Conformational analysis of N-arachidonylethanolamide (anandamide) using nuclear magnetic resonance and theoretical calculations

The conformational properties of cis-5,8,11,14-eicosatetraenoylethanolamide (anandamide) were analysed by the combined use of NMR experimental results plus molecular simulations. The structure of anandamide was found to be a predominantly linear with a seven-atom ring of the ethanolamine group having a hydrogen bond which stabilizes the molecule. The vinylic group present has a cis conformation in solution. The terminal chain has a linear conformation and undergoes isotropic fast motion typical of this structure. Copyright © 2001 John Wiley & Sons, Ltd.     

Experimental and theoretical NMR and IR studies of the side-chain orientation effects on the backbone conformation of dehydrophenylalanine residue

Conformation of N-acetyl-(E)-dehydrophenylalanine N', N'-dimethylamide (Ac-(E)-ΔPhe-NMe(2)) in solution, a member of (E)-α, β-dehydroamino acids, was studied by NMR and infrared spectroscopy and the results were compared with those obtained for (Z) isomer. To support the spectroscopic interpretation, the Φ, Ψ potential energy surfaces were calculated at the MP2/6-31 + G(d,p) level of theory in chloroform solution modeled by the self-consistent reaction field-polarizable continuum model method. All minima were fully optimized by the MP2 method and their relative stabilities were analyzed in terms of π-conjugation, internal H-bonds and dipole interactions between carbonyl groups. The obtained NMR spectral features were compared with theoretical nuclear magnetic shieldings, calculated using Gauge Independent Atomic Orbitals (GIAO) approach and rescaled to theoretical chemical shifts using benzene as reference. The calculated indirect nuclear spin-spin coupling constants were compared with available experimental parameters.     

Configuration and conformation of alfentanil hydrochloride. Conformational study by NMR and theoretical calculations

The configurational and conformational structure of alfentanil hydrochloride (1) was studied by nuclear magnetic resonance and theoretical calculations. Compound 1 is best described by equilibrium between two stereoisomeric piperidinium rings with the N‐substituent always being in equatorial position. Nuclear magnetic resonance spectra demonstrate that, depending on the solvent, 1 adopts the conformation with an axial methoxymethylene group. Computations were crucial in determining the importance of the transannular attractive interaction between the positive charge at the piperidinium N‐atom and the methoxymethyl group in position 4. Copyright © 2014 John Wiley & Sons, Ltd.     

Experimental and theoretical NMR study of selected oxocarboxylic acid oximes

1H and 13C NMR spectra of the oxocarboxylic acid oximes 2-hydroxyiminopropanoic acid (1), 2-(4-methylthiazol-2-yl)-2-(hydroxyimino)acetic acid (2) and 2-cyano-2-(hydroxyimino)acetic acid (3) were measured in DMSO-d6, D2O and acetone-d6 solutions. The data indicate the presence of hydrogen bonding in 1 and 2 and a strong electron-withdrawing effect due to the cyano group in 3. The effect of intra- and intermolecular hydrogen bonding on the hydrogen and carbon chemical shifts in these molecules was studied theoretically. Total energy calculations of the stability of various hydrogen-bonded species, in addition to equilibrium parameters and chemical shifts, were calculated using ab initio methods (RHF, MP2) and density functional theory (B3LYP), implemented in the Gaussian 98 software package. The gauge-including atomic orbital (GIAO) method was used to predict magnetic shielding constants. Chemical shift calculations for the most stable species agree fairly well with the observed data, especially for the hydroxyl protons. Substituents adjacent to the alpha-carbon show some influence of the oximic and carboxyl groups on the 13C chemical shifts, as expected for groups with different polar and anisotropic character.     

Conformational analysis: 3JHCOC and 3JHCCC Karplus relationships for methylene 1H nuclei

NAMFIS (NMR Analysis of Molecular Flexibility In Solution) was applied to 1‐[2‐(benzyloxy)phenyl]ethanone using quantitative ¹H‐¹H NOE distances and ³J proton‐carbon coupling constant (CC) restraints for averaged methylene proton ³J_HCOC and ³J_HCCC pathways H₂‐³J‐X imposed by density functional theory‐generated Karplus relationships. Comparison of the NOE‐only versus the NOE + CC conformational selections illustrates that the experimentally measured average ³J coupling constants of methylene protons can be used for solution conformational analysis, potentially valuable in the study of small‐molecule drugs and natural products which lack the typically studied H₁‐³J‐X Karplus relationships. Copyright © 2015 John Wiley & Sons, Ltd.     

