1
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Brakestad A, Jensen SR, Tantardini C, Pitteloud Q, Wind P, Užulis J, Gulans A, Hopmann KH, Frediani L. Scalar Relativistic Effects with Multiwavelets: Implementation and Benchmark. J Chem Theory Comput 2024; 20:728-737. [PMID: 38181377 PMCID: PMC10809714 DOI: 10.1021/acs.jctc.3c01095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024]
Abstract
The importance of relativistic effects in quantum chemistry is widely recognized, not only for heavier elements but throughout the periodic table. At the same time, relativistic effects are strongest in the nuclear region, where the description of electrons through a linear combination of atomic orbitals becomes more challenging. Furthermore, the choice of basis sets for heavier elements is limited compared with lighter elements where precise basis sets are available. Thanks to the framework of multiresolution analysis, multiwavelets provide an appealing alternative to overcoming this challenge: they lead to robust error control and adaptive algorithms that automatically refine the basis set description until the desired precision is reached. This allows one to achieve a proper description of the nuclear region. In this work, we extended the multiwavelet-based code MRChem to the scalar zero-order regular approximation framework. We validated our implementation by comparing the total energies for a small set of elements and molecules. To confirm the validity of our implementation, we compared both against a radial numerical code for atoms and the plane-wave-based code EXCITING.
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Affiliation(s)
- Anders Brakestad
- Hylleraas
Centre for Quantum Molecular Sciences, UiT
The Arctic University of Norway, Tromsø 9037, Norway
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
| | - Stig Rune Jensen
- Hylleraas
Centre for Quantum Molecular Sciences, UiT
The Arctic University of Norway, Tromsø 9037, Norway
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
| | - Christian Tantardini
- Hylleraas
Centre for Quantum Molecular Sciences, UiT
The Arctic University of Norway, Tromsø 9037, Norway
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
- Department
of Materials Science and NanoEngineering, Rice University, Houston, Texas 77005, United States
| | - Quentin Pitteloud
- Hylleraas
Centre for Quantum Molecular Sciences, UiT
The Arctic University of Norway, Tromsø 9037, Norway
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
| | - Peter Wind
- Hylleraas
Centre for Quantum Molecular Sciences, UiT
The Arctic University of Norway, Tromsø 9037, Norway
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
| | - Jānis Užulis
- Department
of Physics, University of Latvia, Jelgavas iela 3, Riga, Latvia 1004, Latvia
| | - Andris Gulans
- Department
of Physics, University of Latvia, Jelgavas iela 3, Riga, Latvia 1004, Latvia
| | | | - Luca Frediani
- Hylleraas
Centre for Quantum Molecular Sciences, UiT
The Arctic University of Norway, Tromsø 9037, Norway
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
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2
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Zhao L, Zou W. A general method for locating stationary points on the mixed-spin surface of spin-forbidden reaction with multiple spin states. J Chem Phys 2023; 158:2895244. [PMID: 37290081 DOI: 10.1063/5.0151630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
Some chemical reactions proceed on multiple potential energy surfaces and are often accompanied by a change in spin multiplicity, being called spin-forbidden reactions, where the spin-orbit coupling (SOC) effects play a crucial role. In order to efficiently investigate spin-forbidden reactions with two spin states, Yang et al. [Phys. Chem. Chem. Phys. 20, 4129-4136 (2018)] proposed a two-state spin-mixing (TSSM) model, where the SOC effects between the two spin states are simulated by a geometry-independent constant. Inspired by the TSSM model, we suggest a multiple-state spin-mixing (MSSM) model in this paper for the general case with any number of spin states, and its analytic first and second derivatives have been developed for locating stationary points on the mixed-spin potential energy surface and estimating thermochemical energies. To demonstrate the performance of the MSSM model, some spin-forbidden reactions involving 5d transition elements are calculated using the density functional theory (DFT), and the results are compared with the two-component relativistic ones. It is found that MSSM DFT and two-component DFT calculations may provide very similar stationary-point information on the lowest mixed-spin/spinor energy surface, including structures, vibrational frequencies, and zero-point energies. For the reactions containing saturated 5d elements, the reaction energies by MSSM DFT and two-component DFT agree very well within 3 kcal/mol. As for the two reactions OsO+ + CH4 → OOs(CH2)+ + H2 and W + CH4 → WCH2 + H2 involving unsaturated 5d elements, MSSM DFT may also yield good reaction energies of similar accuracy but with some counterexamples. Nevertheless, the energies may be remarkably improved by a posteriori single point energy calculations using two-component DFT at the MSSM DFT optimized geometries, and the maximum error of about 1 kcal/mol is almost independent of the SOC constant used. The MSSM method as well as the developed computer program provides an effective utility for studying spin-forbidden reactions.
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Affiliation(s)
- Long Zhao
- Institute of Modern Physics, Northwest University, Xi'an, Shaanxi 710127, People's Republic of China
- Shaanxi Key Laboratory for Theoretical Physics Frontiers, Xi'an, Shaanxi 710127, People's Republic of China
| | - Wenli Zou
- Institute of Modern Physics, Northwest University, Xi'an, Shaanxi 710127, People's Republic of China
- Shaanxi Key Laboratory for Theoretical Physics Frontiers, Xi'an, Shaanxi 710127, People's Republic of China
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3
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Marques HM. The inorganic chemistry of the cobalt corrinoids - an update. J Inorg Biochem 2023; 242:112154. [PMID: 36871417 DOI: 10.1016/j.jinorgbio.2023.112154] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023]
Abstract
The inorganic chemistry of the cobalt corrinoids, derivatives of vitamin B12, is reviewed, with particular emphasis on equilibrium constants for, and kinetics of, their axial ligand substitution reactions. The role the corrin ligand plays in controlling and modifying the properties of the metal ion is emphasised. Other aspects of the chemistry of these compounds, including their structure, corrinoid complexes with metals other than cobalt, the redox chemistry of the cobalt corrinoids and their chemical redox reactions, and their photochemistry are discussed. Their role as catalysts in non-biological reactions and aspects of their organometallic chemistry are briefly mentioned. Particular mention is made of the role that computational methods - and especially DFT calculations - have played in developing our understanding of the inorganic chemistry of these compounds. A brief overview of the biological chemistry of the B12-dependent enzymes is also given for the reader's convenience.
