Mechanistic investigations of alcohol silylation with isothiourea catalysts.

The mechanism of the asymmetric silylation of alcohols with isothiourea catalysts was studied by employing reaction progress kinetic analysis. These reactions were developed by the Wiskur group, and use triphenyl silyl chloride and chiral isothiourea catalysts to silylate the alcohols. While the order of most reaction components was as expected (catalyst, amine base, alcohol), the silyl chloride was determined to be a higher order. This suggested a multistep mechanism between the catalyst and silyl chloride, with the second equivalent of silyl chloride assisting in the formation of the reactive intermediate leading to the rate-determining step. Through the addition of additives and investigating changes in the silyl chloride, an understanding of the catalyst equilibrium emerged for this reaction and provided pathways for further reaction development.

Understanding Internal Chirality Induction of Triarylsilyl Ethers Formed from Enantiopure Alcohols.

Chirality transmission from point chirality to helical chirality was explored using triarylsilyl ethers. Circular dichroism (CD) spectroscopy was employed to show that the alcohol stereocenter of silylated, enantiopure secondary alcohols can transmit chirality to the aryl groups on the silicon resulting in a higher population of one helical conformation over another. Cotton effects characteristic of the aryl groups organized into one preferred conformation were observed for all of the compounds examined, which included both triphenyl- and trinaphthylsilyl groups. Alcohols with an R configuration typically induced a PMP helical twist, while an S configuration induced a MPM helical twist. Molecular modeling combined with solid-state structures also gave evidence signifying that point chirality adjacent to triphenylsilyl groups could bias the conformation of the phenyl groups. This work helps in our understanding of the origin of selectivity in our silylation-based kinetic resolutions and a role the phenyl groups play in that selectivity.

Silylation-based kinetic resolution of α-hydroxy lactones and lactams.

A silylation-based kinetic resolution has been developed for α-hydroxy lactones and lactams employing the chiral isothiourea catalyst (-)-benzotetramisole and triphenylsilyl chloride as the silyl source. The system is more selective for lactones than lactams, and selectivity factors up to 100 can be achieved utilizing commercially available reagents.

Guanidine hydrochloride-induced unfolding of the three heme coordination states of the CO-sensing transcription factor, CooA.

CooA is a heme-dependent CO-sensing transcription factor that has three observable heme coordination states. There is some evidence that each CooA heme state has a distinct protein conformation; the goal of this study was to characterize these conformations by measuring their structural stabilities through guanidine hydrochloride (GuHCl) denaturation. By studying the denaturation processes of the Fe(III) state of WT CooA and several variants, we were able to characterize independent unfolding processes for each domain of CooA. This information was used to compare the unfolding profiles of various CooA heme activation states [Fe(III), Fe(II), and Fe(II)-CO] to show that the heme coordination state changes the stability of the effector binding domain. A mechanism consistent with the data predicts that all CooA coordination states and variants undergo unfolding of the DNA-binding domain between 2 and 3 M GuHCl with a free energy of unfolding of approximately 17 kJ/mol, while unfolding of the heme domain is variable and dependent on the heme coordination state. The findings support a model in which changes in heme ligation alter the structural stability of the heme domain and dimer interface but do not alter the stability of the DNA-binding domain. These studies provide evidence that the domains of transcription factors are modular and that allosteric signaling occurs through changes in the relative positions of the protein domains without affecting the structure of the DNA-binding region.

Silica-bound copper(II)triazacyclononane as a phosphate esterase: effect of linker length and surface hydrophobicity.

A series of silica-bound Cu(ii) triazacyclononane materials was prepared to study the effect of linker length and surface hydrophobicity on the hydrolysis of phosphate esters. The general synthetic approach for these heterogeneous reagents was rhodium-catalyzed hydrosilation between an alkenyl-modified triazacyclononane and hydride-modified silica followed by metallation with a Cu(ii) salt. Elemental analysis confirmed that organic functionalization of the silica gel was successful and provided an estimate of the surface concentration of triazacyclononane. EPR spectra were consistent with square pyramidal Cu(ii), indicating that Cu(ii) ions were bound to the immobilized macrocycles. The hydrolytic efficacies of these heterogeneous reagents were tested with bis(p-nitrophenyl)phosphate (BNPP) and diethyl 4-nitrophenyl phosphate (paraoxon). The agent that performed best was an octyl-linked, propanol-blocked material. This material had the most hydrophilic surface and the most accessible active site, achieving a rate maximum on par with the other materials, but in fewer cycles and without an induction period.

