Coupling of functional hydrogen bonds in pyridoxal-5'-phosphate-enzyme model systems observed by solid-state NMR spectroscopy

We present a novel series of hydrogen-bonded, polycrystalline 1:1 complexes of Schiff base models of the cofactor pyridoxal-5'-phosphate (PLP) with carboxylic acids that mimic the cofactor in a variety of enzyme active sites. These systems contain an intramolecular OHN hydrogen bond characterized by a fast proton tautomerism as well as a strong intermolecular OHN hydrogen bond between the pyridine ring of the cofactor and the carboxylic acid. In particular, the aldenamine and aldimine Schiff bases N-(pyridoxylidene)tolylamine and N-(pyridoxylidene)methylamine, as well as their adducts, were synthesized and studied using 15N CP and 1H NMR techniques under static and/or MAS conditions. The geometries of the hydrogen bonds were obtained from X-ray structures, 1H and 15N chemical shift correlations, secondary H/D isotope effects on the 15N chemical shifts, or directly by measuring the dipolar 2H-15N couplings of static samples of the deuterated compounds. An interesting coupling of the two "functional" OHN hydrogen bonds was observed. When the Schiff base nitrogen atoms of the adducts carry an aliphatic substituent such as in the internal and external aldimines of PLP in the enzymatic environment, protonation of the ring nitrogen shifts the proton in the intramolecular OHN hydrogen bond from the oxygen to the Schiff base nitrogen. This effect, which increases the positive charge on the nitrogen atom, has been discussed as a prerequisite for cofactor activity. This coupled proton transfer does not occur if the Schiff base nitrogen atom carries an aromatic substituent.     

Systematic study on the structures and reactivity of hydrazobenzenes and azobenzenes bearing a chalcogenophosphoryl group

Hydrazobenzenes 3-5 bearing a chalcogenophosphoryl group were synthesized by palladium-catalyzed cross-coupling reactions. Their X-ray crystallographic analyses and NMR and IR spectra showed the presence of intramolecular hydrogen bonds between the N-H protons and the chalcogenophosphoryl groups. The intermolecular hydrogen bonds in phosphine oxide 3 and selenide 5 were observed in the solid state. Phosphine oxide 3, sulfide 4, and selenide 5 constructed a dimeric structure, a discrete monomeric structure, and a chain structure, respectively. As the chalcogen atom changed, the crystalline structures of the 2-chalcogenophosphorylhydrazobenzenes also changed. The hydrogen bonds affected the oxidation reactions of the hydrazobenzenes, and oxidation of hydrazobenzenes bearing a lighter chalcogen atom was more difficult. For azobenzenes bearing a chalcogenophosphoryl group, X-ray crystallographic analyses and NMR spectra showed little interaction between the azo group and the chalcogenophosphoryl groups. However, in the UV-vis spectra, the red shifts of the absorption maxima due to the n --> pi transitions indicated intramolecular interactions in the excited state, in contrast to the corresponding 4-substituted azobenzenes. In addition, photoirradiation of phosphine oxide (E)-7 gave (Z)-7, whereas that of phosphine sulfide (E)-8 and phosphine selenide (E)-9 did not give (Z)-8 and (Z)-9, suggesting that heavy chalcogen atoms quench excited states by through-space interactions. Introduction of a chalcogenophosphoryl group at the 2-position had a significant effect on the structure, spectral properties, and reactivity of hydrazobenzenes and azobenzenes. Although azobenzene (E)-10 bearing a hydroxyphosphoryl group at the 2-position did not show hydrogen bonding in the crystalline state, its optical properties and photoisomerization ratio were different from those of (E)-7.     

Solution and solid state 13C NMR and X-ray studies of genistein complexes with amines. Potential biological function of the C-7, C-5, and C4'-OH groups

