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Matczak P, Buday P, Kupfer S, Görls H, Mlostoń G, Weigand W. Probing the performance of DFT in the structural characterization of [FeFe] hydrogenase models. J Comput Chem 2024. [PMID: 39417365 DOI: 10.1002/jcc.27515] [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: 06/28/2024] [Revised: 09/20/2024] [Accepted: 10/01/2024] [Indexed: 10/19/2024]
Abstract
In this work, a series of DFT and DFT-D methods is combined with double-ζ basis sets to benchmark their performance in predicting the structures of five newly synthesized hexacarbonyl diiron complexes with a bridging ligand featuring a μ-S2C3 motif in a ring-containing unit functionalized with aromatic groups. Such complexes have been considered as [FeFe] hydrogenase catalytic site models with potential for eco-friendly energetic applications. According to this assessment, r2SCAN is identified as the density functional recommended for the reliable description of the molecular and crystal structures of the herein studied models. However, the butterfly (μ-S)2Fe2 core of the models demonstrates a minor deformation of its optimized geometry obtained from both molecular and periodic calculations. The FeFe bond length is slightly underestimated while the FeS bonds tend to be too long. Adding the D3(BJ) correction to r2SCAN does not lead to any improvement in the calculated structures.
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Affiliation(s)
- Piotr Matczak
- Department of Physical Chemistry, Faculty of Chemistry, University of Lodz, Lodz, Poland
| | - Philipp Buday
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Stephan Kupfer
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Helmar Görls
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Grzegorz Mlostoń
- Department of Organic and Applied Chemistry, Faculty of Chemistry, University of Lodz, Lodz, Poland
| | - Wolfgang Weigand
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
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2
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Kallmeier F, Matthews AJR, Nelmes GR, Lawson NR, Hicks J. Mechanochemical synthesis of iron aluminyl complexes. Dalton Trans 2024; 53:12450-12454. [PMID: 39011575 DOI: 10.1039/d4dt01774a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
A series of iron aluminyl complexes have been synthesised in good crystalline yields from reactions between bulky diamido aluminium iodide complexes and K[Fe(CO)2Cp] in the solid state. The series of metal-metal bonded complexes have been characterised by X-ray crystallography and were investigated using density functional theory to probe the effects of ligand substitution on the Al-Fe bond.
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Affiliation(s)
- Fabian Kallmeier
- Research School of Chemistry, Australian National University, ACT, 2601, Australia.
| | - Aidan J R Matthews
- Research School of Chemistry, Australian National University, ACT, 2601, Australia.
| | - Gareth R Nelmes
- Research School of Chemistry, Australian National University, ACT, 2601, Australia.
| | - Nina R Lawson
- Research School of Chemistry, Australian National University, ACT, 2601, Australia.
| | - Jamie Hicks
- Research School of Chemistry, Australian National University, ACT, 2601, Australia.
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3
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Binacchi F, Giorgi E, Salvadori G, Cirri D, Stifano M, Donati A, Garzella L, Busto N, Garcia B, Pratesi A, Biver T. Exploring the interaction between a fluorescent Ag(I)-biscarbene complex and non-canonical DNA structures: a multi-technique investigation. Dalton Trans 2024; 53:9700-9714. [PMID: 38775704 DOI: 10.1039/d4dt00851k] [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: 06/11/2024]
Abstract
Silver compounds are mainly studied as antimicrobial agents, but they also have anticancer properties, with the latter, in some cases, being better than their gold counterparts. Herein, we analyse the first example of a new Ag(I)-biscarbene that can bind non-canonical structures of DNA, more precisely G-quadruplexes (G4), with different binding signatures depending on the type of G4. Moreover, we show that this Ag-based carbene binds the i-motif DNA structure. Alternatively, its Au(I) counterpart, which was investigated for comparison, stabilises mitochondrial G4. Theoretical in silico studies elucidated the details of different binding modes depending on the geometry of G4. The two complexes showed increased cytotoxic activity compared to cisplatin, overcoming its resistance in ovarian cancer. The binding of these new drug candidates with other relevant biosubstrates was studied to afford a more complete picture of their possible targets. In particular, the Ag(I) complex preferentially binds DNA structures over RNA structures, with higher binding constants for the non-canonical nucleic acids with respect to natural calf thymus DNA. Regarding possible protein targets, its interaction with the albumin model protein BSA was also tested.
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Affiliation(s)
- Francesca Binacchi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Ester Giorgi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Damiano Cirri
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Mariassunta Stifano
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Aurora Donati
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Linda Garzella
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Natalia Busto
- Departamento de Ciencias de la Salud, Universidad de Burgos, Paseo de los Comendadores s/n, 09001 Burgos, Spain
| | - Begona Garcia
- Departamento de Química, Universidad de Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Alessandro Pratesi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
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4
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de Barros Leite NF, Marques RB, Macedo-Filho A, Rocha GB, Martins EPS. Evaluation of DFT methods for predicting geometries and NMR spectra of Bi(III) dithiocarbamate complexes with antitumor properties. J Mol Model 2024; 30:177. [PMID: 38775913 DOI: 10.1007/s00894-024-05969-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/09/2024] [Indexed: 06/07/2024]
Abstract
CONTEXT Bismuth complexes with dithiocarbamate ligands have attracted attention because of their biological applications, such as antimicrobial, antileishmanial, and anticancer properties. These complexes have high cytotoxic activity against cancer cells, being more active than the standard drugs cisplatin, doxorubicin, and tamoxifen. In the present study, we investigated the ability of some DFT methods to reproduce the geometries and NMR spectra of the Bi(III) dithiocarbamate complexes, selected based on their proven antitumor activity. Our investigation revealed that the M06-L/def2-TZVP/ECP/CPCM method presented good accuracy in predicting geometries, while the TPSSh/def2-SVP/ECP/CPCM method proved effective in analyzing the 13C NMR spectra of these molecules. In general, all examined methods exhibited comparable performance in predicting 1H NMR signals. METHODS Calculations were performed with the Gaussian 09 program using the def2-SVP and def2-TZVP basis sets, employing relativistic effective core potential (ECP) for Bi and using the CPCM solvent model. The exchange-correlation functionals BP86, PBE, OLYP, M06-L, B3LYP, B3LYP-D3, M06-2X, TPSSh, CAM-B3LYP, and ωB97XD were used in the study. Geometry optimizations were started from crystallographic structures available at the Cambridge Structural Database. The theoretical results were compared with experimental data using the mean root-mean-square deviation (RMSD), mean absolute deviations (MAD), and linear correlation coefficient (R2).
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Affiliation(s)
| | | | | | - Gerd Bruno Rocha
- Chemistry Department, Exact and Natural Sciences Center, Federal University of Paraíba, João Pessoa, Brazil
| | - Evandro P S Martins
- Graduate Program in Chemistry, State University of Piaui, Teresina, PI, Brazil.
- State University of Piauí, Piripiri, PI, 64260-000, Brazil.
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5
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Rajput J, Ghosh A, Pawar AB, Mondal B. Deciphering the Origin of Regioselectivity in Ru(II)-Catalyzed C-H Annulation of N-Chlorobenzamides with 1,3-Diynes. J Org Chem 2024; 89:6838-6846. [PMID: 38700910 DOI: 10.1021/acs.joc.4c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Understanding the reaction mechanism and origin of regioselectivity in transition metal-catalyzed C-H activation/annulation reactions with 1,3-diynes has remained an intriguing challenge. In this article, to establish the mechanism and decipher the origin of regioselectivity, we report a detailed computational density functional theory-based mechanistic investigation on the recently developed Ru(II)-catalyzed [4 + 2] annulation of N-chlorobenzamides with 1,3-diynes for the synthesis of 3-alkynylated isoquinolone derivatives. Our calculations reveal a redox-neutral pathway for the annulation reaction. The stepwise analysis of the reaction channels indicates the migratory insertion step and the concerted reductive elimination/oxidative addition of the Ru(p-cymene) moiety to form the N-C bond leading to the 3-alkynylated product to be the selectivity- and rate-determining steps, respectively. Finally, the distortion/interaction analysis using the activation-strain model suggests the steric effect as the determining factor for the observed regioselectivity for the formation of the 3-alkynylated product. Overall, the computationally obtained key insights into the catalytic mechanism and the origin of regioselectivity in the C-H activation/annulation reaction can be used as a guide to rationally design and develop novel transformation strategies for heterocycle synthesis.
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Affiliation(s)
- Janavi Rajput
- School of Chemical Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh 175005, India
| | - Arijit Ghosh
- School of Chemical Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh 175005, India
| | - Amit B Pawar
- School of Chemical Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh 175005, India
| | - Bhaskar Mondal
- School of Chemical Sciences, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh 175005, India
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Park J, Lee S, Jafter OF, Cheon J, Lungerich D. Electron beam-induced demetallation of Fe, Co, Ni, Cu, Zn, Pd, and Pt metalloporphyrins: insights in e-beam chemistry and metal cluster formations. Phys Chem Chem Phys 2024; 26:8051-8061. [PMID: 38314818 DOI: 10.1039/d3cp05848d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Electron beams are versatile tools for nanoscale fabrication processes, however, the underlying e-beam chemistry remains in its infancy. Through operando transmission electron microscopy investigations, we elucidate a redox-driven cargo release of individual metal atoms triggered by electron beams. The chosen organic delivery molecule, tetraphenylporphyrin (TPP), proves highly versatile, forming complexes with nearly all metals from the periodic table and being easily processed in solution. A comprehensive cinematographic analysis of the dynamics of single metal atoms confirms the nearly instantaneous ejection of complexed metal atoms under an 80 kV electron beam, underscoring the system's broad versatility. Providing mechanistic insights, we employ density functional theory to support the proposed reductive demetallation pathway facilitated by secondary electrons, contributing novel perspectives to electron beam-mediated chemical reaction mechanisms. Lastly, our findings demonstrate that all seven metals investigated form nanoclusters once ejected from TPP, highlighting the method's potential for studying and developing sustainable single-atom and nanocluster catalysts.
