Simulation of vibrational energy transfer in two-dimensional infrared spectroscopy of amide I and amide II modes in solution

Abstract

Population transfer between vibrational eigenstates is important for many phenomena in chemistry. In solution, this transfer is induced by fluctuations in molecular conformation as well as in the surrounding solvent. We develop a joint electrostatic density functional theory map that allows us to connect the mixing of and thereby the relaxation between the amide I and amide II modes of the peptide building block N-methyl acetamide. This map enables us to extract a fluctuating vibrational Hamiltonian from molecular dynamics trajectories. The linear absorption spectrum, population transfer, and two-dimensional infrared spectra are then obtained from this Hamiltonian by numerical integration of the Schrödinger equation. We show that the amide I/amide II cross peaks in two-dimensional infrared spectra in principle allow one to follow the vibrational population transfer between these two modes. Our simulations of N-methyl acetamide in heavy water predict an efficient relaxation between the two modes with a time scale of 790 fs. This accounts for most of the relaxation of the amide I band in peptides, which has been observed to take place on a time scale of 450 fs in N-methyl acetamide. We therefore conclude that in polypeptides, energy transfer to the amide II mode offers the main relaxation channel for the amide I vibration.

Toward Detecting the Formation of a Single Helical Turn by 2D IR Cross Peaks between the Amide-I and -II Modes

“…[33][34][35] It is quite useful to expand the capability of 2D IR spectroscopic techniques toward other modes, like the amide-A and, as this study demonstrates, amide-II mode. This development necessitates a generalized theoretical framework which can describe the experimental results well.…”

Development and Validation of Transferable Amide I Vibrational Frequency Maps for Peptides

“…The major isotopic form of NMA in D 2 O is N-deuterated NMA (NMAD), as shown in Figure 1a. By performing electronic structure calculations on clusters of NMAD surrounded by D 2 O, frequency maps have been developed that relate the amide I frequency to the electric potential 46,49,55,56,64,66 or electric field 57,58,60,68,69 on different atom sites from the surrounding solvent molecules.…”

Optimization of Model Parameters for Describing the Amide I Spectrum of a Large Set of Proteins

“…A computationally inexpensive way of including solvent effects on the amide I frequencies is to parametrize ab initio calculations of N-methylacetamide (NMA) and water clusters. [16][17][18][19][20][21][22][23][24][25][26][27][28][29][30] This method exploits the linear correlation found between the C=O bond length, stretching frequency and electrostatic potential at the atoms of NMA, 18,31,32 which provides a link between perturbation of molecular (and electronic) structure by the electric field of the solvent and the resulting shift of the vibrational frequency. Parametrized electrostatic calculations using the building block approach have been used in protein amide I sim-ulations of ubiquitin, 10,33 other proteins 34 as well as polypeptides in membrane environment.…”