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Towards Elucidating Structure–Spectra Relationships in Rhamnogalacturonan II: Computational Protocols for Accurate 13C and 1H Shifts for Apiose and Its Borate Esters

Vivek S. Bharadwaj, Luke P. Westawker, Michael F. Crowley
2022 Frontiers in Molecular Biosciences  
Our protocol involved structure optimizations using density functional theory (DFT) followed by isotropic magnetic shielding constant calculations using the gauge-invariant atomic orbital (GIAO) approach  ...  We evaluated the accuracy of 23 different functional–basis set (FBS) combinations with and without implicit solvation for predicting the experimental 1H and 13C shifts of a methyl apioside and its three  ...  Evaluation of the Factors Impacting the Accuracy of 13C NMR Chemical Shift Predictions Using Density Functional Theory-The Advantage of Long-Range Corrected Functionals. J. Chem. Theor.  ... 
doi:10.3389/fmolb.2021.756219 pmid:35141275 pmcid:PMC8820409 fatcat:k3ze6rfbzrebdb5gd6f6lg2tci

Recent progress in understanding chemical shifts

Angel C. de Dios, Eric Oldfield
1996 Solid State Nuclear Magnetic Resonance  
Detailed analysis of chemical shifts may soon become a routine part of solid (and liquid) state NMR structure prediction in chemistry and biology, and this Article covers the development of the topic from  ...  In the past three or four years computer hardware and software developments have reached the stage where the nuclear magnetic resonance (NMR) spectra of many molecular systems can now be accurately evaluated  ...  Acknowledgments We are grateful to C.J. Jameson, P. Pulay and C.E. Dykstra for their continuous flow of advice, and P. Pulay, J.F. Hinton, K. Wolinski and W.  ... 
doi:10.1016/0926-2040(95)01207-9 fatcat:cmqle6zixnbbpi2w3zmsdfjxmy

Evaluation of 13C NMR spectra of cyclopropenyl and cyclopropyl acetylenes by theoretical calculations

Valentine Ananikov
2004 Open Chemistry  
The present article describes in detail the effect of geometry choice, density functional method, basis set and effect of solvent on the accuracy of GIAO calculations of 13C NMR chemical shifts.  ...  GIAO calculations with density functional methods (B3LYP, B3PW91, PBE1PBE) and 6-311+G(2d,p) basis set predict experimental chemical shifts of 3-ethynylcyclopropene (1), 1-ethynylcyclopropane (2) and 1,1  ...  The compounds 1-3 were selected since both experimental 13 C NMR spectra and X-ray structures are available, thus allowing a detailed comparison and analysis.  ... 
doi:10.2478/bf02476190 fatcat:j5rhgzi5fjbsxb4zqi4mvodn5m

Exploring the conformational energy landscape of glassy disaccharides by cross polarization magic angle spinning C13 nuclear magnetic resonance and numerical simulations. II. Enhanced molecular flexibility in amorphous trehalose

Ronan Lefort, Patrice Bordat, Attilio Cesaro, Marc Descamps
2007 Journal of Chemical Physics  
The aim of this article is to assess the ability of chemical shift surfaces to provide structural information on conformational distributions of disaccharides in glassy solid state.  ...  The validity of the general method leading to a simulation of inhomogeneous 13C chemical shift distributions is discussed in detail.  ...  Acknowledgments A.C. is grateful to University Lille I for Visiting Professorship and to hosting LDSMM for hospitality.  ... 
doi:10.1063/1.2409935 pmid:17212504 fatcat:fosjk5tj7rhsznano5ewsne6ye

Conformational Analysis, Experimental and GIAO-DFT 13C NMR Chemical Shift Calculation on 2'-Hydroxy-3,4,5-trimethoxy-chalcone

Fabio Costa, Paulo Gomes, Andressa Silva, Luciano Lião
2017 Journal of the Brazilian Chemical Society  
In this paper we investigated the ability of the GIAO-mPW1PW91/6-31G(d)//mPW1PW91/6-31G(d) level of theory to predict the 13 C nuclear magnetic resonance (NMR) chemical shifts of the 2'-hydroxy-3,4,5-trimethoxy-chalcone  ...  Although, both approaches were able to reproduce the chemical shifts of the 2'-hydroxy-3,4,5-trimethoxy-chalcone, significant differences in the calculated values for C-4 and methoxy carbons were observed  ...  Acknowledgments The authors are grateful to Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Fundação de Amparo  ... 
doi:10.21577/0103-5053.20170060 fatcat:qxjxlxjznfcbvd5lemho2pgpzm