DNA binding by an imidazole-sensing CooA variant is dependent on the heme redox state.

CooA is a transcription factor from Rhodospirillum rubrum that is regulated by the binding of the small molecule effector, CO, to a heme moiety in the protein. The heme in CooA is axially ligated by two endogenous donors in the Fe(III) and Fe(II) states of the protein, and CO binding to the Fe(II) state results in replacement of the distal ligand. Reduction of the heme in the absence of CO results in a ligand switch on the proximal side, in which a cysteine thiolate in the Fe(III) state is replaced by a histidine in the Fe(II) state. Recently, a variant, termed RW CooA, was designed to respond to a new effector; Fe(II) RW CooA shows high specificity and induced DNA-binding activity in the presence of imidazole. Spectroscopic characterization of the imidazole adducts of RW CooA revealed that, unlike CO, imidazole binds to both Fe(III) RW CooA and Fe(II) RW CooA. The spectral characteristics are consistent with normal function of the redox-mediated ligand switch; Fe(III)-imidazole RW CooA bears a thiolate ligand and Fe(II)-imidazole RW CooA bears a neutral donor ligand. Since the effector binds to both redox states, RW CooA was used to probe the role of the redox-mediated ligand switch in the CooA activation mechanism. Functional studies of Fe(III)-imidazole and Fe(II)-imidazole ligated RW CooA demonstrate that only the Fe(II)-imidazole form is active for DNA binding. Thus, the ligand switch is essential for the activating conformational change and may prevent aberrant activation of CooA by other neutral diatomic molecules.

Modeling proline ligation in the heme-dependent CO sensor, CooA, using small-molecule analogs.

CooA, the only protein known to employ proline as a heme ligand, is a CO-activated transcription factor found in the bacterium Rhodospirillum rubrum. Proline is a heme ligand in both the Fe(III) and Fe(II) states; the sixth ligand is cysteinate in Fe(III) CooA and histidine in Fe(II) CooA. When CO binds to Fe(II) CooA, it selectively replaces the proline ligand, activating the protein. The proposed roles of proline are to stabilize the heme pocket during the redox-mediated ligand switch and to form a weak metal-ligand bond that is preferentially cleaved to bind CO. To explore this latter proposal, binding affinity, structural, and density functional theory computational studies were performed using pyrrolidine and 2-methylpyrrolidine as analogs of proline, and imidazole as an analog of histidine. Measurement of the binding properties of these amino acid analogs in two different protein environments, CooA variant deltaP3R4 and myoglobin, revealed that CooA is tailored to accept the bulky proline ligand. Furthermore, the high pKa of proline facilitates selective replacement by CO. Model metalloporphyrin X-ray and computational structures suggest that the key factor leading to lengthening of the Fe-ligand bond and decreased binding affinity is steric hindrance at the C-2 position of the pyrrolidine ring. These data afford a more complete understanding of how CooA utilizes the weak proline ligand to direct CO to the distal position, thus ensuring selective retention of the histidine ligand.

Unexpected NO-dependent DNA binding by the CooA homolog from Carboxydothermus hydrogenoformans.

CooA, the CO-sensing heme protein from Rhodospirillum rubrum, regulates the expression of genes that encode a CO-oxidation system, allowing R. rubrum to use CO as a sole energy source. To better understand the gas-sensing regulation mechanism used by R. rubrum CooA and its homologs in other organisms, we characterized spectroscopically and functionally the Fe(II), Fe(II)-NO, and Fe(II)-CO forms of CooA from Carboxydothermus hydrogenoformans. Surprisingly, and unlike R. rubrum CooA, C. hydrogenoformans CooA binds NO to form a six-coordinate Fe(II)-NO heme that is active for DNA binding in vitro and in vivo. In contrast, R. rubrum CooA, which is exquisitely specific for CO, forms a five-coordinate Fe(II)-NO adduct that is inactive for DNA binding. Based on analyses of protein variants and temperature studies, NO-dependent DNA binding by C. hydrogenoformans CooA is proposed to result from a greater apparent stability of the six-coordinate Fe(II)-NO adduct at room temperature. Results from the present study strengthen the proposal that CO specificity in the CooA activation mechanism is based on the requirement for a small, neutral distal ligand, which in turn affects the relative positioning of the ligand-bound heme.

