Daniel Liotard

IMPROVED METHODS FOR SEMIEMPIRICAL SOLVATION MODELS

We present improved algorithms for the SMx (x = 1, 1a, 2, 3) solvation models presented previously [see the overview in C. J. Cramer and D. G. Truhlar, J. Comp.‐Aided Mol. Design, 6, 629 (1992)]. These models estimate the free energy of solvation by augmenting a semiempirical Hartree‐Fock calculation on the solute with the generalized Born (GB) model for electric polarization of the solvent and a surface tension term based on solvent‐accessible surface area. This article presents three improvements in the algorithms used to carry out such calculations, namely (1) an analytical accessible surface area algorithm, (2) a more efficient radial integration scheme for the dielectric screening computation in the GB model, and (3) a damping algorithm for updating the GB contribution to the Fock update during the iterations to achieve a self‐consistent field. Improvements (1) and (2) decrease the computer time, and improvement (3) leads to more stable convergence. Improvement (2) removes a small systematic numerical error that was explicitly absorbed into the parameterization in the SMx models. Therefore, we have adjusted the parameters for one of the previous models to yield essentially identical performance as was obtained originally while simultaneously taking advantage of improvement (2). The resulting model is called SM2.1. The fact that we obtain similar results after removing the systematic quadrature bias attests to the robustness of the original parameterization.

An efficient procedure for calculating the molecular gradient, using SCF-CI semiempirical wavefunctions with a limited number of configurations

Abstract An effective procedure is presented for calculating analytical derivatives of the energy in Hartree-Fock-type procedures including configuration interaction in cases where the number of configurations is small. This situation commonly arises in calculations involving semiempirical models such as MNDO or AM1. Existing numerical procedures are unsatisfactory, having been designed for ab initio applications where large numbers of configurations must be included.

Universal Solvation Model Based on Conductor-Like Screening Model

Atomic surface tensions are parameterized for use with solvation models in which the electrostatic part of the calculation is based on the conductor‐like screening model (COSMO) and the semiempirical molecular orbital methods AM1, PM3, and MNDO/d. The convergence of the calculated polarization free energies with respect to the numerical parameters of the electrostatic calculations is first examined. The accuracy and precision of the calculated values are improved significantly by adjusting two parameters that control the segmentation of the solvent‐accessible surface that is used for the calculations. The accuracy of COSMO calculations is further improved by adopting an optimized set of empirical electrostatic atomic radii. Finally, the electrostatic calculation is combined with SM5‐type atomic surface tension functionals that are used to compute the nonelectrostatic portions of the solvation free energy. All parameterizations are carried out using rigid (R) gas‐phase geometries; this combination (SM5‐type surface tensions, COSMO electrostatics, and rigid geometries) is called SM5CR. Six air–water and 76 water–solvent partition coefficients are added to the training set of air–solvent data points previously used to parameterize the SM5 suite of solvation models, thereby bringing the total number of data points in the training set to 2266. The model yields free energies of solvation and transfer with mean unsigned errors of 0.63, 0.59, and 0.61 kcal/mol for AM1, PM3, and MNDO/d, respectively, over all 2217 data points for neutral solutes in the training set and mean unsigned errors of 3.0, 2.7, and 3.1 kcal/mol, respectively, for 49 data points for the ions.

Theoretical study of the electronic spectrum of SiH4

Ab initio SCF calculations of the first excited states of SiH4 are reported. Earlier experimental assignments of the three broad peaks in the 107–220 nm range are discussed in terms of the analysis of calculated charge transfer for each state. It is clearly seen that only the first band can be attributed to a pure 4s Rydberg transition, while the others result from an overlapping of diffuse 3d states with the first antibonding Si–H level. The shoulder at 118 nm is assigned to the 5s atomic transition.

Analytical energy gradients of a self-consistent reaction-field solvation model based on CM2 atomic charges

Analytical energy gradients have been derived for an SM5-type solvation model based on Hartree–Fock self-consistent reaction-field theory and CM2 atomic charges. The method is combined with an analytic treatment of the first derivatives of nonelectrostatic first-solvation-shell contributions to the free energy and implemented in the General Atomic and Molecular Electronic Structure System (GAMESS). The resulting equations allow one to use accurate class IV charges to calculate equilibrium geometries of solutes in liquid-phase solutions. The algorithm is illustrated by calculations of optimized geometries and solvation free energies for water, methanol, dimethyl disulfide, and 9-methyladenine in water and 1-octanol.

