Screening of xanthine oxidase inhibitors in complex mixtures using online HPLC coupled with postcolumn fluorescence‐based biochemical detection

Xanthine oxidase (XO) catalyzes the metabolism of hypoxanthine and xanthine to uric acid, the overproduction and/or underexcretion of which could cause the incidence of hyperuricemia such as gout. Herein, the inhibition of XO is recognized as one of the therapeutic approaches to treat gout. In the present study, an off‐line fluorescence‐based microplate method was first developed for an XO assay in which the enzyme converted pterin to its fluorescent metabolite isoxanthopterin. Then, a postcolumn continuous XO assay as a means of bioactivity assessment was coupled to HPLC separation to establish the online HPLC with diode array detection, biochemical detection, and MS/MS system for the screening of XO inhibitors. The availability of the online system was first tested with a positive drug, allopurinol, a well‐known XO inhibitor, and subsequent analysis of Scutellaria baicalensis extract showed that two main bioactive compounds with XO inhibitory activities were observed, indicating that the developed online system was applicable to complex mixtures.     

Own N-layered integrated molecular orbital and molecular mechanics study of the reaction of OH<Superscript>−</Superscript> with polychlorinated hydrocarbons CH<Subscript>(4−n)</Subscript>Cl<Subscript>n</Subscript> (n=2–4)

The reliability of the two-layer own N-layered integrated molecular orbital and molecular mechanics (ONIOM) method was examined for the S_N2 reaction CH_(4–n)Cl_n+OH^–. In the ONIOM calculation, only the methyl chloride and OH^–were treated at a high level and the effect of polychlorination was taken into account only at a low level. The ONIOM results were compared with the target CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ results obtained by Borisov etal. [(2001) J. Phys. Chem. A 105:7724]. The ONIOM[MP2/aug-cc-pVDZ:B3LYP/6-31+G(d)] was found to reproduce well the target geometry and energy at the MP2/aug-cc-pVDZ level. The single-point improved energetics at the ONIOM[CCSD(T)/aug-cc-pVDZ:MP2/6-31+G(d)] is found to give results nearly as accurate as the target CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ results. The substantially reduced cost, 20% for optimization and 5% for single-point improved energy of the target cost for n=4, as well as small errors suggest that ONIOM is a powerful tool for accurate potential-energy surfaces of the reaction of large polyhalohydrocarbons.     

ONIOM and FMO‐EDA study of metabotropic glutamate receptor 1: Quantum insights into the allosteric binding site

The crystal structure of metabotropic glutamate receptor 1 (mGluR1) complexed with 4‐fluoro‐N‐(4‐(6‐(isopropylamino)pyrimidin‐4‐yl)thiazol‐2‐yl)‐N‐methylbenzamide (FITM, a negative allosteric modulator) and its twelve close structural analogs with a broad spectrum of affinities (2.4 nM < IC₅₀ > 10 000 nM) were investigated using quantum mechanical methods. The our own N‐layered integrated molecular orbital and molecular mechanics (ONIOM) was used to optimize the molecular geometries of the receptor with complexed ligands, which were then used to perform the ab initio calculations using the fragment molecular orbitals method with energy decomposition analysis (FMO‐EDA). The results clearly showed that residues Q660^3.28 and/or Y805^6.55 were the anchoring points for all the studied analogs of FITM, while the H‐bond with T815^7.38 determined only the orientation of very active molecules containing an amino substituent in the pyrimidine moiety (e.g., FITM). The orientation of the other parts of ligands resulted from hydrophobic interactions mainly with L757^5.44, F801^6.51, or W798^6.48. The applied ONIOM/FMO–EDA approach facilitated the study of effects related to very small changes in the ligand structure and led to conclusions regarding the significance of individual interactions in the allosteric binding pocket of mGluR1.     