Parent genistein and its new amine complexes with morpholine and piperazine were studied comparatively in the solid and liquid states by X-ray crystallography and 13C and 15N NMR spectroscopy. Biochanine A and its complexes were used as reference. Secondary deuterium isotope effects on 13C chemical shifts in solution were studied in parent isoflavones and their morpholine and piperazine complexes to aid in evaluation of the electronic distribution in both systems. In addition, to quantify the extent of proton transfer as well as to establish strong hydrogen bonding of the 7-OH group in a morpholine complex, proton transfer from the 7-OH group to the piperazine nitrogen atom was also confirmed by 13C NMR in the solid state and by X-ray studies. The effect of 7-OH deprotonation yields a high frequency shift of 7-8 ppm on the C-7 carbon atom of the piperazine complex whereas it is as large as 12 ppm in the morpholine complex in the solid. The former trend is confirmed from solution state concentration studies which also show that the isoflavones have a strong tendency to form complexes with bases. Depending on the pKa difference between the isoflavones and the base this leads either to proton transfer and ion-pair formation or, in the case of a larger pKa difference, to a hydrogen bonded ion pair. The concentration studies show formation of a 1:1 genistein-piperazine complex in DMSO. Addition of water leads to formation of solvent separated ions. The C-5 OH group is involved in strong intramolecular hydrogen bonding leading to a pseudo aromatic ring extending the aromatic part of the drug pharmacophore. The analysis also suggests the way that both the C-7 and C-4' hydroxyl group of genistein may participate in stabilising the ternary inhibitor complexes of tyrosine-specific kinases or DNA topoisomerase II.     

Naryl-substituted anthranilamides with intramolecular hydrogen bonds

Hydrogen bonding interaction as one type of non-covalent force has proven itself to be highly efficient for constructing structurally unique artificial secondary structures. Here, the structure of N_aryl-substituted anthranilamide in solution is demonstrated by various NMR technique, the intramolecular hydrogen bonds between amide attached to arylamine of the same ring is proposed, which is supported by its crystal structure in the solid phase. The substituent on the nitrogen atom of arylamine plays an important role in forming the presence of intramolecular hydrogen bonds. The chemical shift of the N_aryl-H downfield changes obviously, due to the formation of intramolecular hydrogen bonds and the deshielding effect of oxygen, and the neighboring C–H is activated and shows downfield protonic signal too. The presence of intramolecular hydrogen bonds probably provides the explanation for the transformation from N_aryl-substituted anthranilamide to imine, which could be converted into 2-aryl quinazolinone finally.     

Solution and solid-state models of peptide CH...O hydrogen bonds

Fumaramide derivatives were analyzed in solution by (1)H NMR spectroscopy and in the solid state by X-ray crystallography in order to characterize the formation of CH...O interactions under each condition and to thereby serve as models for these interactions in peptide and protein structure. Solutions of fumaramides at 10 mM in CDCl(3) were titrated with DMSO-d(6), resulting in chemical shifts that moved downfield for the CH groups thought to participate in CH...O=S(CD(3))(2) hydrogen bonds concurrent with NH...O=S(CD(3))(2) hydrogen bonding. In this model, nonparticipating CH groups under the same conditions showed no significant change in chemical shifts between 0.0 and 1.0 M DMSO-d(6) and then moved upfield at higher DMSO-d(6) concentrations. At concentrations above 1.0 M DMSO-d(6), the directed CH...O=S(CD(3))(2) hydrogen bonds provide protection from random DMSO-d(6) contact and prevent the chemical shifts for participating CH groups from moving upfield beyond the original value observed in CDCl(3). X-ray crystal structures identified CH...O=C hydrogen bonds alongside intermolecular NH...O=C hydrogen bonding, a result that supports the solution (1)H NMR spectroscopy results. The solution and solid-state data therefore both provide evidence for the presence of CH...O hydrogen bonds formed concurrent with NH...O hydrogen bonding in these structures. The CH...O=C hydrogen bonds in the X-ray crystal structures are similar to those described for antiparallel beta-sheet structure observed in protein X-ray crystal structures.     

Hydrogen Bonds, Tautomers, and Conformation in 2-Hydroxyphenyl 2-hydroxy-2-(β-naphthyl)vinyl Ketone

Single crystal X-ray diffraction and IR spectroscopy have been used to study the conformation of 2-hydroxyphenyl 2-hydroxy-2-(-naphthyl)vinyl ketone in solid state. It was found that one of the two possible enol tautomeric forms is stabilized in the crystal. The 1-hydroxy-3-oxo-1,3-propenylene moiety, O=C—CH=C—OH, shows a strong intramolecular H bond with a definite character of reasonance-assisted hydrogen bond in spite of being in competition with ring intermolecular hydrogen bonds. The comparison of the present results with solution NMR data indicates that the molecular geometry in solid state and in solution are similar.     

Theoretical and experimental study of the vibrational spectrum of N-acetyl-L-alanine

The energies, vibrational frequencies and IR intensities of cis- and trans-N-acetyl-L-alanine (NAAL) are computed using the density functional theory (B3LYP) combined with the 6-311G(d, p) basis set. The trans conformer is characterized by an intramolecular NH ... O hydrogen bond leading to the formation of a five-membered ring and is by 23 kJ mol(-1) more stable than the cis conformer. The difference between the vibrational frequencies and IR intensities computed for the two conformers is discussed. The IR spectra at different temperatures and the Raman spectra of solid NAAL and its deuterated counterpart are investigated and discussed. The frequencies of the v(OH) vibration and the isotopic ratio suggest the formation of short OH ... O hydrogen bonds in the solid state. The NH group seems also to be involved in a weak hydrogen bond.     

