基于两分子和三分子相互作用的流体界面张力研究

提出了一个改进的密度泛函理论模型.该模型同时考虑了流体中两分子和三分子相互作用对体系Helm hlotz自由能的贡献,对Ar,N2,CH4,CO2等四种流体的气液界面张力进行了预测,结果与实验值均吻合良好.通过与仅考虑两分子作用的理论计算值和分子模拟值进行比较,表明流体中的三分子相互作用对描述非均相流体的结构与性质有重要影响.     

Optical investigation of intermolecular action between Si and Cl

Summary The intermolecular action through, Si...Cl bonds in Cl₃Si - CH₂CH₂-Cl and the intermolecular action through Si ...CI in CI₃Si - CH₂CH₂CH₂- Cl were detected in the liquid phase by optical (Raman spectrum) analysis.     

Structure of the EntB multidomain nonribosomal peptide synthetase and functional analysis of its interaction with the EntE adenylation domain

Nonribosomal peptide synthetases are modular proteins that operate in an assembly line fashion to bind, modify, and link amino acids. In the E. coli enterobactin NRPS system, the EntE adenylation domain catalyzes the transfer of a molecule of 2,3-dihydroxybenzoic acid to the pantetheine cofactor of EntB. We present here the crystal structure of the EntB protein that contains an N-terminal isochorismate lyase domain that functions in the synthesis of 2,3-dihydroxybenzoate and a C-terminal carrier protein domain. Functional analysis showed that the EntB-EntE interaction was surprisingly tolerant of a number of point mutations on the surface of EntB and EntE. Mutational studies on EntE support our previous hypothesis that members of the adenylate-forming family of enzymes adopt two distinct conformations to catalyze the two-step reactions.     

Communication: Density functional theory overcomes the failure of predicting intermolecular interaction energies

Density-functional theory (DFT) revolutionized the ability of computational quantum mechanics to describe properties of matter and is by far the most often used method. However, all the standard variants of DFT fail to predict intermolecular interaction energies. In recent years, a number of ways to go around this problem has been proposed. We show that some of these approaches can reproduce interaction energies with median errors of only about 5% in the complete range of intermolecular configurations. Such errors are comparable to typical uncertainties of wave-function-based methods in practical applications. Thus, these DFT methods are expected to find broad applications in modelling of condensed phases and of biomolecules.     

Localized protein interaction surfaces on the EntB carrier protein revealed by combinatorial mutagenesis and selection

Carrier proteins are 80- to 100-residue way stations that are central to polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) enzymatic assembly lines. Because the biosynthetic intermediates for catalytic operations are presented on carrier proteins as covalently attached thioesters (via a 4'-phosphopantetheine prosthetic group), the specific protein-protein interactions between carrier proteins and other NRPS/PKS domains are critical for high-fidelity conversion to the final product. Here we show by combinatorial mutagenesis and selection that the aryl carrier protein of EntB (EntB-ArCP) contains localized protein interaction surfaces. Our strategy involved random mutagenesis of N-terminal regions of EntB-ArCP, then selection for clones that produce enterobactin by plating onto iron-deficient media. We identified several residues that were highly conserved from our selection, two of which (G242 and D244) constitute an interaction surface on EntB-ArCP for the phosphopantetheinyl transferases (PPTases) EntD and Sfp. This PPTase interface is distinct from a previously characterized interface on EntB-ArCP for the downstream elongation module, EntF. These results suggest that different protein components recognize different faces of EntB-ArCP in the enterobactin synthetase and that the majority of EntB-ArCP surface residues are not involved in these interactions. Therefore, designing noncognate carrier protein interactions in PKS and NRPS systems should be possible with very few mutations on a particular carrier protein.     

