Markedly different selectivity in the rhodium catalyzed hydroformylation of vinyl olefins containing a chiral alkoxy or alkyl group: good agreement between theory and experiment

A theoretical investigation on the regio- and stereoselective outcomes of the hydroformylation reaction with an unmodified rhodium catalyst (H-Rh(CO)₃) was carried out at the B3LYP/SBK(d) level on related chiral olefins, namely (1-vinyloxy-ethyl)-benzene (1) and (1-methyl-but-3-enyl)-benzene (2). A thorough and computationally expensive examination of the various possible H-Rh(CO)₃-olefin complex intermediates was performed, in order to determine, interpret, and eventually predict, the regio- and diastereoselectivity of the aforementioned reactions, whose products are a mixture of the linear aldehyde and of two diastereomers of the branched aldehyde. Regio- and diastereoselectivity of the reaction have been experimentally determined via hydroformylation runs at 20° and 100 °C for 1 and at 20 °C for 2. The theoretical results obtained are in good agreement with the experimental ones, which put forward a high chiral discrimination for chiral vinyl ether substrates in contrast to the lack of regio- and diastereoselectivity observed in the hydroformylation of 2. For the hydroformylation of 1, a regioselectivity ratio (B:L) of 72:28 and a diastereoselectivity ratio (b:b^′) of 97:3 have been computed which compare well to the corresponding experimental results (85:15 and 88:12). Therefore, theoretical calculations can give reliable estimates of regio- and diastereoselectivity provided a careful and accurate surface scan is performed for the alkyl-rhodium intermediates and the reaction is carried out at room temperature and, hence, in the absence of branched to linear alkyl isomerization.     

Nucleophilic substitution at the anomeric position of 1,2-O-isopropylidenefuranose derivatives. A novel stereoselective synthesis of cyclic phosphates analogous to cAMP

1,2-O-Isopropylidenefuranose derivatives were treated with various nucleophiles in the presence of either BF(3).OEt(2) or trimethylsilyl trifluoromethanesulfonate (TMSOTf) leading to substitution products in a regio- and stereoselective manner. In particular, nucleophilic substitution of 1,2-O-isopropylidenefuranose derivatives when treated with allyltrimethylsilane was controlled by steric and electronic factors (similar to Woerpel's stereoelectronic model). On the other hand, when 1,2-O-isopropylidenefuranose derivatives were treated with trimethylsilane, in the presence of bis-O-trimethylsilyl-5-iodouracil or bis-O-trimethylsilyl-thymidine, substitution products were generated in high regio- and stereoselectivities via an unusual nucleophilic substitution with opening of the furanose ring. Based on these results, a stereoselective method for the synthesis of neutral cyclic phosphates analogous to cAMP was developed.     

Synthesis of novel 16-spiro steroids: 7-(Aryl)tetrahydro-1H-pyrrolo[1,2-c][1,3]thiazolo estrone hybrid heterocycles

The 1,3-dipolar cycloaddition of azomethine ylides generated in situ from the reaction of isatins or acenaphthylene-1,2-dione and 1,3-thiazolane-4-carboxylic acid to various exocyclic dipolarophiles synthesized from estrone afforded a library of novel C-16 spiro oxindole or acenaphthylene-1-one – 7-(aryl)tetrahydro-1H-pyrrolo[1,2-c][1,3]thiazole – estrone hybrid heterocycles. These reactions occur regio- and stereo-selectively affording a single isomer of the spiro estrones in excellent yields with the formation of two C–C and one C–N bonds along with the generation of four new contiguous stereo-centers in a single step.     

Isotopically sensitive regioselectivity in the oxidative deamination of a homologous series of diamines catalyzed by diamine oxidase.

The equivalence of aminomethylene groups in selected diamine substrates of diamine oxidase was exploited for the determination of intramolecular isotope effects. In the series of substrates, [1,1-2H2]-1,3-diaminopropane, [1,1-2H2]-1,5-diaminopentane, [1,1-2H2]-1,6-diaminohexane, [1,1-2H2]-1,7-diaminoheptane and [alpha,alpha-2H2]-4-(aminomethyl)benzylamine, the preference of the enzyme for reaction at the unlabeled methylene was found to vary from 1.45 to 10.5-fold. The observed partitioning ratios go through a minimum value with 1,5-diaminopentane, the best substrate of diamine oxidase of the compounds tested. The results suggest that fast substrates have less opportunity to reorient into alternate binding conformations while bound to the active site of the enzyme. On the other hand, diamine substrates tested that cannot exist in energetically favorable conformations with internitrogen distances of about 7-8 A showed larger intramolecular isotope effects.     

