Absolute configuration of tert-butyl-1-(2-methylnaphthyl)phosphine oxide

The enantiomers of tert-butyl-1-(2-methylnaphthyl)phosphine oxide 1 have been separated using a homemade HPLC column and an analytical gradient system. Vibrational absorption and circular dichroism spectra for both enantiomers have been measured in CD2Cl2 and CH2Cl2 solutions in the 2000-900 cm(-1) region. The fully relaxed potential energy surface of (S)-tert-butyl-1-(2-methylnaphthyl)phosphine oxide, obtained using the B3LYP functional with a 6-31G basis set, indicated two stable conformers with their populations in a approximately 2:1 ratio. The vibrational absorption and VCD spectra are predicted for these two conformers using the B3LYP functional with a 6-31G basis set. The comparison of predicted and experimental spectra indicated that (+)-tert-butyl-1-(2-methylnaphthyl)phosphine oxide is in the (S)-configuration. This assignment is supported by the ab initio prediction of positive optical rotation for the most stable conformer with an (S)-configuration and the nonequivalence sense of the tert-butyl group chemical shift observed in the 1H NMR spectrum of this enantiomer measured in the presence of (+)-(S)-mandelic acid as a chiral solvating agent.     

Conformational analysis and stereochemical dependences of 31P–1H spin–spin coupling constants of bis(2‐phenethyl)vinylphosphine and related phosphine chalcogenides

Theoretical energy‐based conformational analysis of bis(2‐phenethyl)vinylphosphine and related phosphine oxide, sulfide and selenide synthesized from available secondary phosphine chalcogenides and vinyl sulfoxides is performed at the MP2/6‐311G** level to study stereochemical behavior of their ³¹P–¹H spin–spin coupling constants measured experimentally and calculated at different levels of theory. All four title compounds are shown to exist in the equilibrium mixture of two conformers: major planar s‐cis and minor orthogonal ones, while ³¹P–¹ H spin–spin coupling constants under study are found to demonstrate marked stereochemical dependences with respect to the geometry of the coupling pathways, and to the internal rotation of the vinyl group around the P(X)‐C bonds (X = LP, O, S and Se), opening a new guide in the conformational studies of unsaturated phosphines and phosphine chalcogenides. Copyright © 2009 John Wiley & Sons, Ltd.     

Synthesis and conformational analysis of 6-C-methyl-substituted 2-acetamido-2-deoxy-beta-D-glucopyranosyl mono- and disaccharides

Several 6-C-substituted 2-acetamido-2-deoxy-beta-D-glucopyranosides (beta-D-GlcNAc monosaccharides 1a-3a and 1,4-linked disaccharides 1b-3b) were studied by solution NMR spectroscopy. Conformational analysis of the (6S)- and (6R)-C-methyl-substituted beta-d-GlcNAc monosaccharides indicates that the stereodefined methyl groups impose predictable conformational biases on the exocyclic C-5-C-6 bond, as determined by (1)H-(1)H and (13)C-(1)H coupling constants. Variable-temperature NMR experiments in methanol-d(4) were performed to determine DeltaDeltaH and DeltaDeltaS values derived from the two lowest energy conformers. These indicate that while the influence of 6-C-methyl substitution on conformational enthalpy is in accord with the classic principles of steric interactions, conformational preference in solution can also be strongly affected by other factors such as solvent-solute interactions and solvent reorganization.     

Searching for conformers of nine- to twelve-ring hydrocarbons on the MM2 and MM3 energy surfaces: Stochastic search for interconversion pathways

The stochastic search method was employed to find as many conformers on the MM2 and MM3 energy surfaces as possible for cyclic saturated hydrocarbons with ring sizes from 9 through 12. The number found was 8 MM2 (8 MM3) for 9 rings, 18 MM2 (16 MM3) for 10 rings, 40 MM2 (29 MM3) for 11 rings, and 111 MM2 (90 MM3) for 12 rings. A measure of similarity between pairs of conformers of a compound, called conformational distance, is described. It was used to correlate similar MM2 and MM3 conformers. It was discovered that some conformers on each energy surface are not close to minima on the other surface in rings larger than 9. On refinement with the other optimizer, they changed considerably—going downhill to other previously found minima on the other energy surface or (in a few cases) going to minima which had not been found by direct searches. Conformational distance was also employed as an indication of which pairs of MM2 (or MM3) conformers are likely to interconvert rapidly. A new stochastic procedure of using small kicks was used to search for the most likely interconversion processes among the conformers. There is fairly good agreement between the most facile pathways located by it and unusually short conformational distances. Several additional 12-ring conformers (not found with previous methods) were located through application of this small kick procedure.     