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Affiliation(s)
- Helder M Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa.
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4
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Toda MJ, Lodowski P, Mamun AA, Kozlowski PM. Photoproduct formation in coenzyme B 12-dependent CarH via a singlet pathway. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 232:112471. [PMID: 35644067 DOI: 10.1016/j.jphotobiol.2022.112471] [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: 11/09/2021] [Revised: 03/26/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
The CarH photoreceptor exploits of the light-sensing ability of coenzyme B12 ( adenosylcobalamin = AdoCbl) to perform its catalytic function, which includes large-scale structural changes to regulate transcription. In daylight, transcription is activated in CarH via the photo-cleavage of the Co-C5' bond of coenzyme B12. Subsequently, the photoproduct, 4',5'-anhydroadenosine (anhAdo) is formed inducing dissociation of the CarH tetramer from DNA. Several experimental studies have proposed that hydridocoblamin (HCbl) may be formed in process with anhAdo. The photolytic cleavage of the Co-C5' bond of AdoCbl was previously investigated using photochemical techniques and the involvement of both singlet and triplet excited states were explored. Herein, QM/MM calculations were employed to probe (1) the photolytic processes which may involve singlet excited states, (2) the mechanism of anhAdo formation, and (3) whether HCbl is a viable intermediate in CarH. Time-dependent density functional theory (TD-DFT) calculations indicate that the mechanism of photodissociation of the Ado ligand involves the ligand field (LF) portion of the lowest singlet excited state (S1) potential energy surface (PES). This is followed by deactivation to a point on the S0 PES where the Co-C5' bond remains broken. This species corresponds to a singlet diradical intermediate. From this point, the PES for anhAdo formation was explored, using the Co-C5' and Co-C4' bond distances as active coordinates, and a local minimum representing anhAdo and HCbl formation was found. The transition state (TS) for the formation of the Co-H bond of HCbl was located and its identity was confirmed by a single imaginary frequency of i1592 cm-1. Comparisons to experimental studies and the potential role of rotation around the N-glycosidic bond of the Ado ligand were discussed.
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Affiliation(s)
- Megan J Toda
- Department of Chemistry, University of Louisville, Louisville, KY 40292, United States
| | - Piotr Lodowski
- Institute of Chemistry, Faculty of Science and Technology, University of Silesia in Katowice, Szkolna 9, PL-40 006 Katowice, Poland
| | - Abdullah Al Mamun
- Department of Chemistry, University of Louisville, Louisville, KY 40292, United States
| | - Pawel M Kozlowski
- Department of Chemistry, University of Louisville, Louisville, KY 40292, United States.
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5
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Cuyacot BJR, Novotný J, Berger RJF, Komorovsky S, Marek R. Relativistic Spin–Orbit Electronegativity and the Chemical Bond Between a Heavy Atom and a Light Atom. Chemistry 2022; 28:e202200277. [DOI: 10.1002/chem.202200277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Indexed: 01/30/2023]
Affiliation(s)
- Ben Joseph R. Cuyacot
- CEITEC – Central European Institute of Technology Masaryk University Kamenice 5 62500 Brno Czechia
- Department of Chemistry Faculty of Science Masaryk University Kamenice 5 62500 Brno Czechia
| | - Jan Novotný
- CEITEC – Central European Institute of Technology Masaryk University Kamenice 5 62500 Brno Czechia
- Department of Chemistry Faculty of Science Masaryk University Kamenice 5 62500 Brno Czechia
| | - Raphael J. F. Berger
- Department of Chemistry and Physics of Materials Paris Lodron University of Salzburg Jakob-Haringerstr. 2 A 5020 Salzburg Austria
| | - Stanislav Komorovsky
- Institute of Inorganic Chemistry Slovak Academy of Sciences Dúbravská cesta 9 84536 Bratislava Slovakia
| | - Radek Marek
- CEITEC – Central European Institute of Technology Masaryk University Kamenice 5 62500 Brno Czechia
- Department of Chemistry Faculty of Science Masaryk University Kamenice 5 62500 Brno Czechia
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6
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Braband H, Benz M, Spingler B, Conradie J, Alberto R, Ghosh A. Relativity as a Synthesis Design Principle: A Comparative Study of [3 + 2] Cycloaddition of Technetium(VII) and Rhenium(VII) Trioxo Complexes with Olefins. Inorg Chem 2021; 60:11090-11097. [PMID: 34255507 PMCID: PMC8388117 DOI: 10.1021/acs.inorgchem.1c00995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
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The difference in [3 + 2] cycloaddition reactivity between fac-[MO3(tacn)]+ (M = Re, 99Tc; tacn = 1,4,7-triazacyclononane) complexes has been reexamined
with a selection of unsaturated substrates including sodium 4-vinylbenzenesulfonate,
norbornene, 2-butyne, and 2-methyl-3-butyn-2-ol (2MByOH). None of
the substrates was found to react with the Re cation in water at room
temperature, whereas the 99Tc reagent cleanly yielded the [3 + 2] cycloadducts. Interestingly,
a bis-adduct was obtained as the sole product for 2MByOH, reflecting
the high reactivity of a 99TcO-enediolato monoadduct. On
the basis of scalar relativistic and nonrelativistic density functional
theory calculations of the reaction pathways, the dramatic difference
in reactivity between the two metals has now been substantially attributed to differences in relativistic effects, which are much
larger for the 5d metal. Furthermore, scalar-relativistic ΔG values were found to decrease along the series propene
> norbornene > 2-butyne > dimethylketene, indicating major variations
in the thermodynamic driving force as a function of the unsaturated
substrate. The suggestion is made that scalar-relativistic effects,
consisting of greater destabilization of the valence electrons of
the 5d elements compared with those of the 4d elements, be viewed
as a new design principle for novel 99mTc/Re radiopharmaceuticals,
as well as more generally in heavy-element coordination chemistry. Room temperature cycloaddition reactivity of fac-[99TcO3(tacn)]+ (tacn = 1,4,7-triazacyclononane)
with a variety of unsaturated substrates and the lack of such reactivity
for fac-[ReO3(tacn)]+ appears
largely attributable to much stronger relativistic effects for Re
relative to Tc, based on relativistic density functional theory calculations.
