Theoretical Studies of Molecular Spectroscopy in Simple Liquids and Complex Environments

The combination of quantum mechanics (QM) with molecular modeling (MM) is a powerful tool for studies of molecules and biomolecules [1] in simple and complex environments. This accomplishes the study of solvent effects in molecular spectroscopy and reactivity as well as the effect of a protein environment or a supercritical fluid. This is generally called QM/MM method, because both classical and quantum methodologies are employed. In fact the simulations can be performed both at the classical (e.g. Monte Carlo or Molecular Dynamics) or quantum levels (e.g. Born-Oppenheimer Molecular Dynamics). Further progress may demand inclusion of structural relaxation or even study of molecular reaction in a solvent environment. We have recently combined the Free Energy Gradient (FEG) [2] with the potential provided by the average solvent electrostatic configuration (ASEC) [3] for obtaining an efficient method for free energy calculations [4]. This ASEC-FEG method will be presented and some simple applications will be shown both for ground state geometry changes [4] induced by a solvent as well as the relaxation of excited states [5] promoting deactivation mechanisms [6] and fluorescence decay [7,8]. Finally, Free Energy ASEC-FEG calculations with van der Waals interactions are used to i) perform isomerization [9] of retinal chromophore and ii) in addition, the absorption maxima wavelengths [10] of retinal chromophore covalently bound to rhodopsin-like protein cavity. 

References:

[1] S. Canuto, Ed., Solvation Effects on Molecules and Biomolecules. Computational Methods and Applications. Springer (2008).

[2] N. Okuyama-Yoshida,K. Kataoka, M. Nagaoka, T. Yamabe, J. Chem. Phys. 113, 3519 (2000). 

[3] K. Coutinho, H. C. Georg, T. L. Fonseca, V. Ludwig, S. Canuto, Chem. Phys. Lett. 437, 148 (2007).

[4] H. C. Georg, S. Canuto, J. Phys. Chem. B 116, 11247 (2012).

[5] C. Bistafa, H. C. Georg, S. Canuto, Comp. and Theoret. Chem,, 1040-1041, 312 (2014).

[6] Y. Orozco-Gonzalez, C. Bistafa, S. Canuto, J. Phys. Chem. A 117, 4404 (2013).

[7] Y. Orozco-Gonzalez, K. Coutinho, J. Peón, S. Canuto, J. Chem. Phys. 137, 054307 (2012).

[8] C. Vechi- Suplicy, Y. Orozco-Gonzalez, M. Teresa Lamy, S. Canuto, K. Coutinho, J. Chem. Phys., 153, 244104 (2020)

[9]  D. M. Nikolaev, et al. , J. Chem. Theory and Comp. (2021), in press: https://doi.org/10.1021/acs.jctc.1c00221   

[10] Y. Orozco-Gonzalez et al. , J. Chem. Theory and Comp. 13, 6391 (2017).