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Affiliation(s)
- Jongseong Park
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea.
| | - Sol Lee
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
| | - Orein Francis Jafter
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea.
| | - Jinwoo Cheon
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea.
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Dominik Lungerich
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea
- Department of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea.
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7
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Tolbatov I, Umari P, Marrone A. Mechanism of Action of Antitumor Au(I) N-Heterocyclic Carbene Complexes: A Computational Insight on the Targeting of TrxR Selenocysteine. Int J Mol Sci 2024; 25:2625. [PMID: 38473872 DOI: 10.3390/ijms25052625] [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: 02/15/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
The targeting of human thioredoxin reductase is widely recognized to be crucially involved in the anticancer properties of several metallodrugs, including Au(I) complexes. In this study, the mechanism of reaction between a set of five N-heterocyclic carbene Au(I) complexes and models of the active Sec residue in human thioredoxin reductase was investigated by means of density functional theory approaches. The study was specifically addressed to the kinetics and thermodynamics of the tiled process by aiming at elucidating and explaining the differential inhibitory potency in this set of analogous Au(I) bis-carbene complexes. While the calculated free energy profile showed a substantially similar reactivity, we found that the binding of these Au(I) bis-carbene at the active CysSec dyad in the TrxR enzyme could be subjected to steric and orientational restraints, underlining both the approach of the bis-carbene scaffold and the attack of the selenol group at the metal center. A new and detailed mechanistic insight to the anticancer activity of these Au(I) organometallic complexes was thus provided by consolidating the TrxR targeting paradigm.
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Affiliation(s)
- Iogann Tolbatov
- Department of Physics and Astronomy, University of Padova, Via F. Marzolo 8, 35131 Padova, Italy
| | - Paolo Umari
- Department of Physics and Astronomy, University of Padova, Via F. Marzolo 8, 35131 Padova, Italy
| | - Alessandro Marrone
- Dipartimento di Farmacia, Università "G d'Annunzio" di Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
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8
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Karuth A, Casanola-Martin GM, Lystrom L, Sun W, Kilin D, Kilina S, Rasulev B. Combined Machine Learning, Computational, and Experimental Analysis of the Iridium(III) Complexes with Red to Near-Infrared Emission. J Phys Chem Lett 2024; 15:471-480. [PMID: 38190332 DOI: 10.1021/acs.jpclett.3c02533] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Various coordination complexes have been the subject of experimental and theoretical studies in recent decades because of their fascinating photophysical properties. In this work, a combined experimental and computational approach was applied to investigate the optical properties of monocationic Ir(III) complexes. An interpretative machine learning-based quantitative structure-property relationship (ML/QSPR) model was successfully developed that could reliably predict the emission wavelength of the Ir(III) complexes and provide a foundation for the theoretical evaluation of the optical properties of Ir(III) complexes. A hypothesis was proposed to explain the differences in the emission wavelengths between structurally different individual Ir(III) complexes. The efficacy of the developed model was demonstrated by high R2 values of 0.84 and 0.87 for the training and test sets, respectively. It is worth noting that a relationship between the N-N distance in the diimine ligands of the Ir(III) complexes and emission wavelengths is detected. This effect is most probably associated with a degree of distortion in the octahedral geometry of the complexes, resulting in a perturbed ligand field. This combined experimental and computational approach shows great potential for the rational design of new Ir(III) complexes with the desired optical properties. Moreover, the developed methodology could be extended to other transition-metal complexes.
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Affiliation(s)
- Anas Karuth
- Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Gerardo M Casanola-Martin
- Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Levi Lystrom
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Wenfang Sun
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Dmitri Kilin
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Svetlana Kilina
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Bakhtiyor Rasulev
- Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58108, United States
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9
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Medvedkov IA, Nikolayev AA, He C, Yang Z, Mebel AM, Kaiser RI. One Collision-Two Substituents: Gas-Phase Preparation of Xylenes under Single-Collision Conditions. Angew Chem Int Ed Engl 2023:e202315147. [PMID: 38072833 DOI: 10.1002/anie.202315147] [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: 10/09/2023] [Indexed: 12/21/2023]
Abstract
The fundamental reaction pathways to the simplest dialkylsubstituted aromatics-xylenes (C6 H4 (CH3 )2 )-in high-temperature combustion flames and in low-temperature extraterrestrial environments are still unknown, but critical to understand the chemistry and molecular mass growth processes in these extreme environments. Exploiting crossed molecular beam experiments augmented by state-of-the-art electronic structure and statistical calculations, this study uncovers a previously elusive, facile gas-phase synthesis of xylenes through an isomer-selective reaction of 1-propynyl (methylethynyl, CH3 CC) with 2-methyl-1,3-butadiene (isoprene, C5 H8 ). The reaction dynamics are driven by a barrierless addition of the radical to the diene moiety of 2-methyl-1,3-butadiene followed by extensive isomerization (hydrogen shifts, cyclization) prior to unimolecular decomposition accompanied by aromatization via atomic hydrogen loss. This overall exoergic reaction affords a preparation of xylenes not only in high-temperature environments such as in combustion flames and around circumstellar envelopes of carbon-rich Asymptotic Giant Branch (AGB) stars, but also in low-temperature cold molecular clouds (10 K) and in hydrocarbon-rich atmospheres of planets and their moons such as Triton and Titan. Our study established a hitherto unknown gas-phase route to xylenes and potentially more complex, disubstituted benzenes via a single collision event highlighting the significance of an alkyl-substituted ethynyl-mediated preparation of aromatic molecules in our Universe.
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Affiliation(s)
- Iakov A Medvedkov
- Department of Chemistry, University of Hawai'i at Manoa, Honolulu, HI 96822, USA
| | | | - Chao He
- Department of Chemistry, University of Hawai'i at Manoa, Honolulu, HI 96822, USA
| | - Zhenghai Yang
- Department of Chemistry, University of Hawai'i at Manoa, Honolulu, HI 96822, USA
| | - Alexander M Mebel
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Ralf I Kaiser
- Department of Chemistry, University of Hawai'i at Manoa, Honolulu, HI 96822, USA
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10
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Aarabi M, Gholami S, Grabowski SJ. Double Centrosymmetric Si···π Tetrel Bonds as New Synthons─Evidence from Crystal Structures and DFT Calculations. J Phys Chem A 2023; 127:9995-10007. [PMID: 37975750 DOI: 10.1021/acs.jpca.3c06514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The crystal structure of bis((μ2-ethynylsilyloxo)-dichloro-aluminum), BEDCA, and a few related structures are characterized by the occurrence of tetrel bonds that link molecules. Particularly, centosymmetric dimers in such structures occur that are connected by two equivalent Si···π tetrel bonds. The dimer of BEDCA and dimers of other model species that similarly are linked by two equivalent Si···π tetrel bonds are analyzed theoretically. Some of the complexes calculated here are also characterized by the occurrence of triel bonds. Thus, ωB97XD/aug-cc-pVTZ calculations are performed and these DFT results are further supported by calculations with the use of other theoretical approaches: the quantum theory of atoms in molecules, QTAIM; the natural bond orbital, NBO; the energy decomposition analysis, EDA; and the noncovalent interactions method, NCI. The results show that the tetrel bonds analyzed here are rather weak, and they are not detected by the QTAIM approach; however, they are detected by other approaches, like NBO, for example. On the other hand, the triel bonds that occur in a few complexes discussed here are very strong and possess characteristics of covalent bonds.
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Affiliation(s)
- Mohammad Aarabi
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
| | - Samira Gholami
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
| | - Sławomir J Grabowski
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU & Donostia International Physics Center (DIPC) PK 1072, 20080 Donostia, Spain
- Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain
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11
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Dhimba G, Muller A, Lammertsma K. Chiral-at-Metal Racemization Unraveled for MX 2 (a-chel) 2 by means of a Computational Analysis of MoO 2 (acnac) 2. Chemistry 2023; 29:e202302516. [PMID: 37730887 DOI: 10.1002/chem.202302516] [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: 08/02/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/22/2023]
Abstract
Octahedral chiral-at-metal complexes MX2 (a-chel)2 (a-chel=asymmetric chelate) can rearrange their ligands by four mechanisms known as the Bailar (B), Ray-Dutt (RD), Conte-Hippler (CH), and Dhimba-Muller-Lammertsma (DML) twists. Racemization involves their interconnections, which were computed for MoO2 (acnac)2 (acnac=β-ketoiminate) using density functional theory at ωB97x-D with the 6-31G(d,p) and 6-311G(2d,p) basis sets and LANL2DZ for molybdenum. Racemizing the cis(NN) isomer, being the global energy minimum with trans oriented imine groups, is a three step process (DML-CH-DML) that requires 17.4 kcal/mol, while all three cis isomers (cis(NN), cis(NO), and cis(OO)) interconvert at ≤17.9 kcal/mol. The B and RD twists are energetically not competitive and neither are the trans isomers. The interconnection of all enantiomeric minima and transition structures is summarized in a graph that also visualizes valley ridge inflection points for two of the three CH twists. Geometrical features of the minima and twists are given. Lastly, the influence of N-substitution on the favored racemization pathway is evaluated. The present comprehensive study serves as a template for designing chiral-at-metal MX2 (a-chel)2 catalysts that may retain their chiral integrity.
