1
|
Southern SA, Perras FA. Comparison of methods for the NMR measurement of motionally averaged dipolar couplings. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 364:107710. [PMID: 38901172 DOI: 10.1016/j.jmr.2024.107710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/31/2024] [Accepted: 06/07/2024] [Indexed: 06/22/2024]
Abstract
Motionally averaged dipolar couplings are an important tool for understanding the complex dynamics of catalysts, polymers, and biomolecules. While there is a plethora of solid-state NMR pulse sequences available for their measurement, in can be difficult to gauge the methods' strengths and weaknesses. In particular, there has not been a comprehensive comparison of their performance in natural abundance samples, where 1H homonuclear dipolar couplings are important and the use of large MAS rotors may be required for sensitivity reasons. In this work, we directly compared some of the more common methods for measuring C-H dipolar couplings in natural abundance samples using L-alanine (L-Ala) and the N-formyl-L-methionyl-L-leucyl-L-phenylalanine (fMLF) tripeptide as model systems. We evaluated their performance in terms of accuracy, resolution, sensitivity, and ease of implementation. We found that, despite the presence of 1H homonuclear dipolar interactions, all methods, with the exception of REDOR, were able to yield the reasonable dipolar coupling strengths for both mobile and static moieties. Of these methods, PDLF provides the most convenient workflow and precision at the expense of low sensitivity. In low-sensitivity cases, MAS-PISEMA and DIPSHIFT appear to be the better options.
Collapse
Affiliation(s)
- Scott A Southern
- Chemical and Biological Sciences Division, Ames National Laboratory, Ames, IA 50011, USA
| | - Frédéric A Perras
- Chemical and Biological Sciences Division, Ames National Laboratory, Ames, IA 50011, USA; Department of Chemistry, Iowa State University, Ames, IA 50011, USA.
| |
Collapse
|
2
|
Mathew R, Mazumder A, Kumar P, Matula J, Mohamed S, Brazda P, Hariharan M, Thomas B. Unveiling the topology of partially disordered micro-crystalline nitro-perylenediimide with X-aggregate stacking: an integrated approach. Chem Sci 2024; 15:490-499. [PMID: 38179523 PMCID: PMC10762722 DOI: 10.1039/d3sc05514k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/23/2023] [Indexed: 01/06/2024] Open
Abstract
Profound knowledge of the molecular structure and supramolecular organization of organic molecules is essential to understand their structure-property relationships. Herein we demonstrate the packing arrangement of partially disordered nitro-perylenediimide (NO2-PDI), revealing that the perylenediimide units exhibit an X-shaped packing pattern. The packing of NO2-PDI is derived using a complementary approach that utilises solid-state NMR (ssNMR) and 3D electron diffraction (3D ED) techniques. Perylenediimide (PDI) molecules are captivating due to their high luminescence efficiency and optoelectronic properties, which are related to supramolecular self-assembly. Increasing the alkyl chain length on the imide substituent poses a more significant challenge in crystallizing the resulting molecule. In addition to the alkyl tails, other functional groups, like the nitro group attached as a bay substituent, can also cause disorder. Such heterogeneity could lead to diffuse scattering, which then complicates the interpretation of diffraction experiment data, where perfect periodicity is expected. As a result, there is an unmet need to develop a methodology for solving the structures of difficult-to-crystallize materials. A synergistic approach is utilised in this manuscript to understand the packing arrangement of the disordered material NO2-PDI by making use of 3D ED, ssNMR and density functional theory calculations (DFT). The combination of these experimental and theoretical approaches provides great promise in enabling the structural investigation of novel materials with customized properties across various applications, which are, due to the internal disorder, very difficult to study by diffraction techniques. By effectively addressing these challenges, our methodology opens up new avenues for material characterization, thereby driving exciting advancements in the field.
