Density functional theory study of the structure and energetics of negatively charged oligopyrroles

First‐principles calculations are used to investigate the electronic properties of negatively charged n‐pyrrole oligomers with n = 2–18. Chains of neutral oligomers are bent, whereas the negatively charged oligomers become almost planar due to accumulation of negative charge at the end monomers. Isomers of short oligomers (n < 6) display negative electron affinity although the corresponding anions are energetically stable. For longer oligomers with n ≥ 6, the electron affinity is small and positive, slowly increasing with oligopyrrole length. Doping of 12‐pyrrole with lithium atoms shows that negative oxidation states are possible due to electron transfer from dopant to oligomer at locations close to dopant. These 12‐pyrrole regions support extra negative charge and exhibit a local structural change from benzenoid to quinoid structure in the C? C backbone conjugation. Comparison between neutral and doped polypyrrole (PPy) indicates that doped polymers displays a substantial depletion of the band gap energy and the appearance of dopant‐based bands in the gap for a 50% per monomer doping level. It is predicted that Li‐doped PPy is not metallic. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Ensemble and Single Molecule Studies on the Use of Metallic Nanostructures to Enhance the Intrinsic Emission of Enzyme Cofactors

We present a strategy for enhancing the intrinsic emission of the enzyme cofactors flavin adenine dinucleotide (FAD), flavin mononucleotide (FMN) and nicotinamide adenine dinucleotide (NADH). Ensemble studies show that silver island films (SIFs) are the optimal metal enhanced fluorescence (MEF) substrates for flavins and gave emission enhancements of over 10-fold for both FAD and FMN. A reduction in the lifetime of FAD and FMN on SIFs was also observed. Thermally evaporated aluminum films on quartz slides were found to be the optimal MEF substrate for NADH and gave a 5-fold increase in the emission intensity of NADH. We present finite-difference time-domain (FDTD) calculations that compute the enhancement in the radiated power emitting from an excited state dipole emitting in the wavelength range of NADH in close proximity to an aluminum nanoparticle, and a dipole emitting in the emission wavelength of flavins next to a silver nanoparticle. These calculations confirm that aluminum serves as the optimal MEF substrate for NADH and silver was the optimal MEF substrate for flavins. This is because the plasmon resonance properties of aluminum lie in the UV-blue regime and that of silver lie in the visible region. We also present the results of single molecule studies on FMN which show SIFs can both significantly enhance the intrinsic emission from single FMN molecules, significantly reduce their lifetimes and also significantly reduce FMN blinking. This is the first report of the observation of MEF from cofactors both at the ensemble and single molecule level. We hope this study will serve as a platform to encourage the future use of metallic nanostructures to study cofactors using their intrinsic fluorescence to directly monitor enzyme binding reactions without the need of extrinsic labeling of the molecules.     

Theoretical study of excited state proton transfer in pyrrole-2-carboxylic acid

Pyrrole 2-carboxylic acid (PCA) shows dual emission (310 nm and 430 nm) in water on photo-excitation, which indicates that more than one species is in the excited state. This paper reports on the quantum chemical analysis of pyrrole 2-carboxylic acid (PCA) in the light of a possible excited state proton transfer. Dipole moment, excited state energy and findings in molecular orbital calculations (HOMO, LUMO) establish that PCA is a likely candidate for transfer of a proton from the pyrrole moiety to the C=O of carboxylic moiety (possible zwitterionic form) in the excited state. Overall, the computed predicted results of intramolecular and intermolecular excited state proton transfer corroborates the experimental results.     

Fabrication and characterization of freestanding ultrathin diamond-like carbon targets for high-intensity laser applications

Here, we report the fabrication of diamond-like carbon (DLC) thin films using pulsed laser deposition (PLD). PLD is a well-established technique for deposition of high-quality DLC thin films. Carbon tape target was ablated using a KrF (248 nm, 25 ns, 20 Hz) excimer laser to deposit DLC films on soap-coated substrates. A laser fluence between 8.5 and 14 J/cm² and a target to substrate distance of 10 cm was used. These films were then released from substrates to obtain freestanding DLC thin foils. Foil thicknesses from 20 to 200 nm were deposited using this technique to obtain freestanding targets of up to 1-inch square area. Typically, 100-nm-thick freestanding DLC films were characterized using different techniques such as AFM, XPS, and nano-indentation. AFM was used to obtain the film surface roughness of 9 nm rms of the released film. XPS was utilized to obtain 74 % sp², 23 % sp³, and 3 % C–O bond components. Nano-indentation was used to characterize the film hardness of 10 GPa and Young’s modulus of 110 GPa. Damage threshold properties of the DLC foils were studied (1,064 nm, 6 ns) and found to be 7 × 10¹⁰ W/cm² peak intensity for our best ultrathin DLC foils.     

