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.     

QM/MM study of the active site of free papain and of the NMA-papain complex.

Hybrid quantum mechanical/molecular mechanical (QM/MM) calculations using restricted and unrestricted Hartree-Fock and B3LYP ab initio (QM) and Amber force field (MM), respectively, have been applied to study the catalytic site of papain in both free and substrate bonded forms. Ab initio geometry optimizations have been performed for the active site of papain and the N-methyl-acetamide (NMA)-papain complex within the molecular mechanical treatment of the protein environment. A covalent tetrahedral intermediate structure could be obtained only when the amide N atom of the substrate molecule was protonated through a proton transfer from the His-159 in the catalytic site. Our results support the previous assumption that a proton transfer from His-159 to the amide N atom of the substrate occurs prior to or concerted with the nucleophilic attack of the Cys-25 sulfur atom to the carbonyl group of the substrate. The electron correlation effect will reduce the proton transfer barrier. Therefore, this proton transfer can be easily observed in the B3LYP/6-31G* calculations. The HF/6-31G* method overestimates the reaction barrier against this proton transfer. The sulfur atom of Cys-25 and the imidazole ring of His-159 are found to be coplanar in the free form of the enzyme. However, the rotation of the imidazole ring of His-159 was observed during the formation of the tetrahedral intermediate. Without the papain environment, the coplanar thiolate-imidazolium ion pair RS-...ImH+ is much less stable than the neutral form of RSH....Im. Within the protein environment, however, the thiolate-imidazolium ion pair becomes more stable than its neutral form by 4.1 and 0.4 kcal/mol in HF/6-31G* and B3LYP/6-31G* calculations, respectively. The barrier of proton transfer from S-H group of Cys-25 to the imidazole ring of His-159 was reduced from 22.0 kcal/mol to 15.2 kcal/mol by the protein environment in HF/6-31G* calculations. This barrier is found to be much smaller (2.5 kcal/mol) in B3LYP/6-31G* calculations.     

A computer-aided quantum chemical study of the N<Stack><Subscript>15</Subscript><Superscript>−</Superscript></Stack> cluster

Ab initio (RHF, MP2) and Density Functional Theory (DFT) methods have been used to examine six isomers of the N15m cluster with the 6-31+G* basis set. Different from the known odd-numbered anionic N7m, N9m, and N11m clusters, in which the open-chain structures are the most stable species, the most stable N15m isomer is structure 1 (C1), which may be considered as a complex between the fragments cyclic N5m (D5h) and staggered N10 (D2d). The decomposition pathways of structure 2 (CS), containing two aromatic N5 rings connected by a N5 chain, and the open-chain structure 3 (C2v) were studied at the B3LYP/6-31+G* level of theory. Relative energies were refined at the level of B3LYP/6-311+G(3df,2p)//B3LYP/6-31+G*+ZPE (B3LYP/6-31+G*). The barriers for N2 and N5m (D5h) fission reactions for structure 2 are predicted to be 18.2 and 14.2 kcal x mol(-1), respectively. The corresponding N2+N3m fission barrier for structure 3 is predicted to be 11.2 kcal x mol(-1). Supplementary material is available for this article if you access the article at http://dx.doi.org/10.1007/s00894-003-0118-0. A link in the frame on the left on that page takes you directly to the supplementary material. Figure Structure 1 of the N15m cluster, showing bond distances in A and bond angles in degrees     

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.     

Reactions of 2-thiopyridone and related N-, S- and C-methylated derivatives with [Rh2Cl2(CO)4]: crystal and molecular structure of fac-[Rh(MeC5H3NS)3] containing 6-methyl-2-thiopyridonato ligands

[Rh₂Cl₂(CO)₄] reacts with the ligands L (2-pyridone, 2-thiopyridone, and the isomers 6-methyl-2-thiopyridone, 2-methylmercaptopyridine, and N-methylthiopyridone) to give initially, when L/Rh = 1, the bridged-cleaved compounds cis- [RhCl(CO)₂L]. Further additions of 2-methyl- mercaptopyridine, N-methylthiopyridone, or 2-pyridone caused no further change, but 2- thiopyridone and 6-methyl-2-thiopyridone gave new cis-dicarbonyl species (L/Rh = 2) and eventually monocarbonyl species (L/Rh > 3). All these solutions are air-sensitive and air oxidation of a solution of [Rh₂Cl₂(CO)₄] with an excess of 6-methyl-2- thiopyridone gave fac-[Rh(MeC₅H₃NS)₃] the X-ray structure of which shows three equivalent chelating 6-methyl-2-thiopyridonato ligands.     

