Photophysics of representative ketocyanine dyes: dependence on molecular structure

Spectral properties of a new fluorescent ketocyanine dye have been discussed. The energy of maximum absorption/fluorescence of the dye exhibits bathochromic shift with increasing polarity of the medium. Both dipolarity-polarisability and hydrogen bond donation interaction contribute to solvation of the dye. Study of fluorescence parameters points to existence of different emitting states of the dye for aprotic and protic solvents. While the emitting state is the (1)(π, π*) state for aprotic solvents, fluorescence supposedly take place from a different emitting state involving H-bond formation in the excited state in protic solvents. Fluorescence parameters of the dye have been compared with those for a structurally similar symmetric ketocyanine dye. The faster decay of the dye relative to its symmetric counterpart has been explained as due to an increase of nonradiative decay.     

Sensitivity of polar solvation dynamics to the secondary structures of aqueous proteins and the role of surface exposure of the probe

The structure and dynamics of water around a protein is expected to be sensitive to the details of the adjacent secondary structure of the protein. In this article, we explore this sensitivity by calculating both the orientational dynamics of the surface water molecules and the equilibrium solvation time correlation function of the polar amino acid residues in each of the three helical segments of the protein HP-36, using atomistic molecular dynamics simulations. The solvation dynamics of polar amino acid residues in helix-2 is found to be faster than that of the other two helices (the average time constant is smaller by a factor of 2), although the interfacial water molecules around helix-2 exhibit much slower orientational dynamics than that around the other two helices. A careful analysis shows that the origin of such a counterintuitive behavior lies in the dependence of the solvation time correlation function on the surface exposure of the probe-the more exposed is the probe, the faster the solvation dynamics. We discuss that these results are useful in explaining recent solvation dynamics experiments.     

Photodissociation Dynamics of Benzaldehyde (C6H5CHO) at 266, 248, and 193 nm

The photodissociation of gaseous benzaldehyde (C₆H₅CHO) at 193, 248, and 266 nm using multimass ion imaging and step‐scan time‐resolved Fourier‐transform infrared emission techniques is investigated. We also characterize the potential energies with the CCSD(T)/6‐311+G(3df,2p) method and predict the branching ratios for various channels of dissociation. Upon photolysis at 248 and 266 nm, two major channels for formation of HCO and CO, with relative branching of 0.37:0.63 and 0.20:0.80, respectively, are observed. The C₆H₅+HCO channel has two components with large and small recoil velocities; the rapid component with average translational energy of approximately 25 kJ mol^?1 dominates. The C₆H₆+CO channel has a similar distribution of translational energy for these two components. IR emission from internally excited C₆H₅CHO, ν₃ (v=1) of HCO, and levels v≤2, J≤43 of CO are observed; the latter has an average rotational energy of approximately 13 kJ mol^?1 and vibrational energy of approximately 6 kJ mol^?1. Upon photolysis at 193 nm, similar distributions of energy are observed, except that the C₆H₅+HCO channel becomes the only major channel with a branching ratio of 0.82±0.10 and an increased proportion of the slow component; IR emission from levels ν₁ (v=1) and ν₃ (v=1 and 2) of HCO and v≤2, J≤43 of CO are observed; the latter has an average energy similar to that observed in photolysis at 248 nm. The observed product yields at different dissociation energies are compared to statistical‐theory predicted results based on the computed singlet and triplet potential‐energy surfaces.     

Simplified,interpretable graph convolutional neural networks for small molecule activity prediction

Journal of Computer-Aided Molecular Design - We here present a streamlined, explainable graph convolutional neural network (gCNN) architecture for small molecule activity prediction. We first...     

Experimental investigation for stability and surface properties of TiO2 and Al2O3 water-based nanofluids

Journal of Thermal Analysis and Calorimetry - Nanofluids have gained recent attention because of their potential applications in diverse engineering fields like enhancing thermal transport,...     

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.     

