Analytical derivatives, forces, force constants, molecular geometries, and related response properties in electronic structure theory, WIREs: Comput. Molec. Sci, vol.4, pp.169-181, 2014. ,
Ab initio calculation of force constants and equilibrium geometries in polyatomic molecules, Mol. Phys, vol.17, pp.197-204, 1969. ,
Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme, J. Molec. Biol, vol.103, pp.227-249, 1976. ,
A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations, J. Comput. Chem, vol.11, pp.700-733, 1990. ,
QM/MM Methods for Biolomolecular Systems, Angew. Chem. Int. Ed, vol.48, pp.1198-1229, 2009. ,
The Nobel Prize in Chemistry 2013 -Advanced Information ,
The QM/MM approach for wavefunctions, energies and response functions within self-consistent field and coupled cluster theories, Mol. Phys, vol.100, pp.1813-1828, 2002. ,
Recent applications of a QM/MM scheme at the CASPT2//CASSCF/AMBER (or CHARMM) level of theory in photochemistry and photobiology, J. Phys. Conf. Ser, vol.101, p.12001, 2008. ,
Approximate electrostatic interaction operator for QM/MM calculations, Chem. Phys. Lett, vol.356, pp.331-339, 2002. ,
Unique QM/MM potential energy surface exploration using microiterations, Int. J. Quant. Chem, vol.111, pp.3339-3346, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-01415208
, Combining Quantum Mechanics and Molecular Mechanics. Some Recent Progresses in QM/MM Methods
, Advances in Quantum Chemistry, vol.59, pp.353-400, 2010.
, Combining Quantum Mechanics and Molecular Mechanics. Some Recent Progresses in QM/MM Methods
, Advances in Quantum Chemistry, vol.59, pp.1-15, 2010.
Some Recent Progresses in QM/MM Methods; Sabin, Combining Quantum Mechanics and Molecular Mechanics, vol.59, pp.17-57, 2010. ,
Analytical gradients for MP2, double hybrid functionals, and TD-DFT with polarizable embedding described by fluctuating charges, J. Comput. Chem, vol.36, pp.2271-2290, 2015. ,
Encyclopedia of Biophysics ,
, , pp.2149-2154, 2013.
A new ONIOM implementation in Gaussian98. Part I. The calculation of energies, gradients, vibrational frequencies and electric field derivatives, J. Molec. Struc.: THEOCHEM, pp.1-21, 1999. ,
Molecular properties from combined QM/MM methods. I. Analytical second derivative and vibrational calculations, J. Chem. Phys, vol.112, pp.1133-1149, 2000. ,
, Molecular Properties from Combined QM/MM Methods
, Chemical Shifts in Large Molecules, J. Phys. Chem. B, vol.104, pp.3721-3743, 2000.
Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian, J. Chem. Theor. Comput, vol.7, pp.496-514, 2011. ,
Analytic second derivatives of the energy in the fragment molecular orbital method, J. Chem. Phys, p.164103, 2013. ,
Ab Initio Integrated Multi-Center Molecular Orbitals Method for Large Cluster Systems:â?? Total Energy and Normal Vibration, J. Phys. Chem. A, vol.109, pp.8424-8429, 2005. ,
Enabling ab initio Hessian and frequency calculations of large molecules, J. Chem. Phys, p.234101, 2008. ,
Calculation of IR Spectra with a Fully Polarizable QM/MM Approach Based on Fluctuating Charges and Fluctuating Dipoles, J. Chem. Theory Comput, vol.15, pp.5495-5507, 2019. ,
Analytic QM/MM atomic charge derivatives avoiding the scaling of coupled perturbed equations with the MM subsystem size, J. Chem. Phys, p.41102, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02262433
ATP Binding Turns Plant Cryptochrome Into an Efficient Natural Photoswitch ,
Derivative studies in Hartree-Fock and Møller-Plesset theories, Int. J. Quant. Chem, vol.16, pp.225-241, 1979. ,
All-Atom Calculation of the Normal Modes of Bacteriorhodopsin Using a Sliding Block Iterative Diagonalization Method, J. Chem. Theor. Comput, vol.2, pp.166-174, 2006. ,
Derivative studies in Hartree-Fock and Moller-Plesset theories, Int. J. Quant. Chem.: Quant. Chem. Symp, vol.13, pp.225-241, 1979. ,
Some Recent Advances in Density Matrix Theory, Rev. Mod. Phys, vol.32, pp.335-369, 1960. ,
, , 2016.
Software tools for molecular design ,
URL : https://hal.archives-ouvertes.fr/hal-01820747
General Time Dependent Approach to Vibronic Spectroscopy Including Franck-Condon ,
, J. Chem. Theor. Comput, vol.9, pp.4097-4115, 2013.
Progress in Time-Dependent Density-Functional Theory, Ann. Rev. Phys. Chem, vol.63, pp.287-323, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-01415184
Density-functional thermochemistry. III. The role of exact exchange, J. Chem. Phys, vol.98, pp.5648-5652, 1993. ,
Development of the Colle-Salvetti correlationenergy formula into a functional of the electron density, Phys. Rev. B, vol.37, pp.785-789, 1988. ,
Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis, Can. J. Phys, vol.58, pp.1200-1211, 1980. ,
Fully optimized contracted Gaussian basis sets for atoms Li to Kr, J. Chem. Phys, vol.97, pp.2571-2577, 1992. ,
Fully optimized contracted Gaussian basis sets of triple zeta valence quality for atoms Li to Kr, J. Chem. Phys, vol.100, pp.5829-5835, 1994. ,
Auxiliary basis sets to approximate Coulomb potentials, Chem. Phys. Lett, vol.240, pp.283-290, 1995. ,
Auxiliary basis sets for main row atoms and transition metals and their use to approximate Coulomb potentials, Theor. Chem. Acc, vol.97, pp.119-124, 1997. ,
,
, , 2018.
Theoretical study of electron transfer between the photolyase catalytic cofactor FADH(-) and DNA thymine dimer, J. Am. Chem. Soc, vol.122, p.1057, 2000. ,
Photochemistry of flavoprotein light sensors, Nat. Chem. Biol, vol.10, pp.801-809, 2014. ,
Electronic spectra of flavin in different redox and protonation states: a computational perspective on the effect of the electrostatic environment, Phys. Chem. Chem. Phys, vol.21, pp.16526-16537, 2019. ,
Impact of the redox state of flavin chromophores on the UVâ??vis spectra, redox and acidity constants and electron affinities, J. Photochem. Photobiol. A: Chem, p.112164, 2020. ,
URL : https://hal.archives-ouvertes.fr/hal-02394980
TD-)DFT Calculation of Vibrational and Vibronic Spectra of Riboflavin in Solution, J. Phys. Chem. B, vol.114, pp.10826-10834, 2010. ,
Analytic gradient for the QM/MM-Ewald method using charges derived from the electrostatic potential: Theory, implementation, and application to ab initio molecular dynamics simulation of the aqueous electron, J. Chem. Phys, p.144115, 2019. ,
Vibrational dynamics of polyatomic molecules in solution: assignment, time evolution and mixing of instantaneous normal modes, Theor. Chem. Acc, vol.128, pp.769-782, 2011. ,
Theoretical Investigation of Infrared Spectra and Pocket Dynamics of Photodissociated Carbonmonoxy Myoglobin, Biophys. J, vol.85, pp.3612-3623, 2003. ,
The anharmonic quartic force field infrared spectra of three polycyclic aromatic hydrocarbons: Naphthalene, anthracene, and tetracene, J. Chem. Phys, p.224314, 2015. ,