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Capistran D, Harper JK, Hartman JD. Predicting 35-Cl electric field gradient tensors in crystalline solids using cluster and fragment-corrected planewave density functional theory. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2024; 133:101949. [PMID: 39180993 DOI: 10.1016/j.ssnmr.2024.101949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/29/2024] [Accepted: 07/20/2024] [Indexed: 08/27/2024]
Abstract
Planewave-corrected methods have proven effective for accurately modeling nuclear magnetic resonance (NMR) parameters in crystalline systems. Recent work extended the application of planewave-corrected calculations beyond the second row, predicting EFG tensor parameters for 35Cl using a simple molecular correction to projector augmented-wave (PAW) density functional theory (DFT). Here we extend this work using fragment and cluster-based calculations coupled with polarizable continuum (PCM) methods to improve further the accuracy of planewave-corrected 35Cl EFG tensor calculations. Benchmark data from a test set comprised of 105 individual 35Cl EFG tensor principal components for chlorine-containing molecular crystals and crystalline chloride salts shows fragment-corrected planewave calculations using the PBE0 hybrid density functional improve the accuracy of predicted EFG tensor components by 30 % relative to traditional planewave calculations. We compare the influence of different geometry optimization methods and density functionals on the accuracy of predicted 35Cl EFG tensor parameters. Four cases of spectral assignment are presented to demonstrate the utility of improving the accuracy of predicted 35Cl EFG tensor parameters.
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Affiliation(s)
- Daniel Capistran
- Department of Chemistry, University of CaliforniaRiverside, Riverside, CA, USA.
| | - James K Harper
- Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
| | - Joshua D Hartman
- Department of Chemistry, University of CaliforniaRiverside, Riverside, CA, USA.
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2
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Zhang W, Lucier BEG, Terskikh VV, Chen S, Huang Y. Understanding Cu(i) local environments in MOFs via63/65Cu NMR spectroscopy. Chem Sci 2024; 15:6690-6706. [PMID: 38725502 PMCID: PMC11077522 DOI: 10.1039/d4sc00782d] [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: 02/01/2024] [Accepted: 02/26/2024] [Indexed: 05/12/2024] Open
Abstract
The field of metal-organic frameworks (MOFs) includes a vast number of hybrid organic and inorganic porous materials with wide-ranging applications. In particular, the Cu(i) ion exhibits rich coordination chemistry in MOFs and can exist in two-, three-, and four-coordinate environments, which gives rise to many structural motifs and potential applications. Direct characterization of the structurally and chemically important Cu(i) local environments is essential for understanding the sources of specific MOF properties. For the first time, 63/65Cu solid-state NMR has been used to investigate a variety of Cu(i) sites and local coordination geometries in Cu MOFs. This approach is a sensitive probe of the local Cu environment, particularly when combined with density functional theory calculations. A wide range of structurally-dependent 63/65Cu NMR parameters have been observed, including 65Cu quadrupolar coupling constants ranging from 18.8 to 74.8 MHz. Using the data from this and prior studies, a correlation between Cu quadrupolar coupling constants, Cu coordination number, and local Cu coordination geometry has been established. Links between DFT-calculated and experimental Cu NMR parameters are also presented. Several case studies illustrate the feasibility of 63/65Cu NMR for investigating and resolving inequivalent Cu sites, monitoring MOF phase changes, interrogating the Cu oxidation number, and characterizing the product of a MOF chemical reaction involving Cu(ii) reduction to Cu(i). A convenient avenue to acquire accurate 65Cu NMR spectra and NMR parameters from Cu(i) MOFs at a widely accessible magnetic field of 9.4 T is described, with a demonstrated practical application for tracking Cu(i) coordination evolution during MOF anion exchange. This work showcases the power of 63/65Cu solid-state NMR spectroscopy and DFT calculations for molecular-level characterization of Cu(i) centers in MOFs, along with the potential of this protocol for investigating a wide variety of MOF structural changes and processes important for practical applications. This approach has broad applications for examining Cu(i) centers in other weight-dilute systems.
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Affiliation(s)
- Wanli Zhang
- Department of Chemistry, The University of Western Ontario 1151 Richmond Street London Ontario N6A 5B7 Canada
| | - Bryan E G Lucier
- Department of Chemistry, The University of Western Ontario 1151 Richmond Street London Ontario N6A 5B7 Canada
| | - Victor V Terskikh
- Metrology, National Research Council Canada Ottawa Ontario K1A 0R6 Canada
| | - Shoushun Chen
- College of Chemistry and Chemical Engineering, Lanzhou University Lanzhou 730000 China
| | - Yining Huang
- Department of Chemistry, The University of Western Ontario 1151 Richmond Street London Ontario N6A 5B7 Canada
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3
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Chaloupecká E, Tyrpekl V, Bártová K, Nishiyama Y, Dračínský M. NMR crystallography of amino acids. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2024; 130:101921. [PMID: 38422809 DOI: 10.1016/j.ssnmr.2024.101921] [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: 11/23/2023] [Revised: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
The development of NMR crystallography methods requires a reliable database of chemical shifts measured for systems with known crystal structure. We measured and assigned carbon and hydrogen chemical shifts of twenty solid natural amino acids of known polymorphic structure, meticulously determined using powder X-ray diffraction. We then correlated the experimental data with DFT-calculated isotropic shieldings. The small size of the unit cell of most amino acids allowed for advanced computations using various families of DFT functionals, including generalized gradient approximation (GGA), meta-GGA and hybrid DFT functionals. We tested several combinations of functionals for geometry optimizations and NMR calculations. For carbon shieldings, the widely used GGA functional PBE performed very well, although an improvement could be achieved by adding shielding corrections calculated for isolated molecules using a hybrid functional. For hydrogen nuclei, we observed the best performance for NMR calculations carried out with structures optimized at the hybrid DFT level. The high fidelity of the calculations made it possible to assign additional signals that could not be assigned based on experiments alone, for example signals of two non-equivalent molecules in the unit cell of some of the amino acids.
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Affiliation(s)
- Ema Chaloupecká
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague 2, Czech Republic
| | - Václav Tyrpekl
- Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague 2, Czech Republic
| | - Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic
| | | | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic.
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4
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Holmes ST, Boley CM, Dewicki A, Gardner ZT, Vojvodin CS, Iuliucci RJ, Schurko RW. Carbon-13 chemical shift tensor measurements for nitrogen-dense compounds. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:179-189. [PMID: 38230444 DOI: 10.1002/mrc.5422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/30/2023] [Accepted: 12/13/2023] [Indexed: 01/18/2024]
Abstract
This paper reports the principal values of the 13 C chemical shift tensors for five nitrogen-dense compounds (i.e., cytosine, uracil, imidazole, guanidine hydrochloride, and aminoguanidine hydrochloride). Although these are all fundamentally important compounds, the majority do not have 13 C chemical shift tensors reported in the literature. The chemical shift tensors are obtained from 1 H→13 C cross-polarization magic-angle spinning (CP/MAS) experiments that were conducted at a high field of 18.8 T to suppress the effects of 14 N-13 C residual dipolar coupling. Quantum chemical calculations using density functional theory are used to obtain the 13 C magnetic shielding tensors for these compounds. The best agreement with experiment arises from calculations using the hybrid functional PBE0 or the double-hybrid functional PBE0-DH, along with the triple-zeta basis sets TZ2P or pc-3, respectively, and intermolecular effects modeled using large clusters of molecules with electrostatic embedding through the COSMO approach. These measurements are part of an ongoing effort to expand the catalog of accurate 13 C chemical shift tensor measurements, with the aim of creating a database that may be useful for benchmarking the accuracy of quantum chemical calculations, developing nuclear magnetic resonance (NMR) crystallography protocols, or aiding in applications involving machine learning or data mining. This work was conducted at the National High Magnetic Field Laboratory as part of a 2-week school for introducing undergraduate students to practical laboratory experience that will prepare them for scientific careers or postgraduate studies.
