The role of stereoelectronic interactions in the conformational isomerism of some phosphorus‐containing model compounds

The rotational isomerism of model phosphorus‐containing compounds was evaluated by using theoretical methodologies. The trans rotamer of chloromethylphosphonic acid dichloride ( 1 ) was found to be the prevailing form in the gas phase and in non‐polar solvents, with an inverse behaviour from chloroform solution. Although the use of direct spin–spin coupling constants (SSCCs) do not apply for the quantitative determination of conformers in 1 , due to the small dependence of J with conformation, the observed measurements and calculated individual couplings suggest that the gauche conformer is progressively stabilized with increasing the solvent polarity. In addition, theoretical calculations at the CBS‐Q level for the corresponding phosphine of 1 (compound 2 ) showed the gauche rotamer as the prevailing one in the isolated state. Natural Bond Orbital (NBO) analysis indicated that steric and electrostatic effects rule the rotational isomerism of 1 , while the anomeric effect n_P → σ*_CCl also plays an important role on the conformational equilibrium of 2 . Copyright © 2008 John Wiley & Sons, Ltd.     

Unusual conformational preferences of 1,3‐dimethyl‐3‐isopropoxy‐3‐silapiperidine

The conformational analysis of the first representative of the Si‐alkoxy substituted six‐membered Si,N‐heterocycles, 1,3‐dimethyl‐3‐isopropoxy‐3‐silapiperidine, was performed by low‐temperature ¹H and ¹³C NMR spectroscopy and DFT theoretical calculations. In contrast to the expectations from the conformational energies of methyl and alkoxy substituents, the Me_axi‐PrO_eq conformer was found to predominate in the conformational equilibrium in the ratio Me_axi‐PrO_eq : Me_eqi‐PrO_ax of ca. 2 : 1 as from the ¹H and ¹³C NMR study. The thermodynamic parameters obtained by the complete line shape analysis showed that the main contribution to the barrier to ring inversion originates from the entropy term of the free energy of activation. Copyright © 2012 John Wiley & Sons, Ltd.     

Conformational analysis of 3‐methyl‐3‐silathiane and 3‐fluoro‐3‐methyl‐3‐silathiane

The conformational equilibria of 3‐methyl‐3‐silathiane 5 , 3‐fluoro‐3‐methyl‐3‐silathiane 6 and 1‐fluoro‐1‐methyl‐1‐silacyclohexane 7 have been studied using low temperature ¹³C NMR spectroscopy and theoretical calculations. The conformer ratio at 103 K was measured to be about 5 _ax: 5 _eq = 15:85, 6 _ax: 6 _eq = 50:50 and 7 _ax: 7 _eq = 25:75. The equatorial preference of the methyl group in 5 (0.35 kcal mol^?1) is much less than in 3‐methylthiane 9 (1.40 kcal mol^?1) but somewhat greater than in 1‐methyl‐1‐silacyclohexane 1 (0.23 kcal mol^?1). Compounds 5–7 have low barriers to ring inversion: 5.65 (ax → eq) and 6.0 (eq → ax) kcal mol^?1 ( 5 ), 4.6 ( 6 ), 5.1 (Me_ax → Me_eq) and 5.4 (Me_eq → Me_ax) kcal mol^?1 ( 7 ). Steric effects cannot explain the observed conformational preferences, like equal population of the two conformers of 6 , or different conformer ratio for 5 and 7 . Actually, by employing the NBO analysis, in particular, considering the second order perturbation energies, vicinal stereoelectronic interactions between the Si–X and adjacent C–H, C–S, and C–C bonds proved responsible. Copyright © 2010 John Wiley & Sons, Ltd.     

13C Nuclear Magnetic Resonance Studies of the Conformations of Serine‐3′‐ and 5′‐Thymidine Monophosphate Conjugates

The differences in the backbone conformation between O‐thymidine‐3′‐(1) and 5′‐yl O‐alkyl N‐phosphoryl serine methyl esters (2) have been investigated by solution ¹³C NMR spectroscopy. The stereo‐sensitive vicinal ³¹P–¹³C coupling constants were measured and used in the conformational analysis for the P–O5′–C5′, P–O3′–C3′, and P–N–C_α bonds. Three‐dimensional structural characteristics of dephosphorylation reactions of Compounds are also discussed.     

