Benchmarking Quantum Chemistry Methods in Calculations of Electronic Excitations

Bella L. Grigorenko, Vladimir A. Mironov, Igor V. Polyakov, Alexander V. Nemukhin

Abstract


Quantum chemistry methods are applied to obtain numerical solutions of the Schr¨odinger equation for molecular systems. Calculations of transitions between electronic states of large molecules present one of the greatest challenges in this field which require the use of supercomputer resources. In this work we describe the results of benchmark calculations of electronic excitation in the protein domains which were designed to engineer novel fluorescent markers operating in the near-infrared region. We demonstrate that such complex systems can be efficiently modeled with the hybrid qunatum mechanics/molecular mechanics approach (QM/MM) using the modern supercomputers. More specifically, the time-dependent density functional theory (TD-DFT) method was primarily tested with respect to its performance and accuracy. GAMESS (US) and NWChem software were benchmarked in direct and storage-based TDDFT calculations with the hybrid B3LYP density functional, both showing good scaling up to 32 nodes. We note that conventional SCF calculations greatly outperform direct SCF calculations for our test system. Accuracy of TD-DFT excitation energies was estimated by a comparison to the more accurate ab initio XMCQDPT2 method.


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References


Polyakov, I.V., Grigorenko, B.L., Mironov, V.A., Nemukhin, A.V.: Modeling structure and excitation of biliverdin-binding domains in infrared fluorescent proteins. Chemical Physics Letters (2018), DOI: 10.1016/j.cplett.2018.08.068

Chernov, K.G., Redchuk, T.A., Omelina, E.S., Verkhusha, V.V.: Near-infrared fluorescent proteins, biosensors, and optogenetic tools engineered from phytochromes. Chemical Reviews 117(9), 6423–6446 (2017), DOI: 10.1021/acs.chemrev.6b00700

Sadovnichy, V., Tikhonravov, A., Voevodin, V., Opanasenko, V.: “Lomonosov”: Supercomputing at Moscow State University. In: Vetter, J.S. (ed.) Contemporary High Performance Computing: From Petascale toward Exascale, pp. 283–307. Chapman & Hall/CRC Computational Science, Chapman & Hall/CRC, Boca Raton, United States (2013)

Gordon, M.S., Schmidt, M.W.: Advances in electronic structure theory: GAMESS a decade later. In: Dykstra, C., Frenking, G., Kim, K., Scuseria, G. (eds.) Theory and Applications of Computational Chemistry: The First Forty Years, pp. 1167–1189. Elsevier, Amsterdam (2005), DOI: 10.1016/B978-044451719-7/50084-6

Valiev, M., Bylaska, E., Govind, N., Kowalski, K., Straatsma, T., Van Dam, H., Wang, D., Nieplocha, J., Apra, E., Windus, T., de Jong, W.: NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations. Computer Physics Communications 181(9), 1477–1489 (2010), DOI: 10.1016/j.cpc.2010.04.018

Becke, A.D.: Density-functional exchange-energy approximation with correct asymptotic behavior. Physical Review A 38(6), 3098–3100 (1988), DOI: 10.1103/PhysRevA.38.3098

Schmidt, M.W., Baldridge, K.K., Boatz, J.A., Elbert, S.T., Gordon, M.S., Jensen, J.H., Koseki, S., Matsunaga, N., Nguyen, K.A., Su, S., Windus, T.L., Dupuis, M., Montgomery, J.A.: General atomic and molecular electronic structure system. Journal of Computational Chemistry 14(11), 1347–1363 (1993), DOI: 10.1002/jcc.540141112




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