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991.
A series of N4X (X = O, S, Se) compounds have been examined with ab initio and density functional theory (DFT) methods. To our knowledge,
these compounds, except for the C2v ring and the C3v towerlike isomers of N4O, are first reported here. The ring structures are the most energetically favored for N4X (X = O and S) systems. For N4Se, the cagelike structure is the most energetically favored. Several decomposition and isomerization pathways for the N4X species have been investigated. The dissociation of C2v ring N4O and N4S structures via ring breaking and the barrier height are only 1.1 and −0.2 kcal mol−1 at the CCSD(T)/6-311+G*//MP2/6-311+G* level of theory. The dissociation of the cagelike N4X species is at a cost of 12.1–16.2 kcal mol−1. As for the towerlike and triangle bipyramidal isomers, their decomposition or isomerization barrier heights are all lower
than 10.0 kcal mol−1. Although the CS cagelike N4S isomer has a moderate isomerization barrier (18.3–29.1 kcal mol−1), the low dissociation barrier (−1.0 kcal mol−1) indicates that it will disappear when going to the higher CCSD(T) level.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
992.
Three-dimensional quantitative structure-activity relationship (3D-QSAR) analyses using CoMFA and CoMSIA methods were conducted
on a series of fluoropyrrolidine amides as dipeptidyl peptidase IV (DP-IV) inhibitors. The selected ligands were docked into
the binding site of the 3D model of DP-IV using the GOLD software, and the possible interaction models between DP-IV and the
inhibitors were obtained. Based on the binding conformations of these fluoropyrrolidine amides and their alignment inside
the binding pocket of DP-IV, predictive 3D-QSAR models were established by CoMFA and CoMSIA analyses, which had conventional
r
2 and cross-validated coefficient values () up to 0.982 and 0.555 for CoMFA and 0.953 and 0.613 for CoMSIA, respectively. The predictive ability of these models was
validated by six compounds that were in the testing set. Structure-based investigations and the final 3D-QSAR results provide
the guide for designing new potent inhibitors. 相似文献
993.
994.
Karhánek D Kacer P Kuzma M Splíchalová J Cervený L 《Journal of molecular modeling》2007,13(9):1009-1016
Theoretical investigation of Pt(0)-olefin organometallic complexes containing tertiary phosphine ligands was focused on the
strength of platinum-olefin electronic interaction. DFT theoretical study of electronic effects in a substantial number of
ethylene derivatives was evaluated in terms of the Pt-olefin binding energy using MP2 correlation theory. Organometallics
bearing coordinated olefins with general formula (R1R2C = CR3R4)Pt(PH3)2 [R = various substituents] had been selected, including olefins containing both electron-donor substituents as well as electron-withdrawing
groups. The stability of the corresponding complexes increases with a strengthening electron-withdrawal ability of the olefin
substituents.
Figure Representation of (CH2 = CHR)Pt(PPh3)2 and the stability chart 相似文献
995.
With the help of quantum mechanical calculations, we have examined the series of central system X(ML)3
+(X = O, S, Se; M = Au, Ag, Cu). Using a scalar–relativistic density functional approach, we studied the geometry structures, Mulliken populations and charges of the systems. Structure parameters of the experimental systems are reproduced well with Xα method. The metallophilic interaction energy is analyzed and decomposed. For the systems with different central atoms and different metal atoms, the nature of the metallophilic attraction interaction is analyzed. 相似文献
996.
In this study, we performed a molecular docking and dynamics simulation for a benzoxazinone–human oxytocin receptor system to determine the possible hydrophobic and electrostatic interaction points in the dynamic complex. After the homology modeling, the ligand was docked into the putative active using AutoDock 3.05. After the application of energetic and structural filters, the complexes obtained were further refined with a simulated annealing protocol (AMBER8) to remove steric clashes. Three complexes were selected for subjection to the molecular dynamics simulation (5 ns), and the results on the occurrence of average anchor points showed a stable complex between the benzoxazinone derivative and the receptor. The complex could be used as a good starting point for further analysis with site-directed mutagenesis, or further computational research.
Figure The location of the ligands (complex B – blue; complex E – red; and complex F –
green) in the transmembrane regions (TM1 – red; TM2 – blue; TM3 – yellow; TM4
– purple; TM5 – orange; TM6 – cyan; TM7 – pink) of the hOTR. For clarity, the EC
and IC loops are not shown
Electronic Supplementary Material Supplementary material is available at 相似文献
997.
Understanding the mechanism of the protein stability change is one of the most challenging tasks. Recently, the prediction
of protein stability change affected by single point mutations has become an interesting topic in molecular biology. However,
it is desirable to further acquire knowledge from large databases to provide new insights into the nature of them. This paper
presents an interpretable prediction tree method (named iPTREE-2) that can accurately predict changes of protein stability
upon mutations from sequence based information and analyze sequence characteristics from the viewpoint of composition and
order. Therefore, iPTREE-2 based on a regression tree algorithm exhibits the ability of finding important factors and developing
rules for the purpose of data mining. On a dataset of 1859 different single point mutations from thermodynamic database, ProTherm,
iPTREE-2 yields a correlation coefficient of 0.70 between predicted and experimental values. In the task of data mining, detailed
analysis of sequences reveals the possibility of the compositional specificity of residues in different ranges of stability
change and implies the existence of certain patterns. As building rules, we found that the mutation residues in wild type
and in mutant protein play an important role. The present study demonstrates that iPTREE-2 can serve the purpose of predicting
protein stability change, especially when one requires more understandable knowledge. 相似文献
998.
Botulinum neurotoxins type A (BoNT/A) are highly potent toxins, but are also useful in the treatment of illnesses. We studied
the properties of BoNT/A at various temperatures and pH values in order to understand its toxicity and structure variations.
The pH values of the environment of BoNT/A are obtained by changing the protonation states of certain titratable residue groups.
Our results show that certain parts of the protein are active at acidic pH environments or at high temperatures. The protein
is more stable in neutral environments at normal human body temperature, whereas, at high temperature, the protein is more
stable in acidic environments. Also, the three domains of the protein tend to have relative motion rather than within individual
domains. 相似文献
999.
1000.
Zohar Ibarra-Zatarain Katia Parati Silvia Cenadelli Neil Duncan 《Journal of fish biology》2019,94(3):402-413
The present study investigated the relationship between reproductive success and stress-coping styles in gilthead seabream Sparus aurata in captivity. To characterise stress-coping styles, a total of 22 breeders were submitted to three different individual-based tests, one group-based test and post-handling glucocorticoid quantification. To assess spawning participation, a microsatellite analysis was performed on a total of 2698 larvae, which allowed each offspring to be assigned unambiguously to a single parental couple. Overall, S. aurata showed defined proactive and reactive behavioural traits. Proactive breeders exhibited higher levels of activity and risk taking and lower glucocorticoid blood levels than reactive breeders. The stress-coping style traits were consistent over time and context (different tests). Breeders that contributed to a higher number of progeny exhibited proactive behaviours, while those showing low progeny contribution exhibited reactive behaviour. Therefore, breeders with a high proportion of progeny (> 20%) had significantly higher activity and risk taking and lower cortisol than breeders with low progeny contribution (< 20%). In addition, males were more proactive than females and males exhibited significantly higher activity, risk taking and lower cortisol than females. This study is the first to establish in S. aurata breeders: (a) a relationship between stress-coping styles and spawning success; (b) a relationship between stress-coping styles and gender; and (c) the existence of proactive and reactive traits at the adult stage. 相似文献