1
|
Jessen LM, Sauer SPA. On the performance of HRPA(D) for NMR spin-spin coupling constants: Smaller molecules, aromatic and fluoroaromatic compounds. J Chem Phys 2024; 160:064102. [PMID: 38341775 DOI: 10.1063/5.0189932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/15/2024] [Indexed: 02/13/2024] Open
Abstract
In this study, the performance of the doubles-corrected higher random-phase approximation [HRPA(D)] has been investigated in calculations of nuclear magnetic resonance spin-spin coupling constants (SSCCs) for 58 molecules with the experimental values used as the reference values. HRPA(D) is an approximation to the second-order polarization propagator approximation (SOPPA) and is, therefore, computationally less expensive than SOPPA. HRPA(D) performs comparable and sometimes even better than SOPPA, and therefore, when calculating SSCCs, it should be considered as an alternative to SOPPA. Furthermore, it was investigated whether a coupled-cluster singles, doubles and perturbative triples [CCSD(T)] or Møller-Plesset second order (MP2) geometry optimization was optimal for a SOPPA and a HRPA(D) SSCC calculation for eight smaller molecules. CCSD(T) is the optimal geometry optimization for the SOPPA calculation, and MP2 was optimal for HRPA(D) SSCC calculations.
Collapse
Affiliation(s)
- Louise Møller Jessen
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| |
Collapse
|
2
|
Gleeson R, Aggelund PA, Østergaard FC, Schaltz KF, Sauer SPA. Exploring Alternate Methods for the Calculation of High-Level Vibrational Corrections of NMR Spin-Spin Coupling Constants. J Chem Theory Comput 2024. [PMID: 38299500 DOI: 10.1021/acs.jctc.3c01223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Traditional nuclear magnetic resonance (NMR) calculations typically treat systems with a Born-Oppenheimer-derived electronic wave function that is solved for a fixed nuclear geometry. One can numerically account for this neglected nuclear motion by averaging over property values for all nuclear geometries with a vibrational wave function and adding this expectation value as a correction to an equilibrium geometry property value. Presented are benchmark coupled-cluster singles and doubles (CCSD) vibrational corrections to spin-spin coupling constants (SSCCs) computed at the level of vibrational second-order perturbation theory (VPT2) using the vibrational averaging driver of the CFOUR program. As CCSD calculations of vibrational corrections are very costly, cheaper electronic structure methods are explored via a newly developed Python vibrational averaging program within the Dalton Project. Namely, results obtained with the second-order polarization propagator approximation (SOPPA) and density functional theory (DFT) with the B3LYP and PBE0 exchange-correlation functionals are compared to the benchmark CCSD//CCSD(T) and experimental values. CCSD//CCSD(T) corrections are also combined with literature CC3 equilibrium geometry values to form the highest-order vibrationally corrected values available (i.e., CC3//CCSD(T) + CCSD//CCSD(T)). CCSD//CCSD(T) statistics showed favorable statistics in comparison to experimental values, albeit at an unfavorably high computational cost. A cheaper CCSD//CCSD(T) + B3LYP method showed quite similar mean absolute deviation (MAD) values as CCSD//CCSD(T), concluding that CCSD//CCSD(T) + B3LYP is optimal in terms of cost and accuracy. With reference to experimental values, a vibrational correction was not worth the cost for all of the other methods tested. Finally, deviation statistics showed that CC3//CCSD(T) + CCSD//CCSD(T) vibrational-corrected equilibrium values deteriorated in comparison to CCSD//CCSD(T) attributed to the use of a smaller basis set or lack of solvation effects for the CC3 equilibrium calculations.
