Modeling Dynamic Conformations of Organic Molecules: Alkyne Carotenoids in Solution

0525260 - MBÚ 2021 RIV US eng J - Journal Article
Streckaite, S. - Macernis, M. - Li, F. - Kuthanová Trsková, Eliška - Litvín, Radek - Yang, Ch. - Pascal, A.A. - Valkunas, L. - Robert, B. - Llansola-Portoles, M.J.
Modeling Dynamic Conformations of Organic Molecules: Alkyne Carotenoids in Solution.
Journal of Physical Chemistry A. Roč. 124, č. 14 (2020), s. 2792-2801. ISSN 1089-5639. E-ISSN 1520-5215
R&D Projects: GA MŠMT(CZ) LO1416; GA ČR(CZ) GA19-11494S
Institutional support: RVO:61388971 ; RVO:60077344
Keywords : density-functional theory * light-harvesting complex * resonance raman-spectra
OECD category: Plant sciences, botany; Physical chemistry (BC-A)
Impact factor: 2.781, year: 2020
Method of publishing: Limited access
https://pubs.acs.org/doi/abs/10.1021/acs.jpca.9b11536

Calculating the spectroscopic properties of complex conjugated organic molecules in their relaxed state is far from simple. An additional complexity arises for flexible molecules in solution, where the rotational energy barriers are low enough so that nonminimum conformations may become dynamically populated. These metastable conformations quickly relax during the minimization procedures preliminary to density functional theory calculations, and so accounting for their contribution to the experimentally observed properties is problematic. We describe a strategy for stabilizing these nonminimum conformations in silico, allowing their properties to be calculated. Diadinoxanthin and alloxanthin present atypical vibrational properties in solution, indicating the presence of several conformations. Performing energy calculations in vacuo and polarizable continuum model calculations in different solvents, we found three different conformations with values for the delta dihedral angle of the end ring ca. 0, 180, and 90 degrees with respect to the plane of the conjugated chain. The latter conformation, a nonglobal minimum, is not stable during the minimization necessary for modeling its spectroscopic properties. To circumvent this classical problem, we used a Car-Parinello MD supermolecular approach, in which diadinoxanthin was solvated by water molecules so that metastable conformations were stabilized by hydrogen-bonding interactions. We progressively removed the number of solvating waters to find the minimum required for this stabilization. This strategy represents the first modeling of a carotenoid in a distorted conformation and provides an accurate interpretation of the experimental data.
Permanent Link: http://hdl.handle.net/11104/0309443