Theoretical modeling of peptide α-helical circular dichroism in aqueous solution

Reliable modeling of protein and peptide circular dichroism (CD) spectra in the far UV presents a challenge for current theoretical approaches. In this study, the time-dependent density functional theory (TDDFT), configuration interaction with single excitation (CIS), and transition dipole coupling (TDC) were used to assess the most important factors contributing to the CD spectra of the α-helical secondary structure. The dependence on the peptide chain length and also the role of the flexibility and solvent environment were investigated with a model oligopeptide Ac-(Ala)(N)-NH-Me, (N = 1, ..., 18). Both the TDDFT and TDC-like methods suggest that the CD curve typical for the α-helix arises gradually, but its basic characteristic is discernible already for peptides with 4-5 amino acid residues. The calculated dependence was in a qualitative agreement with experimental spectra of short α-helices stabilized by the histidine-metal binding. The TDDFT computations of the CD were found to be unusually sensitive to the basis set and solvent model. Explicit hydration and temperature fluctuations of the peptide geometry, simulated with the aid of molecular dynamics (MD), significantly influenced the CD and absorption spectral shapes. An extensive averaging over MD configurations is thus required to obtain a converged spectral profile in cluster simulations. On the other hand, both the TDDFT and TDC models indicate only a minor influence of the alanine side chains. The CIS and TDC calculations also point toward a relatively small effect of the helix-helix interaction on the CD spectral profiles. For a model system of two helices, the CIS method predicted larger changes in the spectra than TDC. This suggests other than interactions between peptide chains, such as mutual polarization, can have a minor, but measurable, effect on the CD spectrum.     

Absolute configurational assignment of α-hydroxy acids and α-hydroxy esters from their Cupra A circular dichroism spectra

The in situ formed complexes of cuprammonium solution (Cupra A) with optically active α-hydroxy acids and α-hydroxy esters show circular dichroism spectra suitable for determination of the absolute configuration of both groups of compounds. In the long wavelength spectral region, compounds of R configuration at the α carbon atom display a positive Cotton effect of around 600 nm and a negative one at ca. 720 nm, whereas (S)-α-hydroxy acids and esters exhibit negative and positive Cotton effects, respectively, in the same spectral range.     

Some anomalies in the vibrational spectra of α, β-unsaturated ketones

Summary Some anomalies in the intensities of the bands of the C=C and C=O bonds in the vibrational spectra of , -unsaturated ketones have been explained by a difference in the sequence of the frequencies of the in-phase (_s) and out-of-phase (_as) vibrations of the multiple bonds in their cis (_s<_as) and trans (_s>_as) arrangements.     

Dehydration of α-silylalcohols in the reductive conversion of esters and ketones into alkenes

The conversion of esters and ketones into easily dehydrated α-silylated alcohols, and protodesilylation of the resultant vinylsilanes, gives alkenes under relatively mild acidic conditions.     

The optical activity of β,γ-enones in ground and excited states using circular dichroism and circularly polarized luminescence

The circularly polarized luminescence (CPL) and electronic circular dichroism (CD) spectroscopic parameters corresponding to the n←π* and n→π* transitions, respectively, have been calculated for selected β,γ-enones using density functional theory. For the smallest β,γ-enone, (1R,4R)-bicyclo[2.2.1]hept-5-en-2-one (norbornenone), coupled-cluster calculations have also been carried out. The excited-state potential energy surface for three of the five enones studied reveals two minima with different C[double bond, length as m-dash]OC[double bond, length as m-dash]C dihedral angles, and with rotatory strengths of opposite sign. The relative energies of the minima determine the sign of the CPL intensity, which may be the same or opposite as in the CD spectrum, in agreement with experimental data. The results obtained in this first computational study of CPL demonstrate its usefulness as an indicator of excited-state structures of chiral species.     

Synthesis of β-carbolines from aldehydes and ketones via the α-siloxy α,β-unsaturated esters

We report an efficient method for the synthesis of β-carbolines from α-siloxy α,β-unsaturated esters, which are accessible from a variety of aldehydes and ketones.     

Reductive aldol-type reaction of α,β-unsaturated esters with aldehydes or ketones in the presence of Rh catalyst and Et2Zn

The reaction of RhCl(PPh₃)₃ with Et₂Zn easily generated a rhodium–hydride complex (Rh−H) that added to α,β-unsaturated esters to form rhodium enolate complexes by formal 1,4-reduction. These rhodium enolates gave the corresponding Reformatsky-type reagents through transmetalation, and they reacted with various aldehydes and ketones to give reductive aldol-type products in good to excellent yields.     