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Affiliation(s)
- Henrik Braband
- Department of Chemistry, University of Zurich, Zürich 8057, Switzerland
| | - Michael Benz
- Department of Chemistry, University of Zurich, Zürich 8057, Switzerland
| | - Bernhard Spingler
- Department of Chemistry, University of Zurich, Zürich 8057, Switzerland
| | - Jeanet Conradie
- Department of Chemistry, UiT-The Arctic University of Norway, Tromsø N-9037, Norway.,Department of Chemistry, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - Roger Alberto
- Department of Chemistry, University of Zurich, Zürich 8057, Switzerland
| | - Abhik Ghosh
- Department of Chemistry, UiT-The Arctic University of Norway, Tromsø N-9037, Norway
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7
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Cooper CJ, Zheng K, Rush KW, Johs A, Sanders BC, Pavlopoulos GA, Kyrpides NC, Podar M, Ovchinnikov S, Ragsdale SW, Parks JM. Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation. Commun Biol 2020; 3:320. [PMID: 32561885 PMCID: PMC7305189 DOI: 10.1038/s42003-020-1047-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 05/27/2020] [Indexed: 11/09/2022] Open
Abstract
Bacteria and archaea possessing the hgcAB gene pair methylate inorganic mercury (Hg) to form highly toxic methylmercury. HgcA consists of a corrinoid binding domain and a transmembrane domain, and HgcB is a dicluster ferredoxin. However, their detailed structure and function have not been thoroughly characterized. We modeled the HgcAB complex by combining metagenome sequence data mining, coevolution analysis, and Rosetta structure calculations. In addition, we overexpressed HgcA and HgcB in Escherichia coli, confirmed spectroscopically that they bind cobalamin and [4Fe-4S] clusters, respectively, and incorporated these cofactors into the structural model. Surprisingly, the two domains of HgcA do not interact with each other, but HgcB forms extensive contacts with both domains. The model suggests that conserved cysteines in HgcB are involved in shuttling HgII, methylmercury, or both. These findings refine our understanding of the mechanism of Hg methylation and expand the known repertoire of corrinoid methyltransferases in nature. Connor J. Cooper et al. expressed HgcA and HgcB in Escherichia coli and modeled the structure of the HgcAB complex by combining metagenome sequence data, coevolution analysis, and ab initio structure calculations. This study provides insights into the biochemical mechanism of mercury (Hg) methylation.
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Affiliation(s)
- Connor J Cooper
- Graduate School of Genome Science and Technology, University of Tennessee, F225 Walters Life Science, Knoxville, TN, 37996, USA.,Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831-6038, USA
| | - Kaiyuan Zheng
- Department of Biological Chemistry, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI, 48109-0606, USA
| | - Katherine W Rush
- Department of Biological Chemistry, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI, 48109-0606, USA
| | - Alexander Johs
- Environmental Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831-6038, USA
| | - Brian C Sanders
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831-6038, USA
| | - Georgios A Pavlopoulos
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Institute for Fundamental Biomedical Research, Biomedical Science Research Center "Alexander Fleming", 34 Fleming Street, 16672, Vari, Greece
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory Berkeley, California, USA
| | - Mircea Podar
- Graduate School of Genome Science and Technology, University of Tennessee, F225 Walters Life Science, Knoxville, TN, 37996, USA.,Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831-6038, USA
| | - Sergey Ovchinnikov
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA, 02138, USA
| | - Stephen W Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI, 48109-0606, USA
| | - Jerry M Parks
- Graduate School of Genome Science and Technology, University of Tennessee, F225 Walters Life Science, Knoxville, TN, 37996, USA. .,Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831-6038, USA.
