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Geometry determination of complexes in a molecular liquid mixture using electron-vibration-vibration two-dimensional infrared spectroscopy with a vibrational transition density cube method.

ABSTRACT: We demonstrate the use of a new vibrational transition density cube (VTDC) method for determining the geometry of complexes in a molecular liquid mixture from electron-vibration-vibration two-dimensional infrared (EVV 2DIR) spectra. The VTDC method was used to calculate the electrically-mediated intermolecular vibrational coupling and thereby the EVV 2DIR spectra. Using the 1:1 benzonitrile-phenylacetylene (BN-PA) liquid mixture as a test case, the new method leads to a distance of 3.60 Å between the interacting BN-PA pair, a much more accurate value than the distance previously obtained using a dipolar approximation for the electrical coupling. We also show that molecular dynamics simulations of the liquid mixture predict a modal geometry of complexation which agrees well with the geometry determined from the 2DIR data via VTDC analysis. We therefore conclude the combination of VTDC and EVV 2DIR data is a useful approach for the determination of the geometry of molecular complexes in the condensed phase.

SUBMITTER: Guo R

PROVIDER: S-EPMC3596003 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature

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Geometry determination of complexes in a molecular liquid mixture using electron-vibration-vibration two-dimensional infrared spectroscopy with a vibrational transition density cube method.

Guo Rui R Mukamel Shaul S Klug David R DR

Physical chemistry chemical physics : PCCP 20120919 40

We demonstrate the use of a new vibrational transition density cube (VTDC) method for determining the geometry of complexes in a molecular liquid mixture from electron-vibration-vibration two-dimensional infrared (EVV 2DIR) spectra. The VTDC method was used to calculate the electrically-mediated intermolecular vibrational coupling and thereby the EVV 2DIR spectra. Using the 1:1 benzonitrile-phenylacetylene (BN-PA) liquid mixture as a test case, the new method leads to a distance of 3.60 Å betwee ...[more]

PMID: 22990297

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Project description:Proteins, enzymes, and other biological molecules undergo structural dynamics as an intrinsic part of their biological functions. While many biological processes occur on the millisecond, second, and even longer time scales, the fundamental structural dynamics that eventually give rise to such processes occur on much faster time scales. Many decades ago, chemical kineticists focused on the inverse of the reaction rate constant as the important time scale for a chemical reaction. However, through transition state theory and a vast amount of experimental evidence, we now know that the key events in a chemical reaction can involve structural fluctuations that take a system of reactants to its transition state, the crossing of a barrier, and the eventual relaxation to product states. Such dynamics occur on very fast time scales. Today researchers would like to investigate the fast structural fluctuations of biological molecules to gain an understanding of how biological processes proceed from simple structural changes in biomolecules to the final, complex biological function. The study of the fast structural dynamics of biological molecules requires experiments that operate on the appropriate time scales, and in this Account, we discuss the application of ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy to the study of protein dynamics. The 2D IR vibrational echo experiment is akin to 2D NMR, but it operates on time scales many orders of magnitude faster. In the experiments, a particular vibrational oscillator serves as a vibrational dynamics probe. As the structure of the protein evolves in time, the structural changes are manifested as time-dependent changes in the frequency of the vibrational dynamics probe. The 2D IR vibrational echo experiments can track the vibrational frequency evolution, which we then relate to the time evolution of the protein structure. In particular, we measured protein substate interconversion for mutants of myoglobin using 2D IR chemical exchange spectroscopy and observed well-defined substate interconversion on a sub-100 ps time scale. In another study, we investigated the influence of binding five different substrates to the enzyme cytochrome P450(cam). The various substrates affect the enzyme dynamics differently, and the observed dynamics are correlated with the enzyme's selectivity of hydroxylation of the substrates and with the substrate binding affinity.

Dataset Information

Geometry determination of complexes in a molecular liquid mixture using electron-vibration-vibration two-dimensional infrared spectroscopy with a vibrational transition density cube method.

Publications

Geometry determination of complexes in a molecular liquid mixture using electron-vibration-vibration two-dimensional infrared spectroscopy with a vibrational transition density cube method.

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