Vicinal Bonds Research Articles

Visible-Light Mediated Nickel-Catalyzed Asymmetric Difunctionalizations of Alkenes.

Difunctionalizations of alkenes represent one of the most straightforward protocols to build molecular complexity due to the simultaneous construction of two vicinal bonds cross π-bond of alkenes. It is extremely attractive yet challenging to control the stereochemistry outcome of this event. Over the past years, visible-light and Ni-catalyzed asymmetric difunctionalizations of alkenes provide an environmental benign and promising solution for the construction of saturated carbon centers with the control of regio- and enantioselectivity. In this Concept, the initiative and progress of regio- and enantioselective difunctionalizations of alkenes enabled by visible-light and nickel catalysis has been summarized. Moreover, further efforts and directions for the development of visible-light mediated Ni-catalyzed asymmetric difunctionalizations of alkenes has been discussed.

Structural and mechanistic basis for redox sensing by the cyanobacterial transcription regulator RexT

Organisms have a myriad of strategies for sensing, responding to, and combating reactive oxygen species, which are unavoidable consequences of aerobic life. In the heterocystous cyanobacterium Nostoc sp. PCC 7120, one such strategy is the use of an ArsR-SmtB transcriptional regulator RexT that senses H2O2 and upregulates expression of thioredoxin to maintain cellular redox homeostasis. Different from many other members of the ArsR-SmtB family which bind metal ions, RexT has been proposed to use disulfide bond formation as a trigger to bind and release DNA. Here, we present high-resolution crystal structures of RexT in the reduced and H2O2-treated states. These structures reveal that RexT showcases the ArsR-SmtB winged-helix-turn-helix fold and forms a vicinal disulfide bond to orchestrate a response to H2O2. The importance of the disulfide-forming Cys residues was corroborated using site-directed mutagenesis, mass spectrometry, and H2O2-consumption assays. Furthermore, an entrance channel for H2O2 was identified and key residues implicated in H2O2 activation were pinpointed. Finally, bioinformatics analysis of the ArsR-SmtB family indicates that the vicinal disulfide “redox switch” is a unique feature of cyanobacteria in the Nostocales order, presenting an interesting case where an ArsR-SmtB protein scaffold has been evolved to showcase peroxidatic activity and facilitate redox-based regulation.

Interpretation of anomeric effect in 2-hydroxytetrahydropyrans based on extensive bond interactions

Recently, exchange repulsion and electron delocalization have been a focus of attention as the origin of the anomeric effect. However, the details of these interactions remain unclear. In this study, to elucidate what exchange repulsion and electron delocalization contribute to anomer stabilities of 2-hydroxytetrahydropyran (2-hydroxy-THP), the electronic structures of the anomers were investigated using bond model analysis. The vicinal bond interactions around the anomeric carbon make the equatorial configuration of the hydroxy group more stable than the axial configuration. Exchange repulsions contribute much to this relative stability of the equatorial configuration. However, exchange repulsion and electron delocalization due to 1,3-diaxial interactions and other interactions involving lone pair electrons of oxygen make the axial configuration more stable overall than the equatorial configuration. The anomeric effect in glucose can also be explained in a manner similar to that in 2-hydroxy-THP. Additionally, interactions between the vicinal hydroxy groups contribute to the stabilization of the axial configuration.

Effect of Orbital Interactions between Vicinal Bonds and between Hydroxy Groups on the Conformational Stabilities of 1,2-Ethanediol and 2,3-Butanediols.

