ОПИСАНИЯ МЕЖМОЛЕКУЛЯРНЫХ ВЗАИМОДЕЙСТВИЙ В ДИМЕРАХ (CH4)2, CH4NE, NE2

Проведено сравнительное неэмпирическое исследование межмолекулярных взаимодействий в димерах метан-метан, неон-неон, метан-неон, определенных методом связанных кластеров с учетом одно- и двукратных возбуждений и неитерационной поправки на трехкратные возбуждения (CCSD(T)) с базисными наборами Даннинга, дополненными связевыми функциями, а также явно коррелированным вариантом связанных кластеров (F12-CCSD(T)). Показано, что  усредненная сферически парная электронная плотность, построенная методом связанных кластеров, в случае димера метана имеет минимум, находящийся в его геометрическом центре, только когда используется набор связевых функций, локализованных в этой области. Такой результат обосновывает учет межмолекулярной электронной корреляции для базисных наборов волновых функций, дополненных связевыми функциями. Анализ построенных сечений поверхности потенциальной энергии (ППЭ) позволил провести калибровку набора связевых функций, а также уточнить энергию взаимодействия в димере неона

1. Hobza P., Šponer, J. Toward True DNA Base-Stacking Energies: MP2, CCSD(T), and Complete Basis Set Calculations // Journal of the American Chemical Society, 2002. V.124. Р. 11802–11808. doi: 10.1021/ja026759n.

2. Danilov V.I., Anisimov V.M., Kurita N., Hovorun D. MP2 and DFT studies of the DNA rare base pairs: The molecular mechanism of the spontaneous substitution mutations conditioned by tautomerism of bases // Chemical Physics Letters, 2005. V. 412. P. 285–293. doi: 10.1016/j.cplett.2005.06.123.

3. Chung G., Oh H., Lee D. Tautomerism and isomerism of guanine–cytosine DNA base pair: Ab initio and density functional theory approaches // Journal of Molecular Structure: THEOCHEM, 2005. V. 730. P. 241–249. doi: 10.1016/j.theochem.2005.05.040.

4. Yildirim I., Turner D.H. RNA Challenges for Computational Chemists // Biochemistry, 2005. V. 44. P. 13225–13234. doi: 10.1021/bi051236o.

5. Cysewski P., Czyżnikowska-Balcerak Ż. The MP2 quantum chemistry study on the local minima of guanine stacked with all four nucleic acid bases in conformations corresponding to mean B-DNA // Journal of Molecular Structure: THEOCHEM, 2005. V.757. P.29–36. doi: 10.1016/j.theochem.2005.06.014

6. Jurečka P., Šponer J., Černy J., Hobra P. Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs //Physical Chemistry Chemical Physics, 2006. V.8. P.1985–1993. doi: 10.1039/B600027D

7. Priyakumar U.D., MacKerell A.D. Base Flipping in a GCGC Containing DNA Dodecamer: A Comparative Study of the Performance of the Nucleic Acid Force Fields, CHARMM, AMBER, and BMS // Journal of Chemical Theory and Computation, 2006. V.2. P.187–200. doi: 10.1021/ct0501957

8. Langner K.M., Kedzierski P., Sokalski W.A., Leszczynski J. Physical Nature of Ethidium and Proflavine Interactions with Nucleic Acid Bases in the Intercalation Plane //Journal of Physical Chemistry B, 2006. V. 110. № 19. P. 9720–9727. doi: 10.1021/jp056836b

9. Haley T.P., Graybill E.R., Cybulski S.M. Ab Initio Calc. Dispers. Coefficients Nucleic Acid Base Pairs // Journal of Chemical Physics, 2006. V. 124. № 204301. P. 1–7 doi: 10.1063/1.2197832

10. Fukuzawa K., Komeiji Y., Mochizuki Y., Kato A., Nakano T., Tanaka S. Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab Initio Fragm. Mol. Orbital Study // Journal of Computational Chemistry, 2006. V. 27. P. 948–960. doi: 10.1002/jcc.20399

