A fundamental goal of chemistry research is to understand how to control chemical reactions to most efficiently give desired products. The Coker Group uses and develops new theoretical and computational methods to explore how electronic and vibrational excitation of reactant molecules in different environments can influence the outcome of chemical reactions of these molecules. Because electronic and vibrational relaxation of excited reactants is fundamentally quantum mechanical in nature, the methods they use must accurately describe the transfer of energy between the classical environment and the quantal reactive system.

The various approximate methods the Coker Group has developed to address these types of phenomena have been used to study the influence of environment on excited state photo-chemical reaction dynamics of polyatomic molecules in liquids, solids, clusters, and in the gas phase. Now these methods are being extended to explore photo-chemistry in controllable confining environments such as zeolites. These studies explore the influence of these micro-reactor environments on excited state chemistry. Various other processes being explored with these methods include: the effects of finite temperature on proton transfer reactions in aqueous hydrochloric acid clusters important for atmospheric chemistry of ozone depletion, studies of non-adiabatic excited-state charge transfer reactions that enable computation of cross-sections useful in ionospheric modeling, the influence of non-adiabatic transitions on electronic transport in ionic liquids and polymeric materials, important for understanding the multi-scale phenomena of dielectric break-down, to studies of the ultra-fast excited state photo-physics of biological chromophores such as excited state di-radical ring opening of small nitrogen containing heterocyclic molecules.

Depending on the nature of the problem, they can draw on different approximate methods that they have developed. In some energy or temperature ranges, for example, approximate mixed quantum-classical surface-hopping methods can provide a reliable description of the dynamics. In other situations, high frequency vibrational modes and electronic degrees of freedom need to be treated on the same semi-classical footing while environmental variables can often be incorporated classically. Their approaches take advantage of the “multi-physics” nature that is ubiquitous to these problems. Computationally, this research is extremely demanding both in terms of memory and CPU time. Typically their mixed quantum-classical calculations involve propagating very large ensembles of classical trajectories. For the current application systems, thousands of particles need to be propagated for tens of thousands of nuclear time steps (millions of electronic time steps), and to obtain reasonable statistics, ensembles of several hundred trajectories need to be propagated. For applications where they must use new semi-classical trajectory based methods to incorporate the influence of nuclear quantum coherence on the electronic state amplitudes, there are two significant increases in the computational complexity and demands over the mixed quantum-classical approaches: (1) Each trajectory now has a complex weight determined by its quantum mechanical phase so the contributions of the different trajectories must be added up with these phases to compute the nonadiabatic transition amplitudes. Thus tens of thousands of trajectories may be required and stationary phase filtering methods are needed to achieve convergence. (2) These quantum phases are computed by propagating trajectory stability matrices whose size is the number of degrees of freedom squared for each trajectory so the memory requirements for each trajectory can become very large. They are currently exploring approximations that alleviate these problems to some extent, especially in the calculation of thermally averaged time correlation functions for non-adiabatic processes.

Publications

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications.
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Sanyal S, Coker DF, MacKernan D. How flexible is a protein: simple estimates using FRET microscopy. Mol Biosyst. 2016 Oct 20; 12(10):2988-91. PMID: 27499159.

Lee MK, Coker DF. Modeling Electronic-Nuclear Interactions for Excitation Energy Transfer Processes in Light-Harvesting Complexes. J Phys Chem Lett. 2016 Aug 18; 7(16):3171-8. PMID: 27472379.

Reimers JR, Biczysko M, Bruce D, Coker DF, Frankcombe TJ, Hashimoto H, Hauer J, Jankowiak R, Kramer T, Linnanto J, Mamedov F, Müh F, Rätsep M, Renger T, Styring S, Wan J, Wang Z, Wang-Otomo ZY, Weng YX, Yang C, Zhang JP, Freiberg A, Krausz E. Challenges facing an understanding of the nature of low-energy excited states in photosynthesis. Biochim Biophys Acta. 2016 Sep; 1857(9):1627-40. PMID: 27372198.

Lee MK, Huo P, Coker DF. Semiclassical Path Integral Dynamics: Photosynthetic Energy Transfer with Realistic Environment Interactions. Annu Rev Phys Chem. 2016 May 27; 67:639-68. PMID: 27090842.

Edmonds MT, Tadich A, Carvalho A, Ziletti A, O'Donnell KM, Koenig SP, Coker DF, Özyilmaz B, Neto AH, Fuhrer MS. Creating a Stable Oxide at the Surface of Black Phosphorus. ACS Appl Mater Interfaces. 2015 Jul 15; 7(27):14557-62. PMID: 26126232.

Doganov RA, O'Farrell EC, Koenig SP, Yeo Y, Ziletti A, Carvalho A, Campbell DK, Coker DF, Watanabe K, Taniguchi T, Castro Neto AH, Özyilmaz B. Transport properties of pristine few-layer black phosphorus by van der Waals passivation in an inert atmosphere. Nat Commun. 2015 Apr 10; 6:6647. PMID: 25858614.

Ziletti A, Carvalho A, Campbell DK, Coker DF, Castro Neto AH. Oxygen defects in phosphorene. Phys Rev Lett. 2015 Jan 30; 114(4):046801. PMID: 25679901.

Huo P, Miller TF, Coker DF. Communication: Predictive partial linearized path integral simulation of condensed phase electron transfer dynamics. J Chem Phys. 2013 Oct 21; 139(15):151103. PMID: 24160492.

Rivera E, Montemayor D, Masia M, Coker DF. Influence of site-dependent pigment-protein interactions on excitation energy transfer in photosynthetic light harvesting. J Phys Chem B. 2013 May 9; 117(18):5510-21. PMID: 23597258.

Huo P, Coker DF. Consistent schemes for non-adiabatic dynamics derived from partial linearized density matrix propagation. J Chem Phys. 2012 Dec 14; 137(22):22A535. PMID: 23249072.

Huo P, Coker DF. Influence of environment induced correlated fluctuations in electronic coupling on coherent excitation energy transfer dynamics in model photosynthetic systems. J Chem Phys. 2012 Mar 21; 136(11):115102. PMID: 22443796.

Huo P, Coker DF. Iterative linearized density matrix propagation for modeling coherent excitation energy transfer in photosynthetic light harvesting. J Chem Phys. 2010 Nov 14; 133(18):184108. PMID: 21073214.

Peng J, Castonguay TC, Coker DF, Ziegler LD. Ultrafast H2 and D2 rotational Raman responses in near critical CO2: an experimental and theoretical study of anisotropic solvation dynamics. J Chem Phys. 2009 Aug 7; 131(5):054501. PMID: 19673568.

Ma Z, Coker DF. Quantum initial condition sampling for linearized density matrix dynamics: Vibrational pure dephasing of iodine in krypton matrices. J Chem Phys. 2008 Jun 28; 128(24):244108. PMID: 18601318.

Bonella S, Coker DF. LAND-map, a linearized approach to nonadiabatic dynamics using the mapping formalism. J Chem Phys. 2005 May 15; 122(19):194102. PMID: 16161558.

Causo MS, Ciccotti G, Montemayor D, Bonella S, Coker DF. An adiabatic linearized path integral approach for quantum time correlation functions: electronic transport in metal-molten salt solutions. J Phys Chem B. 2005 Apr 14; 109(14):6855-65. PMID: 16851772.

Bonella S, Montemayor D, Coker DF. Linearized path integral approach for calculating nonadiabatic time correlation functions. Proc Natl Acad Sci U S A. 2005 May 10; 102(19):6715-9. PMID: 15809429.