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The transport of ions and solutes by biological pores is central for cellular processes and has a variety of applications in modern biotechnology. The time scale involved in the polymer transport across a nanopore is beyond the accessibility of conventional MD simulations. Moreover, experimental studies lack sufficient resolution to provide details on the molecular underpinning of the transport mechanisms. BROMOC, the code presented herein, performs Brownian dynamics simulations, both serial and parallel, up to several milliseconds long. BROMOC can be used to model large biological systems. IMC‐MACRO software allows for the development of effective potentials for solute–ion interactions based on radial distribution function from all‐atom MD. BROMOC Suite also provides a versatile set of tools to do a wide variety of preprocessing and postsimulation analysis. We illustrate a potential application with ion and ssDNA transport in MspA nanopore. © 2014 Wiley Periodicals, Inc.  相似文献   

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采用巨正则Monte Carlo方法和分子动力学方法研究了1-丁烯在MCM-22分子筛中的吸附现象和扩散行为,得到了1-丁烯吸附在该分子筛孔道中的相互作用能和在不同孔道中的扩散轨迹和扩散系数.结果表明1-丁烯在MCM-22分子筛中主要存存两个相互作用能区间,1-丁烯优先吸附在十元环孔道中;1-丁烯的扩散和移动主要发生在十二元环超笼的中部,十元环孔道中的1-丁烯扩散速度明显小于十二元环超笼系统中的扩散速度.  相似文献   

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Ion-molecule reactions between the α-phenylvinyl cation (α-PVC) and mono-substituted benzenes have been investigated using a quadrople ion-trap mass spectrometer. The α-PVC, generated by chemical ionization from phenylacetilene, was found to react selectively with mono-substituted benzenes bearing electron withdrawing groups to give the product ions [M + 103](+) and the trans-vinylating product ions [M + 25](+). To characterize the reaction products, a combination of collision-induced dissociation, isotope-labeling experiments and model compounds were used. The results indicate, in addition to direct heteroatom alkylation, high extent of ortho attack. We attributed the positional selectivity of the α-PVC to the nature of the substituent on the neutral molecule. In particular, hydroxy and amino groups promoted the alkenylation at ortho position.  相似文献   

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沈延昌  江国防 《中国化学》2002,20(11):1375-1378
IntroductionRecentlymuchattentionhasbeendevotedtothesynthesisofα ,β unsaturatednitrilessincetheyareim portantstructuralfeatureofseveralnaturallyoccurringbi ologicallyactivecompounds .1,2 Theintroductionoffluo rineortrifluoromethylgroupintobiologicallyactiv…  相似文献   

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A high-performance liquid chromatographic (HPLC) method is described for determination of the ratio of beta-d-mannuronic acid to alpha-l-guluronic acid (M/G ratio) in dietary fibre of edible seaweeds. Total dietary fibre (TDF) content was determined gravimetrically. The TDF fraction was hydrolysed with 12 m and 1 m H(2)SO(4), then neutralized with AG 4 x 4 resin. The uronic acids were separated in a Tracer Extrasil SAX 5 micro m column (25 cm x 4 mm) at 35 degrees C, with 2 mm KH(2)PO(4) containing 5% methanol as mobile phase at a fl ow rate of 1.5 mL/min. The detection wavelength was UV 210 nm. The chromatographic identifications of beta-d-mannuronic acid and alpha-l-guluronic acid were confirmed by liquid chromatography-mass spectrometry (LC-MS). The method precision was 1.4% for beta-d-mannuronic acid and 3.5% for alpha-l-guluronic acid. The method was used to determine M/G ratio in canned seaweeds (Saccorhiza polyschides and Himanthalia elongata) and in dried seaweeds (H. elongata, Laminaria ochroleuca, Undaria pinnatifida, Palmaria sp. and Porphyra sp.).  相似文献   

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IntroductionSingleelectrontransferinaromaticnucleophilicsub stitutionhasattractedmuchattentioninrecentyears .Inadditiontothewell knownSRN1mechanismreportedbyBunnett,1manyotheractivatedaromaticsystems ,i .e .,nitroarylhalides ,dinitrobenzenes ,etc .,havebeenre p…  相似文献   

