Calculating slow-motional electron paramagnetic resonance spectra from molecular dynamics using a diffusion operator approach

A number of groups have utilized molecular dynamics (MD) to calculate slow-motional electron paramagnetic resonance (EPR) spectra of spin labels attached to biomolecules. Nearly all such calculations have been based on some variant of the trajectory method introduced by Robinson, Slutsky and Auteri (J. Chem. Phys. 1992,96, 2609-2616). Here we present an alternative approach that is specifically adapted to the diffusion operator-based stochastic Liouville equation (SLE) formalism that is also widely used to calculate slow-motional EPR line shapes. Specifically, the method utilizes MD trajectories to derive diffusion parameters such as the rotational diffusion tensor, diffusion tilt angles, and expansion coefficients of the orienting potential, which are then used as direct inputs to the SLE line shape program. This approach leads to a considerable improvement in computational efficiency over trajectory-based methods, particularly for high frequency, high field EPR. It also provides a basis for deconvoluting the effects of local spin label motion and overall motion of the labeled molecule or domain: once the local motion has been characterized by this approach, the label diffusion parameters may be used in conjunction with line shape analysis at lower EPR frequencies to characterize global motions. The method is validated by comparison of the MD predicted line shapes to experimental high frequency (250 GHz) EPR spectra.     

Spectroscopic Properties of Fluorescein and Rhodamine Dyes Attached to DNA

We report the spectroscopic properties of fluorescein, x-rhodamine, tetramethyl-rhodamine, attached to single strand, duplex DNA, and to the digestion products by DNAse I. The properties reported include: molar absorptivity, quantum yield, absorbance and fluorescence spectra, fluorescence lifetime, intrinsic lifetime (τ⁰), static quenching (S) and the Förster critical distances (R₀) between fluorescein and x-rhodamine or tetramethyl-rhodamine (acceptors). These spectroscopic properties depend strongly on the local dye environment. Fluorescein was studied: (1) attached to biotin (BF), (2) BF bound to avidin; and attached to two positions in DNA. X-rhodamine and tetramethyl-rhodamine were studied as free dyes and attached at the 5′-end of DNA. We propose a general method to determine the molar absorptivity and τ⁰ of a dye attached to DNA based on the reaction of a biotinylated and dye-labeled oligomer with standardized avidin. The molar absorptivity of a second dye attached to a DNA duplex can be obtained by comparing spectra of doubly and singly labeled sequences. S, arising from dye–DNA interactions can then be determined. R₀ for free and attached dyes showed differences from 1.1 to 4.2 Å. We present evidence for the direct interaction of dyes attached to the termini of various single-stranded DNA sequences.     

Use of the method of metastable defocusing for the analysis of the processes involved in the fragmentation of lycoctonine bases

The metastable transitions in the mass spectra of 21 lycoctonine bases have been studied by the method of metastable defocusing (MD). It has been established that as a criterion of the monotypicity of single-stage fragmentation reactions it is possible to use a linear dependence of the relative intensities of the metastable peaks (MPs) on the stability of the daughter ion. In the MD spectra of the ions formed in several stages, to characterize the generality of the breakdown reactions, in addition to the intensities of the MPs, the accurate positions of their maxima and the general shape of the curve are important.     

Conformational selection or induced fit for Brinker and DNA recognition

Brinker is the key target protein of the Drosophila Decapentaplegic morphogen signalling pathway. Brinker is widely expressed and can bind with DNA. NMR spectra suggest that apo-Brinker is intrinsically unstructured and undergoes a folding transition upon DNA-binding. However, the coupled mechanism of binding and folding is poorly understood. Here, we performed molecular dynamics (MD) simulations for both bound and apo-Brinker to study the mechanism. Room-temperature MD simulations suggest that Brinker becomes more rigid and stable upon DNA-binding. Kinetic analysis of high-temperature MD simulations shows that both bound and apo-Brinker unfold via a two-state process. The time scale of tertiary unfolding is significantly different between bound and apo-Brinker. The predicted Φ-values suggest that there are more residues with native-like transition state ensembles (TSEs) for bound Brinker than for apo-Brinker. The average RMSD differences between bound and apo-Brinker and Kolmogorov-Smirnov (KS) test analysis illustrate that Brinker folding upon DNA-binding might obey induced-fit mechanism based on MD simulations. These methods can be used for the research of other biomolecular folding upon ligand-binding.     

