A computational study of conformational interconversions in 1,4-dithiacyclohexane (1,4-dithiane)

Ab initio molecular orbital theory with the 6-31G(d), 6-31G(d,p), 6-31+G(d), 6-31+G(d,p), 6-31+G(2d,p), 6-311G(d), 6-311G(d,p), and 6-311+G(2d,p) basis sets and density functional theory (BLYP, B3LYP, B3P86, B3PW91) have been used to locate transition states involved in the conformational interconversions of 1,4-dithiacyclohexane (1,4-dithiane) and to calculate the geometry optimized structures, relative energies, enthalpies, entropies, and free energies of the chair and twist conformers. In the chair and 1,4-twist conformers the C-Hax and C-Heq bond lengths are equal at each carbon, which suggest an absence of stereoelectronic hyperconjugative interactions involving carbon-hydrogen bonds. The 1,4-boat transition state structure was 9.53 to 10.5 kcal/mol higher in energy than the chair conformer and 4.75 to 5.82 kcal/mol higher in energy than the 1,4-twist conformer. Intrinsic reaction coordinate (IRC) calculations showed that the 1,4-boat transition state structure was the energy maximum in the interconversion of the enantiomers of the 1,4-twist conformer. The energy difference between the chair conformer and the 1,4-twist conformer was 4.85 kcal/mol and the chair-1,4-twist free energy difference (deltaG degrees (c-t)) was 4.93 kcal/mol at 298.15 K. Intrinsic reaction coordinate (IRC) calculations connected the transition state between the chair conformer and the 1,4-twist conformer. This transition state is 11.7 kcal/mol higher in energy than the chair conformer. The effects of basis sets on the 1,4-dithiane calculations and the relative energies of saturated and unsaturated six-membered dithianes and dioxanes are also discussed.     

Polymers and telomers of perfluoro-1,4-pentadiene

Perfluoro-1,4-pentadiene was prepared by pyrolysis of sodium 3,5,6-trichloroperfluorohexanoate and subsequent dehalogenation. The monomer was polymerized under a number of conditions of temperature and pressure using various periods and various dose rates of γ-ray initiation. The compound was found to undergo doublebond migration producing perfluoro-1,3-pentadiene. The polymer samples, some of them rubbery, others grainy, are assumed to be copolymers of the 1,4-pentadiene and the 1,3 pentadiene, the 1,4-diene polymerizing according to a cyclic mechanism and the 1,3-diene undergoing the 1,4-addition that is characteristic of butadienes under certain conditions. Infrared and nuclear magnetic resonance studies tend to support these assumptions. Under polymerization conditions the monomer also produced four distinct dimers and traces of two monomeric substances.     

A computational study to elucidate the extraordinary reactivity of three-membered heterocycles in nucleophilic substitution reactions

The accelerated rates of small-membered heterocycles relative to acyclic analogues are typically rationalized solely in terms of relief of ring strain. The relative rates of attack of ammonia on oxirane, oxetane, thiirane, and thietane were determined computationally in the gas phase at the MP2(Full)/6-31+G(d) level with respect to the model acyclic compounds methoxyethane and thiomethylethane. Because the cyclic ether and thioether pairs have very similar strain energies, they should react at similar rates by the S(N)2 mechanism if the degree of strain energy release in the transition state is approximately equal. The reactivity of the four-membered rings could be explained almost entirely by relief of strain. The three-membered rings reacted at rates at least 10(6) times faster than calculated from ring strain considerations alone. The electronic distribution of the transition states was determined using AIM methodology and found to indicate that bond cleavage was virtually complete, while bond formation was incomplete. Calculation of atomic charges by the Mulliken, AIM, CHELPG, and NBO methods indicated that positive charge at the reaction center was significantly lower for the three-membered rings than other members of the series. A simple electrostatic model identified differences in energy sufficient to account for the observed rate acceleration. The unique topological features of a three-membered ring make it possible for the partially negatively charged oxygen or sulfur to reduce the positive charge on the reaction center.     

