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1.
NMR structure of a cyclic polyamide-DNA complex   总被引:3,自引:0,他引:3  
The solution structure of a cyclic polyamide ligand complexed to a DNA oligomer, derived from NMR restrained molecular mechanics, is presented. The polyamide, cyclo-gamma-ImPyPy-gamma-PyPyPy-, binds to target DNA with a nanomolar dissociation constant as characterized by quantitative footprinting previously reported. 2D (1)H NMR data were used to generate distance restraints defining the structure of this cyclic polyamide with the DNA duplex d(5'-GCCTGTTAGCG-3'):d(5'-CGCTAACAGGC-3'). Data interpretation used complete relaxation matrix analysis of the NOESY cross-peak intensities with the program MARDIGRAS. The NMR-based distance restraints (276 total) were applied in restrained molecular dynamics calculations using a solvent model, yielding structures with an rmsd for the ligand and binding site of approximately 1 A. The resulting structures indicate some distortion of the DNA in the binding site. The constraints from cyclization lead to altered stacking of the rings in the halves of the cyclic ligand relative to unlinked complexes. Despite this, the interactions with DNA are very similar to what has been found in unlinked complexes. Measurements of ligand amide and DNA imino proton exchange rates indicate very slow dissociation of the ligand and show that the DNA can undergo opening fluctuations while the ligand is bound although the presence of the ligand decreases their frequency relative to the free DNA.  相似文献   

2.
A method for structure validation based on the simultaneous analysis of a 1D (1)H NMR and 2D (1)H - (13)C single-bond correlation spectrum such as HSQC or HMQC is presented here. When compared with the validation of a structure by a 1D (1)H NMR spectrum alone, the advantage of including a 2D HSQC spectrum in structure validation is that it adds not only the information of (13)C shifts, but also which proton shifts they are directly coupled to, and an indication of which methylene protons are diastereotopic. The lack of corresponding peaks in the 2D spectrum that appear in the 1D (1)H spectrum, also gives a clear picture of which protons are attached to heteroatoms. For all these benefits, combined NMR verification was expected and found by all metrics to be superior to validation by 1D (1)H NMR alone. Using multiple real-life data sets of chemical structures and the corresponding 1D and 2D data, it was possible to unambiguously identify at least 90% of the correct structures. As part of this test, challenging incorrect structures, mostly regioisomers, were also matched with each spectrum set. For these incorrect structures, the false positive rate was observed as low as 6%.  相似文献   

3.
A system for structure elucidation based on proton NMR spectra has been developed. The system, named Spec2D (system for spectra from 2D-NMR), incorporates 1H NMR and H-H correlation spectroscopy (COSY) spectral information obtained from 2D-NMR experiments. 2D-NMR is important for the structure elucidation because it provides information about the relationships among differently situated protons in the structures of unknown compounds. The system uses the concepts of molecular graphs. The improved representation of substructures as well as several novel algorithms for structure generation have been devised to solve the combinatorial problem and to reduce the processing time. Spec2D consists of a knowledge base, an analysis module, and a candidate structure generator module. Spec2D proposes candidate structures from only 1H NMR and H-H COSY spectral information of an unknown compound without any 13C NMR spectral or structural information, such as molecular formulas. Spec2D has the capability to propose the "new" structure of an unknown compound, if the corresponding substructures are included in the knowledge base.  相似文献   

