1
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Han C, Zhang D, Xia S, Zhang Y. Accurate Prediction of NMR Chemical Shifts: Integrating DFT Calculations with Three-Dimensional Graph Neural Networks. J Chem Theory Comput 2024; 20:5250-5258. [PMID: 38842505 PMCID: PMC11209944 DOI: 10.1021/acs.jctc.4c00422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024]
Abstract
Computer prediction of NMR chemical shifts plays an increasingly important role in molecular structure assignment and elucidation for organic molecule studies. Density functional theory (DFT) and gauge-including atomic orbital (GIAO) have established a framework to predict NMR chemical shifts but often at a significant computational expense with a limited prediction accuracy. Recent advancements in deep learning methods, especially graph neural networks (GNNs), have shown promise in improving the accuracy of predicting experimental chemical shifts, either by using 2D molecular topological features or 3D conformational representation. This study presents a new 3D GNN model to predict 1H and 13C chemical shifts, CSTShift, that combines atomic features with DFT-calculated shielding tensor descriptors, capturing both isotropic and anisotropic shielding effects. Utilizing the NMRShiftDB2 data set and conducting DFT optimization and GIAO calculations at the B3LYP/6-31G(d) level, we prepared the NMRShiftDB2-DFT data set of high-quality 3D structures and shielding tensors with corresponding experimentally measured 1H and 13C chemical shifts. The developed CSTShift models achieve the state-of-the-art prediction performance on both the NMRShiftDB2-DFT test data set and external CHESHIRE data set. Further case studies on identifying correct structures from two groups of constitutional isomers show its capability for structure assignment and elucidation. The source code and data are accessible at https://yzhang.hpc.nyu.edu/IMA.
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Affiliation(s)
- Chao Han
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Dongdong Zhang
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Song Xia
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Yingkai Zhang
- Department
of Chemistry, New York University, New York, New York 10003, United States
- Simons
Center for Computational Physical Chemistry at New York University, New York, New York 10003, United States
- NYU-ECNU
Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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2
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Shafei R, Strobel PJ, Schmidt PJ, Maganas D, Schnick W, Neese F. A theoretical spectroscopy study of the photoluminescence properties of narrow band Eu 2+-doped phosphors containing multiple candidate doping centers. Prediction of an unprecedented narrow band red phosphor. Phys Chem Chem Phys 2024; 26:6277-6291. [PMID: 38305760 DOI: 10.1039/d3cp06039j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
We have previously presented a computational protocol that is based on an embedded cluster model and operates in the framework of TD-DFT in conjunction with the excited state dynamics (ESD) approach. The protocol is able to predict the experimental absorption and emission spectral shapes of Eu2+-doped phosphors. In this work, the applicability domain of the above protocol is expanded to Eu2+-doped phosphors bearing multiple candidate Eu doping centers. It will be demonstrated that this protocol provides full control of the parameter space that describes the emission process. The stability of Eu doping at various centers is explored through local energy decomposition (LED) analysis of DLPNO-CCSD(T) energies. This enables further development of the understanding of the electronic structure of the targeted phosphors, the diverse interactions between Eu and the local environment, and their impact on Eu doping probability, and control of the emission properties. Hence, it can be employed to systematically improve deficiencies of existing phosphor materials, defined by the presence of various intensity emission bands at undesired frequencies, towards classes of candidate Eu2+-doped phosphors with desired narrow band red emission. For this purpose, the chosen study set consists of three UCr4C4-based narrow-band phosphors, namely the known alkali lithosilicates RbNa[Li3SiO4]2:Eu2+ (RNLSO2), RbNa3[Li3SiO4]4:Eu2+ (RNLSO) and their isotypic nitridolithoaluminate phosphors consisting of CaBa[LiAl3N4]2:Eu2+ (CBLA2) and the proposed Ca3Ba[LiAl3N4]4:Eu2+ (CBLA), respectively. The theoretical analysis presented in this work led us to propose a modification of the CBLA2 phosphor that should have improved and unprecedented narrow band red emission properties. Finally, we believe that the analysis presented here is important for the future rational design of novel Eu2+-doped phosphor materials, with a wide range of applications in science and technology.
