Molecular structure, vibrational spectral investigation and the confirmation analysis of 4-Methylesculetin molecule

WOS: 000333614200003In this work, FT-IR, FT-Raman, and FT-NMR spectra of 4-Methylesculetin molecule are presented for the first time. FT-IR, FT-Raman, and FT-NMR spectra of 4MEC have been recorded and analyzed. The FT-IR and FT-Raman spectra of this molecule are recorded at 4000-400 cm(-1) and 50-3500 cm(-1), respectively. The infrared vibrational frequencies, absolute intensities, potential energy profile, HOMO-LUMO plot and NBO analysis of the molecule have been also predicted using Becke's three-parameter hybrid B3LYP method in the density functional theory DFT method. Calculated and experimental data are in good agreement.Ahi Evran University Research FundAhi Evran University [FEN.4003.12.013]Y. Erdogdu would like to thank Ahi Evran University Research Fund for its financial support. Project Numbers: FEN.4003.12.013. Computing resources used in this work were provided by the National Center for High Performance Computing of Turkey (UYBHM)

Vibrational spectral investigation and natural bond orbital analysis of pharmaceutical compound 7-Amino-2,4-dimethylquinolinium formate – DFT approach

AbstractThe molecular geometry, the normal mode frequencies and corresponding vibrational assignments, natural bond orbital analysis and the HOMO–LUMO analysis of 7-Amino-2,4-dimethylquinolinium formate in the ground state were performed by B3LYP levels of theory using the 6-31G(d) basis set. The optimised bond lengths and bond angles are in good agreement with the X-ray data. The vibrational spectra of the title compound which is calculated by DFT method, reproduces vibrational wave numbers and intensities with an accuracy which allows reliable vibrational assignments. The possibility of N–H⋯O hydrogen bonding was identified using NBO analysis. Natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction

Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.

Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Infrared and Raman spectra, vibrational assignment, NBO analysis and DFT calculations of 6-aminoflavone

WOS: 000282108900005In this study, the experimental and theoretical study on the FT-infrared and FT-Raman spectra of 6-aminoflavone (6AF) are presented. The FT-IR (4000-400 cm(-1)) and FT-Raman (3500-50 cm(-1)) spectral measurements of solid sample of 6AF have been done. The geometric structure, conformational analysis, vibrational wavenumbers of 6AF in the ground state have been calculated by using Density Functional Method (B3LYP) with 6-311++G(d,p) as basis set. The normal modes were assigned by potential energy distribution (PED) calculations. A detailed vibrational spectral analysis was carried out and assignments of the observed bands have been proposed on the basis of fundamentals. Theoretically predicted vibrational wavenumbers were compared with available experimental data of molecule. The present experimental analysis on vibrational modes of 6AF can be well supported by theoretical analysis. (C) 2010 Elsevier B.V. All rights reserved.Ahi Evran UniversityAhi Evran University [A10/2009]This work was supported by the Research Fund of Ahi Evran University Project Number: A10/2009. We would like to thank the central laboratory of METU (ODTU) for recording FT-Raman spectra, Gazi University Art and Science Faculty Department of Chemistry for recording FT-IR spectra and Assoc. Prof. Dr. Mustafa KURT for Gaussian 03W program package

Infrared and Raman spectra, vibrational assignment, NBO analysis and DFT calculations of 6-aminoflavone

In this study, the experimental and theoretical study on the FT-infrared and FT-Raman spectra of 6-aminoflavone (6AF) are presented. The FT-IR (4000-400 cm(-1)) and FT-Raman (3500-50 cm(-1)) spectral measurements of solid sample of 6AF have been done. The geometric structure, conformational analysis, vibrational wavenumbers of 6AF in the ground state have been calculated by using Density Functional Method (B3LYP) with 6-311++G(d,p) as basis set. The normal modes were assigned by potential energy distribution (PED) calculations. A detailed vibrational spectral analysis was carried out and assignments of the observed bands have been proposed on the basis of fundamentals. Theoretically predicted vibrational wavenumbers were compared with available experimental data of molecule. The present experimental analysis on vibrational modes of 6AF can be well supported by theoretical analysis. (C) 2010 Elsevier B.V. All rights reserved

Vibrational spectra and first-order molecular hyperpolarizabilities of p-hydroxybenzaldehyde dimer

WOS: 000284441400003Single crystals of p-hydroxybenzaldehyde (PHBA) were grown by the slow evaporation technique and vibrational spectral analysis was carried out using near-IR Fourier transform Raman and Fourier transform IR spectroscopy. The density functional theoretical (DFT) computations were also performed at the B3LYP/6-311++G(d,p) level to derive the equilibrium geometry, vibrational wavenumbers and intensities. The detailed interpretation of the vibrational spectra has been carried out with the aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology. The various intramolecular interactions that is responsible for the stabilization of the molecule was revealed by natural bond orbital analysis. Vibrational analysis based on the NIR-FT-Raman. FT-IR and computed spectrum reveals that the CH in-plane bending of the aldehyde group interacts with its stretching mode via Fermi Resonance and evidence for intermolecular interaction can be well identified as two CH bands in IR spectra at 2740 and 2804 cm(-1) aldehyde group of the p-hydroxybenzaldehyde dimer. The red shift of the O-H stretching wavenumber is due to the formation of strong O-H center dot center dot center dot O hydrogen bonds by hyperconjugation between the carbonyl oxygen lone electron pairs and the O-H sigma(center dot) anti-bonding orbitals. (C) 2010 Elsevier B.V. All rights reserved

Molecular structure and vibrational spectra of 2,6-bis(benzylidene)cyclohexanone: A density functional theoretical study

WOS: 000287107000016PubMed ID: 21050808The near-infrared Fourier transform (NIR-FT) Raman and Fourier transform infrared (FT-IR) spectral analyses of 2,6-bis(benzylidene)cyclohexanone (BBC) molecule, a potential drugs for the treatment of P388 leukemia cells, were carried out along with density functional computations. The optimized geometry of BBC using density functional theory shows that the energetically favored chair conformation is not observed for central cyclohexanone ring and is found to possess a nearly 'half chair' conformation and shows less expansion of the angles and more rotation about the bonds. The existence of intramolecular C-H center dot center dot center dot O improper, blue-shifted hydrogen bond was investigated by means of the NBO analysis. The lowering of carbonyl stretching vibration can be attributed to the mesomeric effect and the pi-orbital conjugation induced by the unsaturation in the alpha-carbon atoms and co-planarity of the (-CH=C-(C=O)-C=CH-) group. (C) 2010 Elsevier B.V. All rights reserved

Structural Properties of Bioactive Molecule Naphthalene 2-Sulfonic Acid

International audienceNaphthalene 2-sulfonic acid (NSA) and its derivatives are the most important class of organic compounds and are important products of industrial chemical processes.. Bioactive molecule NSA was performed by means of Density Functional Theoretical (DFT) method using standard B3LYP/6-31G (d,p) basis set implemented with Gaussian'09 software package. NBO analysis were performed to provide valuable information about various intermolecular interactions. Optical properties of the NSA molecule were studied using UV-Vis spectral analysis. In addition, Molecular docking was performed for the different receptors for calculating binding affinities and predicting binding sites