1
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Phillips RS, Brown SM, Patel RS. Structural Snapshots of Proteus vulgaris Tryptophan Indole-Lyase Reveal Insights into the Catalytic Mechanism. ACS Catal 2024; 14:11498-11511. [PMID: 39114092 PMCID: PMC11301627 DOI: 10.1021/acscatal.4c03232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 06/24/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024]
Abstract
Tryptophan indole lyase (TIL; [E.C. 4.1.99.1]) is a bacterial pyridoxal-5'-phosphate (PLP)-dependent enzyme that catalyzes reversible β-elimination of indole from L-tryptophan. The mechanism of elimination of indole from L-tryptophan starts with the formation of an external aldimine of the substrate and PLP, followed by deprotonation of the α-CH of the substrate, forming a resonance-stabilized quinonoid intermediate. Proton transfer to C3 of the indole ring and carbon-carbon bond cleavage of the quinonoid intermediate provide indole and aminoacrylate bound to PLP, which then releases indole, followed by iminopyruvate. We have now determined the X-ray crystal structures of TIL complexes with (3S)-dioxindolyl-l-alanine, an inhibitor, and with substrates L-tryptophan, 7-aza-L-tryptophan, and S-ethyl-l-cysteine (SEC) in the presence of benzimidazole (BZI), an isostere of the product indole. These structures show a mixture of gem-diamine, external aldimine, quinonoid, and aminoacrylate intermediates, in both open and closed active site conformations. In the closed conformations of L-tryptophan, (3S)-dioxindolyl-l-alanine, and 7-aza-L-tryptophan complexes, hydrogen bonds form between Asp-133 with N1 of the ligand heterocyclic ring and NE2 of His-458 in the small domain of TIL. This hydrogen bond also forms in the BZI complex with the aminoacrylate intermediates formed from both L-tryptophan and SEC. The closed quinonoid complex of 7-aza-L-tryptophan shows that the azaindole ring in the closed conformation is bent out of plane of the Cβ-C3 bond by about 40°, putting it in a geometry that leads toward the transition-state geometry. Thus, both conformational dynamics and substrate activation play critical roles in the reaction mechanism of the TIL.
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Affiliation(s)
- Robert S. Phillips
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
| | - S. Meredith Brown
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
| | - Ravi S. Patel
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
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2
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Carlson CD, Ma J, Al-Jabiri MH, Insausti A, Xu Y. Conformational adaptation and large amplitude motions of 1-phenyl-2,2,2-trifluoroethanol with two water molecules: a rotational spectroscopic and ab initio investigation. Phys Chem Chem Phys 2024; 26:18067-18075. [PMID: 38895791 DOI: 10.1039/d4cp01516a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The 1 : 2 adduct of 1-phenyl-2,2,2-trifluoroethanol (PhTFE), a chiral fluoroalcohol, with two water molecules (PhTFE⋯2H2O) was investigated via chirped pulse Fourier-transform microwave (CP-FTMW) spectroscopy and theoretical calculations. A systematic search of the PhTFE⋯2H2O conformational landscape identified 38 stable minima at the B3LYP-D3BJ/def2-TZVPPD level of theory, 27 of which are within an energy window of 10 kJ mol-1 after applying zero-point energy corrections. Rotational spectra of a single PhTFE⋯2H2O conformer along with eight deuterated and three oxygen-18 isotopologues were assigned. Interestingly, the observed PhTFE⋯2H2O conformer contains PhTFE II, the second most stable monomer conformer, and the most stable PhTFE I dihydrate is ca. 4 kJ mol-1 higher in energy. In contrast, PhTFE I⋯H2O was identified experimentally and theoretically as the most stable 1 : 1 conformer. Furthermore, the observed dihydrate structure experiences large amplitude motions connecting three theoretical minima which differ only in which water oxygen lone pairs are involved in the hydrogen-bonds, i.e., the free OH pointing directions. Additionally, the ortho and para-H2O tunnelling splittings were detected and attributed to the interchange water hydrogen atoms which interact with the aromatic part of PhTFE but not for the water interacting with PhTFE hydroxy group. Extensive theoretical modelling was carried out to gain insight into the associated large amplitude motions including tunnelling, supported by the experimental isotopic and tunnelling splitting data.
