Biological control of S-nitrosothiol reactivity: potential role of sigma-hole interactions.

S-Nitrosothiols (RSNOs) are ubiquitous biomolecules whose chemistry is tightly controlled in vivo, although the specific molecular mechanisms behind this biological control remain unknown. In this work, we demonstrate, using high-level ab initio and DFT calculations, the ability of RSNOs to participate in intermolecular interactions with electron pair donors/Lewis bases (LBs) via a σ-hole, a region of positive electrostatic potential on the molecular surface at the extension of the N-S bond. Importantly, σ-hole binding is able to modulate the properties of RSNOs by changing the balance between two chemically opposite (antagonistic) resonance components, R-S+[double bond, length as m-dash]N-O- (D) and R-S-/NO+ (I), which are, in addition to the main resonance structure R-S-N[double bond, length as m-dash]O, necessary to describe the unusual electronic structure of RSNOs. σ-Hole binding at the sulfur atom of RSNO promotes the resonance structure D and reduces the resonance structure I, thereby stabilizing the weak N-S bond and making the sulfur atom more electrophilic. On the other hand, increasing the D-character of RSNO by other means (e.g. via N- or O-coordination of a Lewis acid) in turn enhances the σ-hole bonding. Our calculations suggest that in the protein environment a combination of σ-hole bonding of a negatively charged amino acid sidechain at the sulfur atom and N- or O-coordination of a positively charged amino acid sidechain is expected to have a profound effect on the RSNO electronic structure and reactivity.

Lewis Acid Coordination Redirects S-Nitrosothiol Signaling Output.

S-Nitrosothiols (RSNOs) serve as air-stable reservoirs for nitric oxide in biology. While copper enzymes promote NO release from RSNOs by serving as Lewis acids for intramolecular electron-transfer, redox-innocent Lewis acids separate these two functions to reveal the effect of coordination on structure and reactivity. The synthetic Lewis acid B(C6 F5 )3 coordinates to the RSNO oxygen atom, leading to profound changes in the RSNO electronic structure and reactivity. Although RSNOs possess relatively negative reduction potentials, B(C6 F5 )3 coordination increases their reduction potential by over 1 V into the physiologically accessible +0.1 V vs. NHE. Outer-sphere chemical reduction gives the Lewis acid stabilized hyponitrite dianion trans-[LA-O-N=N-O-LA]2- [LA=B(C6 F5 )3 ], which releases N2 O upon acidification. Mechanistic and computational studies support initial reduction to the [RSNO-B(C6 F5 )3 ] radical anion, which is susceptible to N-N coupling prior to loss of RSSR.

Redox-Induced Molecular Actuators: The Case of Oxy-Alternate Bridged Cyclotetraveratrylene.

We report a practical two-step approach for the synthesis of hybrid-bridge macrocyclic molecules that has been used to synthesize two novel oxy-alternate-bridged macrocyclic molecules, oxy-alternate cyclotetraveratrylene (O-altCTTV) and oxy-alternate cyclohexaveratrylene (O-altCHV). Electrochemistry, absorption spectroscopy, X-ray crystallography, and DFT calculations demonstrate that O-altCTTV acts as a redox-induced molecular actuator, as its switches from the open conformation in the neutral state to the closed conformation in the cation-radical state.

Improving Performance of the SMD Solvation Model: Bondi Radii Improve Predicted Aqueous Solvation Free Energies of Ions and pKa Values of Thiols.

Calculation of the solvation free energy of ionic molecules is the principal source of errors in the quantum chemical evaluation of pKa values using implicit polarizable continuum solvent models. One of the important parameters affecting the performance of these models is the choice of atomic radii. Here, we assess the performance of the solvation model based on density (SMD) implicit solvation model employing SMD default radii (SMD) and Bondi radii (SMD-B), a set of empirical atomic radii developed based on the crystallographic data. For a set of 112 ions (60 anions and 52 cations), the SMD-B model showed lower mean unsigned error (MUE) for predicted aqueous solvation free energies (4.0 kcal/mol for anions and 2.4 kcal/mol for cations) compared to the standard SMD model (MUE of 5.0 kcal/mol for anions and 2.9 kcal/mol for cations). In particular, usage of Bondi radii improves the aqueous solvation energies of sulfur-containing ions by >5 kcal/mol compared to the SMD default radii. Indeed, for a set of 45 thiols, the SMD-B model was found to dramatically improve the predicted pKa values, with ∼1 pKa unit mean deviation from the experimental values, compared to ∼7 pKa units mean deviation for the SMD model with the default radii. These findings highlight the importance of the choice of atomic radii on the performance of the implicit solvation models.