Synthesis and anti-proliferative activity of a small library of 7-substituted 5H-pyrrole [1,2-a][3,1]benzoxazin-5-one derivatives

In this study, we investigate the anti-proliferative activity of a small library of 7-substituted 5H-pyrrolo[1,2-a][3,1]benzoxazin-5-one derivatives, against a panel of human cancer cell lines. We reported the synthesis of these compounds in a previous work. 7-Bromo-5H-benzo[d]pyrrolo[2,1-b][1,3]oxazin-5-one showed a promising anti-proliferative effect. As starting material for Suzuki-Miyaura cross coupling reaction, it was selected for the design and the synthesis of six further derivatives, with the aim to better define structure-activity relationships. The anti-proliferative MTT assay revealed a dose-dependent reduction of cell viability, especially for 7-([1,1′-biphenyl]-4-yl)-5H-benzo[d]pyrrolo[2,1-b][1,3]oxazin-5-one. Cell cycle and western blotting analysis suggested apoptosis as possible mechanism for its anti-proliferative activity. These preliminary results encourage our interest for further optimizations.     

Computational prediction of the regio- and diastereoselectivity in a rhodium-catalyzed hydroformylation/cyclization domino process

The regioselectivity of the hydroformylation reaction of 2-methyl-3-(3-acetylpyrrol-1-yl)prop-1-ene catalyzed by an unmodified Rh catalyst has been investigated at the B3LYP/6-31G* level with Rh described by effective core potentials in the LANL2DZ valence basis set. Considering the population of all the H-Rh(CO)3-olefin transition state complexes, a regioselectivity ratio (B:L) of 12:88 has been obtained, in satisfactory agreement with the experiment producing the chiral linear aldehyde as the only product. The aldehyde, after complete diastereoselective cyclization, yields a 1:1 mixture of 1-acetyl-6R(S)-methyl-8R(S)-hydroxy-5,6,7,8-tetrahydroindolizine (having the same configuration on both stereogenic carbon atoms) and 2-acetyl-6-methyl-5,6-dihydroindolizine [Lett Org Chem (2006) 3:10-12]. The reason for such a high degree of diastereoselectivity has been elucidated examining the B3LYP/6-31G* potential energy surface for the reactions leading to the RR and RS diastereomers on a model system (without the acetyl substituent) and the actual compound. In the absence of a catalyst, a very high barrier is found along the reaction pathway, whereas spontaneous annulation occurs to a protonated pentahydroindolizine in the presence of H+. When a counterion (F-) is added, the proton on the newly formed tetrahedral carbon is abstracted, obtaining a structure closer to the final product (tetrahydroindolizine). Replacing H+ with Rh+, an initial adduct along the RS path much more favorable than any of those computed along the RR one is located because of the presence of the acetyl group. Tentative approaching paths obtained using [Rh(CO)3]+, bound to the aldehyde O, feature a higher barrier along the RS one, and offer a convincing explanation for the observed diastereoselectivity.     

Regio- and stereoselective enzymatic esterification of glycerol and its derivatives.

A methodology for regio- and stereoselective preparation of acyl glycerol derivatives is presented. It offers easy access to specific 1,2-, 1,3-diglycerides and triglycerides as well as alkyl glycerol esters, phospholipids and glycolipids. These compounds are prepared by esterification of the corresponding glycerol derivatives such as 2-monoglycerides, alkyl glycerols, glyceryl glycosides, glyceryl phosphate esters, or unsubstituted glycerol. The regio- and stereoselectivity in the esterification is achieved by using fatty acid anhydrides and an enzymatic catalyst, 1,3-specific lipase. NMR methods for determining the regio- and stereoselectivity of esterification are discussed.     

