R. Ow, Comparison of radial pair distribution functions of isobutane simulated with ff03- SPC/E, PM3-PIF3 and the HH-Alkane united atoms potential.[237] Plain lines: RDF. Dashed lines: RDF integral. a: Isobutane center carbon atom (Cc)-water oxygen RDF. b: Isobutane methyl carbon atom (Cme), p.122

P. For and P. , the peptidic correction (PEP) was applied 151 VII List of Figures 5.29 Distribution of the ? improper angle along the gas and the condensed phase dynamics . Comparison between formamide, propanamide and N-methylacetamide

P. For and P. , the peptidic correction (PEP) was applied, p.152

). Cramer and C. J. , 214 XIV Bibliography [1] Szabo, A. Modern Quantum Chemistry, Élements de chimie quantique à l'usage des chimistes; Savoirs actuels Inter Édition/Éditions du CNRS Essentials of Computational Chemistry Theories and Models Second Edition, 1982.

M. P. Allen and D. J. Tildesley, Computer simulation of liquids

U. Oxford, Zeitschrift für Phys, Zeitschrift für Phys, pp.1049-863, 1926.

W. Pauli, Zeitschrift für Phys, pp.31-765, 1925.

J. C. Slater, The Theory of Complex Spectra, Physical Review, vol.35, issue.10, p.1293, 1929.
DOI : 10.1007/BF01379806

C. Roothaan, New Developments in Molecular Orbital Theory, Reviews of Modern Physics, vol.46, issue.2, p.69, 1951.
DOI : 10.1051/jcp/1949460497

C. Møller and M. S. Plesset, Note on an Approximation Treatment for Many-Electron Systems, Physical Review, vol.27, issue.7, p.618, 1934.
DOI : 10.1017/S0305004100010343

M. Head-gordon, J. A. Pople, and M. Frisch, MP2 energy evaluation by direct methods, Chemical Physics Letters, vol.153, issue.6, p.503, 1988.
DOI : 10.1016/0009-2614(88)85250-3

P. Hohenberg and W. Kohn, Inhomogeneous Electron Gas, Physical Review, vol.80, issue.3B, p.864, 1964.
DOI : 10.1088/0370-1328/80/5/307

W. Kohn and L. Sham, Self-Consistent Equations Including Exchange and Correlation Effects, Physical Review, vol.119, issue.4A, p.1133, 1965.
DOI : 10.1103/PhysRev.119.1153

S. Vosko, L. Wilk, M. Nusair, J. P. Perdew, A. Zunger et al., XV Bibliography, Can. J. Phys. Phys. Rev. B Phys. Rev. B, vol.5820, issue.244, 1200.

A. D. Becke, Density-functional exchange-energy approximation with correct asymptotic behavior, Physical Review A, vol.28, issue.6, p.3098, 1988.
DOI : 10.1103/PhysRevB.28.1809

C. Lee, W. Yang, and R. G. Parr, Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Physical Review B, vol.20, issue.2, p.785, 1988.
DOI : 10.1103/PhysRevA.20.397

Y. Zhao and D. G. Truhlar, The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals, Theoretical Chemistry Accounts, vol.103, issue.1-3, p.215, 2008.
DOI : 10.1002/ijch.199300041

S. Grimme, Semiempirical GGA-type density functional constructed with a long-range dispersion correction, Journal of Computational Chemistry, vol.10, issue.15, p.1787, 2006.
DOI : 10.1007/s002140050244

S. Grimme, J. Antony, T. Schwabe, and C. Mück-lichtenfeld, Density functional theory with dispersion corrections for supramolecular structures, aggregates, and complexes of (bio)organic molecules, Org. Biomol. Chem., vol.110, issue.462, p.741, 2007.
DOI : 10.1063/1.479128

A. Dreuw and M. Head-gordon, Single-Reference ab Initio Methods for the Calculation of Excited States of Large Molecules, Chemical Reviews, vol.105, issue.11, p.4009, 2005.
DOI : 10.1021/cr0505627

T. Etienne, X. Assfeld, and A. Monari, Toward a Quantitative Assessment of Electronic Transitions??? Charge-Transfer Character, Journal of Chemical Theory and Computation, vol.10, issue.9, p.3896, 2014.
DOI : 10.1021/ct5003994

W. L. Jorgensen and J. Tirado-rives, The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin, Journal of the American Chemical Society, vol.110, issue.6, p.1657, 1988.
DOI : 10.1021/ja00214a001

M. C. Lee and Y. Duan, Distinguish protein decoys by Using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model, Proteins: Structure, Function, and Bioinformatics, vol.23, issue.3, p.620, 2004.
DOI : 10.1007/s002140050460