Surface structure of sulfuric acid solution relevant to sulfate aerosol: molecular dynamics simulation combined with sum frequency generation measurement

Surface structure of aqueous sulfuric acid solution at a typical atmospheric concentration (0.2x, x: mole fraction) is investigated by close collaboration of molecular dynamics (MD) simulation and sum frequency generation (SFG) measurement. The SFG spectra of both O-H and S-O stretching vibrations are provided with different sets of polarization combination. These sets of experimental spectra are consistently elucidated by the MD calculations. In modeling the surface structure, there exists a major uncertainty about local ion composition at the surface region. To address this uncertainty, we performed MD simulations with various assumptions on the local dissociation constants of sulfuric acid, and searched for the condition to be consistent with the experimental spectra. We have thereby concluded that the first acid dissociation of sulfuric acid is almost complete at the surface, while the second dissociation is more strongly suppressed than in the bulk liquid. The present MD simulation elucidates the ion distribution and molecular orientation at the sulfuric acid solution surface, and also the concentration dependence of the SFG spectrum.     

酰胺型双冠醚的振动光谱分析

对邻苯-二(氧乙酰胺-4'-本并-15-冠-5)、间苯-二(氧乙酰胺-4'-苯并-15-冠-5)、对苯-二(氧乙酰胶-4'-苯并-15-冠-5)三种酰胺型双冠醚和苯并15-冠-5的喇曼光谱及红外光谱进行了测定和归属分析,并与15-冠-5的喇曼及红外光谱进行了比较研究.     

Use of the method of metastable defocusing for the analysis of the processes involved in the fragmentation of lycoctonine bases

The metastable transitions in the mass spectra of 21 lycoctonine bases have been studied by the method of metastable defocusing (MD). It has been established that as a criterion of the monotypicity of single-stage fragmentation reactions it is possible to use a linear dependence of the relative intensities of the metastable peaks (MPs) on the stability of the daughter ion. In the MD spectra of the ions formed in several stages, to characterize the generality of the breakdown reactions, in addition to the intensities of the MPs, the accurate positions of their maxima and the general shape of the curve are important.Institute of the Chemistry of Plant Substances, Academy of Sciences of the Uzbek SSR, Tashkent. Translated from Khimiya Prirodnykh Soedinenii, No. 4, pp. 481–495, July–August, 1984.     

Solid-phase synthesis and 1H and 13C high-resolution magic angle spinning NMR of 13C-labeled resin-bound saccharides

We show how high-resolution magic angle-spinning NMR spectroscopy can be used to characterize 13C-labeled saccharides that have been prepared using solid-phase synthesis techniques while they are still bound to a solid-support resin. With the use of 13C-labeled glucose as the starting material, we have successfully synthesized mono-, di- and trisaccharides with uniform 13C labeling of the saccharide rings. Using these materials, we have been able to assign the 13C and 1H spectra and to characterize various impurities on the resin beads.     

Parametrization, molecular dynamics simulation, and calculation of electron spin resonance spectra of a nitroxide spin label on a polyalanine alpha-helix

The nitroxide spin label 1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl-methanethiosulfonate (MTSSL), commonly used in site-directed spin labeling of proteins, is studied with molecular dynamics (MD) simulations. After developing force field parameters for the nitroxide moiety and the spin label linker, we simulate MTSSL attached to a polyalanine alpha-helix in explicit solvent to elucidate the factors affecting its conformational dynamics. Electron spin resonance spectra at 9 and 250 GHz are simulated in the time domain using the MD trajectories and including global rotational diffusion appropriate for the tumbling of T4 Lysozyme in solution. Analysis of the MD simulations reveals the presence of significant hydrophobic interactions of the spin label with the alanine side chains.     

