scholarly journals Weak Interactions in the Structures of Newly Synthesized (–)-Cytisine Amino Acid Derivatives

Crystals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 146
Author(s):  
Anna K. Przybył ◽  
Anita M. Grzeskiewicz ◽  
Maciej Kubicki
Keyword(s):  
Amino Acid ◽  
Weak Interactions ◽  
Point Interactions ◽  
X Ray ◽  
Depth Analysis ◽  
Weak Hydrogen Bonds ◽  
Geometrical Data ◽  
Topological Characteristics ◽  
Point To Point ◽  
Atoms In Molecules Theory

Eight new (–)-(N-[(AA)-(N-phtaloyl)]cytisines (where AA is amino acid: glycine, β-alanine, D,L-valine, L-valine, L-isoleucine, L-leucine, D-leucine and D,L-phenyloalanine), were synthesized and fully spectroscopically characterized (NMR, FTIR and MS). For two of these compounds, N-[glycine-(N-phtaloyl)]cytisine and N-[L-isoleucine-(N-phtaloyl)]cytisine, X-ray crystal structures were obtained and used as the basis for an in-depth analysis of intermolecular interactions and packing energies. The structural geometrical data (weak hydrogen bonds, π···π interactions, etc.) were compared with the energies of interactions and the topological characteristics (electron density, Laplacian at the appropriate critical point) based on the atoms-in-molecules theory. The results suggest that there is no straightforward connection between the geometry of point-to-point interactions and the molecule-to-molecule energies. Additionally, the usefulness of the transfer of multipolar parameters in estimating of critical points’ characteristics have been confirmed.

An x-ray microprobe based upon a close-coupled focal-spot / glass capillary arrangement

1992 ◽  
Vol 50 (2) ◽  
pp. 1758-1759
Author(s):  
D. A. Carpenter ◽  
M. A. Taylor
Keyword(s):  
Imaging Techniques ◽  
Fluorescence Analysis ◽  
High Sensitivity ◽  
Specimen Preparation ◽  
X Rays ◽  
Glass Capillary ◽  
Close Coupling ◽  
X Ray ◽  
Point To Point ◽  
Beam Damage

The development of intense sources of x rays has led to renewed interest in the use of microbeams of x rays in x-ray fluorescence analysis. Sparks pointed out that the use of x rays as a probe offered the advantages of high sensitivity, low detection limits, low beam damage, and large penetration depths with minimal specimen preparation or perturbation. In addition, the option of air operation provided special advantages for examination of hydrated systems or for nondestructive microanalysis of large specimens.The disadvantages of synchrotron sources prompted the development of laboratory-based instrumentation with various schemes to maximize the beam flux while maintaining small point-to-point resolution. Nichols and Ryon developed a microprobe using a rotating anode source and a modified microdiffractometer. Cross and Wherry showed that by close-coupling the x-ray source, specimen, and detector, good intensities could be obtained for beam sizes between 30 and 100μm. More importantly, both groups combined specimen scanning with modern imaging techniques for rapid element mapping.

Electron probe x-ray microanalysis and electron microscopy of amino acid absorption and transport by the small intestine: inhibition by chemical poisons and correlation to the elemental composition of the epithelial cells

1986 ◽  
Vol 44 ◽  
pp. 134-135
Author(s):  
A. J. Tousimis
Keyword(s):  
Small Intestine ◽  
Amino Acid ◽  
Epithelial Cells ◽  
Elemental Composition ◽  
Isotope Labeling ◽  
Structural Components ◽  
X Ray ◽  
Human Small Intestine ◽  
Transport Studies

The elemental composition of amino acids is similar to that of the major structural components of the epithelial cells of the small intestine and other tissues. Therefore, their subcellular localization and concentration measurements are not possible by x-ray microanalysis. Radioactive isotope labeling: I131-tyrosine, Se75-methionine and S35-methionine have been successfully employed in numerous absorption and transport studies. The latter two have been utilized both in vitro and vivo, with similar results in the hamster and human small intestine. Non-radioactive Selenomethionine, since its absorption/transport behavior is assumed to be the same as that of Se75- methionine and S75-methionine could serve as a compound tracer for this amino acid.