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Affiliation(s)
- Sean T Holmes
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida, USA
- National High Magnetic Field Laboratory, Tallahassee, Florida, USA
| | - Cameron M Boley
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania, USA
| | - Angelika Dewicki
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania, USA
| | - Zachary T Gardner
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania, USA
| | - Cameron S Vojvodin
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida, USA
- National High Magnetic Field Laboratory, Tallahassee, Florida, USA
| | - Robbie J Iuliucci
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania, USA
| | - Robert W Schurko
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida, USA
- National High Magnetic Field Laboratory, Tallahassee, Florida, USA
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5
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Holmes ST, Schönzart J, Philips AB, Kimball JJ, Termos S, Altenhof AR, Xu Y, O'Keefe CA, Autschbach J, Schurko RW. Structure and bonding in rhodium coordination compounds: a 103Rh solid-state NMR and relativistic DFT study. Chem Sci 2024; 15:2181-2196. [PMID: 38332836 PMCID: PMC10848688 DOI: 10.1039/d3sc06026h] [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: 11/10/2023] [Accepted: 12/06/2023] [Indexed: 02/10/2024] Open
Abstract
This study demonstrates the application of 103Rh solid-state NMR (SSNMR) spectroscopy to inorganic and organometallic coordination compounds, in combination with relativistic density functional theory (DFT) calculations of 103Rh chemical shift tensors and their analysis with natural bond orbital (NBO) and natural localized molecular orbital (NLMO) protocols, to develop correlations between 103Rh chemical shift tensors, molecular structure, and Rh-ligand bonding. 103Rh is one of the least receptive NMR nuclides, and consequently, there are very few reports in the literature. We introduce robust 103Rh SSNMR protocols for stationary samples, which use the broadband adiabatic inversion-cross polarization (BRAIN-CP) pulse sequence and wideband uniform-rate smooth-truncation (WURST) pulses for excitation, refocusing, and polarization transfer, and demonstrate the acquisition of 103Rh SSNMR spectra of unprecedented signal-to-noise and uniformity. The 103Rh chemical shift tensors determined from these spectra are complemented by NBO/NLMO analyses of contributions of individual orbitals to the 103Rh magnetic shielding tensors to understand their relationship to structure and bonding. Finally, we discuss the potential for these experimental and theoretical protocols for investigating a wide range of materials containing the platinum group elements.
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Affiliation(s)
- Sean T Holmes
- Department of Chemistry & Biochemistry, Florida State University Tallahassee FL 32306 USA
- National High Magnetic Field Laboratory Tallahassee FL 32310 USA
| | - Jasmin Schönzart
- Department of Chemistry & Biochemistry, Florida State University Tallahassee FL 32306 USA
- National High Magnetic Field Laboratory Tallahassee FL 32310 USA
| | - Adam B Philips
- Department of Chemistry, University at Buffalo, State University of New York Buffalo NY 14260-3000 USA
| | - James J Kimball
- Department of Chemistry & Biochemistry, Florida State University Tallahassee FL 32306 USA
- National High Magnetic Field Laboratory Tallahassee FL 32310 USA
| | - Sara Termos
- Department of Chemistry & Biochemistry, Florida State University Tallahassee FL 32306 USA
- National High Magnetic Field Laboratory Tallahassee FL 32310 USA
| | - Adam R Altenhof
- Department of Chemistry & Biochemistry, Florida State University Tallahassee FL 32306 USA
- National High Magnetic Field Laboratory Tallahassee FL 32310 USA
| | - Yijue Xu
- National High Magnetic Field Laboratory Tallahassee FL 32310 USA
| | - Christopher A O'Keefe
- Department of Chemistry & Biochemistry, University of Windsor Windsor ON N9B 3P4 Canada
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York Buffalo NY 14260-3000 USA
| | - Robert W Schurko
- Department of Chemistry & Biochemistry, Florida State University Tallahassee FL 32306 USA
- National High Magnetic Field Laboratory Tallahassee FL 32310 USA
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Li Y, Zeng P, Lou Q, Su X, Li W, Wang X. Prediction of 19F NMR chemical shifts for organic compounds with ORCA. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 358:107611. [PMID: 38104491 DOI: 10.1016/j.jmr.2023.107611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/11/2023] [Accepted: 12/10/2023] [Indexed: 12/19/2023]
Abstract
Accurate assignment of 19F NMR has long been a challenge, and quantum chemical methods are possible solutions. Herein we reported a scaling method for the prediction of 19F NMR chemical shift with freely available ORCA program package. Performance of 31 DFT functionals coupled with 11 basis sets were evaluated and influence of geometry optimization was also studied with five functionals coupled with three basis sets. The significance of geometry was further examined through the execution of relaxed surface scans of seven flexible compounds, and averaged shieldings of obtained conformers yielded notable improvement of the correlation between calculated isotropic shielidings and experimental chemical shifts. Utilization of the best scaling factor obtained successfully assigned of fluorine atoms in multifluorinated molecules with different conformations. The method reported here was computationally inexpensive, easily available with acceptable accuracy.
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Affiliation(s)
- Yueyang Li
- Institute of Advanced Synthesis, Institute of Chemical Biology and Functional Molecules, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Ping Zeng
- Institute of Advanced Synthesis, Institute of Chemical Biology and Functional Molecules, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Qing Lou
- Institute of Advanced Synthesis, Institute of Chemical Biology and Functional Molecules, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Xiao Su
- Institute of Advanced Synthesis, Institute of Chemical Biology and Functional Molecules, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Wei Li
- Institute of Advanced Synthesis, Institute of Chemical Biology and Functional Molecules, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China; State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China(1)
| | - Xiaojian Wang
- Institute of Advanced Synthesis, Institute of Chemical Biology and Functional Molecules, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China.
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7
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Hartman JD, Spock LE, Harper JK. Benchmark accuracy of predicted NMR observables for quadrupolar 14 N and 17 O nuclei in molecular crystals. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:253-267. [PMID: 36567433 DOI: 10.1002/mrc.5328] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Nuclear quadrupole resonances for 14 N and 17 O nuclei are exquisitely sensitive to interactions with surrounding atoms. As a result, nitrogen and oxygen solid-state nuclear magnetic resonance (ssNMR) provides a powerful tool for investigating structure and dynamics in complex systems. First-principles calculations are increasingly used to facilitate spectral assignment and to evaluate and adjust crystal structures. Recent work combining the strengths of planewave density functional theory (DFT) calculations with a single molecule correction obtained using a higher level of theory has proven successful in improving the accuracy of predicted chemical shielding (CS) tensors and 17 O quadrupolar coupling constants ( C q ). Here we extend this work by examining the accuracy of predicted 14 N and 17 O electric field gradient (EFG) tensor components obtained using alternative planewave-corrections involving cluster and two-body fragment-based calculations. We benchmark the accuracy of CS and EFG tensor predictions for both nitrogen and oxygen using planewave, two-body fragment, and enhanced planewave-corrected techniques. Combining planewave and two-body fragment calculations reduces the error in predicted 17 O C q values by 35% relative to traditional planewave calculations. These enhanced planewave-correction methods improve the accuracy of 17 O and 14 N EFG tensor components by 15% relative to planewave DFT but yield minimal improvement relative to a simple molecular correction. However, in structural environments involving either high symmetry or strong intermolecular interactions, enhanced planewave-corrected methods provide a distinct advantage.
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Affiliation(s)
- Joshua D Hartman
- Department of Chemistry, University of California, Riverside, Riverside, California, USA
| | - Lilian E Spock
- Department of Chemistry, University of California, Riverside, Riverside, California, USA
| | - James K Harper
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
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8
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Iuliucci RJ, Hartman JD, Beran GJO. Do Models beyond Hybrid Density Functionals Increase the Agreement with Experiment for Predicted NMR Chemical Shifts or Electric Field Gradient Tensors in Organic Solids? J Phys Chem A 2023; 127:2846-2858. [PMID: 36940431 DOI: 10.1021/acs.jpca.2c07657] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2023]
Abstract
Ab initio predictions of chemical shifts and electric field gradient (EFG) tensor components are frequently used to help interpret solid-state nuclear magnetic resonance (NMR) experiments. Typically, these predictions employ density functional theory (DFT) with generalized gradient approximation (GGA) functionals, though hybrid functionals have been shown to improve accuracy relative to experiment. Here, the performance of a dozen models beyond the GGA approximation are examined for the prediction of solid-state NMR observables, including meta-GGA, hybrid, and double-hybrid density functionals and second-order Møller-Plesset perturbation theory (MP2). These models are tested on organic molecular crystal data sets containing 169 experimental 13C and 15N chemical shifts and 114 17O and 14N EFG tensor components. To make these calculations affordable, gauge-including projector augmented wave (GIPAW) Perdew-Burke-Ernzerhof (PBE) calculations with periodic boundary conditions are combined with a local intramolecular correction computed at the higher level of theory. Within the context of typical NMR property calculations performed on a static, DFT-optimized crystal structure, the benchmarking finds that the double-hybrid DFT functionals produce errors versus experiment that are no smaller than those of hybrid functionals in the best cases, and they can be larger. MP2 errors versus experiment are even bigger. Overall, no practical advantages are found for using any of the tested double-hybrid functionals or MP2 to predict experimental solid-state NMR chemical shifts and EFG tensor components for routine organic crystals, especially given the higher computational cost of those methods. This finding likely reflects error cancellation benefiting the hybrid functionals. Improving the accuracy of the predicted chemical shifts and EFG tensors relative to experiment would probably require more robust treatments of the crystal structures, their dynamics, and other factors.
