Ab‐initio molecular dynamics and hybrid explicit‐implicit solvation model for aqueous and nonaqueous solvents: GFP chromophore in water and methanol solution as case study

The ONIOM/PMM Model for Effective Yet Accurate Simulation of Optical and Chiroptical Spectra in Solution: Camphorquinone in Methanol as a Case Study

(2020) Sara Del Galdo et al.   Journal of Chemical Theory and Computation

Effect of Ions on the Optical Absorption Spectra of Aqueously Solvated Chromophores

(2019) Sapana V. Shedge et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Toward a general mixed quantum/classical method for the calculation of the vibronic ECD of a flexible dye molecule with different stable conformers: Revisiting the case of 2,2,2-trifluoro-anthrylethanol

(2018) Javier Cerezo et al.   CHIRALITY

Combining the ensemble and Franck-Condon approaches for calculating spectral shapes of molecules in solution

(2018) T. J. Zuehlsdorff et al.   JOURNAL OF CHEMICAL PHYSICS

Exploring Nuclear Photorelaxation of Pyranine in Aqueous Solution: an Integrated Ab-Initio Molecular Dynamics and Time Resolved Vibrational Analysis Approach

(2018) Maria Gabriella Chiariello et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Pyridinium Analogues of Green Fluorescent Protein Chromophore: Fluorogenic Dyes with Large Solvent-Dependent Stokes Shift

(2018) Yulia G. Ermakova et al.   Journal of Physical Chemistry Letters

Comparison of the results of a mean-field mixed quantum/classical method with full quantum predictions for nonadiabatic dynamics: application to the $$\pi \pi ^*/n\pi ^*$$ππ∗/nπ∗ decay of thymine

(2018) Yanli Liu et al.   THEORETICAL CHEMISTRY ACCOUNTS

The mechanism of a green fluorescent protein proton shuttle unveiled in the time-resolved frequency domain by excited state ab initio dynamics

(2018) Greta Donati et al.   Chemical Science

Turn-on fluorescence detection of protein by molecularly imprinted hydrogels based on supramolecular assembly of peptide multi-functional blocks

(2018) Edmondo Battista et al.   Journal of Materials Chemistry B

Unveiling the structure of a novel artificial heme-enzyme with peroxidase-like activity: A theoretical investigation

(2018) Fulvio Perrella et al.   BIOPOLYMERS

Convergence of Computed Aqueous Absorption Spectra with Explicit Quantum Mechanical Solvent

(2017) Joel M. Milanese et al.   Journal of Chemical Theory and Computation

Molecular Vibration Induced Plasmon Decay

(2017) Greta Donati et al.   Journal of Physical Chemistry C

The shape of the electronic circular dichroism spectrum of (2,6-dimethylphenyl)(phenyl)methanol: interplay between conformational equilibria and vibronic effects

(2017) Daniele Padula et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Perspective: Methods for large-scale density functional calculations on metallic systems

(2016) Jolyon Aarons et al.   JOURNAL OF CHEMICAL PHYSICS

Direct ab Initio (Meta-)Surface-Hopping Dynamics

(2016) David B. Lingerfelt et al.   Journal of Chemical Theory and Computation

On the Driving Force of the Excited-State Proton Shuttle in the Green Fluorescent Protein: A Time-Dependent Density Functional Theory (TD-DFT) Study of the Intrinsic Reaction Path

(2016) Alessio Petrone et al.   Journal of Chemical Theory and Computation

“Watching” Polaron Pair Formation from First-Principles Electron–Nuclear Dynamics

(2016) Greta Donati et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Classical or Quantum? A Computational Study of Small Ion Diffusion in II–VI Semiconductor Quantum Dots

(2016) Erica Q. Chong et al.   Journal of Physical Chemistry C

Ab Initio Transient Vibrational Spectral Analysis

(2016) Alessio Petrone et al.   Journal of Physical Chemistry Letters

Does Thermal Breathing Affect Collision Cross Sections of Gas-Phase Peptide Ions? An Ab Initio Molecular Dynamics Study

(2016) Robert Pepin et al.   Journal of Physical Chemistry Letters

Quantum-Classical Calculation of Vibronic Spectra along a Reaction Path: The Case of the ECD of Easily Interconvertible Conformers with Opposite Chiral Responses

(2016) Javier Cerezo et al.   Journal of Physical Chemistry Letters

Single-Crystal and Electronic Structure of a 1.3 nm Indium Phosphide Nanocluster

(2016) Dylan C. Gary et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Electronic spectroscopy of a solvatochromic dye in water: comparison of static cluster/implicit and dynamical/explicit solvent models on structures and energies

(2016) Javier Cerezo et al.   THEORETICAL CHEMISTRY ACCOUNTS

On the different strength of photoacids

(2016) Paola Cimino et al.   THEORETICAL CHEMISTRY ACCOUNTS

Mixed Cation FAxPEA1-xPbI3with Enhanced Phase and Ambient Stability toward High-Performance Perovskite Solar Cells

(2016) Nan Li et al.   Advanced Energy Materials

Organic solvent simulations under non-periodic boundary conditions: A library of effective potentials for the GLOB model

(2015) Giordano Mancini et al.   CHEMICAL PHYSICS LETTERS

Modeling Solvent Broadening on the Vibronic Spectra of a Series of Coumarin Dyes. From Implicit to Explicit Solvent Models

