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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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Quintano M, Moura RT, Kraka E. Exploring Jahn-Teller distortions: a local vibrational mode perspective. J Mol Model 2024; 30:102. [PMID: 38478107 PMCID: PMC11315727 DOI: 10.1007/s00894-024-05882-8] [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: 12/10/2023] [Accepted: 02/20/2024] [Indexed: 04/06/2024]
Abstract
The characterization of normal mode (CNM) procedure coupled with an adiabatic connection scheme (ACS) between local and normal vibrational modes, both being a part of the Local Vibrational Mode theory developed in our group, can identify spectral changes as structural fingerprints that monitor symmetry alterations, such as those caused by Jahn-Teller (JT) distortions. Employing the PBE0/Def2-TZVP level of theory, we investigated in this proof-of-concept study the hexaaquachromium cation case,[ Cr ( OH 2 ) 6 ] 3 + /[ Cr ( OH 2 ) 6 ] 2 + , as a commonly known example for a JT distortion, followed by the more difficult ferrous and ferric hexacyanide anion case,[ Fe ( CN ) 6 ] 4 - /[ Fe ( CN ) 6 ] 3 - . We found that in both cases CNM of the characteristic normal vibrational modes reflects delocalization consistent with high symmetry and ACS confirms symmetry breaking, as evidenced by the separation of axial and equatorial group frequencies. As underlined by the Cremer-Kraka criterion for covalent bonding, from[ Cr ( OH 2 ) 6 ] 3 + to[ Cr ( OH 2 ) 6 ] 2 + there is an increase in axial covalency whereas the equatorial bonds shift toward electrostatic character. From[ Fe ( CN ) 6 ] 4 - to[ Fe ( CN ) 6 ] 3 - we observed an increase in covalency without altering the bond nature. Distinct π back-donation disparity could be confirmed by comparison with the isolated CN- system. In summary, our study positions the CNM/ACS protocol as a robust tool for investigating less-explored JT distortions, paving the way for future applications.
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Affiliation(s)
- Mateus Quintano
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, TX, 75275-0314, USA
| | - Renaldo T Moura
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, TX, 75275-0314, USA
- Department of Chemistry and Physics, Center of Agrarian Sciences, Federal University of Paraiba, Areia, PB, 58397-000, Brazil
| | - 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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Dangat Y, Freindorf M, Kraka E. Mechanistic Insights into S-Depalmitolyse Activity of Cln5 Protein Linked to Neurodegeneration and Batten Disease: A QM/MM Study. J Am Chem Soc 2024; 146:145-158. [PMID: 38055807 DOI: 10.1021/jacs.3c06397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Ceroid lipofuscinosis neuronal protein 5 (Cln5) is encoded by the CLN5 gene. The genetic variants of this gene are associated with the CLN5 form of Batten disease. Recently, the first crystal structure of Cln5 was reported. Cln5 shows cysteine palmitoyl thioesterase S-depalmitoylation activity, which was explored via fluorescent emission spectroscopy utilizing the fluorescent probe DDP-5. In this work, the mechanism of the reaction between Cln5 and DDP-5 was studied computationally by applying a QM/MM methodology at the ωB97X-D/6-31G(d,p):AMBER level. The results of our study clearly demonstrate the critical role of the catalytic triad Cys280-His166-Glu183 in S-depalmitoylation activity. This is evidenced through a comparison of the pathways catalyzed by the Cys280-His166-Glu183 triad and those with only Cys280 involved. The computed reaction barriers are in agreement with the catalytic efficiency. The calculated Gibb's free-energy profile suggests that S-depalmitoylation is a rate-limiting step compared to the preceding S-palmitoylation, with barriers of 26.1 and 25.3 kcal/mol, respectively. The energetics were complemented by monitoring the fluctuations in the electron density distribution through NBO charges and bond strength alterations via local mode stretching force constants during the catalytic pathways. This comprehensive protocol led to a more holistic picture of the reaction mechanism at the atomic level. It forms the foundation for future studies on the effects of gene mutations on both the S-palmitoylation and S-depalmitoylation steps, providing valuable data for the further development of enzyme replacement therapy, which is currently the only FDA-approved therapy for childhood neurodegenerative diseases, including Batten disease.
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Affiliation(s)
- Yuvraj Dangat
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Marek Freindorf
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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Wilson DJD. Extreme NMR shielding in fluoro-nitrogen cations. Phys Chem Chem Phys 2023; 25:25420-25434. [PMID: 37706351 DOI: 10.1039/d3cp03399f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
The structure and NMR shielding of a set of N-F containing cations is reported to near-quantitative accuracy from extensive ab initio calculations. Currently, the shortest experimentally confirmed N-F bond is 1.2461(10) Å in NNF+, however CCSD(T)-F12b/cc-pVQZ-F12 optimised geometries suggest that even shorter N-F bonds are possible for both monocations (1.236 Å, HNF+) and dications (1.098 Å, NF2+). NMR shielding constants have been calculated in a composite manner with individual components from coupled-cluster expansions up to CCSDTQP and basis sets up to aug-cc-pCV8Z, together with vibrational and relativistic corrections. 15N and 19F NMR chemical shifts correlate well with available experimental data. Extreme 19F chemical shifts are predicted for HNF+ (1628.9 ppm) and NH2F2+ (1298.0 ppm), which are by far the largest 19F chemical shifts ever reported and well outside the known range of +865 ppm (F2O2) to -448 ppm (ClF). The 15N chemical shift of -1283.07 ppm in HNF+ is similarly extreme, being well outside the known range of 15N chemical shifts of -730 to 260 ppm (CH3NO2 reference). This work highlights the application of state-of-the-art theoretical techniques, and provides accurate NMR properties of both isolated and yet unknown N-F cations, which can serve to guide and supplement NMR experimentation.
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Affiliation(s)
- David J D Wilson
- Department of Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.
