Molecular properties investigation of a substituted aromatic mannich base: Dynamic and static models

Journal of Chemical Information and Modeling

Volumn 47, Issue 3, 2007, Pages 818-831

  Jezierska, Aneta ^a   Panek, Jarosław J ^a   Filarowski, Aleksander ^a  

^a UNIVERSITY OF WROC AW   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; ELECTRIC DIPOLE MOMENTS; FOURIER TRANSFORMS; HYDROGEN BONDS; INFRARED SPECTROGRAPHS; POTENTIAL ENERGY;

CAR-PARRINELLO MOLECULAR DYNAMICS; ELECTRON DENSITY TOPOLOGY; VIBRATIONAL SCHROEDINGER EQUATION;

AROMATIC COMPOUNDS;

EID: 34250865702     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci600490s     Document Type: Article

References (82)

1. Freddolino, P. L.; Arkhipov, A. S.; Larson, S. B.; McPherson, A.; Schulten, K. Molecular Dynamics Simulations of the Complete Satellite Tobacco Mosaic Virus. Structure 2006, 14, 437-449.
2. Warshel, A. Computer Modeling of Chemical Reactions in Enzymes and Solutions; John Wiley and Sons, Inc.: New York, 1991; p 109.
3. 2. In Quantum Mechanical Simulation Methods For Studying Biological Systems, 1st ed.; Bicout, D., Field, M., Eds.; Springer-Verlag: Berlin, Germany, 1996; pp 119-156.
4. Schäfer, H.: Mark, A. E.; van Gunstern, W. F. Absolute Entropies from Molecular Dynamics Simulation Trajectories. J. Chem. Phys. 2000, 113, 7809-7817.
5. White, R. P.; Meirovitch, H. A Simulation Method for Calculating the Absolute Entropy and Free Energy of Fluids: Application to Liquid Argon and Water. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 9235-9240.
6. Mu, Y.; Stock, G. Conformational Dynamics of Trialanine in Water: A Molecular Dynamics Study. J. Phys. Chem. B 2002, 106, 5294-5301.
7. Kubinyi, H. QSAR and 3D QSAR in Drug Design. Part 1: Methodology. Drug Discovery Today 1997, 2, 457-467.
8. Kubinyi, H. QSAR: Hansch Analysis and Related Approaches, 1st ed.; VCH: Weinheim, Germany, 1993; pp 57-68.
9. Gupta, S. P. QSAR and Molecular Modeling, 1st ed.; Springer-Verlag: London, U. K., 2006.
10. Devillers, J. No-Free-Lunch Molecular Descriptors in QSAR and QSPR. In Topological Indices and Related Descriptors in QSAR and QSPR, 1st ed.; Devillers, J., Balaban, A. T., Eds.; CRC Press: Boca Raton, FL, 2000; pp 1-20.
11. Benigni, R. SARs and QSARs of Mutagens and Carcinogens: Understanding Action Mechanisms and Improving Risk Assessment. In Quantitative Structure-Activity Relationship Models of Mutagens and Carcinogens; Benigni, R., Ed.; CRC Press: Boca Raton, FL, 2003; pp 259-282.
12. Goodsell, D. S.; Morris, G. M.; Olson, A. J. Automated Docking of Flexible Ligands: Applications of AutoDock. J. Mol. Recognit. 1996, 9, 1-5.
13. Rao, M. S.; Olson, A. J. Modelling of Factor Xa-Inhibitor Complexes: A Computational Flexible Docking Approach. Proteins 1999, 34, 173-183.
14. Walters, W. P.; Stahl, M. T.; Murcko, M. A. Virtual Screening - An Overview. Drug Discovery Today 1998, 3, 160-178.
15. Tonmunphean, S.; Kokpol, S.; Parasuk, V.; Wolschann, P.; Winger, R. H.; Liedl, K. R.; Rode, B. M. Comparative Molecular Field Analysis of Artemisinin Derivatives: Ab Initio versus Semiempirical Optimized Structures. J. Comput.-Aided Mol. Des. 1998, 12, 397-409.
16. Buolamwini, J. K.; Assefa, H. CoMFA and CoMSIA 3D QSAR and Docking Studies on Conformationally-Restrained Cinnamoyl HIV-1 Integrase Inhibitors: Exploration of a Binding Mode at the Active Site. J. Med. Chem. 2002, 45, 841-852.
17. Vidossich, P.; Cacsella, M.; Carloni, P. Dynamics and Energetics of Water Permeation through the Aquaporin Channel. Proteins: Struct., Funct., Bioinf. 2004, 56, 844-845.