A computational study on the energetics and reactivity of some xanthene and thioxanthene derivatives

A computational study has been carried out for xanthene and thioxanthene homologous derivatives with keto, hydroxyl, carboxyl, and carboxamide functional groups on position 9, contributing to the understanding of their energetics and reactivity. For that it is presented and compared with the molecular structures, the electrostatic potential energy maps, and the electronic properties of all these heteropolycyclic compounds. The estimation of the standard molar enthalpy of formation, in the gaseous phase, at T = 298.15 K, was made only for the thioxanthydrol, thioxanthene-9-carboxylic acid, and thioxanthene-9-carboxamide using the experimental values available in the literature for the homologous compounds containing oxygen.     

The polymerization of 1,4-pentadiene to [3.3.1]bicyclo-linked chains

1, 4-Pentadiene has been polymerized by Ziegler-Natta catalysts to give amorphous polymers which are up to 64 wt.-% soluble. The polymers all have residual unsaturation which is substantially less than one double bond per mer, some as low as 0.1 double bond per mer. The polymerizations proceed by an unusual double inter-, double intramolecular cyclopolymerization mechanism leading to the formation of [3.3.1] bicyclic repeat units. Some main-chain (internal) unsaturation as well as pendant-group (external) unsaturation is observed. The latter results from incompletely cyclized 1,4-pentadiene units. The former is due to some concurrent isomerization of 1,4- to 1,3 pentadiene, which then copolymerizes with the 1,4 diene. The extent of isomerization varied with the catalyst system used. The soluble polymer fractions were brittle for internal unsaturations of less than about 0.05 double bond per mer and were viscous for higher values. The insoluble fractions were brittle and are believed to be lightly crosslinked.     

Asymmetric radiation-induced inclusion polymerization of 3-methyl-1,4-pentadiene in deoxycholic acid

The radiation-induced polymerization of 3-methyl-1,3-pentadiene (3MPD) as an inclusion complex in deoxycholic acid (DOCA) has produced in good yield the optically active polymer poly(3-methyl-1,4-pentadiene) (P3MPD) whose structure and properties were studied by FT-IR spectroscopy and thermal analysis (TGA, DTG and DTA). The data show that the polymer is essentially trans-1,4-P3MPD as expected for the polymerization in constrained media. Trans-1,4-P3MPD is optically active with [α]_D values comprised between +4.3 and +5.6. The optical rotatory dispersion curve of the P3MPD is completely different from that of DOCA as expected.     

Versatile and cooperative reactivity of a triruthenium polyhydride cluster. A computational study

The reaction of a trinuclear polyhydride complex Ru3H5(C5H5)3 with cyclopentadiene, C5H6, has been studied computationally. A mechanism for the experimentally observed selective C-C bond activation is proposed. All three Ru centers participate in various steps of the mechanism. The catalytic involvement of two cluster hydrides in the transformation of the C5Hn fragment is emphasized.     

Calorimetric and computational study of 1,4-dithiacyclohexane 1,1-dioxide (1,4-dithiane sulfone)

This work reports the enthalpies of formation in the condensed and gas state of 1,4-dithiacyclohexane 1,1-dioxide (1,4-dithiane sulfone, 5), derived from the enthalpy of combustion in oxygen, measured by a rotating bomb calorimeter and the variation of vapor pressures with temperatures determined by the Knudsen effusion technique. The theoretically estimated enthalpy of formation was calculated from high-level ab initio molecular orbital calculations at the G2(MP2) level. The theoretical calculations appear to be in very good agreement with experiment. A comparison of the conversion of thiane sulfone 3 to 1,3-dithiane sulfone 4 and 1,4-dithiane sulfone 5 clearly shows the 1,3 isomer to be 6.7 kJ mol(-1) less stable, probably owing to diminished electrostatic repulsion between the sulfur heteroatoms in 1,4-sulfone 5.     

A computational foray into the formation and reactivity of metallabenzenes

Various metallabenzene complexes, analogues of benzene where one CH unit has been replaced by an organometallic fragment, have been reported in the literature. A detailed theoretical investigation on the chemistry of these complexes is presented here. This includes an evaluation of their aromaticity, the mechanisms of formation of osmium, iridium, and platinum metallabenzene complexes, and one intriguing aspect of their chemistry, the formation of cyclopentadienyl (Cp) complexes. X-ray photoelectron spectroscopy (XPS) measurements on two osmabenzene examples are also presented. In addition, diffuse functions for use with the SDD and SDB-cc-pVDZ basis set-RECP combinations are presented for the transition metals.     