An Electron-Rich Calix[4]arene-Based Receptor with Unprecedented Binding Affinity for Nitric Oxide.

Calixarenes have found widespread application as building blocks for the design and synthesis of functional materials in host-guest chemistry. The ongoing desire to develop a detailed understanding of the nature of NO bonding to multichromophoric π-stacked assemblies led us to develop an electron-rich methoxy derivative of calix[4]arene (3), which we show exists as a single conformer in solution at ambient temperature. Here, we examine the redox properties of this derivative, generate its cation radical (3+. ) using robust chemical oxidants, and determine the relative efficacy of its NO binding in comparison with model calixarenes. We find that 3/3+. is a remarkable receptor for NO+ /NO, with unprecedented binding efficacy. The availability of precise experimental structures of this calixarene derivative and its NO complex, obtained by X-ray crystallography, is critically important both for developing novel functional NO biosensors, and understanding the role of stacked aromatic donors in efficient NO binding, which may have relevance to biological NO transport.

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, △E0≠ = 12.7 kcal/mol, so CH3SNO exists as a cis- or trans-conformer, the latter slightly higher in energy, △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.

Modeling of S-Nitrosothiol-Thiol Reactions of Biological Significance: HNO Production by S-Thiolation Requires a Proton Shuttle and Stabilization of Polar Intermediates.

Nitroxyl (HNO), a reduced form of the important gasotransmitter nitric oxide, exhibits its own unique biological activity. A possible biological pathway of HNO formation is the S-thiolation reaction between thiols and S-nitrosothiols (RSNOs). Our density functional theory (DFT) calculations suggested that S-thiolation proceeds through a proton transfer from the thiol to the RSNO nitrogen atom, which increases electrophilicity of the RSNO sulfur, followed by nucleophilic attack by thiol, yielding a charge-separated zwitterionic intermediate structure RSS+ (R)N(H)O- (Zi), which decomposes to yield HNO and disulfide RSSR. In the gas phase, the proton transfer and the S-S bond formation are asynchronous, resulting in a high activation barrier (>40 kcal mol-1 ), making the reaction infeasible. However, the barrier can decrease below the S-N bond dissociation energy in RSNOs (≈30 kcal mol-1 ) upon transition into an aqueous environment that stabilizes Zi and provides a proton shuttle to synchronize the proton transfer and the S-S bond formation. These mechanistic features suggest that S-thiolation can easily lend itself to enzymatic catalysis and thus can be a possible route of endogenous HNO production.

Metallic-like bonding in plasma-born silicon nanocrystals for nanoscale bandgap engineering.

Based on ab initio molecular dynamics simulations, we show that small nanoclusters of about 1 nm size spontaneously generated in a low-temperature silane plasma do not possess tetrahedral structures, but are ultrastable. Apparently small differences in the cluster structure result in substantial modifications in their electric, magnetic, and optical properties, without the need for any dopants. Their non-tetrahedral geometries notably lead to electron deficient bonds that introduce efficient electron delocalization that strongly resembles the one of a homogeneous electron gas leading to metallic-like bonding within a semiconductor nanocrystal. As a result, pure hydrogenated silicon clusters that form by self-assembly in a plasma reactor possess optical gaps covering most of the solar spectrum from 1.0 eV to 5.2 eV depending simply on their structure and, in turn, on their degree of electron delocalization. This feature makes them ideal candidates for future bandgap engineering not only for photovoltaics, but also for many nano-electronic devices employing nothing else but silicon and hydrogen atoms.

Electrostatic point charge fitting as an inverse problem: Revealing the underlying ill-conditioning.

