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Peluzo BMTC, Moura RT, Kraka E. Extraction of uranyl from spent nuclear fuel wastewater via complexation-a local vibrational mode study. J Mol Model 2024; 30:216. [PMID: 38888814 DOI: 10.1007/s00894-024-06000-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/30/2024] [Indexed: 06/20/2024]
Abstract
CONTEXT The efficient extraction of uranyl from spent nuclear fuel wastewater for subsequent reprocessing and reuse is an essential effort toward minimization of long-lived radioactive waste. N-substituted amides and Schiff base ligands are propitious candidates, where extraction occurs via complexation with the uranyl moiety. In this study, we extensively probed chemical bonding in various uranyl complexes, utilizing the local vibrational modes theory alongside QTAIM and NBO analyses. We focused on (i) the assessment of the equatorial O-U and N-U bonding, including the question of chelation, and (ii) how the strength of the axial U = O bonds of the uranyl moiety changes upon complexation. Our results reveal that the strength of the equatorial uranium-ligand interactions correlates with their covalent character and with charge donation from O and N lone pairs into the vacant uranium orbitals. We also found an inverse relationship between the covalent character of the equatorial ligand bonds and the strength of the axial uranium-oxygen bond. In summary, our study provides valuable data for a strategic modulation of N-substituted amide and Schiff base ligands towards the maximization of uranyl extraction. METHOD Quantum chemistry calculations were performed under the PBE0 level of theory, paired with the relativistic NESCau Hamiltonian, currently implemented in Cologne2020 (interfaced with Gaussian16). Wave functions were expanded in the cc-pwCVTZ-X2C basis set for uranium and Dunning's cc-pVTZ for the remaining atoms. For the bonding properties, we utilized the package LModeA in the local modes analyses, AIMALL in the QTAIM calculations, and NBO 7.0 for the NBO analyses.
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Affiliation(s)
- Bárbara M T C Peluzo
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX, 75275-0314, USA
| | - Renaldo T Moura
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX, 75275-0314, USA
- Department of Chemistry and Physics, Center of Agrarian Sciences, Federal University of Paraíba, Areia, 58397-000, Paraíba, Brazil
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX, 75275-0314, USA.
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2
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Antonio JJ, Kraka E. Metal-ring interactions in group 2 ansa-metallocenes: assessed with the local vibrational mode theory. Phys Chem Chem Phys 2024; 26:15143-15155. [PMID: 38647402 DOI: 10.1039/d4cp00225c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Ansa-metallocenes, a vital class of organometallic compounds, have attracted significant attention due to their diverse structural motifs and their pivotal roles in catalysis and materials science. We investigated 37 distinct group 2 ansa-metallocenes at the B3LYP-D3/def2-TZVP level of theory. Utilizing local mode force constants derived from our local vibrational mode theory, including a special force constant directly targeting the metal-ring interaction, we could unveil latent structural differences between solvated and non-solvated metallocenophanes and the influence of the solvent on complex stability and structure. We could quantify the intrinsic strength of the metal-cyclopentadienyl (M-Cp) bonds and the influence of the bridging motifs on the stiffness of the Cp-M-Cp angles, another determinant of complex stability. LMA was complemented by the analysis of electronic density, utilizing the quantum theory of atoms in molecules (QTAIM), which confirmed both the impact of solvent coordination on the strength of the M-Cp bond(s) and the influence of the bridging motif on the Cp-M-Cp angles. The specific effect of the ansa-motif on the M-Cp interaction was further elucidated by a comparison with linear/bent metallocene structures. In summary, our results identify the local mode analysis as an efficient tool for unraveling the intricate molecular properties of ansa-metallocenes and their unique structural features.
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Affiliation(s)
- Juliana J Antonio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, TX 75275-0314, USA.
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, TX 75275-0314, USA.