P. Ren and J. W. Ponder, Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations, Journal of Computational Chemistry, vol.105, issue.16, p.1497, 2002.
DOI : 10.1021/jp011511q

W. L. Jorgensen and J. Tirado-rives, Monte Carlo vs Molecular Dynamics for Conformational Sampling, The Journal of Physical Chemistry, vol.100, issue.34, p.14508, 1996.
DOI : 10.1021/jp960880x

L. Verlet, Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules, Physical Review, vol.30, issue.1, p.98, 1967.
DOI : 10.1016/0031-8914(64)90224-1

J. Ryckaert, G. Ciccotti, and H. J. Berendsen, Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes, Journal of Computational Physics, vol.23, issue.3, p.327, 1977.
DOI : 10.1016/0021-9991(77)90098-5

D. York and W. Yang, The fast Fourier Poisson method for calculating Ewald sums, The Journal of Chemical Physics, vol.101, issue.4, p.3298, 1994.
DOI : 10.1063/1.445869

S. Nosé, A molecular dynamics method for simulations in the canonical ensemble, Molecular Physics, vol.79, issue.2, p.255, 1984.
DOI : 10.1063/1.446137

G. Monard and K. M. Merz-jr, Combined Quantum Mechanical/Molecular Mechanical Methodologies Applied to Biomolecular Systems, Accounts of Chemical Research, vol.32, issue.10, p.904, 1999.
DOI : 10.1021/ar970218z

G. M. Torrie and J. P. Valleau, Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling, Journal of Computational Physics, vol.23, issue.2, p.187, 1977.
DOI : 10.1016/0021-9991(77)90121-8

T. Huber, A. E. Torda, W. F. Van-gunsteren, F. Wang, and D. P. Landau, XVII Bibliography, J. Comput. Aided. Mol. Des. Phys. Rev. Lett. Comput. Phys. Commun, vol.864, issue.180, p.695, 1961.

I. M. Svishchev, A. Y. Zassetsky, and P. G. Kusalik, Solvation structures in three dimensions, Chemical Physics, vol.258, issue.2-3, p.181, 2000.
DOI : 10.1016/S0301-0104(00)00166-X

M. Allesch, E. Schwegler, and G. Galli, Structure of Hydrophobic Hydration of Benzene and Hexafluorobenzene from First Principles, The Journal of Physical Chemistry B, vol.111, issue.5, p.1081, 2007.
DOI : 10.1021/jp065429c

J. R. Schmidt and S. A. Corcelli, Infrared absorption line shapes in the classical limit: A comparison of the classical dipole and fluctuating frequency approximations, The Journal of Chemical Physics, vol.128, issue.18, p.184504, 2008.
DOI : 10.1016/0378-4371(81)90105-9

W. H. Press, S. A. Teukolosky, W. R. Vetterling, and B. Flannery, Fortran, P. Numerical Recipies in, 1992.

S. Egorov, K. F. Everitt, and J. L. Skinner, Quantum Dynamics and Vibrational Relaxation, The Journal of Physical Chemistry A, vol.103, issue.47, p.9494, 1999.
DOI : 10.1021/jp9919314

J. S. Bader and B. J. Berne, Quantum and classical relaxation rates from classical simulations, The Journal of Chemical Physics, vol.47, issue.11, p.8359, 1994.
DOI : 10.1063/1.462637

J. J. Stewart, Optimization of parameters for semiempirical methods I. Method, Journal of Computational Chemistry, vol.24, issue.2, p.209, 1989.
DOI : 10.1093/comjnl/6.2.163

S. Iuchi, A. Morita, and S. Kato, -Methylacetamide in Aqueous Solution, The Journal of Physical Chemistry B, vol.106, issue.13, p.3466, 2002.
DOI : 10.1021/jp013773y

W. Thiel, Semiempirical methods: current status and perspectives, Tetrahedron, vol.44, issue.24, p.7393, 1988.
DOI : 10.1016/S0040-4020(01)86235-9

R. Pariser and R. G. Parr, A Semi???Empirical Theory of the Electronic Spectra and Electronic Structure of Complex Unsaturated Molecules. I., The Journal of Chemical Physics, vol.46, issue.3, p.466, 1953.
DOI : 10.1063/1.1746930

J. A. Pople, Electron interaction in unsaturated hydrocarbons, Transactions of the Faraday Society, vol.49, p.1375, 1953.
DOI : 10.1039/tf9534901375

J. C. Slater and K. H. Johnson, Cluster Method for Polyatomic Molecules and Solids, Physical Review B, vol.123, issue.3, p.844, 1972.
DOI : 10.1103/PhysRev.123.1219