11. Cauët E., Lièvin J. Radical Cations of the Nucleic Bases and Radiation Damage to DNA: Ab Initio Study // Advances in Quantum Chemistry, 2007. V.52. P. 121–147. doi: 10.1016/S0065-3276(06)52006-

12. Šponer J., Riley K.E., Hobza P. Nature and magnitude of aromatic stacking of nucleic acid bases // Physical Chemistry Chemical Physics, 2008. V. 10. P. 2595–2610. doi: 10.1039/B719370J

13. Rutledge L.R., Campbell-Verduyn L.S., Hunter K.C., Wetmore S.D. Characterization of Nucleobase-Amino Acid Stacking Interactions Utilized by a DNA Repair Enzyme // Journal of Physical Chemistry B, 2006. V. 110. P. 19652–19663. doi: 10.1021/jp061939v

14. Rutledge L.R., Durst H.F., Wetmore S.D. Evidence for Stabilization of DNA/RNA-Protein Complexes Arising from Nucleobase-Amino Acid Stacking and T-Shaped Interactions // Journal of Chemical Theory and Computation, 2009. V. 5. P. 1400–1410. doi: 10.1021/ct800567q

15. Butchosa C., Simon S., Voityuk A.A. Conformational dependence of the electronic coupling for hole transfer between adenine and tryptophan // Computational and Theoretical Chemistry, 2011. V. 975. P. 38–41. doi: 10.1016/j.comptc.2011.04.025

16. Šponer J., Šponer J.E., Petrov A.I., Leontis N.B. Quantum Chemical Studies of Nucleic Acids: Can We Construct a Bridge to the RNA Structural Biology and Bioinformatics Communities? // Journal of Physical Chemistry B, 2010. V. 114. P. 15723–15741. doi: 10.1021/jp104361m

17. Parrish R.M., Sherrill C.D. Spatial assignment of symmetry adapted perturbation theory interaction energy components: The atomic SAPT partition // Journal of Chemical Physics, 2014. V. 141. № 044115. P.1–21. doi: 10.1063/1.4889855

18. Ballesteros F., Dunivan S., Lao K.U. Coupled cluster benchmarks of large noncovalent complexes: The L7 dataset as well as DNA–ellipticine and buckycatcher-fullerene // Journal of Chemical Physics, 2021. V. 154 № 154104. P. 1–12. doi: 10.1063/5.0042906

19. Kříž K., Řezáč J. Benchmarking of Semiempirical Quantum-Mechanical Methods on Systems Relevant to Computer-Aided Drug ˇ Design // Journal of Chemical Information and Modeling, 2020. V. 60. P. 1453–1460. doi: 10.1021/acs.jcim.9b01171

20. Morawietz T., Artrith N. Machine learning-accelerated quantum mechanics-based atomistic simulations for industrial applications // Journal of Computer-Aided Molecular Design, 2021. V. 35. P. 557–586. doi: 10.1007/s10822-020-00346-6

21. Villar R., Gil M.J., García J.I., Martínez-Merino, V. Are AM1 ligand-protein binding enthalpies good enough for use in the rational design of new drugs? // Journal of Computational Chemistry, 2005. V. 26. P. 1347–1358. doi: 10.1002/jcc.20276

22. Li A.H.-T., Chao S.D. Interaction energies of dispersion-bound methane dimer from coupled cluster method at complete basis set // Journal of Molecular Structure: THEOCHEM , V.897. 2009. P. 90. doi: 10.1016/j.theochem.2008.11.026

23. Cybulski S.M., Toczylowski R.R. Ground state potential energy curves for He2, Ne2, Ar2, He–Ne, He–Ar, and Ne–Ar: A coupled-cluster study // Journal of Chemical Physics, 1999. V.111. P.10520 – 10528. doi: 10.1063/1.480430

