Computer-Assisted Structure Determination of Biomacromolecules by NMR

1994 ◽  
pp. 67-85
Author(s):  
Martin Billeter
Keyword(s):  
Structure Determination ◽  
Computer Assisted

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 Logic Structure Determination (LSD) as a Computer Assisted Structure Elucidation (Case) for Molecular Structure Determination of Cytotoxic Cembranoids from Soft Coral

2016 ◽  
Vol 11 (1) ◽  
pp. 1 ◽  
Author(s):  
Hedi Indra Januar ◽  
Neviaty Putri Zamani ◽  
Dedi Soedharma ◽  
Ekowati Chasanah
Keyword(s):  
Molecular Structure ◽  
Experimental Data ◽  
Structure Determination ◽  
Structure Elucidation ◽  
Computer Assisted ◽  
Multiple Quantum ◽  
Soft Corals ◽  
Computer Assisted Structure Elucidation ◽  
Logic Structure

The tropical Indonesian soft corals are a valuable resources that produce pharmacological cytotoxic cembranoids. However, manual structure determination into these compounds requires adequate knowledge of organic chemistry. This study presents the application of Logic Structure Determination (LSD), as a freeware Computer Assisted Structure Elucidation (CASE) for automatic molecular structure determination of cembranoid compounds from soft corals species. 12 Nuclear Magnetic Resonance (NMR) dataset of cytotoxic cembranoids were used to evaluate the accuracy of LSD in generating the possible structures. Results of this study shows LSD  generated numerous possible molecular structures, as the data input file derived only from 2D-NMR HMQC (Heteronuclear Multiple-Quantum Correlation), COSY (Homonuclear Correlation Spectroscopy), and HMBC (Heteronuclear Multiple Bond Correlation). The accuracy significantly enhanced (only 2-4 possible cembranoid structures from each NMR dataset) with addition of H2BC (Heteronuclear  2 Bond Correlation) experimental data. This may indicates that VLRC (Very Long-Range Correlations) affects significantly to LSD capability. Furthermore, LSD with direct 2 bond NMR experimental data is a reliable CASE technique for identification of cembranoid compounds. In general, this freeware-CASE is potential to be applied to other type of small molecule compounds and may serves as a potential solution for elucidation bottleneck step in Indonesian natural products studies.

Computer-Assisted High-Re Solution TEM

1990 ◽  
Vol 48 (1) ◽  
pp. 162-163
Author(s):  
F.A. Ponce ◽  
H. Hikashi
Keyword(s):  
Signal To Noise Ratio ◽  
Accurate Determination ◽  
Computer Software ◽  
Video Camera ◽  
Image Contrast ◽  
Objective Lens ◽  
Computer Assisted ◽  
Optical Parameters ◽  
Astigmatism Correction

The determination of the atomic positions from HRTEM micrographs is only possible if the optical parameters are known to a certain accuracy, and reliable through-focus series are available to match the experimental images with calculated images of possible atomic models. The main limitation in interpreting images at the atomic level is the knowledge of the optical parameters such as beam alignment, astigmatism correction and defocus value. Under ordinary conditions, the uncertainty in these values is sufficiently large to prevent the accurate determination of the atomic positions. Therefore, in order to achieve the resolution power of the microscope (under 0.2nm) it is necessary to take extraordinary measures. The use of on line computers has been proposed [e.g.: 2-5] and used with certain amount of success.We have built a system that can perform operations in the range of one frame stored and analyzed per second. A schematic diagram of the system is shown in figure 1. A JEOL 4000EX microscope equipped with an external computer interface is directly linked to a SUN-3 computer. All electrical parameters in the microscope can be changed via this interface by the use of a set of commands. The image is received from a video camera. A commercial image processor improves the signal-to-noise ratio by recursively averaging with a time constant, usually set at 0.25 sec. The computer software is based on a multi-window system and is entirely mouse-driven. All operations can be performed by clicking the mouse on the appropiate windows and buttons. This capability leads to extreme friendliness, ease of operation, and high operator speeds. Image analysis can be done in various ways. Here, we have measured the image contrast and used it to optimize certain parameters. The system is designed to have instant access to: (a) x- and y- alignment coils, (b) x- and y- astigmatism correction coils, and (c) objective lens current. The algorithm is shown in figure 2. Figure 3 shows an example taken from a thin CdTe crystal. The image contrast is displayed for changing objective lens current (defocus value). The display is calibrated in angstroms. Images are stored on the disk and are accessible by clicking the data points in the graph. Some of the frame-store images are displayed in Fig. 4.

Structure determination of sodium nitrate near the order-disorder phase transition

1984 ◽  
Vol 45 (8) ◽  
pp. 1317-1327 ◽  
Author(s):  
J. Lefebvre ◽  
R. Fouret ◽  
C.M.E. Zeyen
Keyword(s):  
Phase Transition ◽  
Sodium Nitrate ◽  
Structure Determination ◽  
Disorder Phase Transition

Ab initio structure determination of cytochrome c6 by combined reciprocal space-real space approach

2003 ◽  
Vol 218 (1) ◽  
Author(s):  
K. Chowdhury ◽  
S. Ghosh ◽  
M. Mukherjee
Keyword(s):  
Cytochrome C ◽  
Ab Initio ◽  
Structure Determination ◽  
Direct Method ◽  
Real Space ◽  
Reciprocal Space ◽  
Cytochrome C6 ◽  
Ab Initio Structure ◽  
Space Approach

AbstractThe direct method program SAYTAN has been applied successfully to redetermine the structure of cytochrome c

STRUCTURE DETERMINATION OF 5 MEMBERED SILANE RINGS USING MICROWAVE SPECTROSCOPY

2018 ◽  
Author(s):  
Frank Marshall ◽  
G. Grubbs II ◽  
Gamil Guirgis ◽  
Theodore Carrigan-Broda ◽  
Grier Jones ◽  
...  
Keyword(s):  
Structure Determination ◽  
Microwave Spectroscopy

Isolation and Structure Determination of Antiproliferative Secondary Metabolites from the Potato Earthball Mushroom, Scleroderma bovista (Agaricomycetes)

2018 ◽  
Vol 20 (5) ◽  
pp. 411-418 ◽  
Author(s):  
Bernadett Kovacs ◽  
Zoltán Béni ◽  
Miklós Dékány ◽  
Noémi Bózsity ◽  
Istvan Zupko ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Structure Determination
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