Heteroacene-Based Polymer with Fast-Switching Visible-Near Infrared Electrochromic Behavior.

The electrochromic properties and application of electronically conducting polymers (ECPs) (PTRPZ-EDOT) consisting of a 3,4-ethylenedioxythiophene (EDOT) and the heteroacene-based molecular scaffold, 6H-pyrrolo[3,2-b:4,5-b'] bis [1,4] benzothiazine (TRPZ), are reported. Known for its high electron mobility and conducting properties, the novel TRPZ scaffold was synthesized to possess two EDOT molecules termini affording TRPZ-EDOT. Electropolymerization of TRPZ-EDOT resulted in remarkable spectroscopic and conductive properties suitable for electrochromic device fabrication. Using atomic force microscopy (AFM), the average surface roughness and surface topography of PTRPZ-EDOT polymer thin films were determined. Spectroelectrochemical data showed that the polymer achieved switching times of 4.07 (coloration) and 0.47 s (bleaching) at 539 nm. The PTRPZ-EDOT film exhibits an optical contrast of 36-44% at 539 nm between its neutral and colored states, respectively. The NIR region from 1000 to 1700 nm shows the appearance of charge carrier bands with a 0-1 V potential range. An electrochromic device was successfully fabricated from PTRPZ-EDOT, showcasing the potential and applicability of the polymer material for advanced technologies such as smart windows, flexible electrochromic screens, and energy storage devices.

Investigation of cannabidiol's potential targets in limbic seizures. In-silico approach.

Even though the vast armamentarium of FDA-approved antiepileptic drugs is currently available, over one-third of patients do not respond to medication, which arises a need for alternative medicine. In clinical and preclinical studies, various investigations have shown the advantage of specific plant-based cannabidiol (CBD) products in treating certain groups of people with limbic epilepsy who have failed to respond to conventional therapies. This work aims to investigate possible mechanisms by which CBD possesses its anticonvulsant properties. Molecular targets for CBD's treatment of limbic epilepsy, including hyperpolarization-activated cyclic nucleotide-gated channel 1 (HCN1), gamma-aminobutyric acid aminotransferase (GABA-AT), and gamma-aminobutyric acid type A receptor (GABAA), were used to evaluate its binding affinity. Interactions with the CB1 receptor were initially modeled as a benchmark, which further proved the efficiency of proposed here approach. Considering the successful benchmark, we further used the same concept for in silico investigation, targeting proteins of interest. As a result of molecular docking, molecular mechanics, and molecular dynamics simulations models of CBD-receptor complexes were proposed and evaluated. While CBD possessed decently high affinity and stability within the binding pockets of GABA-AT and some binding sites of GABAA, the most effective binding was observed in the CBD complex with HCN1 receptor. 100 ns molecular dynamics simulation revealed that CBD binds the open pore of HCN1 receptor, forming a similar pattern of interactions as potent Lamotrigine. Therefore, we can propose that HCN1 can serve as a most potent target for cannabinoid antiepileptic treatment. Communicated by Ramaswamy H. Sarma.

Homology Modeling and Molecular Dynamics-Driven Search for Natural Inhibitors That Universally Target Receptor-Binding Domain of Spike Glycoprotein in SARS-CoV-2 Variants.

The rapid spread of SARS-CoV-2 required immediate actions to control the transmission of the virus and minimize its impact on humanity. An extensive mutation rate of this viral genome contributes to the virus' ability to quickly adapt to environmental changes, impacts transmissibility and antigenicity, and may facilitate immune escape. Therefore, it is of great interest for researchers working in vaccine development and drug design to consider the impact of mutations on virus-drug interactions. Here, we propose a multitarget drug discovery pipeline for identifying potential drug candidates which can efficiently inhibit the Receptor Binding Domain (RBD) of spike glycoproteins from different variants of SARS-CoV-2. Eight homology models of RBDs for selected variants were created and validated using reference crystal structures. We then investigated interactions between host receptor ACE2 and RBDs from nine variants of SARS-CoV-2. It led us to conclude that efficient multi-variant targeting drugs should be capable of blocking residues Q(R)493 and N487 in RBDs. Using methods of molecular docking, molecular mechanics, and molecular dynamics, we identified three lead compounds (hesperidin, narirutin, and neohesperidin) suitable for multitarget SARS-CoV-2 inhibition. These compounds are flavanone glycosides found in citrus fruits - an active ingredient of Traditional Chinese Medicines. The developed pipeline can be further used to (1) model mutants for which crystal structures are not yet available and (2) scan a more extensive library of compounds against other mutated viral proteins.