4.
The solution structure of the duplex formed by self-pairing of the p-RNA octamer β-D -ribopyranosyl-(2′→4′)-(CGAATTCG) was studied by NMR techniques and, independently, by molecular-dynamics calculations. The resonances of all non-exchanging protons, H-bearing C-atoms, P-atoms, and of most NH protons were assigned. Dihedral angle and distance constraints derived from coupling constants and NOESY spectra are consistent with a single dominant conformer and corroborate the main structural features predicted by qualitative conformational analysis. The duplex displays Watson-Crick pairing with antiparallel strand orientation. The dihedral angles β and ? in the phosphodiester linkages differ considerably from the idealized values. Model considerations indicate that these deviations from the idealized model allow better interstrand stacking and lessen unfavorable interactions in the backbone. The average base-pair axis forms an angle of ca. 40° with the backbone. The resulting interstrand π-π stacking between either two purines, or a purine and a pyrimidine, but not between two pyrimidines, constitutes a characteristic structural feature of the p-RNA duplex. A 1000-ps molecular-dynamics (MD) calculation with the AMBER force field resulted in an average structure of the same conformation type as derived by NMR. For the backbone torsion angle ?, dynamically averaged coupling constants from the MD calculation agree well with the experimental values, but for the angle β, a systematic difference of ca. 25° remains. The two base pairs at the ends of the duplex are calculated to be highly labile, which is consistent with the high exchange rate of the corresponding imino protons found by NMR.  相似文献   

5.
The solution structure of the duplex formed by α‐L ‐arabinopyranosyl‐(4′→2′)‐(CGAATTCG) was studied by NMR. The resonances of all H‐, P‐ and most C‐atoms could be assigned. Dihedral angles and distance estimates derived from coupling constants and NOESY spectra were used as restraints in a simulated annealing calculation, which generated a well‐defined bundle of structures for the six innermost nucleotide pairs. The essential features of the resulting structures are an antiparallel, Watson Crick‐paired duplex with a strong backbone inclination of ca. −50° and, therefore, predominant interstrand base stacking. The very similar inclination and rise parameters of arabinopyranosyl‐(4′→2′)‐oligonucleotides and p‐RNA explain why these two pentapyranosyl isomers are able to cross‐pair.  相似文献   

6.
We recently developed new NMR methods for monitoring the hydrogen exchange rates of tyrosine hydroxyl (Tyr-OH) and cysteine sulfhydryl (Cys-SH) groups in proteins. These methods facilitate the identification of slowly exchanging polar side-chain protons in proteins, which serve as sources of NOE restraints for protein structure refinement. Here, we have extended the methods for monitoring the hydrogen exchange rates of the OH groups of serine (Ser) and threonine (Thr) residues in an 18.2 kDa protein, EPPIb, and thus demonstrated the usefulness of NOE restraints with slowly exchanging OH protons for refining the protein structure. The slowly exchanging Ser/Thr-OH groups were readily identified by monitoring the (13)C(β)-NMR signals in an H(2)O/D(2)O (1:1) mixture, for the protein containing Ser/Thr residues with (13)C, (2)H-double labels at their β carbons. Under these circumstances, the OH groups exist in equilibrium between the protonated and deuterated isotopomers, and the (13)C(β) peaks of the two species are resolved when their exchange rate is slower than the time scale of the isotope shift effect. In the case of EPPIb dissolved in 50 mM sodium phosphate buffer (pH 7.5) at 40 °C, one Ser and four Thr residues were found to have slowly exchanging hydroxyl groups (k(ex) < ~40 s(-1)). With the information for the slowly exchanging Ser/Thr-OH groups in hand, we could collect additional NOE restraints for EPPIb, thereby making a unique and important contribution toward defining the spatial positions of the OH protons, and thus the hydrogen-bonding acceptor atoms.  相似文献   

7.
A home made hydrogen/carbon analyser was used to determine the portion of exchangeable protons in aquatic humic substances. For this purpose, equal sample amounts were dissolved in H2O and D2O, respectively, dried and combusted in a stream of oxygen. The amount of water resulting from combustion was measured by an infrared detector which recorded the OH bending vibration of H2O. The bands stemming from HOD or D2O were not registered by the detection unit. Thus, combustion of organic samples containing exchangeable protons dissolved in D2O resulted in a significantly smaller signal compared to the signal observed for the same sample dissolved in H2O. The relative intensity loss of the H2O signal observed after combustion was used to derive the portion of exchangeable protons in a standard reference material, a humic substance isolated by the International Humic Substances Society (Suwannee River fulvic acid). According to this method about 20% of the sample protons could be identified as exchangeable protons. With regard to titration data the portion of protons bound to non acidic hydroxy functions could be estimated. The validity of this procedure was proved by combustion experiments using commercially available deuterated substances as well as organic model compounds dissolved in D2O and H2O, respectively.  相似文献   