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Madushanka A, Verma N, Freindorf M, Kraka E. Papaya Leaf Extracts as Potential Dengue Treatment: An In-Silico Study. Int J Mol Sci 2022; 23:12310. [PMID: 36293162 PMCID: PMC9610845 DOI: 10.3390/ijms232012310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022] Open
Abstract
Dengue fever (DF), dengue hemorrhagic fever (DHF), and dengue shock syndrome (DSS) cause serious public health problems, with nearly 390 million people affected and 20,000 deaths per year in tropical and subtropical countries. Despite numerous attempts, no antiviral drug or vaccine is currently available to combat the manifestation. The challenge of discovering an efficient vaccine is enhanced by the surplus presence of efficient vectors and drug resistance from the virus. For centuries, papaya (Carica papaya) extracts have been traditionally used to treat DF, DHF, and DSS. In the present study, we systematically investigated seven compounds isolated from papaya leaf extract with regard to their potential as inhibitors for non-structural (NS) proteins, NS3 and NS5, which play a crucial role in viral RNA replication. The computational tools applied stretched across classical molecular docking, molecular dynamics (MD) simulations and SwissADME used to calculate binding affinities; binding free energies; Absorption, Distribution, Metabolism, and Excretion (ADME); and drug-likeness properties, thus, identifying Kaempferol, Chlorogenic acid, and Quercetin as potential candidates, with Kaempferol and Quercetin scoring best. Therefore, for the Kaempferol and Quercetin complexes, hybrid quantum mechanical/molecular mechanical (QM/MM) geometry and frequency calculations were performed, followed by the local mode analysis developed in our group to quantify Kaempferol-NS and Quercetin-NS hydrogen bonding. Given the non-toxic nature and the wide availability of the Kaempferol and Quercetin papaya extract in almost all of the susceptible regions, and our results showing high NS3 and NS5 binding affinities and energies, strong hydrogen bonding with both NS3 and NS5, and excellent ADME properties, we suggest Kaempferol and Quercetin as a strong NS3 and NS5 inhibitor to be further investigated in vitro.
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Affiliation(s)
| | | | | | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, P.O. Box 750314, Dallas, TX 75275, USA
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Freindorf M, Delgado AAA, Kraka E. CO bonding in hexa‐ and pentacoordinate carboxy‐neuroglobin: A quantum mechanics/molecular mechanics and local vibrational mode study. J Comput Chem 2022. [DOI: 10.1002/jcc.26973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marek Freindorf
- Department of Chemistry Southern Methodist University Dallas Texas USA
| | | | - Elfi Kraka
- Department of Chemistry Southern Methodist University Dallas Texas USA
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Mechanistic Details of the Sharpless Epoxidation of Allylic Alcohols—A Combined URVA and Local Mode Study. Catalysts 2022. [DOI: 10.3390/catal12070789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In this work, we investigated the catalytic effects of a Sharpless dimeric titanium (IV)–tartrate–diester catalyst on the epoxidation of allylalcohol with methyl–hydroperoxide considering four different orientations of the reacting species coordinated at the titanium atom (reactions R1–R4) as well as a model for the non-catalyzed reaction (reaction R0). As major analysis tools, we applied the URVA (Unified Reaction Valley Approach) and LMA (Local Mode Analysis), both being based on vibrational spectroscopy and complemented by a QTAIM analysis of the electron density calculated at the DFT level of theory. The energetics of each reaction were recalculated at the DLPNO-CCSD(T) level of theory. The URVA curvature profiles identified the important chemical events of all five reactions as peroxide OO bond cleavage taking place before the TS (i.e., accounting for the energy barrier) and epoxide CO bond formation together with rehybridization of the carbon atoms of the targeted CC double bond after the TS. The energy decomposition into reaction phase contribution phases showed that the major effect of the catalyst is the weakening of the OO bond to be broken and replacement of OH bond breakage in the non-catalyzed reaction by an energetically more favorable TiO bond breakage. LMA performed at all stationary points rounded up the investigation (i) quantifying OO bond weakening of the oxidizing peroxide upon coordination at the metal atom, (ii) showing that a more synchronous formation of the new CO epoxide bonds correlates with smaller bond strength differences between these bonds, and (iii) elucidating the different roles of the three TiO bonds formed between catalyst and reactants and their interplay as orchestrated by the Sharpless catalyst. We hope that this article will inspire the computational community to use URVA complemented with LMA in the future as an efficient mechanistic tool for the optimization and fine-tuning of current Sharpless catalysts and for the design new of catalysts for epoxidation reactions.
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Margaret McCutcheon M, Freindorf M, Kraka E. Bonding in Nitrile Photo-dissociating Ruthenium Drug Candidates --A Local Vibrational Mode Study. J Chem Phys 2022; 157:014301. [DOI: 10.1063/5.0094567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we investigated bonding features 15 ruthenium complexes of the type [Ru(tpy)(L)-(CH3CN)]n+, containing the tridentate tpy ligand (tpy = 2,2':6',2'--terpyridine) and various bidentate ancillary ligands, 12 compounds originally synthesized by Loftus et al. (J. Phys. Chem. C 123, 10291-10299 (2019)) complemented with three additional complexes. The main focus of our work was to relate these local features to the experimental data of Loftus et al. which assess the efficiency of nitrile release in an indirect way via observed quantum yields for ruthenium water association after nitrile release. As a tool to quantitatively assess Ru-NC and Ru-L bonding we utilized the local vibrational mode analysis complemented by the topological analysis of the electron density and the natural bond orbital analysis. Interestingly, the stronger Ru-NC bonds have the greater observed quantum yields, leading to the conclusion that the observed quantum yields are a result of a complex interplay of several processes excluding a direct relationship between QY and Ru-NC or Ru-L bond strengths. We identified the ST splitting as one of the key players and not the Ru-NC bond strength, as one may have thought. In summary, this work has presented a modern computational tool set for the investigation of bonding features applied to nitrile photo-dissociating ruthenium drug candidates forming a valuable basis for future design and fine tuning of nitrile releasing ruthenium compounds, as well as for the understanding of how local properties affect overall experimental outcomes.
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Affiliation(s)
| | | | - Elfi Kraka
- Chemistry, Southern Methodist University, United States of America
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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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BF3–Catalyzed Diels–Alder Reaction between Butadiene and Methyl Acrylate in Aqueous Solution—An URVA and Local Vibrational Mode Study. Catalysts 2022. [DOI: 10.3390/catal12040415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In this study we investigate the Diels–Alder reaction between methyl acrylate and butadiene, which is catalyzed by BF3 Lewis acid in explicit water solution, using URVA and Local Mode Analysis as major tools complemented with NBO, electron density and ring puckering analyses. We considered four different starting orientations of methyl acrylate and butadiene, which led to 16 DA reactions in total. In order to isolate the catalytic effects of the BF3 catalyst and those of the water environment and exploring how these effects are synchronized, we systematically compared the non-catalyzed reaction in gas phase and aqueous solution with the catalyzed reaction in gas phase and aqueous solution. Gas phase studies were performed at the B3LYP/6-311+G(2d,p) level of theory and studies in aqueous solution were performed utilizing a QM/MM approach at the B3LYP/6-311+G(2d,p)/AMBER level of theory. The URVA results revealed reaction path curvature profiles with an overall similar pattern for all 16 reactions showing the same sequence of CC single bond formation for all of them. In contrast to the parent DA reaction with symmetric substrates causing a synchronous bond formation process, here, first the new CC single bond on the CH2 side of methyl acrylate is formed followed by the CC bond at the ester side. As for the parent DA reaction, both bond formation events occur after the TS, i.e., they do not contribute to the energy barrier. What determines the barrier is the preparation process for CC bond formation, including the approach diene and dienophile, CC bond length changes and, in particular, rehybridization of the carbon atoms involved in the formation of the cyclohexene ring. This process is modified by both the BF3 catalyst and the water environment, where both work in a hand-in-hand fashion leading to the lowest energy barrier of 9.06 kcal/mol found for the catalyzed reaction R1 in aqueous solution compared to the highest energy barrier of 20.68 kcal/mol found for the non-catalyzed reaction R1 in the gas phase. The major effect of the BF3 catalyst is the increased mutual polarization and the increased charge transfer between methyl acrylate and butadiene, facilitating the approach of diene and dienophile and the pyramidalization of the CC atoms involved in the ring formation, which leads to a lowering of the activation energy. The catalytic effect of water solution is threefold. The polar environment leads also to increased polarization and charge transfer between the reacting species, similar as in the case of the BF3 catalyst, although to a smaller extend. More important is the formation of hydrogen bonds with the reaction complex, which are stronger for the TS than for the reactant, thus stabilizing the TS which leads to a further reduction of the activation energy. As shown by the ring puckering analysis, the third effect of water is space confinement of the reacting partners, conserving the boat form of the six-member ring from the entrance to the exit reaction channel. In summary, URVA combined with LMA has led to a clearer picture on how both BF3 catalyst and aqueous environment in a synchronized effort lower the reaction barrier. These new insights will serve to further fine-tune the DA reaction of methyl acrylate and butadiene and DA reactions in general.