A TRIR, TREPR and computational study on the reactivity and structure of the 2,2,2-trifluoroethoxycarbonyl radical

The 2,2,2-trifluoroethoxycarbonyl radical, 3b, has been generated by pulsed irradiation of 9-fluorenone oxime 2,2,2-trifluoroethyl oxalate 1b in carbon tetrachloride and acetonitrile solution. It was characterized by time-resolved electron paramagnetic resonance spectroscopy (EPR) and infrared spectroscopy. The radical has a lifetime in the range of microseconds and can be detected within the rise time of our time-resolved equipment before undergoing recombination or reactions with the solvent. No decarbonylation or decarboxylation was observed. In the presence of oxygen, the radical is quenched to yield the 2,2,2-trifluoroethoxycarbonylperoxy radical 4b, which has again a lifetime in the range of several microseconds. Time-resolved electron paramagnetic resonance spectroscopy (TREPR) allowed for the detection of a 1 : 1 : 1 triplet of the fluorene-9-iminyl radical 7 at g = 2.0032 and a 1 : 3 : 3 : 1 quartet with additional hyperfine splitting (HFS) due to proton coupling at g = 2.001 for the trifluoroethoxycarbonyl radical 3b. Calculations indicate that alkoxycarbonyl radicals can exist in conformations that are s-trans or s-cis with respect to the R-O-C(O) x dihedral. A comparison of experimental TREPR spectra with simulations indicates that the s-trans conformer is observed in the case of the ethoxycarbonyl radical, 3a. In the case of the trifluorethoxycarbonyl radical, 3b, however, the additional proton HFS observed shows that it is the s-cis conformer that is formed. As calculations give evidence for a fairly high activation enthalpy for s-cis-s-trans interconversion of alkoxycarbonyl radicals, this discrepancy is likely due to differing conformational preferences of the precursor molecules.     

Mechanism and reactivity of rhodium-catalyzed intermolecular [5 + 1] cycloaddition of 3-acyloxy-1,4-enyne (ACE) and CO: A computational study

The first theoretical study on the mechanism of [RhCl(CO)2]2-catalyzed [5 + 1] cycloadditions of 3-acyloxy-1,4-enyne (ACE) and CO has been performed using density functional theory (DFT) calculations. The effect of ester on reactivity of this reaction has been investigated. The computational results have revealed that the preferred catalytic cycle involves the sequential steps of 1,2-acyloxy migration, CO insertion, reductive elimination to form ketene intermediate, 6π-electroncyclization, and aromatization to afford the resorcinol product. The 1,2-acyloxy migration is found to be the rate-determining step of the catalytic cycle. The electron-rich p-dimethylaminobenzoate substrate promotes 1,2-acyloxy migration and significantly increases the reactivity by stabilizing the positive charge building up in the oxocyclic transition state.     

Calorimetric and computational study of 1,3- and 1,4-oxathiane sulfones

The enthalpies of formation in the condensed and gas states, DeltafH degrees m(cd) and DeltafH degrees m(g), of 1,3- and 1,4-oxathiane sulfones were derived from their respective enthalpies of combustion in oxygen, measured by a rotating bomb calorimeter and the variation of vapor pressures with temperatures determined by the Knudsen effusion technique. Standard ab initio molecular orbital calculations at the G2(MP2) and G3 levels were performed, and a theoretical study on molecular and electronic structure of the compounds has been carried out. Calculated DeltafH degrees m(g) values at the G3 level using atomization reactions agree well with the experimental ones. These experimental and theoretical studies support that the destabilization found in 1,3-oxathiane sulfone, 11.2 kJ mol-1 respecting to 1,4-oxathiane sulfone, is due to the electrostatic repulsion between the negative charges of the axial oxygen of the sulfone and the oxygen of the ring and apparently masks any stabilization originating from the hyperconjugative nO --> sigma*C-SO2 stereoelectronic interaction.     

