Design,synthesis, and NMR structure of linear and cyclic oligomers containing novel furanoid sugar amino acids

Sugar Amino Acids (SAAs) are sugar moieties containing at least one amino and one carboxyl group. The straightforward synthesis of two furanoid SAAs, 3-amino-3-deoxy-1,2-isopropylidene-alpha-D-ribofuranoic acid (f-SAA1) and 3-amino-3-deoxy-1,2-isopropylidene-alpha-D-allofuranoic acid (f-SAA2) starting from diacetone glucose, is described. These SAAs were used as structural templates aiming at new structures for peptidomimetic drug design. f-SAA1 resembles a beta-amino acid, whereas f-SAA2 is a gamma-amino acid mimetic. Thus, for the synthesis of the mixed, linear and cyclic oligomers of f-SAA1, beta-homo-glycine (beta-hGly, also called beta-alanine) was chosen as an amino acid counterpart, while for the oligomer of f-SAA2 gamma-amino butyric acid (GABA) was chosen. Fmoc-[f-SAA1-beta-hGly](3)-OH (3) and cyclo[f-SAA1-beta-hGly](3) (5) resemble linear and cyclic beta-peptides with a very different substitution pattern, compared with the beta-peptides known so far in the literature, whereas Fmoc-[f-SAA2-GABA](3)-OH (4) resembles a gamma-peptide. The linear f-SAA oligomers 3 and 4 were synthesized on the solid-phase using Fmoc strategy. 23 unambiguous interresidue NOE contacts (from a total of 76 NOE values), obtained from extensive NMR studies in C(3)CN, were used in subsequent simulated annealing and MD calculations, to elucidate the 12/10/12-helical structure of oligomer 3 in CH(3)CN. The results indicate that f-SAA1 strongly induces a secondary structure. A characteristic CD curve for the linear oligomer 3 is observed up to 75 degrees C in both CH(3)CN and CH(3)CN/H(2)O, even though 3 contains beta-hGly, which is known to destabilize helices. By contrast, 4 does not seem to form a stable conformation in solution. The cyclic SAA containing oligomer cyclo [f-SAA1-beta-hGly](3) (5) exhibits a C(3) symmetric conformation on the NMR chemical shift time scale.     

Conformational analysis of a tetrasaccharide based on NMR spectroscopy and molecular dynamics simulations

The conformational preference of the human milk oligosaccharide lacto-N-neotetraose, beta-d-Galp-(1 --> 4)-beta-d-GlcpNAc-(1 --> 3)-beta-d-Galp-(1 --> 4)-d-Glcp, has been analyzed using (1)H,(1)H T-ROESY and (1)H,(13)C trans-glycosidic J coupling experiments in isotropic solution and (1)H,(13)C residual dipolar couplings (RDCs) obtained in lyotropic liquid crystalline media. Molecular dynamics simulations of the tetrasaccharide with explicit water as the solvent revealed that two conformational states are significantly populated at the psi glycosidic torsion angle, defined by C(anomeric)-O-C-H, of the (1 --> 3)-linkage. Calculation of order parameters, related to the molecular shape, were based on the inertia tensor and fitting of experimental RDCs to different conformational states showed that psi(+) > 0 degrees is the major and psi(-) < 0 degrees is the minor conformation in solution, in complete agreement with a two-state analysis based on the T-ROESY data. Attention was also given to the effect of salt (200 mM NaCl) in the anisotropic medium, which was a ternary mixture of n-octyl-penta(ethylene glycol), n-octanol, and D(2)O.     

An unusual reverse turn structure adopted by a furanoid sugar amino acid incorporated in gramicidin S

A new reverse turn, replacing one of the native type II' beta-turns in the cyclic peptide antibiotic gramicidin S, induced by a furanoid sugar amino acid is revealed. The C3-hydroxyl function plays a pivotal role by acting as a H-bond acceptor, consequently flipping the amide bond between residues i and i + 1, as was established by NMR and X-ray crystallographic analysis.     

