1
|
Grazioli L, Schleicher LT, Stopkowicz S, Gauss J. Theoretical prediction of closed-shell paramagnetism for scandium and yttrium hydride. J Comput Chem 2024; 45:1215-1223. [PMID: 38334014 DOI: 10.1002/jcc.27305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/19/2023] [Accepted: 12/23/2023] [Indexed: 02/10/2024]
Abstract
Following chemical intuition, one would expect that all closed-shell molecules are diamagnetic. However, it is known that this is not the case for some second-row hydrides with low-lying unoccupied π orbitals due to an unquenching of the total angular momentum in the presence of an external magnetic field. In this article, the transition-metal hydrides ScH and YH are investigated, assuming a similar unquenching effect involving low-lying unoccupied π and δ orbitals formed from the metal d orbitals rather than the p orbitals. We are comparing results obtained with various quantum-chemical methods (HF, CCSD, CCSD(T), CCSDT) and basis sets. The obtained positive values for the magnetizabilities clearly indicate paramagnetic behavior. Vibrational effects on the magnetizability tensor are also considered, but these effects are small and do not change the overall conclusion that both ScH and YH are further examples for closed-shell paramagnetism.
Collapse
Affiliation(s)
- Laura Grazioli
- Department Chemie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Luca T Schleicher
- Department Chemie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Stella Stopkowicz
- Fachrichtung Chemie, Universität des Saarlandes, Saarbrücken, Germany
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, Oslo, Norway
| | - Jürgen Gauss
- Department Chemie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| |
Collapse
|
2
|
Schattenberg C, Kaupp M. Implementation and First Evaluation of Strong-Correlation-Corrected Local Hybrid Functionals for the Calculation of NMR Shieldings and Shifts. J Phys Chem A 2024; 128:2253-2271. [PMID: 38456430 PMCID: PMC10961831 DOI: 10.1021/acs.jpca.3c08507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 03/09/2024]
Abstract
Local hybrid functionals containing strong-correlation factors (scLHs) and range-separated local hybrids (RSLHs) have been integrated into an efficient coupled-perturbed Kohn-Sham implementation for the calculation of nuclear shielding constants. Several scLHs and the ωLH22t RSLH have then been evaluated for the first time for the extended NS372 benchmark set of main-group shieldings and shifts and the TM70 benchmark of 3d transition-metal shifts. The effects of the strong-correlation corrections have been analyzed with respect to the spatial distribution of the sc-factors, which locally diminish exact-exchange admixture at certain regions in a molecule. The scLH22t, scLH23t-mBR, and scLH23t-mBR-P functionals, which contain a "damped" strong-correlation factor to retain the excellent performance of the underlying LH20t functional for weakly correlated situations, tend to make smaller corrections to shieldings and shifts than the "undamped" scLH22ta functional. While the latter functional can also deteriorate agreement with the reference data in certain weakly correlated cases, it provides overall better performance, in particular for systems where static correlation is appreciable. This pertains only to a minority of systems in the NS372 main-group test set but to many more systems in the TM70 transition-metal test set, in particular for high-oxidation-state complexes, e.g., Cr(+VI) complexes and other systems with stretched bonds. Another undamped scLH, the simpler LDA-based scLH21ct-SVWN-m, also tends to provide significant improvements in many cases. The differences between the functionals and species can be rationalized on the basis of one-dimensional plots of the strong-correlation factors, augmented by isosurface plots of the fractional orbital density (FOD). Position-dependent exact-exchange admixture is thus shown to provide substantial flexibility in treating response properties like NMR shifts for both weakly and strongly correlated systems.
Collapse
Affiliation(s)
- Caspar
Jonas Schattenberg
- Research
Unit of Structural Chemistry & Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie
(FMP), Robert-Roessle-Str.
10, 13125 Berlin, Germany
| | - Martin Kaupp
- Institut
für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, D-10623 Berlin, Germany
| |
Collapse
|
3
|
Kleine Büning JB, Grimme S, Bursch M. Machine learning-based correction for spin-orbit coupling effects in NMR chemical shift calculations. Phys Chem Chem Phys 2024; 26:4870-4884. [PMID: 38230684 DOI: 10.1039/d3cp05556f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
As one of the most powerful analytical methods for molecular and solid-state structure elucidation, NMR spectroscopy is an integral part of chemical laboratories associated with a great research interest in its computational simulation. Particularly when heavy atoms are present, a relativistic treatment is essential in the calculations as these influence also the nearby light atoms. In this work, we present a Δ-machine learning method that approximates the contribution to 13C and 1H NMR chemical shifts that stems from spin-orbit (SO) coupling effects. It is built on computed reference data at the spin-orbit zeroth-order regular approximation (ZORA) DFT level for a set of 6388 structures with 38 740 13C and 64 436 1H NMR chemical shifts. The scope of the methods covers the 17 most important heavy p-block elements that exhibit heavy atom on the light atom (HALA) effects to covalently bound carbon or hydrogen atoms. Evaluated on the test data set, the approach is able to recover roughly 85% of the SO contribution for 13C and 70% for 1H from a scalar-relativistic PBE0/ZORA-def2-TZVP calculation at virtually no extra computational costs. Moreover, the method is transferable to other baseline DFT methods even without retraining the model and performs well for realistic organotin and -lead compounds. Finally, we show that using a combination of the new approach with our previous Δ-ML method for correlation contributions to NMR chemical shifts, the mean absolute NMR shift deviations from non-relativistic DFT calculations to experimental values can be halved.
Collapse
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.
| | - Markus Bursch
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
| |
Collapse
|
4
|
Changala PB, Franke PR, Stanton JF, Ellison GB, McCarthy MC. Direct Probes of π-Delocalization in Prototypical Resonance-Stabilized Radicals: Hyperfine-Resolved Microwave Spectroscopy of Isotopic Propargyl and Cyanomethyl. J Am Chem Soc 2024; 146:1512-1521. [PMID: 38170910 DOI: 10.1021/jacs.3c11220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Delocalization of the unpaired electron in π-conjugated radicals has profound implications for their chemistry, but direct and quantitative characterization of this electronic structure in isolated molecules remains challenging. We apply hyperfine-resolved microwave rotational spectroscopy to rigorously probe π-delocalization in propargyl, CH2CCH, a prototypical resonance-stabilized radical and key reactive intermediate. Using the spectroscopic constants derived from the high-resolution cavity Fourier transform microwave measurements of an exhaustive set of 13C- and 2H-substituted isotopologues, together with high-level ab initio calculations of zero-point vibrational effects, we derive its precise semiexperimental equilibrium geometry and quantitatively characterize the spatial distribution of its unpaired electron. Our results highlight the importance of considering both spin-polarization and orbital-following contributions when interpreting the isotropic hyperfine coupling constants of π radicals. These physical insights are strengthened by a parallel analysis of the isoelectronic species cyanomethyl, CH2CN, using new 13C measurements also reported in this work. A detailed comparison of the structure and electronic properties of propargyl, cyanomethyl, and other closely related species allows us to correlate trends in their chemical bonding and electronic structure with critical changes in their reactivity and thermochemistry.
