[1] Goldstein, Herbert. Classical mechanics. Pearson, Harlow, 3rd edition, 2011.Google Scholar

[2] Maksic, Z. B. and Orville-Thomas, W. J., editors. Pauling’s legacy, modern modelling of the chemical bond. Elsevier, Amsterdam, 1st edition, 1999.Google Scholar

[3] Szabo, Attila and Ostlund, Neil S.. Modern quantum chemistry. Dover Publications Inc., New York, 1st edition, 1996.Google Scholar

[4] Jones, R. O.. Density functional theory: Its origins, rise to prominence, and future. Rev. Mod. Phys., 87(3):897–923, 2015.Google Scholar

[5] Hohenberg, P. and Kohn, W. Inhomogeneous electron gas. Phys. Rev., 136(3B):B864– B871, 1964.Google Scholar

[6] Kohn, W. and Sham, L. J.. Self-consistent equations including exchange and correlation effects. Phys. Rev., 140(4A):A1133–A1138, 1965.Google Scholar

[7] Ceperley, David M. and Alder, B. J.. Ground state of the electron gas by a stochastic method. Phys. Rev. Lett., 45(7):566, 1980.Google Scholar

[8] John, P. Perdew and Alex Zunger. Self-interaction correction to density-functional approximations for many-electron systems. Phys. Rev. B, 23(10):5048, 1981.Google Scholar

[9] Becke, A. D.. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A, 38(6):3098–3100, 1988.Google Scholar

[10] Perdew, J. P. and Wang, Y.. Accurate and simple analytic representation of the electron-gas correlation energy. Phys. Rev. B, 45:13244, 1992.CrossRefGoogle ScholarPubMed

[11] Perdew, John P.. Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys. Rev. B, 33(12):8822–8824, 1986.Google Scholar

[12] Perdew, John P., Burke, Kieron, and Ernzerhof, Matthias. Generalized gradient approximation made simple. Phys. Rev. Lett., 77(3):3865–3868, 1996.Google Scholar

[13] Lee, Chengteh, Yang, Weitao, and Parr, Robert G.. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B, 37(2):785–789, 1988.Google Scholar

[14] Perdew, John P., Tao, Jianmin, Staroverov, Viktor N., and Scuseria, Gustavo E.. Meta-generalized gradient approximation: Explanation of a realistic nonempirical density functional. J. Chem. Phys., 120(15):6898–6911, 2004.Google Scholar

[15] Perdew, John P., Staroverov, Viktor N., Tao, Jianmin, and Scuseria, Gustavo E.. Density functional with full exact exchange, balanced nonlocality of correlation, and constraint satisfaction. Phys. Rev. A, 78(5):052513, 2008.Google Scholar

[16] Adamo, Carlo and Barone, Vincenzo. Toward reliable density functional methods without adjustable parameters: The PBE0 model. J. Chem. Phys., 110(13):6158– 6170, 1999.Google Scholar

[17] Heyd, Jochen and Scuseria, Gustavo E.. Efficient hybrid density functional calculations in solids: Assessment of the HeydScuseria-Ernzerhof screened Coulomb hybrid functional. J. Chem. Phys., 121(3):1187, 2004.Google Scholar

[18] Mardirossian, Narbe and Head-Gordon, Martin. How accurate are the Minnesota density functionals for noncovalent interactions, isomerization energies, thermochemistry, and barrier heights involving molecules composed of main-group elements? J. Chem. Theor. Comput., 12(9):4303–4325, 2016.Google Scholar

[19] Grimme, Stefan. Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J. Comput. Chem., 27(15):1787–1799, 2006.Google Scholar

[20] Antony, Jens and Grimme, Stefan. Fully ab initio protein-ligand interaction energies with dispersion corrected density functional theory. J. Comput. Chem., 33(21):1730– 1739, 2012.Google Scholar

[21] Tkatchenko, Alexandre and Scheffler, Matthias. Accurate molecular van der Waals interactions from ground-state electron density and free-atom reference data. Phys. Rev. Lett., 102(7):6–9, 2009.Google Scholar

[22] Zhang, Da W. and Zhang, J. Z. H.. Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy. J. Chem. Phys., 119(7):3599, 2003.Google Scholar

[23] Zhang, Da W., Chen, X. H., and Zhang, John Z. H.. Molecular caps for full quantum mechanical computation of peptide-water interaction energy. J. Comput. Chem., 24(15):1846–1852, 2003.Google Scholar

[24] Gordon, Mark S., Fedorov, Dmitri G., Pruitt, Spencer R., and Slipchenko, Lyudmila V.. Fragmentation methods: A route to accurate calculations on large systems. Chem. Rev., 112(1):632–672, 2012.CrossRefGoogle ScholarPubMed

[25] Datta, S.. Quantum transport: Atom to transistor. Cambridge University Press, Cambridge, 2005.Google Scholar

[26] Cuniberti, G., Richter, K., and Fagas, G.. Introducing molecular electronics. Springer, Berlin, 2005.Google Scholar

[27] Watson, J. D. and Crick, F. H. C.. Molecular structure of nucleic acids. Nature, 171(4356):737–738, 1953.Google Scholar

[28] Chargaff, E., Zamenhof, S., and Green, C.. Human desoxypentose nucleic acid: Composition of human desoxypentose nucleic acid. Nature, 165(4202):756, 1950.Google Scholar

[29] Albuquerque, E. L. and Cottam, M. G.. Superlattice plasmon-polaritons. Phys. Rep., 233(2):67–135, 1993.Google Scholar

[30] Albuquerque, E. L. and Cottam, M. G.. Polaritons in periodic and quasiperiodic structures. Elsevier, Amsterdam, 2004.Google Scholar

[31] Carpena, P., Bernaola-Galván, P., Ivanov, P. Ch., and Stanley, H. E.. Metal-insulator transition in chains with correlated disorder. Nature, 418(6901):955–959, 2002.Google Scholar

[32] Cuniberti, G., Craco, L., Porath, D., and Dekker, C.. Backbone-induced semiconducting behavior in short DNA wires. Phys. Rev. B, 65(24):241314, 2002.Google Scholar

[33] Seeman, N. C.. Nucleic acid junctions and lattices. J. Theor. Biol., 99(2):237–247, 1982.Google Scholar

[34] Seeman, N. C.. DNA in a material world. Nature, 421(6921):427, 2003.Google Scholar

[35] Gu, H., Chao, J., Xiao, S. J., and Seeman, N. C.. Dynamic patterning programmed by DNA tiles captured on a DNA origami substrate. Nat. Nanotechnol., 4(4):245, 2009.Google Scholar

[36] Albuquerque, E. L., Fulco, U. L., Freire, V. N. et al. DNA-based nanobiostructured devices: The role of quasiperiodicity and correlation effects. Phys. Rep., 535(4):139– 209, 2014.Google Scholar

[37] Shechtman, D., Blech, I., Gratias, D., and Cahn, J. W.. Metallic phase with long-range orientational order and no translational symmetry. Phys. Rev. Lett., 53(20):1951, 1984.Google Scholar

[38] Senechal, M.. Quasicrystals and geometry. Cambridge University Press, Cambridge, 1995.Google Scholar

[39] Levine, D. and Steinhardt, P. J.. Quasicrystals: A new class of ordered structures. Phys. Rev. Lett., 53(26):2477, 1984.Google Scholar

[40] Bezerra, C. G. and Albuquerque, E. L.. Localization and scaling properties of spin waves in quasi-periodic magnetic multilayers. Physica A, 255(3–4):285–292, 1998.Google Scholar

[41] Bezerra, C. G., de Araújo, J. M., Chesman, C., and Albuquerque, E. L.. Self-similar magnetoresistance of Fibonacci ultrathin magnetic films. Phys. Rev. B, 60(13):9264, 1999.Google Scholar

[42] Anselmo, D. H. A. L., Cottam, M. G., and Albuquerque, E. L.. Localization and scaling properties of magnetostatic modes in quasiperiodic magnetic superlattices. J. Phys.: Condens. Matter, 12(6):1041, 2000.Google Scholar

[43] Axel, F. and Terauchi, H.. High-resolution X-ray-diffraction spectra of Thue-Morse GaAs-AlAs heterostructures: Towards a novel description of disorder. Phys. Rev. Lett., 66(17):2223, 1991.Google Scholar

[44] Albuquerque, E. L. and Cottam, M. G.. Theory of plasmon-polaritons in Fibonacci-type superlattices with two-dimensionl electron gas layers. Solid State Commun., 81(5):383–386, 1992.CrossRefGoogle Scholar

[45] Vasconcelos, M. S., Mauriz, P. W., de Medeiros, F. F., and Albuquerque, E. L.. Photonic band gaps in quasiperiodic photonic crystals with negative refractive index. Phys. Rev. B, 76(16):165117, 2007.Google Scholar

[46] Ostlund, S., Pandit, R., Rand, D., Schellnhuber, H. J., and Siggia, E. D.. One-dimensional Schrödinger equation with an almost periodic potential. Phys. Rev. Lett., 50(23):1873, 1983.Google Scholar

[47] Kohmoto, M., Kadanoff, L. P., and Tang, C.. Localization problem in one dimension: Mapping and escape. Phys. Rev. Lett., 50(23):1870, 1983.Google Scholar

[48] Nakamura, K.. Quantum chaos: A new paradigm of nonlinear dynamics. Cambridge University Press, Cambridge, 1993.Google Scholar

[49] Lee, P. A. and Ramakrishnan, T. V.. Disordered electronic systems. Rev. Mod. Phys., 57(2):287, 1985.Google Scholar

[50] Ostlund, S. and Pandit, R.. Renormalization-group analysis of the discrete quasiperiodic Schrödinger equation. Phys. Rev. B, 29(3):1394, 1984.Google Scholar

[51] Grimm, U. and Baake, M.. Aperiodic ising models. In Moody, R. V., editor, The mathematics of long-range aperiodic order. Kluwer, Dordrecht, 1997.Google Scholar

[52] Mauriz, P. W., Vasconcelos, M. S., and Albuquerque, E. L.. Specific heat properties of electrons in generalized Fibonacci quasicrystals. Physica A, 329(1–2):101–113, 2003.Google Scholar

[53] Mauriz, P. W., Albuquerque, E. L., and Vasconcelos, M. S.. Electronic specific heat properties in one-dimensional quasicrystals. Physica A, 294(3–4):403–414, 2001.Google Scholar

[54] McCammon, J. A. and Harvey, S. C.. Dynamics of proteins and nucleic acids. Cambridge University Press, Cambridge, 1988.Google Scholar

[55] Boon, E. M., Livingston, A. L., Chmiel, N. H., David, S. S., and Barton, J. K.. DNA-mediated charge transport for DNA repair. Proc. Natl. Acad. Sci. U. S. A., 100(22):12543–12547, 2003.CrossRefGoogle ScholarPubMed

[56] Albuquerque, E. L., Vasconcelos, M. S., Lyra, M. L., and de Moura, F. A. B. F.. Nucleotide correlations and electronic transport of DNA sequences. Phys. Rev. E, 71(2):021910, 2005.Google Scholar

[57] Dyson, F. J.. The S matrix in quantum electrodynamics. Phys. Rev., 75(11):1736, 1949.CrossRefGoogle Scholar