Characteristics investigation on heat transfer growth of sonochemically synthesized ZnO-DW based nanofluids inside square heat exchanger

Journal of Thermal Analysis and Calorimetry - In recent decades, the growth of heat transfer using nanomaterials in the conventional&nbsp;base fluid has caught the attention of researchers...     

Natural Phytocompounds from Common Indian Spices for Identification of Three Potential Inhibitors of Breast Cancer: A Molecular Modelling Approach

Breast cancer is the second most common cancer-related cause of death for women throughout the globe. In spite of some effective measures, the main concerns with traditional anti-cancer chemotherapy are its low bioavailability, physical side effects, acquired resistance of cancer cells and non-specific targeting. Now researchers have taken the initiative to establish natural product-based therapy methods and to identify viable hits for future lead optimization in the development of breast cancer medication. Our study aims to identify the potent phytocompounds from five very popular Indian spices (Zingiber officinale Roscoe, Cuminum cyminum L., Piper nigrum L., Curcuma longa L., and Allium sativum L.). From these spices, a total of 200 phytocompounds were identified and screened against three target genes, namely, cyclin-dependent kinase 8 (CDK 8), progesterone receptor (PR) and epidermal growth factor receptor (EGFR), through structure-based virtual screening using iGEMDOCK 2.1 software. Based on the binding affinity score, the top three phytocompounds against each target protein (cynaroside (−149.66 Kcal/mol), apigetrin (−139.527 Kcal/mol) and curcumin (−138.149 Kcal/mol) against CDK8; apigetrin (−123.298 Kcal/mol), cynaroside (−118.635 Kcal/mol) and xyloglucan (−113.788 Kcal/mol) against PR; cynaroside (−119.18 Kcal/mol), apigetrin (−105.185 Kcal/mol) and xyloglucan (−105.106 Kcal/mol) against EGFR) were selected. Apigetrin, cynaroside, curcumin, and xyloglucan were finally identified for further docking analysis with the respective three target proteins. Autodock 4.2 was applied to screen the optimal binding position and to assess the relative intensity of binding interactions. In addition, the ADME/T property checks and bioactivity scores analysis of were performed to understand the suitability of these four phytocompounds to be potential candidates for developing effective and non-toxic anticancer agents. Based on this in silico analysis, we believe this study could contribute to current efforts to develop new drugs for treating breast cancer.     

Atomistic De-novo Inhibitor Generation-Guided Drug Repurposing for SARS-CoV-2 Spike Protein with Free-Energy Validation by Well-Tempered Metadynamics

Computational drug design is increasingly becoming important with new and unforeseen diseases like COVID-19. In this study, we present a new computational de novo drug design and repurposing method and applied it to find plausible drug candidates for the receptor binding domain (RBD) of SARS-CoV-2 (COVID-19). Our study comprises three steps: atom-by-atom generation of new molecules around a receptor, structural similarity mapping to existing approved and investigational drugs, and validation of their binding strengths to the viral spike proteins based on rigorous all-atom, explicit-water well-tempered metadynamics free energy calculations. By choosing the receptor binding domain of the viral spike protein, we showed that some of our new molecules and some of the repurposable drugs have stronger binding to RBD than hACE2. To validate our approach, we also calculated the free energy of hACE2 and RBD, and found it to be in an excellent agreement with experiments. These pool of drugs will allow strategic repurposing against COVID-19 for a particular prevailing conditions.     

Toward the molecular flashlight: preparation,properties, and photophysics of a hypericin-luciferin tethered molecule

The synthesis of a molecule containing hypericin and luciferin moieties joined by a tether is reported. The light-induced (in vitro) antiviral activity as well as the photophysical properties of this new compound are measured and compared with those of the parent compounds, hypericin and pseudohypericin. This tethered molecule exhibits excited-state behavior that is very similar to that of its parent compounds and antiviral activity that is identical, within experimental error, to that of its more closely related parent compound, pseudohypericin. The implications for a photodynamic therapy that is independent of external light sources are discussed.     

A proof of Howard’s conjecture in homogeneous parallel shear flows

A rigorous mathematical proof of Howard's conjecture which states that the growth rate of an arbitrary unstable wave must approach zero, as the wave length decreases to zero, in the linear instability of nonviscous homogeneous parallel shear flows, is presented here for the first time under the restriction of the boundedness of the second derivative of the basic velocity field with respect to the vertical coordinate in the concerned flow domain.