H. Furukawa, Structure and Function of Glutamate Receptor Amino Terminal Domains, The Journal of Physiology, vol.590, pp.63-72, 2012.

P. Pinheiro, C. K. Mulle, and . Receptors, Cell and Tissue Research, vol.326, pp.457-482, 2006.

S. F. Traynelis, L. P. Wollmuth, C. J. Mcbain, F. S. Menniti, K. M. Vance et al., Glutamate Receptor Ion Channels: Structure, Regulation, and Function, vol.62, pp.405-496, 2010.

S. M. Schmid and M. Hollmann, To Gate or Not to Gate: Are the Delta Subunits in the Glutamate Receptor Family Functional Ion Channels?, Molecular Neurobiology, vol.37, pp.126-141, 2008.

S. L. Kaye, M. S. Sansom, and P. C. Biggin, Molecular Dynamics Simulations of the Ligand-Binding Domain of an N-Methyl-D-Aspartate Receptor, Journal of Biological Chemistry, vol.281, pp.12736-12742, 2006.

C. G. Lau and R. S. Zukin, NMDA Receptor Trafficking in Synaptic Plasticity and Neuropsychiatric Disorders, Nature Reviews. Neuroscience, vol.8, pp.413-439, 2007.

S. G. Cull-candy and D. N. Leszkiewicz, Role of Distinct NMDA Receptor Subtypes at Central Synapses. Science's STKE : Signal Transduction Knowledge Environment, p.16, 2004.

C. G. Parsons, W. Danysz, and G. Quack, Glutamate in CNS Disorders As a Target For Drug Development: An Update, Drug News & Perspectives, vol.11, pp.523-569, 1998.

W. Danysz and C. G. Parsons, Glycine and N-Methyl-D-Aspartate Receptors: Physiological Significance and Possible Therapeutic Applications, Pharmacological reviews, vol.50, pp.597-664, 1998.

I. G. Tikhonova, I. I. Baskin, V. A. Palyulin, and N. S. Zefirov, CoMFA and Homology-Based Models of the Glycine Binding Site of N-Methyl-D-Aspartate Receptor, Journal of Medicinal Chemistry, vol.46, pp.1609-1616, 2003.

M. J. Millan, N-Methyl-D-Aspartate Receptors as a Target for Improved Antipsychotic Agents: Novel Insights and Clinical Perspectives, Psychopharmacology, vol.179, pp.30-53, 2005.

D. Catarzi, V. Colotta, F. Varano, G. Filacchioni, A. Galli et al., Ionotropic Glutamate Receptor Binding Affinity, and Structure-Activity Relationships of a New, vol.44, pp.3157-3165, 2001.

K. T. Nguyen, S. Syed, S. Urwyler, S. Bertrand, D. Bertrand et al., Discovery of NMDA Glycine Site Inhibitors from the Chemical Universe Database GDB, ChemMedChem, vol.3, pp.1520-1524, 2008.

M. C. Regan, A. Romero-hernandez, and H. Furukawa, A Structural Biology Perspective on NMDA Receptor Pharmacology and Function, Current Opinion in Structural Biology, vol.33, pp.68-75, 2015.

J. W. Newcomer and J. H. Krystal, NMDA Receptor Regulation of Memory and Behavior in Humans, Hippocampus, vol.11, pp.529-542, 2001.

M. Ylilauri and O. T. Pentikäinen, Structural Mechanism of N-Methyl-D-Aspartate Receptor Type 1 Partial Agonism, PLoS ONE, vol.7, p.47604, 2012.

M. L. Blanke and A. M. Vandongen, Biology of the NMDA Receptor, 2009.

L. L. Brunton, J. S. Lazo, K. L. Parker, and &. Goodman, Gilman's The Pharmacological Basis of Therapeutics, 2005.

W. R. Forsyth, J. M. Antosiewicz, and A. D. Robertson, Empirical Relationships Between Protein Structure and Carboxyl pKa Values in Proteins, Proteins: Structure, Function and Genetics, vol.48, pp.388-403, 2002.

H. Li, A. D. Robertson, and J. H. Jensen, Very Fast Empirical Prediction and Rationalization of Protein pKa Values, Proteins: Structure, Function and Genetics, vol.61, pp.704-721, 2005.

T. K. Harris and G. J. Turner, Structural Basis of Perturbed pKa Values of Catalytic Groups in Enzyme Active Sites, IUBMB Life, vol.53, pp.85-98, 2002.

S. Sarigul and I. Dogan, Atroposelective Synthesis of Axially Chiral Thiohydantoin Derivatives, The Journal of Organic Chemistry, vol.81, pp.5895-5902, 2016.

C. Hansch, P. P. Maloney, T. Fujita, and R. M. Muir, Correlation of Biological Activity of Phenoxyacetic Acids with Hammett Substituent Constants and Partition Coefficients, Nature, vol.194, pp.178-180, 1962.

Z. Cheng, Y. Zhang, and W. Fu, Predictive QSAR Models of 3-Acylamino-2-Aminopropionic Acid Derivatives as Partial Agonists of the Glycine Site on the NMDA Receptor, Medicinal Chemistry Research, vol.20, pp.1235-1246, 2011.

X. Zhu, H. Cai, Z. Xu, Y. Wang, H. Wang et al., Classification of 5-HT(1A) Receptor Agonists and Antagonists Using GA-SVM Method, Acta Pharmacologica Sinica, vol.32, pp.1424-1430, 2011.

C. Deng, F. Luan, M. Cruz-monteagudo, F. Borges, and M. N. Cordeiro, Recent Advances on QSAR-Based Profiling of Agonist and Antagonist A3 Adenosine Receptor Ligands, Current Topics in Medicinal Chemistry, vol.13, pp.1048-1068, 2013.

H. Djeradi, A. Rahmouni, and A. Cheriti, Antioxidant Activity of Flavonoids: A QSAR Modeling Using Fukui Indices Descriptors, Journal of Molecular Modeling, vol.20, p.2476, 2014.

J. Yosa, M. Blanco, O. Acevedo, and L. Lareo, Molecular Orbital Differentiation of Agonist and Antagonist Activity in the Glycine B-iGluR-NMDA Receptor, European Journal of Medicinal Chemistry, vol.44, pp.2960-2966, 2009.

D. Fabio and R. , Substituted Indole-2-carboxylates as in Vivo Potent Antagonists Acting as the Strychnine-Insensitive Glycine Binding Site, Journal of Medicinal Chemistry, vol.40, pp.841-850, 1997.

S. Urwyler, P. Floersheim, B. L. Roy, and M. Koller, Drug Design, in Vitro Pharmacology, and Structure-Activity Relationships of 3-Acylamino-2-aminopropionic Acid Derivatives, a Novel Class of Partial Agonists at the Glycine Site on the N-Methyl-D-Aspartate (NMDA) Receptor Complex, Journal of Medicinal Chemistry, vol.52, pp.5093-5107, 2009.