A facile 1,3-dipolar cycloaddition of azomethine ylides to 2-arylidene-1,3-indanediones: synthesis of dispiro-oxindolylpyrrolothiazoles and their antimycobacterial evaluation

A facile 1,3-dipolar cycloaddition of azomethine ylide generated in situ from the reaction of 1,3-thiazolane-4-carboxylic acid and isatin to 2-arylidene-1,3-indanediones furnished novel dispiro-oxindolylpyrrolothiazoles regio- and stereo-selectively in moderate to good yields (60-92%). In vitro antitubercular screening of 27 compounds against Mycobacterium tuberculosis H37Rv (MTB) disclosed that spiro[5.3']-5'-nitrooxindolespiro-[6.3″]-1H-inden-1″,3″(2H)-dione-7-(4-bromophenyl)tetrahydro-1H-pyrrolo[1,2-c][1,3]thiazole has the maximum potency with a minimum inhibitory concentration (MIC) of 1.4 μM against MTB, being 3.4 and 5.4 times more potent than ciprofloxacin and ethambutol, respectively.     

Density functional computations of Rh(I)-catalysed hydroacylation of acetic aldehyde and ethene

Density functional theory has been used to study Rh(I)-catalysed hydroacylation of acetic aldehyde and ethene. All the intermediates and the transition states were optimised completely at the B3LYP/6-311+ + G(d,p) level (LANL2DZ(d) for Rh, P). Calculation results confirm that Rh(I)-catalysed hydroacylation of acetic aldehyde and ethene is endothermic, and the total absorbed energy is about 47 kJ/mol. The hydroacylation involves four possible reaction channels, going mainly through Rh–ethene–aldehyde complexes, Rh–ethene–carbonyl complexes, Rh-ethanyl-carbonyl complexes, and Rh-ketone complexes. The formation of Rh–ethene–carbonyl complexes (i.e. Rh(I)-catalysed oxidative addition of aldehyde) is the rate-determinating step for the Rh(I)-catalysed hydroacylation. And the energy barriers of the H-transfer reaction are lower than those of the C–C bond-forming reaction, and thus the H-transfer reaction is prior to the C–C bond-forming reaction. Therefore, the dominant reaction channels predicted theoretically are the reaction channels “a” and “b”, which is well in agreement with the experiments.     

Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling

Soluble epoxide hydrolase (sEH) is an enzyme involved in drug metabolism that catalyzes the hydrolysis of epoxides to form their corresponding diols. sEH has a broad substrate range and shows high regio- and enantioselectivity for nucleophilic ring opening by Asp333. Epoxide hydrolases therefore have potential synthetic applications. We have used combined quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics (MD) simulations (at the AM1/CHARMM22 level) and high-level ab initio (SCS-MP2) QM/MM calculations to analyze the reactions, and determinants of selectivity, for two substrates: trans-stilbene oxide (t-SO) and trans-diphenylpropene oxide (t-DPPO). The calculated free energy barriers from the QM/MM (AM1/CHARMM22) umbrella sampling MD simulations show a lower barrier for phenyl attack in t-DPPO, compared with that for benzylic attack, in agreement with experiment. Activation barriers in agreement with experimental rate constants are obtained only with the highest level of QM theory (SCS-MP2) used. Our results show that the selectivity of the ring-opening reaction is influenced by several factors, including proximity to the nucleophile, electronic stabilization of the transition state, and hydrogen bonding to two active site tyrosine residues. The protonation state of His523 during nucleophilic attack has also been investigated, and our results show that the protonated form is most consistent with experimental findings. The work presented here illustrates how determinants of selectivity can be identified from QM/MM simulations. These insights may also provide useful information for the design of novel catalysts for use in the synthesis of enantiopure compounds.     