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Santos-Jr CV, A. F. de Souza M, Kraka E, Moura Jr RT. Analysis of spectator chemical bonds in SN2@C and @Si reaction mechanisms in the gas phase. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2021.139282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Nanayakkara S, Tao Y, Kraka E. Capturing Individual Hydrogen Bond Strengths in Ices via Periodic Local Vibrational Mode Theory: Beyond the Lattice Energy Picture. J Chem Theory Comput 2021; 18:562-579. [PMID: 34928619 DOI: 10.1021/acs.jctc.1c00357] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Local stretching force constants derived from periodic local vibrational modes at the vdW-DF2 density functional level have been employed to quantify the intrinsic hydrogen bond strength of 16 ice polymorphs, ices Ih, II, III, IV, V, VI, VII, VIII, IX, XI, XII, XIII, XIV, XV, XVII, and XIX, that are stable under ambient to elevated pressures. Based on this characterization on 1820 hydrogen bonds, relationships between local stretching force constants and structural parameters such as hydrogen bond length and angle were identified. Moreover, different bond strength distributions, from uniform to inhomogeneous, were observed for the 16 ices and could be explained in relation to different local structural elements within ices, that is, rings, that consist of different hydrogen bond types. In addition, criteria for the classification of hydrogen bonds as strong, intermediate, and weak were introduced. The latter was used to explore a different dimension of the water-ice phase diagram. These findings will provide important guidelines for assessing the credibility of new ice structures.
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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
| | - 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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Oliveira VP, Marcial BL, Machado FBC, Kraka E. Relating Bond Strength and Nature to the Thermodynamic Stability of Hypervalent Togni-Type Iodine Compounds. Chempluschem 2021; 86:1199-1210. [PMID: 34437775 DOI: 10.1002/cplu.202100285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/09/2021] [Indexed: 11/08/2022]
Abstract
The bond strength and nature of a set of 32 Togni-like reagents have been investigated at the M062X/def2-TZVP(D) level of theory in acetonitrile described with the SMD continuum solvent model, to rationalize the main factors responsible for their thermodynamic stability in different conformations, and trifluoromethylation capabilities. For the assessment of bond strength, we utilized local stretching force constants and associated bond strength orders, complemented with local features of the electron density to access the nature of the bonds. Bond dissociation energies varied from 31.6 to 79.9 kcal/mol depending on the polarizing power of the ligand trans to CF3 . Based on the analysis of the Laplacian of the density, we propose that the charge-shift bond character plays an important role in the stability of the molecules studied, especially for those containing I-O bonds. New insights on the trans influence and on possible ways to fine-tune the stability of these reagents are provided.
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Affiliation(s)
- Vytor Pinheiro Oliveira
- Instituto Tecnológico de Aeronáutica (ITA), Departamento de Química, São José dos Campos, 12228-900, São Paulo, Brazil
| | - Bruna Luana Marcial
- Instituto Federal Goiano (IF Goiano), Núcleo de Química, Campus Morrinhos, Goiás, Brazil
| | - Francisco B C Machado
- Instituto Tecnológico de Aeronáutica (ITA), Departamento de Química, São José dos Campos, 12228-900, São Paulo, Brazil
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas, 75275-0314, USA
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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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Verma N, Tao Y, Kraka E. Systematic Detection and Characterization of Hydrogen Bonding in Proteins via Local Vibrational Modes. J Phys Chem B 2021; 125:2551-2565. [DOI: 10.1021/acs.jpcb.0c11392] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Niraj Verma
- Department of Chemistry, Southern Methodist University, Dallas Texas United States
| | - Yunwen Tao
- Department of Chemistry, Southern Methodist University, Dallas Texas United States
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, Dallas Texas United States
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Nanayakkara S, Tao Y, Kraka E. Comment on "Exploring nature and predicting strength of hydrogen bonds: A correlation analysis between atoms-in-molecules descriptors, binding energies, and energy components of symmetry-adapted perturbation theory". J Comput Chem 2020; 42:516-521. [PMID: 33368440 DOI: 10.1002/jcc.26475] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/29/2020] [Accepted: 11/29/2020] [Indexed: 01/26/2023]
Abstract
We evaluate the correlation between binding energy (BE) and electron density ρ(r) at the bond critical point for 28 neutral hydrogen bonds, recently reported by Emamian and co-workers (J. Comput. Chem., 2019, 40, 2868). As an efficient tool, we use local stretching force constant k HB a derived from the local vibrational mode theory of Konkoli and Cremer. We compare the physical nature of BE versus k HB a , and provide an important explanation for cases with significant deviation in the BE- k HB a relation as well as in the BE-ρ(r) correlation. We also show that care has to be taken when different hydrogen bond strength measures are compared. The BE is a cumulative hydrogen bond strength measure while k HB a is a local measure of hydrogen bond strength covering different aspects of bonding. A simplified and unified description of hydrogen bonding is not always possible and needs an in-depth understanding of the systems involved.
