SDA 7: A modular and parallel implementation of the simulation of diffusional association software

The simulation of diffusional association (SDA) Brownian dynamics software package has been widely used in the study of biomacromolecular association. Initially developed to calculate bimolecular protein–protein association rate constants, it has since been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes, to investigate the adsorption of proteins to inorganic surfaces, and to simulate the dynamics of large systems containing many biomacromolecular solutes, allowing the study of concentration‐dependent effects. These extensions have led to a number of divergent versions of the software. In this article, we report the development of the latest version of the software (SDA 7). This release was developed to consolidate the existing codes into a single framework, while improving the parallelization of the code to better exploit modern multicore shared memory computer architectures. It is built using a modular object‐oriented programming scheme, to allow for easy maintenance and extension of the software, and includes new features, such as adding flexible solute representations. We discuss a number of application examples, which describe some of the methods available in the release, and provide benchmarking data to demonstrate the parallel performance. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Extension of the Taylor Equation for Oil-Water-Surfactant System and Investigating the Impact of Surfactant Concentration over the Quality of Emulsion

Emulsions stand among the most important multiphase fluids, exhibiting various complicated phenomenon. To understand the process of emulsification, the Taylor equation has been extended to incorporate the parameters that depend on molecular mass of oil and their contents and the amount of surfactant added. To test the validity of the proposed equations, four well-defined short chain (n-hexane, n-heptane, n-decane, and kerosene) oils were emulsified in water and the results were compared with the experimental ones. It has been concluded that the extended Taylor equation worked well, even in the presence of surfactant. The quality of the emulsion defined and discussed in terms of size and number of droplets was best near CMC of the surfactant used. A relationship has also been derived between CMC of surfactant and its distribution coefficient, which allows the exact value of one parameter to be determined if other is known.     

Investigating the homogeneity of nylon-6 and polyvinyl alcohol blend

Viscosity measurements were used for measuring the rheological behavior of the nylon-6 and polyvinyl alcohol (PVA) blends in solution and hence their compatibility. The change of different viscosities of various blend compositions showed straight line, curve linear, and S-shape. The effect of concentration of one polymer over the other is also explained. This behavior is explained on the basis of the miscibility of the polymers in various blend compositions. The article is published in the original.     

Crystal Structures of 2-Chloro-3-((3-(trifluoromethyl)phenyl)amino)naphthalene-1,4-dione and 2-Chloro-3-((4-(trifluoromethyl)phenyl)amino)naphthalene-1,4-dione

Crystallography Reports - 2-Chloro-3-((3-(trifluoromethyl)phenyl)amino)naphthalene-1,4-dione (1) and 2-chloro-3-((4-(trifluoromethyl)phenyl)amino)naphthalene-1,4-dione (2) were obtained according...     

Potential COVID-19 Drug Candidates Based on Diazinyl-Thiazol-Imine Moieties: Synthesis and Greener Pastures Biological Study

A novel series of 1-aryl-N-[4-phenyl-5-(arylazo)thiazol-2-yl)methanimines has been synthesized via the condensation of 2-amino-4-phenyl-5-arylazothiazole with various aromatic aldehydes. The synthesized imines were characterized by spectroscopic techniques, namely ¹H and ¹³C-NMR, FTIR, MS, and Elemental Analysis. A molecular comparative docking study for 3a–f was calculated, with reference to two approved drugs, Molnupiravir and Remdesivir, using 7BQY (M^pro; PDB code 7BQY; resolution: 1.7 A°) under identical conditions. The binding scores against 7BQY were in the range of −7.7 to −8.7 kcal/mol for 3a–f. The high scores of the compounds indicated an enhanced binding affinity of the molecules to the receptor. This is due to the hydrophobic interactions and multi-hydrogen bonds between 3a–f ligands and the receptor’s active amino acid residues. The main aim of using in silco molecular docking was to rank 3a–f with respect to the approved drugs, Molnupiravir and Remdesivir, using free energy methods as greener pastures. A further interesting comparison presented the laydown of the ligands before and after molecular docking. These results and other supporting statistical analyses suggested that ligands 3a–f deserve further investigation in the context of potential therapeutic agents for COVID-19. Free-cost, PASS, SwissADME, and Way2drug were used in this research paper to determine the possible biological activities and cytotoxicity of 3a–f.     

