Ligand expansion in ligand-based virtual screening using relevance feedback

Query expansion is the process of reformulating an original query to improve retrieval performance in information retrieval systems. Relevance feedback is one of the most useful query modification techniques in information retrieval systems. In this paper, we introduce query expansion into ligand-based virtual screening (LBVS) using the relevance feedback technique. In this approach, a few high-ranking molecules of unknown activity are filtered from the outputs of a Bayesian inference network based on a single ligand molecule to form a set of ligand molecules. This set of ligand molecules is used to form a new ligand molecule. Simulated virtual screening experiments with the MDL Drug Data Report and maximum unbiased validation data sets show that the use of ligand expansion provides a very simple way of improving the LBVS, especially when the active molecules being sought have a high degree of structural heterogeneity. However, the effectiveness of the ligand expansion is slightly less when structurally-homogeneous sets of actives are being sought.     

Electrochemical determinations of 6-mercaptopurine on the surface of a carbon nanotube-paste electrode modified with a cobalt salophen complex

A mixture of multi-walled carbon nanotube/graphite paste electrode modified with a salophen complex of cobalt was prepared and was applied for the study of the electrochemical behavior of 6-mercaptopurine (MP) using cyclic and differential pulse voltammetry (DPV). An excellent electrocatalytic activity toward the oxidation of MP was achieved, which led to a considerable lowering in the anodic overpotential and remarkable increase in the response sensitivity in comparison with unmodified electrode. Utilizing DPV method, a linear dynamic range of 1–100 μM with detection limit of 0.1 μM was obtained in phosphate buffer of pH 3.0. The electrochemical detection system was very stable, and the reproducibility of the electrode response, based on the six measurements during 1 month, was less than 3.0% for the slope of the calibration curves of MP. The electrochemical method as a simple, sensitive, and selective method was developed for the determination of MP in pharmaceutical dosage form and human plasma without any treatments.     

An Ab Initio Study and NBO Analysis of the Stability and Conformational Properties of Hexakis(trimethylelementhyl)benzene (Element = C,Si, Ge,and Sn)

Ab initio molecular orbital and density functional theory were used to investigate energetic and structural properties of the various conformations of hexa-tertbutylbenzene (1), hexakis(trimethylsilyl)benzene (2), hexakis (trimethylgermyl)benzene (3), and hexakis(trimethylstannyl)benzene (4). HF/3-21G//HF/3-21G and B3LYP/3-21G//HF/3-21G results revealed that the Twist-Boat (TB) conformer of compound 1 is more stable than the 1-Chair (C), 1-Boat (B), and 1-Planar (P) conformers. B3LYP/3-21G//HF/3-21G results show that the 1- TB conformer is more stable than 1- C, 1- B, and 1- P conformers of about 1.13, 4.34, and 99.94 kcal mol^?1 , respectively. Contrary to the stability order of compound 1 conformers, the C conformer of compounds 2–4 is more stable than TB, B, and P conformations, as calculated by B3LYP/3-21G//HF/3-21G and HF/3-21G//HF/3-21G levels of theory. The energy gap between the C and P conformers in compounds 1–4 is decreased in the following order: ΔE(4: C, P) < ΔE (3: C, P) < ΔE(2: C, P) < ΔE (1: C, P). This fact can be explained in terms of the increase of C _aromatic -M (M═C, Si, Ge, and Sn) bond lengths and the decrease of steric (van der Waals) repulsions in the previously discussed compounds. For compounds 1–3, the calculations were also performed at the B3LYP/ 6-31G*//HF/3-21G level of theory. However, the comparison showed that the results at B3LYP/3-21G//HF/3-21G methods correlated well with those obtained at the B3LYP/6-31G*// HF/6-31G method. Further, NBO analysis revealed that in compounds 1–4, the resonance energy associated with the σ_M-C1 to σ*_C2-C3 delocalization is 5.20, 9.68, 11.15, and 12.27 kcal mol^?1, respectively. These resonance energy values could explain the easiness of the ring flipping processes of C, B, and TB conformers of compounds 4 to 1. Also, the NBO results showed that by an increase of the σ_M-C1 → σ *_C2-C3 resonance energies in compounds 1–4, the σ_M-C1 bonding orbital occupancies decrease. This fact could fairly explain the increase of the C_aryl-M bond length from compound 1 to 4. The NBO results are also in good agreement with the calculated energy barriers for the ring flipping of the chair conformations in compounds 1–4, as calculated by B3LYP and HF methods.     

