scholarly journals 15N-Labelling and structure determination of adamantylated azolo-azines in solution

2017 ◽  
Vol 13 ◽  
pp. 2535-2548 ◽  
Author(s):  
Sergey L Deev ◽  
Alexander S Paramonov ◽  
Tatyana S Shestakova ◽  
Igor A Khalymbadzha ◽  
Oleg N Chupakhin ◽  
...  
Keyword(s):  
Structure Determination ◽  
Density Functional ◽  
Nuclear Overhauser Effect ◽  
Coupling Constants ◽  
Computer Assisted ◽  
Hydrogen Atoms ◽  
15N Labelling ◽  
Natural Isotopic Abundance ◽  
Chemical Structures

Determining the accurate chemical structures of synthesized compounds is essential for biomedical studies and computer-assisted drug design. The unequivocal determination of N-adamantylation or N-arylation site(s) in nitrogen-rich heterocycles, characterized by a low density of hydrogen atoms, using NMR methods at natural isotopic abundance is difficult. In these compounds, the heterocyclic moiety is covalently attached to the carbon atom of the substituent group that has no bound hydrogen atoms, and the connection between the two moieties of the compound cannot always be established via conventional 1H-1H and 1H-13C NMR correlation experiments (COSY and HMBC, respectively) or nuclear Overhauser effect spectroscopy (NOESY or ROESY). The selective incorporation of 15N-labelled atoms in different positions of the heterocyclic core allowed for the use of 1H-15N (J HN) and 13C-15N (J CN) coupling constants for the structure determinations of N-alkylated nitrogen-containing heterocycles in solution. This method was tested on the N-adamantylated products in a series of azolo-1,2,4-triazines and 1,2,4-triazolo[1,5-a]pyrimidine. The syntheses of adamantylated azolo-azines were based on the interactions of azolo-azines and 1-adamatanol in TFA solution. For azolo-1,2,4-triazinones, the formation of mixtures of N-adamantyl derivatives was observed. The J HN and J CN values were measured using amplitude-modulated 1D 1H spin-echo experiments with the selective inversion of the 15N nuclei and line-shape analysis in the 1D 13С spectra acquired with selective 15N decoupling, respectively. Additional spin–spin interactions were detected in the 15N-HMBC spectra. NMR data and DFT (density functional theory) calculations permitted to suggest a possible mechanism of isomerization for the adamantylated products of the azolo-1,2,4-triazines. The combined analysis of the J HN and J CN couplings in 15N-labelled compounds provides an efficient method for the structure determination of N-alkylated azolo-azines even in the case of isomer formation. The isomerization of adamantylated tetrazolo[1,5-b][1,2,4]triazin-7-ones in acidic conditions occurs through the formation of the adamantyl cation.

scholarly journals 1,3,4-Thiadiazole-Containing Azo Dyes: Synthesis, Spectroscopic Properties and Molecular Structure

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2822
Author(s):  
Agnieszka Kudelko ◽  
Monika Olesiejuk ◽  
Marcin Luczynski ◽  
Marcin Swiatkowski ◽  
Tomasz Sieranski ◽  
...  
Keyword(s):  
Azo Dyes ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Spectroscopic Properties ◽  
Radiation Absorption ◽  
Functional Theory ◽  
Chemical Structures ◽  
Vis Spectroscopy ◽  
High Yields

Three series of azo dyes derived from 2-amino-5-aryl-1,3,4-thiadiazoles and aniline, N,N-dimethylaniline and phenol were synthesized in high yields by a conventional diazotization-coupling sequence. The chemical structures of the prepared compounds were confirmed by 1H-NMR, 13C-NMR, IR, UV-Vis spectroscopy, mass spectrometry and elemental analysis. In addition, the X-ray single crystal structure of a representative azo dye was presented. For explicit determination of the influence of a substituent on radiation absorption in UV-Vis range, time-dependent density functional theory calculations were performed.

scholarly journals In Silico Modeling of Spirolides and Gymnodimines: Determination of S Configuration at Butenolide Ring Carbon C-4

