Applications of High Performance Computing: Born–Oppenheimer Molecular Dynamics of Complex Formation in Aqueous Solutions

Maria G. Khrenova, Dmitry P. Kapusta, Ilya V. Babchuk, Yulia I. Meteleshko

Abstract


The progress of supercomputer technologies initiated the development of methods of computational chemistry and their applications, particularly molecular dynamic simulations with ab initio potentials. These new methods allow to solve important problems of chemistry and technology. Particularly, solvent extraction and separation techniques are widely used to decrease the amount of radioactive wastes, especially radioactive caesium isotopes present in liquid phases. We demonstrated that the calculated binding constants between the alkali cation and calix[4]arene differ 103 times for Cs+ and Na+ ions, that is in good agreement with the experimental value. We report the results of benchmark calculations of our model system composed of 929 atoms described in the  density functional theory approximation with the GGA-type functional PBE with the empirical dispersion correction D3 and combined basis of Gaussian functions and plane waves DZVP with Goedecker-Teter-Hutter pseudopotentials. We demonstrate that efficiency of calculations decrease to about half if the amount of nodes is 16 on the Lomonosov-2 supercomputer.


Full Text:

PDF

References


Bernardino, R., Costa Cabral, B.: Complexation of calix[4]arene with alkali metal cations: Conformational binding selectivity and cation- driven inclusion. Supramolecular Chemistry 14(1), 57–66 (2002), DOI: 10.1080/10610270290006574

Chinta, J.P., Ramanujam, B., Rao, C.P.: Structural aspects of the metal ion complexes of the conjugates of calix[4]arene: Crystal atructures and computational models. Coordination Chemistry Reviews 256(23-24), 2762–2794 (2012), DOI: 10.1016/j.ccr.2012.09.001

Goedecker, S., Teter, M., Hutter, J.: Separable dual-space gaussian pseudopotentials. Physical Review B 54(3), 1703–1710 (1996), DOI: 10.1103/PhysRevB.54.1703

Gorshkov, V., Ivanov, V., Staina, I.: Selectivity of phenolformaldehyde resins and separation of rare alkali metals. Reactive and Functional Polymers 38(2), 157–176 (1998), DOI: 10.1016/S1381-5148(97)00165-X

Grimme, S., Antony, J., Ehrlich, S., Krieg, H.: A consistent and accurate ab initio parametrization of density functional dispersion correction (dft-d) for the 94 elements h-pu. The Journal of Chemical Physics 132(15), 154104 (2010), DOI: 10.1063/1.3382344

Guilbaud, P., Varnek, A., Wipff, G.: Molecular dynamics study of ptretbutylcalix[4]arenetetraamide and its complexes with neutral and cationic guests. influence of solvation on structures and stabilities. Journal of the American Chemical Society 115(18), 8298–8312 (1993), DOI: 10.1021/ja00071a044

Perdew, J.P., Burke, K., Ernzerhof, M.: Generalized gradient approximation made simple. Phys. Rev. Lett. 77, 3865–3868 (Oct 1996), DOI: 10.1103/PhysRevLett.77.3865

Sadovnichy, V., Tikhonravov, A., Voevodin, Vl., Opanasenko, V.: “Lomonosov”: Supercomputing at Moscow State University. In: Contemporary High Performance Computing: From Petascale toward Exascale, pp. 283–307 (2013)




Publishing Center of South Ural State University (454080, Lenin prospekt, 76, Chelyabinsk, Russia)