Machine Learning-Assisted Computational Screening of Adhesive Molecules Derived from Dihydroxyphenyl Alanine.

Marine mussels adhere to virtually any surface via 3,4-dihydroxyphenyl-L-alanines (L-DOPA), an amino acid largely contained in their foot proteins. The biofriendly, water-repellent, and strong adhesion of L-DOPA are unparalleled by any synthetic adhesive. Inspired by this, we computationally designed diverse derivatives of DOPA and studied their potential as adhesives or coating materials. We used first-principles calculations to investigate the adsorption of the DOPA derivatives on graphite. The presence of an electron-withdrawing group, such as nitrogen dioxide, strengthens the adsorption by increasing the π-π interaction between DOPA and graphite. To quantify the distribution of electron charge and to gain insights into the charge distribution at interfaces, we performed Bader charge analysis and examined charge density difference plots. We developed a quantitative structure-property relationship (QSPR) model using an artificial neural network (ANN) to predict the adsorption energy. Using the three-dimensional and quantum mechanical electrostatic potential of a molecule as a descriptor, the present quantum NN model shows promising performance as a predictive QSPR model.

Development of novel chromones as antioxidant COX2 inhibitors: in vitro, QSAR, DFT, molecular docking, and molecular dynamics studies.

The chromone derivatives are playing a prominent role in many plant cycles, for instance, the regulation of growth, stimulation of oxygen uptake in plants, and essential food constituents with valuable pro-health properties. Determination of the antioxidant activity of these compounds is an interesting approach to drug design and development. The antioxidant activity of the novel fifteen chromone compounds was estimated by using a spectrophotometric Dichloro-5,6-dicyano 1,4-benzoquinone (DDQ) assay method and the mechanism of antioxidant activity was discussed based on the Density functional theory (DFT) calculations. The compounds showed significant antioxidant activity which was correlated to their molecular structure by considering various molecular descriptors. Further, by using regression analysis QSAR-modeled equation was proposed and it has shown a high correlation coefficient value (0.946. We perform molecular docking and molecular dynamics simulations against the cyclooxygenase (COX2) enzyme to investigate the molecule's anti-inflammatory activity and stability of protein-ligand complexes. Molecular docking and dynamics simulations revealed the compounds B3 and B8 were interacting with essential residues TYR385, HIS386, ASN382, TRP387, and HIS388 in the binding site that were crucial for optimizing heme and the resultant peroxidase and cyclooxygenase activities. The root mean square displacement and root mean square fluctuation plots revealed the stability of the B3-COX2 and B8-COX2 complexes. Based on our results, B3 and B8 compounds are considered as best antioxidants as well as COX2 inhibitors.Communicated by Ramaswamy H. Sarma.

Orchestrating the impact of antisites and vacancy defects on the elastic and optoelectronic properties of boron arsenide.

CONTEXT: Cubic boron arsenide (c-BAs), a semiconducting material with ultra-high thermal conductivity and carrier mobilities, has been studied using first-principles calculation. This study examined the elastic and optoelectronic properties of c-BAs. The challenge of subphase boron (B) formation in bulk form owing to the volatile nature of arsenic (As) makes it mandatory to calculate its optoelectronic properties, by producing vacancies and antisite defects with BAs (As atom on a B site) and AsB (B atom on an As site). The mechanical properties including bulk (B), shear (G) moduli, and Poison's ratio of all the systems were studied. It was found that mechanical instability of the structure is observed for the overall vacancy creation, arsenic substitution, and mutual antisite defects. Further, pristine c-BAs showed an indirect bandgap of 1.48 eV. Defect formation reduces the bandgap and shifts the absorption peaks, which improves the overall optoelectronic properties of the host material. In addition, B vacancy formation shows the maximum optical absorption and reflectivity and low energy loss, suggesting its potential applications for optoelectronic devices. The obtained anticipated data from this study is for the optoelectronic and elastic properties of c-BAs, for the device applications in photonics and electronics. METHOD: In this paper, the elastic and optoelectronic properties of the pristine and defected c-BAs were systematically investigated using the Spanish Initiative for Electronic Simulations with Thousands of Atoms (SIESTA). The SIESTA program uses pseudopotentials in the norm-conserving nonlocal forms and pseudo-atomic orbital (PAO) basis set with a double-zeta potential (DZP) which are fundamental for calculating the Hamiltonian and overlap matrices in O(N) operations.