REACTION MECHANISM OF BENZOPHENONE-PHOTOINITIATED CROSSLINKING OF POLYETHYLENE

The radical intermediates, the crosslink microstructures, and the reaction mechanism of benzophenone (BP)-photoinitiated crosslinking of low-density polyethylene (LDPE) and model compounds (MD) have been reviewed in detail.The spin-trapping electron spin resonance (ESR) spectra obtained from the LDPE/BP systems with spin-trap agents showthat two kinds of polymer radical intermediates are mainly formed: tertiary carbon and secondary carbon radicals. The spin-trapping ESR studies of MD/BP systems give further evidence that photocrosslinking reactions of PE predominantly takeplace at sites of tertiary carbon, secondary carbon, and especially allylic carbon when available. The high resolution ~(13)C-NMR spectra obtained from LDPE and MD systems show that the crosslink microstructures have H- and Y-type links andthat their concentrations are of the same order. The fluorescence, ESR ~(13)C and ~1H-NMR spectra from the PE and MDsystems demonstrate that the main photoreduction product of BP(PPB) is benzpinacol formed by the recombination of twodiphenylhydroxymethyl (K·) radical intermediates. Two new PPB products: an isomer of benzpinacol with quinoid structure,1-phenylhydroxymethylene-4-diphenylhydroxymethyl-2, 5-cyclohexadiene and three kinds of α-alkyl-benzhydrols have beendetected and identified. These results provide new experimental evidence for elucidating the reaction mechanism in the BP-photoinitiated crosslinking of polyethylene.     

Anchor-based design of improved cholera toxin and E. coli heat-labile enterotoxin receptor binding antagonists that display multiple binding modes

The action of cholera toxin and E. coli heat-labile enterotoxin can be inhibited by blocking their binding to the cell-surface receptor GM1. We have used anchor-based design to create 15 receptor binding inhibitors that contain the previously characterized inhibitor MNPG as a substructure. In ELISA assays, all 15 compounds exhibited increased potency relative to MNPG. Binding affinities for two compounds, each containing a morpholine ring linked to MNPG via a hydrophobic tail, were characterized by pulsed ultrafiltration (PUF) and isothermal titration calorimetry (ITC). Crystal structures for these compounds bound to toxin B pentamer revealed a conserved binding mode for the MNPG moiety, with multiple binding modes adopted by the attached morpholine derivatives. The observed binding interactions can be exploited in the design of improved toxin binding inhibitors.     

In Silico Design and Selection of New Tetrahydroisoquinoline-Based CD44 Antagonist Candidates

CD44 promotes metastasis, chemoresistance, and stemness in different types of cancer and is a target for the development of new anti-cancer therapies. All CD44 isoforms share a common N-terminal domain that binds to hyaluronic acid (HA). Herein, we used a computational approach to design new potential CD44 antagonists and evaluate their target-binding ability. By analyzing 30 crystal structures of the HA-binding domain (CD44HAbd), we characterized a subdomain that binds to 1,2,3,4-tetrahydroisoquinoline (THQ)-containing compounds and is adjacent to residues essential for HA interaction. By computational combinatorial chemistry (CCC), we designed 168,190 molecules and compared their conformers to a pharmacophore containing the key features of the crystallographic THQ binding mode. Approximately 0.01% of the compounds matched the pharmacophore and were analyzed by computational docking and molecular dynamics (MD). We identified two compounds, Can125 and Can159, that bound to human CD44HAbd (hCD44HAbd) in explicit-solvent MD simulations and therefore may elicit CD44 blockage. These compounds can be easily synthesized by multicomponent reactions for activity testing and their binding mode, reported here, could be helpful in the design of more potent CD44 antagonists.     

Optical absorption spectra from rare-earth ions in polymers: the effect of the polymer host

A Molecular Dynamics (MD) based modified Judd/Ofelt approach has been used to simulate UV-VIS absorption spectra for different concentrations of Er(CF₃SO₃)₃ (erbium triflate) in the amorphous polymer host poly(ethylene oxide), PEO. The simulations have been performed for systems containing both single-chain PEO and PEO with an attached side-chain. Effects on the optical properties of the introduction of side-chains are demonstrated. Qualitative inspection of the calculated spectra would suggest that similarities in the crystal field experienced by individual Er ions in qualitatively different local environments will make structural information difficult to access from this procedure.     

Characterization of an activated iridium water splitting catalyst using infrared photodissociation of H2 tagged ions

We report the vibrational predissociation spectra of two related organometallic half-sandwich iridium species which have been recently reported as activated intermediates in the context of homogenous water oxidation. These compounds are extracted from solution into a cryogenic photofragmentation mass spectrometer and "tagged" with weakly bound H(2) molecules that do not significantly perturb the intrinsic structures of the ions. The resulting spectra display very sharp (～5 cm(-1)), well-resolved bands that provide a stringent test for electronic structure calculations, and are accurately recovered by harmonic predictions for the bare species. The spectra reveal subtle distortions of the ligand structure when a solvent molecule (acetonitrile) is directly coordinated with the metal center.     

