: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Cation-π interaction: its role and relevance in chemistry, biology, and material science.

Significance: Protein S-nitrosylation, the oxidative modification of cysteine by nitric oxide (NO) to form protein S-nitrosothiols (SNOs), mediates redox-based signaling that conveys, in large part, the ubiquitous influence of NO on cellular function. S-nitrosylation regulates protein activity, stability, localization, and protein–protein interactions across myriad physiological processes, and aberrant S-nitrosylation is associated with diverse pathophysiologies. Recent Advances: It is recently recognized that S-nitrosylation endows S-nitroso-protein (SNO-proteins) with S-nitrosylase activity, that is, the potential to trans-S-nitrosylate additional proteins, thereby propagating SNO-based signals, analogous to kinase-mediated signaling cascades. In addition, it is increasingly appreciated that cellular S-nitrosylation is governed by dynamically coupled equilibria between SNO-proteins and low-molecular-weight SNOs, which are controlled by a growing set of enzymatic denitrosylases comprising two ma...

/pdf/protein-s-nitrosylation-determinants-of-specificity-and-54m4xk2n2o.pdf

Protein S-Nitrosylation: Determinants of Specificity and Enzymatic Regulation of S-Nitrosothiol-Based Signaling.

A comparison of the chemistry associated with the biological signaling and actions of nitroxyl (HNO) and nitric oxide (NO).

Cation-π interactions are common in nature, especially in organisms. Their profound influences in chemistry, physics, and biology have been continuously investigated since they were discovered in 1981. However, the importance of cation-π interactions in materials science, regarding carbonaceous nanomaterials, has just been realized. The interplay between cations and delocalized polarizable π electrons of graphene would bring about significant changes to the intrinsic characteristics of graphene and greatly affect the device performance based on graphene and its derivatives. Here, the cation-π interactions in graphene containing systems for water treatment applications (e.g., separation membranes, adsorbents) are highlighted. The cross-linking effects caused by cation-π interactions contribute to membrane stability and selectivity and enhanced adsorption. Their roles in dominating the performance of graphene-based structures for other specific applications are also discussed. Relevant theoretical modeling and calculations are summarized to offer an in-depth understanding of the underlying mechanisms which can help in designing more functional materials and structures. Perspectives on the potential directions that deserve effort are also presented.

Cation-π Interactions in Graphene-Containing Systems for Water Treatment and Beyond.

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...

An Assessment of Theoretical Methods for the Calculation of Accurate Structures and SN Bond Dissociation Energies of S-Nitrosothiols (RSNOs)

Density functional theory methods have been used to investigate the role and effects of Cu+ binding to the S and N centers of the −SNO functional group within S-nitrosothiols (RSNOs), on the lability of the NO group. The binding of Cu+ to the S center is found to weaken the S−N bond, while the N−O bond is concomitantly strengthened, consistent with the notion that Cu+ binding catalyzes NO radical release. In contrast, however, the binding of Cu+ to the N center is found to dramatically shorten and strengthen the S−N bond with a concomitant lengthening of the N−O bond, suggesting stabilization of the RSNOs against NO release. Upon solvation, complexes with Cu+ bound to the N center are stabilized relative to the corresponding S-bound complexes, though remaining slightly higher in energy. The barriers to interconversion between corresponding isomers were also investigated. Implications for biochemical regulation of NO release from RSNOs are discussed.

Influence of Cu+ on the RS−NO Bond Dissociation Energy of S-Nitrosothiols

The interaction of the nitric oxide ions NO+ and NO- with benzene (C6H6) and the aromatic R-groups of the amino acids phenylalanine (Phe), tyrosine (Tyr), histidine (His), and tryptophan (Trp) have been examined using the DFT method B3LYP and the conventional electron correlation method MP2. In particular, the structures and complexation energies of the resulting half-sandwich Ar...NO+/- and sandwich [Ar...NO...Ar]+/- complexes have been considered. For the Ar...NO+ complexes, the presence of an electron rich heteroatom within or attached to the ring is found to not preclude the cation...pi bound complex from being the most stable. Furthermore, unlike the anionic complexes, the pi...cation...pi ([Ar...NO...Ar]+) complexes do not correspond to a "doubling" of the parent half-sandwich.

A computational study on the interaction of the nitric oxide ions NO+ and NO- with the side groups of the aromatic amino acids.

The density functional theory (DFT) method B3P86/6-311+G(2df,p) has been employed to investigate the complexes formed upon interaction of Cu(+) with nitrosylated cysteine (CysNO) and its decarboxylated (H(2)NCH(2)CH(2)SNO) and deaminated (HOOCCH(2)CH(2)SNO) derivatives. Optimized structures, relative enthalpies and relative free energies have been calculated and compared. In addition, the effects of binding an H(2)O molecule to the Cu(+) centre in the resulting complexes have also been considered. It is found that the most stable complexes are formed when Cu(+) coordinates to the S-nitrosothiol via S of the SNO group. This results in dramatic lengthenings of the SN bond with concomitant shortening of the NO bond. In contrast, when Cu(+) coordinates via the nitrogen of the SNO group, a shortening of the SN bond with lengthening of the NO bond is observed. These effects are tempered by the electron donating ability of other functional groups also coordinated with the Cu(+) centre in the complexes and on the coordination state of the Cu(+) ion.

Cristina Baciu

Papers

An Assessment of Theoretical Methods for the Calculation of Accurate Structures and SN Bond Dissociation Energies of S-Nitrosothiols (RSNOs)

Influence of Cu+ on the RS−NO Bond Dissociation Energy of S-Nitrosothiols

A computational study on the interaction of the nitric oxide ions NO+ and NO- with the side groups of the aromatic amino acids.

Ring complexes of S-nitrosothiols with CU+: a density functional theory study.