Free radical abstraction of H atom from peroxides with concerted dissociation of O-O bond

Quantum chemical calculations of the dissociation energy of the C-H bond in the ??-hydroperoxide fragment of Me₂CHOOH were carried out. It was shown that abstraction of H atom is accompanied by dissociation of the O-O bond. Density functional calculations of transition states of the reactions of ^·CH₃, CH₃OO^·, and HO₂ ^· radicals with the C-H bond in the ??-hydroperoxide fragment of Me₂CHOOH were carried out. It was established that H atom abstraction is accompanied by concerted dissociation of the O-O bond. For 45 peroxides R¹R²CHOOH, R¹R²CHOOR³, and R¹R²CHOOC(O)R³ (R¹, R² = H, Me, Et, Ph, H₂C=CH), the enthalpies of H atom abstraction from the C-H bond in the a-hydroperoxide fragment with fragmentation of the peroxides at the O-O bond were calculated. The kinetic parameters for 12 classes of radical abstraction reactions with fragmentation of molecules were calculated from experimental data within the framework of the model of intersecting parabolas. The activation energies and reaction rate constants of H atom abstraction from C-H bonds of a-peroxide fragments involving peroxyl and alkyl radicals were determined for 45 peroxides of different structure.     

Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide

Methodology is discussed for mixed ab initio quantum mechanics/molecular mechanics modeling of systems where the quantum mechanics (QM) and molecular mechanics (MM) regions are within the same molecule. The ab initio QM calculations are at the restricted Hartree–Fock level using the pseudospectral method of the Jaguar program while the MM part is treated with the OPLS force fields implemented in the IMPACT program. The interface between the QM and MM regions, in particular, is elaborated upon, as it is dealt with by “breaking” bonds at the boundaries and using Boys-localized orbitals found from model molecules in place of the bonds. These orbitals are kept frozen during QM calculations. Results from tests of the method to find relative conformational energies and geometries of alanine dipeptides and alanine tetrapeptides are presented along with comparisons to pure QM and pure MM calculations. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1468–1494, 1999     

Theoretical studies of conjugated systems containing CC and CN fragments and their alkyl and amino derivatives

Ab initio molecular orbital theory has been systematically employed to investigate the structures, energies, and conformations of 27 nitrogen-containing compounds. A force field has been developed, on the basis of available experimental and theoretical data, to permit extension of the molecular orbital-based molecular mechanics calculations to hetero-conjugated systems. Structures, heats of formation, and conformations of more than 65 molecules were studied by the developed force field and the results were compared with the available experimental data.     

Force field for computation of conformational energies,structures, and vibrational frequencies of aromatic polyesters

A CFF93¹ all-atom force field for aromatic polyesters based on ab initio calculations is reported. The force field parameters are derived by fitting to quantum mechanical data which include total energies, first and second derivatives of the total energies, and electrostatic potentials. The valence parameters and the ab initio electrostatic potential (ESP) derived charges are then scaled to correct the systematic errors originating from the truncation of the basis functions and the neglect of electron correlation in the HF/6-31G* calculations. Based on the force field, molecular mechanics calculations are performed for homologues of poly(p-hydroxybenzoic acid) (PHBA) and poly(ethylene terephthalate) (PET). The force field results are compared with available experimental data and the ab initio results. © 1994 by John Wiley & Sons, Inc.     

Comparison of ab initio,semiempirical, and molecular mechanics calculations for the conformational analysis of ring systems

The potential energy surfaces of four cyclic alkanes have been examined using molecular mechanics, semiempirical, and ab initio methods to determine if they produce mutually consistent results and investigate the source of any errors between the methods. The C₅ ? C₈ cyclic alkanes were chosen since these structures present a finite set of conformations and transition-state geometries and are still within the computational time and memory limits of the quantum mechanical approaches. We also examined several conformations of 1,2-dideoxyribose to determine the effect of heteroatoms on the results for the 5-membered ring. The molecular mechanics and ab initio calculations are consistent in the relative energies and geometries determined for the conformers of all ring systems. While the semiempirical calculations yielded geometries consistent with the other methods (except for 5-membered rings), the relative energies often deviated substantially. A decomposition analysis of the semiempirical and molecular mechanics energies revealed that the disparities are mainly due to errors in the 1-center energies of the semiempirical calculations. The 2-center bonding and nonbonding energies followed reasonable trends for the conformers. The core-repulsion function, however, is suspected of producing anomalies. A minimum in the attractive Gaussian of this term at 2.1 Å for H? H interactions partly explains the propensity of the 5-membered rings to optimize to near planarity (decreasing 1,2-diaxial hydrogen distances to 2.3 Å) and the underestimation of the relative energy of the boat structure of cyclohexane.     