K. H. Johnson and F. C. Smith-jr, Chemical Bonding of a Molecular Transition-Metal Ion in a Crystalline Environment, Physical Review B, vol.23, issue.3, p.831, 1972.
DOI : 10.1063/1.3022065

A. Warshel and R. M. Weiss, An empirical valence bond approach for comparing reactions in solutions and in enzymes, Journal of the American Chemical Society, vol.102, issue.20, p.6218, 1980.
DOI : 10.1021/ja00540a008

J. Ridley and M. Zerner, An intermediate neglect of differential overlap technique for spectroscopy: Pyrrole and the azines, Theoretica Chimica Acta, vol.54, issue.2, p.111, 1973.
DOI : 10.1007/BF00528484

D. N. Nanda and K. Jug, SINDO1. A semiempirical SCF MO method for molecular binding energy and geometry I. Approximations and parametrization, Theoretica Chimica Acta, vol.52, issue.2, p.95, 1980.
DOI : 10.1007/BF00574898

N. U. Zhanpeisov, A. G. Pel-'menshchikov, and G. M. Zhidomirov, A form of the MINDO/3 method for hydrogen-bonded complexes, Journal of Structural Chemistry, vol.51, issue.No. 1, p.1, 1987.
DOI : 10.1007/BF00749536

K. Jug and G. Geudtner, Treatment of hydrogen bonding in SINDO1, Journal of Computational Chemistry, vol.24, issue.6, p.639, 1993.
DOI : 10.1002/jcc.540140603

M. J. Dewar, E. G. Zoebisch, E. F. Healy, and J. J. Stewart, Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model, Journal of the American Chemical Society, vol.107, issue.13, p.3902, 1985.
DOI : 10.1021/ja00299a024

A. A. Voityuk and N. Rösch, AM1/d Parameters for Molybdenum, The Journal of Physical Chemistry A, vol.104, issue.17, p.4089, 2000.
DOI : 10.1021/jp994394w

P. Winget, A. H. Horn, C. Selçuki, B. Martin, and T. Clark, AM1* parameters for phosphorus, sulfur and chlorine, Journal of Molecular Modeling, vol.9, issue.6, p.408, 2003.
DOI : 10.1007/s00894-003-0156-7

H. Kayi and T. Clark, AM1* parameters for copper and zinc, Journal of Molecular Modeling, vol.4, issue.1, p.965, 2007.
DOI : 10.1002/9780470093399.ch1

H. Kayi and T. Clark, AM1* parameters for vanadium and chromium, Journal of Molecular Modeling, vol.13, issue.1, p.1253, 2009.
DOI : 10.1007/s00894-009-0489-y

H. Kayi and T. Clark, AM1* parameters for bromine and iodine, Journal of Molecular Modeling, vol.114, issue.1, p.295, 2009.
DOI : 10.1007/s00894-008-0419-4

H. Kayi and T. Clark, AM1* parameters for manganese and iron, Journal of Molecular Modeling, vol.13, issue.1, p.1109, 2010.
DOI : 10.1007/s00894-009-0614-y

URL : https://hal.archives-ouvertes.fr/hal-00568333

H. Kayi and T. Clark, AM1* parameters for cobalt and nickel, Journal of Molecular Modeling, vol.13, issue.1, p.29, 2010.
DOI : 10.1007/s00894-009-0503-4

URL : https://hal.archives-ouvertes.fr/hal-00568326

H. Kayi and T. Clark, AM1* parameters for palladium and silver, Journal of Molecular Modeling, vol.13, issue.10, p.2585, 2011.
DOI : 10.1007/s00894-007-0233-4

K. Nam, Q. Cui, J. Gao, and D. M. York, Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions:?? H, O, and P Atoms, Journal of Chemical Theory and Computation, vol.3, issue.2, p.486, 2007.
DOI : 10.1021/ct6002466

K. Y. Burstein and A. N. Isaev, MNDO calculations on hydrogen bonds. Modified function for core-core repulsion, Theoretica Chimica Acta, vol.3, issue.5, p.397, 1984.
DOI : 10.1007/BF00548949

J. J. Stewart, Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements, Journal of Molecular Modeling, vol.73, issue.12, p.1173, 2007.
DOI : 10.1002/jcc.540141106

M. I. Bernal-uruchurtu, M. T. Martins-costa, C. Millot, and M. F. Ruiz-lópez, Improving description of hydrogen bonds at the semiempirical level: water-water interactions as test case, Journal of Computational Chemistry, vol.109, issue.7, p.572, 2000.
DOI : 10.1063/1.477211