NBS or DEAD as effective reagents in α-thiocyanation of enolizable ketones with ammonium thiocyanate

Ketones possessing α-hydrogen undergo smooth thiocyanation with ammonium thiocyanate in the presence of N-bromosuccinimide (NBS) at room temperature in acetonitrile under neutral conditions to produce the corresponding α-ketothiocyanates in excellent yields with high selectivity. The use of NBS makes this procedure simple, convenient and cost effective. In addition, diethyl azodicarboxylate (DEAD) was also found to promote this reaction under mild conditions.     

Stereoselective synthesis of optically active cyclic α- and β-amino esters through lipase-catalyzed transesterification or interesterification processes

A series of cyclic α- and β-amino esters belonging to a family of indolines and quinolines have been efficiently synthesized to study their behavior in lipase-mediated kinetic resolution reactions. The influence of the fused ring structure to the benzene ring and the position of the ester functionality relative to the amino group have been demonstrated, finding excellent values of enantiodiscrimination in the transesterification reaction of methyl indoline-3-carboxylate with n-butanol catalyzed by Candida antarctica lipase B being observed. On the other hand, low to moderate selectivities have been found when using a wide panel of lipases toward methyl indoline-2-carboxylate or 1,2,3,4-tetrahydroquinoline derivatives in alkoxycarbonylation, transesterification or interesterification reactions.     

First-principles study of structural,elastic, electronic and optical properties of rutile GeO2 and α-quartz GeO2

Structural parameters, elastic, electronic, bonding and optical properties of rutile GeO₂ and α-quartz GeO₂ have been investigated using the plane-wave ultrasoft pseudopotential technique based on the first-principles density functional theory (DFT). The ground-state properties obtained by minimizing the total energy are in favorable agreement with the previous work. Two phases of GeO₂ are found to be elastically stable and we have derived the bulk, shear and Young’s modulus, Poisson coefficient for rutile GeO₂ and α-quartz GeO₂. We estimated the Debye temperature of rutile GeO₂ and α-quartz GeO₂ from the acoustic velocity. Electronic and chemical bonding properties have been studied from the calculation of band structure, density of states and charge densities. Furthermore, in order to clarify the mechanism of optical transitions for rutile GeO₂ and α-quartz GeO₂, the complex dielectric function, refractive index, extinction coefficient, optical reflectivity, absorption coefficient, energy-loss spectrum and the complex conductivity function are calculated, which show the significant optical anisotropy in the components of polarization directions (100) and (001) for rutile GeO₂ and α-quartz GeO₂.     

Central-to-axial chirality transfer and induced circular dichroism in 6,7-dihydro-5H-dibenz[c,e]azepine derivatives of α- and β-amino esters

DAZ-Xaa^∗-OMe amino ester derivatives with Xaa^∗ = d/l-Ala, d/l-Val, l-Leu, l-Ile, l-Ser, l-β³-HAla, l-β³-HVal, l-β³-HLeu, (1S,2S)/(1R,2R)-ACHC (2-aminocyclohexanecarboxylic acid) and (1S,2S)/(1R,2R)-ACPC (2-aminocyclopentanecarboxylic acid), N-blocked as 6,7-dihydro-5H-dibenz[c,e]azepines (DAZ), have been synthesized and evaluated for the determination of the absolute configuration of α- and β-amino esters through the induced circular dichroism of the biphenyl chromophore.     

A novel route for the synthesis of α,β-unsaturated esters,ketones and nitriles using dibutyl telluride

In the presence of dibutyl telluride, α-halo-ester, nitrile, and ketone were found to condense easily with aromatic aldehydes to afford α,β-unsaturated esters, nitriles and ketones in high yields as one-pot reaction. A possible reaction machanism was proposed.     

Theoretical investigation on structures, electronic spectra and nonlinear optical properties of gold compounds [X-“Au(PMe3)”2]

The structures, electronic spectra, polarizability and third-order nonlinear optical properties of six gold compounds [X-“Au(PMe₃)”₂] were investigated by density functional theory (DFT) B3LYP and BhandHLYP methods. It was found that the calculation methods and basis set are rational for the object of study, and molecular structures change slightly when PPh₃ is replaced by PMe₃. The spatial effects of the bridging section have a significant influence on the polarizability, but indistinctive to the third-order nonlinear optical (NLO) coefficient. As a result of the conjugated effect in different compounds, the third-order polarizability of molecule 1a is the smallest, while that of molecule 2a is the largest. Au has donor ability in molecule 1a but acceptor ability in molecules 2a–6a by analyzing the electronic spectra and frontier molecular orbitals constitute maximal absorption, which indicates the contribution of Au to NLO properties in the six molecules is different.     

