1
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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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Nakajima Y, Ohmura T, Seino J. Using atomic clustering based on structural and electronic descriptors that consider surrounding environment to evaluate local properties of DFT functionals. J Comput Chem 2024; 45:1870-1879. [PMID: 38686778 DOI: 10.1002/jcc.27375] [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: 11/12/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024]
Abstract
We developed a method for evaluating the accuracies of the local properties of DFT functionals in detail using a clustering method based on machine learning and structural/electronic descriptors. We generated 36 clusters consistent with human intuition using 30,436 carbon atoms from the QM9 dataset. The results were used to evaluate 13C NMR chemical shifts calculated using 84 DFT functionals. Carbon atoms were grouped based on their similar environments, reducing errors within these groups. This enables more accurate assessment of the accuracy using a specific DFT functional. Therefore, the present atomic clustering provides more detailed insight into accuracy verification.
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Affiliation(s)
- Yuya Nakajima
- Waseda Research Institute for Science and Engineering, Tokyo, Japan
| | - Takuto Ohmura
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Junji Seino
- Waseda Research Institute for Science and Engineering, Tokyo, Japan
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
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3
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Oshima K, Kobayashi R, Sakamoto K, Yoza K, Ishida S, Iwamoto T. An Isolable THF-Coordinated Dialkylgermanone. Chem Asian J 2024; 19:e202400111. [PMID: 38380801 DOI: 10.1002/asia.202400111] [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: 01/31/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 02/22/2024]
Abstract
A stable dialkylgermanone was generated by mixing a solid of the corresponding dialkylgermylene and gaseous N2O. While the dialkylgermanone is marginally persistent in solution and gradually converts to its head-to-tail dimer at room temperature, the addition of THF to the dialkylgermanone provided an isolable THF-coordinated dialkylgermanone. The THF-coordinated dialkylgermanone reacts with H2O, THF, and B(C6F5)3 similar to the corresponding base-free two-coordinate dialkylsilanone. The dialkylgermanone undergoes deoxygenation in the presence of triphenylphosphine to provide the corresponding germylene and olefination upon treatment with phosphaylide Ph3PCHPh to afford the corresponding Ge=C bond compound (germa-Wittig reaction).
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Affiliation(s)
- Kazuma Oshima
- Department of Chemistry, Graduate School of Science, Tohoku University Aoba-ku, Sendai, 980-8578, Japan
| | - Ryo Kobayashi
- Department of Chemistry, Graduate School of Science, Tohoku University Aoba-ku, Sendai, 980-8578, Japan
| | - Kengo Sakamoto
- Department of Chemistry, Graduate School of Science, Tohoku University Aoba-ku, Sendai, 980-8578, Japan
| | - Kenji Yoza
- Bruker Japan K. K., 3-9 Moriya-cho, Kanagawa-Ku, Yokohama, 221-0022, Japan
| | - Shintaro Ishida
- Department of Chemistry, Graduate School of Science, Tohoku University Aoba-ku, Sendai, 980-8578, Japan
| | - Takeaki Iwamoto
- Department of Chemistry, Graduate School of Science, Tohoku University Aoba-ku, Sendai, 980-8578, Japan
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4
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Venetos M, Elkin M, Delaney C, Hartwig JF, Persson KA. Deconvolution and Analysis of the 1H NMR Spectra of Crude Reaction Mixtures. J Chem Inf Model 2024; 64:3008-3020. [PMID: 38573053 PMCID: PMC11040730 DOI: 10.1021/acs.jcim.3c01864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is an important analytical technique in synthetic organic chemistry, but its integration into high-throughput experimentation workflows has been limited by the necessity of manually analyzing the NMR spectra of new chemical entities. Current efforts to automate the analysis of NMR spectra rely on comparisons to databases of reported spectra for known compounds and, therefore, are incompatible with the exploration of new chemical space. By reframing the NMR spectrum of a reaction mixture as a joint probability distribution, we have used Hamiltonian Monte Carlo Markov Chain and density functional theory to fit the predicted NMR spectra to those of crude reaction mixtures. This approach enables the deconvolution and analysis of the spectra of mixtures of compounds without relying on reported spectra. The utility of our approach to analyze crude reaction mixtures is demonstrated with the experimental spectra of reactions that generate a mixture of isomers, such as Wittig olefination and C-H functionalization reactions. The correct identification of compounds in a reaction mixture and their relative concentrations is achieved with a mean absolute error as low as 1%.
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Affiliation(s)
- Maxwell
C. Venetos
- Department
of Materials Science and Engineering, University
of California, Berkeley, California 94720, United States
| | - Masha Elkin
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Connor Delaney
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - John F. Hartwig
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Kristin A. Persson
- Department
of Materials Science and Engineering, University
of California, Berkeley, California 94720, United States
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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5
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Hu B, Qian M, Zhang J, Hou X, Wu L. Hyperhenrones: Prenylated α-pyrones with anti-inflammatory activity from Hypericum henryi. PHYTOCHEMISTRY 2024; 220:114007. [PMID: 38296177 DOI: 10.1016/j.phytochem.2024.114007] [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: 10/31/2023] [Revised: 01/24/2024] [Accepted: 01/28/2024] [Indexed: 02/03/2024]
Abstract
Fourteen previously undescribed α-pyrone derivatives (1-14) together with four known analogs (15-18) were isolated from a traditional Chinese medicinal plant Hypericum henryi. Compounds (+)/(-)-1, 2, and 3 share a rare 6/6/4/6/6 polycyclic skeleton. Compound 14 was the first example of a 7,7-dimethyl-pyran-4-one moiety. Their structures were elucidated using comprehensive spectroscopic analyses and electronic circular dichroism calculations. The anti-inflammatory activities of 1-18 were screened in lipopolysaccharide-induced RAW264.7 cells. Among them, compounds 14, (+)-18, and (-)-18 exhibited inhibitory effects against nitric oxide production in LPS-induced RAW264.7 cells. Additionally, compound 14 suppressed the expression of cyclooxygenase-2 and inducible nitric oxide synthase in LPS-induced RAW264.7 cells. Furthermore, preliminary mechanism studies indicated that compound 14 suppressed the phosphorylation and degradation of the inhibitor of NF-κB, and this led to the inhibition of NF-κB activation.