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3
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Xu X, Jiang H, Wu K. Uranyl Affinity between Uranyl Cation and Different Kinds of Monovalent Anions: Density Functional Theory and Quantitative Structure-Property Relationship Model. J Phys Chem A 2024; 128:2960-2970. [PMID: 38576211 DOI: 10.1021/acs.jpca.4c00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
In order to design effective extractants for uranium extraction from seawater, it is imperative to acquire a more comprehensive understanding of the bonding properties between the uranyl cation (UO22+) and various ligands. Therefore, we employed density functional theory to investigate the complexation reactions of UO22+ with 29 different monovalent anions (L-1), exploring both mono- and bidentate coordination. We proposed a novel concept called "uranyl affinity" (Eua) to facilitate the establishment of a standardized scale for assessing the ease or difficulty of coordination bond formation between UO22+ and diverse ligands. Furthermore, we conducted an in-depth investigation into the underlying mechanisms involved. During the process of uranyl complex [(UO2L)+] formation, lone pair electrons from the coordinating atom in L- are transferred to either the lowest unoccupied molecular degenerate orbitals 1ϕu or 1δu of the uranyl ion, which originate from the uranium atom's 5f unoccupied orbitals. In light of discussion concerning the mechanisms of coordination bond formation, quantitative structure-property relationship analyses were conducted to investigate the correlation between Eua and various structural descriptors associated with the 29 ligands under investigation. This analysis revealed distinct patterns in Eua values while identifying key influencing factors among the different ligands.
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Affiliation(s)
- Xiang Xu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Haiyan Jiang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Kechen Wu
- Fujian Key Laboratory of Functional Marine Sensing Materials, Minjiang University, Fuzhou 350108, China
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4
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Freindorf M, Antonio JJ, Kraka E. Iron-histidine bonding in bishistidyl hemoproteins-A local vibrational mode study. J Comput Chem 2024; 45:574-588. [PMID: 38041830 DOI: 10.1002/jcc.27267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 12/04/2023]
Abstract
We investigated the intrinsic strength of distal and proximal FeN bonds for both ferric and ferrous oxidation states of bishistidyl hemoproteins from bacteria, animals, human, and plants, including two cytoglobins, ten hemoglobins, two myoglobins, six neuroglobins, and six phytoglobins. As a qualified measure of bond strength, we used local vibrational force constants ka (FeN) based on local mode theory developed in our group. All calculations were performed with a hybrid QM/MM ansatz. Starting geometries were taken from available x-ray structures. ka (FeN) values were correlated with FeN bond lengths and covalent bond character. We also investigated the stiffness of the axial NFeN bond angle. Our results highlight that protein effects are sensitively reflected in ka (FeN), allowing one to compare trends in diverse protein groups. Moreover, ka (NFeN) is a perfect tool to monitor changes in the axial heme framework caused by different protein environments as well as different Fe oxidation states.
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Affiliation(s)
- Marek Freindorf
- Chemistry Department, Southern Methodist University, Dallas, Texas, USA
| | - Juliana J Antonio
- Chemistry Department, Southern Methodist University, Dallas, Texas, USA
| | - Elfi Kraka
- Chemistry Department, Southern Methodist University, Dallas, Texas, USA
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5
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Ehrman J, Shumilov K, Jenkins AJ, Kasper JM, Vitova T, Batista ER, Yang P, Li X. Unveiling Hidden Shake-Up Features in the Uranyl M 4-Edge Spectrum. JACS AU 2024; 4:1134-1141. [PMID: 38559711 PMCID: PMC10976573 DOI: 10.1021/jacsau.3c00838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 04/04/2024]
Abstract
The M4,5-edge high energy resolution X-ray absorption near-edge structure (HR-XANES) spectra of actinyls offer valuable insights into the electronic structure and bonding properties of heavy-element complexes. To conduct a comprehensive spectral analysis, it is essential to employ computational methods that accurately account for relativistic effects and electron correlation. In this work, we utilize variational relativistic multireference configurational interaction methods to compute and analyze the X-ray M4-edge absorption spectrum of uranyl. By employing these advanced computational techniques, we achieve excellent agreement between the calculated spectral features and experimental observations. Moreover, the calculations unveil significant shake-up features, which arise from the intricate interplay between strongly correlated 3d core-electron and ligand excitations. This research provides important theoretical insights into the spectral characteristics of heavy-element complexes. Furthermore, it establishes the foundation for utilizing M4,5-edge spectroscopy as a means to investigate the chemical activities of such complexes. By leveraging this technique, we can gain a deeper understanding of the bonding behavior and reactivity of heavy-element compounds.