[58] de Oliveira, B. P. W. E. L. Albuquerque, , and Vasconcelos, M. S.. Electronic density of states in sequence dependent DNA molecules. Surf. Sci., 600(18):3770–3774, 2006.CrossRefGoogle Scholar

[59] Sugiyama, H. and Saito, I.. Theoretical studies of GG-specific photocleavage of DNA via electron transfer: Significant lowering of ionization potential and 5-localization of HOMO of stacked GG bases in B-Form DNA. J. Am. Chem. Soc., 118(30):7063– 7068, 1996.Google Scholar

[60] Maciá, E., Triozon, F., and Roche, S.. Contact-dependent effects and tunneling currents in DNA molecules. Phys. Rev. B, 71(11):113106, 2005.Google Scholar

[61] Berlin, Y. A., Burin, A. L., and Ratner, M. A.. Elementary steps for charge transport in DNA: Thermal activation vs. tunneling. Chem. Phys., 275(1–3):61–74, 2002.Google Scholar

[62] Sarmento, R. G., Albuquerque, E. L., Sesion, P. D. Jr, Fulco, U. L., and de Oliveira, B. P. W.. Electronic transport in double-strand poly (dG)-poly (dC) DNA segments. Phys. Lett. A, 373(16):1486–1491, 2009.Google Scholar

[63] Maciá, E.. Electronic structure and transport properties of double-stranded Fibonacci DNA. Phys. Rev. B, 74(24):245105, 2006.Google Scholar

[64] Klotsa, D., Römer, R. A., and Turner, M. S.. Electronic transport in DNA. Biophys. J., 89(4):2187–2198, 2005.CrossRefGoogle ScholarPubMed

[65] Sarmento, R. G., Fulco, U. L., Albuquerque, E. L., Caetano, E. W. S., and Freire, V. N.. A renormalization approach to describe charge transport in quasiperiodic dangling backbone ladder (DBL)-DNA molecules. Phys. Lett. A, 375(45):3993–3996, 2011.Google Scholar

[66] Malyshev, A. V.. DNA double helices for single molecule electronics. Phys. Rev. Lett., 98(9):096801, 2007.Google Scholar

[67] Winfree, E., Liu, F., Wenzler, L. A., and Seeman, N. C.. Design and self-assembly of two-dimensional DNA crystals. Nature, 394(6693):539, 1998.Google Scholar

[68] Porath, D., Bezryadin, A., de Vries, S., and Dekker, C.. Direct measurement of electrical transport through DNA molecules. Nature, 403(6770):635, 2000.Google Scholar

[69] Kasumov, A. Y., Kociak, M., Gueron, S. et al. Proximity-induced superconductivity in DNA. Science, 291(5502):280–282, 2001.Google Scholar

[70] Landauer, R.. Spatial variation of currents and fields due to localized scatterers in metallic conduction. IBMJ. Res. Dev., 1(3):223–231, 1957.Google Scholar

[71] Büttiker, M.. Voltage fluctuations in small conductors. Phys. Rev. B, 35(8):4123, 1987.Google Scholar

[72] Asai, Y.. Theory of electric conductance of DNA molecule. J. Phys. Chem. B, 107(19):4647–4652, 2003.Google Scholar

[73] Stone, A. D., Joannopoulos, J. D., and Chadi, D. J.. Scaling studies of the resistance of the one-dimensional Anderson model with general disorder. Phys. Rev. B, 24(10):5583, 1981.Google Scholar

[74] Bezerril, L. M., Moreira, D. A., Albuquerque, E. L. et al. Current–voltage characteristics of double-strand DNA sequences. Phys. Lett. A, 373(37):3381–3385, 2009.Google Scholar

[75] Xu, M. S., Tsukamoto, S., Ishida, S. et al. Conductance of single thiolated poly (GC)-poly (GC) DNA molecules. Appl. Phys. Lett., 87(8):083902, 2005.Google Scholar

[76] de Almeida, M. L., Ourique, G. S., Fulco, U. L. et al. Charge transport properties of a twisted DNA molecule: A renormalization approach. Chem. Phys., 478:48–54, 2016.Google Scholar

[77] Maciá, E.. Electrical conductance in duplex DNA: Helical effects and low-frequency vibrational coupling. Phys. Rev. B, 76(24):245123, 2007.Google Scholar

[78] Endres, R. G., Cox, D. L., and Singh, R. R. P.. Colloquium: The quest for high-conductance DNA. Rev. Mod. Phys., 76(1):195, 2004.Google Scholar

[79] Zoli, M.. Helix untwisting and bubble formation in circular DNA. J. Chem. Phys., 138(20):205103, 2013.Google Scholar

[80] Fernando, H., Papadantonakis, G. A., Kim, N. S., and LeBreton, P. R.. Conduction-band-edge ionization thresholds of DNA components in aqueous solution. Proc. Natl. Acad. Sci. U. S. A., 95(10):5550–5555, 1998.Google Scholar

[81] Voityuk, A. A. Electronic couplings and on-site energies for hole transfer in DNA: Systematic quantum mechanical/molecular dynamic study. J. Chem. Phys., 128:115101, 2008.Google Scholar

[82] Albuquerque, E. L., Lyra, M. L., and de Moura, F. A. B. F.. Electronic transport in DNA sequences: The role of correlations and inter-strand coupling. Physica A, 370(2):625–631, 2006.Google Scholar

[83] Shao, F. and Barton, J. K.. Long-range electron and hole transport through DNA with tethered cyclometalated iridium (III) complexes. J. Am. Chem. Soc., 129(47):14733– 14738, 2007.Google Scholar

[84] Baylin, S. B.. DNA methylation and gene silencing in cancer. Nat. Rev. Clin. Oncol., 2(S1):S4, 2005.Google Scholar

[85] Smith, Z. D. and Meissner, A.. DNA methylation: Roles in mammalian development. Nat. Rev. Genet., 14(3):204, 2013.Google Scholar

[86] de Almeida, M. L., Oliveira, J. I. N., Lima, J. X. Neto et al. Electronic transport in methylated fragments of DNA. Appl. Phys. Lett., 107(20):203701, 2015.Google Scholar

[87] Becke, A. D.. A new mixing of Hartree-Fock and local density-functional theories. J. Chem. Phys., 98(2):1372–1377, 1993.Google Scholar

[88] Dunning, T. H. Jr. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J. Chem. Phys., 90(2):1007–1023, 1989.Google Scholar

[89] Yu, W., Liang, L., Lin, Z. et al. Comparison of some representative density functional theory and wave function theory methods for the studies of amino acids. J. Comput. Chem., 30(4):589–600, 2009.Google Scholar

[90] Yin, H., Ma, Y., Mu, J., Liu, C., and Rohlfing, M.. Charge-transfer excited states in aqueous DNA: Insights from many-body Greens function theory. Phys. Rev. Lett., 112(22):228301, 2014.Google Scholar

[91] Maul, R., Preuss, M., Ortmann, F., Hannewald, K., and Bechstedt, F.. Electronic excitations of glycine, alanine, and cysteine conformers from first-principles calculations. J. Phys. Chem. A, 111(20):4370–4377, 2007.Google Scholar

[92] Dedachi, K., Natsume, T., Nakatsu, T. et al. Charge transfer through single- and double-strand DNAs: Simulations based on molecular dynamics and molecular orbital methods. Chem. Phys. Lett., 436(1–3):244–251, 2007.Google Scholar

[93] de Moura, F. A. B. F., Lyra, M. L., and Albuquerque, E. L.. Electronic transport in poly (CG) and poly (CT) DNA segments with diluted base pairing. J. Phys.: Condens. Matter, 20(7):075109, 2008.Google Scholar

[94] Hilke, M.. Noninteracting electrons and the metal-insulator transition in two dimensions with correlated impurities. Phys. Rev. Lett., 91(22):226403, 2003.Google Scholar

[95] Mehrez, H. and Anantram, M. P.. Interbase electronic coupling for transport through DNA. Phys. Rev. B, 71(11):115405, 2005.Google Scholar

[96] Tsallis, C., da Silva, L. R., Mendes, R. S., Vallejos, R. O., and Mariz, A. M.. Specific heat anomalies associated with Cantor-set energy spectra. Phys. Rev. E, 56(5):R4922, 1997.CrossRefGoogle Scholar

[97] da Silva, L. R., Vallejos, R. O., Tsallis, C., Mendes, R. S., and Roux, S.. Specific heat of multifractal energy spectra. Phys. Rev. E, 64(1):011104, 2001.Google Scholar

[98] Mauriz, P. W., Albuquerque, E. L., and Vasconcelos, M. S.. Specific heat properties of polariton modes in quasicrystals. Phys. Rev. B, 63(18):184203, 2001.Google Scholar

[99] Yang, I. S. and Anderson, A. C.. Specific heat of deoxyribonucleic acid at temperatures below 5K. Phys. Rev. B, 35(17):9305, 1987.Google Scholar

[100] Macedo, D. X., Guedes, I., and Albuquerque, E. L.. Thermal properties of a DNA denaturation with solvent interaction. Physica A, 404:234–241, 2014.Google Scholar

[101] Moreira, D. A., Albuquerque, E. L., Mauriz, P. W., and Vasconcelos, M. S.. Specific heat spectra of long-range correlated DNA molecules. Physica A, 371(2):441–448, 2006.Google Scholar

[102] Moreira, D. A., Albuquerque, E. L., and Bezerra, C. G.. Specific heat spectra for quasiperiodic ladder sequences. Eur. Phys. J. B, 54(3):393–398, 2006.Google Scholar

[103] Mrevlishvili, G. M.. Low-temperature heat capacity of biomacromolecules and the entropic cost of bound water in proteins and nucleic acids (DNA). Thermochim. Acta, 308(1–2):49–54, 1998.Google Scholar

[104] Moreira, D. A., Albuquerque, E. L., and Anselmo, D. H. A. L.. Specific heat spectra of non-interacting fermions in a quasiperiodic ladder sequence. Phys. Lett. A, 372(31):5233–5238, 2008.Google Scholar

[105] Schrödinger, E.. What is life? The physical aspect of the living cell and mind. Cambridge University Press, Cambridge, 1944.Google Scholar

[106] Anselmo, D. H. A. L., Dantas, A. L., and Albuquerque, E. L.. A multifractal analysis of optical phonon excitations in quasicrystals. Physica A, 362(2):289–294, 2006.Google Scholar

[107] Gell-Mann, M. and Tsallis, C.. Nonextensive entropy: Interdisciplinary applications. Oxford University Press, Oxford, 2004.Google Scholar

[108] Tsallis, C.. Possible generalization of Boltzmann-Gibbs statistics. J. Stat. Phys., 52(1–2):479–487, 1988.CrossRefGoogle Scholar

[109] de Oliveira, I. N. M. L. Lyra, , and Albuquerque, E. L.. Specific heat anomalies of non-interacting fermions with multifractal energy spectra. Physica A, 343:424–432, 2004.Google Scholar

[110] de Oliveira, I. N., Lyra, M. L., Albuquerque, E. L., and da Silva, L. R.. Bosons with multifractal energy spectrum: Specific heat log periodicity and Bose-Einstein condensation. J. Phys.: Condens. Matter, 17(23):3499, 2005.Google Scholar

