Understanding the Anomalous Diffusion of Water in Aqueous Electrolytes Using Machine Learned Potentials

The diffusivity of water in aqueous cesium iodide solutions is larger than that in neat liquid water, and vice versa for sodium chloride solutions. Such peculiar ion-specific behavior, called anomalous diffusion, is not reproduced in typical force field-based molecular dynamics (MD) simulations due to inadequate treatment of ion-water interactions. Herein, this hurdle is tackled using machine learned atomic potentials (MLPs) trained on data from density functional theory calculations. MLP-based atomistic MD simulations of aqueous salt solutions reproduce experimentally determined thermodynamic, structural, dynamical, and transport properties, including their varied trends of water diffusivities across salt concentration. This enables an examination of their intermolecular structure to unravel the microscopic underpinnings of the distinction in their transport. While both ions in CsI solutions contribute to faster diffusion of water molecules, the competition between the heavy retardation by Na-ions and slight acceleration by Cl-ions in NaCl solutions reduces their water diffusivity.Comment: 23 pages, 5 figure

Building Robust Machine Learning Models for Small Chemical Science Data: The Case of Shear Viscosity

Shear viscosity, though being a fundamental property of all liquids, is computationally expensive to estimate from equilibrium molecular dynamics simulations. Recently, Machine Learning (ML) methods have been used to augment molecular simulations in many contexts, thus showing promise to estimate viscosity too in a relatively inexpensive manner. However, ML methods face significant challenges like overfitting when the size of the data set is small, as is the case with viscosity. In this work, we train several ML models to predict the shear viscosity of a Lennard-Jones (LJ) fluid, with particular emphasis on addressing issues arising from a small data set. Specifically, the issues related to model selection, performance estimation and uncertainty quantification were investigated. First, we show that the widely used performance estimation procedure of using a single unseen data set shows a wide variability on small data sets. In this context, the common practice of using Cross validation (CV) to select the hyperparameters (model selection) can be adapted to estimate the generalization error (performance estimation) as well. We compare two simple CV procedures for their ability to do both model selection and performance estimation, and find that k-fold CV based procedure shows a lower variance of error estimates. We discuss the role of performance metrics in training and evaluation. Finally, Gaussian Process Regression (GPR) and ensemble methods were used to estimate the uncertainty on individual predictions. The uncertainty estimates from GPR were also used to construct an applicability domain using which the ML models provided more reliable predictions on another small data set generated in this work. Overall, the procedures prescribed in this work, together, lead to robust ML models for small data sets.Comment: main: 17 pages, 11 figures ; SI: 55 pages, 29 figures ; to be submitted to Journal of Chemical Physic

Role of Lipid Transfer Proteins (LTPs) in the Viral Life Cycle

Viruses are obligate parasites that depend on the host cell machinery for their replication and dissemination. Cellular lipids play a central role in multiple stages of the viral life cycle such as entry, replication, morphogenesis, and egress. Most viruses reorganize the host cell membranes for the establishment of viral replication complex. These specialized structures allow the segregation of replicating viral RNA from ribosomes and protect it from host nucleases. They also facilitate localized enrichment of cellular components required for viral replication and assembly. The specific composition of the lipid membrane governs its ability to form negative or positive curvature and possess a rigid or flexible form, which is crucial for membrane rearrangement and establishment of viral replication complexes. In this review, we highlight how different viruses manipulate host lipid transfer proteins and harness their functions to enrich different membrane compartments with specific lipids in order to facilitate multiple aspects of the viral life cycle

COVID-19 presenting as stroke

© 2020 Elsevier Inc. Objective: Acute stroke remains a medical emergency even during the COVID-19 pandemic. Most patients with COVID-19 infection present with constitutional and respiratory symptoms; while others present with atypical gastrointestinal, cardiovascular, or neurological manifestations. Here we present a series of four patients with COVID-19 that presented with acute stroke. Methods: We searched the hospital databases for patients that presented with acute stroke and concomitant features of suspected COVID-19 infection. All patients who had radiographic evidence of stroke and PCR-confirmed COVID-19 infection were included in the study. Patients admitted to the hospital with PCR- confirmed COVID-19 disease whose hospital course was complicated with acute stroke while inpatient were excluded from the study. Retrospective patient data were obtained from electronic medical records. Informed consent was obtained. Results: We identified four patients who presented with radiographic confirmation of acute stroke and PCR-confirmed SARS-CoV-2 infection. We elucidate the clinical characteristics, imaging findings, and the clinical course. Conclusions: Timely assessment and hyperacute treatment is the key to minimize mortality and morbidity of patients with acute stroke. Stroke teams should be wary of the fact that COVID-19 patients can present with cerebrovascular accidents and should dawn appropriate personal protective equipment in every suspected patient. Further studies are urgently needed to improve current understandings of neurological pathology in the setting of COVID-19 infection