Collapse
Affiliation(s)
- Renny Mathew
- Science Division, New York University Abu Dhabi P.O. Box 129188 Abu Dhabi United Arab Emirates
| | - Aniruddha Mazumder
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM) Maruthamala P.O., Vithura Thiruvananthapuram 695551 Kerala India
| | - Praveen Kumar
- Science Division, New York University Abu Dhabi P.O. Box 129188 Abu Dhabi United Arab Emirates
| | - Julie Matula
- Science Division, New York University Abu Dhabi P.O. Box 129188 Abu Dhabi United Arab Emirates
| | - Sharmarke Mohamed
- Department of Chemistry, Green Chemistry & Materials Modelling Laboratory, Khalifa University of Science and Technology P.O. Box 127788 Abu Dhabi United Arab Emirates
- Advanced Materials Chemistry Center (AMCC), Khalifa University of Science and Technology P.O. Box 127788 Abu Dhabi United Arab Emirates
| | - Petr Brazda
- Institute of Physics of the Czech Academy of Sciences Na Slovance 2/1999 18200 Prague 8 Czech Republic
| | - Mahesh Hariharan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram (IISER TVM) Maruthamala P.O., Vithura Thiruvananthapuram 695551 Kerala India
| | - Brijith Thomas
- Science Division, New York University Abu Dhabi P.O. Box 129188 Abu Dhabi United Arab Emirates
| |
Collapse
|
3
|
Cui J, Prisk TR, Olmsted DL, Su V, Asta M, Hayes SE. Resolving the Chemical Formula of Nesquehonite via NMR Crystallography, DFT Computation, and Complementary Neutron Diffraction. Chemistry 2023; 29:e202203052. [PMID: 36411247 DOI: 10.1002/chem.202203052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022]
Abstract
Nesquehonite is a magnesium carbonate mineral relevant to carbon sequestration envisioned for carbon capture and storage of CO2 . Its chemical formula remains controversial today, assigned as either a hydrated magnesium carbonate [MgCO3 ⋅ 3H2 O], or a hydroxy- hydrated- magnesium bicarbonate [Mg(HCO3 )OH ⋅ 2H2 O]. The resolution of this controversy is central to understanding this material's thermodynamic, phase, and chemical behavior. In an NMR crystallography study, using rotational-echo double-resonance 13 C{1 H} (REDOR), 13 C-1 H distances are determined with precision, and the combination of 13 C static NMR lineshapes and density functional theory (DFT) calculations are used to model different H atomic coordinates. [MgCO3 ⋅ 3H2 O] is found to be accurate, and evidence from neutron powder diffraction bolsters these assignments. Refined H positions can help understand how H-bonding stabilizes this structure against dehydration to MgCO3 . More broadly, these results illustrate the power of NMR crystallography as a technique for resolving questions where X-ray diffraction is inconclusive.
Collapse
Affiliation(s)
- Jinlei Cui
- Department of Chemistry, Washington University in St. Louis, 1 Brookings Drive, Campus Box 1134, St. Louis Missouri, 63130, United States
| | - Timothy R Prisk
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - David L Olmsted
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA, 94720, United States
| | - Vicky Su
- Department of Chemistry, Washington University in St. Louis, 1 Brookings Drive, Campus Box 1134, St. Louis Missouri, 63130, United States
| | - Mark Asta
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA, 94720, United States
| | - Sophia E Hayes
- Department of Chemistry, Washington University in St. Louis, 1 Brookings Drive, Campus Box 1134, St. Louis Missouri, 63130, United States
| |
Collapse
|
4
|
Lund A, Manohara GV, Song AY, Jablonka KM, Ireland CP, Cheah LA, Smit B, Garcia S, Reimer JA. Characterization of Chemisorbed Species and Active Adsorption Sites in Mg-Al Mixed Metal Oxides for High-Temperature CO 2 Capture. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2022; 34:3893-3901. [PMID: 35573112 PMCID: PMC9097159 DOI: 10.1021/acs.chemmater.1c03101] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 03/17/2022] [Indexed: 06/15/2023]
Abstract
Mg-Al mixed metal oxides (MMOs), derived from the decomposition of layered double hydroxides (LDHs), have been purposed as adsorbents for CO2 capture of industrial plant emissions. To aid in the design and optimization of these materials for CO2 capture at 200 °C, we have used a combination of solid-state nuclear magnetic resonance (ssNMR) and density functional theory (DFT) to characterize the CO2 gas sorption products and determine the various sorption sites in Mg-Al MMOs. A comparison of the DFT cluster calculations with the observed 13C chemical shifts of the chemisorbed products indicates that mono- and bidentate carbonates are formed at the Mg-O sites with adjacent Al substitution of an Mg atom, while the bicarbonates are formed at Mg-OH sites without adjacent Al substitution. Quantitative 13C NMR shows an increase in the relative amount of strongly basic sites, where the monodentate carbonate product is formed, with increasing Al/Mg molar ratios in the MMOs. This detailed understanding of the various basic Mg-O sites presented in MMOs and the formation of the carbonate, bidentate carbonate, and bicarbonate chemisorbed species yields new insights into the mechanism of CO2 adsorption at 200 °C, which can further aid in the design and capture capacity optimization of the materials.