18. Piana, S.; Bucher, D.; Carloni, P.; Rothlisberger, U. Reaction Mechanism of HIV-1 Protease by Hybrid Car-Parrinello/Classical MD Simulations. J. Phys. Chem. B 2004, 108, 11139-11150.
19. Gao, M.; Sotomayor, M.; Villa, E.; Lee, E.; Schulten, K. Molecular Mechanisms of Cellular Mechanics. Phys. Chem. Chem. Phys. 2006, 8, 3692-3702.
20. Maiti, A.; Sierka, M.; Andzelm, J.; Golab, J.; Sauer, J. Combined Quantum Mechanics: Interatomic Potential Function Investigation of Rac-Meso Configurational Stability and Rotational Transition in Zirconocene-Based Ziegler-Natta Catalysts. J. Phys. Chem. A 2000, 104, 10932-10938.
21. Deglmann, P.; Ahlrichs, R.; Tsereteli, K. Theoretical Studies of Ligand-Free Cadmium Selenide and Related Semiconductor Clusters. J. Chem. Phys. 2002, 116, 1585-1587.
22. 2 Superlattice. Appl. Phys. Lett. 2005, 88, 013102.
23. Häkkinen, H.; Barnett, R. N.; Scherbakov, A. G.; Landman, U. Nanowire Gold Chains: Formation Mechanisms and Conductance. J. Phys. Chem. B 2000, 104, 9063-9066.
24. Hod, O.; Baer, R.; Rabani, E. Feasible Nanometric Magnetoresistance Devices. J. Phys. Chem. B 2004, 108, 14807-14810.
25. Hod, O.; Baer, R.; Rabani, E. A Parallel Electromagnetic Molecular Logic Gate. J. Am. Chem. Soc. 2005, 127, 1648-1649.
26. Müller, A.; Ratajczak, H.; Junge, W.; Dieman, E.; Zundel, G. Electron and Proton Transfer in Chemistry and Biology; Elsevier: Amsterdam, The Netherlands, 1992.
27. Zundel, G. Proton Polarizability of Hydrogen Bonds: Infrared Methods, Relevance to Electrochemical and Biological Systems. Methods Enzymol. 1986, 127, 439-455.
28. Car, R.; Parrinello, M. Unified Approach for Molecular Dynamics and Density-Functional Theory. Phys. Rev. Lett. 1985, 55, 2471-2474.
29. Doerksen, R. J.; Chen, B.; Klein, M. L. Intramolecular Hydrogen Bonds: Ab Initio Car-Parrinello Simulations of Arylamide Torsions. Chem. Phys. Lett. 2003, 380, 150-157.
30. h- J. Chem. Phys. 2001, 115, 115-123.
31. Rovira, C.; Novoa, J. J.; Ballone, P. Hydrogen Bonding and Collective Proton Modes in Clusters and Periodic Layers of Squaric Acid: A Density Functional Theory. J. Chem. Phys. 2001, 115, 6406-6417.
32. Leung, K.; Rempe, S. B. Ab Initio Molecular Dynamics Study of Glycine Intramolecular Transfer in Water. J. Chem. Phys. 2005, 122, 184506.
33. Boero, M.; Terakura, K.; Ikeshoji, T.; Liew, Ch.; Parrinello, M. Hydrogen Bonding and Dipole Moment of Water at Supercritical Conditions: A First-Principle Molecular Dynamics Study. Phys. Rev. Lett. 2000, 85, 3245-3248.
34. Marx, D.; Hutter, J. Ab Initio Molecular Dynamics: Theory and Implementation. In Modern Methods and Algorithms of Quantum Chemistry; Grotendorst, J., Ed.; NIC: Jülich, Germany, 2000; Vol. 3, pp 329-477.
35. Silvestrelli, P. L.; Bemasconi, M.; Parrinello, M. Ab Initio Liquid Spectrum of Liquid Water. Chem. Phys. Lett. 1997, 277, 478-482.
36. Doltsinis, N. L.; Marx, D. First Principles Molecular Dynamics Involving Excited States and Nonadiabatic Transitions. J. Theor. Comput. Chem. 2002, 1, 319-349.
37. Langer, H.; Doltsinis, N. L. Excited State Tautomerism of the DNA Base Guanine: A Restricted Open-Shell Kohn-Sham Study. J. Chem. Phys. 2003, 118, 5400-5407.
38. Tuckerman, M. E.; Marx, D.; Klein, M. L.; Parrinello, M. On the Quantum Nature of the Shared Proton in Hydrogen Bonds. Science 1997, 275, 817-820.
39. Laio, A.; VandeVondele, J.; Röthlisberger, U. A Hamiltonian Electrostatic Coupling Scheme for Hybrid Car-Parrinello Molecular Dynamics Simulations. J. Chem. Phys. 2002, 116, 6941-6948.
