Using the unusual weak N⋯CO bond as a solvation probe

Molecular Simulation

Volumn 40, Issue 1-3, 2014, Pages 185-195

  Kozlowski, David ^a   Pilmé, Julien ^b   Fleurat Lessard, Paul ^a  

^a UNIVERSITÉ DE LYON   (France)

^b LABORATOIRE DE CHIMIE THÉORIQUE   (France)

Author keywords

atoms in molecules; CPMD; electron localisation function; liquid water; solvation effects

Indexed keywords

ATOMS IN MOLECULES; CPMD; ELECTRON LOCALISATION FUNCTIONS; LIQUID WATER; SOLVATION EFFECT;

CONTINUUM MECHANICS; ELECTRONIC STRUCTURE; LIQUIDS; MOLECULAR MODELING; MOLECULES; PROBES; SOLVENTS; TOPOLOGY;

SOLVATION;

EID: 84896765115     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927022.2013.842995     Document Type: Article

References (60)

1. Simon MO, Li C. Green chemistry oriented organic synthesis in water. Chem Soc Rev. 2012; 41: 1415-1427.
2. Ruppert AM, Weinberg K, Palkovits R. Hydrogenolysis goes bio: from carbohydrates and sugar alcohols to platform chemicals. Angew Chem Int Ed. 2012; 51: 2564-2601.
3. Frassoldati A, Pinel C, Besson M. Promoting effect of water for aliphatic primary and secondary alcohol oxidation over platinum catalysts in dioxane/aqueous solution media. Catal Today. 2011; 173: 81-88.
4. Rideout DC, Breslow R. Hydrophobic acceleration of Diels-Alder reactions. J Am Chem Soc. 1980; 102: 7816-7817.
5. Narayan S, Muldoon J, Finn MG, Fokin VV, Kolb HC, Sharpless KB. "On water" unique reactivity of organic compounds in aqueous suspension. Angew Chem Int Ed. 2005; 44: 3275-3279.
6. Butler RN, Coyne AG. Water: nature's reaction enforcer-comparative effects for organic synthesis "in-water" and "on-water". Chem Rev. 2010; 110: 6302-6337.
7. Gao J. Hybrid quantum and molecular mechanical simulations: an alternative avenue to solvent effects in organic chemistry. Acc Chem Res. 1996; 29: 298-305.
8. Gao J. Methods and applications of combined quantum mechanical and molecular mechanical potentials. In: Lipkowitz KB, Boyd DB., editors. Reviews in computational chemistry. New York: VCH; 1995. p. 119-185.
9. Kaminski G, Jorgensen W. A quantum mechanical and molecular mechanical method based on CM1A charges: applications to solvent effects on organic equilibria and reactions. J Phys Chem B. 1998; 102: 1787-1796.
10. Woo T, Blochl P, Ziegler T. Towards solvation simulations with a combined ab initio molecular dynamics and molecular mechanics approach. J Mol Struct THEOCHEM. 2000; 506: 313-334. 5th World Congress of Theoretically Oriented Chemists (WATOC), Imperial Coll, London, England, Aug 01-06, 1999.
11. Higashi M, Truhlar DG. Combined electrostatically embedded multiconfiguration molecular mechanics and molecular mechanical method: application to molecular dynamics simulation of a chemical reaction in aqueous solution with hybrid density functional theory. J Chem Theor Comput. 2008; 4: 1032-1039.
12. Pilmé J, Berthoumieux H, Robert V, Fleurat-Lessard P. Unusual bond formation in aspartic protease inhibitors: a theoretical study. Chem Eur J. 2007; 13: 5388-5393.
13. Piquemal JP, Pilmé J, Parisel O, Gerard H, Fourre I, Berges J, Gourlaouen C, De La Lande A, Van Severen MC, Silvi B. What can be learnt on biologically relevant systems from the topological analysis of the electron localization function? Int J Quant Chem. 2008; 108: 1951-1969. 3rd International Theoretical Biophysics Symposium, Cetraro, Italy, Jun 16-20, 2007.
14. Leonard NJ, Oki M. Cyclic aminoacyloins and aminoketones 6. Effect of transannular interaction between N and CCO on ultraviolet absorption. J Am Chem Soc. 1955; 77: 6239-6240.
15. Bell MR, Archer S. Conformation of 3-alpha-phenyl-3-beta-tropanyl phynyl ketone-a novel nitrogen carbonyl interaction. J Am Chem Soc. 1960; 82: 151-155.