Infinite Basis Set Extrapolation for Double Hybrid Density Functional Theory 2: Effect of Adding Diffuse Basis Functions

We applied the Infinite Basis (IB) set extrapolation and Double Hybrid Density Functional Theory (DHDF) to calculate the electron affinities, reaction barrier heights, proton affinities, non‐covalent interactions, atomization, ionization, and alkyl bond dissociation energies. We previously found that the mean unsigned error of the B2KPLYP‐IB calculation with the combination of cc‐pVTZ and cc‐pVQZ reach the chemical accuracy limit (～2 kcal/mol) where the largest deviation occurred in the electron affinity calculations and the weak interactions between noble gases and nonpolar molecules. Here, we investigated the basis set effect using the B2KPLYP‐IB extrapolation scheme that involves (1) the addition of extra tight d basis functions to the second row elements (i.e. cc‐pV(L+d)Z), (2) the addition of extra s, p, and d diffuse basis functions, and (3) a comparison between Dunning's Correlation Consistent and Jensen's Polarization Consistent (pc‐L) basis sets. We found that the addition of extra s and p diffuse basis functions formed the minimal augmented basis sets proposed by Truhlar. This addition permitted the B2KPLYP‐IB to reach the chemical accuracy limit with the combination of the double ζ and triple ζ basis sets. Adding extra s, p diffuse functions to the pc‐L series permitted only a small improvement. This small improvement is due to the fact that the pc‐L basis sets already contain a large number of functions for the p block elements. Taken together, the results suggest that this minimal augmented basis sets is useful for due to its accuracy and affordable computational cost.     

Prediction of pKas of Late Transition-Metal Hydrides via a QM/QM Approach

Three implicit solvation models, the conductor-like polarizable continuum model (C-PCM), the conductor-like screening model (COSMO), and universal implicit solvent model (SMD), combined with a hybrid two layer QM/QM approach (ONIOM), were utilized to calculate the pK_a values, using a direct thermodynamic scheme, of a set of Group 10 transition metal (TM) hydrides in acetonitrile. To obtain the optimal combination of quantum methods for ONIOM calculations with implicit solvation models, the influence of factors, such as the choice of density functional and basis set, the atomic radii used to build a cavity in the solvent, and the size of the model system in an ONIOM scheme, was examined. Additionally, the impact of Grimme's empirical dispersion correction and exact exchange was also investigated. The results were calibrated by experimental data. This investigation provides insight about effective models for the prediction of thermodynamic properties of TM-containing complexes with bulky ligands. © 2019 Wiley Periodicals, Inc.     

黄烷类衍生物的合成及其生物活性研究

An efficient and feasible synthetic approach was developed for the synthesis of an array of new flavane derivafives from the substituted benzaldehyde with the reduction of chalcones and subsequent cyclization as the key steps. The purity and structure of the products were confirmed by the elemental analysis and a combination of its IR, ^1H and ^13C NMR, and mass spectra. These synthetic compounds were tested for xanthine oxidase （XO） inhibitions and antifungal actions against Candida albicans, Cryptococcus neoformans, Aspergillus sp. and Trichophyton rubrum. 7-Hydrazinocarbonylmethoxy-4＇-methoxyflavane （9） was found to be the most XO inhibitory with IC50=76.4 μmol/L, and the most potent antifungal compound was 4＇-hydrazinocarbonylmethoxyflavane （12） with minimal inhibition concentration MIC=8 μg/mL against Trichophyton rubrum.     