Conformational analysis of ticagrelor: effect of noncovalent interaction on conformational population

In order to track the source of duplicated peaks in the ¹H-NMR spectrum of Ticagrelor, variable-temperature NMR (VT-NMR) experiment was carried out with temperature increasing from 300 to 343 K. The result showed that the phenomenon was brought forth by coexistence of conformational isomers. Subsequently, conformational search was carried out by molecular mechanics (MM) stimulations associating with quantum mechanics (QM) calculations. The results revealed that the isomers resulting in duplicated proton peaks were introduced by the rotation of 2,4-diflurophenyl group on C^3’position of cyclopropyl. Finally, noncovalent interaction (NCI) topological analysis of the conformers exhibited that CH-π interactions and H-bonds play important roles in controlling the population of conformers of ticagrelor.     

Conformational analysis of 2-aminophenyl-, 2-aminobenzyl-, and 2-nitrobenzyl(diphenyl)phosphine oxides

The polarity and conformations of 2-aminophenyl-, 2-aminobenzyl-, and 2-nitrobenzyl(diphenyl)-phosphine oxides were studied by the dipole moment method, IR spectroscopy, and quantum chemical calculations. 2-Aminophenyl- and 2-aminobenzyl(diphenyl)phosphine oxides were found to exist preferentially as conformers with intramolecular hydrogen bond. 2-Nitrobenzyl(diphenyl)phosphine oxide is likely to be represented by equilibrium mixture of three conformers in which the phosphoryl and nitro groups are oriented syn or anti with respect to the \(PC_{sp^3 } C_{sp^2 } \) fragment.     

Conformation and configuration of tertiary amines via GIAO-derived (13)C NMR chemical shifts and a multiple independent variable regression analysis.

The (13)C chemical shifts of six tertiary amines of unambiguous conformational structure are compared to predicted (13)C NMR chemical shifts obtained via empirically scaled GIAO shieldings for geometries from MM3 molecular mechanics calculations. An average deviation, absolute value of Deltadelta(av), of 0.8 ppm and a maximum deviation, absolute value of Deltadelta(max), of 2.8 ppm between predicted and experimental (13)C shifts of the six tertiary amines of unambiguous structure are found. In several cases of tertiary amines subject to rapid exchange, where experimental (13)C shifts at room temperature are weighted averages of multiple conformers, a comparison of calculated (13)C shifts of all reasonable MM3 predicted conformers with experimental (13)C shifts via a multiple independent variable regression analysis provides an efficient method of determining the major and minor conformers. The examples presented are 2-methyl-2-azabicyclo[2.2.1]heptane and 1,6-diazabicyclo[4.3.1]decane, which each have two expected contributing structures, and 2-(diethylamino)propane and 1,8-diazabicyclo[6.3.1]dodecane, where ten and seven low-energy conformers, respectively, are predicted by MM3 calculations.     

Calculated chemical shifts as a fine tool of conformational analysis: an unambiguous solution for haouamine alkaloids

In this study, for the first time, conformational analysis by calculated chemical shifts (CCS) deals with a real conformational problem of a large biomolecule. This new methodology is applied to haouamine A, which is much more stereodynamically puzzled than the small models used to validate previous CCS-based conformational studies. Thorough NMR experiments by Zubia et al. on this exotic polyfunctional paracyclophane alkaloid could not determine which experimentally detected interconversion of this compound occurs in solution, rotation or N-inversion. The present study uses CCS to locate the lowest energy conformers and thus to identify the observed stereodynamic process. Molecular mechanics calculations were used to explore the conformational space of this polycyclic system, and then the geometry of located conformers was refined by ab initio calculations at the B3LYP/6-31G(d,p) level; an implicit model for acetone solution was employed. Calculated relative energies are considered too inaccurate to identify the lowest energy (i.e., those detectable by NMR) conformers. Instead, rational regression analysis of CCS for carbon atoms using B3LYP/6-31+G(d)//GIAO-based calculations singled out two conformers from a large set of alternative low energy structures, although solvation shell was not explicitly included in the model. For only these two conformers, the differences in CCS (Delta delta) for selected pairs of carbons are very similar to the experimental Delta delta values. Thus, the conformers monitored by NMR have now been identified; their piperideine ring is of (1)Sf and Sf 1 (sofa-shaped) geometry. This azacycle appears to be flexible despite the presence of the ethylenebiphenylene bridge in haouamines. Interconversion between the conformers probably occurs via a concerted process of inversion of the piperideine ring, N-inversion coupled with rotation around the C-N bond, and rotation around two C-C bonds in the ethylenebiphenylene bridge. This CCS method of conformational analysis is sufficiently simple and reliable that if chemical shifts for a pair of the same carbons are sufficiently different in routine (13)C NMR spectra of stereoisomers (ca. > or = 2 ppm), the "resolving power" of the CCS technique may rival that of NMR techniques.     

