Higher Intermolecular Interactions Research Articles

Compositional effects of hybrid MoS2–GO active layer on the performance of unipolar, low-power and multistate RRAM device

Currently, 2D nanomaterials-based resistive random access memory (RRAMs) are explored on account of their tunable material properties enabling fabrication of low power and flexible RRAM devices. In this work, hybrid MoS2–GO based active layer RRAM devices are investigated. A facile hydrothermal co-synthesis approach is used to obtain the hybrid materials and a cost-effective spin coating method adopted for the fabrication of Ag/MoS2–GO/ITO RRAM devices. The performance of the fabricated hybrid active layer RRAM device is analysed with respect to change in material properties of the synthesized hybrid material. The progressive addition of 0.5, 1.5, 2.5 and 4.5 weight % of GO to MoS2, results in a hybrid active layer with higher intermolecular interaction, in the case of Ag/MoS2–GO4.5/ITO RRAM device, resulting in a unipolar resistive switching RRAM behavior with low SET voltage of 1.37 V and high I on/I off of 200 with multilevel resistance states. A space charge limited conduction mechanism is obtained during switching, which may be attributed to the trap states present due to functional groups of GO. The increased number of conduction pathways on account of both Ag+ ions and oxygen vacancies (Vo 2+), participating in the formation of conducting filament, results in higher I on/I off. This is the first report of unipolar Ag/MoS2–GO/ITO RRAM devices, which are particularly important in realizing high density crossbar memories for neuromorphic and in-memory computing as well as enabling flexible 2D nanomaterials-based memristor applications.

Investigating the Potential Pharmacological Applications of 5-Hydroxy-2 (hydroxymethyl)-4H pyran-4 one through Electronic Characterization and MM-GBSA Studies for Oxidative Stress and Tyrosinase Inhibition: A Quantum Chemical Approach

The study thoroughly examines the possible applications of 5 Hydroxy – 2 (hydroxymethyl) – 4 H pyran – 4 one. Through Quantum chemical analysis, the research rigorously evaluates the compound's properties, including its optoelectronics, geometrical structure, and intermolecular interactions. The geometrical structure parameters were optimized using a 6–311++G(d,p) basis set in the DFT/B3LYP method, and the resulting geometrical factors were then scaled to calculate probable vibrational wavenumbers. The Mulliken charges and MEP map were used to locate electrophilic, nucleophilic regions, and chemical reactivity was described using FMOs and Fukui function assessments. The multiwfn was employed to investigate topological analysis (surface distance projection and Hirshfeld maps). The UV-visible spectrum was used to estimate the absorption of maximum wavelengths, which was then correlated with the TD-DFT, DOS, and band structure investigations. The study also calculated parameters, including Total Energies, ZPE, Entropy, Dipole moment, and Heat Capacity for monomeric and dimeric units. Pharmacokinetics were used to determine the biological characteristics of the compound. The MM-GBSA simulation was performed, and the results suggest that this compound has the potential to be an enhancing anti-oxidant protection agent due to its high binding affinity and intermolecular interactions. These findings are crucial in developing therapeutic agents with pharmacological effects and potential toxicities.

Investigation of Rational Design of Amine Solvents for CO2 Capture: A Computational Approach

Solvent selection and design are critical in the CO2 capture process as the choice of solvent directly impacts the cost of the process, capture efficiency, equipment size, and regeneration energy. In the present study, 1MPZ-PZ, PZ, PIP, DEEA and MEA-DEEA are analyzed in terms of interaction intensity (attractive and repulsive) and diffusivity by molecular dynamic simulation. A high intermolecular interaction intensity promotes CO2 absorption, while intra-molecular interaction intensity affects CO2 desorption during the regeneration process. Diffusivity is also an important factor for a fast CO2 uptake rate, which is desirable for efficient CO2 capture. The interpretation of diffusivity and intermolecular interaction intensity findings is conducted through mean square displacement and radial distribution function analysis, respectively. The order of interaction intensity in various amines is DEEA>MEA-DEEA>PIP>1MPZ-PZ. It shows that DEEA can increase the CO2 absorption rate as it shows the highest interaction intensity in pure and blended amine systems. The results of the intramolecular interaction intensity show that it is easier to regenerate DEEA, PIP, PZ, and 1MPZ than MEA. The temperature effect on the interaction intensity is revealed at higher temperatures, where the molecular structure becomes unstable due to higher thermal motion, which is the cause of lower interaction intensity. On the other hand, the mean square displacement analysis for the diffusivity rate shows that PZ shows the highest diffusivity rate compared to other selected solvents. The order of diffusivity rate in various pure and blended amine systems is PZ>PIP>1-MPZ-PZ>MEA-DEEA. The diffusivity of various amine solvent systems increases with temperature. As examined in this current research, assessing solvent characteristics holds significant importance in optimizing the most effective solvent system.

