Use of (S)‐BINOL as NMR chiral solvating agent for the enantiodiscrimination of omeprazole and its analogs

The application of (S)‐1,1′‐binaphthyl‐2,2′‐diol as NMR chiral solvating agent (CSA) for omeprazole, and three of its analogs (lanso‐, panto‐, and rabe‐prazole) was investigated. The formation of diastereomeric host–guest complexes in solution between the CSA and the racemic substrates produced sufficient NMR signal splitting for the determination of enantiomeric excesses by ¹H‐ or ¹⁹F‐NMR spectroscopy. Using of hydrophobic deuterated solvents was mandatory for obtaining good enantiodiscrimination, thus suggesting the importance of intermolecular hydrogen bonds in the stabilization of the complexes. The method was applied to the fast quantification of the enantiomeric purity of in‐process samples of S‐omeprazole. Chirality, 2010. © 2009 Wiley‐Liss, Inc.     

Enantiomeric separation and recognition mechanism of 2-arylpropionic acid derivatives by high-performance liquid chromatography using a chiral column

An optical resolution of the amide derivatives of ibuprofen and the carbamate-alkylester derivatives of the trans-alcohol metabolite of loxoprofen and an analogous compound, CS-670, was studied by chiral high-performance liquid chromatography (HPLC). The chiral columns SUMIPAX OA-4000 and OA-4100 were used to investigate the enantiomeric separation behavior of these derivatives using both reversed and normal mobile phases. A better separation factor (α) of the amide and the carbamate ester derivatives was obtained in the normal mobile phase than in the reversed mobile phase HPLC. In addition, the recognition mechanisms of both amide and carbamate ester enantiomers were investigated by ¹H-nuclear magnetic resonance (NMR). It is suggested that the important driving forces for the enantiomeric separation are the formation of hydrogen bonding and the charge transfer complex between these derivatives and an active site of the chiral stationary phase. © 1995 Wiley-Liss, Inc.     

The influence of solute structure,temperature, and eluent composition on the chiral separation of 21 aminotetralins on a cellulose tris-3,5-dimethylcarbamate stationary phase in high-performance liquid chromatography

In the present study 21 different chiral aminotetralins were used to investigate the mechanism behind their enantiomeric resolution (R_s) on a commercially available high-performance liquid chromatography (HPLC) cellulose tris-3,5-dimethylcarbamate stationary phase. The differences in the chemical structures of the aminotetralins used were never directly located on the chiral carbon. Their chromatographic behavior was studied for two eluent compositions at six different temperatures. Hydrogen bonding and π? π interactions are two possible solute–chiral stationary phase (CSP) interactions. Differences between the enantiomers in their spatial arrangement of positions involved in solute–CSP interactions were the major forces behind enantiomeric separation. Lowering the temperature increased the R_s for the aminotetralins having π-electrons not directly bonded to that part of the molecule where the hydrogen bonding with the CSP is located. Primary amines and secondary amines, with a sufficiently short N-alkyl substituent, showed a decrease of R_s with lower temperatures, all other aminotetralins yielding an increase of R_s with lower temperatures. © 1992 Wiley-Liss, Inc.     

New chiral fluoroanthryl derivatives: Resolution of the enantiomers by chromatography on cellulose esters and their evaluation as chiral solvating agents in NMR spectroscopy

2,2,2-Trifluoro-1-(9-anthryl)ethanol (TFAE) has now been widely used as a powerful chiral solvating agent for NMR spectroscopy. In connection with the development of a new general synthesis of halogenoalkylalkanols, starting from the corresponding ketone or aldehyde, we synthesized some halogenoalkyl-1-(9-anthryl)methanol derivatives liable to work as chiral solvating agents. The racemic anthryl derivatives were preparatively resolved into their corresponding enantiomers by chromatography on triacetyl cellulose (CTA I) or on meta-methylbenzoyl cellulose beads as chiral stationary phases. Their effectiveness as chiral solvating agents was measured as the magnitude of the splitting induced in the ¹H-NMR spectra of 1-phenylethylamine and of (1-phenylethyl)methyl ether in comparison with splitting caused by TFAE. While TFAE induced the largest splitting for 1-phenylethylamine, 2,2,3,3,3-pentafluoro-1-(9-anthryl)propanol 2 was more effective in the case of (1-phenylethyl)methyl ether, pointing out that depending on the substrate, other derivatives of the TFAE type can be very useful as chiral solvating agents.     

