Toward Reliable Modeling of S-nitrosothiol Chemistry: Structure and Properties of Methyl Thionitrite (CH3SNO), an S-nitrosocysteine Model

Methyl thionitrite CH3SNO is an important model of S-nitrosated cysteine aminoacid residue (CysNO), a ubiquitous biological S-nitrosothiol (RSNO) involved in numerous physiological processes. As such, CH3SNO can provide insights into the intrinsic properties of the —SNO group in CysNO, in particular, its weak and labile S—N bond. Here, we report an ab initio computational investigation of the structure and properties of CH3SNO using a composite Feller-Peterson-Dixon scheme based on the explicitly correlated coupled cluster with single, double, and perturbative triple excitations calculations extrapolated to the complete basis set limit, CCSD(T)-F12/CBS, with a number of additive corrections for the effects of quadruple excitations, core-valence correlation, scalar-relativistic and spin-orbit effects, as well as harmonic zero-point vibrational energy with an anharmonicity correction. These calculations suggest that the S—N bond in CH3SNO is significantly elongated (1.814 Å) and has low stretching frequency and dissociation energy values, νS—N = 387 cm−1 and D0 = 32.4 kcal/mol. At the same time, the S—N bond has a sizable rotation barrier, △ role= presentation style= display: inline; font-style: normal; font-weight: normal; line-height: normal; font-size: 20px; text-indent: 0px; text-align: left; text-transform: none; letter-spacing: normal; word-spacing: normal; word-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; padding: 0px 2px 0px 0px; margin: 0px; position: relative; \u3e△△E0≠ role= presentation style= display: inline; font-style: normal; font-weight: normal; line-height: normal; font-size: 12px; text-indent: 0px; text-align: left; text-transform: none; letter-spacing: normal; word-spacing: normal; word-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; padding: 0px 2px 0px 0px; margin: 0px; position: relative; \u3e≠≠ = 12.7 kcal/mol, so CH3SNO exists as a cis- or trans-conformer, the latter slightly higher in energy, △ role= presentation style= display: inline; font-style: normal; font-weight: normal; line-height: normal; font-size: 20px; text-indent: 0px; text-align: left; text-transform: none; letter-spacing: normal; word-spacing: normal; word-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; padding: 0px 2px 0px 0px; margin: 0px; position: relative; \u3e△△E0 = 1.2 kcal/mol. The S—N bond properties are consistent with the antagonistic nature of CH3SNO, whose resonance representation requires two chemically opposite (antagonistic) resonance structures, CH3—S+=N—O−and CH3—S−/NO+, which can be probed using external electric fields and quantified using the natural resonance theory approach (NRT). The calculated S—N bond properties slowly converge with the level of correlation treatment, with the recently developed distinguished cluster with single and double excitations approximation (DCSD-F12) performing significantly better than the coupled cluster with single and double excitations (CCSD-F12), although still inferior to the CCSD(T)-F12 method that includes perturbative triple excitations. Double-hybrid density functional theory (DFT) calculations with mPW2PLYPD/def2-TZVPPD reproduce well the geometry, vibrational frequencies, and the S—N bond rotational barrier in CH3SNO, while hybrid DFT calculations with PBE0/def2-TZVPPD give a better S—N bond dissociation energy

Electronic transport through nanowires: a real-space finite-difference approach

Nanoelectronics is a fast developing ¯eld. Therefore understanding of the electronic transport at the nanoscale is currently of great interest. This thesis "Electronic transport through nanowires: a real-space ¯nite-difference approach" aims at a general theoretical treatment of coherent electronic transport in mesoscopic and mi-\ud croscopic systems by means of Green's function and mode-matching techniques. A general method has been developed for conductance calculations on the basis of the mode-matching technique within the real-space high-order ¯nite-difference scheme for representing a single electron equation. Testing of this real-space ¯nite-di®erence\ud approach for model systems has been done. This approach in combination with the density-functional formalism has been applied to the conductance calculations in nanowires. The stability of even-odd conductance oscillations in monatomic sodium wires with respect to structural variations has been investigated

Fin de Siècle in the Trajectories of Russian Modernity: Novelty and Repetition

Received 13 October 2017. Accepted 20 November 2017. Published online 18 December 2017.The article is devoted to the discussion on fin de siècle in the context of the trajectory the modernity took in the twentieth century Russia. The author follows C. Castoriadis’ definition of modernity through double imaginary of autonomy and rational mastery as well as P. Wagner’s characterisation of modernity as experience and interpretation. He demonstrates how in Russian constellation of modernity autonomy came to be understood as a secondary to rational mastery and how collective autonomy started to dominate over individual one. For this purpose, he discusses details of N. Federov’s “Philosophy of the Common Task” as well as peculiarities of the development of Russian society of the beginning of the last century. Then M. Khomyakov turns to the contemporary fin de siècle and discusses what he sees as a major crisis of modernity in general and democracy, in particular. Thus, the article interprets fin de siècles as inherent to the modernity crises, the main elements of which are revising, reinterpretation, reformulation and renegotiation of the modernity’s fundamentals

On the Structure and Properties of S-Nitrosated Cysteine Models: A Computational Study