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Affiliation(s)
- Robbie J Iuliucci
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania 15301 United States
| | - Joshua D Hartman
- Department of Chemistry, University of California, Riverside, California 92521 United States
| | - Gregory J O Beran
- Department of Chemistry, University of California, Riverside, California 92521 United States
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9
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Hartman JD, Harper JK. Improving the accuracy of GIPAW chemical shielding calculations with cluster and fragment corrections. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 122:101832. [PMID: 36198253 DOI: 10.1016/j.ssnmr.2022.101832] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Ab initio methods for predicting NMR parameters in the solid state are an essential tool for assigning experimental spectra and play an increasingly important role in structural characterizations. Recently, a molecular correction (MC) technique has been developed which combines the strengths of plane-wave methods (GIPAW) with single molecule calculations employing Gaussian basis sets. The GIPAW + MC method relies on a periodic calculation performed at a lower level of theory to model the crystalline environment. The GIPAW result is then corrected using a single molecule calculation performed at a higher level of theory. The success of the GIPAW + MC method in predicting a range of NMR parameters is a result of the highly local character of the tensors underlying the NMR observable. However, in applications involving strong intermolecular interactions we find that expanding the region treated at the higher level of theory more accurately captures local many-body contributions to the N15 NMR chemical shielding (CS) tensor. We propose alternative corrections to GIPAW which capture interactions between adjacent molecules at a higher level of theory using either fragment or cluster-based calculations. Benchmark calculations performed on N15 and C13 data sets show that these advanced GIPAW-corrected calculations improve the accuracy of chemical shielding tensor predictions relative to existing methods. Specifically, cluster-based N15 corrections show a 24% and 17% reduction in RMS error relative to GIPAW and GIPAW + MC calculations, respectively. Comparing the benchmark data sets using multiple computational models demonstrates that N15 CS tensor calculations are significantly more sensitive to intermolecular interactions relative to C13. However, fragment and cluster-based corrections that include direct hydrogen bond partners are sufficient for optimizing the accuracy of GIPAW-corrected methods. Finally, GIPAW-corrected methods are applied to the particularly challenging NMR spectral assignment of guanosine dihydrate which contains two guanosine molecules in the asymmetric unit.
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Affiliation(s)
- Joshua D Hartman
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States.
| | - James K Harper
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, United States.
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10
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Poidevin C, Stoychev GL, Riplinger C, Auer AA. High Level Electronic Structure Calculation of Molecular Solid-State NMR Shielding Constants. J Chem Theory Comput 2022; 18:2408-2417. [PMID: 35353527 PMCID: PMC9009078 DOI: 10.1021/acs.jctc.1c01095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In this work, we
present a quantum mechanics/molecular mechanics
(QM/MM) approach for the computation of solid-state nuclear magnetic
resonance (SS-NMR) shielding constants (SCs) for molecular crystals.
Besides applying standard-DFT functionals like GGAs (PBE), meta-GGAs
(TPSS), and hybrids (B3LYP), we apply a double-hybrid (DSD-PBEP86)
functional as well as MP2, using the domain-based local pair natural
orbital (DLPNO) formalism, to calculate the NMR SCs of six amino acid
crystals. All the electronic structure methods used exhibit good correlation
of the NMR shieldings with respect to experimental chemical shifts
for both 1H and 13C. We also find that local
electronic structure is much more important than the long-range electrostatic
effects for these systems, implying that cluster approaches using
all-electron/Gaussian basis set methods might offer great potential
for predictive computations of solid-state NMR parameters for organic
solids.
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Affiliation(s)
- Corentin Poidevin
- Institut des Sciences Chimiques de Rennes, Av. Général Leclerc, 357000 Rennes, France
| | - Georgi L Stoychev
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | | | - Alexander A Auer
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
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11
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Hartman JD, Mathews A, Harper JK. Fast and Accurate Electric Field Gradient Calculations in Molecular Solids With Density Functional Theory. Front Chem 2021; 9:751711. [PMID: 34692646 PMCID: PMC8529703 DOI: 10.3389/fchem.2021.751711] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/20/2021] [Indexed: 11/24/2022] Open
Abstract
Modern approaches for calculating electric field gradient (EFF) tensors in molecular solids rely upon plane-wave calculations employing periodic boundary conditions (PBC). In practice, models employing PBCs are limited to generalized gradient approximation (GGA) density functionals. Hybrid density functionals applied in the context of gauge-including atomic orbital (GIAO) calculations have been shown to substantially improve the accuracy of predicted NMR parameters. Here we propose an efficient method that effectively combines the benefits of both periodic calculations and single-molecule techniques for predicting electric field gradient tensors in molecular solids. Periodic calculations using plane-wave basis sets were used to model the crystalline environment. We then introduce a molecular correction to the periodic result obtained from a single-molecule calculation performed with a hybrid density functional. Single-molecule calculations performed using hybrid density functionals were found to significantly improve the agreement of predicted 17O quadrupolar coupling constants (C q ) with experiment. We demonstrate a 31% reduction in the RMS error for the predicted 17O C q values relative to standard plane-wave methods using a carefully constructed test set comprised of 22 oxygen-containing molecular crystals. We show comparable improvements in accuracy using five different hybrid density functionals and find predicted C q values to be relatively insensitive to the choice of basis set used in the single molecule calculation. Finally, the utility of high-accuracy 17O C q predictions is demonstrated by examining the disordered 4-Nitrobenzaldehyde crystal structure.
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Affiliation(s)
- Joshua D. Hartman
- Department of Chemistry, Mt. San Jacinto College, Menifee, CA, United States
| | - Amanda Mathews
- Department of Chemistry, Mt. San Jacinto College, Menifee, CA, United States
| | - James K. Harper
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, United States
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12
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Mathews A, Hartman JD. Accurate fragment-based 51-V chemical shift predictions in molecular crystals. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2021; 114:101733. [PMID: 34082261 DOI: 10.1016/j.ssnmr.2021.101733] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/28/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy plays a crucial role in determining molecular structure for complex biological and pharmaceutical compounds. NMR investigations are increasingly reliant on computation for mapping spectral features to chemical structures. Here we benchmark the accuracy of fragment-based 51V chemical shielding tensor calculations using a training set comprised of 10 biologically and pharmaceutically relevant oxovanadium complexes. Using our self-consistent reproduction of the Madelung potential (SCRMP) electrostatic embedding model, we demonstrate comparable performance between fragment methods and computationally demanding cluster-based techniques. Specifically, fragment methods employing hybrid density functionals are capable of reproducing the experimental 51V isotropic chemical shifts with a training set rms error of ~9 ppm, representing a 20% improvement over traditional plane wave techniques. We provide training set-derived linear regression models for mapping the absolute shieldings obtained from computation to the experimentally determined chemical shifts using four common density functionals; PBE0, B3LYP, PBE, and BLYP. Finally, we establish the utility of fragment methods and the reported regression parameters examining four oxovanadium structures excluded from the training set including the tetracoordinate oxovanadium silicate [Formula: see text] , VO15NGlySalbz which contains redox-active ligands, and the solid-state form of the common 51V NMR reference compound VOCl3.
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Affiliation(s)
- Amanda Mathews
- Department of Chemistry, Mt. San Jacinto College, Menifee, CA, USA
| | - Joshua D Hartman
- Department of Chemistry, Mt. San Jacinto College, Menifee, CA, USA.
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Unzueta PA, Greenwell CS, Beran GJO. Predicting Density Functional Theory-Quality Nuclear Magnetic Resonance Chemical Shifts via Δ-Machine Learning. J Chem Theory Comput 2021; 17:826-840. [DOI: 10.1021/acs.jctc.0c00979] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Pablo A. Unzueta
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Chandler S. Greenwell
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Gregory J. O. Beran
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
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14
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Holmes ST, Vojvodin CS, Schurko RW. Dispersion-Corrected DFT Methods for Applications in Nuclear Magnetic Resonance Crystallography. J Phys Chem A 2020; 124:10312-10323. [DOI: 10.1021/acs.jpca.0c06372] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sean T. Holmes
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Cameron S. Vojvodin
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Robert W. Schurko
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
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15
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Abstract
Magnetic shielding depends on molecular structure and noncovalent interactions. This study shows that it is also measurably dependent on the electric field generated by surrounding molecules. This effect has been observed explicitly for 31P nucleus using the adduct under field approach. The results obtained indicate that the field strength experienced by molecules in crystals consisting of molecules with large dipole moments is similar to that in polar solvents. Therefore, magnetic shielding should explicitly depend on solvent polarity. It is important to note that this effect cannot be reproduced correctly within the polarizable continuum model approach.
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Affiliation(s)
- Ilya G Shenderovich
- Institute of Organic Chemistry, University of Regensburg, Universitaetstrasse 31, 93053 Regensburg, Germany
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16
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Unzueta PA, Beran GJO. Polarizable continuum models provide an effective electrostatic embedding model for fragment-based chemical shift prediction in challenging systems. J Comput Chem 2020; 41:2251-2265. [PMID: 32748418 DOI: 10.1002/jcc.26388] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/04/2020] [Accepted: 07/04/2020] [Indexed: 12/25/2022]
Abstract
Ab initio nuclear magnetic resonance chemical shift prediction provides an important tool for interpreting and assigning experimental spectra, but it becomes computationally prohibitive in large systems. The computational costs can be reduced considerably by fragmentation of the large system into a series of contributions from many smaller subsystems. However, the presence of charged functional groups and the need to partition the system across covalent bonds create complications in biomolecules that typically require the use of large fragments and careful descriptions of the electrostatic environment. The present work shows how a model that combines chemical shielding contributions from non-overlapping monomer and dimer fragments embedded in a polarizable continuum model provides a simple, easy-to-implement, and computationally inexpensive approach for predicting chemical shifts in complex systems. The model's performance proves rather insensitive to the continuum dielectric constant, making the selection of the optimal embedding dielectric less critical. The PCM-embedded fragment model is demonstrated to perform well across systems ranging from molecular crystals to proteins.