Collapse
Affiliation(s)
- P Bryan Changala
- Center for Astrophysics|Harvard & Smithsonian, Cambridge, Massachusetts 02138, United States
| | - Peter R Franke
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - John F Stanton
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - G Barney Ellison
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Michael C McCarthy
- Center for Astrophysics|Harvard & Smithsonian, Cambridge, Massachusetts 02138, United States
| |
Collapse
|
5
|
Wilson DJD. Extreme NMR shielding in fluoro-nitrogen cations. Phys Chem Chem Phys 2023; 25:25420-25434. [PMID: 37706351 DOI: 10.1039/d3cp03399f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
The structure and NMR shielding of a set of N-F containing cations is reported to near-quantitative accuracy from extensive ab initio calculations. Currently, the shortest experimentally confirmed N-F bond is 1.2461(10) Å in NNF+, however CCSD(T)-F12b/cc-pVQZ-F12 optimised geometries suggest that even shorter N-F bonds are possible for both monocations (1.236 Å, HNF+) and dications (1.098 Å, NF2+). NMR shielding constants have been calculated in a composite manner with individual components from coupled-cluster expansions up to CCSDTQP and basis sets up to aug-cc-pCV8Z, together with vibrational and relativistic corrections. 15N and 19F NMR chemical shifts correlate well with available experimental data. Extreme 19F chemical shifts are predicted for HNF+ (1628.9 ppm) and NH2F2+ (1298.0 ppm), which are by far the largest 19F chemical shifts ever reported and well outside the known range of +865 ppm (F2O2) to -448 ppm (ClF). The 15N chemical shift of -1283.07 ppm in HNF+ is similarly extreme, being well outside the known range of 15N chemical shifts of -730 to 260 ppm (CH3NO2 reference). This work highlights the application of state-of-the-art theoretical techniques, and provides accurate NMR properties of both isolated and yet unknown N-F cations, which can serve to guide and supplement NMR experimentation.
Collapse
Affiliation(s)
- David J D Wilson
- Department of Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Melosso M, Jiang N, Gauss J, Puzzarini C. Hyperfine-resolved spectra of HDS together with a global ro-vibrational analysis. J Chem Phys 2023; 158:2888208. [PMID: 37139997 DOI: 10.1063/5.0148810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/17/2023] [Indexed: 05/05/2023] Open
Abstract
Despite their chemical simplicity, the spectroscopic investigation of light hydrides, such as hydrogen sulfide, is challenging due to strong hyperfine interactions and/or anomalous centrifugal-distortion effects. Several hydrides have already been detected in the interstellar medium, and the list includes H2S and some of its isotopologues. Astronomical observation of isotopic species and, in particular, those bearing deuterium is important to gain insights into the evolutionary stage of astronomical objects and to shed light on interstellar chemistry. These observations require a very accurate knowledge of the rotational spectrum, which is so far limited for mono-deuterated hydrogen sulfide, HDS. To fill this gap, high-level quantum-chemical calculations and sub-Doppler measurements have been combined for the investigation of the hyperfine structure of the rotational spectrum in the millimeter- and submillimeter-wave region. In addition to the determination of accurate hyperfine parameters, these new measurements together with the available literature data allowed us to extend the centrifugal analysis using a Watson-type Hamiltonian and a Hamiltonian-independent approach based on the Measured Active Ro-Vibrational Energy Levels (MARVEL) procedure. The present study thus permits to model the rotational spectrum of HDS from the microwave to far-infrared region with great accuracy, thereby accounting for the effect of the electric and magnetic interactions due to the deuterium and hydrogen nuclei.
Collapse
Affiliation(s)
- Mattia Melosso
- Dipartimento di Chimica "Giacomo Ciamician," Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Ningjing Jiang
- Dipartimento di Chimica "Giacomo Ciamician," Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Jürgen Gauss
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician," Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| |
Collapse
|
8
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| | | | | |
Collapse
|
9
|
Jackowski K, Słowiński MA. Searching for the Best Values of NMR Shielding and Spin-Spin Coupling Parameters: CH 4-nF n Series of Molecules as the Example. Molecules 2023; 28:molecules28031499. [PMID: 36771162 PMCID: PMC9919152 DOI: 10.3390/molecules28031499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/20/2023] [Accepted: 01/28/2023] [Indexed: 02/09/2023] Open
Abstract
Attempts at the theoretical interpretation of NMR spectra have a very long and fascinating history. Present quantum chemical calculations of shielding and indirect spin-spin couplings permit modeling NMR spectra when small, isolated molecules are studied. Similar data are also available from NMR experiments if investigations are performed in the gas phase. An interesting set of molecules is formed when a methane molecule is sequentially substituted by fluorine atoms-CH4-nFn, where n = 0, 1, 2, 3, or 4. The small molecules contain up to three magnetic nuclei, each with a one-half spin number. The spectral parameters of CH4-nFn can be easily observed in the gas phase and calculated with high accuracy using the most advanced ab initio methods of quantum chemistry. However, the presence of fluorine atoms makes the calculations of shielding and spin-spin coupling constants extremely demanding. Appropriate experimental 19F NMR parameters are good but also require some further improvements. Therefore, there is a real need for the comparison of existing NMR measurements with available state-of-the-art theoretical results for a better understanding of actual limits in the determination of the best shielding and spin-spin coupling values, and CH4-nFn molecules are used here as the exceptionally important case.
Collapse
|
10
|
Fernández-Alarcón A, Autschbach J. Relativistic Density Functional NMR Tensors Analyzed with Spin-free Localized Molecular Orbitals. Chemphyschem 2023; 24:e202200667. [PMID: 36169984 DOI: 10.1002/cphc.202200667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/21/2022] [Indexed: 01/07/2023]
Abstract
The implementation of fast relativistic methods based on density functional theory, in conjunction with localized molecular orbital (LMO) based analysis, allows straightforward interpretations of NMR parameters in terms of contributions from core shells, lone pairs, and bonds, for compounds containing elements from across the periodic table. We present a conceptual review of a frequently used LMO analysis of NMR parameters calculated in the presence of spin-orbit interactions and other relativistic effects. An accompanying example focuses on the 15 N shielding in a heavy metal complex.
