Nitrogen substituted phenothiazine derivatives: Modelling of molecular self-assembling

International Journal of Molecular Sciences

Volumn 12, Issue 5, 2011, Pages 3102-3116

  Bende, Attila ^a   Turcu, Ioan ^a  

^a NATIONAL INSTITUTE FOR RESEARCH AND DEVELOPMENT OF ISOTOPIC AND MOLECULAR TECHNOLOGIES   (Romania)

Author keywords

stacking; Dispersion effects; Intermolecular interaction; Local perturbation method; Nitrogen substituted phenothiazine

Indexed keywords

AZAPHENOTHIAZINE; DIAZAPHENOTHIAZINE; NITROGEN PHENOTHIAZINE DERIVATIVE; PHENOTHIAZINE DERIVATIVE; UNCLASSIFIED DRUG; NITROGEN; PHENOTHIAZINE;

ARTICLE; CHEMICAL ANALYSIS; CHEMICAL INTERACTION; CHEMICAL STRUCTURE; IONIC STRENGTH; MATHEMATICAL COMPUTING; MOLECULAR MODEL; PROCESS OPTIMIZATION; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION;

COMPUTER SIMULATION; MODELS, MOLECULAR; MOLECULAR CONFORMATION; NITROGEN; PHENOTHIAZINES;

EID: 79957797650     PISSN: None     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms12053102     Document Type: Article

References (44)