Pyrene fluorescence quenching and triplet-state formation in the presence of DABCO (1,4-Diazabicyclo[2-2-2]octane): A laser photolysis study

In this paper, we present a study of fluorescence quenching of pyrene by DABCO in cyclohexane solutions. The absorption spectra of pyrene singlet state ¹S-ⁿS have been measured in the presence and in the absence of DABCO; the spectra are practically identical. The de-excitation of singlet pyrene by DABCO seems to be a non-reversible process leading to the triplet state, the probability of formation of this triplet state being near unity in the quenching process.     

Predicting reactivity and stereoselectivity in the Nazarov reaction: a combined computational and experimental study

The Nazarov reaction of pentadienyl cations generated by protonation of either dienones or alkoxytrienes has been examined in detail both experimentally and by DFT calculations. In particular, calculations at the B3LYP/6‐311G** level of theory accurately predicted, and accounted for, the outcome of the Brønsted acid catalyzed electrocyclization of 4π‐electron systems in which one of the double bonds involved in the process was embedded in N‐ and S‐heterocyclic rings. Calculations showed that both heteroatoms are capable of accelerating the ring closure by stabilizing the partial positive charge which develops at C‐6 (C‐2) in the transition state, with S‐heterocyclic derivatives being more reactive than the corresponding N‐containing compounds. In general, pentadienyl cations generated by protonation of alkoxytrienes were expected to react faster than those obtained by protonation of the corresponding dienones, as the latter were stabilized by a hydrogen bond. The presence of a substituent on the heterocyclic ring significantly affects the stereoselectivity (torquoselectivity) only in the case of the N‐heterocyclic derivatives, in which a 2‐alkyl group is axially oriented, providing the cis‐2,5‐disubstituted isomer only. Instead, with substituted S‐heterocyclic compounds, the anticipated torquoselectivity was very low and, in fact, a 3:1 diastereomeric mixture between the trans and cis products was experimentally found after ring closure. For this study, the synthesis of the appropriate N‐ and S‐containing dienones and alkoxytrienes was realized to evaluate the predictivity power of the DFT computations, which was very good in all of the cases examined, both in terms of reactivity and stereoselectivity. The consistency observed between computational and experimental results, therefore, shows the usefulness of DFT calculations at the B3LYP/6‐311G** level of theory as a robust instrument for the prediction of reactivity and stereoselectivity in the Nazarov electrocyclic reaction.     

A theoretical study of the photolytic decomposition of ethane ethylene via a triplet-state ethylidene intermediate

The complete geometrically optimized triplet state of ethane, using the MINDO/2 method, spontaneously dissociates into CH₃H; and H₂. The reaction paths for rearrangement of CH₃CH: to CH₂CH₂ in the triplet state is calculated. The activation energy was determined to be 19.4 kcal/mole. These results are discussed in the context of previously reported experimental results for the gas phase photolyses of alkanes.     

Factors controlling the reactivity of zinc finger cores

Although the Zn(2+) cation in Zn·Cys(4), Zn·Cys(3)His, Zn·Cys(2)His(2), and Zn(2)Cys(6) cores of zinc finger (Zf) proteins typically plays a structural role, the Zn-bound thiolates in some Zf cores are reactive. Such labile Zf cores can serve as drug targets for retroviral or cancer therapies. Previous studies showed that the reactivity of a Zn-bound thiolate toward electrophiles is significantly reduced if it forms S---NH hydrogen bonds with the backbone amide. However, we found several well-known inactive Zf cores containing Cys ligands with no H-bonding interactions. Here, we show that H bonds from the peptide backbone or bonds from a second Zn cation to Zn-bound S atoms suppress the reactivity not only of these S atoms, but also of Zn-bound S* atoms with no interactions. Indeed, two or more indirect NH---S hydrogen bonds raise the free energy barrier for methylation of a Zn-bound S* in a Cys(4) core more than a direct NH---S* hydrogen bond. These findings help to elucidate why several well-known Zf cores have Cys ligands with no H bonds, but are unreactive. They also help to provide guidelines for distinguishing labile Cys-rich Zn sites from structural ones, which in turn help to identify novel potential Zf drug targets.