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8
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Repisky M, Komorovsky S, Kadek M, Konecny L, Ekström U, Malkin E, Kaupp M, Ruud K, Malkina OL, Malkin VG. ReSpect: Relativistic spectroscopy DFT program package. J Chem Phys 2020; 152:184101. [DOI: 10.1063/5.0005094] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Michal Repisky
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Stanislav Komorovsky
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, SK-84536 Bratislava, Slovakia
| | - Marius Kadek
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Lukas Konecny
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Ulf Ekström
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, N-0315 Oslo, Norway
| | - Elena Malkin
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Martin Kaupp
- Technische Universität Berlin, Institute of Chemistry, Strasse des 17 Juni 135, D-10623 Berlin, Germany
| | - Kenneth Ruud
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Olga L. Malkina
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, SK-84536 Bratislava, Slovakia
| | - Vladimir G. Malkin
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, SK-84536 Bratislava, Slovakia
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9
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Zhang Y, Yang DS. Spin-orbit coupling and vibronic transitions of Ce(C 3H 4) and Ce(C 3H 6) formed by the Ce reaction with propene: Mass-analyzed threshold ionization and relativistic quantum computation. J Chem Phys 2020; 152:144304. [PMID: 32295351 DOI: 10.1063/5.0002505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A Ce atom reaction with propene is carried out in a pulsed laser vaporization molecule beam source. Several Ce-hydrocarbon species formed by the C-H and C-C bond activation of propene are observed by time-of-flight mass spectrometry, and Ce(C3Hn) (n = 4 and 6) are characterized by mass-analyzed threshold ionization (MATI) spectroscopy and density functional theory, multiconfiguration, and relativistic quantum chemical calculations. The MATI spectrum of each species consists of two vibronic band systems, each with several vibronic bands. Ce(C3H6) is identified as an inserted species with Ce inserting into an allylic C-H bond of propene and Ce(C3H4) as a metallocycle through 1,2-vinylic dehydrogenation. Both species have a Cs structure with the Ce 4f16s1 ground valence electron configuration in the neutral molecule and the Ce 4f1 configuration in the singly charged ion. The two vibronic band systems observed for each species are attributed to the ionization of two pairs of the lowest spin-orbit coupled states with each pair being nearly degenerate.
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Affiliation(s)
- Yuchen Zhang
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
| | - Dong-Sheng Yang
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
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10
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Kumar M, Francisco JS. Evidence of the Elusive Gold-Induced Non-classical Hydrogen Bonding in Aqueous Environments. J Am Chem Soc 2020; 142:6001-6006. [PMID: 32126169 DOI: 10.1021/jacs.9b05493] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The ability of a gold ion to act as a proton acceptor in hydrogen bonding continues to remain an open question. Heavy-atom effects and secondary competitive interactions in gold complexes make it challenging to precisely establish the identity of gold-ion-induced hydrogen bonding via experimental techniques. In such situations, computational chemistry may play an important role. Herein we have performed Born-Oppenheimer molecular dynamics simulations to study the behavior of [Au(CH3)2)]- in bulk and interfacial aqueous environments. The simulation results suggest that the [Au(CH3)2)]- complex forms one and two gold-ion-induced hydrogen bonds with the water molecules in interfacial and bulk environments, respectively. The calculated probabilities of key hydrogen-bonded configurations of [Au(CH3)2)]-, combined distribution functions, and diffusion coefficients further support this unusual hydrogen-bonding interaction. In summary, the present results suggest that gold-ion-induced hydrogen bonding in an actual solvent environment may be feasible. These results will improve our understanding about the role of weak interactions in transition metal complexes and, thus, will have implications in catalysis and supramolecular assemblies.
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Affiliation(s)
- Manoj Kumar
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Joseph S Francisco
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
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11
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Ricciarelli D, Belpassi L, Harvey JN, Belanzoni P. Spin-Forbidden Reactivity of Transition Metal Oxo Species: Exploring the Potential Energy Surfaces. Chemistry 2020; 26:3080-3089. [PMID: 31846105 DOI: 10.1002/chem.201904314] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Indexed: 11/06/2022]
Abstract
Spin-forbidden reactions are frequently encountered when transition metal oxo species are involved, particularly in oxygen transfer reactivity. The computational study of such reactions is challenging, because reactants and products are located on different spin potential energy surfaces (PESs). One possible approach to describe these reactions is the so-called minimum energy crossing point (MECP) between the diabatic reactants and products PESs. Alternatively, inclusion of spin-orbit coupling (SOC) effects allows to locate a saddle point on a single adiabatic PES (TS SOC). The TS SOC approach is rarely applied because of its high computational cost. Recently evidence for a TS SOC impact on significantly lowering the activation barrier in dioxygen addition to a carbene-gold(I)-hydride complex reaction (Chem. Sci. 2016, 7, 7034-7039) or even on predicting a qualitatively different reaction mechanism in mercury methylation by cobalt corrinoid (Angew. Chem. Int. Ed. 2016, 55, 11503-11506) has been put forward. Using MECP and TS SOC approaches a systematic analysis is provided here of three prototypical transition metal oxo spin-forbidden processes to investigate their implications on reactivity. Cycloaddition of ethylene to chromyl chloride (CrO2 Cl2 +C2 H4 ), iron oxide cation insertion into the hydrogen molecule (FeO+ +H2 ) and H-abstraction from toluene by a MnV -oxo-porphyrin cation (MnOP(H2 O)+ +C6 H5 CH3 ) are case studies. For all these processes the MECP and TS SOC results are compared, which show that the spin-forbidden reactivity of transition metal oxo species can be safely described by a MECP approach, at least for the first-row transition metals investigated here, where the spin-orbit coupling is relatively weak. However, for the Mn-oxo reactivity, the MECP and TS SOC have been found to be crucial for a correct description of the reaction mechanism. In particular, the TS SOC approach allows to straightforwardly explore detailed features of the adiabatic potential energy surface which in principle could affect the overall reaction rate in cases where the involved diabatic PESs are tricky.
