We have developed a new method, i.e., XLOGP3, for logP computation. XLOGP3 predicts the logP value of a query compound by using the known logP value of a reference compound as a starting point. The difference in the logP values of the query compound and the reference compound is then estimated by an additive model. The additive model implemented in XLOGP3 uses a total of 87 atom/group types and two correction factors as descriptors. It is calibrated on a training set of 8199 organic compounds with reliable logP data through a multivariate linear regression analysis. For a given query compound, the compound showing the highest structural similarity in the training set will be selected as the reference compound. Structural similarity is quantified based on topological torsion descriptors. XLOGP3 has been tested along with its predecessor, i.e., XLOGP2, as well as several popular logP methods on two independent test sets: one contains 406 small-molecule drugs approved by the FDA and the other contains 219 oligopeptides. On both test sets, XLOGP3 produces more accurate predictions than most of the other methods with average unsigned errors of 0.24-0.51 units. Compared to conventional additive methods, XLOGP3 does not rely on an extensive classification of fragments and correction factors in order to improve accuracy. It is also able to utilize the ever-increasing experimentally measured logP data more effectively.
For theoreticians, ionic liquids represent a major challenge. This is due to the fact that intermolecular interactions are particularly strong because of ionic liquids' ionicity. This, in turn, causes a subtle interplay between different scales which is encoded in the measured macro- and mesoscopic properties and also in the molecular electrostatic characteristics. Therefore, force fields have to describe the microscopic processes correctly in order to reproduce macroscopic properties accurately over a large range of state variables. Herein, imidazolium-based ionic liquids were studied at different scales, going from the detailed quantum electronic scale to the classical atomistic scale. It is indicated how the information gained at each level could be used for the other scales. In particular, the issue of deriving suitable partial charges for use in classical force fields is addressed. The Blöchl method was employed to generate partial charges reproducing the multipole distribution accurately for bulk systems. This led naturally to absolute ionic charges of less than /l e/, i.e., charge scaling. So, the monopole structure of the herein introduced force field mimics the quantum chemical behaviour observed in the liquid phase. This led to a substantial improvement in the description of dynamical properties of immediate experimental interest, such as electric conductivity. For further insight, the electric dipole moment of the ions was taken as physical indicator of their electronic structure. The electric dipole moment was found to fluctuate strongly and to depend on polarisation. Hence, our scale-combined study offers a gateway to rational design of models, based on the relevant underlying physics rather than on mere numerical parameterisation, and thereby to (possibly) more direct physical interpretation of experimental results.
There are very few root genes that have been described in rice as a monocotyledonous model plant so far. Here, the OsRAA1 (Oryza sativa Root Architecture Associated 1) gene has been characterized molecularly. OsRAA1 encodes a 12.0-kD protein that has 58% homology to the AtFPF1 (Flowering Promoting Factor 1) in Arabidopsis, which has not been reported as modulating root development yet. Data of in situ hybridization and OsRAA1::GUS transgenic plant showed that OsRAA1 expressed specifically in the apical meristem, the elongation zone of root tip, steles of the branch zone, and the young lateral root. Constitutive expression of OsRAA1 under the control of maize (Zea mays) ubiquitin promoter resulted in phenotypes of reduced growth of primary root, increased number of adventitious roots and helix primary root, and delayed gravitropic response of roots in seedlings of rice (Oryza sativa), which are similar to the phenotypes of the wild-type plant treated with auxin. With overexpression of OsRAA1, initiation and growth of adventitious root were more sensitive to treatment of auxin than those of the control plants, while their responses to 9-hydroxyfluorene-9-carboxylic acid in both transgenic line and wild type showed similar results. OsRAA1 constitutive expression also caused longer leaves and sterile florets at the last stage of plant development. Analysis of northern blot and GUS activity staining of OsRAA1::GUS transgenic plants demonstrated that the OsRAA1 expression was induced by auxin. At the same time, overexpression of OsRAA1 also caused endogenous indole-3-acetic acid to increase. These data suggested that OsRAA1 as a new gene functions in the development of rice root systems, which are mediated by auxin. A positive feedback regulation mechanism of OsRAA1 to indole-3-acetic acid metabolism may be involved in rice root development in nature.The growth and development of crops depend on their roots to take up water and nutrient material from soil. The root system of rice (Oryza sativa) consists of embryonic and postembryonic roots. The rice embryonic roots, originating from the radical, emerge after germination. They develop into two forms, one primary root and several seminal roots. Postembryonic roots include adventitious roots that are formed from nodes of the plant and lateral roots that develop on all root types.As is known, plant hormone auxin (indole-3-acetic acid [IAA]) plays an important role in controlling root development, such as inhibiting elongation of a primary root and promoting formation of adventitious roots, lateral roots, and root hairs. In Arabidopsis, it has been reported that genes involved in the auxin signal transduction pathway are able to control the development of roots. For example, mutants of the AUX/IAA gene family, such as SHY2/IAA3, SLR1/ IAA14, IAA28, and MSG2/IAA19, show reduced lateral roots or no lateral roots (for review, see Reed, 2001). Overexpression of AUX1, TIR1, or NAC1 can promote lateral root development (Gray et al., 1999;Xie et al., 2000;Marchant et al., 2002). ...
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