Collapse
Affiliation(s)
- Alberto Fernández-Alarcón
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, NY 14260-3000, USA
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, NY 14260-3000, USA
| |
Collapse
|
11
|
Yesiltepe Y, Govind N, Metz TO, Renslow RS. An initial investigation of accuracy required for the identification of small molecules in complex samples using quantum chemical calculated NMR chemical shifts. J Cheminform 2022; 14:64. [PMID: 36138446 PMCID: PMC9499888 DOI: 10.1186/s13321-022-00587-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/06/2022] [Indexed: 11/24/2022] Open
Abstract
The majority of primary and secondary metabolites in nature have yet to be identified, representing a major challenge for metabolomics studies that currently require reference libraries from analyses of authentic compounds. Using currently available analytical methods, complete chemical characterization of metabolomes is infeasible for both technical and economic reasons. For example, unambiguous identification of metabolites is limited by the availability of authentic chemical standards, which, for the majority of molecules, do not exist. Computationally predicted or calculated data are a viable solution to expand the currently limited metabolite reference libraries, if such methods are shown to be sufficiently accurate. For example, determining nuclear magnetic resonance (NMR) spectroscopy spectra in silico has shown promise in the identification and delineation of metabolite structures. Many researchers have been taking advantage of density functional theory (DFT), a computationally inexpensive yet reputable method for the prediction of carbon and proton NMR spectra of metabolites. However, such methods are expected to have some error in predicted 13C and 1H NMR spectra with respect to experimentally measured values. This leads us to the question–what accuracy is required in predicted 13C and 1H NMR chemical shifts for confident metabolite identification? Using the set of 11,716 small molecules found in the Human Metabolome Database (HMDB), we simulated both experimental and theoretical NMR chemical shift databases. We investigated the level of accuracy required for identification of metabolites in simulated pure and impure samples by matching predicted chemical shifts to experimental data. We found 90% or more of molecules in simulated pure samples can be successfully identified when errors of 1H and 13C chemical shifts in water are below 0.6 and 7.1 ppm, respectively, and below 0.5 and 4.6 ppm in chloroform solvation, respectively. In simulated complex mixtures, as the complexity of the mixture increased, greater accuracy of the calculated chemical shifts was required, as expected. However, if the number of molecules in the mixture is known, e.g., when NMR is combined with MS and sample complexity is low, the likelihood of confident molecular identification increased by 90%.
Collapse
Affiliation(s)
- Yasemin Yesiltepe
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Niranjan Govind
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas O Metz
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA
| | - Ryan S Renslow
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA. .,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| |
Collapse
|
12
|
Begam K, Cohen L, Goobes G, Dunietz BD. Solvent Dependent Nuclear Magnetic Resonance Molecular Parameters Based on a Polarization Consistent Screened Range Separated Hybrid Density Functional Theory Framework. J Chem Theory Comput 2022; 18:5259-5266. [PMID: 35929782 DOI: 10.1021/acs.jctc.2c00275] [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) properties of solvated molecules are significantly affected by the solvent. We, therefore, employ a polarization consistent framework that efficiently addresses the solvent polarizing environment effects. Toward this goal a dielectric screened range separated hybrid (SRSH) functional is invoked with a polarizable continuum model (PCM) to properly represent the orbital gap in the condensed phase. We build on the success of range separated hybrid (RSH) functionals to address the erroneous tendency of traditional density functional theory (DFT) to collapse the orbital gap. Recently, the impact of RSH that properly opens up the orbital gap in gas-phase calculations on NMR properties has been assessed. Here, we report the use of SRSH-PCM that produces properly solute orbital gaps in calculating isotropic nuclear magnetic shielding and chemical shift parameters of molecular systems in the condensed phase. We show that in contrast to simpler DFT-PCM approaches, SRSH-PCM successfully follows expected dielectric constant trends.
Collapse
Affiliation(s)
- Khadiza Begam
- Department of Physics, Kent State University, Kent, Ohio 44242, United States
| | - Lilian Cohen
- Department of Chemistry and Institute for Nanotechnology and Advanced Materials Bar Ilan University, Ramat Gan 5290002, Israel
| | - Gil Goobes
- Department of Chemistry and Institute for Nanotechnology and Advanced Materials Bar Ilan University, Ramat Gan 5290002, Israel
| | - Barry D Dunietz
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| |
Collapse
|
13
|
Quantum Chemical Approaches to the Calculation of NMR Parameters: From Fundamentals to Recent Advances. MAGNETOCHEMISTRY 2022. [DOI: 10.3390/magnetochemistry8050050] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Quantum chemical methods for the calculation of indirect NMR spin–spin coupling constants and chemical shifts are always in progress. They never stay the same due to permanently developing computational facilities, which open new perspectives and create new challenges every now and then. This review starts from the fundamentals of the nonrelativistic and relativistic theory of nuclear magnetic resonance parameters, and gradually moves towards the discussion of the most popular common and newly developed methodologies for quantum chemical modeling of NMR spectra.
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Makulski W. Absolute 13C Nuclear Magnetic Shielding of Simple Isolated Molecules from Gas Phase Measurements. Phys Chem Chem Phys 2022; 24:8950-8961. [DOI: 10.1039/d2cp00231k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The new experimental value of 13C absolute shielding constant in an isolated 13CO molecule was evaluated from the 13C and 3He gas phase NMR measurements performed for 3He/13CO mixtures. The...
Collapse
|
17
|
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: 32] [Impact Index Per Article: 10.7] [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).
Collapse
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
| |
Collapse
|
18
|
Borges R, Colby SM, Das S, Edison AS, Fiehn O, Kind T, Lee J, Merrill AT, Merz KM, Metz TO, Nunez JR, Tantillo DJ, Wang LP, Wang S, Renslow RS. Quantum Chemistry Calculations for Metabolomics. Chem Rev 2021; 121:5633-5670. [PMID: 33979149 PMCID: PMC8161423 DOI: 10.1021/acs.chemrev.0c00901] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 02/07/2023]
Abstract
A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.
Collapse
Affiliation(s)
- Ricardo
M. Borges
- Walter
Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Sean M. Colby
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Susanta Das
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Arthur S. Edison
- Departments
of Genetics and Biochemistry and Molecular Biology, Complex Carbohydrate
Research Center and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - Oliver Fiehn
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Tobias Kind
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Jesi Lee
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Amy T. Merrill
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Kenneth M. Merz
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Thomas O. Metz
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Jamie R. Nunez
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Shunyang Wang
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Ryan S. Renslow
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| |
Collapse
|
19
|
Rusakova IL, Rusakov YY. Quantum chemical calculations of 77 Se and 125 Te nuclear magnetic resonance spectral parameters and their structural applications. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:359-407. [PMID: 33095923 DOI: 10.1002/mrc.5111] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/01/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
An accurate quantum chemical (QC) modeling of 77 Se and 125 Te nuclear magnetic resonance (NMR) spectra is deeply involved in the NMR structural assignment for selenium and tellurium compounds that are of utmost importance both in organic and inorganic chemistry nowadays due to their huge application potential in many fields, like biology, medicine, and metallurgy. The main interest of this review is focused on the progress in QC computations of 77 Se and 125 Te NMR chemical shifts and indirect spin-spin coupling constants involving these nuclei. Different computational methodologies that have been used to simulate the NMR spectra of selenium and tellurium compounds since the middle of the 1990s are discussed with a strong emphasis on their accuracy. A special accent is placed on the calculations resorting to the relativistic methodologies, because taking into account the relativistic effects appreciably influences the precision of NMR calculations of selenium and, especially, tellurium compounds. Stereochemical applications of quantum chemical calculations of 77 Se and 125 Te NMR parameters are discussed so as to exemplify the importance of integrated approach of experimental and computational NMR techniques.