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Affiliation(s)
- Damiano Ricciarelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy
| | - Leonardo Belpassi
- CNR Institute of Chemical Science and Technologies "Giulio Natta" (CNR-SCITEC), via Elce di Sotto 8, 06123, Perugia, Italy.,Consortium for Computational Molecular and Materials Sciences (CMS)2, via Elce di Sotto 8, 06123, Perugia, Italy
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001, Leuven, Belgium
| | - Paola Belanzoni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy.,CNR Institute of Chemical Science and Technologies "Giulio Natta" (CNR-SCITEC), via Elce di Sotto 8, 06123, Perugia, Italy.,Consortium for Computational Molecular and Materials Sciences (CMS)2, via Elce di Sotto 8, 06123, Perugia, Italy
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12
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Zhang Y, Cao W, Yang DS. Spin-orbit coupling and vibronic transitions of two Ce(C4H6) isomers probed by mass-analyzed threshold ionization and relativistic quantum computation. J Chem Phys 2019; 151:124307. [DOI: 10.1063/1.5123729] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Yuchen Zhang
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
| | - Wenjin Cao
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
| | - Dong-Sheng Yang
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA
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13
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Gaggioli CA, Stoneburner SJ, Cramer CJ, Gagliardi L. Beyond Density Functional Theory: The Multiconfigurational Approach To Model Heterogeneous Catalysis. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01775] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Carlo Alberto Gaggioli
- Department of Chemistry, Chemical Theory Center and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Samuel J. Stoneburner
- Department of Chemistry, Chemical Theory Center and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Christopher J. Cramer
- Department of Chemistry, Chemical Theory Center and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Laura Gagliardi
- Department of Chemistry, Chemical Theory Center and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
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14
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Zhao L, Pan S, Holzmann N, Schwerdtfeger P, Frenking G. Chemical Bonding and Bonding Models of Main-Group Compounds. Chem Rev 2019; 119:8781-8845. [DOI: 10.1021/acs.chemrev.8b00722] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Lili Zhao
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Sudip Pan
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
| | - Nicole Holzmann
- Scientific Computing Department, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, United Kingdom
| | - Peter Schwerdtfeger
- The New Zealand Institute for Advanced Study, Massey University (Albany), 0632 Auckland, New Zealand
| | - Gernot Frenking
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Center for Advanced Materials, Nanjing Tech University, Nanjing 211816, China
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, D-35043 Marburg, Germany
- Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain
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15
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Balasubramanian K, Gupta SP. Quantum Molecular Dynamics, Topological, Group Theoretical and Graph Theoretical Studies of Protein-Protein Interactions. Curr Top Med Chem 2019; 19:426-443. [PMID: 30836919 DOI: 10.2174/1568026619666190304152704] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 11/08/2018] [Accepted: 11/28/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Protein-protein interactions (PPIs) are becoming increasingly important as PPIs form the basis of multiple aggregation-related diseases such as cancer, Creutzfeldt-Jakob, and Alzheimer's diseases. This mini-review presents hybrid quantum molecular dynamics, quantum chemical, topological, group theoretical, graph theoretical, and docking studies of PPIs. We also show how these theoretical studies facilitate the discovery of some PPI inhibitors of therapeutic importance. OBJECTIVE The objective of this review is to present hybrid quantum molecular dynamics, quantum chemical, topological, group theoretical, graph theoretical, and docking studies of PPIs. We also show how these theoretical studies enable the discovery of some PPI inhibitors of therapeutic importance. METHODS This article presents a detailed survey of hybrid quantum dynamics that combines classical and quantum MD for PPIs. The article also surveys various developments pertinent to topological, graph theoretical, group theoretical and docking studies of PPIs and highlight how the methods facilitate the discovery of some PPI inhibitors of therapeutic importance. RESULTS It is shown that it is important to include higher-level quantum chemical computations for accurate computations of free energies and electrostatics of PPIs and Drugs with PPIs, and thus techniques that combine classical MD tools with quantum MD are preferred choices. Topological, graph theoretical and group theoretical techniques are shown to be important in studying large network of PPIs comprised of over 100,000 proteins where quantum chemical and other techniques are not feasible. Hence, multiple techniques are needed for PPIs. CONCLUSION Drug discovery and our understanding of complex PPIs require multifaceted techniques that involve several disciplines such as quantum chemistry, topology, graph theory, knot theory and group theory, thus demonstrating a compelling need for a multi-disciplinary approach to the problem.
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Affiliation(s)
- Krishnan Balasubramanian
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, AZ 85287-1604, United States
| | - Satya P Gupta
- Department of Pharmaceutical Technology, Meerut Institute of Engineering Technology, Meerut-250002, India
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16
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Kinetics of Enzymatic Mercury Methylation at Nanomolar Concentrations Catalyzed by HgcAB. Appl Environ Microbiol 2019; 85:AEM.00438-19. [PMID: 31028026 DOI: 10.1128/aem.00438-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/20/2019] [Indexed: 11/20/2022] Open
Abstract
Methylmercury (MeHg) is a potent bioaccumulative neurotoxin that is produced by certain anaerobic bacteria and archaea. Mercury (Hg) methylation has been linked to the gene pair hgcAB, which encodes a membrane-associated corrinoid protein and a ferredoxin. Although microbial Hg methylation has been characterized in vivo, the cellular biochemistry and the specific roles of the gene products HgcA and HgcB in Hg methylation are not well understood. Here, we report the kinetics of Hg methylation in cell lysates of Desulfovibrio desulfuricans ND132 at nanomolar Hg concentrations. The enzymatic Hg methylation mediated by HgcAB is highly oxygen sensitive, irreversible, and follows Michaelis-Menten kinetics, with an apparent Km of 3.2 nM and V max of 19.7 fmol · min-1 · mg-1 total protein for the substrate Hg(II). Although the abundance of HgcAB in the cell lysates is extremely low, Hg(II) was quantitatively converted to MeHg at subnanomolar substrate concentrations. Interestingly, increasing thiol/Hg(II) ratios did not impact Hg methylation rates, which suggests that HgcAB-mediated Hg methylation effectively competes with cellular thiols for Hg(II), consistent with the low apparent Km Supplementation of 5-methyltetrahydrofolate or pyruvate did not enhance MeHg production, while both ATP and a nonhydrolyzable ATP analog decreased Hg methylation rates in cell lysates under the experimental conditions. These studies provide insights into the biomolecular processes associated with Hg methylation in anaerobic bacteria.IMPORTANCE The concentration of Hg in the biosphere has increased dramatically over the last century as a result of industrial activities. The microbial conversion of inorganic Hg to MeHg is a global public health concern due to bioaccumulation and biomagnification of MeHg in food webs. Exposure to neurotoxic MeHg through the consumption of fish represents a significant risk to human health and can result in neuropathies and developmental disorders. Anaerobic microbial communities in sediments and periphyton biofilms have been identified as sources of MeHg in aquatic systems, but the associated biomolecular mechanisms are not fully understood. In the present study, we investigate the biochemical mechanisms and kinetics of MeHg formation by HgcAB in sulfate-reducing bacteria. These findings advance our understanding of microbial MeHg production and may help inform strategies to limit the formation of MeHg in the environment.
