scholarly journals A Volumetric Analysis of the 1H NMR Chemical Shielding in Supramolecular Systems

2021 ◽  
Vol 22 (7) ◽  
pp. 3333
Author(s):  
Jiří Czernek ◽  
Jiří Brus
Keyword(s):  
Chemical Shift ◽  
1H Nmr ◽  
Model Compound ◽  
Structural Information ◽  
Volumetric Analysis ◽  
Basis Set ◽  
Supramolecular Systems ◽  
Chemical Shielding ◽  
A Value ◽  
Previous Experimental Study

The liquid state NMR chemical shift of protons is a parameter frequently used to characterize host–guest complexes. Its theoretical counterpart, that is, the 1H NMR chemical shielding affected by the solvent (1H CS), may provide important insights into spatial arrangements of supramolecular systems, and it can also be reliably obtained for challenging cases of an aggregation of aromatic and antiaromatic molecules in solution. This computational analysis is performed for the complex of coronene and an antiaromatic model compound in acetonitrile by employing the GIAO-B3LYP-PCM approach combined with a saturated basis set. Predicted 1H CS values are used to generate volumetric data, whose properties are thoroughly investigated. The 1H CS isosurface, corresponding to a value of the proton chemical shift taken from a previous experimental study, is described. The presence of the 1H CS isosurface should be taken into account in deriving structural information about supramolecular hosts and their encapsulation of small molecules.

Synthesis, Conformational Analysis, Infrared, Raman and UV-Visible Spectra of Novel Schiff Bases compiled with DFT Calculations

2020 ◽  
Vol 23 (7) ◽  
pp. 568-586
Author(s):  
Samy M. Ahmed ◽  
Ibrahim A. Shaaban ◽  
Elsayed H. El-Mossalamy ◽  
Tarek A. Mohamed
Keyword(s):  
Schiff Bases ◽  
1H Nmr ◽  
Electronic Absorption Spectra ◽  
Chemical Shifts ◽  
Basis Set ◽  
Oh Groups ◽  
Vibrational Assignments ◽  
Cartesian Coordinate ◽  
Surface Scan ◽  
Ir And Raman

Objective: Two novel Schiff bases named, 2-((2-Hydroxybenzylidene)amino)-4,5,6,7- tetrahydrobenzo[b] thiophene-3-carbonitrile (BESB1) and 2-((Furan-2-ylmethylene)amino)-4,5,6, 7-tetrahydro-benzo[b]thiophene-3-carbonitrile (BESB2) were synthesized. Methods: The structures were characterized based on CHN elemental analysis, mid-infrared (400– 4000 cm-1), Raman (100-4000 cm-1), 1H NMR, mass and UV-Vis spectroscopic measurements. In addition, quantum mechanical calculations using DFT-B3LYP method at 6-31G(d) basis set were carried out for both Schiff bases. Initially, we have carried out complete geometry optimizations followed by frequency calculations for the proposed conformational isomers; BESB1 (A–E) and BESB2 (F–J) based on the orientations of both CN and OH groups against the azomethine lonepair (NLP) in addition to the 3D assumption. Results: The computational outcomes favor conformer A for BESB1 in which the C≡N and OH moieties are cis towards the NLP while conformer G is preferred for BESB2 (the C≡N/furan-O are cis/trans towards the NLP) which was found consistent with the results of relaxed potential energy surface scan. Aided by normal coordinate analysis of the Cartesian coordinate displacements, we have suggested reliable vibrational assignments for all observed IR and Raman bands. Moreover, the electronic absorption spectra for the favored conformers were predicted in DMSO solution using TD-B3LYP/6-31G(d) calculations. Similarly, the 1H NMR chemical shifts were also estimated using GIAO approach implementing PCM including solvent effects (DMSO-d6). Conclusion: Proper interpretations of the observed electronic transition, chemical shifts, IR and Raman bands were presented in this study.