O. I. Arillo-flores, M. F. Ruiz-lópez, and M. I. Bernal-uruchurtu, Can semi-empirical models describe HCl dissociation in water?, Theoretical Chemistry Accounts, vol.4, issue.2, p.425, 2007.
DOI : 10.1007/s00214-003-0454-2

S. K. Ignatov, A. G. Razuvaev, V. N. Kokorev, and Y. A. Alexandrov, Extension of the PM3 Method on s,p,d Basis. Test Calculations on Organochromium Compounds, The Journal of Physical Chemistry, vol.100, issue.15, p.6354, 1996.
DOI : 10.1021/jp9528572

W. Thiel and A. A. Voityuk, Extension of the MNDO formalism tod orbitals: Integral approximations and preliminary numerical results, Theoretica Chimica Acta, vol.180, issue.6, p.391, 1992.
DOI : 10.1002/ijch.198000010

W. Thiel and A. A. Voityuk, Extension of MNDO to d Orbitals:?? Parameters and Results for the Second-Row Elements and for the Zinc Group, The Journal of Physical Chemistry, vol.100, issue.2, p.616, 1996.
DOI : 10.1021/jp952148o

B. Ahlswede and K. Jug, Consistent modifications of SINDO1: I. Approximations and parameters, Journal of Computational Chemistry, vol.9, issue.6, p.563, 1999.
DOI : 10.1002/(SICI)1096-987X(19990430)20:6<563::AID-JCC1>3.0.CO;2-2

M. Kolb and W. Thiel, Beyond the MNDO model: Methodical considerations and numerical results, Journal of Computational Chemistry, vol.110, issue.7, p.775, 1993.
DOI : 10.1002/ijch.198000010

W. Weber and W. Thiel, Orthogonalization corrections for semiempirical methods, Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), vol.103, issue.6, p.495, 2000.
DOI : 10.1007/s002149900083

D. T. Chang, G. K. Schenter, and B. C. Garrett, Self-consistent polarization neglect of diatomic differential overlap: Application to water clusters, The Journal of Chemical Physics, vol.37, issue.16, p.164111, 2008.
DOI : 10.1146/annurev.pc.16.100165.000435

B. Martin and T. Clark, Dispersion treatment for NDDO-based semiempirical MO techniques, International Journal of Quantum Chemistry, vol.91, issue.5, p.1208, 2006.
DOI : 10.1007/s00214-003-0454-2

G. I. Csonka and J. G. Ángyán, The origin of the problems with the PM3 core repulsion function, Journal of Molecular Structure: THEOCHEM, vol.393, issue.1-3, p.31, 1997.
DOI : 10.1016/S0166-1280(96)04872-5

M. Elstner, The SCC-DFTB method and its application to biological systems, Theoretical Chemistry Accounts, vol.401, issue.1-3, p.316, 2006.
DOI : 10.1002/cphc.200390047

L. Oleari, G. De-michelis, and L. Di-sipio, The evaluation of the one-centre integrals in the semi-empirical molecular orbital theory, Molecular Physics, vol.10, issue.2, p.97, 1966.
DOI : 10.1021/ja01062a001

M. J. Dewar and W. Thiel, A semiempirical model for the two-center repulsion integrals in the NDDO approximation, Theoretica Chimica Acta, vol.13, issue.2, p.89, 1977.
DOI : 10.1524/zpch.1957.13.3_4.140

K. E. Riley, M. Pitonák, P. Jurecka, and P. Hobza, Stabilization and Structure Calculations for Noncovalent Interactions in Extended Molecular Systems Based on Wave Function and Density Functional Theories, Chemical Reviews, vol.110, issue.9, p.5023, 2010.
DOI : 10.1021/cr1000173

E. Thiriot and G. Monard, Combining a genetic algorithm with a linear scaling semiempirical method for protein???ligand docking, Journal of Molecular Structure: THEOCHEM, vol.898, issue.1-3, p.31, 2009.
DOI : 10.1016/j.theochem.2008.12.041

M. I. Bernal-uruchurtu and M. F. Ruiz-lópez, Beyond standard quantum chemistry: Applications from gas to condensed phases Chapter Eigen and Zundel ions in aqueous environments. A theoretical study uising semi-empirical force fields, pp.65-86, 2007.

M. Sprik, . Chem, . Phys, K. Nam, J. Gao et al., XXIII Bibliography, J. Chem. Theory Comput J. Chem. Theory Comput, vol.258, issue.8, p.3565, 0195.

