Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling

The W191G cavity of cytochrome c peroxidase is useful as a model system for introducing small molecule oxidation in an artificially created cavity. A set of small, cyclic, organic cations was previously shown to bind in the buried, solvent-filled pocket created by the W191G mutation. We docked these ligands and a set of non-binders in the W191G cavity using AutoDock 3.0. For the ligands, we compared docking predictions with experimentally determined binding energies and X-ray crystal structure complexes. For the ligands, predicted binding energies differed from measured values by +/- 0.8 kcal/mol. For most ligands, the docking simulation clearly predicted a single binding mode that matched the crystallographic binding mode within 1.0 A RMSD. For 2 ligands, where the docking procedure yielded an ambiguous result, solutions matching the crystallographic result could be obtained by including an additional crystallographically observed water molecule in the protein model. For the remaining 2 ligands, docking indicated multiple binding modes, consistent with the original electron density, suggesting disordered binding of these ligands. Visual inspection of the atomic affinity grid maps used in docking calculations revealed two patches of high affinity for hydrogen bond donating groups. Multiple solutions are predicted as these two sites compete for polar hydrogens in the ligand during the docking simulation. Ligands could be distinguished, to some extent, from non-binders using a combination of two trends: predicted binding energy and level of clustering. In summary, AutoDock 3.0 appears to be useful in predicting key structural and energetic features of ligand binding in the W191G cavity.     

Structures and bonding of the complexes [M(η<Superscript>5</Superscript>-E<Subscript>5</Subscript>)] and [M(η<Superscript>5</Superscript>-E<Subscript>5</Subscript>)<Subscript>2</Subscript>] (M = Sc,Y, E = N,P): a DFT study

The mono- and bisligands complexes formed by rare earth cation (Sc, Y) with pentazolato anion or cyclo-P₅⁻ anion, the all-nitrogen counterparts of metallocenes or the all-phosphorus counterparts of metallocenes, have been studied at hybrid basis sets level with the DFT method. The geometric parameters, binding energy and the charge distributions of these complexes were characterized. And their stable orders were obtained. Monoligand complexes incline to become bisligands complexes due to their destabilization. The charge transferring between ligand and metallic cation has affinity with the stability of complex. The possibility of forming stable [M(η ⁵-E₅)₂] (M = Sc, Y, E = N, P) complexes is predicted and they are viable synthetic targets theoretically, especially Sc(η ⁵-N₅)₂.     

Voltammetric determination of the trace amounts of bromate in drinking water after pre-concentration on hydrous γ-Al<Subscript>2</Subscript>O<Subscript>3</Subscript>

A differential pulse voltammetric (DPV) method for the determination of bromate in drinking water, after pre-concentration on γ-Al₂O₃, is proposed. The reduction peak of bromate has been observed at the potential E _p -−1.6 V in an ammonia buffer as a supporting electrolyte. The method has been successfully applied to determine a bromate concentration of 2.5 μg·l⁻¹ in drinking water (RSD=6.1%, n=7). A sample pre-treatment with a column filled with mixed cation-exchange resin in Ag, Ba and H forms was needed before pre-concentration of bromate on alumina.     

Phase-pure nanocrystalline Li<Subscript>4</Subscript>Ti<Subscript>5</Subscript>O<Subscript>12</Subscript> for a lithium-ion battery

Phase-pure nanocrystalline Li₄Ti₅O₁₂ with BET surface areas between 183 and 196 m²/g was prepared via an improved synthetic protocol from lithium ethoxide and titanium(IV) butoxide. The phase purity was proved by X-ray powder diffraction, Raman spectroscopy and cyclic voltammetry. Thin-film electrodes were prepared from two nanocrystalline samples of Li₄Ti₅O₁₂ and one microcrystalline commercial sample. Li-insertion behavior of these electrodes was related to the particle size.Presented at the 3rd International Meeting on Advanced Batteries and Accumulators, 16–20 June 2002, Brno, Czech Republic     

Hydrothermal synthesis and thermodynamic properties of 2CaO·3B<Subscript>2</Subscript>O<Subscript>3</Subscript>·H<Subscript>2</Subscript>O

2CaO·3B₂O₃·H₂O which has non-linear optical (NLO) property was synthesized under hydrothermal condition and identified by XRD, FTIR and TG as well as by chemical analysis. The molar enthalpy of solution of 2CaO·3B₂O₃·H₂O in HCl·54.572H₂O was determined. From a combination of this result with measured enthalpies of solution of H₃BO₃ in HCl·54.501H₂O and of CaO in (HCl+H₃BO₃) solution, together with the standard molar enthalpies of formation of CaO(s), H₃BO₃(s), and H₂O(l), the standard molar enthalpy of formation of −(5733.7±5.2) kJ mol⁻¹ of 2CaO·3B₂O₃·H₂O was obtained. Thermodynamic properties of this compound were also calculated by a group contribution method.     