The geometries of the two hydroxy groups in 1,2-ethanediol or 2,3-butanediols are more stable in a gauche orientation than those in an anti orientation. This has been generally explained in terms of the gauche effect, which is stabilization due to antiperiplanar electron delocalization between an antibonding orbital of the C-O bond (σCO*) and a bonding orbital of the C-H or C-C bond (σCH or σCC). However, a C-C single bond rotation simultaneously determines the geometries of the six vicinal bonds. Therefore, it is important to understand the effects on conformational stability of other interactions of the bond orbitals adjacent to the rotating C1-C2 bond. Bond model analysis revealed that antiperiplanar bond orbital interactions as a whole contribute to the higher stabilities of hydroxy/hydroxy gauche conformers, where the C-O/C-H or C-O/C-C combination including the σCO*/σCH or σCO*/σCC delocalization is not the dominant interaction stabilizing hydroxy/hydroxy gauche conformers. Rather, our results show that a large destabilization due to the antiperiplanar C-O/C-O combination in hydroxy/hydroxy anti conformers relatively increases the stabilities of hydroxy/hydroxy gauche conformers. This destabilization results mainly from the repulsion between the antiperiplanar bonding orbitals (σCO/σCO), which have a larger overlap compared to the synclinal σCO/σCO combination. The sum of the interbond energies between the vicinal bond orbitals of these 1,2-alkanediols is more advantageous for stability in gauche conformers. In addition, interactions between the gauche-oriented hydroxy groups provide large stabilization energies and the corresponding interactions in anti conformers are negligible. The relative conformational stabilities of 1,2-ethanediol and erythro-2,3-butanediol can be explained by the interactions between the antiperiplanar bond orbitals, between the vicinal bond orbitals, or between the hydroxy groups in addition to the combination of interactions between the vicinal bond orbitals and between the hydroxy groups. In contrast, in threo-2,3-butanediol, differences in the relative stabilities of the three conformers can be understood by the combination of the interactions between the vicinal bond orbitals and between the hydroxy groups.

Fluid transition layer between rigid solute and liquid solvent: is there depletion or enrichment?

The fluid layer between solute and liquid solvent is studied by combining the density functional theory with the probabilistic hydrogen bond model. This combination allows one to obtain the equilibrium distribution of fluid molecules, taking into account the hydrogen bond contribution to the external potential whereto they are subjected near the solute. One can find the effective width of the fluid solvent-solute transition layer and fluid average density in that layer, and determine their dependence on temperature, solvent-solute affinity, vicinal hydrogen bond (hb) energy alteration ratio, and solute radius. Numerical calculations are performed for the solvation of a plate and spherical solutes of four different radii in two model solvents (associated liquid and non-associated one) in the temperature range from 293 K to 333 K for various solvent-solute affinities and hydrogen bond energy alteration ratios. The predictions of our model for the effective width and average density of the transition layer are consistent with experiments and simulations. The small-to-large crossover lengthscale for hydrophobic hydration is expected to be about 3-5 nm. Remarkably, characterizing the transition layer with the average density, one can observe that for small hydrophobes, the transition layer becomes enriched with rather than depleted of fluid when the solvent-solute affinity and hb-energy alteration ratio become large enough. The boundary values of solvent-solute affinity and hb-energy alteration ratio, needed for the "depletion-to-enrichment" crossover (in the smoothed density sense), are predicted to decrease with increasing temperature.

Effect of Water Hydrogen Bonding on the Solvent-Mediated "Oscillatory" Repulsion of C60 Fullerenes in Water.

The solvent-mediated interaction of C60 fullerenes in liquid water is examined by using the combination of the probabilistic hydrogen bond model with the density functional theory. This combination allows one to take into account the effect of hydrogen bonding between water molecules on their interaction with fullerenes and to construct an approximation for the distribution of water molecules in the system, which provides an efficient foundation for studying hydrophobic phenomena. Our numerical evaluations predict the solvent-induced interaction of two C60 fullerenes in water at 293 K to have an oscillatory-repulsive character (previously observed in molecular dynamics simulations) only when the vicinal water-water hydrogen bonds are slightly weaker than bulk ones. Besides indicating the direction of the energetic alteration of water-water hydrogen bonds near C60 fullerenes, our model also suggests that the hydrogen bonding ability of water plays a defining role in the solvent-mediated C60-C60 repulsion.

ChemInform Abstract: A Metal‐Free Dyotropic‐Like Rearrangement of 2‐Oxa Allylic Alcohols in the Presence of Organoboronic Acids.

The first example of a dyotropic-like rearrangement of 2-oxa allylic alcohols in the presence of catalytic amounts of Selectfluor and DABCO was reported, which provides a facile access to organoboronates. This reaction represents an unprecedented dyotropic rearrangement consisting of cleavage of two vicinal bonds (one C–C bond and one CC bond).