Axially Chiral Bis(α-amino Acid)s and Their Deamino Analogues. Synthesis and Configurational Assignment

1998 ◽  
Vol 63 (2) ◽  
pp. 211-221 ◽  
Author(s):  
Miloš Tichý ◽  
Luděk Ridvan ◽  
Miloš Buděšínský ◽  
Jiří Závada ◽  
Jaroslav Podlaha ◽  
...  
Keyword(s):  
Amino Acid ◽  
Nmr Spectra ◽  
Building Blocks ◽  
X Ray Diffraction ◽  
Amino Groups ◽  
X Ray ◽  
Configurational Assignment ◽  
Symmetry Properties ◽  
Axially Chiral ◽  
Polymeric Structures

The axially chiral bis(α-amino acid)s cis-2 and trans-2 as possible building blocks for polymeric structures of novel type of helicity were prepared. Their configuration has been determined by NMR spectroscopy and, in the case of the trans-isomer, confirmed by single-crystal X-ray diffraction. Analogous pair of stereoisomeric diacids cis-3 and trans-3, devoid of the amino groups, was also prepared and their configuration assigned. The observed differences in the NMR spectra of cis- and trans-isomers of 2 and 3 are discussed from the viewpoint of their different symmetry properties.

Resolution of a protein sequence ambiguity by X-ray crystallographic and mass spectrometric methods

1992 ◽  
Vol 25 (2) ◽  
pp. 205-210 ◽  
Author(s):  
L. J. Keefe ◽  
E. E. Lattman ◽  
C. Wolkow ◽  
A. Woods ◽  
M. Chevrier ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Electron Density ◽  
Mass Spectrometric ◽  
Amino Acid Sequences ◽  
Data Matrix ◽  
Protein Crystal ◽  
Insertion Mutant ◽  
Laser Desorption Mass Spectrometry ◽  
X Ray

Ambiguities in amino acid sequences are a potential problem in X-ray crystallographic studies of proteins. Amino acid side chains often cannot be reliably identified from the electron density. Many protein crystal structures that are now being solved are simple variants of a known wild-type structure. Thus, cloning artifacts or other untoward events can readily lead to cases in which the proposed sequence is not correct. An example is presented showing that mass spectrometry provides an excellent tool for analyzing suspected errors. The X-ray crystal structure of an insertion mutant of Staphylococcal nuclease has been solved to 1.67 Å resolution and refined to a crystallographic R value of 0.170 [Keefe & Lattman (1992). In preparation]. A single residue has been inserted in the C-terminal α helix. The inserted amino acid was believed to be an alanine residue, but the final electron density maps strongly indicated that a glycine had been inserted instead. To confirm the observations from the X-ray data, matrix-assisted laser desorption mass spectrometry was employed to verify the glycine insertion. This mass spectrometric technique has sufficient mass accuracy to detect the methyl group that distinguishes glycine from alanine and can be extended to the more common situation in which crystallographic measurements suggest a problem with the sequence, but cannot pinpoint its location or nature.

scholarly journals Chemical in‐depth analysis of (Ca/Sr)F 2 core–shell like nanoparticles by X‐ray photoelectron spectroscopy with tunable excitation energy

2021 ◽  
Vol 53 (5) ◽  
pp. 494-508
Author(s):  
Anja Müller ◽  
Thoralf Krahl ◽  
Jörg Radnik ◽  
Andreas Wagner ◽  
Carsten Kreyenschulte ◽  
...  
Keyword(s):  
Excitation Energy ◽  
Photoelectron Spectroscopy ◽  
Core Shell ◽  
X Ray ◽  
Depth Analysis

scholarly journals High-Throughput Sequencing of Phage Display Libraries Reveals Parasitic Enrichment of Indel Mutants Caused by Amplification Bias

2021 ◽  
Vol 22 (11) ◽  
pp. 5513
Author(s):  
Sander Plessers ◽  
Vincent Van Deuren ◽  
Rob Lavigne ◽  
Johan Robben
Keyword(s):  
Amino Acid ◽  
Phage Display ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Target Selection ◽  
Acid Modification ◽  
Phage Display Technology ◽  
Amplification Bias ◽  
Large Deletions ◽  
Depth Analysis

The combination of phage display technology with high-throughput sequencing enables in-depth analysis of library diversity and selection-driven dynamics. We applied short-read sequencing of the mutagenized region on focused display libraries of two homologous nucleic acid modification eraser proteins—AlkB and FTO—biopanned against methylated DNA. This revealed enriched genotypes with small indels and concomitant doubtful amino acid motifs within the FTO library. Nanopore sequencing of the entire display vector showed additional enrichment of large deletions overlooked by region-specific sequencing, and further impacted the interpretation of the obtained amino acid motifs. We could attribute enrichment of these corrupted clones to amplification bias due to arduous FTO display slowing down host cell growth as well as phage production. This amplification bias appeared to be stronger than affinity-based target selection. Recommendations are provided for proper sequence analysis of phage display data, which can improve motive discovery in libraries of proteins that are difficult to display.

