Molecular mechanics Poisson–Boltzmann surface area (MM-PBSA), a method to estimate interaction free energies, has been increasingly used in the study of biomolecular interactions. Recently, this ...method has also been applied as a scoring function in computational drug design. Here a new tool g_mmpbsa, which implements the MM-PBSA approach using subroutines written in-house or sourced from the GROMACS and APBS packages is described. g_mmpbsa was developed as part of the Open Source Drug Discovery (OSDD) consortium. Its aim is to integrate high-throughput molecular dynamics (MD) simulations with binding energy calculations. The tool provides options to select alternative atomic radii and different nonpolar solvation models including models based on the solvent accessible surface area (SASA), solvent accessible volume (SAV), and a model which contains both repulsive (SASA-SAV) and attractive components (described using a Weeks–Chandler–Andersen like integral method). We showcase the effectiveness of the tool by comparing the calculated interaction energy of 37 structurally diverse HIV-1 protease inhibitor complexes with their experimental binding free energies. The effect of varying several combinations of input parameters such as atomic radii, dielectric constant, grid resolution, solute–solvent dielectric boundary definition, and nonpolar models was investigated. g_mmpbsa can also be used to estimate the energy contribution per residue to the binding energy. It has been used to identify those residues in HIV-1 protease that are most critical for binding a range of inhibitors.
Abstract
Follicle-stimulating hormone (FSH) is critical for ovarian folliculogenesis and essential for female fertility. FSH binds to FSH receptors (FSHRs) and regulates estrogen production in ...ovarian granulosa cells to orchestrate female reproductive physiology. Ovarian senescence that occurs as a function of aging results in loss of estrogen production, and this is believed to be the major reason for bone loss in postmenopausal women. Although conflicting, studies in rodents and humans during the last decade have provided genetic, pharmacological, and physiological evidence that elevated FSH levels that occur in the face of normal or declining estrogen levels directly regulate bone mass and adiposity. Recently, an efficacious blocking polyclonal FSHβ antibody was developed that inhibited ovariectomy-induced bone loss and triggered white-to-brown fat conversion accompanied by mitochondrial biogenesis in mice. Moreover, additional nongonadal targets of FSH action have been identified, and these include the female reproductive tract (endometrium and myometrium), the placenta, hepatocytes, and blood vessels. In this mini-review, I summarize these studies in mice and humans and discuss critical gaps in our knowledge, yet unanswered questions, and the rationale for developing novel genetic models to unambiguously address the extragonadal actions of FSH.
Controversy exists with regard to extra-gonadal actions of FSH. This mini-review summarizes the controversies, identifies the critical gaps, and provides the rationale to develop new genetic models.
Adsorption of methylene blue (MB, cationic) and methyl orange (MO, anionic) dyes by graphene oxide (GO) and reduced graphene oxide (rGO) were investigated experimentally. To understand the adsorption ...properties of rGO with dyes, dye-rGO interaction was analysed by density functional theory (DFT). The GO was predominantly decorated by oxygen functional groups and rGO was characterised by both oxygen functional groups and vacancy defects. Fast and efficient adsorption of both MB and MO dyes was observed by rGO while GO showed higher adsorption of MB compared to MO. Studies reveal that the interaction of cationic dye with GO was found to be facilitated by oxygen functional groups via electrostatic interaction whereas interaction of cationic and anionic dyes with rGO was found to be facilitated by oxygen functional groups and vacancy defects, via electrostatic and π – π interactions. The results could be useful for the designing and understanding of adsorbents capable of removing cationic and anionic dyes (mixed dye) from waste water.
Adsorption process of Graphene oxide and Reduced graphene oxide towards Methylene Blue and Methyl orange dyes. Display omitted
•GO and rGO are subjected to adsorption of anionic and cationic dyes.•GO adsorbs cationic dye and rGO adsorbs both cationic and anionic dye.•rGO show adsorption capacity of 145 and 244 mg/g for MB and MO respectively.•DFT study reveal electrostatic and π-π interactions between rGO and dye molecules.