Exploring the potential of naturally-derived ionic liquids for sustainable vegetable oil deacidification

This work investigated two different approaches for vegetable oil deacidification using an ionic liquid (IL), composed of cholinium cation ([Ch]) and oleate anion ([OLE]), as a solvent to form oligomeric ILs (OILs) potentially, and reactive extraction to form multicomponent ILs (MILs) from different acids. The OIL approach (adding an excess acid into the IL through hydrogen bonding) removed oleic acid (∼80%) from a commercial vegetable soybean oil, previously acidified, possibly due to high intermolecular interactions. Through MIL approach, the FFA removal was up to 85%. In this case, the MIL formation occurred concomitant to deacidification as a driving force. Both strategies were evaluated in crude vegetable oil, and the high removal indexes were maintained. Concerning the oil loss, the MIL and OIL approaches result in a significantly lower oil loss (up to 5%) than conventional chemical processes (up to 50%). Finally, envisioning integrated processes, MIL was reused in a new deacidification process, achieving good results (removal of FFA up to 85%). Alternatively, reused MILs and OILs were employed in the β-carotene and astaxanthin recovery from P. rhodozyma wet biomass, indicating that the obtained IL-based systems could be further used as green solvents for other sustainable extraction processes.

Effect of Monomer Type on the Synthesis and Properties of Poly(Ethylene Furanoate).

This work aimed to produce bio-based poly(ethylene furanoate) (PEF) with a high molecular weight using 2,5-furan dicarboxylic acid (FDCA) or its derivative dimethyl 2,5-furan dicarboxylate (DMFD), targeting food packaging applications. The effect of monomer type, molar ratios, catalyst, polycondensation time, and temperature on synthesized samples' intrinsic viscosities and color intensity was evaluated. It was found that FDCA is more effective than DMFD in producing PEF with higher molecular weight. A sum of complementary techniques was employed to study the structure-properties relationships of the prepared PEF samples, both in amorphous and semicrystalline states. The amorphous samples exhibited an increase in glass transition temperature of 82-87 °C, and annealed samples displayed a decrease in crystallinity with increasing intrinsic viscosity, as analyzed by differential scanning calorimetry and X-ray diffraction. Dielectric spectroscopy showed moderate local and segmental dynamics and high ionic conductivity for the 2,5-FDCA-based samples. The spherulite size and nuclei density of samples improved with increased melt crystallization and viscosity, respectively. The hydrophilicity and oxygen permeability of the samples were reduced with increased rigidity and molecular weight. The nanoindentation test showed that the hardness and elastic modulus of amorphous and annealed samples is higher at low viscosities due to high intermolecular interactions and degree of crystallinity.

Castor oil-based, robust, non-leaching and durable antibacterial waterborne polyurethane/polyhexamethylene guanidine composites prepared via an electrostatic self-assembly strategy

Antibacterial materials with durable antibacterial properties and high mechanical strength from renewable resources recently have attracted extensive attention. In this study, a facile and environmentally friendly electrostatic self-assembly strategy was adopted to prepare a series of castor oil-based waterborne polyurethane/polyhexamethylene guanidine (WPU/PHMG) composites. The relationship between performance (antibacterial properties, mechanical properties, etc.) and the chemical structures of these resulting composite films has been systematically investigated. The results showed that the antibacterial rate of these antibacterial composite films against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) was more than 99.9%. Interestingly, the obtained composite films still demonstrated long-lasting antibacterial properties after 42 days of immersion in water and six cycles of antibacterial testing due to the synergistic effect of electrostatic interaction and intermolecular hydrogen bonds. In addition, the tensile strength of the obtained composite films was significantly improved up to 30 MPa, 2 times higher than the original polyurethane films, and the toughness was high up to 70 MJ/m3, which could easily pull up to 19,000 times their own weight. Furthermore, the water absorption of the obtained composite films was greatly reduced from 56.4% to 6.6% due to their high crosslinking densities and intermolecular interaction. The technique reported in this study provides a facile and simple strategy for development of high mechanical properties and durable antibacterial properties of bio-based polymer composites, which would find promising applications in medical devices, product packaging, and so on.