S. Krishnamurty and S. Pal, Intermolecular Reactivity Trends Using the Concept of Group Softness, The Journal of Physical Chemistry A, vol.104, pp.7639-7645, 2000.

R. Vijayaraj, V. Subramanian, and P. K. Chattaraj, Comparison of Global Reactivity Descriptors Calculated Using Various Density Functionals: A QSAR Perspective, Journal of Chemical Theory and Computation, vol.5, pp.2744-2753, 2009.

R. G. Pearson, Hard and Soft Acids and Bases, vol.85, pp.3533-3539, 1963.

R. G. Pearson, Acids and Bases, Science, vol.151, pp.172-177, 1966.

R. G. Pearson, Chemical Hardness

-. Wiley and . Vch, , 1997.

J. Padmanabhan, R. Parthasarathi, M. Elango, V. Subramanian, B. Krishnamoorthy et al., Multiphilic Descriptor for Chemical Reactivity and Selectivity, Journal of Physical Chemistry A, vol.111, pp.9130-9138, 2007.

S. X. Cai, Z. L. Zhou, J. C. Huang, E. R. Whittemore, Z. O. Egbuwoku et al., Synthesis and Structure-Activity Relationships of 1,2,3,4-Tetrahydroquinoline-2,3,4-trione 3-Oximes: Novel and Highly Potent Antagonists for NMDA Receptor Glycine Site, Journal of Medicinal Chemistry, vol.39, pp.3248-3255, 1996.

K. A. Joshi, D. D. Patil, and S. P. Gejji, Molecular Electrostatic Potentials in Aromatic Substituted 4-hydroxyquino-2-lones: Glycine/NMDA Receptor Antagonists, Journal of Molecular Modeling, vol.15, pp.383-390, 2009.

E. Karakas, N. Simorowski, and H. Furukawa, Subunit Arrangement and Phenylethanolamine Binding in GluN1/GluN2B NMDA Receptors, Nature, vol.475, pp.249-253, 2011.

A. Inanobe, H. Furukawa, and E. Gouaux, Mechanism of Partial Agonist Action at the NR1 Subunit of NMDA Receptors, Neuron, vol.47, pp.71-84, 2005.

N. Armstrong and E. Gouaux, Mechanisms for Activation and Antagonism of an AMPA-Sensitive Glutamate Receptor: Crystal Structures of the GluR2 Ligand Binding Core, Neuron, vol.28, pp.165-181, 2000.

M. L. Mayer, Crystal Structures of the GluR5 and GluR6 Ligand Binding Cores: Molecular Mechanisms Underlying Kainate Receptor Selectivity, Neuron, vol.45, pp.539-552, 2005.

M. L. Mayer and N. Armstrong, Structure and Function of Glutamate Receptor Ion Channels, Annual Review of Physiology, vol.66, pp.161-181, 2004.

M. L. Mayer, Glutamate Receptors at Atomic Resolution, Nature, vol.440, pp.456-462, 2006.

H. Furukawa and E. Gouaux, Mechanisms of Activation, Inhibition and Specificity: Crystal Structures of the NMDA Receptor NR1 Ligand-Binding Core, The EMBO Journal, vol.22, pp.2873-2885, 2003.

T. Kvist, T. S. Bielefeldt, J. R. Greenwood, F. Mehrzad-tabrizi, K. B. Hansen et al., Crystal Structure and Pharmacological Characterization of a Novel N-Methyl-D-Aspartate (NMDA) Receptor Antagonist at the GluN1 Glycine Binding Site, Journal of Biological Chemistry, vol.288, pp.33124-33135, 2013.

R. Jin, T. G. Banke, M. L. Mayer, S. F. Traynelis, and E. Gouaux, Structural Basis for Partial Agonist Action at Ionotropic Glutamate Receptors, Nature Neuroscience, vol.6, pp.803-810, 2003.

K. L. Dürr, L. Chen, R. A. Stein, R. De-zorzi, I. M. Folea et al., Structure and Dynamics of AMPA Receptor GluA2 in Resting, Pre-open, and Desensitized States, Cell, vol.158, pp.778-792, 2014.

H. Furukawa, S. K. Singh, R. Mancusso, and E. Gouaux, Subunit Arrangement and Function in NMDA receptors, Nature, vol.438, pp.185-192, 2005.

K. M. Vance, N. Simorowski, S. F. Traynelis, and H. Furukawa, Ligand-Specific Deactivation Time Course of GluN1/GluN2D NMDA Receptors, Nature Communications, vol.2, p.294, 2011.

Y. Yao, J. Belcher, A. J. Berger, M. L. Mayer, and A. Y. Lau, Conformational Analysis of NMDA Receptor GluN1, GluN2, and GluN3 Ligand-Binding Domains Reveals Subtype-Specific Characteristics, Structure, vol.21, pp.1788-1799, 2013.

K. B. Hansen, N. Tajima, R. Risgaard, R. E. Perszyk, L. Jørgensen et al., Structural Determinants of Agonist Ffficacy at the Glutamate Binding Site of N-methyl-D-aspartate Receptors, Molecular Pharmacology, vol.84, pp.114-127, 2013.

E. Yuriev, M. Agostino, and P. A. Ramsland, Challenges and Advances in Computational Docking: 2009 in Review, Journal of Molecular Recognition, vol.24, pp.149-164, 2011.

X. Meng, H. Zhang, M. Mezei, and M. Cui, Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery. Current Computer-Aided Drug Design, vol.7, pp.146-157, 2011.

N. S. Pagadala, K. Syed, and J. Tuszynski, Software for Molecular Docking: A Review, Biophysical Reviews, vol.9, pp.91-102, 2017.

R. W. Zwanzig, High Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases, Journal of Chemical Physics, vol.22, pp.1420-1426, 1954.

T. P. Lybrand, J. A. Mccammon, and G. Wipff, Theoretical Calculation of Relative Binding Affinity in Host-Guest Systems, Proceedings of the National Academy of Sciences of the United States of America, vol.83, pp.833-835, 1986.

J. Aqvist, C. Medina, and J. E. Samuelsson, A New Method for Predicting Binding Affinity in Computer-Aided Drug Design, Protein Engineering, vol.7, pp.385-391, 1994.

P. A. Kollman, I. Massova, C. Reyes, B. Kuhn, S. Huo et al., Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models, Accounts of Chemical Research, vol.33, pp.889-897, 2000.

J. Wang, P. Morin, W. Wang, and P. A. Kollman, Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA, Journal of the American Chemical Society, vol.123, pp.5221-5230, 2001.

D. L. Beveridge and F. M. Dicapua, Free Energy via Molecular Simulation: Applications to Chemical and Biomolecular Systems, Annual Review of Biophysics and Biophysical Chemistry, vol.18, pp.431-492, 1989.

C. Chipot, X. Rozanska, and S. B. Dixit, Can Free Energy Calculations Be Fast and Accurate at the Same Time? Binding of Low-Affinity, Non-Peptide Inhibitors to the SH2 Domain of the SRC, Protein. Journal of Computer-Aided Molecular Design, vol.19, pp.765-770, 2005.