Xanthate sulfur as a hydrogen bond acceptor: the free xanthate anion and ligand sulfur in nickel tris ethylxanthate

Xanthates, like thiolates, form a variety of complexes with metals in which coordinating sulfur can serve as a hydrogen bond acceptor. Nickel tris xanthate complexes [Ni(xan)₃]⁻, (xan = o-ethylxanthate, N-(carbamoylmethyl)ethylxanthate) have been synthesized and compared by a combination of X-ray crystallographic and spectroscopic measurements. Recent results from our studies of N-H?S hydrogen bonding interactions in metal-xanthate complexes shows N-S distances to be longer than those in related thiolate complexes, indicative of weaker hydrogen bonds for the xanthates. The complex (Et₄N)[N-(carbamoylmethyl)ethylxanthate)] adopts an extended conformation in both the solid state and solution and lacks either intraligand or intermolecular N-H?S hydrogen bonds. The complex (CTA)[Ni(exa)₃] exhibits N-H?S hydrogen bonds between the amide group of the counterion and the ligand sulfur. The amide-sulfur N-H?S distance is 3.567 Å.     

The structural chemistry of triorganotin(IV) derivatives of 3-amino-5-mercapto-1,2,4-triazole: Supramolecular structures involving intermolecular N-H?N and N-H?S hydrogen bonding

Four new triorganotin complexes of 3-amino-5-mercapto-1,2,4-triazole with the type of R₃Sn(SC₂N₃HNH₂-3) (R = Me, 1; n-Bu, 2; Ph, 3; PhCH₂, 4) have been synthesized. All the complexes have been characterized by elemental analysis, IR, ¹H NMR and ¹³C NMR spectra. Complexes 1, 3 and 4 have been characterized by X-ray crystallography analyses too. The geometry about Sn of complex 1 is distorted trigonal bipyramidal and the supramolecular structures of complex 1 has been found consist of channels built up by intermolecular N-H?N hydrogen bonding. The geometry of tin atoms in complexes 3 and 4 are distorted tetrahedron and 1D polymers connected by intermolecular N-H?N hydrogen bonding or N-H?N and N-H?S hydrogen bonding. Additionally, 1D polymer of complex 3 aggregated in 2D layer by intermolecular N-H?S hydrogen bonding.     

Probing the “fingers” domain binding pocket of Hepatitis C virus NS5B RdRp and D559G resistance mutation via molecular docking,molecular dynamics simulation and binding free energy calculations

