Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins.

Following chemical reactions in atomistic detail is one of the most challenging aspects of current computational approaches to chemistry. In this chapter the application of adiabatic reactive MD (ARMD) and its multistate version (MS-ARMD) are discussed. Both methods allow to study bond-breaking and bond-forming processes in chemical and biological processes. Particular emphasis is put on practical aspects for applying the methods to investigate the dynamics of chemical reactions. The chapter closes with an outlook of possible generalizations of the methods discussed.

Grotthus-type and diffusive proton transfer in 7-hydroxyquinoline.(NH(3))(n) clusters.

Proton translocation along ammonia wires is investigated in 7-hydroxyquinoline.(NH(3))(n) clusters, both experimentally by laser spectroscopy and theoretically by Hartree-Fock and density functional (DFT) calculations. These clusters serve as realistic finite-size models for proton transfer along a chain of hydrogen-bonded solvent molecules. In the enol tautomer of 7-hydroxyquinoline (7-HQ), the OH group acts as a proton injection site into the (NH(3))(n)cluster. Proton translocation along a chain of three NH(3) molecules within the cluster can take place, followed by reprotonation of 7-HQ at the quinolinic N atom, forming the 7-ketoquinoline tautomer. Exoergic proton transfer from the OH group of 7-HQ to the closest NH(3) molecule within the cluster giving a zwitterion 7-HQ-.(NH(3))(6)H+ (denoted PT-A) occurs at a threshold cluster size of n = 6 in the DFT calculations and at n = 5 or 6 experimentally. Three further locally stable zwitterion clusters denoted PT-B, PT-B', and PT-C, the keto tautomer, and several transition structures along the proton translocation path were characterized theoretically. Grotthus-type proton-hopping mechanisms occur for three of the proton transfer steps, which have low barriers and are exoergic or weakly endoergic. The step with the highest barrier involves a complex proton transfer mechanism, involving structural reorganization and large-scale diffusive motions of the cluster.

The Dynamics of N(2)-O(3) and N(2)-SO(2) Probed by Microwave Spectroscopy.

The microwave spectra of N(2)-O(3) and N(2)-SO(2) have been recorded in the 6-18 GHz range using a pulsed-nozzle, Fourier transform microwave spectrometer. C-type transitions have been observed for both complexes which are slightly shifted by internal tunneling motions of the O(3) or SO(2) moieties. In addition, unshifted a-type transitions have been observed for N(2)-O(3). The nuclear hyperfine pattern is typical of equivalent nitrogen nuclei. Two sets of rotational and hyperfine constants are required to fit the symmetric and antisymmetric nuclear spin states, indicating that the equivalence arises from tunneling rotation of the nitrogen molecule. Internal tunneling motions along three tunneling pathways have been identified, although no information on the N(2) tunneling frequency is available from the spectra. From the N(2)-O(3) data the tunneling frequencies cannot be decorrelated from the rotational parameters; however, the O(3) tunneling frequency upper limit is estimated to be 2.0 MHz and the frequency of the concerted tunneling motion of both moieties is estimated to be about 8.9 MHz. For N(2)-SO(2), the SO(2) tunneling frequency is 11.5 kHz and the concerted frequency 173.9 kHz. Both complexes are roughly T shaped with the N(2) axis approximately perpendicular to the O(3) or SO(2) plane. In the equilibrium structures of both complexes, the a-c inertial plane is a plane of symmetry. The centers of mass separations are estimated from the rotational parameters to be 3.582 Å for N(2)-O(3) and 3.875 Å for N(2)-SO(2). The angle between the symmetry axes of the O(3) or SO(2) and the line joining their centers of mass have been calculated as 130.84 degrees (or 49.16 degrees ) and 119.71 degrees (or 60.29 degrees ), respectively. From the quadrupole analysis, the average angle between the N(2) axis and the a-inertial axis is 32.12 degrees for N(2)-O(3) and 27.81 degrees for N(2)-SO(2). Model electrostatic and ab initio calculations confirm these structures. Differences between the experimental and calculated structural parameters highlight the role of tunneling dynamics in these complexes. Copyright 2000 Academic Press.