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Affiliation(s)
- Bo Hu
- School of Pharmacy, Anhui Medical University Hefei, 230032, People's Republic of China
| | - Mengyu Qian
- School of Pharmacy, Anhui Medical University Hefei, 230032, People's Republic of China
| | - Jiayue Zhang
- School of Pharmacy, Anhui Medical University Hefei, 230032, People's Republic of China
| | - Xingcun Hou
- School of Pharmacy, Anhui Medical University Hefei, 230032, People's Republic of China
| | - Lin Wu
- School of Pharmacy, Anhui Medical University Hefei, 230032, People's Republic of China.
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6
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Zhu G, Lin Y, Zhou W, Song H, Li Z. Study of the electronic effect and quantitative spectra predictions of o-methoxyaniline-terminated monoazonaphthols: a combined experimental and DFT study. RSC Adv 2023; 13:33736-33742. [PMID: 38020020 PMCID: PMC10655066 DOI: 10.1039/d3ra05518c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/13/2023] [Indexed: 12/01/2023] Open
Abstract
A combined experimental and density functional theory (DFT) study on the UV-Vis spectra of o-methoxyaniline-terminated mono azo dyes was conducted. By applying time-dependent-DFT calculations, details of excitation processes were determined and visualization by hole-electron analysis was undertaken. Fragment-divided analysis revealed the contributions of different parts of the structures for the UV-Vis spectra, that richer/poorer electron density on aromatic rings lead to greater/less maximum absorption wavelengths (λmax) and larger/smaller half peak width (W1/2). Combining theoretical prediction with experimental verification, we answered the question of how the electronegativities of substituents affected the electron densities and how it affected the spectra. In addition, a linear model connecting the λmax and W1/2 to the chemical shifts obtained by NMR spectroscopy was constructed, which laid the foundation for construction of a spectral library.
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Affiliation(s)
- Guoxun Zhu
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences, China National Analytical Centre Guangzhou 510070 P. R. China
| | - Yan Lin
- FSPG Hi-Tech Co., Ltd Foshan 528000 P. R. China
| | - Wenxian Zhou
- WINDA OPTO-Electronics Co., Ltd Foshan 528136 P. R. China
| | - Huacan Song
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences, China National Analytical Centre Guangzhou 510070 P. R. China
| | - Zhengquan Li
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences, China National Analytical Centre Guangzhou 510070 P. R. China
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7
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Kleine Büning JB, Grimme S. Computation of CCSD(T)-Quality NMR Chemical Shifts via Δ-Machine Learning from DFT. J Chem Theory Comput 2023. [PMID: 37262324 DOI: 10.1021/acs.jctc.3c00165] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
NMR spectroscopy undoubtedly plays a central role in determining molecular structures across different chemical disciplines, and the accurate computational prediction of NMR parameters is highly desirable. In this work, a new Δ-machine learning approach is presented to correct DFT-computed NMR chemical shifts using input features from the calculation and in addition highly accurate reference data at the CCSD(T)/pcSseg-2 level of theory with a basis set extrapolation scheme. The model is trained on a data set containing 1000 optimized and geometrically distorted structures of small organic molecules comprising most elements of the first three periods and containing data for 7090 1H and 4230 13C NMR chemical shifts. Applied to the PBE0/pcSseg-2 method, the mean absolute deviation (MAD) on the internal NMR shift test set is reduced by 81% for 1H and 92% for 13C at virtually no additional computational cost. For 12 different DFT functional and basis set combinations, the MAD of the ML-corrected NMR shifts ranges from 0.021 to 0.039 ppm (1H) and from 0.38 to 1.07 ppm (13C). Importantly, the new method consistently outperforms the simple and widely used linear regression correction technique. This behavior is reproduced on three different external benchmark sets, confirming the generality and robustness of the correction scheme, which can easily be applied in DFT-based spectral simulations.
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Affiliation(s)
- Julius B Kleine Büning
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
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8
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Wong J, Ganoe B, Liu X, Neudecker T, Lee J, Liang J, Wang Z, Li J, Rettig A, Head-Gordon T, Head-Gordon M. An in-silico NMR laboratory for nuclear magnetic shieldings computed via finite fields: Exploring nucleus-specific renormalizations of MP2 and MP3. J Chem Phys 2023; 158:164116. [PMID: 37114707 PMCID: PMC10148725 DOI: 10.1063/5.0145130] [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: 02/03/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
We developed and implemented a method-independent, fully numerical, finite difference approach to calculating nuclear magnetic resonance shieldings, using gauge-including atomic orbitals. The resulting capability can be used to explore non-standard methods, given only the energy as a function of finite-applied magnetic fields and nuclear spins. For example, standard second-order Møller-Plesset theory (MP2) has well-known efficacy for 1H and 13C shieldings and known limitations for other nuclei such as 15N and 17O. It is, therefore, interesting to seek methods that offer good accuracy for 15N and 17O shieldings without greatly increased compute costs, as well as exploring whether such methods can further improve 1H and 13C shieldings. Using a small molecule test set of 28 species, we assessed two alternatives: κ regularized MP2 (κ-MP2), which provides energy-dependent damping of large amplitudes, and MP2.X, which includes a variable fraction, X, of third-order correlation (MP3). The aug-cc-pVTZ basis was used, and coupled cluster with singles and doubles and perturbative triples [CCSD(T)] results were taken as reference values. Our κ-MP2 results reveal significant improvements over MP2 for 13C and 15N, with the optimal κ value being element-specific. κ-MP2 with κ = 2 offers a 30% rms error reduction over MP2. For 15N, κ-MP2 with κ = 1.1 provides a 90% error reduction vs MP2 and a 60% error reduction vs CCSD. On the other hand, MP2.X with a scaling factor of 0.6 outperformed CCSD for all heavy nuclei. These results can be understood as providing renormalization of doubles amplitudes to partially account for neglected triple and higher substitutions and offer promising opportunities for future applications.