S. Genheden and U. Ryde, How to Obtain Statistically Converged MM/GBSA Results, Journal of Computational Chemistry, vol.31, pp.837-846, 2010.

G. Rastelli, G. Degliesposti, A. Del-rio, and M. Sgobba, Binding Estimation After Refinement, A New Automated Procedure for the Refinement and Rescoring of Docked Ligands in Virtual Screening, Chemical Biology & Drug Design, vol.73, pp.283-286, 2009.

J. Kongsted and U. Ryde, An Improved Method to Predict the Entropy Term with the MM/PBSA Approach, Journal of Computer-Aided Molecular Design, vol.23, pp.63-71, 2009.

S. M. Dravid, P. B. Burger, A. Prakash, M. T. Geballe, R. Yadav et al., Structural Determinants of D-cycloserine Efficacy at the NR1/NR2C NMDA Receptors, The Journal of Neuroscience : The Official Journal of the Society for Neuroscience, vol.30, pp.2741-2754, 2010.

P. A. Postila, M. Ylilauri, and O. T. Pentikäinen, Full and Partial Agonism of Ionotropic Glutamate Receptors Indicated by Molecular Dynamics Simulations, Journal of Chemical Information and Modeling, vol.51, pp.1037-1047, 2011.

T. Mamonova, K. Speranskiy, and M. Kurnikova, Interplay Between Structural Rigidity and Electrostatic Interactions in the Ligand Binding Domain of GluR2, Proteins, vol.73, pp.656-671, 2008.

D. M. Dolino, D. Cooper, S. Ramaswamy, H. Jaurich, C. F. Landes et al., Structural Dynamics of the Glycine-Binding Domain of the N-Methyl-D-Aspartate Receptor, The Journal of Biological Chemistry, vol.290, pp.797-804, 2015.

G. Çifci, V. Aviyente, E. D. Akten, and G. Monard, Assessing Protein-Ligand Binding Modes with Computational Tools: The Ccase of PDE4B, Journal of Computer-Aided Molecular Design, vol.31, pp.563-575, 2017.

C. N. Pace, G. R. Grimsley, and J. M. Scholtz, Protein Ionizable Groups: pKa Values and Their Contribution to Protein Stability and Solubility, Journal of Biological Chemistry, vol.284, pp.13285-13289, 2009.

J. Kim, J. Mao, and M. R. Gunner, Are Acidic and Basic Groups in Buried Proteins Predicted to Be Ionized?, Journal of Molecular Biology, vol.348, pp.1283-1298, 2005.

C. Ji, Y. Mei, and J. Z. Zhang, Developing Polarized Protein-Specific Charges for Protein Dynamics: MD Free Energy Calculation of pKa Shifts for Asp26/Asp 20 in Thioredoxin, Biophysical Journal, vol.95, pp.1080-1088, 2008.

D. G. Isom, C. A. Castaneda, B. R. Cannon, E. Garcia-moreno, and B. , Large Shifts in pKa Values of Lysine Residues Buried Inside a Protein, Proceedings of the National Academy of Sciences, vol.108, pp.5260-5265, 2011.

H. Li, A. D. Robertson, and J. H. Jensen, The Determinants of Carboxyl pKa Values in Turkey Ovomucoid Third Domain, Proteins: Structure, Function and Genetics, vol.55, pp.689-704, 2004.

D. E. Anderson, W. J. Becktel, and F. W. Dahlquist, pH-Induced Denaturation of Proteins: A Single Salt Bridge Contributes 3-5 kcal/mol to the Free Energy of Folding of T4 Lysozyme, Biochemistry, vol.29, pp.2403-2408, 1990.

H. Schmidt, G. Shah, L. Sperling, and C. Rienstra, NMR Determination of Protein pKa Values in the Solid State, Journal of Physical Chemistry Letters, vol.1, pp.1623-1628, 2010.

E. Oksanen, J. C. Chen, and S. Z. Fisher, Neutron Crystallography for the Study of Hydrogen Bonds in Macromolecules, vol.22, pp.1-26, 2017.

M. D. Liptak and G. C. Shields, Accurate pK a Calculations for Carboxylic Acids Using Complete Basis Set and Gaussian-n Models Combined with CPCM Continuum Solvation Methods, Journal of the American Chemical Society, vol.123, pp.7314-7319, 2001.

M. D. Liptak, K. C. Gross, P. G. Seybold, S. Feldgus, and G. C. Shields, Absolute pK a Determinations for Substituted Phenols, Journal of the American Chemical Society, vol.124, pp.6421-6427, 2002.

A. M. Rebollar-zepeda and A. Galano, First Principles Calculations of pKa Values of Amines in Aqueous Solution: Application to Neurotransmitters, International Journal of Quantum Chemistry, vol.112, pp.3449-3460, 2012.

B. Thapa and H. B. Schlegel, Calculations of pKa's and Redox Potentials of Nucleobases with Explicit Waters and Polarizable Continuum Solvation, Journal of Physical Chemistry A, vol.119, pp.5134-5144, 2015.

R. Casasnovas, J. Ortega-castro, J. Frau, J. Donoso, and F. Muñoz, Theoretical pKa Calculations with Continuum Model Solvents, Alternative Protocols to Thermodynamic Cycles, International Journal of Quantum Chemistry, vol.114, pp.1350-1363, 2014.

J. Zhang, T. Kleinoder, and J. Gasteiger, Prediction of pK a Values for Aliphatic Carboxylic Acids and Alcohols with Empirical Atomic Charge Descriptors, Journal of Chemical Information and Modeling, vol.46, pp.2256-2266, 2006.

F. Milletti, L. Storchi, G. Sforna, and G. Cruciani, New and Original pKa Prediction Method Using Grid Molecular Interaction Fields, Journal of Chemical Information and Modeling, vol.47, pp.2172-2181, 2007.

L. Xing and R. C. Glen, Novel Methods for the Prediction of logP, pKa, and logD, Journal of Chemical Information and Computer Sciences, vol.42, pp.796-805, 2002.

L. Xing, R. C. Glen, and R. D. Clark, Predicting pKa by Molecular Tree Structured Fingerprints and PLS, Journal of Chemical Information and Computer Sciences, vol.43, pp.870-879, 2003.

R. Parthasarathi, J. Padmanabhan, M. Elango, K. Chitra, and V. Subra-manian, Chattaraj, P. K. pKa Prediction Using Group Philicity, Journal of Physical Chemistry A, vol.110, pp.6540-6544, 2006.

L. Tao, J. Han, and F. M. Tao, Correlations and Predictions of Carboxylic Acid pKa Values Using Intermolecular Structure and Properties of Hydrogen-Bonded Complexes, Journal of Physical Chemistry A, vol.112, pp.775-782, 2008.

A. J. Abkowicz-bienko and Z. Latajka, Density Functional Study on Phenol Derivative-Ammonia Complexes in the Gas Phase, Journal of Physical Chemistry A, vol.104, pp.1004-1008, 2000.