Heteroacene-Based Amphiphile as a Molecular Scaffold for Bioimaging Probes.

The challenges faced with current fluorescence imaging agents have motivated us to study two nanostructures based on a hydrophobic dye, 6H-pyrrolo[3,2-b:4,5-b']bis [1,4]benzothiazine (TRPZ). TRPZ is a heteroacene with a rigid, pi-conjugated structure, multiple reactive sites, and unique spectroscopic properties. Here we coupled TRPZ to a tert-butyl carbamate (BOC) protected 2,2-bis(hydroxymethyl)propanoic acid (bisMPA) dendron via azide-alkyne Huisgen cycloaddition. Deprotection of the protected amine groups on the dendron afforded a cationic terminated amphiphile, TRPZ-bisMPA. TRPZ-bisMPA was nanoprecipitated into water to obtain nanoparticles (NPs) with a hydrodynamic radius that was <150 nm. For comparison, TRPZ-PG was encapsulated in pluronic-F127 (Mw = 12 kD), a polymer surfactant to afford NPs almost twice as large as those formed by TRPZ-bisMPA. Size and stability studies confirm the suitability of the TRPZ-bisMPA NPs for biomedical applications. The photophysical properties of the TRPZ-bisMPA NPs show a quantum yield of 49%, a Stokes shift of 201 nm (0.72 eV) and a lifetime of 6.3 ns in water. Further evidence was provided by cell viability and cellular uptake studies confirming the low cytotoxicity of TRPZ-bisMPA NPs and their potential in bioimaging.

Computational studies on binding, solvent, and pH effects on (S)-propranolol and methacrylic acid complex.

Density functional theory methods have been applied to understand binding of (s)-propranolol, a template, to a methacrylic acid molecule acting as a functional monomer using basic 1:1 model. The model has been expanded to study the effect of various pH by adding hydronium and hydroxide ions solvated by water molecules to the template-monomer system, to mimic acidic and basic environments, respectively. This could be considered a model study towards a potential use of molecular imprinting method for the design of a transdermal patch for a topical and direct delivery of (s)-propranolol to hemangiomas. In addition, this study provides detailed binding site analysis of the template and functional monomer verified by the theoretical IR spectra analysis, as well as solvent and pH effects on template-monomer binding energy.

N-arylnaphthylamines as inhibitors of human immunodeficiency virus integrase - lens epithelium-derived growth factor interactions: theoretical studies.

Presented work reports a comprehensive theoretical study on the inhibitory nature of N-arylnaphthylamines in Human Immunodeficiency Virus Integrase (HIV IN) - Lens Epithelium-Derived Growth Factor (LEDGF/p75) complexes. Factors influencing the inhibition efficiency in AlphaScreen% assay are evaluated and explained through the structure- and ligand-based studies; including molecular docking, molecular dynamics calculations, and quantitative structure-activity relationship (QSAR) approach. It has been shown that N-arylnaphthylamines possess a wide variety of binding poses. Three QSAR models have been developed using structural descriptors and descriptors derived from docking calculations. The activity of untested N-arylnaphthylamines have been predicted using the most successful model. Proposed here technique could become a useful tool for ligand selection, accelerating the development of a new generation of anti-HIV medications. [Formula: see text] Communicated by Ramaswamy H. Sarma.

Protein reliability analysis and virtual screening of natural inhibitors for SARS-CoV-2 main protease (Mpro) through docking, molecular mechanic & dynamic, and ADMET profiling.

