Crystallographic investigation, Hirshfeld surface analysis, NLO characterization and experimental spectral (UV and NMR) studies with DFT probe on(R)-9-(2-hydroxy propyl)adenine.

In this study, (R)-9-(2-hydroxy propyl)adenine (HPA) is the molecule of interest for investigation. The XRD from single crystal of HPA has been used to extract its structural features. Since HPA crystallised in a non-centro symmetric space group P212121, its NLO property was studied and it was found to exhibit very good SHG activity. To explore the intermolecular interactions the generated Hirshfeld surface has been investigated along with 2D-fingerprint plots. The experimental electronic and NMR spectra taken in the UV-visible and radio frequency regions respectively for HPA have been corroborated in correlation with theoretical predictions at Density Function Theory using 6-311++g (d, p) basis set. The experimental XRD geometrical parameters, chemical shifts of 13C and 1H and λmax values of HPA fit satisfactorily with the corresponding theoretically obtained numerical values as well as the stimulated spectrograms with the experimental ones. Further to explore the electronic structure, the MESP surface has been generated and investigated. The thermodynamic, kinetic and chemical reactivity features have been explored by means of frontier molecular orbitals of HPA.

Crystallographic, spectral and computational studies on (S)-4-(4-aminobenzyl) oxazolidin-2-one.

The experimental geometry (XRD), vibrational (IR and Raman), electronic (UV-visible) and NMR spectra of (S)-4-(4-Amino-benzyl)-oxazolidin-2-one (ABO) have been corroborated with the corresponding first principle calculated values at DFT using hybrid B3LYP exchange correlation functional invoking 6-311++g(d, p) basis set. The optimized geometrical parameters were found to be in satisfactory agreement with the experimental values obtained from the X-ray diffraction structural features of ABO. The scaled down computed vibrational frequencies with appropriate scaling factors were in good correspondence with the experimental observations. Room-temperature 1H and 13C nuclear magnetic resonance (NMR) studies were supported by advanced density functional theory calculations. The theoretical spectrograms of FT-IR, FT-Raman, 1H NMR, 13C NMR and UV of the title compound have been constructed and compared with experimental spectra and Hirshfeld surface analysis has also been made to study the intermolecular interactions. The electronic structure of the title compound has also been studied in terms of HOMO, LUMO and MESP diagrams.

Formulations for delivering Trichoderma atroviridae spores as seed coatings, effects of temperature and relative humidity on storage stability.

AIMS: We aimed to evaluate different formulations for their ability to adhere Trichoderma atroviridae spores to wheat seeds, and promote survival during storage at a range of temperatures and relative humidities (RH). METHODS AND RESULTS: We tested a range of formulations for their ability to adhere T. atroviridae spores to wheat seeds. Treated seeds were stored for 6 months at a range of temperatures and RH, and spore viability among formulation was compared over time. Spore survival within formulations interacted significantly with environmental conditions. Notably, under optimum conditions (low temperatures and RH) best spore survival was recorded with a xanthan-gum-based formulation. Conversely under suboptimum conditions (high temperatures and RH), survival of spores was best in a waxy-starch formulation, but very poor in the xanthan-gum formulation. CONCLUSIONS: These results indicate that T. atroviridae spores can be effectively delivered on to seeds and that a xanthan-gum formulation is promising when optimal storage conditions can be maintained. SIGNIFICANCE AND IMPACT OF THE STUDY: Most published formulation papers/patents only report survival of organisms over time at a single or limited number of temperatures and RH. For the first time, this study shows how different formulations are better suited to certain temperature and RH combinations.

Cardioprotective properties of Crataegus oxycantha extract against ischemia-reperfusion injury.