Application of infrared spectroscopy to investigation of the structure of tetrafluoroethylene telomers in acetone and their intermolecular interaction

Measured FTIR spectra of the products of the radiation-chemical telomerization of tetrafluoroethylene in acetone have been compared with the spectra calculated by density functional theory for oligomers with the structural formula H(C₂F₄) _n CH₂COCH₃, n ≥ 3, and the dimer of the latter. Inhomogeneous broadening, splittings, and shifts of the CH, CC, and CO vibration bands in the terminal groups on the oligomers relative to the associates of acetone molecules confirm the structural formula of the oligomers and show that strong hydrogen bonds are formed between their end groups.     

A fourth scale sensitive to the magnetic field; intermolecular frequency symmetry in a specific interaction between protein and low-molecular compound

We found a new method that a specific interaction between prion, i.e., high-molecular compound, and Cp-60, i.e., low-molecular one, could be successfully elucidated with intermolecular frequency symmetry (IFS). To accomplish this, the former sequence is analyzed with a sequence Fourier analysis used average nuclear (N) resonant frequency scale as a fourth one, and the latter structure with a 13C-NMR software. Further, such the symmetry could be observed in a specific interaction between a segment of human immunodeficiency virus (HIV)gag and PA-457 or between 1918 neuraminidase and peramivir. Therefore, the IFS rule seems to be evolutionarily conserved as a necessary condition even in a specific protein-organic compound interaction.     

Extender unit and acyl carrier protein specificity of ketosynthase domains of the 6-deoxyerythronolide B synthase

Polyketide synthases (PKSs) catalyze the production of numerous biologically important natural products via repeated decarboxylative condensation reactions. Modular PKSs, such as the 6-deoxyerythronolide B synthase (DEBS), consist of multiple catalytic modules, each containing a unique set of covalently linked catalytic domains. To better understand the engineering opportunities of these assembly lines, the extender unit and acyl carrier protein (ACP) specificity of keto synthase (KS) domains from modules 3 and 6 of DEBS were analyzed. These studies were undertaken with a newly developed didomain [KS][AT] construct, which lacks its own ACP domain and can therefore be interrogated with homologous or heterologous ACP or acyl-ACP substrates. By substituting the natural methylmalonyl extender unit with a malonyl group, a modest role was demonstrated for the KS in recognition of the nucleophilic substrate. The KS domain from module 3 of DEBS was found to exhibit a distinct ACP-recognition profile from the KS domain of module 6. On the basis of the above kinetic insights, a hybrid module was constructed ([KS3][AT3][KR5][ACP5][TE]) which displayed substrate recognition and elongation capabilities consistent with the natural module 3 protein. Unlike module 3, however, which lacks a ketoreductase (KR) domain, the hybrid module was able to catalyze reduction of the beta-ketothioester product of chain elongation. The high expression level and functionality of this hybrid protein demonstrates the usefulness of kinetic analysis for hybrid module design.     

A computational and experimental investigation of the interaction between the template molecule and the functional monomer used in the molecularly imprinted polymer

A computational approach to screening monomer for preparing molecularly imprinted polymer (MIP) was proposed, using the binding energy, ΔE, of a template molecule and a monomer as a measure of their interaction. For a specified template molecule, a monomer of higher ΔE is suitable for preparing the MIP. To examine the validity of this approach, theophylline (THO) was chosen as the template molecule and methacrylic acid (MAA), acrylamide (AA) and 2-(trifluoromethyl)acrylic acid (TFMAA) were as the functional monomers, respectively. Density functional theory (DFT) at B3LYP/6-31+G**//B3LYP/3-21G level was used to calculate ΔE. It was shown that TFMAA gave the largest ΔE while AA gave the smallest. The details of the interaction between the THO with these monomers were also given by this computing approach. The adsorption of THO on the MIP synthesized using different monomers was studied. The MIP synthesized using TFMAA as monomer showed the highest selectivity to THO while the MIP from AA gave the lowest, as predicted from the ΔE calculation. ¹H NMR spectroscopy showed that, compared to MAA and AA, a stronger H-bond interaction is formed between TFMAA and THO. FT-IR analysis of the MIPs prepared using these three monomers confirmed the existence of CO and OH groups, which forms H-bond with THO. The results described above have given an insight into the interaction between THO and the monomers, and shown the use of ΔE to facilitate the selection of monomers for the synthesis of MIP.     