Mobile Point-of-Care Device Using Molecularly Imprinted Polymer-Based Chemosensors Targeting Interleukin-1ß Biomarker.

Molecularly imprinted polymers (MIPs) have garnered significant attention as a promising material for engineering specific biological receptors with superior chemical complementarity to target molecules. In this study, we present an electrochemical biosensing platform incorporating MIP films for the selective detection of the interleukin-1ß (IL-1ß) biomarker, particularly suitable for mobile point-of-care testing (POCT) applications. The IL-1ß-imprinted biosensors were composed of poly(eriochrome black T (EBT)), including an interlayer of poly(3,4-ethylene dioxythiophene) and a 4-aminothiophenol monolayer, which were electrochemically polymerized simultaneously with template proteins (i.e., IL-1ß) on custom flexible screen-printed carbon electrodes (SPCEs). The architecture of the MIP films was designed to enhance the sensor sensitivity and signal stability. This approach involved a straightforward sequential-electropolymerization process and extraction for leaving behind cavities (i.e., rebinding sites), resulting in the efficient production of MIP-based biosensors capable of molecular recognition for selective IL-1ß detection. The electrochemical behaviors were comprehensively investigated using cyclic voltammograms and electrochemical impedance spectroscopy responses to assess the imprinting effect on the MIP films formed on the SPCEs. In line with the current trend in in vitro diagnostic medical devices, our simple and effective MIP-based analytical system integrated with mobile POCT devices offers a promising route to the rapid detection of biomarkers, with particular potential for periodontitis screening.

Depolymerized Chitosan-g-[Poly(MMA-co-HEMA-cl-EGDMA)] Based Nanogels for Controlled Local Release of Bupivacaine.

This study is designed to formulate and characterize chitosan-based nanogels that provide the controlled delivery of anesthetic drugs, such as bupivacaine (BPV), for effective postoperative pain management over prolonged periods of time. Drug carriers of chitosan/poly (MMA-co-HEMA-cl-EGDMA) (CsPMH) nanogels were prepared by varying the composition of comonomers such as MMA, HEMA, and redox initiator CAN. The nanogels were then characterized using FTIR, TGA, SEM, and TEM. The CsPMH nanogels showed greater encapsulation efficiencies from 43.20-91.77%. Computational studies were also conducted to evaluate the interaction between the drug and CsPMH nanoparticles. Finally, BPV-loaded nanoparticles were used to examine their in vitro release behavior. At pH 7.4, all the drug carriers displayed the "n" value around 0.7, thus the BPV release follows anomalous diffusion. Drug carrier 7 demonstrated a steady and sustained release of BPV for approximately 24 h and released about 91% of BPV, following the K-P mechanism of drug release. On the other hand, drug carrier 6 exhibited controlled release for approximately 12 h and released only 62% of BPV.

Machine-Learning Approach in Prediction of the Wettability of a Surface Textured with Microscale Pillars.

Tuning the wettability of a flat surface by introducing an array of microscale pillars finds wide applications, especially in engineering a superhydrophobic surface. The wettability of such a pillared surface is quantified by the contact angle (CA) of a water droplet. It is desired to know the CA prior to construction of pillars, in order to obviate the trial-and-errors in experimenting with many different topographies. Given an accurate theoretical prediction of CA has been elusive, we propose a convolutional neural network (CNN) model of CA for a surface patterned with rectangular or cylindrical pillars. By employing a three-dimensional descriptor of the surface topography, the present CNN model can predict experimental CAs within errors comparable to the uncertainties in measuring CAs.

Molecular modeling and simulation of transition metal-doped molybdenum disulfide biomarkers in exhaled gases for early detection of lung cancer.

