude without compromise in accuracy.     

Pyrrolizidine alkaloids necine bases: Ab initio,semiempirical, and molecular mechanics approaches to molecular properties

The structural stabilities of endo and exo conformations of retronecine and heliotridine molecules were analyzed using different ab initio, semiempirical, and molecular mechanics methods. All electron and pseudopotential ab initio calculations at the Hartree-Fock level of theory with 6-31G* and CEP-31G* basis sets provided structures in excellent agreement with available experimental results obtained from X-ray crystal structure and ¹H-NMR (nuclear magnetic resonance) studies in D₂O solutions. The exo conformations showed a greater stability for both molecules. The most significant difference between the calculations was found in the ring planarity of heliotridine, whose distortion was associated with the interaction between the O(11)H group and the C(1)-C(2) double bond as well as with a hydrogen bond between O(11)H and N(4). The discrepancy between pseudopotential and all-electron optimized geometries was reduced after inclusion of the innermost electrons of C(1), C(2), and N(4) in the core potential calculation. The MNDO, AM1, and PM3 semiempirical results showed poor agreement with experimental data. The five-membered rings were observed to be planar for AM1 and MNDO calculations. The PM3 calculations for exo-retronecine showed a greater stability than the endo conformer, in agreement with ab initio results. A good agreement was observed between MM3 and ab initio geometries, with small differences probably due to hydrogen bonds. While exo-retronecine was calculated to be more stable than the endo conformer, the MM3 calculations suggested that endo-heliotridine was slightly more stable than the exo form. © 1996 by John Wiley & Sons, Inc.     

Ab initio molecular orbital calculations

A series of non-empirical calculations on furan, pyrrole and 1,2,5-oxadiazole are reported in which the effect of polarisation functions added to the minimal 7s 3p basis on each atom is studied. The effect on these planar molecules is largely through the rather than the-system. A comparison with the results of work with scaled functions is reported. Both series are shown to lead to much improved agreement with the electron spectroscopy energy levels. The effect on the dipole moments of these changes in basis is more variable but, with the exception of furan, the agreement with experiment is improved in the present method.

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Zusammenfassung Für die Moleküle Furan, Pyrrol und 1,2,5-Oxadiazol wurde eine Reihe von nichtempirischen Rechnungen durchgeführt, in denen der Einfluß von zusätzlichen Polarisationsfunktionen zur minimalen 7s 3p-Basis an jedem Atom untersucht wird. Die Ergebnisse werden mehr durch die Art der Beschreibung des Systems der-Elektronen als durch diejenige der-Elektronen beeinflußt. Ein Vergleich mit den Ergebnissen bei Verwendung skalierter Funktionen wird durchgeführt. Beide Reihen von Ergebnissen zeigen eine verbesserte Übereinstimmung zu den Energiemeßwerten der Elektronenspektroskopie. Die Änderungen des berechneten Dipolmoments bei derartigen Basisvariationen sind größer als bei früheren Methoden. Die Übereinstimmung mit dem Experiment wird, mit Ausnahme von Furan, jedoch verbessert.

     

Ab initio molecular electrostatic potentials

The ab initio isopotential map of guanine is given and compared to that of adenine. It shows that in contrast to the situation in adenine, the most basic site of guanine is N₇ with a secondary potential minimum at O₆. These results as well as those concerning the secondary out-of-plane attractive regions over the NH₂ group and C₈ H bonds of the two molecules are discussed in connection with the available experimental knowledge concerning the bonding of alkylating carcinogens and mutagens.     

Halon thermochemistry: Ab initio calculations of the enthalpies of formation of fluoroethanes

The ab initio G2, G2(MP2), CBS-4 and CBS-Q quantum mechanical protocols and the parameterized BAC-MP4 procedure were used to calculate the enthalpies of formation (Δ_fH⁰) of ethane and the complete series of fluoroethanes, C₂H_xF_6−x, x = 0−5. Results from all methods exhibited significant negative deviations from experiment. With the exception of the CBS-4 and BAC-MP4 procedures, the negative errors in the calculated enthalpies were observed to be linearly dependent upon the number of CF bonds in the molecule. Application of a bond additivity correction (BAC) parameter, Δ_CF, derived in an earlier investigation of fluoro- and chlorofluoromethanes, removed some although not all of the systematic deviations. Introduction of a heavy atom interaction parameter, representing the effect of an attached carbon on the CF bond error, yielded corrected enthalpies which agree with experiment to within the reported uncertainties. The BAC-MP4 method, which has already been parameterized with generalized BACs, yields calculated enthalpies which average approximately 10 kJ mol⁻¹ below the experimental values of Δ_fH⁰ in the fluoroethanes.     

Ab initio and molecular mechanics study of n-phenyl phthalimide and its crystal structure

Ab initio molecular orbital calculations are reported on the energetics for torsional motion of N-phenyl phthalimide using 3-21G, 6-31G, and 6-31G^** basis sets and incorporating electron correlation effects for selected geometries. With the largest basis set, a minimum energy is found for a torsion angle of 59.2°. Atomic charges are assigned to the molecules on the basis of a least-squares fit to the molecular electrostatic potential. This information is then used in molecular mechanics calculations of the crystal structure, where the calculated unit cell parameters are in good agreement with those observed experimentally.     