Crystal structure of 3-diethylaminomethyl-2,2′-biphenol

Crystals of 3-diethylaminomethyl-2,2′-biphenol were examined using X-ray diffraction and FT-IR spectroscopy. Their space group is P2₁/c with a=7.305(1), b=13.816(2), c=29.232(4) Å, β=92.411(3)° and Z=8. The unit cell contains two symmetry-independent zwitterions. The hydrogen atom of the protonated diethylaminomethyl group is linked to the negatively charged phenolate oxygen atom, which in turn is linked to the hydroxyl group by a short hydrogen bond (molecule a: NO=2.604(3), OO=2.512(3) Å; molecule b: NO=2.593(4), OO=2.489(4) Å). The OHO⁻H⁺N bifurcated intramolecular hydrogen bonds are crystallographically asymmetric. The IR spectrum of the crystals confirms very well the results obtained by the X-ray study. Instead of continuous absorption, only broad bands are found indicating relatively low proton polarisability in the two types of intramolecular hydrogen bonds.     

Intramolecular hydrogen bond in the push–pull CF3-aminoenones: DFT and FTIR study,NBO analysis

Postulated conformers of trifluoromethylated β-aminoenones stabilized by intramolecular NH?O and N?HO bonds were studied by IR and NMR spectroscopy and evaluated with quantum chemical calculations (B3LYP/6-311+G(d,p), MP2/6-311+G(d,p)//B3LYP/6-311+G(d,p) and MP2/6-31G(d,p)) and NBO analysis. The influence of the nature of EWG, substituents at the nitrogen atom and double bond, and of orbital interactions of heteroatoms and double bonds in these structures on the proton affinity of basic and acid centers, strength of hydrogen bonds, and the energy of tautomeric transfers is discussed. The theoretical results agree satisfactorily with the experimental observations.     

Helically chiral ferrocene peptides containing 1'-aminoferrocene-1-carboxylic acid subunits as turn inducers

We present a detailed structural study of peptide derivatives of 1'-aminoferrocene-1-carboxylic acid (ferrocene amino acid, Fca), one of the simplest organometallic amino acids. Fca was incorporated into di- to pentapeptides with D- and L-alanine residues attached to either the carboxy or amino group, or to both. Crystallographic and spectroscopic studies (circular dicroism (CD), IR, and NMR) of about two dozen compounds were used to gain a detailed insight into their structures in the solid state as well as in solution. Four derivatives were characterized by single-crystal X-ray analysis, namely Boc-Fca-Ala-OMe (16), Boc-Fca-D-Ala-OMe (17), Boc-Fca-beta-Ala-OMe (18), and Boc-Ala-Fca-Ala-Ala-OMe (21) (Boc=tert-butyloxycarbamyl). CD spectroscopy is an extremely useful tool to elucidate the helical chirality of the metallocene core. Unlike in all other known ferrocene peptides, the helical chirality of the ferrocene is governed solely by the chirality of the amino acid attached to the N terminus of Fca. Depending on the degree of substitution of both cyclopentadiene (Cp) rings, different hydrogen-bonding patterns are realized. (1)H NMR and IR spectroscopy, together with the results from X-ray crystallography, give detailed information regarding not only the hydrogen-bonding patterns of the compounds, but also the equilibria between different conformers in solution. Differences in chemical shifts of NH protons in dimethyl sulfoxide ([D(6)]DMSO) and CDCl(3), that is, the variation ratio (vr), is used for the first time as a measure of the hydrogen-bonding strength of individual COHN bonds in ferrocenoyl peptides. In dipeptides with one intramolecular hydrogen bond between the pendant chains, for example, in dipeptide 16, an equilibrium between hydrogen-bonded and open forms is observed, as testified by a vr value of around 0.5. Higher peptides, such as tetrapeptide 21, are able to form two intramolecular hydrogen bonds stabilizing one single conformation in CDCl(3) solution (vr approximately 0). Due to the low barrier of Cp-ring rotation, new and unnatural hydrogen-bonding patterns are emerging. The systematic work described herein lays a solid foundation for the rational design of metallocene peptides with unusual structures and properties.     