8.
9.
Solid-state (1)H, (17)O MAS NMR, (1)H-(93)Nb TRAPDOR NMR, and (1)H double quantum 2D MAS NMR experiments were used to characterize the oxygen, water, and hydroxyl environments in the monoprotonated hexaniobate material, Na(7)[HNb(6)O(19)].15H(2)O. These solid-state NMR experiments demonstrate that the proton is located on the bridging oxygen of the [Nb(6)O(19)](8-) cluster. The solid-state NMR results also show that the NbOH protons are spatially isolated from similar protons, but undergo proton exchange with the water species located in the crystal lattice. On the basis of double quantum (1)H MAS NMR measurements, it was determined that the water species in the crystal lattice have restricted motional dynamics. Two-dimensional (1)H-(17)O MAS NMR correlation experiments show that these restricted waters are preferentially associated with the bridging oxygen. Solution (17)O NMR experiments show that the hydroxyl proton is also attached to the bridging oxygen for the compound in solution. In addition, solution (17)O NMR kinetic studies for the hexaniobate allowed the measurement of relative oxygen exchange rates between the bridging, terminal, and hydroxyl oxygen and the oxygen of the solvent as a function of pH and temperature. These NMR experiments are some of the first investigations into the proton location, oxygen and proton exchange processes, and water dynamics for a base stable polyoxoniobate material, and they provide insight into the chemistry and reactivity of these materials.  相似文献   

10.
Gossypol was obtained as an yellow platelike crystal with m.p. 210-214 . In CDCl3 there were three tautomers of gossypol: Ⅰ aldehyde, Ⅱ lactol, Ⅲ ketal, in equilibrium .Their total 1H NMR spectra were assigned by means of 1D and 2D NMR techniques including 1H-1H cosy ,DEPT, HMQC (1H Detected Heteronuclear Multiple Quantum Coherence) and HMBC (1H Detected Heteronuclear Multiple Bond Connectivity) experiments.This paper first reported that we took use of the 2D NMR techniques to assign all of 1H NMR chemical shifts of each tautomer , through the assignments of each peaks we investigated the tautomerism of gossypol . We concluded that when gossypol ( Ⅰ ) was put into CDCl3 , it would tautomerized three tautomers, they stable existed and attained tautomeric equilibrium in a molar ratio of 6:2:1 according to peaks intensity ratios in CDCl3. The result listed in table 1.Table 1. The 1H spectroscopy chemical shifts (ppm) for gossypol (Ⅰ), (Ⅱ) and (Ⅲ)All spectra were recorded at room tempreture in CDCl3 using TMS as an internal standard reported in δ units,hydroxyl protons were identified by D2O exchange.  相似文献   

11.
三对节中两个新环烯醚萜甙的研究   总被引:1,自引:0,他引:1  
从三对节的叶子中分离得到4个化合物,经化学和光谱方法鉴定其为7-O-p-Coumaroyloxyugandoside(1),7-O-cinnamoyloxyugandoside(2),acteoside(3)和martynoside(4),其中前两者是新环烯醚萜甙化合物,后两者为首次从该植物中获得的苯丙素甙类化合物。  相似文献   

12.
Well-ordered cubic mesoporous silicas SBA-1 functionalized with sulfonic acid groups have been synthesized through in situ oxidation of mercaptopropyl groups with H(2)O(2) via co-condensation of tetraethoxysilane (TEOS) and 3-mercaptopropyltrimethoxysilane (MPTMS) templated by cetyltriethylammonium bromide (CTEABr) under strong acidic conditions. Various synthesis parameters such as the amounts of H(2)O(2) and MPTMS on the structural ordering of the resultant materials were systematically investigated. The materials thus obtained were characterized by a variety of techniques including powder X-ray diffraction (XRD), multinuclear solid-state Nuclear Magnetic Resonance (NMR) spectroscopy, (29)Si{(1)H} 2D HETCOR (heteronuclear correlation) NMR spectroscopy, thermogravimetric analysis (TGA), and nitrogen sorption measurements. By using (13)C CPMAS NMR technique, the status of the incorporated thiol groups and their transformation to sulfonic acid groups can be monitored and, as an extension, to define the optimum conditions to be used for the oxidation reaction to be quantitative. In particular, (29)Si{(1)H} 2D HETCOR NMR revealed that the protons in sulfonic acid groups are in close proximity to the silanol Q(3) species, but not close enough to form a hydrogen bond.  相似文献   