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Affiliation(s)
- Pablo A Unzueta
- Department of Chemistry, Univeristy of California, Riverside, California, USA
| | - Gregory J O Beran
- Department of Chemistry, Univeristy of California, Riverside, California, USA
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17
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Hodgkinson P. NMR crystallography of molecular organics. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 118-119:10-53. [PMID: 32883448 DOI: 10.1016/j.pnmrs.2020.03.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/25/2020] [Accepted: 03/13/2020] [Indexed: 06/11/2023]
Abstract
Developments of NMR methodology to characterise the structures of molecular organic structures are reviewed, concentrating on the previous decade of research in which density functional theory-based calculations of NMR parameters in periodic solids have become widespread. With a focus on demonstrating the new structural insights provided, it is shown how "NMR crystallography" has been used in a spectrum of applications from resolving ambiguities in diffraction-derived structures (such as hydrogen atom positioning) to deriving complete structures in the absence of diffraction data. As well as comprehensively reviewing applications, the different aspects of the experimental and computational techniques used in NMR crystallography are surveyed. NMR crystallography is seen to be a rapidly maturing subject area that is increasingly appreciated by the wider crystallographic community.
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Affiliation(s)
- Paul Hodgkinson
- Department of Chemistry, Durham University, Stockton Road, Durham DH1 3LE, UK.
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18
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Zhao D, Shen X, Cheng Z, Li W, Dong H, Li S. Accurate and Efficient Prediction of NMR Parameters of Condensed-Phase Systems with the Generalized Energy-Based Fragmentation Method. J Chem Theory Comput 2020; 16:2995-3005. [DOI: 10.1021/acs.jctc.9b01298] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Dongbo Zhao
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
- Kuang Yaming Honors School, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Xiaoling Shen
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Zheng Cheng
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, 210023 Nanjing, People’s Republic of China
- Institute for Brain Sciences, Nanjing University, 210023 Nanjing, People’s Republic of China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People’s Republic of China
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19
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Holmes ST, Engl OG, Srnec MN, Madura JD, Quiñones R, Harper JK, Schurko RW, Iuliucci RJ. Chemical Shift Tensors of Cimetidine Form A Modeled with Density Functional Theory Calculations: Implications for NMR Crystallography. J Phys Chem A 2020; 124:3109-3119. [DOI: 10.1021/acs.jpca.0c00421] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sean T. Holmes
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Olivia G. Engl
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania 15301, United States
| | - Matthew N. Srnec
- Department of Chemistry, Physics, & Engineering, Franciscan University, Steubenville, Ohio 43952, United States
| | - Jeffry D. Madura
- Department of Chemistry & Biochemistry, Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Rosalynn Quiñones
- Department of Chemistry, Marshall University, Huntington, West Virginia 25755, United States
| | - James K. Harper
- Department of Chemistry & Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Robert W. Schurko
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Robbie J. Iuliucci
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania 15301, United States
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20
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Zhao Z, Li E, Qin Y, Liu X, Zou Y, Wu H, Zhu T. Density functional theory (DFT) studies of vanadium-titanium based selective catalytic reduction (SCR) catalysts. J Environ Sci (China) 2020; 90:119-137. [PMID: 32081309 DOI: 10.1016/j.jes.2019.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/01/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
Based on density functional theory (DFT) and basic structure models, the chemical reactions on the surface of vanadium-titanium based selective catalytic reduction (SCR) denitrification catalysts were summarized. Reasonable structural models (non-periodic and periodic structural models) are the basis of density functional calculations. A periodic structure model was more appropriate to represent the catalyst surface, and its theoretical calculation results were more comparable with the experimental results than a non-periodic model. It is generally believed that the SCR mechanism where NH3 and NO react to produce N2 and H2O follows an Eley-Rideal type mechanism. NH2NO was found to be an important intermediate in the SCR reaction, with multiple production routes. Simultaneously, the effects of H2O, SO2 and metal on SCR catalysts were also summarized.
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Affiliation(s)
- Ziwei Zhao
- National Engineering Laboratory for Hydrometallurgical Cleaner Production Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Erwei Li
- National Engineering Laboratory for Hydrometallurgical Cleaner Production Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Yu Qin
- State Key Laboratory of Solid Waste Reuse for Building Materials, Beijing Building Materials Academy of Science Research, Beijing 100041, China
| | - Xiaolong Liu
- National Engineering Laboratory for Hydrometallurgical Cleaner Production Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
| | - Yang Zou
- National Engineering Laboratory for Hydrometallurgical Cleaner Production Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Heng Wu
- National Engineering Laboratory for Hydrometallurgical Cleaner Production Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Tingyu Zhu
- National Engineering Laboratory for Hydrometallurgical Cleaner Production Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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21
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Ludwig M, Himmel D, Hillebrecht H. GIAO versus GIPAW: Comparison of Methods To Calculate 11B NMR Shifts of Icosahedral Closo-Heteroboranes toward Boron-Rich Borides. J Phys Chem A 2020; 124:2173-2185. [PMID: 31999459 DOI: 10.1021/acs.jpca.9b06582] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we perform first-principle density functional theory calculations with the Perdew-Burke-Ernzerhof (PBE) exchange correlation functional to compare the results of the gauge-including atomic orbital (GIAO) method with the gauge-including projector-augmented wave (GIPAW) approach for isotropic 11B nuclear magnetic resonance shifts. GIPAW had been used successfully for the theoretical calculation of nuclear magnetic parameters of 11B species in strong ionic solid-phase compounds such as borates but had been applied very rarely to structures where boron is mainly involved in complex covalent bonding situations, for example, in icosahedra of boron-rich borides. Thus, we investigate the accuracy of both well-known methods and reliability of the effective treatment of core electrons on a test set containing 16 experimentally known closo-(hetero)dodecaboranes. In general, we find very good agreement between GIAO and GIPAW when compared to experimental observations. However, accidental degeneracies of the shift values are better predicted by GIPAW. The optimized molecular geometries on the PBE level agree well with gaseous electron diffraction data and lead to theoretical isotropic chemical 11B shifts with root-mean-square errors of 2.1 and 1.0 ppm depending on the used model of converting absolute shieldings to chemical shifts. The comparison with results from hybrid functionals (B3LYP, B3LYP-D2, and PBE0) shows a minor improvement in accuracy, which is in agreement with 13C shifts of sp3-hybridized species. In order to prove the reliability of the conversion parameters obtained by PBE, we report the calculated 11B shifts of 1,2-, 1,7-, and 1,12-PCB10H11 with GIAO and GIPAW to our knowledge for the first time. Additionally, Bader's analysis is carried out on the converged electron density for all boron species within the molecular test set, yielding no simple direct relation between charge and isotropic shifts.
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Affiliation(s)
- Martin Ludwig
- Institut für Anorganische und Analytische Chemie, Albert-Ludwigs-Universität, Albertstraße 21, 79104 Freiburg, Germany
| | - Daniel Himmel
- Institut für Anorganische und Analytische Chemie, Albert-Ludwigs-Universität, Albertstraße 21, 79104 Freiburg, Germany
| | - Harald Hillebrecht
- Institut für Anorganische und Analytische Chemie, Albert-Ludwigs-Universität, Albertstraße 21, 79104 Freiburg, Germany
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22
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Martel L, Kovács A, Popa K, Bregiroux D, Charpentier T. 31P MAS NMR and DFT study of crystalline phosphate matrices. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2020; 105:101638. [PMID: 31810014 DOI: 10.1016/j.ssnmr.2019.101638] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/15/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
We present the study of the phosphorus local environment by using 31P MAS NMR in a series of seven double monophosphates MIIMIV(PO4)2 (MII and MIV being divalent and tetravalent cations, respectively) of yavapaiite and low-yavapaiite type crystal structures. Solid-state and cluster DFT calculations were found to be efficient for predicting the 31P isotropic chemical shift and chemical shift anisotropy. To achieve this performance, however, a proper computational optimisation of the experimental structural data was required. From the three optimisation methods tested, the full optimisation provided the best reference structure for the calculation of the NMR parameters of the studied phosphates. Also, a better prediction of the chemical shifts was possible by using a correction to the GIPAW calculated shielding.