CuSO<Subscript>4</Subscript> as a Mild,Green, and Efficient Catalyst for the One-pot Conversion of <Emphasis Type="Italic">THP</Emphasis> Ethers to Acetates

Summary. An efficient direct conversion of THP ethers into the corresponding acetates was achieved with acetic anhydride in the presence of CuSO₄ · 5H₂O as an available and green catalyst in high yields.     

Electronic structure and chemical bonding in K<Subscript>2</Subscript>V<Subscript>3</Subscript>O<Subscript>8</Subscript>

The calculations of the electronic structure of layered polyvanadate K₂V₃O₈ were made employing the spin-polarized tight-binding LMTO method. Calculated magnetic moment for K₄V₆O₁₆ compound phase equals 1.97 μ_B. V-O interactions were established to be dominating in the chemical bonding generation in this polyvanadate according to the estimated crystal orbital overlap population. The covalent bonds V(2)-V(2) in V(2)₂O₇ groups and electron density localization on vanadium atoms in isolated pyramids V(1)O₅ were found.     

Hydrothermal synthesis,structure and photocatalytic property of nano-TiO<Subscript>2</Subscript>-MnO<Subscript>2</Subscript>

TiCl₄ and MnSO₄· H₂O as raw materials are hydrolyzed stiochiometrically, following the intermediate of oxide hydrating reacts at 150°C, 0.5 MPa in high-pressure reactor, after filtering, washing and drying, nanometric TiO₂-MnO₂ (Ti_1-X Mn _X O₂) is prepared. The effects of the reaction temperature and time on nanometric TiO₂-MnO₂ are also discussed. XRD shows that the product is TiO₂-MnO₂ with amorphous phase. After being sintered at above 780 °C, it transfers into Ti_1-X Mn _X O₂ with a rutile structure. TEM shows that TiO₂-MnO₂ is the spherical particle. And the average diameter of the particles is 20 nm. The optical absorbance was determined by UV-265 spectrophotometer after dispersing the sample in the mixture of water and glycerol with the ratio of 1 : 1 equably. It is found that the nano-material possesses the advantages of both nano-TiO₂ and nano-MnO₂, and it has strong absorption in the UV and visible region. Photodegradation of dyes in an aqueous solution is investigated using nanometricTiO₂-MnO₂ as a photocatalyst. The results show that after 60 min illumination, the decolorization rate of the acidic red B and acidic black 234 dye can be as high as 100%.     

Influence of protonation on substrate and inhibitor interactions at the active site of human monoamine oxidase-A

Although substrate conversion mediated by human monoaminooxidase (hMAO) has been associated with the deprotonated state of their amine moiety, data regarding the influence of protonation on substrate binding at the active site are scarce. Thus, in order to assess protonation influence, steered molecular dynamics (SMD) runs were carried out. These simulations revealed that the protonated form of the substrate serotonin (5-HT) exhibited stronger interactions at the protein surface compared to the neutral form. The latter displayed stronger interactions in the active site cavity. These observations support the possible role of the deprotonated form in substrate conversion. Multigrid docking studies carried out to rationalize the role of 5-HT protonation in other sites besides the active site indicated two energetically favored docking sites for the protonated form of 5-HT on the enzyme surface. These sites seem to be interconnected with the substrate/inhibitor cavity, as revealed by the tunnels observed by means of CAVER program. pK(a) calculations in the surface loci pointed to Glu32?, Asp32?, His???, and Asp132 as candidates for a possible in situ deprotonation step. Docking analysis of a group of inhibitors (structurally related to substrates) showed further interactions with the same two docking access sites. Interestingly, the protonated/deprotonated amine moiety of almost all compounds attained different docking poses in the active site, none of them oriented to the flavin moiety, thus producing a more variable and less productive orientations to act as substrates. Our results highlight the role of deprotonation in facilitating substrate conversion and also might reflect the necessity of inhibitor molecules to adopt specific orientations to achieve enzyme inhibition.     