Collapse
Affiliation(s)
- Irina L Rusakova
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russian Federation
| | - Yuriy Yu Rusakov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russian Federation
| |
Collapse
|
20
|
Schattenberg CJ, Kaupp M. Implementation and Validation of Local Hybrid Functionals with Calibrated Exchange-Energy Densities for Nuclear Shielding Constants. J Phys Chem A 2021; 125:2697-2707. [PMID: 33730855 DOI: 10.1021/acs.jpca.1c01135] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A recently reported coupled-perturbed Kohn-Sham implementation to compute nuclear shielding constants with gauge-including atomic orbitals and local hybrid functionals has been extended to cover higher derivatives of the density in the local mixing function (LMF) of the local hybrid as well as the calibration function (CF) needed to deal with the ambiguity of exchange-energy densities. This allowed the first evaluation of state-of-the-art local hybrids with "calibrated" exchange-energy densities for nuclear shieldings. Compared to previously evaluated simpler local hybrids without a CF, appreciable improvements are found for proton shieldings. Furthermore, the recent LH20t functional is still competitive with the outstanding performance of the uncalibrated LH12ct-SsirSVWN and LH12ct-SsifSVWN LHs for heavier nuclei, suggesting that LH20t is possibly the most robust choice of any rung-four functional for computing the nuclear shieldings of main-group nuclei so far. Interestingly, the presence of a CF in the functional significantly reduces the number of artifacts introduced by the widely used Maximoff-Scuseria framework to treat the local kinetic energy τ. The latter occurs in so-called t-LMFs used in many of the present local hybrids. In any case, the use of Dobson's current-density functional framework is also recommended with more advanced calibrated τ-dependent local hybrid functionals.
Collapse
Affiliation(s)
- Caspar Jonas Schattenberg
- Theoretische Chemie/Quantenchemie, Institut für Chemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Martin Kaupp
- Theoretische Chemie/Quantenchemie, Institut für Chemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, D-10623 Berlin, Germany
| |
Collapse
|
21
|
Jinger R, Fliegl H, Bast R, Dimitrova M, Lehtola S, Sundholm D. Spatial Contributions to Nuclear Magnetic Shieldings. J Phys Chem A 2021; 125:1778-1786. [PMID: 33605721 PMCID: PMC8023705 DOI: 10.1021/acs.jpca.0c10884] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/05/2021] [Indexed: 01/09/2023]
Abstract
We develop a methodology for calculating, analyzing, and visualizing nuclear magnetic shielding densities which are calculated from the current density via the Biot-Savart relation. Atomic contributions to nuclear magnetic shielding constants can be estimated within our framework with a Becke partitioning scheme. The new features have been implemented in the GIMIC program and are applied in this work to the study of the 1H and 13C nuclear magnetic shieldings in benzene (C6H6) and cyclobutadiene (C4H4). The new methodology allows a visual inspection of the spatial origins of the positive (shielding) and negative (deshielding) contributions to the nuclear magnetic shielding constant of a single nucleus, something which has not been hitherto easily accomplished. Analysis of the shielding densities shows that diatropic and paratropic current-density fluxes yield both shielding and deshielding contributions, as the shielding or deshielding is determined by the direction of the current-density flux with respect to the studied nucleus instead of the tropicity. Becke partitioning of the magnetic shieldings shows that the magnetic shielding contributions mainly originate from the studied atom and its nearest neighbors, confirming the localized character of nuclear magnetic shieldings.
Collapse
Affiliation(s)
- Rahul
Kumar Jinger
- Indian
Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Heike Fliegl
- Karlsruhe
Institute of Technology, Institute of Nanotechnology, Hermann-von-Helmholtz Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Radovan Bast
- Department
Information Technology, UiT Arctic University
Norway, Tromsø, Norway
| | - Maria Dimitrova
- Department
of Chemistry, Faculty of Science, University
of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Susi Lehtola
- Department
of Chemistry, Faculty of Science, University
of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
- Molecular
Sciences Software Institute, Blacksburg, Virginia 24061, United States
| | - Dage Sundholm
- Department
of Chemistry, Faculty of Science, University
of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| |
Collapse
|
22
|
Costa FLP, de Albuquerque ACF, Fiorot RG, Lião LM, Martorano LH, Mota GVS, Valverde AL, Carneiro JWM, dos Santos Junior FM. Structural characterisation of natural products by means of quantum chemical calculations of NMR parameters: new insights. Org Chem Front 2021. [DOI: 10.1039/d1qo00034a] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this review, we focus in all aspects of NMR simulation of natural products, from the fundamentals to the new computational toolboxes available, combining advanced quantum chemical calculations with upstream data processing and machine learning.