Asymmetric reduction and oxidation of aromatic ketones and alcohols using W110A secondary alcohol dehydrogenase from Thermoanaerobacter ethanolicus

An enantioselective asymmetric reduction of phenyl ring-containing prochiral ketones to yield the corresponding optically active secondary alcohols was achieved with W110A secondary alcohol dehydrogenase from Thermoanaerobacter ethanolicus (W110A TESADH) in Tris buffer using 2-propanol (30%, v/v) as cosolvent and cosubstrate. This concentration of 2-propanol was crucial not only to enhance the solubility of hydrophobic phenyl ring-containing substrates in the aqueous reaction medium, but also to shift the equilibrium in the reduction direction. The resulting alcohols have S-configuration, in agreement with Prelog's rule, in which the nicotinamide-adenine dinucleotide phosphate (NADPH) cofactor transfers its pro-R hydride to the re face of the ketone. A series of phenyl ring-containing ketones, such as 4-phenyl-2-butanone (1a) and 1-phenyl-1,3-butadione (2a), were reduced with good to excellent yields and high enantioselectivities. On the other hand, 1-phenyl-2-propanone (7a) was reduced with lower ee than 2-butanone derivatives. (R)-Alcohols, the anti-Prelog products, were obtained by enantiospecific oxidation of (S)-alcohols through oxidative kinetic resolution of the rac-alcohols using W110A TESADH in Tris buffer/acetone (90:10, v/v).     

Microwave-assisted synthesis and characterization of novel metal-free and metallophthalocyanines containing four 14-membered tetraaza macrocycles

The novel tetrasubstituted metal-free phthalocyanine (6) and metallophthalocyanines (7, 8) bearing four 14-membered tetraaza macrocycles moieties on peripheral positions have been synthesized by cyclotetramerization reaction of phthalonitrile derivative (5) in a multi-step reaction sequence. The new compounds were characterized by a combination of IR, ¹H NMR, ¹³C NMR, UV-vis, elemental analysis and MS spectral data.     

An inexact modified subgradient algorithm for nonconvex optimization

We propose and analyze an inexact version of the modified subgradient (MSG) algorithm, which we call the IMSG algorithm, for nonsmooth and nonconvex optimization over a compact set. We prove that under an approximate, i.e. inexact, minimization of the sharp augmented Lagrangian, the main convergence properties of the MSG algorithm are preserved for the IMSG algorithm. Inexact minimization may allow to solve problems with less computational effort. We illustrate this through test problems, including an optimal bang-bang control problem, under several different inexactness schemes.     

Chemical constituents of Fumaria densiflora and the effects of some isolated spirobenzylisoquinoline alkaloids on murine isolated ileum and perfused heart

Abstract

Twenty-two alkaloids, were isolated from Fumaria densiflora. Two of these alkaloids, N-methyl-5-hydroxystylopine chloride and fumaricine N-oxide, were isolated for the first time from natural sources. Parfumine and fumaritine, in concentrations ranging from 3?×?10^?7 to 9?×?10^?4?M, caused concentration–dependent relaxation of ileum longitudinal segment. Also, parfumine and fumaritine in concentrations ranging from 3?×?10^?4 to 9?×?10^?2?M, caused concentration – dependent decrease in heart rate of the isolated perfused heart. A concentration of parfumine of 3?×?10^?2?M increased but a higher concentration (9?×?10^?2?M) decreased the amplitude of contraction of the isolated perfused heart. On the other hand, fumaritine, in concentrations ranging from 3?×?10^?4 to 3?×?10^?2?M, caused concentration – dependent increase, but a higher concentration (9?×?10^?2?M) caused a decrease in the amplitude of contraction of the isolated perfused heart.

     

Synthesis and Characterization of Biologically Potent Di‐organotin(IV) Complexes of Mono‐Methyl Glutarate

The synthesis and characterization of some novel compounds of organotin(IV) chlorides with monomethyl glutarate is reported; the ligand molecule appears to be bound to the tin atom through the carbonyl oxygen. The results obtained through ¹H‐¹³C‐¹¹⁹Sn NMR, FT‐IR and ¹¹⁹Sn Mössbauer spectra show that the diorganotin(IV) complexes have hexacoordination with octahedral geometry. Biological screening of the complexes reveals that the diorganotin(IV) complexes show significant activity against all microorganisms.