Toward the quantum chemical calculation of nuclear magnetic resonance chemical shifts of proteins

Andrea Frank, Ionut Onila, Heiko M. Möller, Thomas E. Exner
2011 Proteins: Structure, Function, and Bioinformatics  
We present here, quantum chemical calculations of NMR chemical shifts for many proteins based on our fragment-based quantum chemical method: the adjqstable density matrix assembler (AD MA).  ...  Despite the many protein structures solved successfully by nuclear magnetic resonance (NMR) spectroscopy, quality control of NMR structures is still by far not as well established and standardized as in  ...  ACKNOWLEDGMENTS The authors thank the Common Ulm Stuttgart Server (CUSS) and the Baden-Wiirttemberg grid (bwGRiD), which is part of the D-Grid system, for providing the computer resources making the computations  ... 
doi:10.1002/prot.23041 pmid:21557322 fatcat:mryoggepbjftvfkjuap25nqcuy

Evaluation of the ONIOM(B3PW91:HF) hybrid method for modeling butyltin chlorides

Piotr Matczak
2013 Open Chemistry  
Unfortunately, the hybrid method turned out to be ineffective in reproducing the 1H, 13C and 119Sn NMR chemical shifts in XnSnCl4-n accurately.  ...  The values of molecular properties obtained by ONIOM(B3PW91:HF) were compared in a statistical manner with the reference values calculated by B3PW91.  ...  Acknowledgements The CYFRONET AGH Academic Computer Center is acknowledged for access to the Baribal supercomputer (Computational Grant No. MEiN/SGI3700/ UŁódzki/078/2006).  ... 
doi:10.2478/s11532-013-0261-0 fatcat:ifuj6frzh5auhe5actpaejvboy

A guide to small-molecule structure assignment through computation of (1H and 13C) NMR chemical shifts

Patrick H Willoughby, Matthew J Jansma, Thomas R Hoye
2014 Nature Protocols  
(with, e.g., MacroModel) to generate a library of conformers; (ii) using density functional theory (DFt) calculations (with, e.g., Gaussian 09) to determine optimal geometry, free energies and chemical  ...  this protocol is intended to provide chemists who discover or make new organic compounds with a valuable tool for validating the structural assignments of those new chemical entities. experimental 1 H  ...  standard: Enter the experimental 1H chemical shift of the reference standard: Enter the computed 13C NMR shielding tensor of the reference standard: Enter the experimental 13C chemical shift of the reference  ... 
doi:10.1038/nprot.2014.042 pmid:24556787 fatcat:i6uxsbt7bje3plwk36qt77pedm

13C Chemical Shifts in Proteins: A Rich Source of Encoded Structural Information [chapter]

Jorge A. Vila, Yelena A. Arnautova
2018 Springer Series on Bio- and Neurosystems  
, to determination of the fraction of the tautomeric forms of the imidazole ring of histidine in proteins as a function of pH or to accurate detection of structural flaws, at a residuelevel, in NMR-determined  ...  In this chapter, the basis of a novel methodology of computing, at the quantum chemical level of theory, the 13 C α shielding for the amino acid residues in proteins is described.  ...  as a function of the size of the basis set chosen and the Density Functional Theory (DFT) model adopted.  ... 
doi:10.1007/978-3-319-95843-9_20 fatcat:rkrbx3tzlnhk3pnnkrhlqrpxl4

1H and 13C NMR for the Profiling of Natural Product Extracts: Theory and Applications [chapter]