The aim of the study was to investigate the cardioprotective effect and mechanism of Crataegus oxycantha (COC) extract, a well-known natural antioxidant-based cardiotonic, against ischemia/reperfusion (I/R) injury. Electron paramagnetic resonance studies showed that COC extract was capable of scavenging superoxide, hydroxyl, and peroxyl radicals, in vitro. The cardioprotective efficacy of the extract was studied in a crystalloid perfused heart model of I/R injury. Hearts were subjected to 30min of global ischemia followed by 45min of reperfusion. During reperfusion, COC extract was infused at a dose rate of 1mg/ml/min for 10min. Hearts treated with COC extract showed a significant recovery in cardiac contractile function, reduction in infarct size, and decrease in creatine kinase and lactate dehydrogenase activities. The expressions of xanthine oxidase and NADPH oxidase were significantly reduced in the treated group. A significant upregulation of the anti-apoptotic proteins Bcl-2 and Hsp70 with simultaneous downregulation of the pro-apoptotic proteins cytochrome c and cleaved caspase-3 was observed. The molecular signaling cascade including phospho-Akt (ser-473) and HIF-1alpha that lead to the activation or suppression of apoptotic pathway also showed a significant protective role in the treatment group. No significant change in phospho-p38 levels was observed. The results suggested that the COC extract may reduce the oxidative stress in the reperfused myocardium, and play a significant role in the inhibition of apoptotic pathways leading to cardioprotection.

FT-IR, FT-Raman, ab initio and DFT structural and vibrational frequency analysis of 6-aminopenicillanic acid.

Quantum mechanical calculations of energies, geometries and vibrational wavenumbers of 6-aminopenicillanic acid were carried out by using ab initio HF and density functional theory (DFT/B3LYP) methods with 6-311G(d,p) basis set. The optimized geometrical parameters obtained by HF and DFT calculations are in good agreement with experimental X-ray data. A detailed interpretation of the infrared spectra has also been reported. The theoretical IR and Raman spectrograms have been constructed and compared with the experimental FT-IR and FT-Raman spectra. The differences between the observed and scaled wavenumber values of most of the fundamentals are very small. The thermodynamic parameters have also been computed.

PDBe: Protein Data Bank in Europe.

The Protein Data Bank in Europe (PDBe) (http://www.ebi.ac.uk/pdbe/) is actively working with its Worldwide Protein Data Bank partners to enhance the quality and consistency of the international archive of bio-macromolecular structure data, the Protein Data Bank (PDB). PDBe also works closely with its collaborators at the European Bioinformatics Institute and the scientific community around the world to enhance its databases and services by adding curated and actively maintained derived data to the existing structural data in the PDB. We have developed a new database infrastructure based on the remediated PDB archive data and a specially designed database for storing information on interactions between proteins and bound molecules. The group has developed new services that allow users to carry out simple textual queries or more complex 3D structure-based queries. The newly designed 'PDBeView Atlas pages' provide an overview of an individual PDB entry in a user-friendly layout and serve as a starting point to further explore the information available in the PDBe database. PDBe's active involvement with the X-ray crystallography, Nuclear Magnetic Resonance spectroscopy and cryo-Electron Microscopy communities have resulted in improved tools for structure deposition and analysis.

FT-IR and FT-Raman vibrational assignment of 2-bromobenzoic acid with the help of ab initio and DFT calculations.

The vibrational spectra of 2-bromobenzoic acid (2BBA) have been experimentally recorded (FT-IR and FT-Raman) and compared with the harmonic vibrational frequencies calculated at HF and B3LYP level of theories using 6-311+G(d,p) basis set with appropriate scaling factors. The XRD geometrical parameters show satisfactory agreement with the theoretical prediction at Hartree-Fock and B3LYP levels. The scaled vibrational frequencies at B3LYP/6-311+G(d,p) seem to coincide with the experimentally observed values with acceptable deviations. The theoretical spectrograms (IR and Raman) have been constructed and compared with the experimental FT-IR and FT-Raman spectra.

Vibrational spectroscopic studies and DFT calculations of 4-aminoantipyrine.

The pyrazole derivative, 4-aminoantipyrine (4AAP), used as an intermediate for the synthesis of pharmaceuticals especially antipyretic and analgesic drugs has been analyzed experimentally and theoretically for its vibrational frequencies. The FTIR and FT Raman spectra of the title compound have been compared with the theoretically computed frequencies invoking the standard 6-311g(d,p) and cc-pVDZ basis sets at DFT level of theory (B3LYP). The harmonic vibrational frequencies at B3LYP/cc-pVDZ after appropriate scaling method seem to coincide satisfactorily with the experimental observations rather than B3LYP/6-311g(d,p) results. The theoretical spectrograms for FT-IR and FT-Raman spectra of 4AAP have been also constructed and compared with the experimental spectra. Additionally, thermodynamic data have also been calculated and discussed.