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Affiliation(s)
- George Dhimba
- Department of Chemical Sciences, University of Johannesburg, Auckland Park, Johannesburg, 2006, South Africa
| | - Alfred Muller
- Department of Chemical Sciences, University of Johannesburg, Auckland Park, Johannesburg, 2006, South Africa
| | - Koop Lammertsma
- Department of Chemical Sciences, University of Johannesburg, Auckland Park, Johannesburg, 2006, South Africa
- Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
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12
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Martínez JP, Trzaskowski B. An Anthracene-Thiolate-Ligated Ruthenium Complex: Computational Insights into Z-Stereoselective Cross Metathesis. J Phys Chem A 2023; 127:9465-9472. [PMID: 37916964 PMCID: PMC10658622 DOI: 10.1021/acs.jpca.3c05021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023]
Abstract
Stereoselective control of the cross metathesis of olefins is a crucial aspect of synthetic procedures. In this study, we utilized density functional theory methods to calculate thermodynamic and kinetic descriptors to explore the stereoselectivity of cross metathesis between allylbenzene and 2-butene-1,4-diyl diacetate. A ruthenium-based complex, characterized primarily by an anthracene-9-thiolate ligand, was designed in silico to completely restrict the E conformation of olefins through a bottom-bound mechanism. Our investigation of the kinetics of all feasible propagation routes demonstrated that Z-stereoisomers of metathesis products can be synthesized with an energy cost of only 13 kcal/mol. As a result, we encourage further research into the synthetic strategies outlined in this work.
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Affiliation(s)
- Juan Pablo Martínez
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warszawa, Poland
| | - Bartosz Trzaskowski
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warszawa, Poland
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13
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Song Z, Wang S, Gao R, Wang Y, Gou Q, Zheng G, Feng H, Fan G, Lai J. Recent Advancements in Mechanistic Studies of Palladium- and Nickel-Catalyzed Ethylene Copolymerization with Polar Monomers. Polymers (Basel) 2023; 15:4343. [PMID: 38006069 PMCID: PMC10675468 DOI: 10.3390/polym15224343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 11/26/2023] Open
Abstract
The introduction of polar functional groups into polyolefin chain structures creates opportunities to enhance specific properties, such as adhesion, dyeability, printability, compatibility, thermal stability, and electrical conductivity, which widen the range of potential applications for these modified materials. Transition metal catalysts, especially late transition metals, have proven to be highly effective in copolymerization processes due to their reduced Lewis acidity and electrophilicity. However, when compared to the significant progress and summary of synthetic methods, there is a distinct lack of a comprehensive summary of mechanistic studies pertaining to the catalytic systems involved in ethylene copolymerization catalyzed by palladium and nickel catalysts. In this review, we have provided a comprehensive summary of the latest developments in mechanistic studies of ethylene copolymerization with polar monomers catalyzed by late-transition-metal complexes. Experimental and computational methods were employed to conduct a detailed investigation of these organic and organometallic systems. It is mainly focused on ligand substitution, changes in binding modes, ethylene/polar monomer insertion, chelate opening, and β-H elimination. Factors that control the catalytic activity, molecular weight, comonomer incorporation ratios, and branch content are analyzed, these include steric repulsions between ligands and monomers, electronic effects arising from both ligands and monomers, and so on.
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Affiliation(s)
- Zhihui Song
- Department of Polyethylene, SINOPEC (Beijing) Research Institute of Chemical Industry Co., Ltd., Beijing 100013, China; (R.G.); (Y.W.); (Q.G.); (G.Z.); (G.F.); (J.L.)
| | - Shaochi Wang
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA;
| | - Rong Gao
- Department of Polyethylene, SINOPEC (Beijing) Research Institute of Chemical Industry Co., Ltd., Beijing 100013, China; (R.G.); (Y.W.); (Q.G.); (G.Z.); (G.F.); (J.L.)
| | - Ying Wang
- Department of Polyethylene, SINOPEC (Beijing) Research Institute of Chemical Industry Co., Ltd., Beijing 100013, China; (R.G.); (Y.W.); (Q.G.); (G.Z.); (G.F.); (J.L.)
| | - Qingqiang Gou
- Department of Polyethylene, SINOPEC (Beijing) Research Institute of Chemical Industry Co., Ltd., Beijing 100013, China; (R.G.); (Y.W.); (Q.G.); (G.Z.); (G.F.); (J.L.)
| | - Gang Zheng
- Department of Polyethylene, SINOPEC (Beijing) Research Institute of Chemical Industry Co., Ltd., Beijing 100013, China; (R.G.); (Y.W.); (Q.G.); (G.Z.); (G.F.); (J.L.)
| | - Huasheng Feng
- Department of Catalytic Science, SINOPEC (Beijing) Research Institute of Chemical Industry Co., Ltd., Beijing 100013, China;
| | - Guoqiang Fan
- Department of Polyethylene, SINOPEC (Beijing) Research Institute of Chemical Industry Co., Ltd., Beijing 100013, China; (R.G.); (Y.W.); (Q.G.); (G.Z.); (G.F.); (J.L.)
| | - Jingjing Lai
- Department of Polyethylene, SINOPEC (Beijing) Research Institute of Chemical Industry Co., Ltd., Beijing 100013, China; (R.G.); (Y.W.); (Q.G.); (G.Z.); (G.F.); (J.L.)
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14
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van Dam A, van Schendel R, Gangarapu S, Zuilhof H, Smulders MMJ. DFT Study of Imine-Exchange Reactions in Iron(II)-Coordinated Pincers. Chemistry 2023; 29:e202301795. [PMID: 37560922 DOI: 10.1002/chem.202301795] [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: 06/05/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/11/2023]
Abstract
The imine bond is among the most applied motifs in dynamic covalent chemistry. Although its uses are varied and often involve coordination to a transition metal for stability, mechanistic studies on imine exchange reactions so far have not included metal coordination. Herein, we investigated the condensation and transimination reactions of an Fe2+ -coordinated diimine pyridine pincer, employing wB97XD/6-311G(2d,2p) DFT calculations in acetonitrile. We first experimentally confirmed that Fe2+ is strongly coordinated by these pincers, and is thus a justified model ion. When considering a four-membered ring-shaped transition state for proton transfers, the required activation energies for condensation and transimination reaction exceeded the values expected for reactions known to be spontaneous at room temperature. The nature of the incoming and exiting amines and the substituents on the para-position of the pincer had no effect on this. Replacing Fe2+ with Zn2+ or removing it altogether did not reduce it either. However, the addition of two ethylamine molecules lowered the energy barriers to be compatible with experiment (19.4 and 23.2 kcal/mol for condensation and transimination, respectively). Lastly, the energy barrier of condensation of a non-coordinated pincer was significantly higher than found for Fe2+ -coordinating pincers, underlining the catalyzing effect of metal coordination on imine exchange reactions.
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Affiliation(s)
- Annemieke van Dam
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Robin van Schendel
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Satesh Gangarapu
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
- School of Pharmaceutical Sciences and Technology, Tianjin University, 92 Weijin Road, Tianjin, 300072, P.R. China
| | - Maarten M J Smulders
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
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15
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Giricheva NI, Sliznev VV, Alikhanyan AS, Morozova EA, Girichev GV. Molecular Structure of Gaseous Oxopivalate Co(II): Electronic States of Various Multiplicities. Int J Mol Sci 2023; 24:13224. [PMID: 37686030 PMCID: PMC10487729 DOI: 10.3390/ijms241713224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
Synchronous electron diffraction/mass spectrometry was used to study the composition and structure of molecular forms existing in a saturated vapor of cobalt(II) oxopivalate at T = 410 K. It was found that monomeric complexes Co4O(piv)6 dominate in the vapor. The complex geometry possesses the C3 symmetry with bond lengths Co-Oc = 1.975(5) Å and Co-O = 1.963(5) Å, as well as bond angles Oc-Co-O = 111.8(3)°, Co-Oc-Co = 110.4(6)°, O-Co-O = 107.1(3)° in the central OcCo4 fragment and four OcCoO3 fragments. The presence of an open 3d shell for each Co atom leads to the possibility of the existence of electronic states of the Co4O(piv)6 complex with Multiplicities 1, 3, 5, 7, 9, 11, and 13. For them, the CASSCF and XMCQDPT2 calculations predict similar energies, identical shapes of active orbitals, and geometric parameters, the difference between which is comparable with the error of determination by the electron diffraction experiment. QTAIM and NBO analysis show that the Co-Oc and Co-O bonds can be attributed to ionic (or coordination) bonds with a significant contribution of the covalent component. The high volatility and simple vapor composition make it possible to recommend cobalt (II) oxopivalate as precursors in the preparation of oxide films or coatings in the CVD technologies. The features of the electronic and geometric structure of the Co4O(piv)6 complex allows for the conclude that only a very small change in energy is required for the transition from antiferromagnetically to ferromagnetically coupled Co atoms.
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Affiliation(s)
- Nina I. Giricheva
- Nanomaterial Research Institute, Ivanovo State University, Ermak Str. 39, 153025 Ivanovo, Russia;
| | - Valery V. Sliznev
- Department of Physics, Ivanovo State University of Chemistry and Technology, Sheremetevsky Ave. 7, 153000 Ivanovo, Russia;
| | - Andrey S. Alikhanyan
- Kurnakov Institute of General and Inorganic Chemistry RAS, Leninsky Prospect 31, 119991 Moscow, Russia; (A.S.A.); (E.A.M.)
| | - Ekaterina A. Morozova
- Kurnakov Institute of General and Inorganic Chemistry RAS, Leninsky Prospect 31, 119991 Moscow, Russia; (A.S.A.); (E.A.M.)
| | - Georgiy V. Girichev
- Department of Physics, Ivanovo State University of Chemistry and Technology, Sheremetevsky Ave. 7, 153000 Ivanovo, Russia;
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16
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Boychuk BTA, Wetmore SD. Assessment of Density Functional Theory Methods for the Structural Prediction of Transition and Post-Transition Metal-Nucleic Acid Complexes. J Chem Theory Comput 2023. [PMID: 37399186 DOI: 10.1021/acs.jctc.3c00127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Understanding the structure of metal-nucleic acid systems is important for many applications such as the design of new pharmaceuticals, metal detection platforms, and nanomaterials. Herein, we explore the ability of 20 density functional theory (DFT) functionals to reproduce the crystal structure geometry of transition and post-transition metal-nucleic acid complexes identified in the Protein Data Bank and Cambridge Structural Database. The environmental extremes of the gas phase and implicit water were considered, and analysis focused on the global and inner coordination geometry, including the coordination distances. Although gas-phase calculations were unable to describe the structure of 12 out of the 53 complexes in our test set regardless of the DFT functional considered, accounting for the broader environment through implicit solvation or constraining the model truncation points to crystallographic coordinates generally afforded agreement with the experimental structure, suggesting that functional performance for these systems is likely due to the models rather than the methods. For the remaining 41 complexes, our results show that the reliability of functionals depends on the metal identity, with the magnitude of error varying across the periodic table. Furthermore, minimal changes in the geometries of these metal-nucleic acid complexes occur upon use of the Stuttgart-Dresden effective core potential and/or inclusion of an implicit water environment. The overall top three performing functionals are ωB97X-V, ωB97X-D3(BJ), and MN15, which reliably describe the structure of a broad range of metal-nucleic acid systems. Other suitable functionals include MN15-L, which is a cheaper alternative to MN15, and PBEh-3c, which is commonly used in QM/MM calculations of biomolecules. In fact, these five methods were the only functionals tested to reproduce the coordination sphere of Cu2+-containing complexes. For metal-nucleic acid systems that do not contain Cu2+, ωB97X and ωB97X-D are also suitable choices. These top-performing methods can be utilized in future investigations of diverse metal-nucleic acid complexes of relevance to biology and material science.