Theoretical study of the ligand-CYP2B4 complexes: effect of structure on binding free energies and heme spin state

The molecular origins of temperature-dependent ligand-binding affinities and ligand-induced heme spin state conversion have been investigated using free energy analysis and DFT calculations for substrates and inhibitors of cytochrome P450 2B4 (CYP2B4), employing models of CYP2B4 based on CYP2C5(3LVdH)/CYP2C9 crystal structures, and the results compared with experiment. DFT calculations indicate that large heme-ligand interactions (ca. -15 kcal/mol) are required for inducing a high to low spin heme transition, which is correlated with large molecular electrostatic potentials (approximately -45 kcal/mol) at the ligand heteroatom. While type II ligands often contain oxygen and nitrogen heteroatoms that ligate heme iron, DFT results indicate that BP and MF heme complexes, with weak substrate-heme interactions (ca. -2 kcal/mol), and modest MEPS minima (>-35 kcal/mol) are high spin. In contrast, heme complexes of the CYP2B4 inhibitor, 4PI, the product of benzphetamine metabolism, DMBP, and water are low spin, have substantial heme-ligand interaction energies (<-15 kcal/mol) and deep MEPS minima (<-45 kcal/mol) near their heteroatoms. MMPBSA analysis of MD trajectories were made to estimate binding free energies of these ligands at the heme binding site of CYP2B4. In order to initially assess the realism of this approach, the binding free energy of 4PI inhibitor was computed and found to be a reasonable agreement with experiment: -7.7 kcal/mol [-7.2 kcal/mol (experiment)]. BP was determined to be a good substrate [-6.3 kcal/mol (with heme-ligand water), -7.3 kcal/mol (without ligand water)/-5.8 kcal/mol (experiment)], whereas the binding of MF was negligible, with only marginal binding binding free energy of -1.7 kcal/mol with 2-MF bound [-3.8 kcal/mol (experiment)], both with and without retained heme-ligand water. Analysis of the free energy components reveal that hydrophobic/nonpolar contributions account for approximately 90% of the total binding free energy of these substrates and are the source of their differential and temperature-dependent CYP2B4 binding. The results indicate the underlying origins of the experimentally observed differential binding affinities of BP and MF, and indicate the plausibility of the use of models derived from moderate sequence identity templates in conjunction with approximate free energy methods in the estimation of ligand-P450 binding affinities.     

Formation of α-1,2- and α-1,3-linked mannose disaccharides from dolichyl mannosyl phosphate by rat liver membrane enzymes

Dolichyl mannosyl phosphate and GDPmannose were active substrates for the transfer of mannose to methyl-α-d-mannose, p-nitrophenyl-α-d-mannose, and free mannose with rat liver microsomal membranes. The products formed during dolichyl mannosyl phosphate incubation with methyl-α-d-mannose or with mannose were α-linked. The dissaccharides formed by incubation of dolichyl mannosyl phosphate or GDPmannose with mannose were identified by paper chromatography and electrophoresis as mannose-α-1,2-mannose and mannose-α-1,3-mannose. Synthesis of each product was dependent on the assay conditions used and was most markedly affected by the presence of detergent. Transfer of mannose from either substrate to form mannose-α-1,3-mannose was severely inhibited by Triton X-100.     

The application of dimethyldioxirane for the selective oxidation of polyfunctional steroids

Oxidation and epoxidation reactions of a series of structurally different steroids related to methyl 5 beta-cholanoates having hydroxyl groups and/or double bonds by treatment with dimethyldioxirane (DMDO) are described. Steroidal alcohols, olefines, and unsaturated alcohols and conjugated enones with DMDO were transformed into ketones, epoxides, and epoxy-ketones, respectively, in good isolated yields. The regio- and stereoselectivities for DMDO reaction differing from those observed for organic peracids, tert-butyl hydroperoxide and alkaline hydrogen peroxide are also discussed.     

Rhodium catalysts bound to functionalized mesoporous silica

Phosphine and amine functionalized mesoporous silica materials were metallated with Rh(CO)₂(i-Pr₂NH)Cl or Rh₂(CO)₄Cl₂, respectively, to yield catalysts containing the Rh(PPh₂R)₂(CO)Cl or Rh(CO)₂(NH₂R)Cl, where R is a propyl chain bonded to the silica surface, reactive centers. In order to ascertain the effect of pore size on rates of hydroformylation catalysis both 35 and 45 Å pore size materials were used. Using the hydroformylation of octene as a reference reaction, the phosphine based, 45 Å catalysts were 1.5-1.3 times faster than the amine based, 45 Å catalysts, and the 45 Å materials were 2.6-2.1 times faster than the 35 Å materials. The orientation of the catalyst relative to the functionalized surface, and the steric environment around the catalyst active site appear to be significant in determining rate of reaction. The ability of the surface bound phosphine catalysts to affect hydroformylation was strongly influenced by the steric constraints of the substrate. Terminal alkenes were readily hydroformylated and norbornene was slowly hydroformylated, but pinene, trans-cyclododecene, cyclohexene and cholesterol were nonreactive to the catalytic center.     