Candidate Genes and Pathways in Cervical Cancer: A Systematic Review and Integrated Bioinformatic Analysis.

Cervical cancer is the leading cause of cancer-related death among women in developing countries. However, no comprehensive molecular mechanism for cervical cancer has been established, as many studies were small-cohort studies conducted with small sample sizes. A thorough literature search was performed using the PubMed, Scopus, EBSCOhost, and Science Direct databases. Medical Subject Heading (MeSH) terms such as "Uterine Cervical Neoplasms" and "gene expression" were used as the keywords in all fields. A total of 4027 studies were retrieved, and only clinical studies, which used the microarray method to identify differentially expressed genes (DEGs) in the cervical tissue of cervical cancer patients, were selected. Following the screening, 6 studies were selected and 1128 DEGs were extracted from the data. Sixty-two differentially expressed genes from at least two studies were selected for further analysis by DAVID, STRING, and Cytoscape software. In cervical cancer pathogenesis, three significant clusters with high intermolecular interactions from the Protein-Protein Interaction (PPI) network complex revealed three major molecular mechanisms, including cell signaling, cell cycle, and cell differentiation. Subsequently, eight genes were chosen as the candidate genes based on their involvement in the relevant gene ontology (GO) and their interaction with other genes in the PPI network through undirected first neighbor nodes. The present systematic review improves our understanding of the molecular mechanism of cervical cancer and the proposed genes that can be used to expand the biomarker panel in the screening for cervical cancer. The targeted genes may be beneficial for the development of better treatment strategies.

Insight into the glycerol extraction from biodiesel using deep eutectic solvents

The main challenge of large-scale biofuel production is related to the extraction of its undesired impurities including glycerol, water, methanol, soap/catalyst, free fatty acids, glycerides, and others. There are many ways to remove glycerol, and herein, the one alternative is the extraction of glycerol from biodiesel by deep eutectic solvents. In this regard, the mixture of a choline chloride (ChCl) and urea, methyltriphenylphosphonium chloride (MTPPCl), and ethylene glycol (EGL), as a deep eutectic solvent (DES), is effective in removing glycerol from biofuel. In this work, we have investigated the formation mechanism of ChCl and urea, and then MTPPCl and EGL, as a DES, and then extraction of glycerol from biofuel via DES implementing density functional theory (DFT)by Gaussian09 software, B3LYP basis set, and classical all-atom molecular dynamics (MD) simulationsby Gromacs software, GROMOS force field. DFT approximation demonstrates that Cl ion plays an important binding role in the formation of complexes ChCl/urea-based DES + biofuel and in MTPPCl/EGL-based DES + biofuel. We have also considered the formation and change of hydrogen bonds upon the formation of these systems using the DFT method. Large HOMO-LUMO gaps in ChCl/urea-based DES + biofuel and in MTPPCl/urea-based DES + biofuel demonstrate the stability of the complexes. The results of MD work have stated that the chloride ion formed bonding with the choline/ethylene glycol EGL, while still weakly intermolecular interacting with the urea/methyltriphenylphosphonium in ChCl/urea- and MTPPCl/EGL-based DESs. Further results of MD simulations stated that the DESs had a higher intermolecular interaction with glycerol in comparison with biofuel, thereby favoring the extraction process of glycerol from model biofuel. • Intermolecular interactions of choline chloride and urea, methyl triphenyl phosphonium chloride, and ethylene glycol-based DESs and their applications in the extraction of glycerol from biofuel studied by DFT calculations and classical all-atom molecular dynamics simulations. • Calculated outputs of DFT calculations and classical all-atom molecular dynamics simulations for DESs and their applications in the extraction of glycerol from biofuel were discussed in detail. • The molecular formation mechanism of choline and methyl triphenyl phosphonium-based DESs and their application in the extraction process of glycerol from biofuel were summarized.