A metal-free dyotropic-like rearrangement of 2-oxa allylic alcohols in the presence of organoboronic acids.

The first example of a dyotropic-like rearrangement of 2-oxa allylic alcohols in the presence of catalytic amounts of Selectfluor and DABCO was reported, which provides a facile access to organoboronates. This reaction represents an unprecedented dyotropic rearrangement consisting of cleavage of two vicinal bonds (one C-C bond and one C=C bond).

Experimental and Theoretical Investigation of 1JCC and nJCC Coupling Constants in Strychnine

A relatively unexplored and unexploited means of establishing molecular structure, stereochemistry, and probing vicinal bond angles is through the use of long-range (13)C-(13)C coupling constants. The measurement of these multifunctional, diagnostic (3)J(CC) couplings has not been reported on sample amounts viable for the practicing organic chemist. A generalized protocol for the measurement of (1)J(CC) and (3)J(CC) couplings using a 4.6 mg sample of strychnine as a model compound is described, and the utility of DFT calculations for the prediction of these useful molecular descriptors and the congruence of the calculated and experimental data is demonstrated.

Predominance of the Participation of the Geminal over Vicinal Bonds: Torquoselectivity of Retro-Nazarov Reactions

Torquoselectivities of electrocyclic ring-opening reactions have been proposed to be controlled by the participation of electron-donating σ-bonds (σ-EDB) geminal to the breaking σ-bond and/or vicinal electron-accepting σ-bonds (σ-EAB) or lone pair(s) of the substituent(s). We designed reactions in which the effects of the vicinal bonds should be significantly diminished by the cationic nature of the reactants. The calculated enthalpies of activation of the retro-Nazarov reactions of some 3-substituted cyclopentenyl cations show inward rotation of the geminal σ-EDB, which is consistent with the theory of geminal bond participation.

Geometry and conformation of cyclopropane derivatives having σ-acceptor and σ-donor substituents: a theoretical and crystal structure database study

The structures of cyclopropane rings which carry σ-acceptor or σ-donor substituents have been studied using density-functional theory (DFT), and mean bond lengths and conformational parameters retrieved from the Cambridge Structural Database. It is confirmed that σ-acceptor substituents, e.g. halogens, generate positive ring bond-length asymmetry in which there is lengthening of the distal bond (opposite to the point of substitution), and shorterning of the two vicinal bonds. This is due to withdrawal of electron density from the cyclopropane 1e'' orbitals, which are bonding for the distal bond and antibonding for the vicinal bonds. For σ-donor substituents such as SiH(3) or Si(CH(3))(3), the DFT and crystal structure data show negative ring bond-length asymmetry (distal bond shortened, vicinal bonds lengthened), owing to electron donation into the 4e' ring orbital, which are also bonding for the distal bond and antibonding for the vicinal bonds. The results also show that -OH substituents induce weak positive asymmetry, but that the effects of methyl or amino substituents are either non-existent or extremely small, certainly too small to measure using crystal structure information.

Blue-shifted A–H stretching frequencies in complexes with methanol: the decisive role of intramolecular coupling

The presence of a blue shift of A-H stretching frequencies in intermolecular complexes is directly related to the intramolecular coupling between A-H and vicinal A-X bonds in isolated molecules. The intramolecular coupling between vicinal bonds is the decisive parameter that determines whether a general molecule is a candidate for displaying blue-shifted A-H stretching frequencies in intermolecular complexes, with or without hydrogen bonding. The structures and vibrational spectra of dimeric complexes of methanol with H(2)O, HF, HCN, HNC, HOF, HNO, and HSN are investigated at the MP2/6-311++G(2d,2p) approach. Blue- and red-shifts of the methyl C-H stretches of methanol and the various other A-H stretching frequencies in the complexes can be predicted by normal coordinate analyses of methanol and the partner molecules. It is, hence, suggested that conventional normal coordinate analysis is the appropriate predictive tool to decide beforehand whether a given molecule is a promising candidate for the observation of blue shifts in intermolecular complexes.