Anion effect on the conformational equilibrium of sulfamide and its N,N′‐diindolyl derivative: Insights on anion transportation

The relatively high acidity of the sulfamide hydrogens suggests a potential for the development of sulfamide derivatives as novel anion receptors. The interactions of sulfamide with F^?, Cl^?, CH₃COO^?, and H₂PO₄^? anions were spectroscopically (¹H and ¹⁹F NMR) and theoretically (density functional theory) analyzed, and the complexation through hydrogen bonds was confirmed by changes in the NMR signals and theoretical calculations. The replacement of 2 sulfamide hydrogens with indolyl groups yields the N,N′‐diindolylsulfamide ( DIS , N‐1H‐indol‐4‐yl‐N′‐1H‐indol‐7‐ylsulfuric diamide), whose bond rotations allow the interaction of 4 H(N) atoms with anions. The conformational preferences of DIS change upon the presence of anions, but they are practically insensitive to the anion type. According to the quantum theory of atoms in molecules, natural bond orbital analysis, and NMR chemical shifts, as well as to a thermodynamic cycle, the complex with fluoride is the most stable, followed by the oxoanion‐derived models.     

Conformational analysis of 3,3‐dimethyl‐3‐silathiane, 2,3,3‐trimethyl‐3‐silathiane and 2‐trimethylsilyl‐3,3‐dimethyl‐3‐silathiane—preferred conformers,barriers to ring inversion and substituent effects

The first conformational analysis of 3‐silathiane and its C‐substituted derivatives, namely, 3,3‐dimethyl‐3‐silathiane 1 , 2,3,3‐trimethyl‐3‐silathiane 2 , and 2‐trimethylsilyl‐3,3‐dimethyl‐3‐silathiane 3 was performed by using dynamic NMR spectroscopy and B3LYP/6‐311G(d,p) quantum chemical calculations. From coalescence temperatures, ring inversion barriers ΔG^≠ for 1 and 2 were estimated to be 6.3 and 6.8 kcal/mol, respectively. These values are considerably lower than that of thiacyclohexane (9.4 kcal/mol) but slightly higher than the one of 1,1‐dimethylsilacyclohexane (5.5 kcal/mol). The conformational free energy for the methyl group in 2 (?ΔG° = 0.35 kcal/mol) derived from low‐temperature ¹³C NMR data is fairly consistent with the calculated value. For compound 2 , theoretical calculations give ΔE value close to zero for the equilibrium between the 2 ‐Me_ax and 2 ‐Me_eq conformers. The calculated equatorial preference of the trimethylsilyl group in 3 is much more pronounced (?ΔG° = 1.8 kcal/mol) and the predominance of the 3 ‐SiMe_{3 eq} conformer at room temperature was confirmed by the simulated ¹H NMR and 2D NOESY spectra. The effect of the 2‐substituent on the structural parameters of 2 and 3 is discussed. Copyright © 2010 John Wiley & Sons, Ltd.     

Isosteres of peptides: boron analogs as dipolar forms of α‐amino acids – a theoretical study

Modification of peptides to produce peptidomimetics is of great interest, with the aim of designing potent, selective, and metabolically stable analogs having certain conformational properties. Organoboranes have been reported in the literature with a wide range of therapeutic applications. One of the therapeutically important class of molecules is amine‐carboxyboranes derived from amino acids by replacement of the Cα atom of an amino acid/peptide by boron. The conformational preferences of these peptides, with respect to backbone ω, ?, and ψ torsion angles, have been investigated by theoretical calculations. The amide bond in these molecules has the same geometry in the ground and transition states as the natural peptides. However, the boron isosteres of glycine and alanine peptides are less structured than their natural derivatives, but are distinguished by structures with a positive value for the ? angle, which is normally disfavored for natural peptides. This property could be used to build peptides with a geometry not usually seen in natural peptides. Copyright © 2007 John Wiley & Sons, Ltd.     

