Structural properties and isomerisation of simple S-nitrosothiols: ab initio studies with a simplified treatment of correlation effects
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 RSNOsprotein S-nitrosationhas 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.
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TL;DR: The first experimental derivation and theoretical calculations of the S -NO bond energies for two series of thiol-containing model compounds are reported, where the NO+ and NO• affinities of the model thiols are determined.
Abstract: Recent years have witnessed substantial research activities in the field of chemistry and biochemistry of nitric oxide (NO) because of the remarkable discoveries of its key roles in a wide range of human physiological processes. 1 As a unique class of such NO-carrying vehicles, S-nitrosothiols (RSNOs) are generally believed to take a most active part in many biological functions of nitric oxide especially in the processes of NO-storage, transport, and delivery. 2-8 Despite its obvious importance, the S -NO bondenergy scale, which registers the thermodynamic driving forces for NO release and NO capture, has yet not been reported. As part of our efforts to understand the NO-related physiological processes at a molecular level, we have conducted a solution NO affinity study9 for a series ofR π-acceptor-bearingN-nitroso compounds 12 in terms of the heterolytic and homolytic Y -NO bond dissociation energies. Similarly, typical O -NO13 and N-NO14 bond energies were later determined. Although the instability of thioanion and thio-radical (and to a less extent, the parentS-nitroso) species under the required experimental conditions prohibits application of the established method 12-14 to derive the S-NO bond energies (i.e., NO affinities) of biologically more relevant RSNOs, in the present work we report the first experimental derivation and theoretical calculations of the S -NO bond energies for two series of thiol-containing model compounds (1 and2), where the NO+ and NO• affinities of the model thiol
97 citations
TL;DR: In this article, the authors describe a computationally efficient ab initio many-body method that can be used as a packageable approximation for computing excited state properties for small to large molecular systems, including those of multiconfigurational character.
Abstract: We describe a computationally efficient ab initio many-body method that can be used as a “packageable approximation” for computing excited state properties for small to large molecular systems, including those of multiconfigurational character. The method is based on first order multi-reference many-body perturbation theory (MR-MBPT), where the unoccupied valence orbitals are obtained by using an extension of Huzinaga’s improved virtual orbital (IVO) generation technique. Because the method employs a complete active space (CAS) which contains singly, doubly, and higher excited state configurations with respect to the zeroth order ground state configuration, the approach (IVO-CASCI) is capable of providing a more accurate description of the excited states than the widely used packageable configuration interaction with singles (CIS) at a fraction of computational labor. Moreover, unlike the CASSCF approach this IVO-CASCI method does not require iterations and therefore is more computationally efficient and ...
96 citations
TL;DR: In this paper, both aryl and alkyl thionitrites (RSNO) were prepared quantitatively by the reaction of thiols with dinitrogen tetraoxide (N2O4) under mild conditions.
Abstract: Both aryl and alkyl thionitrites (RSNO) were prepared quantitatively by the reaction of thiols with dinitrogen tetraoxide (N2O4) under mild conditions. Unstable thionitrites were identified by i.r. or u.v. spectra at low temperatures (e.g. 0 °C) or by their further reactions with nucleophiles leading to known derivatives. The spectroscopic data of these thionitrites are summarized and the highly reactive thionitrites were found to react readily with other nucleophiles such as thiols, sulphinic acids, alcohols, and secondary amines at ca.–5 °C. Treatment of thionitrites with other thiols or sulphinic acids was found to yield the corresponding unsymmetrical disulphides or thiolsulphonates in good yields. Similar treatment of thionitrites with secondary amines or alcohols gave the corresponding N-nitrosoamines, or disulphides and nitrites.
80 citations
TL;DR: Previous quantum-chemical data on RSNOs are reexamined based on the new insight into the SNO electronic structure obtained from the present high-level calculations on HSNO, indicating that the electronic structure of the SNo group possesses multireference character.
Abstract: High-level ab initio calculations employing the CCSD and CCSD(T) coupled cluster methods with a series of systematically convergent correlation-consistent basis sets have been performed to obtain accurate molecular geometry and energetic properties of the simplest S-nitrosothiol (RSNO), HSNO. The properties of the S–N bond, which are central to the physiological role of RSNOs in the storage and transport of nitric oxide, are highlighted. Following corrections for quadruple excitations, core-valence correlation and relativistic effects, the CCSD(T) method extrapolated to the complete basis set (CBS) limit yielded values of 1.85 A and 29.2 kcal mol−1 for the S–N bond length and the dissociation energy for homolysis of the S–N bond, respectively, in the energetically most stable trans-conformer of HSNO. The properties of the S–N bond strongly depend on the basis-set size and the inclusion of triple, and, to a lesser extent, quadruple excitations in the coupled cluster expansion. CCSD calculations systematically underestimate the S–N equilibrium distance and S–N bond dissociation energy by 0.05–0.07 A and 6–7 kcal mol−1, respectively. The significant differences between the CCSD(T) and CCSD descriptions of HSNO, the high values of the coupled clusterT1 (0.027) and D1 (0.076) diagnostics, as well as the instability of the reference restricted Hartree–Fock (RHF) wavefunction indicate that the electronic structure of the SNO group possesses multireference character. Previous quantum-chemical data on RSNOs are reexamined based on the new insight into the SNO electronic structure obtained from the present high-level calculations on HSNO.
70 citations
TL;DR: In this paper, the ability of conventional electron correlation (MP2 and QCISD) and density functional theory (B3LYP and B3P86) methods to provide accurate and reliable optimized structures, and homolytic S−N bond dissociation energies (BDEs), for a range of S-nitrosothiols (RSNOs) has been investigated.
Abstract: The ability of conventional electron correlation (MP2 and QCISD) and density functional theory (B3LYP and B3P86) methods to provide accurate and reliable optimized structures, and homolytic S−N bond dissociation energies (BDEs), for a range of S-nitrosothiols (RSNOs) has been investigated. It is found that, in general, for any given method the 6-311+G(2df,p) or larger basis set must be used to obtain reliable structures. With a suitably large basis set, the different methods generally give optimized structures in close agreement with each other. However, the B3LYP method consistently overestimates the RS−NO bond length. The trends observed are found to be due in part to the fact that the RS−NO bond does not possess considerable double-bond character as previously suggested, but rather is a long single S−N bond, with the −NO moiety possessing considerable multiple-bond character. The B3P86/6-311+G(2df,p) method consistently gives BDEs in best agreement with values obtained with higher accuracy methods, e.g...
62 citations