Collapse
Affiliation(s)
| | - Ana C. F. de Albuquerque
- Departamento de Química Orgânica
- Instituto de Química
- Universidade Federal Fluminense
- Niterói-RJ
- Brazil
| | - Rodolfo G. Fiorot
- Departamento de Química Orgânica
- Instituto de Química
- Universidade Federal Fluminense
- Niterói-RJ
- Brazil
| | - Luciano M. Lião
- Instituto de Química
- Universidade Federal de Goiás
- 74690-900 Goiânia-GO
- Brazil
| | - Lucas H. Martorano
- Departamento de Química Orgânica
- Instituto de Química
- Universidade Federal Fluminense
- Niterói-RJ
- Brazil
| | - Gunar V. S. Mota
- Faculdade de Ciências Naturais/Instituto de Ciências Exatas e Naturais
- Universidade Federal do Pará
- Belém-PA
- Brazil
| | - Alessandra L. Valverde
- Departamento de Química Orgânica
- Instituto de Química
- Universidade Federal Fluminense
- Niterói-RJ
- Brazil
| | - José W. M. Carneiro
- Departamento de Química Inorgânica
- Instituto de Química
- Universidade Federal Fluminense
- Niterói-RJ
- Brazil
| | | |
Collapse
|
23
|
Sethio D, Raggi G, Lindh R, Erdélyi M. Halogen Bond of Halonium Ions: Benchmarking DFT Methods for the Description of NMR Chemical Shifts. J Chem Theory Comput 2020; 16:7690-7701. [PMID: 33136388 PMCID: PMC7726912 DOI: 10.1021/acs.jctc.0c00860] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Indexed: 12/20/2022]
Abstract
Because of their anisotropic electron distribution and electron deficiency, halonium ions are unusually strong halogen-bond donors that form strong and directional three-center, four-electron halogen bonds. These halogen bonds have received considerable attention owing to their applicability in supramolecular and synthetic chemistry and have been intensely studied using spectroscopic and crystallographic techniques over the past decade. Their computational treatment faces different challenges to those of conventional weak and neutral halogen bonds. Literature studies have used a variety of wave functions and DFT functionals for prediction of their geometries and NMR chemical shifts, however, without any systematic evaluation of the accuracy of these methods being available. In order to provide guidance for future studies, we present the assessment of the accuracy of 12 common DFT functionals along with the Hartree-Fock (HF) and the second-order Møller-Plesset perturbation theory (MP2) methods, selected from an initial set of 36 prescreened functionals, for the prediction of 1H, 13C, and 15N NMR chemical shifts of [N-X-N]+ halogen-bond complexes, where X = F, Cl, Br, and I. Using a benchmark set of 14 complexes, providing 170 high-quality experimental chemical shifts, we show that the choice of the DFT functional is more important than that of the basis set. The M06 functional in combination with the aug-cc-pVTZ basis set is demonstrated to provide the overall most accurate NMR chemical shifts, whereas LC-ωPBE, ωB97X-D, LC-TPSS, CAM-B3LYP, and B3LYP to show acceptable performance. Our results are expected to provide a guideline to facilitate future developments and applications of the [N-X-N]+ halogen bond.
Collapse
Affiliation(s)
- Daniel Sethio
- Department of Chemistry—BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Gerardo Raggi
- Department of Chemistry—BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Roland Lindh
- Department of Chemistry—BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Máté Erdélyi
- Department of Chemistry—BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| |
Collapse
|
24
|
Santa Cruz T, Aucar GA. On the invariance of polarization propagators at SOPPA level of approach under unitary transformations of MOs. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.138027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
25
|
Jaszuński M, Sauer SPA, Faber R, Wilson DJD. NMR parameters of FNNF as a test for coupled-cluster methods: CCSDT shielding and CC3 spin-spin coupling. Phys Chem Chem Phys 2020; 22:21350-21359. [PMID: 32936148 DOI: 10.1039/d0cp02730h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
NMR shielding and spin-spin coupling constants of cis and trans isomers of FNNF have been determined to near-quantitative accuracy from ab initio calculations. The FNNF system, containing multiple N-F bonds and fluorine atoms, provides a severe test of computational methods. Coupled-cluster methods were used with large basis sets and complete basis set (CBS) extrapolations of the equilibrium geometry results, with vibrational and relativistic corrections. Shielding constants were calculated with basis sets as large as aug-cc-pCV7Z, together with coupled-cluster expansions up to CCSDT, at the all-electron CCSD(T)/aug-cc-pCVQZ optimized geometries. Spin-spin coupling constants have been determined with specialized versions of the correlation consistent basis sets ccJ-pVXZ, further augmented with diffuse functions. All-electron coupled-cluster methods up to CC3 were applied in these calculations. The results of this work highlight the application of state-of-the-art theoretical techniques, and provide the most accurate NMR properties of FNNF to date, which can serve to guide and supplement NMR experimentation.
Collapse
Affiliation(s)
- Michał Jaszuński
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44-52, 01-224 Warsaw, Poland
| | | | | | | |
Collapse
|
26
|
Auer AA, Tran VA, Sharma B, Stoychev GL, Marx D, Neese F. A case study of density functional theory and domain-based local pair natural orbital coupled cluster for vibrational effects on EPR hyperfine coupling constants: vibrational perturbation theory versus ab initio molecular dynamics. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1797916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
| | - Van Anh Tran
- MPI für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Bikramjit Sharma
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, Bochum, Germany
| | | | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, Bochum, Germany
| | - Frank Neese
- MPI für Kohlenforschung, Mülheim an der Ruhr, Germany
| |
Collapse
|
27
|
Matthews DA, Cheng L, Harding ME, Lipparini F, Stopkowicz S, Jagau TC, Szalay PG, Gauss J, Stanton JF. Coupled-cluster techniques for computational chemistry: The CFOUR program package. J Chem Phys 2020; 152:214108. [DOI: 10.1063/5.0004837] [Citation(s) in RCA: 214] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Devin A. Matthews
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, USA
| | - Lan Cheng
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Michael E. Harding
- Institut für Physikalische Chemie, Karlsruher Institut für Technologie (KIT), Kaiserstr. 12, D-76131 Karlsruhe, Germany
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Stella Stopkowicz
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Thomas-C. Jagau
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Péter G. Szalay
- ELTE Eötvös Loránd University, Institute of Chemistry, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - Jürgen Gauss
- Department Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - John F. Stanton
- Quantum Theory Project, Departments of Chemistry and Physics, University of Florida, Gainesville, Florida 32611, USA
| |
Collapse
|
28
|
Aerts A, Brown A. A revised nuclear quadrupole moment for aluminum: Theoretical nuclear quadrupole coupling constants of aluminum compounds. J Chem Phys 2019; 150:224302. [PMID: 31202232 DOI: 10.1063/1.5097151] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The nuclear quadrupole moment of aluminum (27Al) has been re-evaluated by determining the electric field gradients at this nucleus for AlF and AlCl using the coupled cluster method with single, double, and perturbative triple excitations [CCSD(T)]/aug-cc-pwCVXZ (X = T and Q) accounting for both vibrational averaging and core-core/core-valence electron correlation and then comparing to the experimentally measured nuclear quadrupole coupling constants (NQCCs). The new recommended value is Q(27Al) = 148.2 ± 0.5 mb, which can be compared to the previous value of 146.6 ± 1 mb. Using the new value of the nuclear quadrupole moment, the accuracy is assessed for several computational approaches [i.e., Hartree-Fock, Møller-Plesset perturbation theory to the second order, quadratic configuration interaction with single and double excitations, CCSD, CCSD(T), and density functional theory (DFT) with the B3LYP, PBE0, and M06-2X functionals] and basis sets (the aug-cc-pVXZ and aug-cc-pwCVXZ families) for determining the nuclear quadruple coupling constants for AlCN, AlNC, AlSH, AlOH, and AlCCH, where experimental measurements are available. From the results at equilibrium geometries of the polyatomic molecules, it has been determined that (i) the CCSD(T)/aug-cc-pwCVXZ approach is needed to obtain results within 4% of the experimental measurements, (ii) typical DFT values are only within 10%-15% of the experimental measurements, and (iii) the aug-cc-pVXZ family of basis sets is not recommended for computing the electric field gradients at aluminum. The present results also suggest that the NQCC for AlOH should be remeasured. Using the recommended CCSD(T)/aug-cc-pwCVXZ approach, the equilibrium geometries and corresponding NQCCs for AlCH3 and AlCCCN were determined, and the NQCCs are in excellent agreement with previously reported experimental values.