Effect of the frequency of intramolecular motions on the NMR relaxation in liquid state temperature regime

Equations for the spectral densities of complex motion of a spin pair undergoing internal motion and isotropic/anisotropic overall rotation have been considered. The fluctuations of the interproton distances, caused by internal motion, have been taken into account in the theoretical equations. A method allowing a distinction between the isotropic and the anisotropic overall rotation of molecules has been proposed. The effect of the activation parameters of internal motions (known from the solid state study) on the measured T ₁ relaxation of the ¹³C and ¹H–¹H cross-relaxation rates has been analysed for methyl-β-D-galactopyranoside in DMSO-d6 solution. The conformational trans-gauche jumps of the methylene group are not fast enough to affect the T ₁ value of carbon C6 in the liquid state temperatures regime. Only the methyl group rotation is a very fast internal motion. This motion influences the carbon C7 relaxation and methyl protons–anomeric proton cross-relaxation. The values of interatomic distances between anomeric H(C1) and H(C5) as well as the three methyl protons H(C7) have been calculated from the cross-relaxation rates. The distance H(C1)–H(C7) fluctuates due to the rotation of methyl group. The application of the ‘model-free approach’ to study molecular dynamics in solutions is discussed.     

13C NMR relaxation and computational study of anisole and derivatives in the solution state

¹³C NMR spin–lattice relaxation times and nuclear Overhauser effects were measured at several temperatures for the methoxyl methyl carbon and the phenyl ring carbons in neat samples and in dilute cyclohexane solution for anisole, 4‐methylanisole, and 4‐chloroanisole. Similar measurements were made for 2‐methylanisole, 2‐methyl‐4‐bromoanisole, and 2,4,6‐trimethylanisole in dilute cyclohexane solution. Density functional theory (DFT) computations were performed on anisole, 4‐chloroanisole and 2,4,6‐trimethylanisole to obtain the minimum energy structures and the potential energy barriers to the internal rotations of the methoxyl group. The shortest distance between a methoxyl methyl hydrogen and the ortho hydrogen in anisole is 1.920 Å. The DFT results point to steric interactions that arise thereof as the principal source of the energy barriers to the internal rotation of the methyl or of the methoxyl group. The carbon relaxation data are consistent with the existence of noncovalent intermolecular interaction, especially π ? π stacking interaction. The nuclear magnetic resonance and DFT results are discussed with reference to the rotational characteristics of the methoxyl methyl and the anisotropy in the reorientational motion of anisole and its derivatives in dilute cyclohexane solution. Copyright © 2012 John Wiley & Sons, Ltd.     

Solvation thermodynamics of xylitol in water and in aqueous amino acids at 298.15 K

The scaled particle theory has been applied to calculate the free energy, ΔG_solv, enthalpy, ΔH_solv, and entropy, ΔS_solv of solvation for xylitol in water and in aqueous amino acids (glycine, alanine and valine) at 298.15 K. The solvation energy, enthalpy and entropy of xylitol are expressed in terms of their various ingredients. The results show that the interaction terms contribute favorably to the process of solvation. The results suggest that the cavity formation for accommodation of xylitol molecules in aqueous amino acids is an enthalpy‐dominated process. Furthermore, the investigated parameters indicate that xylitol–amino acid interactions follow the sequence: glycine alanine valine water. The findings of the present work may help to throw light on the role that xylitol can play to stabilize macromolecules like proteins in aqueous solutions. Copyright © 2012 John Wiley & Sons, Ltd.     

Substituent effects on conformational preference in α‐substituted α‐fluorophenylacetic acid methyl ester model systems for chiral derivatizing agents

