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Journal ArticleDOI

Structural properties and isomerisation of simple S-nitrosothiols: ab initio studies with a simplified treatment of correlation effects

03 Mar 2020-Molecular Physics (Taylor & Francis)-Vol. 118, Iss: 5
TL;DR: In this paper, the structure-stability relationship in S-Nitrosothiols (RSNOs) that govern their activity in vivo is not well understood, and useful structural information is provided.
Abstract: Despite the enormous biological significance, the structure-stability relationship in S-Nitrosothiols (RSNOs) that govern their activity in vivo is not well understood We provide useful structural
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TL;DR: It is suggested that RSNO reactions in vivo should be tightly controlled by the protein environment via modulation of the RSNO electronic structure through a 'ligand effect map' (LEM) approach.
Abstract: There is currently great interest in S-nitrosothiols (RSNOs) because formation of protein-based RSNOsprotein S-nitrosationhas been recently recognized as a major pathway of the biological function of nitric oxide, NO. Despite the growing number of S-nitrosated proteins identified in vivo, enzymatic processes that control reactions of biological RSNOs are still not well understood. In this article, we use a range of models to computationally demonstrate that specific interactions of RSNOs with charged and polar residues in proteins can result in dramatic modification of RSNO structure, stability, and reactivity. This unprecedented sensitivity of the −SNO group toward interactions with charged species is related to their unusual electronic structure that can be elegantly expressed in terms of antagonistic resonance structures. We propose a ‘ligand effect map’ (LEM) approach as an efficient way to estimate the environment effects on the −SNO groups in proteins without performing electronic structure calculations. Furthermore, the calculated ¹⁵N NMR signatures of these specific interactions suggest that ¹⁵N NMR spectroscopy can be an effective technique to identify and study these interactions experimentally. Overall, the results of this study suggest that RSNO reactions in vivo should be tightly controlled by the protein environment via modulation of the RSNO electronic structure.

6 citations

Journal Article
TL;DR: In this article, the pairing matrix fluctuation was used to estimate the excitation energies of the N-electron system through particle-particle random phase approximation (pp-RPA) and particleparticle Tamm-Dancoff approximation(pp-TDA).
Abstract: Double, Rydberg, and charge transfer (CT) excitations have been great challenges for time-dependent density functional theory (TDDFT). Starting from an (N ± 2)-electron single-determinant reference, we investigate excitations for the N-electron system through the pairing matrix fluctuation, which contains information on two-electron addition/removal processes. We adopt the particle-particle random phase approximation (pp-RPA) and the particle-particle Tamm-Dancoff approximation (pp-TDA) to approximate the pairing matrix fluctuation and then determine excitation energies by the differences of two-electron addition/removal energies. This approach captures all types of interesting excitations: single and double excitations are described accurately, Rydberg excitations are in good agreement with experimental data and CT excitations display correct 1/R dependence. Furthermore, the pp-RPA and the pp-TDA have a computational cost similar to TDDFT and consequently are promising for practical calculations.

2 citations

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Journal ArticleDOI
TL;DR: A new multi-reference perturbation approach developed at second order, based on a Jeziorski-Mokhorst expansion using individual Slater determinants as perturbers, strongly reducing the computational cost of these two approaches with respect to other determinant-based perturbations theories.
Abstract: The present paper introduces a new multi-reference perturbation approach developed at second order, based on a Jeziorsky-Mokhorst expansion using individual Slater determinants as perturbers. Thanks to this choice of perturbers, an effective Hamiltonian may be built, allowing for the dressing of the Hamiltonian matrix within the reference space, assumed here to be a CAS-CI. Such a formulation accounts then for the coupling between the static and dynamic correlation effects. With our new definition of zeroth-order energies, these two approaches are strictly size-extensive provided that local orbitals are used, as numerically illustrated here and formally demonstrated in the appendix. Also, the present formalism allows for the factorization of all double excitation operators, just as in internally contracted approaches, strongly reducing the computational cost of these two approaches with respect to other determinant-based perturbation theories. The accuracy of these methods has been investigated on ground-state potential curves up to full dissociation limits for a set of six molecules involving single, double and triple bond breaking. The spectroscopic constants obtained with the present methods are found to be in very good agreement with the full configuration interaction (FCI) results. As the present formalism does not use any parameter or numerically unstable operation, the curves obtained with the two methods are smooth all along the dissociation path.

