The N−H···S Hydrogen Bond in (TACN)2Fe2S6 (TACN = Triazacyclononane) and in Model Systems Involving the Persulfido Moiety: An ab Initio and DFT Study

Participation of S and Se in hydrogen and chalcogen bonds

The heavier chalcogen atoms S, Se, and Te can each participate in a range of different noncovalent interactions. They can serve as both proton donor and acceptor in H-bonds. Each atom can also act as electron acceptor in a chalcogen bond.

Conformational preferences of furan- and thiophene-based arylamides: a combined computational and experimental study

We examine the conformational preferences of the furan- and thiophene-based arylamides, N-methylfuran-2-carboxamide (3) and N-methylthiophene-2-carboxamide (4), using a combination of computational methods and NMR experiments. The compound choice stems from their use as foldamer building blocks. We quantify the differences in the conformational rigidity of the two compounds, which governs corresponding foldamer conformations. Specifically, we demonstrate the effects of intramolecular hydrogen bonding (H-bonding), geometrical patterns and solvent polarity on arylamide conformations by comparing 3, 4 and previously studied ortho-methoxy N-methylbenzamide (1) and ortho-methylthio N-methylbenzamide (2). The study reveals that compound 3, despite its non-optimal S(5)-type H-bond geometry, retains a large portion of the H-bonded (eclipsed) conformation even in polar protic solvents. This behaviour is consistent with the quantum mechanical (QM) torsional energy profile. The percentages of H-bonded conformers that 3 retains are just slightly smaller than those of 1, which has a stronger S(6)-type H-bond. As for 2 and 4, the replacement of the O atom in 1 by an S atom in 2 results in a 70–90% loss of the H-bonded conformer in solution. However, the equivalent O to S replacement in 3 (leading to 4) causes only 15–30% loss of the eclipsed conformers in 4. Therefore, conformational preferences of 4 are very different from 2, in contrast to the similarity between 3 and 1. This study shows how the interplay of several forces modulates the conformational flexibility of arylamides. It also attests the strategy we are developing, which leads to accurate prediction of foldamer structure. The vital component of this strategy is the re-parameterization of critical force field parameters based on QM potential energy profiles, as well as validation of these parameters using experimental data in solution.

S K-edge XAS and DFT calculations on square-planar NiII-thiolate complexes: effects of active and passive H-bonding

S K-edge XAS for a low-spin NiII-thiolate complex shows a 0.2 eV shift to higher pre-edge energy but no change in Ni-S bond covalency upon H-bonding. This is different from the H-bonding effect we observed in high-spin FeIII-thiolate complexes where there is a significant decrease in Fe-S bond covalency but no change in energy due to H-bonding (Dey, A.; Okamura, T.-A.; Ueyama, N.; Hedman, B.; Hodgson, K. O.; Solomon, E. I. J. Am. Chem. Soc. 2005, 127, 12046-12053). These differences were analyzed using DFT calculations, and the results indicate that two different types of H-bonding interactions are possible in metal-thiolate systems. In the high-spin FeIII-thiolate case, the H-bonding involves a thiolate donor orbital which is also involved in bonding with the metal (active), while in the low-spin NiII-thiolate, the orbital involved in H-bonding is nonbonding with respect to the M-S bonding (passive). The contributions of active and passive H-bonds to the reduction potential and Lewis acid properties of a metal center are evaluated.

Computational Study of the Interaction between TIBO Inhibitors and Y181 (C181), K101, and Y188 Amino Acids