13.
Density functional theory calculations are used to compute proton nuclear magnetic resonance (NMR) chemical shifts, interatomic distances, atom–atom interaction energies, and atomic charges for partial structures and conformers of α‐D‐glucopyranose, β‐D‐glucopyranose, and α‐D‐galactopyranose built up by introducing OH groups into 2‐methyltetrahydropyran stepwisely. For the counterclockwise conformers, the most marked effects on the NMR shift and the charge on the OH1 proton are produced by OH2, those of OH3 and OH4 being somewhat smaller. This argues for a diminishing cooperative effect. The effect of OH6 depends on the configuration of the hydroxymethyl group and the position, axial or equatorial, of OH4, which controls hydrogen bonding in the 1,3‐diol motif. Variations in the interaction energies reveal that a “new” hydrogen bond is sometimes formed at the expense of a preexisting one, probably due to geometrical constraints. Whereas previous work showed that complexing a conformer with pyridine affects only the nearest neighbour, successive OH groups increase the interaction energy of the N⋯H1 hydrogen bond and reduce its length. Analogous results are obtained for the clockwise conformers. The interaction energies for C―H⋯OH hydrogen bonding between axial CH protons and OH groups in certain conformers are much smaller than for O―H⋯OH bonds but they are largely covalent, whereas those of the latter are predominantly coulombic. These interactions are modified by complexation with pyridine in the same way as O―H⋯OH interactions: the computed NMR shifts of the CH protons increase, the atom–atom distances are shorter, and interaction energies are enhanced.  相似文献   

14.
In a wide variety of proteins, insolubility presents a challenge to structural biology, as X-ray crystallography and liquid-state NMR are unsuitable. Indeed, no general approach is available as of today for studying the three-dimensional structures of membrane proteins and protein fibrils. We here demonstrate, at the example of the microcrystalline model protein Crh, how high-resolution 3D structures can be derived from magic-angle spinning solid-state NMR distance restraints for fully labeled protein samples. First, we show that proton-mediated rare-spin correlation spectra, as well as carbon-13 spin diffusion experiments, provide enough short, medium, and long-range structural restraints to obtain high-resolution structures of this 2 x 10.4 kDa dimeric protein. Nevertheless, the large number of 13C/15N spins present in this protein, combined with solid-state NMR line widths of about 0.5-1 ppm, induces substantial ambiguities in resonance assignments, preventing 3D structure determination by using distance restraints uniquely assigned on the basis of their chemical shifts. In the second part, we thus demonstrate that an automated iterative assignment algorithm implemented in a dedicated solid-state NMR version of the program ARIA permits to resolve the majority of ambiguities and to calculate a de novo 3D structure from highly ambiguous solid-state NMR data, using a unique fully labeled protein sample. We present, using distance restraints obtained through the iterative assignment process, as well as dihedral angle restraints predicted from chemical shifts, the 3D structure of the fully labeled Crh dimer refined at a root-mean-square deviation of 1.33 A.  相似文献   

15.
Abstract

Molecular Dynamics (MD) calculations have been performed on nystose in water. According to these calculations the glycosidic linkages of the molecule are flexible. Structures obtained with MD calculations are compared with NMR data of several inulin related oligosaccharides and inulin, resulting in a model for the conformation of their fructofuranosyl residues. To extend the set of available NMR data of inulin related oligosaccharides, the complete assignment of the 1H and 13C NMR signals of β-D-fructofuranosyl-(2->l)-ß-D-fructofuranosyl-(2->l)-ß-D-fructofuranosyl-(2->l)-ß-D-fructofuranosyl-(2->l)-α-D-glucopyranoside has been given here, using several 2D homo- and heteronuclear NMR experiments. Accurate coupling constants have been obtained by simulation of the 600 MHz 1D NMR spectra.  相似文献   