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Affiliation(s)
- Rami Shafei
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
- Department of Chemistry, Faculty of Science, Beni-Suef University, Salah Salem Str., 62511 Beni-Suef, Egypt
| | - Philipp Jean Strobel
- Lumileds Phosphor Center Aachen, Lumileds Germany GmbH, Philipsstraße 8, 52068 Aachen, Germany
| | - Peter J Schmidt
- Lumileds Phosphor Center Aachen, Lumileds Germany GmbH, Philipsstraße 8, 52068 Aachen, Germany
| | - Dimitrios Maganas
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
| | - Wolfgang Schnick
- Department of Chemistry, University of Munich (LMU), Butenandtstraße 5-13, 81377 München, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
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3
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Ke Z, Weng J, Xu X. Calculating 13 C NMR chemical shifts of large molecules using the eXtended ONIOM method at high accuracy with a low cost. J Comput Chem 2023; 44:2347-2357. [PMID: 37572044 DOI: 10.1002/jcc.27201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/15/2023] [Accepted: 07/24/2023] [Indexed: 08/14/2023]
Abstract
Fragmentation-based methods for nuclear magnetic resonance (NMR) chemical shift calculations have become more and more popular in first-principles calculations of large molecules. However, there are many options for a fragmentation-based method to select, such as theoretical methods, fragmentation schemes, the number of levels of theory, etc. It is important to study the optimal combination of the options to achieve a good balance between accuracy and efficiency. Here we investigate different combinations of options used by a fragmentation-based method, the eXtended ONIOM (XO) method, for 13 C chemical shift calculations on a set of organic and biological molecules. We found that: (1) introducing Hartree-Fock exchange into density functional theory (DFT) could reduce the calculation error due to fragmentation in contrast to pure DFT functionals, while a hybrid functional, xOPBE, is generally recommended; (2) fragmentation schemes generated from the molecular tailoring approach (MTA) with small level parameter n, for example, n = 2 and the degree-based fragmentation method (DBFM) with n = 1, are sufficient to achieve satisfactory accuracy; (3) the two-level XO (XO2) NMR calculation is superior to the calculation with only one level of theory, as the second level (i.e., low level) of theory provides a way to well describe the long-range effect. These findings are beneficial to practical applications of fragmentation-based methods for NMR chemical shift calculations of large molecules.
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Affiliation(s)
- Zhipeng Ke
- Institute of Photochemistry and Photofunctional Materials, University of Shanghai for Science and Technology, Shanghai, China
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, China
| | - Jingwei Weng
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, China
- Hefei National Laboratory, Hefei, China
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4
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Tran VA, Teucher M, Galazzo L, Sharma B, Pongratz T, Kast SM, Marx D, Bordignon E, Schnegg A, Neese F. Dissecting the Molecular Origin of g-Tensor Heterogeneity and Strain in Nitroxide Radicals in Water: Electron Paramagnetic Resonance Experiment versus Theory. J Phys Chem A 2023; 127:6447-6466. [PMID: 37524058 PMCID: PMC10424240 DOI: 10.1021/acs.jpca.3c02879] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/01/2023] [Indexed: 08/02/2023]
Abstract
Nitroxides are common EPR sensors of microenvironmental properties such as polarity, numbers of H-bonds, pH, and so forth. Their solvation in an aqueous environment is facilitated by their high propensity to form H-bonds with the surrounding water molecules. Their g- and A-tensor elements are key parameters to extracting the properties of their microenvironment. In particular, the gxx value of nitroxides is rich in information. It is known to be characterized by discrete values representing nitroxide populations previously assigned to have different H-bonds with the surrounding waters. Additionally, there is a large g-strain, that is, a broadening of g-values associated with it, which is generally correlated with environmental and structural micro-heterogeneities. The g-strain is responsible for the frequency dependence of the apparent line width of the EPR spectra, which becomes evident at high field/frequency. Here, we address the molecular origin of the gxx heterogeneity and of the g-strain of a nitroxide moiety (HMI: 2,2,3,4,5,5-hexamethylimidazolidin-1-oxyl, C9H19N2O) in water. To treat the solvation effect on the g-strain, we combined a multi-frequency experimental approach with ab initio molecular dynamics simulations for structural sampling and quantum chemical EPR property calculations at the highest realistically affordable level, including an explicitly micro-solvated HMI ensemble and the embedded cluster reference interaction site model. We could clearly identify the distinct populations of the H-bonded nitroxides responsible for the gxx heterogeneity experimentally observed, and we dissected the role of the solvation shell, H-bond formation, and structural deformation of the nitroxide in the creation of the g-strain associated with each nitroxide subensemble. Two contributions to the g-strain were identified in this study. The first contribution depends on the number of hydrogen bonds formed between the nitroxide and the solvent because this has a large and well-understood effect on the gxx-shift. This contribution can only be resolved at high resonance frequencies, where it leads to distinct peaks in the gxx region. The second contribution arises from configurational fluctuations of the nitroxide that necessarily lead to g-shift heterogeneity. These contributions cannot be resolved experimentally as distinct resonances but add to the line broadening. They can be quantitatively analyzed by studying the apparent line width as a function of microwave frequency. Interestingly, both theory and experiment confirm that this contribution is independent of the number of H-bonds. Perhaps even more surprisingly, the theoretical analysis suggests that the configurational fluctuation broadening is not induced by the solvent but is inherently present even in the gas phase. Moreover, the calculations predict that this broadening decreases upon solvation of the nitroxide.