Collapse
Affiliation(s)
- Ronan Gleeson
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Patrick A Aggelund
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Kasper F Schaltz
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
| |
Collapse
|
3
|
Quantum Chemical Approaches to the Calculation of NMR Parameters: From Fundamentals to Recent Advances. MAGNETOCHEMISTRY 2022. [DOI: 10.3390/magnetochemistry8050050] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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
|
4
|
Soares JV, Dal Poggetto G, Viesser RV, Couto UR, Tormena CF. Stereoelectronic interactions: A booster for 4 J HF transmission. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:481-488. [PMID: 35023222 DOI: 10.1002/mrc.5248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/04/2022] [Accepted: 01/10/2022] [Indexed: 05/21/2023]
Abstract
Long-range proton-fluorine coupling constants (n JHF ) are helpful for the structure elucidation of fluorinated molecules. However, their magnitude and sign can change with the relative position of coupled nuclei and the presence of substituents. Here, trans-4-tert-butyl-2-fluorocyclohexanone was used as a model compound for the study of the transmission of 4 JHF . In this compound, the 4 JH6axF was measured to be +5.1 Hz, which is five times larger than the remaining 4 JHF in the same molecule (4 JH4F = +1.0 Hz and 4 JH6eqF = +1.0 Hz). Through a combination of experimental data, natural bond orbital (NBO) and natural J-coupling (NJC) analyses, we observed that stereoelectronic interactions involving the π system of the carbonyl group are involved in the transmission pathway for the 4 JH6axF . Interactions containing the π system as an electron acceptor (e.g., σC6H6ax → π*C═O and σCF → π*C═O ) increase the value of the 4 JH6axF , while the interaction of the π system as an electron donor (e.g., πC═O → σ*CF ) decreases it. Additionally, the carbonyl group was shown not to be part of the transmission pathway of the diequatorial 4 JH6eqF coupling in cis-4-tert-butyl-2-fluorocyclohexanone, revealing that there is a crucial symmetry requirement that must be fulfilled for the π system to influence the value of the 4 JHF in these systems.
Collapse
Affiliation(s)
- João Vitor Soares
- Institute of Chemistry, University of Campinas-UNICAMP, Campinas, Brazil
| | | | - Renan V Viesser
- Institute of Chemistry, University of Campinas-UNICAMP, Campinas, Brazil
| | - Uenifer R Couto
- Institute of Chemistry, University of Campinas-UNICAMP, Campinas, Brazil
| | - Cláudio F Tormena
- Institute of Chemistry, University of Campinas-UNICAMP, Campinas, Brazil
| |
Collapse
|
5
|
Steinmann C, Sauer SPA. The aug-cc-pVTZ-J basis set for the p-block fourth-row elements Ga, Ge, As, Se, and Br. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:1134-1145. [PMID: 33929770 DOI: 10.1002/mrc.5166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
The aug-cc-pVTZ-J basis set family is extended to include the fourth-row p-block elements Ga, Ge, As, Se, and Br. We use the established approach outlined by Sauer and coworkers (J. Chem. Phys. 115, 1324 [2001], J. Chem. Phys. 133, 054308 [2010], J. Chem. Theory Comput. 7, 4070 [2011], and J. Chem. Theory Comput. 7, 4077 [2011]) where the completely uncontracted aug-cc-pVTZ basis set is saturated with tight s-, p-, d-, and f-functions to form the aug-cc-pVTZ-Juc basis set for the tested elements. The saturation is carried out on the simplest hydrides possible for the tested elements GaH, GeH4 , AsH3 , H2 Se, and HBr until an improvement is less than 0.01% for all s-, p-, and d-functions added. f-Functions are added to an improvement less than or equal to 1.0% due to the computational expense these functions add. The saturated aug-cc-pVTZ-Juc (26s16p12d5f) is then recontracted using the molecular orbital coefficients from self-consistent field calculations on the simple hydrides to improve computational efficiency. During contraction of the basis set, we observe that the linear hydrogen bromide molecule has a slower convergence than the other tested molecules which sets a limit on the accuracy obtained. All calculations with the contracted aug-cc-pVTZ-J [17s10p7d5f] gives results that are within 1.0% of the uncontracted results at considerable computational savings.