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Affiliation(s)
- Jonathan Wong
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Brad Ganoe
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Xiao Liu
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Tim Neudecker
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Joonho Lee
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Jiashu Liang
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Zhe Wang
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Jie Li
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Adam Rettig
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
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9
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Hill A, Wang F. Intramolecular O···H Hydrogen Bonding of Salicylic Acid: Further Insights from O 1s XPS and 1H NMR Spectra Using DFT Calculations. J Phys Chem A 2023; 127:2705-2716. [PMID: 36939708 DOI: 10.1021/acs.jpca.2c08981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
Intramolecular hydrogen bonding (HB) is a complex phenomenon that extends beyond a simple valence event, affecting the core electrons of a molecule. Salicylic acid (SA) and its conformers provide an excellent model compound for studying intramolecular HB as the proton donor (H) and acceptor (O) can be toggled by rotating the C-O and C-C bonds to form up to seven potential conformers through various HB. In this study, we computationally investigated intramolecular interactions in SA conformers with and without such HB, by examining their calculated O 1s core electron-binding energy (CEBE) and 1H NMR chemical shifts validated using recent measurements. The quantum mechanically stable SA conformers are fully defined by three rotatable bonds in the compound, which are abstracted as SA(η1η2η3) digital structures, where ηi = 0 if the ηi angles match the most stable SA conformer (000) and ηi = 1 otherwise. Our findings suggest that the stability is dominated by the appearance of the intergroup intramolecular HB of Hp···O (where O is in the carboxylic acid functional group and Hp is the phenolic proton in -OHp), and η3 serves as a switch of such HB. As a result, the (η1η20) SA conformers containing such Hp···O HB are more stable than other SA conformers (η1η21) without such the Hp···O HB. The present density functional theory calculations reveal that this Hp···O HB results in splitting of the O 1s CEBEs of two hydroxyl groups (-OH) by up to 1 eV and deshielding the Hp proton 1H NMR (δHp) up to 11.68 ppm for the (η1η20) conformers. Without such Hp···O HB, the O 1s XPS binding energies of two -OH groups will be closely located in the same band, and the 1H NMR chemical shift of the Hp atom will be as small as an 4.09 ppm SA conformer [SA-G(101)]. The present study indicates that the O 1s CEBE splitting between two -OH groups serves as an indicator of the presence of the Hp···O HB in SA conformers, which is also supported by the 1H NMR results.
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Affiliation(s)
- Alexander Hill
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
| | - Feng Wang
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
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10
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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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11
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Cohen RD, Wood JS, Lam YH, Buevich AV, Sherer EC, Reibarkh M, Williamson RT, Martin GE. DELTA50: A Highly Accurate Database of Experimental 1H and 13C NMR Chemical Shifts Applied to DFT Benchmarking. Molecules 2023; 28:molecules28062449. [PMID: 36985422 PMCID: PMC10051451 DOI: 10.3390/molecules28062449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/30/2023] Open
Abstract
Density functional theory (DFT) benchmark studies of 1H and 13C NMR chemical shifts often yield differing conclusions, likely due to non-optimal test molecules and non-standardized data acquisition. To address this issue, we carefully selected and measured 1H and 13C NMR chemical shifts for 50 structurally diverse small organic molecules containing atoms from only the first two rows of the periodic table. Our NMR dataset, DELTA50, was used to calculate linear scaling factors and to evaluate the accuracy of 73 density functionals, 40 basis sets, 3 solvent models, and 3 gauge-referencing schemes. The best performing DFT methodologies for 1H and 13C NMR chemical shift predictions were WP04/6-311++G(2d,p) and ωB97X-D/def2-SVP, respectively, when combined with the polarizable continuum solvent model (PCM) and gauge-independent atomic orbital (GIAO) method. Geometries should be optimized at the B3LYP-D3/6-311G(d,p) level including the PCM solvent model for the best accuracy. Predictions of 20 organic compounds and natural products from a separate probe set had root-mean-square deviations (RMSD) of 0.07 to 0.19 for 1H and 0.5 to 2.9 for 13C. Maximum deviations were less than 0.5 and 6.5 ppm for 1H and 13C, respectively.
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Affiliation(s)
- Ryan D Cohen
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ 07079, USA
| | - Jared S Wood
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28409, USA
| | - Yu-Hong Lam
- Department of Computational and Structural Chemistry, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Alexei V Buevich
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Edward C Sherer
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Mikhail Reibarkh
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - R Thomas Williamson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28409, USA
| | - Gary E Martin
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ 07079, USA
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12
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Cedillo–Cruz A, Villalobos–López DC, Aguilar MI, Trejo–Soto PJ, Hernández–Campos A, Jung–Cook H. Praziquanamine enantiomers: crystal structure, Hirshfeld surface analysis, and quantum chemical studies. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
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13
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Antifungal polyketides from the marine-derived fungus Nigrospora sp. MG36-1. Fitoterapia 2023; 165:105406. [PMID: 36572117 DOI: 10.1016/j.fitote.2022.105406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022]
Abstract
Three new polyketides, a griseofulvin derivative 1, a hydroanthraquinone derivative 8 and a pyranolactone derivative 10, together with eight known compounds (2-7, 9 and 11), were isolated from the marine-derived fungus Nigrospora sp. MG36-1. The structures of the three new compounds were unambiguously determined by nuclear magnetic resonance (NMR), mass spectrometry, 13C NMR calculation in combination with DP4+ and ECD calculations. The antitumor, antibacterial and antifungal activities of the compounds 1-9 were evaluated in vitro. Compound 1 showed antibacterial activity against Acinetobacter baumannii with MIC 42.5 μg/mL. Compounds 1 and 8 exhibited antifungal activity against Candida albicans with MICs 21.5 μg/mL and 17.5 μg/mL, respectively.