Quantum-chemical modelling of nanotubes of titanium silicocarbides Ti<Subscript>2</Subscript>SiC,Ti<Subscript>3</Subscript>SiC<Subscript>2</Subscript>, and Ti<Subscript>4</Subscript>SiC<Subscript>3</Subscript>

Atomic models are proposed for nanotubes of the titanium silicocarbides Ti₂SiC, Ti₃SiC₂, and Ti₄SiC₃, and their electronic structure and interatomic interactions are investigated by the density functional tight-binding method (DFTB) in comparison with the corresponding crystalline phases. Translated from Teoreticheskaya i éksperimental’naya Khimiya, Vol. 45, No. 2, pp. 88-92, March-April, 2009.     

Preparation and characterization of LiFePO<Subscript>4</Subscript> from NH<Subscript>4</Subscript>FePO<Subscript>4</Subscript>·H<Subscript>2</Subscript>O under different microwave heating conditions

Olivine-type LiFePO₄ is a very promising polyanion-type cathode material for lithium-ion batteries. In this work, LiFePO₄ with high specificity capacity is obtained from a novel precursor NH₄FePO₄·H₂O via microwave processing. The grains grow up in the duration of sintering until they reach the decomposition temperature. The apparent conductivity of the samples rises rapidly with the irradiation time and influences the electrochemical performance of the material greatly at high current density. As a result, the LiFePO₄ cathode material obtained with a sintering time of 15 min has good electrochemical performance. Between 2.5 and 4.2 V versus Li, a reversible capacity is as high as 156 mAh g⁻¹ at 0.05 C.     

Electrochemical properties of <Emphasis Type="Italic">n</Emphasis>-sulfonatothiacalyx[4]arene complexes with Fe<Superscript>3+</Superscript> and [Co(dipy)<Subscript>3</Subscript>]<Superscript>3+</Superscript> ions

The electrochemical properties of n-sulfonatothiacalyx[4]arene (H₄XNa₄) complexes with [Co(dipy)₃]³⁺ and Fe³⁺ ions were studied by means of cyclic voltammetry in aqueous solution at pH 2.5. The observed single-electron reduction of [Co(dipy)₃]³⁺ bound extraspherically to the upper rim and Fe³⁺ ion bound intraspherically to the lower rim of n-sulfonatothiacalyx[4]arene in binary [Co(dipy)₃]³⁺ · H₃X^5?, H₃X^5? · Fe³⁺, and ternary [Co(dipy)₃]³⁺ · H₃X^5? · Fe³⁺ heterometal complexes was more difficult than in the free state. The reversible single-electron transfer to the metal ion results in lower binding energy ([Co(dipy)₃]³⁺, ΔΔG ₀ = 3.9 kJ/mol) or in full fast dissociation of the complex (Fe³⁺). The ternary complex in the solution forms the aggregates, in which inner encapsulated Fe(III) and Co(III) ions are not reduced on the electrode. Their quantitative reduction takes place by the relay mechanism of intra- and intermolecular electron transfer through electrochemically generated [Co(dipy)₃]²⁺ outer ions.     

Laser assisted selective chemical metalization of Al<Subscript>2</Subscript>O<Subscript>3</Subscript> films

Thick aluminum oxide films are prepared on Al plates by anodizing. On the ceramic surface thus obtained a very thin Ag film is deposited via vacuum thermal evaporation. The Ag/Al₂O₃/Al samples prepared are irradiated by Nd:YAG laser through a suitable metal mask in order to remove the top metal film in the exposed areas. Thus, a negative silver image of the copied mask is obtained. Further, the samples are processed in Ni electroless chemical bath activated by the rest of silver. All processing steps are studied by scanning electron microscopy (SEM). EDS X-ray mapping is applied to study the final distribution of Al and Ni in the processed areas. In addition, the DC conductivity of the fabricated Ni wires obtained is measured. The proposed new method for selective chemical deposition of electroconductive Ni onto laser microstructured Ag/Al₂O₃/Al samples is simple, versatile and not restricted to the metal/ceramic system studied as well as to the electroless deposited metal.     