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Affiliation(s)
- Laura Martel
- European Commission, Joint Research Centre (JRC), Postfach 2340, D-76125, Karlsruhe, Germany.
| | - Attila Kovács
- European Commission, Joint Research Centre (JRC), Postfach 2340, D-76125, Karlsruhe, Germany
| | - Karin Popa
- European Commission, Joint Research Centre (JRC), Postfach 2340, D-76125, Karlsruhe, Germany
| | - Damien Bregiroux
- Sorbonne Université, CNRS, Chimie de la Matière Condensée de Paris, LCMCP, F-75005, Paris, France
| | - Thibault Charpentier
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay 91191 Gif-sur-Yvette, France
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23
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McKinley JL, Beran GJO. Improving Predicted Nuclear Magnetic Resonance Chemical Shifts Using the Quasi-Harmonic Approximation. J Chem Theory Comput 2019; 15:5259-5274. [PMID: 31442040 DOI: 10.1021/acs.jctc.9b00481] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ab initio nuclear magnetic resonance chemical shift prediction plays an important role in the determination or validation of crystal structures. The ability to predict chemical shifts more accurately can translate to increased confidence in the resulting chemical shift or structural assignments. Standard electronic structure predictions for molecular crystal structures neglect thermal expansion, which can lead to an appreciable underestimation of the molar volumes. This study examines this volume error and its impact on 68 13C- and 28 15N-predicted chemical shifts taken from 20 molecular crystals. It assesses the ability to recover more realistic room-temperature crystal structures using the quasi-harmonic approximation and how refining the structures impacts the chemical shifts. Several pharmaceutical molecular crystals are also examined in more detail. On the whole, accounting for quasi-harmonic expansion changes the 13C and 15N chemical shifts by 0.5 and 1.0 ppm on average. This, in turn, reduces the root-mean-square errors relative to experiment by 0.3 ppm for 13C and 0.7 ppm for 15N. Although the statistical impacts are modest, changes in individual chemical shifts can reach multiple ppm. Accounting for thermal expansion in molecular crystal chemical shift prediction may not be needed routinely, but the systematic trend toward improved accuracy with the experiment could be useful in cases where discrimination between structural candidates is challenging, as in the pharmaceutical theophylline.
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Affiliation(s)
- Jessica L McKinley
- Department of Chemistry , University of California , Riverside , California 92521 , United States
| | - Gregory J O Beran
- Department of Chemistry , University of California , Riverside , California 92521 , United States
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24
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Young RP, Lewis CR, Yang C, Wang L, Harper JK, Mueller LJ. TensorView: A software tool for displaying NMR tensors. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:211-223. [PMID: 30230009 PMCID: PMC6736611 DOI: 10.1002/mrc.4793] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 09/12/2018] [Accepted: 09/12/2018] [Indexed: 05/29/2023]
Abstract
The representation of nuclear magnetic resonance (NMR) tensors as surfaces on three-dimensional molecular models is an information-rich presentation that highlights the geometric relationship between tensor principal components and the underlying molecular and electronic structure. Here, we describe a new computational tool, TensorView, for depicting NMR tensors on the molecular framework. This package makes use of the graphical interface and built-in molecular display functionality present within the Mathematica programming environment and is robust for displaying tensor properties from a broad range of commercial and user-specific computational chemistry packages. Two mathematical forms for representing tensor interaction surfaces are presented, the popular ellipsoidal construct and the more technically correct "ovaloid" form. Examples are provided for chemical shielding and shift tensors, dipole-dipole and quadrupolar couplings, and atomic anisotropic displacement parameters (thermal ellipsoids) derived from NMR crystallography.
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Affiliation(s)
- Robert P. Young
- Department of Chemistry, University of California, Riverside, California 92521
| | - Corbin R. Lewis
- Department of Chemistry, University of California, Riverside, California 92521
| | - Chen Yang
- Department of Chemistry, University of California, Riverside, California 92521
| | - Luther Wang
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, FL 32816
| | - James K. Harper
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Orlando, FL 32816
| | - Leonard J. Mueller
- Department of Chemistry, University of California, Riverside, California 92521
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25
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Chernyshov IY, Vener MV, Shenderovich IG. Local-structure effects on 31P NMR chemical shift tensors in solid state. J Chem Phys 2019; 150:144706. [PMID: 30981271 DOI: 10.1063/1.5075519] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The effect of the local structure on the 31P NMR chemical shift tensor (CST) has been studied experimentally and simulated theoretically using the density functional theory gauge-independent-atomic-orbital approach. It has been shown that the dominating impact comes from a small number of noncovalent interactions between the phosphorus-containing group under question and the atoms of adjacent molecules. These interactions can be unambiguously identified using the Bader analysis of the electronic density. A robust and computationally effective approach designed to attribute a given experimental 31P CST to a certain local morphology has been elaborated. This approach can be useful in studies of surfaces, complex molecular systems, and amorphous materials.
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Affiliation(s)
- Ivan Yu Chernyshov
- Department of Quantum Chemistry, D. Mendeleev University of Chemical Technology, Moscow 125047, Russia
| | - Mikhail V Vener
- Department of Quantum Chemistry, D. Mendeleev University of Chemical Technology, Moscow 125047, Russia
| | - Ilya G Shenderovich
- Institute of Organic Chemistry, University of Regensburg, 93053 Regensburg, Germany
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26
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Holmes ST, Schurko RW. A DFT/ZORA Study of Cadmium Magnetic Shielding Tensors: Analysis of Relativistic Effects and Electronic-State Approximations. J Chem Theory Comput 2019; 15:1785-1797. [PMID: 30721042 DOI: 10.1021/acs.jctc.8b01296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Theoretical considerations are discussed for the accurate prediction of cadmium magnetic shielding tensors using relativistic density functional theory (DFT). Comparison is made between calculations that model the extended lattice of the cadmium-containing solids using periodic boundary conditions and pseudopotentials with calculations that use clusters of atoms. The all-electron cluster-based calculations afford an opportunity to examine the importance of (i) relativistic effects on cadmium magnetic shielding tensors, as introduced through the ZORA Hamiltonian at either the scalar (SC) or spin-orbit (SO) levels and (ii) variation in the class of the DFT approximation. Twenty-three combinations of pseudopotentials or all-electron methods, DFT functionals, and relativistic treatments are assessed for the prediction of the principal components of the magnetic shielding tensors of 30 cadmium sites. We find that the inclusion of SO coupling can increase the cadmium magnetic shielding by as much as ca. 1100 ppm for a certain principal values; these effects are most pronounced for cadmium sites featuring bonds to other heavy atoms such as cadmium, iodine, or selenium. The best agreement with experimental values is found at the ZORA SO level in combination with a hybrid DFT method featuring a large admixture of Hartree-Fock exchange such as BH&HLYP. Finally, a theoretical examination is presented of the magnetic shielding tensor of the Cd(I) site in Cd2(AlCl4)2.
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Affiliation(s)
- Sean T Holmes
- Department of Chemistry and Biochemistry , University of Windsor , Windsor , ON , Canada N9B 3P4
| | - Robert W Schurko
- Department of Chemistry and Biochemistry , University of Windsor , Windsor , ON , Canada N9B 3P4
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27
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Oliveira JPC, Rivelino R. Close Relationships between NMR J-Coupling Alternation (JCA) and Molecular Properties of Carbon Chains. J Chem Theory Comput 2019; 15:1605-1615. [PMID: 30730735 DOI: 10.1021/acs.jctc.8b01141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose a J-coupling alternation (JCA) value that is demonstrated to be a suitable parameter to evaluate the nuclear magnetic resonance (NMR) indirect spin-spin coupling constants (SSCCs) as a function of molecular properties of chains by increasing their length. As an application, we report a theoretical study of the SSCCs for the interactions between neighbor nuclei in increasingly patterned carbon chains within density functional theory. First, we examine the J-coupling constants between 1H and 13C nuclei ( n JHC) considering the separation distance, as well as between two adjacent 13C nuclei (1 JCC) considering their relative positions in polyynes and cumulenes. Further, we define and determine JCA in terms of the differences of 1 JCC, which is investigated as a function of several molecular properties, e.g., cohesive energy, characteristic vibrational frequency, average polarizability, and energy gap of the systems. We also determine JCA for other types of carbon chains, such as diphenyl-capped polyynes, polyacetylene and polythiophene. The behavior of JCA as a function of the energy gap may be related to highly π-conjugated low-band-gap carbon chains. Overall, JCA correlates very well with the electronic properties of these chains, especially with their energy gap, exhibiting positive values for pristine polyyne and polythiophene and negative values for pristine cumulene and plyacetylene. These findings indicate an alternative way to establish an appropriate SSCC descriptor that characterizes the electronic nature of the system, such as the proposed JCA value averaging the whole system, instead of using only the individual J-coupling values to give insights into the properties of large and extended systems.
