Conformational study of a strained tolanophane by dynamic 1H NMR spectroscopy and computational methods

The existence of a short C–H ⋯ π (alkyl–alkyne) interaction in the structure of a strained and relatively rigid tolanophane is expected to hinder the rotation about the C–C sp³ single bond. Variable-temperature NMR experiments (performed in three solvents, CDCl₃, THF-d₈, and acetone-d₆) and ab initio density functional calculations were carried out to investigate its dynamic nature. An energy barrier of 48.6 kJ/mol is determined at coalescence (210 K) with acetone-d₆ which is in good agreement with calculation result (54 kJ/mol). Correspondence: Hossein Reza Darabi, Chemistry and Chemical Engineering Research Center of Iran, Pajoohesh Blvd., km 17, Karaj Hwy, 14968-13151 Tehran, Iran.     

Predicting NMR spectra by computational methods: structure revision of hexacyclinol

[structure: see text] The structure of the natural product hexacyclinol was reassigned from endoperoxide 1 to the diepoxide 7 on the basis of calculated (13)C chemical shift data using HF/3-21G geometries and mPW1PW91/6-31G(d,p) GIAO NMR predictions. These predictions correlate very well with experimental data for three other highly oxygenated natural products, elisapterosin B, maoecrystal V, and elisabethin A. Hexacyclinol is proposed to arise from acid-catalyzed rearrangement of panepophenanthrin in the presence of methanol.     

Aromatic-carbohydrate interactions: an NMR and computational study of model systems

The interactions of simple carbohydrates with aromatic moieties have been investigated experimentally by NMR spectroscopy. The analysis of the changes in the chemical shifts of the sugar proton signals induced upon addition of aromatic entities has been interpreted in terms of interaction geometries. Phenol and aromatic amino acids (phenylalanine, tyrosine, tryptophan) have been used. The observed sugar-aromatic interactions depend on the chemical nature of the sugar, and thus on the stereochemistries of the different carbon atoms, and also on the solvent. A preliminary study of the solvation state of a model monosaccharide (methyl beta-galactopyranoside) in aqueous solution, both alone and in the presence of benzene and phenol, has also been carried out by monitoring of intermolecular homonuclear solvent-sugar and aromatic-sugar NOEs. These experimental results have been compared with those obtained by density functional theory methods and molecular mechanics calculations.     

Interfering with the sugar code: design and synthesis of oligosaccharide mimics

Oligosaccharide determinants of cellular glycoconjugates interact with protein receptors triggering a variety of cellular responses within a wide range of physiological and pathological processes and with exquisitely tuned selectivity. This has led to the formulation of the hypothesis that a sugar code exists and that sugar-binding proteins (lectins) act to decipher it and translate it into biological responses. Interference with these recognition events by functional mimics of carbohydrates could thus be used to modulate or alter signal transmission, or to prevent the onset of diseases. Attempts to design and prepare glycomimetic inhibitors of well-known target lectins (cholera toxin, DC-SIGN) are reviewed in this concept paper.     

Conformational study of 1,2-cycloundecadiene by dynamic NMR spectroscopy and computational methods

Solutions of 1,2-cycloundecadiene in propane were studied by low-temperature (13)C NMR spectroscopy. A total of 17 peaks were observed at -166.7 degrees C, corresponding to two conformations of similar populations, one of C(1) symmetry (11 peaks) and the other of C(2) symmetry. The line shapes show that the predominant pathway for exchange of the topomers (C(1) and C(1)') of the C(1) conformation does not include the C(2) conformation. From the (13)C spectra, free-energy barriers of 8.38 +/- 0.15, 9.45 +/- 0.15, and 9.35 +/- 0.15 kcal/mol were determined for the C(1) to C(1)', (C(1) + C(1)') to C(2), and C(2) to (C(1) + C(1)') conversions, respectively, at -72.2 degrees C. The NMR results for this compound are discussed in terms of the conformations predicted by molecular mechanics calculations obtained with Allinger's MM3 program. Ab initio calculations of free energies are also reported at the HF/ 6-311G level for 25 conformations.     

