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VeloxChem: GPU-Accelerated Fock Matrix Construction Enabling Complex Polarization Propagator Simulations of Circular Dichroism Spectra of G-Quadruplexes
KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.ORCID iD: 0000-0001-6508-8355
KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.ORCID iD: 0000-0002-9720-5429
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.ORCID iD: 0000-0002-1191-4954
2025 (English)In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 129, no 2, p. 633-642Article in journal (Refereed) Published
Abstract [en]

An automatic code generated C++/HIP/CUDA implementation of the (auxiliary) Fock, or Kohn-Sham, matrix construction for execution in GPU-accelerated hardware environments is presented. The module is developed as part of the quantum chemistry software package VeloxChem, employing localized Gaussian atomic orbitals. The performance and scaling characteristics are analyzed in view of the specific requirements for self-consistent field optimization and response theory calculations. As an example, the electronic circular dichroism spectrum of a G-quadruplex is calculated at the level of time-dependent density functional theory in conjunction with the range-separated CAM-B3LYP exchange-correlation functional. Computational issues due to the high-density of states following the adoption of large-scale model systems are here bypassed with use of the complex polarization propagator approach. The origin of the negative Cotton effect in the long-wavelength onset of the experimental spectrum is elucidated in large-scale modeling and shown to be associated with the TTA nucleobase linkers in the G-quadruplex.

Place, publisher, year, edition, pages
American Chemical Society (ACS) , 2025. Vol. 129, no 2, p. 633-642
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-359305DOI: 10.1021/acs.jpca.4c07510ISI: 001387038800001PubMedID: 39739694Scopus ID: 2-s2.0-85215269952OAI: oai:DiVA.org:kth-359305DiVA, id: diva2:1932632
Note

QC 20250130

Available from: 2025-01-29 Created: 2025-01-29 Last updated: 2025-01-30Bibliographically approved

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Li, XinLinares, MathieuNorman, Patrick

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