“Spectroscopic” Calculations of CH Bond Dissociation Energies for Ethane, Propane, Butane, Isobutane, Pentane, Hexane, and Neopentane Using Fundamental Vibration Frequencies

The fundamental spectrum and the parameters of the potential function of a number of saturated hydrocarbon molecules are calculated in an anharmonic approximation. The calculation is performed by the variational technique using a minimal Morse-harmonic basis. The potential function is taken as the sum of the Morse function for CH bonds and the harmonic function for the skeletal and deformation vibrations. The initial approximation for the potential function is found by ab initio calculations in a 6-31G basis and refined by solving the inverse problem. The calculated CH bond dissociation energies depend significantly on the molecular structure and on the position of CH bonds in the molecule. These energies correlate well with the experimental cleavage energies of these bonds. The changes in the dipole moment of the molecule induced by vibrations were found by ab initio calculations in a 6-31G basis. The calculated IR transmission curves are in good agreement with the experimental curves.     

A charge-conserving approximation method for ab initio calculations

A new method is presented for approximate ab initio calculations in quantum chemistry. It is called CCAM (charge conserving approximation method). The calculation method does not include the use of empirical parameters. We use Slater type orbitals as basis set, replacing STO's by STO-2G functions to evaluate three- and four-center integrals and making the STO-2G two-orbital charge distributions have the same total charge as STO. The results are presented for test calculations on five molecules. In view of these results, CCAM is better than ab initio calculations over STO-6G in the results on total energies, kinetic energies and occupied orbital energies. In atomic populations, dipole moments and unoccupied orbital energies, CCAM is also satisfactory. We estimate that CCAM would be as fast as ab initio calculations over STO-2G in evaluating molecular integrals.     

A molecular mechanics treatment of the anomeric effect

The tendency of C? O bond lengths to change as a function of the torsional angles at an acetal carbon has been included in a new version of the molecular mechanics program MM 2(82), based on the observed behavior of molecules of this class as indicated by ab initio calculations and experimental structural data. The experimental geometries and energies are reasonably well reproduced.     

Ab initio crystal structure predictions for flexible hydrogen‐bonded molecules. Part II. Accurate energy minimization

A method is described to perform ab initio energy minimization for crystals of flexible molecules. The intramolecular energies and forces are obtained directly from ab initio calculations, whereas the intermolecular contributions follow from a potential that had been parameterized earlier on highly accurate quantum‐chemical calculations. Glycol and glycerol were studied exhaustively as prototypes. Lists of hypothetical crystal structures were generated using an empirical force field, after which ab initio energy minimizations were performed for a few hundreds of these. The experimental crystal structures were found among the structures with lowest energy, provided that sufficiently large basis sets were used. Moreover, their crystal geometries were well reproduced. This approach enables a systematic comparison between the merits of force fields at various levels of sophistication. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 805–815, 2001     

Ab initioMODPOT/VRDDO/MERGE calculations on energetic compounds. III. Nitroexplosives: Polyaminopolynitrobenzenes (including DATB,TATB, and tetryl)

Quantum chemical ab initio MODPOT /VRDDO calculations have been carried out on the following aminonitrobenzenes for which crystal structures had been determined experimentally: 4-nitroaniline; N,N-dimethyl-p-nitroaniline; 2,4,6-trinitroaniline; 1,3-diamino-2,4,6-trinitrobenzene (DATB—Form I); 1,3,5-triamino-2,4,6-trinitrobenzene (TATB); 2,3,4,6-tetranitroaniline; N-methyl-N,2,4,6-tetranitroaniline (Tetryl); and N-(β,β,β-trifluoroethyl)-N,2,4,6-tetranitroaniline. These quantum chemical calculations were performed on the molecules in their conformations as found in their crystal structures. The calculations were carried out with our own ab initio programs which also incorporate as options several desirable features for calculations on large molecules: ab initio effective core model potentials (MODPOT) which enable calculations of valence electrons only explicitly, yet accurately, and a charge conserving integral prescreening evaluation (which we named VRDDO-variable retention of diatomic differential overlap) especially effective for spatially extended molecules. Aminonitrobenzenes are especially interesting since there are inherent intramolecular ring distortions and deviations from planarity and intramolecular hydrogen bonds as well as intermolecular hydrogen bonds causing further deviations from planarity. The theoretical indices resulting from the quantum chemical calculations are relevant to a number of properties and behavioral characteristics of these molecules, both intramolecular and intermolecular. The charges on the atoms [from the gross atomic populations (GAP 's)] are needed for calculation of the atomic multipole–atomic multipole electrostatic contributions (a dominant factor) to the intermolecular interaction energies. These electrostatic interaction energies are part of the input necessary for calculations on the crystal packing and densities of these molecules. These GAP 's are also of value in interpreting the experimental photoelectron and ESCA spectra of these molecules. The total overlap populations (TOP 's) between atoms are related to the inherent bond strengths and can serve as a quantitative replacement for the old empirical bond length-bond order-bond energy relationship still used by explosives chemists to identify the “target bonds” (the weakest bonds). The TOP 's are of considerable value in predicting and tracing initiation and subsequent steps of explosive phenomena. The molecular orbital energies of the lowest unoccupied orbitals are of interest since nitroexplosives have been implicated in testicular toxicity and the initial metabolic activation appears to proceed through a one-electron reduction of the nitroexplosive.     