Intermediates involved in serotonin oxidation catalyzed by Cu bound Aβ peptides

The degradation of neurotransmitters is a hallmark feature of Alzheimer''s disease (AD). Copper bound Aβ peptides, invoked to be involved in the pathology of AD, are found to catalyze the oxidation of serotonin (5-HT) by H₂O₂. A combination of EPR and resonance Raman spectroscopy reveals the formation of a Cu(ii)–OOH species and a dimeric, EPR silent, Cu₂O₂ bis-μ-oxo species under the reaction conditions. The Cu(ii)–OOH species, which can be selectively formed in the presence of excess H₂O₂, is the reactive intermediate responsible for 5-HT oxidation. H₂O₂ produced by the reaction of O₂ with reduced Cu(i)–Aβ species can also oxidize 5-HT. Both these pathways are physiologically relevant and may be involved in the observed decay of neurotransmitters as observed in AD patients.

The mononuclear copper hydroperoxo species (Cu(ii)–OOH) of Cu–Aβ is the active oxidant responsible for serotonin oxidation by Cu–Aβ in the presence of physiologically relevant oxidants like O₂ and H₂O₂, which can potentially cause oxidative degradation of neurotransmitters, a marker of Alzheimer''s disease.     

Self-Assembly of Benzimidazole-Derived Tris-NHC Ligands and AgI-Ions to Hexanuclear Organometallic Cages and Their Unusual Transmetalation Chemistry

Multi-ligand self-assembly to attain the Ag^I-N-heterocyclic carbene (NHC)-built hexanuclear organometallic cages of composition [Ag₆( 3 a , b )₄](PF₆)₆ from the reaction of benzimidazole-derived tris(azolium) salts [H₃- 3 a , b ](PF₆)₃ with Ag₂O was achieved. The molecular structures of the cages were established by X-ray diffraction studies along with NMR and MS analyses. The existence of a single assembly in solution was supported by diffusion-ordered spectroscopy (DOSY) ¹H NMR spectra. Further, transmetalation reactions of these self-assembled complexes, [Ag₆( 3 a , b )₄](PF₆)₆, with Cu^I/Au^I-ions provided various coinage metal-NHC complexes having diverse molecular compositions, which included the first example of a hexanuclear Cu^I-dodecacarbene complex, [Cu₆( 3 b )₄](PF₆)₆.     

Leveraging an enzyme/artificial substrate system to enhance cellular persulfides and mitigate neuroinflammation

Persulfides and polysulfides, collectively known as the sulfane sulfur pool along with hydrogen sulfide (H₂S), play a central role in cellular physiology and disease. Exogenously enhancing these species in cells is an emerging therapeutic paradigm for mitigating oxidative stress and inflammation that are associated with several diseases. In this study, we present a unique approach of using the cell''s own enzyme machinery coupled with an array of artificial substrates to enhance the cellular sulfane sulfur pool. We report the synthesis and validation of artificial/unnatural substrates specific for 3-mercaptopyruvate sulfurtransferase (3-MST), an important enzyme that contributes to sulfur trafficking in cells. We demonstrate that these artificial substrates generate persulfides in vitro as well as mediate sulfur transfer to low molecular weight thiols and to cysteine-containing proteins. A nearly 100-fold difference in the rates of H₂S production for the various substrates is observed supporting the tunability of persulfide generation by the 3-MST enzyme/artificial substrate system. Next, we show that the substrate 1a permeates cells and is selectively turned over by 3-MST to generate 3-MST-persulfide, which protects against reactive oxygen species-induced lethality. Lastly, in a mouse model, 1a is found to significantly mitigate neuroinflammation in the brain tissue. Together, the approach that we have developed allows for the on-demand generation of persulfides in vitro and in vivo using a range of shelf-stable, artificial substrates of 3-MST, while opening up possibilities of harnessing these molecules for therapeutic applications.

A persulfide/hydrogen sulfide generation strategy through artificial substrates for 3-mercaptopyruvate sulfurtransferase (3-MST) is reported, which enhances cellular persulfides, attenuates reactive oxygen species (ROS), and alleviates inflammation.