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Affiliation(s)
- João P C Oliveira
- Instituto de Física , Universidade Federal da Bahia , 40210-340 Salvador , Bahia , Brazil.,Centro de Ciência e Tecnologia em Energia e Sustentabilidade , Universidade Federal do Recôncavo da Bahia , 44085-132 Feira de Santana , Bahia , Brazil
| | - Roberto Rivelino
- Instituto de Física , Universidade Federal da Bahia , 40210-340 Salvador , Bahia , Brazil
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28
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Dračínský M, Unzueta P, Beran GJO. Improving the accuracy of solid-state nuclear magnetic resonance chemical shift prediction with a simple molecular correction. Phys Chem Chem Phys 2019; 21:14992-15000. [PMID: 31237586 DOI: 10.1039/c9cp01666j] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A fast, straightforward method for computing NMR chemical shieldings of crystalline solids is proposed. The method combines the advantages of both conventional approaches: periodic calculations using plane-wave basis sets and molecular computational approaches. The periodic calculations capture the periodic nature of crystalline solids, but the computational level of the electronic structure calculation is limited to general-gradient-approximation (GGA) density functionals. It is demonstrated that a correction to the GGA result calculated on an isolated molecule at a higher level of theory significantly improves the correlations between experimental and calculated chemical shifts while adding almost no additional computational cost. Corrections calculated with a hybrid density functional improved the accuracy of 13C, 15N and 17O chemical shift predictions significantly and allowed identifying errors in previously published experimental data. Applications of the approach to crystalline isocytosine, methacrylamide, and testosterone are presented.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo 2, Prague, Czech Republic.
| | - Pablo Unzueta
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Gregory J O Beran
- Department of Chemistry, University of California, Riverside, California 92521, USA
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29
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Afonin AV, Pavlov DV, Vashchenko AV. Case study of 2-vinyloxypyridine: Quantitative assessment of the intramolecular C H⋯N hydrogen bond energy and its contribution to the one-bond 13C1H coupling constant. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.08.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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30
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Pilar K, Deng Z, Preefer MB, Cooley JA, Clément R, Seshadri R, Cheetham AK. Ab initio computation for solid-state 31P NMR of inorganic phosphates: revisiting X-ray structures. Phys Chem Chem Phys 2019; 21:10070-10074. [PMID: 31049516 DOI: 10.1039/c9cp01420a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The complete 31P NMR chemical shift tensors for 22 inorganic phosphates obtained from ab initio computation are found to correspond closely to experimentally obtained parameters. Further improvement was found when structures determined by diffraction were geometry optimized. Besides aiding in spectral assignment, the cases where correspondence is significantly improved upon geometry optimization point to the crystal structures requiring correction.
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Affiliation(s)
- Kartik Pilar
- Materials Research Laboratory, University of California Santa Barbara, California 93106, USA
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31
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Hartman JD, Beran GJO. Accurate 13-C and 15-N molecular crystal chemical shielding tensors from fragment-based electronic structure theory. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2018; 96:10-18. [PMID: 30273904 DOI: 10.1016/j.ssnmr.2018.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/14/2018] [Accepted: 09/14/2018] [Indexed: 06/08/2023]
Abstract
Standard nuclear magnetic resonance (NMR) spectroscopy experiments measure isotropic chemical shifts, but measuring the chemical shielding anisotropy (CSA) tensor can provide additional insights into solid state chemical structures. Interpreting the principal components of these tensors is facilitated by first-principles chemical shielding tensor predictions. Here, the ability to predict molecular crystal CSA tensor components for 13C and 15N nuclei with fragment-based electronic structure techniques is explored. Similar to what has been found previously for isotropic chemical shifts, the benchmarking demonstrates that fragment-based techniques can accurately reproduce CSA tensor components. The use of hybrid density functionals like PBE0 or B3LYP provide higher accuracy than generalized gradient approximation functionals like PBE. Unlike for planewave density functional techniques, hybrid density functionals can be employed routinely with modest computational cost in fragment approaches. Finally, good consistency between the regression parameters used to map either isotropic shieldings or CSA tensor components is demonstrated, providing further evidence for the quality of the models and highlighting that models trained for isotropic shifts can also be applied to CSA tensor components.
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Affiliation(s)
- Joshua D Hartman
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
| | - Gregory J O Beran
- Department of Chemistry, University of California, Riverside, CA, 92521, USA.
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32
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Alkan F, Dybowski C. Spin-orbit effects on the 125Te magnetic-shielding tensor: A cluster-based ZORA/DFT investigation. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2018; 95:6-11. [PMID: 30189330 DOI: 10.1016/j.ssnmr.2018.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 08/24/2018] [Accepted: 08/24/2018] [Indexed: 06/08/2023]
Abstract
Cluster-based calculations of 125Te magnetic-shielding tensors demonstrate that inclusion of spin-orbit effects is necessary to obtain the best agreement of theoretical predictions with experiment. The spin-orbit contribution to shielding depends on the oxidation state and stereochemistry of the 125Te site. Comparison of the performance of various density functionals indicates that GGA functionals behave similarly to each other in predicting NMR magnetic shielding. The use of hybrid functionals improves the predictive ability on average for a large set of 125Te-containing materials. The amount of Hartree-Fock exchange affects the predicted parameters. Inclusion of larger Hartree-Fock exchange contributions in hybrid functionals results in larger slopes of the correlation between calculated magnetic-shielding and experimental chemical-shift principal components, by 10-15% from the ideal value.
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Affiliation(s)
- Fahri Alkan
- Department of Chemistry, Kansas State University, Manhattan, KS, 66506, USA
| | - Cecil Dybowski
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.
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33
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Lu M, Sarkar S, Wang M, Kraus J, Fritz M, Quinn CM, Bai S, Holmes ST, Dybowski C, Yap GPA, Struppe J, Sergeyev IV, Maas W, Gronenborn AM, Polenova T. 19F Magic Angle Spinning NMR Spectroscopy and Density Functional Theory Calculations of Fluorosubstituted Tryptophans: Integrating Experiment and Theory for Accurate Determination of Chemical Shift Tensors. J Phys Chem B 2018; 122:6148-6155. [PMID: 29756776 DOI: 10.1021/acs.jpcb.8b00377] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The 19F chemical shift is a sensitive NMR probe of structure and electronic environment in organic and biological molecules. In this report, we examine chemical shift parameters of 4F-, 5F-, 6F-, and 7F-substituted crystalline tryptophan by magic angle spinning (MAS) solid-state NMR spectroscopy and density functional theory. Significant narrowing of the 19F lines was observed under fast MAS conditions, at spinning frequencies above 50 kHz. The parameters characterizing the 19F chemical shift tensor are sensitive to the position of the fluorine in the aromatic ring and, to a lesser extent, the chirality of the molecule. Accurate calculations of 19F magnetic shielding tensors require the PBE0 functional with a 50% admixture of a Hartree-Fock exchange term, as well as taking account of the local crystal symmetry. The methodology developed will be beneficial for 19F-based MAS NMR structural analysis of proteins and protein assemblies.
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Affiliation(s)
- Manman Lu
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Sucharita Sarkar
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Jodi Kraus
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Matthew Fritz
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Shi Bai
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Sean T Holmes
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Cecil Dybowski
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Glenn P A Yap
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Jochem Struppe
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Ivan V Sergeyev
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Werner Maas
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Angela M Gronenborn
- Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States.,Department of Structural Biology , University of Pittsburgh School of Medicine , 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
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34
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Fritz M, Quinn CM, Wang M, Hou G, Lu X, Koharudin LMI, Struppe J, Case DA, Polenova T, Gronenborn AM. Determination of accurate backbone chemical shift tensors in microcrystalline proteins by integrating MAS NMR and QM/MM. Phys Chem Chem Phys 2018; 20:9543-9553. [PMID: 29577158 PMCID: PMC5892194 DOI: 10.1039/c8cp00647d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chemical shifts are highly sensitive probes of local conformation and overall structure. Both isotropic shifts and chemical shift tensors are readily accessible from NMR experiments but their quantum mechanical calculations remain challenging. In this work, we report and compare accurately measured and calculated 15NH and 13Cα chemical shift tensors in proteins, using the microcrystalline agglutinin from Oscillatoria agardhii (OAA). Experimental 13Cα and 15NH chemical tensors were obtained by solid-state NMR spectroscopy, employing tailored recoupling sequences, and for their quantum mechanics/molecular mechanics (QM/MM) calculations different sets of functionals were evaluated. We show that 13Cα chemical shift tensors are primarily determined by backbone dihedral angles and dynamics, while 15NH tensors mainly depend on local electrostatic contributions from solvation and hydrogen bonding. In addition, the influence of including crystallographic waters, the molecular mechanics geometry optimization protocol, and the level of theory on the accuracy of the calculated chemical shift tensors is discussed. Specifically, the power of QM/MM calculations in accurately predicting the unusually upfield shifted 1HN G26 and G93 resonances is highlighted. Our integrated approach is expected to benefit structure refinement of proteins and protein assemblies.