A new series of luminescent cyclometalated platinum complexes with triarylborane-functionalized acetylacetonate ligands is reported. The complexes exhibit solid state luminescence and phosphorescence ...under ambient conditions. The luminescence color can be tuned from green to red by varying the cyclometalating ligand 2-phenylpyridine (for 1 and 2), 2-thiophenylpyridine (for 3 and 4), 2-thianapthenylpyridine (for 5 and 6). The luminescence originates from mixed 3MLCT/3IL MLCT, metal to ligand charge transfer; IL, intraligand states of square planar platinum and borane moieties. The π spacer (phenyl or duryl) which connects the boryl and platinum entities has a significant role in determining the photoluminescence efficiency. The bulky duryl spacer in 2, 4, and 6 significantly reduces π–π stacking of the square planar platinum moiety in the solid state and provides a rigid backbone, thereby increasing their quantum yield significantly. The role of Lewis-acidic borane on the photoluminescence features is evaluated by fluoride binding experiments.
Tin-based perovskite materials have the drawbacks of high density of Sn vacancies, structural deformations of SnI6 – octahedra, and oxidation of unstable Sn2+ states, resulting in poor chemical ...stability processed at inert and open atmosphere. In this work, we demonstrate the temperature effects on reduction of Sn vacancies (Vsn) in polymorphic CsSnI3 perovskite solar cells. Evidence of light-induced I– ion diffusion and an interplay between iodide and Sn vacancies were briefly presented. We have observed by X-ray photoelectron spectroscopy that the formation of iodide vacancies (VI) are highly activated at 60 °C, contributing to the reduction of acceptor defects, mainly Sn vacancies (Vsn). The formation of SnO– and SnO2 – at high temperature mitigates the Sn–I interaction and eventually increases the trap density at Au/CsSnI3 interfaces. We have observed by time-of-flight secondary ion mass spectrometry that the delocalized I– ions are accumulated near the metal contacts and form AuI– ions which diffuse through the material, inhibiting the exciton transport.
•CuO nanoparticles from two different starting precursors show different properties.•CuO–distilled water nanofluids give superior thermal conductivity results.•Thermal conductivity is more sensitive ...to volume percent change at higher concentration.•CuO–distilled water nanofluids show higher thermal conductivity sensitivity.
In the present work CuO nanoparticles have been synthesized using wet chemical method and characterized using UV–Vis, PL, DLS, SEM, TEM and XRD. To evaluate effect of precursor salt CuO nanoparticles were synthesized using two different starting precursors viz copper acetate and copper sulphate. It was observed that keeping all other parameters fixed, CuO nanoparticles synthesized from copper sulphate were of regular shape and smaller size as compared to copper acetate based CuO nanoparticles. CuO nanoparticles synthesized from copper sulphate precursor were used for preparation of nanofluids in distilled water, ethylene glycol and engine oil base fluids using two step approach. These prepared nanofluids were examined for their potential of modulation in thermal conductivity. Thermal conductivity was measured using KD2 Pro which is based on transient line heat source method. 40% increment in thermal conductivity was observed for distilled water based nanofluids for change in temperature from 10 to 70°C and concentration variation from 0 to 2vol%. In case of ethylene glycol and engine oil based nanofluids thermal conductivity enhancement was 27% and 19%. Sensitivity analysis for thermal conductivity was also performed. Sensitivity analysis shows that at higher concentration sensitivity increases and varies significantly for different base fluids.
The lack of highly efficient, cost effective and stable ammonia gas sensors functionable at room temperature even in extreme humid environments poses significant challenge for the future generation ...gas sensors. The prime factors that impede the development of such next generation gas sensors are the strong interference of humidity and sluggish selectivity. Herein, we fabricated tungsten doped molybdenum disulphide/reduced graphene oxide composite by an in-situ hydrothermal method to exploit the adsorption, dissolution (solubility), ionization and transmission process of ammonia and thereby to effectuate its trace level detection even in indispensable humid environments. The protype based on 5 at.% Tungsten doped MoS2/RGO (W5) gas sensor exhibited 3.8-fold increment in its response to 50 ppm of ammonia when the relative humidity varied from 20 % to 70 % with ultra-high selectivity at room temperature. The as prepared gas sensor revealed a practical detection limit down to 1 ppm with a substantial response and rapid recovery time. Furthermore, W5 gas sensor exhibited a 42-fold increment in response to 50 ppm of ammonia relative to its pristine (MoS2/RGO) MG composite with a RH of 70 %. The proton hopping mechanism accountable for such an enormous enhancement in ammonia sensing and its potential for breath sensor are briefly annotated.
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