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Protein-protein complexes play an important role in the physiology and the pathology of cellular functions, and therefore are attractive therapeutic targets. A small subset of residues known as “hot spots”, accounts for most of the protein-protein binding free energy. Computational methods play a critical role in identifying the hotspots on the proteinprotein interface. In this paper, we use a computational alanine scanning method with all-atom force fields for predicting hotspots for 313 mutations in 16 protein complexes of known structures. We studied the effect of force fields, solvation models, and conformational sampling on the hotspot predictions. We compared the calculated change in the protein-protein interaction energies upon mutation of the residues in and near the protein-protein interface, to the experimental change in free energies. The AMBER force field (FF) predicted 86% of the hotspots among the three commonly used FF for proteins, namely, AMBER FF, Charmm27 FF, and OPLS-2005 FF. However, AMBER FF also showed a high rate of false positives, while the Charmm27 FF yielded 74% correct predictions of the hotspot residues with low false positives. Van der Waals and hydrogen bonding energy show the largest energy contribution with a high rate of prediction accuracy, while the desolvation energy was found to contribute little to improve the hot spot prediction. Using a conformational ensemble including limited backbone movement instead of one static structure leads to better predicttion of hotpsots.

The synthesis of 4,4′-arylmethylene-bis(3-(trifluoromethyl)-1-phenyl-1 H -pyrazol-5-ol) was performed effectively in aqueous media without catalyst by the reaction of aryl aldehydes and 1-phenyl-3-trifluoromethylpyrazol-5-one. All of the compounds obtained were characterized by elemental analysis, FTIR and 1 H NMR. The structure of compound 3g was further confirmed by the X-ray single crystal diffraction. The method has the advantages of mild condition, without any catalyst, high yields and environmentally benign procedure.

A series of novel alpha,alpha,alpha-trifluoro-m-tolyl pyridazinone derivatives was synthesised. Herbicidal activities of the two intermediate compounds and 15 pyridazinone derivatives were evaluated through barnyardgrass and rape cup tests and Spirodela polyrrhiza (L.) Schleiden tests. Selected compounds were also evaluated under greenhouse conditions. Bleaching activities were observed at 10 microg ml(-1) and some compounds exhibited herbicidal activities at a rate of 300 g ha(-1). The relationship between crystal structures and herbicidal activities is discussed through a comparison of two compounds (5a and 5f).

The structures of methyl 5-[2-chloro-4-(trifluoromethyl)phenoxy]-2-nitrobenzoate, C15H9ClF3N3O5, (I), methyl 2-chloro-5-[3-methyl-2,6-dioxo-4-(trifluoromethyl)-1,2,3,6-tetrahydropyrimidin-1-yl]benzoate, C14H10ClF3N2O4, (II), and 2-[4-chloro-2-fluoro-5-(prop-2-ynyloxy)phenyl]-4-(trifluoromethyl)piperidine-2,6-dione, C15H10ClF4NO3, (III), are similar in their dihedral angles and in the distances between the farthest two atoms. There are two independent molecules in the structure of (I). The dihedral angles between the two aromatic rings in each molecule in (I), between the benzene and tetrahydropyrimidine rings in (II), and between the benzene ring and the five-atom planar portion of the piperidine-2,6-dione ring in (III) are 80.78 (11)/89.75 (11), 89.13 (9) and 87.52 (13) degrees , respectively. The distances between the farthest two atoms, viz. O...F in the two molecules of (I), and Cl...F in (II) and (III), are 11.763 (7)/11.953 (6), 10.734 (10) and 10.889 (9) A, respectively. In all three crystal structures, the molecules are linked to generate sheets of molecules via C-H...O interactions.

The molecular structures of 2-[4-chloro-2-fluoro-5-(prop-2-ynyloxy)phenyl]-1,3,4,5,6,7-hexahydroisoindole-1,3-dione, C17H13ClFNO3, (I), and the isomeric compound 2-[4-chloro-2-fluoro-5-(prop-2-ynyloxy)phenyl]-cis-1,3,3a,4,7,7a-hexahydroisoindole-1,3-dione, (II), are, as anticipated, significantly different in their conformations and in the distances between the farthest two atoms. The six-membered ring of the 1,3,4,5,6,7-hexahydroisoindole-1,3-dione moiety in (I) adopts a half-chair conformation. The dihedral angle between the five-membered dione ring of (I) and the benzene ring is 50.96 (7) degrees . The six-membered ring of the cis-1,3,3a,4,7,7a-hexahydroisoindole-1,3-dione moiety in (II) adopts a boat conformation. The dihedral angle in (II) between the five-membered dione ring and the benzene ring is 61.03 (13) degrees . In the crystal structures, the molecules are linked by C-H...O hydrogen bonds and weak pi-pi interactions. Compound (I) is a much more potent herbicide than (II). The Cl...H distances between the farthest two atoms in (I) and (II) are 11.37 and 9.97 A, respectively.