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14
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de Oliveira MT, Alves JMA, Vrech NL, Braga AAC, Barboza CA. A comprehensive benchmark investigation of quantum chemical methods for carbocations. Phys Chem Chem Phys 2023; 25:1903-1922. [PMID: 36541431 DOI: 10.1039/d2cp04603b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The application of various density functional approximations (DFAs) and an emphasis on popular methods without any consensus have prevailed in computational studies dedicated to carbocations. More importantly, an extensive and rigorous benchmark investigation on density functionals for the class is still lacking. To close this gap, we present a comprehensive benchmark study of quantum chemical methods on a series of classical and nonclassical carbocations, the CARBO33 dataset. We evaluate a total of 107 DFT methods from all rungs giving particular attention to double hybrid density functionals as the potential of the class has been largely undermined in the context of carbocations. To support our findings, DLPNO-CCSD(T) at the complete basis set (CBS) limit and W1-F12 are used as reference methods. Our results indicate that the composite CBS-QB3 method performs poorly and should not be adopted for target energies. Oftentimes, the tested DFAs of a lower rung perform better than several DFAs in a higher rung of Perdew's "Jacob's ladder". Nonetheless, double hybrids DSD-PBEP86-NL and ωB97X-2-D3(BJ) stand out by showing the overall best performance. Among the hybrids evaluated, about half of them show mean absolute deviation (MAD) below 1.1 kcal mol-1, including the popular hybrids M06-2X and mPW1PW91. In this family, MN15-D3(BJ) performs particularly well (MAD = 0.77 kcal mol-1) displaying reliable results across various tests. Highly popular B3LYP exhibited one of the worst performances (MAD = 4.74 kcal mol-1), and we do not recommend its application to carbocations. We also assess the 24 general-purpose basis sets of single- up to quadruple-ζ quality. The best compromise between accuracy and computational cost is achieved with cc-pVTZ followed by def2-TZVP. Computations on larger structures of general interest, including terpene carbocations, are also presented for selected DFT methods confirming general trends in the results.
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Affiliation(s)
- Marcelo T de Oliveira
- Department of Chemistry and Physics, La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne, Victoria 3086, Australia. .,Chemistry Institute of São Carlos, University of São Paulo, Av. Trabalhador São Carlense 400, 13566-590, São Carlos, SP, Brazil
| | - Júlia M A Alves
- Chemistry Institute of São Carlos, University of São Paulo, Av. Trabalhador São Carlense 400, 13566-590, São Carlos, SP, Brazil
| | - Natália L Vrech
- Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil
| | - Ataualpa A C Braga
- Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil
| | - Cristina A Barboza
- Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland.,Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, Warsaw, Poland
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15
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Liang J, Wang Z, Li J, Wong J, Liu X, Ganoe B, Head-Gordon T, Head-Gordon M. Efficient Calculation of NMR Shielding Constants Using Composite Method Approximations and Locally Dense Basis Sets. J Chem Theory Comput 2023. [PMID: 36594660 DOI: 10.1021/acs.jctc.2c00933] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
This paper presents a systematic study of applying composite method approximations with locally dense basis sets (LDBS) to efficiently calculate NMR shielding constants in small and medium-sized molecules. The pcSseg-n series of basis sets are shown to have similar accuracy to the pcS-n series when n ≥ 1 and can slightly reduce computational costs. We identify two different LDBS partition schemes that perform very effectively for density functional calculations. We select a large subset of the recent NS372 database containing 290 H, C, N, and O shielding values evaluated by reference methods on 106 molecules to carefully assess methods of the high, medium, and low computational costs to make practical recommendations. Our assessment covers conventional electronic structure methods (density functional theory and wave function) with global basis calculations, as well as their use in one of the satisfactory LDBS approaches, and a range of composite approaches, also with and without LDBS. Altogether 99 methods are evaluated. On this basis, we recommend different methods to reach three different levels of accuracy and time requirements across the four nuclei considered.
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Affiliation(s)
- Jiashu Liang
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California94720, United States
| | - Zhe Wang
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California94720, United States
| | - Jie Li
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California94720, United States
| | - Jonathan Wong
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California94720, United States
| | - Xiao Liu
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California94720, United States
| | - Brad Ganoe
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California94720, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California94720, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
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16
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Bakker MJ, Mládek A, Semrád H, Zapletal V, Pavlíková Přecechtělová J. Improving IDP theoretical chemical shift accuracy and efficiency through a combined MD/ADMA/DFT and machine learning approach. Phys Chem Chem Phys 2022; 24:27678-27692. [PMID: 36373847 DOI: 10.1039/d2cp01638a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This work extends the multi-scale computational scheme for the quantum mechanics (QM) calculations of Nuclear Magnetic Resonance (NMR) chemical shifts (CSs) in proteins that lack a well-defined 3D structure. The scheme couples the sampling of an intrinsically disordered protein (IDP) by classical molecular dynamics (MD) with protein fragmentation using the adjustable density matrix assembler (ADMA) and density functional theory (DFT) calculations. In contrast to our early investigation on IDPs (Pavlíková Přecechtělová et al., J. Chem. Theory Comput., 2019, 15, 5642-5658) and the state-of-the art NMR calculations for structured proteins, a partial re-optimization was implemented on the raw MD geometries in vibrational normal mode coordinates to enhance the accuracy of the MD/ADMA/DFT computational scheme. In addition, machine-learning based cluster analysis was performed on the scheme to explore its potential in producing protein structure ensembles (CLUSTER ensembles) that yield accurate CSs at a reduced computational cost. The performance of the cluster-based calculations is validated against results obtained with conventional structural ensembles consisting of MD snapshots extracted from the MD trajectory at regular time intervals (REGULAR ensembles). CS calculations performed with the refined MD/ADMA/DFT framework employed the 6-311++G(d,p) basis set that outperformed IGLO-III calculations with the same density functional approximation (B3LYP) and both explicit and implicit solvation. The partial geometry optimization did not universally improve the agreement of computed CSs with the experiment but substantially decreased errors associated with the ensemble averaging. A CLUSTER ensemble with 50 structures yielded ensemble averages close to those obtained with a REGULAR ensemble consisting of 500 MD frames. The cluster based calculations thus required only a fraction of the computational time.