Synthesis and Stereochemistry of Substituted 1,3-Dioxa-2-silacyclohexanes: VII. Synthesis and Stereochemistry of Substituted 2-Vinyl-2-methyl-1,3-dioxa-2-silacyclohexanes

The stereochemistry of substituted 2-vinyl-2-methyl-1,3-dioxa-2-silacyclohexanes was studied by ^1Hand ^13C NMR spectroscopy. The configurational and conformational assignment of a mixture of 2-vinyl-2,4-dimethyl-1,3-dioxa-2-silacyclohexane diastereomers with various ratios of the cis and trans forms was made. The molecules of both conformers occur chiefly in the chair conformartion with equatorial location of the methyl group at the C⁴ atom. The experimental data were confirmed by AM1 and MM+ optimization of the molecular geometry.     

Conformational Composition of Stereoisomers of 2-Alkyl-5-isopropyl-4-methyl-1,3,2-dioxaborinanes

¹H and ¹³C NMR spectroscopy was used to assign the configuration of a mixture of stereoisomers of 2-alkyl-5-isopropyl-4-methyl-1,3,2-dioxaborinanes with different ratios of the cis and trans forms. These forms differ in the configuration of C⁽⁴⁾ in the ring. The results of MM+ and AM1 calculations for the optimal geometry indicate high conformational flexibility of both isomers, which exist in an equilibrium mixture of sofa and half-chair conformers.     

Trivinylphosphine and trivinylphosphine chalcogenides: stereochemical trends of ³¹P-¹H spin-spin coupling constants

A combined theoretical and experimental study of the stereochemical behavior of (31)P-(1)H spin-spin coupling constants has been performed in the series of trivinylphosphine and related trivinylphosphine oxide, sulfide and selenide. Theoretical energy-based conformational analysis of the title compounds performed at the MP2/6-311G** level reveals that each of the four compounds of this series exists in the equilibrium mixture of five true-minimum conformers, namely s-cis-s-cis-s-cis, s-cis-s-cis-gauche, syn-s-cis-gauche-gauche, anti-s-cis-gauche-gauche and gauche-gauche-gauche, which were taken into account in the conformational averaging of (31)P-(1)H spin-spin couplings calculated at the second-order polarization propagator approach/aug-cc-pVTZ-J level of theory. All (31)P-(1)H spin-spin coupling constants involving phosphorus and either of the vinyl protons are found to demonstrate a marked stereochemical dependences with respect to the geometry of the coupling pathway and internal rotation of the vinyl group around the P-C bond which is of major importance in the stereochemical studies of the unsaturated phosphines and phosphine chalcogenides.     

Conformational properties of the macrocyclic trichothecene mycotoxin verrucarin A in solution

Phase-sensitive nuclear Overhauser enhancement spectroscopy (NOESY) experiments, (3)J couplings and computational molecular modeling (MM2* and MMFF force fields) were employed to examine the conformational properties of verrucarin A in chloroform solutions. The MMFF force field calculations resulted in a family of 12 low-energy structures along with their populations, the latter being determined by the NMR analysis of molecular flexibility in solution(NAMFIS) deconvolution analysis. The concluded model was capable of reproducing successfully the experimental NOESY cross-peak volumes and the proton-coupling constants. Among the 12 conformers, the one which was similar to the structure of verrucarin A in the solid state was the predominant accounting for 75% of the total relative population, although other low-energy conformations contributed to a lesser degree in order to explain the experimental data.     