Ab initio study of bond stretching: Implications in force-field parametrization for molecular mechanics and dynamics

We report a theoretical study of the stretching of chemical bonds and its implications on the force-field parametrization. Computations were performed at the SCF and MCSCF levels by using minimal, split-valence, and large extended and polarized basis sets. The stretching energy profiles were determined considering up to 25 perturbed geometries of 11 different bonds (6 singles, 2 doubles, and 3 triples). The energy profiles and stretching parameters are compared with the experimental data compiled in the most popular force fields. MCSCF stretching energy profiles are mainly anharmonic and can be only roughly reproduced by quadratic equations. The use of Allinger's MM2 quasiharmonic expression appears as the best choice because it fits with reasonable accuracy a large percentage of the stretching profile without increasing the complexity of the formalism and of the parametrization procedure. MCSCF computations are needed to obtain reliable stretching force parameters. In this respect, MCSCF calculations considering as active space only the bonded and nonbonded orbitals of the perturbed bond seems to be the best strategy to obtain good results at a minimum computational cost, especially if small split-valence basis sets like the 3-21G are used. Results obtained at this level of sophistication are completely comparable to stretching parameters compiled on empirical force fields. © 1993 John Wiley & Sons, Inc.     

Ab initio thermochemistry and kinetics for carbon-centered radical addition and beta-scission reactions

A quantitative comparison of ab initio calculated rate coefficients using five computational methods and five different approaches of treating hindered internal rotation and tunneling with experimental values of rate coefficients for nine carbon-centered radical additions/beta scissions at 300, 600, and 1000 K is performed. The high-accuracy compound methods, CBS-QB3 and G3B3, and the density functionals, MPW1PW91, BB1K, and BMK, have been evaluated using the following approaches: (i) the harmonic oscillator approximation; (ii) the hindered internal rotor approximation for the internal rotation about the forming/breaking bond in the transition state and product; and the hindered internal rotation approximation combined with (iii) Wigner, (iv) Skodje and Truhlar, and (v) Eckart zero-curvature tunneling corrections. The density functional theory (DFT) based values for beta-scission rate coefficients deviate significantly from the experimental ones at 300 K, and the DFT methods do not accurately predict the equilibrium coefficient. The hindered rotor approximation offers a significant improvement in the agreement with experimental rate coefficients as compared to the harmonic oscillator treatment, especially at higher temperatures. Tunneling correction factors are smaller than 1.40 at 300 K and 1.03 at 1000 K. For both the CBS-QB3 method, including the hindered rotor treatment but excluding tunneling corrections, and the G3B3 method, including hindered rotor and Eckart tunneling corrections, a mean factor of deviation with experimentally observed values of 3 is found.     

Ab initio mass tensor molecular dynamics

Mass tensor molecular dynamics method was first introduced by Bennett [J. Comput. Phys. 19, 267 (1975)] for efficient sampling of phase space through the use of generalized atomic masses. Here, we show how to apply this method to ab initio molecular dynamics simulations with minimal computational overhead. Test calculations on liquid water show a threefold reduction in computational effort without making the fixed geometry approximation. We also present a simple recipe for estimating the optimal atomic masses using only the first derivatives of the potential energy.     

Ab initio aqueous thermochemistry: application to the oxidation of hydroxylamine in nitric acid solution

Ab initio molecular orbital calculations were performed and thermochemical parameters estimated for 46 species involved in the oxidation of hydroxylamine in aqueous nitric acid solution. Solution-phase properties were estimated using the several levels of theory in Gaussian03 and using COSMOtherm. The use of computational chemistry calculations for the estimation of physical properties and constants in solution is addressed. The connection between the pseudochemical potential of Ben-Naim and the traditional standard state-based thermochemistry is shown, and the connection of these ideas to computational chemistry results is established. This theoretical framework provides a basis for the practical use of the solution-phase computational chemistry estimates for real systems, without the implicit assumptions that often hide the nuances of solution-phase thermochemistry. The effect of nonidealities and a method to account for them is also discussed. A method is presented for estimating the solvation enthalpy and entropy for dilute aqueous solutions based on the solvation free energy from the ab initio calculations. The accuracy of the estimated thermochemical parameters was determined through comparison with (i) enthalpies of formation in the gas phase and in solution, (ii) Henry's law data for aqueous solutions, and (iii) various reaction equilibria in aqueous solution. Typical mean absolute deviations (MAD) for the solvation free energy in room-temperature water appear to be ~1.5 kcal/mol for most methods investigated. The MAD for computed enthalpies of formation in solution was 1.5-3 kcal/mol, depending on the methodology employed and the type of species (ion, radical, closed-shell) being computed. This work provides a relatively simple and unambiguous approach that can be used to estimate the thermochemical parameters needed to build detailed ab initio kinetic models of systems in aqueous solution. Technical challenges that limit the accuracy of the estimates are highlighted.     