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Affiliation(s)
- Van Anh Tran
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Markus Teucher
- Max-Planck-Institut
für Chemische Energiekonversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Laura Galazzo
- Department
of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva, Switzerland
- Faculty
of Chemistry and Biochemistry, Ruhr-Universität
Bochum, 44780 Bochum, Germany
| | - Bikramjit Sharma
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität
Bochum, 44780 Bochum, Germany
| | - Tim Pongratz
- Fakultät
für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Stefan M. Kast
- Fakultät
für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Dominik Marx
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität
Bochum, 44780 Bochum, Germany
| | - Enrica Bordignon
- Department
of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva, Switzerland
- Faculty
of Chemistry and Biochemistry, Ruhr-Universität
Bochum, 44780 Bochum, Germany
| | - Alexander Schnegg
- Max-Planck-Institut
für Chemische Energiekonversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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5
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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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6
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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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7
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Jaworski A, Hedin N. Electron correlation and vibrational effects in predictions of paramagnetic NMR shifts. Phys Chem Chem Phys 2022; 24:15230-15244. [PMID: 35703010 DOI: 10.1039/d2cp01206e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electronic structure calculations are fundamentally important for the interpretation of nuclear magnetic resonance (NMR) spectra from paramagnetic systems that include organometallic and inorganic compounds, catalysts, or metal-binding sites in proteins. Prediction of induced paramagnetic NMR shifts requires knowledge of electron paramagnetic resonance (EPR) parameters: the electronic g tensor, zero-field splitting D tensor, and hyperfine A tensor. The isotropic part of A, called the hyperfine coupling constant (HFCC), is one of the most troublesome properties for quantum chemistry calculations. Yet, even relatively small errors in calculations of HFCC tend to propagate into large errors in the predicted NMR shifts. The poor quality of A tensors that are currently calculated using density functional theory (DFT) constitutes a bottleneck in improving the reliability of interpretation of the NMR spectra from paramagnetic systems. In this work, electron correlation effects in calculations of HFCCs with a hierarchy of ab initio methods were assessed, and the applicability of different levels of DFT approximations and the coupled cluster singles and doubles (CCSD) method was tested. These assessments were performed for the set of selected test systems comprising an organic radical, and complexes with transition metal and rare-earth ions, for which experimental data are available. Severe deficiencies of DFT were revealed but the CCSD method was able to deliver good agreement with experimental data for all systems considered, however, at substantial computational costs. We proposed a more computationally tractable alternative, where the A was computed with the coupled cluster theory exploiting locality of electron correlation. This alternative is based on the domain-based local pair natural orbital coupled cluster singles and doubles (DLPNO-CCSD) method. In this way the robustness and reliability of the coupled cluster theory were incorporated into the modern formalism for the prediction of induced paramagnetic NMR shifts, and became applicable to systems of chemical interest. This approach was verified for the bis(cyclopentadienyl)vanadium(II) complex (Cp2V; vanadocene), and the metal-binding site of the Zn2+ → Co2+ substituted superoxide dismutase (SOD) metalloprotein. Excellent agreement with experimental NMR shifts was achieved, which represented a substantial improvement over previous theoretical attempts. The effects of vibrational corrections to orbital shielding and hyperfine tensor were evaluated and discussed within the second-order vibrational perturbation theory (VPT2) framework.