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Affiliation(s)
- Michael J Bakker
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic.
| | - Arnošt Mládek
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic.
| | - Hugo Semrád
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic. .,Department of Chemistry, Faculty of Science, Masaryk University, Kotlářská 267/2, 611 37 Brno, Czech Republic
| | - Vojtěch Zapletal
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic.
| | - Jana Pavlíková Přecechtělová
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic.
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17
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Cuadrado C, Daranas AH, Sarotti AM. May the Force (Field) Be with You: On the Importance of Conformational Searches in the Prediction of NMR Chemical Shifts. Mar Drugs 2022; 20:699. [PMID: 36355022 PMCID: PMC9694776 DOI: 10.3390/md20110699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 10/29/2022] [Accepted: 11/04/2022] [Indexed: 09/21/2023] Open
Abstract
NMR data prediction is increasingly important in structure elucidation. The impact of force field selection was assessed, along with geometry and energy cutoffs. Based on the conclusions, we propose a new approach named mix-J-DP4, which provides a remarkable increase in the confidence level of complex stereochemical assignments-100% in our molecular test set-with a very modest increment in computational cost.
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Affiliation(s)
- Cristina Cuadrado
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), 38206 La Laguna, Tenerife, Spain
| | - Antonio Hernández Daranas
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), 38206 La Laguna, Tenerife, Spain
| | - Ariel M. Sarotti
- Instituto de Química Rosario (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
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18
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Zhu H, Guo X, Si Y, Du Q, Cheng Y, Wang L, Li X. Insights into pathways and solvent effects of fructose dehydration to 5-hydroxymethylfurfural in acetone-water solvent. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.118352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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19
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Wei J, Chen X, Ge Y, Yin Q, Wu X, Tang J, Zhang Z, Wu B. Citrinin Monomer, Trimer, and Tetracyclic Alkaloid Derivatives from the Hydrothermal Vent-Associated Fungus Penicillium citrinum TW132-59. J Org Chem 2022; 87:13270-13279. [PMID: 36131357 DOI: 10.1021/acs.joc.2c01856] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Five new unusual citrinin-derived alkaloids with a tetracyclic core, citrinidines A-E (1-5), two new amide alkaloids, methyl (2S,8E)-1'-(2-methyl-3-oxodec-8-enamido) butanoate (6) and (2S,8E)-2-methyl-3-oxodec-8-enamide (7), a new unusual citrinin trimer, tricitrinol C (8), a new citrinin acetal-ketal derivative, citrininol (9), together with four known citrinin monomers (10-13), and three known citrinin dimers (14-16), were isolated from the fermentation of hydrothermal vent-associated fungus Penicillium citrinum TW132-59. Their structures were unambiguously determined by nuclear magnetic resonance (NMR), mass spectrometry, Mosher's method, 13C NMR calculation in combination with DP4+, and ECD calculations. A plausible biosynthetic pathway of all new compounds (1-9) was proposed. Citrinin trimer (8) exhibited potent cytotoxicity activity with an IC50 value of 1.34 ± 0.11 μM, and compounds 1 and 15 showed moderate cytotoxicity with IC50 values of 17.50 ± 1.43 and 9.45 ± 0.55 μM, respectively, against A549 cell line.
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Affiliation(s)
- Jihua Wei
- Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Xuexia Chen
- Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Yichao Ge
- Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Qizhao Yin
- Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Xiaodan Wu
- Center of Analysis, Zhejiang University, Hangzhou 310058, China
| | - Jinshan Tang
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Zunjing Zhang
- Lishui Hospital of Traditional Chinese Medicine, Lishui 323000, China
| | - Bin Wu
- Ocean College, Zhejiang University, Zhoushan 316021, China
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20
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Stadelmann T, Balmer C, Riniker S, Ebert MO. Impact of solvent interactions on 1H and 13C chemical shifts investigated using DFT and a reference dataset recorded in CDCl 3 and CCl 4. Phys Chem Chem Phys 2022; 24:23551-23560. [PMID: 36129319 PMCID: PMC9533371 DOI: 10.1039/d2cp03205h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
1H and 13C chemical shifts of 35 small, rigid molecules were measured under standardized conditions in chloroform-d and in tetrachloromethane. The solvent change mainly affects carbon shifts of polar functional groups. This difference due to specific interactions with CDCl3 cannot be adequately reproduced by DFT calculations in implicit solvent. The new dataset provides an accurate basis for the validation and calibration of shift calculations, especially with respect to improved solvent models. 1H and 13C chemical shifts of 35 small, rigid molecules were measured under standardized conditions in CDCl3 and in CCl4. Specific solvent interactions lead to chemical shift differences that cannot be reproduced by DFT in implicit solvent.![]()
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Affiliation(s)
- Thomas Stadelmann
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland.
| | - Chantal Balmer
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland.
| | - Sereina Riniker
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland.
| | - Marc-Olivier Ebert
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland.