In Situ Compatibilized Blends of PLA/PCL/CAB Melt-Blown Films with High Elongation: Investigation of Miscibility, Morphology, Crystallinity and Modelling.

Ternary-blended, melt-blown films of polylactide (PLA), polycaprolactone (PCL) and cellulose acetate butyrate (CAB) were prepared from preliminary miscibility data using a rapid screening method and optical ternary phase diagram (presented as clear, translucent, and opaque regions) as a guide for the composition selection. The compositions that provided optically clear regions were selected for melt blending. The ternary (PLA/PCL/CAB) blends were first melt-extruded and then melt-blown to form films and characterized for their tensile properties, tensile fractured-surface morphology, miscibility, crystallinity, molecular weight and chemical structure. The results showed that the tensile elongation at the break (%elongation) of the ternary-blended, melt-blown films (85/5/10, 75/10/15, 60/15/25 of PLA/PCL/CAB) was substantially higher (>350%) than pure PLA (ca. 20%). The range of compositions in which a significant increase in %elongation was observed at 55−85% w/w PLA, 5−20% w/w PCL and 10−25% w/w CAB. Films with high %elongation all showed good interfacial interactions between the dispersed phase (PCL and CAB) and matrix (PLA) in FE-SEM and showed improvements in miscibility (higher intermolecular interaction and mixing) and a decrease in the glass transition temperature, when compared to the low %elongation films. The decrease in Mw and Mn and the formation of the new NMR peaks (1H NMR at 3.68−3.73 ppm and 13C NMR at 58.54 ppm) were observed in only the high %elongation films. These are expected to be in situ compatibilizers that are generated during the melt processing, mostly by chain scission. In addition, mathematical modelling was used to study the optimal ratio and cost-effectiveness of blends with optimised mechanical properties. These ternary-blended, melt-blown films have the potential for use in both packaging and medical devices with excellent mechanical performance as well as inherent economic and environmental capabilities.

Pharmacological inhibition of cathepsin C (CatC) as a potential approach for cancer therapeutics

Studies have established that proteolytic enzyme inhibition holds significant promise in cancer prevention and treatment. Cathepsin C (CatC) is conserved lysosomal cysteine dipeptidyl aminopeptidase, which is the key for pro-inflammatory neutrophil serine protease activation and biological functioning. This makes CatC as a promising therapeutic drug target for the management of different cancer types. Considering this, using a wide range of computer aided drug-designing applications, several inhibitors are shortlisted against CatC active pocket, which interact with the enzyme with high affinity and form strong intermolecular interaction network. Compared to control, three molecules ASN_06916232, ASN_06917112 and ASN_06916892 are filtered as best binders of the CatC active pocket with binding energy value of −10.9 kcal/mol, −10.9 kcal/mol and −10.7 kcal/mol, respectively. These compounds interact with several important active side residues of CatC such as Ser233, Cys234, Gly277, Asn380 and His38. Furthermore, the complexes of these compounds with CatC reveal very stable dynamics with average RMSD value less than 3 Å. The binding energy analysis further indicates the compounds to have very stable van der Waals and electrostatic energies. In conclusion, these molecules are promising and require experimental validation to prove them as anti-CatC molecules. Communicated by Ramaswamy H. Sarma

Perfluorocycloparaphenylenes

Perfluorinated aromatic compounds, the so-called perfluoroarenes, are widely used in materials science owing to their high electron affinity and characteristic intermolecular interactions. However, methods to synthesize highly strained perfluoroarenes are limited, which greatly limits their structural diversity. Herein, we report the synthesis and isolation of perfluorocycloparaphenylenes (PFCPPs) as a class of ring-shaped perfluoroarenes. Using macrocyclic nickel complexes, we succeeded in synthesizing PF[n]CPPs (n = 10, 12, 14, 16) in one-pot without noble metals. The molecular structures of PF[n]CPPs (n = 10, 12, 14) were determined by X-ray crystallography to confirm their tubular alignment. Photophysical and electrochemical measurements revealed that PF[n]CPPs (n = 10, 12, 14) exhibited wide HOMO–LUMO gaps, high reduction potentials, and strong phosphorescence at low temperature. PFCPPs are not only useful as electron-accepting organic materials but can also be used for accelerating the creation of topologically unique molecular nanocarbon materials.

