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Photochemistry of hydrogen-bonded aromatic pairs: Quantum dynamical calculations for the pyrrole-pyridine complex.

ABSTRACT: The photochemical dynamics of the pyrrole-pyridine hydrogen-bonded complex has been investigated with computational methods. In this system, a highly polar charge-transfer state of (1)pipi* character drives the proton transfer from pyrrole to pyridine, leading to a conical intersection of S(1) and S(0) energy surfaces. A two-sheeted potential-energy surface including 39 in-plane nuclear degrees of freedom has been constructed on the basis of ab initio multiconfiguration electronic-structure data. The non-Born-Oppenheimer nuclear dynamics has been treated with time-dependent quantum wave-packet methods, including the two or three most relevant nuclear degrees of freedom. The effect of the numerous weakly coupled vibrational modes has been taken into account with reduced-density-matrix methods (multilevel Redfield theory). The results provide insight into the mechanisms of excited-state deactivation of hydrogen-bonded aromatic systems via the electron-driven proton-transfer process. This process is believed to be of relevance for the ultrafast excited-state deactivation of DNA base pairs and may contribute to the photostability of the molecular encoding of the genetic information.

SUBMITTER: Lan Z

PROVIDER: S-EPMC2529040 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature

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Photochemistry of hydrogen-bonded aromatic pairs: Quantum dynamical calculations for the pyrrole-pyridine complex.

Lan Zhenggang Z Frutos Luis Manuel LM Sobolewski Andrzej L AL Domcke Wolfgang W

Proceedings of the National Academy of Sciences of the United States of America 20080728 35

The photochemical dynamics of the pyrrole-pyridine hydrogen-bonded complex has been investigated with computational methods. In this system, a highly polar charge-transfer state of (1)pipi* character drives the proton transfer from pyrrole to pyridine, leading to a conical intersection of S(1) and S(0) energy surfaces. A two-sheeted potential-energy surface including 39 in-plane nuclear degrees of freedom has been constructed on the basis of ab initio multiconfiguration electronic-structure data ...[more]

PMID: 18663223

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Project description:Ribonucleotide:protein interactions play crucial roles in a number of biological processes. Unlike the RNA:protein interface where van der Waals contacts are prevalent, the recognition of a single ribonucleotide such as ATP by a protein occurs predominantly through hydrogen-bonding interactions. As a first step toward understanding the role of hydrogen bonding in ribonucleotide:protein recognition, the present work employs density functional theory to provide a detailed quantum-mechanical analysis of the structural and energetic characteristics of 18 unique hydrogen-bonded pairs involving the nucleobase/nucleoside moiety of four canonical ribonucleotides and the side chains of three polar amino-acid residues (arginine, glutamine, and glutamic acid) of proteins. In addition, we model five new pairs that are till now not observed in crystallographically identified ribonucleotide:protein complexes but may be identified in complexes crystallized in the future. We critically examine the characteristics of each pair in its ribonucleotide:protein crystal structure occurrence and (gas phase and water phase) optimized intrinsic structure. We further evaluated the interaction energy of each pair and characterized the associated hydrogen bonds using a number of quantum mechanics-based relationships including natural bond orbital analysis, quantum theory atoms in molecules analysis, Iogansen relationships, Nikolaienko-Bulavin-Hovorun relationships, and noncovalent interaction-reduced density gradient analysis. Our analyses reveal rich variability in hydrogen bonds in the crystallographic as well as intrinsic structure of each pair, which includes conventional O/N-H···N/O and C-H···O hydrogen bonds as well as donor/acceptor-bifurcated hydrogen bonds. Further, we identify five combinations of nucleobase and amino acid moieties; each of which exhibits at least two alternate (i.e., multimodal) structures that interact through the same nucleobase edge. In fact, one such pair exhibits four multimodal structures; one of which possesses unconventional "amino-acceptor" hydrogen bonding with comparable (-9.4 kcal mol-1) strength to the corresponding conventional (i.e., amino:donor) structure (-9.2 kcal mol-1). This points to the importance of amino-acceptor hydrogen bonds in RNA:protein interactions and suggests that such interactions must be considered in the future while studying the dynamics in the context of molecular recognition. Overall, our study provides preliminary insights into the intrinsic features of ribonucleotide:amino acid interactions, which may help frame a clearer picture of the molecular basis of RNA:protein recognition and further appreciate the role of such contacts in biology.

Dataset Information

Photochemistry of hydrogen-bonded aromatic pairs: Quantum dynamical calculations for the pyrrole-pyridine complex.

Publications

Photochemistry of hydrogen-bonded aromatic pairs: Quantum dynamical calculations for the pyrrole-pyridine complex.

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