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Affiliation(s)
- Briana T A Boychuk
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB T1K 3M4, Canada
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17
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Parra RD. Bracelet-like Complexes of Lithium Fluoride with Aromatic Tetraamides, and Their Potential for LiF-Mediated Self-Assembly: A DFT Study. Molecules 2023; 28:4812. [PMID: 37375366 DOI: 10.3390/molecules28124812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Geometries and binding energies of complexes between a LiF molecule and a model aromatic tetraamide are obtained using various DFT methods. The tetraamide consists of a benzene ring and four amides positioned so that the LiF molecule can bind via Li⋯O=C or N-H⋯F interactions. The complex with both interactions is the most stable one, followed by the complex with only N-H⋯F interactions. Doubling the size of the former resulted in a complex with a LiF dimer sandwiched between the model tetraamides. In turn, doubling the size of the latter resulted in a more stable tetramer with bracelet-like geometry having the two LiF molecules also sandwiched but far apart from each other. Additionally, all methods show that the energy barrier to transition to the more stable tetramer is small. The self-assembly of the bracelet-like complex mediated by the interactions of adjacent LiF molecules is demonstrated by all computational methods employed.
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Affiliation(s)
- Rubén D Parra
- Department of Chemistry and Biochemistry, DePaul University, Chicago, IL 60614, USA
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18
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Mononuclear half-sandwich nd 7 metallo drug complexes based on bidentate N∩N dendritic scaffolds: DFT (B3LYP; BP86 and B3PW91) examination. J Mol Graph Model 2023; 120:108417. [PMID: 36706572 DOI: 10.1016/j.jmgm.2023.108417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 01/24/2023]
Abstract
Through an use of three functionals (B3PW91, B3LYP and BP86) associated to a generic basis set LanL2DZ for transition metals (as well as halogen atoms) and 6-311+G (d,p) for others atoms, an examination of the bonding properties of a series of mononuclear half-sandwich nd7 transition metal (anticancer) complexes based on N∩N dendritic scaffolds (L) has been done. Collectively, complexes studied have adopted the piano-stool environment. An examination of the performance of each functional has shown that for the most reliable geometrical analysis of Metal-Nitrogen and Metal-Halogen bonds, the B3LYP and B3PW91 functionalities are suitable respectively. Regardless of the halogen ligand adopted, the B3LYP metal-nitrogen bond lengths are the most widely overestimated. A correlation has been built between the retained charge on each divalent transition metal cation and its metal ion affinity (MIA). Topological examinations reveal the higher instability of metal-N bonds compared to metal-X ones (X = Cl and Br). By the mean of the energy decomposition analysis, a predominant electrostatic character of metal … halogen and [LCP]- … [MX]+ interaction has been demonstrated. The transition metal atom … (hydrophobic) surface (Cp*) interaction is most pronounced for the chloride rhodium complexes of rhodium (combined with (E)-N-(pyridin-2-ylmethylene) Propan-1-amine and 2,2'- dipyridylketone ligands and iridium combined with 2,2'- dipyridylketone ligand. The charge decomposition analysis displays the weakening of the [Formula: see text] bonds in the studied complexes.
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19
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Shayesteh Zadeh A, Khan SA, Vandervelden C, Peters B. Site-Averaged Ab Initio Kinetics: Importance Learning for Multistep Reactions on Amorphous Supports. J Chem Theory Comput 2023; 19:2873-2886. [PMID: 37093705 DOI: 10.1021/acs.jctc.3c00160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Single-atom centers on amorphous supports include catalysts for polymerization, partial oxidation, metathesis, hydrogenolysis, and more. The disordered environment makes each site different, and the kinetics exponentially magnifies these differences to make ab initio site-averaged kinetics calculations extremely difficult. This work extends the importance learning algorithm for efficient and precise site-averaged kinetics estimates to ab initio calculations and multistep reaction mechanisms. Specifically, we calculate site-averaged proton transfer relaxation rates on an ensemble of cluster models representing Brønsted acid sites on silica-alumina. We include direct and water-assisted proton transfer pathways and simultaneously estimate the water adsorption and activation enthalpies for forward and backward proton transfers. We use density functional theory (DFT) to obtain a site-averaged rate, somewhat like a turnover frequency, for the proton transfer relaxation rate. Finally, we show that importance learning can provide orders-of-magnitude acceleration over standard sampling methods for site-averaged rate calculations in cases where the rate is dominated by a few highly active sites.
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Affiliation(s)
- Armin Shayesteh Zadeh
- Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Salman A Khan
- Delaware Energy Institute (DEI), University of Delaware, Newark, Delaware 19711, United States
| | | | - Baron Peters
- Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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20
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Ninković D, Moncho S, Petrović P, Hall MB, Zarić SD, Brothers EN. Improving a Methane C-H Activation Complex by Metal and Ligand Alterations from Computational Results. Inorg Chem 2023; 62:5058-5066. [PMID: 36946599 PMCID: PMC10848199 DOI: 10.1021/acs.inorgchem.2c03342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Indexed: 03/23/2023]
Abstract
We present results for a series of complexes derived from a titanium complex capable of activating C-H bonds under mild conditions (PNP)Ti═CHtBu(CH2tBu), where PNP = N[2-PiPr2-4-methylphenyl]2-. In addition to the initial activation of methane, a tautomerization reaction to a terminal methylidene is also explored due to methylidene's potential use as a synthetic starting point. Analogous complexes with other low-cost 3d transition metals were studied, such as scandium, titanium, vanadium, and chromium as both isoelectronic and isocharged complexes. Our results predict that V(IV) and V(V) complexes are promising for methane C-H bond activation. The V(V) complex has a low rate-determining barrier for methane activation, specifically 16.6 kcal/mol, which is approximately 12 kcal/mol less than that for the Ti complex, as well as having a moderate tautomerization barrier of 29.8 kcal/mol, while the V(IV) complex has a methane activation barrier of 19.0 kcal/mol and a tautomerization barrier of 31.1 kcal/mol. Scandium and chromium complexes are much poorer for C-H bond activation; scandium has very high barriers, while chromium strongly overstabilizes the alkylidene intermediate, potentially stopping the further reaction. In addition to the original PNP ligand, some of the most promising ligands from a previous work were tested, although (as shown previously) modification of the ligand does not typically have large effects on the activity of the system. Our best ligand modification improves the performance of the V(V) complex via the substitution of the nitrogen in PNP by phosphorus, which reduces the tautomerization barrier by 5 to 24.4 kcal/mol.
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Affiliation(s)
- Dragan
B. Ninković
- Department
of Chemistry, Texas A&M University at
Qatar, P.O. Box 23874 Doha, Qatar
- Innovation
Center of the Faculty of Chemistry, University
of Belgrade, Belgrade 11000, Serbia
| | - Salvador Moncho
- Department
of Chemistry, Texas A&M University at
Qatar, P.O. Box 23874 Doha, Qatar
| | - Predrag Petrović
- Department
of Chemistry, Texas A&M University at
Qatar, P.O. Box 23874 Doha, Qatar
| | - Michael B. Hall
- Department
of Chemistry, Texas A&M University College
Station, College Station, Texas 77843-3255, United States
| | - Snežana D. Zarić
- Department
of Chemistry, Texas A&M University at
Qatar, P.O. Box 23874 Doha, Qatar
- University
of Belgrade – Faculty of Chemistry, Studentski trg 12-16, Belgrade 11000, Serbia
| | - Edward N. Brothers
- Department
of Chemistry, Texas A&M University at
Qatar, P.O. Box 23874 Doha, Qatar
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21
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Varadwaj PR, Varadwaj A, Marques HM, Yamashita K. The Tetrel Bond and Tetrel Halide Perovskite Semiconductors. Int J Mol Sci 2023; 24:6659. [PMID: 37047632 PMCID: PMC10094773 DOI: 10.3390/ijms24076659] [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: 02/26/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 04/05/2023] Open
Abstract
The ion pairs [Cs+•TtX3-] (Tt = Pb, Sn, Ge; X = I, Br, Cl) are the building blocks of all-inorganic cesium tetrel halide perovskites in 3D, CsTtX3, that are widely regarded as blockbuster materials for optoelectronic applications such as in solar cells. The 3D structures consist of an anionic inorganic tetrel halide framework stabilized by the cesium cations (Cs+). We use computational methods to show that the geometrical connectivity between the inorganic monoanions, [TtX3-]∞, that leads to the formation of the TtX64- octahedra and the 3D inorganic perovskite architecture is the result of the joint effect of polarization and coulombic forces driven by alkali and tetrel bonds. Depending on the nature and temperature phase of these perovskite systems, the Tt···X tetrel bonds are either indistinguishable or somehow distinguishable from Tt-X coordinate bonds. The calculation of the potential on the electrostatic surface of the Tt atom in molecular [Cs+•TtX3-] provides physical insight into why the negative anions [TtX3-] attract each other when in close proximity, leading to the formation of the CsTtX3 tetrel halide perovskites in the solid state. The inter-molecular (and inter-ionic) geometries, binding energies, and charge density-based topological properties of sixteen [Cs+•TtX3-] ion pairs, as well as some selected oligomers [Cs+•PbI3-]n (n = 2, 3, 4), are discussed.