C6‐substituted purine derivatives: an experimental and theoretical 1H, 13C and 15N NMR study

We measured the ¹H, ¹³ C and ¹⁵ N chemical shifts for a series of purine derivatives bearing a norbornane substituent in position 9 and various substituents in position 6. The experimental data were complemented with density functional theory (DFT) calculations. The comparison of the calculated and experimental chemical shifts provided us with information about the tautomer and conformational equilibria of the studied compounds. Copyright © 2012 John Wiley & Sons, Ltd.     

A comparative study between para‐aminophenyl and ortho‐aminophenyl benzothiazoles using NMR and DFT calculations

Ortho‐substituted and para‐substituted aminophenyl benzothiazoles were synthesised and characterised using NMR spectroscopy. A comparison of the proton chemical shift values reveals significant differences in the observed chemical shift values for the NH protons indicating the presence of a hydrogen bond in all ortho‐substituted compounds as compared to the para compounds. The presence of intramolecular hydrogen bond in the ortho amino substituted aminophenyl benzothiazole forces the molecule to be planar which may be an additional advantage in developing these compounds as Alzheimer's imaging agent because the binding to amyloid fibrils prefers planar compounds. The splitting pattern of the methylene proton next to the amino group also showed significant coupling to the amino proton consistent with the notion of the existence of slow exchange and hydrogen bond in the ortho‐substituted compounds. This is further verified by density functional theory calculations which yielded a near planar low energy conformer for all the o‐aminophenyl benzothiazoles and displayed a hydrogen bond from the amine proton to the nitrogen of the thiazole ring. A detailed analysis of the ¹H, ¹³C and ¹⁵N NMR chemical shifts and density functional theory calculated structures of the compounds are described. Copyright © 2014 John Wiley & Sons, Ltd.     

Conformational analysis of 2-halocyclopentanones by NMR and IR spectroscopies and theoretical calculations

The conformational isomerism of 2-chlorocyclopentanone and 2-bromocyclopentanone has been determined through the solvent dependence of the ¹H NMR ³J_HH coupling constants, theoretical calculations and infrared data, using the solvation theory for the treatment of NMR data. In 2-chlorocyclopentanone, the energy difference (E_Ψ-e − E_Ψ-a), in the isolated molecule at B3LYP level of theory, between the pseudo-equatorial (Ψ-e) and pseudo-axial (Ψ-a) conformers is 0.42 kcal mol⁻¹, which decreases in CCl₄ and in acetonitrile solutions, in good agreement with infrared data (ν_CO), despite the uncertainties of the latter method. The conformational equilibrium for 2-bromocyclopentanone is also between the Ψ-e and Ψ-a conformations, with an energy difference (E_Ψ-e − E_Ψ-a), in the isolated molecule at B3LYP level of theory, is 0.85 kcal mol⁻¹ which decreases in CCl₄ and in acetonitrile solutions, also in good agreement with infrared data.     

A theoretical study of multinuclear coupling constants in pyrazoles

The 243 coupling constants of eight N-R-pyrazoles [R=H, CH3, C6H5, COCH3, NH2, NO2, SO2CF3, Si(CH3)3] have been calculated and compared with 131 experimental values. The agreement is good and can be used to estimate new couplings. The whole collection has been statistically analyzed.     

Conformational analysis of N-benzyl-N-o-tolyl-p-methylbenzene-sulfonamides from dynamic H NMR experiments and theoretical calculations

Theoretical studies of molecular conformations of four N-benzyl-N-o-tolyl-p-methylbenzenesulfonamides, by means of semiempirical PM3, ab initio (RHF and MP2) methods, and DFT approach, are presented and discussed in comparison with the experimental data. The free energy (ΔG^#) of rotation obtained by the dynamic shape analysis of the ¹H NMR spectra is ca. 16 kcal/mol for those systems for which the barrier has been probed experimentally. Failure to determine the barrier in the experimental spectra in the case of one system is attributed to the chiral conformation of the global minimum. The rotational profile was established at the PM3 level and verified at the DFT level of theory. The solvent effect, the 0th-order vibrational corrections, and the temperature dependence of the Boltzman distribution of conformers and kinetic equilibrium are discussed.     