Cryospectroscopic and ab initio anharmonic studies of acetylene–trimethylamine H-bonded complex

The FTIR spectra of C 2H 2 in mixtures with trimethylamine (TMA) have been studied in liquefied Kr in the frequency range of ∼800–7000 cm −1. The data obtained for C 2H 2 subunit suggest the formation of 1:1 complexes stabilized by a moderate strength conventional H-bond. CH and CN stretching vibrations, related to the vicinal bonds of proton acceptor, were found to shift in opposite directions – blue in the former and red in the latter case. New weak bands, revealed in the range of ∼6000–7000 cm −1, were ascribed to the overtone and combination bands of C H stretching vibrations of acetylene which participates in the H-bond formation. The relative stability of the complex has been determined in a series of temperature ( T = 118–157 K) measurements of integrated intensities of vibrational bands ascribed to monomer and complex species. Ab initio MP2/6-311++G(2d,2p) a priory counterpoise corrected calculations, made for acetylene, TMA, and the complex reproduce the main spectroscopic observations. They suggest that the most stable non-linear structure of the complex is very floppy. Evaluations of anharmonic effects on position and integrated intensity of selected bands of C H stretching modes of C 2H 2 subunit have been made within perturbation theory on the basis of single point potential energy surface (PES) and dipole moment function calculations.

Origin of methyl torsional barrier in 1-methyl-2(1H)-pyridinimine and 3-methyl-2(1H)-pyridone: II. Ground state

To get the insight into the electronic structure-methyl torsion correlation in nitrogen heterocyclic molecules, a comparative study on torsion of the methyl group in 1-methyl-2(1H)pyridone (1MPY), 1-methyl-2(1H)pyridinimine (1MPI), and 3-methyl-2(1H)pyridone (3MPY) was carried out using ab initio calculations. To understand the barrier forming mechanism in the ground state and its consequence on the molecular structure, the ground state torsional potential has been investigated by partitioning the barrier energy using the natural bond orbital (NBO) theoretical framework. The NBO analysis reveals that the delocalization energy is the barrier forming term whereas the Lewis energy is always antibarrier for all these molecules. To get further insight into the effect of local electronic structure on the methyl torsional barrier, the individual bond-antibond interactions and structural energy contributions have been investigated. It was found that when the bond order difference between the vicinal bonds does not change appreciably during the course of methyl rotation, the local electronic interactions with the methyl group do not play any decisive role in barrier formation as observed in the case of 1MPY and 1MPI. In these cases, it is the skeletal relaxation during methyl rotation that plays an important role in determining the barrier. On the other hand, if the bond order change is appreciable as is the case for 3MPY, the local interactions alone suffice to describe the origin of the torsional barrier of the methyl group.

Conformational Characteristics of Poly(ethylene sulfide) and Poly(ethylene oxide): Solvent Dependence of Attractive and Repulsive Gauche Effects