V. M. Anisimov and A. A. Bliznyuk, Charge Transfer Effects in the GroEL???GroES Chaperonin Tetramer in Solution, The Journal of Physical Chemistry B, vol.116, issue.22, p.6261, 2012.
DOI : 10.1021/jp211385e

G. Murdachaew, C. J. Mundy, G. K. Schenter, T. Laino, and J. Hutter, Semiempirical Self-Consistent Polarization Description of Bulk Water, the Liquid???Vapor Interface, and Cubic Ice, The Journal of Physical Chemistry A, vol.115, issue.23, p.6046, 2011.
DOI : 10.1021/jp110481m

G. Csonka, Analysis of the core-repulsion functions used in AM1 and PM3 semiempirical calculations: Conformational analysis of ring systems, Journal of Computational Chemistry, vol.82, issue.8, p.895, 1993.
DOI : 10.1002/jcc.540140803

G. Csonka, K. Éliás, and I. G. Csizmadia, Ab initio and density functional study of the conformational space of1C4 ?-L-fucose, Journal of Computational Chemistry, vol.14, issue.3, p.330, 1997.
DOI : 10.1107/S0567740877007808

E. Clementi and G. Corongiu, Van der Waals Interaction Energies of Helium, Neon, and Argon with Naphthalene, The Journal of Physical Chemistry A, vol.105, issue.45, p.10379, 2001.
DOI : 10.1021/jp011509z

J. A. Pople, M. Head-gordon, and K. Raghavachari, Quadratic configuration interaction. A general technique for determining electron correlation energies, The Journal of Chemical Physics, vol.87, issue.10, p.5968, 1987.
DOI : 10.1063/1.447214

V. V. Struzhkin, B. Militzer, W. L. Mao, H. Mao, and R. J. Hemley, Hydrogen Storage in Molecular Clathrates, Chemical Reviews, vol.107, issue.10, p.4133, 2007.
DOI : 10.1021/cr050183d

A. Khan, Theoretical studies of CH4(H2O)20, (H2O)21, (H2O)20, and fused dodecahedral and tetrakaidecahedral structures: How do natural gas hydrates form?, The Journal of Chemical Physics, vol.110, issue.24, p.11884, 1999.
DOI : 10.1021/jp970768e

A. Schäfer, C. Huber, and R. Ahlrichs, Fully optimized contracted Gaussian basis sets of triple zeta valence quality for atoms Li to Kr, The Journal of Chemical Physics, vol.100, issue.8, p.5829, 1994.
DOI : 10.1016/0009-2614(90)85472-O

P. R. Rablen, J. W. Lockman, and W. L. Jorgensen, Ab Initio Study of Hydrogen-Bonded Complexes of Small Organic Molecules with Water, The Journal of Physical Chemistry A, vol.102, issue.21, p.3782, 1998.
DOI : 10.1021/jp980708o

F. J. Luque, N. Reuter, A. Cartier, and M. F. Ruiz-lópez, Calibration of the Quantum/Classical Hamiltonian in Semiempirical QM/MM AM1 and PM3 Methods, The Journal of Physical Chemistry A, vol.104, issue.46, p.10923, 2000.
DOI : 10.1021/jp001974g

M. Gaigeot, Theoretical spectroscopy of floppy peptides at room temperature. A DFTMD perspective: gas and aqueous phase, Physical Chemistry Chemical Physics, vol.68, issue.409, p.3336, 2010.
DOI : 10.1103/PhysRevB.56.12847

U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee et al., A smooth particle mesh Ewald method, The Journal of Chemical Physics, vol.100, issue.19, p.8577, 1995.
DOI : 10.1063/1.470043

C. Sagui and T. A. Darden, In Simulation and Theory of Electrostatic Interactions in Solution, Eds, pp.104-113, 1999.

A. Toukmaji, C. Sagui, J. Board, and T. Darden, Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions, The Journal of Chemical Physics, vol.94, issue.24, p.10913, 2000.
DOI : 10.1063/1.466407

C. Sagui, L. G. Pedersen, and T. A. Darden, Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations, The Journal of Chemical Physics, vol.34, issue.1, pp.73-74, 2004.
DOI : 10.1103/PhysRev.52.191

L. Rossato, F. Rossetto, and P. L. Silvestrelli, Aqueous Solvation of Methane from First Principles, The Journal of Physical Chemistry B, vol.116, issue.15, p.4552, 2012.
DOI : 10.1021/jp300774z

L. Dang and D. Feller, Molecular Dynamics Study of Water???Benzene Interactions at the Liquid/Vapor Interface of Water, The Journal of Physical Chemistry B, vol.104, issue.18, p.4403, 2000.
DOI : 10.1021/jp000054v