Investigation of structure and dynamics in a photochromic molecular crystal by NMR crystallography

A photochromic anil, N-(3,5-di-t-butylsalicylidene)-4-amino-pyridine, has been studied by single-crystal X-ray diffraction, multinuclear magic-angle spinning NMR, and first-principles density functional theory (DFT) calculations. Interpretation of the solid-state NMR data on the basis of calculated chemical shifts confirms the structure is primarily composed of molecules in the ground-state enol tautomer, whereas thermally activated cis-keto and photoisomerised trans-keto states exist as low-level defects with populations that are too low to detect experimentally. Variable temperature ¹³C NMR data reveal evidence for solid-state dynamics, which is found to be associated with fast rotational motion of t-butyl groups and 180° flips of the pyridine ring, contrasting the time-averaged structure obtained by X-ray diffraction. Comparison of calculated chemical shifts for the full crystal structure and an isolated molecule also reveals evidence for an intermolecular hydrogen bond involving the pyridine ring and an adjacent imine carbon, which facilitates the flipping motion. The DFT calculations also reveal that the molecular conformation in the crystal structure is very close to the energetic minimum for an isolated molecule, indicating that the ring dynamics arise as a result of considerable steric freedom of the pyridine ring and which also allows the molecule to adopt a favourable conformation for photochromism.     

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.     

Polymorphism for a novel phosphoramidate; NMR and X-ray crystallography

Abstract  

New phosphoramidates with formula 3-NC₅H₄C(O)NHP(O)XY (X=Y=Cl (1), X=Y=NH–C(CH₃)₃ (2a,2b), X=Y=N(C₄H₉)₂ (3), X=Cl, Y=N(C₂H₅)₂ (4) were synthesized and characterized by IR, ¹H-, ¹³C-, ³¹P-NMR spectroscopy and CHN elemental analysis. Surprisingly, the reaction of compound 2a with LaCl₃, 7H₂O in 3:1 M ratio leads to a polymorph of this compound (2b). NMR spectra indicate that ² J(PNH_amide) in 2b (7.0 Hz) is very much greater than in 2a (4.1 Hz), while δ(³¹P) values are identical for both of them. In IR spectra, υ(P=O) is weaker but υ(C=O) is stronger in 2a than in 2b. The structures of 2a, 2b were determined by X-ray crystallography. These compounds form centrosymmetric dimers via two intermolecular P=O……H–N hydrogen bonds. Strong intermolecular N–H…N, N–H…O and weak C–H…O hydrogen bonds lead to a three-dimensional polymeric cluster in the 2a while intermolecular strong N–H……N and weak C–H……O hydrogen bonds form a two-dimensional polymeric chain in 2b.     

1,n′-Disubstituted ferrocenoyl amino acids and dipeptides: Conformational analysis by CD spectroscopy, X-ray crystallography, and DFT calculations

An experimental and computational study on the conformational preference of 1,n′-disubstituted ferrocenoyl amino acids and dipeptides is presented. Only l-amino acids were used for the synthesis of Fe[C₅H₄-CO-Met-Met-OMe]₂ (4), but according to the X-ray structure a 4:1 mixture of l,d,M,d,l and l,d,M,l,l isomers is obtained (l describes amino acid chirality and M the helical chirality of the ferrocene core). This result is in agreement with IR and CD solution phase data and can be explained with a racemization by 1 M NaOH during the synthesis. In order to determine the relative stabilities of the different conformations, DFT calculations on model compounds Fe[C₅H₄-CO-Gly-NH₂]₂ (5) and Fe[C₅H₄-CO-Ala-OMe]₂ (6) were performed using the B3LYP/LanL2DZ method with ECPs on the heavy atoms. Conformers 5A-5C with different hydrogen bond patterns have significantly different stabilities with a stabilization by about 30 kJ mol⁻¹ per hydrogen bond. The “Herrick conformation” 5A with two hydrogen bonds is the most stable in the gas phase, in accordance with the solution and solid phase data. In contrast, only small energetic differences (less than 10 kJ mol⁻¹) were calculated for conformers l,P,l-6A, l,P,d-6A and d,P,d-6A, which differ only in amino acid chirality.     

Studies on synthesis and molecular dynamics simulation of dendrimers containing amino acids and peptides

A series of poly(ether-amide) dendrimers with amino acids and peptides as the peripheral functional groups was synthesized, and their structures were confirmed by nuclear magnetic resonance (NMR) and electrospray ionization-mass spectrometry (ESI-MS) spectrometry. Molecular dynamics simulation of the peptide dendrimers in solution was performed, indicating that, the prior conformations of the dendrimers were atom number dependent, i.e., with the increases of the atom number, the prior conformations were more spherical. Also, the amino acid α-C atom radial distribution indicated that, with larger peripheral groups, more back-folding of the dendrimers occurred. __________ Translated from Acta Chimica Sinica, 2007, 65(1): 21–26 [译自: 化学 通报]     

Conformational analysis of oxazolidines by molecular and quantum mechanics and NMR spectroscopy

A combined experimental (¹HNMR) and theoretical (molecular mechanics and PCILO) study of (4S,5S,6R)-4-carbome-thoxyethylenyl-N-carbobenzyloxy-5-methyl-6-phenyl oxazolidine has been carried out with the purpose of contributing to a better understanding of the steric and electronic factors responsible for the observed diastereoisomeric selectivity in the dihydroxylation of oxazolidines leading to optically active α, β dialkoxyaldehydes.     

