Clickable 9-azido-(9-deoxy)-Cinchona alkaloids: synthesis and conformation

The synthesis and conformational preferences of 9-azido-(9-deoxy)-Cinchona alkaloids constituting a novel class of Cinchona alkaloid derivatives of both natural and 9-epi configurations are described. One and two-step preparative syntheses of 9-azido-(9-deoxy)-Cinchona alkaloids have been developed, allowing for their easy access on a multigram scale. The stereochemical integrity of these azides has been confirmed from their circular dichroism and specific rotation data. The conformations of the 9-azido Cinchona alkaloids, deduced from both ¹H NMR and DFT calculations, show that this class of Cinchona derivatives largely reflect the conformational preferences of the corresponding Cinchona bases; this strategy, therefore, offers a defined chiral and clickable scaffold.     

Analyzing coordination preferences of Mg2+ complexes: insights from computational and database study

Solvation of metal cations has attracted substantial interest on account of its functional importance in biological systems. In the present study, we undertake a comprehensive analysis of hydrated complexes of Mg²⁺ with up to 20 water molecules using MP2/cc-pVTZ and density functional theory (DFT) calculations. The effect of first, second, and higher solvation shells on magnesium coordination has been systematically analyzed by considering Mg²⁺(H₂O) _n complexes. Numerous competing conformations for each of the metal ion complexes have been explored and the minima structures obtained were further analyzed. The study probes the relative preferences among various coordination numbers and unambiguously establishes that coordination number 6 is the most optimal choice. The relative abundance of Mg²⁺ ion and its coordination with water and other ligands has been analyzed in the Protein Data Bank and Cambridge Structural Database. It is noted that the M–O distance and charge transfer to metal ion increase as the number of solvating water molecules increases. The computational studies are in excellent agreement with the experimental observations, and provide support to multiple coordinate site preferences for Mg²⁺.     

On the conformational structure of cyclohexadecane,the corresponding ketone,the 1,9-dione and the corresponding ketals

The title compounds have been prepared, and their structures have been studied using molecular mechanics calculations, together with dipole moment measurements, and thermodynamic and spectroscopic data reported in the literature. It is concluded that the parent hydrocarbon exists to a very large extent in a “square” diamondoid conformation (D_2d symmetry). Other conformations (rectangular, nearly D₂, and puckered, (D_2d) are considerably higher in energy. The ketone consists of a mixture of both square and rectangular conformations with the CO group in several different positions. The monoethylene ketal exists primarily in a conformation which is square, with the ketal group on a corner. The diketone, diketal, and monoketal of the dione are considered in the light of the above, and conclusions are drawn regarding their conformations. The dipole moments of the difunctional compounds are in agreement with the conformational conclusions reached by the calculations.     

Synthesis and conformational behaviour of lower-rim tetraacetylated thiacalix[4]arenes

The acylation of thiacalix[4]arenes with AcCl or Ac₂O gave the corresponding lower-rim tetraacetoxy derivatives. In contrast to classical calix[4]arenes, tetraacetylated thiacalix[4]arenes are conformationally mobile in solution and represent a thermodynamic equilibrium of three different conformers at room temperature. As proven by a dynamic ¹H NMR study, conformational preferences of acetylated thiacalix[4]arenes considerably depend on the upper-rim substitution. Hence, t-Bu thiacalixarene prefers 1,3-alternate and 1,2-alternate conformations (43% and 38%, respectively), while the upper-rim unsubstituted compound adopts preferably the partial cone conformation (70%).     

Molecular modelling and conformational analysis of a GABAB antagonist

Summary Crystallographic database studies and molecular dynamics simulations in different media have enabled us to sample the conformational space of a GABA_B antagonist. As a result, we have defined a pharmacophoric pattern for GABA_B antagonists. This study has led us to compare the conformational preferences deduced from database studies and molecular dynamics simulations. The influence of the medium on the conformations has also been investigated.     

