Structure of sodiated polyglycines

The intrinsic folding of peptides about a sodium ion has been investigated in detail by using infrared multiple photon dissociation (IRMPD) spectroscopy and a combination of theoretical methods. IRMPD spectroscopy was carried out on sodiated polyglycines G(n)-Na(+) (n=2-8), in both the fingerprint and N-H/O-H stretching regions. Interplay between experimental and computational approaches (classical and quantum) enables us to decipher most structural details. The most stable structures of the small peptides up to G(6)-Na(+) maximize metal-peptide interactions with all peptidic C=O groups bound to sodium. In addition, direct interactions between peptide termini are possible for G(6)-Na(+) and larger polyglycines. The increased flexibility of larger peptides leads to more complex folding and internal peptide structuration through γ or β turns. A structural transition is found to occur between G(6)-Na(+) and G(7)-Na(+), leading to a structure with sodium coordination that becomes tri-dimensional for the latter. This transition was confirmed by H/D exchange experiments on G(n)-Na(+) (n=3-8). The most favorable hydrogen-bonding pattern in G(8)-Na(+) involves direct interactions between the peptide termini and opens the way to salt-bridge formation; however, there is only good agreement between experimental and computational data over the entire spectral range for the charge solvation isomer.     

IRMPD spectroscopy of metal-ion/tryptophan complexes

Infrared multiple-photon dissociation (IRMPD) spectroscopy is employed to obtain detailed binding information on singly charged silver and alkali metal-ion/tryptophan complexes in the gas phase. For these complexes the presence of the salt bridge (i.e. zwitterionic) tautomer can be virtually excluded, except for perhaps a few percent in the case of Li+. Two low-energy structures having the charge solvation form are shown to be likely, where the metal cation is either in a tridentate N/O/Ring conformation or in a bidentate O/Ring conformation. These two structures can be conveniently discriminated and their relative quantities can be approximated by IR spectroscopy, based principally on diagnostic modes near approximately 1150 (N/O/Ring) and 1400 (O/Ring) cm(-1). Interestingly, the smaller cation complexes (i.e. Ag+ and Li+) display exclusively the N/O/Ring conformation, whereas the O/Ring conformer becomes progressively more abundant with increasing alkali metal size, eventually representing the majority of the ion population for Rb+ and Cs+. These spectroscopic findings are in excellent agreement with thermochemical density functional theory (DFT) calculations, giving support to the utility of high-level quantum-chemical calculations for such systems. Moreover, in contrast to other mass spectrometry-based techniques, IRMPD spectroscopy allows clear differentiation and semi-quantitative approximation of these metal-ligand binding motifs, thereby underlining its importance in thermochemical model benchmarking.     

IRMPD spectroscopy of anionic group II metal nitrate cluster ions

Anionic group II metal nitrate clusters of the formula [M₂(NO₃)₅]⁻, where M₂ = Mg₂, MgCa, Ca₂, and Sr₂, are investigated by infrared multiple photon dissociation (IRMPD) spectroscopy to obtain vibrational spectra in the mid-IR region. The IR spectra are dominated by the symmetric and the antisymmetric nitrate stretches, with the latter split into high and low-frequency components due to the distortion of nitrate anion symmetry by interactions with the cation. Density functional theory (DFT) is used to predict geometries and vibrational spectra for comparison to the experimental spectra. Calculations yield two stable isomers: the first one contains two terminal nitrate anions on each cation and a single bridging nitrate (“mono-bridging”), while the second structure features a single terminal nitrate on each cation with three bridging nitrate ligands (“tri-bridging”). The tri-bridging isomer is calculated to be lower in energy than the mono-bridging one for all species. Theoretical spectra of the tri-bridging structure provide a better qualitative match to the experimental infrared spectra of [Mg₂(NO₃)₅]⁻ and [MgCa(NO₃)₅]⁻. However, the profile of the low-frequency ν ₃ band for the Mg₂ complex suggests a third possible isomer not predicted by theory. The IRMPD spectra of the Ca₂ and Sr₂ complexes are better reconciled by a weighted summation of the spectra of both isomers suggesting that a mixture of structures is present.     

Internal rotation in enaminonitriles: Investigation by dynamic NMR spectroscopy and molecular modeling

Rotational isomerism in enaminonitriles was studied using dynamic NMR spectroscopy and molecular modeling. It was found that the barrier to rotation about C_vinyl-NH bond was higher for enaminonitriles derived from aliphatic amines than that of enaminonitriles derived from aromatic amines. It was also found that the rotational isomerism about the C_ar-C_vinyl bond also exists in enaminonitriles.     