Molecular structure and vibrational spectra of 3-amino-5-hydroxypyrazole by density functional method.

In this work, we report a combined experimental and theoretical study on molecular and vibrational structure of 3-amino-5-hydroxypyrazole (3A5HP). The Fourier transform infrared and Fourier transform Raman spectra of 3A5HP were recorded in the solid phase. The molecular geometry and vibrational frequencies of 3A5HP in the ground state have been calculated by using the density functional method B3LYP with basis sets, 6-311++G(d,p), 6-311+G(3df,2p), 6-311+G(3df,2pd), CC-pVDZ, aug-CC-pVDZ and CC-pVTZ. The optimized geometrical parameters obtained by B3LYP show best agreement with the experimental values. The theoretical spectrograms for FT-IR and FT-Raman spectra of the title molecule have been constructed.

Harmonic analysis of vibrations of morpholine-4-ylmethylthiourea: a DFT, midinfrared and Raman spectral study.

The FTIR and FT-Raman spectra of morpholine-4-ylmethylthiourea (MMTU) were recorded in the region of mid-IR (400-4,000 cm(-1)). Initial geometry generated from the standard geometrical parameters was relaxed without any constraint on the potential energy surface at MP2 and DFT levels adopting the standard 6-31++G and 6-311+G basis set. With the help of two specific scaling procedures the computed harmonic frequencies have been compared with the observed vibrational wave numbers of FTIR and FT-Raman spectra and assigned to different normal modes of the molecule. Most of the vibrational modes have wave numbers in the expected range. The appropriate theoretical spectrograms of the IR spectra of MMTU have been also constructed.

Experimental (FTIR and FT-Raman) and ab initio and DFT study of vibrational frequencies of 5-amino-2-nitrobenzoic acid.

The FTIR and FT-Raman spectra of 5-amino-2-nitrobenzoic acid (ANB) have been recorded in the region 400-4000 cm(-1). The observed frequencies were assigned to different modes of vibrations on the basis of fundamental, combination and overtones. The geometry has been optimized with complete relaxation on the potential energy surface at HF, MP2 and B3LYP level of theories using 6-311++G(d,p) basis set and compared with the crystal data. The possible hydrogen bond interaction has been estimated taking a model compound. Further harmonic vibrational frequency calculations have been carried out at HF and B3LYP levels and the scaled values were in good agreement with majority of the experimental observations. The theoretically constructed spectra coincide satisfactorily with those of experimental spectra.

E-MSD: the European Bioinformatics Institute Macromolecular Structure Database.

The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool.

The gene ygdP, associated with the invasiveness of Escherichia coli K1, designates a Nudix hydrolase, Orf176, active on adenosine (5')-pentaphospho-(5')-adenosine (Ap5A).

ygdP, a gene associated with the invasion of brain microvascular endothelial cells by Escherichia coli K1 (Badger, J. L., Wass, C. A., and Kim, K. S. (2000) Mol. Microbiol. 36, 174-182), the primary Gram-negative bacterium causing meningitis in newborns, has been cloned and expressed in E. coli. The protein, YgdP, was purified to near homogeneity and identified as a member of the Nudix hydrolase subfamily of dinucleoside oligophosphate pyrophosphatases. It catalyzes the hydrolysis of diadenosine tetra-, penta-, and hexa-phosphates with a preference for diadenosine penta-phosphate, from which it forms ATP and ADP. The enzyme has a requirement for a divalent metal cation that can be met with Mg2+, Zn2+, or Mn2+ and, like most of the Nudix hydrolases, has an alkaline pH optimum between 8.5 and 9. This is the second identification of a gene associated with the invasiveness of a human pathogen as a member of the Nudix hydrolase subfamily of dinucleoside oligophosphate pyrophosphatases, and an examination of homologous proteins in other invasive bacteria suggests that this may be a common feature of cellular invasion.