Empirical force-field and ab initio calculations on delocalized open chain cations

Force-field calculations are reported for large delocalized cations. The results for the geometries, heats of formation, and π-electron densities agree well with MP2(full)/6–31G^* ab initio calculations. Both methods give similar results for the distortion of the carbon skeletons of unsubstituted cations by hyperconjugating methyl groups. Because of the SCF treatment of π-interactions, the MMP2 force-field technique enables calculations of resonance energies in delocalized cations. The additional resonance stabilization produced by extending conjugation is directly related to the π-charge on the carbon at which a vinyl group is substituted. The good agreement of MMP2 results for nonbonded resonance effects in large delocalized cationic π-systems with ab initio data suggests that MMP2 can be used to study the influence of these interactions in cationic π-systems too large to be calculated by correlated ab initio methods. © 1997 by John Wiley & Sons, Inc.     

Decomposition analyses of the intermolecular interaction energies in two π?π stacking complexes: Quinhydrone and N,N,N′, N′-tetramethyl-P-diaminobenzene-chloranil complex

Although there is a similarity in the orbital interaction scheme between quinhydrone and N,N,N′,N′-tetramethyl-p-diaminobenzene-chloranil complex, the stacking conformations are different from each other. The former prefers the half-stacked conformation, whereas the latter prefers the completely stacked conformation. We have done ab initio molecular orbital calculations and decomposition analyses of the intermolecular interaction energies to clarify the origin of the different stacking conformations. It was concluded that the main origin is the difference in the steric part of the interaction energies. © 1994 by John Wiley & Sons, Inc.     

A systematic preparation of new contracted Gaussian-type orbital sets. VI. Ab initio calculation on molecules containing Na through Cl

Compact contracted Gaussian basis sets introduced in the preceding article are tested for ab initio molecular calculations on molecules containing third-row atoms (Na through Cl). It is found that the effect of splitting valence orbitals is essential for these molecules and addition of polarization functions to split basis sets can yield computed geometries, spectroscopic constants, and atomization energies in close agreement with the result of near Hartree–Fock calculations.     

A new method for empirical force field calculations on localized and delocalized carbocations

A new empirical force field method for localized and delocalized carbocations is described. Additional geometry parameters for carbocations were added to Allinger's MMP2 molecular mechanics program, which can treat delocalized π-systems. The effect of hyperconjugation in carbocations is introduced via a quantum chemical term into force field calculations for the first time. The calculated heats of formation are in excellent agreement with a wide range of experimental data; the largest deviations are about 3.5 kcal/mol. The calculated structures agree very well with those computed at correlated ab initio levels (MP2(full)/6-31G*). The relative energies and geometries of different conformations of representative carbocations also were in good agreement with MP4/6-31G*//MP2(full)/6-31G* results. © 1996 by John Wiley & Sons, Inc.     

Molecular mechanics of peroxides. I. Parametrization and conformational analysis of linear compounds

A force field has been developed for use in MM2 calculations of geometric and energy data for linear peroxides R₁? O? O? R₂ and tested in some of them (R₁, R₂ = H, Me, Et, Prⁱ, Bu^t). The field obtained yield results that agree considerably better with experimental and ab initio data than those afforded by the only set of estimated parameters hitherto available.     

Molecular mechanics (MM2) and conformational analysis of compounds with N?C?O units. Parametrization of the force field and anomeric effect

A molecular mechanics force field was developed for systems bearing the N? C? O unit on the basis of 6-31G* and 4-21G “ab initio” calculations with full optimization of the geometry and experimental heats of formation. The parameters used, which implicitly included the anomeric effect, provided good geometric and energetic results, both for the compounds on which the parametrization was based and for others on which the validity of the predictions was checked.     

Accurate molecular electrostatic potentials based on modified PRDDO/M wave functions. I. Electrostatic potential derived atomic charges

A new approach for the calculation of electrostatic potential derived atomic charges is presented. Based on molecular orbital calculations in the PRDDO/M approximation, the new parametrized electrostatic potential (PESP) method is parametrized against ab initio MP2/6-31G** calculations. For a data set of 820 atoms in 145 molecules containing H, C, N. O, F, P, S, Cl, and Br (including hypervalent species), the PESP method achieves a mean absolute error of 0.037 e⁻ with a correlation coefficient of 0.990. Unlike other approximate approaches, no scaling factor is required to improve the agreement between PESP charges and the underlying ab initio results. PESP calculations are an order of magnitude faster than the simplest ab initio calculation (STO-3G) on large molecules while achieving a level of accuracy that rivals much more elaborate ab initio methods. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 955–969, 1997     

A molecular mechanics study of alkyl peroxides

Studies have been carried out on alkyl peroxides with MM3 that have led to a parameter set that allows the calculation of geometries, energies, vibrational frequencies, and heats of formation for alkyl hydroperoxides (R? O? O? H) and dialkyl peroxides (R₁? O? O? R₂). The results obtained are in agreement with the available experimental and theoretical data. A similar, although less good, parameter set has been developed for MM2. © 1993 John Wiley & Sons, Inc.