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Affiliation(s)
- Colton D Carlson
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada.
| | - Jiarui Ma
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada.
| | - Mohamad H Al-Jabiri
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada.
| | - Aran Insausti
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada.
- Departamento de Quimica Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV-EHU), Bilbao 48080, Spain
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada.
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3
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D'Anania O, Romano E, Barone V, Talarico G. Predicting the propene stereoselectivity on transition metal catalysts: A daunting task for density functional theory. J Comput Chem 2024; 45:1483-1492. [PMID: 38470153 DOI: 10.1002/jcc.27343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024]
Abstract
Thanks to recent developments in hardware and software, quantum chemical methods are increasingly used for interpreting the complex mechanisms underlying polymerization reaction by homogeneous catalysis. Unfortunately, the dimensions of even the smallest realistic models are too large to permit the use of state-of-the-art composite wave function methods. Under these circumstances, density functional theory still offers the best compromise between cost and accuracy. However, comprehensive benchmarks of different functionals are not yet available for this important research field. The main aim of the present paper is to fill this gap by performing an unbiased comparison of several density functionals and continuum solvent models for the stereo-control in the propylene polymerization on prototypical catalysts inducing different reaction mechanisms. While it was not possible to define a unique computational protocol providing the best results in all the situations, the B3PW91 functional in conjunction with D3 empirical dispersions and the solvent model density solvent model performs remarkably well for three out of the four investigated catalysts. Under such circumstances, it is recommended to compare the results delivered by different models when approaching additional classes of catalysts.
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Affiliation(s)
- Olga D'Anania
- Scuola Superiore Meridionale, Napoli, Italy
- Scuola Normale Superiore, Pisa, Italy
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Eugenio Romano
- Scuola Superiore Meridionale, Napoli, Italy
- Scuola Normale Superiore, Pisa, Italy
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Napoli, Italy
| | | | - Giovanni Talarico
- Scuola Superiore Meridionale, Napoli, Italy
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Napoli, Italy
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4
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Sornambigai M, Roselin Pavithra AS, Hansda S, Senthil Kumar S. Fabrication of an all-in-one self-enhanced solid-state electrochemiluminescence sensing platform for the selective detection of spermine. Analyst 2024; 149:3555-3563. [PMID: 38780058 DOI: 10.1039/d4an00357h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
The fabrication of an all-in-one solid-state ECL sensing platform is beneficial not only for expediting the miniaturization of sensing devices, but also, more importantly, for enabling point-of-care applications. In the present work, a self-enhanced solid-state ECL sensing platform is fabricated using newly synthesised silica polyethylene nanoparticles (SiO2-PEI NPs) which generate a co-reactant in situ and easily self-assemble with Ru(bpy)32+ and shows selective and sensitive detection of spermine at physiological pH (7.4). Spermine induces the maximum ECL emission intensity compared to other biogenic amines due to the presence of two secondary amines. A possible ECL reaction mechanism has been proposed based on CV and ECL experiments, DFT calculations, and in situ ECL spectrum analysis. The developed solid-state sensor showed a linear increase in ECL intensity with increasing spermine concentration in the range of 10 nM to 100 nM with an LOD of 12.2 nM. Compared to other biogenic amines in previous works, chemically synthesised SiO2-PEI NPs used in the present study act as an effective label- and enzyme-free sensor, and the new method is observed to be simple and cost-effective, to overcome various limitations of solution-phase ECL and to avoid the usage of any noble metals.
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Affiliation(s)
- Mathavan Sornambigai
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 20100, Uttar Pradesh, India
- CSIR-Central Electrochemical Research Institute (CSIR-CECRI) campus, Karaikudi-630003, Tamil Nadu, India.