The NS5B RdRp polymerase is a prominent enzyme for the replication of Hepatitis C virus (HCV). During the HCV replication, the template RNA binding takes place in the “fingers” sub-domain of NS5B. The “fingers” domain is a new emerging allosteric site for the HCV drug development. The inhibitors of the “fingers” sub-domain adopt a new antiviral mechanism called RNA intervention. The details of essential amino acid residues, binding mode of the ligand, and the active site intermolecular interactions of RNA intervention reflect that this mechanism is ambiguous in the experimental study. To elucidate these details, we performed molecular docking analysis of the fingers domain inhibitor quercetagetin (QGN) with NS5B polymerase. The detailed analysis of QGN-NS5B intermolecular interactions was carried out and found that QGN interacts with the binding pocket amino acid residues Ala97, Ala140, Ile160, Phe162, Gly283, Gly557, and Asp559; and also forms π?π stacking interaction with Phe162 and hydrogen bonding interaction with Gly283. These are found to be the essential interactions for the RNA intervention mechanism. Among the strong hydrogen bonding interactions, the QGN?Ala140 is a newly identified important hydrogen bonding interaction by the present work and this interaction was not resolved by the previously reported crystal structure. Since D559G mutation at the fingers domain was reported for reducing the inhibition percentage of QGN to sevenfold, we carried out molecular dynamics (MD) simulation for wild and D559G mutated complexes to study the stability of protein conformation and intermolecular interactions. At the end of 50?ns MD simulation, the π?π stacking interaction of Phe162 with QGN found in the wild-type complex is altered into T-shaped π stacking interaction, which reduces the inhibition strength. The origin of the D559G resistance mutation was studied using combined MD simulation, binding free energy calculations and principal component analysis. The results were compared with the wild-type complex. The mutation D559G reduces the binding affinity of the QGN molecule to the fingers domain. The free energy decomposition analysis of each residue of wild-type and mutated complexes revealed that the loss of non-polar energy contribution is the origin of the resistance.

Communicated by Ramaswamy H. Sarma     

Effect of solvent environment on the CO band position in the infrared spectrum of trans-[Fe(CN)4(CO)2]

Density functional theory (DFT) is used to understand the effect of hydrogen bonding solvents on the CO band position in the infrared (IR) spectrum of a mono-iron complex, trans-[Fe^II(CN)₄(CO)₂]²⁻. This mono-iron complex has received much attention recently due its potential relation to the biosynthesis of Fe-only hydrogenase enzymes. Our calculations show that the polar solvent molecules preferentially hydrogen bond to the cyano ligands in this complex. The effect of such hydrogen bonding on the electron density distribution is analyzed in terms of the population in natural bond orbitals (NBO). Our results show that the presence of hydrogen bonding to the cyano ligands decreases the extent of back bonding from the metal to the carbonyl ligand. This results in decreased electron density in the π^∗ orbitals of the carbonyl bond leading to a strengthening of the CO bond and a consequent blue shift in the IR band position of the carbonyl group. We also show that the extent of blue shift correlates with the number of nearest neighbor solvent molecules.     

A systematic evaluation of different hydrogen bonding patterns in unsymmetrical 1,n′-disubstituted ferrocenoyl peptides

The synthesis and spectroscopic characterization of 21 l,l′-disubstituted ferrocenoyl peptides of the general formula [Fe(C₅H₄-CO-Aal-OR) (C₅H₄-CO-Aa2-OR′)] is reported, with Aal and Aa2 being different amino acids. The one-pot synthesis from activated ferrocene-l,l′-dicarboxylic acid and two different amino acid esters gives the unsymmetrical ferrocenoyl peptides in yields between 27% and 42%, which can be easily separated from their symmetrical byproducts by column chromatography. All new compounds are comprehensively characterized by mass spectrometry (El and FAB, including high-resolution EI-MS), ¹H and ¹³C NMR, and UV/Vis spectroscopy. CD spectroscopy in conjunction with ¹H NMR is used to elucidate the solution structures. Using the achiral glycine (Gly) as Aal permits to determine qualitatively the structure-determining influence of the different amino acids Aa2. Helically chiral structures in ferrocene amino acids in this study are stabilized by hydrogen bonds. If one hydrogen bond partner is systematically moved away by the introduction of methylene groups, then indeed the strength of the hydrogen bond decreases as indicated by ¹H NMR chemical shifts of the amide protons and the strength of characteristic CD bands. As proline (Pro) is the only naturally accuring secondary amino acid it cannot contribute any amide proton to intra-strand hydrogen bonding. DFT calculations on the compound [Fe(C₅H₄-CO-Gly-OMe)(C₅H₄-CO-Pro-OMe)] with one achiral and one secondary amino acid were therefore performed to quantify the more subtle influence of the relative orientations of the ferrocene carbonyl groups and the cis-/trans-conformation of both amide bonds. Not unexpectedly, the conformations with both amide bonds in cis orientation are highest in energy. Surprisingly, the calculations suggest the presence of a low-energy conformation with a non-classical hydrogen bond between the proline ester carbonyl oxygen and a glycine H_α atom. However, a second conformation with no apparent intra-strand contacts but optimal positioning of all relevant groups is similar in energy. Although two conformations were observed in solution for this compound, the experimental data did not permit to assign those two conformations.     