G. Caballero-garcía, G. Mondragón-solórzano, R. Torres-cadena, M. Díaz-garcía, J. Sandoval-lira et al., Calculation of Vs,Max and Its Use as a Descriptor for the Theoretical Calculation of pKa Values for Carboxylic Acids, Molecules, p.24, 2019.

C. Grüber and V. Buß, Quantum-Mechanically Calculated Properties for the Development of Quantitative Structure-Activity Relationships (QSAR'S). pKA-Values of Phenols and Aromatic and Aliphatic Carboxylic Acids, Chemosphere, vol.19, pp.1595-1609, 1989.

E. Soriano, S. Cerdán, and P. Ballesteros, Computational Determination of pKa Values. A Comparison of Different Theoretical Approaches and a Novel Procedure, Journal of Molecular Structure: THEOCHEM, vol.684, pp.121-128, 2004.

F. H. Clarke and N. M. Cahoon, Ionization Constants by Curve Fitting: Determination of Partition and Distribution Coefficients of Acids and Bases and Their Ions, Journal of Pharmaceutical Sciences, vol.76, pp.611-620, 1987.

S. L. Dixon and P. C. Jurs, Estimation of pKa for Organic Oxyacids Using Calculated Atomic Charges, Journal of Computational Chemistry, vol.14, pp.1460-1467, 1993.

M. J. Citra, Estimating the pKa of Phenols, Carboxylic Acids and Alcohols from Semi-Empirical Quantum Chemical Methods, Chemosphere, vol.38, pp.191-206, 1999.

R. S. Varekova, S. Geidl, C. M. Ionescu, O. Skrehota, M. Kudera et al., Predicting pKa Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes, Journal of Chemical Information and Modeling, vol.51, pp.1795-1806, 2011.

I. Ugur, A. Marion, S. Parant, J. H. Jensen, and G. Monard, Rationalization of the pK a Values of Alcohols and Thiols Using Atomic Charge Descriptors and Its Application to the Prediction of Amino Acid pK a 's, Journal of Chemical Information and Modeling, vol.54, pp.2200-2213, 2014.

W. M. Haynes and . Ed, CRC Handbook of Chemistry and Physics, 2018.

S. Zhang, J. Baker, and P. Pulay, A Reliable and Efficient First Principles-Based Method for Predicting pK a Values. 2. Organic Acids, The Journal of Physical Chemistry A, vol.114, pp.432-442, 2010.

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.37, pp.785-789, 1988.

A. Becke, Density-Functional Exchange-Energy Approximation with Correct Asymptotic Behavior, Physical Review A, General Physics, vol.38, pp.3098-3100, 1988.

A. Becke, A New Mixing of Hartree-Fock and Local Density-Functional Theories, The Journal of Chemical Physics, vol.98, pp.1372-1377, 1993.

N. C. Handy and A. J. Cohen, Left-Right Correlation Energy, Molecular Physics, vol.99, pp.403-412, 2001.

J. P. Perdew, K. Burke, and M. Ernzerhof, Generalized Gradient Approximation Made Simple, Physical Review Letters, vol.77, pp.3865-3868, 1996.

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.120, pp.215-241, 2008.

Y. Zhao and D. G. Truhlar, Density Functionals with Broad Applicability in Chemistry, Accounts of Chemical Research, vol.41, pp.157-167, 2008.

A. V. Marenich, C. J. Cramer, and D. G. Truhlar, Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions, The Journal of Physical Chemistry B, vol.113, pp.6378-6396, 2009.

G. Scalmani and M. J. Frisch, Continuous Surface Charge Polarizable Continuum Models of Solvation. I. General Formalism, The Journal of Chemical Physics, p.114110, 2010.

V. Barone and M. Cossi, Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model, Journal of Physical Chemistry A, vol.102, 1995.

R. S. Mulliken, Electronic Population Analysis on LCAO-MO Molecular Wave Functions. I. The Journal of Chemical Physics, vol.23, pp.1833-1840, 1955.

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.18, pp.365-375, 1950.

A. E. Reed, R. B. Weinstock, and F. Weinhold, Natural Population Analysis, The Journal of Chemical Physics, vol.83, pp.735-746, 1985.

J. M. Fraile, G. Lafuente, J. A. Mayoral, and A. Pallarés, Synthesis and Reactivity of 5-Methylenehydantoins, Tetrahedron, vol.67, pp.8639-8647, 2011.

A. Al-obaid, H. El-subbagh, A. Khodair, and M. Elmazar, 5-Substituted-2-Thiohydantoin Analogs as a Novel Class of Antitumor Agents. Anti-Cancer Drugs, vol.7, pp.873-880, 1996.

A. A. El-barbary, A. I. Khodair, E. B. Pedersen, C. Nielsen, and . S-glucosylated, Hydantoins as New Antiviral Agents, Journal of Medicinal Chemistry, vol.37, pp.73-77, 1994.

J. Marton, J. Enisz, S. Hosztafi, and T. Timar, Preparation and Fungicidal Activity of 5-Substituted Hydantoins and Their 2-Thio Analogs, Journal of Agricultural and Food Chemistry, vol.41, pp.148-152, 1993.

J. V. Marx, D. A. Richert, and W. W. Westerfeld, Peripheral Inhibition of Thyroxine by Thiohydantoins Derived from Amino Acids, Journal of Medicinal Chemistry, vol.13, pp.1179-1181, 1970.

J. E. Tompkins, 5-Diaryl-2-Thiohydantoins and 5,5-Diaryl N3-Substituted 2-Thiohydantoins as Potential Hypolipidemic Agents, Journal of Medicinal Chemistry, vol.5, pp.855-859, 1986.

J. Elwood, D. A. Richert, and W. Westerfeld, A Comparison of Hypolipidemic Drugs in the Prevention of an Orotic Acid Fatty Liver, Biochemical Pharmacology, vol.21, pp.1127-1134, 1972.

A. Takahashi, H. Matsuoka, Y. Ozawa, and Y. Uda, Antimutagenic Properties of 3,5-Disubstituted 2-Thiohydantoins, Journal of Agricultural and Food Chemistry, vol.46, pp.5037-5042, 1998.

E. Froelich, A. Fruehan, M. Jackman, F. K. Kirchner, E. J. Alexander et al., New Antitubercular Agent. Journal of the American Chemical Society, vol.76, pp.3099-3100, 1954.

H. P. Das and G. Mahapatra, New 2-Thiohydantoins as Potential Pesticides, Indian Journal of Chemistry. Section B, vol.21, pp.162-164, 1982.

R. T. Pardasani, P. Pardasani, C. K. Ojha, D. Sherry, V. Chaturvedi et al., Syntheses of Indigoid Dye Precursors and Bioactive Compounds Via Condensation of 1,2-and 1,4-Diones with Thiohydantoins. Phosphorus, Sulfur, and Silicon and the Related Elements, vol.177, pp.2435-2443, 2002.