16. Kirby AJ, Komarov IV, Bilenko VA, Davies JE, Rawson JM. Structure and chemistry of a zwitterionic amine-aldehyde adduct. Chem Commun. 2002;18: 2106-2107.
17. Gautier A, Pitrat D, Hasserodt J. An unusual functional group interaction and its potential to reproduce steric and electrostatic features of the transition states of peptidolysis. Bioorg Med Chem. 2006; 14: 3835-3847.
18. Waibel M, Pitrat D, Hasserodt J. On the inhibition of HIV-1 protease by hydrazino-ureas displaying the N → CO interaction. Bioorg Med Chem. 2009; 17: 3671-3679.
19. Tomasi J, Mennucci B, Cammi R. Quantum mechanical continuum solvation models. Chem Rev. 2005; 105: 2999-3093.
20. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ. Gaussian 09 revision A.1. Wallingford, CT: Gaussian Inc; 2009.
21. Dapprich S, Komáromi I, Byun KS, Morokuma K, Frisch MJ. A new ONIOM implementation in Gaussian 98. 1. The calculation of energies, gradients and vibrational frequencies and electric field derivatives. J Mol Struct THEOCHEM. 1999; 462: 1-21.
22. Vreven T, Byun KS, Komáromi I, Dapprich S, Montgomery JA Jr, Morokuma K, Frisch MJ. Combining quantum mechanics methods with molecular mechanics methods in ONIOM. J Chem Theory Comput. 2006; 2: 815-826.
23. Car R, Parrinello M. Unified approach for molecular dynamics and density-functional theory. Phys Rev Lett. 1985; 55: 2471-2474.
24. Andreoni W, Curioni A. New advances in chemistry and material science with CPMD and parallel computing. Parallel Comput. 2000; 26: 819-842.
25. Laio A, VandeVondele J, Rothlisberger U. A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations. J Chem Phys. 2002; 116: 6941-6947.
26. Laio A, Gervasio FL, VandeVondele J, Sulpizi M, Rothlisberger U. A variational definition of electrostatic potential derived charges. J Phys Chem B. 2004; 108: 7963-7968.
27. Becke AD. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A. 1988; 38: 3098-3100.
28. Perdew JP. Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys Rev B. 1986; 33: 8822-8824.
29. Bader R. Atoms in molecules: a quantum theory. USA: Oxford University Press; 1994.
30. Bader RFW. A quantum theory of molecular structure and its applications. Chem Rev. 1991; 91: 893-928.
31. Becke AD, Edgecombe KE. A simple measure of electron localization in atomic and molecular systems. J Chem Phys. 1990; 92: 5397-5403.
32. Bergès J, Fourré I, Pilmé J, Kozelka J. Quantum chemical topology study of the water-platinum(II) interaction. Inorg Chem. 2013; 52: 1217-1227.
33. Andres J, Berski S, Domingo LR, Polo V, Silvi B. Describing the molecular mechanism of organic reactions by using topological analysis of electronic localization function. Curr Org Chem. 2011; 15: 3566-3575.
34. Gillespie RJ. Fifty years of the VSEPR model. Coord Chem Rev. 2008; 252: 1315-1327.
35. Contreras-Garca J, Recio JM. On bonding in ionic crystals. J Phys Chem C. 2011; 115: 257-263.
36. De La Lande A, Salahub DR, Maddaluno J, Scemama A, Pilmé J, Parisel O, Gerard H, Caffarel M, Piquemal JP. Rapid communication spin-driven activation of dioxygen in various metalloenzymes and their inspired models. J Comput Chem. 2011; 32: 1178-1182.
37. Silvi B, Savin A. Classification of chemical bonds based on topological analysis of electron localization functions. Nature. 1994; 371: 683-686.
38. Pilmé J, Piquemal JP. Advancing beyond charge analysis using the electronic localization function: chemically intuitive distribution of electrostatic moments. J Comput Chem. 2008; 29: 1440-1449.
39. Raub S, Jansen G. A quantitative measure of bond polarity from the electron localization function and the theory of atoms in molecules. Theor Chem Acc. 2001; 106: 223-232. 10.1007/s002140100268.