BACKGROUND: The presence of volatile organic compounds (VOCs) in the exhaled breath of lung cancer patients is the only available source for detecting the disease at its initial stage. Exhaled breath analysis depends purely on the performance of the biosensors. The interaction between VOCs and pristine MoS2 is repulsive in nature. Therefore, modifying MoS2 via surficial adsorption of the transition metal nickel is of prime importance. The surficial interaction of six VOCs with Ni-doped MoS2 led to substantial variations in the structural and optoelectronic properties compared to those of the pristine monolayer. The remarkable improvement in the conductivity, thermostability, good sensing response, and recovery time of the sensor exposed to six VOCs revealed that a Ni-doped MoS2 exhibits impressive properties for the detection of exhaled gases. Different temperatures have a significant impact on the recovery time. Humidity has no effect on the detection of exhaled gases upon exposure to VOCs. The obtained results may encourage the use of exhaled breath sensors by experimentalists and oncologists to enable potential advancements in lung cancer detection. METHODS: The surface adsorption of transition metal and its interaction with volatile organic compounds on a MoS2 surface was studied by using Spanish Initiative for Electronic Simulations with Thousands of Atoms (SIESTA). The pseudopotentials used in the SIESTA calculations are norm-conserving in their fully nonlocal forms. The atomic orbitals with finite support were used as a basis set, allowing unlimited multiple-zeta and angular momenta, polarization, and off-site orbitals. These basis sets are the key for calculating the Hamiltonian and overlap matrices in O(N) operations. The present hybrid density functional theory (DFT) is a combination of PW92 and RPBE methods. Additionally, the DFT+U approach was employed to accurately ascertain the coulombic repulsion in the transition elements.

Computer simulation approach to the identification of visfatin-derived angiogenic peptides.

Angiogenesis plays an essential role in various normal physiological processes, such as embryogenesis, tissue repair, and skin regeneration. Visfatin is a 52 kDa adipokine secreted by various tissues including adipocytes. It stimulates the expression of vascular endothelial growth factor (VEGF) and promotes angiogenesis. However, there are several issues in developing full-length visfatin as a therapeutic drug due to its high molecular weight. Therefore, the purpose of this study was to develop peptides, based on the active site of visfatin, with similar or superior angiogenic activity using computer simulation techniques.Initially, the active site domain (residues 181∼390) of visfatin was first truncated into small peptides using the overlapping technique. Subsequently, the 114 truncated small peptides were then subjected to molecular docking analysis using two docking programs (HADDOCK and GalaxyPepDock) to generate small peptides with the highest affinity for visfatin. Furthermore, molecular dynamics simulations (MD) were conducted to investigate the stability of the protein-ligand complexes by computing root mean square deviation (RSMD) and root mean square fluctuation(RMSF) plots for the visfatin-peptide complexes. Finally, peptides with the highest affinity were examined for angiogenic activities, such as cell migration, invasion, and tubule formation in human umbilical vein endothelial cells (HUVECs). Through the docking analysis of the 114 truncated peptides, we screened nine peptides with a high affinity for visfatin. Of these, we discovered two peptides (peptide-1: LEYKLHDFGY and peptide-2: EYKLHDFGYRGV) with the highest affinity for visfatin. In an in vitrostudy, these two peptides showed superior angiogenic activity compared to visfatin itself and stimulated mRNA expressions of visfatin and VEGF-A. These results show that the peptides generated by the protein-peptide docking simulation have a more efficient angiogenic activity than the original visfatin.

Molecular Simulation Study on the Wettability of a Surface Texturized with Hierarchical Pillars.

By using molecular dynamics simulation, we investigate the wettability of a surface texturized with a periodic array of hierarchical pillars. By varying the height and spacing of the minor pillars on top of major pillars, we investigate the wetting transition from the Cassie-Baxter (CB) to Wenzel (WZ) states. We uncover the molecular structures and free energies of the transition and meta-stable states existing between the CB and WZ states. The relatively tall and dense minor pillars greatly enhance the hydrophobicity of a pillared surface, in that, the CB-to-WZ transition requires an increased activation energy and the contact angle of a water droplet on such a surface is significantly larger.

Modulating Optoelectronic and Elastic Properties of Anatase TiO2 for Photoelectrochemical Water Splitting.

Titanium dioxide (TiO2) has been investigated for solar-energy-driven photoelectrical water splitting due to its suitable band gap, abundance, cost savings, environmental friendliness, and chemical stability. However, its poor conductivity, weak light absorption, and large indirect bandgap (3.2 eV) has limited its application in water splitting. In this study, we precisely targeted these limitations using first-principle techniques. TiO2 only absorbs near-ultraviolet radiation; therefore, the substitution (2.1%) of Ag, Fe, and Co in TiO2 significantly altered its physical properties and shifted the bandgap from the ultraviolet to the visible region. Cobalt (Co) substitution in TiO2 resulted in high absorption and photoconductivity and a low bandgap energy suitable for the reduction in water without the need for external energy. The calculated elastic properties of Co-doped TiO2 indicate the ductile nature of the material with a strong average bond strength. Co-doped TiO2 exhibited fewer microcracks with a mechanically stable composition.