Collapse
Affiliation(s)
- Casper Steinmann
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
6
|
Kjellgren ER, Jensen HJA. Multi-configurational short-range density functional theory can describe spin-spin coupling constants of transition metal complexes. J Chem Phys 2021; 155:084102. [PMID: 34470359 DOI: 10.1063/5.0059128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The multi-configurational short-range (sr) density functional theory has been extended to the calculation of indirect spin-spin coupling constants (SSCCs) for nuclear magnetic resonance spectroscopy. The performance of the new method is compared to Kohn-Sham density functional theory and the ab initio complete active space self-consistent field for a selected set of molecules with good reference values. Two density functionals have been considered, the local density approximation srLDA and srPBE from the GGA class of functionals. All srDFT calculations are of Hartree-Fock-type HF-srDFT or complete active space-type CAS-srDFT. In all cases, the calculated SSCC values are of the same quality for srLDA and srPBE functionals, suggesting that one should use the computationally cost-effective srLDA functionals in applications. For all the calculated SSCCs in organic compounds, the best choice is HF-srDFT; the more expensive CAS-srDFT does not provide better values for these single-reference molecules. Fluorine is a challenge; in particular, the FF, FC, and FO couplings have much higher statistical errors than the rest. For SSCCs involving fluorine and a metal atom CAS-srDFT with singlet, generalized Tamm-Dancoff approximation is needed to get good SSCC values although the reference ground state is not a multi-reference case. For VF6 -1, all other considered models fail blatantly.
Collapse
Affiliation(s)
- Erik Rosendahl Kjellgren
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Hans Jørgen Aagaard Jensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| |
Collapse
|
7
|
Theibich YA, Sauer SP, Leggio LL, Hedegård ED. Estimating the accuracy of calculated electron paramagnetic resonance hyperfine couplings for a lytic polysaccharide monooxygenase. Comput Struct Biotechnol J 2020; 19:555-567. [PMID: 33510861 PMCID: PMC7807142 DOI: 10.1016/j.csbj.2020.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/11/2020] [Accepted: 12/13/2020] [Indexed: 11/07/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are enzymes that bind polysaccharides followed by an (oxidative) disruption of the polysaccharide surface, thereby boosting depolymerization. The binding process between the LPMO catalytic domain and polysaccharide is key to the mechanism and establishing structure-function relationships for this binding is therefore crucial. The hyperfine coupling constants (HFCs) from EPR spectroscopy have proven useful for this purpose. Unfortunately, EPR does not provide direct structural data and therefore the experimental EPR parameters have to be supported with parameters calculated with density functional theory. Yet, calculated HFCs are extremely sensitive to the employed computational setup. Using the LPMO Ls(AA9)A catalytic domain, we here quantify the importance of several choices in the computational setup, ranging from the use of specialized basis, the underlying structures, and the employed exchange-correlation functional. We show that specialized basis sets are an absolute necessity, and also that care has to be taken in the optimization of the underlying structure: only by allowing large parts of the protein around the active site to structurally relax could we obtain results that uniformly reproduced experimental trends. We compare our results to previously published X-ray structures and experimental HFCs for Ls(AA9)A as well as to recent experimental/theoretical results for another (AA10) family of LPMOs.
