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List of works by Nicolas Ferré

A new three-layer hybrid method (LSCF/MM/Madelung) devoted to the study of chemical reactivity in zeolites. Preliminary results

Additive Decomposition of the Physical Components of the Magnetic Coupling from Broken Symmetry Density Functional Theory Calculations

scientific article published on July 2013

An Average Solvent Electrostatic Configuration Protocol for QM/MM Free Energy Optimization: Implementation and Application to Rhodopsin Systems

scientific article published on 7 November 2017

An Effective Procedure for Analyzing Molecular Vibrations in Terms of Local Fragment Modes

scientific article published on 19 September 2016

An artificial molecular switch that mimics the visual pigment and completes its photocycle in picoseconds

scholarly article

Anabaena sensory rhodopsin is a light-driven unidirectional rotor

scientific article

Analysis of the physical contributions to magnetic couplings in broken symmetry density functional theory approach

scientific article published on 01 September 2012

Analytic Energy, Gradient, and Hessian of Electrostatic Embedding QM/MM Based on Electrostatic Potential-Fitted Atomic Charges Scaling Linearly with the MM Subsystem Size

scientific article published on 07 December 2020

Analytic QM/MM atomic charge derivatives avoiding the scaling of coupled perturbed equations with the MM subsystem size

scientific article published on 01 July 2019

Application of the local self-consistent-field method to core-ionized and core-excited molecules, polymers, and proteins: True orthogonality between ground and excited states

Approximate electrostatic interaction operator for QM/MM calculations

Are the bio- and chemiluminescence states of the firefly oxyluciferin the same as the fluorescence state?

scientific article

Assessing the accuracy of a QM/MM//MD combined protocol to compute spectromagnetic properties of polyfunctional nitroxides in solution

Assessment of Density Functional Theory for Describing the Correlation Effects on the Ground and Excited State Potential Energy Surfaces of a Retinal Chromophore Model

scientific article published on 13 August 2013

Assignment of the EPR spectrum of 5,5-dimethyl-1-pyrroline N-oxide (DMPO) superoxide spin adduct

scientific article published in February 2005

Can the Closed-Shell DFT Methods Describe the Thermolysis of 1,2-Dioxetanone?

scientific article published on 24 September 2012

Characterization of the conical intersection of the visual pigment rhodopsin at the CASPT2//CASSCF/AMBER level of theory

Chemi- and Bioluminescence of Cyclic Peroxides.

scientific article published in March 2018

Chemical Tuning of Magnetic Exchange Couplings Using Broken-Symmetry Density Functional Theory

scientific article published on 26 September 2018

Chemiluminescence and Fluorescence States of a Small Model for Coelenteramide and Cypridina Oxyluciferin: A CASSCF/CASPT2 Study

scientific article published on 11 November 2011

Chemiluminescence of Coelenterazine and Fluorescence of Coelenteramide: A Systematic Theoretical Study

scientific article published on 23 July 2012

Color-tuning mechanism of firefly investigated by multi-configurational perturbation method

scientific article published in January 2010

Computation of the Isotropic Hyperfine Coupling Constant: Efficiency and Insights from a New Approach Based on Wave Function Theory

scientific article published on 17 January 2017

CpHMD-Then-QM/MM Identification of the Amino Acids Responsible for the Anabaena Sensory Rhodopsin pH-Dependent Electronic Absorption Spectrum

scientific article published on 02 July 2019

DNA nucleobase properties and photoreactivity: Modeling environmental effects

Effect of point mutations on the ultrafast photo-isomerization of Anabaena sensory rhodopsin

scientific article published in February 2018

Effects of water re-location and cavity trimming on the CASPT2//CASSCF/AMBER excitation energy of Rhodopsin

Electronic Basis of the Comparable Hydrogen Bond Properties of Small H2CO/(H2O)nand H2NO/(H2O)nSystems (n= 1, 2)

scientific article published on 18 October 2007

Electrostatic interactions in peptides. Polarisation effects due to an α-helix

Further insights into the environmental effects on the computed hyperfine coupling constants of nitroxides in aqueous solution

scientific article published in November 2009

Geometrical Embedding Governs a Dramatic Variation of Electron Paramagnetic Resonance Hyperfine Coupling Constants of Disulfide Radical Anions

scientific article published on 04 May 2011

Hybrid QM/MM simulations of the obelin bioluminescence and fluorescence reveal an unexpected light emitter.

scientific article published on 6 March 2014

Imidazoline-N-oxyl: a DFT study of its protonation reaction.

scientific article published in October 2009

Improved evaluation of spin-polarization energy contributions using broken-symmetry calculations

scientific article published on 01 August 2020

Infrared spectroscopy from electrostatic embedding QM/MM: local normal mode analysis of infrared spectra of arabidopsis thaliana plant cryptochrome

scientific article published on 08 January 2021

MOLCAS 7: the next generation

scientific article

Magnetic exchange coupling in bis-nitroxides: a theoretical analysis of the solvent effects

scientific article published on 12 March 2012

Mapping the ultrafast vibrational dynamics of all-trans and 13-cis retinal isomerization in Anabaena Sensory Rhodopsin

scientific article published on 01 December 2018

Mechanism of the Initial Conformational Transition of a Photomodulable Peptide

scientific article published on 01 September 2005

Modeling the fluorescence of protein-embedded tryptophans with ab initio multiconfigurational quantum chemistry: the limiting cases of parvalbumin and monellin

scientific article published in December 2009

Modeling, preparation, and characterization of a dipole moment switch driven by Z/E photoisomerization

scientific article published on July 2010

Modern quantum chemistry with [Open]Molcas

scientific article published on 01 June 2020

Molcas8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table

scientific article (publication date: 12 November 2015)