The non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) are an important class of drugs employed in anti-HIV chemotherapy. TIBO compounds, which belong to the NNRTIs class, are potent inhibitors of the HIV-1 reverse transcriptase enzyme (HIV-1 RT). However, mutations in the amino acids present in the active site of these inhibitors limit their clinical use. In this work, the intermolecular interactions taking place between compounds of the TIBO family and Y181 (C181), K101, and Y188 amino acids are investigated. For this purpose the coordinates of three RT crystalline structures complexed with TIBO were taken from PDB database, and were analyzed by means of the B3LYP/6-31+G(d,p) model. The natural bond orbital (NBO) and atoms in molecules (AIM) methods indicate that not only does the Y181C mutation lead to loss of favorable interactions between the TIBO side chains and tyrosine, but it also affects the interaction between the inhibitor and K101 and Y188. Results also revealed that the interaction between TIBO and K101 is stabilized by N-H...O and N-H...S hydrogen bonds. This is the first time that the presence of the latter hydrogen bond (N-H...S) is reported to play an important role in the stabilization of the interaction between TIBO and K101. In addition the NBO and natural population analyses (NPA) indicate that the 8 Cl-TIBO inhibitor presents a more effective interaction with the Y181, K101, and Y188 than that of 9 Cl-TIBO.

X-ray Absorption Spectroscopy and Density Functional Theory Studies of [(H3buea)FeIII-X]n- (X = S2-, O2-, OH-): Comparison of Bonding and Hydrogen Bonding in Oxo and Sulfido Complexes

Iron L-edge, iron K-edge, and sulfur K-edge X-ray absorption spectroscopy was performed on a series of compounds [Fe(III)H(3)buea(X)](n-) (X = S(2-), O(2-), OH(-)). The experimentally determined electronic structures were used to correlate to density functional theory calculations. Calculations supported by the data were then used to compare the metal-ligand bonding and to evaluate the effects of H-bonding in Fe(III)(-)O vs Fe(III)(-)S complexes. It was found that the Fe(III)(-)O bond, while less covalent, is stronger than the Fe(III)(-)S bond. This dominantly reflects the larger ionic contribution to the Fe(III)(-)O bond. The H-bonding energy (for three H-bonds) was estimated to be -25 kcal/mol for the oxo as compared to -12 kcal/mol for the sulfide ligand. This difference is attributed to the larger charge density on the oxo ligand resulting from the lower covalency of the Fe-O bond. These results were extended to consider an Fe(IV)(-)O complex with the same ligand environment. It was found that hydrogen bonding to Fe(IV)(-)O is less energetically favorable than that to Fe(III)(-)O, which reflects the highly covalent nature of the Fe(IV)(-)O bond.

Sulfur K-edge XAS and DFT calculations on P450 model complexes: effects of hydrogen bonding on electronic structure and redox potentials

Hydrogen bonding (H-bonding) is generally thought to play an important role in tuning the electronic structure and reactivity of metal-sulfur sites in proteins. To develop a quantitative understanding of this effect, S K-edge X-ray absorption spectroscopy (XAS) has been employed to directly probe ligand-metal bond covalency, where it has been found that protein active sites are significantly less covalent than their related model complexes. Sulfur K-edge XAS data are reported here on a series of P450 model complexes with increasing H-bonding to the ligated thiolate from its substituent. The XAS spectroscopic results show a dramatic decrease in preedge intensity. DFT calculations reproduce these effects and show that the observed changes are in fact solely due to H-bonding and not from the inductive effect of the substituent on the thiolate. These calculations also indicate that the H-bonding interaction in these systems is mainly dipolar in nature. The -2.5 kcal/mol energy of the H-bonding interaction was small relative to the large change in ligand-metal bond covalency (30%) observed in the data. A bond decomposition analysis of the total energy is developed to correlate the preedge intensity change to the change in Fe-S bonding interaction on H-bonding. This effect is greater for the reduced than the oxidized state, leading to a 260 mV increase in the redox potential. A simple model shows that E degrees should vary approximately linearly with the covalency of the Fe-S bond in the oxidized state, which can be determined directly from S K-edge XAS.

