Ab initio Computational Modeling of Glyphosate Analogs: Conformational Perspective

A historical perspective on the application of conformational analysis to structure-based ligand design approach is presented. The application of isodensity molecular electrostatic potential surfaces with the conformational energy surfaces (CES) have allowed us to reach pertinent conclusions for aiding synthetic and biochemical studies. Here we illustrate such an application on the modeling of the potent analogs of an important, environmentally stringent herbicidal compound glyphosate by constructing conformational energy surfaces. The systems were modeled by substituting F, Cl, and NH— OH moiety to the position of pharmacophoric nitrogen center in glyphosate structure. All the calculations were thoroughly performed with ab initio MO theory at Hartree–Fock method using 3-21G(d) basis functions. On the basis of the results, we identified the bioactive conformations for N-fluoro-glyphosate, N-chloro-glyphosate, and N-hydroxyamino-glyphosate as (−38^∘, 77^∘), (−61^∘, 111^∘), and (−167^∘, −169^∘), respectively. Geometry optimization of certain selected conformations of these compounds using hybrid DFT method with 6–31+G(d) basis functions provides nearly equal values of φ and ψ. Moreover, the results indicate that the global minimum structures of N-fluoro and N-chloro analogs of glyphosate show cyclic conformation whereas the N-hydroxyamino-glyphosate global minimum structure shows spyrocyclic and zig-zag conformation. Also, the predicted bioactive conformation of N-hydroxyamino analog optimally overlaps with glyphosate backbone in EPSPS complex with 0.1 Å RMSD value. However, the other two compounds slightly deviate from the backbone of glyphosate with RMSD of 0.92 Å for N-fluoro-glyphosate and 0.83 Å for N-chloro-glyphosate. The linear N-hydroxyamino-glyphosate exhibits relatively more number of intermolecular hydrogen bond interactions as compared to the other two analogs. Further, comparison of CES of previously studied glyphosate analogs such as N-hydroxy-glyphosate (2.2 μM) and N-amino-glyphosate (0.61 μM) with the present systems reveals the order of activity as: N-hydroxyamino-glyphosate > N-fluoro-glyphosate > N-chloro-glyphosate based on CES flexibility. Also, the calculated heats of formation of N-fluoro-glyphosate, N-chloro-glyphosate, and N-hydroxyamino-glyphosate are −288, −209, and −288 kcal/mol, respectively, which clearly indicate that the N-hydroxyamino and N-fluoro analogs of glyphosate are thermodynamically more stable than N-amino-glyphosate (−278 kcal/mol).     

Effect of Erosive Agents on Surface Characteristics of Nano-Fluorapatite Ceramic: An In-Vitro Study

Erosive beverages cause dissolution of natural teeth and intra-oral restorations, resulting in surface characteristic changes, particularly roughness and degradation. The purpose of this study was to evaluate the surface roughness and topography of a dental ceramic following immersion in locally available erosive solutions. A total of 160 disc specimens of a nano-fluorapatite type ceramic (12 mm diameter and 2 mm thickness) were fabricated and equally distributed into two groups (n = 80) and then evenly distributed among the following five testing groups (n = 16): lemon juice, citrate buffer solution, 4% acetic acid, soft cola drink, and distilled water which served as a control. The surface roughness (Ra) and topography were evaluated using a profilometer and scanning electron microscope at baseline, 24 h, 96 h, and 168 h respectively. Data were analyzed using ANOVA and Tukey’s multiple comparisons (p ≤ 0.05). Surface changes were observed upon exposure to all acidic beverages except distilled water. Amongst all immersion media, 4% acetic acid produced the most severe surface roughness across all time periods (i.e., baseline, 24 h, 96 h, and 168 h). A statistically significant difference in the surface roughness values between all immersion media and across all four time intervals was observed. Erosive agents had a negative effect on the surface roughness and topography of the tested ceramic. The surface roughness increased with increased storage time intervals.     

Viscosity approximation methods for nonexpansive multimaps in Banach spaces

We prove strong convergence of the viscosity approximation process for nonexpansive nonself multimaps. Furthermore, an explicit iteration process which converges strongly to a fixed point of multimap T is constructed. It is worth mentioning that, unlike other authors, we do not impose the condition ＂Tz = {z}＂ on the map T.     