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Affiliation(s)
- Matthew Fritz
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Caitlin M. Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Xingyu Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Leonardus M. I. Koharudin
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - David A. Case
- Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854-8087, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
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35
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Marín-Luna M, Alkorta I, Elguero J. A theoretical NMR study of selected benzazoles: Comparison of GIPAW and GIAO-PCM (DMSO) calculations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:164-171. [PMID: 29077221 DOI: 10.1002/mrc.4674] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/14/2017] [Accepted: 10/16/2017] [Indexed: 06/07/2023]
Abstract
This paper compares the absolute shieldings obtained by gauge-including-projected-augmented-wave (GIPAW) to those obtained by gauge-invariant atomic orbital/Becke, 3-parameter, Lee-Yang-Parr (GIAO/B3LYP)/6-311++G(d,p)-polarizable continuum model (PCM, dimethyl sulfoxide) for nine benzazoles (benzimidazoles, indazoles, and benzotriazoles) recorded in the solid-state. Three nuclei were explored, 13 C, 15 N, and 19 F, and the gauge-including-projected-augmented-wave approach only proved better for 15 N MAS NMR.
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Affiliation(s)
- Marta Marín-Luna
- Departamento de Química Orgánica, Universidad de Vigo, Vigo, Spain
| | - Ibon Alkorta
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006, Madrid, Spain
| | - José Elguero
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006, Madrid, Spain
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36
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How reliable are Minnesota density functionals for modeling phosphorus–hydrogen NMR spin–spin coupling constants? Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2182-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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37
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Hartman JD, Balaji A, Beran GJO. Improved Electrostatic Embedding for Fragment-Based Chemical Shift Calculations in Molecular Crystals. J Chem Theory Comput 2017; 13:6043-6051. [PMID: 29139294 DOI: 10.1021/acs.jctc.7b00677] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Fragment-based methods predict nuclear magnetic resonance (NMR) chemical shielding tensors in molecular crystals with high accuracy and computational efficiency. Such methods typically employ electrostatic embedding to mimic the crystalline environment, and the quality of the results can be sensitive to the embedding treatment. To improve the quality of this embedding environment for fragment-based molecular crystal property calculations, we borrow ideas from the embedded ion method to incorporate self-consistently polarized Madelung field effects. The self-consistent reproduction of the Madelung potential (SCRMP) model developed here constructs an array of point charges that incorporates self-consistent lattice polarization and which reproduces the Madelung potential at all atomic sites involved in the quantum mechanical region of the system. The performance of fragment- and cluster-based 1H, 13C, 14N, and 17O chemical shift predictions using SCRMP and density functionals like PBE and PBE0 are assessed. The improved embedding model results in substantial improvements in the predicted 17O chemical shifts and modest improvements in the 15N ones. Finally, the performance of the model is demonstrated by examining the assignment of the two oxygen chemical shifts in the challenging γ-polymorph of glycine. Overall, the SCRMP-embedded NMR chemical shift predictions are on par with or more accurate than those obtained with the widely used gauge-including projector augmented wave (GIPAW) model.
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Affiliation(s)
- Joshua D Hartman
- Department of Chemistry, University of California, Riverside , Riverside, California 92521, United States
| | - Ashwin Balaji
- Department of Chemistry, University of California, Riverside , Riverside, California 92521, United States
| | - Gregory J O Beran
- Department of Chemistry, University of California, Riverside , Riverside, California 92521, United States
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38
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Alkan F, Holmes ST, Dybowski C. Role of Exact Exchange and Relativistic Approximations in Calculating 19F Magnetic Shielding in Solids Using a Cluster Ansatz. J Chem Theory Comput 2017; 13:4741-4752. [DOI: 10.1021/acs.jctc.7b00555] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Fahri Alkan
- Department
of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Sean T. Holmes
- Department
of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Cecil Dybowski
- Department
of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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39
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Szeleszczuk Ł, Pisklak DM, Zielińska-Pisklak M, Wawer I. Spectroscopic and structural studies of the diosmin monohydrate and anhydrous diosmin. Int J Pharm 2017; 529:193-199. [PMID: 28663085 DOI: 10.1016/j.ijpharm.2017.06.078] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 10/19/2022]
Abstract
Diosmin, a flavone glycoside frequently used in therapy of various veins diseases in monohydrate form, exhibits poor solubility in water and low bioavailability. Due to the fact that the anhydrous forms of drugs generally have better bioavailability than the corresponding hydrates, the aim of this study was to analyze the conversion of diosmin monohydrate (DSNM) to anhydrous diosmin (DSNA) that occurs upon heating. The mechanism of this transformation was examined as well as advanced structural studies of each form were performed using 13C CP/MAS SSNMR, DSC, FT-IR and PXRD techniques. Spectroscopic findings were supported by CASTEP-DFT calculations of NMR and IR parameters. The pathway of reversible transformation was specified as follows: DSNM upon heating for 24h at temperature up to 110°C losses non-crystalline water and converts into metastable form (DSNM*) that turns into DSNA during heating at temperature 140°C for next 24h. Under room temperature DSNA spontaneously absorbs moisture from air and turns into a DSNM within 72h. The detailed analysis of CP kinetic parameters (T1ρI) revealed presence of metastable, intermediate form of diosmin (DSNM*) and allowed its characterization. The results are essential for further studies comparing dissolution and bioavailability of DSNM and DSNA. The study provided an understanding of the conversion pathway of the diosmin monohydrate into its anhydrate form when it is exposed to increased temperature.
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Affiliation(s)
- Łukasz Szeleszczuk
- Faculty of Pharmacy with The Laboratory Medicine Division, Medical University of Warsaw, Department of Physical Chemistry, Banacha 1, 02-093 Warsaw Poland.
| | - Dariusz Maciej Pisklak
- Faculty of Pharmacy with The Laboratory Medicine Division, Medical University of Warsaw, Department of Physical Chemistry, Banacha 1, 02-093 Warsaw Poland
| | - Monika Zielińska-Pisklak
- Faculty of Pharmacy with the Laboratory Medicine Division, Medical University of Warsaw, Department of Biomaterials Chemistry, Chair and Department of Inorganic and Analytical Chemistry, Banacha 1, 02-093 Warsaw Poland
| | - Iwona Wawer
- Faculty of Pharmacy with The Laboratory Medicine Division, Medical University of Warsaw, Department of Physical Chemistry, Banacha 1, 02-093 Warsaw Poland
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40
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Soss SE, Flynn PF, Iuliucci RJ, Young RP, Mueller LJ, Hartman J, Beran GJO, Harper JK. Measuring and Modeling Highly Accurate
15
N Chemical Shift Tensors in a Peptide. Chemphyschem 2017; 18:2225-2232. [DOI: 10.1002/cphc.201700357] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/08/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Sarah E. Soss
- Department of Chemistry University of Utah Salt Lake City UT 84112 USA
| | - Peter F. Flynn
- Department of Chemistry University of Utah Salt Lake City UT 84112 USA
| | - Robbie J. Iuliucci
- Department of Chemistry Washington and Jefferson College 60 Lincoln Street Washington PA 15301 USA
| | - Robert P. Young
- Department of Chemistry University of California Riverside CA 92521 USA
| | | | - Joshua Hartman
- Department of Chemistry University of California Riverside CA 92521 USA
| | | | - James K. Harper
- Department of Chemistry University of Central Florida 4111 Libra Drive Orlando FL 32816 USA
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41
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Holmes ST, Bai S, Iuliucci RJ, Mueller KT, Dybowski C. Calculations of solid‐state
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Ca NMR parameters: A comparison of periodic and cluster approaches and an evaluation of DFT functionals. J Comput Chem 2017; 38:949-956. [DOI: 10.1002/jcc.24763] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/29/2016] [Accepted: 01/30/2017] [Indexed: 01/18/2023]
Affiliation(s)
- Sean T. Holmes
- Department of Chemistry and BiochemistryUniversity of DelawareNewark Delaware19716
| | - Shi Bai
- Department of Chemistry and BiochemistryUniversity of DelawareNewark Delaware19716
| | - Robbie J. Iuliucci
- Department of ChemistryWashington and Jefferson CollegeWashington Pennsylvania15301
| | - Karl T. Mueller
- Department of ChemistryPennsylvania State University, University Park Pennsylvania16802
- Physical and Computational Sciences Directorate, Pacific Northwest National LaboratoryRichland Washington99352
| | - Cecil Dybowski
- Department of Chemistry and BiochemistryUniversity of DelawareNewark Delaware19716
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42
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Holmes ST, Iuliucci RJ, Mueller KT, Dybowski C. Semi-empirical refinements of crystal structures using 17O quadrupolar-coupling tensors. J Chem Phys 2017; 146:064201. [DOI: 10.1063/1.4975170] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Sean T. Holmes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Robbie J. Iuliucci
- Department of Chemistry, Washington and Jefferson College, Washington, Pennsylvania 15301, USA
| | - Karl T. Mueller
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Cecil Dybowski
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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43