40. Fatmi, M. Q.; Hofer, T. S.; Randolf, B. R.; Rode, B. M. An Extended ab Initio QM/MM MD Approach to Structure and Dynamics of Zn(II) in Aqueous Solution. J. Chem. Phys. 2005, 123, 054514.
41. Das, D.; Eurenius, K. P.; Billings, E. M.; Sherwood, P.; Chatfield, D. C.; Hodošček, M.; Brooks, B. R. Optimization of Quantum Mechanical Molecular Mechanical Partitioning Schemes: Gaussian Delocalization of Molecular Mechanical Charges and the Double Link Atom Method. J. Chem. Phys. 2002, 117, 10534-10547.
42. Fedorowicz, A.; Mavri, J.; Bala, P.; Koll, A. Molecular Dynamics Study of the Tautomeric Equilibrium in the Mannich Base. 1998, 259, 457-462.
43. Merzel, F.; Hodošček, M.; Janežič, D.; Sanson, A. New Force Field for Calcium Binding Sites in Annexin-Membrane Complexes. J. Comput. Chem. 2006, 27, 446-452.
44. Sulpizi, M.; Rothlisberger, U.; Carloni, P. Molecular Dynamics Studies of Caspase-3. Biophys. J. 2003, 84, 2207-2216.
45. Hohenberg, P.; Kohn, W. Inhomogeneous Electron Gas. Phys. Rev. 1964, 136, B864-B871.
46. Møller, C.; Plesset, M. S. Note on an Approximation Treatment for Many-Electron Systems. Phys. Rev. 1934, 46, 618-622.
47. Vashishtha, S. C.; Zello, G. A.; Nienaber, K. H.; Balzarini, J.; De Clercq, E.; Stables, J. P.; Dimmock, J. R. Cytotoxic and Anticonvulsant Aryloxyaryl Mannich Bases and Related Compounds. Eur. J. Med. Chem. 2004, 39, 27-35.
48. Pandeya, S. N.; Sriram, D.; Nath, G.; De Clercq, E. Synthesis, Antibacterial, Antifungal and Anti-HIV Evaluation of Norfloxacin Mannich Bases. Sci. Pharm. 1999, 67, 103-111.
49. Varma, R. S.; Nobles, W. L. Antiviral, Antibacterial, and Antifungal Activities of Isatin N-Mannich Bases. J. Pharm. Sci. 1975, 64, 881-882.
50. Pandeya, S. N.; Sriram, D.; Nath, G.; De Clercq, E. Synthesis, Antibacterial, Antifungal and Anti-HIV Evaluation of Schiff and Mannich Bases of Isatin Derivatives with 3-Amino-2-methylmercapto quinazolin-4(3H)-one. Pharm. Acta Helv. 1999, 74, 11-17.
51. Pandeya, S. N.; Sriram, D.; Nath, G.; De Clercq, E. Synthesis and Antimicrobial Activity of Schiff and Mannich Bases of Isatin and Its Derivatives with Pyrimidine. Farmaco 1999, 54, 624-628.
52. Varma, R. S.; Nobles, W. L. Synthesis and Antiviral and Antibacterial Activity of Certain N-Dialkylaminomethylisatin Beta-Thiosemicarbazones. J. Med. Chem. 1967, 10, 972-974.
53. Logan, J. C.; Fox, M. P.; Morgan, J. M.; Makohon, A. M.; Pfau, C. J. Arenavirus Inactivation on Contact with N-Substituted Isatin BetaThiosemicarbazones and Certain Cations. J. Gen. Virol. 1975, 28, 271-283.
54. Imam, S. A.; Varma, R. S. Isatin-3-anils as Excystment and Cysticidal Agents against Schizopyrenus russelli. Experienta 1975, 31, 1287-1288.
55. Holla, B, S.; Udupa, K. V. Synthesis of Novel 5-Mercapto-s-triazolo[3,4- c]-as-triazino[5,6-b]indoles and Their Mannich Bases. Heterocycles 1991, 32, 1081-1088.
56. Mitsch, A.; Wissner, P.; Sattler, I.; Schlitzer, M. Non-Thiol Famesyltransferase Inhibitors: Structure-Activity Relationships of Aralkylsubsituted Benzophenones. Arch. Pharm. Med. Chem. 2001, 334, 40-44.
57. Sasse, A.; Ligneau, X.; Sadek, B.; Elz, S.; Pertz, H.; Ganelin, C. R.; Arrang, J. M.; Schwanz, J. C.; Schunack, W. Benzophenone Derivatives and Related Compounds as Potent Histamine H3-reCeptor Antagonists and Potential PET/SPECT Ligands. Arch. Pharm. Med. Chem. 2001, 334, 45-52.
58. Tramontini, M.; Angiolini, L.; Ghednini, W. Mannich Bases in Polymer Chemistry. Polymer 1988, 29, 771-788.
59. Koll, A.; Wolschann, P. Mannich Bases as Model Compounds for Intramolecular Hydrogen Bonding. I. Solid State Structures and Molecular Calculations. Monatsh. Chem. 1996, 127, 475-486.