A. C. Curran, Patent, vol.3, p.430, 1976.

B. Mo, J. Li, and S. Liang, Chemical Carboxy-Terminal Sequence Analysis of Peptides Using Acetyl Isothiocyanate, Analytical Biochemistry, vol.252, pp.169-176, 1997.

S. S. Kandil, G. B. El-hefnawy, and E. A. Baker, Thermal and Spectral Studies of 5-(Phenylazo)-2-Thiohydantoin and 5-(2-Hydroxyphenylazo)-2-Thiohydantoin Complexes of Cobalt(II), Nickel(II) and Copper(II), Thermochimica Acta, vol.414, pp.105-113, 2004.

M. Ichitani, S. Kitoh, K. Tanaka, S. Fujinami, M. Suda et al., Synthesis and Crystal Structure of (S)-5-Isopropyl-5-Methyl-2-Thiohydantoin, European Journal of Chemistry, vol.4, pp.350-352, 2013.

M. A. Metwally and E. Abdel-latif, Thiohydantoins: Synthetic Strategies and Chemical Reactions, Journal of Sulfur Chemistry, vol.33, pp.229-257, 2012.

T. Kawabata, S. Kawakami, and K. Fuji, Enantioselective ?-allylation of a phenylalanine derivative under the control of aggregation of a chiral nonracemic enolate, Tetrahedron Letters, vol.43, pp.1465-1467, 2002.

Y. Aydeniz, F. Oguz, A. Yaman, A. S. Konuklar, I. Dogan et al., Barriers to Internal Rotation Around the C-N Bond in 3-(o-Aryl)-5-Methyl-Rhodanines Using NMR Spectroscopy and Computational Studies. Electron Density Topological Analysis of the Transition States. Organic and Biomolecular Chemistry, vol.2, pp.2426-2436, 2004.

A. Yildirim, F. A. Konuklar, S. Catak, V. Van-speybroeck, and M. Waroquier, Dogan, I.; Aviyente, V. Solvent-Catalyzed Ring-Chain-Ring Tautomerization in Axially Chiral Compounds, Chemistry -A European Journal, vol.18, pp.12725-12732, 2012.

E. M. Yilmaz and I. Dogan, Axially Chiral N-(o-Aryl)-2-Thioxo-oxazolidine-4-one and Rhodanine Derivatives: Enantiomeric Separation and Determination of Racemization Barriers, Tetrahedron: Asymmetry, vol.19, pp.2184-2191, 2008.

V. Belot, D. Farran, M. Jean, M. Albalat, N. Vanthuyne et al., Steric Scale of Common Substituents from Rotational Barriers of N-(o-Substituted aryl)thiazoline-2-thione Atropisomers, The Journal of Organic Chemistry, vol.82, pp.10188-10200, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01682730

D. Bonne and J. Rodriguez, Enantioselective Syntheses of Atropisomers Featuring a Five-Membered Ring, Chemical Communications, vol.53, pp.12385-12393, 2017.
URL : https://hal.archives-ouvertes.fr/medihal-01705653

D. Bonne and J. Rodriguez, A Bird's Eye View of Atropisomers Featuring a Five-Membered Ring, European Journal of Organic Chemistry, pp.2417-2431, 2018.

G. Bringmann, A. J. Mortimer, P. A. Keller, M. J. Gresser, and J. Garner, Breuning, M. Atroposelective Synthesis of Axially Chiral Biaryl Compounds, Angewandte Chemie International Edition, vol.44, pp.5384-5427, 2005.

S. Erol and I. Dogan, Axially Chiral 2-Arylimino-3-aryl-thiazolidine-4-one Derivatives: Enantiomeric Separation and Determination of Racemization Barriers by Chiral HPLC. The Journal of Organic Chemistry, vol.72, pp.2494-2500, 2007.

E. Kumarasamy, R. Raghunathan, M. P. Sibi, and J. Sivaguru, Nonbiaryl and Heterobiaryl Atropisomers: Molecular Templates with Promise for Atropselective Chemical Transformations, Chemical Reviews, vol.115, pp.11239-11300, 2015.

P. Renzi, Organocatalytic Synthesis of Axially Chiral Atropisomers, Organic & Biomolecular Chemistry, vol.15, pp.4506-4516, 2017.

S. D. Jacob, J. L. Brooks, and A. J. Frontier, No Acid Required: 4? and 6? Electrocyclization Reactions of Dienyl Diketones for the Synthesis of Cyclopentenones and 2H-Pyrans, The Journal of Organic Chemistry, vol.79, pp.10296-10302, 2014.

B. Pem and V. Vr?ek, Substituent Effects on the Stability of 1,4-Benzodiazepin-2-one Tautomers: A Density Functional Study, International Journal of Quantum Chemistry, vol.118, p.25523, 2018.

C. Tian, P. Xiu, Y. Meng, W. Zhao, Z. Wang et al., Enantiomerization Mechanism of Thalidomide and the Role of Water and Hydroxide Ions, Chemistry -A European Journal, vol.18, pp.14305-14313, 2012.

T. Kawabata, S. Majumdar, K. Tsubaki, and D. Monguchi, Memory of Chirality in Intramolecular Conjugate Addition of Enolates: A Novel Access to Nitrogen Heterocycles with Contiguous Quaternary and Tertiary Stereocenters, Organic & Biomolecular Chemistry, 1609.

J. A. Pople and G. A. Segal, Approximate Self-Consistent Molecular Orbital Theory. II. Calculations with Complete Neglect of Differential Overlap, The Journal of Chemical Physics, vol.43, pp.136-151, 1965.

J. A. Pople, D. L. Beveridge, and P. A. Dobosh, Approximate Self-Consistent Molecular-Orbital Theory. V. Intermediate Neglect of Differential Overlap, The Journal of Chemical Physics, vol.47, pp.2026-2033, 1967.

J. A. Pople, D. P. Santry, and G. A. Segal, Approximate Self-Consistent Molecular Orbital Theory. I. Invariant Procedures, The Journal of Chemical Physics, vol.43, pp.129-135, 1965.

M. J. Dewar and W. Thiel, Ground States of Molecules. 38. The MNDO Method. Approximations and Parameters, Journal of the American Chemical Society, vol.99, pp.4899-4907, 1977.

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, pp.3902-3909, 1985.

J. J. Stewart, Optimization of Parameters for Semiempirical Methods I. Method. Journal of Computational Chemistry, vol.10, pp.209-220, 1989.

D. M. Ceperley and B. J. Alder, Ground State of the Electron Gas by a Stochastic Method, Physical Review Letters, vol.45, pp.566-569, 1980.

S. H. Vosko, L. Wilk, and M. Nusair, Accurate Spin-Dependent Eelectron Liquid Correlation Energies for Local Spin Density Calculations: A Critical Analysis, Canadian Journal of Physics, vol.58, pp.1200-1211, 1980.

J. P. Perdew and A. Zunger, Self-Interaction Correction to Density-Functional Approximations for Many-Electron Systems, Physical Review B, vol.23, pp.5048-5079, 1981.