Theoretical and Experimental Studies of Hydrogen Bonded Dihydroxybenzene Isomers Polyurethane Adhesive Material.

Hydrogen bonding in polyurethane (PU) is imposed by molecular parameters. In this study, the effect of structural isomerism of certain monomers on hydrogen bonding of waterborne polyurethane (WBPU) was studied theoretically and experimentally. Two dihydroxybenzene (DHB)-based structural isomers such as catechol (CC) and hydroquinone (HQ), with different OH positions on the inner benzene core, had been used. Two series of WBPU dispersions were prepared using CC and HQ with defined contents. The binding energies between the catechol (CC)/hydroquinone (HQ) (respective OH group) and urethane/urea were calculated theoretically. By using a density functional theory (DFT) method, it was found that the largest binding energy between the urea and CC was higher than that of urea and HQ. The FT-IR analysis of synthesized polymer was also carried out to compare the results with the theoretical values. The CC-based polymers showed a stronger hydrogen bond both theoretically and experimentally than those for HQ-based polymers. The higher level of hydrogen bond was reflected in their properties of CC-based polymers. The adhesive strength, thermal stability, and hydrophobicity were higher for CC-based materials than those for HQ-based materials. The adhesive strength was increased 25% with the addition of 2.0 wt% CC content. This adhesive strength slightly deviated at a moderately high temperature of 80 °C.

A Combination of Pharmacophore-Based Virtual Screening, Structure-Based Lead Optimization, and DFT Study for the Identification of S. epidermidis TcaR Inhibitors.

The transcriptional regulator (TcaR) enzyme plays an important role in biofilm formation. Prevention of TcaR-DNA complex formation leads to inhibit the biofilm formation is likely to reveal therapeutic ways for the treatment of bacterial infections. To identify the novel ligands for TcaR and to provide a new idea for drug design, two efficient drug design methods, such as pharmacophore modeling and structure-based drug design, were used for virtual screening of database and lead optimization, respectively. Gemifloxacin (FDA-approved drug) was considered to generate the pharmacophore model for virtual screening of the ZINC database, and five hits, namely ZINC77906236, ZINC09550296, ZINC77906466, ZINC09751390, and ZINC01269201, were identified as novel inhibitors of TcaR with better binding energies. Using structure-based drug design, a set of 7a-7p inhibitors of S. epidermidis were considered, and Mol34 was identified with good binding energy and high fitness score with improved pharmacological properties. The active site residues ARG110, ASN20, HIS42, ASN45, ALA38, VAL63, VAL68, ALA24, VAL43, ILE57, and ARG71 are playing a promising role in inhibition process. In addition, we performed DFT simulations of final hits to understand the electronic properties and their significant role in driving the inhibitor to adopt apposite bioactive conformations in the active site. Conclusively, the newly identified and designed hits from both the methods are promising inhibitors of TcaR, which can hinder biofilm formation.

Molecular Modelling of Optical Biosensor Phosphorene-Thioguanine for Optimal Drug Delivery in Leukemia Treatment.

Thioguanine is an anti-cancer drug used for the treatment of leukemia. However, thioguanine has weak aqueous solubility and low biocompatibility, which limits its performance in the treatment of cancer. In the present work, these inadequacies were targeted using density functional theory-based simulations. Three stable configurations were obtained for the adsorption of thioguanine molecules on the phosphorene surface, with adsorption energies in the range of -76.99 to -38.69 kJ/mol, indicating physisorption of the drug on the phosphorene surface. The calculated bandgap energies of the individual and combined geometries of phosphorene and thioguanine were 0.97 eV, 2.81 eV and 0.91 eV, respectively. Owing to the physisorption of the drug molecule on the phosphorene surface, the bandgap energy of the material had a direct impact on optical conductivity, which was significantly altered. All parameters that determine the potential ability for drug delivery were calculated, such as the dipole moment, chemical hardness, chemical softness, chemical potential, and electrophilicity index. The higher dipole moment (1.74 D) of the phosphorene-thioguanine complex reflects its higher biodegradability, with no adverse physiological effects.