Toxins ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 685
Author(s):  
Christian Zurhelle ◽  
Tilmann Harder ◽  
Urban Tillmann ◽  
Jan Tebben
Keyword(s):  
In Silico ◽  
Density Functional ◽  
Nuclear Overhauser Effect ◽  
Resonance Spectroscopy ◽  
Functional Theory ◽  
Relative Configuration ◽  
Overhauser Effect ◽  
In Silico Modeling ◽  
Nuclear Overhauser

Only few naturally occurring cyclic imines have been fully structurally elucidated or synthesized to date. The configuration at the C-4 carbon plays a pivotal role in the neurotoxicity of many of these metabolites, for example, gymnodomines (GYMs) and spirolides (SPXs). However, the stereochemistry at this position is not accessible by nuclear Overhauser effect—nuclear magnetic resonance spectroscopy (NOE-NMR) due to unconstrained rotation of the single carbon bond between C-4 and C-5. Consequently, the relative configuration of GYMs and SPXs at C-4 and its role in protein binding remains elusive. Here, we determined the stereochemical configuration at carbon C-4 in the butenolide ring of spirolide- and gymnodimine-phycotoxins by comparison of measured 13C NMR shifts with values obtained in silico using force field, semiempirical and density functional theory methods. This comparison demonstrated that modeled data support S configuration at C-4 for all studied SPXs and GYMs, suggesting a biosynthetically conserved relative configuration at carbon C-4 among these toxins.

scholarly journals Estudo do tautomerismo ceto-enólico da 7-epi-clusianona através de cálculos teóricos de deslocamentos químicos de RMN

2020 ◽  
Author(s):  
Ana Carolina Ferreira de Albuquerque ◽  
José Walkimar de Mesquita Carneiro ◽  
Fernando Martins dos Santos Junior
Keyword(s):  
Natural Products ◽  
Structural Characterization ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Chemical Shifts ◽  
Coupling Constants ◽  
Spectroscopic Techniques ◽  
Chemical Structures ◽  
Nmr Parameters

The properties of natural products, including their biological and pharmacological activities, are directly correlated with their chemical structures. Thus, a correct structural characterization of these compounds is a crucial step to the understanding of their biological activities. However, despite the recent advances in spectroscopic techniques, structural studies of natural products can be challenging. This way, theoretical calculations of Nuclear Magnetic Resonance (NMR) parameters (such as chemical shifts and coupling constants) have proven to be a powerful and low-cost tool for the aid to experimental techniques traditionally used for the structural characterization of natural products. One of the several applications of quantum-mechanical calculations of NMR parameters is the study of tautomerism. Since chemical shifts are sensitive to the tautomeric equilibrium, this technique can provide crucial informations. In this work, it was applied a protocol for theoretical calculations of ¹³C chemical shifts in order to study the tautomerism of the natural product 7-epi-clusianone, isolated from Rheedia gardneriana. This protocol consists in a Monte Carlo conformational search, followed by geometry optimization and shielding tensors calculations, both using a density functional level of theory. After comparison of theoretical and experimental data, it was possible to confirm the two tautomers present in equilibrium in the experimental solution. Furthermore, this study highlights how this theoretical protocol can be an effective method in identifying the preferred tautomeric form in solution.

First crystal-structure determination of natural lansfordite, MgCO3·5H2O

2017 ◽  
Vol 81 (5) ◽  
pp. 1063-1071 ◽  
Author(s):  
Fabrizio Nestola ◽  
Anatoly V. Kasatkin ◽  
Sergey S. Potapov ◽  
Olga YA. Chervyatsova ◽  
Arianna Lanza
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Single Crystal ◽  
Structure Determination ◽  
Room Temperature ◽  
Crystal Structure Determination ◽  
Hydrogen Atoms ◽  
Synthetic Analogues ◽  
X Ray

AbstractThis study presents the first crystal-structure determination of natural MgCO3·5H2O, mineral lansfordite, in comparison with previous structural works performed on synthetic analogues. A new prototype single-crystal X-ray diffractometer allowed us to measure an extremely small crystal (i.e. 0.020 mm × 0.010 mm × 0.005 mm) and refine anisotropically all non-hydrogen atoms in the structure and provide a robust hydrogen-bond arrangement. Our new data confirm that natural lansfordite can be stable for several months at room temperature, in contrast with previous works, which reported that such a mineral could be stable only below 10°C.