First principles study and database analyses of structural preferences for sodium ion (Na+) solvation and coordination

Extensive computations were performed on aqueous clusters of monovalent sodium cation [Na⁺(H₂O) _n ; (n = 1–20)] using MP2/cc-pVTZ and density functional theory. The structure, energy, and coordination number (CN) preference of a large number of competing conformations of different complexes have been explored. For complexes up to n = 12, the CN 4 is most preferred while 5, 6 CNs are favored in case of larger complexes containing up to 20 water molecules. These results are in very good agreement with experimental observations. The strength of hydrogen bonding among the waters coordinated to the Na⁺ ion is found to play a major role in the stability of the complexes. The varying preferences for CN of Na⁺ ion were explored by screening two important databases: Protein Databank and Cambridge Structural Database. A linear correlation is observed between the M (Metal)–O distance and the charge on metal ion in complex with the increase in CN of metal ion.     

Conformational stability of trivinylborane from vibrational spectra and ab initio calculations

The conformational stability, barriers to internal rotation and vibrational frequencies of trivinylborane have been determined from the vibrational spectra and ab initio calculations. The ab initio calculations have been carried out utilizing the RHF/3-21G, RHF/6-31G*, and MP2/6-31G* basis sets and support the vibrational data that there are two stable conformations in the fluid phases separated by a relatively small energy difference. One of the conformations is a near-planar form which has the three vinyl groups twisted out of the BC₃ plane and belongs to the C₃ point group. The other conformer has a non-planar structure and belongs to the C₁ point group. These and other calculated results are compared to the corresponding quantities obtained from the experiment.     

Heterodiene syntheses—XII : The conformational analysis of cis and trans 2-alkoxy-4-phenyl-2,3-dihydropyran[2,3-c] pyrazoles: Steric interactions and the anomeric effect

The conformational equilibria of a homogeneous series of cis and trans 2-alkoxy-4-phenyl-2,3-dihydropyran[2,3-c] pyrazoles have been investigated by a graphical method, and the preferences are rationalized in terms of steric interactions between the 4 and 5-substituents and of the anomeric effect.The anomeric interaction depends upon the nature of the alkoxy group and the conformational free-energy differences correlate with the steric parameters E_s.     

Exploring structural and conformational behaviour of cyclophanes incorporating imidazole-2-thiones

New cyclophanes containing two imidazole-2-thione moieties linked by two xylylene groups have been synthesized by the reaction of imidazolium-linked cyclophanes with sulfur in the presence of K₂CO₃. The conformational behaviour of the new cyclophanes was explored by NMR spectroscopy and X-ray diffraction studies. In cyclophanes containing o-xylylene or 2,4,6-trimethyl-m-xylylene linking groups, the imidazole-2-thione groups were mutually syn in both the solid state and in solution, the cyclophanes adopting a conformation reminiscent of the cone conformation of calix[4]arenes. Cyclophanes containing p-xylylene or m-xylylene linking groups exhibited two conformations in solution, one in which the imidazole-2-thione groups are mutually syn, the other in which they are mutually anti, and these conformations did not interconvert on the NMR timescale. Both conformations co-crystallised in the m-xylylene linked cyclophane, while for the p-xylylene-linked cyclophane the anti conformation crystallised separately.     

Peculiarities of interactions between the DNA molecule and different isomers and modifications of binuclear coordination compounds of platinum(II)

A comparison has been made of conformational changes in the DNA molecule during its interaction in solution with different binuclear coordination compounds of platinum [Pt(NH₃)₂Cl-R-Pt(NH₃)₂Cl]Cl₂ in cis and trans conformations, which contain cytosine, pyrazine, and carboxypyrazine as the common ligand (R). The influence of concentration of the components, and in particular, of ionic strength of the solution on the complexation process was studied. The influence of the nature of the common ligand, and of cis and trans conformations of coordination compounds on the character of their interaction with DNA was considered. A comparison was made between the structures of DNA complexes with mono-and binuclear compounds with the same set of ligands in the platinum coordination sphere.     

Conformational studies on chloramphenicol and related molecules

A conformational analysis has been performed on chloramphenicol and related molecules by potential energy functions, NMR and IR spectroscopy. Specific solvent effects have been considered via calculation in the case of chloramphenicol. The results establish that essentially only one conformer of chloramphenicol exists in solution with respect to the C_αC_β bond, but that this stabilization is not due to hydrogen bonding as proposed in a previous study. The importance of stabilization of polar solute conformations in polar media is also discussed.     