G. Ortiz and P. Ballone, Correlation Energy, Structure Factor, Radial Distribution Function, and Momentum Distribution of the Spin-Polarized Uniform Electron Gas, Physical Review B, vol.50, pp.1391-1405, 1994.

C. J. Cramer, Essentials of Computational Chemistry : Theories and Models, 2004.

B. Miehlich, A. Savin, H. Stoll, and H. Preuss, Results Obtained with the Correlation Energy Density Functionals of Becke and Lee, Yang and Parr, Chemical Physics Letters, vol.157, pp.200-206, 1989.

M. Guidon, J. Hutter, and J. Vandevondele, Auxiliary Density Matrix Methods for Hartree-Fock Exchange Calculations, Journal of Chemical Theory and Computation, vol.6, pp.2348-2364, 2010.

C. Adamo and V. Barone, Toward Reliable Density Functional Methods Without Adjustable Parameters: The PBE0 Model, The Journal of Chemical Physics, vol.110, pp.6158-6170, 1999.

Y. Zhao and D. G. Truhlar, A New Local Density Functional for Main-group Thermochemistry, Transition Metal Bonding, Thermochemical Kinetics, and Noncovalent Interactions, The Journal of Chemical Physics, vol.125, 2006.

R. Ditchfield, W. J. Hehre, and J. A. Pople, Self-Consistent Molecular-Orbital Methods. IX. An Extended Gaussian-Type Basis for Molecular-Orbital Studies of Organic Molecules, The Journal of Chemical Physics, vol.54, pp.724-728, 1971.

A. R. Leach, Molecular Modelling : Principles and Applications

F. L. Hirshfeld, Bonded-Atom Fragments for Describing Molecular Charge Densities, Theoretica Chimica Acta, vol.44, pp.129-138, 1977.

A. V. Marenich, S. V. Jerome, C. J. Cramer, and D. G. Truhlar, Charge Model 5: An Extension of Hirshfeld Population Analysis for the Accurate Description of Molecular Interactions in Gaseous and Condensed Phases, Journal of Chemical Theory and Computation, vol.8, pp.527-541, 2012.

S. Miertu?, E. Scrocco, and J. Tomasi, Electrostatic Interaction of a Solute with a Continuum. A Direct Utilizaion of AB Initio Molecular Potentials for the Prevision of Solvent Effects, Chemical Physics, vol.55, pp.117-129, 1981.

V. Barone and M. Cossi, Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model, Journal of Pjysical Chemistry A, vol.102, 1995.

B. Mennucci, E. Cancès, and J. Tomasi, Evaluation of Solvent Effects in Isotropic and Anisotropic Dielectrics and in Ionic Solutions with a Unified Integral Equation Method: Theoretical Bases, Computational Implementation, and Numerical Applications, The Journal of Physical Chemistry B, vol.101, pp.10506-10517, 1997.

B. Mennucci and J. Tomasi, Continuum Solvation Models: A New Approach to the Problem of Solute's Charge Distribution and Cavity Boundaries, The Journal of Chemical Physics, vol.106, pp.5151-5158, 1997.

W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz et al., A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules, Journal of the American Chemical Society, vol.117, pp.5179-5197, 1995.

L. Verlet, Computer Experiments on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules. Physical Review, vol.159, pp.98-103, 1967.

, Hockney

W. and R. , The Potential Calculation and Some Applications, Computational Physics, vol.9, pp.136-211, 1970.

W. C. Swope, H. C. Andersen, P. H. Berens, and K. R. Wilson, Computer Simulation Method for the Calculation of Equilibrium Constants for the Formation of Physical Clusters of Molecules: Application to Small Water Clusters, The Journal of Chemical Physics, vol.76, pp.637-649, 1982.

D. S. Cerutti and D. A. Case, Multi-Level Ewald: A Hybrid Multigrid / Fast Fourier Transform Approach to the Electrostatic Particle-Mesh Problem, Journal of Chemical Theory and Computation, vol.6, pp.443-458, 2010.

H. C. Andersen, Molecular Dynamics Simulations at Constant Pressure and/or Temperature, The Journal of Chemical Physics, vol.72, pp.2384-2393, 1980.

H. J. Berendsen, J. P. Postma, W. F. Van-gunsteren, A. Dinola, and J. R. Haak, Molecular Dynamics with Coupling to an External Bath, The Journal of Chemical Physics, vol.81, pp.3684-3690, 1984.

S. F. Sousa, P. A. Fernandes, and M. J. Ramos, Protein-Ligand Docking: Current Status and Future Challenges, Proteins: Structure, Function, and Bioinformatics, vol.65, pp.15-26, 2006.

L. F. Ten-eyck, J. Mandell, V. A. Roberts, and M. E. Pique, Surveying Molecular Interactions with DOT, Proceedings of the 1995 ACM/IEEE conference on Supercomputing (CDROM) -Supercomputing '95, 1995.

I. A. Vakser, Evaluation of GRAMM Low-Resolution Docking Methodology on the Hemagglutinin-Antibody Complex, Proteins, vol.1, pp.226-230, 1997.

R. Chen and Z. Weng, Docking Unbound Proteins Using Shape Complementarity, Desolvation, and Electrostatics, Proteins, vol.47, pp.281-294, 2002.

T. N. Hart, R. J. Read, and . Multiple, Proteins: Structure, Function, and Genetics, vol.13, pp.206-222, 1992.

D. S. Goodsell, H. Lauble, C. D. Stout, and A. J. Olson, Automated Docking in Crystallography: Analysis of the Substrates of Aconitase, Proteins: Structure, Function, and Genetics, vol.17, pp.1-10, 1993.

C. M. Oshiro, I. D. Kuntz, and J. S. Dixon, Flexible Ligand Docking Using a Genetic Algorithm, Journal of Computer-Aided Molecular Design, vol.9, pp.113-130, 1995.

G. Jones, P. Willett, R. C. Glen, A. R. Leach, and R. Taylor, Development and Validation of a Genetic Algorithm for Flexible Docking, Journal of Molecular Biology, vol.267, pp.727-748, 1997.

G. M. Morris, D. S. Goodsell, R. S. Halliday, R. Huey, W. E. Hart et al., Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function, Journal of Computational Chemistry, vol.19, pp.1639-1662, 1998.

D. B. Kitchen, H. Decornez, J. R. Furr, and J. Bajorath, Docking and Scoring in Virtual Screening for Drug Discovery: Methods and Applications, Nature Reviews Drug Discovery, vol.3, pp.935-949, 2004.

C. Sotriffer, Virtual Screening : Principles, Challenges, and Practical Guidelines, p.519, 2011.

E. C. Meng, B. K. Shoichet, and I. D. Kuntz, Automated Docking with Grid-Based Energy Evaluation, Journal of Computational Chemistry, vol.13, pp.505-524, 1992.

A. N. Jain, Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine, Journal of Medicinal Chemistry, vol.46, pp.499-511, 2003.