Discriminating the helical forms of peptides by NMR and molecular dynamics simulation

The HNCO NMR pulse sequence was applied to three selectively labeled (15)N and (13)C isotopic homologues of the peptide Ac-WAAAH(AAARA)(3)A-NH(2) to probe directly for hydrogen bonds between residues 8 and 11 (characteristic of a 3(10)-helix), 8 and 12 (alpha-helix), and 8 and 13 (pi-helix). The experiments demonstrate conclusively, and in agreement with circular dichroism studies, that the center of the peptide is alpha-helical; there is no discernible 3(10)- or pi-helix at these specific positions. Molecular dynamics simulations of the preceding peptide and Ac-(AAAAK)(3)A-NH(2) in water using the potential energy parameter set CHARMM22/CMAP correctly yield an alpha-helix, in contrast to simulations with the set CHARMM22, which result in a pi-helix.     

Conformational analysis of dehydrodidemnin B (aplidine) by NMR spectroscopy and molecular mechanics/dynamics calculations.

Dehydrodidemnin B (DDB or aplidine), a potent antitumoral natural product currently in phase II clinical trials, exists as an approximately 1:1 mixture of two slowly interconverting conformations. These are sufficiently long-lived so as to allow their resolution by HPLC. NMR spectroscopy shows that this phenomenon is a consequence of restricted rotation about the Pyr-Pro(8) terminal amide bond of the molecule's side chain. The same technique also indicates that the overall three-dimensional structures of both the cis and trans isomers of DDB are similar despite the conformational change. Molecular dynamics simulations with different implicit and explicit solvent models show that the ensembles of three-dimensional structures produced are indeed similar for both the cis and trans isomers. These studies also show that hydrogen bonding patterns in both isomers are alike and that each one is stabilized by a hydrogen bond between the pyruvyl unit at the terminus of the molecule's side chain and the Thr(6) residue situated at the junction betwen the macrocycle and the molecule's side chain. Nevertheless, each conformational isomer forms this hydrogen bond using a different pyruvyl carbonyl group: CO(2) in the case of the cis isomer and CO(1) in the case of the trans isomer.     

Conformational studies of N-carbomethoxy-2-alkoxyindolenines by dynamic NMR, crystallography, and molecular mechanics

The synthesis of N-carbomethoxy-2-alkoxyindolenines and the transformation to their tautomeric indoles is reported. Variable-temperature ¹H NMR studies of these 2-alkoxyindolenines evidenced dynamic processes involving two low-energy E and Z equilibrating conformers around the N-C(O) carbamate bond, for which the barriers (ΔG^≠) between the two conformations are in the order of 12.5-13.9 kcal/mol, as deduced from computational NMR line shape simulations. The rotational barrier decreases as the bulkiness of the alkoxyl group increases, with the E conformer being always more stable. Molecular mechanics calculations evidenced a preferred quasi-axial position of the alkoxyl group in the five-membered ring as the steric effect increases, in agreement with X-ray diffraction studies.     

Conformational analysis of thia crown ether derivatives by NMR spectroscopy and molecular mechanics calculations

Summary Addition of sulfur dichloride to tetrachlorocatechol-bisallylether (1) yields the 9- and 10-ring thia crown ether derivatives2 and3, respectively, together with the dithia-18-crown-6-ether4. The 10-membered ring compound3 represents the first thia macrocycle containing bothMarkovnikov andanti-Markovnikov constitution of the -chloro-thio structural segments in the same molecule. By¹H and¹³C NMR spectroscopy, equal amounts of two preferred conformers of the only isolated diastereomer of3 were observed at temperatures below –50°C. The signals were assigned to these conformers using COSY, HETCOR, and phase sensitive NOESY spectra at low temperatures. The preferred conformations and the relative configuration were determined using the different effects of _gauche -and _anti -positions in¹³C NMR chemical shifts and analyzing vicinal³ J _H,H coupling constants. These results were confirmed by molecular mechanics calculations.Dedicated to Prof. Dr.Rolf Borsdorf on the occasion of his 65^th birthday     