A theoretical study of the isomerization process in tris(2-thienyl)methyl radical

An INDO study has shown that the title compound exists in two diastereomeric propeller-like conformations, a cis form (C₃ symmetry), and a trans form (C₁ symmetry). The cis form is more stable than the trans form by 0·75 kcal/mole. The two forms undergo ready conformational interconversion by the two-ring flip mechanism, with activation energies of ca. 6 kcal/mole.     

Concerning some unusual trimethylsilyl proton chemical shifts

Proton and ¹³C NMR data are presented for six different compounds containing the fragment C₆H₅? C? CH₂SiMe₃. In a number of instances it was observed that, in the ¹H NMR spectrum, the SiMe₃ groups had a chemical shift significantly upfield from internal tetramethylsilane (δ = ?0·14 to ?0·36). These unexpected upfield chemical shifts of the SiMe₃ groups are suggested to result from the predominance, on a time averaged basis, of conformations which place the methyl groups attached to silicon in the face of an aromatic ring. The preference for such conformations is, in turn, the result of rotational preferences exhibited by the ‘flat’ aromatic ring. These results suggest that conformational analysis of systems containing a phenyl ring should take more explicit account of the fact that the preferred orientation of this phenyl ring can have a profound influence on the conformation adopted by the remainder of the molecule. In addition, the preferred conformation of the phenyl ring can have a significant effect upon the observed ¹H NMR chemical shifts, while the ¹³C chemical shifts are relatively insensitive to conformational factors and can be explained by well-known substituent effects previously delineated for all-carbon systems.     

Data-mining the diaryl(thio)urea conformational landscape: Understanding the contrasting behavior of ureas and thioureas with quantum chemistry

The conformations adopted by urea and thiourea functional groups influence catalysis and binding. We combine data-mining with quantum chemical calculations to understand the differences in conformational behavior for these two important structural motifs. We developed a Python tool to automate the compilation of X-ray structural information and perform conformational clustering and visualization, based on SMILES input. While diarylureas have an overwhelming preference for the anti,anti-conformer, diarylthioureas adopt a mixture of anti,anti- and anti,syn-conformers. Computations show the anti,anti-thiourea conformer is destabilized by out-of-plane rotations which avoid a steric clash with the sulfur atom. These conformational preferences were studied computationally under a variety of conditions, and apart from in the gas-phase, a preference for anti,anti-ureas was found. Consistent with experiments, this preference increases in more polar environments. Quantitative predicted ratios are sensitive to the computational treatment of solvation effects, with COSMO-RS giving more realistic amounts of the anti,anti-conformer in THF and DMSO.     

Fourier transform infrared spectroscopy and solid-state nuclear magnetic resonance studies of octadecyl modified metal oxides obtained from different silane precursors

Octadecyl (C₁₈) modified metal oxide substrates, including titania, zirconia, hafnia, and alumina, are prepared using two types of silylating reagents, n-octadecyltrihydridosilane and n-octadecyltrichlorosilane. Fourier transform infrared (FTIR) and solid-state ²⁹Si nuclear magnetic resonance (NMR) measurements are performed to examine the cross-linking of the silanes. Solid-state ¹³C NMR spectroscopy provides information about the conformation and mobility of surface-immobilized alkyl chains. Variable temperature FTIR investigations are carried out to study the influence of the organosilane precursors and metal oxides on the conformational order of the alkyl modified systems. It is found that grafting by means of n-octadecyltrichlorosilane yields higher grafting densities than surface modification with n-octadecyltrihydridosilane. Combined pyridine adsorption and diffuse reflectance infrared Fourier transform (DRIFT) measurements are performed on the titania and hafnia substrates to evaluate potential surface heterogeneities, i.e. Lewis and Brønsted sites. Differences in the alkyl chain conformational order within the series of C₁₈ modified metal oxides are explained by the presence of island structures. The reduced C₁₈ conformational order for the samples grafted with n-octadecyltrihydridosilane is traced back to the lower grafting density which in turn points to a lower reactivity of this silylating reagent. The most striking result is the higher conformational order of the C₁₈ chains grafted in the present surface modified metal oxides when compared with silica-based systems. This finding is attributed to the lower porosity of the metal oxide supports along with more closely packed chains on the surface.     