Model systems for flavoenzyme activity. The effects of specific hydrogen bonds on the 13C and 1H NMR of flavins

We have developed a family of receptors designed to bind flavin derivatives using specific hydrogen bond interactions. These synthetic host molecules provide a model for specific flavoenzyme–cofactor interactions, allowing isolation and observation of the effects of hydrogen bonding on flavin NMR. We describe here the use of one of these receptors to study the effects of hydrogen bonding to O(2), N(3), and O(4) on flavin ¹H and ¹³C NMR.     

Evaluation of (R)-(-)-α-methoxy phenyl acetic acid as a chiral shift reagent for resolution and determination of R and S enantiomers of modafinil in bulk drugs and formulations by 1H NMR spectroscopy

(R)-(-)-α-Methoxy phenyl acetic acid, (S)-(-)-1,1'-(2-naphthol), and (R)-(+)-α-methoxy-α-trifluoromethyl phenyl acetic acid were evaluated as chiral shift reagents (CSRs) for (1)H NMR spectroscopic resolution and determination of R and S enantiomers of modafinil (MDL) in bulk drugs and formulations. Effects of the nature of CSR and the weight ratio of substrate to shift reagent on enantiomeric discrimination were investigated. Intramolecular and intermolecular hydrogen bonding interactions between the drug and the CSR seem to be the driving force for desired resolution. A mechanism was proposed to explain the interactions between (R, S)-enantiomers of MDL and (R)-(-)-α-methoxy phenyl acetic acid. The method was validated and applied successfully to determine the enantiomeric purity of MDL in tablet formulations.     

An improved method for determining enantiomeric excess by 13C‐NMR in chiral liquid crystal media

By using a combination of inverse gated ¹H decoupled ¹³C‐NMR experiments 1 with short acquisition times and NMR Cryo‐probe technology, the sample requirements and experimental times necessary to accurately measure enantiomeric excess of small chiral molecules has been reduced 16‐fold. Quality ¹³C‐NMR spectra can now be obtained from a 1 to 5 mg sample in 12 minutes. The enantiomeric excess determination achieved from the average integration of all the ¹³C‐resonances in the spectrum is comparable to enantiomeric excess measured by chiral SFC. The advantage of the NMR method is that enantiomeric excess can rapidly be measured in situ on practical amounts of enantioselective reaction products without the need for chromatographic separation or chemical modification and with substantially less solvent waste. Chirality, 2010. © 2010 Wiley‐Liss, Inc.     

Disordered hydrogen bonding in N-(1-deoxy-β-d-fructopyranos-1-yl)-N-allylaniline

We report on a ¹³C NMR and a single-crystal X-ray diffraction study of N-(1-deoxy-β-d-fructopyranos-1-yl)-N-allylaniline (d-fructose-N-allylaniline). In solution, an equilibrium of α-pyranose, β-pyranose, α-furanose, β-furanose, and acyclic keto tautomers of the carbohydrate was detected in the following respective proportions: 2.2%, 47.4%, 4.5%, 33.6%, and 12.3%. In the crystalline state, the compound exists exclusively as the β-pyranose form, in the normal ²C₅ chair conformation. Bond lengths and valence angles compare well with the average values from a number of β-fructopyranose derivatives. The structure displays two unusual features for this class of compounds. First, the molecule assumes an eclipsed conformation around the C1-C2 bond, apparently stabilized by an intramolecular O2-H···N hydrogen bond. Second, the O3, O4, and O5 hydroxyl groups are involved in an intermolecular hydrogen bonding, which forms 12-membered homodromic cycles. In the cycles, each determined hydrogen atom site is half occupied, possibly due to the ···H-O···H-O··· ? ···O-H···O-H··· flip-flop type disorder.     