Due to an outbreak of COVID-19, the number of research papers devoted to in-silico drug discovery of potential antiviral drugs is increasing every day exponentially. Still, there is no specific drug to prevent or treat this novel coronavirus (SARS-CoV-2) disease. Thus, the screening for a potential remedy presents a global challenge for scientists. Up to date over a hundred crystallographic structures of SARS-CoV-2 Mpro have been deposited to Protein Data Bank. With many known proteins, the demand for a reliable target has become higher than ever, so as the choice of an efficient computational methods. Therefore, in this study comparative methods have been used for receptor-based virtual screening, targeting 9 selected structures of viral Mpro. Reliability analyses followed by re-docking of the specific co-crystallized ligand provided the best reproductivity for structures with PDB ID 6LU7, 6Y2G and 6Y2F. The influence of crystallographic water on an outcome of a virtual screening against selected targets was also investigated. Once the most reliable targets were selected, the library of easy purchasable natural compounds were retrieved from the MolPort database (10,305 compounds) and docked against the selected Mpro proteins. To ensure the efficiency of the selected compounds, binding energies for top-15 hit ligands were calculated using Molecular Mechanics as well as their absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties were predicted. Based on predicted binding energies and toxicities, top-5 compounds were selected and subjected to Molecular Dynamics simulation and found to be stable in complex to act as possible inhibitors for SARS-CoV-2. Communicated by Ramaswamy H. Sarma.

Structural, optical, photocatalytic, and optoelectronic properties of Zn2SnO4 nanocrystals prepared by hydrothermal method.

Zn2SnO4 (ZTO) nanocrystals are extensively studied in various fields. However, size-dependent ZTO nanocrystals are still challenging to understand their structural, optical, photocatalytic, and optoelectronic properties. ZTO nanocrystals are synthesized by a facile hydrothermal reaction method. The structural properties of the synthesized ZTO nanocrystals are studied by x-ray diffraction and transmission electron microscope. The sizes of the ZTO nanocrystals are controlled by the pH values of the precursor and the molar ratios of the Zn:Sn in the starting materials. ZTO nanocrystals with the small size of 6 nm and large size of 270 nm are obtained by our method. The Eu3+ ions are doped into ZTO nanocrystals to probe size-dependent Eu doping sites, which shows significant potential applications in light emitting diode phosphors. Moreover, the photocatalytic activity of ZTO nanocrystals on rhodamine (RhB) decoloration are investigated, and the results show that 6 nm ZTO nanocrystals show better performance in the photocatalytic decoloration of RhB compared to 270 nm nanocrystals. Most importantly, we design and fabricate optoelectronic devices to detect IR light based on our nanocrystals and a self-prepared NIR cyanine dye. The device based on small sized ZTO nanocrystals exhibits better device performance under 808 nm IR light compared to that of the large sized ZTO nanocrystals. We believe this work represents ZTO size-dependent properties in term of structural, optical, photocatalytic, and optoelectronic properties as a multifunctional material.

Antioxidant Activity of Selected Phenolic Acids-Ferric Reducing Antioxidant Power Assay and QSAR Analysis of the Structural Features.

Phenolic acids are naturally occurring compounds that are known for their antioxidant and antiradical activity. We present experimental and theoretical studies on the antioxidant potential of the set of 22 phenolic acids with different models of hydroxylation and methoxylation of aromatic rings. Ferric reducing antioxidant power assay was used to evaluate this property. 2,3-dihydroxybenzoic acid was found to be the strongest antioxidant, while mono hydroxylated and methoxylated structures had the lowest activities. A comprehensive structure-activity investigation with density functional theory methods elucidated the influence of compounds topology, resonance stabilization, and intramolecular hydrogen bonding on the exhibited activity. The key factor was found to be a presence of two or more hydroxyl groups being located in ortho or para position to each other. Finally, the quantitative structure-activity relationship approach was used to build a multiple linear regression model describing the dependence of antioxidant activity on structure of compounds, using features exclusively related to their topology. Coefficients of determination for training set and for the test set equaled 0.9918 and 0.9993 respectively, and Q2 value for leave-one-out was 0.9716. In addition, the presented model was used to predict activities of phenolic acids that haven't been tested here experimentally.

Pyridyl CO2 Fixation Enabled by a Secondary Hydrogen Bonding Coordination Sphere.