Collapse
Affiliation(s)
- Yusuf A. Theibich
- Department of Chemistry, University of University, Copenhagen, Denmark
| | | | - Leila Lo Leggio
- Department of Chemistry, University of University, Copenhagen, Denmark
| | - Erik D. Hedegård
- Division of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden
| |
Collapse
|
8
|
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
|
9
|
|
10
|
Schnack-Petersen AK, Haase PAB, Faber R, Provasi PF, Sauer SPA. RPA(D) and HRPA(D): Two new models for calculations of NMR indirect nuclear spin-spin coupling constants. J Comput Chem 2019; 39:2647-2666. [PMID: 30515901 DOI: 10.1002/jcc.25712] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/26/2018] [Accepted: 09/23/2018] [Indexed: 01/21/2023]
Abstract
In this article, the RPA(D) and HRPA(D) models for the calculation of linear response functions are presented. The performance of the new RPA(D) and HRPA(D) models is compared to the performance of the established RPA, HRPA, and SOPPA models in calculations of indirect nuclear spin-spin coupling constants using the CCSD model as a reference. The doubles correction offers a significant improvement on both the RPA and HRPA models; however, the improvement is more dramatic in the case of the RPA model. For all coupling types investigated in this study, the results obtained using the HRPA(D) model are comparable in accuracy to those given by the SOPPA model, while requiring between 30% and 90% of the calculation time needed for SOPPA. The RPA(D) model, while of slightly lower accuracy compared to the CCSD model than HRPA(D), offered calculation times of only approximately 25% of those required for SOPPA for all the investigated molecules. © 2018 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
| | - Pi A B Haase
- Van Swinderen Institute, University of Groningen, Groningen, The Netherlands
| | - Rasmus Faber
- Department of Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Patricio F Provasi
- Department of Physics-IMIT, Northeastern University-CONICET, Corrientes, Argentina
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
11
|
Krivdin LB. Theoretical calculations of carbon-hydrogen spin-spin coupling constants. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 108:17-73. [PMID: 30538048 DOI: 10.1016/j.pnmrs.2018.10.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/09/2018] [Accepted: 10/11/2018] [Indexed: 06/09/2023]
Abstract
Structural applications of theoretical calculations of carbon-hydrogen spin-spin coupling constants are reviewed covering papers published mainly during the last 10-15 years with a special emphasis on the most notable studies of hybridization, substitution and stereoelectronic effects together with the investigation of hydrogen bonding and intermolecular interactions. The wide scope of different applications of calculated carbon-hydrogen couplings in the structural elucidation of particular classes of organic and bioorganic molecules is reviewed, concentrating mainly on saturated, unsaturated, aromatic and heteroaromatic compounds and their functional derivatives, as well as on natural compounds and carbohydrates. The review is dedicated to Professor Emeritus Michael Barfield in view of his invaluable pioneering contribution to this field.
Collapse
Affiliation(s)
- 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
|
12
|
Caputo MC, Alkorta I, Provasi PF, Sauer SPA. Analysis of the interactions in FCCF:(H 2O) and FCCF:(H 2O) 2 complexes through the study of their indirect spin–spin coupling constants. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1488006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- María Cristina Caputo
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires y IFIBA – CONICET-UBA, Ciudad Universitaria, Buenos Aires, Argentina
| | - Ibon Alkorta
- Instituto de Química Médica (C.S.I.C.), Madrid, Spain
| | - Patricio F. Provasi
- Department of Physics – IMIT – CONICET, Northeastern University, Corrientes, Argentina
| | | |
Collapse
|
13
|
Aggelund PA, Sauer SPA, Jensen F. Development of polarization consistent basis sets for spin-spin coupling constant calculations for the atoms Li, Be, Na, and Mg. J Chem Phys 2018; 149:044117. [PMID: 30068157 DOI: 10.1063/1.5034109] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The pcJ-n basis set, optimized for spin-spin coupling constant calculations using density functional theory methods, are expanded to also include the s-block elements Li, Be, Na, and Mg, by studying several small molecules containing these elements. This is done by decontracting the underlying pc-n basis sets, followed by augmentation with additional tight functions. As was the case for the p-block elements, the convergence of the results can be significantly improved by augmentation with tight s-functions. For the p-block elements, additional tight functions of higher angular momentum were also needed, but this is not the case for the s-block elements. A search for the optimum contraction scheme is carried out using the criterion that the contraction error should be lower than the inherent error of the uncontracted pcJ-n relative to the uncontracted pcJ-4 basis set. A large search over possible contraction schemes is done for the Li2 and Na2 molecules, and based on this search contracted pcJ-n basis sets for the four atoms are recommended. This work shows that it is more difficult to contract the pcJ-n basis sets, than the underlying pc-n basis sets. However, it also shows that the pcJ-n basis sets for Li and Be can be more strongly contracted than the pcJ-n basis sets for the p-block elements. For Na and Mg, the contractions are to the same degree as for the p-block elements.
Collapse
Affiliation(s)
- Patrick A Aggelund
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Frank Jensen
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| |
Collapse
|