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21
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Ge Y, Ma Y, Zhao M, Wei J, Wu X, Zhang Z, Yang H, Lei H, Wu B. Exploring gabosine and chlorogentisyl alcohol derivatives from a marine-derived fungus as EcGUS inhibitors with informatic assisted approaches. Eur J Med Chem 2022; 242:114699. [PMID: 36001934 DOI: 10.1016/j.ejmech.2022.114699] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/02/2022] [Accepted: 08/15/2022] [Indexed: 11/04/2022]
Abstract
β-Glucuronidase catalyzes the cleavage of glucuronosyl-O-bonds, whose inhibitors reduce the level of toxic substances present in the intestine caused by anti-cancer and anti-inflammatory therapies. Herein, we presented a new tool, Bioactive Fractions Filtering Platform (BFFP), which is able to reliably discern active candidate node from crude extracts. The source code for the BFFP is available on GitHub (https://github.com/BioGavin/msbff). With the assistant of BFFP, 25 gabosine and chlorogentisyl alcohol derivatives including 19 new compounds were isolated from a marine-derived fungus Epicoccum sp. GST-5. Compounds 7, 9-15 possessed an unusual hybrid skeleton of gabosine and chlorogentisyl alcohol units. Compounds 9-12, 16 and 17 possessed a novel three-membered spiral ring skeleton with one/two gabosine and one/two chlorogentisyl alcohol units. Compound 25 represented new gabosine-derived skeleton possessing an unusual 6/6/6/5/6 condensed ring system. All isolates were evaluated for in vitro E. coli β-glucuronidase (EcGUS) inhibitory activity. 14 Compounds demonstrated superior inhibitory activity (IC50 = 0.24-4.61 μM) to that of standard d-saccharic acid 1,4-lactone (DSL, IC50 = 56.74 ± 4.01 μM). Compounds with chlorogentisyl alcohol moiety, such as 17 (IC50 = 0.24 ± 0.02 μM) and 1 (IC50 = 0.74 ± 0.03 μM), exhibited the most potent inhibitory activity. Furthermore, literature based QSAR profiling by applying PCA and OPLS analysis was carried out to analyze the features of compounds against EcGUS, revealing that the introduction of substituents able to form polar interactions with binding sites of receptor would lead to more active structures.
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Affiliation(s)
- Yichao Ge
- Ocean College, Zhejiang University, Zhoushan, 321000, China.
| | - Yihan Ma
- Ocean College, Zhejiang University, Zhoushan, 321000, China.
| | - Meilu Zhao
- Ocean College, Zhejiang University, Zhoushan, 321000, China.
| | - Jihua Wei
- Ocean College, Zhejiang University, Zhoushan, 321000, China.
| | - Xiaodan Wu
- Center of Analysis, Zhejiang University, Hangzhou, 310058, China.
| | - Zunjing Zhang
- Lishui Hospital of Traditional Chinese Medicine, Lishui, 323000, China.
| | - Han Yang
- Ocean College, Zhejiang University, Zhoushan, 321000, China.
| | - Houxing Lei
- Lishui Hospital of Traditional Chinese Medicine, Lishui, 323000, China.
| | - Bin Wu
- Ocean College, Zhejiang University, Zhoushan, 321000, China.
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22
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Zhang T, Zhang C, Ma X, Quan H. Substitution Effects on the Reactivity and Thermostability of Five-Membered Ring Fluorides. ACS OMEGA 2022; 7:25476-25490. [PMID: 35910138 PMCID: PMC9330182 DOI: 10.1021/acsomega.2c02461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recently, five-membered ring fluorides (c-C5Fs) have been significantly desirable in green chlorofluorocarbon substitutes due to their practically flexible application in various fields and environmental friendliness. Detailed knowledge regarding different substitution effects on their environmental properties and thermal stability is very limited due to their high-cost experiments. Here, comprehensive density functional theory and ab initio molecular dynamics calculations were performed to explore the relative electrophilic and nucleophilic reactivity and thermostability of c-C5F chemicals. The electronic properties induced by substitution effects of c-C5Fs were first explored. The environmental friendliness of c-C5Fs including 1,1,2,2,3,3-hexafluorocyclopentane (F6A), 1,1,2,2,3,3,4-heptafluorocyclopentane (F7A), cis-1,1,2,2,3,3,4,5-octafluorocyclopentane (F8A), 3,3,4,4,5,5-hexafluorocyclopentene (F6E), 1,3,3,4,4,5,5-heptafluorocyclopentene (F7E), octafluorocyclopentene (F8E), 1-chloro-3,3,4,4,5,5-hexafluorocyclopent-1-ene (F6-1), and 1-chloro-2,3,3,4,4,5,5-heptafluorocyclopent-1-ene (F7-1) was validly confirmed. Besides, their thermal stabilities at 600 K temperature were concluded due to their flexible carbon skeletons, where both in-plane stability and slight aromaticity of F6E were in peculiar found to contribute substantially. We also would like to stress the future application of F6-1 due to its significant out-plane stability. This study may pave the way for the development of chlorofluorocarbon substitutes.