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Affiliation(s)
- Aleksander Jaworski
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Niklas Hedin
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
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8
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Shafei R, Maganas D, Strobel PJ, Schmidt PJ, Schnick W, Neese F. Electronic and Optical Properties of Eu 2+-Activated Narrow-Band Phosphors for Phosphor-Converted Light-Emitting Diode Applications: Insights from a Theoretical Spectroscopy Perspective. J Am Chem Soc 2022; 144:8038-8053. [PMID: 35471974 PMCID: PMC9100680 DOI: 10.1021/jacs.2c00218] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
In this work, we
present a computational protocol that is able
to predict the experimental absorption and emission spectral shapes
of Eu2+-doped phosphors. The protocol is based on time-dependent
density functional theory and operates in conjunction with an excited-state
dynamics approach. It is demonstrated that across the study set consisting
of representative examples of nitride, oxo-nitride, and oxide Eu2+-doped phosphors, the energy distribution and the band shape
of the emission spectrum are related to the nature of the 4f–5d
transitions that are probed in the absorption process. Since the 4f
orbitals are very nearly nonbonding, the decisive quantity is the
covalency of the 5d acceptor orbitals that become populated in the electronically excited state that leads
to emission. The stronger the (anti) bonding interaction between the
lanthanide and the ligands is in the excited state, the larger will
be the excited state distortion. Consequently, the corresponding emission
will get broader due to the vibronic progression that is induced by
the structural distortion. In addition, the energy separation of the
absorption bands that are dominated by states with valence 4f–5d
and a metal to ligand charge transfer character defines a measure
for the thermal quenching of the studied Eu2+-doped phosphors.
Based on this analysis, simple descriptors are identified that show
a strong correlation with the energy position and bandwidth of the
experimental emission bands without the need for elaborate calculations.
Overall, we believe that this study serves as an important reference
for designing new Eu2+-doped phosphors with desired photoluminescence
properties.
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Affiliation(s)
- Rami Shafei
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany.,Department of Chemistry, Faculty of Science, Beni-Suef University, Salah Salem Str, Beni-Suef 62511, Egypt
| | - Dimitrios Maganas
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Philipp Jean Strobel
- Lumileds Phosphor Center Aachen, Lumileds (Germany) GmbH, Philipsstraße 8, Aachen 52068 , Germany
| | - Peter J Schmidt
- Lumileds Phosphor Center Aachen, Lumileds (Germany) GmbH, Philipsstraße 8, Aachen 52068 , Germany
| | - Wolfgang Schnick
- Department of Chemistry, University of Munich (LMU), Butenandtstraße 5-13, München 81377, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
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9
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Yan W, Xu X. Accurate Prediction of Nuclear Magnetic Resonance Parameters via the XYG3 Type of Doubly Hybrid Density Functionals. J Chem Theory Comput 2022; 18:2931-2946. [PMID: 35467852 DOI: 10.1021/acs.jctc.2c00055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful and versatile tools in elucidating molecular structures. To eliminate ambiguities of experimental assignments, accurate calculations of NMR spectra are of great importance. Here, a method for theoretical evaluation of the NMR shielding constants by analytic derivatives using gauge including atomic orbitals (GIAO) has been implemented for the XYG3 type of doubly hybrid density functionals (xDH), namely, the GIAO-xDH method. Benchmark calculations on shielding constants and chemical shifts demonstrate the remarkable accuracy of the GIAO-xDH method, compared to the accurate CCSD(T) references. It is shown here that the XYGJ-OS functional is able to give a mean absolute deviation (MAD) of ∼3.0 ppm in the calculated shielding constants for 13C, 15N, 17O, 19F, while both XYGJ-OS and xDH-PBE0 functionals are able to provide a satisfactory estimation of chemical shifts with MADs of ∼0.03 and 1.0 ppm for 1H and 13C, respectively. The basis set influence upon the method has been examined and a computational scheme considering both accuracy and efficiency has been proposed and tested to predict the experimental 13C chemical shifts of five medium-sized natural product molecules, yielding a MAD of ∼1.0 ppm, which demonstrates the practical feasibility of the GIAO-xDH method.
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Affiliation(s)
- Wenjie Yan
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, 200433, China
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10
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Santra G, Martin JML. Do Double-Hybrid Functionals Benefit from Regularization in the PT2 Term? Observations from an Extensive Benchmark. J Phys Chem Lett 2022; 13:3499-3506. [PMID: 35417181 PMCID: PMC9036584 DOI: 10.1021/acs.jpclett.2c00718] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
We put to the test a recent suggestion [Shee, J., et al. J. Phys. Chem. Lett. 2021, 12 (50), 12084-12097] that MP2 regularization might improve the performance of double-hybrid density functionals. Using the very large and chemically diverse GMTKN55 benchmark, we find that κ-regularization is indeed beneficial at lower percentages of Hartree-Fock exchange, especially if spin-component scaling is not applied [such as in B2GP-PLYP or ωB97M(2)]. This benefit dwindles for DSD and DOD functionals and vanishes entirely in the ∼70% HF exchange region optimal for them.