Conformational characteristics of poly(ethylene sulfide) (PES), poly(ethylene oxide) (PEO), and their oligomeric model compounds have been investigated by the rotational isomeric state (RIS) analysis of ab initio molecular orbital (MO) calculations, NMR vicinal coupling constants, characteristic ratios, and dipole moment ratios. Conformational energies of PES were determined from 1H and 13C NMR vicinal constants of its monomeric model compound, 1,2-bis(methylthio)ethane (BMTE), and ab initio MO calculations for BMTE at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31G(d) and MP2/6-311+G(3df,2p)//HF/6-31G(d) levels. By the NMR analysis, the firs-order interaction energies for the gauche states around the C−C and C−S bonds, designated as Eσ and Eρ respectively, were evaluated as follows: in benzene, Eσ = 0.41 kcal mol-1 and Eρ = −0.74 kcal mol-1; in chloroform, Eσ = 0.31 kcal mol-1 and Eρ = −0.41 kcal mol-1. The C−C and C−S bonds were shown to prefer the trans and gauche conformations, respectively. These tendencies are consistent with the MO calculations: B3LYP, Eσ = 1.39 kcal mol-1 and Eρ = −0.24 kcal mol-1; MP2, Eσ = 0.89 kcal mol-1 and Eρ = −0.41 kcal mol-1. Inasmuch as the MO calculations represent gaseous BMTE, the conformational energies were indicated to have large solvent dependence. Ab initio MO calculations at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31G(d) and MP2/6-311+G(3df,2p)//HF/6-31G(d) levels and by the complete basis set (CBS-Q) method were carried out for 1,2-dimethoxyethane (DME), a model compound of PEO. All of the MO calculations showed the presence of the (C−H)···O attraction in the g±g∓ conformations for the C−C/C−O bond pairs. The MP2 calculations gave the first-order interaction energies (Eσ and Eρ) for the gauche states around the C−C and C−O bonds as 0.32 and 1.22 kcal mol-1, respectively. The conformational energy Eω representing the (C−H)···O interaction was evaluated as −1.12 kcal mol-1. In the RIS scheme, bond conformations of PEO in 1,4-dioxane and dipole moment ratios of PEO in benzene were simultaneously simulated, and the conformational energies of PEO in nonpolar organic solvents were determined: Eσ = −0.25, Eρ = 1.17, and Eω = −0.79 kcal mol-1. Ours and Abe and Mark's data [Eσ = −0.5, Eρ = 0.9, and Eω = 0.4 kcal mol-1, Abe, A.; Mark, J. E. J. Am. Chem. Soc. 1976, 98, 6468] show that the Eσ and Eω values of PEO so widely vary with solvent as to change the signs. Configurational entropies of 200 mers of PES and PEO were calculated to be 5.8−6.3 and 5.0−5.1 cal mol-1 K-1, respectively. Thus, the difference in melting point between PES (216 °C) and PEO (68 °C) was indicated to come from that in enthalpy (ΔHu) of fusion: ΔHu (PES) > ΔHu (PEO). The natural bond orbital analysis for BMTE and DME revealed the following facts. For BMTE and DME, vicinal bond−antibond interactions around the C−C bond cause the gauche preference. For BMTE, however, a steric S···S repulsion considerably reduces the gauche stability, and hence the trans preference appears in the C−C bond. Bond−antibond and lone pair-antibond interactions around the C−X bond (X = S or O) stabilize the gauche conformation for BMTE but the trans state for DME. Both MO calculations and NMR experiments for BMTE showed that the most stable states are g±tg∓, in which electron delocalization in the S−C−C−S antibonds is maximized and a large antiparallel dipole−dipole interaction is formed. Thus, the g±tg∓ conformations have a smaller free energy than g±tg± by ca. 0.2 kcal mol-1, being found in BMTE and PES crystals.

Anomalous Behavior of the Ethyl Group in the Aminolysis of S-Phenyl Acetate with Benzylamine in Acetonitrile

The rates of the aminolysis of S-phenyl substituted-acetate series <TEX>$(RC(=O)SC_6H_4Z$</TEX>, with R=Me, Et, i-Pr, t-Bu and Bn) with benzylamines <TEX>$(XC_6H_4CH_2NH_2)$</TEX> are not correlated simply with the Taft's polar <TEX>$({\sigma}^{\ast})$</TEX> and/or steric effect constants <TEX>$(E_s)$</TEX> of the substituents due to abnormally enhanced rate of the substrate with R=Et. Furthermore, the cross-interaction constant, <TEX>${\rho}x_z$</TEX> , is the largest with R=Et. These anomalous behaviors can only be explained by invoking the vicinal bond <TEX>$({\sigma})$</TEX>-antibond <TEX>$({\sigma}^{\ast})$</TEX> charge transfer interaction between C-<TEX>$C{\alpha}$</TEX> and C-S bonds. In the tetrahedral zwitterionic intermediate, <TEX>$T^{\pm}$</TEX> , formed with R=Et the vicinal <TEX>${\sigma}_{c-c}-{\sigma}^{\ast}_{c-s}$</TEX> delocalization is the strongest with an optimum antiperiplanar arrangement and a narrow energy gap, <TEX>${\Delta}{\varepsilon}={\varepsilon}_{{\sigma}^{\ast}}-{\varepsilon}_{\sigma}$</TEX>. Due to this charge transfer interaction, the stability of the intermediate increases (with the concomitant increase in the equilibrium constant K (= <TEX>$k_a/k_{-a}$</TEX>)) and also the leaving ability of the thiophenolate leaving group increases (and hence <TEX>$k_b$</TEX> increases) so that the overall rate, <TEX>$k_n\;=\;Kk_b$</TEX>, is strongly enhanced. Theoretical support is provided by the natural bond orbital (NBO) analyses at the B3LYP/6-31+<TEX>$G^{\ast}$</TEX> level. The anomaly exhibited by R=Et attests to the stepwise reaction mechanism in which the leaving group departure is rate limiting.

