Overview

We are theoretical and computational chemistry research group with primary focus in exploring complex molecular-level phenomena in chemistry, biology, and materials, by means of computer simulations. We develop new models and use existing computational and quantum chemistry methodology to exploit primarily electron-driven and photoinduced processes. The main research directions we pursue at the moment are:

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Electronic structure of metastable electronic states

Metastable electronic states are states that lie in the autodetachment continuum, i.e. that have enough energy to eject an electron, and, yet, live long enough to be experimentally detected or even cause a chemical reaction. Metastable states, or electronic resonances, are commonly formed upon electron capture by molecular system or though excitation into highly-excited states. They serve as intermediates in such processes DNA building blocks radiation damage, are routinely formed in highly energetic environments, and possibly act as gateway states for formation of stable anions in the interstellar medium.

As resonances belong to the continuous spectrum of the Hamiltonian, they cannot be described using conventional quantum-chemistry methods. We develop new methods for describing energies and lifetimes of these states by combing Non-Hermitian quantum mechanics with advanced quantum chemistry electronic structure methods. We also exploit developed and existing techniques to study electronic structure of metastable electronic states and mechanism of electron capture by molecules. Several representative references on theory development and applied computational studies are listed below.

Theory:

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A.A. Kunitsa and K.B. Bravaya; Feshbach projection XMCQDPT2 model for metastable electronic states, [arXiv.org].

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A.A. Kunitsa, A.A. Granovsky, and K.B. Bravaya; CAP-XMCQDPT2 method for molecular electronic resonances, J. Chem. Phys., 2017, 146, 184107, [http].

Applications:

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Z. Li, M.M. Dawley, I. Carmichael, K.B. Bravaya, and S. Ptasińska; Dipole-supported electronic resonances mediate electron-induced amide bond cleavage, Phys. Rev. Lett., 2019, 22, 073002, [http].

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Ragesh Kumar T.P., J. Kocisek, K.B. Bravaya, and J. Fedor; Electron-induced vibrational excitation and dissociative electron attachment in methyl formate, Phys. Chem. Chem. Phys., 2020, 22, 518–524, [http].

Computational electrochemistry

We explore the capabilities of modern computational chemistry for predictive simulations of redox potentials of molecules in different environments, from solutions to proteins. Redox reactions play key role in various biological processes, including respiration, photosynthesis, oxidative stress protection. As experimental characterization of redox properties of complex systems such as proteins is often challenging, predictive theoretical tools are highly desirable. Simulation of redox potentials of molecules in heterogeneous and flexible environments, such as biological micromoles, requires multi-level approaches. We have proposed a computational protocol exploiting quantum and classical approaches that accounts for protein structural fluctuations, long-range electrostatic interactions, and environment polarization, that yields accurate description of redox thermodynamics.

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R.N. Tazhigulov, P. Kumar Gurunathan, Y. Kim, L.V. Slipchenko and K.B. Bravaya; Polarizable Embedding for Simulating Redox Potentials of Biomolecules, Phys. Chem. Chem. Phys., 2019, 21, 11642–11650, [http].

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R.N. Tazhigulov and K.B. Bravaya; Accurate redox half-reactions free energies from the first principle calculations, J. Phys. Chem. Lett., 2016, 7, 2490–2495, [http].

Electron trasfer in proteins

Electron transfer processes are ubiquitous in biology. They are exploited by signaling proteins, play key role in photosynthesis, and drive enzymatic processes. We pursue two directions in theoretical description of electron transfer: identifying critical chemical players in electron transfer and providing accurate description of the energetics and dynamics of electron transfer.

To identify aminoacid residues or co-factors playing key role in electron transfer in proteins we develop an eMap application (https://emap.bu.edu). Using protein structural information as the input the software predicts and visualizes potentially efficient electron hopping pathways in proteins.

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R.N. Tazhigulov, J.R. Gayvert, M. Wei, and K.B. Bravaya; eMap: Web application for robust identification, mapping, and visualization of electron transfer channels in proteins, J. Phys. Chem. B, 2019, 123, 6946– 6951, [http].

While qualitative information provided by eMap analysis can be useful to guide the experimental studies and can contribute to mechanistic understanding of the proteins functions, qualitative estimates of the electron transfer rates are highly desrible. To address this challenge we work on developing computational protocols that combine advanced quantum chemistry and quantum dynamics approaches to obtain accurate energetic parameters as well as the dynamical description of the process.

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R.N. Tazhigulov, D. Coker, J. Provazza, K.B. Bravaya Photoactivation of Cryptochromes Invokes Competing Inter- and Intramolecular Electron Transfer, [ChemrXiv].