40. Noury S, Krokidis X, Fuster F, Silvi B. Computational tools for the electron localization function topological analysis. Comput Chem. 1999; 23: 597-604.
41. Kozlowski D, Pilmé J. New insights in quantum chemical topology studies using numerical grid-based analyses. J Comput Chem. 2011; 32: 3207-3217.
42. Flukiger P, Luthi HP, Portmann S, Weber J. Molekel version 4.3. Manno (Switzerland): Swiss Centre for Scientific Computing; 2000.
43. Chalmet S, Ruiz-Lopez MF. Molecular dynamics simulation of formamide in water using density functional theory and classical potentials. J Chem Phys. 1999; 111: 1117-1125.
44. Lankhorst D, Schriever J, Leyte JC. Determination of the rotational correlation time of water by proton NMR relaxation in H217O and some related results. Ber Bunsen-Ges Phys Chem. 1982; 86: 215-221.
45. van der Spoel D, Maarenvan PJ, Berendsen HJC. A systematic study of water models for molecular simulation: derivation of water models optimized for use with a reaction field. J Chem Phys. 1998; 108: 10220-10230.
46. Pendás AM, Blanco MA, Francisco E. The nature of the hydrogen bond: a synthesis from the interacting quantum atoms picture. J Chem Phys. 2006; 125: 184112.
47. Devereux M, Popelier PLA. The effects of hydrogen-bonding environment on the polarization and electronic properties of water molecules. J Phys Chem A. 2007; 111: 1536-1544.
48. Bergner A, Dolg M, Kuechle W, Stoll H, Preuss H. Ab initio energy-adjusted pseudopotentials for elements of groups 13-17. Mol Phys. 1993;80: 1431-1441.
49. Sierraalta A, Ruette F. A comparative study of effective core potential and full-electron calculations in Mo compounds. I. An analysis of topological properties of bond charge distribution. J Comput Chem. 1994; 15: 313-321.
50. Vyboishchikov SF, Sierraalta A, Frenking G. Topological analysis of electron density distribution taken from a pseudopotential calculation. J Comput Chem. 1998; 18: 416-429.
51. Frenking G, Antes I, Böhme M, Dapprich S, Ehlers AW, Jones V, Neuhaus A, Otto M, Stegmann R. Methods and applications of combined quantum mechanical and molecular mechanical potentials. In: Lipkowitz KB, Boyd DB., editors. Reviews in computational chemistry. New York: VCH; 1996. p. 63-92.
52. Keith TA, Frisch MJ. Subshell fitting of relativistic atomic core electron densities for use in QTAIM analyses of ECP-based wave functions. J Phys Chem A. 2011; 115: 12879-12894.
53. Tiana D, Francisco E, Blanco MA, Pendás AM. Using pseudopotentials within the interacting quantum atoms approach. J Phys Chem A. 2009; 113: 7963-7971.
54. Kerdcharoen T, Morokuma K. ONIOM-XS: an extension of the ONIOM method for molecular simulation in condensed phase. Chem Phys Lett. 2002; 355: 257-262.
55. Heyden A, Lin H, Truhlar DG. Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations. J Phys Chem B. 2007; 111: 2231-3341.
56. Bulo RE, Ensing B, Sikkema J, Visscher L. Toward a practical method for adaptive QM/MM simulations. J Chem Theory Comput. 2009; 5: 2212-2221.
57. + in liquid water determined from high level ab initio molecular dynamics simulations. J Chem Theory Comput. 2012; 8: 3526-3535.
58. Bernstein N, Varnai C, Solt I, Winfield SA, Payne MC, Simon I, Fuxreiter M, Csanyi G. QM/MM simulation of liquid water with an adaptive quantum region. Phys Chem Chem Phys. 2012; 14: 646-656.
59. Bulo RE, Michel C, Fleurat-Lessard P, Sautet P. Multi-scale modeling of chemistry in water: are we there yet? J Chem Theory Comput,. Forthcoming 2013.
60. Tang W, Sanville E, Henkelman G. A grid-based Bader analysis algorithm without lattice bias. J Phys Condens Matter. 2009; 21: 084204.