In connection with study of chiral derivatizing agents (CDAs) for NMR determination of absolute configuration of organic compounds, factors controlling the conformational preference between syn‐ and anti‐forms in α‐substituted α‐fluorophenylacetic acid methyl ester (FC(X)(Ph)COOMe) model systems were theoretically investigated. Substituents X at the stereogenic carbon atom were X = H, C?CH and CH₃, the electronic and steric properties of which were significantly different from each other. The model system with X = C?CH and that with X = CH₃ were found to be possible candidates for fluorine‐containing CDAs. The syn conformation is stable compared with the anti one by 0.7 kcal mol^?1 for the ester with X = C?CH. On the other hand, the anti conformation is stable compared with the syn one by 0.5 kcal mol^?1 for the ester with X = CH₃. Both natural bond orbital (NBO) analysis and deletion of selected orbitals based on the donor–acceptor NBO scheme were adopted for semi‐quantitative estimation of factors responsible for the conformational preference as well as a qualitative inspection of occupied canonical molecular orbitals (MOs). It was shown that [σ–(σ* + π*)(C?O)] and [σ–σ*(Ph) and π(Ph)–σ*] hyperconjugations are the main factors controlling the conformational preferences between the syn and anti conformations. Other types of effects such as electrostatic effects were also investigated. The role of the fluorine atom was also clarified. Copyright © 2009 John Wiley & Sons, Ltd.     

Gas-phase quasi-degeneracy of zwitterionic and canonical tautomers of glycine and proline induced by the presence of the MAlF4 (M = Li,Na, K) salts

The ionic MAlF₄ salts (M = Li, Na, K) are postulated to act as effective stabilising agents with respect to glycine and proline zwitterionic tautomers. On the basis of ab-initio MP2/6-311++G(d,p) theoretical calculations, it is demonstrated that strong electrostatic interactions between the polar MAlF₄ moiety and either Gly and Pro zwitterion should allow to suppress the intra-molecular proton transfer in the amino acid and thus render the zwitterion tautomer stable in the gas phase. Among the systems proposed, the K⁺AlF₄^– turned out to be the most efficient stabilising compound as its presence is expected to lead to the energetic quasi-degeneracy of the canonical and zwitterionic tautomers of glycine and proline.     

Influence of ortho substituents on 17O NMR chemical shifts in phenyl esters of substituted benzoic acids

¹⁷O NMR spectra for 29 phenyl esters of ortho‐, para,‐ and meta‐substituted benzoic acids, X‐C₆H₄CO₂C₆H₅, at natural abundance in acetonitrile were recorded. The δ(¹⁷O) values of carbonyl and the single‐bonded oxygens for para derivatives gave good correlation with the σ⁺ constants. The δ(¹⁷O) values for meta derivatives correlated well with the σ_m constants. The influence of ortho substituents on the δ(¹⁷O) values of carbonyl oxygen and the single‐bonded oxygens was analyzed using the Charton equation containing the inductive, σ_I, resonance, σ⁺_R, and steric, E, substituent constants. For ortho derivatives, excellent correlations with the Charton equation were obtained when the data treatment was performed separately for derivatives containing electron‐donating +R and electron‐attracting ?R substituents. The electron‐donating substituents in ortho‐, meta‐, and para‐substituted esters resulted in shielding of the ¹⁷O signal and the electron‐withdrawing groups caused deshielding. In phenyl ortho‐substituted benzoates, the substituent‐induced positive inductive (ρ_I > 0), resonance (ρ_R > 0), and steric (δ_orthoE > 0) effects were found. The steric interaction of ortho substituents with ester group was found to produce a deshielding effect on the carbonyl and single‐bonded oxygens. For ortho derivatives with ?R substituents, the resonance term was insignificant and the steric term was ca. twice weaker as compared to that for derivatives with +R substituents. The δ(¹⁷O) values for ortho‐substituted nitrobenzenes, acetophenones, and benzoyl chlorides showed a good correlation with the Charton equation as well. In ortho‐substituted nitrobenzenes the inductive, resonance and steric effect were found to be ca. 1.7 times stronger as compared to that for phenyl ortho‐substituted benzoates. Copyright © 2010 John Wiley & Sons, Ltd.     