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Affiliation(s)
| | - Yunwen Tao
- Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
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18
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Haags A, Reichmann A, Fan Q, Egger L, Kirschner H, Naumann T, Werner S, Vollgraff T, Sundermeyer J, Eschmann L, Yang X, Brandstetter D, Bocquet FC, Koller G, Gottwald A, Richter M, Ramsey MG, Rohlfing M, Puschnig P, Gottfried JM, Soubatch S, Tautz FS. Kekulene: On-Surface Synthesis, Orbital Structure, and Aromatic Stabilization. ACS NANO 2020; 14:15766-15775. [PMID: 33186031 PMCID: PMC7690051 DOI: 10.1021/acsnano.0c06798] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/03/2020] [Indexed: 05/08/2023]
Abstract
We revisit the question of kekulene's aromaticity by focusing on the electronic structure of its frontier orbitals as determined by angle-resolved photoemission spectroscopy. To this end, we have developed a specially designed precursor, 1,4,7(2,7)-triphenanthrenacyclononaphane-2,5,8-triene, which allows us to prepare sufficient quantities of kekulene of high purity directly on a Cu(111) surface, as confirmed by scanning tunneling microscopy. Supported by density functional calculations, we determine the orbital structure of kekulene's highest occupied molecular orbital by photoemission tomography. In agreement with a recent aromaticity assessment of kekulene based solely on C-C bond lengths, we conclude that the π-conjugation of kekulene is better described by the Clar model rather than a superaromatic model. Thus, by exploiting the capabilities of photoemission tomography, we shed light on the question which consequences aromaticity holds for the frontier electronic structure of a π-conjugated molecule.
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Affiliation(s)
- Anja Haags
- Peter
Grünberg Institut (PGI-3), Forschungszentrum
Jülich, 52425 Jülich, Germany
- Jülich
Aachen Research Alliance (JARA), Fundamentals of Future Information
Technology, 52425 Jülich, Germany
- Experimentalphysik
IV A, RWTH Aachen University, 52074 Aachen, Germany
| | - Alexander Reichmann
- Institut
für Physik, Karl-Franzens-Universität Graz, NAWI Graz, 8010 Graz, Austria
| | - Qitang Fan
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Larissa Egger
- Institut
für Physik, Karl-Franzens-Universität Graz, NAWI Graz, 8010 Graz, Austria
| | - Hans Kirschner
- Physikalisch-Technische
Bundesanstalt (PTB), 10587 Berlin, Germany
| | - Tim Naumann
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Simon Werner
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Tobias Vollgraff
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Jörg Sundermeyer
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Lukas Eschmann
- Institut
für Festkörpertheorie, Westfälische
Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Xiaosheng Yang
- Peter
Grünberg Institut (PGI-3), Forschungszentrum
Jülich, 52425 Jülich, Germany
- Jülich
Aachen Research Alliance (JARA), Fundamentals of Future Information
Technology, 52425 Jülich, Germany
- Experimentalphysik
IV A, RWTH Aachen University, 52074 Aachen, Germany
| | - Dominik Brandstetter
- Institut
für Physik, Karl-Franzens-Universität Graz, NAWI Graz, 8010 Graz, Austria
| | - François C. Bocquet
- Peter
Grünberg Institut (PGI-3), Forschungszentrum
Jülich, 52425 Jülich, Germany
- Jülich
Aachen Research Alliance (JARA), Fundamentals of Future Information
Technology, 52425 Jülich, Germany
| | - Georg Koller
- Institut
für Physik, Karl-Franzens-Universität Graz, NAWI Graz, 8010 Graz, Austria
| | | | - Mathias Richter
- Physikalisch-Technische
Bundesanstalt (PTB), 10587 Berlin, Germany
| | - Michael G. Ramsey
- Institut
für Physik, Karl-Franzens-Universität Graz, NAWI Graz, 8010 Graz, Austria
| | - Michael Rohlfing
- Institut
für Festkörpertheorie, Westfälische
Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Peter Puschnig
- Institut
für Physik, Karl-Franzens-Universität Graz, NAWI Graz, 8010 Graz, Austria
| | - J. Michael Gottfried
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Serguei Soubatch
- Peter
Grünberg Institut (PGI-3), Forschungszentrum
Jülich, 52425 Jülich, Germany
- Jülich
Aachen Research Alliance (JARA), Fundamentals of Future Information
Technology, 52425 Jülich, Germany
| | - F. Stefan Tautz
- Peter
Grünberg Institut (PGI-3), Forschungszentrum
Jülich, 52425 Jülich, Germany
- Jülich
Aachen Research Alliance (JARA), Fundamentals of Future Information
Technology, 52425 Jülich, Germany
- Experimentalphysik
IV A, RWTH Aachen University, 52074 Aachen, Germany
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19
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Chen Y, Wang F. Intermolecular Interactions Involving Heavy Alkenes H 2Si=TH 2 (T = C, Si, Ge, Sn, Pb) with H 2O and HCl: Tetrel Bond and Hydrogen Bond. ACS OMEGA 2020; 5:30210-30225. [PMID: 33251455 PMCID: PMC7689927 DOI: 10.1021/acsomega.0c04682] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 10/28/2020] [Indexed: 06/12/2023]
Abstract
The intermolecular interactions between the heavy alkenes H2Si=TH2 (T = C, Si, Ge, Sn, Pb) and H2O or HCl have been explored at the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVDZ level. The various hydrogen bond (HB) and tetrel bond (TB) complexes can be located on the basis of molecular electrostatic potential maps of the isolated monomers. The competition between TB and HB interactions has been investigated through the relaxed potential energy surface scan. The results indicate that the HB complexes become more and more unstable relative to the TB complexes with the increase of the T atomic number, and cannot even retain as a minimum in some cases, for H2Si=TH2···H2O systems. In contrast, the HB complexes are generally more stable than TB complexes, and the TB complexes exhibit rather weak binding strength, for H2Si=TH2···HCl systems. The majority of the TB complexes formed between H2Si=TH2 and H2O possesses very strong binding strength with covalent characteristics. The noncovalent TB complexes can be divided into two types on the basis of the orbital interactions: π-hole complexes, with binding angles ranging from 91 to 111°, and hybrid σ/π-hole complexes, with binding angles ranging from 130 to 165°. The interplay between different molecular interactions has been explored, and an interesting result is that the covalent TB interaction is significantly abated and becomes noncovalent because of the competitive effect.
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20
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Haags A, Reichmann A, Fan Q, Egger L, Kirschner H, Naumann T, Werner S, Vollgraff T, Sundermeyer J, Eschmann L, Yang X, Brandstetter D, Bocquet FC, Koller G, Gottwald A, Richter M, Ramsey MG, Rohlfing M, Puschnig P, Gottfried JM, Soubatch S, Tautz FS. Kekulene: On-Surface Synthesis, Orbital Structure, and Aromatic Stabilization. ACS NANO 2020; 14:15766-15775. [PMID: 33186031 DOI: 10.26434/chemrxiv.12771254.v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We revisit the question of kekulene's aromaticity by focusing on the electronic structure of its frontier orbitals as determined by angle-resolved photoemission spectroscopy. To this end, we have developed a specially designed precursor, 1,4,7(2,7)-triphenanthrenacyclononaphane-2,5,8-triene, which allows us to prepare sufficient quantities of kekulene of high purity directly on a Cu(111) surface, as confirmed by scanning tunneling microscopy. Supported by density functional calculations, we determine the orbital structure of kekulene's highest occupied molecular orbital by photoemission tomography. In agreement with a recent aromaticity assessment of kekulene based solely on C-C bond lengths, we conclude that the π-conjugation of kekulene is better described by the Clar model rather than a superaromatic model. Thus, by exploiting the capabilities of photoemission tomography, we shed light on the question which consequences aromaticity holds for the frontier electronic structure of a π-conjugated molecule.