Conformational manifold of alpha-aminoisobutyric acid (Aib) containing alanine-based tripeptides in aqueous solution explored by vibrational spectroscopy, electronic circular dichroism spectroscopy, and molecular dynamics simulations

Replacement of the alpha-proton of an alanine residue to generate alpha-aminoisobutyric acid (Aib) in alanine-based oligopeptides favors the formation of a 3(10) helix when the length of the oligopeptide is about four to six residues. This research was aimed at experimentally identifying the structural impact of an individual Aib residue in an alanine context of short peptides in water and Aib's influence on the conformation of nearest-neighbor residues. The amide I band profile of the IR, isotropic and anisotropic Raman, and vibrational circular dichroism (VCD) spectra of Ac-Ala-Ala-Aib-OMe, Ac-Ala-Aib-Ala-OMe, and Ac-Aib-Ala-Ala-OMe were measured and analyzed in terms of different structural models by utilizing an algorithm that exploits the excitonic coupling between amide I' modes. The conformational search was guided by the respective 1H NMR and electronic circular dichroism spectra of the respective peptides, which were also recorded. From these analyses, all peptides adopted multiple conformations. Aib predominantly sampled the right-handed and left-handed 3(10)-helix region and to a minor extent the bridge region between the polyproline (PPII) and the helical regions of the Ramachandran plot. Generally, alanine showed the anticipated PPII propensity, but its conformational equilibrium was shifted towards helical conformations in Ac-Aib-Ala-Ala-OMe, indicating that Aib can induce helical conformations of neighboring residues positioned towards the C-terminal direction of the peptide. An energy landscape exploration by molecular dynamics simulations corroborated the results of the spectroscopic studies. They also revealed the dynamics and pathways of potential conformational transitions of the corresponding Aib residues.     

Solvation and aggregation of n,n'-dialkylimidazolium ionic liquids: a multinuclear NMR spectroscopy and molecular dynamics simulation study

The solvation and aggregation of the ionic liquid (IL) 1-n-butyl-3-methylimidazolium chloride ([C4mim]Cl) in water and dimethylsulfoxide (DMSO) were examined by analysis of (1)H and (35/37)Cl chemical shift perturbations and molecular dynamics (MD) simulations. Evidence of aggregation of the IL n-butyl chains in aqueous environments at IL concentrations of 75-80 wt% was observed both in the NMR experiments and in the MD simulations. The studies also show that [C4mim]Cl behaves as a typical electrolyte in water, with both ions completely solvated at low concentrations. On the other hand, the data reveal that the interactions between the [C4mim](+) and Cl(-) ions strengthen as the DMSO content of the solutions increases, and IL-rich clusters persist in this solvent even at concentrations below 10 wt%. These results provide an experimentally supported atomistic explanation of the effects that these two solvents have on some of the macroscopic properties of [C4mim]Cl. The implications that these findings could have on the design of IL-based solvent systems are briefly discussed.     

Conformational analysis of phorboxazole bis-oxazole oxane fragment analogs by NMR spectroscopy and molecular modeling simulations

We present a detailed conformational study of a simplified synthetic analog of the bis-oxazole oxane fragment found in the cytostatic agents phorboxazole A and B based on results from NMR spectroscopy and molecular modeling simulations. Complete 1H and 13C resonance assignments for the bis-oxazole oxane system were carried out through the use of COSY, HSQC, HMBC, TOCSY, and HSQC-TOCSY experiments, and its conformational preferences in solution were investigated by analysis of 3J(HH) coupling constants and NOE enhancements obtained from 1D and 2D NOESY experiments. In order to solve inconsistencies from our preliminary structural studies, simulated annealing studies were performed to thoroughly sample the phase space available to the molecule. Our results reveal that the six-membered oxane ring, which constitutes the most important moiety regarding the three-dimensional (3D) structure and flexibility of the analog, exists in rapid equilibrium between its two accessible chair conformers in an approximate ratio of 70:30. The information gathered from these studies will be of critical importance in our efforts to prepare novel compounds with phorboxazole-like structure and activity.     