Reversible CO2 binders under ambient conditions are of significant interest for multiple applications in sensing and capture technologies. In this paper, a general systematic way to evaluate CO2 receptors with π-systems is put forward. A series of receptors (five pyridine-based and one triazine-based) are evaluated as CO2 binders in terms of number of hydrogen bonding sites, strength of hydrogen bond donors, and number of nucleophilic sites. The binding of CO2 to the receptors was probed by computational models, absorption spectroscopy, fluorescence spectroscopy, cyclic voltammetry, and 1H NMR studies. Multiple solvents with varying ionic strength additives are probed to analyze the effects on CO2-bound intermediates. The receptors were screened progressively down-selecting through the different analytical techniques arriving at a promising pyridine receptor, which shows evidence of CO2 binding with each of the analytical techniques. The diaminopyridine motif demonstrates reversible CO2 binding and has convenient substitution sites for derivatization to incorporate into functional sensor systems.

A DFT study of isolated histidine interactions with metal ions (Ni2+, Cu2+, Zn2+) in a six-coordinated octahedral complex.

Understanding the role that metal ions play in biological and material processes is critical to addressing a number of diseases and problems facing society today. There have been a number of studies that have begun to approach this concern from a myriad of different perspectives. However, there is still a considerable lack of understanding concerning the mechanisms and structures of metal-related problems, specifically biological and medical-related issues. Understanding the mechanism of ingestion and uptake of metals into the human body is critical to addressing many diseases such as Alzheimer's and certain types of cancers. Using computational techniques, this work adds to the overall understanding of metal interactions with proteins by focusing on metal ion interactions with the amino acid, histidine, one of the most common sites of metal attachment. In this work, the geometries of single and dual histidines attached to Ni2+, Cu2+, and Zn2+ ions at B3LYP/6-311G(d) are presented. The results show stable octahedral complexes associated with each of the metal ions. Free energy calculations suggest that all three complexes are spontaneous in the formation of the dual histidine-metal complexes. Nickel and copper are spontaneous in the formation of the single histidine complex, although the copper complex undergoes slight geometric changes. Zinc is found to be nonspontaneous in forming the single histidine complex. Finally, the reduction potential of the single histidine-metal complex is presented. All of the complexes show positive reduction potentials. However, the nickel and copper complexes undergo geometrical changes to adopt a square planar conformation. Graphical abstract The impact of metal ions in biological systems is of great importance to understanding a diverse number of diseases. By understanding the fundamentals of select ions complexed with histidines, greater understanding of the mechanisms of actions these ions play in health may be elucidated. This work presents initial structures and thermodynamics of histidine complexes with nickel, copper, and zinc metal ions.

Development of Human Host Defense Antimicrobial Peptide-Conjugated Biochar Nanocomposites for Combating Broad-Spectrum Superbugs.

Infectious diseases by multidrug-resistant superbugs, which cannot be cured using commercially available antibiotics, are the biggest threat for our society. Due to the lack of discovery of effective antibiotics in the last two decades, there is an urgent need for the design of new broad-spectrum antisuperbug biomaterials. Herein, we report the development of antisuperbug nanocomposites using human host defense antimicrobial peptide-conjugated biochar. To develop an economically viable technology, biochar, a carbon-rich material from naturally abundant resource, has been used. For combating broad-spectrum superbugs, a nanocomposite has been designed by combining biochar with α-defensin human neutrophil peptide-1 (HNP-1), human ß-defensin-1 (hBD-1), and human cathelicidin LL-37 antimicrobial peptide. The designed three-dimensional (3D) nanocomposites with pore size between 200 and 400 nm have been used as channels for water passage and captured superbugs. The reported data demonstrated that antimicrobial nanocomposite can be used for efficient capture and eradication of Gram-negative carbapenem-resistant Enterobacteriaceae (CRE) Escherichia coli (E. coli) and Klebsiella pneumoniae (KPN) superbugs, as well as Gram-positive methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) superbugs. Possible mechanisms for broad-spectrum antisuperbug activities using hydrogel have been discussed.

How water affects mercury-halogen interaction in the atmosphere.