S-Nitrosation of cysteine (Cys) residues, a covalent modification of its S atom by NO group, is a major post-translational modification of proteins. Despite the importance of S-nitrosoproteins in numerous physiological processes, lability of the S-nitrosothiol (-SNO) group hinders the research progress. In this work, computational chemistry methods were applied to S-nitrosated cysteine (CysNO) models to gain a deeper insight into its structure and properties. First, we obtained the most accurate at the moment computational estimation of the molecular structure and properties of CH3SNO model molecule using Feller-Peterson-Dixon (FPD) ab initio protocol. The S–N bond length in cis- CH3SNO is calculated as 1.814 Å, and its dissociation energy (BDE) is 32.4 kcal/mol. We found that although the vibrational frequency of the S–N stretch is unusually low for a covalent bond (398 cm-1), the S–N bond has a remarkably harmonic character. After the benchmarking of the density functional theory (DFT) methods against the FPD reference, we recommend MPW2PLYP and MPW2PLYPD double hybrid functionals for calculation of the geometric properties, vibrational frequencies and isomerization barriers of S-nitrosothiols, and PBE0 (PBE0-GD3) hybrid functional for the S–N BDEs. Further, we evaluated the influence of charged amino acid residues and steric constraints on the conformational dynamics of CysNO, using an a-helix model and a DJ-1 (PARK7) protein using hybrid quantum mechanics/molecular mechanics (QM/MM) approach. We found that while the rotational barrier around the S–N bond is ca. 13 kcal/mol in free CysNO, it can vary between 10 and 24 kcal/mol in the protein environment due to the effect of neighboring charged amino acids. Finally, to address a long-standing problem of the CysNO identification in proteins, we computationally designed a novel CysNO labeling reaction, (3+2) dipolar cycloaddition between the -SNO group activated by N-coordinated Lewis acid and a strain-activated alkene. We show that the most effective labeling reagent should covalently link both crucial reaction components—the Lewis acid and the dipolarophile—into one molecule, to lower the entropic penalty and corresponding reaction barrier

Towards Reliable Modeling of S-Nitrosothiol Chemistry: Explicitly-Correlated Coupled Cluster and DFT Studies

In this work, we apply recently proposed explicitly-correlated coupled cluster methods, CCSD(T)-F12x, as well as density functional theory methods, to study the acid-base properties of HSNO molecule in gas phase. Used in this work approach theoretical efficiently alleviates excessive computational cost of the traditional ab initio methods, used in computational chemistry, with identical level of accuracy. Our high-level reference calculations show that protonation of HSNO molecule will most readily occur at the S atom (with energy release ~ 17 kcal/mol), compared to N atom (energy release ~ 5 kcal/mol) or O atom (energy release ~ 7 kcal/mol). S-N bond in HSNO elongates by 0.572 Å and weakens by 11.1 kcal/mol upon protonation at the S at-om, gaining noticeable anharmonic character. Deprotonation of HSNO is thermodynami-cally unfavorable, with energy loss ~ 170 kcal/mol, accompanied with S-N bond shorten-ing by 0.149 Å. Based on generated in this work the reference values, we tested and ranked the performance of total 45 different DFT functionals of various families and rungs of the DFT Jacob\u27s ladder , applied to HSNO in neutral or protonated and deprotonated forms. Best performing functionals are identified for the future computational studies of the bio-logically relevant reactions involving S-nitrosothiols

Simulation of near-term climate change at target sites in West and East Africa

We describe the generation of synthetic sequences of precipitation and maximum and minimum daily temperatures at two locations, in western and eastern Africa respectively. The sequences are generated at the monthly time scale and incorporate both explicitly modelled annual-to-decadal variability, based on the observational record, and long-range (i.e., climate change) trends, as inferred from an ensemble of global climate models. Annual-to-decadal variability is modelled as a first-order vector autoregressive (VAR) process, and the simulations are temporally downscaled to monthly time resolution using a nonparametric resampling scheme. The modelled sequences reproduce well the observed covariances as well as serial autocorrelation in individual variables. The simulations are intended to drive agricultural or other applications models to investigate responses to a range of plausible trends, on which are superimposed decade-scale climate fluctuations whose likelihood of occurrence can be estimated

BRICS and Global South: Towards Multilateral Educational Collaboration

Received 23 October 2018. Accepted 3 December 2018. Published online 15 December 2018.The article is devoted to the discussion of the educational policies of the BRICS countries in the context of rising Global South. The author argues that BRICS grouping is better understood not as a union of the countries based upon common identity or a set of the values, but as a group, which is held together by certain imaginaries. These imaginaries are a vision of alternative world order on the one hand and of the emerging Global South on the other hand. Education, then, pays a pivotal role in BRICS collaboration, because it helps to develop and to spread these imaginaries. The article analyses multilateral educational collaboration in BRICS in comparison with excellence programmes devoted to establishment of elite worldclass universities and oriented at indicators of the main international academic rankings. The author argues that such projects as BRICS Network University are much more relevant to the tasks of South-South collaboration than the excellence programmes such as Russian 5/100 one. In conclusion, the author attracts readers’ attention to the multiple modernities theories as possible rationale for BRICS cooperation or South-South collaboration in general.The work was supported by the Russian Science Foundation (RSF) grant number 18-18-00236

Substrate-induced bandgap in graphene on hexagonal boron nitride

We determine the electronic structure of a graphene sheet on top of a lattice-matched hexagonal boron nitride (h-BN) substrate using ab initio density functional calculations. The most stable configuration has one carbon atom on top of a boron atom, the other centered above a BN ring. The resulting inequivalence of the two carbon sites leads to the opening of a gap of 53 meV at the Dirac points of graphene and to finite masses for the Dirac fermions. Alternative orientations of the graphene sheet on the BN substrate generate similar band gaps and masses. The band gap induced by the BN surface can greatly improve room temperature pinch-off characteristics of graphene-based field effect transistors.Comment: 5 pages, 4 figures, Phys. Rev. B, in pres