M. Allesch, F. C. Lightstone, E. Schwegler, and G. Galli, First principles and classical molecular dynamics simulations of solvated benzene, The Journal of Chemical Physics, vol.128, issue.1, p.14501, 2008.
DOI : 10.1109/SC.2005.40

M. P. Mateus, N. Galamba, and B. Costa-cabral, Structure and electronic properties of a benzene-water solution, The Journal of Chemical Physics, vol.4, issue.1, p.14507, 2012.
DOI : 10.1021/jp980761c

R. S. Mulliken, Electronic Population Analysis on LCAO???MO Molecular Wave Functions. I, The Journal of Chemical Physics, vol.207, issue.10, p.1833, 1955.
DOI : 10.1063/1.1747438

P. Löwdin, On the Non???Orthogonality Problem Connected with the Use of Atomic Wave Functions in the Theory of Molecules and Crystals, The Journal of Chemical Physics, vol.188, issue.3, p.365, 1950.
DOI : 10.1098/rspa.1947.0003

C. Singh, U. Kollman, and P. A. , An approach to computing electrostatic charges for molecules, Journal of Computational Chemistry, vol.77, issue.2, p.129, 1984.
DOI : 10.1063/1.444325

A. E. Reed, R. B. Weinstock, and F. Weinhold, Natural population analysis, The Journal of Chemical Physics, vol.83, issue.2, p.735, 1985.
DOI : 10.1063/1.1674408

B. Stuart, . Infrared, and . Spectroscopy, Fundamentals and Applications, 2004.

T. J. Lee, J. M. Martin, and P. R. Taylor, and isotopomers, The Journal of Chemical Physics, vol.102, issue.1, p.254, 1995.
DOI : 10.1063/1.454382

J. Greathouse, R. T. Cygan, and B. Simmons, Vibrational Spectra of Methane Clathrate Hydrates from Molecular Dynamics Simulation, The Journal of Physical Chemistry B, vol.110, issue.13, p.6428, 2006.
DOI : 10.1021/jp060471t

G. Varsányi, Vibrational spectra of benzene derivatives, 1969.

J. Fidler and P. M. Rodger, Solvation Structure around Aqueous Alcohols, The Journal of Physical Chemistry B, vol.103, issue.36, p.7695, 1999.
DOI : 10.1021/jp9907903

T. S. Van-erp and E. J. Meijer, molecular dynamics study of aqueous solvation of ethanol and ethylene, The Journal of Chemical Physics, vol.105, issue.19, p.8831, 2003.
DOI : 10.1103/PhysRevLett.82.3308

N. W. Larsen and F. M. Nicolaisen, Far-infrared gas spectra of phenol, 4-fluorophenol, thiophenol and some deuterated species: barrier to internal rotation, Journal of Molecular Structure, vol.22, issue.1, p.29, 1974.
DOI : 10.1016/0022-2860(74)80065-7

G. Berden, W. Leo-meerts, M. Schmitt, and K. Kleinermanns, High resolution UV spectroscopy of phenol and the hydrogen bonded phenol???water cluster, The Journal of Chemical Physics, vol.104, issue.3, p.972, 1996.
DOI : 10.1063/1.1742731

B. T. Mmereki and D. J. Donaldson, Ab Initio and Density Functional Study of Complexes between the Methylamines and Water, The Journal of Physical Chemistry A, vol.106, issue.13, p.3185, 2002.
DOI : 10.1021/jp013694m

R. C. Rizzo and W. L. Jorgensen, OPLS All-Atom Model for Amines:?? Resolution of the Amine Hydration Problem, Journal of the American Chemical Society, vol.121, issue.20, p.4827, 1999.
DOI : 10.1021/ja984106u

H. Hesske and K. Gloe, Hydration Behavior of Alkyl Amines and Their Corresponding Protonated Forms. 1. Ammonia and Methylamine, The Journal of Physical Chemistry A, vol.111, issue.39, p.9848, 2007.
DOI : 10.1021/jp073154a

M. Feigel and T. Strassner, A semiempirical AM1, MNDO and PM3 study of the rotational barriers of various ureas, thioureas, amides and thioamides, Journal of Molecular Structure: THEOCHEM, vol.283, p.33, 1993.
DOI : 10.1016/0166-1280(93)87112-Q

S. Chalmet and M. F. Ruiz-lópez, Molecular dynamics simulation of formamide in water using density functional theory and classical potentials, The Journal of Chemical Physics, vol.111, issue.3, p.1117, 1999.
DOI : 10.1016/S0009-2614(98)00486-2

