Chemical fragmentation in quantum mechanical methods

Optimal virtual orbitals to relax wave functions built up with transferred extremely localized molecular orbitals

Extremely localized molecular orbitals (ELMOs), namely orbitals strictly localized on molecular fragments, are easily transferable from one molecule to another one. Hence, they provide a natural way to set up the electronic structure of large molecules using a data base of orbitals obtained from model molecules. However, this procedure obviously increases the energy with respect to a traditional MO calculation. To gain accuracy, it is important to introduce a partial electron delocalization. This can be carried out by defining proper optimal virtual orbitals that supply an efficient set for nonorthogonal configurations to be employed in VB-like expansions.

Transferability of parameters of strictly local geminals' wave function and possibility of sequential derivation of molecular mechanics

The problem of substantiation of molecular mechanics (MM) remains actual due to growing popularity of hybrid quantum/classical (QM/MM) schemes. Recently proposed deductive molecular mechanics (DMM) seems to be a natural tool to derive mechanistic models of molecular energy (classical force fields) from a suitable quantum mechanical (QM) description of molecular structure. It is based on an assumption that the trial wave function underlying the MM description is one of the antisymmetrized product of strictly local geminals (SLG). A proof of transferability of electronic structure parameters (ESPs) in this approximation is an essential component of a logical framework for the transition from the QM to an MM description because it allows constructing expressions for potential energy surfaces by proper consideration of the response of the ESPs to the variations of geometry parameters. In the present article the ESPs defining density matrix elements and basis one-electron states (hybrid orbitals-HOs) in the SLG approximation are formally considered. The transferability of the density matrix elements with respect to the parameters of molecular electronic structure and the linear response relations for the HOs are proven to take place under very nonrestrictive conditions. Special attention is paid to numerical estimates of the ESPs' features giving an "experimental" support to approximate expressions for the molecular energy.

Unexpected reactivity difference between iodo-alkene moieties of steroids possessing remote lactame or cycloalkane structural units: a theoretical approach

The steroidal ring A possessing cyclohexane vs. delta-valerolactame structures shows a 'long-range effect' on the reactivity of the 'iodovinyl' functionality of the ring D. The strikingly different reactivity of 17-iodo-16-ene functionality of steroids is explained on the basis of the redistribution of kinetic energy of the system. The vibrational energy localized on the 'iodovinyl' moiety proved to be determinant in the CI bond-breaking process. The appearance of the lactame moiety in the ring A supports a redistribution of the kinetic energy on the molecule. As a result, a drastic decrease in C-I bond stretching has been obtained, which could diminish the C-I bond breaking, and therefore, results in decreased reactivity of the iodovinyl moiety in agreement with experimental findings.

Hydride transfer catalyzed by xylose isomerase: mechanism and quantum effects

We have applied molecular dynamics umbrella-sampling simulation and ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT) to calculate the reaction rate of xylose-to- xylulose isomerization catalyzed by xylose isomerase in the presence of two Mg2+ ions. The calculations include determination of the free energy of activation profile and ensemble averaging in the transmission coefficient. The potential energy function is approximated by a combined QM/MM/SVB method involving PM3 for the quantum mechanical (QM) subsystem, CHARMM22 and TIP3P for the molecular mechanical (MM) environment, and a simple valence bond (SVB) local function of two bond distances for the hydride transfer reaction. The simulation confirms the essential features of a mechanism postulated on the basis of kinetics and X-ray data by Whitlow et al. (Whitlow, M.; Howard, A. J.; Finzel, B. C.; Poulos, T. L.; Winborne, E.; Gilliland, G. L. Proteins 1991, 9, 153) and Ringe, Petsko, and coworkers (Labie, A.; Allen, K.-N.; Petsko, G. A.; Ringe, D. Biochemistry 1994, 33, 5469). This mechanism involves a rate-determining 1,2-hydride shift with prior and post proton transfers. Inclusion of quantum mechanical vibrational energy is important for computing the free energy of activation, and quantum mechanical tunneling effects are essential for computing kinetic isotope effects (KIEs). It is found that 85% of the reaction proceeds by tunneling and 15% by overbarrier events. The computed KIE for the ratio of hydride to deuteride transfer is in good agreement with the experimental results. The molecular dynamics simulations reveal that proton and hydride transfer reactions are assisted by breathing motions of the mobile Mg2+ ion in the active site, providing evidence for concerted motion of Mg2+ during the hydride transfer step.

Specific force field parameters determination for the hybrid ab initio QM/MM LSCF method

The pure quantum mechanics method, called Local Self-Consistent Field (LSCF), that allows to optimize a wave function within the constraint that some predefined spinorbitals are kept frozen, is discussed. These spinorbitals can be of any shape, and their occupation numbers can be 0 or 1. Any post-Hartree-Fock method, based on the restricted or unrestricted Hartree-Fock Slater determinant, and Kohn-Sham-based DFT method are available. The LSCF method is easily applied to hybrid quantum mechanics/molecular mechanics (QM/MM) procedure where the quantum and the classical parts are covalently bonded. The complete methodology of our hybrid QM/MM scheme is detailed for studies of macromolecular systems. Not only the energy but also the gradients are derived; thus, the full geometry optimization of the whole system is feasible. We show that only specific force field parameters are needed for a correct description of the molecule, they are given for some general chemical bonds. A careful analysis of the errors induced by the use of molecular mechanics in hybrid computation show that a general procedure can be derived to obtain accurate results at low computation effort. The methodology is applied to the structure determination of the crambin protein and to Menshutkin reactions between primary amines and chloromethane.