The redox behavior of the heme in cystathionine beta-synthase is sensitive to pH.

Human cystathionine beta-synthase (CBS) is a unique pyridoxal-5'-phosphate-dependent enzyme in which heme is also present as a cofactor. Because the function of heme in this enzyme has yet to be elucidated, the study presented herein investigated possible relationships between the chemistry of the heme and the strong pH dependence of CBS activity. This study revealed, via study of a truncation variant, that the catalytic core of the enzyme governs the pH dependence of the activity. The heme moiety was found to play no discernible role in regulating CBS enzyme activity by sensing changes in pH, because the coordination sphere of the heme is not altered by changes in pH over a range of pH 6-9. Instead, pH was found to control the equilibrium amount of ferric and ferrous heme present after reaction of CBS with one-electron reducing agents. A variety of spectroscopic techniques, including resonance Raman, magnetic circular dichroism, and electron paramagnetic resonance, demonstrated that at pH 9 Fe(II) CBS is dominant while at pH 6 Fe(III) CBS is favored. At low pH, Fe(II) CBS forms transiently but reoxidizes by an apparent proton-gated electron-transfer mechanism. Regulation of CBS activity by the iron redox state has been proposed as the role of the heme moiety in this enzyme. Given that the redox behavior of the CBS heme appears to be controlled by pH, interplay of pH and oxidation state effects must occur if CBS activity is redox regulated.

Investigation of the role of the N-terminal proline, the distal heme ligand in the CO sensor CooA.

A unique feature of CooA, a heme-containing transcription factor, is that the N-terminal proline is the distal heme ligand in the ferrous state, and this ligand is displaced upon CO binding. To investigate the importance of Pro(2) in CO-dependent DNA binding, several CooA variants that alter N-terminal ligation were characterized. Electronic absorption, electron paramagnetic resonance, and magnetic circular dichroism spectra of these variants provide the most definitive evidence that Pro(2) is the distal ligand in Fe(III) CooA. Furthermore, the functional and spectroscopic properties of these proteins depended on whether a weak ligand occupied the distal heme coordination site: for CooA variants in which distal coordination is disrupted, the DNA-binding affinities and Fe(II)-CO spectral properties showed an unexpected dependence on the order of CO addition and heme reduction. If N-terminal variant samples were incubated with CO before the heme was reduced, the proteins displayed DNA-binding affinities and Fe(II)-CO spectral characteristics similar to those of wild-type (WT) CooA. However, if the same samples were incubated with CO after the heme was reduced, the extent of functional and spectral similarity to WT CooA negatively correlated with the amount of high-spin heme present in the ferric state. From these data, it was inferred that the absence of a distal heme ligand in the ferric state prevents WT-like CO binding to the ferrous state, and it was hypothesized that correct CO binding is inhibited by the collapse of the distal heme pocket upon reduction. Together with the observation that L116H CooA, a variant in which His(116) replaces Pro(2) as the distal heme ligand, binds CO more slowly than WT CooA, these data indicate that the presence of a weak distal heme ligand, not specifically ligation by the N-terminal proline, is crucial for proper function. The role of Pro(2) in CooA is apparently to direct CO to bind on the distal side of heme and to help maintain the integrity of the distal heme pocket during the redox-mediated ligand switch.

A comparison of the ring conformational properties of two derivatives prepared from the same diene diacetate precursor.

Results of single-crystal X-ray experiments performed for the title compounds, (1S,2R,3S,4R,5R)-4-benzyloxy-2-[1-(benzyloxy)allyl]-5-hydroxymethyl-2,3,4,5-tetrahydrofuran-3-ol, C(22)H(26)O(5), (I), and (3R,5S,6S,7S,8S)-3,6-bis(benzyloxy)-5-iodomethyl-2,3,4,5-tetrahydrofuro[3,2-b]furan-2-one, C(21)H(21)IO(5), (II), demonstrate that the tetrahydrofuran ring that is common to both structures adopts a different conformation in each molecule. Structural analyses of (I) and (II), which were prepared from the same precursor, indicate that their different conformations are caused by hydrogen-bonding interactions in the case of (I) and the presence of a fused bicyclic ring system in the case of (II). Density functional theory calculations on simplified analogs of (I) and (II) are also presented.

A 1,2,4-diazaphospholane complex of rhodium.