Syntheses, structures and bioactivities of fluorine-containing phenylimino-thia(oxa)zolidine derivatives as agricultural bioregulators

From insight into the structure of trehazolin as trehalase inhibitor, six series of fluorine-containing phenylimino-thiazolidines (oxazolidines) derivatives were designed and prepared through a convenient synthesis of fluoroaryl isothiocyanate and a one-pot facile synthesis in high yield of fluorophenyl aminobenzoxazoles by cyclodesulfurization. The structures of the target compounds were confirmed with using IR, NMR, MS and elemental analysis. Their X-ray crystal analysis suggested that there were novel intermolecular (sp²CF?H₃C) and intramolecular (sp²CF?HN) hydrogen bonds between the fluorine atom on benzene ring and hydrogen atom of methyl group or amino group on five-membered heterocycle. Their fungicidal activities against Rhizoctonia solani and Pyricuraria oryzae at 100 ppm were determined.     

Intramolecular Resonance-assisted Hydrogen Bonds in N-Salicylidene-anilines

In the crystal structures of N-salicylidene-anilines, the ortho-OH group with the central N atom forms a planar six-membered ring through intramolecular hydrogen bonds (Fig. 1). The pseudo-aromatic ring is coplanar with its attached phenyl ring. The resonance strengthens the H-bond through proton transfer between the O and N atoms (Fig.1,Ⅰ←→Ⅱ): dco and dcc become shorter and dCN longer significantly. The d1～d6 are also changed regularly. According to the geometries obtained from X-ray analysis and retrieved from the Cambridge Structural Database (CSD, version 5.21), we believe that the main resonance, at least in solid state, is the molecular keto form (Ⅱ, Fig. 1) instead of the zwitterionic one (Ⅲ, Fig.1).     

Two copper(II) complexes with 4-benzoylpyridine ligand: synthesis, crystal structure and luminescent properties

Two new copper(II) complexes Cu(NCS)2(4-Bzpy)2 (1) and Cu(NO3)2(4-Bzpy)4 (2) (4-Bzpy=4-benzoylpyridine) have been synthesized and characterized by IR, UV, elemental analysis and X-ray crystallography. Cu(II) atom has a square planar environment for 1 and an distorted octahedral environment for 2, respectively. In solid state there are C-H?π interactions and C-H?S hydrogen bonds between adjacent molecules in complex 1. The molecule of complex 2 is further connected by multiform π-π interactions, C-H?π interactions and C-H?O hydrogen bonds to form a three-dimensional supramolecular structure. The luminescent properties of the complexes 1 and 2 were both investigated in H2O solution and in solid state at room temperature, respectively.     

Structure and absorption sepctra of 3-phenyl-4-hydroxyisoquinoline

It was shown by IR spectroscopy that 3-phenyl-4-hydroxyisoquinoline exists in the hydroxy form in solution in organic nonpolar solvents. The splitting of the ^vOH band in the IR absorption spectra was assigned to the S-cis and S-trans orientations of the OH group relative to the phenyl ring. An intramolecular hydrogen bond is formed in the cis form of 3-phenyl-4-hydroxyisoquinoline due to interaction of the hydroxyl hydrogen atom with the -electron system of the phenyl ring. An interpretation of the first two absorption maxima in the electronic spectra of the neutral and ionic forms of the 4-hydroxyisoquinoline and 3-phenyl-4-hydroxyisoquinoline molecules is given within the framework of the MO method and the Pariser-Parr-Pople approximation. It is shown that the introduction of a phenyl group in the 3 position of 4-hydroxyisoquinoline, protonation of the ring nitrogen atom, the ionization of the exocyclic -hydroxyl group affect the energy of the upper occupied molecular orbital, leaving the lower vacant molecular orbital of 4-hydroxyisoquinoline almost unchanged.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 6, pp. 805–809, June. 1977.     

Normal coordinate analysis of bilirubin vibrational spectra: Effects of intramolecular hydrogen bonding

Normal coordinate analyses are presented for half-bilirubin molecules. Calculations for the AB pyrromethenone include intramolecular hydrogen bonds, while those for the CD chromophore exclude intramolecular hydrogen bonds. Valence force-field parameters have been optimized to correlate closely with the IR and Raman spectra of the target molecules. The results of the calculations are compared with the spectra of bilirubin IXa and various model compounds in the solid state and solution.     