24. Burcl R., Chałasiński G., Bukowski R., Szczȩśniak M.M. On the role of bond functions in interaction energy calculations: Ar· · ·HCl, Ar· · ·H2O, (HF)2 // Journal of Chemical Physics, 1995. V. 103. Iss. 4. P. 1–11. doi: 10.1063/1.469771

25. Chałasiński G., Szczȩśniak M.M. State of the Art and Challenges of the ab Initio Theory of Intermolecular Interactions // Chemical Reviews, 2000. V.100. №11. P.4227–4252. doi: 10.1021/cr990048z

26. Tao F.-M., Pan Y.-K. Møller-Plesset perturbation investigation of the He2 potential and the role of midbond basis functions // Journal of Chemical Physics, 1992. V.97. P.4989–4995. doi: 10.1063/1.463852

27. Rutskoy B.V., Bezrukov D.S. Ab Initio Description of the Structure and Interaction Energy of Perhalomethane Dimers // Russian Journal of Physical Chemistry A, 2019. V.93. P.1519–1524. doi: 10.1134/S0036024419080259

28. Rutskoy B.V., Ozerov G.K., Bezrukov D.S. The Role of Bond Functions in Describing Intermolecular Electron Correlation for Van der Waals Dimers: A Study of (CH4)2 and Ne2 // International Journal of Molecular Sciences, 2024. V.25. №3. P.1472. doi: 10.3390/ijms25031472

29. Baerends E.J., Gritsenko O.V. A Quantum Chemical View of Density Functional Theory. // Journal of Physical Chemistry A , 1997. V. 101. P. 5383 – 5403. doi: 10.1021/jp9703768

30. Kong L., Bischoff F., Valeev E.F. Explicitly Correlated R12/F12 Methods for Electronic Structure // Chemical Reviews, 2011. V. 112. P. 75 – 107. doi: 10.1021/cr200204r

31. Pan X.-Y., Sahnia V. Integral coalescence conditions in D ⩾ 2 dimension space // Journal of Chemical Physics, 2003. V. 119. P. 7083–7086. doi: 10.1063/1.1605933

32. Gauss J., Stanton J.F., Bartlett R.J. Coupled-cluster open-shell analytic gradients: Implementation of the direct product decomposition approach in energy gradient calculations // Journal of Chemical Physics, 1991. V. 95. P.2623–2638. doi: 10.1063/1.460915

33. Stanton J.F., Gauss J., Watts J.D., Bartlett R.J. A direct product decomposition approach for symmetry exploitation in many-body methods. I. Energy calculations // Journal of Chemical Physics, 1991. V 94. P. 4334–4345. doi: 10.1063/1.460620

34. Fitzgerald G., Harrison R.J., Bartlett R.J. Analytic energy gradients for general coupled-cluster methods and fourth-order many-body perturbation theory // Journal of Chemical Physics, 1986. V. 85. P. 5143–5150. doi: 10.1063/1.451823

35. Scheiner A.C., Scuseria G.E., Rice J.E., Lee, T.J., Schaefer H.F. Analytic evaluation of energy gradients for the single and double excitation coupled cluster (CCSD) wave function: Theory and application // Journal of Chemical Physics, 1987. V. 87. P. 5361–5373. doi: 10.1063/1.453655

36. Fitzgerald G., Harrison R., Laidig W.D., Bartlett R.J. Analytic energy gradients for general coupled-cluster methods and fourth-order many-body perturbation theory // Chemical Physics Letters, 1985. V. 117. P. 433–436. doi: 10.1063/1.451823

37. Salter E.A., Trucks G.W., Bartlett R.J. Analytic energy derivatives in many- body methods. I. First derivatives // Journal of Chemical Physics, 1989. V. 90. P. 1752–1766. doi: 10.1063/1.456069

38. Gauss J., Stanton J.F. Analytic gradients for the coupled-cluster singles, doubles, and triples (CCSDT) model //Journal of Chemical Physics, 2002. V.116. P.1773–1782. doi: 10.1063/1.1429244