Collapse
Affiliation(s)
- Alicia Lund
- Materials
Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - G. V. Manohara
- Research
Center for Carbon Solutions (RCCS), School of Engineering and Physical
Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K.
| | - Ah-Young Song
- Materials
Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Kevin Maik Jablonka
- Laboratory
of Molecular Simulation (LSMO), Institut
des Sciences et Ingénierie Chimiques, École Polytechnique
Fédérale de Lausanne (EPFL), Rue de l’Industrie 17, Sion CH-1951, Switzerland
| | - Christopher P. Ireland
- Laboratory
of Molecular Simulation (LSMO), Institut
des Sciences et Ingénierie Chimiques, École Polytechnique
Fédérale de Lausanne (EPFL), Rue de l’Industrie 17, Sion CH-1951, Switzerland
| | - Li Anne Cheah
- Research
Center for Carbon Solutions (RCCS), School of Engineering and Physical
Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K.
| | - Berend Smit
- Laboratory
of Molecular Simulation (LSMO), Institut
des Sciences et Ingénierie Chimiques, École Polytechnique
Fédérale de Lausanne (EPFL), Rue de l’Industrie 17, Sion CH-1951, Switzerland
| | - Susana Garcia
- Research
Center for Carbon Solutions (RCCS), School of Engineering and Physical
Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K.
| | - Jeffrey A. Reimer
- Materials
Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| |
Collapse
|
5
|
Liu Z, Liang L, Xiao D, Ji Y, Zhao Z, Xu J, Hou G. 89Y chemical shift anisotropy: a sensitive structural probe of layered yttrium hydroxides revealed by solid-state NMR spectroscopy and DFT calculations. Phys Chem Chem Phys 2021; 23:27244-27252. [PMID: 34859801 DOI: 10.1039/d1cp04247e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Anion-exchangeable Y2(OH)5X·nH2O (LYH-X, X = monovalent anions, n ≈ 1.5) materials are an ideal platform for incorporating the unique properties of layered metal hydroxides and rare-earth (RE) ions, and thus have exhibited promising prospects for various applications. To further improve the performance of LYH-X and related functional materials, their structure-property relationships must be explored. However, due to the intrinsic felxibility, extracting the local structural details of these materials is particularly challenging. In this work, we utilized a combined approach of 89Y solid-state NMR (ssNMR) spectroscopy and density functional theory (DFT) calculations to reveal the response of 89Y chemical shift anisotropy (CSA) in LYH-X to the structural changes including a small displacement of cationic yttrium hydroxide layers and intercalated anions. Such subtle structural changes are often associated with dehydration/rehydration, anion-exchange, exfoliation, and the self-assembly process of LYH-X and related functional materials, which are exceedingly difficult to detect using other techniques. The principal components of 89Y CSA show a larger variation range than isotropic chemical shifts, making CSA a more sensitive probe. In addition, it is found that the response of 89Y CSA to structural changes is distinct for Y sites with different local coordination environments, opening great opportunities to analyze each Y site within these materials. All these observations suggest that the strategy involving both experimental (89Y ssNMR) and theoretical (DFT) approaches can be utilized to extract previously unavailable ultrafine structural information of LYH-X and related materials, and provide fruitful insights into their thorough structure-property relationships.
Collapse
Affiliation(s)
- Zhengmao Liu
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lixin Liang
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Xiao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Yi Ji
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenchao Zhao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Jun Xu
- Center for Rare Earth and Inorganic Functional Materials, Tianjin Key Lab for Rare Earth Materials and Applications, School of Materials Science and Engineering & National Institute for Advanced Materials, Nankai University, Tianjin 300350, China.