Highlights and perspectives of the JLab spin physics program

Nucleon spin structure has been an active, exciting and intriguing subject of interest for the last three decades. Recent precision spin-structure data from Jefferson Lab have significantly advanced our knowledge of nucleon structure in the valence quark (high-x) region and improved our understanding of higher-twist effects, spin sum rules and quark-hadron duality. First, results of spin sum rules and polarizabilities in the low to intermediate Q ² region are presented. Comparison with theoretical calculations, in particular with Chiral Perturbation Theory (ChPT) calculations, are discussed. Surprising disagreements of ChPT calculations with experimental results on the generalized spin polarizability, δ _LT, were found. Then, precision measurements of the spin asymmetry, A ₁, in the high-x region are presented. They provide crucial input for global fits to world data to extract polarized parton distribution functions. The up and down quark spin distributions in the nucleon were extracted. The results for Δd/d disagree with the leading-order pQCD prediction assuming hadron helicity conservation. Results of precision measurements of the g ₂ structure function to study higher-twist effects are presented. The data indicate a significant higher-twist (twist-3 or higher) effect. The second moment of the spin structure functions and the twist-3 matrix element d ₂ results were extracted. The high Q ² result was compared with a Lattice QCD calculation. Results on the resonance spin-structure functions in the intermediate Q ² range are presented, which, in combination with DIS data, enable a detailed study of quark-hadron duality in spin-structure functions. Finally, an experiment to study neutron transversity and transverse spin asymmetries is discussed. A future plan with the 12 GeV energy upgrade at JLab is briefly outlined.     

Solution conformational preferences of glutaric, 3‐hydroxyglutaric, 3‐methylglutaric acid,and their mono‐ and dianions

Conformational preferences of glutaric, 3‐hydroxyglutaric and 3‐methylglutaric acid, and their mono‐ and dianions have been investigated with the aid of NMR spectroscopy. In contrast to succinic acid, glutaric acid displays essentially statistical conformational equilibria in polar and non‐polar solutions of high and low hydrogen‐bonding ability with no clear evidence for intramolecular hydrogen‐bonding interactions. The acid ionization constant ratios, K ₁/K₂, in D₂O and DMSO of glutaric, 3‐hydroxyglutaric, and 3‐methylglutaric acids also indicate that intramolecular interactions are much less important than, or indeed insignificant, for shorter‐chain acids. FTIR studies on 3‐methylglutaric acid indicate some preference for either association with solvent or dimerization, depending on the solvent, rather than intramolecular hydrogen bonding. Copyright © 2008 John Wiley & Sons, Ltd.     

The influence of steric effects on the kinetics and mechanism of SNAr reactions of 1‐phenoxy‐nitrobenzenes with aliphatic primary amines in acetonitrile

Rate constants are reported for the reactions of 1‐phenoxy‐dinitrobenzenes, 3 , 1‐phenoxy‐dinitrotrifluoromethylbenzenes, 4 , with n‐propylamine, and 1‐methylheptylamine in acetonitrile as solvent. The results are compared with results reported previously for n‐butylamine, pyrrolidine, and piperidine. Decreasing ring activation leads to lower values of k₁ for nucleophilic attack although this may be mediated by reduced steric congestion around the reaction centre. Specific steric effects, leading to rate retardation, are noted for the ortho‐CF₃ group. In general, reactant‐bearing ortho‐CF₃ group were subject to base catalysis irrespective of the amine nucleophile and values of k_Am/k_?1 are reduced as the size of the amine get bulkier. This is likely to reflect increases in values of k_?1 coupled with decreases in values of k_Am as the proton transfer from zwitterionic intermediates to catalysing amine becomes less thermodynamically favourable.     

Influence of solvent on the ortho substituent effect in the alkaline hydrolysis of phenyl esters of substituted benzoic acids

The second‐order rate constants k (dm³ mol^?1 s^?1) for the alkaline hydrolysis of phenyl esters of meta‐, para‐ and ortho‐substituted benzoic acids in aqueous 5.3 M NaClO₄ and 1.0 M Bu₄NBr were measured by UV/Vis spectrophotometry at 25 °C. The variations in the ortho inductive, ortho resonance, as well as meta and para polar effects with solvent parameters were studied using data for the alkaline hydrolysis of phenyl esters of substituted benzoic acids in various media. The dependence of the ortho substituent effect on solvent can be precisely described with the following equation: Δlog k_ortho = log k_ortho ? log k_H = 0.059 + 2.19σ_I + 0.304σ°_R + 2.79E ? 0.016ΔEσ_I ? 0.085ΔEσ°_R, where ΔE is the solvent electrophilicity, ΔE = E_S ? E_H2O, characterizing the hydrogen‐bond donating power of the solvent. The increase in the meta and para polar substituent effects with decrease in the solvent hydrogen‐bond donor capacity (electrophilicity) was approximately to the same extent (?0.068ΔEσ°_m,p) as the resonance term for the ortho substituents. The steric term of ortho substituents was independent of the solvent parameters. The variations in the ortho inductive, ortho resonance, as well as meta and para polar substituent effects with the solvent electrophilicity were to the same extent as in phenyl benzoates containing the substituents in the phenyl part. The substituent effects in the alkaline hydrolysis of ethyl benzoates appeared to vary with the solvent electrophilicity nearly to the same extent as in the alkaline hydrolysis of substituted phenyl esters of benzoic acids. Copyright © 2009 John Wiley & Sons, Ltd.     