D. M. Benoit and D. C. Clary, Quantum Simulation of Phenol???Water Clusters, The Journal of Physical Chemistry A, vol.104, issue.23, p.5590, 2000.
DOI : 10.1021/jp994420q

J. Max, S. Daneault, and C. Chapdos, 1-Propanol hydrate by IR spectroscopy, Canadian Journal of Chemistry, vol.93, issue.1, p.113, 2002.
DOI : 10.1021/j100343a008

T. Yamashita and K. Takatsuka, mixed quantum-classical study, The Journal of Chemical Physics, vol.126, issue.7, p.74304, 2007.
DOI : 10.1063/1.465445

M. Petkovi´cpetkovi´c, O???H Stretch in Phenol and Its Hydrogen-Bonded Complexes: Band Position and Relaxation Pathways, The Journal of Physical Chemistry A, vol.116, issue.1, p.364
DOI : 10.1021/jp209897y

S. Ataka, H. Takeuchi, and M. Tasumi, Infrared studies of the less stable cis form of N-methylformmaide and N-methylacetamide in low-temperature nitrogen matrices and vibrational analyses of the trans and cis forms of these molecules, Journal of Molecular Structure, vol.113, p.147, 1984.
DOI : 10.1016/0022-2860(84)80140-4

J. Kubelka and T. A. Keiderling, -Methyl Acetamide, The Journal of Physical Chemistry A, vol.105, issue.48, p.10922, 2001.
DOI : 10.1021/jp013203y

M. Gaigeot, Unravelling the Conformational Dynamics of the Aqueous Alanine Dipeptide with First-Principle Molecular Dynamics, The Journal of Physical Chemistry B, vol.113, issue.30, p.10059, 2009.
DOI : 10.1021/jp903745r

A. N. Drozdov, A. Grossfield, and R. V. Pappu, Role of Solvent in Determining Conformational Preferences of Alanine Dipeptide in Water, Journal of the American Chemical Society, vol.126, issue.8, p.2574, 2004.
DOI : 10.1021/ja039051x

K. Kwac, K. Lee, J. B. Han, K. Oh, and M. Cho, Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: Comparisons with IR and vibrational circular dichroism spectra, The Journal of Chemical Physics, vol.128, issue.10, p.105106, 2008.
DOI : 10.1366/0003702963905970

J. Vymetal and J. Vondrásek, Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides ??? The Alanine Dipeptide Case Study, The Journal of Physical Chemistry B, vol.114, issue.16, p.5632, 2010.
DOI : 10.1021/jp100950w

W. Chin, F. Piuzzi, J. Dognon, I. Dimicoli, and M. Mons, Gas-phase models of ?? turns: Effect of side-chain/backbone interactions investigated by IR/UV spectroscopy and quantum chemistry, The Journal of Chemical Physics, vol.25, issue.8, p.84301, 2005.
DOI : 10.1021/ja00071a046

URL : https://hal.archives-ouvertes.fr/hal-00084292

H. S. Biswal, Y. Loquais, B. Tardivel, E. Gloaguen, and M. Mons, XXVII Bibliography, Chem. Chem. Phys. J. Am. Chem. Soc, vol.9285, issue.133, pp.4491-3931, 2007.

R. E. Riter, D. M. Willard, and N. E. Levinger, Water Immobilization at Surfactant Interfaces in Reverse Micelles, The Journal of Physical Chemistry B, vol.102, issue.15, p.2705, 1998.
DOI : 10.1021/jp973330n

J. Faeder and B. M. Ladanyi, Molecular Dynamics Simulations of the Interior of Aqueous Reverse Micelles, The Journal of Physical Chemistry B, vol.104, issue.5, p.1033, 2000.
DOI : 10.1021/jp993076u

J. Faeder and B. M. Ladanyi, Solvation Dynamics in Aqueous Reverse Micelles:?? A Computer Simulation Study, The Journal of Physical Chemistry B, vol.105, issue.45, p.11148, 2001.
DOI : 10.1021/jp010632n

M. R. Harpham, B. M. Ladanyi, N. E. Levinger, and K. W. Herwig, Water motion in reverse micelles studied by quasielastic neutron scattering and molecular dynamics simulations, The Journal of Chemical Physics, vol.66, issue.16, p.7855, 2004.
DOI : 10.1139/p67-025

I. R. Piletic, D. E. Moilanen, D. B. Spry, N. E. Levinger, and M. D. Fayer, Testing the Core/Shell Model of Nanoconfined Water in Reverse Micelles Using Linear and Nonlinear IR Spectroscopy, The Journal of Physical Chemistry A, vol.110, issue.15, p.4985, 2006.
DOI : 10.1021/jp061065c