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A parallel finite element simulator, ichannel, is developed for ion transport through three‐dimensional ion channel systems that consist of protein and membrane. The coordinates of heavy atoms of the protein are taken from the Protein Data Bank and the membrane is represented as a slab. The simulator contains two components: a parallel adaptive finite element solver for a set of Poisson–Nernst–Planck (PNP) equations that describe the electrodiffusion process of ion transport, and a mesh generation tool chain for ion channel systems, which is an essential component for the finite element computations. The finite element method has advantages in modeling irregular geometries and complex boundary conditions. We have built a tool chain to get the surface and volume mesh for ion channel systems, which consists of a set of mesh generation tools. The adaptive finite element solver in our simulator is implemented using the parallel adaptive finite element package Parallel Hierarchical Grid (PHG) developed by one of the authors, which provides the capability of doing large scale parallel computations with high parallel efficiency and the flexibility of choosing high order elements to achieve high order accuracy. The simulator is applied to a real transmembrane protein, the gramicidin A (gA) channel protein, to calculate the electrostatic potential, ion concentrations and IV curve, with which both primitive and transformed PNP equations are studied and their numerical performances are compared. To further validate the method, we also apply the simulator to two other ion channel systems, the voltage dependent anion channel (VDAC) and α‐Hemolysin (α‐HL). The simulation results agree well with Brownian dynamics (BD) simulation results and experimental results. Moreover, because ionic finite size effects can be included in PNP model now, we also perform simulations using a size‐modified PNP (SMPNP) model on VDAC and α‐HL. It is shown that the size effects in SMPNP can effectively lead to reduced current in the channel, and the results are closer to BD simulation results. © 2013 Wiley Periodicals, Inc.  相似文献   

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The [4+2] reactions of N‐acyliminium ions, produced from 2‐aryl‐3‐hydroxy‐2,3‐dihydroisoindol‐1‐ones or 5‐hydroxy‐1‐phenyl‐2,5‐dihydro/2,3,4,5‐tetrahydropyrrol‐2‐ones in the presence of BF3OEt2, with α,β‐unsaturated ketones or esters were examined, and the dependence of these reactions on the substituents at double bonds was clarified. For β‐aryl substituted α,β‐unsaturated ketones and esters such as 4‐aryl‐3‐buten‐2‐ones, chalcones and methyl cinnamate, the [4+2] reactions could proceed smoothly at room temperature to afford 6‐acyl‐5,6,6a,11‐tetrahydroisoindolo[2,1‐a]quinolin‐11‐ones and 4‐acyl‐1,3a,4,5‐tetrahydropyrrolo[1,2‐a]quinolin‐ 1‐ones or 4‐acyl‐1,2,3,3a,4,5‐hexahydropyrrolo[1,2‐a]quinolin‐1‐ones in moderate to high yields; while for simple α,β‐unsaturated ketones and esters such as methyl crotonate and ethyl 3‐methylbut‐2‐enoate, except mesityloxide, the [4+2] reactions were difficult to proceed. The cycloaddition reactions were highly stereoselective, and only one stereoisomer was produced in each reaction.  相似文献   

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Diastereomeric clusters of general formula [MAB(2)](+) and [MA(2)B](+) (M = Li(I), Na(I), Ag(I), Ni(II)-H, or Cu(II)-H; A = (R)-(-)- and (S)-(+)-(1-aminopropyl)phosphonic acid; B = (1R)-(-)- and (1S)-(+)-(1-aminohexyl)phosphonic acid) have been readily generated in the electrospray ionization (ESI) source of a triple-quadrupole mass spectrometer and their collision-induced dissociation (CID) investigated. CID of diastereomeric complexes, e.g. [MA(S)(B(S))(2)](+) and [MA(R)(B(S))(2)](+), leads to fragmentation patterns characterized by R(homo) = [MA(S)B(S)](+)/[M(B(S))(2)](+) and R(hetero) = [MA(R)B(S)](+)/[M(B(S))(2)](+) abundance ratios, which depend upon the relative stability of the diastereomeric [MA(S)B(S)](+) and [MA(R)B(S)](+) complexes in the gas phase. The chiral resolution factor R(chiral) = R(homo)/R(hetero) is found to depend not only on the nature of the M ion but also on that of the fragmenting species, whether [MAB(2)](+) or [MA(2)B](+). The origin of this behavior is discussed.  相似文献   