Configurational stability of chiral lithiated cyclopropylnitriles: a density functional study

Chiral, configurationally stable lithiated nitriles would be valuable intermediates for asymmetric carbon-carbon bond-forming reactions. To gain insight into the design of such species, Walborsky's attempted enantioselective deprotonation/trapping reactions of a chiral cyclopropylnitrile were studied computationally up to the MP2(fc)/6-31+G* and B3LYP/6-31+G* levels. Investigation of cyclopropylnitrile/LiNH(2) deprotonation transition structures demonstrated a significant (20-23 kcal/mol) kinetic preference for N-lithiation, and a facile (4-6 kcal/mol barrier) "conducted tour" racemization pathway for the N-lithiated nitrile product. Addition of a model directing group (formyl) to the beta-carbon of the cyclopropyl ring is predicted to significantly favor C-lithiation over N-lithiation, both kinetically and thermodynamically. Thus, chiral beta-Lewis base substituted cyclopropylnitriles may serve as precursors to chiral, configurationally stable organolithium reagents.     

Density functional studies of the substituent effect on absorption and emission properties of 1, 8-naphthalimide derivatives

Using TD-PBE1PBE/6-31G* and TD-B3LYP/6-31G* approaches, we calculated the absorption and emission spectra of 1,8-naphthalmide derivatives in gas-phase. The geometric structures optimized by HF/6-31G* and B3LYP/6-31G* models and the absorption and emission maxima were in good agreement with existed experimental measurements. It was also found that the lowest singlet states corresponded mainly to the electronic transition from the highest occupied orbital (HOMO) to the lowest unoccupied molecular orbital (LUMO). Intramolecular charge transfer occurred between substituents and naphthalimic rings. Study also showed that most compounds with low absorption excitation energies had low vertical ionization potentials. Finally, the delocalization electronic energies between substituents and naphthalimic rings of isomers were investigated to obtain further sight into their stability.     

Polaron binding energy in polymers: poly[methyl(phenyl)silylene]

This paper presents a theoretical approach to the evaluation of polaron binding energy in polymers. Quantum chemical calculations were performed on a model polymer, poly[methyl(phenyl)silylene], employing the B3LYP and CAM-B3LYP method. The polaron binding energy consists of two terms: the molecular deformation energy and electron-phonon term. Its value was found to be about 0.23 eV at the CAM-B3LYP/6-31G* level of theory.     

Syntheses of Terpenes by the Condensation of Aliphatic Compounds

Treatment of mesityloxide with basic condensing agents resulted in formation of isoxylitones-A, B, C and D and isophorone. These compounds were purely isolated and assigned their structures from spectroscopic and chemical evidences. Isoxylitone-A and isoxylitone-B were conformers of 1-acetyl-2, 4, 6, 6-tetramethyl-1, 3-cyclohexadiene separated by the rotational barrier of acetyl group and interconversional barrier of cyclohexadiene ring. Isoxylitone-C was 4-isopropenyl-1, 5, 5-trimethyl-1-cyclohexen-3-one. Isoxylitone-D was 5, 5-dimethyl-3-(1-isobutenyl)-2-cyclohexen-1-one.     

QM/MM study of energy storage and molecular rearrangements due to the primary event in vision

The energy storage and the molecular rearrangements due to the primary photochemical event in rhodopsin are investigated by using quantum mechanics/molecular mechanics hybrid methods in conjunction with high-resolution structural data of bovine visual rhodopsin. The analysis of the reactant and product molecular structures reveals the energy storage mechanism as determined by the detailed molecular rearrangements of the retinyl chromophore, including rotation of the (C11-C12) dihedral angle from -11 degrees in the 11-cis isomer to -161 degrees in the all-trans product, where the preferential sense of rotation is determined by the steric interactions between Ala-117 and the polyene chain at the C13 position, torsion of the polyene chain due to steric constraints in the binding pocket, and stretching of the salt bridge between the protonated Schiff base and the Glu-113 counterion by reorientation of the polarized bonds that localize the net positive charge at the Schiff-base linkage. The energy storage, computed at the ONIOM electronic-embedding approach (B3LYP/6-31G*:AMBER) level of theory and the S0-->S1 electronic-excitation energies for the dark and product states, obtained at the ONIOM electronic-embedding approach (TD-B3LYP/6-31G*//B3LYP/6-31G*:AMBER) level of theory, are in very good agreement with experimental data. These results are particularly relevant to the development of a first-principles understanding of the structure-function relations in prototypical G-protein-coupled receptors.     