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Asaduzzaman A, Riccardi D, Afaneh AT, Cooper CJ, Smith JC, Wang F, Parks JM, Schreckenbach G. Environmental Mercury Chemistry - In Silico. Acc Chem Res 2019; 52:379-388. [PMID: 30689347 DOI: 10.1021/acs.accounts.8b00454] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Mercury (Hg) is a global environmental contaminant. Major anthropogenic sources of Hg emission include gold mining and the burning of fossil fuels. Once deposited in aquatic environments, Hg can undergo redox reactions, form complexes with ligands, and adsorb onto particles. It can also be methylated by microorganisms. Mercury, especially its methylated form methylmercury, can be taken up by organisms, where it bioaccumulates and biomagnifies in the food chain, leading to detrimental effects on ecosystem and human health. In support of the recently enforced Minamata Convention on Mercury, a legally binding international convention aimed at reducing the anthropogenic emission of-and human exposure to-Hg, its global biogeochemical cycle must be understood. Thus, a detailed understanding of the molecular-level interactions of Hg is crucial. The ongoing rapid development of hardware and methods has brought computational chemistry to a point that it can usefully inform environmental science. This is particularly true for Hg, which is difficult to handle experimentally due to its ultratrace concentrations in the environment and its toxicity. The current account provides a synopsis of the application of computational chemistry to filling several major knowledge gaps in environmental Hg chemistry that have not been adequately addressed experimentally. Environmental Hg chemistry requires defining the factors that determine the relative affinities of different ligands for Hg species, as they are critical for understanding its speciation, transformation and bioaccumulation in the environment. Formation constants and the nature of bonding have been determined computationally for environmentally relevant Hg(II) complexes such as chlorides, hydroxides, sulfides and selenides, in various physical phases. Quantum chemistry has been used to determine the driving forces behind the speciation of Hg with hydrochalcogenide and halide ligands. Of particular importance is the detailed characterization of solvation effects. Indeed, the aqueous phase reverses trends in affinities found computationally in the gas phase. Computation has also been used to investigate complexes of methylmercury with (seleno)amino acids, providing a molecular-level understanding of the toxicological antagonism between Hg and selenium (Se). Furthermore, evidence is emerging that ice surfaces play an important role in Hg transport and transformation in polar and alpine regions. Therefore, the diffusion of Hg and its ions through an idealized ice surface has been characterized. Microorganisms are major players in environmental mercury cycling. Some methylate inorganic Hg species, whereas others demethylate methylmercury. Quantum chemistry has been used to investigate catalytic mechanisms of enzymatic Hg methylation and demethylation. The complex interplay between the myriad chemical reactions and transport properties both in and outside microbial cells determines net biogeochemical cycling. Prospects for scaling up molecular work to obtain a mechanistic understanding of Hg cycling with comprehensive multiscale biogeochemical modeling are also discussed.