16.
We have determined by X-ray crystallography the structures of three dinuclear zirconium(IV) complexes containing the heptadentate ligand dhpta (where H(5)dhpta = 1,3-diamino-2-propanol-N,N,N',N'-tetraacetic acid, 1) and different countercations: K(2)[Zr(2)(dhpta)(2)].5H(2)O (2.5H(2)O), Na(2)[Zr(2)(dhpta)(2)].7H(2)O.C(2)H(5)OH (3.7H(2)O.C(2)H(5)OH), and Cs(2)[Zr(2)(dhpta)(2)].H(5)O(2).Cl.4H(2)O (4.H(5)O(2).Cl.4H(2)O). In the K(I) complex 2, crystallized from water, the two Zr(IV) ions are 3.5973(4) A apart and bridged via two alkoxo groups (average Zr-O 2.165 A). Each Zr(IV) is eight-coordinate and also bound to two N atoms (average Zr-N 2.448 A), and four carboxylate O atoms (average Zr-O 2.148 A). The two dhpta ligands in the dinuclear unit have different conformations. One face of the complex contains an array of 14 oxygen atoms and interacts strongly with the two K(I) ions, one of which is 6-coordinate, the other 8-coordinate, which are 3.922(4) A apart and bridged by a carboxylate O and by two water molecules. The structures of the dinuclear anion [Zr(2)(dhpta)(2)](2-) in the Na(I) complex 3 and in the Cs(I) complex 4 are essentially identical to that found in complex 2, although the alkali metal ions coordinate differently to the oxygen-rich face. All Zr(IV) ions have a distorted triangulated dodecahedral geometry. Although the crystal structure of complex 2 does not indicate the presence of acidic protons, in 4 an [H(5)O(2)](+) unit is strongly H-bonded to an oxygen atom of a coordinated carboxylate group. 1D and 2D (1)H and (13)C NMR spectroscopic and potentiometric studies reveal two deprotonations with pK(a) values of 9.0 and 10.0. At low pH, two carboxylate groups appear to undergo protonation accompanied by chelate ring-opening, and the complex exhibits dynamic fluxional behavior in which the two magnetically nonequivalent dhpta ligands exchange at a rate of 11 s(-1) at pH 3.30, 298 K, as determined from 2D EXSY NMR studies. Ligand interchange is not observed at high pH (>11). The same crystals of complex 2 were obtained from solutions at pH 3 or 12. The dynamic configurational change is therefore mediated by the aqueous solvent.  相似文献   

17.
In the hydrogen ion titration of micelles, the degree of ionization of the micelle at a given pH has to be evaluated to obtain a pKa value of micelles (Ka being the proton dissociation constant) at the pH. We compared the degree of ionization obtained from 13C and 1H NMR spectra with that obtained from the stoichiometric method. We used dodecyldimethylamine oxide (C12DMAO) and hexyldimethylamine oxide (C6DMAO) to examine the titration behavior of micelles and monomers, respectively. We determined pKa values of amine oxides both in H2O and D2O. As to the monomer (C6DMAO), the degree of ionization from NMR, alpha(NMR), coincided with that from the conventional stoichiometric method alpha. The difference of pK1 of amine oxide monomer between D2O and H2O was about 0.5: pK1(D) approximately pK1(H) + 0.5. The difference was about the same as that for carboxylic acids. As to the C12DMAO micelle, alphaNMR did not coincide with alpha over a considerable range of alpha. The NMR chemical shift might be influenced by micellar structure changes induced by the ionization, such as the sphere-to-rod transition. The intrinsic logarithmic dissociation constants of the micelle were 5.9+/-0.1 for H2O, and 6.5+/-0.1 for D2O.  相似文献   