B. Guillot and Y. Guissani, How to build a better pair potential for water, The Journal of Chemical Physics, vol.23, issue.15, p.6720, 2001.
DOI : 10.1063/1.1315991

M. W. Feyereisen, D. Feller, and D. A. Dixon, Hydrogen Bond Energy of the Water Dimer, The Journal of Physical Chemistry, vol.100, issue.8, p.2993, 1996.
DOI : 10.1021/jp952860l

S. S. Xantheas, Cooperativity and hydrogen bonding network in water clusters, Chemical Physics, vol.258, issue.2-3, p.225, 2000.
DOI : 10.1016/S0301-0104(00)00189-0

F. N. Keutsch, J. D. Cruzan, and R. J. Saykally, The Water Trimer, Chemical Reviews, vol.103, issue.7, p.2533, 2003.
DOI : 10.1021/cr980125a

E. E. Dahlke, R. M. Olson, H. R. Leverentz, and D. G. Truhlar, Assessment of the Accuracy of Density Functionals for Prediction of Relative Energies and Geometries of Low-Lying Isomers of Water Hexamers, The Journal of Physical Chemistry A, vol.112, issue.17, p.3976, 2008.
DOI : 10.1021/jp077376k

J. Kuo, C. V. Ciobanu, L. Ojamäe, I. Shavitt, and S. J. Singer, Short H-bonds and spontaneous self-dissociation in (H2O)20: Effects of H-bond topology, The Journal of Chemical Physics, vol.118, issue.8, p.3583, 2003.
DOI : 10.1063/1.469654

A. Lenz and L. Ojamäe, = 6???22, 28, 30) and Identification of Spectral Contributions from Different H-Bond Conformations in Gaseous and Liquid Water, The Journal of Physical Chemistry A, vol.110, issue.50, p.13388, 2006.
DOI : 10.1021/jp066372x

M. I. Bernal-uruchurtu and I. Ortega-blake, On the Molecular Basis of Water Hydrolysis. A Detailed ab Initio Study, The Journal of Physical Chemistry A, vol.103, issue.7, pp.884-892, 1999.
DOI : 10.1021/jp982573s

B. L. Trout and M. Parrinello, The dissociation mechanism of H2O in water studied by first-principles molecular dynamics, Chemical Physics Letters, vol.288, issue.2-4, p.343, 1998.
DOI : 10.1016/S0009-2614(98)00286-3

W. C. Natzle and C. B. Moore, Recombination of hydrogen ion (H+) and hydroxide in pure liquid water, The Journal of Physical Chemistry, vol.89, issue.12, p.2605, 1985.
DOI : 10.1021/j100258a035

H. Chang, C. Wu, and J. Kuo, Recent advances in understanding the structures of medium-sized protonated water clusters, International Reviews in Physical Chemistry, vol.7, issue.3-4, p.553, 2005.
DOI : 10.1021/jp020242g

S. Mcdonald, L. Ojama, and S. J. Singer, Graph Theoretical Generation and Analysis of Hydrogen-Bonded Structures with Applications to the Neutral and Protonated Water Cube and Dodecahedral Clusters, The Journal of Physical Chemistry A, vol.102, issue.17, p.2824, 1998.
DOI : 10.1021/jp9803539

R. Vuilleumier and D. Borgis, An extended empirical valence bond model for describing proton transfer in H+(H2O)n clusters and liquid water, Chemical Physics Letters, vol.284, issue.1-2, p.71, 1998.
DOI : 10.1016/S0009-2614(97)01365-1

M. P. Hodges and D. Wales, Global minima of protonated water clusters, Chemical Physics Letters, vol.324, issue.4, p.279, 2000.
DOI : 10.1016/S0009-2614(00)00584-4

P. Parkkinen, S. Riikonen, and L. Halonen, Revisited, The Journal of Physical Chemistry A, vol.116, issue.44, p.10826, 2012.
DOI : 10.1021/jp307608k

M. Eigen and . Angew, Chemie Int, 1964.

D. J. Anick, J. Mrázek, J. V. Burda, S. Karthikeyan, N. J. Singh et al., XXIX Bibliography [329], J. Mol. Struct. THEOCHEM J. Chem. Phys. J. Phys. Chem. A, vol.574, issue.112, pp.6527-6559, 2001.

L. Ojamäe, I. Shavitt, and S. J. Singer, Potential models for simulations of the solvated proton in water, The Journal of Chemical Physics, vol.11, issue.13, p.5547, 1998.
DOI : 10.1063/1.470962