Melting thermodynamics of oligonucleic acids conjugated with relatively solvophobic linear polymers: A coarse‐grained molecular simulation study

Oligonucleic acids (ONAs), such as DNA and RNA, are used in various biotechnology and nanotechnology applications due to their ability to form a double helix that is stable at low temperature and melts at high temperatures. The melting temperature (T_m) of ONA duplexes can be tuned by the ONA composition, sequence, length and concentration, solvent quality, and salt concentration and by conjugation to other macromolecules. In this article, we use coarse‐grained (CG) molecular simulations to study ONAs conjugated with linear homopolymers that are relatively more solvophobic than the ONA. We study charged and stiff 8‐mer ONAs (e.g., DNA) and neutral and flexible 8‐mer ONAs (e.g., peptide nucleic acids or PNA), and vary the composition (or G‐C content) and sequence of ONA, conjugated homopolymer lengths and solvent quality for the polymer. For neutral and flexible ONAs, as the solvent quality worsens for the polymer, the ONA melting temperature increases from that of unconjugated ONA. The melting curves broaden with polymer length and worsening solvent quality, especially for ONAs with higher G‐C content. For charged and stiff ONAs, as the solvent quality worsens, the ONA melting temperature decreases compared to unconjugated ONA while the width of the melting curve remains the same. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 1196–1208     

Synthesis,characterization, and anti-cancer activity of chalcone derivatives as-potent anaplastic lymphoma kinase inhibitors

Structural Chemistry - Chalcone derivatives (7a–k) have been synthesized and characterized by 1H-NMR, 13C-NMR, mass, and elemental analysis. The synthesized compounds 7a, 7d, and 7g have been...     

Synthesis,Spectroscopic Analysis,and In-Vitro Antimicrobial Evaluation of some Tetrahydrobenzo[a]Xanthene-11-Thiones

Abstract

A series of 12-aryl-8,9,10,12-tetrahydrobenzo[a]xanthene-11-thiones were synthesized by the reaction of substituted 12-aryl-8,9,10,12-tetrahydrobenzo[a]xanthene-11-ones with Lawesson's Reagent in toluene under standard reaction conditions. All synthesized compounds were characterized by IR, NMR (¹H and ¹³C), and mass spectra. Moreover, 2D-NMR (HOMOCOSY, HSQC, and HMBC) studies were also performed for compound 10b. The synthesized compounds were also screened for their antibacterial activities.

[Supplementary materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfer, and Silicon and the Related Elements for the following free supplemental files: Additional figures.]     

A Comprehensive Review on Therapeutic Perspectives of Phytosterols in Insulin Resistance: A Mechanistic Approach

Natural products in the form of functional foods have become increasingly popular due to their protective effects against life-threatening diseases, low risk of adverse effects, affordability, and accessibility. Plant components such as phytosterol, in particular, have drawn a lot of press recently due to a link between their consumption and a modest incidence of global problems, such as Type 2 Diabetes mellitus (T2DM), cancer, and cardiovascular disease. In the management of diet-related metabolic diseases, such as T2DM and cardiovascular disorders, these plant-based functional foods and nutritional supplements have unquestionably led the market in terms of cost-effectiveness, therapeutic efficacy, and safety. Diabetes mellitus is a metabolic disorder categoriszed by high blood sugar and insulin resistance, which influence major metabolic organs, such as the liver, adipose tissue, and skeletal muscle. These chronic hyperglycemia fallouts result in decreased glucose consumption by body cells, increased fat mobilisation from fat storage cells, and protein depletion in human tissues, keeping the tissues in a state of crisis. In addition, functional foods such as phytosterols improve the body’s healing process from these crises by promoting a proper physiological metabolism and cellular activities. They are plant-derived steroid molecules having structure and function similar to cholesterol, which is found in vegetables, grains, nuts, olive oil, wood pulp, legumes, cereals, and leaves, and are abundant in nature, along with phytosterol derivatives. The most copious phytosterols seen in the human diet are sitosterol, stigmasterol, and campesterol, which can be found in free form, as fatty acid/cinnamic acid esters or as glycosides processed by pancreatic enzymes. Accumulating evidence reveals that phytosterols and diets enriched with them can control glucose and lipid metabolism, as well as insulin resistance. Despite this, few studies on the advantages of sterol control in diabetes care have been published. As a basis, the primary objective of this review is to convey extensive updated information on the possibility of managing diabetes and associated complications with sterol-rich foods in molecular aspects.     