| | - Guangjin Hou
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| |
Collapse
|
6
|
Mames A, Pietrzak M, Bernatowicz P, Kubas A, Luboradzki R, Ratajczyk T. NMR Crystallography Enhanced by Quantum Chemical Calculations and Liquid State NMR Spectroscopy for the Investigation of Se-NHC Adducts*. Chemistry 2021; 27:16477-16487. [PMID: 34606111 DOI: 10.1002/chem.202102800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Indexed: 11/11/2022]
Abstract
N-heterocyclic carbene ligands (NHC) are widely utilized in catalysis and material science. They are characterized by their steric and electronic properties. Steric properties are usually quantified on the basis of their static structure, which can be determined by X-ray diffraction. The electronic properties are estimated in the liquid state; for example, via the 77 Se liquid state NMR of Se-NHC adducts. We demonstrate that 77 Se NMR crystallography can contribute to the characterization of the structural and electronic properties of NHC in solid and liquid states. Selected Se-NHC adducts are investigated via 77 Se solid state NMR and X-ray crystallography, supported by quantum chemical calculations. This investigation reveals a correlation between the molecular structure of adducts and NMR parameters, including not only isotropic chemical shifts but also the other chemical shift tensor components. Afterwards, the liquid state 77 Se NMR data is presented and interpreted in terms of the quantum chemistry modelling. The discrepancy between the structural and electronic properties, and in particular the π-accepting abilities of adducts in the solid and liquid states is discussed. Finally, the 13 C isotropic chemical shift from the liquid state NMR and the 13 C tensor components are also discussed, and compared with their 77 Se counterparts. 77 Se NMR crystallography can deliver valuable information about NHC ligands, and together with liquid state 77 Se NMR can provide an in-depth outlook on the properties of NHC ligands.
Collapse
Affiliation(s)
- Adam Mames
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Mariusz Pietrzak
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Piotr Bernatowicz
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Adam Kubas
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Roman Luboradzki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Tomasz Ratajczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| |
Collapse
|
7
|
Lang T, Wang J, Han T, Cai M, Fang S, Zhong Y, Peng L, Cao S, Liu B, Polisadova E, Korepanov V, Yakovlev A. Enhancing Structural Rigidity via a Strategy Involving Protons for Creating Water-Resistant Mn 4+-Doped Fluoride Phosphors. Inorg Chem 2021; 60:1832-1838. [PMID: 33476132 DOI: 10.1021/acs.inorgchem.0c03284] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The poor water resistance property of a commercial Mn4+-activated narrow-band red-emitting fluoride phosphor restricts its promising applications in high-performance white LEDs and wide-gamut displays. Herein, we develop a structural rigidity-enhancing strategy using a novel KHF2:Mn4+ precursor as a Mn source to construct a proton-containing water-resistant phosphor K2(H)TiF6:Mn4+ (KHTFM). The parasitic [HMnF6]- complexes in the interstitial site from the fall off the KHF2:Mn4+ are also transferred to the K2TiF6 host by ion exchange to form KHTFM with rigid bonding networks, improving the water resistance and thermostability of the sample. The KHTFM sample retains at least 92% of the original emission value after 180 min of water immersion, while the non-water-resistant K2TiF6:Mn4+(KTFM) phosphor maintains only 23%. Therefore, these findings not only illustrate the effect of protons on fluoride but also provide a novel insight into commercial water-resistant fluoride phosphors.