1. Hollingsworth, M.D. Crystal Engineering: from Structure to Function. Science 2002, 295, 2410-2413.
2. Leininger, S.; Olenyuk, B.; Stang, P.J. Self-Assembly of Discrete Cyclic Nanostructures Mediated by Transition Metals. Chem. Rev. 2000, 100, 853-908.
3. Venkataramanan, B.; Saifudin, M.-A.; Jagadese, V.J.; Suresh, V. Self-assembly of methacrylamides assisted by an interplay of N-H...O, C-H...O, C-H...π and π-π interactions. Cryst. Eng. Commun. 2004, 6, 284-289.
4. Colquhoun, H.M.; Zhu, Z.; Cardin, C.J.; Gan, Y.; Drew, M.G.B. Sterically Controlled Recognition of Macromolecular Sequence Information by Molecular Tweezers. J. Am. Chem. Soc. 2007, 129, 16163-16174.
5. Burley, S.K.; Petsko, G.A. Aromatic-aromatic interaction: A mechanism of protein structure stabilization. Science 1985, 229, 23-28.
6. Loakes, D. The applications of universal DNA base analogues. Nucleic Acids Res. 2001, 29, 2437-2447.
7. Rutledge, L.R.; Campbell-Verduyn, L.S.; Wetmore, S.D. Characterization of the stacking interactions between DNA or RNA nucleobases and the aromatic amino acids. Chem. Phys. Lett. 2007, 444, 167-175.
8. Hunter, C.A.; Sanders, K.M. The nature of π-π interactions. J. Am. Chem. Soc. 1990, 112, 5525-5534.
9. Járai-Szabó, F.; Aştilean, S.; Néda, Z. Understanding self-assembled nanosphere patterns. Chem. Phys. Lett. 2005, 408, 241-246.
10. Love, J.C.; Estroff, L.A.; Kriebel, J.K.; Nuzzo, R.G.; Witheside, G.M. Self-Assembled Monolayers of Thiolates on Metals as a Form of Nanotechnology. Chem. Rev. 2005, 105, 1103-1170.
11. Bende, A.; Grosu, I.; Turcu, I. Molecular modeling of phenothiazine derivatives: Self-assembling properties. J. Phys. Chem. A 2010, 114, 12479-12489.
12. Wang, W.; Hobza, P. Theoretical Study on the Complexes of Benzene with Isoelectronic Nitrogen-Containing Heterocycles. ChemPhysChem 2008, 9, 1003-1009.
13. Mignon, P.; Loverix, S.; Steyaert, J.; Geerlings, P. Influence of the π-π interaction on the hydrogen bonding capacity of stacked DNA/RNA bases. Nucl. Acid. Res. 2005, 33, 1779-1789.
14. Mignon, P.; Loverix, S.; de Proft, F.; Geerlings, P. Influence of Stacking on Hydrogen Bonding: Quantum Chemical Study on Pyridine-Benzene Model Complexes. J. Phys. Chem. A 2004, 108, 6038-6044.
15. Mishra, B.K.; Arey, J.S.; Sathyamurthy, N. Stacking and Spreading Interaction in N-Heteroaromatic Systems. J. Phys. Chem. A 2010, 114, 9606-9616.
16. Główka, M.L.; Martynowski, D.; Kozłowska, K. Stacking of six-membered aromatic rings in crystals. J. Mol. Struct. 1999, 474, 81-89.
17. Wheaton, C.A.; Dobrowolski, S.L.; Millen, A.L.; Wetmore, S.D. Nitrosubstituted aromatic molecules as universal nucleobases: Computational analysis of stacking interactions. Chem. Phys. Lett. 2006, 428, 157-166.
18. Pulay, P. Localizability of dynamic electron correlation. Chem. Phys. Lett. 1983, 100, 151-154.
19. Saebo, S.; Pulay, P. Local Treatment of Electron Correlation. Annu. Rev. Phys. Chem. 1993, 44, 213-236.
20. Hampel, C.; Werner, H.-J. Local treatment of electron correlation in coupled cluster theory. J. Chem. Phys. 1996, 104, 6286-6297.
21. Hetzer, G.; Schütz, M.; Stoll, H.; Werner, H.-J. Low-order scaling local correlation methods II: Splitting the Coulomb operator in linear scaling local second-order MøllerPlesset perturbation theory. J. Chem. Phys. 2000, 113, 9443-9455.
22. Schütz, M. Low-order scaling local electron correlation methods. III. Linear scaling local perturbative triples correction (T). J. Chem. Phys. 2000, 113, 9986-10001.
23. Schütz, M.; Werner, H.-J. Low-order scaling local electron correlation methods. IV. Linear scaling local coupled-cluster (LCCSD). J. Chem. Phys. 2001, 114, 661-681.
24. Vahtras, O.; Almlöf, J.; Feyereisen, M.W. Integral approximations for LCAO-SCF calculations. Chem. Phys. Lett. 1993, 213, 514-518.
25. Schütz, M.; Rauhut, G.; Werner, H.-J. Local Treatment of Electron Correlation in Molecular Clusters: Structures and Stabilities of (H2O)n, n = 2-4. J. Phys. Chem. A 1998, 102, 5997-6003.
26. Hill, J.G.; Platts, J.A.; Werner, H.-J. Calculation of intermolecular interactions in the benzene dimer using coupled-cluster and local electron correlation methods. Phys. Chem. Chem. Phys. 2006, 8, 4072-4078.
27. Grimme, S. Improved second-order Møller-Plesset perturbation theory by separate scaling of parallel and antiparallel-spin pair correlation energies. J. Chem. Phys. 2003, 118, 9095-10002.
28. Hill, J.G.; Platts, J.A. Spin-Component Scaling Methods for Weak and Stacking Interactions. J. Chem. Theory Comput. 2007, 3, 80-85.
29. Jurečka, P.; Šponer, J.; Černý, J.; Hobza, 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. Phys. Chem. Chem. Phys. 2006, 8, 1985-1993.
30. Distasio, R.A., Jr.; Head-Gordon, M. Optimized spin-component scaled second-order Møller-Plesset perturbation theory for intermolecular interaction energies. Mol. Phys. 2007, 105, 1073-1083.
31. Grimme, S. Semiempiricall GGA-type density functional constructed with a long-range dispersion correction. J. Comput. Chem. 2006, 27, 1787-1799.
32. Elstner, M.; Porezag, D.; Jungnickel, G.; Elsner, J.; Haugk, M.; Frauenheim, T.; Suhai, S.; Seifert, G. Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties. Phys. Rev. B 1998, 58, 7260-7268.
33. Elstner, M.; Jalkanen, K.J.; Knapp-Mohammady, M.; Frauenheim, T.; Suhai, S. DFT studies on helix formation in N-acetyl-(L-alanyl)n-N'-methylamide for n = 1-20. Chem. Phys. 2000, 256, 15-27.
34. Elstner, M.; Jalkanen, K.J.; Knapp-Mohammady, M.; Frauenheim, T.; Suhai, S. Energetics and structure of glycine and alanine based model peptides: Approximate SCC-DFTB, AM1 and PM3 methods in comparison with DFT, HF and MP2 calculations. Chem. Phys. 2001, 263, 203-219.
35. Elstner, M.; Hobza, P.; Frauenheim, T.; Suhai, S.; Kaxiras, E. Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment. J. Chem. Phys. 2001, 114, 5149-5155.
36. Liu, H.Y.; Elstner, M.; Kaxiras, E.; Frauenheim, T.; Hermans, J.; Yang, W.T. Quantum mechanics simulation of protein dynamics on long timescale. Proteins: Struct. Funct., Bioinf. 2001, 44, 484-489.
37. Kubař, T.; Jurečka, P.; Černý, J.; Řezáč, J.; Otyepka, M.; Valdés, H.; Hobza, P. Density-Functional, Density-Functional Tight-Binding, and Wave Function Calculations on Biomolecular Systems. J. Phys. Chem. A 2007, 111, 5642-5647.
38. Werner, H.-J.; Knowles, P.J.; Lindh, R.; Manby, F.R.; Schütz, M.; Celani, P.; Korona, T.; Mitrushenkov, A.; Rauhut, G.; Adler, T.B.; et al. MOLPRO, a Package of ab initio Programs, version 2009.1. Available online: http://www.molpro.net (accessed on 11 May 2011).
39. Dunning, T.H., Jr. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J. Chem. Phys. 1989, 90, 1007-1023.
40. Kendall, R.A.; Dunning, T.H., Jr.; Harrison, R.J. Electron affinities of the first-row atoms revisited. Systematic basis sets and wave functions. J. Chem. Phys. 1992, 96, 6796-6806.
41. Pipek, J.; Mezey, P.G. A fast intrinsic localization procedure applicable for ab initio and semiempirical linear combination of atomic orbital wave functions. J. Chem. Phys. 1989, 90, 4916-4926.
42. Allouche, A.R. Gabedit-A graphical user interface for computational chemistry softwares. J. Comput. Chem. 2010, 32, 174-182.
43. Korth, M.; Pitoňák, M.; Řezáč, J.; Hobza, P. A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods. J. Chem. Theory Comput. 2010, 6, 344-352.
44. Allinger, N.L.; Lii, J.-H. Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals' potentials and crystal data for aliphatic and aromatic hydrocarbons. J. Am. Chem. Soc. 1989, 111, 8576-8582.