Cyclobutanone mimics of penicillins: effects of substitution on conformation and hemiketal stability

The tendency for carbocyclic analogues of penicillins to undergo hydrate and hemiketal formation is central to their ability to function as beta-lactamase inhibitors. 2-Thiabicyclo[3.2.0]heptan-6-one-4-carboxylates with alkoxy functionality at C3 have been prepared through two complementary diastereoselective substitution reactions following a highly stereoselective chlorination with sulfuryl chloride. We have found that carbocyclic analogues with 3beta substituents favor an endo envelope conformation in solution, the solid state, and the gas phase, whereas those with 3alpha substituents adopt an exo envelope. Evidence from X-ray crystal structures and ab initio calculations suggests that an anomeric effect contributes to the large conformational preference of the tetrahydrothiophene ring that favors the C3 substituent in an axial orientation. In addition, the envelope conformation of the bicycle, which is determined by the stereochemistry of the C3 substituent, has a dramatic effect on the ability of the cyclobutanone to undergo hemiketal formation in methanol-d4.     

DFT and NMR parameterized conformation of valeranone

A Monte Carlo random search using molecular mechanics, followed by geometry optimization of each minimum energy structure employing density functional theory (DFT) calculations at the B3LYP/6-31G* level and a Boltzmann analysis of the total energies, generated accurate molecular models which describe the conformational behavior of the antispasmodic bicyclic sesquiterpene valeranone (1). The theoretical H-C-C-H dihedral angles gave the corresponding 1H, 1H vicinal coupling constants using a generalized Karplus-type equation. In turn, the 3J(H,H) values were used as initial input data for the spectral simulation of 1, which after iteration provided an excellent correlation with the experimental 1H NMR spectrum. The calculated 3J(H,H) values closely predicted the experimental values, excepting the coupling constant between the axial hydrogen alpha to the carbonyl group and the equatorial hydrogen beta to the carbonyl group (J(2beta, 3beta)). The difference is explained in terms of the electron density distribution found in the highest occupied molecular orbital (HOMO) of 1. The simulated spectrum, together with 2D NMR experiments, allowed the total assignment of the 1H and 13C NMR spectra of 1.     

The conformation of epinephrine in polar solvents: an NMR study

Structural Chemistry - Epinephrine (Epi) is a physiologically important catecholamine. Molecular conformation of Epi controls the interactions with other molecules and its biological effects. There...     

NMR experiments on acetals—56 : Conformational study of 1,3-dioxene

From the ¹H-NMR parameters, extracted from the spectra of 1,3-dioxene, 5-Me-1,3-diox-4-ene, 4,5-diMe-1,3-diox-4-ene and of 2,4,5-triMe-1,3-diox-4-ene, it follows that the preferred conformations are the 1,2-diplanar (sofa) C₂ form (Fig. 1B). The barrier to ring reversal in 5-Me-1,3-dioxene was found to be 7·2±0·2 kcal/mole at ?123° (in freon-21).     

NMR spectra and conformation of cembrene in solution

Using dimeric NMR spectroscopy, a complete interpretation of the¹H and¹³C NMR spectra of the diterpene hydrocarbon cembrene has been made. The experimental values of the SSCs for the¹H atoms in the PMR spectra of cembrene agree well with those calculated for the lowest-energy (“crystal”) conformation. In the light of the observation of intramolecular NOEs and of the low-temperature¹³C NMR spectra, it has been concluded that the cembrene molecule retains the “crystal” conformation in solution.     

NMR spectra and conformation of cembrene in solution

Using dimeric NMR spectroscopy, a complete interpretation of the¹H and¹³C NMR spectra of the diterpene hydrocarbon cembrene has been made. The experimental values of the SSCs for the¹H atoms in the PMR spectra of cembrene agree well with those calculated for the lowest-energy (crystal) conformation. In the light of the observation of intramolecular NOEs and of the low-temperature¹³C NMR spectra, it has been concluded that the cembrene molecule retains the crystal conformation in solution.Institute of Organic Chemistry, Siberian Branch, Academy of Sciences of the USSR, Novosibirsk. Translated from Khimiya Prirodnykh Soedinenii, No. 4, pp. 455–459, July–August, 1991.     