Fabian M. Dayrit, Angel C. de Dios
2017 Spectroscopic Analyses - Developments and Applications  
Various applications of 1H and 13C NMR for the proiling of natural products are described. The use of two-dimensional 1H NMR has been used to overcome problems of spectral overlap.  ...  Although 1H NMR is more sensitive, 13C NMR spectra are simpler with less overlapping signals and are less afected by diferent magnetic ield strengths.  ...  The solvent system must balance the ability to perform a comprehensive extraction with solvent complexity and reproducibility.  ... 
doi:10.5772/intechopen.71040 fatcat:ertk2hrsuzef7dwxbymtzk3yby

Benchmark fragment-based 1H, 13C, 15N and 17O chemical shift predictions in molecular crystals

Joshua D. Hartman, Ryan A. Kudla, Graeme M. Day, Leonard J. Mueller, Gregory J. O. Beran
2016 Physical Chemistry, Chemical Physics - PCCP  
The performance of fragment-based ab initio1H, 13C, 15N and 17O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals.  ...  density functional theory, especially if electrostatic embedding models are employed to mimic the crystal lattice. 12, 13 Accordingly, a two-body fragment model approximates the shielding tensor as  ...  Thus, comparison of predicted shifts with experimental NMR spectra requires mapping between the computed absolute shieldings s i and the experimentally referenced chemical shift d i .  ... 
doi:10.1039/c6cp01831a pmid:27431490 pmcid:PMC4991946 fatcat:xmpkukjt4fdillfdcax2c4iowa

The binding site of sodium in the gramicidin A channel: comparison of molecular dynamics with solid-state NMR data

T.B. Woolf, B. Roux
1997 Biophysical Journal  
The results are compared with carbonyl 13C chemical shift anisotropy solid-state NMR experimental data previously obtained with oriented GA:DMPC samples.  ...  Predictions are made for other solid-state NMR properties that could be observed experimentally.  ...  A representative configuration extracted from the simulation is the amplitude of calculated normal mode displacement vectors to reproduce the experimental N-H NMR backbone order parameters (Briischweiler  ... 
doi:10.1016/s0006-3495(97)78839-8 pmid:9129798 pmcid:PMC1184390 fatcat:yczniypbprbldhhvm7dr6ol4ge

13C Chemical Shifts in Proteins: A Rich Source of Encoded Structural Information [chapter]

Jorge A. Vila, Yelena A. Arnautova
2014 Springer Series in Bio-/Neuroinformatics  
, to determination of the fraction of the tautomeric forms of the imidazole ring of histidine in proteins as a function of pH or to accurate detection of structural flaws, at a residue-level, in NMR-determined  ...  In this chapter, the basis of a novel methodology of computing, at the quantum chemical level of theory, the 13 C α shielding for the amino acid residues in proteins is described.  ...  as a function of the size of the basis set chosen and the Density Functional Theory (DFT) model adopted.  ... 
doi:10.1007/978-3-642-28554-7_19 fatcat:vuwcmveozfhujgrhoodfnpag7a

A QM/MM approach for the study of monolayer-protected gold clusters

Sandipan Banerjee, John A. Montgomery, José A. Gascón
2012 Journal of Materials Science  
As an example, we demonstrate that calculations of the 1H and 13C NMR shielding constants with our proposed QM/MM model maintain the qualitative features of a full DFT calculation, with an order-of-magnitude  ...  We envision that such an approach will lead to an accurate description of key structural and electronic signatures at a fraction of the cost of a full quantum chemical treatment.  ...  In this work we develop MM and QM/MM models, explore different implementations, and evaluate their ability to reproduce experimental data.  ... 
doi:10.1007/s10853-012-6356-8 fatcat:udfvsgpmrveszifhaobs5qfgsi

Computational NMR of Carbohydrates: Theoretical Background, Applications, and Perspectives

Leonid B Krivdin
2021 Molecules  
This review is written amid a marked progress in the calculation of NMR parameters of carbohydrates substantiated by a vast amount of experimental data coming from several laboratories worldwide.  ...  The main idea of the present review was only to outline general trends and perspectives in this dynamically developing area on the background of a marked progress in theoretical and computational NMR.  ...  In addition to that study [158] , Shao and coworkers [159] investigated the ability of DFT with using the PBE exchange-correlation functional to reproduce experimental principal components for trehalose  ... 
doi:10.3390/molecules26092450 pmid:33922318 fatcat:ejatbuumurcshnndlvavjvdqji
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