Thioamide substitution to probe the hydroxyproline recognition of VHL ligands

Thioamide substitution influences hydrogen bond and n → π¹ interactions involved in the conformational stability of protein secondary structures and oligopeptides. Hydroxyproline is the key recognition element of small molecules targeting the von Hippel-Lindau (VHL) E3 ligase, which are of interest as probes of hypoxia signaling and ligands for PROTAC conjugation. We hypothesized that VHL ligands could be a privileged model system to evaluate the contribution of these interactions to protein:ligand complex formation. Herein we report the synthesis of VHL ligands bearing thioamide substitutions at the central hydroxyproline moiety, and characterize their binding by fluorescence polarization, isothermal titration calorimetry, X-ray crystallography and molecular modeling. In spite of a conserved binding mode, the substitution pattern had a pronounced impact on the ligand affinities. Together the results underscore the role of hydrogen bond and n → π¹ interactions in fine tuning hydroxyproline recognition by VHL.     

A fast protein-ligand docking algorithm based on hydrogen bond matching and surface shape complementarity

With the rapid development of structural determination of target proteins for human diseases, high throughout virtual screening based drug discovery is gaining popularity gradually. In this paper, a fast docking algorithm (H-DOCK) based on hydrogen bond matching and surface shape complementarity was developed. In H-DOCK, firstly a divide-and-conquer strategy based enumeration approach is applied to rank the intermolecular modes between protein and ligand by maximizing their hydrogen bonds matching, then each docked conformation of the ligand is calculated according to the matched hydrogen bonding geometry, finally a simple but effective scoring function reflecting mainly the van der Waals interaction is used to evaluate the docked conformations of the ligand. H-DOCK is tested for rigid ligand docking and flexible one, the latter is implemented by repeating rigid docking for multiple conformations of a small molecule and ranking all together. For rigid ligands, H-DOCK was tested on a set of 271 complexes where there is at least one intermolecular hydrogen bond, and H-DOCK achieved success rate (RMSD<2.0?Å) of 91.1%. For flexible ligands, H-DOCK was tested on another set of 93 complexes, where each case was a conformation ensemble containing native ligand conformation as well as 100 decoy ones generated by AutoDock [1], and the success rate reached 81.7%. The high success rate of H-DOCK indicates that the hydrogen bonding and steric hindrance can grasp the key interaction between protein and ligand. H-DOCK is quite efficient compared with the conventional docking algorithms, and it takes only about 0.14 seconds for a rigid ligand docking and about 8.25 seconds for a flexible one on average. According to the preliminary docking results, it implies that H-DOCK can be potentially used for large scale virtual screening as a pre-filter for a more accurate but less efficient docking algorithm.     

Membrane channel forming polypeptides. 270-MHz proton magnetic resonance studies of the aggregation of the 11-21 fragment of suzukacillin in organic solvents

270-MHz 1H NMR studies of the 11-21 suzukacillin fragment Boc-Gln-Aib-Leu-Aib-Gly-Leu-Aib-Pro-Val-Aib-Aib-OMe (11-G) and its analogue Boc-Ala-Aib-Leu-Aib-Gly-Leu-Aib-Pro-Val-Aib-Aib-OMe (11-A) have been carried out in CDCl3 and (CD3)2SO. The NH chemical shifts and their temperature coefficients have been measured as a function of peptide concentration in both solvents. It is established that replacement of Gln by Ala is without effect on backbone conformation. Both peptides adopt highly folded 310 helical conformations stabilized by seven intramolecular 4 leads to hydrogen bonds. Nonlinear temperature dependences are demonstrated for free NH groups in the Gln(1) peptide. Aggregation is mediated by intermolecular hydrogen bonds formed by solvent-exposed NH groups. A major role for the Gln side chain in peptide association is suggested by differences in the NMR behavior of the Gln(1) and Ala(1) peptides. For the Gln(1) peptide in CDCl3, the carboxamide side chain carbonyl group forms an intramolecular hydrogen bond to the peptide backbone, while the trans side chain NH shows evidence for intermolecular interactions. In (CD3)2SO, the cis carboxamide NH is involved in intermolecular hydrogen bonding. The possible role of the central Gln residue in stabilizing aggregates of peptide channel formers is discussed, and a model for hexameric association is postulated.     