Collapse
Affiliation(s)
- Tianchun Lang
- Chongqing Key Laboratory of Materials Surface & Interface Science, Research Institute for New Materials Technology, Chongqing University of Arts and Sciences, Chongqing 402160, China.,School of Advanced Manufacturing Technologies, National Research Tomsk Polytechnic University, Tomsk 634050, Russia
| | - Jinyu Wang
- Chongqing Key Laboratory of Materials Surface & Interface Science, Research Institute for New Materials Technology, Chongqing University of Arts and Sciences, Chongqing 402160, China.,School of Material Science and Engineering, Chongqing University of Technology, No. 319, Honghe Road, Yongchuan District, Chongqing 400054, China
| | - Tao Han
- Chongqing Key Laboratory of Materials Surface & Interface Science, Research Institute for New Materials Technology, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Mingsheng Cai
- School of Advanced Manufacturing Technologies, National Research Tomsk Polytechnic University, Tomsk 634050, Russia
| | - Shuangqiang Fang
- School of Advanced Manufacturing Technologies, National Research Tomsk Polytechnic University, Tomsk 634050, Russia
| | - Yang Zhong
- School of Advanced Manufacturing Technologies, National Research Tomsk Polytechnic University, Tomsk 634050, Russia
| | - Lingling Peng
- Chongqing Key Laboratory of Materials Surface & Interface Science, Research Institute for New Materials Technology, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Shixiu Cao
- Chongqing Key Laboratory of Materials Surface & Interface Science, Research Institute for New Materials Technology, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Bitao Liu
- Chongqing Key Laboratory of Materials Surface & Interface Science, Research Institute for New Materials Technology, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Elena Polisadova
- School of Advanced Manufacturing Technologies, National Research Tomsk Polytechnic University, Tomsk 634050, Russia
| | - Vladimir Korepanov
- School of Advanced Manufacturing Technologies, National Research Tomsk Polytechnic University, Tomsk 634050, Russia
| | - Aleksey Yakovlev
- School of Advanced Manufacturing Technologies, National Research Tomsk Polytechnic University, Tomsk 634050, Russia
| |
Collapse
|
8
|
Xu J, Terskikh VV, Chu Y, Zheng A, Huang Y. 13 C chemical shift tensors in MOF α-Mg 3 (HCOO) 6 : Which component is more sensitive to host-guest interaction? MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:1082-1090. [PMID: 31659777 DOI: 10.1002/mrc.4944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/23/2019] [Accepted: 09/16/2019] [Indexed: 06/10/2023]
Abstract
Metal-organic frameworks (MOFs) are a class of important porous materials with many current and potential applications. Their applications almost always involve the interaction between host framework and guest species. Therefore, understanding of host-guest interaction in MOF systems is fundamentally important. Solid-state NMR spectroscopy is an excellent technique for investigating host-guest interaction as it provides information complementary to that obtained from X-ray diffraction. In this work, using MOF α-Mg3 (HCOO)6 as an example, we demonstrated that 13 C chemical shift tensor of organic linker can be utilized to probe the host-guest interaction in MOFs. Obtaining 13 C chemical shift tensor components (δ11 , δ22 , and δ33 , where δ11 ≥ δ22 ≥ δ33 ) in this MOF is particularly challenging as there are six coordinatively equivalent but crystallographically non-equivalent carbons in the unit cell with very similar local coordination environment. Two-dimensional magic-angle-turning experiments were employed to measure the 13 C chemical shift tensors of each individual crystallographically non-equivalent carbon in three microporous α-Mg3 (HCOO)6 samples with different guest species. The results indicate that the δ22 component (with its direction approximately being co-planar with the formate anion and perpendicular to the C-H bond) is more sensitive to the adsorbate molecules inside the MOF channel due to the weak C-H···O hydrogen bonding or the ring current effect of benzene. The 13 C isotropic chemical shift, on the other hand, seems much less sensitive to the subtle changes in the local environment around formate linker induced by adsorption. The approach described in this study may be used in future studies on host-guest interaction within MOFs.
Collapse
Affiliation(s)
- Jun Xu
- Center for Rare Earth and Inorganic Functional Materials, Tianjin Key Lab for Rare Earth Materials and Applications, School of Materials Science and Engineering & National Institute for Advanced Materials, Nankai University, Tianjin, 300350, P.R. China
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Victor V Terskikh
- Department of Chemistry, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Yueying Chu
- Chinese Academy of Sciences, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Wuhan, 430071, P.R. China
| | - Anmin Zheng
- Chinese Academy of Sciences, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Wuhan, 430071, P.R. China
| | - Yining Huang
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| |
Collapse
|
9
|
Haghighatlari M, Li J, Heidar-Zadeh F, Liu Y, Guan X, Head-Gordon T. Learning to Make Chemical Predictions: the Interplay of Feature Representation, Data, and Machine Learning Methods. Chem 2020; 6:1527-1542. [PMID: 32695924 PMCID: PMC7373218 DOI: 10.1016/j.chempr.2020.05.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Recently supervised machine learning has been ascending in providing new predictive approaches for chemical, biological and materials sciences applications. In this Perspective we focus on the interplay of machine learning method with the chemically motivated descriptors and the size and type of data sets needed for molecular property prediction. Using Nuclear Magnetic Resonance chemical shift prediction as an example, we demonstrate that success is predicated on the choice of feature extracted or real-space representations of chemical structures, whether the molecular property data is abundant and/or experimentally or computationally derived, and how these together will influence the correct choice of popular machine learning methods drawn from deep learning, random forests, or kernel methods.