Interaction of hypericin with serum albumins: surface-enhanced Raman spectroscopy, resonance Raman spectroscopy and molecular modeling study

Surface-enhanced Raman spectroscopy, resonance Raman spectroscopy and molecular modeling were employed to study the interaction of hypericin (Hyp) with human (HSA), rat (RSA) and bovine (BSA) serum albumins. The identification of the binding site of Hyp in serum albumins as well as the structural model for Hyp/HSA complex are presented. The interactions mainly reflect: (1) a change of the strength of H bonding at the N1-H site of Trp; (2) a change of the Trp side-chain conformation; (3) a change of the hydrophobicity of the Trp environment; and (4) a formation of an H-bond between the carbonyl group of Hyp and a proton donor in HSA and RSA which leads to a protonated-like carbonyl in Hyp. Our results indicate that Hyp is rigidly bound in IIA subdomain of HSA close to Trp214 (distance 5.12 A between the centers of masses). In the model presented the carbonyl group of Hyp is hydrogen bonded to Asn458. Two other candidates for hydrogen bonds have been identified between the bay-region hydroxyl group of Hyp and the carbonyl group of the Trp214 peptidic link and between the peri-region hydroxyl group of Hyp and the Asn458 carbonyl group. It is shown that the structures of the Hyp/HSA and Hyp/RSA complexes are similar to, and in some aspects different from, those found for the Hyp/BSA complex. The role of aminoacid sequence in the IIA subdomains of HSA, RSA and BSA is discussed to explain the observed differences.     

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.     

Bibracchial diazatetralactams. Structure and molecular modeling of calcium complexes

Doubly-armed diazatetralactams constitute a new series of easily synthesized tetralactams. The structural study of the calcium complexes of their N,N′-dimethyl acetamido and (2-pyridylmethyl) derivatives was performed by IR, ¹H, ¹³C NMR spectroscopies and molecular modeling. These complexes showed a C₂ symmetry and a high number (8–9) of coordination around the calcium atom.     

Study of the complexation of resveratrol with cyclodextrins by spectroscopy and molecular modeling

In present work the complexation of Res with two kinds of cyclodextrins (CDs), native β-cyclodextrin (β-CD) and modified hydroxypropyl-β-cyclodextrin (HP-CD), have been investigated by fluorescence spectroscopy, ¹H-NMR spectroscopy and molecular modeling methods. The stoichiometric ratios, inclusion constants and thermodynamic parameters have been determined by the fluorescence data. In all cases 1:1 inclusion complexes are formed. The inclusion ability of HP-CD is larger than that of β-CD. Both inclusion processes have negative ?G, negative ?H and positive ?S. Thermodynamic analysis suggests that Van der Waals force of guest-host interactions and the release of high-enthalpy water molecules from the cavity of CDs play important roles in driving complex formation. The study of molecular modeling shows that part of the A-ring and the B-ring of Res are placed in the cavity of β-CD, and the hydroxyl groups are projected outside. As for Res in HP-CD, the B-ring of Res is included in the cavity of HP-CD, and part of the A-ring is pointed outside. ¹H-NMR spectroscopy results show that H_2, H₃, H₄ and H₅ protons of Res are more affected by the complexatin, indicating that they are located inside the torus of CDs, which are in agreement with the result of the molecular modeling.     

Molecular mechanism of interaction between norfloxacin and trypsin studied by molecular spectroscopy and modeling

The molecular mechanism of the binding of norfloxacin (NRF) to trypsin was investigated by fluorescence, synchronous fluorescence and UV–vis absorbance spectroscopy and molecular modeling at physiological conditions. The quenching mechanism and the binding mode were investigated in terms of the association constants and basic thermodynamic parameters. The results of spectroscopic measurements suggested that NRF have a strong ability to quench the intrinsic fluorescence of trypsin through static quenching procedure. Moreover, fluorescence experiments were also performed at different values of pH to elucidate the effect of pH on the binding. The NRF–trypsin complex was stabilized by hydrophobic forces and hydrogen bonding, via tryptophan residue as indicated from the thermodynamic parameters, which was consistent with the results of molecular docking and accessible surface area calculations.     

Competition between HF And HCl molecular elimination in IRMPD of 1,2-dichloro-1,2-difluoroethane

The infrared multiple-photon decomposition of 1,2-dichloro-1,2-difluoroethane has been studied using time-resolved infrared emission. Vibrationally excited parent molecules dissociate competitively via two channels to form vibrationally excited HCl and HF, depending strongly on CO₂ laser fluence. The yield of HF elimination increases with fluence, while that of HCl elimination reaches a plateau and then decreases.     

光谱-分子模拟法分析杨梅素与人血清白蛋白的分子作用机制

在模拟生理条件下,用多种光谱法结合分子对接法测定了杨梅素(MY)与人血清白蛋白(HSA)的相互作用.研究结果表明,MY能够明显猝灭HSA的荧光,MY与HSA的相互作用为复合式静态结合过程,结合强度较强.热力学和分子对接结果表明,MY与HSA是自发结合的,维持MY与HSA的相互作用力主要是氢键和范德华力.能量转移结果表明...     

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.     