119Sn, 13C and 1H NMR Spectra of Tris(1-butyl)stannyl D-Glucuronate

1997 ◽  
Vol 62 (8) ◽  
pp. 1169-1176 ◽  
Author(s):  
Antonín Lyčka ◽  
Jaroslav Holeček ◽  
David Micák
Keyword(s):  
Chemical Shift ◽  
Carbonyl Group ◽  
1H Nmr ◽  
Equatorial Plane ◽  
Title Compound ◽  
Nmr Spectra ◽  
Hydroxyl Groups ◽  
Carboxylic Group ◽  
H Nmr ◽  
Oxygen Atoms

The 119Sn, 13C and 1H NMR spectra of tris(1-butyl)stannyl D-glucuronate have been measured in hexadeuteriodimethyl sulfoxide, tetradeuteriomethanol and deuteriochloroform. The chemical shift values have been assigned unambiguously with the help of H,H-COSY, TOCSY, H,C-COSY and 1H-13C HMQC-RELAY. From the analysis of parameters of 119Sn, 13C and 1H NMR spectra of the title compound and their comparison with the corresponding spectra of tris(1-butyl)stannyl acetate and other carboxylates it follows that in solutions of non-coordinating solvents (deuteriochloroform) the title compound is present in the form of more or less isolated individual molecules with pseudotetrahedral environment around the central tin atom and with monodentately bound carboxylic group. The interaction of tin atom with oxygen atoms of carbonyl group and hydroxyl groups of the saccharide residue - if they are present at all - are very weak. In solutions in coordinating solvents (hexadeuteriodimethyl sulfoxide or tetradeuteriomethanol), the title compound forms complexes with one molecule of the solvent. Particles of these complexes have a shape of trigonal bipyramid with the 1-butyl substituents in equatorial plane and the oxygen atoms of monodentate carboxylic group and coordinating solvent in axial positions.

scholarly journals DP4-AI Automated NMR Data Analysis: Straight from Spectrometer to Structure

2020 ◽  
Author(s):  
Alexander Howarth ◽  
Kristaps Ermanis ◽  
Jonathan Goodman
Keyword(s):  
1H Nmr ◽  
Open Source Software ◽  
Processing Speed ◽  
Structure Elucidation ◽  
Structural Information ◽  
Fold Increase ◽  
Structural Uncertainty ◽  
Large Sets ◽  
Nmr Data ◽  
Objective Model

<div> <p>A robust system for automatic processing and assignment of raw 13C and 1H NMR data DP4-AI has been developed and integrated into our computational organic molecule structure elucidation workflow. Starting from a molecular structure with undefined stereochemistry or other structural uncertainty, this system allows for completely automated structure elucidation. Methods for NMR peak picking using objective model selection and algorithms for matching the calculated 13C and 1H NMR shifts to peaks in noisy experimental NMR data were developed. DP4-AI achieved a 60-fold increase in processing speed, and near-elimination of the need for scientist time, when rigorously evaluated used a challenging test set of molecules. DP4-AI represents a leap forward in NMR structure elucidation and a step-change in the functionality of DP4. It enables high-throughput analyses of databases and large sets of molecules, which were previously impossible, and paves the way for the discovery of new structural information through machine learning. This new functionality has been coupled with an intuitive GUI and is available as open-source software at https://github.com/KristapsE/DP4-AI.</p> </div> <br>

scholarly journals Protein structure refinement using a quantum mechanics-based chemical shielding predictor

2016 ◽  
Author(s):  
Lars A. Bratholm ◽  
Jan H. Jensen
Keyword(s):  
Quantum Mechanics ◽  
Simulated Annealing ◽  
Chemical Shift ◽  
Force Field ◽  
Chemical Shifts ◽  
Protein Structures ◽  
Empirical Methods ◽  
Structural Refinement ◽  
Chemical Shielding ◽  
Chemical Shift Prediction

The accurate prediction of protein chemical shifts using quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of protein backbone and CB chemical shifts (ProCS15, PeerJ 2016, 3:e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: Simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1 - 0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If a residue-specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiment that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differs in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural change may be due to force field deficiencies. The overall accuracy of the empirical methods are slightly improved by annealing the CHARMM structure with ProCS15, which may suggest that the minor structural changes introduced by ProCS15-based annealing improves the accuracy of the protein structures. Having established that QM-based chemical shift prediction can deliver the same accuracy as empirical shift predictors we hope this can help increase the accuracy of related approaches such as QM/MM or linear scaling approaches or interpreting protein structural dynamics from QM-derived chemical shift.

From simple amphiphilic to surfactant behavior: Analysis of 1H NMR chemical shift variations

2007 ◽  
Vol 316 (1) ◽  
pp. 31-36 ◽  
Author(s):  
Cristiano Andrade-Dias ◽  
Sérgio Lima ◽  
José J.C. Teixeira-Dias
Keyword(s):  
Chemical Shift ◽  
Behavior Analysis ◽  
1H Nmr ◽  
Nmr Chemical Shift ◽  
1H Nmr Chemical Shift
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