Collapse
Affiliation(s)
- Mojtaba Haghighatlari
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, CA, USA
| | - Jie Li
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, CA, USA
| | - Farnaz Heidar-Zadeh
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, CA, USA
- Center for Molecular Modeling (CMM), Ghent University, B-9052 Ghent, Belgium
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Yuchen Liu
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, CA, USA
| | - Xingyi Guan
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, CA, USA
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, CA, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| |
Collapse
|
10
|
Liu S, Li J, Bennett KC, Ganoe B, Stauch T, Head-Gordon M, Hexemer A, Ushizima D, Head-Gordon T. Multiresolution 3D-DenseNet for Chemical Shift Prediction in NMR Crystallography. J Phys Chem Lett 2019; 10:4558-4565. [PMID: 31305081 PMCID: PMC6922005 DOI: 10.1021/acs.jpclett.9b01570] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We have developed a deep learning algorithm for chemical shift prediction for atoms in molecular crystals that utilizes an atom-centered Gaussian density model for the 3D data representation of a molecule. We define multiple channels that describe different spatial resolutions for each atom type that utilizes cropping, pooling, and concatenation to create a multiresolution 3D-DenseNet architecture (MR-3D-DenseNet). Because the training and testing time scale linearly with the number of samples, the MR-3D-DenseNet can exploit data augmentation that takes into account the property of rotational invariance of the chemical shifts, thereby also increasing the size of the training data set by an order of magnitude without additional cost. We obtain very good agreement for 13C, 15N, and 17O chemical shifts when compared to ab initio quantum chemistry methods, with the highest accuracy found for 1H chemical shifts that is comparable to the error between the ab initio results and experimental measurements. Principal component analysis (PCA) is used to both understand these greatly improved predictions for 1H , as well as indicating that chemical shift prediction for 13C, 15N, and 17O, which have far fewer training environments than the 1H atom type, will improve once more unique training samples are made available to exploit the deep network architecture.
Collapse
Affiliation(s)
- Shuai Liu
- Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Jie Li
- Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Kochise C Bennett
- Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Brad Ganoe
- Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Tim Stauch
- Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Martin Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Alexander Hexemer
- Advanced Light Source , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Daniela Ushizima
- Computational Research Division, Center for Advanced Mathematics for Energy Research Applications (CAMERA) , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Teresa Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, Department of Bioengineering, Department of Chemical and Biomolecular Engineering , University of California , Berkeley , California 94720 , United States
| |
Collapse
|
11
|
Czernek J, Brus J. Exploring Accuracy Limits of Predictions of the 1H NMR Chemical Shielding Anisotropy in the Solid State. Molecules 2019; 24:E1731. [PMID: 31058873 PMCID: PMC6539467 DOI: 10.3390/molecules24091731] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 04/25/2019] [Accepted: 04/30/2019] [Indexed: 11/16/2022] Open
Abstract
The 1H chemical shielding anisotropy (CSA) is an NMR parameter that is exquisitely sensitive to the local environment of protons in crystalline systems, but it is difficult to obtain it experimentally due to the need to concomitantly suppress other anisotropic interactions in the solid-state NMR (SSNMR) pulse sequences. The SSNMR measurements of the 1H CSA are particularly challenging if the fast magic-angle-spinning (MAS) is applied. It is thus important to confront the results of both the single-crystal (SC) and fast-MAS experiments with their theoretical counterparts. Here the plane-waves (PW) DFT calculations have been carried out using two functionals in order to precisely characterize the structures and the 1H NMR chemical shielding tensors (CSTs) of the solid forms of maleic, malonic, and citric acids, and of L-histidine hydrochloride monohydrate. The level of agreement between the PW DFT and either SC or fast-MAS SSNMR 1H CSA data has been critically compared. It has been found that for the eigenvalues of the 1H CSTs provided by the fast-MAS measurements, an accuracy limit of current PW DFT predictions is about two ppm in terms of the standard deviation of the linear regression model, and sources of this error have been thoroughly discussed.
Collapse
Affiliation(s)
- Jiří Czernek
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovsky Square 2, 16206 Prague, Czech Republic.
| | - Jiří Brus
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovsky Square 2, 16206 Prague, Czech Republic.
| |
Collapse
|