Molecular Insights on the Wetting Behavior of a Surface Corrugated with Nanoscale Domed Pillars.

Using all-atom molecular dynamics simulation, we investigated the wettability of a surface texturized with nanoscale pillars of domed, rectangular, or cylindrical shapes. The dewetted and wetted states of the gaps between the pillars were related to the Cassie-Baxter (CB) and Wenzel (WZ) states of a macroscopic water droplet resting on top of the pillars. We uncovered the structures and free energies of the intermediate states existing between the CB and WZ states. The contact line of the liquid-vapor-solid interface could not be depinned for the domed pillars due to their smooth curvatures unlike for the rectangular or cylindrical pillars. The liquid symmetrically penetrated down into the gap between the domed pillars by a liquid-vapor interface shape like a paraboloid, while the penetration for the rectangular or cylindrical pillars was often asymmetrical, giving a half-tubular liquid-vapor interface.

Wetting Behavior of a Surface with Dual-Scale Structures.

Theoretical and numerical studies were conducted to investigate the transitional interpillar spacing for dual-scale structures, where wetting transition between the Wenzel and Cassie-Baxter states occurs in the primary and secondary pillars. A theoretical formula was derived for the transitional interpillar spacing based on the continuum picture of water. Molecular dynamics (MD) simulations were carried out by varying the interpillar spacing for the primary pillars for single- and dual-scale structures with various pillar heights. The results obtained from the theoretical formula agreed reasonably well with the results obtained from MD simulations, especially when the primary pillar height was relatively high. The transitional interpillar spacing increases as the pillar height and the number of secondary pillars increase. The effect of the secondary pillars on the transitional interpillar spacing was also evaluated using the difference in the grand potentials between the Wenzel and Cassie-Baxter states. These results show that the dual-scale structures increase the transitional interpillar spacing with an increase in the surface hydrophobicity.

A density functional theory study on the underwater adhesion of catechol onto a graphite surface.

Mussel foot proteins (MFPs) strongly adhere to both hydrophilic and hydrophobic surfaces under wet conditions. This water-resistant adhesion of MFP is ascribed to catechol (1,2-dihydroxybenzene) which is highly contained in the MFP. Currently, little is known about the molecular details of the underwater adhesion of catechol onto a nonpolar hydrophobic surface. By using the density functional theory, we investigate the adhesion of catechol onto a wet graphite surface. We unveil the molecular geometry and energy in the course of the wet adhesion of catechol. Catechol adheres through π-π stacking with the underlying graphite. The surrounding water molecules further strengthen the adhesion by forming hydrogen bonds with catechol. In addition, a significant charge transfer has been observed from wet graphite to the catechol. Consequently, catechol adheres onto the present hydrophobic surface as strongly as onto a hydrophilic silica surface.

A New Series of EDOT Based Co-Sensitizers for Enhanced Efficiency of Cocktail DSSC: A Comparative Study of Two Different Anchoring Groups.

Herein, we report the design and synthesis strategy of a new class of five EDOT based co-sensitizers (CSGR1-5) by introducing different donors (2,3,4-trimethoxypheny, 2,4-dibutoxyphenyl, and 2,4-difluorophenyl) and anchoring groups (rhodamine-3-acetic acid and cyanoacetic acid) systematically. The synthesized metal-free organic co-sensitizers were employed for cocktail dye-sensitized solar cells along with N749 (black dye). The DSSC devices with a mixture of co-sensitizers (CSGR1-5) and N749 have shown a 7.95%, 8.40%, 7.81%, 6.56% and 6.99% power conversion efficiency (PCE) respectively, which was more than that of single N749 dye PCE (6.18%). Enhanced efficiency could be ascribed to the increased short circuit current (Jsc) and open circuit voltage (Voc). The increased Jsc was achieved due to enhanced light harvesting nature of N749 device upon co-sensitization with CSGR dyes and feasible energy levels of both the dyes. The Voc was improved due to better surface coverage which helps in decreasing the rate of recombination. The detailed optical and electrochemical properties were investigated and complimented with theoretical studies (DFT).