Solvent-Free Acetylation of Thiols Under Catalysis of MgBr2·OEt2

Solvent-free protection of aromatic and aliphatic thiols with acetic anhydride was performed at room temperature under trace quantities of magnesium bromide ethyl etherate, affording rapid formation of various thiol esters in excellent yields.     

Crystal-packing trends for a series of 6,9,12,15,18-pentaaryl-1-hydro[60]fullerenes

The relationship between the size of the substituents of aryl groups in a series of fifteen 6,9,12,15,18-pentaaryl-1-hydro[60]fullerenes and the solid-state structures and packing motifs of these compounds has been analyzed. Pentaarylfullerenes have a characteristic "badminton shuttlecock" shape that causes several derivatives to crystallize into columnar stacks. However, many pentaarylfullerenes form non-stacked structures with, for example, dimeric, layered, diamondoid, or feather-in-cavity relationships between molecules. Computational modeling gave a qualitative estimate of the best shape match between the ball and socket surfaces of each pentaarylfullerene. The best match was for pentaarylfullerenes with large, spherically shaped para-substituents on the aryl groups. The series of pentaarylfullerenes was characterized by single-crystal X-ray diffraction. A total of 34 crystal structures were obtained as various solvates and were categorized by their packing motifs.     

Graphene arrested in laponite-water colloidal glass

Graphene production in water from graphite sources is an important technological route toward harvesting the unique properties of this material. Graphene forms thermodynamically unstable dispersions in water, limiting the use of this solvent due to aggregation. We show that graphene-water dispersions can be controlled kinetically to produce graphene by using laponite clay. Laponite exhibits rapid gelation kinetics when dispersed in water above its gelation concentration, allowing graphene aggregation to be halted after exfoliation in water at ambient conditions. The transparency of laponite colloidal glass and films is important in examining the extent of graphene exfoliation.     

Determination of tryptophan in raw materials, rat brain and human plasma by RP-HPLC technique

This paper describes tryptophan (TRP) estimation in raw human plasma and rat brain by reversed-phase high-performance liquid chromatography (RP-HPLC). Estimation was carried out on a Purospher STAR C18 column using water-acetonitrile (90:10 v/v, at pH 2.7) mixture at a rate of 1.5 mL/min as mobile phase. Eluents were monitored at 273 nm by an ultraviolet detector. The method was linear (R(2) > 0.999), precise (intra-day and inter-day precision <2%) in the range of 0.25-20 μg/mL. The detection and quantification limits were 0.0144 μg/mL and 0.0437 μg/mL, respectively. In human plasma, Day 1 and Day 2 precision were 0.054-2.29% and 1.66-3.7%; whereas precisions in rat brain were 1.23-2.3% and 0.677-4.2%, respectively. The method was applied to study TRP level in human smokers and in arthritic rat brain. An efficient RP-HPLC method was developed for TRP determination that worked for clinical and research purposes.     

A New and Simple Electrocatalyst for Formaldehyde Oxidation; Nickel/poly(o‐Anisidine)/Film Modified Ionic Liquid Carbon Paste Electrode

In present work, the ionic liquid, 1‐butyl‐3‐methylimidazolium bis (trifluoromethylsulfonyl) imide was incorporated in the carbon paste electrode as the binder (IL‐CPE). O‐anisidine (OA) monomer is electropolymerized in the presence of an aqueous acidic solution onto IL‐CPE (POA/IL‐CPE). The as‐prepared substrate is used as a porous matrix for dispersion of Ni(II) ions by immersing the modified electrode in a nickel(II) nitrite solution. The modified electrodes are characterized by scanning electron microscopy (SEM) and electrochemical methods. The POA/IL‐CPE was applied successfully to highly efficient (current density of 18.2 mA cm^?2) electrocatalytic oxidation of formaldehyde in alkaline medium. Finally, the rate constant for chemical reaction between formaldehyde and redox sites of the electrode was calculated.     

Diammonium Hydrogen Phosphate: An Efficient and Versatile Catalyst for the One‐Pot Synthesis of Tetrahydrobenzo[b]pyran Derivatives in Aqueous Media

Diammonium hydrogen phosphate was used as a mild, efficient, neutral, and cheap catalyst for the synthesis of various 4H‐benzo[b]pyran derivatives via a one‐pot, three‐component condensation of aromatic aldehydes, active methylene compounds, and dimedone in aqueous media.