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Affiliation(s)
- Tongyun Zhang
- School
of Chemical Engineering, Northwest University, 229 Taibai North Road, Xi’an, Shaanxi 710069, China
| | - Chengping Zhang
- School
of Chemistry and Chemical Engineering, Beijing
Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China
| | - Xiaoxun Ma
- School
of Chemical Engineering, Northwest University, 229 Taibai North Road, Xi’an, Shaanxi 710069, China
| | - Hengdao Quan
- School
of Chemistry and Chemical Engineering, Beijing
Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China
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23
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Trung NQ, Mechler A, Hoa NT, Vo QV. Calculating bond dissociation energies of X-H (X=C, N, O, S) bonds of aromatic systems via density functional theory: a detailed comparison of methods. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220177. [PMID: 35706655 PMCID: PMC9174704 DOI: 10.1098/rsos.220177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/06/2022] [Indexed: 05/03/2023]
Abstract
In this study, the performance of 17 different density functional theory functionals was compared for the calculation of the bond dissociation energy (BDE) values of X-H (X=C, N, O, S) bonds of aromatic compounds. The effect of the size of the basis set (expansions of 6-31(G)) was also assessed for the initial geometry and zero-point energy calculations, followed by the single-point BDE calculations with different model chemistries with the 6-311 + (3df,2p) basis set. It was found that the size of the basis set for geometry optimization has a much smaller effect on the accuracy of BDE than the choice of functional for the following single-point calculations. The M06-2X, M05-2X and M08-HX functionals yielded highly accurate BDE values compared to experimental data (with the average mean unsigned error MUE = 1.2-1.5 kcal mol-1), performing better than any of the other functionals. The results suggest that geometry optimization may be performed with B3LYP functional and a small basis set, whereas the M06-2X, M05-2X and M08-HX density functionals with a suitably large basis set offer the best method for calculating BDEs of ArX-H (X=C, N, O, S) bonds.
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Affiliation(s)
- Nguyen Quang Trung
- Department of Chemistry, The University of Danang - University of Science and Education, Da Nang 550000, Vietnam
- Quality Assurance and Testing Center 2, Danang 550000, Vietnam
| | - Adam Mechler
- Department of Chemistry and Physics, La Trobe University, Victoria 3086, Australia
| | - Nguyen Thi Hoa
- Academic Affairs, The University of Danang - University of Technology and Education, Danang 550000, Vietnam
| | - Quan V. Vo
- Faculty of Chemical Technology – Environment, The University of Danang - University of Technology and Education, Danang 550000, Vietnam
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24
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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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25
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Li X, Ge Y, Ma Y, Wang S, Li S, Yin Q, Liu X, Wie J, Wu X, Wu B. New Cytotoxic Secondary Metabolites from Two Deep-Sea-Derived Fungi and the Co-Culture Impact on the Secondary Metabolic Patterns. Chem Biodivers 2022; 19:e202200055. [PMID: 35229447 DOI: 10.1002/cbdv.202200055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 02/12/2022] [Indexed: 11/05/2022]
Abstract
In this study, chemical profiles for two co-existing deep-sea-derived Penicillium fungal strains were thoroughly investigated. Two new compounds and 11 known compounds were identified from Penicillium sp. LXY140-R, while one new compound and 12 known compounds were isolated from Penicillium sp. LXY140-3. Their structures were elucidated by extensive 1D and 2D NMR experiments, which were supported by HR-ESI-MS data. The antiproliferative activities of all isolates against HCT-116, A549 and Bel-7402 cell lines were also evaluated. Compounds 2, 5, 6, 10 and 13 showed potent antiproliferative activity. To reveal the metabolic relationship of the two strains, we conducted co-culture experiments to discover cross-talk molecules by a device that allows only small molecule to communicate. Extensive HPLC/MS2 experiments were applied to identify the disturbance of the chemical profiles within the synthetic Penicillium-Penicillium community. The fungal strain LXY140-R was found to accumulate mono or multiple-acetylation derivatives of deoxynivalenol (DON) sesquiterpenes as responsible molecules by the disturbance of the metabolites produced by the LXY140-3 strain.
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Affiliation(s)
- Xuanyi Li
- Ocean College, Zhejiang University, Zhoushan, 321000, China
| | - Yichao Ge
- Ocean College, Zhejiang University, Zhoushan, 321000, China
| | - Yihan Ma
- Ocean College, Zhejiang University, Zhoushan, 321000, China
| | - Shoubao Wang
- Beijing Key Laboratory of Drug Target and Screening Research, Beijing, 100050, China
| | - Sihui Li
- Ocean College, Zhejiang University, Zhoushan, 321000, China
| | - Qizhao Yin
- Ocean College, Zhejiang University, Zhoushan, 321000, China
| | - Xiaowan Liu
- Ocean College, Zhejiang University, Zhoushan, 321000, China.,The State Key Laboratory of Marine Pollution and Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Jihua Wie
- Ocean College, Zhejiang University, Zhoushan, 321000, China
| | - Xiaodan Wu
- Center of Analysis, Zhejiang University, Hangzhou, 310058, China
| | - Bin Wu
- Ocean College, Zhejiang University, Zhoushan, 321000, China
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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
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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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27
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Zhao WY, Sun CP, Chang YB, Wang WY, Yan JK, Lv X, Wang C, Ma XC. Unprecedented diterpenoid dimers with soluble epoxide hydrolase inhibitory effect from Euphorbia fischeriana. Org Biomol Chem 2022; 20:2508-2517. [PMID: 35266497 DOI: 10.1039/d2ob00053a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Biseuphoids A (1) and B (2), two unprecedented ent-abietane-type diterpenoid dimers linked by monomeric blocks through C-17-C-12' and C-17-C-11', respectively, were isolated from Euphorbia fischeriana, along with their biogenesis related diterpenoid monomers, 17-hydroxyjolkinolide B (3), caudicifolin (4), and fischeriabietane C (5). Their structures were elucidated by extensive spectroscopy assisted by quantum chemical NMR and ECD calculations. The unusual dimeric skeletons are possibly derived from the adduct of diterpenoid monomers through Michael-like reactions. The novel dimers 1 and 2 exhibited inhibitory activities on soluble epoxide hydrolase (sEH) with IC50 values of 8.17 and 5.61 μM, respectively. Molecular dynamics studies illustrated that both 1 and 2 can occupy the catalytic pocket of sEH by forming stable hydrogen bonds with the key amino acid residues including Gln384, Asn378, Pro361, Ala365, Asn366, and Asn472.
