Time-Dependent Perspective for the Intramolecular Couplings of the N-H Stretches of Protonated Tryptophan.

Alexander Kaiser,William L Hase,Yuxuan Yao,Xinyou Ma,Roland Wester,Bhumika Jayee

doi:10.1021/acs.jpca.0c01611

Abstract

Quasi-classical direct dynamics simulations, performed with the B3LYP-D3/cc-pVDZ electronic structure theory, are reported for vibrational relaxation of the three NH stretches of the −NH3+ group of protonated tryptophan (TrpH+), excited to the n = 1 local mode states. The intramolecular vibrational energy relaxation (IVR) rates determined for these states, from the simulations, are in good agreement with the experiment. In accordance with the experiment, IVR for the free NH stretch is slowest, with faster IVR for the remaining two NH stretches which have intermolecular couplings with an O atom and a benzenoid ring. For the free NH and the NH coupled to the benzenoid ring, there are beats (i.e., recurrences) in their relaxations versus time. For the free NH stretch, 50% of the population remained in n = 1 when the trajectories were terminated at 0.4 ps. IVR for the free NH stretch is substantially slower than for the CH stretch in benzene. The agreement found in this study between quasi-classical direct dynamics simulations and experiments indicates the possible applicability of this simulation method to larger biological molecules. Because IVR can drive or inhibit reactions, calculations of IVR time scales are of interest, for example, in unimolecular reactions, mode-specific chemistry, and many photochemical processes.

Highlights

Vibrational spectroscopy is an important experimental means for obtaining structural information for biological molecules.[1−4] Of particular interest are the secondary structures of proteins and peptides, which are affected by their conformations, protonation sites, and hydrogen bonding
The property determined from the simulations is the probability P(n,t) that TrpH+ remained in the n = 1 local mode state versus time
P(n,t) is the quasi-classical trajectory (QCT) analogue of |cs(t)|2 in eq 1.24 The quasi-classical binning model was used to identify if the trajectory was in the local mode state n = 1; that is, the trajectory was assumed to be in n = 1 if the energy for the local mode was in the energy interval [En−1/2,En+1/2] of the initially prepared local mode

Summary

Introduction

Vibrational spectroscopy is an important experimental means for obtaining structural information for biological molecules.[1−4] Of particular interest are the secondary structures of proteins and peptides, which are affected by their conformations, protonation sites, and hydrogen bonding. The Greek letters α, β, γ label the three hydrogen atoms in the protonated amino group. NH(α) is the mode with the largest amplitude of vibration of H toward the side group, NH(β) is influenced by the electrostatic bond of H to the oxygen atom, and NH(γ) is basically a free NH stretch (displacement vectors are shown in Figure S1 in the Supporting Information)

Methods

Results

Conclusion