Synthesis,Coordination Chemistry and Bonding of Strong N‐Donor Ligands Incorporating the 1H‐Pyridin‐(2E)‐Ylidene (PYE) Motif

A range of N‐donor ligands based on the 1H‐pyridin‐(2E)‐ylidene (PYE) motif have been prepared, including achiral and chiral examples. The ligands incorporate one to three PYE groups that coordinate to a metal through the exocyclic nitrogen atom of each PYE moiety, and the resulting metal complexes have been characterised by methods including single‐crystal X‐ray diffraction and NMR spectroscopy to examine metal–ligand bonding and ligand dynamics. Upon coordination of a PYE ligand to a proton or metal‐complex fragment, the solid‐state structures, NMR spectroscopy and DFT studies indicate that charge redistribution occurs within the PYE heterocyclic ring to give a contribution from a pyridinium–amido‐type resonance structure. Additional IR spectroscopy and computational studies suggest that PYE ligands are strong donor ligands. NMR spectroscopy shows that for metal complexes there is restricted motion about the exocyclic C? N bond, which projects the heterocyclic N‐substituent in the vicinity of the metal atom causing restricted motion in chelating‐ligand derivatives. Solid‐state structures and DFT calculations also show significant steric congestion and secondary metal–ligand interactions between the metal and ligand C? H bonds.     

Heterocyclic tautomerism. V. 2-Guanidinobenzimidazole

A single-crystal X-ray structure analysis of 2-guanidinobenzimidazole shows the molecule exists in the solid state as tautomer 1 , with an intramolecular hydrogen bond between the benzimidazole-N3 and a guanidino-NH₂. The guanidino group is inclined at an angle of 13.8° to the benzimidazole plane. Other nitrogen atoms and their attached hydrogens are involved in additional intermolecular hydrogen bonds that connect the molecules in a complex three-dimensional network.     

Synthesis and structure of 5,7-Di(<Emphasis Type="Italic">tert</Emphasis>-butyl)-2-(8-methanesulfonyloxyquinolin-2-yl)-1,3-tropolone

5,7-Di(tert-butyl)-2-(8-methanesulfonyloxyquinolin-2-yl)-1,3-tropolone whose structure was established by X-ray diffraction analysis and confirmed by ¹H and ¹³C NMR, IR spectroscopy, and mass spectrometry, was obtained by the reaction of 2-methyl-8-methanesulfonyloxyquinoline with 3,5-di(tert-butyl)-1,2-benzoquinone. According to X-ray diffraction study, this sulfonyloxyquinolinotropolone exists in the NH tautomeric form with methanesulfonyloxy group in the exo position to the tropolone ring and the sixmembered chelate ring produced by the quinoline and tropolone moieties stabilized by strong intramolecular hydrogen bond. The strong intramolecular hydrogen bond between the phenolic oxygen atom and the six-membered chelate ring provides supplementary contribution to the stabilization of the NH tautomeric form.     

The intramolecular hydrogen bond in 2-hydroxy-benzamides

The two crystal structures of 5-chloro-2-hydroxy-benzamide and 2-hydroxy-N,N-diethyl-benzamide were determined by X-ray diffraction at 100 K. The intramolecular and intermolecular hydrogen bonds were found in these structurally similar 2-hydroxy-benzamides. Analysis of the hydrogen bonding was carried out on the basis of X-ray data, infrared spectra, and DFT calculations. Disruption of the intramolecular hydrogen bonding in the solid state by a steric effect is shown. Conformational analysis and potential energy calculations as functions of the turning angle around the C_aryl–C_alkyl bond were conducted. The values obtained for the HOMA index indicate mutual compensation of the amide and hydroxyl groups (due to the high degree aromaticity of the phenyl ring).     

Conjugation and hyperconjugation in conformational analysis of cyclohexene derivatives containing an exocyclic double bond

The equilibrium geometry, ring-inversion pathway barriers for analogues of cyclohexene with an exocyclic double bond have been studied using the MP2/6-311 G(d,p) level of theory. The equilibrium conformation of the ring depends on conjugation between the endocyclic and exocyclic double bonds. Interactions between conjugated double bonds include the pi-pi conjugation and interactions between the lone pair of the heteroatom of the exocyclic double bond and the sigma-antibonding orbital of the endocyclic single bond. In the case of the tetrahydrocycles with double bonds separated by a methylene group the balance between the pi --> sigma* hyperconjugation interactions between the exocyclic double bond and the neighboring methylene group and the n --> sigma* interaction between the lone pair of the heteroatom and the sigma-antibonding orbitals of the C(sp(2))-C(sp(3)) bond determine the geometrical parameters of the ring. The character of the potential-energy surface around the saddle point depends on the position of the exocyclic double bond and the orientation of the hydrogen atom attached to the heteroatom of the V group of the periodic table in the tetrahydrocycles with double bonds separated by a methylene group.