Mechanism of substrate dephosphorylation in low Mr protein tyrosine phosphatase.

Substrate dephosphorylation by the low molecular weight protein tyrosine phosphatases proceeds via nucleophilic substitution at the phosphorous atom yielding a cysteinyl phosphate intermediate. However, several questions regarding the exact reaction mechanism remain unanswered. Starting from the crystal structure of the enzyme we study the energetics of this reaction, using the empirical valence bond method in combination with molecular dynamics and free energy perturbation simulations. The free energy profiles of two mechanisms corresponding to different protonation states of the reacting groups are examined along stepwise and concerted pathways. The activation barriers calculated relative to the enzyme-substrate complex are very similar for both monoanionic and dianionic substrates, but taking the substrate binding step into account shows that hydrolysis of monoanionic substrates is strongly favored by the enzyme, because a dianionic substrate will not bind when the reacting cysteine is ionized. The calculated activation barrier for dephosphorylation of monoanionic phenyl phosphate according to this novel mechanism is 14 kcal mol(-1), which is in good agreement with experimental data. Proteins 1999;36:370-379.     

Purification and characterization of a new type of alpha-glucosidase from Paecilomyces lilacinus that has transglucosylation activity to produce alpha-1,3- and alpha-1,2-linked oligosaccharides

A fungus producing an alpha-glucosidase that synthesizes alpha-1,3- and alpha-1,2-linked glucooligosaccharides by transglucosylation was isolated and identified as Paecilomyces lilacinus. The cell-bound enzyme responsible for the synthesis was extracted by suspension of mycelia with 0.1 M phosphate buffer (pH 8.0), and the extract was purified. The molecular weight and the isoelectric point were estimated to be 54,000 and 9.1, respectively. The enzyme was most active at pH 5.0 and 65 degres C. The enzyme hydrolyzed maltose, nigerose, and kojibiose. The enzyme also hydrolyzed soluble starch and amylose with the rate toward maltose. p-Nitro-phenyl alpha-glucoside and isomaltose were not good substrates. The enzyme had high transglucosylation activity to synthesize oligosaccharides containing alpha-1,3- and alpha-1,2-linkages. At an early stage of the reaction, considerable maltotriose, 4-O-alpha-nigerosyl-D-glucose, and 4-O-alpha-kojibiosyl-D-glucose were synthesized. Afterwards, nigerose and kojibiose were accumulated gradually with glucose as an acceptor.     

Free energy calculations on binding and catalysis by alpha-lytic protease: the role of substrate size in the P1 pocket

We present free energy calculations using molecular dynamics on different substrates of alpha-lytic protease in the gas phase, in solution, while forming a noncovalent Michaelis complex with the enzyme, and in a tetrahedral structure representing a transition state/intermediate for acylation by the enzyme. Various P1 substrates were studied, with P1 = Gly, Ala, Val, and Leu. In qualitative agreement with experiment, the enzyme was calculated to bind and catalyze most effectively substrates with P1 = Ala over those with P1 = Gly, Val or Leu. Also, the calculated relative solvation free energies of Gly----Ala and Ala----Val were in qualitative agreement with experimental values in corresponding model systems. However, the level of quantitative agreement with experiment achieved in our earlier study of relative binding and catalysis of native subtilisin and an Asn-155----Ala mutant was not achieved. We surmise that this is due to the greater difficulty in quantitatively simulating effects that are predominantly van der Waals and hydrophobic compared to those that are hydrogen bonding/electrostatic.     