60. Filarowski, A.; Szemik-Hojniak, A.; Gowiak, T.; Koll, A. Anomalous Strengthening of the Intramolecular Hydrogen Bond by Steric Repulsion. J. Mol. Struct. 1997, 404, 67-74.
61. CPMD; IBM Corp.: Armonk, NY, 1990-2004; MPI fuer Festkoer-perforschung Stuttgart: Stuttgart, Germany, 1997-2001.
62. Schlegel, H. B. Estimating the Hessian for Gradient-Type Geometry Optimizations. Theor. Chim. Acta 1984, 66, 333-340.
63. Perdew, J. P.; Burke, K.; Emzerhof, M. Generalized Gradient Approximation Made Simple. Phys. Rev. Lett. 1996, 77, 3865-3868.
64. Troullier, N.; Martins, J. L. Efficient Pseudopotentials for Plane-Wave Calculations. Phys. Rev. B: Condens. Matter Mater. Phys. 1991, 43, 1993-2006.
65. Marzari, N.; Vanderbilt, D. Maximally Localized Generalized Wannier Functions for Composite Energy Bands. Phys. Rev. B: Condens. Matter Mater. Phys. 1997, 56, 12847-12865.
66. Silvestrelli, P. L. Maximally Localized Wannier Functions for Simulations with Supercells of General Symmetry. Phys. Rev. B: Condens. Matter Mater. Phys. 1999, 59, 9703-9706.
67. 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.
68. Woon, D. E.; Dunning, T. H., Jr. Gaussian Basis Sets for Use in Correlated Molecular Calculations, in. The Atoms Aluminum through Argon. J. Chem. Phys. 1993, 98, 1358-1371.
69. Becke, A. D. Density-Functional Thermochemistry. III. The Role of Exact Exchange. J. Chem. Phys. 1993, 98, 5648-5652.
70. Lee, C.; Yang, W.; Parr, R. G. Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density. Phys. Rev. B: Condens. Matter Mater. Phys. 1988, 37, 785-789.
71. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Kiene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision C.02; Gaussian, Inc., Wallingford CT, 2004.
72. Panek, J.; Stare, J.; Hadži, D. From the Isolated Molecule to Oligomers and the Crystal: A Static Density Functional Theory and CarParrinello Molecular Dynamics Study of Geometry and Potential Function Modifications of the Short Intramolecular Hydrogen Bond in Picolinic Acid N-Oxide. J. Phys. Chem. A 2004, 108, 7417-7423.
73. Stare, J.; Mavri, J. Numerical Solving of the Vibrational Time-Independent Schrödinger Equation in One and Two Dimensions Using the Variational Method. Comput. Phys. Commun. 2002, 143, 222240.
74. Bader, R. F. W. Atoms in Molecules - A Quantum Theory, 1st ed.; Oxford University Press: Oxford, U. K., 1990; pp 169-351.
75. Koch, U.; Popelier, P. L. A. Characterization of C-H-O Hydrogen Bonds Based on the Charge Density J. Phys. Chem. 1995, 99, 97479754.
76. Biegler-König, F. W.; Bader, R. F. W.; Tang, T.-H. Calculation of the Average Properties of Atoms in Molecules. II. J. Comput. Chem. 1982, 3, 317-328.
77. Portmann, S.; Lüthi, H. P. MOLEKEL: An Interactive Molecular Graphics Tool. Chimia 2000, 54, 766-770.
78. Macrae, C. F.; Edgington, P. R.; McCabe, P.; Pidcock, E.; Shields, G. P.; Taylor, E.; Towler, M.; van de Streek, J. Mercury: Visualization and Analysis of Crystal Structures. J. Appl. Crystallogr. 2006, 39, 453-457.
79. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Clarendon Press: Oxford, U. K., 1994; pp 58-64.
80. Rutkowski, K.; Koll, A. Gas Phase IR Spectra of Systems with Intramolecular Hydrogen Bonds. J. Mol. Struct. 1994, 322, 195-203.
81. s(OH) Absorption Bands in Bent Hydrogen Bonds in orrto-Dialkylaminomethylphenols. Vib. Spectrosc. 1996, 12, 15-24.
82. Silvestrelli, P. .L; Matzari, N.; Vanderbilt, D.; Parrinello, M. Maximally-Localized Wannier Functions for Disordered Systems: Application to Amorphous Silicon. Solid State Commun. 1998, 107, 7-11.