Stereoelectronic, torsional, and steric effects on rates of enolization of ketones.

The stereoselectivities of base-catalyzed enolizations of ketones have been studied by quantum mechanical methods. Transition structures of exo and endo deprotonation of camphor, norcamphor, and dehydronorcamphor have been located with two model bases. Stereoelectronic, torsional, and steric effects on activation energies were assessed. These calculations demonstrate the importance of torsional strain between partial bonds and vicinal bonds on the rates of deprotonation and on related reactions involving the formation of enolates or reactions of enols and enolates.

Theoretical studies on the iminium ion-forming reaction

The iminium ion forming reactions of YC6H4NHCH2NH3+(I) and the corresponding carbon analog, YC6H4CH2CH2NH3+ (II) were studied theoretically at the MP2/6–31G*//RHF/6–31G* level. The iminium ion-forming reactions are favored mainly due to a large amount of electron donation (0.05–0.06e) from the nitrogen to the antibonding orbital of the cleaving bond, nN σ*(r3), by a first-neighbor vicinal charge-transfer interaction. At ca 50% progress of reaction, i.e. bond cleavage in the SN1 transition state (TS), bond contraction of the geminal bond (r2) is greater by ca 10% (60%), which is also greater than bond stretching of a vicinal bond (50%). The reaction through the imbalanced TS provides the minimum energy path in accordance with the basic laws of nature. The Hammett ρ values for the iminium ion-forming activation and equilibrium processes are ca −1.3 and −4.3, respectively. The negative activation energies for the SN2 processes with I in the gas phase are consistent with the experimental direct nucleophilic displacement by a strong nucleophile at the iminium ion-forming substrate in water. Copyright © 1999 John Wiley & Sons, Ltd.

The Cubane Cage – A Sensitive Probe for Assessing Substituent Effects on a Four-Membered Ring, Part II

The crystal structures of methyl 4-methoxycubane-1-carboxylate (1), 1-acetamido-4-fluorocubane (2), methyl 4-acetoxycubane-1-carboxylate (3), 1,4-difluorocubane (4), 1,4-dichlorocubane (5), and N,N-diisopropylcubane-1,4-dicarboxamide (6) have been investigated by means of X-ray diffraction analysis. Fluorine and chlorine substituents cause a shortening of the vicinal bonds, as is seen in the 4-halocubane-1-carboxylates. The cage bonds vicinal to the ester substituent, with a favorable orientation with regard to the π-acceptor influence of this group become longer than the CH–CH bonds. Furthermore, the influence on bond length with respect to the orientation of this group relative to bonds within the cubane skeleton has been investigated experimentally. The effect of the methoxy group has also been found to depend on the orientation. The cage bond antiperiplanar to the methyl group is shortened, while the cage bonds in gauche orientation to this group are lengthened. As seen in the case of the halogen-substituted derivatives, the bonds bearing the acetoxy substituent are shortened due to the σ-acceptor property of this group. Ab initio calculations on compounds 1, 2, 4, and 5 performed at the 6-31G* level confirm the experimental results.

A theoretical study on the complexation of sp, sp 2 and sp 3 nitrogen-containing species by Cu +

A study of the cationization of NH 3, NH 2CH 3, NHCH 2 and HCN with Cu + in the gas-phase is performed at the B3LYP, B3PW91 and G2 levels of theory. A comparison of the geometries, binding energies and harmonic vibrational frequencies indicate that these DFT methods are a good option for this kind of system when the size of the molecule makes higher levels of theory difficult. The nature of the CuN bond through the series, as well as the character of the hybridization of the orbitals involved have been analyzed by means of the Bader topological analysis and NBO method. As Cu + has a covalent interaction with N, the possible activation of the different CN vicinal bonds by the effect of copper cation complexation is discussed.