Carbon and silicon substitution in (4, 4) aluminum nitride nanotube — Density functional study of 27Al and 14N electric field gradient tensors

2008 ◽  
Vol 86 (8) ◽  
pp. 745-750 ◽  
Author(s):  
Ahmad Seif ◽  
Mehran Aghaie ◽  
Hossein Aghaie
Keyword(s):  
Density Functional Theory ◽  
Aluminum Nitride ◽  
Density Functional ◽  
Computational Study ◽  
Coupling Constants ◽  
Functional Study ◽  
Hydrogen Atoms ◽  
Functional Theory ◽  
Aluminum Nitride Nanotube ◽  
Electronic Environments

A computational study at the level of density functional theory (DFT) was performed to investigate the influence of Si and C substitution on the 14N and 27Al quadrupole coupling constants (CQ) in the armchair single-walled aluminum nitride nanotube (SWAlNNT). To this aim, a 1 nm AlNNT consisting of 28 Al and 28 N atoms was considered in which both mouths of the nanotube are capped by hydrogen atoms. Additionally, two other forms of this model of AlNNT were considered in which five Si and five C atoms were substituted in place of the five Al and five N atoms, with two rings in the length of nanotube, like a wire, in the first form; and three Si and three C atoms were substituted in place of three Al and three N atoms as a central ring on the surface of the AlNNT in the second form. The calculated CQ values for three optimized AlNNT systems (raw and Si- and C-substituted) reveal diverse electronic environments in the above-mentioned systems. All the calculations were carried out using the Gaussian 98 software package.Key words: armchair nanotube, density functional theory, nuclear quadrupole resonance.

scholarly journals Accuracy in determining interproton distances using Nuclear Overhauser Effect data from a flexible molecule

2011 ◽  
Vol 7 ◽  
pp. 145-150 ◽  
Author(s):  
Catharine R Jones ◽  
Craig P Butts ◽  
Jeremy N Harvey
Keyword(s):  
Nuclear Overhauser Effect ◽  
Coupling Constants ◽  
Scalar Coupling ◽  
Dynamical Analysis ◽  
Flexible Molecules ◽  
Large Numbers ◽  
Distance Restraints ◽  
Nuclear Overhauser ◽  
Interproton Distances

The determination of accurate NOE-derived interproton distances and confirmation/prediction of relative populations in multi-conformer, flexible small molecules was investigated with the model compound 4-propylaniline. The low accuracy assumed for semi-quantitative NOE distance restraints is typically taken to suggest that large numbers of constraints need to be used in the dynamical analysis of flexible molecules, and this requires, for example, the measurement and Karplus-type analysis of scalar coupling constants (3 J CH and 3 J HH). Herein we demonstrate that, contrary to this common perception, NOE measurements alone are accurate enough to establish interproton distances, and hence conformational detail, in flexible molecules to within a few percent of their ensemble-averaged values, hence reducing the demand for additional restraints in such dynamic analyses.

Structural analysis of dexrazoxane: Exploring tautomeric conformations

2021 ◽  
pp. 1-8
Author(s):  
Farnoosh Behboodyzad ◽  
Tahereh Mohseniabbasabadi ◽  
Nahal Ghanemnia ◽  
Ebrahim Balali
Keyword(s):  
Structural Analysis ◽  
Density Functional ◽  
Distribution Patterns ◽  
Heterocyclic Ring ◽  
Coupling Constants ◽  
Original Structure ◽  
Hydrogen Atoms ◽  
Functional Theory ◽  
Quadrupole Coupling

Structural analysis of dexrazoxane, as a cardioprotective agent, was done in this work by exploring formations of tautomeric conformations and investigating the corresponding effects. Density functional theory (DFT) calculations were performed to optimize the structures to evaluate their molecular and atomic descriptors. In addition to the original structure of dexrazoxane, eight tautomers were obtained with lower stability than the original compound. Movements of two hydrogen atoms in between nitrogen and oxygen atoms of heterocyclic ring put such significant effects. Moreover, electronic molecular orbital features showed effects of such tautomerism processes on distribution patterns and surfaces, in which evaluating the quadrupole coupling constants helped to show the role of atomic sites for resulting the features. As a consequence, the results indicated that the tautomeric formations could significantly change the features of dexrazoxane reminding the importance of carful medication of this drug for patients.

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