Atom-centered point charge (PC) model of the molecular electrostatics-a major workhorse of the atomistic biomolecular simulations-is usually parameterized by least-squares (LS) fitting of the point charge values to a reference electrostatic potential, a procedure that suffers from numerical instabilities due to the ill-conditioned nature of the LS problem. To reveal the origins of this ill-conditioning, we start with a general treatment of the point charge fitting problem as an inverse problem and construct an analytical model with the point charges spherically arranged according to Lebedev quadrature which is naturally suited for the inverse electrostatic problem. This analytical model is contrasted to the atom-centered point-charge model that can be viewed as an irregular quadrature poorly suited for the problem. This analysis shows that the numerical problems of the point charge fitting are due to the decay of the curvatures corresponding to the eigenvectors of LS sum Hessian matrix. In part, this ill-conditioning is intrinsic to the problem and is related to decreasing electrostatic contribution of the higher multipole moments, that are, in the case of Lebedev grid model, directly associated with the Hessian eigenvectors. For the atom-centered model, this association breaks down beyond the first few eigenvectors related to the high-curvature monopole and dipole terms; this leads to even wider spread-out of the Hessian curvature values. Using these insights, it is possible to alleviate the ill-conditioning of the LS point-charge fitting without introducing external restraints and/or constraints. Also, as the analytical Lebedev grid PC model proposed here can reproduce multipole moments up to a given rank, it may provide a promising alternative to including explicit multipole terms in a force field.

A deeper insight into strain for the sila-bi[6]prismane ( Si18H12) cluster with its endohedrally trapped silicon atom, Si19H12.

A new family of over-coordinated hydrogenated silicon nanoclusters with outstanding optical and mechanical properties has recently been proposed. For one member of this family, namely the highly symmetric Si19 H12 nanocrystal, strain calculations have been presented with the goal to question its thermal stability and the underlying mechanism of ultrastability and electron-deficiency aromaticity. Here, the invalidity of these strain energy (SE) calculations is demonstrated mainly based on a fundamentally wrong usage of homodesmotic reactions, the miscounting of atomic bonds, and arithmetic errors. Since the article in question is entirely anchored on those erroneous SE values, all of its conclusions and predictions become without meaning. We provide evidence here that the nanocrystal in question suffers from such low levels of strain that its thermodynamical stability should be largely sufficient for device fabrication in a realistic plasma reactor. Most remarkably, the two "alternative," irregular isomers explicitly proposed in the aforementioned article are also electron-deficient, nontetrahedral, ultrastable, and aromatic nicely underlining the universality of the ultrastability concept for nanometric hydrogenated silicon clusters.

Genetic algorithm optimization of point charges in force field development: challenges and insights.

Evolutionary methods, such as genetic algorithms (GAs), provide powerful tools for optimization of the force field parameters, especially in the case of simultaneous fitting of the force field terms against extensive reference data. However, GA fitting of the nonbonded interaction parameters that includes point charges has not been explored in the literature, likely due to numerous difficulties with even a simpler problem of the least-squares fitting of the atomic point charges against a reference molecular electrostatic potential (MEP), which often demonstrates an unusually high variation of the fitted charges on buried atoms. Here, we examine the performance of the GA approach for the least-squares MEP point charge fitting, and show that the GA optimizations suffer from a magnified version of the classical buried atom effect, producing highly scattered yet correlated solutions. This effect can be understood in terms of the linearly independent, natural coordinates of the MEP fitting problem defined by the eigenvectors of the least-squares sum Hessian matrix, which are also equivalent to the eigenvectors of the covariance matrix evaluated for the scattered GA solutions. GAs quickly converge with respect to the high-curvature coordinates defined by the eigenvectors related to the leading terms of the multipole expansion, but have difficulty converging with respect to the low-curvature coordinates that mostly depend on the buried atom charges. The performance of the evolutionary techniques dramatically improves when the point charge optimization is performed using the Hessian or covariance matrix eigenvectors, an approach with a significant potential for the evolutionary optimization of the fixed-charge biomolecular force fields.

Structure, stability, and substituent effects in aromatic S-nitrosothiols: the crucial effect of a cascading negative hyperconjugation/conjugation interaction.

Aromatic S-nitrosothiols (RSNOs) are of significant interest as potential donors of nitric oxide and related biologically active molecules. Here, we address a number of poorly understood properties of these species via a detailed density functional theory and the natural bond orbital (NBO) investigation of the parent PhSNO molecule. We find that the characteristic perpendicular orientation of the -SNO group relative to the phenyl ring is determined by a combination of the steric factors and the donor-acceptor interactions including, in particular, a cascading orbital interaction involving electron delocalization from the oxygen lone pair to the σ-antibonding S-N orbital and then to the π*-aromatic orbitals, an unusual negative hyperconjugation/conjugation long-range delocalization pattern. These interactions, which are also responsible for the relative weakness of the S-N bond in PhSNO and the modulation of -SNO group properties in substituted aromatic RSNOs, can be interpreted as a resonance stabilization of the ionic resonance component RS(-)/NO(+) of the RSNO electronic structure by the aromatic ring, similar to the resonance stabilization of PhS(-) anion. These insights into the chemistry and structure-property relationships in aromatic RSNOs can provide an important theoretical foundation for rational design of new RSNOs for biomedical applications.