Density functional investigation of the interaction of acetone with small gold clusters

The structural evolution of Au(n) (n=2, 3, 5, 7, 9, and 13) clusters and the adsorption of organic molecules such as acetone, acetaldehyde, and diethyl ketone on these clusters are studied using a density functional method. The detailed study of the adsorption of acetone on the Au(n) clusters reveals two main points. (1) The acetone molecule interacts with one gold atom of the gold clusters via the carbonyl oxygen. (2) This interaction is mediated through back donation mainly from the spd-hybridized orbitals of the interacting gold atom to the oxygen atom of the acetone molecule. In addition, a hydrogen bond is observed between a hydrogen atom of the methyl group and another gold atom (not involved in the bonding with carbonyl oxygen). Interestingly, the authors notice that the geometries of Au(9) and Au(13) undergo a significant flattening due to the adsorption of an acetone molecule. They have also investigated the role of the alkyl chain attached to the carbonyl group in the adsorption process by analyzing the interaction of Au(13) with acetaldehyde and diethyl ketone.     

The role of tandem acyl carrier protein domains in polyunsaturated fatty acid biosynthesis

Acyl carrier protein (ACP) plays an essential role in fatty acid and polyketide biosynthesis, and most of the fatty acid synthases (FASs) and polyketide synthases (PKSs) known to date are characterized with a single ACP for each cycle of chain elongation. Polyunsaturated fatty acid (PUFA) biosynthesis is catalyzed by the PUFA synthase, and all PUFA synthases known to date contain tandem ACPs (ranging from 5 to 9). Using the Pfa PUFA synthase from Shewanella japonica as a model system, we report here that these tandem ACPs are functionally equivalent regardless of their physical location within the PUFA synthase subunit, but the total number of ACPs controls the overall PUFA titer. These findings set the stage to interrogate other domains and subunits of PUFA synthase for their roles in controlling the final PUFA products and could potentially be exploited to improve PUFA production.     

Photoemission investigation of interaction between L-cysteine and silver surface

In this study, the formation of Ag–S bond was systematically elucidated by thickness-dependent ultraviolet photoelectron spectroscopy (UPS) in order to understand the L-cysteine interaction with silver surface. A clean Ag(111) as the model system for silver surface was used, and L-cysteine films on silver substrate were formed by vacuum evaporation. The orbital configurations at the interface was estimated including work function, secondary electron cutoff (SECO), highest occupied molecular orbital (HOMO) onset, position of an interface state, charge injection barrier, and ionization energy. A clear spectral feature was appeared in between Fermi edge and HOMO of L-cysteine, and the feature can be attributed to the formation of Ag–S bonding. In the case of SECO, the maximum shift was 0.46 eV to the higher binding energy side at the nominal thickness of 1 Å. However, from the nominal thickness of 2 Å, SECO started to shift to the lower binding energy side, and at 16 Å, the SECO shifted to a value of around 0.4 eV to the lower binding energy side to almost cancel the initial vacuum level shift. This behavior can be attributed to weakening of the silver-sulfur bond with increasing of L-cysteine coverage referring to the literature. The photoelectron yield spectroscopy (PYS) was also performed as an additional spectroscopic work, which exhibited that the work function of silver once decreased and then recovered at low coverage. This behavior can also be assigned to a weakening the interaction of L-cysteine with silver by increasing of L-cysteine coverage.     