Conformational studies of novel estrogen receptor ligands by 1D and 2D NMR spectroscopy and computational methods

The solution conformations of the novel estrogen receptor ligands (17α,20E)‐(p‐trifluoromethylphenyl)vinylestradiol ( 1 ) and (17α,20E)‐(o‐trifluoromethylphenyl)vinylestradiol ( 2 ) were investigated in 2D and 1D NOESY studies and by comparison of ¹³C NMR chemical shifts with theoretical shieldings. The ¹H and ¹³C assignments of 1 and 2 were determined by DEPT, COSY and HMQC experiments. The conformations of the 17α‐phenylvinyl substituents of 1 and 2 are of interest because of their differing receptor binding affinities and effects in in vivo uterotrophic growth assays. A statistical method of evaluating contributing conformers of 1 and 2 from predicted ¹³C shifts of possible structures correlated fairly well with conformational conclusions derived from the NOE data. The 17α substituents of 1 and 2 apparently exist in similar conformational equilibria, suggesting that while 1 and 2 would occupy a similar receptor volume, interactions with the protein may shift the equilibrium and thereby influence the expression of the ligand. Copyright © 2003 John Wiley & Sons, Ltd.     

Analysis of flavonoids: tandem mass spectrometry, computational methods, and NMR

Due to the increasing understanding of the health benefits and chemopreventive properties of flavonoids, there continues to be significant effort dedicated to improved analytical methods for characterizing the structures of flavonoids and monitoring their levels in fruits and vegetables, as well as developing new approaches for mapping the interactions of flavonoids with biological molecules. Tandem mass spectrometry (MS/MS), particularly in conjunction with liquid chromatography (LC), is the dominant technique that has been pursued for elucidation of flavonoids. Metal complexation strategies have proven to be especially promising for enhancing the ionization of flavonoids and yielding key diagnostic product ions for differentiation of isomers. Of particular value is the addition of a chromophoric ligand to allow the application of infrared (IR) multiphoton dissociation as an alternative to collision-induced dissociation (CID) for the differentiation of isomers. CID, including energy-resolved methods, and nuclear magnetic resonance (NMR) have also been utilized widely for structural characterization of numerous classes of flavonoids and development of structure/activity relationships.The gas-phase ion chemistry of flavonoids is an active area of research particularly when combined with accurate mass measurement for distinguishing between isobaric ions. Applications of a variety of ab initio and chemical computation methods to the study of flavonoids have been reported, and the results of computations of ion and molecular structures have been shown together with computations of atomic charges and ion fragmentation. Unambiguous ion structures are obtained rarely using MS alone. Thus, it is necessary to combine MS with spectroscopic techniques such as ultraviolet (UV) and NMR to achieve this objective. The application of NMR data to the mass spectrometric examination of flavonoids is discussed.     

Study of three-dimensional structures of benzoylpyridine oximes and their ethers by 1H and 13C NMR spectroscopy

The ¹H and ¹³C NMR spectra of the E and Z isomers of 2-, 3-, and 4-benzoylpyridine oximes and their ethers were analyzed thoroughly, and the ¹H-¹³C spin-spin coupling constants (SSCC) were determined. It was established that the magnitude of the effect for the quaternary carbon atoms in the E and Z isomers depends on the site of substitution in the pyridine ring. It was assumed that the intermolecular hydrogen bond is stronger in the E form than in the Z form. The existence of the Z isomer of 2-benzoylpyridine oxime in deuterochloroform with an intramolecular hydrogen bond was proved.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 2, pp. 203–208, February, 1990.     