A theoretical study of the structure and bonding of UOX4 (X = F, Cl, Br, I) molecules: the importance of inverse trans influence.

During nitroxide-mediated polymerization (NMP) in the presence of a nitroxide R2(R1)NO*, the reversible formation of N-alkoxyamines [P-ON(R1)R2] reduces significantly the concentration of polymer radicals (P*) and their involvement in termination reactions. The control of the livingness and polydispersity of the resulting polymer depends strongly on the magnitude of the bond dissociation energy (BDE) of the C-ON(R1)R2 bond. In this study, theoretical BDEs of a large series of model N-alkoxyamines are calculated with the PM3 method. In order to provide a predictive tool, correlations between the calculated BDEs and the cleavage temperature (T(c)), and the dissociation rate constant (k(d)), of the N-alkoxyamines are established. The homolytic cleavage of the N-OC bond is also investigated at the B3P86/6-311++G(d,p)//B3LYP/6-31G(d), level. Furthermore, a natural bond orbital analysis is carried out for some N-alkoxyamines with a O-C-ON(R1)R2 fragment, and the strengthening of their C-ON(R1)R2 bond is interpreted in terms of stabilizing anomeric interactions.     

Conformational and configurational analysis of an N,N carbonyl dipyrrinone-derived oximate and nitrone by NMR and quantum chemical calculations

The geometries and relative energies of new N,N carbonyl dipyrrinone-derived oxime molecules (E/Z-s-cis 4a and E/Z-s-cis 4b) have been investigated. The calculated energies, molecular geometries, and (1) H/(13) C NMR chemical shifts agree with experimental data, and the results are presented herein. The E-s-cis conformations of 4a and 4b and the Z-s-cis conformation of 5b were found to be the thermodynamically most stable isomers with the oxime hydrogen atom or the methyl functional group adopting an anti-orientation with respect to the dipyrrinone group. This conformation was unambiguously supported by a number of 2D NMR experiments.     

Conformational evaluation and detailed 1H and 13C NMR assignments of eremophilanolides

Extensive application of 1D and 2D NMR methodology, combined with molecular modeling, allowed the complete 1H and 13C NMR assignments of eremophilanolides from Senecio toluccanus. Comparison of the experimental 1H, 1H coupling constant values with those generated employing a generalized Karplus-type relationship, using dihedral angles extracted from MMX and DFT calculations, revealed that the epoxidized eremophilanolides 1 and 2 show conformational rigidity at room temperature, whereas molecules 3-6, containing an isolated double bond, are conformationally mobile.     

Synthesis and spectroscopy of N3P3X5OCH=CH2 (X = Cl, F, OCH3, OCH2CF3, N(CH3)2) and N3P3X4(OCH=CH2)2 (X = Cl, N(CH3)2). Correlations of ultraviolet photoelectron spectroscopy and nuclear magnetic resonance data to electronic and geometrical structure

The syntheses of the vinyloxycyclotriphosphazene derivatives N3P3X5OCH=CH2 (X = OMe, OCH2CF3) and the N3P3(NMe2)4(OCH=CH2)2 isomeric mixture along with improved preparations of N3P3X5OCH=CH2 (X = F, NMe2) are reported. The interactions between the vinyloxy function and the cyclophosphazene in these and the previously reported N3P3Cl5 (OCH=CH2) and N3P3F6-n(OCH=CH2)n (n = 1-4) have been examined by ultraviolet photoelectron spectroscopy (UPS) and NMR spectroscopy. The UPS data for the chloro and fluoro derivatives show a strong electron-withdrawing effect of the phosphazene on the olefin that is mediated with decreasing halogen substitution. The 1H and 13C NMR data for N3P3X5OCH=CH2 (X = F, Cl, OMe, OCH2CF3, NMe2) show significant changes as a function of the phosphazene substituent. There is a linear correlation between the beta-carbon chemical shift on the vinyloxy unit and the phosphorus chemical shift at the vinyloxyphosphorus centers. The chemical shifts of the different phosphorus centers on each ring are also related in a linear fashion. These relationships may be understood in terms of the relative electron donor-acceptor abilities of the substituents on the phosphazene ring. The 1H NMR spectra of the N3P3(NMe2)4(OCH-CH2)2 isomeric mixture allow for assignment of the relative amounts of cis and trans isomers. A model for the observed cis preference in the formation of N3P3Cl4(OCH=CH)2 is presented.     