[111] Moreira, D. A., Albuquerque, E. L., da Silva, L. R., and Galvao, D. S.. Low-temperature specific heat spectra considering nonextensive long-range correlated quasiperiodic DNA molecules. Physica A, 387(22):5477–5482, 2008.Google Scholar

[112] Lyra, M. L. and Tsallis, C.. Nonextensivity and multifractality in low-dimensional dissipative systems. Phys. Rev. Lett., 80(1):53, 1998.CrossRefGoogle Scholar

[113] Coronado, A. V. and Carpena, P.. Study of the log-periodic oscillations of the specific heat of Cantor energy spectra. Physica A, 358(2–4):299–312, 2005.Google Scholar

[114] Peyrard, M.. Nonlinear dynamics and statistical physics of DNA. Nonlinearity, 17(2):R1, 2004.Google Scholar

[115] Peyrard, M. and Bishop, A. R.. Statistical mechanics of a nonlinear model for DNA denaturation. Phys. Rev. Lett., 62(23):2755, 1989.Google Scholar

[116] Dauxois, T., Peyrard, M., and Bishop, A. R.. Thermodynamics of a nonlinear model for DNA denaturation. Physica D, 66(1–2):35–42, 1993.Google Scholar

[117] Dauxois, T. and Peyrard, M.. Entropy-driven transition in a one-dimensional system. Phys. Rev. E, 51(5):4027, 1995.Google Scholar

[118] Joyeux, M. and Buyukdagli, S.. Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation. Phys. Rev. E, 72(5):051902, 2005.CrossRefGoogle ScholarPubMed

[119] Weber, G.. Sharp DNA denaturation due to solvent interaction. Europhys. Lett., 73(5):806, 2006.Google Scholar

[120] Sulaiman, A., Zen, F. P., Alatas, H., and Handoko, L. T.. The thermal denaturation of the Peyrard-Bishop model with an external potential. Phys. Scr., 86(1):015802, 2012.Google Scholar

[121] Dauxois, T., Peyrard, M., and Bishop, A. R.. Entropy-driven DNA denaturation. Phys. Rev. E, 47(1):R44, 1993.Google Scholar

[122] Dauxois, T. and Peyrard, M.. Energy localization in nonlinear lattices. Phys. Rev. Lett., 70(25):3935, 1993.Google Scholar

[123] Dauxois, T., Peyrard, M., and Bishop, A. R.. Dynamics and thermodynamics of a nonlinear model for DNA denaturation. Phys. Rev. E, 47(1):684, 1993.Google Scholar

[124] Wildes, A., Theodorakopoulos, N., Valle-Orero, J., Cuesta-Lopez, S., Garden, J. L., and Peyrard, M.. Thermal denaturation of DNA studied with neutron scattering. Phys. Rev. Lett., 106(4):048101, 2011.Google Scholar

[125] Owczarzy, R., You, Y., Moreira, B. G. et al. Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures. Biochemistry, 43(12):3537–3554, 2004.Google Scholar

[126] van Erp, T. S. and Peyrard, M.. The dynamics of the DNA denaturation transition. Europhys. Lett., 98(4):48004, 2012.Google Scholar

[127] Jelesarov, I. and Bosshard, H. R.. Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition. J. Mol. Recognit., 12(1):3–18, 1999.Google Scholar

[128] Eley, D. D. and Spivey, D. I.. Semiconductivity of organic substances. Part 9. Nucleic acid in the dry state. Trans. Faraday Soc., 58:411–415, 1962.Google Scholar

[129] Gomez, Eliot F., Venkatraman, Vishak, Grote, James G., and Steckl, Andrew. J.. Exploring the potential of nucleic acid bases in organic light emitting diodes. Adv. Mater., 27(46):7552–7562, 2015.Google Scholar

[130] Chan, M. K. Y. and Ceder, Gerbrand. Efficient band gap prediction for solids. Phys. Rev. Lett., 105(19):196403, 2010.Google Scholar

[131] da Silva, M. B., Francisco, T. S., Maia, F. F., Jr. et al. Improved description of the structural and optoelectronic properties of DNA/RNA nucleobase anhydrous crystals: Experiment and dispersion-corrected density functional theory calculations. Phys. Rev. B, 96(8):085206, 2017.Google Scholar

[132] Gomez, Eliot F., Venkatraman, Vishak, Grote, James G., and Steckl, Andrew J.. DNA bases thymine and adenine in bio-organic light emitting diodes. Sci. Rep., 4:7105, 2014.Google Scholar

[133] Runge, Erich and Gross, Eberhard K. U.. Density-functional theory for time-dependent systems. Phys. Rev. Lett., 52(12):997, 1984.Google Scholar

[134] Delley, Bernard. From molecules to solids with the DMol³ approach. J. Chem. Phys., 113(18):7756–7764, 2000.Google Scholar

[135] Barker, D. L. and Marsh, R. E.. The crystal structure of cytosine. Acta Cryst., 17(12):1581–1587, 1964.Google Scholar

[136] Parry, Go So. The crystal structure of uracil. Acta Cryst., 7(4):313–320, 1954.Google Scholar

[137] Berland, Kristian, Cooper, Valentino R., Lee, Kyuho et al. Van der Waals forces in density functional theory: A review of the vdW-DF method. Rep. Prog. Phys., 78(6):066501, 2015.Google Scholar

[138] Pfrommer, Bernd G., Côté, Michel, Louie, Steven G., and Cohen, Marvin L.. Relaxation of crystals with the quasi-Newton method. J. Comput. Phys., 131(1):233–240, 1997.Google Scholar

[139] Mulliken, Robert S.. Electronic population analysis on LCAO-MO molecular wave functions. I. J. Chem. Phys., 23(10):1833–1840, 1955.Google Scholar

[140] Hirshfeld, Fred L.. Bonded-atom fragments for describing molecular charge densities. Theor. Chim. Acta, 44(2):129–138, 1977.Google Scholar

[141] Wang, C. S. and Pickett, W. E.. Density-functional theory of excitation spectra of semiconductors: Application to Si. Phys. Rev. Lett., 51(7):597, 1983.Google Scholar

[142] Klamt, A., Moya, C., and Palomar, J.. A comprehensive comparison of the IEFPCM and SS(V)PE continuum solvation methods with the COSMO approach. J. Chem. Theor. Comput., 11(9):4220–4225, 2015.Google Scholar

[143] Maia, F. F., Jr., Freire, V. N., Caetano, E. W. S. et al. Anhydrous crystals of DNA bases are wide gap semiconductors. J. Chem. Phys., 134(17):05B601, 2011.Google Scholar

[144] Šponer, Jiří, Riley, Kevin E., and Hobza, Pavel. Nature and magnitude of aromatic stacking of nucleic acid bases. Phys. Chem. Chem. Phys., 10(19):2595–2610, 2008.Google Scholar

[145] Roy, Ram Kinkar, Pal, Sourav, and Hirao, Kimihiko. On non-negativity of Fukui function indices. J. Chem. Phys., 110(17):8236–8245, 1999.Google Scholar

[146] Verstraelen, Toon, Sukhomlinov, Sergey V., Speybroeck, Veronique Van, Waroquier, Michel, and Smirnov, Konstantin S. Computation of charge distribution and electrostatic potential in silicates with the use of chemical potential equalization models. J. Phys. Chem. C, 116(1):490–504, 2012.Google Scholar

[147] Silaghi, S. D., Friedrich, M., Cobet, C. et al. Dielectric functions of DNA base films from near–infrared to ultra–violet. Phys. Status Solidi B, 242(15):3047–3052, 2005.Google Scholar

[148] Bhushan, Bharat, editor. Springer handbook of nanotechnology. Springer, Heidelberg, 1st edition, 2005.Google Scholar

[149] Aviram, Arieh and Ratner, Mark A.. Molecular rectifiers. Chem. Phys. Lett., 29(2):277–283, 1974.Google Scholar

[150] Carter, F. L., Siatkowski, R. E., and Wohltjen, H., editors. Molecular electronic devices. North Holland, Amsterdam, 1st edition, 1988.Google Scholar

[151] Petty, M. C., Bryce, M. R., and Bloor, D., editors. Introduction to molecular electronics. Oxford University Press, Oxford, 1st edition, 1995.Google Scholar

[152] Kraatz, Heinz-Bernhard, Irene Bediako-Amoa, Samuel H Gyepi-Garbrah, and Todd C Sutherland. Electron transfer through H-bonded peptide assemblies. J. Phys. Chem. B, 108(52):20164–20172, 2004.Google Scholar

[153] Oliveira, J. I. N., Albuquerque, E. L., Fulco, U. L., Mauriz, P. W., and Sarmento, R. G.. Electronic transport through oligopeptide chains: An artificial prototype of a molecular diode. Chem. Phys. Lett., 612:14–19, 2014.Google Scholar

[154] Kojima, Shuichi, Kuriki, Yukino, Yoshihiro Sato et al. Synthesis of α-helix-forming peptides by gene engineering methods and their characterization by circular dichro-ism spectra measurements. Biochim. Biophys. Acta, 1294(2):129–137, 1996.Google Scholar

[155] Bezerril, L. M., Fulco, U. L., Oliveira, J. I. N. et al. Charge transport in fibrous/not fibrous α 3-helical and (5Q, 7Q)α3 variant peptides. Appl. Phys. Lett., 98(5):053702, 2011.Google Scholar

[156] Mendes, G. A., Albuquerque, E. L., Fulco, U. L. et al. Electronic specific heat of an α3-helical polypeptide and its biochemical variants. Chem. Phys. Lett., 542:123– 127, 2012.Google Scholar

[157] Oliveira, J. I. N., Albuquerque, E. L., Fulco, U. L. et al. Conductance of single microR-NAs chains related to the autism spectrum disorder. Europhys. Lett., 107(6):68006, 2014.Google Scholar

[158] Metzger, Robert M.. Unimolecular electrical rectifiers. Chem. Rev., 103(9):3803– 3834, 2003.Google Scholar

[159] Bravaya, K. B., Kostko, O., Dolgikh, S. et al. Electronic structure and spectroscopy of nucleic acid bases: Ionization energies, ionization-induced structural changes, and photoelectron spectra. J. Phys. Chem. A., 114:12305–12317, 2010.Google Scholar

[160] Huang, J. and Kertesz, M.. Validation of intermolecular transfer integral and bandwidth calculations for organic molecular materials. J. Chem. Phys., 122:234707, 2005.Google Scholar

[161] Peach, M. J. G., Benfield, P., Helgaker, T., and Tozer, D. J.. Excitation energies in density functional theory: An evaluation and a diagnostic test. J. Chem. Phys., 128:044118, 2008.Google Scholar

[162] Cardamone, David M. and Kirczenow, George. Single-molecule device prototypes for protein-based nanoelectronics: Negative differential resistance and current rectification in oligopeptides. Phys. Rev. B, 77(16):165403, 2008.Google Scholar

[163] Pauling, Linus, Corey, Robert B., and Branson, Herman R.. The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain. Proc. Natl. Acad. Sci. U. S. A., 37(4):205–211, 1951.Google Scholar