Theoretical study of the SN2 reaction of Cl−(H2O)+CH3Cl using our own N-layered integrated molecular orbital and molecular mechanics polarizable continuum model method (ONIOM, PCM)

The effects of solvation in the S_N2 reaction Cl^–(H₂O)+CH₃Cl were investigated using our own N-layered integrated molecular orbital and molecular mechanics (ONIOM) polarizable continuum model (PCM) method [Vreven T, Mennucci B, da Silva CO, Morokuma K, Tomasi J (2001) J Chem Phys 115:62–72], which surrounds the microsolvated ONIOM system with a polarizable continuum. The microsolvating water molecule tends to stay in the vicinity of the original chloride ion. In the ONIOM calculations, Cl^–+CH₃Cl was considered as the model system and was handled with the high-level method, while the explicit water molecule in the microsolvated complex was treated at the low-level. The molecular orbital (MO) and ONIOM(MO:MO) calculations allow us to assess the errors introduced by the ONIOM extrapolation, as well as the effects of microsolvation on the potential-energy surfaces. We find that ONIOM[B3LYP/6-31+G(d,p):HF/6-31+G(d,p)] and ONIOM[B3LYP/6-31+G(d,p):HF/6-31+G(d,p)]-PCM methods are good approximations to the target B3LYP/6-31+G(d,p) and B3LYP/6-31+G(d,p)-PCM methods. In addition, several approximate (computationally less expensive) schemes in the ONIOM-PCM method have been compared to the exact scheme, and all are shown to perform well.Contribution to the Jacopo Tomasi Honorary Issue     

Construction of hole‐transported MoO3‐x coupled with CdS nanospheres for boosting photocatalytic performance via oxygen‐defects‐mediated Z‐scheme charge transfer

The establishment of Z‐scheme charge transfer between semiconductors is an effective method to improve the performance of hybridized semiconductor photocatalysts. Herein, the novel photocatalysts consisting of MoO_3‐x and varying amounts of cadmium sulfide (CdS) nanospheres were successfully prepared via the one‐pot hydrothermal method in the presence of polyvinylpyrrolidone (PVP). It is indicated that the PVP not only served as the reducing agent for the formation of oxygen defects in MoO_3‐x, but also the cross‐linking agent for the coupling between MoO_3‐x and CdS. The CdS/MoO_3‐x composite allowed for higher visible‐light photocatalytic performance for enhanced removal of methylene blue and tetracycline with an efficiency of 97.6% and 85.5%, respectively. The improved performance of the CdS/MoO_3‐x composite was found to be mainly attributable to the remarkable charge carrier separation and transfer between CdS and MoO_3‐x based on the favorable hole‐transporting nature and oxygen deficiencies of MoO_3‐x. In addition, the hole‐oxidized photocorrosion of CdS was efficiently suppressed due to the presence of hole‐attractive MoO_3‐x. At the solid interface, an oxygen‐defects‐mediated Z‐scheme charge carrier transfer pathway was proposed as the underlying mechanism for the superior photocatalytic reaction.     

On the use of symmetry in the ab initio quantum mechanical simulation of nanotubes and related materials

Nanotubes can be characterized by a very high point symmetry, comparable or even larger than the one of the most symmetric crystalline systems (cubic, 48 point symmetry operators). For example, N = 2n rototranslation symmetry operators connect the atoms of the (n,0) nanotubes. This symmetry is fully exploited in the CRYSTAL code. As a result, ab initio quantum mechanical large basis set calculations of carbon nanotubes containing more than 150 atoms in the unit cell become very cheap, because the irreducible part of the unit cell reduces to two atoms only. The nanotube symmetry is exploited at three levels in the present implementation. First, for the automatic generation of the nanotube structure (and then of the input file for the SCF calculation) starting from a two‐dimensional structure (in the specific case, graphene). Second, the nanotube symmetry is used for the calculation of the mono‐ and bi‐electronic integrals that enter into the Fock (Kohn‐Sham) matrix definition. Only the irreducible wedge of the Fock matrix is computed, with a saving factor close to N. Finally, the symmetry is exploited for the diagonalization, where each irreducible representation is separately treated. When M atomic orbitals per carbon atom are used, the diagonalization computing time is close to Nt, where t is the time required for the diagonalization of each 2M × 2M matrix. The efficiency and accuracy of the computational scheme is documented. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

An ONIOM and DFT study of water and ammonia adsorption on anatase TiO2 (001) cluster