M. Rarey, B. Kramer, T. Lengauer, and G. Klebe, A Fast Flexible Docking Method Using an Incremental Construction Algorithm, Journal of Molecular Biology, vol.261, pp.470-489, 1996.

I. Muegge and . Scoring-revisited, Journal of Medicinal Chemistry, vol.49, pp.5895-5902, 2006.

H. F. Velec, H. Gohlke, and G. Klebe, DrugScore (CSD)-Knowledge-Based Scoring Function Derived from Small Molecule Crystal Data with Superior Recognition Rate of Near-Native Ligand Poses and Better Affinity Prediction, Journal of Medicinal Chemistry, vol.48, pp.6296-6303, 2005.

Y. Shao, L. Molnar, Y. Jung, J. Kussmann, C. Ochsenfeld et al., Advances in Methods and Algorithms in a Modern Quantum Chemistry Program Package, Phys. Chem. Chem. Phys, vol.8, pp.3172-3191, 2006.

P. Hohenberg and W. Kohn, Inhomogeneous Electron Gas. Physical Review, vol.136, pp.864-871, 1964.

W. Kohn and L. J. Sham, Self-Consistent Equations Including Exchange and Correlation Effects, Physical Review, vol.140, pp.1133-1138, 1965.

M. Orio, D. A. Pantazis, and F. Neese, Density Functional Theory, Photosynthesis Research, vol.102, pp.443-453, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00169803

M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, and M. A. Robb, Cheeseman, J. R, 2009.

E. Cancès, B. Mennucci, and J. Tomasi, A New Integral Equation Formalism for the Polarizable Continuum Model: Theoretical Background and Applications to Isotropic and Anisotropic Dielectrics, The Journal of Chemical Physics, vol.107, pp.3032-3041, 1997.

R. G. Parr and R. G. Pearson, Absolute Hardness: Companion Parameter to Absolute Electronegativity, Journal of the American Chemical Society, vol.105, pp.7512-7516, 1983.

M. Buhl, M. Kaupp, O. L. Malkina, and V. G. Malkin, The DFT Route to NMR Chemical Shifts, Journal of Computational Chemistry, vol.20, pp.91-105, 1999.

R. Ditchfield, Self-Consistent Perturbation Theory of Diamagnetism, Molecular Physics, vol.27, pp.789-807, 1974.

K. Wolinski, J. F. Hinton, and P. Pulay, Efficient Implementation of the Gauge-Independent Atomic Orbital Method for NMR Chemical Shift Calculations, Journal of the American Chemical Society, vol.112, pp.8251-8260, 1990.

C. Miranda, F. Escarti, L. ;. Lamarque, M. Yunta, P. Navarro et al., New 1H-Pyrazole-Containing Polyamine Receptors Able To Complex l-Glutamate in Water at Physiological pH Values, Journal of the American Chemical Society, vol.126, pp.823-833, 2003.

R. Bischoff and H. Schlüter, Amino acids: Chemistry, Functionality and Selected Non-Enzymatic Post-Translational Modifications, Journal of Proteomics, vol.75, pp.2275-2296, 2012.

L. Moretti, O. T. Pentikäinen, L. Settimo, and M. S. Johnson, Model Structures of the N-Methyl-D-Aspartate Receptor Subunit NR1 Explain the Molecular Recognition of Agonist and Antagonist Ligands, Journal of Structural Biology, vol.145, pp.205-215, 2004.

A. Rios, T. L. Amyes, and J. P. Richard, Formation and Stability of Organic Zwitterions in Aqueous Solution: Enolates of the Amino Acid Glycine and Its Derivatives, Journal of American Chemical Society, vol.122, pp.9373-9385, 2000.

A. Agarwal and E. W. Taylor, 3-D QSAR for Intrinsic Activity of 5-HT1A Receptor Ligands by the Method of Comparative Molecular Field Analysis, Journal of Computational Chemistry, vol.14, pp.237-245, 1993.

F. Osterberg, G. M. Morris, M. F. Sanner, A. J. Olson, and D. S. Goodsell, Automated Docking to Multiple Target Structures: Incorporation of Protein Mobility and Structural Water Heterogeneity in AutoDock, Proteins, vol.46, pp.34-40, 2002.

M. Schapira, R. Abagyan, and M. Totrov, Nuclear Hormone Receptor Targeted Virtual Screening, Journal of Medicinal Chemistry, vol.46, pp.3045-3059, 2003.

C. M. Venkatachalam, X. Jiang, T. Oldfield, and M. Waldman, LigandFit: A Novel Method for the Shape-Directed Rapid Docking of Ligands to Protein Active Sites, Journal of Molecular Graphics & Modelling, vol.21, pp.289-307, 2003.

M. R. Mcgann, H. R. Almond, A. Nicholls, J. A. Grant, and F. K. Brown, Gaussian Docking Functions, Biopolymers, vol.68, pp.76-90, 2003.

R. A. Friesner, J. L. Banks, R. B. Murphy, T. A. Halgren, J. J. Klicic et al., A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy, Journal of Medicinal Chemistry, vol.47, pp.1739-1749, 2004.

O. Trott and A. J. Olson, Software News and Update AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading, Journal of Computational Chemistry, vol.31, pp.455-461, 2010.

C. R. Corbeil, C. I. Williams, and P. Labute, Variability in Docking Success Rates due to Dataset Preparation, Journal of Computer-Aided Molecular Design, vol.26, pp.775-786, 2012.

H. Zhao and A. Caflisch, Discovery of ZAP70 Inhibitors by High-Throughput Docking into a Conformation of its Kinase Domain Generated by Molecular Dynamics, Bioorganic & Medicinal Chemistry Letters, vol.23, pp.5721-5726, 2013.

S. Ruiz-carmona, D. Alvarez-garcia, N. Foloppe, A. B. Garmendia-doval, S. Juhos et al., rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids, PLoS Computational Biology, p.10, 2014.

W. J. Allen, T. E. Balius, S. Mukherjee, S. R. Brozell, D. T. Moustakas et al., DOCK 6: Impact of New Features and Current Docking Performance, Journal of Computational Chemistry, vol.36, pp.1132-1156, 2015.

G. M. Morris, R. Huey, W. Lindstrom, M. F. Sanner, R. K. Belew et al., AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility, Journal of Computational Chemistry, vol.30, pp.2785-2791, 2009.

D. Case, I. Ben-shalom, S. Brozell, D. Cerutti, T. C. Cruzeiro et al., , 2018.

W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, Comparison of Simple Potential Functions for Simulating Liquid Water, The Journal of Chemical Physics, vol.79, pp.926-935, 1983.

J. A. Maier, C. Martinez, K. Kasavajhala, L. Wickstrom, and K. E. Hauser, Simmerling, C. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB, Journal of Chemical Theory and Computation, vol.11, pp.3696-3713, 2015.

J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, and D. A. Case, Development and Testing of a General Amber Force Field, Journal of Computational Chemistry, vol.25, pp.1157-1174, 2004.

