Diffusion and single molecule dynamics on biomolecular interface binding energy landscape

We propose a new approach to study the diffusion dynamics on biomolecular interface binding energy landscape. The resulting mean first passage time (MFPT) has 'U'curve dependence on the temperature. It is shown that the large specificity ratio of gap to roughness of the underlying binding energy landscape not only guarantees the thermodynamic stability and the specificity [P.A. Rejto, G.M. Verkhivker, in: Proc. Natl. Acad. Sci. 93 (1996) 8945; C.J. Tsai, S. Kumar, B. Ma, R. Nussinov, Protein Sci. 8 (1999) 1181; G.A. Papoian, P.G. Wolynes, Biopolymers 68 (2003) 333; J. Wang, G.M. Verkhivker, Phys. Rev. Lett. 90 (2003) 198101] but also the kinetic accessibility. The complex kinetics and the associated fluctuations reflecting the structures of the binding energy landscape emerge upon temperature changes. The theory suggests a way of connecting the models/simulations with single molecule experiments by analysing the kinetic trajectories.

Single-molecule dynamics reveals cooperative binding-folding in protein recognition

The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape-inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure ( the Go model). With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state.

Blue organic light-emitting diodes based on an oxadiazole-containing organic molecule exhibiting excited state intramolecular proton transfer

A blue organic light-emitting device based on an emissive layer of 2-(2-hydroxyphenyl)-5-phenyl-1,3,4-oxadiazole (HOXD), which exhibits excited state intramolecular proton transfer (ESIPT), was presented. The device had a luminance efficiency of 0.8 cd/A and a maximum brightness of 870 cd/m(2). Our studies indicate that some EL may originate from the triplet excitation state of the enol form of HOXD.

Synthesis and structural characterization of a new molecule-based complex constructed from dodecamolybdophosphoric acid and imidazole

A new compound, (CH5N2)(3)(PMo12O40CH4N23H2O)-C-.-H-. (1), was synthesized and structurally characterized by elemental analyses, IR spectra, UV spectra, NMR spectra and ESR spectra. This is, to our knowledge, the first example of an imidazole-polyoxometalate species. The compound was recrystallized from N,N-dimethylformamide (DMF), and then black block-like crystals of (C3H5N2)(4)((PMoMo11O40)-Mo-V-O-VI)(.)4C(3)H(7)NO(.) 2H(2)O (2), were obtained. It crystallizes in a triclinic space group P (1) over bar with n=12.423(3) Angstrom, b=12.666(3) Angstrom, c=13.341(3) Angstrom, alpha=70.56(3)degrees, beta=71.16(3)degrees, gamma=64.18(3)degrees, V= 1742.3(6) Angstrom(3), Z=1, R1 = 0.0585, wR2 = 0.1885. An X-ray crystallographic study showed that the crystal structure is constructed by electrostatic attractions and hydrogen bonds between a dodecamolybdophosphoric anion and an imidazole. The imidazole and DMF molecules occupy cavities in a polyoxometalate lattice ordered along a c-axis. The structure of (2) is similar to that of (1) from a comparison of both IR spectra and TGA Curves.

Applications of the method of three-dimensional projection of a molecule in quantitative structure-activity relationship of phenol derivatives

Five variables for phenol derivatives were calculated by molecular projection in three-dimensional space which were combined with eight quantum-chemical parameters and three Am indices. These variables were selected by using leaps-and-bounds regression analysis. Multiple linear regression analysis and artificial neural networks' were performed, and the results obtained by using. artificial neural networks are superior than that obtained by using multiple linear regression.

Gas-phase ion-molecule reactions of C-60 with the plasma of methyl acrylate

The gas-phase ion-molecule reactions of C-60 with the plasma generated from methyl acrylate under self-chemical ionization conditions were studied by use of a triple-quadrupole mass spectrometer. The adduct cation [C60C3H3O](+) and protonated molecular ion [C60H](+) were observed as the major product ions. The former adduct ion is formed by electrophilic reaction of C-60 with the ion [CH2=CHCO](+), a main fragment ion resulting from the methyl acrylate molecular ion [CH2=CHCOOCH3](+) through alpha cleavage. The latter ion is generated by proton transfer from protonated methyl acrylate to C-60. Semi-empirical quantum chemical calculations have been performed for the eight possible isomers of [C60C3H3O](+) at the Hartree-Fock level by use of the AMI method. The results show three types of cycloadducts as the most stable structures among the possible isomers.

Study on polymer micelles of hydrophobically modified ethyl hydroxyethyl cellulose using single-molecule force spectroscopy

Individual hydrophobically modified ethyl hydroxyethyl cellulose (HM-EHEC) molecules under different conditions were elongated using a new atomic force microscope (AFM) based technique-single-molecule force spectroscopy (SMFS). The critical concentration of HM-EHEC for micelle-like clusters at a solid/liquid interface was around 0.8 wt %, which is lower than that in solution. The different mechanical properties of HM-EHEC below and above the critical concentration were displayed on force-extension curves. Through a comparison with unmodified hydroxyethyl cellulose, substituent-induced effects on nanomechanical features of HM-EHEC were investigated. Because of hydrophobic interactions and cooperative binding with the polymer, surfactants such as sodium dodecyl sulfate (SDS) dramatically influence the elastic properties of HM-EHEC below the critical concentration, and further addition of SDS reduces the interactions between the hydrophobic groups and the surfactant.

The algorithm on ring perception of molecule

It's important to identify ring in the process of structure elucidation. In this paper, all rings and the smallest set of smallest ring(SSSR) of structure are obtained from two-dimensional connection table. The results are satisfactory by using this algorithm in ESESOC expert system as constraint.