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Affiliation(s)
- Jordan
N. Ehrman
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Kirill Shumilov
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Andrew J. Jenkins
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Joseph M. Kasper
- Theoretical
Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Tonya Vitova
- Institute
for Nuclear Waste Disposal (INE), Karlsruhe
Institute of Technology, P.O. Box 3640, Karlsruhe D-76021, Germany
| | - Enrique R. Batista
- Theoretical
Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Ping Yang
- Theoretical
Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Xiaosong Li
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
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Peluzo BMTC, Makoś MZ, Moura RT, Freindorf M, Kraka E. Linear versus Bent Uranium(II) Metallocenes─A Local Vibrational Mode Study. Inorg Chem 2023. [PMID: 37478353 DOI: 10.1021/acs.inorgchem.3c01761] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Uranium metallocenes have recently attracted attention driven by their use as catalysts in organometallic synthesis. In addition to bent U(IV) and U(III), an U(II) metallocene [(η5-C5i Pr5)2U] was synthesized with an unusual linear Cp-U-Cp angle. In this work, we investigated 22 U(II) metallocenes, (i) assessing the intrinsic strength of the U-ring interactions in these complexes with a novel bond strength measure based on our local vibrational mode analysis and (ii) systematically exploring what makes these U(II) metallocenes bent. We included relativistic effects through the NESCau Hamiltonian and complemented the local mode analysis with natural bonding orbital (NBO) and quantum theory of atoms in molecules (QTAIM) data. Our study led to the following results: (i) reduction of bulky U-ring ligand substituents does not lead to bent complexes for alkyl substituents (iPr and iBu) in contrast to SiMe3 ring substituents, which are all bent. (ii) The most bent complexes are [(η5-C5H4SiMe3)2U] (130°) and [η5-P5H5)2U] (143°). (iii) Linear complexes showed one hybridized NBO with s/d character, while bent structures were characterized by s/d/f mixing. (iv) We did not observe a correlation between the strength of the U-ring interaction and the amount of the ring-U-ring bend; the strongest interaction was found for [η5-Cp)2U] and the weakest for [η5-P5H5)2U]. In conclusion, our results provide a foundation for the design of U(II) metallocenes with specific physicochemical properties and increased reactivity.
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Affiliation(s)
- Bárbara M T C Peluzo
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Małgorzata Z Makoś
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Renaldo T Moura
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
- Department of Chemistry and Physics, Center of Agrarian Sciences, Federal University of Paraíba, Areia 58397-000, Paraíba, Brazil
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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7
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Carneiro Neto AN, Moura RT, Carlos LD, Malta OL, Sanadar M, Melchior A, Kraka E, Ruggieri S, Bettinelli M, Piccinelli F. Dynamics of the Energy Transfer Process in Eu(III) Complexes Containing Polydentate Ligands Based on Pyridine, Quinoline, and Isoquinoline as Chromophoric Antennae. Inorg Chem 2022; 61:16333-16346. [PMID: 36201622 PMCID: PMC9580001 DOI: 10.1021/acs.inorgchem.2c02330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In this work, we investigated from a theoretical point
of view
the dynamics of the energy transfer process from the ligand to Eu(III)
ion for 12 isomeric species originating from six different complexes
differing by nature of the ligand and the total charge. The cationic
complexes present the general formula [Eu(L)(H2O)2]+ (where L = bpcd2– = N,N′-bis(2-pyridylmethyl)-trans-1,2-diaminocyclohexane N,N′-diacetate;
bQcd2– = N,N′-bis(2-quinolinmethyl)-trans-1,2-diaminocyclohexane N,N′-diacetate; and bisoQcd2– = N,N′-bis(2-isoquinolinmethyl)-trans-1,2-diaminocyclohexane N,N′-diacetate), while the neutral complexes present
the Eu(L)(H2O)2 formula (where L = PyC3A3– = N-picolyl-N,N′,N′-trans-1,2-cyclohexylenediaminetriacetate; QC3A3– = N-quinolyl-N,N′,N′-trans-1,2-cyclohexylenediaminetriacetate;
and isoQC3A3– = N-isoquinolyl-N,N′,N′-trans-1,2-cyclohexylenediaminetriacetate).