Effects of particle size distribution of potato starch granules on rheological properties of model dough underwent multiple freezing-thawing cycles

In order to elucidate the mechanism underlying the effect of different-sizes potato starch on dough during freeze–thaw treatment, the rheological properties, moisture distribution, secondary structure, and relative crystallinity of dough were investigated. The results showed that the storage modulus (G′), loss modulus (G″), and complex modulus (|G*|) of dough increased as a result of the freeze–thaw treatment, and the effect was more obvious as the starch granular sizes increased. The higher β -sheet and T22 contents reflected the higher viscoelasticity and freeze–thaw sensitivity, which may be related to the higher degree expansion of amylose. In contrast, dough with small-sized starch had higher intermolecular interactions, and denser structure, lower water migration, showing that this has better resistance and higher stability. The presented mechanisms may contribute to the better understanding of the effects of freeze–thaw process on model dough properties.

Facile preparation of polybenzimidazole membrane crosslinked with three-dimensional polyaniline for high-temperature proton exchange membrane

Phosphoric acid (PA) doped polybenzimidazole (PBI) membrane has been regarded as one of most effective high temperature proton exchange membrane (HT-PEM). However, it has to face poor mechanical properties at high acid doping levels (ADLs) and significant acid loss at high temperature during the operation of fuel cell. Herein, we prepare cross-linked PBI membranes containing different contents of the cross-linker three-dimensional polyaniline (PANI) via a facile N-substitution reaction. The obtained cross-linked PBI membrane exhibits superior tensile strength, stability and proton conductivity. More importantly, robust mechanical strength and good acid retention of the PA-doped cross-linked PBI membrane are demonstrated even at high ADL (above 20). The cross-linked PANI-30%-g-OPBI membrane exhibits a high ADL of 22.9, high proton conductivity of 122.8 mS cm−1 at 160 °C. Furthermore, the peak power density reaches 447 mW cm−2 at 160 °C, which is 2.5 times than that based on the corresponding PBI membrane. Molecular dynamics simulation results indicate that the decreased mobility of polymer chains improve the mechanical properties of the cross-linked membranes, and the high intermolecular interaction energy of the aniline-biphosphate ion pair significantly decrease PA leaching in the membranes due to the introduction of 3D molecular structure of PANI.

High-sulfur bitumen amplifies the effect of polyphosphoric acid

This study examines the effect of polyphosphoric acid (PPA) in bitumens with low-sulfur content and high-sulfur (10% sulfur) content. The recently lowered limit on the sulfur content of marine fuel will result in increased sulfur content of the bitumen remaining at the bottom of the barrel. Since the effect of PPA on bitumen's performance highly depends on bitumen’s composition, we hypothesize that high-sulfur bitumen, with an increased content of sulfoxide due to aging, will have higher intermolecular interactions with PPA leading to increase in bitumen’s elasticity. We used computational modeling and laboratory experiments to examine this hypothesis. Based on the results, under laboratory aging, the content of sulfoxide is increased for bitumen samples containing sulfur; a greater increase is observed for high-sulfur bitumen. Our molecular modeling, showed that H-bonding and H-transfer interactions of PPA’s terminal OH with sulfoxide’s polar group (S = O) are responsible for the effective interaction between the two components. The H-transfer interaction has a considerable binding energy (-70.0 kcal/mol), although it is not dominant. H-bonding interactions, with lower binding energy (−(17–22) kcal/mol), are dominant. The high concentration of sulfoxides and dominant contribution of H-bonding interactions can provide an impressive improvement in bitumen’s performance. Upon the introduction of PPA to each bitumen, high–sulfur bitumen showed about 22% increase in percent recovery, while low-sulfur bitumen showed about 12% increase in percent recovery. A higher percent recovery is an indicator of enhanced elasticity. This was also evidenced in a significantly higher complex shear modulus in high-sulfur bitumen compared to low-sulfur bitumen.