Liquid structure of room-temperature ionic liquid, 1-Ethyl-3-methylimidazolium bis-(trifluoromethanesulfonyl) imide

The liquid structure of 1-ethyl-3-methylimidazolium bis-(trifluoromethanesulfonyl) imide (EMI(+)TFSI(-)) has been studied by means of large-angle X-ray scattering (LAXS), (1)H, (13)C, and (19)F NMR, and molecular dynamics (MD) simulations. LAXS measurements show that the ionic liquid is highly structured with intermolecular interactions at around 6, 9, and 15 A. The intermolecular interactions at around 6, 9, and 15 A are ascribed, on the basis of the MD simulation, to the nearest neighbor EMI(+)...TFSI(-) interaction, the EMI(+)...EMI(+) and TFSI(-)...TFSI(-) interactions, and the second neighbor EMI+...TFSI(-) interaction, respectively. The ionic liquid involves two conformers, C(1) (cis) and C(2) (trans), for TFSI(-), and two conformers, planar cis and nonplanar staggered, for EMI(+), and thus the system involves four types of the EMI(+)...TFSI(-) interactions in the liquid state by taking into account the conformers. However, the EMI(+)...TFSI(-) interaction is not largely different for all combinations of the conformers. The same applies alsoto the EMI(+)...EMI(+) and TFSI(-)...TFSI(-) interactions. It is suggested from the 13C NMR that the imidazolium C(2) proton of EMI(+) strongly interacts with the O atom of the -SO(2)(CF(3)) group of TFSI(-). The interaction is not ascribed to hydrogen-bonding, according to the MD simulation. It is shown that the liquid structure is significantly different from the layered crystal structure that involves only the nonplanar staggered EMI(+) and C(1) TFSI(-) conformers.     

Meso-porphyrinylphosphine oxides: mono- and bidentate ligands for supramolecular chemistry and the crystal structures of monomeric {[10,20-diphenylporphyrinatonickel(II)-5,15-diyl]-bis-[P(O)Ph(2)] and polymeric self-coordinated {[10,20-diphenylporphyrinatozinc(II)-5,15-diyl]-bis-[P(O)Ph(2)]}

A series of porphyrins substituted in one or two meso positions by diphenylphosphine oxide groups has been prepared by the palladium-catalyzed reaction of diphenylphosphine or its oxide with the corresponding bromoporphyrins. Compounds {MDPP-[P(O)Ph2]n} (M = H2, Ni, Zn; H2DPP = 5,15-diphenylporphyrin; n = 1, 2) were isolated in yields of 60-95%. The reaction is believed to proceed via the conventional oxidative addition, phosphination, and reductive elimination steps, as the stoichiometric reaction of eta(1)-palladio(II) porphyrin [PdBr(H2DPP)(dppe)] (H2DPP = 5,15-diphenylporphyrin; dppe = 1,2-bis(diphenylphosphino)ethane) with diphenylphosphine oxide also results in the desired mono-porphyrinylphosphine oxide [H2DPP-P(O)Ph2]. Attempts to isolate the tertiary phosphines failed due to their extreme air-sensitivity. Variable-temperature 1H NMR studies of [H2DPP-P(O)Ph2] revealed an intrinsic lack of symmetry, while fluorescence spectroscopy showed that the phosphine oxide group does not behave as a "heavy atom" quencher. The electron-withdrawing effect of the phosphine oxide group was confirmed by voltammetry. The ligands were characterized by multinuclear NMR and UV-visible spectroscopy, as well as mass spectrometry. Single-crystal X-ray crystallography showed that the bis(phosphine oxide) nickel(II) complex {[NiDPP-[P(O)Ph2]2} is monomeric in the solid state, with a ruffled porphyrin core and the two P=O fragments on the same side of the average plane of the molecule. On the other hand, the corresponding zinc(II) complex formed infinite chains through coordination of one Ph2PO substituent to the neighboring zinc porphyrin through an almost linear P=O...Zn unit, leaving the other Ph2PO group facing into a parallel channel filled with disordered water molecules. These new phosphine oxides are attractive ligands for supramolecular porphyrin chemistry.     

On the optical activity of paraffinic hydrocarbons

An expression for potential energy as a function of torsion angle about a saturated CC bond is developed analytically. This equation is used in the development of two methods for the conformational analysis of paraffins-one based on consideration only of exactly staggered conformers and one giving consideration to energy at 1° intervals of torsion angle. Two methods of assigning molecular rotations to hydrocarbon conformers are considered. Various combinations of results so obtained are compared as ways to calculate rotations for paraffins.     