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Cross-beta amyloid is implicated in over 20 human diseases. Experiments suggest that specific sequence elements within amyloidogenic proteins play a major role in seeding amyloid formation. Identifying these seeding sequences is important for rationalizing the molecular mechanisms of amyloid formation and for elaborating therapeutic strategies that target amyloid. Theoretical techniques play an important role in facilitating the identification and structural characterization of putative seeding sequences; most amyloid species are not amenable to high resolution experimental structure techniques. In this study we have combined a coarse-grained physicochemical protein model with a highly efficient Monte Carlo sampling technique to identify amyloidogenic sequences in four proteins for which respective experimental peptide fragmentation data exist. Peptide sequences were defined as amyloidogenic if the ensemble structure predicted for three interacting peptides described a stable and regular three-stranded beta-sheet. For such peptides, free energies were calculated to provide a measure of amyloid propensity. The overall agreement between the experimental and predicted data is good, and we correctly identify several self-recognition motifs proposed to define the cross-beta amyloid fibril architectures of two of the proteins. Our results compare very favorably with those obtained using atomistic molecular dynamics methods, though our simulations are 30-40 times faster.  相似文献   

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Collision‐induced dissociation mass spectra of anions derived from α‐hydroxy carboxylic acids (AHAs) show a diagnostic peak at m/z 45. Product ion spectra recorded from this m/z 45 ion confirm that it represents the hydroxycarbonyl anion ( ), and not the formate anion ( ) as sometimes described in the literature. For example, the formate anion is not only defiant to further fragmentation but is also unreactive toward CO2. In contrast, the hydroxycarbonyl anion easily fragments to produce a peak at m/z 17 for the hydroxyl anion, and also readily reacts with CO2 to produce a peak at m/z 61 for the bicarbonate anion. The hydrogen atom in the hydroxycarbonyl anion and that in the formate anion are not mobile within the skeletal framework of the ions, since the two ions did not manifest any interconversion under the conditions and time scales of our mass spectrometric experiments. The other significant product ion peak in the spectra of deprotonated AHAs represents a 46‐Da loss. MS/MS data from appropriately deuteriated compounds confirmed that one hydrogen atom from the C‐2 position, and the other from the hydroxy group are specifically removed for this loss of elements of formic acid. Moreover, the two oxygen atoms eliminated for the HCOOH loss originate exclusively from the carboxylate group. Copyright © 2008 John Wiley & Sons, Ltd.  相似文献   

14.
A Monte‐Carlo simulation approach has been applied to describe the spatial distribution of characteristic x‐rays in W/Al film targets of different combinations of film thicknesses for the optimal design of a small‐sized x‐ray source having a high x‐ray intensity. The result has led to optimal combinations of W and Al film targets for 100 kV electrons, e.g. W(1 µm)/Al(20 µm), W(3 µm)/Al(15 µm) and W(5 µm)/Al(8 µm). These Al/W targets could be used as x‐ray sources for a medical instrument currently under development. Copyright © 2004 John Wiley & Sons, Ltd.  相似文献   

15.
Ion/molecule reactions of +CH2OCH2. with alpha-dicarbonyl compounds were performed via pentaquadrupole mass spectrometry. Besides the previously known [3+ + 2] 1,3-cycloaddition reaction that forms cyclic 1,3-dioxonium ions, an unprecedented reaction proceeding formally by [4 + 1+] cycloaddition of ionized methylene (CH2+.) to the alpha-dicarbonyl compounds occurs competitively, leading to the gas-phase synthesis of several ionized 2-unsubstituted 1,3-dioxoles. This novel cycloaddition reaction may therefore be added to the set of methods available for the synthesis of 1,3-dioxoles.  相似文献   

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The key problem in polypeptide‐structure prediction is with regard to thermodynamics. Two factors limit prediction in ab initio computer simulations. First, the thermodynamically dominant conformations must be found from an extremely large number of possible conformations. Second, these low‐energy forms must deviate little from the experimental structures. Here, we report on the application of the diffusion‐controlled Monte Carlo approach to predict four α‐helical hairpins with 34–38 residues by global optimization, using an energy optimized on other supersecondary structures. A total of seven simulations is carried out for each protein starting from fully extended conformations. Three proteins are correctly folded (within 3.0 Å rms from the experimental structures), but the fourth protein cannot distinguish between several equienergetic conformations. Possible improvement of the energy model is suggested. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 582–589, 2000  相似文献   

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