Etude théorique de l'isomérisation syn-anti dans la Formaldoxime

Semi empirical CNDO and “ab initio” methods are applied to the analysis of syn-anti isomerization mechanism of formaldoxime. Semi empirical calculations are carried out with complete geometry optimization and lead to predicted inversion barrier equal to 37.5 kcal/mole. A bicentric partitioning of the total energy and the expression of the density matrix in hybride basis set reveal the chemical origin of the shape of the potential line.

Reaction mechanism studies made simple using simulated annealing. Potential energy surface exploration

Abstract A new and easy way to study reaction mechanisms by theoretical means is proposed. Simulated annealing is used to explore the potential energy surface of three different systems. This approach enables a facile finding of most stationary points involved in the various possible reaction paths arising from a given molecular system and thus allows one to determine a whole set of competing reactions. Therefore, by a comparison of the activation barriers, we can qualitatively estimate whether a reaction should be stereoselective or if side-products may arise. This paper deals with the [2+2] cycloaddition leading to β-lactones and the thermolysis of thiirane and thiiranium cation.

Analysis of the topological features of the conformational potential energy surfaces of spiro [2.5] octanes by molecular mechanics calculations

Abstract Allingers force field MM2 is expanded to the calculation of the static and dynamic properties of 1-hetero spiro[2.5]octanes by additional parameters. This model is shown to reproduce satisfactorily trends in conformational energies of these compounds. A detailed map of the chair →- chair inversion process is constructed and the calculated rates are compared to experimental data. For the exploration of the interconversion paths, a new method including a quadratic procedure is used which makes it possible to avoid the pitfalls of the exhaustive point-by-point mapping technique and provides high accuracy in the search for saddle points. Finally, the conformational potential energy surface is analyzed in terms of the relationships which exist between the number of critical points of various orders.

Theoretical studies of [n]paracyclophanes and their valence isomers

SummaryThe valence isomerisations of benzene, [6]- and [7]paracyclophane to their Dewar benzene and prismane isomers are studied with the MNDO method using the unrestricted Hartree-Fock (UHF) and the configuration interaction (C.I.) approximations. The enthalpy of the reaction Dewar benzene → benzene is ΔH°r=−68.9 kcal/mol and the activation enthalpy is ΔH°‡=27.9 kcal/mol (with C.I.). The reaction path hasC2v symmetry.The determination of several points of the lowest potential energy surface of [6]- and [7]paracyclophanes leads to a minimum reaction path having the same topology as for the potential energy surface of the nonbridged benzene. The only difference is a quantitative change in the energy values of the aromatic isomers due to the deformation introduced by the alkyl chain. For [6]paracyclophane, the activation enthalpy is ΔH°‡=24.6 kcal/mol and the activation entropy is ΔS0‡=0.6 cal K−1 mol−1 calculated with C.I.The enthalpy of the reaction prismane → Dewar benzene is ΔH°r≈−32 kcal/mol and the activation enthalpy is ΔH°‡≈19 kcal/mol. The highest molecular symmetry group common to both molecules isC2v, whereas the symmetry group of the reaction path is lowered toCs. Along this reaction path is located a biradicaloid intermediate, separated by low activation barriers from the products. No significant changes of the potential energy surfaces are found for the bridged [n]prismanes and the [n]Dewar benzenes.All the calculated values, reaction enthalpies, activation enthalpies and entropies, are in a good agreement with literature experimental data.

Conformational equilibria of TADDOL-s in solution investigated by vibrational circular dichroism.

Six enantiomeric pairs of TADDOL-s gathered in two series with either methyl (series A) or phenyl (series B) substituent in 2-position of the dioxolane ring were studied by vibrational circular dichroism (VCD). Experimental IR and VCD spectra associated with density functional theory (DFT) calculations showed that the two series exhibit quite different conformations in solution. In series A, the conformer with anti C-O bonds and stabilized by intramolecular OH...OH hydrogen bonding prevails, whereas in series B the conformer with gauche C-O bonds and intramolecular OH...π hydrogen bonding is favored. The shape and sign of the VCD bands in the O-H stretching region revealing the nature of the intramolecular hydrogen bonding were clearly identified. Polarimetric measurements showed that, within the same absolute configuration, compounds in series A and in series B have opposite signs of optical rotation.