Simulation of carbohydrate-protein interactions: Computer-aided design of a second generation GM1 mimic

The oligosaccharide of ganglioside GM1 [Gal1-3GalNAc1-4(NeuAc2-3)Gal1-4Glc1-1Cer] is the cellular target of two bacterial enterotoxins: the cholera toxin (CT) and the heat-labile toxin of E.coli (LT). We recently reported that the pseudosaccharide 2[Gal1-3GalNAc1-4(NeuAc2-3)DCCHD] is a high-affinity ligand for CT, and thus a functional mimic of GM1 (Bernardi, A., Checchia, A., Brocca, P., Sonnino, S. and Zuccotto, F., J. Am. Chem. Soc., 121 (1999) 2032–2036). In this paper we describe the design of a second-generation mimic, formally obtained from 2 by inverting the configuration of a single stereocenter, thus transforming a N-acetyl galactosamine into a N-acetyl glucosamine. The design process involved modeling of the free ligand and its LT complex, followed by qualitative and quantitative comparison with the corresponding structures of 2. The protocol employed relied on both conformational search and molecular dynamics methodologies to account for the flexibility of both the ligand and the protein receptor. The conformational search of the LT:inhibitor complex showed that, compared to 2, the new compound can insert one more hydroxy group within the protein binding site. Molecular dynamics simulations showed that, in turn, this may trigger a series of rearrangements and reorientations of side chains and crystallographic water molecules in the toxin, leading to new H-bond contacts which may result in enhanced affinity of the new inhibitor. FEP calculations were performed by mutating the structure of 2 in solution and in the protein complex, and the prediction was made that the second-generation mimic should be a stronger binder than its parent compound.     

Quantitative ROESY analysis of computational models: structural studies of citalopram and β‐cyclodextrin complexes by 1H‐NMR and computational methods

Complexation of racemic citalopram with β‐cyclodextrin (β‐CD) in aqueous medium was investigated to determine atom‐accurate structure of the inclusion complexes. ¹H‐NMR chemical shift change data of β‐CD cavity protons in the presence of citalopram confirmed the formation of 1 : 1 inclusion complexes. ROESY spectrum confirmed the presence of aromatic ring in the β‐CD cavity but whether one of the two or both rings was not clear. Molecular mechanics and molecular dynamic calculations showed the entry of fluoro‐ring from wider side of β‐CD cavity as the most favored mode of inclusion. Minimum energy computational models were analyzed for their accuracy in atomic coordinates by comparison of calculated and experimental intermolecular ROESY peak intensities, which were not found in agreement. Several least energy computational models were refined and analyzed till calculated and experimental intensities were compatible. The results demonstrate that computational models of CD complexes need to be analyzed for atom‐accuracy and quantitative ROESY analysis is a promising method. Moreover, the study also validates that the quantitative use of ROESY is feasible even with longer mixing times if peak intensity ratios instead of absolute intensities are used. Copyright © 2015 John Wiley & Sons, Ltd.     

Conformational analysis of indole alkaloids corynantheine and dihydrocorynantheine by dynamic 1H NMR spectroscopy and computational methods: steric effects of ethyl vs vinyl group

1H NMR (400 MHz) spectra of the indole alkaloid dihydrocorynantheine recorded at room temperature show the presence of two conformers near coalescence. Low temperature 1H NMR allowed characterization of the conformational equilibrium, which involves rotation of the 3-methoxypropenoate side chain. Line-shape analysis yielded enthalpy of activation DeltaH(double dagger) = 71 +/- 6 kJ/mol, and entropy of activation DeltaS(double dagger) = 33 +/- 6 J/mol.K. The major and minor conformation contains the methyl ether group above and below the plane of the ring, respectively, as determined by low-temperature NOESY spectra, with free energy difference DeltaG degrees = 1.1 kJ/mol at -40 degrees C. In contrast to dihydrocorynantheine, the corresponding rotamers of corynantheine are in the fast exchange limit at room temperature. The activation parameters determined for corynantheine were DeltaH(double dagger) = 60 +/- 6 kJ/mol and DeltaS(double dagger) = 24 +/- 6 J/mol.K, with DeltaG degrees = 1.3 kJ/mol at -45 degrees C. The difference in the exchange rates of the rotamers of corynantheine and dihydrocorynantheine (respectively, 350 s(-1) and 9 s(-1) at 0 degrees C) reflects the difference in the steric bulk of the vinyl and the ethyl group. The conformational equilibria involving the side chain rotation as well as inversion of the bridgehead nitrogen in corynantheine and dihydrocorynantheine was studied by force-field (Amber and MMFF) and ab initio (density-functional theory at the B3LYP/6-31G level) computational methods, the results of which were in good agreement with the 1H NMR data. However, the calculations identified the rotamers as essentially isoenergetic, the experimental energy differences being to small to be reproduced exactly by the theory. Comparison of density-functional and force-field calculations with experimental results identified Amber as giving the most accurate results in the present case.     