22 citations

Journal ArticleDOI
TL;DR: Spectre IR du thionitrite de methyle en matrice d'Ar a 12 K indiquant une conformation cis et trans; Par irradiation a 485-590 nm isomerisation cis⇄trans selectivement induite as mentioned in this paper.
Abstract: Spectre IR du thionitrite de methyle en matrice d'Ar a 12 K indiquant une conformation cis et trans; Par irradiation a 485-590 nm isomerisation cis⇄trans selectivement induite. DG 298 0 (cis→trans)=5,56±0,76 kJ mole −1

20 citations

Journal ArticleDOI
TL;DR: The present work clearly illustrates that the IVO-CASCI analytical gradient method provides a good description of the complicated electronic quasi-degeneracies during the geometry optimization process for the radicaloid anions.
Abstract: The improved virtual orbital-complete active space configuration interaction (IVO-CASCI) method enables an economical and reasonably accurate treatment of static correlation in systems with significant multireference character, even when using a moderate basis set. This IVO-CASCI method supplants the computationally more demanding complete active space self-consistent field (CASSCF) method by producing comparable accuracy with diminished computational effort because the IVO-CASCI approach does not require additional iterations beyond an initial SCF calculation, nor does it encounter convergence difficulties or multiple solutions that may be found in CASSCF calculations. Our IVO-CASCI analytical gradient approach is applied to compute the equilibrium geometry for the ground and lowest excited state(s) of the theoretically very challenging 2,6-pyridyne, 1,2,3-tridehydrobenzene and 1,3,5-tridehydrobenzene anionic systems for which experiments are lacking, accurate quantum calculations are almost completely absent, and commonly used calculations based on single reference configurations fail to provide reasonable results. Hence, the computational complexity provides an excellent test for the efficacy of multireference methods. The present work clearly illustrates that the IVO-CASCI analytical gradient method provides a good description of the complicated electronic quasi-degeneracies during the geometry optimization process for the radicaloid anions. The IVO-CASCI treatment produces almost identical geometries as the CASSCF calculations (performed for this study) at a fraction of the computational labor. Adiabatic energy gaps to low lying excited states likewise emerge from the IVO-CASCI and CASSCF methods as very similar. We also provide harmonic vibrational frequencies to demonstrate the stability of the computed geometries.

19 citations

Journal ArticleDOI
TL;DR: The overall stability and structural preference of two pharmacologically relevant S-nitrosothiol molecules were studied in detail and it was observed that the structure and the stability of these molecules can be directly related to the formation of stabilizing hydrogen-bond and chalcogen-chalcogen intramolecular interactions.
Abstract: Nowadays, S-nitrosothiols (RSNOs) represent a promising class of nitric oxide (NO) donors that could be successfully used as drugs to compensate the decrease of NO production that usually arises in conjunction with cardiovascular diseases. Nevertheless, notwithstanding their pharmacological interest, the structure–stability relationship in RSNOs is still unclear, and this issue, together with the mechanism of NO donation in the physiological medium, deserves further investigation. As a first step forward in this direction, in this paper, the overall stability and structural preference of two pharmacologically relevant S-nitrosothiol molecules were studied in detail by means of computational strategies. In particular, performing calculations in implicit solvent (water) on the S-nitroso-N-acetylpenicillamine and the S-nitroso-N-acetylcysteine and analyzing the noncovalent interactions networks of their most stable conformers, we observed that the structure and the stability of these molecules can be directl...

18 citations

Journal ArticleDOI
TL;DR: In electronic structure theory, restricted single-reference coupled cluster (CC) captures weak correlation but fails catastrophically under strong correlation as discussed by the authors, and the spin-projected unrestricted Hartree-F...
Abstract: In electronic structure theory, restricted single-reference coupled cluster (CC) captures weak correlation but fails catastrophically under strong correlation. Spin-projected unrestricted Hartree-F...

15 citations