Literature DB >> 27431490

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

Joshua D Hartman1, Ryan A Kudla, Graeme M Day, Leonard J Mueller, Gregory J O Beran.   

Abstract

The performance of fragment-based ab initio(1)H, (13)C, (15)N and (17)O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (pan class="Chemical">PBE0, B3LYP, TPSSh, On>n class="Chemical">PBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. (1)H, (13)C, (15)N, and (17)O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same (1)H, (13)C, (15)N, and (17)O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tert-butyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2.

Entities:  

Year:  2016        PMID: 27431490      PMCID: PMC4991946          DOI: 10.1039/c6cp01831a

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  56 in total

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Journal:  Phys Rev Lett       Date:  1996-10-28       Impact factor: 9.161

Review 2.  A review of oxygen-17 solid-state NMR of organic materials--towards biological applications.

Authors:  V Lemaître; M E Smith; A Watts
Journal:  Solid State Nucl Magn Reson       Date:  2004 Nov-Dec       Impact factor: 2.293

3.  Ab initio NMR spectra for molecular systems with a thousand and more atoms: a linear-scaling method.

Authors:  Christian Ochsenfeld; Jörg Kussmann; Felix Koziol
Journal:  Angew Chem Int Ed Engl       Date:  2004-08-27       Impact factor: 15.336

4.  Climbing the density functional ladder: nonempirical meta-generalized gradient approximation designed for molecules and solids.

Authors:  Jianmin Tao; John P Perdew; Viktor N Staroverov; Gustavo E Scuseria
Journal:  Phys Rev Lett       Date:  2003-09-30       Impact factor: 9.161

5.  Combined first-principles computational and experimental multinuclear solid-state NMR investigation of amino acids.

Authors:  Christel Gervais; Ray Dupree; Kevin J Pike; Christian Bonhomme; Mickaël Profeta; Chris J Pickard; Francesco Mauri
Journal:  J Phys Chem A       Date:  2005-08-11       Impact factor: 2.781

6.  Coupling of functional hydrogen bonds in pyridoxal-5'-phosphate-enzyme model systems observed by solid-state NMR spectroscopy.

Authors:  Shasad Sharif; David Schagen; Michael D Toney; Hans-Heinrich Limbach
Journal:  J Am Chem Soc       Date:  2007-03-20       Impact factor: 15.419

7.  Solid-state acid-base interactions in complexes of heterocyclic bases with dicarboxylic acids: crystallography, hydrogen bond analysis, and 15N NMR spectroscopy.

Authors:  Z Jane Li; Yuriy Abramov; Jon Bordner; Jason Leonard; Ales Medek; Andrew V Trask
Journal:  J Am Chem Soc       Date:  2006-06-28       Impact factor: 15.419

8.  A solid-state (17)O nuclear magnetic resonance study of nucleic acid bases.

Authors:  Gang Wu; Shuan Dong; Ramsey Ida; Nitin Reen
Journal:  J Am Chem Soc       Date:  2002-02-27       Impact factor: 15.419

9.  Photochemically driven shape changes of crystalline organic nanorods.

Authors:  Rabih O Al-Kaysi; Astrid M Müller; Christopher J Bardeen
Journal:  J Am Chem Soc       Date:  2006-12-20       Impact factor: 15.419

10.  Chemical shift referencing in MAS solid state NMR.

Authors:  Corey R Morcombe; Kurt W Zilm
Journal:  J Magn Reson       Date:  2003-06       Impact factor: 2.229

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  16 in total

1.  Accurate Backbone 13 C and 15 N Chemical Shift Tensors in Galectin-3 Determined by MAS NMR and QM/MM: Details of Structure and Environment Matter.

Authors:  Jodi Kraus; Rupal Gupta; Manman Lu; Angela M Gronenborn; Mikael Akke; Tatyana Polenova
Journal:  Chemphyschem       Date:  2020-06-04       Impact factor: 3.102

2.  TensorView: A software tool for displaying NMR tensors.

Authors:  Robert P Young; Corbin R Lewis; Chen Yang; Luther Wang; James K Harper; Leonard J Mueller
Journal:  Magn Reson Chem       Date:  2018-11-06       Impact factor: 2.447

3.  Quantum mechanical force fields for condensed phase molecular simulations.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Phys Condens Matter       Date:  2017-08-17       Impact factor: 2.333

4.  NMR Crystallography of a Carbanionic Intermediate in Tryptophan Synthase: Chemical Structure, Tautomerization, and Reaction Specificity.

Authors:  Bethany G Caulkins; Robert P Young; Ryan A Kudla; Chen Yang; Thomas J Bittbauer; Baback Bastin; Eduardo Hilario; Li Fan; Michael J Marsella; Michael F Dunn; Leonard J Mueller
Journal:  J Am Chem Soc       Date:  2016-11-11       Impact factor: 15.419

5.  Ab initio random structure searching of organic molecular solids: assessment and validation against experimental data.

Authors:  Miri Zilka; Dmytro V Dudenko; Colan E Hughes; P Andrew Williams; Simone Sturniolo; W Trent Franks; Chris J Pickard; Jonathan R Yates; Kenneth D M Harris; Steven P Brown
Journal:  Phys Chem Chem Phys       Date:  2017-10-04       Impact factor: 3.676

6.  The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine.

Authors:  Xiaozhou Li; Marcus A Neumann; Jacco van de Streek
Journal:  IUCrJ       Date:  2017-02-15       Impact factor: 4.769

7.  Enhanced NMR Discrimination of Pharmaceutically Relevant Molecular Crystal Forms through Fragment-Based Ab Initio Chemical Shift Predictions.

Authors:  Joshua D Hartman; Graeme M Day; Gregory J O Beran
Journal:  Cryst Growth Des       Date:  2016-10-04       Impact factor: 4.076

8.  Chemical shifts in molecular solids by machine learning.

Authors:  Federico M Paruzzo; Albert Hofstetter; Félix Musil; Sandip De; Michele Ceriotti; Lyndon Emsley
Journal:  Nat Commun       Date:  2018-10-29       Impact factor: 14.919

9.  Mechanochemical Formation of Racemic Praziquantel Hemihydrate with Improved Biopharmaceutical Properties.

Authors:  Debora Zanolla; Dritan Hasa; Mihails Arhangelskis; Gabriela Schneider-Rauber; Michele R Chierotti; Jennifer Keiser; Dario Voinovich; William Jones; Beatrice Perissutti
Journal:  Pharmaceutics       Date:  2020-03-23       Impact factor: 6.321

10.  Bridging photochemistry and photomechanics with NMR crystallography: the molecular basis for the macroscopic expansion of an anthracene ester nanorod.

Authors:  Kevin R Chalek; Xinning Dong; Fei Tong; Ryan A Kudla; Lingyan Zhu; Adam D Gill; Wenwen Xu; Chen Yang; Joshua D Hartman; Alviclér Magalhães; Rabih O Al-Kaysi; Ryan C Hayward; Richard J Hooley; Gregory J O Beran; Christopher J Bardeen; Leonard J Mueller
Journal:  Chem Sci       Date:  2020-10-30       Impact factor: 9.825

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