Conformational analysis,part 43. A theoretical and LIS/NMR investigation of the conformations of substituted benzamides

A refined Lanthanide‐Induced‐Shift Analysis (LISA) is used with molecular mechanics and ab initio calculations to investigate the conformations of benzamide ( 1 ), N‐methylbenzamide ( 2 ), N,N‐dimethylbenzamide ( 3 ) and the conformational equilibria of 2‐fluoro ( 4 ), 2‐chloro ( 5 ) and N‐methyl‐2‐methoxy benzamide ( 6 ). The amino group in 1 is planar in the crystal but is calculated to be pyramidal with the CO/phenyl torsional angle (ω) of 20–25°. The LISA analysis gave acceptable agreement factors (Rcryst ≤ 1%) for the ab initio geometries when ω was decreased to 0°, the other geometries were not as good. In 2 , the N‐methyl is coplanar with the carbonyl group in all the geometries. Good agreement was obtained for the RHF geometries, with ω 25°, the other geometries were only acceptable with increased values of ω. In 3 , good agreement for the RHF and PCModel geometries was found when ω was changed from the calculated values of 40° (RHF) and 90° (PCModel) to ca. 60°, the X‐ray and B3LYP geometries were not as good. The two substituted compounds 4 , 5 and 6 are interconverting between the cis (O,X) and trans (O,X) conformers. The more stable trans conformer is planar in 4 and 6 but the cis form non‐planar. Both the cis and trans conformers of 5 are non‐planar. There is an additional degree of freedom in 6 due to the 2‐methoxy group, which can be either planar or orthogonal to the phenyl ring in both conformers. The conformer ratios were obtained from the LISA analysis to give Ecis‐Etrans in 4 > 2.3 kcal/mol (CDCl₃) and 1.7 kcal/mol (CD₃CN), in 5 0.0 kcal/mol (CD₃CN) and in 6 > 2.5 kcal/mol (CDCl₃) and 2.0 kcal/mol (CD₃CN). These values were used with the observed versus calculated ¹H shifts to determine the conformer ratios and energies in DMSO solvent to give Ecis‐Etrans 1.1, ?0.1 and 1.8 kcal/mol for ( 4 ), ( 5 ) and ( 6 ). Comparison of the observed versus calculated conformer energies show that both the MM and ab initio calculations overestimate the NH..F hydrogen bond in ( 4 ) by ca. 2 kcal/mol. Copyright © 2015 John Wiley & Sons, Ltd.     

Structure elucidation of 11-amino-8-hydroxypentacyclo[5.4.0.0(2, 6).0(3, 10).0(5, 9)]undecane-8,11-lactam through selective acetylation and complete 1H and 13C NMR spectral assignment of the mono-, di- and triacetates

NMR techniques cannot unambiguously distinguish between 11-amino-8-hydroxypentacyclo[5.4.0.0(2, 6).0(3, 10).0(5, 9)]undecane-8,11-lactam and 8-amino-11-hydroxypentacyclo[5.4.0.0(2, 6).0(3, 10).0(5, 9)]undecane-8,11-lactam, both of which are possible products during the reaction of pentacyclo[5.4.0.0(2, 6).0(3, 10).0(5, 9)]undecane-8,11-dione with Strecker reagents. Treatment of 11-amino-8-hydroxy-pentacyclo[5.4.0.0(2, 6).0(3, 10).0(5, 9)]undecane-8,11-lactam with acetic anhydride at room temperature produced a monoacetate. With acetic anhydride containing sodium acetate, a triacetate was obtained at reflux temperature. Treatment with acetyl chloride and N,N-dimethylaniline produced a diacetate. High-field 1H and 13C NMR techniques were used in the structure elucidation and assignment of the different NMR resonances of these three acetylated compounds.     