Computational prediction of selectivities in nonreversible and reversible hydroformylation reactions catalyzed by unmodified rhodium-carbonyls

The regio- and stereoselectivities of the hydroformylation reaction catalyzed by an unmodified Rh catalyst have been investigated at the B3P86/6-31G* level with Rh described by effective core potentials in the LANL2DZ valence basis set for a number of either mono- or (1,1-, 1,2-, 1,3-) di-substituted substrates and compared with a variety of earlier results of ours, supplemented with free energy results when not already available. The computational prediction of regio- and stereoselectivities in nonreversible hydroformylations performed under mild reaction conditions is seemingly possible provided a careful conformational search for TS structures is carried out and all the low energy conformers are taken into account. The internal energy can be used to compute both the regio- and stereoselectivities in the hydroformylation of 1,1- and 1,3-substituted substrates with satisfactory results, whereas for 1,2-substituted substrates the regioselectivity determined from the internal energy is in good agreement with the experiment in the case of aliphatic olefins just for the lowest terms in the series (i.e., methyl and ethyl substituents), while the ratios are only qualitatively correct for the slightly bulkier iso-propyl and tert-butyl moieties. The theory/experiment agreement becomes decidedly better using the free energy differences instead.     

Density functional computations of enantioselective alkynylation of aldehyde catalyzed by chiral zinc(II)-complexes

The enantioselective alkynylation of aldehyde catalyzed by chiral zinc(II)-complexes was studied by means of the density functional theory (DFT). All the structures were optimized completely at the B3LYP/6-31G(d,p) level. To obtain more exact energies, single-point energy calculations at B3LYP/6-31+G(d,p) level were carried out on the B3LYP/6-31G(d,p) geometries. As shown, this enantioselective alkynylation was endothermic. The chirality-determining step for the alkynylation was the formation of the catalyst–ethanol complexes and the transition states for this step involved a six-membered ring. The dominant products predicted theoretically were of (R)-chirality, in good agreement with experiment.      

Synthetic and quantum chemical study on the regioselective addition of amines to methyl maleamate

Synthetic and theoretical studies were performed to gain insight into the regioselectivity in the mechanism of aspartyl-isoaspartyl formation, modeled by additions of ammonia and primary amines to methyl maleamate. Reactions between maleamate and aliphatic, araliphatic amines or O-methyl acetimidate lead to the formation of N-substituted isoasparaginates. The size of the amine and the activating effect of the amide and ester group on the double bond are the determining factors of the site of addition. The formation of both isomers was observed only in the case of ammonia addition. The regioselectivity was predicted on the basis of the charge distribution for low-energy methyl maleamate conformers, calculated at the B3LYP/6-311++G(2df,2pd)//B3LYP/6-31+G(d) level, both in gas phase and in methanol. The methyl isoasparaginate over methyl asparaginate product ratio was computed based on the free energy Boltzmann distribution of their conformers. The calculated 2 : 1 ratio is in agreement with the experimental regioselectivity of the addition of nitrogen nucleophiles.

Structural and electronic properties of 4H-cyclopenta[2,1-b,3;4-b′]dithiophene S-oxide (BTO) derivatives with an S, S=O, O, SiH2, or BH2 bridge: semi-empirical and DFT study

In this paper, we theoretically studied the geometries, stabilities, and the electronic and thermodynamic properties of 4H-cyclopenta[2,1-b,3;4-b']dithiopene S-oxide derivatives (BTO-X, with X = BH(2), SiH(2), S, S=O, or O) using semi-empirical methods, ab initio methods, and density functional theory. The geometries and thermodynamic parameters calculated by PM3 were in good agreement with those calculated with B3LYP/6-31 G*. The band gap calculated using B3LYP/6-31 G* ranged from 3.94 eV (BTO-O) to 3.16 eV (BTO-B). The absorption λ(max) calculated using B3LYP/6-31 G* was shifted to longer wavelengths when X = BH(2), SiH(2), or S=O (due to their electron-withdrawing effects) and to shorter wavelengths for BTO-S and BTO-O as compared to the λ(max) for the thiophene S-oxide (2TO) dimer. The changes in ΔH°, ΔS°, and ΔG° calculated using both semi-empirical and DFT methods were quite similar.     

ONIOM DFT/PM3 calculation on the interaction between STI-571 and abelson tyrosine kinase

The ONIOM2 (B3LYP/6–31G (d, p): PM3) and B3LYP/6–31G (d, p) methods were applied to investigate the interaction between STI-571 and abelson tyrosine kinase binding site. The complex of N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)- phenyl]-benzamide (part of STI-571) and related 16 amino acid residues were found at B3LYP/6–31G (d, p) level to have hydrogen bonds and π....π stacking interaction, their binding energy via HAF optimization was −20.4 kcal mol⁻¹. The results derived from this study agreed well with the reported observation. Figure Optimized structure of STI-571 and Thr315 in abelson tyrosine kinase based on ONIOM2 method     

A Comparative Semiempirical, Ab initio and DFT Study of Decarbonylation of Cyclic Ketones Part 1: Thermal Fragmentation of Cyclopropanone