FTIR-ATR <Emphasis Type="Italic">in situ</Emphasis> observation on the efflorescence and deliquescence processes of Mg(NO<Subscript>3</Subscript>)<Subscript>2</Subscript> aerosols

The efflorescence and deliquescence processes of Mg(NO₃)₂ aerosol particles deposited on ZnSe substrate have been investigated through in situ Fourier transform infrared-attenuated total reflection (FTIR-ATR) technique at the molecular level. At relative humidity (RH) of ∼3%, Mg(NO₃)₂ particles existed as amorphous states. The amorphous Mg(NO₃)₂ particles were transformed into crystalline Mg(NO₃)₂ · nH₂O (n ≤ 5) with slight increasing of RH. Thermodynamically stable Mg(NO₃)₂·6H₂O crystals were gradually formed on the particle surface and started to be dissolved at the saturation point (∼53% RH). At the same time, a continuous phase transition from Mg(NO₃)₂ · nH₂O (n≤5) to Mg(NO₃)₂·6H₂O occurred on the particle surface. This led the solid particles to completely deliquesce at 76% RH, which was much higher than the saturation point of 53% RH. In the efflorescence process, Mg(NO₃)₂ droplets entered into the supersaturated region due to the gradual evaporation of water. Finally, amorphous particles were formed when RH decreased below 5%. In the FTIR-ATR spectra of the supersaturated Mg(NO₃)₂ droplets, the absorbance of the symmetric stretching vibration of NO ₃ ⁻ (v ₁- NO ₃ ⁻ ) clearly became stronger. It resulted from the continuous formation of solvent share ion pairs (SIPs), and even the contact ion pairs (CIPs) between Mg²⁺ and NO ₃ ⁻ . Supported by the Trans-Century Program Foundation for the Talents by the Ministry of Education of China, the National Natural Science Foundation of China (Grant Nos. 20073004, 20473012, and 20673010), the 111 Project (B07012), and the State Key Laboratory of Physical Chemistry for Solid Surface of Xiamen University     

Study of Endogen Substrates,Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics

Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coarse grained, and umbrella sampling molecular dynamics simulations (AA-MDS and CG-MDS, respectively). The results showed that the three MRP4 structures had significantly different conformations at given sites, leading to differences in the docking scores (DS) and binding sites of three different groups of molecules. Folic acid (FA) had the highest variation in DS on G187W concerning WT-MRP4. WT-MRP4, G187W, Y556C, and FA had different conformations through 25 ns AA-MD. Umbrella sampling simulations indicated that the Y556C-FA complex was the most stable one with or without ATP. In Y556C, the cyclic adenosine monophosphate (cAMP) and ceefourin-1 binding sites are located out of the entrance of the inner cavity, which suggests that both cAMP and ceefourin-1 may not be transported. The binding site for cAMP and ceefourin-1 is quite similar and the affinity (binding energy) of ceefourin-1 to WT-MRP4, G187W, and Y556C is greater than the affinity of cAMP, which may suggest that ceefourin-1 works as a competitive inhibitor. In conclusion, the nsSNPs G187W and Y556C lead to changes in protein conformation, which modifies the ligand binding site, DS, and binding energy.     

Modeling the active centers of V<Subscript>2</Subscript>O<Subscript>5</Subscript>/SiO<Subscript>2</Subscript> and V<Subscript>2</Subscript>O<Subscript>5</Subscript>/TiO<Subscript>2</Subscript> supported catalysts. DFT theoretical analysis of optical properties

Within the framework of the density functional theory (DFT), the electronic structure of monooxodioxovanadium functional groups in tetrahedral coordination, which model the active centers (ACs) of fine supported catalysts V₂O₅/SiO₂ and V₂O₅/TiO₂, has been analyzed. The optimal structures of three ACs as possible models of monomeric and polymeric oxovanadium forms on the carriers with low vanadium content were determined. The modified DFT method involving the time dependence of Kohn-Sham equation (TDDFT) was used for the adopted AC models to calculate the energies of the excited states, and optical spectra of the absorption in 25000–60000 cm^?1 region were reconstructed on their base. The spectrum in this region is due to O → V charge transfer. The features of electronic spectra with the charge transfer for V₂O₅/SiO₂ and V₂O₅/TiO₂ catalysts and the vibrational spectra of three AC models corresponding to the monomeric and dimeric oxovanadium forms of the supported catalysts V₂O₅/SiO₂ and V₂O₅/TiO₂ were defined. The detailed interpretation of normal vibration frequencies is given. The frequencies typical of the monomeric and dimeric oxovanadium forms on the carrier surface were identified.     

