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Chyba J, Hruzíková A, Knor M, Pikulová P, Marková K, Novotný J, Marek R. Nature of NMR Shifts in Paramagnetic Octahedral Ru(III) Complexes with Axial Pyridine-Based Ligands. Inorg Chem 2023; 62:3381-3394. [PMID: 36763803 PMCID: PMC10017024 DOI: 10.1021/acs.inorgchem.2c03282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
In recent decades, transition-metal coordination compounds have been extensively studied for their antitumor and antimetastatic activities. In this work, we synthesized a set of symmetric and asymmetric Ru(III) and Rh(III) coordination compounds of the general structure (Na+/K+/PPh4+/LH+) [trans-MIIIL(eq)nL(ax)2]- (M = RuIII or RhIII; L(eq) = Cl, n = 4; L(eq) = ox, n = 2; L(ax) = 4-R-pyridine, R = CH3, H, C6H5, COOH, CF3, CN; L(ax) = DMSO-S) and systematically investigated their structure, stability, and NMR properties. 1H and 13C NMR spectra measured at various temperatures were used to break down the total NMR shifts into the orbital (temperature-independent) and hyperfine (temperature-dependent) contributions. The hyperfine NMR shifts for paramagnetic Ru(III) compounds were analyzed in detail using relativistic density functional theory (DFT). The effects of (i) the 4-R substituent of pyridine, (ii) the axial trans ligand L(ax), and (iii) the equatorial ligands L(eq) on the distribution of spin density reflected in the "through-bond" (contact) and the "through-space" (pseudocontact) contributions to the hyperfine NMR shifts of the individual atoms of the pyridine ligands are rationalized. Further, we demonstrate the large effects of the solvent on the hyperfine NMR shifts and discuss our observations in the general context of the paramagnetic NMR spectroscopy of transition-metal complexes.
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Affiliation(s)
- Jan Chyba
- CEITEC─Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Anna Hruzíková
- CEITEC─Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Michal Knor
- CEITEC─Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Petra Pikulová
- CEITEC─Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Kateřina Marková
- CEITEC─Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Jan Novotný
- CEITEC─Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia.,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia.,Institute of Inorganic Chemistry, Slovak Academy of Science, Dúbravská cesta 9, SK-84536 Bratislava, Slovakia
| | - Radek Marek
- CEITEC─Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia.,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
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Ravera E, Gigli L, Czarniecki B, Lang L, Kümmerle R, Parigi G, Piccioli M, Neese F, Luchinat C. A Quantum Chemistry View on Two Archetypical Paramagnetic Pentacoordinate Nickel(II) Complexes Offers a Fresh Look on Their NMR Spectra. Inorg Chem 2021; 60:2068-2075. [PMID: 33478214 PMCID: PMC7877564 DOI: 10.1021/acs.inorgchem.0c03635] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
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Quantum chemical methods for calculating paramagnetic NMR observables are becoming
increasingly accessible and are being included in the inorganic chemistry practice.
Here, we test the performance of these methods in the prediction of proton hyperfine
shifts of two archetypical high-spin pentacoordinate nickel(II) complexes (NiSAL-MeDPT
and NiSAL-HDPT), which, for a variety of reasons, turned out to be perfectly suited to
challenge the predictions to the finest level of detail. For NiSAL-MeDPT, new NMR
experiments yield an assignment that perfectly matches the calculations. The slightly
different hyperfine shifts from the two “halves” of the molecules related
by a pseudo-C2 axis, which are experimentally divided into
two well-defined spin systems, are also straightforwardly distinguished by the
calculations. In the case of NiSAL-HDPT, for which no X-ray structure is available, the
quality of the calculations allowed us to refine its structure using as a starting
template the structure of NiSAL-MeDPT. State-of-the-art
quantum chemical methods and paramagnetism-tailored
NMR experiments provide a deep insight on the relation between the
spectra and the electronic structure for two paramagnetic pentacoordinate
nickel(II) complexes.
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Affiliation(s)
- Enrico Ravera
- Department of Chemistry "Ugo Schiff″, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Lucia Gigli
- Department of Chemistry "Ugo Schiff″, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Barbara Czarniecki
- Bruker Biospin Corporation, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Lucas Lang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Rainer Kümmerle
- Bruker Biospin Corporation, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Giacomo Parigi
- Department of Chemistry "Ugo Schiff″, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Mario Piccioli
- Department of Chemistry "Ugo Schiff″, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Claudio Luchinat
- Department of Chemistry "Ugo Schiff″, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Magnetic Resonance Center, University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
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Khan S, Pollet R, Vuilleumier R, Kowalewski J, Odelius M. An ab initio CASSCF study of zero field splitting fluctuations in the octet ground state of aqueous [Gd(iii)(HPDO3A)(H2O)]. J Chem Phys 2017; 147:244306. [DOI: 10.1063/1.5010347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Shehryar Khan
- Department of Physics, Stockholm University, AlbaNova University Center, 106 91 Stockholm, Sweden
| | - Rodolphe Pollet
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Rodolphe Vuilleumier
- PASTEUR, Département de Chimie, École Normale Supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005 Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, École Normale Supérieure, CNRS, Processus d’Activation Sélective par Transfert d’Énergie Uni-Électronique ou Radiatif (PASTEUR), 75005 Paris, France
| | - Jozef Kowalewski
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden
| | - Michael Odelius
- Department of Physics, Stockholm University, AlbaNova University Center, 106 91 Stockholm, Sweden
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4
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Håkansson P. Prediction of low-field nuclear singlet lifetimes with molecular dynamics and quantum-chemical property surface. Phys Chem Chem Phys 2017; 19:10237-10254. [DOI: 10.1039/c6cp08394c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular dynamics and quantum chemistry methods are implemented to quantify nuclear spin-1/2 pair singlet-state relaxation rates. Illustrated is the relevant spin-internal-motion mechanism (SIM).