NMR spectroscopic and theoretical study on the isomerism of dimethyl benzodiazepine(diylidene)diacetates

The isomerism of dimethyl 2,2′-(7,8-dichloro-1H-benzo[b][1,4]diazepine-2,4-(3H,5H)diylidene)diacetate ( 1a ) and dimethyl 2,2′-(7,8-dichloro-3-methyl-1H-benzo[b][1,4]diazepine-2,4-(3H,5H)diylidene)diacetate ( 1b ) was investigated by ¹H, ¹³C and ¹⁵N nuclear magnetic resonance (NMR) spectroscopy. In CDCl₃ solution, inversion of the diazepine ring was observed, whereas in (D₆)DMSO and (D₇)DMF solution, besides the ring inversion, a partial cleavage of one chelate ring appeared connected with (E/Z) isomerization about one of the exocyclic C=C bonds. Gibbs free energies (ΔG) and free activation energies (ΔG^≠) were calculated based on B3PW91-SCRF/ZVP DFT computations. Agreement between NMR data and density functional theory (DFT) computations was found.     

Predicting the NMR spectra of nucleotides by DFT calculations: cyclic uridine monophosphate

We present an experimental and quantum chemical NMR study of the mononucleotide cyclic uridine monophosphate in water. Spectral parameters ((1)H and (13)C chemical shifts and (1)H--(1)H, (13)C--(1)H, (31)P--(13)C and (31)P--(1)H spin-spin coupling constants) have been carefully obtained experimentally and calculated using DFT methods including the solvent effect and the conformational flexibility of the solute. This study confirms that the (1)H and (13)C spectra of polar, flexible molecules in aqueous solution can be predicted with a high level of accuracy, comparable to that obtained for less complex systems.     

Synthesis and 1H and 13C NMR structural analysis of cis‐ and trans‐2‐imino‐1,3‐ and ‐3,1‐perhydrobenzoxazines and their 3‐ and 1‐N‐methyl derivatives

cis‐ and trans‐2‐imino‐1,3‐ and ‐3,1‐perhydrobenzoxazines and the N‐methyl derivatives of the latter were synthesized from the corresponding cyclic 1,3‐amino alcohol with cyanogen bromide. The configurations of the studied compounds were confirmed by ¹H and ¹³C NMR spectra. All trans‐fused compounds exist in biased chair–chair conformations as expected, whereas the cis‐fused 1,3‐benzoxazines attain exclusively the O‐in conformations. The cis‐fused 3,1‐benzoxazines, especially the 1‐methyl‐substituted derivatives, tend to favor the N‐out form, obviously owing to the favorable axial orientation of this N‐methyl. Copyright © 2003 John Wiley & Sons, Ltd.     

Stereochemistry and conformations of natural 1,2-epoxy-guaianolides based on 1D and 2D NMR data and semiempirical calculations

From detailed study of 1D and 2D NMR spectra of ten natural 1,2-epoxyguaianolides (bis-1,2:3,4-epoxyguaianolides and guaianolide-1,2-epoxychlorohydrins), we identified general spectral traits helpful for stereochemical assignment of such sesquiterpene lactones. We found that the chemical shifts of certain (1)H and (13)C nuclei are consistently dependent on the configuration of 1,2-epoxy-ring which could be used as a simple rule for establishing this configuration. Then, from 1D and 2D (COSY, NOESY, HMQC, HMBC) NMR data, applying the observed rule, the structure and stereochemistry of two new, diastereomeric guaianolide-1,2-epoxychlorohydrins, isolated from Achillea serbica, are determined. The NMR data, namely, nuclear overhauser enhancement (NOE) correlations, pointed out two conformations of guaianolide's cycloheptane ring. The semiempirical calculations (AM1 and PM3 methods), performed in order to gain additional information regarding conformations, resulted in three geometries of investigated lactones. Even so, the conformations derived from the NMR data agreed well with those calculated by semiempirical methods.