The crystal structure of a prospective olefin catalyst, namely [2-[1-acetyl-5-(2-hydroxyphenyl)-4-phenyl-1,2,4-diazaphospholan-3-yl]phenyl acetate-kappaP]chloro(eta(4)-cycloocta-1,5-diene)rhodium(I) dichloromethane solvate, [RhCl(C(8)H(12))(C(24)H(23)N(2)O(4)P)].CH(2)Cl(2), has been determined at 173 K. The five-membered heterocycle of the phosphine ligand is in a slightly distorted twist conformation. An intramolecular N1-H1.Cl1 hydrogen bond contributes to the adopted conformation and may additionally participate in secondary interactions with substrates during catalysis.

"Inverse-electron-demand" ligand substitution in palladium(0)-olefin complexes.

Ligand substitution reactions are ubiquitous in transition-metal chemistry and catalysis. Investigation of ligand substitution reactions for a series of electron-rich palladium(0)-olefin complexes, (bathocuproine)Pd(nitrostyrene) reveals an unprecedented mechanism in which the metal serves as the nucleophilic partner in an "associative" substitution pathway.

Chemistry of the aromatic 9-germafluorenyl dianion and some related silicon and carbon species.

Dipotassio-9-germafluorenyl dianion (3b) was synthesized by reduction of 9,9-dichloro-9-germafluorene (4b) with sodium/potassium alloy in tetrahydrofuran. The X-ray crystal structure of 3b, like that for the analogous silicon compound 3a, shows C-C bond length equalization in the five-membered metallole rings and C-C bond length alternation in the six-membered benzenoid rings, indicating aromatic delocalization of electrons into the germole ring of 3b. Calculated nucleus independent chemical shift (NICS) values indicate that the five-membered ring is more aromatic than the six-membered rings in 3a and 3b. Derivatization of 3b with Me(3)SiCl gave 9,9-bis(trimethylsilyl)-9-germafluorene (5). Controlled oxidation of 3b yielded dipotassio-9,9'-digerma-9,9'-bifluorenyl dianion (6). Reaction of 6 with MeOH yielded 9,9'-digerma-9,9'-bifluorene (7). The X-ray structure of 6 indicates C-C bond length alternation in the five-membered rings. Thus dianion 6, like its silicon analogue 8, has the negative charges localized at metal atoms and no aromatic character. Dipotassio-9,9'-bifluorenyl dianion (9), the carbon analogue of 6, exhibits aromaticity with its X-ray crystal structure showing the C-C bond length equalization in both the five- and six-membered rings. Derivatization of 9 with MeI gave 9,9'-dimethyl-9,9'-bifluorene (10). The structure of 10 shows that the two fluorenyl rings are cis to each other with a torsional angle of 59 degrees and a long C-C single bond (1.60 A) connecting them.

Analysis of the L116K variant of CooA, the heme-containing CO sensor, suggests the presence of an unusual heme ligand resulting in novel activity.

CooA is the CO-sensing transcriptional activator from Rhodospirillum rubrum, in which CO binding to its heme prosthetic group triggers a conformational change of CooA that allows the protein to bind its cognate target DNA sequence. By a powerful in vivo screening method following the simultaneous randomization of the codons for two C-helix residues, 113 and 116, near the distal heme pocket of CooA, we have isolated a series of novel CooA variants. In vivo, these show very high CO-independent activities (comparable with that of wild-type CooA in the presence of CO) and diminished CO-dependent activities. Sequence analysis showed that this group of variants commonly contains lysine at position 116 with a variety of residues at position 113. DNA-binding analysis of a representative purified variant, L116K CooA, revealed that this protein is competent to bind target DNA with K(d) values of 56 nm for Fe(III), 36 nm for Fe(II), and 121 nm for Fe(II)-CO CooA forms. Electron paramagnetic resonance and electronic absorption spectroscopies, combined with additional mutagenic studies, showed that L116K CooA has a new ligand replacing Pro(2) in both Fe(III) and Fe(II) states. The most plausible replacement ligand is the substituted lysine at position 116, so that the ligands of Fe(III) L116K CooA are Cys(75) and Lys(116) and those in the Fe(II) form are His(77) and Lys(116). A possible explanation for CO-independent activity in L116K CooA is that ligation of Lys(116) results in a repositioning of the C-helices at the CooA dimer interface. This result is consistent with that repositioning being an important aspect of the activation of wild-type CooA by CO.