Hunig's base catalyzed synthesis of new 1-(2,3-dihydro-1H-inden-1-yl)-3-aryl urea/ thiourea derivatives as potent antioxidants and 2HCK enzyme growth inhibitors

A series of 1-(2,3-dihydro-1H-indan-1-yl)-3-aryl urea/thiourea derivatives (4a-j) have been synthesized from the reaction of 2,3-dihydro-1H-inden-1-amine (2) with various aryl isocyanates/isothiocyanates (3a-j) by using N,N-DIPEA base (Hunig's base) catalyst in THF at reflux conditions. All of them are structurally confirmed by spectral (IR, 1H & 13C NMR and MASS) and elemental analysis and screened for their in-vitro antioxidant activity against DPPH and NO free radicals and found that compounds 4b, 4i, 4h & 4g are potential antioxidants. The obtained in vitro results were compared with the molecular docking, ADMET, QSAR and bioactivity study results performed for them and identified that the recorded in silico binding affinities were observed in good correlation with the in vitro antioxidant results. The Molecular docking analysis had unveiled the strong hydrogen bonding interactions of synthesized ligands with ARG 160 residue of protein tyrosine kinase (2HCK) enzyme and plays an effective role in its inhibition. Toxicology studies have assessed the potential risks of 4a-j and inferred that all of them were in the limits of potential drugs. The conformational analysis of 4a-j inferred that the urea/thiourea spacer linking 2,3-dihydro-1H-inden-1-amino and substituted aryl units has facilitated all these molecules to effectively bind with ARG 160 amino acid residue present on the α-helix of the protein tyrosine kinase (2HCK) enzyme specifically on chain A of hemopoetic cell kinase. Collectively this study has established a relationship between the antioxidant potentiality and ligands binding with ARG 160 amino acid residue of chain A of 2HCK enzyme to inhibit its growth as well as proliferation of reactive oxygen species in vivo

PHYTOCHEMICALS OF CHRISTIA VESPERTILIONIS LEAF EXTRACT: ANTIOXIDANT, ANTIDIABETIC AND TOXICITY CAPABILITIES

Phytochemicals of Christia vespertilionis plant is known for medicinal properties and used to treat various health problems. The present study revealed medicinal properties of the leaf extract of Christia vespertilionis plant as its total phenolic content derived is screened for their antioxidant, antidiabetic and toxicity properties by Folin-Ciocalteu method, DPPH assay with butylated hydroxytoluene standard, α-amylase inhibition assay with metformin standard, brine shrimp lethality bioassay respectively

SYNTHESIS, CHARACTERIZATION, AND BIOLOGICAL EVALUATION OF UREA DERIVATIVES OF p- XYLYLENEDIAMINE

A novel and efficient method hasbeendeveloped for the synthesis of 1,1'-(1,4-phenylesubstituted-bis(methylene))bis(3-phenylurea) derivatives from 1,4-phenylene-dimethanamine and aryl isocyanates

Multiple molecular targets mediated antioxidant activity, molecular docking, ADMET, QSAR and bioactivity studies of halo substituted urea derivatives of α-Methyl-l-DOPA

A series of novel α-methyl-l-DOPA urea derivatives viz., 3-(3,4-dihydroxyphenyl)-2-methyl-2-(3-halo/trifluoromethyl substituted phenyl ureido)propanoic acids (6a-e) have been synthesized from the reaction of α-methyl-l-DOPA (3) with various aryl isocyanates (4a-e) by using triethylamine (5, TEA) as a base catalyst in THF at reflux conditions. The synthesized compounds are structurally characterized by spectral (IR, 1H & 13C NMR and MASS) and elemental analysis studies and screened for their in-vitro antioxidant activity against DPPH, NO and H2O2 free radical scavenging assays and identified compounds 6c & 6d as potential antioxidants. The acquired in vitro results were correlated with the results of molecular docking, ADMET, QSAR and bioactivity studies performed for them and predicted that the recorded in silico binding affinities are in good correlation with the in vitro antioxidant activity results. The molecular docking analysis has comprehended the strong hydrogen bonding interactions of 6a-e with 1CB4, 1N8Q, 3MNG, 1OG5, 1DNU, 3NRZ, 2CDU, 1HD2 and 2HCK proteins of their respective SOD, LO, PRXS5, CP450, MP, XO, NO, PRY5 and HCK enzymes. This has sustained the effective binding of 6a-e and resulted in functional inhibition of selective aminoacid residues to be pronounced as multiple molecular targets mediated antioxidant potent compounds. In addition, the evaluated toxicology risks of 6a-e are identified with in the potential limits of drug candidates. The conformational analysis of 6c & 6d prominently infers that urea moiety uniting α-methyl-l-DOPA with halo substituted aryl units into a distinctive orientation to comply good structure-activity to inhibit the proliferation of reactive oxygen species in vivo