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Affiliation(s)
- Anja Haags
- Peter Grünberg Institut (PGI-3), Forschungszentrum Jülich, 52425 Jülich, Germany
- Jülich Aachen Research Alliance (JARA), Fundamentals of Future Information Technology, 52425 Jülich, Germany
- Experimentalphysik IV A, RWTH Aachen University, 52074 Aachen, Germany
| | - Alexander Reichmann
- Institut für Physik, Karl-Franzens-Universität Graz, NAWI Graz, 8010 Graz, Austria
| | - Qitang Fan
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Larissa Egger
- Institut für Physik, Karl-Franzens-Universität Graz, NAWI Graz, 8010 Graz, Austria
| | - Hans Kirschner
- Physikalisch-Technische Bundesanstalt (PTB), 10587 Berlin, Germany
| | - Tim Naumann
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Simon Werner
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Tobias Vollgraff
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Jörg Sundermeyer
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Lukas Eschmann
- Institut für Festkörpertheorie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Xiaosheng Yang
- Peter Grünberg Institut (PGI-3), Forschungszentrum Jülich, 52425 Jülich, Germany
- Jülich Aachen Research Alliance (JARA), Fundamentals of Future Information Technology, 52425 Jülich, Germany
- Experimentalphysik IV A, RWTH Aachen University, 52074 Aachen, Germany
| | - Dominik Brandstetter
- Institut für Physik, Karl-Franzens-Universität Graz, NAWI Graz, 8010 Graz, Austria
| | - François C Bocquet
- Peter Grünberg Institut (PGI-3), Forschungszentrum Jülich, 52425 Jülich, Germany
- Jülich Aachen Research Alliance (JARA), Fundamentals of Future Information Technology, 52425 Jülich, Germany
| | - Georg Koller
- Institut für Physik, Karl-Franzens-Universität Graz, NAWI Graz, 8010 Graz, Austria
| | | | - Mathias Richter
- Physikalisch-Technische Bundesanstalt (PTB), 10587 Berlin, Germany
| | - Michael G Ramsey
- Institut für Physik, Karl-Franzens-Universität Graz, NAWI Graz, 8010 Graz, Austria
| | - Michael Rohlfing
- Institut für Festkörpertheorie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Peter Puschnig
- Institut für Physik, Karl-Franzens-Universität Graz, NAWI Graz, 8010 Graz, Austria
| | - J Michael Gottfried
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Serguei Soubatch
- Peter Grünberg Institut (PGI-3), Forschungszentrum Jülich, 52425 Jülich, Germany
- Jülich Aachen Research Alliance (JARA), Fundamentals of Future Information Technology, 52425 Jülich, Germany
| | - F Stefan Tautz
- Peter Grünberg Institut (PGI-3), Forschungszentrum Jülich, 52425 Jülich, Germany
- Jülich Aachen Research Alliance (JARA), Fundamentals of Future Information Technology, 52425 Jülich, Germany
- Experimentalphysik IV A, RWTH Aachen University, 52074 Aachen, Germany
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21
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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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22
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Martins JBL, Quintino RP, Politi JRDS, Sethio D, Gargano R, Kraka E. Computational analysis of vibrational frequencies and rovibrational spectroscopic constants of hydrogen sulfide dimer using MP2 and CCSD(T). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 239:118540. [PMID: 32502813 DOI: 10.1016/j.saa.2020.118540] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/18/2020] [Accepted: 05/24/2020] [Indexed: 06/11/2023]
Abstract
Previous studies have shown that the weakly bonded H2S dimer demands high level quantum chemical calculations to reproduce experimental values. We investigated the hydrogen bonding of H2S dimer using MP2 and CCSD(T) levels of theory in combination with aug-cc-pV(D,T,Q)Z basis sets. More precisely, the binding energies, potential energy curves, rovibrational spectroscopic constants, decomposition lifetime, and normal vibrational frequencies were calculated. In addition, we introduced the local mode analysis of Konkoli-Cremer to quantify the hydrogen bonding in the H2S dimer as well as providing for the first time the comprehensive decomposition of normal vibrational modes into local modes contributions, and a decomposition lifetime based on rate constant. The local mode force constant of the H2S dimer hydrogen bond is smaller than that of the water dimer, in accordance with the weaker hydrogen bonding in the H2S dimer.
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Affiliation(s)
- João B L Martins
- Institute of Chemistry, University of Brasília, Brasília, DF 70910-900, Brazil.
| | - Rabeshe P Quintino
- Institute of Chemistry, University of Brasília, Brasília, DF 70910-900, Brazil
| | - José R Dos S Politi
- Institute of Chemistry, University of Brasília, Brasília, DF 70910-900, Brazil
| | - Daniel Sethio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, United States
| | - Ricardo Gargano
- Institute of Physics, University of Brasília, Brasília, DF 70910-900, Brazil
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, United States
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23
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Freindorf M, Kraka E. Critical assessment of the FeC and CO bond strength in carboxymyoglobin: a QM/MM local vibrational mode study. J Mol Model 2020; 26:281. [DOI: 10.1007/s00894-020-04519-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/26/2020] [Indexed: 12/15/2022]
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24
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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: 16] [Impact Index Per Article: 4.0] [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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25
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26
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Exploring the Mechanism of Catalysis with the Unified Reaction Valley Approach (URVA)—A Review. Catalysts 2020. [DOI: 10.3390/catal10060691] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The unified reaction valley approach (URVA) differs from mainstream mechanistic studies, as it describes a chemical reaction via the reaction path and the surrounding reaction valley on the potential energy surface from the van der Waals region to the transition state and far out into the exit channel, where the products are located. The key feature of URVA is the focus on the curving of the reaction path. Moving along the reaction path, any electronic structure change of the reacting molecules is registered by a change in their normal vibrational modes and their coupling with the path, which recovers the curvature of the reaction path. This leads to a unique curvature profile for each chemical reaction with curvature minima reflecting minimal change and curvature maxima, the location of important chemical events such as bond breaking/forming, charge polarization and transfer, rehybridization, etc. A unique decomposition of the path curvature into internal coordinate components provides comprehensive insights into the origins of the chemical changes taking place. After presenting the theoretical background of URVA, we discuss its application to four diverse catalytic processes: (i) the Rh catalyzed methanol carbonylation—the Monsanto process; (ii) the Sharpless epoxidation of allylic alcohols—transition to heterogenous catalysis; (iii) Au(I) assisted [3,3]-sigmatropic rearrangement of allyl acetate; and (iv) the Bacillus subtilis chorismate mutase catalyzed Claisen rearrangement—and show how URVA leads to a new protocol for fine-tuning of existing catalysts and the design of new efficient and eco-friendly catalysts. At the end of this article the pURVA software is introduced. The overall goal of this article is to introduce to the chemical community a new protocol for fine-tuning existing catalytic reactions while aiding in the design of modern and environmentally friendly catalysts.