Study of conformation of cryptahemispherands by two-dimensional NMR spectroscopy

Two-dimensional NMR spectroscopy (NOESY, COSY-DQF) has been used in a study of nitrogen-containing cryptahemispherands and their complexes with alkali metals. On the basis of experimentally established interproton distances, the preferred conformations of these molecules have been established. It has been shown that the important features of structure determining the molecular conformation are (a) the orientation of the N-CH₂(Ar) bond relative to the plane of the crown ether and (b) the length of the methylene bridge (spacer). The spatial and torsional angles have been determined. It has been established that as the length of the bridge is increased, the structure of these molecules approaches a betaine structure, with mutually parallel positions of the phenyl rings. Upon complexation, their orientation changes to mutually perpendicular, and this leads to enlargement of the inner cavity of the molecule and a corresponding rearrangement of its dimensions toward the ionic radius of the alkali metal.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 406–411, March, 1993.     

Addressing non-idealities in NMR experiments on rotating liquid crystals

Unequivocal evidence for a biaxial nematic phase in low-molar-mass calamitic thermotropic liquid crystals has been challenging to generate. Recently we provided NMR evidence that nonlinear calamitic mesogens based on the oxadiazole heterocycle exhibit a biaxial nematic phase (Phys. Rev. Lett., 2004, 92, 145505). Herein we probe the robustness of that claim by exploring potential variations of the director distribution from the ideal one that would apply to nematics rotated about an axis perpendicular to the spectrometer magnetic field. Moreover, we demonstrate that our methodology, when applied to the high temperature uniaxial nematic TBBA, yields a biaxial order parameter η = 0.0, thereby confirming the validity of our procedures. Our findings suggest that the original claim of biaxial order (η∼0.1) as reflected by probe molecule studies of oxadiazole mesogens is still valid.     

NMR and rotational angles in solution conformation of polypeptides

Professor San-Ichiro Mizushima and Professor Yonezo Morino's classical contributions provided unique means and firm basis for understanding of conformational states and internal rotation in polypeptide molecules. Now the NMR spectroscopy is the best choice to study molecular conformation, mechanism of action and structure-functional relationships of peptide and proteins in solution under conditions approaching those of their physiological environments. Crucial details of spatial structure and interactions of these molecules in solution are revealed by using proton-proton and carbon-proton vicinal coupling constants, proton nuclear Overhauser effect and spectral perturbation techniques. The results of NMR conformational analysis are presented for valinomycin “bracelet”, gramicidin A double helices, honey-bee neurotoxin apamin, scorpion insectotoxins and snake neurotoxins of long and short types.     

Sedum alkaloids-VI : Resolution enhanced proton NMR and 13C NMR spectroscopic studies on the solution conformation of Sedum acre alkaloids

The preferred solution conformation of 9 Sedum alkaloids and derivatives (sedinine, dihydrosedinine. 8-episedinine, diacetylsedinine, sedinone, 2-episedinone, sedacrine, 2-episedacrine and sedacryptine) was established by high resolution ¹H and¹³C NMR spectroscopy. These compounds may be divided into three classes based on the existence or the absence of an intramolecular hydrogen bond between the nitrogen atom and the hydroxyl group at C8 or at C10. In all of them (except sedacryptine) the N-CH₃ group was found to be axially oriented.     

