A tunable QM/MM approach to chemical reactivity, structure and physico-chemical properties prediction

Altoè, Piero; Stenta, Marco; Bottoni, Andreà; Garavelli, Marco

doi:10.1007/s00214-007-0275-9

Cited by 80 publications

(120 citation statements)

References 87 publications

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“…A two-step QM/MM refinement was performed with our software package Cobramm 19 : an initial Hartree-Fock energy minimization run for 30 steps was followed by a complete active space self-consistent field (CASSCF) 20 minimization. An active space of eight electrons and eight orbitals (i.e.…”

Section: Methodsmentioning

confidence: 99%

Tracking Conformational Dynamics of Polypeptides by Nonlinear Electronic Spectroscopy of Aromatic Residues: A First‐Principles Simulation Study

et al. 2014

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The ability of non-linear electronic spectroscopy to track folding/unfolding processes of proteins in solution by monitoring aromatic interactions is investigated by first-principle simulations of two-dimensional (2D) electronic spectra of a model peptide. A dominant reaction pathway approach is employed to determine the unfolding pathway of a tetrapeptide, connecting the initial folded configuration with stacked aromatic side chains and the final unfolded state with distant non-interacting aromatic residues. π-stacking and excitonic coupling effects are included via ab-initio simulations based on multiconfigurational methods within a hybrid QM/MM scheme. We show that linear absorption spectroscopy in the ultraviolet (UV) is unable to resolve the unstacking dynamics characterized by the three-step process: T-shaped→twisted offset stacking→unstacking. Conversely, pump-probe spectroscopy can be used to resolve aromatic interactions by probing in the visible (Vis) the excited state absorptions (ESA) that involve charge transfer (CT) states. 2DUV spectroscopy offers the highest sensitivity to the unfolding process, providing the disentanglement of ESA signals belonging to different aromatic chromophores and high correlation between the conformational dynamics and the quartic splitting.

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Section: Methodsmentioning

confidence: 99%

Tracking Conformational Dynamics of Polypeptides by Nonlinear Electronic Spectroscopy of Aromatic Residues: A First‐Principles Simulation Study

et al. 2014

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“…Other properties highly dependent on the basis set, like the dipole moment, do change more prominently in the Pople-type basis set even though the mapped PEH appears to be qualitatively similar. This might have some implications in external perturbations to the wave function such as those given for QM/MM schemes [75][76][77], where solvation is described as dipole-driven electrostatic interactions between the solvent and the solute, and thus a more accurate characterization of the dipole moment may be important.…”

Section: Caspt2//casscfmentioning

confidence: 99%

Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2

et al. 2016

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Abstract:The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies. A direct comparison between these strategies is drawn, yielding qualitatively similar results within a static framework. A number of analyses are performed to assess the accuracy of these different computational strategies under study based on a variety of numerical thresholds and optimization methods. Several basis sets and active spaces have also been calibrated to understand to what extent they can influence the resulting geometries and subsequent interpretation of the photochemical decay channels. The study shows small discrepancies between CASSCF and CASPT2 PEHs, displaying a shallow planar or twisted 1 (ππ*) minimum, respectively, and thus featuring a qualitatively similar scenario for supporting the ultrafast bi-exponential deactivation registered in thymine upon UV-light exposure. A deeper knowledge of the PEHs at different levels of theory provides useful insight into its correct characterization and subsequent interpretation of the experimental observations. The discrepancies displayed by the different methods studied here are then discussed and framed within their potential consequences in on-the-fly non-adiabatic molecular dynamics simulations, where qualitatively diverse outcomes are expected.

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“…The residue was diluted with CH 2 Cl 2 (5 mL), and the biphasic mixture was washed with H 2 O (2 ϫ 5 mL). The organic layer was dried with Na 2 Computational Details: All calculations were carried out with the COBRAMM [18] suite of programs, which was used as an interface between the TURBOMOLE [19] and the GAUSSIAN 03 packages. [20] This approach allowed us to combine the accurate optimisation algorithms implemented in GAUSSIAN 03 and the TUR-BOMOLE approximated DFT [21] potential.…”

mentioning

confidence: 99%

Synthesis of Ethyl 5‐Hydroxyisoxazolidine‐4‐carboxylates via Michael Addition/Intramolecular Hemiketalisation

Benfatti¹,

Bottoni²,

Cardillo³

et al. 2008

Eur J Org Chem

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A tunable QM/MM approach to chemical reactivity, structure and physico-chemical properties prediction

Cited by 80 publications

References 87 publications

Tracking Conformational Dynamics of Polypeptides by Nonlinear Electronic Spectroscopy of Aromatic Residues: A First‐Principles Simulation Study

Tracking Conformational Dynamics of Polypeptides by Nonlinear Electronic Spectroscopy of Aromatic Residues: A First‐Principles Simulation Study

Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2

Synthesis of Ethyl 5‐Hydroxyisoxazolidine‐4‐carboxylates via Michael Addition/Intramolecular Hemiketalisation

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