(2015) Javier Cerezo et al.   Journal of Chemical Theory and Computation

Calibration of Energy-Specific TDDFT for Modeling K-edge XAS Spectra of Light Elements

(2015) Patrick J. Lestrange et al.   Journal of Chemical Theory and Computation

Absorption and Emission Spectral Shapes of a Prototype Dye in Water by Combining Classical/Dynamical and Quantum/Static Approaches

(2015) Alessio Petrone et al.   JOURNAL OF PHYSICAL CHEMISTRY A

The Lineshape of the Electronic Spectrum of the Green Fluorescent Protein Chromophore, Part I: Gas Phase

(2014) Mehdi D. Davari et al.   CHEMPHYSCHEM

The Lineshape of the Electronic Spectrum of the Green Fluorescent Protein Chromophore, Part II: Solution Phase

(2014) Francisco J. Avila Ferrer et al.   CHEMPHYSCHEM

Electronic Absorption Spectra and Solvatochromic Shifts by the Vertical Excitation Model: Solvated Clusters and Molecular Dynamics Sampling

(2014) Aleksandr V. Marenich et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Large-Scale Density Functional Theory Transition State Searching in Enzymes

(2014) Greg Lever et al.   Journal of Physical Chemistry Letters

Understanding THz and IR Signals beneath Time-Resolved Fluorescence from Excited-State Ab Initio Dynamics

(2014) Alessio Petrone et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

From charge-transfer to a charge-separated state: a perspective from the real-time TDDFT excitonic dynamics

(2014) Alessio Petrone et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Ultrafast excited state dynamics of the green fluorescent protein chromophore and its kindling fluorescent protein analogue

(2013) Kiri Addison et al.   FARADAY DISCUSSIONS

Benchmarking Time-Dependent Density Functional Theory for Excited State Geometries of Organic Molecules in Gas-Phase and in Solution

(2013) Ciro A. Guido et al.   Journal of Chemical Theory and Computation

First-Principles Characterization of the Energy Landscape and Optical Spectra of Green Fluorescent Protein along the A→I→B Proton Transfer Route

(2013) Bella L. Grigorenko et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Electrostatic spectral tuning mechanism of the green fluorescent protein

(2013) Ville R. I. Kaila et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

On the optical absorption of the anionic GFP chromophore in vacuum, solution, and protein

(2013) Alessio Petrone et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

A polarizable embedding DFT study of one-photon absorption in fluorescent proteins

(2013) Maarten T. P. Beerepoot et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Spectrum simulation and decomposition with nuclear ensemble: formal derivation and application to benzene, furan and 2-phenylfuran

(2012) Rachel Crespo-Otero et al.   THEORETICAL CHEMISTRY ACCOUNTS

Molecular dynamics simulations of rigid and flexible water models: Temperature dependence of viscosity

(2011) J.S. Medina et al.   CHEMICAL PHYSICS

Effect of microhydration on the electronic structure of the chromophores of the photoactive yellow and green fluorescent proteins

(2011) Dmitry Zuev et al.   JOURNAL OF CHEMICAL PHYSICS

Vibrational analysis of x-ray absorption fine structure thermal factors by ab initio molecular dynamics: The Zn(II) ion in aqueous solution as a case study

(2011) Nadia Rega et al.   JOURNAL OF CHEMICAL PHYSICS

Bathochromic Shift in Green Fluorescent Protein: A Puzzle for QM/MM Approaches

(2011) Claudia Filippi et al.   Journal of Chemical Theory and Computation

Excited states of the green fluorescent protein chromophore: Performance of ab initio and semi-empirical methods

(2011) Marius Wanko et al.   PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS

Orbital pathways for Mn2+-carriersp−dexchange in diluted magnetic semiconductor quantum dots

(2011) Rémi Beaulac et al.   PHYSICAL REVIEW B

Absorption Spectrum of the Green Fluorescent Protein Chromophore: A Difficult Case for ab Initio Methods?

(2009) Claudia Filippi et al.   Journal of Chemical Theory and Computation

Quantum Chemical Benchmark Studies of the Electronic Properties of the Green Fluorescent Protein Chromophore: 2.Cis−TransIsomerization in Water

(2009) Igor Polyakov et al.   Journal of Chemical Theory and Computation

Quantum Chemical Benchmark Studies of the Electronic Properties of the Green Fluorescent Protein Chromophore. 1. Electronically Excited and Ionized States of the Anionic Chromophore in the Gas Phase

(2009) Evgeny Epifanovsky et al.   Journal of Chemical Theory and Computation

The Properties of Water: Insights from Quantum Simulations†

(2009) Francesco Paesani et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Validation of the DFT/N07D computational model on the magnetic, vibrational and electronic properties of vinyl radical

(2009) Vincenzo Barone et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Quantum Mechanical Computations and Spectroscopy: From Small Rigid Molecules in the Gas Phase to Large Flexible Molecules in Solution

(2008) Vincenzo Barone et al.   ACCOUNTS OF CHEMICAL RESEARCH

A hybrid explicit/implicit solvation method for first-principle molecular dynamics simulations

(2008) Giuseppe Brancato et al.   JOURNAL OF CHEMICAL PHYSICS

Theoretical modeling of open-shell molecules in solution: a QM/MM molecular dynamics approach

(2008) Giuseppe Brancato et al.   THEORETICAL CHEMISTRY ACCOUNTS