[164] Day, Paul N. and Pachter, Ruth. A study of aqueous glutamic acid using the effective fragment potential method. J. Chem. Phys., 107(8):2990–2999, 1997.Google Scholar

[165] Davis, K. M. C., Eley, D. D., and Snart, R. S.. Semiconductivity in proteins and hæmoglobin: Enhanced semiconductivity in protein complexes. Nature, 188(4752):724, 1960.Google Scholar

[166] Rakvin, Boris, Maltar-Strmečki, Nadica, Ramsey, Chris M., and Dalal, Naresh S.. Heat capacity and electron spin echo evidence for low frequency vibrational modes and lattice disorder in L-alanine at cryogenic temperatures. J. Chem. Phys, 120(14):6665–6673, 2004.Google Scholar

[167] Starikov, Evgeni B.. Many faces of entropy or bayesian statistical mechanics. ChemPhysChem, 11(16):3387–3394, 2010.Google Scholar

[168] Linhart, George A.. Correlation of heat capacity, absolute temperature and entropy. J. Chem. Phys., 1(11):795–797, 1933.Google Scholar

[169] Lee, Rosalind C., Feinbaum, Rhonda L., and Ambros, Victor. The c. elegans hete-rochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75(5):843–854, 1993.Google Scholar

[170] Abrahams, Brett S. and Geschwind, Daniel H.. Advances in autism genetics: On the threshold of a new neurobiology. Nat. Rev. Genet., 9(5):341, 2008.Google Scholar

[171] Senthilkumar, Kittusamy, Grozema, Ferdinand C., Célia Fonseca Guerra et al. Absolute rates of hole transfer in DNA. J. Am. Chem. Soc., 127(42):14894–14903, 2005.Google Scholar

[172] Willett, R. L., Baldwin, K. W., West, K. W., and Pfeiffer, L. N.. Differential adhesion of amino acids to inorganic surfaces. Proc. Natl. Acad. Sci. U. S. A., 102(22):7817– 7822, 2005.Google Scholar

[173] Stroscio, Michael A. and Dutta, Mitra. Integrated biological-semiconductor devices. Proc. IEEE, 93(10):1772–1783, 2005.Google Scholar

[174] Cândido-Júnior, J. R., Sales, F. A. M., Costa, S. N. et al. Monoclinic and orthorhombic cysteine crystals are small gap insulators. Chem. Phys. Lett., 512(4–6):208–210, 2011.Google Scholar

[175] Silva, A. M., Silva, B. P., Sales, F. A. M. et al. Optical absorption and DFT calculations in L-aspartic acid anhydrous crystals: Charge carrier effective masses point to semiconducting behavior. Phys. Rev. B, 86(19):195201, 2012.Google Scholar

[176] Caetano, E. W. S., Fulco, U. L., Albuquerque, E. L. et al. Anhydrous proline crystals: Structural optimization, optoelectronic properties, effective masses and frenkel exciton energy. J. Phys. Chem. Solids, 121:36–48, 2018.Google Scholar

[177] Costa, S. N., Sales, F. A. M., Freire, V. N. et al. L-serine anhydrous crystals: structural, electronic, and optical properties by first-principles calculations, and optical absorption measurement. Cryst. Growth Des., 13(7):2793–2802, 2013.Google Scholar

[178] Silva, A. M., Costa, S. N., Sales, F. A. M. et al. Vibrational spectroscopy and phonon-related properties of the L-aspartic acid anhydrous monoclinic crystal. J. Phys. Chem. A, 119(49):11791–11803, 2015.Google Scholar

[179] Silva, A. M., Costa, S. N., Silva, B. P. et al. Assessing the role of water on the electronic structure and vibrational spectra of monohydrated L-aspartic acid crystals. Cryst. Growth Des., 13(11):4844–4851, 2013.Google Scholar

[180] Monkhorst, Hendrik J. and Pack, James D.. Special points for Brillouin-zone integrations. Phys. Rev. B, 13(12):5188, 1976.Google Scholar

[181] Kerr, K. A. and Ashmore, J. P.. Structure and conformation of orthorhombic L-cysteine. Acta Cryst., B29(10):2124–2127, 1973.Google Scholar

[182] Bordallo, Heloisa N., Boldyreva, Elena V., Fischer, Jennifer et al. Observation of subtle dynamic transitions by a combination of neutron scattering, X-ray diffraction and DSC: A case study of the monoclinic L–cysteine. Biophys. Chem., 148(1–3): 34–41, 2010.Google Scholar

[183] Fox, A. M., editor. Optical properties of solids. Oxford University Press, Oxford, 1st edition, 2001.Google Scholar

[184] Higgs, Paul G. and Pudritz, Ralph E.. A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code. Astrobiology, 9(5):483–490, 2009.Google Scholar

[185] Kistenmacher, Thomas J., Rand, George A., and Marsh, Richard E.. Refinements of the crystal structures of DL-serine and anhydrous L-serine. Acta Cryst., B30(11):2573–2578, 1974.Google Scholar

[186] Ramachandran, G. N. and Kartha, Gopinath. Structure of collagen. Nature, 176(4482):593, 1955.Google Scholar

[187] Lee, Tu and Lin, Yu Kun. The origin of life and the crystallization of aspartic acid in water. Cryst. Growth Des., 10(4):1652–1660, 2010.Google Scholar

[188] Plimmer, R. H. A., editor. The chemical constitution of the proteins. Longmans, Green and Co., London, 1st edition, 1908.Google Scholar

[189] Derissen, J. L., Endeman, H. J., and Peerdeman, A. F.. The crystal and molecular structure of L-aspartic acid. Acta Cryst., B24(10):1349–1354, 1968.Google Scholar

[190] Matei, Adriana, Drichko, Natalia, Gompf, Bruno, and Dressel, Martin. Far-infrared spectra of amino acids. Chem. Phys., 316(1–3):61–71, 2005.Google Scholar

[191] Lopes, Rui P., Valero, Rosendo, John Tomkinson, M. Paula M. Marques, and Luís A. E. Batista de Carvalho. Applying vibrational spectroscopy to the study of nucleobases-adenine as a case-study. New J. Chem., 37(9):2691–2699, 2013.Google Scholar

[192] Makhatadze, George I.. Heat capacities of amino acids, peptides and proteins. Biophys. Chem., 71(2–3):133–156, 1998.Google Scholar

[193] Kapoor, Deepti, Navnit K. Misra, Poonam Tandon, and V. D. Gupta. Phonon dispersion and heat capacity of poly (L-aspartic acid). Eur. Polym. J., 34(12):1781– 1791, 1998.Google Scholar

[194] Umadevi, K., Anitha, K., Sridhar, B., Srinivasan, N., and Rajaram, R. K.. L-aspartic acid monohydrate. Acta Cryst., E59(7):o1073–o1075, 2003.Google Scholar

[195] Jones, Susan and Janet M. Thornton. Principles of protein-protein interactions. Proc. Natl. Acad. Sci. U. S. A., 93(1):13–20, 1996.CrossRefGoogle ScholarPubMed

[196] Schwikowski, Benno, Peter Uetz, and Stanley Fields. A network of protein-protein interactions in yeast. Nat. Biotechnol., 18(12):1257–1261, 2000.Google Scholar

[197] Rain, Jean-Christophe, Luc Selig, Hilde De Reuse et al. The protein-protein interaction map of Helicobacter pylori. Nature, 409(6817):211–215, 2001.Google Scholar

[198] Shen, Juwen, Jian Zhang, Xiaomin Luo et al. Predicting protein-protein interactions based only on sequences information. Proc. Natl. Acad. Sci. U. S. A., 104(11):4337– 4341, 2007.Google Scholar

[199] Schueler-Furman, Ora, Chu Wang, Phil Bradley, Kira Misura, and David Baker. Progress in modeling of protein structures and interactions. Science, 310(5748):638– 642, 2005.Google Scholar

[200] Berman, Helen M.. The protein data bank: A historical perspective. Acta Cryst., A64(1):88–95, 2008.Google Scholar

[201] Berman, Helen M., Westbrook, John, Feng, Zukang et al. The protein data bank. Nucleic Acids Res., 28(1):235–242, 2000.Google Scholar

[202] Berman, Helen, Kim Henrick, and Haruki Nakamura. Announcing the worldwide protein data bank. Nat. Struct. Mol. Biol., 10(12):980, 2003.Google Scholar

[203] Markosian, Christopher, Luigi Di Costanzo, Monica Sekharan et al. Analysis of impact metrics for the Protein Data Bank. Sci. Data, 5:180212, 2018.Google Scholar

[204] Berendsen, Herman J. C., David van der Spoel, and Rudi van Drunen. GROMACS: A message-passing parallel molecular dynamics implementation. Comput. Phys. Commun., 91(1–3):43–56, 1995.Google Scholar

[205] Pearlman, David A., David A. Case, James W. Caldwell et al. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun., 91(1–3):1–41, 1995.Google Scholar

[206] Phillips, James C., Rosemary Braun, Wei Wang et al. Scalable molecular dynamics with NAMD. J. Comput. Chem., 26(16):1781–1802, 2005.Google Scholar

[207] Martínez, Leandro, Ricardo Andrade, Ernesto G Birgin, and José Mario Martínez. PACKMOL: A package for building initial configurations for molecular dynamics simulations. J. Comput. Chem., 30(13):2157–2164, 2009.Google Scholar

[208] Buch, Ignasi, Toni Giorgino, and Gianni De Fabritiis. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proc. Natl. Acad. Sci. U. S. A., 108(25):10184–10189, 2011.Google Scholar

[209] Ganesan, Aravindhan, Michelle L. Coote, and Khaled Barakat. Molecular dynamics-driven drug discovery: Leaping forward with confidence. Drug Discov. Today, 22(2):249–269, 2017.Google Scholar

[210] Warwicker, J.. Improved continuum electrostatic modelling in proteins, with comparison to experiment. J. Mol. Biol., 236(3):887–903, 1994.Google Scholar

[211] Song, Xueyu. An inhomogeneous model of protein dielectric properties: Intrinsic polarizabilities of amino acids. J. Chem. Phys., 116(21):9359–9363, 2002.Google Scholar

[212] Bagchi, Biman. Water dynamics in the hydration layer around proteins and micelles. Chem. Rev., 105(9):3197–3219, 2005.Google Scholar

[213] Schutz, Claudia N. and Arieh Warshel. What are the dielectric constants of proteins and how to validate electrostatic models? Prot.: Struct., Funct., Bioinf., 44(4):400– 417, 2001.Google Scholar

[214] Sternberg, Michael J. E., Fiona R. F. Hayes, Alan J. Russell, Paul G. Thomas, and Alan R. Fersht. Prediction of electrostatic effects of engineering of protein charges. Nature, 330(6143):86–88, 1987.Google Scholar

[215] Nymeyer, Hugh and Huan-Xiang Zhou. A method to determine dielectric constants in nonhomogeneous systems: Application to biological membranes. Biophys. J., 94(4):1185–1193, 2008.Google Scholar