Conformational dynamics in nitrogen-fused azabicycles

Using molecular mechanics (MM3 force field)-based methodology, conformational dynamics have been studied for 1-azabicyclo[2.2.0]hexane, 1-azabicylo[3.3.0]octane, and 1-azabicylo[4.4.0]decane. Obtained conformational schemes describe the flexibity of these parent azabicyles as well as permit us to estimate conformational mobility in related N-fused systems. Quantum mechanics ab initio calculations have been used in order to check the reliability of molecular mechanics-provided estimates of relative energy of conformers. The previous dynamic NMR (DNMR) data have been reinterpreted for some polycyclic alkaloids.     

Synthesis of Glycosylphosphine Oxides and Related Compounds

The benzyl-protected glycosyl acetates 1 , 6 , 11 , and 15 react with MeOPPh₂ under catalysis by TMSOTf to yield diastereoselectively the glycosylphosphine oxides 2 , 3 , 8 , 12 , 13 , and 16 , with a strong preference for the 1,2-cis-configurated anomers. Hydrogenolysis of the major products gave the crystalline, unprotected phosphine oxides 4 , 9 , 14 , and 17 , of which 4 was transformed in to the acetate 5 , and 9 into the benzoate 10 . The benzylated phosphine oxides 4 , 8 , 12 , and 16 were reduced with Cl₃SiH in the presence of a tertiary amine to form the phosphines 18 , 21 , 24 , and 26 , which were transformed into the phosphine sulfides 19 , 22 , 25 , and 27 . Moreover, 18 and 21 , were characterized as the borane adducts 20 , and 23 . The structure of the (arabinofuranosyl)phosphine oxide 12 , the corresponding sulfide 25 , and of the borane complex 20 were established by X-ray analysis. According to NMR spectroscopy, the equatorial pyranosylphosphine oxide 8 , the sulfide 22 , and the borane complex 23 adopt a ⁴C₁ conformation. The axial phosphine oxide 2 is a flattened ⁴C₁, the sulfide 19 exists as a B_2,5, and the borane complex 20 is a flattened ⁴C₁ in the solid sate and a B_2,5 in solution. Thus, the conformational behavior of these α-D -glucopyranose derivatives reflects the steric requirement of the P-substituents.     

Conformational study of (8alpha,8'beta)-bis(substituted phenyl)-lignano-9,9'-lactones by means of combined computational, database mining, NMR, and chemometric approaches

Beta-(3,4-Methylenedioxybenzyl)-gamma-butyrolactone (MDBL) and (-)-hinokinin (HK) were obtained by partial synthesis and characterized by 1H NMR and computational methods (conformational analysis, molecular modeling, structural data mining and chemometrics). Three conformers were detected for MDBL and nine were found for HK. The energy differences are around 1 and 2 kcal mol(-1) and rotation barriers are less than 3 and 5 kcal mol(-1) for MDBL and HK conformers, respectively. The geometries of these conformers, obtained from semiempirical PM3 and density functional theory (DFT) B3LYP 6-31G** calculations agree satisfactorily with 1H NMR data (vicinal proton-proton coupling constants) and structures retrieved from the Cambridge Structural Database (torsion angles). DFT combined with some variants of the Haasnoot-de Leeuuw-Altona equations gives the best predictions for the coupling constants. The molecular conformation of MDBL, of HK, and of related systems depends not only on intramolecular interactions but also on crystal packing forces and solvent-solute interactions, in particular hydrogen bonds and polar interactions. Hydration favors more stable HK conformers, which can be important for their behavior in chemical and biological systems.     

Conformational analysis of phorboxazole bis-oxazole oxane fragment analogs by NMR spectroscopy and molecular modeling simulations

We present a detailed conformational study of a simplified synthetic analog of the bis-oxazole oxane fragment found in the cytostatic agents phorboxazole A and B based on results from NMR spectroscopy and molecular modeling simulations. Complete 1H and 13C resonance assignments for the bis-oxazole oxane system were carried out through the use of COSY, HSQC, HMBC, TOCSY, and HSQC-TOCSY experiments, and its conformational preferences in solution were investigated by analysis of 3J(HH) coupling constants and NOE enhancements obtained from 1D and 2D NOESY experiments. In order to solve inconsistencies from our preliminary structural studies, simulated annealing studies were performed to thoroughly sample the phase space available to the molecule. Our results reveal that the six-membered oxane ring, which constitutes the most important moiety regarding the three-dimensional (3D) structure and flexibility of the analog, exists in rapid equilibrium between its two accessible chair conformers in an approximate ratio of 70:30. The information gathered from these studies will be of critical importance in our efforts to prepare novel compounds with phorboxazole-like structure and activity.