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11
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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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12
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Shi BX, Kapil V, Zen A, Chen J, Alavi A, Michaelides A. General embedded cluster protocol for accurate modeling of oxygen vacancies in metal-oxides. J Chem Phys 2022; 156:124704. [DOI: 10.1063/5.0087031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The O vacancy (Ov) formation energy, EOv, is an important property of a metal-oxide, governing its performance in applications such as fuel cells or heterogeneous catalysis. These defects are routinely studied with density functional theory (DFT). However, it is well-recognized that standard DFT formulations (e.g., the generalized gradient approximation) are insufficient for modeling the Ov, requiring higher levels of theory. The embedded cluster method offers a promising approach to compute EOv accurately, giving access to all electronic structure methods. Central to this approach is the construction of quantum(-mechanically treated) clusters placed within suitable embedding environments. Unfortunately, current approaches to constructing the quantum clusters either require large system sizes, preventing application of high-level methods, or require significant manual input, preventing investigations of multiple systems simultaneously. In this work, we present a systematic and general quantum cluster design protocol that can determine small converged quantum clusters for studying the Ov in metal-oxides with accurate methods, such as local coupled cluster with single, double, and perturbative triple excitations. We apply this protocol to study the Ov in the bulk and surface planes of rutile TiO2 and rock salt MgO, producing the first accurate and well-converged determinations of EOv with this method. These reference values are used to benchmark exchange–correlation functionals in DFT, and we find that all the studied functionals underestimate EOv, with the average error decreasing along the rungs of Jacob’s ladder. This protocol is automatable for high-throughput calculations and can be generalized to study other point defects or adsorbates.
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Affiliation(s)
- Benjamin X. Shi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Venkat Kapil
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Churchill College, University of Cambridge, Storey’s Way, Cambridge CB3 0DS, United Kingdom
| | - Andrea Zen
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Monte S. Angelo, I-80126 Napoli, Italy
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Ji Chen
- School of Physics, Peking University, Beijing 100871, China
| | - Ali Alavi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Angelos Michaelides
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
- Thomas Young Centre and London Centre for Nanotechnology, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
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13
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EPR Spectroscopy of Cu(II) Complexes: Prediction of g-Tensors Using Double-Hybrid Density Functional Theory. MAGNETOCHEMISTRY 2022. [DOI: 10.3390/magnetochemistry8040036] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Computational electron paramagnetic resonance (EPR) spectroscopy is an important field of applied quantum chemistry that contributes greatly to connecting spectroscopic observations with the fundamental description of electronic structure for open-shell molecules. However, not all EPR parameters can be predicted accurately and reliably for all chemical systems. Among transition metal ions, Cu(II) centers in inorganic chemistry and biology, and their associated EPR properties such as hyperfine coupling and g-tensors, pose exceptional difficulties for all levels of quantum chemistry. In the present work, we approach the problem of Cu(II) g-tensor calculations using double-hybrid density functional theory (DHDFT). Using a reference set of 18 structurally and spectroscopically characterized Cu(II) complexes, we evaluate a wide range of modern double-hybrid density functionals (DHDFs) that have not been applied previously to this problem. Our results suggest that the current generation of DHDFs consistently and systematically outperform other computational approaches. The B2GP-PLYP and PBE0-DH functionals are singled out as the best DHDFs on average for the prediction of Cu(II) g-tensors. The performance of the different functionals is discussed and suggestions are made for practical applications and future methodological developments.