Time-dependent density functional theory (TD-DFT) calculations provided
the energy of the ligand excited donor states, distances between donor
and acceptor orbitals involved in the energy transfer mechanism (RL), spin-orbit coupling matrix elements, and
excited-state reorganization energies. The intramolecular energy transfer
(IET) rates for both singlet-triplet intersystem crossing and ligand-to-metal
(and vice versa) involving a multitude of ligand and Eu(III) levels
and the theoretical overall quantum yields (ϕovl)
were calculated (the latter for the first time without the introduction
of experimental parameters). This was achieved using a blend of DFT,
Judd–Ofelt theory, IET theory, and rate equation modeling.
Thanks to this study, for each isomeric species, the most efficient
IET process feeding the Eu(III) excited state, its related physical
mechanism (exchange interaction), and the reasons for a better or
worse overall energy transfer efficiency (ηsens)
in the different complexes were determined. The spectroscopically
measured ϕovl values are in good agreement with the
ones obtained theoretically in this work. Photophysical properties of 12 Eu(III)
complexes with pyridine,
quinoline, and isoquinoline ligands in aqueous solutions were elucidated
and predicted through a theoretical protocol using a blend of DFT,
Judd−Ofelt theory, intramolecular energy transfer theory, and
coupled rate equation modeling calculations. The theoretical procedure
is general and can be extended to any lanthanide-based complexes.
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Affiliation(s)
- Albano N Carneiro Neto
- Physics Department and CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193Aveiro, Portugal
| | - Renaldo T Moura
- Department of Chemistry and Physics, Federal University of Paraíba, 58397-000Areia, Brazil.,Department of Chemistry, Southern Methodist University, Dallas, Texas75275-0314, United States
| | - Luís D Carlos
- Physics Department and CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193Aveiro, Portugal
| | - Oscar L Malta
- Department of Fundamental Chemistry, Federal University of Pernambuco, 50740-560Recife, Brazil
| | - Martina Sanadar
- Dipartimento Politecnico di Ingegneria e Architettura, Laboratorio di Tecnologie Chimiche, University of Udine, 33100Udine, Italy
| | - Andrea Melchior
- Dipartimento Politecnico di Ingegneria e Architettura, Laboratorio di Tecnologie Chimiche, University of Udine, 33100Udine, Italy
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, Dallas, Texas75275-0314, United States
| | - Silvia Ruggieri
- Luminescent Materials Laboratory, Department of Biotechnology, University of Verona and INSTM, UdR Verona, 37134Verona, Italy
| | - Marco Bettinelli
- Luminescent Materials Laboratory, Department of Biotechnology, University of Verona and INSTM, UdR Verona, 37134Verona, Italy
| | - Fabio Piccinelli
- Luminescent Materials Laboratory, Department of Biotechnology, University of Verona and INSTM, UdR Verona, 37134Verona, Italy
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Costa Peluzo BMT, Kraka E. Uranium: The Nuclear Fuel Cycle and Beyond. Int J Mol Sci 2022; 23:ijms23094655. [PMID: 35563047 PMCID: PMC9101921 DOI: 10.3390/ijms23094655] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 01/01/2023] Open
Abstract
This review summarizes the recent developments regarding the use of uranium as nuclear fuel, including recycling and health aspects, elucidated from a chemical point of view, i.e., emphasizing the rich uranium coordination chemistry, which has also raised interest in using uranium compounds in synthesis and catalysis. A number of novel uranium coordination features are addressed, such the emerging number of U(II) complexes and uranium nitride complexes as a promising class of materials for more efficient and safer nuclear fuels. The current discussion about uranium triple bonds is addressed by quantum chemical investigations using local vibrational mode force constants as quantitative bond strength descriptors based on vibrational spectroscopy. The local mode analysis of selected uranium nitrides, N≡U≡N, U≡N, N≡U=NH and N≡U=O, could confirm and quantify, for the first time, that these molecules exhibit a UN triple bond as hypothesized in the literature. We hope that this review will inspire the community interested in uranium chemistry and will serve as an incubator for fruitful collaborations between theory and experimentation in exploring the wealth of uranium chemistry.