Total synthesis and structure confirmation of elatenyne: success of computational methods for NMR prediction with highly flexible diastereomers

Elatenyne is a small dibrominated natural product first isolated from Laurencia elata. The structure of elatenyne was originally assigned as a pyrano[3,2-b]pyran on the basis of NMR methods. Total synthesis of the originally proposed pyrano[3,2-b]pyran structure of elatenyne led to the gross structure of the natural product being reassigned as a 2,2'-bifuranyl. The full stereostructure of this highly flexible small molecule was subsequently predicted by Boltzmann-weighted DFT calculations of (13)C NMR chemical shifts for all 32 potential diastereomers, with the predicted structure being in accord with the proposed biogenesis outlined below. Herein we report two complementary total syntheses of elatenyne, which confirm the computer-predicted stereostructure. Additionally, the total syntheses of (E)-elatenyne and a related 2,2'-bifuranyl, laurendecumenyne B, are reported. This work has not only allowed the full structure determination of all of these natural products but also provides excellent supporting evidence for their proposed biogenesis. The total synthesis of elatenyne demonstrates that DFT calculations of (13)C NMR chemical shifts coupled with biosynthetic postulates, comprise a very useful method for distinguishing among large numbers of highly flexible, closely related molecules.     

Conformational analysis of ochratoxin a by NMR spectroscopy and computational molecular modeling

Two-dimensional NMR spectroscopy has been used for a complete assignment of the proton and carbon-13 spectra of the metabolite from Aspergillus ochraceus, ochratoxin A. In addition, phase-sensitive nuclear Overhauser effect spectrometry experiments and computational molecular modeling (MM2 and MMFF force field programs) have been employed to examine the conformational properties of ochratoxin A in chloroform solutions. Particular attention has been given to intramolecular hydrogen-bonding formation involving the phenolic group on dihydroisocoumarin, which may be responsible for the toxic mechanism of ochratoxin A.     

Short-range structure of a GM3 ganglioside membrane: comparison between experimental WAXS and computer simulation results

The local structure of a GM3 ganglioside bilayer, whose wide-angle X-ray spectrum is reconstructed from molecular dynamics simulations, is found to compare quantitatively well with the experimental one. By separating inter- and intramolecular contributions, correlations between distinct head groups are shown to contribute in a substantial way to the total scattering intensity. This finding supports the hypothesis of a strong local head group order as recently formulated on the basis of calorimetry and X-ray experimental data.     

Carbohydrate chain of ganglioside GM1 as a ligand: identification of the binding strategies of three 15 mer peptides and their divergence from the binding modes of growth-regulatory galectin-1 and cholera toxin

The branched pentasaccharide chain of ganglioside GM1 is a prominent cell surface ligand, for example, for cholera toxin or tumor growth-regulatory homodimeric galectins. This activity profile via protein recognition prompted us to examine the binding properties of peptides with this specificity. Our study provides insights into the mechanism of molecular interaction of this thus far unexplored size limit of the protein part. We used three pentadecapeptides in a combined approach of mass spectrometry, NMR spectroscopy and molecular modelling to analyze the ligand binding in solution. Availability of charged and hydrophobic functionalities affected the intramolecular flexibility of the peptides differently. Backfolding led to restrictions in two cases; the flexibility was not reduced significantly by association of the ligand in its energetically privileged conformations. Major contributions to the interaction energy arise from the sialic acid moiety contacting Arg/Lys residues and the N-terminal charge. Considerable involvement of stacking between the monovalent ligand and aromatic rings could not be detected. This carbohydrate binding strategy is similar to how an adenoviral fiber knob targets sialylated glycans. Rational manipulation for an affinity enhancement can now be directed to reduce the flexibility, exploit the potential for stacking and acquire the cross-linking capacity of the natural lectins by peptide attachment to a suitable scaffold.     