Ligand Displacement and Oxidation Reactions of Methyl(oxo)rhenium(V) Complexes

Compounds that contain the anion [MeReO(edt)(SPh)](-) (3-) were synthesized with the countercations 2-picolinium (PicH+3-) and 2,6-lutidinium (LutH+3-), where edt is 1,2-ethanedithiolate. Both PicH+3- and MeReO(edt)(tetramethylthiourea) (4) were crystallographically characterized. The rhenium atom in each of these compounds exists in a five-coordinate distorted square pyramid. In the solid state, PicH+3- contains an anion with a short (d(SH) = 232 pm) and nearly linear hydrogen-bonded (N-H.S) interaction to the cation. Ligand substitution reactions were studied in chloroform. Displacement of PhSH by PPh(3) follows second-order kinetics, d[MeReO(edt)(PPh(3))]/dt = k[PicH+3-][PPh3], whereas with pyridines an unusual form was found, d[MeReO(edt)(Py)]/dt = k[PyH+3-][Py](2), in which the conversion of PicH+3- to PyH+3- has been incorporated. Further, added Py accelerates the formation of [MeReO(edt)(PPh3)], v = k.[PicH+3-].[PPh3].[Py]. Compound 4, on the other hand, reacts with both PPh(3) and pyridines, L, at a rate given by d[MeReO(edt)(L)]/dt = k.[4].[L]. When PicH+3- reacts with pyridine N-oxides, a three-stage reaction was observed, consistent with ligand replacement of SPh(-) by PyO, N-O bond cleavage of the PyO assisted by another PyO, and eventual decomposition of MeRe(O)(edt)(OPy) to MeReO(3). Each of first two steps showed a large substituent effect; Hammett analysis gave rho(1) = -5.3 and rho(2) = -4.3.

Research on Soluble Metal Sulfides: From Polysulfido Complexes to Functional Models for the Hydrogenases

Results from this laboratory are surveyed, emphasizing the synthesis of metal sulfides. Four themes are described. Continuing studies exploit the exothermic desulfurization of polysulfido complexes as a means to generate new clusters and rings. Illustrative inorganic rings prepared in this way include 1,5-[L(2)M](2)(S(3))(2) and 1,4-[L(2)M](2)(S(2))(2), where L(2)M = CpRu(PPh(3)) and Cp(2)Ti. Fundamentally new clusters prepared in this project included the cubanes [(C(5)R(5))MS](4) for M = Ti, V, Ru, Ir. Associated redox studies led to the discovery of the phenomenon of mobile metal-metal bonds, as manifested in [Cp(4)Ir(4)S(4)](2+) wherein the localized Ir-Ir bond migrates over the six Ir- - -Ir edges of the cluster. Other desulfurization experiments led to the preparation of the reactive species Ir(II)(2)S(2)(PPh(3))(4) from [IrS(16)](3)(-) and the synthesis of the first high polymers of ferrocene, [(RC(5)H(3)S)(2)Fe](n) (n approximately 500). A second theme uncovered the useful role of donor solvents on the reaction of metals with sulfur. It was found that pyridine accelerates the low temperature conversion of Cu to crystalline CuS via the intermediacy of the cluster Cu(4)(S(5))(2)L(4). Related synthetic methodology led to a family of amine-stabilized zinc polysulfides, e.g. ZnS(6)(tmeda), an efficient sulfur-transfer agent. A third theme explored the organic and organometallic chemistry of the tetrathiometalates. The sulfido analogue of OsO(4), ReS(4)(-) was shown to be broadly reactive toward unsaturated organic substrates such as alkenes, alkynes, nitriles, and isocyanides. The final and still emerging theme focuses on the preparation of functional and structural models for bio-organometallic reaction centers. Studies on models for the Fe-only hydrogenases began with the synthesis of the highly reducing species [Fe(2)(SR)(2)(CN)(2)(CO)(4)](2)(-) where (SR)(2) also includes the proposed azadithiolate cofactor HN(CH(2)S(-))(2). Systematic studies on the cyanide substitution process led to the preparation of [HFe(2)(SR)(2)(CN)(CO)(4)(PMe(3))], which efficiently catalyzes the reduction of protons to H(2). Work on the hydrogenases was expanded to include modeling of acetyl Co-A synthase, leading to the preparation of mixed valence Ni(2) models containing bound CO substrate.