Density functional theory (DFT) calculations at ONIOM DFT B3LYP/ 6‐31G**‐MD/UFF level are employed to study molecular and dissociative water and ammonia adsorption on anatase TiO₂ (001) surface represented by partially relaxed Ti₂₀O₃₅ ONIOM cluster. DFT calculations indicate that water molecule is dissociated on anatase TiO₂ (001) surface by a nonactivated process with an exothermic relative energy difference of 58.12 kcal/mol. Dissociation of ammonia molecule on the same surface is energetically more favorable than molecular adsorption of ammonia (?37.17 kcal/mol vs. ?23.28 kcal/mol). The vibration frequency values also are computed for the optimized geometries of adsorbed water and ammonia molecules on anatase TiO₂ (001) surface. The computed adsorption energy and vibration frequency values are comparable with the values reported in the literature. Finally, several thermodynamical properties (ΔH°, ΔS°, and ΔG°) are calculated for temperatures corresponding to the experimental studies. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Evaluation of the ONIOM(B3PW91:HF) hybrid method for modeling butyltin chlorides

The ONIOM(B3PW91:HF) hybrid method has been evaluated for the purposes of modeling butyltin chlorides, X_nSnCl_4-n (X = n-butyl, sec-butyl, isobutyl, tert-butyl; n = 1, 2, 3). Three different partitioning schemes of a molecule within ONIOM(B3PW91:HF) were taken into account. For each of these partitioning schemes, conformational analyses of the X_nSnCl_4-n molecules were performed and then several molecular properties of the resulting rotamers were calculated. The values of molecular properties obtained by ONIOM(B3PW91:HF) were compared in a statistical manner with the reference values calculated by B3PW91. A careful choice of partitioning scheme for X_nSnCl_4-n allowed ONIOM(B3PW91:HF) to achieve a significant saving in computational cost, together with a relatively small decrease in the accuracy of the X_nSnCl_4-n molecular properties routinely obtained from conformational analysis (structural parameters, etc.). Unfortunately, the hybrid method turned out to be ineffective in reproducing the ¹H, ¹³C and ¹¹⁹Sn NMR chemical shifts in X_nSnCl_4-n accurately.      

Systematic Study of Selected Diagonalization Methods for Configuration Interaction Matrices

Several modifications to the Davidson algorithm are systematically explored to establish their performance for an assortment of configuration interaction (CI) computations. The combination of a generalized Davidson method, a periodic two‐vector subspace collapse, and a blocked Davidson approach for multiple roots is determined to retain the convergence characteristics of the full subspace method. This approach permits the efficient computation of wave functions for large‐scale CI matrices by eliminating the need to ever store more than three expansion vectors ( b _i) and associated matrix‐vector products ( σ _i), thereby dramatically reducing the I/O requirements relative to the full subspace scheme. The minimal‐storage, single‐vector method of Olsen is found to be a reasonable alternative for obtaining energies of well‐behaved systems to within μE_h accuracy, although it typically requires around 50% more iterations and at times is too inefficient to yield high accuracy (ca. 10^?10 E_h) for very large CI problems. Several approximations to the diagonal elements of the CI Hamiltonian matrix are found to allow simple on‐the‐fly computation of the preconditioning matrix, to maintain the spin symmetry of the determinant‐based wave function, and to preserve the convergence characteristics of the diagonalization procedure. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1574–1589, 2001     

The H‐Bond activation mechanism and enantioselectivity in stepwise conjugate amine addition promoted by hydroxyl‐thiourea catalyst

The H‐bond activation mechanism and enantioselectivity of hydroxyl‐thiourea catalyst in conjugate amine addition of O‐benzyl hydroxylamine to pyrazole crotonate is investigated using density functional theory (DFT) calculations. Two competing activation models are explored in detail. C? N bond formation is stepwise in both of the two models. The enantioselective (S)‐channel is more favorable than (R)‐channel via the calculated barriers. The enantioselectivity originated from si face preferable than re face can be attributed to the H‐bonded network provided by thiourea and hydroxyl groups in rate‐determining step. The enantiomeric excess (ee) values predicted through ONIOM calculations are in line with the experiment. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