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Affiliation(s)
- Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
| | - Helder M. Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1, Tokyo 113-8656, Japan
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22
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Bayach I, Sarfaraz S, Sheikh NS, Alamer K, Almutlaq N, Ayub K. Hydrogen Dissociation Reaction on First-Row Transition Metal Doped Nanobelts. MATERIALS (BASEL, SWITZERLAND) 2023; 16:2792. [PMID: 37049085 PMCID: PMC10096363 DOI: 10.3390/ma16072792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 06/19/2023]
Abstract
Zigzag molecular nanobelts have recently captured the interest of scientists because of their appealing aesthetic structures, intriguing chemical reactivities, and tantalizing features. In the current study, first-row transition metals supported on an H6-N3-belt[6]arene nanobelt are investigated for the electrocatalytic properties of these complexes for the hydrogen dissociation reaction (HDR). The interaction of the doped transition metal atom with the nanobelt is evaluated through interaction energy analysis, which reveals the significant thermodynamic stability of TM-doped nanobelt complexes. Electronic properties such as frontier molecular orbitals and natural bond orbitals analyses are also computed, to estimate the electronic perturbation upon doping. The highest reduction in the HOMO-LUMO energy gap compared to the bare nanobelt is seen in the case of the Zn@NB catalyst (4.76 eV). Furthermore, for the HDR reaction, the Sc@NB catalyst displays the best catalytic activity among the studied catalysts, with a hydrogen dissociation barrier of 0.13 eV, whereas the second-best catalytic activity is observed for the Zn@NB catalyst (0.36 eV). It is further found that multiple active sites, i.e., the presence of the metal atom and nitrogen atom moiety, help to facilitate the dissociation of the hydrogen molecule. These key findings of this study enhance the understanding of the relative stability, electronic features, and catalytic bindings of various TM@NB catalysts.
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Affiliation(s)
- Imene Bayach
- Department of Chemistry, College of Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Sehrish Sarfaraz
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Nadeem S. Sheikh
- Chemical Sciences, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong BE1410, Brunei
| | - Kawther Alamer
- Department of Chemistry, College of Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Nadiah Almutlaq
- Department of Chemistry, College of Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Khurshid Ayub
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
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23
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Tatebe CJ, Fromel E, Bellas MK, Zeller M, Genna DT. Mechanistic Investigation of the Synthesis of Dianionic In-Derived Coordination Polymers. Inorg Chem 2023; 62:5881-5885. [PMID: 37001027 DOI: 10.1021/acs.inorgchem.3c00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
The mechanism of formation of crystalline coordination polymers is as complex as the architectures themselves. In this Communication, we detail a three-tiered approach using density functional theory (DFT) analysis, synthesis, and in situ Raman spectroscopy to study the formation of coordination polymers. Specifically, the previously reported coordination polymers YCM-22 and YCM-51 containing the [In(CO2R)2X3]2- (X = halogen) molecular building unit (MBU) were investigated. DFT revealed two potential pathways of formation, involving the initial formation of either [InCl4]- or [In(CO2R)Cl3]-. A molecular dimeric In species (8a) containing two [In(CO2R)Cl4]2- centers bridged by 2,5-thiophenedicarboxylic acid was isolated. When a suspension of 8a was treated with a solution of 2,5-thiophenedicarboxylic acid, an isomer of the coordination polymer YCM-22 (denoted as YCM-22') was formed. In situ Raman analysis of the formation of YCM-22 confirms that [InCl4]- forms at the onset of the reaction and that the [In(CO2R)2X3]2- MBU forms at its expense. The totality of the data presented support a mechanism of formation of one-dimensional In-derived coordination polymers and present a roadmap for future investigations into the formation of other crystalline coordination polymers.
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Affiliation(s)
- Caleb J. Tatebe
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, United States
| | - Emily Fromel
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, United States
| | - Michael K. Bellas
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, United States
| | - Matthias Zeller
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Douglas T. Genna
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, United States
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24
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Grabowski SJ. Halogen bonds with carbenes acting as Lewis base units: complexes of imidazol-2-ylidene: theoretical analysis and experimental evidence. Phys Chem Chem Phys 2023; 25:9636-9647. [PMID: 36943198 DOI: 10.1039/d3cp00348e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
ωB97XD/aug-cc-pVDZ and ωB97XD/aug-cc-pVTZ calculations were performed on complexes of imidazol-2-ylidene that are linked by halogen bonds. This singlet carbene acts as the Lewis base through a lone electron pair located at the carbon centre. The XCCH, XCN and X2 units were chosen here as those that interact through the X Lewis acid halogen centre (X = Cl, Br and I); if X = F the complexes are linked by interactions which are not classified as halogen bonds. The properties of interactions that occur in complexes are analyzed using the results of DFT calculations which are supported by parameters derived from the Quantum Theory of Atoms in Molecules, QTAIM, and the Natural Bond Orbital, NBO, approaches. The energy decomposition analysis, EDA, applied here provided additional characteristics of interactions linking complexes analyzed. The majority of complexes are linked by the medium in strength and strong halogen bonds which often possess characteristics typical for covalent bonds. Searches through the Cambridge Structural Database were also performed and structures analogues to complexes analyzed theoretically were found, and these structures are also discussed in this study.
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Affiliation(s)
- Sławomir J Grabowski
- Faculty of Chemistry, University of the Basque Country and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Spain
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.
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25
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Souza JR, Curutchet C, Aoto YA, Homem-De-Mello P. Benchmarking DFT functionals for photophysics of pyranoflavylium cations. J Mol Graph Model 2023; 122:108460. [PMID: 37004417 DOI: 10.1016/j.jmgm.2023.108460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/07/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023]
Abstract
An intense absorption, phosphorescence, a long triplet excited state lifetime and singlet oxygen generation capabilities are characteristics of pyranoflavylium cations, analogues to pyranoanthocyanidins originated in the maturation process of red wine. Such properties make these compounds potential photosensitizers to be applied in photodynamic therapy. In this context, the photophysical processes underlying that treatment critically depend on the electronic structure of the pyranoflavylium molecules. When employing density functional theory to describe the electronic structure of molecules, the choice of the most suitable functional is not trivial, and benchmark studies are needed to orient practitioners in the field. In this work, a benchmark of seven of the most commonly used density functionals in addressing the photophysical properties of a set of eight pyranoflavylium cations is reported. Ground and excited state geometries, molecular orbitals, and absorption, fluorescence and phosphorescence transition energies were calculated using density functional theory approaches, and evaluated and compared to experimental data and monoreferential wave function-based methodologies. Statistical analysis of the results indicates that global-hybrid functionals allow an excellent description of absorption and emission energies, with errors around 0.05 eV, while range-separated variants led to somewhat larger errors in the range 0.1-0.2 eV. In contrast, range-separated functionals display excellent phosphorescence energies with errors close to 0.05 eV, in this case global-hybrids showing increased discrepancies around 0.5-0.1 eV.
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26
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Bíró L, Tóth B, Lihi N, Farkas E, Buglyó P. Interaction between [(η 6- p-cym)M(H 2O) 3] 2+ (M II = Ru, Os) or [(η 5-Cp*)M(H 2O) 3] 2+ (M III = Rh, Ir) and Phosphonate Derivatives of Iminodiacetic Acid: A Solution Equilibrium and DFT Study. Molecules 2023; 28:molecules28031477. [PMID: 36771142 PMCID: PMC9918899 DOI: 10.3390/molecules28031477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The pH-dependent binding strengths and modes of the organometallic [(η6-p-cym)M(H2O)3]2+ (MII = Ru, Os; p-cym = 1-methyl-4-isopropylbenzene) or [(η5-Cp*)M(H2O)3]2+ (MIII = Rh, Ir; Cp* = pentamethylcyclopentadienyl anion) cations towards iminodiacetic acid (H2Ida) and its biorelevant mono- and diphosphonate derivatives N-(phosphonomethyl)-glycine (H3IdaP) and iminodi(methylphosphonic acid) (H4Ida2P) was studied in an aqueous solution. The results showed that all three of the ligands form 1:1 complexes via the tridentate (O,N,O) donor set, for which the binding mode was further corroborated by the DFT method. Although with IdaP3- and Ida2P4- in mono- and bis-protonated species, where H+ might also be located at the non-coordinating N atom, the theoretical calculations revealed the protonation of the phosphonate group(s) and the tridentate coordination of the phosphonate ligands. The replacement of one carboxylate in Ida2- by a phosphonate group (IdaP3-) resulted in a significant increase in the stability of the metal complexes; however, this increase vanished with Ida2P4-, which was most likely due to some steric hindrance upon the coordination of the second large phosphonate group to form (5 + 5) joined chelates. In the phosphonate-containing systems, the neutral 1:1 complexes are the major species at pH 7.4 in the millimolar concentration range that is supported by both NMR and ESI-TOF-MS.
