scholarly journals Extending the applicability of P3D for structure determination of small molecules

2020 ◽  
Author(s):  
Alain Ibáñez de Opakua ◽  
Markus Zweckstetter
Keyword(s):  
Small Molecules ◽  
Small Molecule ◽  
Structure Determination ◽  
Structural Characteristics ◽  
Discrimination Power ◽  
Partially Ordered ◽  
Nmr Parameters ◽  
Structural Assignment ◽  
Nmr Data

Abstract. The application of anisotropic NMR parameters for the correct structural assignment of small molecules requires the use of partially ordered media. Previously we demonstrated that the use of P3D simulations using PBLG as alignment medium allows the determination of the correct diastereomer from extremely sparse NMR data. Through the analysis of the structural characteristics of small molecules in different alignment media we here show that when steric or electrostatic factors dominate the alignment, P3D-PBLG retains its diastereomer discrimination power. We also demonstrate that P3D simulations can define the different conformations of a flexible small molecule from sparse NMR data.

scholarly journals Extending the applicability of P3D for structure determination of small molecules

2021 ◽  
Vol 2 (1) ◽  
pp. 105-116
Author(s):  
Alain Ibáñez de Opakua ◽  
Markus Zweckstetter
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Small Molecules ◽  
Structure Determination ◽  
Structural Characteristics ◽  
Discrimination Power ◽  
Nmr Parameters ◽  
Structural Assignment ◽  
Nmr Data

Abstract. The application of anisotropic nuclear magnetic resonance (NMR) parameters for the correct structural assignment of small molecules requires the use of partially ordered media. Previously we demonstrated that the use of P3D simulations using poly(γ-benzyl-L-glutamate) (PBLG) as an alignment medium allows for the determination of the correct diastereomer from extremely sparse NMR data. Through the analysis of the structural characteristics of small molecules in different alignment media, here we show that when steric or electrostatic factors dominate the alignment, P3D-PBLG retains its diastereomer discrimination power. We also demonstrate that P3D simulations can define the different conformations of a flexible small molecule from sparse NMR data.

scholarly journals Simultaneous Assignment and Structure Determination of Proteins From Sparsely Labeled NMR Datasets

2021 ◽  
Vol 8 ◽  
Author(s):  
Arup Mondal ◽  
Alberto Perez
Keyword(s):  
Bayesian Approach ◽  
Structure Determination ◽  
Structure Prediction ◽  
Critical Assessment ◽  
Limited Data ◽  
Computational Tools ◽  
Nmr Data

Sparsely labeled NMR samples provide opportunities to study larger biomolecular assemblies than is traditionally done by NMR. This requires new computational tools that can handle the sparsity and ambiguity in the NMR datasets. The MELD (modeling employing limited data) Bayesian approach was assessed to be the best performing in predicting structures from sparsely labeled NMR data in the 13th edition of the Critical Assessment of Structure Prediction (CASP) event—and limitations of the methodology were also noted. In this report, we evaluate the nature and difficulty in modeling unassigned sparsely labeled NMR datasets and report on an improved methodological pipeline leading to higher-accuracy predictions. We benchmark our methodology against the NMR datasets provided by CASP 13.

scholarly journals Structure determination of small molecule compounds by an electron diffractometer for 3D ED/MicroED

CrystEngComm ◽  
2021 ◽  
Author(s):  
Sho Ito ◽  
Fraser J. White ◽  
Eiji Okunishi ◽  
Yoshitaka Aoyama ◽  
Akihito Yamano ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Small Molecule ◽  
Structure Determination

Development of a diffractometer specialized for electron diffraction experiments.

Reaktion von 1.4-Dienen mit Metallkomplexen, I Darstellung und Röntgenstrukturanalyse eines π-enyl-Komplexes der Zusammensetzung (C8H13PdCl)2/ Reaction of 1,4-Dienes with Metal Complexes, I Synthesis and X-ray Structure Determination of a π-enyl Complex of Composition (C8H18PdCl)2

1976 ◽  
Vol 31 (4) ◽  
pp. 455-462 ◽  
Author(s):  
Peter Feldhaus ◽  
Richard Ratka ◽  
Hermann Schmid ◽  
Manfred L. Ziegler
Keyword(s):  
Metal Complexes ◽  
Structure Determination ◽  
Three Dimensional ◽  
Fourier Methods ◽  
X Ray ◽  
H Nmr ◽  
Nmr Data ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

Reaction of (C6H5CN)2PdCl2 and 1,3-dimethylenecyclohexane led to an exocyclic π-enyl complex of formula (C8H13PdCl)2-bis(η3-2-methylene-6-methylcyclohexyl)(di-µ-chloro)-dipalladium. IR and 1H NMR data are in agreement with this formulation.The compound is monoclinic, with unit cell dimensions α = 499.97 ± 0.08, b =1342.26 ± 0.19, c =1379.60 ± 0.20 pm, β = 99.43 ± 0.02°, space group C5h2-P21/C, Ζ = 2, dX-ray = 1.83 g/cm3.The structure was determined from three-dimensional X-ray data by Patterson and Fourier methods. Least squares refinement by use of 1045 independent reflections has reached R1 = 5.6%.

Potential Anticancer Agents, XI. X-Ray Structure Determination of Acantholide [1]

1979 ◽  
Vol 34 (9-10) ◽  
pp. 677-682 ◽  
Author(s):  
H. Lotter ◽  
H. Wagner ◽  
A. A. Saleh ◽  
G. A. Cordell ◽  
N. R. Famsworth
Keyword(s):  
Solid State ◽  
Antitumor Activity ◽  
Sesquiterpene Lactone ◽  
Anticancer Agents ◽  
Structure Determination ◽  
Direct Methods ◽  
X Ray ◽  
Activity Evaluation ◽  
Nmr Data

Abstract The X-ray structure of acantholide, a melampolide sesquiterpene lactone from Acanthosper­mum glabratum (D C .) Willd. was determined by the aid of direct methods. The compound was cy­totoxic but displayed no antitumor activity. Evaluation of the X-ray and NMR data indicated that the same conformation exists in the solid state as in solution.

New procedure to obtain Bragg-reflection intensities from FULLPROF suite for powder crystal-structure determination using GEST and PECKCRYST programs

2010 ◽  
Vol 25 (4) ◽  
pp. 374-376
Author(s):  
Zhen Jie Feng ◽  
Yong Lei Zheng ◽  
Yu Ling Su ◽  
Biao Shao ◽  
Ming Tao Li ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Small Molecules ◽  
Powder Diffraction ◽  
Structure Determination ◽  
Bragg Reflection ◽  
Crystal Structure Determination ◽  
Diffraction Determination ◽  
Good Agreement

A useful procedure is described to rapidly obtain Bragg-reflection intensities from the FULLPROF suite, and the Bragg intensities can then be input into the GEST and the PECKCRYST programs for crystal-structure determination of small molecules. An example on using the new procedure for the structure determination from powder diffraction determination of hydrochlorothiazide (C7H8ClN3O4S2) is presented, and the powder-structure results obtained by the PECKCRYST program are in good agreement with previously reported single-crystal results.

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