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Affiliation(s)
- Abu Asaduzzaman
- Department of Chemistry, University of Manitoba, Winnipeg, MB Canada, R3T 2N2
- School of Science, Engineering and Technology, Penn State Harrisburg, 777 West Harrisburg Pike, Middletown, Pennsylvania 17057, United States
| | - Demian Riccardi
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, Tennessee 37996, United States
| | - Akef T. Afaneh
- Department of Chemistry, University of Manitoba, Winnipeg, MB Canada, R3T 2N2
- Department of Chemistry, Faculty of Science, Al-Balqa Applied University, P.O. Box 19117,
postal code 19117, Al-Salt, Jordan
| | - Connor J. Cooper
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jeremy C. Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, Tennessee 37996, United States
| | - Feiyue Wang
- Centre for Earth Observation Science and Department of Environment and Geography, University of Manitoba, Winnipeg, MB Canada, R3T 2N2
| | - Jerry M. Parks
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Georg Schreckenbach
- Department of Chemistry, University of Manitoba, Winnipeg, MB Canada, R3T 2N2
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Alemayehu AB, McCormick LJ, Vazquez-Lima H, Ghosh A. Relativistic Effects on a Metal-Metal Bond: Osmium Corrole Dimers. Inorg Chem 2019; 58:2798-2806. [PMID: 30730723 DOI: 10.1021/acs.inorgchem.8b03391] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of metal-metal bonded osmium corrole dimers, {Os[T pXPC]}2, were synthesized in reasonably good yields (35-46%) via the interaction of the corresponding free-base meso-tris( p-X-phenyl)corroles (H3[T pXPC], X = CF3, H, CH3, and OCH3), Os3(CO)12, and potassium carbonate in 1,2,4-trichlorobenzene under an inert atmosphere at 180 °C over several hours. The complexes are only the second class of Os corroles reported to date (the first being OsVIN corroles) and also the second class of metal-metal bonded metallocorrole dimers (the other being Ru corrole dimers). Comparison of the X-ray structures, redox potentials, and optical spectra of analogous Ru and Os corrole dimers, along with scalar-relativistic DFT calculations, has provided an experimentally calibrated account of relativistic effects in these complexes. Three of the Os corrole dimers (X = CF3, H, and OCH3) were analyzed with single-crystal X-ray diffraction analysis, revealing inversion-related corrole rings with eclipsed Os-N bonds and Os-Os distances of ∼2.24 Å that are ∼0.06 Å longer than the Ru-Ru distances in the analogous Ru corrole dimers. Interestingly, a comparison of scalar-relativistic and nonrelativistic DFT calculations indicates that this difference in metal-metal bond distance does not, in fact, reflect a differential relativistic effect. For a given corrole ligand, the Ru and Os corrole dimers exhibit nearly identical oxidation potentials but dramatically different reduction potentials, with the Os values ∼0.5 V lower relative to Ru, suggesting that whereas oxidation occurs in a ligand-centered manner, reduction is substantially metal-centered, which indeed was confirmed by scalar-relativistic calculations. The calculations further indicate that approximately a third of the ∼0.5 V difference in reduction potentials can be ascribed to relativity. The somewhat muted value of this relativistic effect appears to be related to the finding that reduction of an Os corrole dimer is not exclusively metal-based but that a significant amount of spin density is delocalized over to the corrole ligand; in contrast, reduction of an Ru corrole dimer occurs exclusively on the Ru-Ru linkage. For isoelectronic complexes, the Ru and Os corrole dimers exhibit substantially different UV-vis spectra. A key difference is a strong near-UV feature of the Os series, which in energy terms is blue-shifted by ∼0.55 V relative to the analogous feature of the Ru series. TDDFT calculations suggest that this difference may be related to higher-energy Os(5d)-based LUMOs in the Os case relative to analogous MOs for Ru.
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Affiliation(s)
- Abraham B Alemayehu
- Department of Chemistry , UiT - The Arctic University of Norway , N-9037 Tromsø , Norway
| | - Laura J McCormick
- Advanced Light Source , Lawrence Berkeley National Laboratory , Berkeley , California 94720-8229 , United States
| | - Hugo Vazquez-Lima
- Department of Chemistry , UiT - The Arctic University of Norway , N-9037 Tromsø , Norway
| | - Abhik Ghosh
- Department of Chemistry , UiT - The Arctic University of Norway , N-9037 Tromsø , Norway
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Regnell O, Watras CJ. Microbial Mercury Methylation in Aquatic Environments: A Critical Review of Published Field and Laboratory Studies. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:4-19. [PMID: 30525497 DOI: 10.1021/acs.est.8b02709] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Methylmercury (MeHg) is an environmental contaminant of concern because it biomagnifies in aquatic food webs and poses a health hazard to aquatic biota, piscivorous wildlife and humans. The dominant source of MeHg to freshwater systems is the methylation of inorganic Hg (IHg) by anaerobic microorganisms; and it is widely agreed that in situ rates of Hg methylation depend on two general factors: the activity of Hg methylators and their uptake of IHg. A large body of research has focused on the biogeochemical processes that regulate these two factors in nature; and studies conducted within the past ten years have made substantial progress in identifying the genetic basis for intracellular methylation and defining the processes that govern the cellular uptake of IHg. Current evidence indicates that all Hg methylating anaerobes possess the gene pair hgcAB that encodes proteins essential for Hg methylation. These genes are found in a large variety of anaerobes, including iron reducers and methanogens; but sulfate reduction is the metabolic process most often reported to show strong links to MeHg production. The uptake of Hg substrate prior to methylation may occur by passive or active transport, or by a combination of both. Competitive inhibition of Hg uptake by Zn speaks in favor of active transport and suggests that essential metal transporters are involved. Shortly after its formation, MeHg is typically released from cells, but the efflux mechanisms are unknown. Although methylation facilitates Hg depuration from the cell, evidence suggests that the hgcAB genes are not induced or favored by Hg contamination. Instead, high MeHg production can be linked to high Hg bioavailability as a result of the formation of Hg(SH)2, HgS nanoparticles, and Hg-thiol complexes. It is also possible that sulfidic conditions require strong essential metal uptake systems that inadvertently bring Hg into the cytoplasm of Hg methylating microbes. In comparison with freshwaters, Hg methylation in open ocean waters appears less restricted to anoxic environments. It does seem to occur mainly in oxygen deficient zones (ODZs), and possibly within anaerobic microzones of settling organic matter, but MeHg (CH3Hg+) and Me2Hg ((CH3)2Hg) have been shown to form also in surface water samples from the euphotic zone. Future studies may disclose whether several different pathways lead to Hg methylation in marine waters and explain why Me2Hg is a significant Hg species in oceans but seemingly not in most freshwaters.