Preparation of crown compounds containing allyloxymethyl or butenyl groups for attachment to silica gel or containing long chain lipophilic groups for use in liquid membrane systems

Several new macrocyclic polyether ligands have been prepared for use in the separation of metal ions from aqueous solutions. Four of the crown ethers reported contain 1,2,4-triazole or 4-pyridone protonionizable subcyclic units and lipophilic groups. The remaining crown ethers are not proton-ionizable but contain alkene groups and were prepared for attachment to silica gel. The crowns were prepared by reacting the appropriate glycols with the appropriate ditosylates or dichloride in the case of the 1,2,4-triazole subcyclic unit. The crowns with proton-ionizable and lipophilic substituents were tested in liquid membrane transport systems and some of the crowns with alloxymethyl or butenyl substituents were attached to silica gel. The log K values for the interaction of these silica gel-bound macrocycles with certain metal ions were nearly the same (± 10%) as those for the association of the unbound macrocycles with the same metal ions.     

Optical absorption of methoxy and carboethoxy derivatives of 1,3-diphenyl-1H-pyrazolo[3,4-b]quinoline

Paper deals with experimental investigations and quantum chemical calculations of the optical absorption spectra of methoxy and carboethoxy 1,3-diphenyl derivatives of the pyrazoloquinoline ([PQ]): 6-methoxy-1,3-dyphenil-[PQ], 6-methoxy-1,3-(p-methoxyphenyl)-[PQ], 6-methoxy-1-(p-methoxyphenyl)-[PQ] and 6-carboethoxy-1,3-diphenyl-[PQ]. The quantum chemical calculations are performed by means of the semiempirical quantum chemical methods (AM1 or PM3) applied to: (a) the equilibrium molecular conformation in vacuo (T=0 K); (b) the molecular dynamic (MD) trajectory (T=300 K) which includes the dynamics of a certain molecular fragment (moiety) only (fragmental MD simulations); or (c) the MD trajectory obtained for most general case within the total MD simulations at T=300 K. The results of these calculations are compared with the measured spectra of the optical absorption. The quantum chemical simulations show that the dynamics of the methoxy or carboethoxy groups practically does not influence the absorption spectrum whereas the strongest its modification (300相似文献   

Mass spectrometry of 4-amino-4′-nitroazobenzene compounds

The mass spectra of 32 substituted 4-amino-4′-nitroazobenzene compounds have been recorded and the most intense peaks have been used to characterize these spectra. It was found that the spectra of 4-amino-4′-nitroazobenzene compounds are characterized by peaks due to: (1) molecular ions, (2) fragment ions formed by cleavage of one of the carbon-nitrogen bonds adjacent to the azo linkage with the positive charge remaining with the amine fragment, (3) ions formed by cleavage alpha to the amine nitrogen with the charge remaining with the amine substituent, (4) ions formed by cleavage beta to the amine nitrogen with the loss of the amine substituent fragment, (5) secondary ions formed by cleavage beta to the amine nitrogen with the loss of the amine substituent fragment from the primary amine fragment (2), and (6) ions formed by loss of NO from the molecular ion. This work shows that 4-amino-4′-nitroazobenzene compounds exhibit fragmentation which is dependent in a consistent manner on the types of substituents. This work provides a basis for a systematic approach to the identification of 4-amino-4′-nitroazobenzene compounds.     

Application of Fourier transform Raman spectroscopy to a range of compounds of pharmaceutical interest

Fourier transform (FT) Raman spectra have been obtained for a range of synthetic and semisynthetic samples to evaluate the utility of the technique for the characterization of compounds of pharmaceutical interest. These spectra are compared with the IR KBr disc spectra. Examples of the additional, important information which may be extracted from Raman data in comparison with IR spectroscopy are reported for the range of chemical structures studied. The superior ability of Raman to characterize the stretching modes of the CH bond compared with IR spectroscopy is demonstrated for several compounds.The characterization of highly symmetric vibrational modes is one of the most prominent and useful advantages of Raman spectroscopy and several examples of this primary application are also cited. These include the assignment of the ring breathing frequency of monosubstituted benzene rings, the CCC symmetric skeletal mode of a tricyclic fused ring system, the NO symmetric stretch of aromatic nitro groups and the stretching vibrations of various double bonds, several of which possess a high degree of local symmetry.     