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Zheng XJ, Bacha RUS, Su DM, Pan QJ. Relativistic DFT Probe for Reaction Energies and Electronic/Bonding Properties of Polypyrrolic Hetero-Bimetallic Actinide Complexes: Effects of Uranyl endo-Oxo Functionalization. Inorg Chem 2021; 60:5747-5756. [PMID: 33826313 DOI: 10.1021/acs.inorgchem.1c00008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A series of hetero-bimetallic actinide complexes of the Schiff-base polypyrrolic macrocycle (L), featuring cation-cation interactions (CCIs), were systematically investigated using relativistic density functional theory (DFT). The tetrahydrofuran (THF) solvated complex [(THF)(OUVIOUIV)(THF)(L)]2+ has high reaction free energy (ΔrG), and its replacement with electron-donating iodine promotes the reaction thermodynamics to obtain uranyl iodide [(I)(OUVIOUIV)(I)(L)]2+ (UVI-UIV). Retaining this coordination geometry, calculations have been extended to other An(IV) (An = Th, Pa, Np, Pu), i.e., for the substitution of U(IV) to obtain UVI-AnIV. As a consequence, the reaction free energy is appreciably lowered, suggesting the thermodynamic feasibility for the experimental synthesis of these bimetallic complexes. Among all UVI-AnIV, the electron-spin density and high-lying occupied orbitals of UVI-PaIV show a large extent of electron transfer from electron-rich Pa(IV) to electron-deficient U(VI), leading to a more stable UV-PaV oxidation state. Additionally, the shortest bond distance and the comparatively negative Eint of the Pa-Oendo bond suggest more positive and negative charges (Q) of Pa and endo-oxo atoms, respectively. As a result of the enhanced Pa-Oendo bond and strong CCI in UVI-PaIV along with the corresponding lowest reaction free energy among all of the optimized complexes, uranyl species is a better candidate for the experimental synthesis in the ultimate context of environmental remediation.