Ab initio and molecular mechanics (MM3) calculations of protonated-neutral diamine hydrogen bonds

Ab initio calculations of cation-neutral diamine complexes have been carried out at the MP2/6-311+G** level. The geometry and energetics of the charge-reinforced hydrogen bond are analyzed with respect to the alkyl substitution of both the protonated and neutral nitrogen atoms, and these results have been used to improve the quality of the MM3(2000) force field. In addition, specialized hydrogen bond parameters optimized for MM3(2000) are presented. These parameters allow very accurate gas-phase modeling of the charge-neutral diamine environment. Molecular mechanics calculations can model effectively protonated amine-neutral amine hydrogen bonds in the gas phase and solution (continuum dielectric) through a combination of charge-dipole interactions and explicit hydrogen-bonding terms.     

Ab initio calculation of molecular chiroptical properties

This review describes the first-principles calculation of chiroptical properties such as optical rotation, electronic and vibrational circular dichroism, and Raman optical activity. Recent years have witnessed a flurry of activity in this area, especially in the advancement of density-functional and coupled cluster methods, with two ultimate goals: the elucidation of the fundamental relationship between chiroptical properties and detailed molecular structure, and the development of a suite of computational tools for the assignment of the absolute configurations of chiral molecules. The underlying theory and the basic principles of such calculations are given for each property, and a number of representative applications are discussed.     

Ab initio investigation of benzene clusters: molecular tailoring approach

An exhaustive study on the clusters of benzene (Bz)(n), n = 2-8, at MP2/6-31++G(??) level of theory is reported. The relative strengths of CH-π and π-π interactions in these aggregates are examined, which eventually govern the pattern of cluster formation. A linear scaling method, viz., molecular tailoring approach (MTA), is efficiently employed for studying the energetics and growth patterns of benzene clusters consisting up to eight benzene (Bz) units. Accuracy of MTA-based calculations is appraised by performing the corresponding standard calculations wherever possible, i.e., up to tetramers. For benzene tetramers, the error introduced in energy is of the order of 0.1 mH (～0.06 kcal/mol). Although for higher clusters the error may build up, further corrections based on many-body interaction energy analysis substantially reduce the error in the MTA-estimate. This is demonstrated for a prototypical case of benzene hexamer. A systematic way of building up a cluster of n monomers (n-mer) which employs molecular electrostatic potential of an (n-1)-mer is illustrated. The trends obtained using MTA method are essentially identical to those of the standard methods in terms of structure and energy. In summary, this study clearly brings out the possibility of effecting such large calculations, which are not possible conventionally, by the use of MTA without a significant loss of accuracy.     

Ab initio calculations on peptide-derived oxazoles and thiazoles: Improved molecular mechanics parameters for the AMBER* force field

Ab initio calculations at the RHF/6-31G* and MP2/6- 31G*//RHF/6-31G* levels of theory are performed for 2-methyl-4-carboxamido-oxazoles and -thiazoles, including rotational profiles for the ring-carboxamide bond, which showed the expected conjugation and hydrogen bonding effects. On the basis of these data, newly optimised stretch, bend and torsional parameters for the AMBER* force field are derived, along with CHELPG-fitted partial atomic charges.     

Ab initio molecular orbital studies of polyethylene deformation

A molecular LCAO Hartree-Fock procedure was used to calculate total energies of axially stretched normal paraffins containing up to nine carbon atoms. The results are used to model the mechanical properties of polyethylene.     

Ab initio molecular dynamics simulation of ionic liquids

Ab initio Car-Parinnello molecular dynamics is used to simulate the structure and the dynamics of 1-butyl-3-methylimidazolium iodide ([bmim]I) ionic liquid at 300 K. Site-site pair correlation functions reveal that the anion has a strong interaction with any three C-H's of the imidazolium ring. The ring bends over and wraps around the anion such that the two nitrogen atoms take a distance to the anion. Electron donating butyl group contributes the electronic polarization in addition to geometrical (out-of-plane) polarization of the ring due to the liquid environment. This facilitates bending of the ring along the axis passing through nitrogen atoms. The average bending angle depends largely on the alkyl chain length and slightly on the anion type. Redistribution of electron density over the ring caused by the electron donating alkyl group provides additional independent evidence to the instability of lattice structure, hence the low melting point of the ionic liquid. Simulated viscosity and diffusion coefficients of [bmim]I are in quite agreement with the experiments.     

Ab initio molecular dynamics study of liquid methanol

We present a density-functional theory based molecular-dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare well with recent neutron diffraction data, except for an underestimate of the oxygen–oxygen correlation. We observe that, in line with infrared spectroscopic data, the hydroxyl stretching mode is significantly red-shifted in the liquid. A substantial enhancement of the dipole moment is accompanied by significant fluctuations due to thermal motion. Our results provide valuable data for improvement of empirical potentials.