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Patel TR, Ganguly B. Metal‐Free Catalytic Functionalization of Second −
C
sp
2
−H Bond of 1‐Methyl Pyrrole Using Bishomocubane‐Derived Aminoborane Frustrated Lewis Pairs: A Computational Study. ChemistrySelect 2023. [DOI: 10.1002/slct.202202728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Tulsi R. Patel
- Computation and Simulation Unit (Analytical & Environmental Science Division and Centralized Instrument Facility) CSIR-Central Salt & Marine Chemicals Research Institute Bhavnagar 364 002 Gujarat India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical & Environmental Science Division and Centralized Instrument Facility) CSIR-Central Salt & Marine Chemicals Research Institute Bhavnagar 364 002 Gujarat India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
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28
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Aprajita, Choudhary M. New Ni(II) and Cu(II) Schiff base coordination complexes derived from 5-Bromo-salicylaldehyde and 3-picoyl amine/ethylenediamine: Synthesis, structure, Hirshfeld surface and molecular docking study with SARS-CoV-2 7EFP-main protease. Polyhedron 2023. [DOI: 10.1016/j.poly.2023.116296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Abstract
To expand the existing genetic letters beyond the natural four nucleotides, such as G, C, A, and T, it is necessary to design robust nucleotides that can not only produce stable and unperturbed DNA but also function naturally in living cells. Although hydrophobic bases, such as d5SICS (2,6-dimethyl-2H-isoquiniline-1-thione) and dNaM (2-methoxy-3-methylnaphthalene) were shown to be replicated in bacterial cells, the d5SICS:dNaM base-pair was found to perturb the structure of the duplex DNA. Therefore, it is necessary to design nucleobases that can form base pairs like the natural G:C and A:T pairs. Here, a reliable dispersion-corrected density functional theory has been used to design several nucleobases that can produce three-hydrogen-bonded base pairs like the G:C pair. In doing so, the Watson-Crick faces of d5SICS and dNaM were modified by replacing the hydrophobic groups with hydrogen bond donors and acceptors. As dNaM contains an unnatural C-glycosidic bond (C-dNaM), it was also modified to contain the natural N-glycosidic bond (N-dNaM). This technique produced 91 new bases (N-d5SICS-X (X = 1-33), C-dNaM-X (X = 1-35), and N-dNaM-X (X = 1-23), where X is the different types of modifications applied to d5SICS and dNaM) and 259 base-pairs. Among these base pairs, 76 base pairs are found to be more stable than the G:C pair. Interestingly, the N-d5SICS-32:C-dNaM-32 and N-d5SICS-32:N-dNaM-20 pairs are found to be the most stable with binding energies of about -28.0 kcal/mol. The base-pair patterns of these pairs are also analogous to that of the G:C pair. Hence, it is proposed that N-d5SICS-32, C-dNaM-32, and N-dNaM-20 would act as efficient new genetic letters to produce stable and unperturbed artificial DNA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- N R Jena
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design, and Manufacturing, Khamaria, Jabalpur, India
| | - P Das
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design, and Manufacturing, Khamaria, Jabalpur, India
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Spectroscopic, structural, and intermolecular interactions of 4-(2‑hydroxy-3-methoxybenzylideneamino)-N-(5-methylisoxazol-3-yl)benzenesulfonamide enol-imine and keto-amine isomers. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.134978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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31
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Martínez JP, Trzaskowski B. Electrophilicity of Hoveyda-Grubbs Olefin Metathesis Catalysts as the Driving Force that Controls Initiation Rates. Chemphyschem 2022; 23:e202200580. [PMID: 36062870 DOI: 10.1002/cphc.202200580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/01/2022] [Indexed: 01/05/2023]
Abstract
The dissociative mechanism of initiation for a series of Hoveyda-Grubbs type metathesis catalysts modified at the para and meta positions in the isopropoxybenzylidene ligand is investigated by means of DFT calculations. The electron donating/withdrawing capacity of the ligand was screened through the incorporation of various substituents such as halogens, nitro, alkoxides, ketones, esters, amines, and amides. Variations in structural parameters, energy barriers for the Ru-O bond dissociation, and Ru-O bond strength were examined as a function of the Hammett constant. It was found that electronic properties of the catalysts such as chemical potential, hardness, and electrophilicity correlate linearly with the dissociative energy barriers. These findings enable a systematic rationalization and prediction of rate of precatalyst initiation through the calculation of only the HOMO-LUMO gap of catalysts, as the faster the initiation, the more electrophilic the catalyst.
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32
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On the stereoselectivity of the cross metathesis of olefins catalyzed by a second-generation catalyst. CATAL COMMUN 2022. [DOI: 10.1016/j.catcom.2022.106552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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33
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Corinti D, Paciotti R, Coletti C, Re N, Chiavarino B, Crestoni ME, Fornarini S. Elusive intermediates in cisplatin reaction with target amino acids: Platinum(II)-cysteine complexes assayed by IR ion spectroscopy and DFT calculations. J Inorg Biochem 2022; 237:112017. [PMID: 36209532 DOI: 10.1016/j.jinorgbio.2022.112017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/12/2022] [Accepted: 09/27/2022] [Indexed: 01/18/2023]
Abstract
The reactivity of a widely used metal based antineoplastic drug, cisplatin, cis-PtCl2(NH3)2, with L-cysteine (Cys) has been investigated using a combination of electrospray ionization mass spectrometry (ESI-MS), IRMPD gas phase ion spectroscopy and DFT calculations. The cysteine lateral chain represents one of the main platination sites in proteins, which is believed to be related to the resistance mechanisms to cisplatin. The vibrational features of the mass-selected substitution product cis-[PtCl(NH3)2(Cys)]+ and the intercepted cis-[PtCl(NH3)2(H2O)(Cys)]+ intermediate complex were compared to calculated IR spectra, enabling the assessment of the sampled ions structures. In cis-[PtCl(NH3)2(Cys)]+, cysteine was found to bind platinum through the sulfur atom as a thiolate zwitterion, highlighting the enhanced acidity of the cysteine thiol group upon metal coordination. The cis-[PtCl(NH3)2(H2O)(Cys)]+ structure complies with the non-covalent encounter complex, formed by cis-[PtCl(NH3)2(H2O)]+ and neutral cysteine. This species is able to undergo the substitution process to produce cis-[PtCl(NH3)2(Cys)]+ when activated as a mass-isolated ion suggesting its participation in the reaction mechanism of cisplatin with cysteine in solution. Finally, the DFT-calculated energy profile for the substitution reaction was correlated with the peculiar gas-phase reactivity of this non-covalent complex, resulting to be 10-fold less reactive toward substitution than the corresponding methionine complex.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma, "La Sapienza", I-00185 Roma, Italy.
| | - Roberto Paciotti
- Dipartimento di Farmacia, Università G. D'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy.
| | - Cecilia Coletti
- Dipartimento di Farmacia, Università G. D'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Nazzareno Re
- Dipartimento di Farmacia, Università G. D'Annunzio Chieti-Pescara, Via dei Vestini 31, Chieti I-66100, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma, "La Sapienza", I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma, "La Sapienza", I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma, "La Sapienza", I-00185 Roma, Italy
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Dhimba G, Muller A, Lammertsma K. Racemization Pathway for MoO 2(acac) 2 Favored over Ray-Dutt, Bailar, and Conte-Hippler Twists. Inorg Chem 2022; 61:14918-14923. [PMID: 35980189 PMCID: PMC9516665 DOI: 10.1021/acs.inorgchem.2c00824] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Indexed: 11/28/2022]
Abstract
Chiral cis-MoO2(acac)2 racemizes via four pathways that agree with and extend upon Muetterties' topological analysis for dynamic MX2(chel)2 complexes. Textbook Ray-Dutt and Bailar twists are the least favored with barriers of 27.5 and 28.7 kcal/mol, respectively. Rotating both acac ligands of the Bailar structure by 90° gives the lower Conte-Hippler twist (20.0 kcal/mol), which represents a valley-ridge inflection that invokes the trans isomer. The most favorable is a new twist that was found by 90° rotation of only one acac ligand of the Bailar structure. The gas-phase barrier of 17.4 kcal/mol for this Dhimba-Muller-Lammertsma twist further decreases upon inclusion of the effects of solvents to 16.3 kcal/mol (benzene), 16.2 kcal/mol (toluene), and 15.4 kcal/mol (chloroform), which are in excellent agreement with the reported experimental values.
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Affiliation(s)
- George Dhimba
- Department
of Chemical Sciences, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Alfred Muller
- Department
of Chemical Sciences, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Koop Lammertsma
- Department
of Chemical Sciences, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
- Department
of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, Amsterdam 1081 HZ, The Netherlands
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Enhancing Effects of the Cyano Group on the C-X∙∙∙N Hydrogen or Halogen Bond in Complexes of X-Cyanomethanes with Trimethyl Amine: CH3−n(CN)nX∙∙∙NMe3, (n = 0–3; X = H, Cl, Br, I). Int J Mol Sci 2022; 23:ijms231911289. [PMID: 36232589 PMCID: PMC9570363 DOI: 10.3390/ijms231911289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/28/2022] Open
Abstract
In this paper, density functional theory and wave function theory calculations are carried out to investigate the strength and nature of the intermolecular C-X∙∙∙N bond interaction as a function of the number of cyano groups, CN, in the X-bond donor while maintaining the X-bond acceptor as fixed. Specifically, complexes of X-cyanomethanes with trimethyl amine CH3−n(CN)nX∙∙∙NMe3 (n = 0–3; X = H, Cl, Br, I) are used as model systems. Geometrical parameters and vibrational C-X-stretching frequencies as well as interaction energies are used as relevant indicators to gauge hydrogen or halogen bond strength in the complexes. Additional characteristics of interactions that link these complexes, i.e., hydrogen or halogen bonds, are calculated with the use of the following theoretical tools: the atoms in molecules (AIM) approach, the natural bond orbital (NBO) method, and energy decomposition analysis (EDA). The results show that, for the specified X-center, the strength of C-X∙∙∙N interaction increases significantly and in a non-additive fashion with the number of CN groups. Moreover, the nature (noncovalent or partly covalent) of the interactions is revealed via the AIM approach.