A ‘stack’ model of rate-independent polycrystals

A novel ‘stack’ model of a rate-independent polycrystal, which extends the ‘ALAMEL’ model of Van Houtte et al. (2005) is proposed. In the ‘stack’ model, stacks of N neighboring ‘ALAMEL’ domains collectively accommodate the imposed macroscopic deformation while deforming such that velocity and traction continuity with their neighbors is maintained. The flow law and consistency conditions are derived and an efficient solution methodology based on the linear programming technique is given. The present model is applied to study plastic deformation of an idealized two-dimensional polycrystal under macroscopically imposed plane-strain tension and simple shear constraints. Qualitative and quantitative variations in the predicted macroscopic and microscopic response with N are presented. The constraint on individual ‘ALAMEL’ domains diminishes with stack size N but saturates for large N. Computational effort associated with the present model is analyzed and found to be well within one order of magnitude greater than that required to solve the classical Taylor model. Furthermore, implementation of the consistency conditions is found to reduce computation time by at least 50%.     

Improved semiempirical heats of formation through the use of bond and group equivalents

Deficiencies in energetics obtained using the common semiempirical methods, AM1, PM3, and MNDO, may partly be traced to the use of pseudoatomic equivalents for conversion of molecular energies to heats of formation at 298 K. We present an alternative scheme based on the use of bond and group equivalents. Values for the 61 bond and group equivalents necessary for treatment of molecules containing the common organic elements, hydrogen, carbon, nitrogen, and oxygen have been derived. For a set of 583 neutral, closed-shell molecules mean absolute errors in AM1, PM3, and MNDO heats of formation are reduced from 6.6, 4.2, and 8.2 kcal/mol to 2.3, 2.2, and 3.0 kcal/mol, respectively. Several systematic problems are overcome in the present scheme including relative stabilities of branched hydrocarbons, energetics of conjugated systems, heats of formation of long chain hydrocarbons, and enthalpies of molecules containing multiple heteroatoms. Although the approach is restricted to molecules with well-defined functional groups, the equivalents are easy to incorporate and are chemically relevant. This revised procedure allows semiempirical methods to be used for far more reliable evaluations of heats of reactions. Estimates are made of the errors inherent in these semiempirical formalisms, arising from integral approximations and the neglect of explicit treatment of electron correlation effects, while excluding those from inadequate parameterization.     

Pressure-induced ordering in adamantane: a Monte Carlo simulation study

Isothermal-isobaric ensemble Monte Carlo simulation of adamantane has been carried out with a variable shape simulation cell. The low-temperature crystalline phase and the room-temperature plastic crystalline phases have been studied employing the modified Williams potential. We show that at room temperature, the plastic crystalline phase transforms to the crystalline phase on increase in pressure. Further, we show that this is the same phase as the low-temperature ordered tetragonal phase of adamantane. The high-pressure ordered phase appears to be characterized by a slightly larger shift of the first peak toward a lower value of r in C-C, C-H, and H-H radial distribution functions as compared to the low-temperature tetragonal phase. The coexistence curve between the crystalline and plastic crystalline phase has been obtained approximately up to a pressure of 4 GPa.     

D-branes on Calabi–Yau Manifolds and Superpotentials

We show how to compute terms in an expansion of the world-volume superpotential for fairly general D-branes on the quintic Calabi-Yau using linear sigma model techniques, and show in examples that this superpotential captures the geometry and obstruction theory of bundles and sheaves on this Calabi-Yau.Louis Michel Professor