Which is more likely in trichodiene biosynthesis: hydride or proton transfer?

The mechanisms proposed for enzyme-catalyzed formation of the sesquiterpene natural product trichodiene consistently include a step involving a 1,4-hydride transfer. Using quantum chemical methods (B3LYP/6-31+G(d,p) and mPW1PW91/6-31+G(d,p)), we discovered two alternative pathways for transformation of the intermediate bisabolyl cation to the cuprenyl cation, one of which--a proton-transfer pathway--appears to be much more energetically favorable (by more than 10 kcal/mol) than the hydride transfer pathways usually proposed.     

Hydrodynamics and microphase ordering in block copolymers: are hydrodynamics required for ordered phases with periodicity in more than one dimension?

We use Brownian dynamics (BD), molecular dynamics, and dissipative particle dynamics to study the phase behavior of diblock copolymer melts and to determine if hydrodynamics is required in the formation of phases with greater than one-dimensional periodicity. We present a phase diagram for diblock copolymers predicted by BD and provide a relationship between the inverse dimensionless temperature epsilon/k(B)T and the Flory-Huggins chi parameter, allowing for a quantitative comparison between methods and to mean field predictions. Our results concerning phase behavior are in good qualitative agreement with the theoretical predictions of Matsen and Bates [M. W. Matsen and F. S. Bates, Macromolecules 29, 1091 (1996)]; however, fluctuation effects arising from finite polymer lengths substantially alter the phase boundaries. Our results pertaining to the hydrodynamics are in contrast to earlier work by Groot et al. [R. D. Groot, T. J. Madden, and D. J. Tildesley, J. Chem. Phys. 110, 9739 (1999); D. Frenkel and B. Smit, Understanding Molecular Simulation, 2nd ed. (Academic, New York, 2001)]. In particular, we obtain the hexagonal ordered cylinder phase with BD, a method that does not include hydrodynamics.     

Anion plays a more important role than cation in affecting gas hydrate stability in electrolyte solution? — a recognition from experimental results

An interesting phenomenon that cation and anion play different roles in inhibiting hydrate formation in electrolyte solution has been recognized from experimental results: gas hydrate stability condition in electrolyte solution is mainly determined by anion but comparatively few by cation. This difference is qualitatively attributed to the difference of cation and anion in affecting the ambient water networks due to their hydration characteristics in electrolyte solution, although more researches is needed to verify the phenomenon and understand its mechanism.     

Is vanadium a more versatile target in the activity of primordial life forms than hitherto anticipated?

The two predominant forms of vanadium occurring in the geo-, aqua- and biosphere, soluble vanadate(V) and insoluble oxovanadium(IV) (vanadyl), are subject to bacterial activity and transformation. Bacteria belonging to genera such as Shewanella, Pseudomonas and Geobacter can use vanadate as a primary electron acceptor in dissimilation or respiration, an important issue in the context of biomineralisation and soil detoxification. Azotobacter, which can employ vanadium as an essential element in nitrogen fixation, secretes a vanadophore which enables the uptake of vanadium(V). Siderophores secreted by other bacteria competitively (to ferric iron) take up vanadyl and thus interfere with iron supply, resulting in bacteriostasis. The halo-alkaliphilic Thioalkalivibrio nitratireducens possibly uses vanadium as a constituent of an alternative, molybdopterin-free nitrate reductase. Marine macro-algae can generate a variety of halogenated organic compounds by use of vanadate-dependent haloperoxidases, and a molecular vanadium compound, amavadin, from Amanita mushrooms has turned out to be an efficient catalyst in oxidation reactions. The present account is a focused and critical review of the current knowledge of the interplay of bacteria and other primitive forms of life (cyanobacteria, algae, fungi and lichens) with vanadium, with the aim to provide perspectives for applications and further investigations.     

Are stone-wales defect sites always more reactive than perfect sites in the sidewalls of single-wall carbon nanotubes?