Solution state structure determination of silicate oligomers by 29SI NMR spectroscopy and molecular modeling

Evidence for nine new solution state silicate oligomers has been discovered by (29)Si NMR homonuclear correlation experiments of (29)Si-enriched samples. In addition to enhancing signal sensitivity, the isotopic enrichment increases the probability of the (29)Si-(29)Si two-bond scalar couplings that are necessary for the observation of internuclear correlations in 2-D experiments. The proposed assignments are validated by comparisons of experimental and simulated cross-peaks obtained with high digital resolution. The internuclear connectivity indicated by the NMR data suggests that several of these oligomers can have multiple stereoisomers, including conformers and/or diastereomers. The stabilities of these oligomers and their possible stereoisomers have been investigated by electronic structure calculations.     

Studies on the binding of nevadensin to human serum albumin by molecular spectroscopy and modeling

The binding of nevadensin to human serum albumin (HSA) in aqueous solution was investigated for the first time by molecular spectroscopy and modeling at pH 7.4. Spectrophotometric observations are rationalized in terms of a static quenching process and binding constant (K_a, K_b) and the number of binding sites (n ≈ 1) were evaluated by fluorescence quenching methods. Thermodynamic data showed that nevadensin was included in the hydrophobic cavity of HSA mainly via hydrophobic interactions. The value of 3.09 nm for the distance r between the donor (HSA) and acceptor (nevadensin) was derived from the fluorescence resonance energy transfer. Spectrophotometric techniques were also applied to investigate the structural information of HSA molecules on the binding of nevadensin and the results showed that the binding of nevadensin to HSA did not change significantly molecular conformation of HSA in our experimental conditions. Furthermore, the study of molecular modeling also indicated that nevadensin could strongly bind to the site I (subdomain IIA) of HSA mainly by a hydrophobic interaction and there are hydrogen bond interactions between nevadensin and the residues Arg-218, Arg-222, Lys-195, and Asp-451. As compared to the other flavonoids, the flavonoids containing methoxy groups which are in aromatic rings can bind to HSA with higher affinity.     

Studies on the binding of vinpocetine to human serum albumin by molecular spectroscopy and modeling

The interaction between vinpocetine(VPC) and human serum albumin(HSA) in physiological buffer(pH 7.40) was investigated by fluorescence,FT-IR,UV-vis absorption and molecular modeling.VPC effectively quenched the intrinsic fluorescence of HSA via static quenching.The binding site number n and apparent binding constant K_a,corresponding thermodynamic parametersΔG,ΔH andΔS at different temperatures were calculated.The synchronous fluorescence and FT-IR spectra were used to investigate the structural change of HSA molecules with addition of VPC.Molecular modeling indicated that VPC could bind to the site I of HSA and hydrophobic interaction was the major acting force,which was in agreement with the binding mode study.     

Investigation of the interaction between human hemoglobin and five antioxidants by fluorescence spectroscopy and molecular modeling

L-ascorbic acid, α-tocopherol, procyanidin B3, β-carotene, and astaxanthin are five classic dietary antioxidants. In this study, the interaction between the five antioxidants and human hemoglobin (HHb) was investigated by fluorescence spectroscopy and molecular modeling. The quenching mechanisms of HHb by the five antioxidants are all static quenching. The downward curvature of the Stern–Volmer plots for HHb–procyanidin B3 system at higher concentrations of procyanidin B3 come from the reason for the variation in the number of accessible tryptophan (Trp) residues toward HHb. The upward curvature of the Stern–Volmer plots for HHb–β-carotene system at higher concentrations of β-carotene predominantly by the “sphere of action” quenching mechanism. The binding constants of HHb with the five antioxidants are in the following order as: astaxanthin > L-ascorbic acid > β-carotene > α-tocopherol > procyanidin B3 at 298 K. The binding processes of the five antioxidants to HHb are all entropy process. Thermodynamic analysis and molecular modeling suggest that the hydrophobic forces are the main interaction force in the binding of the five antioxidants to HHb and hydrogen bond interactions between HHb and L-ascorbic acid/α-tocopherol/procyanidin B3/astaxanthin should be also considered. The fluorescence experimental results are in agreement with the results obtained by molecular modeling study.     

Structure and vibrational spectroscopy of salt water/air interfaces: predictions from classical molecular dynamics simulations

We report the sum frequency generation (SFG) spectra of aqueous sodium iodide interfaces computed with the methodology outlined by Morita and Hynes (J. Phys. Chem. B 2002, 106, 673), which is based on molecular dynamics simulations. The calculated spectra are in qualitative agreement with experiment. Our simulations show that the addition of sodium iodide to water leads to an increase in SFG intensity in the region of 3400 cm(-1), which is correlated with an increase in ordering of hydrogen-bonded water molecules. Depth-resolved orientational distribution functions suggest that the ion double layer orders water molecules that are approximately one water layer below the Gibbs dividing surface. We attribute the increase in SFG intensity to these ordered subsurface water molecules that are present in the aqueous sodium iodide/air interfaces but are absent in the neat water/air interface.