Isolation from atelia herbert-smithii pittier (sophoreae, leguminosae) and x-ray structure of cis-1-amino-3-hydroxymethyl-cyclobutane-1-carboxylic acid, an achiral non-protein amino acid

Tetrahedron ◽  
1987 ◽  
Vol 43 (8) ◽  
pp. 1857-1861 ◽  
Author(s):  
Geoffrey N. Austin ◽  
Peter D. Baird ◽  
Hak-Fun Chow ◽  
L.E. Fellows ◽  
G.W.J. Fleet ◽  
...  
Keyword(s):  
Amino Acid ◽  
Carboxylic Acid ◽  
Protein Amino Acid ◽  
X Ray

Developing structure-based models to predict substrate specificity of D-group (Type II) molybdenum enzymes: application to a molybdo-enzyme of unknown function from Archaeoglobus fulgidus

2006 ◽  
Vol 34 (1) ◽  
pp. 118-121 ◽  
Author(s):  
E.J. Dridge ◽  
D.J. Richardson ◽  
R.J. Lewis ◽  
C.S. Butler
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Sequence Analysis ◽  
Archaeoglobus Fulgidus ◽  
Substrate Selectivity ◽  
Type Ii ◽  
Amino Acid Residues ◽  
Sequence Alignments ◽  
X Ray ◽  
Group Type

The AF0174–AF0176 gene cluster in Archaeoglobus fulgidus encodes a putative oxyanion reductase of the D-type (Type II) family of molybdo-enzymes. Sequence analysis reveals that the catalytic subunit AF0176 shares low identity (31–32%) and similarity (41–42%) to both NarG and SerA, the catalytic components of the respiratory nitrate and selenate reductases respectively. Consequently, predicting the oxyanion substrate selectivity of AF0176 has proved difficult based solely on sequence alignments. In the present study, we have modelled both AF0176 and SerA on the recently determined X-ray structure of the NAR (nitrate reductase) from Escherichia coli and have identified a number of key amino acid residues, conserved in all known NAR sequences, including AF0176, that we speculate may enhance selectivity towards trigonal planar (NO3−) rather than tetrahedral (SeO42− and ClO4−) substrates.

Distinguishment of Weak Interactions of Hydrogen Atoms Bound to Carbon Atoms: X-Ray Crystal Structural and Hirshfeld Surface Analyses of 2-Hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene with the 2-Methoxylated Homologue

2021 ◽  
Vol 19 ◽  
Author(s):  
Kikuko Iida ◽  
Toyokazu Muto ◽  
Miyuki Kobayashi ◽  
Hiroaki Iitsuka ◽  
Kun Li ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Molecular Conformation ◽  
Weak Interactions ◽  
Carbonyl Oxygen ◽  
Hirshfeld Surface ◽  
Molecular Surface ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Classical Hydrogen Bond

Abstract: X-ray crystal and Hirshfeld surface analyses of 2-hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene and its 2-methoxylated homologue show quantitatively and visually distinct molecular contacts in crystals and minute differences in the weak intermolecular interactions. The title compound has a helical tubular packing, where molecules are piled in a two-folded head-to-tail fashion. The homologue has a tight zigzag molecular string lined up behind each other via nonclassical intermolecular hydrogen bonds between the carbonyl oxygen atom and the hydrogen atom of the naphthalene ring. The dnorm index obtained from the Hirshfeld surface analysis quantitatively demonstrates stronger molecular contacts in the homologue, an ethereal compound, than in the title compound, an alcohol, which is consistent with the higher melting temperature of the former than the latter. Stabilization through the significantly weak intermolecular nonclassical hydrogen bonding interactions in the homologue surpasses the stability imparted by the intramolecular C=O…H–O classical hydrogen bonds in the title compound. The classical hydrogen bond places the six-membered ring in the concave of the title molecule. The hydroxy group opposingly disturbs the molecular aggregation of the title compound, as demonstrated by the distorted H…H interactions covering the molecular surface, owing to the rigid molecular conformation. The position of effective interactions predominate over the strength of the classical/nonclassical hydrogen bonds in the two compounds.

Sign in / Sign up

Export Citation Format

Share Document