J. P. 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, pp.327-341, 1977.

G. D. Hawkins, C. J. Cramer, and D. G. Truhlar, Pairwise Solute Descreening of Solute Charges from a Dielectric Medium, Chemical Physics Letters, vol.246, pp.122-129, 1995.

G. D. Hawkins, C. J. Cramer, and D. G. Truhlar, Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium, Journal of Physical Chemistry, vol.100, pp.19824-19839, 1996.

V. Tsui and D. A. Case, Theory and Applications of the Generalized Born Solvation Model in Macromolecular Simulations, Biopolymers, vol.56, pp.275-291, 2000.

A. Onufriev, D. Bashford, and D. A. Case, Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model, Proteins, vol.55, pp.383-394, 2004.

J. Mongan, C. Simmerling, J. A. Mccammon, D. A. Case, and A. Onufriev, Generalized Born Model with a Simple, Robust Molecular Volume Correction, Journal of Chemical Theory and Computation, vol.3, pp.156-169, 2007.

H. Nguyen, D. R. Roe, and C. Simmerling, Improved Generalized Born Solvent Model Parameters for Protein Simulations, Journal of Chemical Theory and Computation, vol.9, pp.2020-2034, 2013.

J. Weiser, P. S. Shenkin, and W. C. Still, Approximate Atomic Surfaces from Linear Combinations of Pairwise Overlaps (LCPO), Journal of Computational Chemistry, vol.20, pp.217-230, 1999.

Y. Zhao and D. G. Truhlar, Density Functionals with Broad Applicability in Chemistry, Accounts of Chemical Research, vol.41, pp.157-167, 2008.

U. C. Singh and P. A. Kollman, An approach to Computing Electrostatic Charges for Molecules, Journal of Computational Chemistry, vol.5, pp.129-145, 1984.

C. M. Breneman and K. B. Wiberg, Determining Atom-Centered Monopoles from Molecular Electrostatic Potentials. The Need for High Sampling Density in Formamide Conformational Analysis, Journal of Computational Chemistry, vol.11, pp.361-373, 1990.

G. R. Grimsley, J. M. Scholtz, and C. N. Pace, A Summary of the Measured pKa Values of the Ionizable Groups in Folded Proteins, Protein Science, vol.18, pp.247-251, 2008.

R. L. Thurlkill, G. R. Grimsley, J. M. Scholtz, and C. N. Pace, pKa Values of the Ionizable Groups of Proteins, vol.15, pp.1214-1218, 2006.

P. D. Leeson, R. Baker, R. W. Carling, J. J. Kulagowski, I. M. Mawer et al., Amino Acid Bioisosteres: Design of 2-Quinolone Derivatives as Glycine-Site N-Methyl-D-Aspartate Receptor Antagonists, Bioorganic & Medicinal Chemistry Letters, vol.3, pp.299-304, 1993.

W. H. Brown, Organic chemistry

. Brooks/cole-cengage and . Learning, , 2009.

L. Liu, D. Malhotra, R. S. Paton, K. N. Houk, and G. B. Hammond, The [4+2], not [2+2], Mechanism Occurs in the Gold-Catalyzed Intramolecular Oxygen Transfer Reaction of 2-Alkynyl-1,5-Diketones, Angewandte Chemie International Edition, vol.49, pp.9132-9135, 2010.

D. Cantillo and C. O. Kappe, A Unified Mechanistic View on the Morita-Baylis-Hillman Reaction: Computational and Experimental Investigations, The Journal of Organic Chemistry, vol.75, pp.8615-8626, 2010.

S. Catak, K. Hemelsoet, L. Hermosilla, M. Waroquier, and V. Van-speybroeck, Competitive Reactions of Organophosphorus Radicals on Coke Surfaces, Chemistry -A European Journal, vol.17, pp.12027-12036, 2011.

J. M. Winne, S. Catak, M. Waroquier, and V. Van-speybroeck, Scope and Mechanism of the (4+3) Cycloaddition Reaction of Furfuryl Cations, Angewandte Chemie International Edition, vol.50, pp.11990-11993, 2011.

W. Pluempanupat, M. Abraham, L. Brecker, P. Wolschann, A. Karpfen et al., Synthesis and Conformation of Chiral Biheteroaryls. The Journal of Organic Chemistry, vol.76, pp.3222-3230, 2011.

L. Degennaro, R. Mansueto, E. Carenza, R. Rizzi, S. Florio et al., Nitrogen Dynamics and Reactivity of Chiral Aziridines: Generation of Configurationally Stable Aziridinyllithium Compounds, Chemistry -A European Journal, vol.17, pp.4992-5003, 2011.

K. Mollet, S. Catak, M. Waroquier, V. Van-speybroeck, M. D'hooghe et al., Stereoselective Synthesis of cis -3,4-Disubstituted Piperidines through Ring Transformation of 2-(2-Mesyloxyethyl)azetidines. The Journal of Organic Chemistry, vol.76, pp.8364-8375, 2011.

K. Fukui, The Path of Chemical Reactions -the IRC Approach, Accounts of Chemical Research, vol.14, pp.363-368, 1981.

E. Cancès and B. Mennucci, Comment on Reaction Field Treatment of Charge Penetration, The Journal of Chemical Physics, vol.114, p.4744, 2001.

T. Kawabata, K. Yahiro, and K. Fuji, Memory of Chirality: Enantioselective Alkylation Reactions at an Asymmetric Carbon Adjacent to a Carbonyl Group, Journal of the American Chemical Society, vol.113, pp.9694-9696, 1991.

D. Zhang, X. Xing, and G. D. Cuny, Synthesis of Hydantoins from Enantiomerically Pure ?-Amino Amides without Epimerization, Journal of Organic Chemistry, vol.71, pp.1750-1753, 2006.

J. E. Baldwin, Rules for Ring Closure, Journal of the Chemical Society, p.734, 1976.

J. E. Baldwin, J. Cutting, W. Dupont, L. Kruse, L. Silberman et al., 5-Endo-Trigonal Reactions: A Disfavoured Ring Closure, Journal of the Chemical Society, p.736, 1976.

J. E. Baldwin, R. C. Thomas, L. I. Kruse, and L. Silberman, Rules for Ring Closure: Ring Formation by Conjugate Addition of Oxygen Nucleophiles, The Journal of Organic Chemistry, vol.42, pp.3846-3852, 1977.

C. Chatgilialoglu, C. Ferreri, M. Guerra, V. Timokhin, and G. Froudakis, Gimisis, T. 5-Endo-trig Radical Cyclizations: Disfavored or Favored Processes?, Journal of American Chemical Society, vol.124, pp.10765-10772, 2002.

Y. Zhao and D. G. Truhlar, Density Functional Theory for Reaction Energies: Test of Meta and Hybrid Meta Functionals, Range-Separated Functionals, and Other High-Performance Functionals, Journal of Chemical Theory and Computation, vol.7, pp.669-676, 2011.