Gas‐phase structure and new vibrational study of methyl trifluoroacetate (CF3C(O)OCH3)

The molecular structure of methyl trifluoroacetate (CF₃C(O)OCH₃) has been determined in the gas phase from electron‐diffraction data supplemented by ab initio (MP2) and DFT calculations using different basis sets. Experimental data revealed an anti conformation with a dihedral angle θ (CCOC) = 180°. Quantum mechanical calculations indicate the possible existence of two conformers, differing by a rotation about the C(O) O bond. The global minimum represents a C_s‐symmetric structure in which the CF₃ group has the anti orientation with respect to the CH₃ group, but there is another potential minimum, much higher in energy, representing a C_s‐symmetric structure with a cis conformation. The preference for the anti conformation was studied using the total energy scheme and the natural bond orbital (NBO) partition scheme. Additionally, the total potential energy has been deconvoluted using a six‐fold decomposition in terms of a Fourier‐type expansion, showing that the electrostatic and steric contributions are dominant in stabilizing the anti conformer. Infrared spectra of CF₃C(O)OCH₃ were obtained for the gaseous and liquid phases, while the Raman spectrum was recorded for the liquid phase. Harmonic vibrational frequencies and a scaled force field have been calculated, leading to a final root mean‐square deviation of 9 cm⁻¹ when comparing experimental and calculated frequencies. Copyright © 2009 John Wiley & Sons, Ltd.     

Exploring the reaction of iodine with α‐diazo esters

In this paper we describe the unprecedented reaction between α‐diazo esters 1 and iodine. The reaction, carried out in the presence of aqueous NaHCO₃, afforded the Z‐isomer of the corresponding unsaturated‐2‐iodo ester 8 . The configuration of compounds 8 was determined using the ³J_{C? H} coupling between carbonyl carbon atom and alkene proton. Mechanistic considerations accounting for the observed phenomena and including quantum chemical calculations are proposed. Copyright © 2008 John Wiley & Sons, Ltd.     

Conformational flexibility of xanthene‐based covalently linked dimers

The conformational flexibility of three covalently linked dimers consisting of two xanthene‐based moieties connected by a diphenyl ether linker was studied using NMR spectroscopy, X‐ray crystallography, and density functional theory (DFT) calculations. The three dimers interconvert as a function of pH: the doubly cationic dimer (Xan⁺)₂ exists in acidic solutions (pH < 0.5), the mono‐alcohol monocation Xan⁺–Xan‐OH at intermediate pH values (pH = 1–3), and the neutral diol at the highest pH‐values (pH > 3). Each dimer exhibits conformational degrees of freedom associated with rotations of either the xanthene moiety or of the diphenyl ether (DPE) linker. The barriers for rotation of the xanthylium moiety were evaluated using DFT calculations, yielding values of 23 kcal/mol for (Xan⁺)₂ and 11 kcal/mol for (Xan‐OH)₂, respectively. The rotational barrier for the diphenyl ether linker in Xan⁺–Xan‐OH (15 kcal/mol) was experimentally determined using variable temperature NMR measurements. The relative orientation of the two –OH groups in (Xan‐OH)₂ diol was investigated in solution and the solid state using NMR spectroscopy and X‐ray crystallography. The conformer observed in the solid state was found to be the In–Out conformer, while free rotation of the xanthenol units is thought to occur on the NMR timescale at room temperature. These studies are relevant for the design of linkers for efficient water oxidation catalysts. Copyright © 2016 John Wiley & Sons, Ltd.