Collapse
Affiliation(s)
- Antoine Aerts
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| |
Collapse
|
29
|
Wang K, Sun M, Cui D, Shen T, Wu A, Xu X. Accurate prediction of nuclear magnetic resonance shielding constants: An extension of the focal-point analysis method for magnetic parameter calculations (FPA-M) with improved efficiency. J Chem Phys 2018; 149:184101. [PMID: 30441917 DOI: 10.1063/1.5041979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Previously, we have proposed a method, FPA-M, for focal-point analysis of magnetic parameter calculations [Sun et al., J. Chem. Phys. 138, 124113 (2013)], where the shielding constants at equilibrium geometries σe are calculated with the second order Møller-Plesset perturbation (MP2) approach, which are extrapolated to the complete basis set (CBS) limit and then augmented by the [σe(CCSD(T)) - σe(MP2)] difference at a valence triple-ζ (VTZ) basis set, where CCSD(T) stands for the coupled cluster singles and doubles model with a perturbative correction for triple excitations. This FPA-M(MP2) method provides satisfactory results to approach to the corresponding CCSD(T)/CBS values for elements of the first two rows in the periodic tables. A series of extensions have been explored here, which replace the MP2/CBS with the Hartree-Fock (HF)/CBS for efficiency. In particular, the [σe(CCSD(T)) - σe(MP2)] VTZ difference is replaced by a step-wise correction from the [σe(CCSD(T)) - σe(MP2)] difference at a valence double-ζ basis set plus the [σe(MP2) - σe(HF)] VTZ difference, leading to a new scheme, denoted here as FPA-M(HF'). A systematical comparison has demonstrated that the FPA-M(HF') method provides an excellent balance between accuracy and efficiency, which makes routinely accurate calculations of the shielding constants for medium-sized organic molecules and biomolecules feasible.
Collapse
Affiliation(s)
- Kangli Wang
- Department of Chemistry, College of Chemistry and Chemical Engineering, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 361005, China
| | - Meng Sun
- Department of Chemistry, College of Chemistry and Chemical Engineering, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 361005, China
| | - Deng Cui
- Department of Chemistry, College of Chemistry and Chemical Engineering, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 361005, China
| | - Tonghao Shen
- MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Anan Wu
- Department of Chemistry, College of Chemistry and Chemical Engineering, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 361005, China
| | - Xin Xu
- MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China
| |
Collapse
|
30
|
Rusakov YY, Rusakova IL, Krivdin LB. Relativistic heavy atom effect on the 31 P NMR parameters of phosphine chalcogenides. Part 1. Chemical shifts. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:1061-1073. [PMID: 29775489 DOI: 10.1002/mrc.4752] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/27/2018] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
Four-component density functional theory calculations of 31 P NMR chemical shifts have been performed for the representative series of 56 phosphine chalcogenides in order to investigate an influence of different functional groups on the heavy atom relativistic effect on the NMR chemical shifts of light phosphorous atoms (Heavy Atom on Light Atom effect). The validity of the 4-component density functional theory approach used for the wide-scale calculations of the phosphorous chemical shifts in a wide series of phosphine chalcogenides has been confirmed on a small series of 5 representative compounds with the aid of high-quality coupled cluster singles and doubles calculations taking into account solvent, vibrational, and the relativistic corrections in comparison with the experiment.
Collapse
Affiliation(s)
- Yury Yu Rusakov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033, Irkutsk, Russia
| | - Irina L Rusakova
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033, Irkutsk, Russia
| | - Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033, Irkutsk, Russia
| |
Collapse
|
31
|
An automated framework for NMR chemical shift calculations of small organic molecules. J Cheminform 2018; 10:52. [PMID: 30367288 PMCID: PMC6755567 DOI: 10.1186/s13321-018-0305-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/09/2018] [Indexed: 12/04/2022] Open
Abstract
When using nuclear magnetic resonance (NMR) to assist in chemical identification in complex samples, researchers commonly rely on databases for chemical shift spectra. However, authentic standards are typically depended upon to build libraries experimentally. Considering complex biological samples, such as blood and soil, the entirety of NMR spectra required for all possible compounds would be infeasible to ascertain due to limitations of available standards and experimental processing time. As an alternative, we introduce the in silico Chemical Library Engine (ISiCLE) NMR chemical shift module to accurately and automatically calculate NMR chemical shifts of small organic molecules through use of quantum chemical calculations. ISiCLE performs density functional theory (DFT)-based calculations for predicting chemical properties—specifically NMR chemical shifts in this manuscript—via the open source, high-performance computational chemistry software, NWChem. ISiCLE calculates the NMR chemical shifts of sets of molecules using any available combination of DFT method, solvent, and NMR-active nuclei, using both user-selected reference compounds and/or linear regression methods. Calculated NMR chemical shifts are provided to the user for each molecule, along with comparisons with respect to a number of metrics commonly used in the literature. Here, we demonstrate ISiCLE using a set of 312 molecules, ranging in size up to 90 carbon atoms. For each, calculation of NMR chemical shifts have been performed with 8 different levels of DFT theory, and with solvation effects using the implicit solvent Conductor-like Screening Model. The DFT method dependence of the calculated chemical shifts have been systematically investigated through benchmarking and subsequently compared to experimental data available in the literature. Furthermore, ISiCLE has been applied to a set of 80 methylcyclohexane conformers, combined via Boltzmann weighting and compared to experimental values. We demonstrate that our protocol shows promise in the automation of chemical shift calculations and, ultimately, the expansion of chemical shift libraries.
![]()
Collapse
|
32
|
Rusakov YY, Rusakova IL. Relativistic heavy atom effect on 13 C NMR chemical shifts initiated by adjacent multiple chalcogens. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:716-726. [PMID: 29412478 DOI: 10.1002/mrc.4720] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/21/2018] [Accepted: 01/23/2018] [Indexed: 06/08/2023]
Abstract
In this paper, we have investigated the cumulative peculiarity of the "heavy atom on light atom" effect on the 13 C NMR chemical shifts, initiated by the adjacent chalcogens. For this purpose, the most accurate hybrid computational scheme for the calculation of chemical shifts of carbon nuclei, directly bonded with several heavy chalcogens, is introduced and attested on the representative series of molecules. The best hybrid scheme combines the nonrelativistic coupled cluster-based approach with the different types of corrections, including vibrational, solvent, and relativistic. The dependences of the total relativistic corrections to carbon shielding constants in 2 series of model compounds, namely, X═13 C═Y (X, Y = O, S, Se, Te) and C(XH)m (YH)n (ZH)p (QH)s H1-m H1-n H1-p H1-s (X, Y, Z, Q = S, Se, Te and m, n, p, s = 0, 1), on the total atomic number of the adjacent chalcogens have been obtained.