Key Role of End-Capping Groups in Optoelectronic Properties of Poly-p-phenylene Cation Radicals.

Poly-p-phenylenes (PPs) are prototype systems for understanding the charge transport in π-conjugated polymers. In a combined computational and experimental study, we demonstrate that the smooth evolution of redox and optoelectronic properties of PP cation radicals toward the polymeric limit can be significantly altered by electron-donating iso-alkyl and iso-alkoxy end-capping groups. A multiparabolic model (MPM) developed and validated here rationalizes this unexpected effect by interplay of the two modes of hole stabilization: due to the framework of equivalent p-phenylene units and due to the electron-donating end-capping groups. A symmetric, bell-shaped hole in unsubstituted PPs becomes either slightly skewed and shifted toward an end of the molecule in iso-alkyl-capped PPs or highly deformed and concentrated on a terminal unit in PPs with strongly electron-donating iso-alkoxy capping groups. The MPM shows that the observed linear 1/n evolution of the PP cation radical properties toward the polymer limit originates from the hole stabilization due to the growing chain of p-phenylene units, while shifting of the hole toward electron-donating end-capping groups leads to early breakdown of these 1/n dependencies. These insights, along with the readily applicable and flexible multistate parabolic model, can guide studies of complex donor-spacer-acceptor systems and doped molecular wires to aid the design of the next generation materials for long-range charge transport and photovoltaic applications.

On the possible biological relevance of HSNO isomers: a computational investigation.

Thionitrous acid (HSNO), the smallest S-nitrosothiol, has been identified as a potential biologically active molecule that connects the biochemistries of two important gasotransmitters, nitric oxide (NO) and hydrogen sulfide (H2S). Here, we computationally explore possible isomerization reactions of HSNO that may occur under physiological conditions using high-level coupled-cluster as well as density functional theory and composite CBS-QB3 methodology calculations. Gas-phase calculations show that the formation of the tautomeric form HONS and the Y-isomer SN(H)O is thermodynamically feasible, as they are energetically close, within ∼6 kcal mol(-1), to HSNO, while the recently proposed three-membered ring isomer is not thermodynamically or kinetically accessible. The gas-phase intramolecular proton-transfer reactions required for HSNO isomerization into HONS and SN(H)O are predicted to have prohibitively high reaction barriers, 30-50 kcal mol(-1). However, the polar aqueous environment and water-assisted proton shuttle should decrease these barriers to ∼9 kcal mol(-1), which makes these two isomers kinetically accessible under physiological conditions. Our calculations also support the possibility of an aqueous reaction between the Y-isomer SN(H)O and H2S leading to biologically active nitroxyl HNO. These results suggest that the formation of HSNO in biological milieu can lead to various derivative species with their own, possibly biologically relevant, activity.

Photoexcitation and charge-transfer-to-solvent relaxation dynamics of the I(-)(CH3CN) complex.

Photoexcitation of iodide-acetonitrile clusters, I(-)(CH3CN)n, to the charge-transfer-to-solvent (CTTS) state and subsequent cluster relaxation could result in the possible formation of cluster analogues of the bulk solvated electron. In this work, the relaxation process of the CTTS excited iodide-acetonitrile binary complex, [I(-)(CH3CN)]*, is investigated using rigorous ab initio quantum chemistry calculations and direct-dynamics simulations to gain insight into the role and motion of iodine and acetonitrile in the relaxation of CTTS excited I(-)(CH3CN)n. Computed potential energy curves and profiles of the excited electron vertical detachment energy for [I(-)(CH3CN)]* along the iodine-acetonitrile distance coordinate reveal for the first time significant dispersion effects between iodine and the excited electron, which can have a significant stabilizing effect on the latter. Results of direct-dynamics simulations demonstrate that [I(-)(CH3CN)]* undergoes dissociation to iodine and acetonitrile fragments, resulting in decreased stability of the excited electron. The present work provides strong evidence of solvent translational motion and iodine ejection as key aspects of the early time relaxation of CTTS excited I(-)(CH3CN)n that can also have a substantial impact on the subsequent electron solvation processes and further demonstrates that intricate details of the relaxation process of CTTS excited iodide-polar solvent molecule clusters make it heavily solvent-dependent.

Computational design of S-nitrosothiol "click" reactions.