NMR in natural products: understanding conformation, configuration and receptor interactions

Covering: up to 2011. Natural products are of tremendous importance in both traditional and modern medicine. For medicinal chemistry natural products represent a challenge, as their chemical synthesis and modification are complex processes, which require many, often stereo-selective, synthetic steps. A prerequisite for the design of analogs of natural products, with more accessible synthetic routes, is the availability of their bioactive conformation. Nuclear Magnetic Resonance (NMR) spectroscopy and X-ray crystallography are the two techniques of choice to investigate the structure of natural products. In this review, I describe the most recent advances in NMR to study the conformation of natural products either free in solution or bound to their cellular receptors. In chapter 2, I focus on the use of residual dipolar couplings (RDC). On the basis of a few examples, I discuss the benefit of complementing classical NMR parameters, such as NOEs and scalar couplings, with dipolar couplings to simultaneously determine both the conformation and the relative configuration of natural products in solution. Chapter 3 is dedicated to the study of the structure of natural products in complex with their cellular receptors and is further divided in two sections. In the first section, I describe two solution-state NMR methodologies to investigate the binding mode of low-affinity ligands to macromolecular receptors. The first approach, INPHARMA (Interligand Noes for PHArmacophore Mapping), is based on the observation of interligand NOEs between two small molecules binding competitively to a common receptor. INPHARMA reveals the relative binding mode of the two ligands, thus allowing ligand superimposition. The second approach is based on paramagnetic relaxation enhancement (PRE) of ligand resonances in the presence of a receptor containing a paramagnetic center. In the second section, I focus on solid-state NMR spectroscopy as a tool to access the bioactive conformation of natural products in complex with macromolecular receptors.     

NMR experiments on acetals—57 : Conformational study of 5-alkylidene-1,3-dioxanes

From an extensive ¹H-NMR comparative study (homo-INDOR-, and nmdr-assisted) of a series of 2-, 4- and 2,4-substituted 5-alkylidene-1,3-dioxanes it is concluded that the basic conformation is a flattened chair (Fig. 5c,f). This is substantiated by the low barrier to ring reversal in 5-methylidene- and 5-propylidene-1,3-dioxane of ?G^≠ ～ 5·5 kcal/mole (T_c resp. ?158° and ?161°).     

Study on conformation interconversion of 3-alkyl-4-acetyl-3,4-dihydro-2H-1,4-benzoxazines from dynamic NMR experiments and ab initio density functional calculations

Variable-temperature NMR experiments and ab initio density functional calculations were carried out to investigate the conformation interconversion of novel chiral 3-alkyl-3,4-dihydro-2H-benzo[1,4]oxazine derivatives. With CDCl3 as the solvent, the coalescence temperatures of H2, H3, H11, and H19 of product 1 are about 289, 304, 292, and 316 K, with the corresponding activation free energies at 58.0 +/- 6.7, 60.9 +/- 7.1, 58.3 +/- 6.8, and 59.6 +/- 6.9 kJ.mol(-1), respectively. When dimethyl sulfoxide (DMSO-d6) was used as the solvent, 1H and 13C NMR signals were completely assigned at 375 K. The effects of solvent and temperature were investigated through a polarizable continuum model. At each theoretical level (MP2 or B3LYP), the changing tendencies of the calculated activation free energies and interconversion rates agree well with those of the NMR results. In addition, the interconversion rate at each specified temperature was calculated to be about 1.5 times faster in DMSO-d6 than in CDCl3. Accordingly, we failed to observe the coalescence phenomena of H3 and H19 in DMSO-d6 by NMR measurements from 296 to 375 K. The substitution effect at the R1-R5 positions was considered using density functional calculations, with the activation barriers decreasing as follows: product 6 > 3 > 1 > 7 > 2. This sequence is consistent with that of the reaction heats, except for product 7, implying that the interconversion processes may be thermodynamically controlled. Surprisingly, the substituted groups near the acetyl group in product 2 and 7 do not elevate the activation barrier but, instead, lower it somewhat, with the possible reasons for this provided in the paper.     