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14
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Neese F. Software update: The
ORCA
program system—Version 5.0. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1606] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Frank Neese
- Max Planck Institut für Kohlenforschung Mülheim an der Ruhr Germany
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15
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Dumouilla V, Dussap CG. Online analysis of D-glucose and D-mannose aqueous mixtures using Raman spectroscopy: an in silico and experimental approach. Bioengineered 2021; 12:4420-4431. [PMID: 34308749 PMCID: PMC8806848 DOI: 10.1080/21655979.2021.1955550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/08/2021] [Indexed: 11/30/2022] Open
Abstract
Raman spectroscopy was applied to an aqueous solution containing D-mannose and D-glucose at a fixed dry matter content. The Raman measurement apparatus was adapted online at the industrial scale to monitor a bioprocess including an epimerization reaction. Online Raman spectroscopy and deconvolution techniques were successfully applied to monitor in real time the D-mannose and D-glucose concentrations using the Raman shifts at 960 cm-1 and 974 cm-1 respectively. The two anomeric forms, α and β of D-mannose in the pyranose conformation were quantified. In silico analysis of vibrational frequencies and Raman intensities of hydrated structure of D-mannose and D-glucose in the pyranose form for α and β anomers were carried out using a two-step procedure. First molecular dynamics was used to generate the theoretical carbohydrates' structures keeping the experimental dry matter content, then quantum mechanics was used to compute the Raman frequencies and intensities. Computed vibrational frequencies are in satisfactory agreement with the experimental spectra considering a hydration shell approach. Raman intensities are qualitatively in accordance with the experimental data. The interpretation of Raman frequencies and intensities led to acceptable results regarding the current possible structures of D-mannose and D-glucose in aqueous solution. Online Raman spectroscopy coupled with in silico approaches such as quantum mechanics and molecular dynamics methodology is proved to be a valuable tool to quantify the carbohydrates and stereoisomers content in complex aqueous mixtures. This methodology offers a new way to monitor any bioprocesses that encounter aqueous mixtures of D-glucose and D-mannose.
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Affiliation(s)
- Vincent Dumouilla
- CNRS, SIGMA Clermont, Institut Pascal, Université Clermont Auvergne, Clermont-Ferrand, France
- Biotechnology and Process Department, Roquettes Frères, Lestrem, France
| | - Claude Gilles Dussap
- CNRS, SIGMA Clermont, Institut Pascal, Université Clermont Auvergne, Clermont-Ferrand, France
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16
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Santra G, Semidalas E, Martin JML. Surprisingly Good Performance of XYG3 Family Functionals Using a Scaled KS-MP3 Correlation. J Phys Chem Lett 2021; 12:9368-9376. [PMID: 34550706 DOI: 10.1021/acs.jpclett.1c02838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
By adding a GLPT3 (third-order Görling-Levy perturbation theory, or KS-MP3) term E3 to the XYG7 form for a double hybrid, we are able to bring down WTMAD2 (weighted total mean absolute deviation) for the very large and chemically diverse GMTKN55 benchmark to an unprecedented 1.17 kcal/mol, competitive with much costlier composite wave function ab initio approaches. Intriguingly, (a) the introduction of E3 makes an empirical dispersion correction redundant; (b) generalized gradient approximation (GGA) or meta-GGA semilocal correlation functionals offer no advantage over the local density approximation (LDA) in this framework; (c) if a dispersion correction is retained, then simple Slater exchange leads to no significant loss in accuracy. It is possible to create a six-parameter functional with WTMAD2 = 1.42 that has no post-LDA density functional theory components and no dispersion correction in the final energy.
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Affiliation(s)
- Golokesh Santra
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Emmanouil Semidalas
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Jan M L Martin
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
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17
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14N, 13C, and 119Sn solid-state NMR characterization of tin(II) carbodiimide Sn(NCN). ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL SCIENCES 2021. [DOI: 10.1515/znb-2021-0122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
We report the first magic-angle spinning (MAS) nuclear magnetic resonance (NMR) study on Sn(NCN). In this compound the spatially elongated (NCN)2− ion is assumed to develop two distinct forms: either cyanamide (N≡C–N2−) or carbodiimide (−N=C=N−). Our 14N MAS NMR results reveal that in Sn(NCN) the (NCN)2− groups exist exclusively in the form of symmetric carbodiimide ions with two equivalent nitrogen sites, which is in agreement with the X-ray diffraction data. The 14N quadrupolar coupling constant
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C
Q
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$\vert {C}_{\text{Q}}\vert $
≈ 1.1 MHz for the −N=C=N− ion in Sn(NCN) is low when compared to those observed in molecular compounds that comprise cyano-type N≡C– moieties (
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C
Q
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$\vert {C}_{\text{Q}}\vert $
> 3.5 MHz). This together with the information from 14N and 13C chemical shifts indicates that solid-state NMR is a powerful tool for providing atomic-level insights into anion species present in these compounds. The experimental NMR results are corroborated by high-level calculations with quantum chemistry methods.