[216] Martins, A. C. V., de Lima Neto, P., Caetano, E. W. S., and Freire, V. N.. An improved quantum biochemistry description of the glutamate-GluA2 receptor binding within an inhomogeneous dielectric function framework. New J. Chem., 41(14):6167–6179, 2017.Google Scholar

[217] Keskin, Ozlem, Nurcan Tuncbag, and Attila Gursoy. Predicting protein-protein interactions from the molecular to the proteome level. Chem. Rev., 116(8):4884– 4909, 2016.Google Scholar

[218] Scott, Duncan E., Andrew R. Bayly, Chris Abell, and John Skidmore. Small molecules, big targets: Drug discovery faces the protein–protein interaction challenge. Nat. Rev. Drug Discov., 15(8):533, 2016.Google Scholar

[219] Kroto, Harold W., Heath, James R., O’Brien, Sean C., Curl, Robert F., and Smalley, Richard E.. C60: Buckminsterfullerene. Nature, 318(6042):162–163, 1985.Google Scholar

[220] Kroto, Harold W.. C60: Buckminsterfullerene, the celestial sphere that fell to earth. Angew. Chem. Int. Ed., 31(2):111–129, 1992.Google Scholar

[221] Santos, S. G., Santana, J. V., Maia, F. F., Jr et al. Adsorption of ascorbic acid on the C60 fullerene. J. Phys. Chem. B, 112(45):14267–14272, 2008.Google Scholar

[222] Hadad, André, David L. Azevedo, Ewerton W. S. Caetano et al. Two-level adsorption of ibuprofen on C60 fullerene for transdermal delivery: Classical molecular dynamics and density functional theory computations. J. Phys. Chem. C, 115(50):24501– 24511, 2011.Google Scholar

[223] Dantas, Diego S., Jonas I. N. Oliveira, José X. Lima Neto et al. Quantum molecular modelling of ibuprofen bound to human serum albumin. RSC Adv., 5(61):49439– 49450, 2015.Google Scholar

[224] Milanesio, M., R. Bianchi, Piero Ugliengo, Carla Roetti, and D. Viterbo. Vitamin C at 120 K: Experimental and theoretical study of the charge density. J. Mol. Struct.: Theochem, 419(1–3):139–154, 1997.Google Scholar

[225] Mora, M. A. and F. J. Melendez. Conformational ab initio study of ascorbic acid. J. Mol. Struct.: Theochem, 454(2–3):175–185, 1998.Google Scholar

[226] Juhasz, Jason R., Pisterzi, Luca F., Gasparro, Donna M., Almeida, David R. P., and Csizmadia, Imre G.. The effects of conformation on the acidity of ascorbic acid: A density functional study. J. Mol. Struct.: Theochem, 666:401–407, 2003.Google Scholar

[227] Jubert, Alicia, Legarto, María Leticia, Massa, Néstor E., Tévez, Leonor López, and Okulik, Nora Beatriz. Vibrational and theoretical studies of non-steroidal anti-inflammatory drugs ibuprofen [2-(4-isobutylphenyl) propionic acid]; naproxen [6-methoxy-α-methyl-2-naphthalene acetic acid] and tolmetin acids [1-methyl-5-(4-methylbenzoyl)-1h-pyrrole-2-acetic acid]. J. Mol. Struct., 783(1–3):34–51, 2006.Google Scholar

[228] He, Xiao Min and Carter, Daniel C.. Atomic structure and chemistry of human serum albumin. Nature, 358(6383):209–215, 1992.Google Scholar

[229] Ghuman, Jamie, Zunszain, Patricia A., Petitpas, Isabelle et al. Structural basis of the drug–binding specificity of human serum albumin. J. Mol. Biol., 353(1):38–52, 2005.Google Scholar

[230] Stierand, Katrin and Rarey, Matthias. Drawing the PDB: Protein-ligand complexes in two dimensions. ACS Med. Chem. Lett., 1(9):540–545, 2010.Google Scholar

[231] Watanabe, Hiroshi, Tanase, Sumio, Nakajou, Keisuke et al. Role of arg-410 and tyr-411 in human serum albumin for ligand binding and esterase-like activity. Biochem. J., 349(3):813–819, 2000.Google Scholar

[232] Gallivan, Justin P. and Dougherty, Dennis A.. A computational study of cation-π interactions vs salt bridges in aqueous media: Implications for protein engineering. J. Am. Chem. Soc., 122(5):870–874, 2000.Google Scholar

[233] Xie, Meng-Xia, Mei Long, Yuan Liu, Chuan Qin, and Ying-Dian Wang. Characterization of the interaction between human serum albumin and morin. Biochim. Biophys. Acta, Gen. Subj., 1760(8):1184–1191, 2006.Google Scholar

[234] Sato, Hiroki, Victor Tuan Giam Chuang, Keishi Yamasaki et al. Differential effects of methoxy group on the interaction of curcuminoids with two major ligand binding sites of human serum albumin. PloS One, 9(2):e87919, 2014.Google Scholar

[235] Colmenarejo, Gonzalo. In silico prediction of drug-binding strengths to human serum albumin. Med. Res. Rev., 23(3):275–301, 2003.Google Scholar

[236] Musa, Klefah A. K. and Leif A. Eriksson. Theoretical study of ibuprofen phototoxi-city. J. Phys. Chem. B, 111(46):13345–13352, 2007.Google Scholar

[237] Gofman, John W., Lindgren, Frank, Elliott, Harold et al. The role of lipids and lipoproteins in atherosclerosis. Science, 111(2877):166–186, 1950.Google Scholar

[238] Bloch, Konrad. The biological synthesis of cholesterol. Science, 150(3692):19–28, 1965.Google Scholar

[239] Blumenthal, Roger S.. Statins: Effective antiatherosclerotic therapy. Am. Heart J., 139(4):577–583, 2000.Google Scholar

[240] Libby, Peter. Cholesterol and atherosclerosis. Biochim. Biophys. Acta, 1529:299– 309, 2000.Google Scholar

[241] Blum, Conrad B.. Comparison of properties of four inhibitors of 3-hydroxy-3-methylglutaryl-coenzyme a reductase. Am. J. Cardiol., 73(14):D3–D11, 1994.Google Scholar

[242] da Costa, Roner F., Freire, Valder N., Bezerra, Eveline M., Benildo S. Cavada, Ewerton W. S. Caetano, José L. de Lima Filho, and Eudenilson L. Albuquerque. Explaining statin inhibition effectiveness of HMG-CoA reductase by quantum biochemistry computations. Phys. Chem. Chem. Phys., 14(4):1389–1398, 2012.Google Scholar

[243] Istvan, Eva S. and Deisenhofer, Johann. Structural mechanism for statin inhibition of HMG-CoA reductase. Science, 292(5519):1160–1164, 2001.Google Scholar

[244] Carbonell, Teresa and Freire, Ernesto. Binding thermodynamics of statins to HMG-CoA reductase. Biochemistry, 44(35):11741–11748, 2005.Google Scholar

[245] Zhang, Qing Y., Jian Wan, Xin Xu et al. Structure-based rational quest for potential novel inhibitors of human HMG-CoA reductase by combining CoMFA 3D QSAR modeling and virtual screening. J. Comb. Chem., 9(1):131–138, 2007.Google Scholar

[246] da Silva, Vinicius B., Carlton A. Taft, and Carlos H. T. P Silva. Use of virtual screening, flexible docking, and molecular interaction fields to design novel HMG-CoA reductase inhibitors for the treatment of hypercholesterolemia. J. Phys. Chem. A, 112(10):2007–2011, 2008.Google Scholar

[247] Kee, Emily A., Maura C. Livengood, Erin E. Carter, Megan McKenna, and Mauricio Cafiero. Aromatic interactions in the binding of ligands to HMG-CoA reductase. J. Phys. Chem. B, 113(44):14810–14815, 2009.Google Scholar

[248] Silvestrelli, Pier Luigi. van der Waals interactions in density functional theory using Wannier functions. J. Phys. Chem. A, 113(17):5224–5234, 2009.Google Scholar

[249] Ortmann, F., Wolf Gero Schmidt, and Friedhelm Bechstedt. Attracted by long-range electron correlation: Adenine on graphite. Phys. Rev. Lett., 95(18):186101, 2005.Google Scholar

[250] Harrison, Charlotte. The patent cliff steepens. Nat. Rev. Drug Discov., 10(1):12–14, 2011.Google Scholar

[251] Jones, Peter H., Michael H. Davidson, Evan A. Stein et al. Comparison of the efficacy and safety of rosuvastatin versus atorvastatin, simvastatin, and pravastatin across doses (STELLAR Trial). Am. J. Cardiol., 92(2):152–160, 2003.Google Scholar

[252] Smith, M. C., N. Burns, J. R. Sayers et al. Bacteriophage collagen. Science, 279(5358):1834, 1998.Google Scholar

[253] Shoulders, Matthew D. and Raines, Ronald T.. Collagen structure and stability. Annu. Rev. Biochem., 78:929–958, 2009.Google Scholar

[254] Prockop, Darwin J. and Kivirikko, Kari I.. Collagens: Molecular biology, diseases, and potentials for therapy. Annu. Rev. Biochem., 64(1):403–434, 1995.Google Scholar

[255] Kramer, Rachel Z., Jordi Bella, Barbara Brodsky, and Helen M. Berman. The crystal and molecular structure of a collagen-like peptide with a biologically relevant sequence. J. Mol. Biol., 311(1):131–147, 2001.Google Scholar

[256] Schumacher, Maria, Kazunori Mizuno, and Hans Peter Bächinger. The crystal structure of the collagen-like polypeptide (glycyl-4 (r)-hydroxyprolyl-4 (r)-hydroxyprolyl) 9 at 1.55 å resolution shows up-puckering of the proline ring in the Xaa position. J. Biol. Chem., 280(21):20397–20403, 2005.Google Scholar

[257] Kramer, Rachel Z., Jordi Bella, Patricia Mayville, Barbara Brodsky, and Helen M. Berman. Sequence dependent conformational variations of collagen triple-helical structure. Nat. Struct. Mol. Biol., 6(5):454–457, 1999.Google Scholar

[258] De Simone, Alfonso, Vitagliano, Luigi, and Rita Berisio. Role of hydration in collagen triple helix stabilization. Biochem. Biophys. Res. Commun., 372(1):121– 125, 2008.Google Scholar

[259] Streeter, Ian and Nora H. de Leeuw. Atomistic modeling of collagen proteins in their fibrillar environment. J. Phys. Chem. B, 114(41):13263–13270, 2010.Google Scholar

[260] Krishnamoorthy, Navaneethakrishnan, Yacoub, Magdi H., and Yaliraki, Sophia N.. A computational modeling approach for enhancing self-assembly and biofunction-alisation of collagen biomimetic peptides. Biomaterials, 32(30):7275–7285, 2011.Google Scholar

[261] Parthasarathi, R., Madhan, B., Subramanian, V., and Ramasami, T.. Ab initio and density functional theory based studies on collagen triplets. Theor. Chem. Acc., 110(1):19–27, 2003.Google Scholar

[262] Hsien, Midas I. Tsai, Yujia Xu, and J. J. Dannenberg. Completely geometrically optimized DFT/ONIOM triple-helical collagen-like structures containing the ProProGly, ProProAla, ProProDAla, and ProProDSer triads. J. Am. Chem. Soc., 127(41):14130–14131, 2005.Google Scholar