Targeting norovirus infection-multivalent entry inhibitor design based on NMR experiments

Noroviruses attach to their host cells through histo blood group antigens (HBGAs), and compounds that interfere with this interaction are likely to be of therapeutic or diagnostic interest. It is shown that NMR binding studies can simultaneously identify and differentiate the site for binding HBGA ligands and complementary ligands from a large compound library, thereby facilitating the design of potent heterobifunctional ligands. Saturation transfer difference (STD) NMR experiments, spin-lock filtered NMR experiments, and interligand NOE (ILOE) experiments in the presence of virus-like particles (VLPs), identified compounds that bind to the HBGA binding site of human norovirus. Based on these data two multivalent prototype entry-inhibitors against norovirus infection were synthesized. A surface plasmon resonance based inhibition assay showed avidity gains of 1000 and one million fold over a millimolar univalent ligand. This suggests that further rational design of multivalent inhibitors based on our strategy will identify potent entry-inhibitors against norovirus infections.     

Effects of antidepressants on the conformation of phospholipid headgroups studied by solid-state NMR

The effect of tricyclic antidepressants (TCA) on phospholipid bilayer structure and dynamics was studied to provide insight into the mechanism of TCA-induced intracellular accumulation of lipids (known as lipidosis). Specifically we asked if the lipid-TCA interaction was TCA or lipid specific and if such physical interactions could contribute to lipidosis. These interactions were probed in multilamellar vesicles and mechanically oriented bilayers of mixed phosphatidylcholine-phosphatidylglycerol (PC-PG) phospholipids using (31)P and (14)N solid-state NMR techniques. Changes in bilayer architecture in the presence of TCAs were observed to be dependent on the TCA's effective charge and steric constraints. The results further show that desipramine and imipramine evoke distinguishable changes on the membrane surface, particularly on the headgroup order, conformation and dynamics of phospholipids. Desipramine increases the disorder of the choline site at the phosphatidylcholine headgroup while leaving the conformation and dynamics of the phosphate region largely unchanged. Incorporation of imipramine changes both lipid headgroup conformation and dynamics. Our results suggest that a correlation between TCA-induced changes in bilayer architecture and the ability of these compounds to induce lipidosis is, however, not straightforward as imipramine was shown to induce more dramatic changes in bilayer conformation and dynamics than desipramine. The use of (14)N as a probe was instrumental in arriving at the presented conclusions.     

Ligand conformation in lanthanide complexes by NMR paramagnetic shifts: L-proline and L-valine

A fitting procedure is descdribede to establish the conformation and molecular dynamics of flexible molecules co-ordinated to lanthanide cations from NMR paramagnetic shift data of ¹H and ¹³C resonances. The results from L -proline and L -valine in aqueous solution at low pH values are consistent with peak assignments given by independent methods. A free rotation of the pyrrolidine ring is proposed in the case of L -proline, and a rigid lock in the case of L -valine, and angle and distance values are given for the cation and ligand positions in the complex.     

Solution conformation of tripeptides by NMR spectroscopy and force-field calculations

The solution conformation of three linear tripeptides Boc-Ala-Val-Val-OMe1, Boc-Ala-Pro-Val-OMe2, and Boc-Ala-(D)Pro-Val-OMe3 was studied by NMR spectroscopy and accompanying force-field calculations. In one case,2, as preferred conformation the-turnall trans conformer was found.     

Characterization of stereochemistry and molecular conformation using solid-state NMR tensors

A solid-state NMR technique is described for establishing stereochemistry using the natural product terrein as a model compound. This method involves comparison of experimental (13)C tensor principal values with ab initio computed values for all possible computer-generated stereoisomers. In terrein the relative stereochemistry is confirmed by NMR to be 2R*,3S with high statistical probability (>99.5%). The proposed approach also simultaneously verifies the molecular conformation of the two hydroxy groups in terrein established by X-ray data. It is sufficient to use only shift tensor values at carbons 2 and 3, the stereocenters, to characterize both the stereochemistry and molecular conformations. The solid-state NMR method appears to be especially useful for determining relative stereochemistry of compounds or their derivatives that are difficult to crystallize.