Density functional computations show, in contrast to general assumptions, that the reactions at the 7-7 ring fusions of Stone-Wales defects in the sidewalls of armchair (5,5) single-wall carbon nanotubes are much less exothermic than reactions at perfect sites. In addition, the peripheral 5-6 and 6-7 ring fusions of the defect are much more reactive.     

A study of anhydrocelluloses--is a cellulose structure with residues in a 1C4-conformation more prone to hydrolysis?

A study of the effect of introduction of 3,6-anhydroglucose residues in the cellulose structure on glycoside hydrolysis rate was performed. A cellotetrose with an 3,6-anhydroglucose as the third residue was synthesised. Acidic hydrolysis of this tetrasaccharide showed that hydrolysis of the 3,6-anhydro-β-D-glucoside linkage was 31.400 times faster than hydrolysis of cellobiose. A series of different 3,6-anhydrocelluloses with different degree of substitution were prepared by tosylation of cellulose with varying amounts of tosyl chloride in dimethylacetamide and subsequent treatment with sodium hydroxide. Anhydrocelluloses with degrees of substitution of 0.02, 0.07, 0.31 and 0.74 were obtained. The anhydrocelluloses were subjected to acidic hydrolysis in 2.0 M aqueous HCl and the rate of hydrolysis monitored by ion chromatography analysis of the amount of glucose and/or cellobiose formed. All 3,6-anhydrocelluloses hydrolyzed with a faster rate than cellulose, but the anhydrocellulose with a low degree of substitution (ds = 0.07) hydrolyzed fastest which was 90 times faster than cellulose.     

Synthesis and NMR spectroscopic conformational analysis of esters of 4-hydroxy-cyclohexanone—the more polar the molecule the more stable the axial conformer

The esters of 4-hydroxy-cyclohexanone and a series of carboxylic acids R–COOH with R of different electronic and steric influence (R=Me, Et, n-Pr, i-Pr, n-Bu, i-Bu, sec-Bu, t-Bu, CF₃, CH₂Cl, CHCl₂, CCl₃, CH₂Br, CHBr₂, and CBr₃) were synthesized and the conformational equilibria studied by ¹H and ¹³C NMR spectroscopy at 103 K and at 295 K, respectively. The geometry of optimized structures of the axial/equatorial chair conformers was computed at the ab initio MO and DFT levels of theory. Only one preferred conformation was obtained for the axial and the equatorial conformer as well. When comparing the conformational equilibria of the cyclohexanone esters with those of the corresponding cyclohexyl esters a certain polarity contribution of the cyclohexanone framework was revealed, which is independent of the substituent effects and increases the stability of the axial conformers by a constant amount.     

The more gold--the more enantioselective: cyclohydroaminations of γ-allenyl sulfonamides with mono-, bis-, and trisphospholane gold(I) catalysts

A series of chiral mono-, di-, and trinuclear gold(I) complexes have been prepared and used as precatalysts in the asymmetric cyclohydroamination of N-protected γ-allenyl sulfonamides. The stereodirecting ligands were mono-, di-, and tridentate 2,5-diphenylphospholanes, which possessed C(1), C(2), and C(3) symmetry, respectively, thereby rendering the catalytic sites in the di- and trinuclear complexes symmetry equivalent. The C(3)-symmetric trinuclear complex displayed the highest activity and enantioselectivity (up to 95?% ee), whilst its mono- and dinuclear counterparts exhibited considerably lower enantioselectivities and activities. A similar trend was observed in a series of mono-, di-, and trinuclear 2,5-dimethylphospholane gold(I) complexes. Aurophilic interactions were established from the solid-state structures of the trinuclear gold(I) complexes, thereby raising the question as to whether these secondary forces were responsible for the different catalytic behavior observed.     

Phenyloxenium ions: more like phenylnitrenium ions than isoelectronic phenylnitrenes?