39. Taube A.G., Bartlett R.J. Improving upon CCSD(T): ΛCCSD(T). I. Potential energy surfaces // Journal of Chemical Physics, 2008. V. 128. P. 1–13. doi: 10.1063/1.2830236

40. Jørgensen P., Helgaker T. Møller-Plesset energy derivatives // Journal of Chemical Physics, 1988. V. 89. P. 1560–1570. doi: 10.1063/1.455152

41. Helgaker T., Jørgensen P. Analytical Calculation of Geometrical Derivatives in Molecular Electronic Structure Theory // Advances in Quantum Chemistry, 1988. V. 19. P. 183–245. doi: 10.1016/S0065-3276(08)60616-4

42. Gauss J., Stanton J.F. Coupled-cluster calculations of nuclear magnetic resonance chemical shifts // Journal of Chemical Physics, 1995. V.103. P. 3561–3577. doi: 10.1063/1.470240

43. Gauss J., Stanton J.F., Bartlett R.J. Analytic evaluation of energy gradients at the coupled-cluster singles and doubles level using quasi-restricted Hartree-Fock open-shell reference functions // Journal of Chemical Physics, 1991. V. 95. P. 2639–2645. doi: 10.1063/1.460916

44. Lebedev V.I. Quadratures on the sphere // USSR Computational Mathematics and Mathematical Physics,1976. V.16. P.10–24. doi: 10.1016/0041-5553(76)90100-2

45. Lebedev V.I. Spherical quadrature formulas exact to orders 25-29 // Siberian Mathematical Journal, 1977. V. 18. P. 99–107. doi: 10.1007/bf00966954

46. Werner H.-J., Knowles P.J., Knizia G., Manby F.R., etc. MOLPRO, Version 2015.1, a Package of Ab Initio Programs, 2015. [Электронный ресурс]. URL: http://www.molpro.net. [дата обращения 23.09.2024].

47. Saad Y., Schultz M.H. GMRES: A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear Systems // SIAM Journal on Scientific Computing.1986. V.7. P. 856–869. doi: 10.1137/0907058

48. Yang C., Brabec J., Veis L., Williams-Young, D.B., Kowalski K. Solving Coupled Cluster Equations by the Newton Krylov Method //Theoretical and Computational Chemistry, 2020. V.7. P. 856–869. doi: 10.3389/fchem.2020.590184

49. Pulay P. Convergence acceleration of iterative sequences. the case of SCF iteration // Chemical Physics Letters, 1980. V.73. P. 393–398. doi: 10.1016/0009-2614(80)80396-4

50. Scuseria G.E., Lee T.J., Schaefer H.F. Accelerating the convergence of the coupled-cluster approach //Chemical Physics Letters., 1986. V.130. P.236–239. doi:10.1016/0009-2614(86)80461-4

51. Ito T., Hayami K. Preconditioned GMRES methods for least squares problems // Japan Journal of Industrial and Applied Mathematics, 2008. V. 25. P. 185–207. doi: 10.1007/BF03167519

52. Halkier A., Helgaker T., Jorgensen P., Klopper W., Koch H., Olsen J., Wilson A.K. Basis-set convergence in correlated calculations on Ne, N2, and H2O // Chemical Physics Letters, 1998 V. 286. P. 243 – 252. doi: 10.1016/S0009-2614(98)00111-0

53. Woon D.A., Dunning T.H. Gaussian basis sets for use in correlated molecular calculations. IV. Calculation of static electrical response properties // Journal of Chemical Physics, 1994 V. 100. P. 2975 – 2988. doi: 10.1063/1.466439

54. Van Mourik T.V., Wilson A.K., Dunning T.H. Benchmark Calculations with Correlated Molecular Wavefunctions. XIII. Potential Energy Curves for He2, Ne2 and Ar2 using Correlation Consistent Basis Sets through Augmented Sextuple Zeta // Molecular Physics, 1999. V. 96 P. 529-547. doi: 10.1080/00268979909482990