Collapse
Affiliation(s)
- Yu Yu Rusakov
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033, Irkutsk, Russia
| | - I L Rusakova
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033, Irkutsk, Russia
| |
Collapse
|
33
|
Stoychev GL, Auer AA, Neese F. Efficient and Accurate Prediction of Nuclear Magnetic Resonance Shielding Tensors with Double-Hybrid Density Functional Theory. J Chem Theory Comput 2018; 14:4756-4771. [DOI: 10.1021/acs.jctc.8b00624] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Georgi L. Stoychev
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr 45470, Germany
| | - Alexander A. Auer
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr 45470, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr 45470, Germany
| |
Collapse
|
34
|
Roggatz CC, Lorch M, Benoit DM. Influence of Solvent Representation on Nuclear Shielding Calculations of Protonation States of Small Biological Molecules. J Chem Theory Comput 2018; 14:2684-2695. [PMID: 29566332 DOI: 10.1021/acs.jctc.7b01020] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this study, we assess the influence of solvation on the accuracy and reliability of isotropic nuclear magnetic shielding calculations for amino acids in comparison to experimental data. We focus particularly on the performance of solvation methods for different protonation states, as biological molecules occur almost exclusively in aqueous solution and are subject to protonation with pH. We identify significant shortcomings of current implicit solvent models and present a hybrid solvation approach that improves agreement with experimental data by taking into account the presence of direct interactions between amino acid protonation state and water molecules.
Collapse
|
35
|
Gajda Ł, Kupka T, Broda MA, Leszczyńska M, Ejsmont K. Method and basis set dependence of the NICS indexes of aromaticity for benzene. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:265-275. [PMID: 29211311 DOI: 10.1002/mrc.4690] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 11/21/2017] [Accepted: 11/24/2017] [Indexed: 05/24/2023]
Abstract
The role of theory level in prediction of benzene magnetic indexes of aromaticity is analysed and compared with calculated nuclear magnetic shieldings of 3 He used as NMR probe. Three closely related nucleus-independent chemical shift (NICS) based indexes were calculated for benzene at SCF-HF, MP2, and DFT levels of theory and the impact of basis set on these quantities was studied. The changes of benzene NICS(0), NICS(1), and NICS(1)zz parameters calculated using SCF-HF, MP2 and several density functionals were within 1 to 3 ppm. Similar deviations between magnetic indexes of aromaticity were observed for values calculated with selected basis sets. Only very small effect of polar solvent on benzene aromaticity was predicted. The 3 He nuclear magnetic isotropic shielding (σ) and its zz-components (σzz ) of helium atom approaching the centre of benzene ring from above produced similar curves versus benzene-He distance to NICS parameters calculated for similarly moving Bq ghost atom. We also propose an experimental verification of NICS calculations by designing the 3 He NMR measurement for benzene saturated with helium gas or in low temperature matrices.
Collapse
Affiliation(s)
- Łukasz Gajda
- Faculty of Chemistry, University of Opole, 48, Oleska Street, 45-052, Opole, Poland
| | - Teobald Kupka
- Faculty of Chemistry, University of Opole, 48, Oleska Street, 45-052, Opole, Poland
| | - Małgorzata A Broda
- Faculty of Chemistry, University of Opole, 48, Oleska Street, 45-052, Opole, Poland
| | | | - Krzysztof Ejsmont
- Faculty of Chemistry, University of Opole, 48, Oleska Street, 45-052, Opole, Poland
| |
Collapse
|
36
|
Stoychev GL, Auer AA, Izsák R, Neese F. Self-Consistent Field Calculation of Nuclear Magnetic Resonance Chemical Shielding Constants Using Gauge-Including Atomic Orbitals and Approximate Two-Electron Integrals. J Chem Theory Comput 2018; 14:619-637. [DOI: 10.1021/acs.jctc.7b01006] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Georgi L. Stoychev
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Alexander A. Auer
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Róbert Izsák
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
37
|
|
38
|
Field-Theodore TE, Olejniczak M, Jaszuński M, Wilson DJD. NMR shielding constants in group 15 trifluorides. Phys Chem Chem Phys 2018; 20:23025-23033. [DOI: 10.1039/c8cp04056g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By combining large basis and complete basis set (CBS) extrapolations of the coupled-cluster equilibrium geometry results with rovibrational and relativistic corrections, we demonstrate that it is possible to achieve near-quantitative accuracy for the NMR shielding constants in three group 15 trifluorides – NF3, PF3 and AsF3.
Collapse
Affiliation(s)
- Terri E. Field-Theodore
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
| | | | - Michał Jaszuński
- Institute of Organic Chemistry
- Polish Academy of Sciences
- 01-224 Warszawa
- Poland
| | - David J. D. Wilson
- Department of Chemistry and Physics
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
| |
Collapse
|
39
|
Iron MA. Evaluation of the Factors Impacting the Accuracy of 13C NMR Chemical Shift Predictions using Density Functional Theory-The Advantage of Long-Range Corrected Functionals. J Chem Theory Comput 2017; 13:5798-5819. [PMID: 29016125 DOI: 10.1021/acs.jctc.7b00772] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The various factors influencing the accuracy of 13C NMR calculations using density functional theory (DFT), including the basis set, exchange-correlation (XC) functional, and isotropic shielding calculation method, are evaluated. A wide selection of XC functionals (over 70) were considered, and it was found that long-range corrected functionals offer a significant improvement over the other classes of functionals. Based on a thorough study, it is recommended that for calculating NMR chemical shifts (δ) one should use the CSGT method, the COSMO solvation model, and the LC-TPSSTPSS exchange-correlation functional in conjunction with the cc-pVTZ basis set. A selection of problems in natural product identification are considered in light of the newly recommended level of theory.