The geometries and energies of the electronic states of phenyloxenium ion 1 (Ph-O(+)) were computed at the multireference CASPT2/pVTZ level of theory. Despite being isoelectronic to phenylnitrene 4, the phenyloxenium ion 1 has remarkably different energetic orderings of its electronic states. The closed-shell singlet configuration ((1)A(1)) is the ground state of the phenyloxenium ion 1, with a computed adiabatic energy gap of 22.1 kcal/mol to the lowest-energy triplet state ((3)A(2)). Open-shell singlet configurations ((1)A(2), (1)B(1), (1)B(2), 2(1)A(1)) are significantly higher in energy (>30 kcal/mol) than the closed-shell singlet configuration. These values suggest a revision to the current assignments of the ultraviolet photoelectron spectroscopy bands for the phenoxy radical to generate the phenyloxenium ion 1. For para-substituted phenyloxenium ions, the adiabatic singlet-triplet energy gap (ΔE(ST)) is found to have a positive linear free energy relationship with the Hammett-like σ(+)(R)/σ(+) substituent parameters; for meta substituents, the relationship is nonlinear and negatively correlated. CASPT2 analyses of the excited states of p-aminophenyloxenium ion 5 and p-cyanophenyloxenium ion 10 indicate that the relative orderings of the electronic states remain largely unperturbed for these para substitutions. In contrast, meta-donor-substituted phenyloxenium ions have low-energy open-shell states (open-shell singlet, triplet) due to stabilization of a π,π* diradical state by the donor substituent. However, all of the other phenyloxenium ions and larger aryloxenium ions (naphthyl, anthryl) included in this study have closed-shell singlet ground states. Consequently, ground-state reactions of phenyloxenium ions are anticipated to be more closely related to closed-shell singlet arylnitrenium ions (Ar-NH(+)) than their isoelectronic arylnitrene (Ar-N) counterparts.     

Sulfonyl vs. carbonyl group: which is the more electron-withdrawing?

Unexpectedly high reactivity of nitrogenated aromatics protected as amides or carbamates, when compared to sulfonamides, can be explained by a decrease of the aromaticity due to a greater ability of the carbon-centered groups to achieve delocalisation of the nitrogen lone pair, resulting in stronger global withdrawing effects.     

New bioorganic reagents: evolved cyclohexanone monooxygenase--why is it more selective?

Four mutants of the cyclohexanone monooxygenase (CHMO) evolved as catalysts for Baeyer-Villiger oxidation of 4-hydroxycyclohexanone were investigated as catalysts for a variety of 4-substituted and 4,4-disubstituted cyclohexanones. Several excellent catalytic matches (mutant/substrate) were identified. The most important, however, is the finding that, in a number of cases, a mutant with a single exchange, Phe432Ser, was shown to be as robust and more selective as a catalyst than the wild-type CHMO. All biotransformations were performed on a laboratory scale, allowing full characterization of the products. The absolute configurations of two products were established. A model suggesting a possible role of the 432 serine residue in enantioselectivity control is proposed.     

Can an α-anomer of the trinitro form of D-glucopyranose be more easily hydrolyzed in alkaline environment than the β-anomer? A detailed theoretical analysis

Comprehensive computational investigations of detailed alkaline hydrolysis reaction pathways of the α-anomeric form of nitrocellulose monomer (2,3,6-trinitro-α-D-glucopyranose) in the (4)C(1) chair conformation within the S(N)2 framework in the gas phase and in bulk water solution are reported. Geometries of reactant complexes, transition states, intermediates, and completely denitrated product were optimized at the density functional theory (DFT) level using the B3LYP functional and the 6-311G(d,p) basis set both in the gas phase and in the bulk water solution. The effect of bulk water was modeled using the polarizable continuum model (PCM) approach. The nature of the potential energy surface of the local minima and transition states was ascertained through vibrational frequency analysis. Intrinsic reaction coordinate (IRC) calculations were also performed to validate the computed transition state structures. Effect of electron correlation on computed energies was considered through a single point energy calculation at the MP2 level using the cc-pVTZ basis set. It was revealed that the presence of hydrogen bonds between the attacking OH(-) ion and various hydrogen bond donating sites (including CH sites) of monomer was necessary for stabilization of the transition state. It was revealed that the α-anomer will be more reactive than the β-anomer with regard to the denitration reaction. The role of entropy and the denitration ability of various sites are also discussed.     