Thermal Effect on Positive Patterned Self-Assembled Monolayer Grown from a Droplet of Alkanethiol.

Atomic force microscope technique is widely used for the spatial narrow deposition of molecules inside the bare space of preexisting self-assembled monolayer (SAM) matrix. Using molecular dynamics simulation, we studied the formation of positively patterned SAM from a globule of 1-octadecanethiol (ODT) on predesigned SAM matrix of 1-dodecanethiol (DDT) and effect of temperature on it. The alkyl chains of ODT SAM were densely packed and ordered by means of chemisorption through sulfur atoms. The circular SAM of ODT contained defects due to the molecules those were standing upside down or trapped inside ODT SAM. We found that with the increase of temperature, these defects moved out by flipping of inverted ODT molecules or building spaces to be adsorbed on Au surface. The ODT molecules on the top of the pile of stable circular SAM or those are upside down and trapped disperse in a unique fashion namely serial pushing through which molecules firstly make a free space to enter inside the adsorbed thiol molecules and then push neighboring molecules to get enough space to be adsorbed on the gold surface. The stability of ODT SAM was confirmed by analyzing different structural properties such as tilt angle, tilt orientation. and backbone orientation. We also calculated the diffusion coefficient of the ODT molecules which were on the top of SAM island. © 2019 Wiley Periodicals, Inc.

Adenine-Based Zn(II)/Cd(II) Metal-Organic Frameworks as Efficient Heterogeneous Catalysts for Facile CO2 Fixation into Cyclic Carbonates: A DFT-Supported Study of the Reaction Mechanism.

We synthesized two new adenine-based Zn(II)/Cd(II) metal-organic frameworks (MOFs), namely, [Zn2(H2O)(stdb)2(5H-Ade)(9H-Ade)2]n (PNU-21) and [Cd2(Hstdb)(stdb)(8H-Ade)(Ade)]n (PNU-22), containing auxiliary dicarboxylate ligand (stdb = 4,4'-stilbenedicarboxylate). Both MOFs were characterized by multiple analytical techniques such as single-crystal X-ray diffraction (SXRD), powder X-ray diffraction, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, thermogravimetric analysis, scanning electron microscopy, as well as temperature program desorption and Brunauer-Emmett-Teller measurements. Both MOFs were structurally robust and possessed unsaturated Lewis acidic metal centers [Zn(II) and Cd(II)] and free basic N atoms of adenine molecules. They were used as heterogeneous catalysts for the fixation of CO2 into five-membered cyclic carbonates. Significant conversion of epichlorohydrin (ECH) was attained at a low CO2 pressure (0.4 MPa) and moderate catalyst (0.6 mol %)/cocatalyst (0.3 mol %) amounts, with over 99% selectivity toward the ECH carbonate. They showed comparable or even higher catalytic activity than other previously reported MOFs. Because of high thermal stability and robust architecture of PNU-21/PNU-22, both catalysts could be reused with simple separation up to five successive cycles without any considerable loss of their catalytic activity. Densely populated acidic and basic sites in both Zn(II)/Cd(II) MOFs facilitated the conversion of ECH to ECH carbonate in high yields. The reaction mechanism of the cycloaddition reaction between ECH and CO2 is described by possible intermediates, transition states, and pathways, from the density functional theory calculation in correlation with the SXRD structure of PNU-21.

Molecular features of hydration layers probed by atomic force microscopy.

Structurally-ordered layers of water are universally formed on a solid surface in aqueous solution or under ambient conditions. Although such hydration layers are commonly probed via atomic force microscopy (AFM), the current understanding on how the hydration layers manifest themselves in an AFM experiment is far from complete. By using molecular dynamics simulation, we investigate the hydration layers on a hydrophilic or hydrophobic surface probed by a nanoscale tip. We study the density and molecular orientation of water, the free energy, and the force on the tip by varying the tip-surface distance. The force-distance curve oscillates due to the transition between the mono-, bi-, and tri-layers of water confined between the tip and the surface. If both the tip and the surface are hydrophobic, water confined between the tip and the surface evaporates due to the dewetting transition, giving a hydrophobic force without oscillation. The periodicity of oscillation in the force differs from the structural periodicity of water. With a close proximity of the tip, the molecular dipoles align parallel to the surface, regardless of whether the tip and the surface are hydrophilic or hydrophobic.