Intramolecular steric effects and hydrogen bonding in regular conformations of polyamino acids

A survey has been made, by using computer methods, of the types of helices which polypeptide chains can form, taking into account steric requirements and intramolecular hydrogen-bonding interactions. The influence on these two requirements, of small variations in the bond angles of the peptide residues, or of small changes in the overall dimensions of the helix (pitch and residues per turn), have been assessed for the special case of the α-helix. Criteria for the formation of acceptable hydrogen bonds have also been applied to helices of other types, viz., the 3, γ^?, ω^?, and π-helices. It was shown that the N? H … O and H … O? C angles in hydrogen bonds are sensitive to changes in either the NC^αC′ bond angle or in the rotational angles about the N? C^α and C^α? C′ bonds. However, the variants of the α-helix observed experimentally in myoglobin can all be constructed without distortion of the hydrogen bonds. For α-helices, the steric and hydrogen bonding requirements are more easily fulfilled with an NC^αC′ bond angle of 111°, rather than 109.5°. The decreased stability observed for the left-handed α-helix relative to the right-handed one for L -amino acids is due essentially only to interactions of the C^β atom of the side chains with atoms in adjacent peptide units in the backbone, and interactions with atoms in adjacent turns of the helical backbone are not significantly different in the two helices. Restrictions in the freedom of rotation of bulky side chains may have significant kinetic effects during the formation of the α-helix from the “random coil” state.     

Crystal packing driven by metal-ligand interactions, hydrogen bonds, π-π stacking and anion-π stacking

Two polymeric copper(II) compounds have been synthesized with the ligand bis(pyrimidin-2yl)amine (dipm), by means of coordination bonds, Watson-Crick type hydrogen bond interactions and π-π stacking. Both supramolecules hold the same cationic building block, namely [Cu(dipm)₂(H₂O)₂]²⁺. However, their crystal structure significantly differs and this variation apparently arises from the nature of the anion which induces dissimilar crystal packings. The crystal growth is driven by several synergistic intermolecular interactions, i.e., coordination and hydrogen bonds, π-π and anion-π stacks.     

The competition of C-X⋯O=P halogen bond and π-hole⋯O=P bond between halopentafluorobenzenes C6F5X (X=F, Cl, Br, I) and triethylphosphine oxide

Calculation predicted the interacting forms of halopentafluorobenzene C₆F₅X (X=F, Cl, Br, I) with triethylphosphine oxide which is biologically interested and easily detected by ³¹P NMR. The interaction energy and geometric parameters of resultant halogen or π-hole bonding complexes were estimated and compared. Moreover, the bonding constants were determined by ³¹P NMR. Both theory and experiments indicated the C₆F₆ and C₆F₅Cl interact with triethylphosphine oxide by π-hole bonding pattern, while C₆F₅I by halogen/σ-hole bonding form. For C₆F₅Br, two interactions are comparative and should coexist competitively. The calculated interaction energies of σ-hole bonding complexes, ?5.07 kcal mol^?1 for C₆F₅Br?O=P and ?8.25 kcal mol^?1 for C₆F₅I?O=P, and π-hole bonding complexes, ?7.29 kcal mol^?1 for C₆F₆?O=P and ?7.24 kcal mol^?1 for C₆F₅Cl?O=P, are consistent with the changing tendency of bonding constants measured by ³¹P NMR, 4.37, 19.7, 2.42 and 2.23 M^?1, respectively.