[263] Rodrigues, C. R. F., Oliveira, J. I. N., Fulco, U. L. et al. Quantum biochemistry study of the T3–785 tropocollagen triple-helical structure. Chem. Phys. Lett., 559:88–93, 2013.Google Scholar

[264] Bezerra, Katyanna S., Jonas I. N. Oliveira, José X. Lima Neto et al. Quantum binding energy features of the T3–785 collagen-like triple-helical peptide. RSC Adv., 7(5):2817–2828, 2017.Google Scholar

[265] Ourique, G. S., J. F. Vianna, J. X. Lima Neto et al. A quantum chemistry investigation of a potential inhibitory drug against the dengue virus. RSC Adv., 6(61):56562– 56570, 2016.Google Scholar

[266] Sales Bezerra, Katyanna, J. X. Lima Neto, Jonas Ivan Nobre Oliveira et al. Computational investigation of the α2β1 integrin-collagen triple helix complex interaction. New J. Chem., 42(20):17115–17125, 2018.Google Scholar

[267] Dolinsky, Todd J., Jens E. Nielsen, J. Andrew McCammon, and Nathan A. Baker. PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res., 32(suppl 2):W665–W667, 2004.Google Scholar

[268] MacKerell, Alex D., Jr., Donald Bashford, M. L. D. R. Bellott et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B, 102(18):3586–3616, 1998.Google Scholar

[269] Derewenda, Zygmunt S., Linda Lee, and Urszula Derewenda. The occurence of C-H···O hydrogen bonds in proteins. J. Mol. Biol., 252(2):248–262, 1995.Google Scholar

[270] Gallivan, Justin P. and Dougherty, Dennis A.. Cation-π interactions in structural biology. Proc. Natl. Acad. Sci. U. S. A., 96(17):9459–9464, 1999.Google Scholar

[271] Fallas, Jorge A., Lesley E. R. O’Leary, and Jeffrey D. Hartgerink. Synthetic collagen mimics: Self-assembly of homotrimers, heterotrimers and higher order structures. Chem. Soc. Rev., 39(9):3510–3527, 2010.Google Scholar

[272] Bronco, Simona, Chiara Cappelli, and Susanna Monti. Understanding the structural and binding properties of collagen: A theoretical perspective. J. Phys. Chem. B, 108(28):10101–10112, 2004.Google Scholar

[273] Monti, Susanna, Simona Bronco, and Chiara Cappelli. Toward the supramolec-ular structure of collagen: A molecular dynamics approach. J. Phys. Chem. B, 109(22):11389–11398, 2005.Google Scholar

[274] Ortmann, F., F. Bechstedt, and W. G. Schmidt. Semiempirical van der Waals correction to the density functional description of solids and molecular structures. Phys. Rev. B, 73(20):205101, 2006.Google Scholar

[275] Persikov, Anton V., John A. M. Ramshaw, Alan Kirkpatrick, and Barbara Brodsky. Amino acid propensities for the collagen triple-helix. Biochemistry, 39(48):14960– 14967, 2000.Google Scholar

[276] Rich, Alexander and Crick, F. H. C.. The molecular structure of collagen. J. Mol. Biol., 3(5):483–506, 1961.Google Scholar

[277] Ramachandran, G. X. and Chandrasekharan, R.. Interchain hydrogen bonds via bound water molecules in the collagen triple helix. Biopolymers, 6(11):1649–1658, 1968.Google Scholar

[278] Bella, Jordi and Berman, Helen M. Crystallographic evidence for Cα-H···O=C hydrogen bonds in a collagen triple helix. J. Mol. Biol., 264(4):734–742, 1996.Google Scholar

[279] Bhatnagar, Rajendra S., Pattabiraman, N., Keith, R. et al. Inter-chain proline: Proline contacts contribute to the stability of the triple helical conformation. J. Biomol. Struct. Dyn., 6(2):223–233, 1988.Google Scholar

[280] Hongo, Chizuru, Keiichi Noguchi, Kenji Okuyama et al. Repetitive interactions observed in the crystal structure of a collagen-model peptide, [(Pro-Pro-Gly)₉]₃. J. Biochem., 138(2):135–144, 2005.Google Scholar

[281] Okuyama, Kenji, Narita, Hirotaka, Kawaguchi, Tatsuya et al. Unique side chain conformation of a leu residue in a triple-helical structure. Biopolymers, 86(3):212– 221, 2007.Google Scholar

[282] Juliano, Rudolph L. and Haskill, S.. Signal transduction from the extracellular matrix. J. Cell Biol., 120(3):577–585, 1993.Google Scholar

[283] Calderwood, David A., Iain D. Campbell, and David R. Critchley. Talins and kindlins: Partners in integrin-mediated adhesion. Nat. Rev. Mol. Cell Biol., 14(8):503–517, 2013.Google Scholar

[284] Hemler, Martin E.. VLA proteins in the integrin family: Structures, functions, and their role on leukocytes. Annu. Rev. Immunol., 8(1):365–400, 1990.Google Scholar

[285] Znoyko, Iya, Naondo Sohara, Samuel S. Spicer, Maria Trojanowska, and Adrian Reuben. Expression of oncostatin M and its receptors in normal and cirrhotic human liver. J. Hepatol., 43(5):893–900, 2005.Google Scholar

[286] Emsley, Jonas, C. Graham Knight, Richard W. Farndale, Michael J. Barnes, and Robert C. Liddington. Structural basis of collagen recognition by integrin α2β1. Cell, 101(1):47–56, 2000.Google Scholar

[287] Van de Walle, Gerlinde R., Karen Vanhoorelbeke et al. Two functional active conformations of the integrin α2β1, depending on activation condition and cell type. J. Biol. Chem., 280(44):36873–36882, 2005.Google Scholar

[288] Zhao, Yan and Truhlar, Donald G.. 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. Theor. Chem. Acc., 120(1–3):215– 241, 2008.Google Scholar

[289] Case, David A., Cheatham III, Thomas E. et al. The Amber biomolecular simulation programs. J. Comp. Chem., 26(16):1668–1688, 2005.Google Scholar

[290] Ulf Ryde and Par Soderhjelm. Ligand-binding affinity estimates supported by quantum-mechanical methods. Chem. Rev., 116(9):5520–5566, 2016.Google Scholar

[291] Welch, K. M. A.. Drug therapy of migraine. N. Engl. J. Med., 329(20):1476–1483, 1993.Google Scholar

[292] Durham, Paul and Papapetropoulos, Spyros. Biomarkers associated with migraine and their potential role in migraine management. Headache, 53(8):1262–1277, 2013.Google Scholar

[293] Pietrobon, Daniela and Jörg Striessnig. Neurological diseases: Neurobiology of migraine. Nat. Rev. Neurosci., 4(5):386–398, 2003.Google Scholar

[294] Del Bello, Fabio, Antonio Cilia, Antonio Carrieri et al. The versatile 2-substituted imidazoline nucleus as a structural motif of ligands directed to the serotonin 5-HT_1A receptor. ChemMedChem, 11(20):2287–2298, 2016.Google Scholar

[295] Lima Neto, José X., Vanessa P. Soares-Rachetti, Eudenilson L. Albuquerque, Vinicius Manzoni, and Umberto L. Fulco. Outlining migrainous through dihydroergotamine-serotonin receptor interactions using quantum biochemistry. N. J. Chem., 42(4):2401–2412, 2018.Google Scholar

[296] Wang, Chong, Yi Jiang, Jinming Ma, Huixian Wu et al. Structural basis for molecular recognition at serotonin receptors. Science, 340(6132):610–614, 2013.Google Scholar

[297] Córdova-Sintjago, Tania, Nancy Villa, Clinton Canal, and Raymond Booth. Human serotonin 5-HT2C G protein-coupled receptor homology model from the β2 adreno-ceptor structure: Ligand docking and mutagenesis studies. Int. J. Quantum Chem., 112(1):140–149, 2012.Google Scholar

[298] Schoenen, Jean. Migraine and serotonin: The quest for the holy grail goes on. Cephalalgia, 34(3):163–164, 2014.Google Scholar

[299] Silberstein, Stephen D. and McCrory, Douglas C.. Ergotamine and dihydroergotamine: History, pharmacology, and efficacy. Headache, 43(2):144–166, 2003.Google Scholar

[300] Roth, Bryan L.. Drugs and valvular heart disease. N. Engl. J. Med., 356(1):6–9, 2007.Google Scholar

[301] Rao, Bijan K., Samanta, Devleena, Joshi, Shawn et al. Receptor-ligand interaction at 5-HT3 serotonin receptors: A cluster approach. J. Phys. Chem. A, 118(37):8471– 8476, 2014.Google Scholar

[302] McCorvy, John D. and Roth, Bryan L.. Structure and function of serotonin G protein-coupled receptors. Pharmacol. Ther., 150:129–142, 2015.Google Scholar

[303] Zanatta, G., Barroso-Neto, I. L., Bambini-Junior, V. et al. Quantum biochemistry description of the human dopamine D3 receptor in complex with the selective antagonist eticlopride. Proteomics Bioinf., 5:155–162, 2012.Google Scholar

[304] Hebert, Hans. The crystal structure and absolute configuration of (-)-dihydroergotamine methanesulfonate monohydrate. Acta Crystallogr. B, 35(12): 2978–2984, 1979.Google Scholar

[305] Zanatta, Geancarlo, Gustavo Nunes, Eveline M. Bezerra et al. Antipsychotic haloperidol binding to the human dopamine D3 receptor: Beyond docking through QM/MM refinement toward the design of improved schizophrenia medicines. ACS Chem. Neurosci., 5(10):1041–1054, 2014.Google Scholar

[306] Heifetz, Alexander, Ewa I. Chudyk, Laura Gleave et al. The fragment molecular orbital method reveals new insight into the chemical nature of GPCR-ligand interactions. J. Chem. Inf. Model., 56(1):159–172, 2015.Google Scholar

[307] Zanatta, Geancarlo, Gustavo Della Flora Nunes, Eveline M. Bezerra et al. Two binding geometries for risperidone in dopamine D3 receptors: Insights on the fast-off mechanism through docking, quantum biochemistry, and molecular dynamics simulations. ACS Chem. Neurosci., 7(10):1331–1347, 2016.Google Scholar

[308] Venkatakrishnan, A. J., Xavier Deupi, Guillaume Lebon et al. Molecular signatures of G-protein-coupled receptors. Nature, 494(7436):185–194, 2013.Google Scholar

[309] Brinkmann, Levin, Eugene Heifets, and Lev Kantorovich. Density functional calculations of extended, periodic systems using coulomb corrected molecular fractionation with conjugated caps method (CC-MFCC). Phys. Chem. Chem. Phys., 16(39):21252–21270, 2014.Google Scholar

[310] Magnus, Jogvan Haugaard Olsen, Nanna Holmgaard List, Kasper Kristensen, and Jacob Kongsted. Accuracy of protein embedding potentials: An analysis in terms of electrostatic potentials. J. Chem. Theor. Comput., 11(4):1832–1842, 2015.Google Scholar