The retention characteristics of 25 2-cyano-3-methylthio-3substituted amine-acrylates are determined using reversed-phase thin-layer chromatography (RP-TLC) with methanol‐water mixtures as eluents. The relationship between R m values and partition coefficients (C log P ) are established. The R m values decrease linearly with increasing methanol concentration in the eluent. The R m values extrapolated to zero organic modifier concentration (R m0 ) in the eluent are highly related to C log P. The R m0 value can be used to evaluate the lipophilicity of this kind of compound.

A series of fourteen O-ethyl O-phenyl N-isopropyl phosphoroamidothioate enantiomers containing a phosphorus atom as a chiral center have been separated by high-performance liquid chromatography on a Pirkle model chiral stationary phase. Chromatography data, the capacity factor (k′) and the separation factor (α) of all solutes are presented. The influence of chromatographic conditions was investigated. The probable mechanism for chiral recognition is proposed.

A series of 2-(3-(trifluoromethyl)-5-(alkoxy)-1H-pyrazol-1-yl)-4-aryloxypyrimidine derivatives were designed and synthesized. The structures of all the title compounds were confirmed by 1H NMR and elementary analysis. These compounds were screened for herbicidal activity against rape and barnyard grass. Compound B13 exhibited moderate herbicidal activity.

A series of novel 6,7,8,9-tetrahydro-2-(2-aryloxypyrimidin-4-yl)-2H-[1,2,4]triazolo[4,3-a]azepin-3(5H)-ones were designed and efficiently synthesized. Their structures were determined by IR, 13C and 1H NMR, mass spectroscopy, and elemental analysis. These compounds were screened for herbicidal activities against rape and barnyard grass. Compounds 5a-5f and 5m exhibited moderate herbicidal activity against rape. In addition, the synthesis of the intermediate 1-(azepan-2-ylidene)-2-(2-chloropyrimidin-4-yl)-hydrazine (3) was studied and the reason for the low yield in the initial procedure is discussed as well.

Ethyl 5-amino-3-trifluoromethyl-1H-pyrazole-4-carboxylate (1) was efficiently synthesized via the condensation of ethyl cyanoacetate and trifluoroacetic anhydride, followed by chloridization and the condensation with aqueous hydrazine. Its unique reactivity was exploited for the synthesis of trifluoromethylated pyrazolo[1,5-a]pyrimidine (5) and pyrazolo[5,1-d][1,2,3,5]tetrazine-4(3H)-ones (8a–j). Among them, 5 was firstly found to be a novel fluorescent molecule that might be exploited as an attractive fluorophore for possessing many binding sites, and its fluorescence intensity was obviously stronger than its methyl analogue. 8 were found to be a new chemical class of potential monocotyledonous Echinochloa crus-galli L. Beauv inhibitors, and were more active than their methyl analogues.

A series of novel sulfone-containing pyrazolo[1,5-a]pyrimidines (2-3) and pyrazolo[5,1-d][1,2,3,5]tetra-zine-4(3H)-ones (5a-5k) were designed and efficiently synthesized, some of which have been identified as being potential rape inhibitors. These results widen the structural diversity of rape inhibitors and confirm the perspectives of further investigations in this area. Moreover, a plausible reaction mechanism is outlined.

The molecular structures of ethyl 5-amino-3-(4,6-dimethylpyrimidin-2-ylamino)-1-methyl-1H-pyrazole-4-carboxylate, C13H18N6O2, (I), and ethyl 5-amino-3-(4,6-dimethylpyrimidin-2-ylamino)-1-(2-nitrophenylsulfonyl)-1H-pyrazole-4-carboxylate, C18H19N7O6S, (II), have been determined. There are two intramolecular N-H...O bonds and one intermolecular N-H...O hydrogen bond in (I). The rings formed by the N-H...O hydrogen bonds are almost planar. In (II), three intramolecular N-H...O hydrogen bonds exist.

Phytoalexins are low-molecular-weight chemicals that immune systems of plants produce and accumulate in response to infections, especially those of fungal origin. Although their content is not high in plants, yet they have shown unique fungicidal activity and played an important role in the defence system of plants. In searching for novel environmentally benign fungicides with high activity, the structures of flavanone derivatives, one of the most important phytoalexins groups, have been modified via bioisosteric substitution and a series of 2-heteroaryl-4-chromanones were designed and synthesized. They showed good fungicidal activities against rice blast disease, Pyricularia grisea (Sacc). Their IC50 values were tested in vitro and the relationship between structure and fungicidal activity was analyzed quantitatively using a Hansch–Fujita approach. The results showed that hydrophobicity was very important for fungicidal activity and there is apparently an optimum hydrophobic property for the molecules at a log Pow value of about 2.7. In addition, the results indicated that electronic effects played an important role in binding with the receptor and that the CO group was probably a electron-accepting site. The quantitative structure–retention correlative equation of the title compounds was also established. © 2002 Society of Chemical Industry