VeloxChem: Complex Polarisation Propagator Simulations of Circular Dichroism Spectra on GPUs

Theoretical studies of microscopic structures and chemical and physical processes in molecular systems provide valuable insight into the understanding of macroscopic functions by relating the molecular and electronic structures to properties and observables. Among the theoretical methods for performing such simulations, time- dependent density functional theory (TDDFT) is perhaps the most impactful due to its ability to study large, complex systems with manageable computational cost. However, in systems with multiple interacting chromophores (parts of molecules within a compound that absorb some frequencies of light and hence make the compound appear coloured), TDDFT calculations remain challenging due to the requirement of simulating a large quantum mechanical (QM) region and the difficulty of tackling the many systems within that region that are close to each other and also in excited states.

The complex polarization propagator (CPP) formulation of response theory provides an alternative approach for studying a discretised frequency window of interest within the spectrum of light that is being emitted by the systems that are under investigation. The convergence of CPP can also be made robust and efficient by solving many response equations simultaneously. Based on recent developments in the VeloxChem quantum chemistry program (for calculating molecular properties and simulating a variety of spectroscopies), we have implemented real and complex linear responses where GPU-accelerated CPP calculations are realised by efficient evaluation of symmetric and antisymmetric auxiliary Fock matrices. The details of the implementation are summarised and documented in our preprint on ChemRxiv [1].

As an example, we carried out CPP calculations for the electronic circular dichroism spectrum of a G-quadruplex. We used three models of different sizes, and the largest model includes the whole G-quadruplex and surrounding water molecules as the QM region, plus an additional layer of water molecules as the molecular mechanical (MM) region, as shown in the figure above. All three models present clear bisignated signal characteristics of the G-quadruplex (see graph below); however, only the largest model reproduced the experimentally observed small negative band in the long-wavelength region. Our analysis of individual orbital excitations suggests that the negative band can be ascribed, at least partially, to transitions centred on the thymine nucleotides as well as the presence of potassium ions [1].

References

1. X. Li, M. Linares, P. Norman, “VeloxChem: GPU-accelerated Fock matrix construction enabling complex polarization propagator simulations of circular dichroism spectra of G-quadruplexes”. ChemRxiv. (2024) doi.org/10.26434/chemrxiv-2024-rk6w2
2. J. Kypr, I. Kejnovska, D. Renciuk, M. Vorlickova, “Circular dichroism and conformational polymorphism of DNA”. Nucleic Acids Res. (2009) 37, 1713–1725.