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Affiliation(s)
- Pär Håkansson
- School of Chemistry
- University of Southampton
- SO17 1BJ Southampton
- UK
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Gaita-Ariño A, Prima-García H, Cardona-Serra S, Escalera-Moreno L, Rosaleny LE, Baldoví JJ. Coherence and organisation in lanthanoid complexes: from single ion magnets to spin qubits. Inorg Chem Front 2016. [DOI: 10.1039/c5qi00296f] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Molecular magnetism is reaching a degree of development that will allow for the rational design of sophisticated systems.
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Affiliation(s)
| | - Helena Prima-García
- Instituto de Ciencia Molecular (ICMol)
- Universidad de Valencia
- 46980 Paterna
- Spain
| | | | | | - Lorena E. Rosaleny
- Instituto de Ciencia Molecular (ICMol)
- Universidad de Valencia
- 46980 Paterna
- Spain
| | - José J. Baldoví
- Instituto de Ciencia Molecular (ICMol)
- Universidad de Valencia
- 46980 Paterna
- Spain
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
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Chan SHS, Waudby CA, Cassaignau AME, Cabrita LD, Christodoulou J. Increasing the sensitivity of NMR diffusion measurements by paramagnetic longitudinal relaxation enhancement, with application to ribosome-nascent chain complexes. JOURNAL OF BIOMOLECULAR NMR 2015; 63:151-163. [PMID: 26253948 PMCID: PMC4924603 DOI: 10.1007/s10858-015-9968-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 07/13/2015] [Indexed: 05/27/2023]
Abstract
The translational diffusion of macromolecules can be examined non-invasively by stimulated echo (STE) NMR experiments to accurately determine their molecular sizes. These measurements can be important probes of intermolecular interactions and protein folding and unfolding, and are crucial in monitoring the integrity of large macromolecular assemblies such as ribosome-nascent chain complexes (RNCs). However, NMR studies of these complexes can be severely constrained by their slow tumbling, low solubility (with maximum concentrations of up to 10 μM), and short lifetimes resulting in weak signal, and therefore continuing improvements in experimental sensitivity are essential. Here we explore the use of the paramagnetic longitudinal relaxation enhancement (PLRE) agent NiDO2A on the sensitivity of (15)N XSTE and SORDID heteronuclear STE experiments, which can be used to monitor the integrity of these unstable complexes. We exploit the dependence of the PLRE effect on the gyromagnetic ratio and electronic relaxation time to accelerate recovery of (1)H magnetization without adversely affecting storage on N z during diffusion delays or introducing significant transverse relaxation line broadening. By applying the longitudinal relaxation-optimized SORDID pulse sequence together with NiDO2A to 70S Escherichia coli ribosomes and RNCs, NMR diffusion sensitivity enhancements of up to 4.5-fold relative to XSTE are achieved, alongside ~1.9-fold improvements in two-dimensional NMR sensitivity, without compromising the sample integrity. We anticipate these results will significantly advance the use of NMR to probe dynamic regions of ribosomes and other large, unstable macromolecular assemblies.
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Affiliation(s)
- Sammy H S Chan
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 6BT, UK
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 6BT, UK
| | - Anaïs M E Cassaignau
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 6BT, UK
| | - Lisa D Cabrita
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 6BT, UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London WC1E 6BT, UK
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Ouyang W, Dou W, Subotnik JE. Surface hopping with a manifold of electronic states. I. Incorporating surface-leaking to capture lifetimes. J Chem Phys 2015; 142:084109. [PMID: 25725714 DOI: 10.1063/1.4908032] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate the incorporation of the surface-leaking (SL) algorithm into Tully's fewest-switches surface hopping (FSSH) algorithm to simulate some electronic relaxation induced by an electronic bath in conjunction with some electronic transitions between discrete states. The resulting SL-FSSH algorithm is benchmarked against exact quantum scattering calculations for three one-dimensional model problems. The results show excellent agreement between SL-FSSH and exact quantum dynamics in the wide band limit, suggesting the potential for a SL-FSSH algorithm. Discrepancies and failures are investigated in detail to understand the factors that will limit the reliability of SL-FSSH, especially the wide band approximation. Considering the easiness of implementation and the low computational cost, we expect this method to be useful in studying processes involving both a continuum of electronic states (where electronic dynamics are probabilistic) and processes involving only a few electronic states (where non-adiabatic processes cannot ignore short-time coherence).
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Affiliation(s)
- Wenjun Ouyang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Wenjie Dou
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Joseph E Subotnik
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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8
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Mareš J, Vaara J. Solvation structure and dynamics of Ni2+(aq) from a polarizable force field. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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