Predicting glass transition of amorphous polymers by application of cheminformatics and molecular dynamics simulations

Predicting the glass-transition temperatures (Tg) of glass-forming polymers is of critical importance as it governs the thermophysical properties of polymeric materials. The cheminformatics approaches based on machine learning algorithms are becoming very useful in predicting the quantitative relationships between key molecular descriptors and various physical properties of materials. In this work, we developed a modeling framework by integrating the cheminformatics approach and coarse-grained molecular dynamics (CG-MD) simulations to predict Tg of a diverse set of polymers. The developed machine learning-based QSPR model identified the most prominent molecular descriptors influencing the Tg of a hundred of polymers. Informed by the QSPR model, CG-MD simulations are performed to further delineate mechanistic interpretation and systematic dependence of these influential molecular features on Tg by investigating three major CG model parameters, namely the cohesive interaction, chain stiffness, and grafting density. The CG-MD simulations reveal that the higher intermolecular interaction and chain stiffness increase the Tg of CG polymers, where their relative influences are coupled with the existence of side chains grafted on the backbone. This synergistic modeling framework provides valuable insights into the roles of key molecular features influencing the Tg of polymers, paving the way to establishing a materials-by-design framework for polymeric materials via molecular engineering.

Development of whey protein isolate/chitosan/microcrystalline cellulose‐based bilayer films using surface‐pretreated polyethylene terephthalate substrate

AbstractPolyethylene terephthalate (PET) has been widely used in food packaging due to its excellent comprehensive properties, but has relatively low barrier properties towards small molecules. In this study, whey protein isolate (WPI)/chitosan (CS)/microcrystalline cellulose (MCC) solution was sprayed evenly on PET which pretreated by corona discharge (CD) and uniform glow discharge (UGD) plasma to prepare WPI/CS/MCC/PET bilayer film, and the properties, structure, and morphology of films were characterized. The water contact angle of UGD treated PET was significantly decreased by 79.01% due to increased polar functional groups. After coated with WPI/CS/MCC film, the reduced oxygen and carbon dioxide transmission rates of untreated and pretreated PET was in the range of 71.74–94.64%, and UGD pretreatment was more efficient to improve gas barrier properties than CD, but the mechanical and water vapor barrier properties of pretreated bilayer film weakened a little. There was a high intermolecular interaction between hydroxyl and amino groups of WPI/CS/MCC film and polar groups, such as COC and CH bonds, carbonyl, and methyl groups, of UGD‐pretreated PET, as verified by Fourier transform infrared with attenuated total reflection. In conclusion, UGD‐pretreated WPI/CS/MCC/PET bilayer film was significantly efficient to enhance the gas barrier properties of single‐layer PET.Practical ApplicationsPolyethylene terephthalate (PET) has relatively low barrier properties and its application has been limited in food high air tightness packaging. The present study aimed to develop biopolymer‐based high barrier bilayer film using surface‐pretreated PET substrate. The thermogravimetric analysis, mechanical, and barrier properties were investigated, and the structural characterization and morphology of bilayer films were investigated by Fourier transform infrared with attenuated total reflection analysis, environmental scanning electron microscopy, and atomic force microscope. This work provides a foundation for enhancing the gas barrier properties of single‐layer PET using the combination of biopolymer‐based coating and surface pretreatment.

High-density polyethylene/asphaltene composites: Thermal, mechanical and morphological properties

In this work, a series of high-density polyethylene (HDPE)/asphaltene composites were fabricated via the melt blending method. The composites were characterized, and the degradability, thermal, and mechanical stabilities of the products were analyzed. TGA results showed that HDPE/asphaltene composites had better thermal properties, e.g. higher degradation temperatures than asphaltene-free pristine HDPE. The high intermolecular interactions between the asphaltene and HDPE resulted in the degradation mechanism break, delaying the decomposition of composites and increasing their thermal stabilities. The results of DSC analysis indicated that the presence of asphaltene induces higher crystallinity and melting temperature in the composite matrix. According to the XRD results, the crystalline size was increased by increasing the asphaltene loading level due to the nucleating effect of asphaltene and the proper interactions developed between the asphaltene particles and HDPE chains. The proper dispersion of asphaltene in the composite matrix was confirmed by SEM images. The obtained results from the hardness analysis indicated higher mechanical stability for the composites, proportional to the content of the incorporated asphaltene to the composite. The results showed that asphaltene can be considered as an appropriate choice to improve the HDPE properties.