Autoxidation catalysis with N-hydroxyimides: more-reactive radicals or just more radicals?

A first-principles analysis reveals that the catalytic efficiency of nitroxyl radicals in alkane oxidations is not simply correlated with their reactivity toward the substrate.     

With regard to the hydrogen bonding in complexes of pyridylureas, less is more. a role for shape complementarity and CH...O interactions?

A pyridylurea.tetraazaanthracenedione complex with three hydrogen bonds is more stable than an analogous complex with four hydrogen bonds. An X-ray analysis and modeling suggests a steric mismatch destabilizing the latter and a CH...O contact enhancing the stability of the former.     

One electron less or one proton more: how do they differ?

From the NIST website and the literature, we have collected the Ionisation Energies (IE) of 3,052 and the Proton Affinities (PA) of 1,670 compounds. For 614 of these, both the IE and PA are known; this enables a study of the relationships between these quantities for a wide variety of molecules. From the IE and PA values, the hydrogen atom affinities (HA) of molecular ions M^?+ may also be assessed. The PA may be equated to the heterolytic bond energy of [MH]⁺ and HA to the homolytic bond energy. Plots of PA versus IE for these substances show (in agreement with earlier studies) that, for many families of molecules, the slope of the ensuing line is less negative than ?1, i.e. changes in the PA are significantly less than the concomitant opposite changes in IE. At one extreme (high PA, low IE) are the metals, their oxides and hydroxides, which show a slope of close to ?1, at the other extreme (low PA, high IE) are the hydrogen halides, methyl halides and noble gases, which show a slope of ca. ?0.3; other molecular categories show intermediate behaviour. One consequence of a slope less negative than ?1 is that the changes in ionic enthalpies of the protonated species more closely follow the changes in the enthalpies of the neutral molecules compared with changes in the ion enthalpies of the corresponding radical cations. This is consistent with findings from ab initio calculations from the literature that the incoming proton, once attached to the molecule, may retain a significant amount of its charge. These collected data allow a comparison of the thermodynamic stability of protonated molecules in terms of their homolytic or heterolytic bond cleavages. Protonated nitriles are particularly stable by virtue of the very large hydrogen atom affinities of their radical cations.     

Stepwise diels-alder: more than just an oddity? A computational mechanistic study

We have employed hybrid DFT and SCS-MP2 calculations at the SMD-PCM-6-311++G(2d,2p)//6-31+G(d) level to investigate the relationship between three possible channels for forming a Diels-Alder adduct from a highly nucleophilic diene and moderately to highly electrophilic dienophiles. We discuss geometries optimized using the B3LYP and M06-2X functionals with the 6-31+(d) basis set. The transition states and intermediates are characterized on the basis of geometric and electronic properties, and we also address the possibility of predicting detectability of a zwitterionic intermediate based on its relative stability. Our results show that a conventional Diels-Alder transition state conformation yields intermediates in all four investigated cases, but that these are too short-lived to be detected experimentally for the less activated reactants. The stepwise trans pathway, beginning with a conjugate addition-like transition state, becomes increasingly competitive with more activated reactants and is indeed favored for the most electrophilic dienophiles. Addition of a trans diene leads to a dead-end as the trans intermediates have insurmountable rotation barriers that prohibit formation of the second bond, unless another, heterocyclic intermediate is formed. We also show that introduction of a hydrogen bond donating catalyst favors a stepwise pathway even for less activated dienophiles.