[311] Liu, Jinfeng, Xianwei Wang, John Z. H. Zhang, and Xiao He. Calculation of protein-ligand binding affinities based on a fragment quantum mechanical method. RSC Adv., 5(129):107020–107030, 2015.Google Scholar

[312] Lloyd, K. and Hornykiewicz, O.. Parkinson’s disease: Activity of l-dopa decarboxy-lase in discrete brain regions. Science, 170(3963):1212–1213, 1970.Google Scholar

[313] Kish, Stephen J., Kathleen Shannak, and Oleh Hornykiewicz. Uneven pattern of dopamine loss in the striatum of patients with idiopathic Parkinson’s disease. N. Engl. J. Med., 318(14):876–880, 1988.Google Scholar

[314] Adamiak, Urszula, Maria Kaldonska, Gabriela Klodowska-Duda et al. Pharmacokinetic-pharmacodynamic modeling of levodopa in patients with advanced Parkinson disease. Clin. Neuropharmacol., 33(3):135–141, 2010.Google Scholar

[315] Steinmetz, Nicole F., Vu Hong, Erik D. Spoerke et al. Buckyballs meet viral nanoparticles: Candidates for biomedicine. J. Am. Chem. Soc., 131(47):17093– 17095, 2009.Google Scholar

[316] Calne, Donald B.. Treatment of Parkinson’s disease. N. Engl. J. Med., 329(14):1021– 1027, 1993.Google Scholar

[317] Frazao, Nilton F., Eudenilson L. Albuquerque, Umberto L. Fulco et al.Four-level levodopa adsorption on C60 fullerene for transdermal and oral administration: A computational study. RSC Adv., 2(22):8306–8322, 2012.Google Scholar

[318] Frazão, N. F., Albuquerque, E. L., Fulco, U. L., Mauriz, P. W., and Azevedo, D. L.. Conformational, optoelectronic and vibrational properties of the entacapone molecule: A quantum chemistry study. J. Nanosci. Nanotechnol., 16(5):4825–4834, 2016.Google Scholar

[319] Hedberg, Kenneth, Lise Hedberg, Donald S. Bethune et al. Bond lengths in free molecules of buckminsterfullerene, C60, from gas-phase electron diffraction. Science, 254(5030):410–412, 1991.Google Scholar

[320] Cooper, Valentino R., T. Thonhauser, and David C. Langreth. An application of the van der Waals density functional: Hydrogen bonding and stacking interactions between nucleobases. J. Chem. Phys., 128(20):204102, 2008.Google Scholar

[321] Hess, Berk, Carsten Kutzner, David Van Der Spoel, and Erik Lindahl. GROMACS4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theor. Comput., 4(3):435–447, 2008.Google Scholar

[322] Jorgensen, William L., David S. Maxwell, and Julian Tirado-Rives. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc., 118(45):11225–11236, 1996.Google Scholar

[323] Bussi, Giovanni, Davide Donadio, and Michele Parrinello. Canonical sampling through velocity rescaling. J. Chem. Phys., 126(1):014101, 2007.Google Scholar

[324] Singh, U. Chandra and Kollman, Peter A.. An approach to computing electrostatic charges for molecules. J. Comput. Chem., 5(2):129–145, 1984.Google Scholar

[325] Parr, Robert G. and Yang, Weitao. Density functional approach to the frontier-electron theory of chemical reactivity. J. Am. Chem. Soc., 106(14):4049–4050, 1984.Google Scholar

[326] Foster, J. P. and Weinhold, F.. Natural hybrid orbitals. J. Am. Chem. Soc., 102(24):7211–7218, 1980.Google Scholar

[327] Bonaccorsi, Rosanna, Eolo Scrocco, and Jacopo Tomasi. Molecular SCF calculations for the ground state of some three-membered ring molecules:(CH ₂ )₃ ,(CH₂ ) ₂ NH, (CH₂ )₂ NH⁺₂ ,(CH₂) ₂₀ ,(CH₂ )₂ s,(CH)₂ CH₂ , and N₂ CH₂ . J. Chem. Phys., 52(10): 5270–5284, 1970.Google Scholar

[328] Nalewajski, Roman F. and Robert G. Parr. Information theory, atoms in molecules, and molecular similarity. Proc. Natl. Acad. Sci. U. S. A., 97(16):8879–8882, 2000.Google Scholar

[329] Henriques, J. M., E. W. S. Caetano, V. N. Freire, J. A. P. da Costa, and E. L. Albuquerque. Structural, electronic, and optical absorption properties of orthorhombic CaSnO3 through ab initio calculations. J. Phys. Condens. Matter, 19(10): 106214, 2007.Google Scholar

[330] Moreira, E., Henriques, J. M., Azevedo, D. L. et al. Structural, optoelectronic, infrared and raman spectra of orthorhombic SrSnO3 from DFT calculations. J. Solid State Chem., 184(4):921–928, 2011.Google Scholar

[331] Medeiros, S. K., Albuquerque, E. L., Maia, F. F., Jr., Caetano, E. W. S., and Freire, V. N.. Structural, electronic, and optical properties of CaCO3 aragonite. Chem. Phys. Lett., 430(4–6):293–296, 2006.Google Scholar

[332] Fast, Patton L., Jose Corchado, Maria Luz Sanchez, and Donald G. Truhlar. Optimized parameters for scaling correlation energy. J. Phys. Chem. A, 103(17):3139– 3143, 1999.Google Scholar

[333] George, Philip and Bock, Charles W.. A test of the AM1 model for calculating energies and structural properties of benzene, toluene, naphthalene, 1-methyl and 2-methylnaphthalene. Tetrahedron, 45(3):605–616, 1989.Google Scholar

[334] Poon, Kinning, Linda M. Nowak, and Robert E. Oswald. Characterizing single-channel behavior of GluA3 receptors. Biophys. J., 99(5):1437–1446, 2010.Google Scholar

[335] Lodge, David. The history of the pharmacology and cloning of ionotropic glutamate receptors and the development of idiosyncratic nomenclature. Neuropharmacology, 56(1):6–21, 2009.Google Scholar

[336] Jin, Rongsheng, Tue G. Banke, Mark L. Mayer, Stephen F. Traynelis, and Eric Gouaux. Structural basis for partial agonist action at ionotropic glutamate receptors. Nat. Neurosci., 6(8):803–810, 2003.Google Scholar

[337] Fenwick, Michael K. and Robert E. Oswald. NMR spectroscopy of the ligand-binding core of ionotropic glutamate receptor 2 bound to 5-substituted willardiine partial agonists. J. Mol. Biol., 378(3):673–685, 2008.Google Scholar

[338] Lima Neto, José X., Umberto L. Fulco, Eudenilson L. Albuquerque et al. A quantum biochemistry investigation of willardiine partial agonism in AMPA receptors. Phys. Chem. Chem. Phys., 17(19):13092–13103, 2015.Google Scholar

[339] Mayer, Mark L.. Glutamate receptors at atomic resolution. Nature, 440(7083):456– 462, 2006.Google Scholar

[340] Madden, Dean R.. Ion channel structure: The structure and function of glutamate receptor ion channels. Nat. Rev. Neurosci., 3(2):91–101, 2002.Google Scholar

[341] Sobolevsky, Alexander I., Rosconi, Michael P., and Gouaux, Eric. X-ray structure, symmetry and mechanism of an AMPA-subtype glutamate receptor. Nature, 462(7274):745–756, 2009.Google Scholar

[342] Dong, Hao and Zhou, Huan-Xiang. Atomistic mechanism for the activation and desensitization of an AMPA-subtype glutamate receptor. Nat. Commun., 2:354, 2011.Google Scholar

[343] Lau, Albert Y. and Roux, Benoît. The hidden energetics of ligand binding and activation in a glutamate receptor. Nat. Struct. Mol. Biol., 18(3):283–287, 2011.Google Scholar

[344] Mayer, Mark L. and Armstrong, Neali. Structure and function of glutamate receptor ion channels. Annu. Rev. Physiol., 66:161–181, 2004.Google Scholar

[345] Maltsev, Alexander S., Ahmed, Ahmed H., Fenwick, Michael K., Jane, David E., and Oswald, Robert E.. Mechanism of partial agonism at the GluR2 AMPA receptor: Measurements of lobe orientation in solution. Biochemistry, 47(40):10600–10610, 2008.Google Scholar

[346] Wu, Emilia L., Ye Mei, Ke Li Han, and John Z. H. Zhang. Quantum and molecular dynamics study for binding of macrocyclic inhibitors to human α-thrombin. Biophys. J., 92(12):4244–4253, 2007.Google Scholar

[347] Frandsen, Anne, Darryl S. Pickering, Bente Vestergaard et al. Tyr702 is an important determinant of agonist binding and domain closure of the ligand-binding core of GluR2. Mol. Pharmacol., 67(3):703–713, 2005.Google Scholar

[348] Martinez, Madeline, Ahmed, Ahmed H., Loh, Adrienne P., and Oswald, Robert E.. Thermodynamics and mechanism of the interaction of willardiine partial agonists with a glutamate receptor: Implications for drug development. Biochemistry, 53(23):3790–3795, 2014.Google Scholar

[349] Hill, Ronald A., Wallace, Lane J., Miller, Duane D. et al. Structure-activity studies for α-amino-3-hydroxy-5-methyl-4-isoxazolepropanoic acid receptors: Acidic hydrox-yphenylalanines. J. Med. Chem., 40(20):3182–3191, 1997.Google Scholar

[350] Ahmed, Ahmed H., Christopher P. Ptak, Michael K. Fenwick et al. Dynamics of cleft closure of the GluA2 ligand-binding domain in the presence of full and partial agonists revealed by hydrogen-deuterium exchange. J. Biol. Chem., 288(38):27658– 27666, 2013.Google Scholar

[351] Pøhlsgaard, Jacob, Karla Frydenvang, Ulf Madsen, and Jette Sandholm Kastrup. Lessons from more than 80 structures of the GluA2 ligand-binding domain in complex with agonists, antagonists and allosteric modulators. Neuropharmacology, 60(1):135–150, 2011.Google Scholar

[352] da Silva Ribeiro, Tamires C., Roner F. da Costa, Eveline M. Bezerra et al. The quantum biophysics of the isoniazid adduct NADH binding to its InhA reductase target. N. J. Chem., 38(7):2946–2957, 2014.Google Scholar

[353] Postila, Pekka A., Mikko Ylilauri, and Olli T. Pentiküinen. Full and partial agonism of ionotropic glutamate receptors indicated by molecular dynamics simulations. J. Chem. Inf. Model., 51(5):1037–1047, 2011.Google Scholar

[354] Armstrong, Neali and Gouaux, Eric. Mechanisms for activation and antagonism of an AMPA-sensitive glutamate receptor: Crystal structures of the GluR2 ligand binding core. Neuron, 28(1):165–181, 2000.Google Scholar

[355] Boström, Jonas, Anders Hogner, and Stefan Schmitt. Do structurally similar ligands bind in a similar fashion? J. Med. Chem., 49(23):6716–6725, 2006.Google Scholar