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Affiliation(s)
- Wen-Yu Zhao
- College of Pharmacy, College (Institute) of Integrative Medicine, Dalian Medical University, Dalian 116044, China.
| | - Cheng-Peng Sun
- College of Pharmacy, College (Institute) of Integrative Medicine, Dalian Medical University, Dalian 116044, China.
| | - Yi-Bo Chang
- College of Pharmacy, College (Institute) of Integrative Medicine, Dalian Medical University, Dalian 116044, China. .,Pharmaceutical Research Center, Second Affiliated Hospital, Dalian Medical University, Dalian 116027, China.
| | - Wei-Yi Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Jian-Kun Yan
- Analysis Center of College of Science & Technology, Hebei Agricultural University, Cangzhou, China
| | - Xia Lv
- College of Pharmacy, College (Institute) of Integrative Medicine, Dalian Medical University, Dalian 116044, China.
| | - Chao Wang
- College of Pharmacy, College (Institute) of Integrative Medicine, Dalian Medical University, Dalian 116044, China.
| | - Xiao-Chi Ma
- Pharmaceutical Research Center, Second Affiliated Hospital, Dalian Medical University, Dalian 116027, China.
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Stückrath JB, Gasevic T, Bursch M, Grimme S. Benchmark Study on the Calculation of 119Sn NMR Chemical Shifts. Inorg Chem 2022; 61:3903-3917. [PMID: 35180346 DOI: 10.1021/acs.inorgchem.1c03453] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A new benchmark set termed SnS51 for assessing quantum chemical methods for the computation of 119Sn NMR chemical shifts is presented. It covers 51 unique 119Sn NMR chemical shifts for a selection of 50 tin compounds with diverse bonding motifs and ligands. The experimental reference data are in the spectral range of ±2500 ppm measured in seven different solvents. Fifteen common density functional approximations, two scalar- and one spin-orbit relativistic approach are assessed based on conformer ensembles generated using the CREST/CENSO scheme and state-of-the-art semiempirical (GFN2-xTB), force field (GFN-FF), and composite DFT methods (r2SCAN-3c). Based on the results of this study, the spin-orbit relativistic method combinations of SO-ZORA with PBE0 or revPBE functionals are generally recommended. Both yield mean absolute deviations from experimental data below 100 ppm and excellent linear regression determination coefficients of ≤0.99. If spin-orbit calculations are not affordable, the use of SR-ZORA with B3LYP or X2C with ωB97X or M06 may be considered to obtain qualitative predictions if no severe spin-orbit effects, for example, due to heavy nuclei containing ligands, are expected. An empirical linear scaling correction is demonstrated to be applicable for further improvement, and respective empirical parameters are given. Conformational effects on chemical shifts are studied in detail but are mostly found to be small. However, in specific cases when the ligand sphere differs substantially between conformers, chemical shifts can change by up to several hundred ppm.
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Affiliation(s)
- Julius B Stückrath
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Thomas Gasevic
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Markus Bursch
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
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Schattenberg CJ, Kaupp M. Extended Benchmark Set of Main-Group Nuclear Shielding Constants and NMR Chemical Shifts and Its Use to Evaluate Modern DFT Methods. J Chem Theory Comput 2021; 17:7602-7621. [PMID: 34797677 DOI: 10.1021/acs.jctc.1c00919] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An extended theoretical benchmark set, NS372, for light main-group nuclear shieldings and NMR shifts has been constructed based on high-level GIAO-CCSD(T)/pcSseg-3//CCSD(T)/cc-pVQZ reference data. After removal of the large static-correlation cases O3, F3-, and BH from the statistical evaluations for the 17O, 19F, and 11B subsets, the benchmark comprises overall 372 shielding values in 117 molecules with a wide range of electronic-structure situations, containing 124 1H, 14 11B, 93 13C, 43 15N, 31 17O, 47 19F, 14 31P, and 6 33S shielding constants. The CCSD(T)/pcSseg-3 data are shown to be close to the basis-set and method limit and thus provide an excellent benchmark to evaluate more approximate methods, such as density functional approaches. This dataset has been used to evaluate Hartree-Fock (HF) and MP2, and a wide range of exchange-correlation functionals from local density approximation (LDA) to generalized gradient approximations (GGAs) and meta-GGAs (focusing on their current-density functional implementations), as well as global hybrid, range-separated hybrid, local hybrid, and double-hybrid functionals. Starting with absolute shielding constants, the DSD-PBEP86 double hybrid is confirmed to provide the highest accuracy, with an aggregate relative mean absolute error (rel. MAE) of only 0.9%, followed by MP2 (1.1%). MP2 and double hybrids only show larger errors for a few systems with the largest static-correlation effects. The double-hybrid B2GP-PLYP, the two local hybrids cLH12ct-SsirPW92 and cLH12ct-SsifPW92, and the current-density functional meta-GGA cB97M-V follow closely behind (all 1.5%), as do some further functionals, cLH20t and cMN15-L (both 1.6%), as well as B2PLYP and KT3 (both 2.0%). Functionals on the lower rungs of the usual ladder offer the advantage of lower computational cost and access to larger molecules. Closer examination also reveals the best-performing methods for individual nuclei in the test set. Different ways of treating τ-dependent functionals are evaluated. When moving from absolute shielding constants to chemical shifts, some of the methods can benefit from systematic error compensation, and the overall error range somewhat narrows. Further methods now achieve the 2% threshold of relative MAEs, including functionals based on TPSS (TPSSh, cmPSTS).
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Affiliation(s)
- Caspar Jonas Schattenberg
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Martin Kaupp
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Straße des 17. Juni 135, D-10623 Berlin, Germany
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