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36
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Grabowski SJ, Parra RD. Sandwich, Triple-Decker and Other Sandwich-like Complexes of Cyclopentadienyl Anions with Lithium or Sodium Cations. Molecules 2022; 27:molecules27196269. [PMID: 36234808 PMCID: PMC9571536 DOI: 10.3390/molecules27196269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Density functional theory, DFT, calculations were carried out on complexes containing cyclopentadienyl anions and lithium or sodium cations; half-sandwich, sandwich and sandwich-like complexes (among them triple-decker ones) are analyzed. Searches performed through the Cambridge Structural Database revealed that crystal structures containing these motifs exist, mostly structures with sodium cations. The DFT calculations performed here include geometry optimization and frequency calculations of the complexes at the ωB97XD/aug-cc-pVTZ level, followed by the partitioning of the energy of interaction via the Energy Decomposition Analysis scheme, EDA, at the BP86-D3/TZ2P level. Additional calculations and analyses were performed using both the Quantum Theory of Atoms in Molecules, QTAIM, and the Natural Bond Orbital analyses, NBO. The results of this work show that the electrostatic interaction energy is the most important attractive contribution to the total interaction energy of each of the complex systems analyzed here, and that complexation itself leads to minor electron charge shifts.
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Affiliation(s)
- Sławomir J. Grabowski
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU & Donostia International Physics Center (DIPC) PK 1072, 20080 Donostia, Spain
- Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain
- Correspondence: (S.J.G.); (R.D.P.)
| | - Rubén D. Parra
- Department of Chemistry and Biochemistry, DePaul University, Chicago, IL 60614, USA
- Correspondence: (S.J.G.); (R.D.P.)
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37
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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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38
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Efremenko I, Montag M. Revisiting C–C and C–H Bond Activation in Rhodium Pincer Complexes: Thermodynamics and Kinetics Involving a Common Agostic Intermediate. Organometallics 2022. [DOI: 10.1021/acs.organomet.2c00176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Irena Efremenko
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76000, Israel
| | - Michael Montag
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76000, Israel
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Paciotti R, Fish RH, Marrone A. MD-DFT Computational Studies on the Mechanistic and Conformational Parameters for the Chemoselective Tyrosine Residue Reactions of G-Protein-Coupled Receptor Peptides with [Cp*Rh(H 2O) 3](OTf) 2 in Water To Form Their [(η 6-Cp*Rh-Tyr #)-GPCR peptide] 2+ Complexes: Noncovalent H-Bonding Interactions, Molecular Orbital Analysis, Thermodynamics, and Lowest Energy Conformations. Organometallics 2022. [DOI: 10.1021/acs.organomet.2c00259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Roberto Paciotti
- Dipartimento di Farmacia, Università “G d’Annunzio” di Chieti-Pescara, Chieti 5130, Italy
| | - Richard H. Fish
- Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720, United States
| | - Alessandro Marrone
- Dipartimento di Farmacia, Università “G d’Annunzio” di Chieti-Pescara, Chieti 5130, Italy
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40
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Liu H, Zhou Y, An D, Wang G, Zhu F, Yamaguchi T. Structure of Aqueous KNO 3 Solutions by Wide-Angle X-ray Scattering and Density Functional Theory. J Phys Chem B 2022; 126:5866-5875. [PMID: 35895329 DOI: 10.1021/acs.jpcb.2c02247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure of aqueous KNO3 solutions was studied by wide-angle X-ray scattering (WAXS) and density functional theory (DFT). The interference functions were subjected to empirical potential structure refinement (EPSR) modeling to extract the detailed hydration structure information. In aqueous KNO3 solutions with a concentration from 0.50 to 2.72 mol·dm-3, water molecules coordinate K+ with a mean coordination number (CN) from 6.6 ± 0.9 to 5.8 ± 1.2, respectively, and a K-OW(H2O) distance of 2.82 Å. To further describe the hydration properties of K+, a hydration factor (fh) was defined based on the orientational angle between the water O-H vector and the ion-oxygen vector. The fh value obtained for K+ is 0.792, 0.787, 0.766, and 0.765, and the corresponding average hydration numbers (HN) are 5.2, 5.1, 4.8, and 4.5. The reduced HN is compensated by the direct binding of oxygen atoms of NO3- with the average CN from 0.3 ± 0.7 to 2.6 ± 1.7, respectively, and the K-ON(NO3-) distance of 2.82 Å. The average number of water molecules around NO3- slightly reduces from 10.5 ± 1.5 to 9.6 ± 1.7 with rN-OW = 3.63 Å. K+-NO3- ion association is characterized by K-ON and K-N pair correlation functions (PCFs). A K-N peak is observed at 3.81 Å as the main peak with a shoulder at 3.42 Å in gK-N(r). This finding indicates that two occupancy sites are available for K+, i.e., the edge-shared bidentate (BCIP) and the corner-shared monodentate (MCIP) contact ion pairs. The structure and stability of the KNO3(H2O)10 cluster were investigated by a DFT method and cross-checked with the results from WAXS.
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Affiliation(s)
- Hongyan Liu
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources; Key Laboratory of Salt Lake Resources Chemistry of Qinghai Province; Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, Qinghai 810008, China
| | - Yongquan Zhou
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources; Key Laboratory of Salt Lake Resources Chemistry of Qinghai Province; Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, Qinghai 810008, China
| | - Dong An
- Department of Chemical Engineering, Qinghai University, Xining 810016, China
| | - Guangguo Wang
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources; Key Laboratory of Salt Lake Resources Chemistry of Qinghai Province; Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, Qinghai 810008, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fayan Zhu
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources; Key Laboratory of Salt Lake Resources Chemistry of Qinghai Province; Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, Qinghai 810008, China
| | - Toshio Yamaguchi
- Key Laboratory of Comprehensive and Highly Efficient Utilization of Salt Lake Resources; Key Laboratory of Salt Lake Resources Chemistry of Qinghai Province; Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, Qinghai 810008, China.,Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan, Fukuoka 814-0180, Japan
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41
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Preparation of Deuterium-Labeled Armodafinil by Hydrogen–Deuterium Exchange and Its Application in Quantitative Analysis by LC-MS. Metabolites 2022; 12:metabo12070578. [PMID: 35888702 PMCID: PMC9317911 DOI: 10.3390/metabo12070578] [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] [Received: 06/03/2022] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 11/17/2022] Open
Abstract
Armodafinil, the R enantiomer of modafinil, was approved in 2007 by the US Food and Drug Administration as a wake-promoting agent for excessive sleepiness treatment. Due to its abuse by students and athletes, there is a need of its quantification. Quantitative analysis by liquid chromatography-mass spectrometry, however, though very common and sensitive, frequently cannot be performed without isotopically labeled standards which usually have to be specially synthesized. Here we reported our investigation on the preparation of deuterated standard of armodafinil based on the simple and inexpensive hydrogen–deuterium exchange reaction at the carbon centers. The obtained results clearly indicate the possibility of introduction of three deuterons into the armodafinil molecule. The introduced deuterons do not undergo back exchange under neutral and acidic conditions. Moreover, the deuterated and non-deuterated armodafinil isotopologues revealed co-elution during the chromatographic analysis. The ability to control the degree of deuteration using different reaction conditions was determined. The proposed method of deuterated armodafinil standard preparation is rapid, cost-efficient and may be successfully used in its quantitative analysis by LC-MS.
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42
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Bresciani G, Zacchini S, Pampaloni G, Bortoluzzi M, Marchetti F. η 6-Coordinated ruthenabenzenes from three-component assembly on a diruthenium μ-allenyl scaffold. Dalton Trans 2022; 51:8390-8400. [PMID: 35587270 DOI: 10.1039/d2dt01071b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The room temperature reactions with internal alkynes, RCCR, of the μ-allenyl acetonitrile complex [Ru2Cp2(CO)2(NCMe){μ-η1:η2-C1HC2C3Me2}]BF4 (1-NCMe), freshly prepared from the tricarbonyl precursor [Ru2Cp2(CO)3{μ-η1:η2-C1HC2C3Me2}]BF4, 1, proceeded with alkyne insertion into ruthenium-allenyl bond and allenyl-CO coupling, affording compounds [Ru2Cp2(CO)2{μ-η2:η5-C(R)C(R)C1HC2(C3MeCH2)C(OH)}]BF4 (R = Ph, 2; R = CO2Me, 3; R = CO2Et, 4) in 83-94% yields. Deprotonation of 2-4 by triethylamine gave [Ru2Cp2(CO)2{μ-η2:η5-C(R)C(R)CHC(CMeCH2)C(O)}] (R = Ph, 5; R = CO2Me, 6; R = CO2Et, 7) in 75-88% yields, and 2-4 could be recovered upon HBF4·Et2O addition to 5-7. All the products, 2-7, were fully characterized by elemental analysis, IR and multinuclear NMR spectroscopy. The structure of 2 was ascertained by single crystal X-ray diffraction and investigated by DFT calculations, revealing a six-membered ruthenacycle with Shannon aromaticity index in line with related compounds. The formation of ruthenium-coordinated ruthenabenzenes from a preexistent diruthenium scaffold is a versatile but underdeveloped approach exploiting cooperative effects typical of a dimetallic core.