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18
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Engel EA, Kapil V, Ceriotti M. Importance of Nuclear Quantum Effects for NMR Crystallography. J Phys Chem Lett 2021; 12:7701-7707. [PMID: 34355903 DOI: 10.1021/acs.jpclett.1c01987] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The resolving power of solid-state nuclear magnetic resonance (NMR) crystallography depends heavily on the accuracy of computational predictions of NMR chemical shieldings of candidate structures, which are usually taken to be local minima in the potential energy. To test the limits of this approximation, we systematically study the importance of finite-temperature and quantum nuclear fluctuations for 1H, 13C, and 15N shieldings in polymorphs of three paradigmatic molecular crystals: benzene, glycine, and succinic acid. The effect of quantum fluctuations is comparable to the typical errors of shielding predictions for static nuclei with respect to experiments, and their inclusion improves the agreement with measurements, translating to more reliable assignment of the NMR spectra to the correct candidate structure. The use of integrated machine-learning models, trained on first-principles energies and shieldings, renders rigorous sampling of nuclear fluctuations affordable, setting a new standard for the calculations underlying NMR structure determinations.
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Affiliation(s)
- Edgar A Engel
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Venkat Kapil
- Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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19
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Ma Z, Lu C, Chen J, Rokicińska A, Kuśtrowski P, Coridan R, Dronskowski R, Slabon A, Jaworski A. CeTiO 2N oxynitride perovskite: paramagnetic 14N MAS NMR without paramagnetic shifts. ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL SCIENCES 2021. [DOI: 10.1515/znb-2021-0031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
14N magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of diamagnetic LaTiO2N perovskite oxynitride and its paramagnetic counterpart CeTiO2N are presented. The latter, to the best of our knowledge, constitutes the first high-resolution 14N MAS NMR spectrum collected from a paramagnetic solid material. The unpaired 4f-electrons in CeTiO2N do not induce a paramagnetic 14N NMR shift. This is remarkable given the direct Ce−N contacts in the structure for which ab initio calculations predict substantial Ce→14N contact shift interaction. The same effect is revealed with 14N MAS NMR for SrWO2N (unpaired 5d-electrons).
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Affiliation(s)
- Zili Ma
- Chair of Solid-State and Quantum Chemistry, Institute of Inorganic Chemistry, RWTH Aachen University , Landoltweg 1, D-52056 Aachen , Germany
| | - Can Lu
- Chair of Solid-State and Quantum Chemistry, Institute of Inorganic Chemistry, RWTH Aachen University , Landoltweg 1, D-52056 Aachen , Germany
| | - Jianhong Chen
- Department of Materials and Environmental Chemistry , Stockholm University , SE-106 91 , Stockholm , Sweden
| | - Anna Rokicińska
- Faculty of Chemistry, Jagiellonian University , Gronostajowa 2, 30-387 Kraków , Poland
| | - Piotr Kuśtrowski
- Faculty of Chemistry, Jagiellonian University , Gronostajowa 2, 30-387 Kraków , Poland
| | - Robert Coridan
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , AR 72701 , USA
| | - Richard Dronskowski
- Chair of Solid-State and Quantum Chemistry, Institute of Inorganic Chemistry, RWTH Aachen University , Landoltweg 1, D-52056 Aachen , Germany
| | - Adam Slabon
- Department of Materials and Environmental Chemistry , Stockholm University , SE-106 91 , Stockholm , Sweden
| | - Aleksander Jaworski
- Department of Materials and Environmental Chemistry , Stockholm University , SE-106 91 , Stockholm , Sweden
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20
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Attia AAA, Reinholdt P, Kongsted J. Modeling One‐ and Two‐Photon Excitation of 4′‐(Hydroxymethyl)‐4,5′,8‐trimethylpsoralen in Complex with DNA: Solving Electron Spill‐Out Problems in Polarizable QM/MM Calculations. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202000294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Amr A. A. Attia
- Faculty of Chemistry and Chemical Engineering Babeş‐Bolyai University Cluj‐Napoca Romania
| | - Peter Reinholdt
- Department of Physics Chemistry and Pharmacy University of Southern Denmark Campusvej 55 Odense M DK–5230 Denmark
| | - Jacob Kongsted
- Department of Physics Chemistry and Pharmacy University of Southern Denmark Campusvej 55 Odense M DK–5230 Denmark
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