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27
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Makoś MZ, Zou W, Freindorf M, Kraka E. Metal–ring interactions in actinide sandwich compounds: A combined normalized elimination of the small component and local vibrational mode study. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1768314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Małgorzata Z. Makoś
- Computational and Theoretical Chemistry Group (CATCO), Southern Methodist University, Dallas, TX, USA
| | - Wenli Zou
- Institute of Modern Physics, Northwest University, and Shaanxi Key Laboratory for Theoretical Physics Frontiers, Xi'an, Shaanxi, People's Republic of China
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Southern Methodist University, Dallas, TX, USA
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Southern Methodist University, Dallas, TX, USA
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28
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Kraka E, Zou W, Tao Y. Decoding chemical information from vibrational spectroscopy data: Local vibrational mode theory. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1480] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Elfi Kraka
- Department of Chemistry Southern Methodist University Dallas Texas USA
| | - Wenli Zou
- Institute of Modern Physics Northwest University and Shaanxi Key Laboratory for Theoretical Physics Frontiers, Xi'an Shaanxi PR China
| | - Yunwen Tao
- Department of Chemistry Southern Methodist University Dallas Texas USA
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29
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Tao Y, Qiu Y, Zou W, Nanayakkara S, Yannacone S, Kraka E. In Situ Assessment of Intrinsic Strength of X-I⋯OA-Type Halogen Bonds in Molecular Crystals with Periodic Local Vibrational Mode Theory. Molecules 2020; 25:molecules25071589. [PMID: 32235623 PMCID: PMC7181175 DOI: 10.3390/molecules25071589] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/20/2020] [Accepted: 03/24/2020] [Indexed: 12/03/2022] Open
Abstract
Periodic local vibrational modes were calculated with the rev-vdW-DF2 density functional to quantify the intrinsic strength of the X-I⋯OA-type halogen bonding (X = I or Cl; OA: carbonyl, ether and N-oxide groups) in 32 model systems originating from 20 molecular crystals. We found that the halogen bonding between the donor dihalogen X-I and the wide collection of acceptor molecules OA features considerable variations of the local stretching force constants (0.1–0.8 mdyn/Å) for I⋯O halogen bonds, demonstrating its powerful tunability in bond strength. Strong correlations between bond length and local stretching force constant were observed in crystals for both the donor X-I bonds and I⋯O halogen bonds, extending for the first time the generalized Badger’s rule to crystals. It is demonstrated that the halogen atom X controlling the electrostatic attraction between the σ-hole on atom I and the acceptor atom O dominates the intrinsic strength of I⋯O halogen bonds. Different oxygen-containing acceptor molecules OA and even subtle changes induced by substituents can tweak the n→σ∗(X-I) charge transfer character, which is the second important factor determining the I⋯O bond strength. In addition, the presence of the second halogen bond with atom X of the donor X-I bond in crystals can substantially weaken the target I⋯O halogen bond. In summary, this study performing the in situ measurement of halogen bonding strength in crystalline structures demonstrates the vast potential of the periodic local vibrational mode theory for characterizing and understanding non-covalent interactions in materials.
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Affiliation(s)
- Yunwen Tao
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA; (Y.T.); (S.N.); (S.Y.)
| | - Yue Qiu
- Grimwade Centre for Cultural Materials Conservation, School of Historical and Philosophical Studies, Faculty of Arts, University of Melbourne, Parkville, VIC 3052, Australia;
| | - Wenli Zou
- Institute of Modern Physics, Northwest University, and Shaanxi Key Laboratory for Theoretical Physics Frontiers, Xi’an 710127, China;
| | - Sadisha Nanayakkara
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA; (Y.T.); (S.N.); (S.Y.)
| | - Seth Yannacone
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA; (Y.T.); (S.N.); (S.Y.)
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA; (Y.T.); (S.N.); (S.Y.)
- Correspondence:
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30
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Kraka E, Freindorf M. Characterizing the Metal–Ligand Bond Strength via Vibrational Spectroscopy: The Metal–Ligand Electronic Parameter (MLEP). TOP ORGANOMETAL CHEM 2020. [DOI: 10.1007/3418_2020_48] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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31
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Oliveira VP, Marcial BL, Machado FBC, Kraka E. Metal-Halogen Bonding Seen through the Eyes of Vibrational Spectroscopy. MATERIALS 2019; 13:ma13010055. [PMID: 31861904 PMCID: PMC6982077 DOI: 10.3390/ma13010055] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 12/09/2019] [Accepted: 12/15/2019] [Indexed: 11/17/2022]
Abstract
Incorporation of a metal center into halogen-bonded materials can efficiently fine-tune the strength of the halogen bonds and introduce new electronic functionalities. The metal atom can adopt two possible roles: serving as halogen acceptor or polarizing the halogen donor and acceptor groups. We investigated both scenarios for 23 metal–halogen dimers trans-M(Y2)(NC5H4X-3)2 with M = Pd(II), Pt(II); Y = F, Cl, Br; X = Cl, Br, I; and NC5H4X-3 = 3-halopyridine. As a new tool for the quantitative assessment of metal–halogen bonding, we introduced our local vibrational mode analysis, complemented by energy and electron density analyses and electrostatic potential studies at the density functional theory (DFT) and coupled-cluster single, double, and perturbative triple excitations (CCSD(T)) levels of theory. We could for the first time quantify the various attractive contacts and their contribution to the dimer stability and clarify the special role of halogen bonding in these systems. The largest contribution to the stability of the dimers is either due to halogen bonding or nonspecific interactions. Hydrogen bonding plays only a secondary role. The metal can only act as halogen acceptor when the monomer adopts a (quasi-)planar geometry. The best strategy to accomplish this is to substitute the halo-pyridine ring with a halo-diazole ring, which considerably strengthens halogen bonding. Our findings based on the local mode analysis provide a solid platform for fine-tuning of existing and for design of new metal–halogen-bonded materials.
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Affiliation(s)
- Vytor P. Oliveira
- Departamento de Química, Instituto Tecnológico de Aeronáutica (ITA), São José dos Campos, 12228-900 São Paulo, Brazil; (V.P.O.); (F.B.C.M.)
| | - Bruna L. Marcial
- Núcleo de Química, Instituto Federal Goiano (IF Goiano), Campus Morrinhos, 75650-000 Goiás, Brazil;
| | - Francisco B. C. Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica (ITA), São José dos Campos, 12228-900 São Paulo, Brazil; (V.P.O.); (F.B.C.M.)