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Beran GJO, Hartman JD, Heit YN. Predicting Molecular Crystal Properties from First Principles: Finite-Temperature Thermochemistry to NMR Crystallography. Acc Chem Res 2016; 49:2501-2508. [PMID: 27754668 DOI: 10.1021/acs.accounts.6b00404] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Molecular crystals occur widely in pharmaceuticals, foods, explosives, organic semiconductors, and many other applications. Thanks to substantial progress in electronic structure modeling of molecular crystals, attention is now shifting from basic crystal structure prediction and lattice energy modeling toward the accurate prediction of experimentally observable properties at finite temperatures and pressures. This Account discusses how fragment-based electronic structure methods can be used to model a variety of experimentally relevant molecular crystal properties. First, it describes the coupling of fragment electronic structure models with quasi-harmonic techniques for modeling the thermal expansion of molecular crystals, and what effects this expansion has on thermochemical and mechanical properties. Excellent agreement with experiment is demonstrated for the molar volume, sublimation enthalpy, entropy, and free energy, and the bulk modulus of phase I carbon dioxide when large basis second-order Møller-Plesset perturbation theory (MP2) or coupled cluster theories (CCSD(T)) are used. In addition, physical insight is offered into how neglect of thermal expansion affects these properties. Zero-point vibrational motion leads to an appreciable expansion in the molar volume; in carbon dioxide, it accounts for around 30% of the overall volume expansion between the electronic structure energy minimum and the molar volume at the sublimation point. In addition, because thermal expansion typically weakens the intermolecular interactions, neglecting thermal expansion artificially stabilizes the solid and causes the sublimation enthalpy to be too large at higher temperatures. Thermal expansion also frequently weakens the lower-frequency lattice phonon modes; neglecting thermal expansion causes the entropy of sublimation to be overestimated. Interestingly, the sublimation free energy is less significantly affected by neglecting thermal expansion because the systematic errors in the enthalpy and entropy cancel somewhat. Second, because solid state nuclear magnetic resonance (NMR) plays an increasingly important role in molecular crystal studies, this Account discusses how fragment methods can be used to achieve higher-accuracy chemical shifts in molecular crystals. Whereas widely used plane wave density functional theory models are largely restricted to generalized gradient approximation (GGA) functionals like PBE in practice, fragment methods allow the routine use of hybrid density functionals with only modest increases in computational cost. In extensive molecular crystal benchmarks, hybrid functionals like PBE0 predict chemical shifts with 20-30% higher accuracy than GGAs, particularly for 1H, 13C, and 15N nuclei. Due to their higher sensitivity to polarization effects, 17O chemical shifts prove slightly harder to predict with fragment methods. Nevertheless, the fragment model results are still competitive with those from GIPAW. The improved accuracy achievable with fragment approaches and hybrid density functionals increases discrimination between different potential assignments of individual shifts or crystal structures, which is critical in NMR crystallography applications. This higher accuracy and greater discrimination are highlighted in application to the solid state NMR of different acetaminophen and testosterone crystal forms.
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Affiliation(s)
- Gregory J. O. Beran
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Joshua D. Hartman
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yonaton N. Heit
- Department of Chemistry, University of California, Riverside, California 92521, United States
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44
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Hartman J, Day GM, Beran GJO. Enhanced NMR Discrimination of Pharmaceutically Relevant Molecular Crystal Forms through Fragment-Based Ab Initio Chemical Shift Predictions. CRYSTAL GROWTH & DESIGN 2016; 16:6479-6493. [PMID: 27829821 PMCID: PMC5095663 DOI: 10.1021/acs.cgd.6b01157] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/09/2016] [Indexed: 05/10/2023]
Abstract
Chemical shift prediction plays an important role in the determination or validation of crystal structures with solid-state nuclear magnetic resonance (NMR) spectroscopy. One of the fundamental theoretical challenges lies in discriminating variations in chemical shifts resulting from different crystallographic environments. Fragment-based electronic structure methods provide an alternative to the widely used plane wave gauge-including projector augmented wave (GIPAW) density functional technique for chemical shift prediction. Fragment methods allow hybrid density functionals to be employed routinely in chemical shift prediction, and we have recently demonstrated appreciable improvements in the accuracy of the predicted shifts when using the hybrid PBE0 functional instead of generalized gradient approximation (GGA) functionals like PBE. Here, we investigate the solid-state 13C and 15N NMR spectra for multiple crystal forms of acetaminophen, phenobarbital, and testosterone. We demonstrate that the use of the hybrid density functional instead of a GGA provides both higher accuracy in the chemical shifts and increased discrimination among the different crystallographic environments. Finally, these results also provide compelling evidence for the transferability of the linear regression parameters mapping predicted chemical shieldings to chemical shifts that were derived in an earlier study.
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Affiliation(s)
- Joshua
D. Hartman
- Department
of Chemistry, University of California, Riverside, California 92521 United States
| | - Graeme M. Day
- School
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Gregory J. O. Beran
- Department
of Chemistry, University of California, Riverside, California 92521 United States
- E-mail:
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45
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Alkan F, Holmes ST, Iuliucci RJ, Mueller KT, Dybowski C. Spin-orbit effects on the (119)Sn magnetic-shielding tensor in solids: a ZORA/DFT investigation. Phys Chem Chem Phys 2016; 18:18914-22. [PMID: 27354312 DOI: 10.1039/c6cp03807g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Periodic-boundary and cluster calculations of the magnetic-shielding tensors of (119)Sn sites in various co-ordination and stereochemical environments are reported. The results indicate a significant difference between the predicted NMR chemical shifts for tin(ii) sites that exhibit stereochemically-active lone pairs and tin(iv) sites that do not have stereochemically-active lone pairs. The predicted magnetic shieldings determined either with the cluster model treated with the ZORA/Scalar Hamiltonian or with the GIPAW formalism are dependent on the oxidation state and the co-ordination geometry of the tin atom. The inclusion of relativistic effects at the spin-orbit level removes systematic differences in computed magnetic-shielding parameters between tin sites of differing stereochemistries, and brings computed NMR shielding parameters into significant agreement with experimentally-determined chemical-shift principal values. Slight improvement in agreement with experiment is noted in calculations using hybrid exchange-correlation functionals.
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Affiliation(s)
- Fahri Alkan
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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46
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Hartman JD, Kudla RA, Day GM, Mueller LJ, Beran GJO. Benchmark fragment-based (1)H, (13)C, (15)N and (17)O chemical shift predictions in molecular crystals. Phys Chem Chem Phys 2016; 18:21686-709. [PMID: 27431490 DOI: 10.1039/c6cp01831a] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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 (PBE0, B3LYP, TPSSh, OPBE, 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.
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Affiliation(s)
- Joshua D Hartman
- Department of Chemistry, University of California, Riverside, California 92521, USA.
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Effects of structural differences on the NMR chemical shifts in cinnamic acid derivatives: Comparison of GIAO and GIPAW calculations. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.04.075] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Holmes ST, Alkan F, Iuliucci RJ, Mueller KT, Dybowski C. Analysis of the bond‐valence method for calculating
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Si and
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P magnetic shielding in covalent network solids. J Comput Chem 2016; 37:1704-10. [DOI: 10.1002/jcc.24389] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/14/2016] [Accepted: 03/27/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Sean T. Holmes
- Department of Chemistry and BiochemistryUniversity of DelawareNewark Delaware19716
| | - Fahri Alkan
- Department of Chemistry and BiochemistryUniversity of DelawareNewark Delaware19716
| | - Robbie J. Iuliucci
- Department of ChemistryWashington and Jefferson CollegeWashington Pennsylvania15301
| | - Karl T. Mueller
- Department of ChemistryPennsylvania State UniversityUniversity Park Pennsylvania16802
- Physical and Computational Sciences DirectoratePacific Northwest National LaboratoryRichland Washington99352
| | - Cecil Dybowski
- Department of Chemistry and BiochemistryUniversity of DelawareNewark Delaware19716
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Abstract
Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California , Riverside, California 92521, United States
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Dračínský M, Bouř P, Hodgkinson P. Temperature Dependence of NMR Parameters Calculated from Path Integral Molecular Dynamics Simulations. J Chem Theory Comput 2016; 12:968-73. [PMID: 26857802 DOI: 10.1021/acs.jctc.5b01131] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The influence of temperature on NMR chemical shifts and quadrupolar couplings in model molecular organic solids is explored using path integral molecular dynamics (PIMD) and density functional theory (DFT) calculations of shielding and electric field gradient (EFG) tensors. An approach based on convoluting calculated shielding or EFG tensor components with probability distributions of selected bond distances and valence angles obtained from DFT-PIMD simulations at several temperatures is used to calculate the temperature effects. The probability distributions obtained from the quantum PIMD simulations, which includes nuclear quantum effects, are significantly broader and less temperature dependent than those obtained with conventional DFT molecular dynamics or with 1D scans through the potential energy surface. Predicted NMR observables for the model systems were in excellent agreement with experimental data.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry , Flemingovo nám. 2, 16610 Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry , Flemingovo nám. 2, 16610 Prague, Czech Republic
| | - Paul Hodgkinson
- Department of Chemistry, Durham University , South Road, DH1 3LE Durham, United Kingdom
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