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Affiliation(s)
- Olof Regnell
- Department of Biology/Aquatic Ecology , Lund University , SE-223 62 Lund , Sweden
| | - Carl J Watras
- Bureau of Water Quality , Wisconsin Department of Natural Resources , Madison , Wisconsin 53703 , United States
- Center for Limnology , University of Wisconsin-Madison , 3110 Trout Lake Station Drive , Boulder Junction , Wisconsin 54512 , United States
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20
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Knecht S, Jensen HJA, Saue T. Relativistic quantum chemical calculations show that the uranium molecule U2 has a quadruple bond. Nat Chem 2018; 11:40-44. [DOI: 10.1038/s41557-018-0158-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 09/13/2018] [Indexed: 12/31/2022]
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21
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Jerabek P, Vondung L, Schwerdtfeger P. Tipping the Balance between Ligand and Metal Protonation due to Relativistic Effects: Unusually High Proton Affinity in Gold(I) Pincer Complexes. Chemistry 2018; 24:6047-6051. [DOI: 10.1002/chem.201800755] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Paul Jerabek
- Centre for Theoretical Chemistry and Physics, The New Zealand Institute for Advanced Study; the Institute for Natural and Mathematical Sciences; Massey University Albany; Auckland New Zealand
| | - Lisa Vondung
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Str. 4 35032 Marburg Germany
| | - Peter Schwerdtfeger
- Centre for Theoretical Chemistry and Physics, The New Zealand Institute for Advanced Study; the Institute for Natural and Mathematical Sciences; Massey University Albany; Auckland New Zealand
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22
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Battaglia S, Keller S, Knecht S. Efficient Relativistic Density-Matrix Renormalization Group Implementation in a Matrix-Product Formulation. J Chem Theory Comput 2018; 14:2353-2369. [DOI: 10.1021/acs.jctc.7b01065] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stefano Battaglia
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Sebastian Keller
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Stefan Knecht
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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23
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Takayanagi T, Nakatomi T. Automated reaction path searches for spin-forbidden reactions. J Comput Chem 2018; 39:1319-1326. [PMID: 29504140 DOI: 10.1002/jcc.25202] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/02/2018] [Accepted: 02/14/2018] [Indexed: 01/09/2023]
Abstract
Many catalytic and biomolecular reactions containing transition metals involve changes in the electronic spin state. These processes are referred to as "spin-forbidden" reactions within nonrelativistic quantum mechanics framework. To understand detailed reaction mechanisms of spin-forbidden reactions, one must characterize reaction pathways on potential energy surfaces with different spin states and then identify crossing points. Here we propose a practical computational scheme, where only the lowest mixed-spin eigenstate obtained from the diagonalization of the spin-coupled Hamiltonian matrix is used in reaction path search calculations. We applied this method to the 6,4 FeO+ + H2 → 6,4 Fe+ + H2 O, 6,4 FeO+ + CH4 → 6,4 Fe+ + CH3 OH, and 7 Mn+ + OCS → 5 MnS+ + CO reactions, for which crossings between the different spin states are known to play essential roles in the overall reaction kinetics. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Toshiyuki Takayanagi
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-Ku, Saitama City, Saitama, 338-8570, Japan
| | - Taiki Nakatomi
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-Ku, Saitama City, Saitama, 338-8570, Japan
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De Santis M, Rampino S, Quiney HM, Belpassi L, Storchi L. Charge-Displacement Analysis via Natural Orbitals for Chemical Valence in the Four-Component Relativistic Framework. J Chem Theory Comput 2018; 14:1286-1296. [DOI: 10.1021/acs.jctc.7b01077] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Matteo De Santis
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Sergio Rampino
- Istituto di Scienze e Tecnologie Molecolari, Consiglio Nazionale delle Ricerche c/o Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Harry M. Quiney
- ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, The University of Melbourne, 3010 Victoria, Australia
| | - Leonardo Belpassi
- Istituto di Scienze e Tecnologie Molecolari, Consiglio Nazionale delle Ricerche c/o Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
- Consortium for Computational Molecular and Materials Sciences (CMS)2, Via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Loriano Storchi
- Istituto di Scienze e Tecnologie Molecolari, Consiglio Nazionale delle Ricerche c/o Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
- Dipartimento di Farmacia, Università degli Studi ‘G. D’Annunzio’, Via dei Vestini 31, 66100 Chieti, Italy
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25
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Gaggioli CA, Belpassi L, Tarantelli F, Harvey JN, Belanzoni P. Spin-Forbidden Reactions: Adiabatic Transition States Using Spin-Orbit Coupled Density Functional Theory. Chemistry 2017; 24:5006-5015. [DOI: 10.1002/chem.201704608] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Carlo Alberto Gaggioli
- Department of Chemistry; Chemical Theory Center and Supercomputing Institute; University of Minnesota; 207 Pleasant Street SE 55455-0431 Minneapolis Minnesota USA
| | - Leonardo Belpassi
- Institute of Molecular Science and Technologies (ISTM)-; CNR; via Elce di Sotto 8 06123 Perugia Italy
- Consortium for Computational Molecular and Materials Sciences (CMS); via Elce di Sotto 8 06123 Perugia Italy
| | - Francesco Tarantelli
- Institute of Molecular Science and Technologies (ISTM)-; CNR; via Elce di Sotto 8 06123 Perugia Italy
- Consortium for Computational Molecular and Materials Sciences (CMS); via Elce di Sotto 8 06123 Perugia Italy
- Department of Chemistry; Biology and Biotechnology; University of Perugia; via Elce di Sotto 8 06123 Perugia Italy
| | - Jeremy N. Harvey
- Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgium
| | - Paola Belanzoni
- Institute of Molecular Science and Technologies (ISTM)-; CNR; via Elce di Sotto 8 06123 Perugia Italy
- Consortium for Computational Molecular and Materials Sciences (CMS); via Elce di Sotto 8 06123 Perugia Italy
- Department of Chemistry; Biology and Biotechnology; University of Perugia; via Elce di Sotto 8 06123 Perugia Italy
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