The solvation of mercury and halogens ions in water is essential for studying the reaction kinetics of various mercury depletion reactions in the atmosphere. Here, we use two approaches. The first one is the implementation of transition state theory to study the recombination reactions of Hg2+and Hal- with the introduction of a water molecule as a third body part. The inclusion of solvation corrections to the total energy enables one to localize the barrier for such diatomic systems with explicit water molecule participation. The second approach is the molecular modeling of three mercuric halide ion pairs in water complexes [HgHal(H2O)n]+ (Hal = Cl, Br, I) by using the semiempirical tight-binding molecular dynamics combined with density functional theory calculations. Various [Hg-Hal]+ ion pairs behave similarly when hydrated and tend to adopt clathrate-like configurations with a [Hg2+(H2O)6] central motif and halogen ions residing on the external surface of the water complex. Contact ion pairs are energetically favorable for all complexes up to 50 water molecules. Further increase in the level of hydration stabilized the solvent-separated forms of [Hg-Hal]+ ion pairs, which matches the water affinity rule. The balance between the contact and the solvated ion pairs was shown to be ion-pair specific and temperature dependent. Graphical abstractThe structure of stable water complexes of mercury halides reflects the competition between water-water, Hg2+ -water, and Hal -water interactions.

Indolizine-Cyanine Dyes: Near Infrared Emissive Cyanine Dyes with Increased Stokes Shifts.

Molecular engineering strategies designed to red-shift cyanine dye absorptions and emissions further into the near-infrared (NIR) spectral region are explored. Through the use of a novel donor group, indolizine, with varying cyanine bridge lengths, dye absorptions and emissions, were shifted deeper into the NIR region than common indoline-cyanines. Stokes shifts resulting from intramolecular steric interactions of up to ∼60 nm in many cases were observed and explained computationally. Molecular brightnesses of up to 5800 deep into the NIR region were observed. Structure-property relationships are explored for the six indolizine-cyanine dyes with varying cyanine bridge length and indolizine substituents showing broad absorption and emission tunability. The dyes are characterized by crystallography, and the photophysical properties are probed by varying solvent for absorption and emission studies. Computational data show involvement of the entire indolizine π-system during light absorption, which suggests these systems can be tunable even further into the NIR region through select derivatizations.

Theoretical study of the pre- and post-translational effects of adenine and thymine tautomers and methyl derivatives.

The study of pre-translational effects (ionization, tautomerization) and post-translational effects (methylation) of adenine and thymine has only recently been the focus of some studies. These effects can potentially help regulate gene expression as well as potentially disrupt normal gene function. Because of this wide array of roles, greater insight into these effects in deoxyribonucleic acids (DNA) are paramount. There has been considerable research of each phenomenon (tautomerization, methylation and ionization) individually. In this work, we attempt to shed light upon the pre-translational effects and post translational effects of adenine and thymine by investigating the electron affinities (EAs) and ionization potentials (IPs) of the major and minor tautomers and their methyl derivatives. We performed all calculations using the density functional theory (DFT) B3LYP functional accompanied with 6-311G(d,p), 6-311+G(d,p) and 6-311++G(df,pd) basis sets. Our results reveal that the thymine tautomer has a higher EA and IP than the adenine tautomers. The higher EA suggests that an electron that attaches to the AT base pair would predominately attach to the thymine instead of adenine. The higher IP would suggest that an electron that is removed from the AT base pair would be predominately removed from the adenine within the base pair. Understanding how tautomerization, ionization and methylation differences change effects, discourages, or promotes one another is lacking. In this work, we begin the steps of integrating these effects with one another, to gain a greater understanding of molecular changes in DNA bases.

Theoretical investigation on monomer and solvent selection for molecular imprinting of nitrocompounds.