On the accuracy factors and computational cost of the GIAO–DFT calculation of 15N NMR chemical shifts of amides

The main factors affecting the accuracy and computational cost of Gauge‐independent Atomic Orbital–density functional theory (GIAO–DFT) calculation of ¹⁵N NMR chemical shifts in the benchmark series of 16 amides are considered. Among those are the choice of the DFT functional and basis set, solvent effects, internal reference conversion factor and applicability of the locally dense basis set (LDBS) scheme. Solvent effects are treated within the polarizable continuum model (PCM) scheme as well as at supermolecular level with solvent molecules considered in explicit way. The best result is found for Keal and Tozer's KT3 functional used in combination with Jensen's pcS‐3 basis set with taking into account solvent effects within the polarizable continuum model. The proposed LDBS scheme implies pcS‐3 on nitrogen and pc‐2 elsewhere in the molecule. The resulting mean average error for the calculated ¹⁵N NMR chemical shifts is about 6 ppm. The application of the LDBS approach tested in a series of 16 amides results in a dramatic decrease in computational cost (more than an order of magnitude in time scale) with insignificant loss of accuracy.     

Flotation‐Spectrophotometric Determination of Trace Amounts of Thorium

A simple, sensitive and reproducible flotation‐spectrophotometric method for the determination of thorium is reported. The method is based on the ion‐associate formation between thorium, xylenol orange (XO) and cethyltrimethyl ammonium bromide (CTAB) which is floated in the interface of the aqueous phase and n‐hexane by vigorous shaking. By discarding the aqueous solution and n‐hexane, the adsorbed ion‐associate (Th‐XO‐CTAB) on the wall of a separating funnel was dissolved in a small volume of ethanol solvent, and its absorbance was measured at 568 nm. The effects of different parameters such as pH, concentrations of HCl, XO, and CTAB, volume of n‐hexane, and standing and shaking time were studied. The calibration graph was linear in the concentration range of 2–200 ng mL^?1 of thorium(r = 0.9994). The limit of detection (LOD) is 1.4 ng mL^?1. The relative standard deviations (RSD) at 50 and 175 ng mL^?1 of thorium were 2.5% and 1.0% (n = 7), respectively. The method was successfully applied to the determination of thorium in gas mantel samples.     

DOX: A new computational protocol for accurate prediction of the protein–ligand binding structures

Molecular docking techniques have now been widely used to predict the protein–ligand binding modes, especially when the structures of crystal complexes are not available. Most docking algorithms are able to effectively generate and rank a large number of probable binding poses. However, it is hard for them to accurately evaluate these poses and identify the most accurate binding structure. In this study, we first examined the performance of some docking programs, based on a testing set made of 15 crystal complexes with drug statins for the human 3‐hydroxy‐3‐methylglutaryl coenzyme A reductase (HMGR). We found that most of the top ranking HMGR–statin binding poses, predicted by the docking programs, were energetically unstable as revealed by the high theoretical‐level calculations, which were usually accompanied by the large deviations from the geometric parameters of the corresponding crystal binding structures. Subsequently, we proposed a new computational protocol, DOX, based on the joint use of molecular Docking, ONIOM, and eXtended ONIOM (XO) methods to predict the accurate binding structures for the protein–ligand complexes of interest. Our testing results demonstrate that the DOX protocol can efficiently predict accurate geometries for all 15 HMGR‐statin crystal complexes without exception. This study suggests a promising computational route, as an effective alternative to the experimental one, toward predicting the accurate binding structures, which is the prerequisite for all the deep understandings of the properties, functions, and mechanisms of the protein–ligand complexes. © 2015 Wiley Periodicals, Inc.