Gas-phase ion - Molecule reactions of neutral C-60 with the plasmas of alkyl methyl ethers and primary alcohols

The gas-phase ion-molecule reactions of C-60 with the methoxymethyl ion [CH3O=CH2](+) and the 1-hydroxyethyl ion [CH3CH=OH](+) generated under the self-chemical-ionization (self-CI) conditions of alkyl methyl ethers and primary alcohols were studied in the ion source of a mass spectrometer. The adduct ions [C60C2H5O](+) and protonated molecules [C60H](+) were observed as the major products of C-60 with the plasma of alkyl methyl ethers. On the contrary, the reactions of C-60 With the plasmas of primary alcohols produced few corresponding adduct ions. The AM1 semiempirical molecular orbital calculations were carried out on 14 possible structures. The calculated results showed that the most stable structure among the possible isomers of [C60C2H5O](+) is the [3+2] cycloadduct. According to experimental and theoretical results, the pathway for the formation of the adduct was presented.

Phase transition temperature of HPT(2,3,6,7,10,11-hexa-n-pentyloxytriphenylene) from molecule dynamic simulation

Molecule dynamics simulation was used on HPT(2,3,6,7,10,11-hexa-n-pentyloxytriphenylene), which is a discotic Liquid crystal. From analyzing the energy and displacement varying with the temperature, the phase transition temperature of PM6MPP can be predicted. The deviations of T-g, T-m and T-i due to the MD time scale are small enough that it should be possibly used to predict the material properties especially when more powerful computers are available.

Gas-phase ion-molecule reactions of C-60 with methyl ethers CH3OCnH2n+1

Gas-phase ion-molecule reactions of buckminsterfullerene (C-60) with the ion systems generated from the self-chemical-ionization of alkyl methyl ethers(CH3OCnH2n+1, n =2 , 3, 4) were studied in the ion source of a mass spectrometer. The adduct cation [C60C2H5O](+) and protonated molecular ion [C60H](+) were observed as the major products, The former was produced by the reactions.of C-60 with the methoxymethyl ion [CH3O = CH2](+) , the latter corresponded to the proton transfer reactions from the protonated alkyl methyl ethers to C60 It is suggested that the [3+2] cycloadduct is the most favorable structure among the probable isomers with special chemical properties, Our investigation provides the guidance for the synthesis of this compound in condensed phase.

Gas-phase ion-molecule reactions of neutral C-60 with alkyl methyl ethers under chemical ionization conditions

Gas-phase ion-molecule reactions of buckminsterfullerene (C-60) with the ion systems generated from the self-chemical ionization of alkyl methyl ethers (CH3OR, R = n-C2H5, n-C3H7, n-C4H9) were studied in the ion source of a mass spectrometer. The adduct cation [C60C2H5O](+) and protonated molecule [C60H](+) were observed as the major products. The former adduct ion was produced by the reactions of C-60 with the methoxymethyl ion [CH3OCH2](+), and the latter resulted from the proton transfer reactions from protonated alkyl methyl ethers to C-60 It is suggested that the [3+2] cycloadduct to a 6-6 bond of C-60 (a C-C bond common to two annulated six-membered rings) is the most favorable structure among the probable isomers of [C60C2H5O](+). (C) 1998 John Wiley & Sons, Ltd.

Ion-molecule reactions of cis- and trans-cyclopropane derivatives with methane, acetone and vinyl acetate under chemical ionization conditions

Ion-molecule reactions of four isomeric cyclopropane derivatives were investigated under chemical ionization(CI) conditions, using methane, acetone and vinyl acetate as reagent gases, The methane positive-ion CI mass spectra of each of two isomer pairs 1,2 and 3,4 are identical, and so are the collision-induced dissociation (CTD) spectra of the protonated molecules of each of the two isomer pairs, The protonation reactions for the isomer pairs 1,2 and 3,4 occurred on the sites of the carboxyl groups and the R groups, respectively, Differences between isomers 1 and 2 are observed in their acetone (A) positive-ion CI mass spectra and in the CID spectra of their adduct ions ([M+H+A](+)), The adduct ions of compounds 2, 3 and 4 with protonated acetone and with protonated acetone dimer are observed in their CI mass spectra, However, only the adduct ions of compound 1 with protonated acetone appear in its CI mass spectrum, The protonated dimers of each of the four compounds are found in their vinyl acetate positive-ion CI mass spectra, and the CID spectra of these dimers for isomers 1 and 2 can also reflect their stereostructural difference. (C) 1998 John Wiley & Sons, Ltd.

Studies on the product of ion-molecule reaction of halogeno-benzene in gas phase by MS/MS

The fragmentations of the product ions produced by the ion-molecule reaction of the halogeno-benzene (chlorobenzene, bromobenzene and iodobenzene) were studied using the collision-induced dissociation, The main product ions of the ion-molecule reaction of three kinds of halogeno-beneze include the dimeric ions, m/z(2M-X) ions and m/z(2M-2X) ions, The CID spectra of these ions were compared with that of the protonated bromodiphenyl and biphenyl, The formation mechanism and the structure of the product ions were obtained.

Formation of heterocyclic C-60 derivative by gas-phase ion/molecule reaction

Ion/molecule reactions of C-60 with vinyl acetate under chemical ionization conditions have been studied here. Compared with C2H3O+ from acetone, C2H3O+ from vinyl acetate undergoes the reactions more easily, a new heterocycle between C-60 and the studied ion is formed The generation of two sigma-bonds and little angle tensile force of pentatomic ring make it more stable.