Demystifying the catalytic pathway of Mycobacterium tuberculosis isocitrate lyase

Pulmonary tuberculosis, caused by Mycobacterium tuberculosis, is one of the most persistent diseases leading to death in humans. As one of the key targets during the latent/dormant stage of M. tuberculosis, isocitrate lyase (ICL) has been a subject of interest for new tuberculosis therapeutics. In this work, the cleavage of the isocitrate by M. tuberculosis ICL was studied using quantum mechanics/molecular mechanics method at M06-2X/6-31+G(d,p): AMBER level of theory. The electronic embedding approach was applied to provide a better depiction of electrostatic interactions between MM and QM regions. Two possible pathways (pathway I that involves Asp108 and pathway II that involves Glu182) that could lead to the metabolism of isocitrate was studied in this study. The results suggested that the core residues involved in isocitrate catalytic cleavage mechanism are Asp108, Cys191 and Arg228. A water molecule bonded to Mg2+ acts as the catalytic base for the deprotonation of isocitrate C(2)–OH group, while Cys191 acts as the catalytic acid. Our observation suggests that the shuttle proton from isocitrate hydroxyl group C(2) atom is favourably transferred to Asp108 instead of Glu182 with a lower activation energy of 6.2 kcal/mol. Natural bond analysis also demonstrated that pathway I involving the transfer of proton to Asp108 has a higher intermolecular interaction and charge transfer that were associated with higher stabilization energy. The QM/MM transition state stepwise catalytic mechanism of ICL agrees with the in vitro enzymatic assay whereby Asp108Ala and Cys191Ser ICL mutants lost their isocitrate cleavage activities.

Human Rhinovirus Inhibition Through Capsid "Canyon" Perturbation: Structural Insights into The Role of a Novel Benzothiophene Derivative.

The challenge in targeting human rhinoviruses (HRV) over the years has been attributed to the wide variety in HRV serotypes. Nonetheless, the search for therapeutic agents against HRV continues unabated. These efforts have been augmented by the recent discovery of the novel benzothiophene derivative shown to inhibit HRV viral replication. Bound to subtype HRV-B14, the compound showed similar inhibitory activity as Pleconaril, a known capsid inhibitor. However, the molecular and structural basis of this inhibition remains unclear. In this in silico report, residue interaction network analysis revealed that the binding of the benzothiophene derivative into the "canyon" region of the active site of HRV-B14 distorts its initially extensively networked and compact residue profile. This was characterized by fewer inter-residue hydrogen bonds, reduced van der Waals interactions, and increased residue flexibility. Interestingly, however, the binding of this benzothiophene derivative decreased the flexibility of the north-south wall around the canyon region possibly impeding the "breathing motion" of HRV-B14, hence its inhibition. Atomistic insights also revealed the cruciality of Tyr152 toward inhibitor binding at HRV-B14. This was justified by the amino acid's high intermolecular interaction with both inhibitors. Findings provide important structural insights in the inhibitory activity the novel benzothiophene derivative, and reaffirm its promising potential as an alternative capsid inhibitor toward common cold therapy upon further experimental validation.

Study to improve an amphoteric sulfonate alkyl ester surfactant by mixing with nonionic surfactant to reduce brine\u2013waxy oil interfacial tension and to increase oil recovery in sandstone reservoir: T-KS field, Indonesia

Crude oil with a high wax content and high pour point can be very challenging when enhanced oil recovery by surfactant flooding is to be applied. High wax content in crude oil will lead to high intermolecular interaction because of the increasing cohesion forces. It causes interfacial (IFT) tension between oil and brine to be high. Hence, oil recovery is relatively low. This paper presents formulation of an amphoteric sulfonate alkyl ester (SAE) surfactant with a nonionic surfactant (ester group) to reduce oil–brine IFT in waxy oil of T-KS field, in Indonesia. The ion–dipole forces may occur between SAE surfactant and nonionic cosurfactant molecules. The forces cause sulfonate chain to be attracted to oil phase. The formulated surfactant produces low interfacial tension between brine and waxy oil of T-KS oil field. Its ability to displace remaining oil in the pore space was also tested using coreflood tests. These tests demonstrate considerably good incremental recovery.