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Affiliation(s)
- Xiu-Jun Zheng
- Institute of Food and Environmental Engineering, East University of Heilongjiang, Harbin 150066, China
| | - Raza Ullah Shah Bacha
- Key Laboratory of Functional Inorganic Material Chemistry, School of Chemistry and Materials Science, Heilongjiang University, Harbin 150080, China
| | - Dong-Mei Su
- State-Owned Assets Management Division, Harbin University, Harbin 150086, China
| | - Qing-Jiang Pan
- Key Laboratory of Functional Inorganic Material Chemistry, School of Chemistry and Materials Science, Heilongjiang University, Harbin 150080, China
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Makoś MZ, Freindorf M, Tao Y, Kraka E. Theoretical Insights into [NHC]Au(I) Catalyzed Hydroalkoxylation of Allenes: A Unified Reaction Valley Approach Study. J Org Chem 2021; 86:5714-5726. [PMID: 33780251 DOI: 10.1021/acs.joc.1c00208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Hydroxylation is an effective approach for the synthesis of carbon-oxygen bonds and allylic ethers. The [NHC]Au(I) catalyzed intermolecular hydroalkoxylation of allene was studied at the DFT and Coupled Cluster level of theory. Using the Unified Reaction Valley Approach (URVA), we carry out a comprehensive mechanistic analysis of [NHC]Au(I)-catalyzed and noncatalyzed reactions. The URVA study of several possible reaction pathways reveal that the [NHC]Au(I) catalyst enables the hydroalkoxylation reaction to occur via a two step mechanism based upon the Au ability to switch between π- and σ-complexation. The first step of the mechanism involves the formation of a CO bond after the transition state with no energy penalty. Following the CO bond breakage, the OH bond breaks and CH bond forms during the second step of the mechanism, as the catalyst transforms into the more stable π-Au complex. The URVA results were complemented with local vibrational mode analysis to provide measures of intrinsic bond strength for Au(I)-allene interactions of all stationary points, and NBO analysis was applied in order to observe charge transfer events along the reaction pathway. Overall, the π-Au C═C interactions of the products are stronger than those of the reactants adding to their exothermicity. Our work on the hydroxylation of allene provides new insights for the design of effective reaction pathways to produce allylic ethers and also unravels new strategies to form C-O bonds by activation of C═C bonds.
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Affiliation(s)
- Małgorzata Z Makoś
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Yunwen Tao
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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11
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Beiranvand N, Freindorf M, Kraka E. Hydrogen Bonding in Natural and Unnatural Base Pairs-A Local Vibrational Mode Study. Molecules 2021; 26:2268. [PMID: 33919989 PMCID: PMC8071019 DOI: 10.3390/molecules26082268] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 12/13/2022] Open
Abstract
In this work hydrogen bonding in a diverse set of 36 unnatural and the three natural Watson Crick base pairs adenine (A)-thymine (T), adenine (A)-uracil (U) and guanine (G)-cytosine (C) was assessed utilizing local vibrational force constants derived from the local mode analysis, originally introduced by Konkoli and Cremer as a unique bond strength measure based on vibrational spectroscopy. The local mode analysis was complemented by the topological analysis of the electronic density and the natural bond orbital analysis. The most interesting findings of our study are that (i) hydrogen bonding in Watson Crick base pairs is not exceptionally strong and (ii) the N-H⋯N is the most favorable hydrogen bond in both unnatural and natural base pairs while O-H⋯N/O bonds are the less favorable in unnatural base pairs and not found at all in natural base pairs. In addition, the important role of non-classical C-H⋯N/O bonds for the stabilization of base pairs was revealed, especially the role of C-H⋯O bonds in Watson Crick base pairs. Hydrogen bonding in Watson Crick base pairs modeled in the DNA via a QM/MM approach showed that the DNA environment increases the strength of the central N-H⋯N bond and the C-H⋯O bonds, and at the same time decreases the strength of the N-H⋯O bond. However, the general trends observed in the gas phase calculations remain unchanged. The new methodology presented and tested in this work provides the bioengineering community with an efficient design tool to assess and predict the type and strength of hydrogen bonding in artificial base pairs.
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Affiliation(s)
| | | | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, TX 75275-0314, USA; (N.B.); (M.F.)