NQR and NMR study of hydrogen bonding interactions in anhydrous and monohydrated guanine cluster model: A computational study

In this paper extensive systematic computational study has been carried out to justify hydrogen bonding interactions and their influence on the oxygen, nitrogen and hydrogen NQR and NMR parameters of the anhydrous and monohydrated guanine crystal structures at two different levels, B3LYP and MP2, using 6-311++G** and D95** basis sets. These theoretical data have been compared with experimental NMR and NQR measurements. For further investigation, results of cluster calculation have been compared with that of a single molecule. Our theoretical NQR and NMR parameters of ¹⁷O, ¹⁵N and ²H atoms of anhydrous and monohydrated guanine exhibited extreme sensitivity to electron distribution around mentioned nuclei caused by cooperative influences of various types of hydrogen bonding interactions. Fortunately, our calculated isotropic shielding values and CS tensors for the ¹⁷O and ¹⁵N nuclei as well as obtained ¹⁴N-NQR parameters are in excellent agreement with experimental data. Therefore, we can undoubtedly conclude that for anhydrous and monohydrated guanine tetrameric clusters including intermolecular interactions, our theoretical estimates are in better agreement with observed experimental values than those in which these interactions have been ignored.     

Chiral thiols: the assignment of their absolute configuration by 1H NMR

A general NMR spectroscopy protocol for determination of absolute configuration of thiols, that includes the introduction of new aryl-tert-butoxyacetic acids as chiral derivatizing agents (CDAs), is described.     

Copper cation interactions with biologically essential types of ligands: a computational DFT study

This work presents a systematic theoretical study on Cu(I) and Cu(II) cations in variable hydrogen sulfide-aqua-ammine ligand fields. These ligands model the biologically most common environment for Cu ions. Molecular structures of the complexes were optimized at the density functional theory (DFT) level. Subsequent thorough energy analyses revealed the following trends: (i) The ammine complexes are the most stable, followed by those containing the aqua and hydrogen sulfide ligands, which are characterized by similar stabilization energies. (ii) The most preferred Cu(I) coordination number is 2 in ammine or aqua ligand fields. A qualitatively different binding picture was obtained for complexes with H(2)S ligands where the 4-coordination is favored. (iii) The 4- and 5-coordinated structures belong to the most stable complexes for Cu(II), regardless of the ligand types. Vertical and adiabatic ionization potentials of Cu(I) complexes were calculated. Charge distribution (using the natural population analysis (NPA) method) and molecular orbital analyses were performed to elucidate the nature of bonding in the examined systems. The results provide in-depth insight into the Cu-binding properties and can be, among others, used for the calibration of bioinorganic force fields.     

Conformational study of cis-1,4-di-tert-butylcyclohexane by dynamic NMR spectroscopy and computational methods. Observation of chair and twist-boat conformations

[reaction: see text] Low-temperature 13C NMR spectra of cis-1,4-di-tert-butylcyclohexane (1) showed signals for the twist-boat (1a) and chair (1b) conformations. 13C NMR signals were assigned to specific carbons based on the different populations, different symmetries (time-averaged C(2v) for 1a and time-averaged C(s) for 1b), and calculated chemical shifts (GIAO, HF/6-311+G*). In addition to slow ring inversion and interconversion of the chair and twist-boat conformations, slow rotation of the tert-butyl groups was found. Most of the expected 13C peaks were observed. Free-energy barriers of 6.83 and 6.35 kcal/mol were found for interconversion of 1a (major) and 1b (minor) at -148.1 degrees C. Conformational space was searched with Allinger's MM3 and MM4 programs, and free energies were obtained for several low-energy conformations 1a-c. Calculations were repeated with ab initio methods up to the HF/6-311+G* level. Molecular symmetries, relative free energies, relative enthalpies and entropies, frequencies, and NMR chemical shifts were obtained. A boat conformation (1d; C(2v) symmetry) was generated and optimized as a transition state by ab initio, MM3, and MM4 calculations.