Noncommuting selfmaps and invariant approximations

Common fixed-point results are established for a new class of noncommuting selfmaps. We apply them to obtain several invariant approximation results which unify, extend, and complement well-known results.     

Double Suzuki cross‐coupling reaction of pyrimidine boronic acid: synthesis of new versatile dielectrophile

The double Suzuki cross‐coupling reaction has successfully been applied for the synthesis of 5,5′‐(5‐butoxy‐1,3‐phenylene)bis(2‐chloropyrimidine) with two reactive chloro groups and an alkoxy side chain starting from 2‐chloropyrimidin‐5‐ylboronic acid and 1,3‐dibromo‐5‐butoxybenzene. The reactivity of this dielectrophile was tested by reaction with aniline and phenol, a nitrogen and oxygen nucleophile, respectively. The new dielectrophile would further provide an ideal platform for the construction of large hetero‐atom bridged macrocycles for desired properties and functions in supramolecular and material chemistry. Copyright © 2012 John Wiley & Sons, Ltd.     

Steric and Electronic Influence on the Coordination Aptitude of 4‐Formylpiperazine‐1‐Carbodithioate Towards Triorganotin(IV) Moieties

A fascinating ligand, 4‐formylpiperazinium 4‐formylpiperazine‐1‐carbodithioate (L‐salt) has been reacted with two electronically and sterically different trimethyltin(IV) chloride and triphenyltin(IV) chloride. The complexes 1 and 2 were characterized by elemental analysis, spectroscopic techniques, and X‐ray single crystal analysis. The latter technique confirmed the polymeric and monomeric nature of 1 and 2 , respectively. Both 1 and 2 showed intriguing molecular packing properties in the solid state. However, the packing of 1 is more interesting and unique where one‐dimensional polymer chains self assemble in two‐over‐two saltire‐shaped fashion to provide an overall multilayered structure. The different behavior of L toward two different tin(IV) compounds can be attributed to different electronic and steric environments around metal center.     

Deciphering the Role of Filamin B Calponin-Homology Domain in Causing the Larsen Syndrome,Boomerang Dysplasia,and Atelosteogenesis Type I Spectrum Disorders via a Computational Approach

Filamins (FLN) are a family of actin-binding proteins involved in regulating the cytoskeleton and signaling phenomenon by developing a network with F-actin and FLN-binding partners. The FLN family comprises three conserved isoforms in mammals: FLNA, FLNB, and FLNC. FLNB is a multidomain monomer protein with domains containing an actin-binding N-terminal domain (ABD 1–242), encompassing two calponin-homology domains (assigned CH1 and CH2). Primary variants in FLNB mostly occur in the domain (CH2) and surrounding the hinge-1 region. The four autosomal dominant disorders that are associated with FLNB variants are Larsen syndrome, atelosteogenesis type I (AOI), atelosteogenesis type III (AOIII), and boomerang dysplasia (BD). Despite the intense clustering of FLNB variants contributing to the LS-AO-BD disorders, the genotype-phenotype correlation is still enigmatic. In silico prediction tools and molecular dynamics simulation (MDS) approaches have offered the potential for variant classification and pathogenicity predictions. We retrieved 285 FLNB missense variants from the UniProt, ClinVar, and HGMD databases in the current study. Of these, five and 39 variants were located in the CH1 and CH2 domains, respectively. These variants were subjected to various pathogenicity and stability prediction tools, evolutionary and conservation analyses, and biophysical and physicochemical properties analyses. Molecular dynamics simulation (MDS) was performed on the three candidate variants in the CH2 domain (W148R, F161C, and L171R) that were predicted to be the most pathogenic. The MDS analysis results showed that these three variants are highly compact compared to the native protein, suggesting that they could affect the protein on the structural and functional levels. The computational approach demonstrates the differences between the FLNB mutants and the wild type in a structural and functional context. Our findings expand our knowledge on the genotype-phenotype correlation in FLNB-related LS-AO-BD disorders on the molecular level, which may pave the way for optimizing drug therapy by integrating precision medicine.