Fully quantum mechanical energy optimization for protein-ligand structure

We present a quantum mechanical approach to study protein-ligand binding structure with application to a Adipocyte lipid-binding protein complexed with Propanoic Acid. The present approach employs a recently develop molecular fractionation with a conjugate caps (MFCC) method to compute protein-ligand interaction energy and performs energy optimization using the quasi-Newton method. The MFCC method enables us to compute fully quantum mechanical ab initio protein-ligand interaction energy and its gradients that are used in energy minimization. This quantum optimization approach is applied to study the Adipocyte lipid-binding protein complexed with Propanoic Acid system, a complex system consisting of a 2057-atom protein and a 10-atom ligand. The MFCC calculation is carried out at the Hartree-Fock level with a 3-21G basis set. The quantum optimized structure of this complex is in good agreement with the experimental crystal structure. The quantum energy calculation is implemented in a parallel program that dramatically speeds up the MFCC calculation for the protein-ligand system. Similarly good agreement between MFCC optimized structure and the experimental structure is also obtained for the streptavidin-biotin complex. Due to heavy computational cost, the quantum energy minimization is carried out in a six-dimensional space that corresponds to the rigid-body protein-ligand interaction.     

Solvothermal Synthesis and Structure Characterization of a 3D Hydrogen-bonded Copper Compound [Cu(H_2dhpmc)_2]·2H_2O

1 INTRODUCTION The controlled assembly of inorganic and coordination polymers from simple building blocks is an important challenge in the design of high- dimensionality systems. In the crystal engineering 'toolbox'[1], hydrogen bonding moieties are perhaps the implements used the most in the design of such supramolecular systems[2], and have been particularly strongly applied towards the synthesis of molecular magnetic materials[3~6]. Copper complexes play an important role in catalyzin…     

Incorporation of FT-IR spectral data in a computer-assisted prediction of globular protein structure

Currently, much effort is being directed to the determination of the three-dimensional structure of proteins. Two classes of research are of interest; spectrometric techniques which include Fourier transform infrared (FT-IR) spectrometry, and non-spectrometric prediction schemes. The spectra obtained using FT-IR spectrometry, are analyzed to determine the percentages of alpha-helices, beta-pleated sheets, and non-structured coils in a protein. Unfortunately, FT-IR, as well as other spectrometric techniques, cannot be used to determine the exact secondary structure of a protein reliably. Non-spectrometric prediction methods yield information on the exact secondary structure, but are not always accurate. Most prediction methods relate the primary amino acid sequence to the secondary structure of a protein, allowing sequential secondary structure information for the protein examined to be obtained. The goal of this research is to incorporate FT-IR with a prediction method, resulting in an improvement in the accuracy of the prediction.     

Analytical applications of picolinealdehyde salicyloylhydrazone: Spectrophotometric determination of nickel and zinc

With a view to the use of picolinealdehyde salicyloylhydrazone as analytical reagent, a study of the physical properties and chemical reactions of this substance has been carried out. It reacts with nickel (λ_max = 375 nm, ? = 3.9 × 10⁴M^?1cm^?1) or zinc (λ_max = 365 nm, ? = 4.8 × 10⁴M^?1cm^?1) to produce a yellow 1:2 complex in both cases. Spectrophotometric determinations of trace amounts of nickel and zinc have been established.     

Synthesis and Crystal Structure of MnSm_4(SiO_4)_3O

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Synthesis and Crystal Structure of Trigadolinium Bromoorthosilicate，Gd_3Br（SiO_4）_2

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Liquid structure of vanadium tetrachloride from neutron diffraction study

Assuming the separation of the intermolecular scattering function into the radial and angular parts and using Egelstaffet al’s orientational model for tetrachlorides, the structure of liquid vanadium tetrachloride has been studied. It has been observed that such a separation is approximate for this liquid and the introduction of a third correction term is required to account for the molecular structure function. The chlorine-chlorine partial structure and effective angleaveraged intermolecular chlorine-chlorine potential in the liquid has been evaluated. Without taking the third correction term, introduced to generate theoretically the molecular structure function, the centre structure function has been obtained in an approximate way from the experimentally observed molecular structure function and from it the centre radial distribution function, centre direct correlation function and the angle-averaged vanadium-vanadium effective potential has been evaluated.     

Trigonal-planare CuX3-Gruppen in Cu2Mo6X14, X = Cl,Br, I

Trigonal Planar CuX₃-Groups in Cu₂Mo₆X₁₄, X = Cl, Br, I Cu₂Mo₆Cl₁₄ (I), Cu₂Mo₆Br₁₄ (II) and Cu₂Mo₆I₁₄ (III) were synthesized by thermal treatment of corresponding mixtures of copper(I) and molybdenum(II) halides. The crystal structures were determined by single crystal X-ray analyses. I and II show isotypism, cubic, Pn3 (no. 201, sec. setting), Z = 4, I: a = 12.772(3) Å, II: a = 13.350(2) Å. III shows a new structural type, orthorhombic, Pbca (No. 61), Z = 4, a = 16.058(3) Å, b = 10.643(2) Å, c = 16.963(3) Å. Trigonal planar CuX₃ units were found in I? III. Structural behaviour relations are discussed, especially with regard to ionic conductivity.     

Synthese und Strukturuntersuchungen von Ba2H[α-FeO4W12O36] · 26 H2O

Synthesis and Structure Studies of Ba₂H[α-FeO₄W₁₂O₃₆] · 26 H₂O The heteropolyanion compound Ba₂H[α-FeO₄W₁₂O₃₆] · 26 H₂O (I) crystallizes in the tetragonal space group P4 n2 with the lattice parameters a = 12.398(6), c = 18.721(6) Å; Z = 2; D_x = 4.128 g · cm^?3. The structure was solved on a twinned crystal from 1029 observed reflections and refined to an index R of 7.6%. The calculations were done by means of a modified ORFLS-programme by Eitel and Bärnighausen. The heteropolyanion [α-FeO₄W₁₂O₃₆]^5? has the well known α-Keggin structure. The average distance of the four central oxygen atoms to the Fe^III position (0, 0, 0) is 1.84 Å. The angles ? O? Fe? O are 112.3° (4X) and 103.9 (2X), respectively, which leads to an disphenoidal distortion of the FeO₄ tetrahedron. The powder and single crystal ESR spectra of I show the anisotropy of the Fe^III fine structure transition 1/2 ? ?1/2. The Mößbauer spectra confirm the tetragonal distortion of the central FeO₄ tetrahedron (quadrupole splitting Δ ≈ 0.50 mm · s^?1).     

小分子配体诱导合成N,N-二苄基二硫代氨基甲酸镉(II)配合物及晶体结构

4,4'-联吡啶与二苄基二硫代氨基甲酸镉配合物[Cd(DBTC)₂]₂ (1)反应得到加合物[Cd(DBTC)₂(4,4'-bipy)] (2) (DBTC＝N,N-二苄基二硫代氨基甲酸), 通过晶体结构分析及红外光谱等研究其结构与性质. 结果表明: 引入小分子配体会破坏[Cd(DBTC)₂]₂ (1)的二聚结构, 加入吡啶则得到单核的吡啶加合物[Cd(DBTC)₂py] (3), 而引入4,4'-联吡啶后其结构变为新型的一维链状结构的配位聚合物2, 这种结构在二硫代氨基甲酸金属配合物中少见报道. 也比较了不同配体如吡啶及4,4'-联吡啶对Cd(II)及Zn(II)配合物结构的影响.