Zinc(II) tetraarylporphyrins anchored to TiO2, ZnO, and ZrO2 nanoparticle films through rigid-rod linkers

A series of six Zn(II) tetraphenylporphyrins (ZnTPP), with a phenyl (P) or oligophenyleneethynylene (OPE = (PE) n ) rigid-rod bridge varying in length (9-30 A) and terminated with an isophthalic acid (Ipa) anchoring unit, were prepared as model dyes for the study of sensitization processes on metal oxide semiconductor nanoparticle surfaces (MO(n) = TiO(2), ZnO, and insulating ZrO(2)). The dyes were designed such that the electronic properties of the central porphyrin chromophore remained consistent throughout the series, with the rigid-rod anchoring unit allowing each porphyrin unit to be located at a fixed distance from the metal oxide nanoparticle surface. Electronic communication between the porphyrin and the rigid-rod unit was not desired. Rigid-rod porphyrins ZnTPP-Ipa, ZnTPP-P-Ipa, ZnTPP-PE-Ipa, ZnTPP-(PE)(2)-Ipa, ZnTPP-(PE)(3)-Ipa, and ZnTMP-Ipa (with mesityl substituents on the porphyrin ring) were synthesized using combinations of mixed aldehyde condensations and Pd-catalyzed cross-coupling reactions. Their properties, in solution and bound, were compared with that of Zn(II) 5,10,15,20-tetra(4-carboxyphenyl)porphyrin ( p-ZnTCPP) as the reference compound. Solution UV-vis and steady-state fluorescence spectra for all six rigid-rod-Ipa porphyrins were almost identical to each other and to that of p-ZnTCPP. Cyclic voltammetry and differential pulse voltammetry scans of the methyl ester derivatives of the six rigid-rod-Ipa porphyrins, recorded in dichloromethane/electrolyte, exhibited redox behavior typical of ZnTPP porphyrins, with the first oxidation in the range +0.99 to 1.09 V vs NHE. All six rigid-rod-Ipa porphyrins and p-ZnTCPP were bound to metal oxide (MO(n) = TiO(2), ZnO, and insulating ZrO(2)) nanoparticle films. The Fourier transform infrared attenuated total reflectance spectra of all compounds bound to MO n films showed a broad band at 1553-1560 cm(-1) assigned to the v(CO(2)(-)) asymmetric stretching mode. Splitting of the Soret band into two bands at 411 and 423 nm in the UV-vis spectra of the bound compounds, and broadening and convergence of both fluorescence emission bands in the fluorescence spectra of the porphyrins bound to insulating ZrO(2) were also observed. Such changes were less evident for ZnTMP-Ipa, which has mesityl substituents on the porphyrin ring to prevent aggregation. Steady-state fluorescence emission of rigid-rod-Ipa porphyrins bound to TiO(2) and ZnO through the longest bridges (>14 A) showed residual fluorescence emission, while fluorescence quenching was observed for the shortest compounds.     

A new mechanism of benzophenone photoreduction in photoinitiated crosslinking of polyethylene and its model compounds

The photolytic products and a new photoreduction mechanism of benzophenone (BP) as a photoinitiator in the photocrosslinking of polyethylene (PE) and its model compounds (MD) have been studied by means of fluorescence, ESR, ¹³C and ¹H NMR spectroscopy. The fluorescence spectra from the PE and MD systems demonstrate that the main photoreduction product of BP (PPB) is benzpinacol formed by the recombination of two diphenylhydroxymethyl (K^•) radical intermediates. The ESR spectrum obtained from the UV irradiation of the MD/BP system gives positive evidence of K^• radicals. Two new PPB products: an isomer of benzpinacol with quinoid structure, 1‐phenyl‐hydroxymethylene‐4‐diphenyl‐hydroxymethyl‐2,5‐cyclohexa‐diene and three kinds of α‐alkylbenzhydrols have been detected and identified for the first time by ¹³C and ¹H NMR spectroscopy from the MD systems. The latter could be formed by the reactions of K^• radicals with alkyl radicals produced by hydrogen abstraction of the excited triplet state ³(BP)* from polyethylene or its model compounds. These results provide new experimental evidence for elucidating the photoreduction mechanism of BP in the photoinitiated crosslinking of polyethylene. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 999–1005, 2000