X-ray structures of 4-chlorocatechol 1,2-dioxygenase adducts with substituted catechols: New perspectives in the molecular basis of intradiol ring cleaving dioxygenases specificity

The crystallographic structures of 4-chlorocatechol 1,2-dioxygenase (4-CCD) complexes with 3,5-dichlorocatechol, protocatechuate (3,4-dihydroxybenzoate), hydroxyquinol (benzen-1,2,4-triol) and pyrogallol (benzen-1,2,3-triol), which act as substrates or inhibitors of the enzyme, have been determined and analyzed. 4-CCD from the Gram-positive bacterium Rhodococcus opacus 1CP is a Fe(III) ion containing enzyme specialized in the aerobic biodegradation of chlorocatechols.The structures of the 4-CCD complexes show that the catechols bind the catalytic iron ion in a bidentate mode displacing Tyr169 and the benzoate ion (found in the native enzyme structure) from the metal coordination sphere, as found in other adducts of intradiol dioxygenases with substrates. The analysis of the present structures allowed to identify the residues selectively involved in recognition of the diverse substrates.Furthermore the structural comparison with the corresponding complexes of catechol 1,2-dioxygenase from the same Rhodococcus strain (Rho-1,2-CTD) highlights significant differences in the binding of the tested catechols to the active site of the enzyme, particularly in the orientation of the aromatic ring substituents. As an example the 3-substituted catechols are bound with the substituent oriented towards the external part of the 4-CCD active site cavity, whereas in the Rho-1,2-CTD complexes the 3-substituents were placed in the internal position. The present crystallographic study shed light on the mechanism that allows substrate recognition inside this class of high specific enzymes involved in the biodegradation of recalcitrant pollutants.     

Density functional computations of Rh(I)-catalysed hydroacylation and hydrogenation of ethene using formic acid

The rhodium-catalysed hydroacylation of alkene is one of the most useful C–H bond activation processes. The C–C bond-forming reactions via C–H bond activation have extensively been the focus of study in the fields of organic and organometallic chemistry. In this work, density functional theory has been used to study Rh(I)-catalysed hydroacylation and hydrogenation of ethene with formic acid. All the intermediates and the transition states were optimised completely at the B3LYP/6-311++G(d,p) level (LANL2DZ(d) for Rh, P). Calculation results confirm that Rh(I)-catalysed hydroacylation of ethene is exothermic and the released Gibbs free energy is ? 60.39 kJ/mol. Rh(I)-catalysed hydrogenation of ethene is also exothermic and the released Gibbs free energy is ? 150.97 kJ/mol. Rh(I)-catalysed hydroacylation of ethene is the dominant reaction mode for Rh(I)-catalysed hydroacylation and hydrogenation of ethene with formic acid. In Rh(I)-catalysed hydroacylation of ethene, the H-transfer reaction is prior to the C–C bond-forming reaction. Therefore, the reaction mode ‘a’ (i.e. ca → M1 → TS1 → M2 → TS2a → M3a → TS3a → M4 → P1) is the dominant reaction pathway for Rh(I)-catalysed hydroacylation and hydrogenation of ethene. The theoretically predicted dominant product is propane acid.     

Analysis of functional coupling: mitochondrial creatine kinase and adenine nucleotide translocase

The mechanism of functional coupling between mitochondrial creatine kinase (MiCK) and adenine nucleotide translocase (ANT) in isolated heart mitochondria is analyzed. Two alternative mechanisms are studied: 1), dynamic compartmentation of ATP and ADP, which assumes the differences in concentrations of the substrates between intermembrane space and surrounding solution due to some diffusion restriction and 2), direct transfer of the substrates between MiCK and ANT. The mathematical models based on these possible mechanisms were composed and simulation results were compared with the available experimental data. The first model, based on a dynamic compartmentation mechanism, was not sufficient to reproduce the measured values of apparent dissociation constants of MiCK reaction coupled to oxidative phosphorylation. The second model, which assumes the direct transfer of substrates between MiCK and ANT, is shown to be in good agreement with experiments—i.e., the second model reproduced the measured constants and the estimated ADP flux, entering mitochondria after the MiCK reaction. This model is thermodynamically consistent, utilizing the free energy profiles of reactions. The analysis revealed the minimal changes in the free energy profile of the MiCK-ANT interaction required to reproduce the experimental data. A possible free energy profile of the coupled MiCK-ANT system is presented.