[356] Holm, Mai Marie, Naur, Peter, Bente Vestergaard et al. A binding site tyrosine shapes desensitization kinetics and agonist potency at GluR2. a mutagenic, kinetic, and crystallographic study. J. Biol. Chem., 280(42):35469–35476, 2005.Google Scholar

[357] McFeeters, Robert L. and Oswald, Robert E.. Structural mobility of the extracellular ligand-binding core of an ionotropic glutamate receptor: Analysis of NMR relaxation dynamics. Biochemistry, 41(33):10472–10481, 2002.Google Scholar

[358] Ahmed, Ahmed H., Thompson, Melissa D., Fenwick, Michael K. et al. Mechanisms of antagonism of the GluR2 AMPA receptor: Structure and dynamics of the complex of two willardiine antagonists with the glutamate binding domain. Biochemistry, 48(18):3894–3903, 2009.Google Scholar

[359] Jin, Rongsheng and Gouaux, Eric. Probing the function, conformational plasticity, and dimer-dimer contacts of the GluR2 ligand-binding core: Studies of 5-substituted willardiines and GluR2 S1S2 in the crystal. Biochemistry, 42(18):5201–5213, 2003.Google Scholar

[360] Okada, Okimasa, Kei Odai, Tohru Sugimoto, and Etsuro Ito. Molecular dynamics simulations for glutamate-binding and cleft-closing processes of the ligand-binding domain of GluR2. Biophys. Chem., 162:35–44, 2012.Google Scholar

[361] Ahmed, Ahmed H., Shu Wang, Huai-Hu Chuang, and Robert E. Oswald. Mechanism of AMPA receptor activation by partial agonists dissulfice trapping of closed lobe conformations. J. Biol. Chem., 286(40):35257–35266, 2011.Google Scholar

[362] Begley, C. Glenn and Ellis, Lee M.. Drug development: Raise standards for preclini-cal cancer research. Nature, 483(7391):531, 2012.Google Scholar

[363] Byun, David J., Wolchok, Jedd D., Lynne M. Rosenberg, and Monica Girotra. Cancer immunotherapy-immune checkpoint blockade and associated endocrinopathies. Nat. Rev. Endocrinol., 13(4):195–207, 2017.Google Scholar

[364] Mota, K. B., Lima Neto, J. X., Lima Costa, A. H. et al. A quantum biochemistry model of the interaction between the estrogen receptor and the two antagonists used in breast cancer treatment. Comput. Theor. Chem., 1089:21–27, 2016.Google Scholar

[365] Lima Neto, José X., Katyanna S. Bezerra, Dalila N. Manso et al. Energetic description of cilengitide bound to integrin. New J. Chem, 41(19):11405–11412, 2017.Google Scholar

[366] Tavares, Ana Beatriz M. L. A., José X. Lima Neto, Umberto L. Fulco, and Eudenilson L. Albuquerque. Inhibition of the checkpoint protein PD-1 by the therapeutic antibody pembrolizumab outlined by quantum chemistry. Sci. Rep., 8(1):1840, 2018.Google Scholar

[367] Tavares, Ana Beatriz M. L. A., José X. Lima Neto, Umberto L. Fulco, and Eudenilson L. Albuquerque. A quantum biochemistry approach to investigate checkpoint inhibitor drugs for cancer. New J. Chem., 43:7185–7189, 2019.Google Scholar

[368] Rivenbark, Ashley G., Siobhan M. OConnor, and William B. Coleman. Molecular and cellular heterogeneity in breast cancer: Challenges for personalized medicine. Am. J. Pathol., 183(4):1113–1124, 2013.Google Scholar

[369] Fukuzawa, Kaori, Kitaura, Kazuo, Uebayasi, Masami et al. Ab initio quantum mechanical study of the binding energies of human estrogen receptor α with its ligands: An application of fragment molecular orbital method. J. Comput. Chem., 26(1):1–10, 2005.Google Scholar

[370] Jordan, V. Craig and Morrow, Monica. Tamoxifen, raloxifene, and the prevention of breast cancer. Endocr. Rev., 20(3):253–278, 1999.Google Scholar

[371] Gomathi, G., Srinivasan, T., Velmurugan, D., and Gopalakrishnan, R.. A bluish-green emitting organic compound methyl 3-[(E)-(2-hydroxy-1-naphthyl) methyli-dene] carbazate: Spectroscopic, thermal, fluorescence, antimicrobial and molecular docking studies. RSC Adv., 5(56):44742–44748, 2015.Google Scholar

[372] Shiau, Andrew K., Barstad, Danielle, Loria, Paula M. et al. The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell, 95(7):927–937, 1998.Google Scholar

[373] Brzozowski, Andrzej M., Ashley C. W. Pike, Zbigniew Dauter et al. Molecular basis of agonism and antagonism in the oestrogen receptor. Nature, 389(6652):753–758, 1997.Google Scholar

[374] Clegg, Nicola J., Sreenivasan Paruthiyil, Dale C. Leitman, and Thomas S. Scanlan. Differential response of estrogen receptor subtypes to 1, 3-diarylindene and 2, 3-diarylindene ligands. J. Med. Chem., 48(19):5989–6003, 2005.Google Scholar

[375] Watanabe, Chiduru, Kaori Fukuzawa, Shigenori Tanaka, and Sachiko Aida-Hyugaji. Charge clamps of lysines and hydrogen bonds play key roles in the mechanism to fix helix 12 in the agonist and antagonist positions of estrogen receptor α: Intramolecular interactions studied by the ab initio fragment molecular orbital method. J. Phys. Chem. B, 118(19):4993–5008, 2014.Google Scholar

[376] Desgrosellier, Jay S. and David A. Cheresh. Integrins in cancer: Biological implications and therapeutic opportunities. Nat. Rev. Cancer, 10(1):9–22, 2010.Google Scholar

[377] Prowse, Andrew B. J., Fenny Chong, Peter P. Gray, and Trent P. Munro. Stem cell integrins: Implications for ex-vivo culture and cellular therapies. Stem Cell Res., 6(1):1–12, 2011.Google Scholar

[378] Su, Yang, Xia, Wei, Li, Jing, Walz, Thomas et al. Relating conformation to function in integrin α5β1. Proc. Natl. Acad. Sci. U. S. A., 113(27):E3872–E3881, 2016.Google Scholar

[379] Corso, Alberto Dal, Pignataro, Luca, Laura Belvisi, and Cesare Gennari. αvβ3 integrin-targeted peptide/peptidomimetic-drug conjugates: In-depth analysis of the linker technology. Curr. Top. Med. Chem., 16(3):314–329, 2016.Google Scholar

[380] Vasile, Francesca, Gloria Menchi, Elena Lenci et al. Insight to the binding mode of triazole RGD-peptidomimetics to integrin-rich cancer cells by NMR and molecular modeling. Bioorg. Med. Chem., 24(5):989–994, 2016.Google Scholar

[381] Chen, JianFeng, Salas, Azucena, and Springer, Timothy A.. Bistable regulation of integrin adhesiveness by a bipolar metal ion cluster. Nat. Struct. Mol. Biol., 10(12):995–1001, 2003.Google Scholar

[382] Honjo, Tasuku. Cancer immunotherapy by PD-1 blockade. Cancer Sci., 109:197– 197, 2018.Google Scholar

[383] Wei, Spencer C., Duffy, Colm R., and Allison, James P.. Fundamental mechanisms of immune checkpoint blockade therapy. Cancer Discov., 8(9):1069–1086, 2018.Google Scholar

[384] Chowdhury, P. S., Chamoto, K., and Honjo, T.. Combination therapy strategies for improving PD-1 blockade efficacy: A new era in cancer immunotherapy. J. Intern. Med., 283(2):110–120, 2018.Google Scholar

[385] Sharma, Padmanee and Allison, James P.. The future of immune checkpoint therapy. Science, 348(6230):56–61, 2015.Google Scholar

[386] Iwai, Yoshiko, Hamanishi, Junzo, Chamoto, Kenji, and Honjo, Tasuku. Cancer immunotherapies targeting the PD-1 signaling pathway. J. Biomed. Sci, 24(1):26, 2017.Google Scholar

[387] Khoja, Leila, Marcus O. Butler, S. Peter Kang, Scot Ebbinghaus, and Anthony M. Joshua. Pembrolizumab. J. Immunother. Cancer, 3(1):36, 2015.Google Scholar

[388] Shin, Daniel Sanghoon, Zaretsky, Jesse M., Escuin-Ordinas, Helena et al. Primary resistance to PD-1 blockade mediated by JAK1/2 mutations. Cancer Discov., 7(2):188–201, 2017.Google Scholar

[389] Zak, Krzysztof M., Grudnik, Przemyslaw, Magiera, Katarzyna, Dömling, Alexander, Dubin, Grzegorz, and Holak, Tad A.. Structural biology of the immune checkpoint receptor PD-1 and its ligands PD-L1/PD-L2. Structure, 25(8):1163–1174, 2017.Google Scholar

[390] Viricel, Clement, Ahmed, Marawan, and Barakat, Khaled. Human PD-1 binds differently to its human ligands: A comprehensive modeling study. J. Mol. Graph. Model., 57:131–142, 2015.Google Scholar

[391] Zak, Krzysztof M., Przemyslaw Grudnik, Katarzyna Guzik et al. Structural basis for small molecule targeting of the programmed death ligand 1 (PD-L1). Oncotarget, 7(21):30323–30335, 2016.Google Scholar

[392] Ivashko, Igor N. and Kolesar, Jill M.. Pembrolizumab and nivolumab: PD-1 inhibitors for advanced melanoma. Am. J. Health Syst. Pharm., 73(4):193–201, 2016.Google Scholar

[393] Horita, Shoichiro, Nomura, Yayoi, Sato, Yumi et al. High-resolution crystal structure of the therapeutic antibody pembrolizumab bound to the human PD-1. Sci. Rep., 6:35297, 2016.Google Scholar

[394] Nishimura, Hiroyuki, Nose, Masato, Hiai, Hiroshi, Minato, Nagahiro, and Honjo, Tasuku. Development of lupus-like autoimmune diseases by disruption of the PD-1 gene encoding an ITIM motif-carrying immunoreceptor. Immunity, 11(2):141–151, 1999.Google Scholar

[395] Tan, Shuguang, Zhang, Hao, Chai, Yan et al. An unexpected n-terminal loop in PD-1 dominates binding by nivolumab. Nat. Commun., 8:14369, 2017.Google Scholar

[396] Lima Costa, Aranthya H., Clemente, Washington S. et al. Computational biochemical investigation of the binding energy interactions between an estrogen receptor and its agonists. New J. Chem., 42(24):19801–19810, 2018.Google Scholar

[397] Alder, Berni Julian and Wainwright, Thomas Everett. Phase transition for a hard sphere system. J. Chem. Phys., 27(5):1208–1209, 1957.Google Scholar

[398] Perutz, M. F. F.. New x-ray evidence on the configuration of polypeptide chains: Polypeptide chains in poly-γ -benzyl-l-glutamate, keratin and hæmoglobin. Nature, 167(4261):1053, 1951.Google Scholar

[399] Ramachandran, G. N., Ramakrishnan, C., and Sasisekharan, V.. Stereochemistry of polypeptide chain configurations. J. Mol. Biol., 7:95–99, 1963.Google Scholar