[NMR paper] Towards Relatively General and Accurate Quantum Chemical Predictions of Solid-State (17)O NMR Chemical Shifts in Various Biologically Relevant Oxygen-containing Compounds.
Towards Relatively General and Accurate Quantum Chemical Predictions of Solid-State (17)O NMR Chemical Shifts in Various Biologically Relevant Oxygen-containing Compounds.
Towards Relatively General and Accurate Quantum Chemical Predictions of Solid-State (17)O NMR Chemical Shifts in Various Biologically Relevant Oxygen-containing Compounds.
J Phys Chem B. 2015 Aug 14;
Authors: Rorick A, Michael MA, Yang L, Zhang Y
Abstract
Oxygen is an important element in most biologically significant molecules and experimental solid-state (17)O NMR studies have provided numerous useful structural probes to study these systems. However, computational predictions of solid-state (17)O NMR chemical shift tensor properties are still challenging in many cases and in particular each of the prior computational work is basically limited to one type of oxygen-containing systems. This work provides the first systematic study of the effects of geometry refinement, method and basis sets for metal and non-metal elements in both geometry optimization and NMR property calculations of some biologically relevant oxygen-containing compounds with a good variety of XO bonding groups, X= H, C, N, P, and metal. The experimental range studied is 1455 ppm, a major part of the reported (17)O NMR chemical shifts in organic and organometallic compounds. A number of computational factors towards relatively general and accurate predictions of (17)O NMR chemical shifts were studied to provide helpful and detailed suggestions for future work. For the studied various kinds of oxygen-containing compounds, the best computational approach results in a theory-versus-experiment correlation coefficient R(2) of 0.9880 and mean absolute deviation of 13 ppm (1.9% of the experimental range) for isotropic NMR shifts and R(2) of 0.9926 for all shift tensor properties. These results shall facilitate future computational studies of (17)O NMR chemical shifts in many biologically relevant systems, and the high accuracy may also help refinement and determination of active-site structures of some oxygen-containing substrate bound proteins.
PMID: 26274812 [PubMed - as supplied by publisher]
[NMR paper] AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.
AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.
Related Articles AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.
J Biomol NMR. 2015 Aug 2;
Authors: Swails J, Zhu T, He X, Case DA
Abstract
We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects...
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08-04-2015 03:00 PM
AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules
AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules
Abstract
We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poissonâ??Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation...
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08-02-2015 07:10 AM
[NMR paper] Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.
Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.
Related Articles Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.
Adv Exp Med Biol. 2015;827:49-70
Authors: Zhu T, Zhang JZ, He X
Abstract
The performance of quantum mechanical methods on the calculation of protein NMR chemical shifts is reviewed based on the recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. By using the...
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11-14-2014 08:33 AM
[NMR paper] NMRDSP: An Accurate Prediction of Protein Shape Strings from NMR Chemical Shifts and Sequence Data.
NMRDSP: An Accurate Prediction of Protein Shape Strings from NMR Chemical Shifts and Sequence Data.
Related Articles NMRDSP: An Accurate Prediction of Protein Shape Strings from NMR Chemical Shifts and Sequence Data.
PLoS One. 2013;8(12):e83532
Authors: Mao W, Cong P, Wang Z, Lu L, Zhu Z, Li T
Abstract
Shape string is structural sequence and is an extremely important structure representation of protein backbone conformations. Nuclear magnetic resonance chemical shifts give a strong correlation with the local protein structure, and are...
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01-01-2014 03:05 PM
[NMR paper] Determination of accurate 1H positions of an alanine tripeptide with anti-parallel and parallel ?-sheet structures by high resolution 1H solid state NMR and GIPAW chemical shift calculation.
Determination of accurate 1H positions of an alanine tripeptide with anti-parallel and parallel ?-sheet structures by high resolution 1H solid state NMR and GIPAW chemical shift calculation.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.rsc.org-images-entities-char_z_RSClogo.gif Related Articles Determination of accurate 1H positions of an alanine tripeptide with anti-parallel and parallel ?-sheet structures by high resolution 1H solid state NMR and GIPAW chemical shift calculation.
Chem Commun (Camb). 2012 Nov 25;48(91):11199-201
...
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03-30-2013 12:59 PM
Chemical Shifts for the Unusual DNA Structure in Pf1 Bacteriophage from Dynamic-Nuclear-Polarization-Enhanced Solid-State NMR Spectroscopy
Chemical Shifts for the Unusual DNA Structure in Pf1 Bacteriophage from Dynamic-Nuclear-Polarization-Enhanced Solid-State NMR Spectroscopy
Ivan V. Sergeyev, Loren A. Day, Amir Goldbourt and Ann E. McDermott
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja2043062/aop/images/medium/ja-2011-043062_0007.gif
Journal of the American Chemical Society
DOI: 10.1021/ja2043062
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/EeKgo5vg1K0
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11-30-2011 10:45 PM
Chemical Shifts for the Unusual DNA Structure in Pf1 Bacteriophage from Dynamic-Nuclear-Polarization-Enhanced Solid-State NMR Spectroscopy.
Chemical Shifts for the Unusual DNA Structure in Pf1 Bacteriophage from Dynamic-Nuclear-Polarization-Enhanced Solid-State NMR Spectroscopy.
Chemical Shifts for the Unusual DNA Structure in Pf1 Bacteriophage from Dynamic-Nuclear-Polarization-Enhanced Solid-State NMR Spectroscopy.
J Am Chem Soc. 2011 Aug 22;
Authors: Sergeyev IV, Day LA, Goldbourt A, McDermott AE
Abstract
Solid state NMR spectra, including dynamic nuclear polarization enhanced 400 MHz spectra acquired at 100K, as well as non-DNP spectra at a variety of field strengths and...
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08-23-2011 04:03 PM
Rapid, Accurate and Simple Model to Predict NMR Chemical Shifts for Biological Molecu
Rapid, Accurate and Simple Model to Predict NMR Chemical Shifts for Biological Molecules.
Rapid, Accurate and Simple Model to Predict NMR Chemical Shifts for Biological Molecules.
J Phys Chem B. 2010 Nov 18;
Authors: Atieh Z, Aubert-Fre?con M, Allouche AR
We present a new model to predict chemical shifts for biological molecules. It is simple, fast, and involves a limited number of parameters. It is particularly adapted to be used in molecular dynamics studies with a molecular mechanic potential. We test the model for polyamines, which are rather...