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Affiliation(s)
- Giulio Bresciani
- University of Pisa, Department of Chemistry and Industrial Chemistry, Via G. Moruzzi 13, I-56124 Pisa, Italy. .,CIRCC, Via Celso Ulpiani 27, I-70126 Bari, Italy
| | - Stefano Zacchini
- University of Bologna, Department of Industrial Chemistry "Toso Montanari", Viale Risorgimento 4, I-40136 Bologna, Italy.,CIRCC, Via Celso Ulpiani 27, I-70126 Bari, Italy
| | - Guido Pampaloni
- University of Pisa, Department of Chemistry and Industrial Chemistry, Via G. Moruzzi 13, I-56124 Pisa, Italy. .,CIRCC, Via Celso Ulpiani 27, I-70126 Bari, Italy
| | - Marco Bortoluzzi
- University of Venezia "Ca' Foscari", Department of Molecular Science and Nanosystems, Via Torino 155, I-30170 Mestre (VE), Italy.,CIRCC, Via Celso Ulpiani 27, I-70126 Bari, Italy
| | - Fabio Marchetti
- University of Pisa, Department of Chemistry and Industrial Chemistry, Via G. Moruzzi 13, I-56124 Pisa, Italy. .,CIRCC, Via Celso Ulpiani 27, I-70126 Bari, Italy
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Aslam MR, Khera RA, El-Badry YA, Rafiq M, Naveed A, Shehzad MT, Iqbal J. Tuning of diphenylamine subphthalocyanine based small molecules with efficient photovoltaic parameters for organic solar cells. J Mol Graph Model 2022; 112:108146. [DOI: 10.1016/j.jmgm.2022.108146] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 01/07/2022] [Accepted: 02/02/2022] [Indexed: 10/19/2022]
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Yuan M, Gutierrez O. Mechanisms, Challenges, and Opportunities of Dual Ni/Photoredox-Catalyzed C(sp 2)-C(sp 3) Cross-Couplings. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2022; 12:e1573. [PMID: 35664524 PMCID: PMC9162266 DOI: 10.1002/wcms.1573] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/09/2021] [Indexed: 12/28/2022]
Abstract
The merging of photoredox and nickel catalysis has revolutionized the field of C-C cross-coupling. However, in comparison to the development of synthetic methods, detailed mechanistic investigations of these catalytic systems are lagging. To improve the mechanistic understanding, computational tools have emerged as powerful tools to elucidate the factors controlling reactivity and selectivity in these complex catalytic transformations. Based on the reported computational studies, it appears that the mechanistic picture of catalytic systems is not generally applicable, but is rather dependent on the specific choice of substrate, ligands, photocatalysts, etc. Given the complexity of these systems, the need for more accurate computational methods, readily available and user-friendly dynamics simulation tools, and data-driven approaches is clear in order to understand at the molecular level the mechanisms of these transformations. In particular, we anticipate that such improvement of theoretical methods will become crucial to advance the understanding of excited-state properties and dynamics of key species, as well as to enable faster and unbiased exploration of reaction pathways. Further, with greater collaboration between computational, experimental, and spectroscopic communities, the mechanistic investigation of photoredox/Ni dual-catalytic reactions is expected to thrive quickly, facilitating the design of novel catalytic systems and promoting our understanding of the reaction selectivity.
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Sahu K, Dutta J, Nayak S, Nayak P, Biswal HS, Kar S. Investigation of the Nature of Intermolecular Interactions in Tetra(thiocyanato)corrolato-Ag(III) Complexes: Agostic or Hydrogen Bonded? Inorg Chem 2022; 61:6539-6546. [PMID: 35442024 DOI: 10.1021/acs.inorgchem.2c00353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Tetra(thiocyanato)corrolato-Ag(III) complexes presented here constitute a new class of metallo-corrole complexes. The spectroscopic properties of these complexes are quite unusual and interesting. For example, the absorption spectra of these β-substituted corrolato-Ag(III) complexes are very different from those of the β-unsubstituted corrolato-Ag(III) derivatives. Single-crystal XRD analysis of a representative tetra(thiocyanato)corrolato-Ag(III) derivative reveals C-H···Ag interactions. The C-H···Ag interactions are rarely demonstrated in the crystal lattice of a discrete coordination/organometallic compound. Optimization of the hydrogen positions of the crystal structure discloses the geometrical parameters of the said interaction as a Ag···H distance of 2.597 Å and ∠C-H···Ag of 109.62°. The natural bond orbital analysis provides information about the donor-acceptor orbitals involved in the interactions and their interaction energies. It was observed that the σC-H orbital overlaps with the vacant d-orbital of Ag with an interaction energy of 17.93 kJ/mol. The filled d-orbital of Ag overlaps with the σ*C-H orbital with an interaction energy of 4.79 kJ/mol. The highlights of this work are that the H···Ag distance is outside of the distance range for the typical agostic interaction but fitted with the weak H-bond distance. However, the ∠C-H···Ag angle is within the range of the agostic interaction. Both crystallographic data and electronic structure calculations reveal that these kinds of intermolecular interactions in square-planar d8 Ag(III) complexes are intermediate in nature. Thus, they cannot be categorically called either hydrogen bonding or agostic interaction.
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Affiliation(s)
- Kasturi Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India
| | - Srimoy Nayak
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India
| | - Panisha Nayak
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India
| | - Sanjib Kar
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400 094, India
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Pradhan TR, Paudel M, Feoktistova T, Cheong PHY, Park JK. Silaborative Assembly of Allenamides and Alkynes: Highly Regio- and Stereocontrolled Access to Bi- or Trimetallic Skipped Dienes. Angew Chem Int Ed Engl 2022; 61:e202116154. [PMID: 35142019 DOI: 10.1002/anie.202116154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Indexed: 12/16/2022]
Abstract
A highly stereo- and regiocontrolled multicomponent approach to skipped 1,4-dienes decorated with one boryl and two silyl functionalities is described. This Pd-catalyzed atom-economical union of allenamides, alkynes, and Me2 PhSiBpin (or Et3 SiBpin) proceeds without the use of phosphine ligands, instead relying on chelation through the internal amide group of the allenamide sulfonyl. A variety of alkynes, including those derived from complex bioactive molecules, can be efficiently coupled with allenamides and Me2 PhSiBpin in good yields and with excellent selectivity. The synthetic potential was demonstrated through multiple valuable chemoselective transformations, establishing new disconnections for functionalized dienes. Density functional theory calculations revealed that the reaction first proceeded through borylation of the allenamide, followed by silylation of the alkyne and then reductive elimination, which convergently assemble the skipped 1,4-diene.
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Affiliation(s)
- Tapas R Pradhan
- Department of Chemistry and Institution for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Mukti Paudel
- Department of Chemistry and Institution for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | | | | | - Jin Kyoon Park
- Department of Chemistry and Institution for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
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Hajali N, Taghva Manesh A, Seif A. Formations of bimolecular barbituric acid complexes through hydrogen bonding interactions: DFT analyses of structural and electronic features. MAIN GROUP CHEMISTRY 2022. [DOI: 10.3233/mgc-210102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Formations of bimolecular barbituric acid (BA) complexes through hydrogen-bonding (HB) interactions were investigated in this work. BA has been known as a starting compound of pharmaceutical compounds developments, in which the molecular and atomic features of parent BA in homo-paring with another BA molecule were investigated here. The models were optimized to reach the stabilized structures and their properties were evaluated at the molecular and atomic scales. Density functional theory (DFT) calculations were performed to provide required information for achieving the goal of this work. Six dimer models were obtained finally according to examining all possible starting dimers configurations for involving in optimization calculations. N-H . . . O and C-H . . . O interactions were also involved in dimers formations besides participation of the X-center of parent BA in interaction. Molecular and atomic scales features were evaluated for characterizing the dimers formations. As a consequence, several configurations of BA dimers were obtained showing the importance of performing such structural analyses for developing further compounds from BA.
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Affiliation(s)
- Narjes Hajali
- Department of Chemistry, Faculty of Science, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Afshin Taghva Manesh
- Department of Chemistry, Faculty of Science, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Ahmad Seif
- Department of Chemistry, Faculty of Science, Central Tehran Branch, Islamic Azad University, Tehran, Iran
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Ovalle S, Malardier-Jugroot C. Choice of Functional for Iron Porphirin Density Functional Theory Studies: Geometry, Spin-State, and Binding Energy Analysis. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Brown J, Ovens J, Richeson D. Elucidating Two Distinct Pathways for Electrocatalytic Hydrogen Production Using Co II Pincer Complexes. CHEMSUSCHEM 2022; 15:e202102542. [PMID: 35041773 DOI: 10.1002/cssc.202102542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/02/2022] [Indexed: 06/14/2023]
Abstract
Hydrogen gas is a sustainable energy source with water as the sole combustion product. As a result, efforts to catalyze H2 production are pertinent and widespread. The electrocatalytic H2 generating capabilities of two CoII complexes, [Co(κ3 -2,6-{Ph2 PNR}2 (NC5 H3 ))Br2 ] with R=H (I) or R=Me (II), were presented for a variety of proton sources including trifluoroacetic acid (TFA), acetic acid (AA), and trifluoroethanol (TFE). Cyclic voltammetry and controlled potential coulometry demonstrated that electrocatalysis from I and II occurred at two different potentials and are associated with different reduction processes. Density functional theory analysis provided insight into the identities of the catalyst and supported two distinct reaction pathways for electrocatalytic proton reduction. Specifically, stronger acids (e. g., AA, TFA) proceeded at -1.31 to -1.45 V through a MI /MIII pathway while sources with higher pKa values (e. g., TFE, H2 O) generated hydrogen at -2.4 V via M0 /MII ligand-assisted metal-centered reduction.
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Affiliation(s)
- Josh Brown
- Department of Chemistry and Biomolecular Sciences Centre for Catalysis Research and Innovation, University of Ottawa, 10 Marie Curie, Ottawa, ON K1 N 6 N5, Canada
| | - Jeffrey Ovens
- Department of Chemistry and Biomolecular Sciences Centre for Catalysis Research and Innovation, University of Ottawa, 10 Marie Curie, Ottawa, ON K1 N 6 N5, Canada
| | - Darrin Richeson
- Department of Chemistry and Biomolecular Sciences Centre for Catalysis Research and Innovation, University of Ottawa, 10 Marie Curie, Ottawa, ON K1 N 6 N5, Canada
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Pradhan TR, Paudel M, Feoktistova T, Cheong PH, Park JK. Silaborative Assembly of Allenamides and Alkynes: Highly Regio‐ and Stereocontrolled Access to Bi‐ or Trimetallic Skipped Dienes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tapas R. Pradhan
- Department of Chemistry and Institution for Functional Materials Pusan National University Busan 46241 Republic of Korea
| | - Mukti Paudel
- Department of Chemistry and Institution for Functional Materials Pusan National University Busan 46241 Republic of Korea
| | | | | | - Jin Kyoon Park
- Department of Chemistry and Institution for Functional Materials Pusan National University Busan 46241 Republic of Korea
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