Collapse
Affiliation(s)
- Mark A Iron
- Computational Chemistry Unit, Department of Chemical Research Support, Weizmann Institute of Science , Rehovot 7610001, Israel
| |
Collapse
|
40
|
Martínez FA, Aucar GA. Intermolecular magnetic interactions in stacked DNA base pairs. Phys Chem Chem Phys 2017; 19:27817-27827. [PMID: 28990030 DOI: 10.1039/c7cp04484d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The influence of pi-stacking on the magnetic properties of atoms that belong to adenine-thymine and guanine-cytosine pairs in sequences of three and five layers of DNA base pairs was analysed. As probes we used NMR spectroscopic parameters, which are among the most useful tools to learn about the transmission of magnetic interactions in molecules. Four DFT functionals were employed: B3LYP, BHANDLYP, KT2 and KT3, together with the SOPPA method. Besides, given that the number of non-hydrogen atoms of the supramolecular systems studied here is larger than 50 we applied a locally dense basis set scheme. Our results show that the piling up of a few Watson-Crick base pairs above and below a given pair modifies its NMR spectroscopic parameters by an amount that may be measurable and the percentage of variation does not depend on dispersion. We found that magnetic shieldings are more sensitive than J-couplings, and also that some atoms are more sensitive than others. Stacking affects the shielding of non-hydrogen atoms like nitrogens, that are donors in hydrogen bonds, HBs, and the carbons bonded to them. The amount of variation of these shieldings was found to be from 2% to 5% when the pairs are considered first as isolated, and then, placed in the middle of a sequence of three layers of base pairs. Such a variation becomes vanishingly small when the sequence contains more than three layers, showing that the stacking effect on NMR spectroscopic parameters has a local nature. We have also found a pattern for shieldings. First, equivalent atoms of similar monomers (thymine and adenine, or guanine and cytosine) have similar values of absolute shieldings in isolated pairs, and the amount of variation from isolated pairs to aggregates of a few pairs is also similar, meaning that equivalent atoms are affected in a similar manner by pi-stacking. Second, the hydrogen atoms which belong to hydrogen bonds are more sensitive to the piling up than the non-hydrogen atoms.
Collapse
Affiliation(s)
- Fernando A Martínez
- Instituto de Modelado e Innovación Tecnológica, CONICET, and Departamento de Física - Facultad de Ciencias Exactas y Naturales, UNNE, Avda Libertad 5460, W3404AAS, Corrientes, Argentina.
| | | |
Collapse
|
41
|
Karadakov PB, Kirsopp J. Magnetic Shielding Studies of C2
and C2
H2
Support Higher than Triple Bond Multiplicity in C2. Chemistry 2017; 23:12949-12954. [DOI: 10.1002/chem.201703051] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Peter B. Karadakov
- Department of Chemistry; University of York; Heslington York YO10 5DD UK
| | - Josh Kirsopp
- Department of Chemistry; University of York; Heslington York YO10 5DD UK
| |
Collapse
|
42
|
Rusakov YY, Rusakova IL, Krivdin LB. On the significant relativistic heavy atom effect on 13C NMR chemical shifts of β- and γ-carbons in seleno- and telluroketones. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1350292] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Yuriy Yu. Rusakov
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russian Federation
| | - Irina L. Rusakova
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russian Federation
| | - Leonid B. Krivdin
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russian Federation
| |
Collapse
|
43
|
Field-Theodore TE, Wilson DJD. A coupled cluster study of the magnetisability, rotational g-tensor and quadrupole moment of NF3, PF3 and AsF3. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1349346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Terri E. Field-Theodore
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - David J. D. Wilson
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| |
Collapse
|
44
|
Fedorov SV, Rusakov YY, Krivdin LB. Quantum-chemical calculations of NMR chemical shifts of organic molecules: XV. Relativistic calculations of 29Si NMR chemical shifts of silanes. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1070428017050013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
45
|
Yamamoto K, Kanematsu Y, Nagashima U, Ueda A, Mori H, Tachikawa M. Multicomponent DFT study of geometrical H/D isotope effect on hydrogen-bonded organic conductor, κ-H 3 (Cat EDT-ST) 2. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.073] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
46
|
Bertani R, Mozzon M, Sgarbossa P, Tamburini S, Casarin M, Mangione G, Casella G, Venzo A, Rizzato S, Albinati A. Pt(II) nitrile complexes: New insights on old complexes from a combined experimental and theoretical study. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2016.07.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
47
|
Buß A, Koch R. Simulation of NMR chemical shifts in heterocycles: a method evaluation. J Mol Model 2016; 23:9. [DOI: 10.1007/s00894-016-3172-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/16/2016] [Indexed: 12/11/2022]
|
48
|
Bhowmick A, Brookes DH, Yost SR, Dyson HJ, Forman-Kay JD, Gunter D, Head-Gordon M, Hura GL, Pande VS, Wemmer DE, Wright PE, Head-Gordon T. Finding Our Way in the Dark Proteome. J Am Chem Soc 2016; 138:9730-42. [PMID: 27387657 PMCID: PMC5051545 DOI: 10.1021/jacs.6b06543] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The traditional structure-function paradigm has provided significant insights for well-folded proteins in which structures can be easily and rapidly revealed by X-ray crystallography beamlines. However, approximately one-third of the human proteome is comprised of intrinsically disordered proteins and regions (IDPs/IDRs) that do not adopt a dominant well-folded structure, and therefore remain "unseen" by traditional structural biology methods. This Perspective considers the challenges raised by the "Dark Proteome", in which determining the diverse conformational substates of IDPs in their free states, in encounter complexes of bound states, and in complexes retaining significant disorder requires an unprecedented level of integration of multiple and complementary solution-based experiments that are analyzed with state-of-the art molecular simulation, Bayesian probabilistic models, and high-throughput computation. We envision how these diverse experimental and computational tools can work together through formation of a "computational beamline" that will allow key functional features to be identified in IDP structural ensembles.
Collapse
Affiliation(s)
- Asmit Bhowmick
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
| | - David H. Brookes
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Shane R. Yost
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - H. Jane Dyson
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California 92037
| | - Julie D. Forman-Kay
- Molecular Structure and Function Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Daniel Gunter
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley CA, 94720
| | | | - Gregory L. Hura
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley CA, 94720
| | - Vijay S. Pande
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - David E. Wemmer
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Peter E. Wright
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Teresa Head-Gordon
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley CA, 94720
| |
Collapse
|
49
|
Giménez CA, Maldonado AF, Aucar GA. Relativistic and electron correlation effects on NMR J-coupling of Sn and Pb containing molecules. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1952-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
50
|
Faber R, Buczek A, Kupka T, Sauer SPA. On the convergence of zero-point vibrational corrections to nuclear shieldings and shielding anisotropies towards the complete basis set limit in water. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1210831] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Rasmus Faber
- Department of Chemistry, University of Copenhagen, Copenhagen Ø, Denmark
| | - Aneta Buczek
- Faculty of Chemistry, University of Opole, Opole, Poland
| | - Teobald Kupka
- Faculty of Chemistry, University of Opole, Opole, Poland
| | | |
Collapse
|