Photophysics of acetophenone interacting with DNA: why the road to photosensitization is open

scientific article

Population of triplet states in acetophenone: A quantum dynamics perspective

article

Prediction of nitroxide hyperfine coupling constants in solution from combined nanosecond scale simulations and quantum computations

scientific article published in June 2008

Probing the Photodynamics of Rhodopsins with Reduced Retinal Chromophores

scientific article published on 7 December 2015

Probing the rhodopsin cavity with reduced retinal models at the CASPT2//CASSCF/AMBER level of theory

scientific article

Properties of the emitting state of the green fluorescent protein resolved at the CASPT2//CASSCF/CHARMM level.

scientific article published in August 2005

QM/MM study on the light emitters of aequorin chemiluminescence, bioluminescence, and fluorescence: a general understanding of the bioluminescence of several marine organisms

scientific article published on 13 May 2013

Quantitative evaluation of the aqueous dihydronitroxide nitrogen hyperfine coupling constant from QM/MM//MD computations

Quantum Chemical Modeling and Preparation of a Biomimetic Photochemical Switch

scholarly article by Flavio Lumento et al published 8 January 2007 in Angewandte Chemie International Edition

Quantum chemical modeling of rhodopsin mutants displaying switchable colors

scientific article

Relationship between the excited state relaxation paths of rhodopsin and isorhodopsin

scientific article

Sampling the protonation states: the pH-dependent UV absorption spectrum of a polypeptide dyad

scientific article published on 01 September 2018

Shape of Multireference, Equation-of-Motion Coupled-Cluster, and Density Functional Theory Potential Energy Surfaces at a Conical Intersection

scientific article published on 11 June 2014

Simulation and Analysis of the Spectroscopic Properties of Oxyluciferin and Its Analogues in Water

scientific article published on 16 March 2018

Specific force field parameters determination for the hybrid ab initio QM/MM LSCF method

scientific article published in April 2002

Spin decontamination of broken-symmetry density functional theory calculations: deeper insight and new formulations

scientific article published on 01 June 2015

Structural and atoms-in-molecules analysis of hydrogen-bond network around nitroxides in liquid water

scientific article published on 01 September 2010

Structure and Spectromagnetic Properties of the Superoxide Radical Adduct of the DMPO in Water: Elucidation by Theoretical Investigations

Structure and spectromagnetic properties of the superoxide radical adduct of DMPO in water: elucidation by theoretical investigations

scientific article published in September 2010

Structure of the intersection space associated with ZIE photoisomerization of retinal in rhodopsin proteins

scientific article published in January 2004

Structure, initial excited-state relaxation, and energy storage of rhodopsin resolved at the multiconfigurational perturbation theory level

scientific article

Systematic Theoretical Investigation on the Light Emitter of Firefly

scientific article published on 16 February 2011

The Molecular Mechanism of Thermal Noise in Rod Photoreceptors ⬇️

scientific article published on September 7, 2012

The OpenMolcas <i>Web</i>: A Community-Driven Approach to Advancing Computational Chemistry

scientific article published in 2023

The Ultrafast Photoisomerizations of Rhodopsin and Bathorhodopsin Are Modulated by Bond Length Alternation and HOOP Driven Electronic Effects ⬇️

scientific article published on February 22, 2011

The amide bond: pitfalls and drawbacks of the link atom scheme

The chemistry of bioluminescence: an analysis of chemical functionalities.

scientific article published on 13 October 2011

The color of rhodopsins at the ab initio multiconfigurational perturbation theory resolution

scholarly article

Theoretical Study of the Photochemical Initiation in Nitroxide-Mediated Photopolymerization

scientific article published on 12 June 2014

Theoretical study of the photochemical generation of triplet acetophenone.

scientific article

Toward a computational photobiology

Towards an accurate treatment of σ∗←σ transitions: Moving onto

Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry

scholarly article

Triplet state photochemistry and the three-state crossing of acetophenone within time-dependent density-functional theory

scientific article published on 01 April 2014

UV-visible absorption spectrum of FAD and its reduced forms embedded in a cryptochrome protein

scientific article published on 27 May 2020

Understanding Bacterial Bioluminescence: A Theoretical Study of the Entire Process, from Reduced Flavin to Light Emission

scientific article published on 13 May 2014

Unique QM/MM potential energy surface exploration using microiterations

What Are the Physical Contents of Hubbard and Heisenberg Hamiltonian Interactions Extracted from Broken Symmetry DFT Calculations in Magnetic Compounds?

scientific article published on 17 October 2017

pH-Dependent absorption spectrum of a protein: a minimal electrostatic model of Anabaena sensory rhodopsin

scientific article

pH-Dependent absorption spectrum of oxyluciferin analogues in the active site of firefly luciferase

scientific article published on 28 September 2020

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