To address a long-standing problem of finding efficient reactions for chemical labeling of protein-based S-nitrosothiols (RSNOs), we computationally explored hitherto unknown (3+2) cycloaddition RSNO reactions with alkynes and alkenes. Nonactivated RSNO cycloaddition reactions have high activation enthalpy (>20 kcal/mol at the CBS-QB3 level) and compete with alternative S-N bond insertion pathway. However, the (3+2) cycloaddition reaction barriers can be dramatically lowered by coordination of a Lewis acid to the N atom of the -SNO group. To exploit this effect, we propose to use reagents with Lewis acid and a strain-activated carbon-carbon multiple bond linked by a rigid scaffold, which can react with RSNOs with small activation enthalpies (∼5 kcal/mol) and high reaction exothermicities (∼40 kcal/mol). The proposed efficient RSNO cycloaddition reactions can be used for future development of practical RSNO labeling reactions.

No longer a complex, not yet a molecule: a challenging case of nitrosyl O-hydroxide, HOON.

HOON might be an elusive intermediate of atmospheric photochemical reactions of HONO or recombination of the parent nitrene HN and molecular oxygen. However, no reliable data on HOON structure and stability are available, and the nature of the O-O bond is not well understood. In this study, we used high-level single- [CCSD(T) and, CCSDTQ] and multireference [CASPT2, MR-AQCC] ab initio calculations to determine properties of HOON: geometry, harmonic and anharmonic vibrational frequencies, thermodynamic stability, and electronic structure. HOON has bonding minima only in the (1)A' electronic state that correspond to cis- and trans-conformers; trans-HOON is more stable by 6.4-8.5 kJ/mol. The O-O bond in trans-HOON is unusually long, R(O-O) = 1.89 Å, and weak, D(O-O) = 33.3 kJ/mol; however, trans-HOON might be stable enough to be identified in cryogenic matrices. Though the electronic structure of the NO moiety in HOON most resembles nitric oxide, some nitrene character as well nitrosyl cation character are also important; therefore, the current name of HOON, hydroperoxynitrene, is misleading; instead, we propose the name "nitrosyl O-hydroxide" or "isonitrosyl hydroxide".

Protein control of S-nitrosothiol reactivity: interplay of antagonistic resonance structures.

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 (15)N NMR signatures of these specific interactions suggest that (15)N 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.

Photochemical electrocyclic ring closure and leaving group expulsion from N-(9-oxothioxanthenyl)benzothiophene carboxamides.

N-(9-Oxothioxanthenyl)benzothiophene carboxamides bearing leaving groups (LG(-) = Cl(-), PhS(-), HS(-), PhCH(2)S(-)) at the C-3 position of the benzothiophene ring system photochemically cyclize with nearly quantitative release of the leaving group, LG(-). The LG(-) photoexpulsions can be conducted with 390 nm light or with a sunlamp. Solubility in 75% aqueous CH(3)CN is achieved by introducing a carboxylate group at the C-6 position of the benzothiophene ring. The carboxylate and methyl ester derivatives regiospecifically cyclize at the more hindered C-1 position of the thioxanthone ring. Otherwise, the photocyclization favors the C-3 position of the thioxanthone. Quantum yields for reaction are 0.01-0.04, depending on LG(-) basicity. Electronic structure calculations for the triplet excited state show that excitation transfer occurs from the thioxanthone to the benzothiophene ring. Subsequent cyclization in the triplet excited state is energetically favourable and initially generates the triplet excited state of the zwitterionic species. Expulsion of LG(-) is thought to occur once this species converts to the closed shell ground state.

Unprecedented External Electric Field Effects on S-Nitrosothiols: Possible Mechanism of Biological Regulation?

Reactions of S-nitrosothiols (RSNOs), ubiquitous carriers of nitric oxide NO and its physiological activity, are tightly regulated in biological systems, but the mechanisms of this regulation are not well understood. Here, we computationally demonstrate that RSNO properties can be dramatically altered by biologically accessible external electric fields (EEFs) by modulation of the two minor antagonistic resonance structures of RSNOs, which have opposite formal charge distributions and bonding patterns. As these resonance contributions relate to the two competing modes of RSNO reactivity with nucleophiles, via N- or S-atom directed nucleophilic attack, EEFs are predicted to be efficient in controlling biologically important RSNO reactions with thiols. For instance, EEF catalysis might be one of the mechanisms behind the high selectivity of protein trans-S-nitrosation reactions, or putative nitroxyl HNO formation via RSNO S-thiolation reactions.