Reformatsky-type addition of esters of α-halogeno carboxylic acids to aldehydes and ketones in the presence of Fe(CO)5

Reformatsky-type addition of esters of α-halogeno carboxylic acids to aldehydes and ketones in the presence of Fe(CO)₅ and an activating agent (CBrCl₃ or I₂) afforded the corresponding esters of β-hydroxy acids in good yields. Possible reaction mechanisms are discussed. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1132–1138, June, 1999.     

Assignment of the molecular absolute configuration through the ab initio Hartree-Fock calculation of the optical rotation: can the circular dichroism data help in reducing basis set requirements?

In this paper the calculation of the optical rotation (OR) of some rigid organic molecules, using the Hartree-Fock method with small (6-31G, DZP) basis sets, has been studied thoroughly to carefully evaluate the scope and limitations of this method, previously introduced by other authors. Calculations on test molecules (compounds 1-13) together with a careful analysis of their CD spectra allow a simple criterion for the reliability of this approach to be formulated: for unsaturated and/or aromatic (i.e., absorbing in the near-UV region) molecules, if the [alpha](D) is quantitatively determined by the lowest energy Cotton effect (at wavelengths >220 nm), then the HF/6-31G result is reliable. The usefulness of this method for the experimental organic chemist has been further demonstrated because the OR (sign and order of magnitude) of compounds 14-19 (i.e., large molecules having considerable interest in organic chemistry), which fulfill the above criterion and for which an extended basis set treatment is not feasible owing to their size, is correctly predicted.     

Spectrophotometric determination of α-naphthol, β-naphthol,and oxine in aqueous solution

Diazotized orthanilic acid reagent has been devised as a novel chromogen for the trace determination of α-naphthol, β-naphthol, and oxine in aqueous solution. The developed method is characterized by simplicity and rapidness and does not resort to either temperature control or solvent extraction.     

Conversion of methyl ketones and methyl sulfones into α-deutero-α,α-difluoromethyl ketones and α-deutero-α,α-difluoromethyl sulfones in three synthetic steps

Deuterodifluoromethyl ketones and sulfones were assembled in three synthetic steps from methyl ketones and sulfones, respectively. The key synthetic transformation is the deuteration of the difluorocarbanion generated by the release of trifluoroacetate from highly α-fluorinated gem-diols. High levels of deuterium on the “CF₂D” group were routinely observed. This strategy is mild and versatile and it can be applied to both ketones and sulfones without additional concerns of over- or under-fluorination. Additional examples address issues of over-deuteration when compounds with other acidic protons are subjected to the reaction conditions. This process not only demonstrates a new method to install a “CF₂D” group but also extends the scope of trifluoroacetate release to sulfones.     

Direct synthesis of 2,4,5-trisubstituted imidazoles and di/tri-substituted pyrimidines via cycloadditions of α,β-unsaturated ketones/aldehydes and N′-hydroxyl imidamides

An efficient route for the synthesis of 5-acetylimidazoles and di/trisubstituted pyrimidines via iron-catalyzed cross-dehydrogenative coupling (CDC), with excellent tolerance and yields, has been developed. In this report, α,β-unsaturated aldehydes/ketones and N′-hydroxyl imidamides undergo [3+2] and [3+3] cycloadditions in two processes, involving iron-mediated Michael reaction, Robinson Annulation and 1,5-electrocyclization.     

Iridium-catalyzed [2+2+2] cycloaddition of α,ω-diynes with alkynyl ketones and alkynyl esters

We found that the combination of [Ir(cod)Cl]₂ and rac-BINAP served as an efficient catalyst for the [2+2+2] cycloaddition of 2,7-nonadiyne derivatives and related compounds with alkynyl ketones and alkynyl esters. The corresponding products were obtained in high yields under mild reaction conditions.     

Theoretical investigation of the complexation,structural, and electronic properties of complexes between oseltamivir drug and cucurbit[n = 6–9]urils

Structural Chemistry - The structural geometries of cucurbit[n]uril CB[n]&nbsp;with n?=?6–9 and their complexes with oseltamivir (OST) drug were obtained using the density...