Ammonia gas sensor based on a spinel semiconductor,Co<Subscript>0.8</Subscript>Ni<Subscript>0.2</Subscript>Fe<Subscript>2</Subscript>O<Subscript>4</Subscript> nanomaterial

Thick film of nanocrystalline Co_0.8Ni_0.2Fe₂O₄ was obtained by sol–gel citrate method for gas sensing application. The synthesized powder was characterized by X-ray diffraction (XRD) and transmission electron microscopy. The XRD pattern shows spinel type structure of Co_0.8Ni_0.2Fe₂O₄. XRD of Co_0.8Ni_0.2Fe₂O₄ revels formation of solid solution with average grain size of about 30 nm. From gas sensing properties it observed that nickel doping improves the sensor response and selectivity towards ammonia gas and very low response to LPG, CO, and H₂S at 280 °C. Furthermore, incorporation of Pd improves the sensor response and stability of ammonia gas and reduced the operating temperature upto 210 °C. The sensor is a promising candidate for practical detector of ammonia.     

Formation of Composites Based on CsHSO<Subscript>4</Subscript> and Cs<Subscript>5</Subscript>H<Subscript>3</Subscript>(SO<Subscript>4</Subscript>)<Subscript>4</Subscript> and Mechanism of Their Protonic Conduction

Vibrational spectra of finely divided amorphous CsHSO₄,Cs₅H₃(SO₄)₄ · H₂O, and composites based on these are measured and analyzed. An analysis of the spectra indicates the occurrence of substantial changes in the system of hydrogen bonds and in the spectral range of the sulfate group of acid sulfates in the composites. Structural dynamics of the SO₄ tetrahedrons is in full conformance with protonic conduction and the data of x-ray diffraction analyses accompanied by differential scanning calorimetry. It is shown that mobility of protons in the composites increases. A mechanism of the formation of the composites and their conduction is proposed.__________Translated from Elektrokhimiya, Vol. 41, No. 5, 2005, pp. 640–645.Original Russian Text Copyright © 2005 by Ponomareva, Lavrova, Burgina.     

Exploring the binding of serotonin to the 5-HT3 receptor by density functional theory

The 5-HT3 receptor is a typical ligand-gated ion channel of the Cys-loop superfamily, which is activated by binding of serotonin (5-HT). Models of the binding site of this protein reveal potential interactions between 5-HT and Tyr143, Tyr153, and Tyr234. Here we describe a series of ab initio calculations, based on density functional theory, to assess the effects of mutating these tyrosine residues on the binding of 5-HT. A series of mutations to these tyrosines, previously studied experimentally, were tested, and the binding energies compared with the available experimental data. Our results show that Tyr153 could form a hydrogen bond with the tertiary amine of 5-HT, and that mutation in this location revealed binding energies broadly in line with experimentally determined EC50s. Tyr143 could also form a hydrogen bond, but as EC50s do not relate to binding energies, it is unlikely that such a bond is formed here. Tyr234 is quite distinct in that it may interact with 5-HT via a mixed hydrogen bond/cation-pi interaction.     

Generation of fullerenyl radicals and chemiluminescence in the (C<Subscript>60</Subscript>—R<Subscript>3</Subscript>Al)—O<Subscript>2</Subscript> system

Fullerenyl radicals (FR) RC₆₀ ^· and chemiluminescence (CL) are generated in the presence of O₂ in C₆₀—R₃Al (R = Et, Buⁱ) solutions in toluene (T = 298 K). The FR are formed due to the addition of the R^· radical, which is an intermediate of R₃Al autooxidation, to C₆₀. Mass spectroscopy and HPLC were used to identify Et_nC₆₀H_m (n, m = 1–6), Et_pC₆₀ (p = 2–6), and dimer EtC₆₀C₆₀Et as stable products of FR transformations. As found by ESR, the EtC₆₀ ^· radical (g = 2.0037) is also generated by photolysis of solutions obtained after interaction in the (C₆₀— R₃Al)—O₂ system. In the presence of dioxygen, the FR is not oxidized but yields complexes with O₂, which appear as broadening of the ESR signals. Chemiluminescence arising in the (C₆₀—R₃Al)—O₂ system is much brighter (I _max = 1.86·10⁸ photon s⁻¹ mL⁻¹) than the known background CL (I _max = 6.0·10⁶ photon s⁻¹ mL⁻¹) for the autooxidation of R₃Al and is localized in a longer-wavelength spectral region (λ_max = 617 and 664 nm). This CL is generated as a result of energy transfer from the primary emitter ³CH₃CHO* to the products of FR transformation: R_nC₆₀H_m, R_pC₆₀, and EtC₆₀C₆₀Et. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 205–213, February, 2007.