Epikatonic acid from Austroplenckia populnea: structure elucidation by 2D NMR spectroscopy and X‐ray crystallography

From the chloroform extract of Austroplenckia populnea, epikatonic acid, friedelin, populnonic acid, abruslactone A, salaspermic acid and 22β‐epi‐maytenfolic acid were isolated. The structure and stereochemistry of epikatonic acid were established by two‐dimensional NMR spectroscopic techniques (HMQC, HMBC and NOESY) and later confirmed by single crystal X‐ray diffraction as 3β‐hydroxy‐olean‐12‐en‐29‐oic acid, which unambiguously established the configuration of the hydroxyl group at C‐3 as 3β‐OH and the carboxyl group at C‐20 as 20α‐COOH. The crystal structure shows two independent molecules in the asymmetric unit. The crystal packing is stabilized by four O–H·O intermolecular hydrogen bonds, which give rise to infinite double chains along the c axis. Copyright © 2002 John Wiley & Sons, Ltd.     

A 500-ps molecular dynamics simulation trajectory of cardiotoxin II from Taiwan cobra venom in solution: Correlation with NMR and X-ray crystallography data

Molecular dynamics simulation of a small, basic, all β-sheet cardiotoxin, CTX II, from Taiwan cobra venom, with proper treatment of long-range electrostatic interactions, was carried out to examine the backbone mobility of CTX II in solution and aid in interpretation of order parameters of C_α H bonds obtained from NMR experiments based on the Lipari–Szabo theory. The calculated order parameters of C_α H bonds and B-factors of CTX II in solution were compared with NMR-derived backbone order parameters and the crystal structure data, respectively. An overall qualitative agreement was obtained and, quantitatively, the calculated values and experimental results of many residues were also in good agreement. The discrepancies between the results computed herein and the experimental values, physical bases, and plausible biological functions are discussed. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 546–562, 1999     

A novel crown ether generation containing different heteroaromatic cations: synthesis, characterization, solid-phase (13)C NMR, X-ray crystal structure, and selective amino acid recognition

The synthesis and structural characterization of a novel generation of crown ethers, 3, 5 and 6 containing pyrilium, thiopyrilium, and pyridinium subunits, respectively, are reported. The crown ether unit is potentially capable of forming host-guest complexes with inorganic and organic cations, while the heteroaromatic cationic unit is suitable to bind with anions. A variety of physicochemical methods including electrospray mass spectrometry, UV-vis spectroscopy, solution and solid-phase NMR, and X-ray crystallography were applied for structural characterization of the new crown ether derivatives. The (1)H and (13)C NMR studies indicate rapid rotation of the B9C3 unit about the C-C bond that connects the two units to each other. Single crystals for 3, 4, and 5 were successfully obtained, and their X-ray crystal structures were resolved. The perchlorate anion in 3 (orthorhombic, space group P2(1)2(1)2(1)) and 5 (orthorhombic, space group P2(1)) is far from O(+) and close to S(+). The solid-phase structure of 3 and 5 show small deviation from planarity for the four aromatic rings, whereas two of the aromatic rings in 4 are out of heteroaromatic ring. Spectrophotometric studies in methanol solution revealed that the ligand 3 can be successfully applied to selective amino acid recognition.     

Benzoxazine oligomers: evidence for a helical structure from solid-state NMR spectroscopy and DFT-based dynamics and chemical shift calculations

A combination of molecular modeling, DFT calculations, and advanced solid-state NMR experiments is used to elucidate the supramolecular structure of a series of benzoxazine oligomers. Intramolecular hydrogen bonds are characterized and identified as the driving forces for ring-shape and helical conformations of trimeric and tetrameric units. In fast MAS (1)H NMR spectra, the resonances of the protons forming the hydrogen bonds can be assigned and used for validating and refining the structure by means of DFT-based geometry optimizations and (1)H chemical-shift calculations. Also supporting these proposed structures are homonuclear (1)H[bond](1)H double-quantum NMR spectra, which identify the local proton-proton proximities in each material. Additionally, quantitative (15)N[bond](1)H distance measurements obtained by analysis of dipolar spinning sideband patterns confirm the optimized geometry of the tetramer. These results clearly support the predicted helical geometry of the benzoxazine polymer. This geometry, in which the N...H...O and O...H...O hydrogen bonds are protected on the inside of the helix, can account for many of the exemplary chemical properties of the polybenzoxazine materials. The combination of advanced experimental solid-state NMR spectroscopy with computational geometry optimizations, total energy, and NMR spectra calculations is a powerful tool for structural analysis. Its results provide significantly more confidence than the individual measurements or calculations alone, in particular, because the microscopic structure of many disordered systems cannot be elucidated by means of conventional methods due to lack of long-range order.