18.
Aqueous solutions of five ionic liquids (ILs) of the 1-n-alkyl-3-methylimidazolium bromide family, [C(n)mim]Br (n = 4, 6, 8, 10, 12), were investigated by NMR measurements at 298.2 K as a function of IL concentrations. Critical aggregation concentrations and aggregation numbers of these ILs were determined by 1H NMR except for [C4mim]Br in D2O. The effects of the alkyl chain length of the cations were examined on the aggregation behavior of the ILs. 1H NMR data of the solvent D2O were used to investigate the hydration of the ILs in D2O, and it was found that the ionic hydration and the cation-anion association or aggregation of the ILs offset each other. The microenvironment of different protons of cations of the ILs in the aggregates was probed by determining the spin-lattice relaxation rate (1/T1). It is suggested that the imidazolium rings in the aggregates are exposed to water and that the molecular motion of the aggregates is more restricted than that of the monomers of the ILs. Furthermore, a stair-like microscopic aggregation structure is suggested for the [C(n)mim]Br/D2O (n = 6, 8, 10) systems from 2-D 1H-1H NOESY measurements.  相似文献   

19.
Proton transfer reactions and dynamics of the hydrophilic group (-SO(3)H) in Nafion? were studied at low hydration levels using the complexes formed from CF(3)SO(3)H, H(3)O(+) and nH(2)O, 1 ≤n≤ 3, as model systems. The equilibrium structures obtained from DFT calculations suggested at least two structural diffusion pathways at the -SO(3)H group namely, the "pass-through" and "pass-by" mechanisms. The former involves the protonation and deprotonation at the -SO(3)H group, whereas the latter the proton transfer in the adjacent Zundel complex. Analyses of the asymmetric O-H stretching frequencies (ν(OH)) of the hydrogen bond (H-bond) protons showed the threshold frequencies (ν(OH*)) of proton transfer in the range of 1700 to 2200 cm(-1). Born-Oppenheimer Molecular Dynamics (BOMD) simulations at 350 K anticipated slightly lower threshold frequencies (ν(A)(OH*,MD)), with two characteristic asymmetric O-H stretching frequencies being the spectral signatures of proton transfer in the H-bond complexes. The lower frequency (ν(A)(OH,MD))) is associated with the oscillatory shuttling motion and the higher frequency (ν(B)(OH,MD))) the structural diffusion motion. Comparison of the present results with BOMD simulations on protonated water clusters indicated that the -SO(3)H group facilitates proton transfer by reducing the vibrational energy for the interconversion between the two dynamic states (Δν), resulting in a higher population of the H-bonds with the structural diffusion motion. One could therefore conclude that the -SO(3)H groups in Nafion? act as active binding sites which provide appropriate structural, energetic and dynamic conditions for effective structural diffusion processes in a proton exchange membrane fuel cell (PEMFC). The present results suggested for the first time a possibility to discuss the tendency of proton transfer in H-bond using Δν(BA)(OH,MD)) and provided theoretical bases and guidelines for the investigations of proton transfer reactions in theory and experiment.  相似文献   

20.
In situ solid-state NMR spectroscopy was employed to study the kinetics of hydrogen/deuterium exchange and scrambling as well as (13)C scrambling reactions of labeled propane over Al(2)O(3)-promoted sulfated zirconia (SZA) catalyst under mild conditions (30-102 degrees C). Three competitive pathways of isotope redistribution were observed during the course of the reaction: (1) a regioselective H/D exchange between acidic protons of the solid surface and the deuterons of the methyl group of propane-1,1,1,3,3,3-d(6), monitored by in situ (1)H MAS NMR; (2) an intramolecular H/D scrambling between methyl deuterons and protons of the methylene group, without exchange with the catalyst surface, monitored by in situ (2)H MAS NMR; (3) a intramolecular (13)C scrambling, by skeletal rearrangement process, favored at higher temperatures, monitored by in situ (13)C MAS NMR. The activation energy of (13)C scrambling was estimated to be very close to that of (2)H scrambling, suggesting that these two processes imply a common transition state, responsible for both vicinal hydride migration and protonated cyclopropane formation. All pathways are consistent with a classical carbenium ion-type mechanism.  相似文献   

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