Synthesis and conformational analysis of N-aryl-N-(6-azulenyl)acetamides

We synthesized a series of N-(6-azulenyl)-N-arylacetamides, and investigated their conformational preferences in solution and in the crystalline state by means of NMR and X-ray analyses. The results indicated that the conformational preferences of these amides are dependent on both the relative π-electron densities of the N-aromatic parts and the three-dimensional relationship of the carbonyl group to the aryl groups. The N-(6-azulenyl) group has a very different effect from the previously reported N-(2-azulenyl) group on the conformational preferences of aromatic amides.     

Combined use of three forms of chiroptical spectroscopies in the study of the absolute configuration and conformational properties of 3-phenylcyclopentanone, 3-phenylcyclohexanone,and 3-phenylcycloheptanone

Three forms of chiroptical spectroscopies, electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and optical rotatory dispersion (ORD) have been employed to study the configuration and conformational properties of the three molecules: (S)-3-phenylcyclopentanone, (S)-3-phenylcyclohexanone, and (S)-3-phenylcycloheptanone (including (S)-3-phenylcyclopentanone-2,2,5,5-d₄ and (S)-3-phenylcyclohexanone-2,2,6,6-d₄). ECD and VCD spectra in the mid-IR for the three molecular systems are marginally dependent on fine conformational details, as interpreted in terms of standard DFT computational methods, with common spectroscopic features to the three systems clearly identified. Accounting for vibronic coupling mechanisms reproduces the structuring of ECD n→π^∗ band. The ORD curves are quite similar for the three types of molecules, but their interpretation highlights a crucial role played by conformations of the cycloalkanone ring in the case of (S)-3-phenylcycloheptanone. The same conclusions are reached by considering the VCD spectra in the CH-stretching region.     

Conformational analysis-V.: A lanthanide induced shift (L.I.S.) N.M.R. investigation of conformational isomerism in aromatic aldehydes and ketones

An L.I.S. N.M.R. investigation of conformational isomerism in meta-nitrobenzaldehyde and furan- and thiophene-3-aldehydes, and of the conformation of acetophenone has been carried out. With the diamagnetic (complexation) contributions to the observed shifts removed by means of experiments with La (fod)₃ and the application of our previously-described lanthanide ion complexing model, the pseudo-contact shifts have been used to obtain the precise conformational preferences of the aldehydes. They exist to the extent of 45%, 100% and 80% respectively in the $\text{O}$-$\text{trans}$ conformation, findings which are good agreement with the previously-reported values. The L.I.S.'s for acetophenone are in best agreement with a planar molecule, although the definition is not as good in this case. These examples suggest that the L.I.S. technique is of general applicability in the determination of conformer populations and the conformations of aromatic aldehydes and ketones.     

Uncovering the Contributions of Charge Regulation to the Stability of Single Alpha Helices**

The single alpha helix (SAH) is a recurring motif in biology. The consensus sequence has a di-block architecture that includes repeats of four consecutive glutamate residues followed by four consecutive lysine residues. Measurements show that the overall helicity of sequences with consensus E₄K₄ repeats is insensitive to a wide range of pH values. Here, we use the recently introduced q-canonical ensemble, which allows us to decouple measurements of charge state and conformation, to explain the observed insensitivity of SAH helicity to pH. We couple the outputs from separate measurements of charge and conformation with atomistic simulations to derive residue-specific quantifications of preferences for being in an alpha helix and for the ionizable residues to be charged vs. uncharged. We find a clear preference for accommodating uncharged Glu residues within internal positions of SAH-forming sequences. The stabilities of alpha helical conformations increase with the number of E₄K₄ repeats and so do the numbers of accessible charge states that are compatible with forming conformations of high helical content. There is conformational buffering whereby charge state heterogeneity buffers against large-scale conformational changes thus making the overall helicity insensitive to large changes in pH. Further, the results clearly argue against a single, rod-like alpha helical conformation being the only or even dominant conformation in the ensembles of so-called SAH sequences.