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Abstract
We systematically investigated iodine–metal and iodine–iodine bonding in van Koten’s pincer complex and 19 modifications changing substituents and/or the transition metal with a PBE0–D3(BJ)/aug–cc–pVTZ/PP(M,I) model chemistry. As a novel tool for the quantitative assessment of the iodine–metal and iodine–iodine bond strength in these complexes we used the local mode analysis, originally introduced by Konkoli and Cremer, complemented with NBO and Bader’s QTAIM analyses. Our study reveals the major electronic effects in the catalytic activity of the M–I–I non-classical three-center bond of the pincer complex, which is involved in the oxidative addition of molecular iodine I2 to the metal center. According to our investigations the charge transfer from the metal to the σ* antibonding orbital of the I–I bond changes the 3c–4e character of the M–I–I three-center bond, which leads to weakening of the iodine I–I bond and strengthening of the metal–iodine M–I bond, facilitating in this way the oxidative addition of I2 to the metal. The charge transfer can be systematically modified by substitution at different places of the pincer complex and by different transition metals, changing the strength of both the M–I and the I2 bonds. We also modeled for the original pincer complex how solvents with different polarity influence the 3c–4e character of the M–I–I bond. Our results provide new guidelines for the design of pincer complexes with specific iodine–metal bond strengths and introduce the local vibrational mode analysis as an efficient tool to assess the bond strength in complexes.
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Nanayakkara S, Freindorf M, Tao Y, Kraka E. Modeling Hydrogen Release from Water with Borane and Alane Catalysts: A Unified Reaction Valley Approach. J Phys Chem A 2020; 124:8978-8993. [PMID: 33064477 DOI: 10.1021/acs.jpca.0c07244] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The unified reaction valley approach combined with the local vibrational mode and ring puckering analysis is applied to investigate the hydrogen evolution from water in the presence of small hydrides such as BH3, metal hydrides as AlH3, and their derivatives. We studied a series of reactions involving BH3, AlH3, B2H6, Al2H6, and AlH3BH3 with one- and two-water molecules, considering multiple reaction paths. In addition, the influence of the aqueous medium was examined. A general reaction mechanism was identified for most of the reactions. Those that deviate could be associated with unusually high reaction barriers with no hydrogen release. The charge transfer along the reaction path suggests that a viable hydrogen release is achieved when the catalyst adopts the role of a charge donor during the chemical processes. The puckering analysis showed that twistboat and boat forms are the predominant configurations in the case of an intermediate six-membered ring formation, which influences the activation barrier. The local mode analysis was used as a tool to detect the H-H bond formation as well as to probe catalyst regenerability. Based on the correlation between the activation energy and the change in the charge separation for cleaving O-H and B(Al)-H bonds, two promising subsets of reactions could be identified along with prescriptions for lowering the reaction barrier individually with electron-donating/withdrawing substituents.
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Affiliation(s)
- Sadisha Nanayakkara
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Yunwen Tao
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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Local Vibrational Mode Analysis of π–Hole Interactions between Aryl Donors and Small Molecule Acceptors. CRYSTALS 2020. [DOI: 10.3390/cryst10070556] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
11 aryl–lone pair and three aryl–anion π –hole interactions are investigated, along with the argon–benzene dimer and water dimer as reference compounds, utilizing the local vibrational mode theory, originally introduced by Konkoli and Cremer, to quantify the strength of the π –hole interaction in terms of a new local vibrational mode stretching force constant between the two engaged monomers, which can be conveniently used to compare different π –hole systems. Several factors have emerged which influence strength of the π –hole interactions, including aryl substituent effects, the chemical nature of atoms composing the aryl rings/ π –hole acceptors, and secondary bonding interactions between donors/acceptors. Substituent effects indirectly affect the π –hole interaction strength, where electronegative aryl-substituents moderately increase π –hole interaction strength. N-aryl members significantly increase π –hole interaction strength, and anion acceptors bind more strongly with the π –hole compared to charge neutral acceptors (lone–pair donors). Secondary bonding interactions between the acceptor and the atoms in the aryl ring can increase π –hole interaction strength, while hydrogen bonding between the π –hole acceptor/donor can significantly increase or decrease strength of the π –hole interaction depending on the directionality of hydrogen bond donation. Work is in progress expanding this research on aryl π –hole interactions to a large number of systems, including halides, CO, and OCH3− as acceptors, in order to derive a general design protocol for new members of this interesting class of compounds.
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