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA
- Correspondence: ; Tel.: +1-214-768-2611
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Oliveira VP, Kraka E, Machado FBC. Pushing 3c–4e Bonds to the Limit: A Coupled Cluster Study of Stepwise Fluorination of First-Row Atoms. Inorg Chem 2019; 58:14777-14789. [DOI: 10.1021/acs.inorgchem.9b02458] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Vytor P. Oliveira
- Instituto Tecnológico de Aeronáutica (ITA), Departamento de Química, São José dos Campos, 12228-900 São Paulo, Brazil
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Francisco B. C. Machado
- Instituto Tecnológico de Aeronáutica (ITA), Departamento de Química, São José dos Campos, 12228-900 São Paulo, Brazil
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Lyu S, Beiranvand N, Freindorf M, Kraka E. Interplay of Ring Puckering and Hydrogen Bonding in Deoxyribonucleosides. J Phys Chem A 2019; 123:7087-7103. [PMID: 31323178 DOI: 10.1021/acs.jpca.9b05452] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The Cremer-Pople ring puckering analysis and the Konkoli-Cremer local mode analysis supported by the topological analysis of the electron density were applied for the first comprehensive analysis of the interplay between deoxyribose ring puckering and intramolecular H-bonding in 2'-deoxycytidine, 2'-deoxyadenosine, 2'-deoxythymidine, and 2'-deoxyguanosine. We mapped for each deoxyribonucleoside the complete conformational energy surface and the corresponding pseudorotation path. We found only incomplete pseudorotation cycles, caused by ring inversion, which we coined as pseudolibration paths. On each pseudolibration path a global and a local minimum separated by a transition state were identified. The investigation of H-bond free deoxyribonucleoside analogs revealed that removal of the H-bond does not restore the full conformational flexibility of the sugar ring. Our work showed that ring puckering predominantly determines the conformational energy; the larger the puckering amplitude, the lower the conformational energy. In contrast no direct correlation between conformational energy and H-bond strength was found. The longest and weakest H-bonds are located in the local minimum region, whereas the shortest and strongest H-bonds are located outside the global and local minimum regions at the turning points of the pseudolibration paths, i.e., H-bonding determines the shape and length of the pseudolibration paths. In addition to the H-bond strength, we evaluated the covalent/electrostatic character of the H-bonds applying the Cremer-Kraka criterion of covalent bonding. H-bonding in the puric bases has a more covalent character whereas in the pyrimidic bases the H-bond character is more electrostatic. We investigated how the mutual orientation of the CH2OH group and the base influences H-bond formation via two geometrical parameters describing the rotation of the substituents perpendicular to the sugar ring and their tilting relative to the ring center. According to our results, rotation is more important for H-bond formation. In addition we assessed the influence of the H-bond acceptor, the lone pair (N, respectively O), via the delocalization energy. We found larger delocalization energies corresponding to stronger H-bonds for the puric bases. The global minimum conformation of 2'-deoxyguanosine has the strongest H-bond of all conformers investigated in this work with a bond strength of 0.436 which is even stronger than the H-bond in the water dimer (0.360). The application of our new analysis to DNA deoxyribonucleotides and to unnatural base pairs, which have recently drawn a lot of attention, is in progress.
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Affiliation(s)
- Siying Lyu
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry , Southern Methodist University , 3215 Daniel Ave , Dallas , Texas 75275-0314 , United States
| | - Nassim Beiranvand
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry , Southern Methodist University , 3215 Daniel Ave , Dallas , Texas 75275-0314 , United States
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry , Southern Methodist University , 3215 Daniel Ave , Dallas , Texas 75275-0314 , United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry , Southern Methodist University , 3215 Daniel Ave , Dallas , Texas 75275-0314 , United States
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34
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Sethio D, Daku LML, Hagemann H, Kraka E. Quantitative Assessment of B-B-B, B-H b -B, and B-H t Bonds: From BH 3 to B 12 H 12 2. Chemphyschem 2019; 20:1967-1977. [PMID: 31063616 DOI: 10.1002/cphc.201900364] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/06/2019] [Indexed: 12/28/2022]
Abstract
We report the thermodynamic stabilities and the intrinsic strengths of three-center-two-electron B-B-B and B-Hb -B bonds ( H b : bridging hydrogen), and two-center-two-electron B-Ht bonds ( H t : terminal hydrogen) which can be served as a new, effective tool to determine the decisive role of the intermediates of hydrogenation/dehydrogenation reactions of borohydride. The calculated heats of formation were obtained with the G4 composite method and the intrinsic strengths of B-B-B, B-Hb -B, and B-Ht bonds were derived from local stretching force constants obtained at the B3LYP-D2/cc-pVTZ level of theory for 21 boron-hydrogen compounds, including 19 intermediates. The Quantum Theory of Atoms in Molecules (QTAIM) was used to deepen the inside into the nature of B-B-B, B-Hb -B, and B-Ht bonds. We found that all of the experimentally identified intermediates hindering the reversibility of the decomposition reactions are thermodynamically stable and possess strong B-B-B, B-Hb -B, and B-Ht bonds. This proves that thermodynamic data and intrinsic B-B-B, B-Hb -B, and B-Ht bond strengths form a new, effective tool to characterize new (potential) intermediates and to predict their role for the reversibility of the hydrogenation/dehydrogenation reactions.
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Affiliation(s)
- Daniel Sethio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas, 75275-0314, United States
| | - Latévi Max Lawson Daku
- Department of Physical Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland
| | - Hans Hagemann
- Department of Physical Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland
| | - 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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35
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New insights into Fe–H$$_{2}$$ and Fe–H$$^{-}$$ bonding of a [NiFe] hydrogenase mimic: a local vibrational mode study. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2463-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Abstract
The intrinsic bonding nature of λ 3 -iodanes was investigated to determine where its hypervalent bonds fit along the spectrum between halogen bonding and covalent bonding. Density functional theory with an augmented Dunning valence triple zeta basis set ( ω B97X-D/aug-cc-pVTZ) coupled with vibrational spectroscopy was utilized to study a diverse set of 34 hypervalent iodine compounds. This level of theory was rationalized by comparing computational and experimental data for a small set of closely-related and well-studied iodine molecules and by a comparison with CCSD(T)/aug-cc-pVTZ results for a subset of the investigated iodine compounds. Axial bonds in λ 3 -iodanes fit between the three-center four-electron bond, as observed for the trihalide species IF 2 − and the covalent FI molecule. The equatorial bonds in λ 3 -iodanes are of a covalent nature. We explored how the equatorial ligand and axial substituents affect the chemical properties of λ 3 -iodanes by analyzing natural bond orbital charges, local vibrational modes, the covalent/electrostatic character, and the three-center four-electron bonding character. In summary, our results show for the first time that there is a smooth transition between halogen bonding → 3c–4e bonding in trihalides → 3c–4e bonding in hypervalent iodine compounds → covalent bonding, opening a manifold of new avenues for the design of hypervalent iodine compounds with specific properties.