Calculations using different quantum mechanical methods including semiempirical (MNDO,AM1 and PM3), ab initio (RHF and MP2 calculations using the 6-311G and 6-311++G^** basis sets), and density functional theory (LSDA, BP, MIXBP and B3LYP, i.e., B3LYP/6-311+G**//B3LYP/6-31G*) have been performed on the thermal fragmentation of cyclopropanone to ethylene and carbon monoxide. All RHF calculations predict a concerted single step mechanism for this conversion. The estimated activation energies vary from 34.4 to 54.6 kcal·mol^-1, mainly localized around 37±2 kcal·mol^-1, depending on the method. Whereas the calculated RHF reaction energies also varied from 14.5 to -33.3 kcal·mol^-1, the B3LYP/6-311+G**//B3LYP/6-31G* method predicts the experimental value (-17.7 kcal·mol^-1) within experimental uncertainties. Remarkably, semiempirical AM1 and PM3 methods and simple DFT calculations, LSDA, predict comparable results to the more advanced methods. UHF ab initio calculations predict the same single step mechanism, whereas a multistep biradical mechanism with an unrealistically low activation energy is favored by the semiempirical methods. Structures of the activated complex of the single step mechanism, estimated by different methods, are very similar and consistent with a nonlinear cheletropic [_2s + _2a] reaction, as predicted by the orbital symmetry rules and earlier EHT calculations.Electronic Supplementary Material available.     

An ONIOM investigation on anion recognition of alkali–metal complexes with diurea calix[4]arene receptor

The ONIOM(B3LYP/6-31G(d):AM1) optimized structures of complexes of diurea calix[4]arene receptor (L) with alkali metals Li(+), Na(+) and K(+) and their complexes with halide ions F(-), Cl(-), Br(-), oxygen-containing anions HCO(3)(-), HSO(4)(-) and CH(3)COO(-) ions were obtained. Binding energies and thermodynamic properties of complex receptors LiL(+), NaL(+) and KL(+) with these anions were determined. The binding stabilities according to binding energies of LiL(+), NaL(+) and KL(+) associated with anions computed either at the ZPVE-corrected ONIOM(B3LYP/6-31G(d):AM1) or BSSE-corrected B3LYP/6-31 + G(d,p)//ONIOM(B3LYP/6-31G(d):AM1) are in the same order: F(-) > CH(3)COO(-) ≈ HCO(3)(-) > Br(-) ≈ HSO(4)(-) ≈ Cl(-). All the receptors LiL(+), NaL(+) and KL(+) were found to be selective toward fluoride ion.     

Racemization of the gastrointestinal antisecretory chiral drug esomeprazole magnesium via the pyramidal inversion mechanism: A theoretical study

The pyramidal inversion mechanisms of the 6‐methoxy and the 5‐methoxy tautomers of (S)‐omeprazole were studied, employing ab initio and DFT methods. The conformational space of the model molecule (S)‐2‐[(3‐methyl‐2‐pyridinyl)methyl]sulfinyl‐1H‐benzimidazole was calculated, with respect to rotations around single bonds, at the B3LYP/6‐311G(d,p) level. All of the resulting conformations were used as starting points for full optimizations of (S)‐omeprazole, at B3LYP/6‐31G(d), B3LYP/6‐311G(d,p), B3LYP/6‐311++G(d,p), B3LYP/6‐311G(2df,2pd), MP2/6‐31G(d), and MP2/6‐311G(d,p) levels. Four distinct pathways were found for enantiomerization via the pyramidal inversion mechanism for each of the tautomers of (S)‐omeprazole. Each transition state, in which the sulfur, the oxygen and the two carbon atoms connected directly to the sulfur are in one plane, connects two diastereomeric minima. The enantiomerization is completed by free rotation around the sulfur–methylene bond, and around the methylene–pyridine ring bond. The effective Gibbs' free energy barrier for racemization ΔG of the two tautomers of (S)‐omeprazole are 39.8 kcal/mol (5‐methoxy tautomer) and 40.0 kcal/mol (6‐methoxy tautomer), indicating that the enantiomers of omeprazole are stable at room temperature (in the gas phase). The 5‐methoxy tautomer of (S)‐omeprazole was found to be slightly more stable than the 6‐methoxy tautomer, in the gas phase. The energy barrier (ΔG^?) for the(S,M) (S,P) diastereomerization of (S)‐omeprazole due to the rotation around the pyridine chiral axis was very low, 5.8 kcal/mole at B3LYP/6‐311G(d,p). Chirality 2010. © 2010 Wiley‐Liss, Inc.     

Further phloroglucinol derivatives in the fruits of Mallotus japonicus

Two new rottlerin-like phloroglucinol derivatives were detected from the fruits of Mallotus japonicus and identified as 3-(3,3-dimethylallyl)-5-(3-acetyl-2,4-dihydroxy-5-methyl-6-methoxybenzyl)-phlorobutyrophenone and -phloroisobutyrophenone by spectral studies. 2,6-Dihydroxy-3-methyl-4-methoxyacetophenone was also isolated