Electrochemical investigation of the interaction between lysozyme-shelled microbubbles and vitamin C

We report loading of vitamin C (ascorbic acid) on to lysozyme-shelled microbubbles. The interaction between lysozyme-shelled microbubbles and vitamin C was studied by use of cyclic and differential pulse voltammetry, zeta potential measurements, and scanning electron microscopy. The effect of microbubbles on electrochemical measurement of ascorbic acid was evaluated. The linear range for ascorbic acid obtained for differential pulse measurement in the presence of 1 mg mL^?1 microbubbles was 1–50 μmol L^?1 (y?=?0.067x?+?0.130, r ²?=?0.995), with a detection limit of 0.5 μmol L^?1. The experimental conditions, i.e., pH and ionic strength, were optimized to improve the interaction between ascorbic acid and lysozyme-shelled microbubbles. The results were satisfactory when the interaction was performed for 1 h in aqueous solution at pH 6. The amount of vitamin C loaded on the microbubbles (90 % of the analyte added, RSD _inter-expt. = 3 %, n?=?6) and the stability of microbubbles–ascorbic acid complex (until 72 h at 25 °C) were also evaluated by use of differential pulse voltammetry and zeta potential measurements.

光谱法研究喜树碱与牛血清白蛋白的相互作用

采用多种光谱技术对喜树碱和牛血清白蛋白的相互作用进行了研究.结果表明喜树碱和牛血清白蛋白可形成基态复合物,引起牛血清白蛋白内源荧光猝灭.通过计算获得了二者在不同温度下的结合常数及结合位点数.根据喜树碱和牛血清白蛋白结合的热力学参数,确定了二者之间主要为疏水作用力.根据F(o)rster非辐射能量转移理论确定了喜树碱和牛血清白蛋白的作用距离.同步荧光光谱显示喜树碱主要与蛋白中色氨酸残基发生相互作用,改变其周围的局部构象.红外光谱提示喜树碱可引起蛋白的构象发生改变,α-螺旋二级结构减少.     

Fluorescence spectroscopic investigation of the interaction between triphenyltin and humic acids

The interaction between triphenyltin (TPT) and humic acid (HA) was investigated using UV-vis and fluorescence spectra techniques. The experimental results showed that the fluorescence quenching of HA by TPT was a result of the interaction of TPT with HA. The binding constant K(b) and corresponding thermodynamic parameters were measured at different temperatures. The binding of TPT molecule to HA is a spontaneous molecular interaction procedure in which entropy increased and Gibbs free energy decreased. Hydrophobic interaction force plays a major role in stabilizing the TPT-HA complex. The three-dimensional fluorescence contour spectra revealed that TPT could enter into the hydrophobic cavities in some domain of HA.     

Density functional theory study of the interaction between formamide and uracil

The hydrogen bonding of complexes formed between the formamide and uracil molecule has been fully investigated in the present study using the density functional theory (DFT) method at varied basis set levels from 6‐31G to 6‐311++G(d,p). Eight stable cyclic structures with two hydrogen bonds involved in the interaction are found on the potential energy surface (PES). The four structures are seven‐membered rings; the others are eight‐membered rings. The eight‐membered ring is preferred over the seven‐membered one by analyzing the hydrogen bond lengths and the interaction energies. The infrared (IR) spectrum frequencies, IR intensities, and the vibrational frequency shifts are reported. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

肾上腺素与胞嘧啶相互作用的密度泛函理论研究

采用密度泛函理论（DFT）B3LYP方法和6-311＋G（d,p）基组对肾上腺素-胞嘧啶复合物进行结构优化和频率计算,得到15种稳定的复合物.研究发现,所有的复合物进行基组重叠误差（BSSE）校正后的相互作用能为-11.43^-48.96kJ/mol,符合氢键能量范围,相互作用能主要由氢键所贡献.结构和振动频率分析显示,氢键的形成使相应O（N）—H键的键长变长,对称伸缩振动频率减小,说明复合物中形成的氢键都是正常的红移型氢键.应用自然键轨道（NBO）理论和分子中的原子（AIM）理论对15种复合物的氢键性质和特征进行分析,发现氢键对于复合物的稳定性起着重要作用,当复合物形成2个或更多的氢键时,氢键的数目、类型及强度共同决定着复合物的稳定性,复合物基本符合三氢键〉二氢键〉单氢键的稳定顺序,三氢键复合物4是最稳定的,复合物3存在单氢键O—H…O,比部分二氢键复合物要稳定.