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37
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Correlation between molecular acidity (pKa) and vibrational spectroscopy. J Mol Model 2019; 25:48. [DOI: 10.1007/s00894-019-3928-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/03/2019] [Indexed: 12/17/2022]
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38
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Sethio D, Oliveira V, Kraka E. Quantitative Assessment of Tetrel Bonding Utilizing Vibrational Spectroscopy. Molecules 2018; 23:E2763. [PMID: 30366391 PMCID: PMC6278569 DOI: 10.3390/molecules23112763] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/19/2018] [Accepted: 10/20/2018] [Indexed: 01/15/2023] Open
Abstract
A set of 35 representative neutral and charged tetrel complexes was investigated with the objective of finding the factors that influence the strength of tetrel bonding involving single bonded C, Si, and Ge donors and double bonded C or Si donors. For the first time, we introduced an intrinsic bond strength measure for tetrel bonding, derived from calculated vibrational spectroscopy data obtained at the CCSD(T)/aug-cc-pVTZ level of theory and used this measure to rationalize and order the tetrel bonds. Our study revealed that the strength of tetrel bonds is affected by several factors, such as the magnitude of the σ-hole in the tetrel atom, the negative electrostatic potential at the lone pair of the tetrel-acceptor, the positive charge at the peripheral hydrogen of the tetrel-donor, the exchange-repulsion between the lone pair orbitals of the peripheral atoms of the tetrel-donor and the heteroatom of the tetrel-acceptor, and the stabilization brought about by electron delocalization. Thus, focusing on just one or two of these factors, in particular, the σ-hole description can only lead to an incomplete picture. Tetrel bonding covers a range of -1.4 to -26 kcal/mol, which can be strengthened by substituting the peripheral ligands with electron-withdrawing substituents and by positively charged tetrel-donors or negatively charged tetrel-acceptors.
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Affiliation(s)
- Daniel Sethio
- Computational and Theoretical Chemistry Group, Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA.
| | - Vytor Oliveira
- Computational and Theoretical Chemistry Group, Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA.
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group, Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA.
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39
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Freindorf M, Tao Y, Sethio D, Cremer D, Kraka E. New mechanistic insights into the Claisen rearrangement of chorismate – a Unified Reaction Valley Approach study. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1530464] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Yunwen Tao
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Daniel Sethio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
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Setiawan D, Sethio D, Cremer D, Kraka E. From strong to weak NF bonds: on the design of a new class of fluorinating agents. Phys Chem Chem Phys 2018; 20:23913-23927. [PMID: 30206587 DOI: 10.1039/c8cp03843k] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A set of 50 molecules with NF bonds was investigated to determine the factors that influence the strength of a NF bond, with the aim of designing a new class of fluorinating agents. The intrinsic bond strength of the NF bonds was used as bond strength measure, derived from local stretching NF force constants obtained at the CCSD(T)/aug-cc-pVTZ and ωB97XD/aug-cc-pVTZ levels of theory. The investigation showed that the NF bond is a tunable covalent bond, with bond strength orders ranging from 2.5 (very strong) to 0.1 (very weak). NF bond strengthening is caused by a combination of different factors and can be achieved by e.g. ionization. Whereas, the NF bond weakening can be achieved by hypervalency on the N atom, using a N→Ch (Ch: O, S, Se) donor-acceptor type bond with different electron-withdrawing groups. These new insights into the nature of the NF bond were used to propose and design a new class of fluorinating agents. Hypervalent amine-chalcogenides turned out as most promising candidates for efficient electrophilic fluorinating agents.
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Affiliation(s)
- Dani Setiawan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
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Oliveira V, Cremer D, Kraka E. The Many Facets of Chalcogen Bonding: Described by Vibrational Spectroscopy. J Phys Chem A 2017; 121:6845-6862. [PMID: 28782954 DOI: 10.1021/acs.jpca.7b06479] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A diverse set of 100 chalcogen-bonded complexes comprising neutral, cationic, anionic, divalent, and double bonded chalcogens has been investigated using ωB97X-D/aug-cc-pVTZ to determine geometries, binding energies, electron and energy density distributions, difference density distributions, vibrational frequencies, local stretching force constants, and associated bond strength orders. The accuracy of ωB97X-D was accessed by CCSD(T)/aug-cc-pVTZ calculations of a subset of 12 complexes and by the CCSD(T)/aug-cc-pVTZ //ωB97X-D binding energies of 95 complexes. Most of the weak chalcogen bonds can be rationalized on the basis of electrostatic contributions, but as the bond becomes stronger, covalent contributions can assume a primary role in the strength and geometry of the complexes. Covalency in chalcogen bonds involves the charge transfer from a lone pair orbital of a Lewis base into the σ* orbital of a divalent chalcogen or a π* orbital of a double bonded chalcogen. We describe for the first time a symmetric chalcogen-bonded homodimer stabilized by a charge transfer from a lone pair orbital into a π* orbital. New polymeric materials based on chalcogen bonds should take advantage of the extra stabilization granted by multiple chalcogen bonds, as is shown for 1,2,5-telluradiazole dimers.
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Affiliation(s)
- Vytor Oliveira
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
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42
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Chemistry is about energy and its changes: A critique of bond-length/bond-strength correlations. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.03.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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43
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Cremer D, Kraka E. Generalization of the Tolman electronic parameter: the metal–ligand electronic parameter and the intrinsic strength of the metal–ligand bond. Dalton Trans 2017; 46:8323-8338. [DOI: 10.1039/c7dt00178a] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The MLEP is a new, generally applicable measure of the metal–ligand bond strength based on vibrational spectroscopy, replacing the TEP.
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Affiliation(s)
- Dieter Cremer
- Computational and Theoretical Chemistry Group (CATCO)
- Department of Chemistry
- Southern Methodist University
- Dallas
- USA
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO)
- Department of Chemistry
- Southern Methodist University
- Dallas
- USA
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44
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Setiawan D, Kraka E, Cremer D. Quantitative Assessment of Aromaticity and Antiaromaticity Utilizing Vibrational Spectroscopy. J Org Chem 2016; 81:9669-9686. [DOI: 10.1021/acs.joc.6b01761] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dani Setiawan
- Computational and Theoretical
Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave., Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical
Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave., Dallas, Texas 75275-0314, United States
| | - Dieter Cremer
- Computational and Theoretical
Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave., Dallas, Texas 75275-0314, United States
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