The aim of this work is to serve as a guideline for the initial selection of monomer and solvent for the synthesis of the nitrocompound-based molecularly imprinted polymers, MIPs. Reported data include evaluation of six systems with the ability to form noncovalently bonded monomer-template complexes. These systems are represented by the following aliphatic and aromatic molecules: acrolein, acrylonitrile, 2,6-bisacrylamide, 4-ethylenebenzoic acid, methyl methacrylate, and 2-vinylpyridine. Cave models for selected monomers are also presented and supported by binding energy analysis under various conditions. Solvent effects on monomer-template binding energy have been studied for four solvents: acetone, acetonitrile, chloroform, and methanol. Additionally, systems such as 2,4-dinitrotoluene (2,4-DNT), 2,6-dinitrotoluene (2,6-DNT), pentachlorophenol (PCP), and 3,6-dichloro-2-methoxybenzoic acid (Dicamba) have been used to study selectivity of acrolein-based MIP toward TNT detection. The density functional theory, DFT, method has been used for all structural, vibrational frequency, and solvent calculations.

Conventional strain energies of azetidine and phosphetane: can density functional theory yield reliable results?

The conventional strain energies for azetidine and phosphetane are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies and zero-point vibrational energies are computed for all pertinent molecular systems using self-consistent field theory, second-order perturbation theory, and density functional theory and using the correlation consistent basis sets cc-pVDZ, cc-pVTZ, and cc-pVQZ. Single point fourth-order perturbation theory, CCSD, and CCSD(T) calculations using the cc-pVTZ and the cc-pVQZ basis sets are computed using the MP2/cc-pVTZ and MP2/cc-pVQZ optimized geometries, respectively, to ascertain the contribution of higher order correlation effects and to determine if the quadruple-zeta valence basis set is needed when higher order correlation is included. In the density functional theory study, eight different functionals are used including B3LYP, wB97XD, and M06-2X to determine if any functional can yield results similar to those obtained at the CCSD(T) level.

Conformational analysis of flephedrone using quantum mechanical models.

Flephedrone is an analogue of cathinone - chemically similar to ephedrine, cathine and other amphetamines. Conformations of all isomers of flephedrone have been studied at the quantum-chemical level. Calculations have been performed using DFT and MP2 methods with two basis sets - 6-31G and 6-31G(d,p). Results show that there are low energy conformers for the ortho, meta, and para isomers that are connected by way of low-barrier transition states. Boltzmann distribution of population predicts the highest population for the 1-meta conformer with a 10% increase in solution. The molecular electrostatic potential surface data for each molecule has been calculated revealing likely reaction sites.

Density functional theory study on the interaction between keto-9H guanine and aspartic acid.

A theoretical study was performed using density functional theory (DFT) to investigate hydrogen bonding interactions in signature complexes formed between keto-9H guanine (Gua) and aspartic acid (Asp) at neutral pH. Optimized geometries, binding energies and the theoretical IR spectra of guanine, aspartic acid and their corresponding complexes (Gua-Asp) were calculated using the B3LYP method and the 6-31+G(d) basis set. Stationary points found to be at local minima on the potential energy surface were verified by second derivative harmonic vibrational frequency calculations at the same level of theory. AIM theory was used to analyze the hydrogen bonding characteristics of these DNA base complex systems. Our results show that the binding motif for the most stable complex is strikingly similar to a Watson-Crick motif observed in the guanine-cytosine base pair. We have found a range of hydrogen bonding interactions between guanine and aspartic acid in the six complexes. This was further verified by theoretical IR spectra of ω(C-H--O-H) cm(-1) stretches for the Gua-Asp complexes. The electron density plot indicates strong hydrogen bonding as shown by the 2p(z) dominant HOMO orbital character.

The evolution of bonding and thermodynamic properties of boron-doped small carbon clusters: an ab initio study.

Theoretical studies on BC(n) (n=1-6) clusters are carried out using density functional theory, Møller-Plesset second-order perturbation theory (MP2), coupled-cluster calculations including up to triple excitations (CCSD(T)), and higher-level approaches. All possible isomers depending on the positions of the boron atom are generated and the lowest-energy isomers are determined for doublet and quartet electronic states. The three potential evolution paths of the clusters are determined as a function of their size. The energetic and electronic consequences for the increased size of structures differ significantly, which leads to representatives of the ground electronic state from different structural groups. The ab initio calculated thermal functions allow enhancements to the available atomization energies and improve the agreement between the calculated and experimental heat content.