- Electrodics and Electrocatalysis Division, CSIR-CECRI, Karaikudi-630003, Tamil Nadu, India
| | | | - Shekhar Hansda
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 20100, Uttar Pradesh, India
- Corrosion and Material Protection Division, CSIR-CECRI, Karaikudi-630003, Tamil Nadu, India
| | - Shanmugam Senthil Kumar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 20100, Uttar Pradesh, India
- CSIR-Central Electrochemical Research Institute (CSIR-CECRI) campus, Karaikudi-630003, Tamil Nadu, India.
- Electrodics and Electrocatalysis Division, CSIR-CECRI, Karaikudi-630003, Tamil Nadu, India
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5
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Kusza DA, Venter GA, Mabunda M, Biwi J, Samanta SK, Klinck JD, Singh SV, Hunter R, Kaschula CH. Finding the Ajoene Sweet-Spot: Structure-Activity Relations that Govern its Blood Stability and Cancer Cytotoxicity. ChemMedChem 2024; 19:e202400087. [PMID: 38532643 DOI: 10.1002/cmdc.202400087] [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] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 03/28/2024]
Abstract
Ajoene is an organosulfur compound found in crushed garlic that exerts its anti-cancer activity by S-thiolating cysteine residues on proteins. Its development is hampered due to limited bioavailability, so in this study, we synthesised analogues of ajoene to probe the significance of the ajoene vinyl disulfide/sulfoxide core with respect to cytotoxicity and blood stability. Polar side groups were also incorporated to improve aqueous solubility. It was found that derivatives containing a vinyl disulfide functional group (4-7, as in ajoene), were more cytotoxic compared to analogues in which the double bond was removed, although the latter showed superior blood stability. It was also found that the allyl-S sulfur of the disulfide was more electrophilic to S-thiolysis based on the global electrophilicity index (ω) and the condensed electrophilic Fukui functionf k + ${{ f}_{\rm{k}}^{\rm{ + }} }$ . S-Thiolysis was found to be exergonic for the vinyl disulfides based on entropy and enthalpy computations with a deprotonated thiolate. Derivatisation to the dihydro (10, 12) and deoxydihydroajoenes (9, 11) produced analogues that were slightly less potent but with greatly improved blood stability. Taken together, the deoxydihydroajoenes present themselves as good candidates for further therapeutic development.
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Affiliation(s)
- Daniel A Kusza
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
| | - Gerhard A Venter
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
| | - Mandla Mabunda
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
| | - James Biwi
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
| | - Suman K Samanta
- Faculty of Science, Assam down town University, Sankar Madhab Path, Gandi Nagar, Panikhaiti, Guwahati, 781026, Assam, India
| | - Johan D Klinck
- Department of Chemistry and Polymer Science, Stellenbosch University, Matieland, 7600, South Africa
| | - Shivendra V Singh
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh School of Medicine, UPMC Hillman Cancer Centre, Pittsburgh, Pennsylvania, USA
| | - Roger Hunter
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
| | - Catherine H Kaschula
- Department of Chemistry and Polymer Science, Stellenbosch University, Matieland, 7600, South Africa
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6
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Scherz F, Bauer M, Domenianni LI, Hoyer C, Schmidt J, Sarkar B, Vöhringer P, Krewald V. Ultrafast photogeneration of a metal-organic nitrene from 1,1'-diazidoferrocene. Chem Sci 2024; 15:6707-6715. [PMID: 38725494 PMCID: PMC11077559 DOI: 10.1039/d4sc00883a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
Ferrocene and its derivatives have fascinated chemists for more than 70 years, not least due to the analogies with the properties of benzene. Despite these similarities, the obvious difference between benzene and ferrocene is the presence of an iron ion and hence the availability of d-orbitals for properties and reactivity. Phenylnitrene with its rich photochemistry can be considered an analogue of nitrenoferrocene. As with most organic and inorganic nitrenes, nitrenoferrocene can be obtained by irradiating the azide precursor. We study the photophysical and photochemical processes of dinitrogen release from 1,1'-diazidoferrocene to form 1-azido-1'-nitrenoferrocene with UV-pump-mid-IR-probe transient absorption spectroscopy and time-dependent density functional theory calculations including spin-orbit coupling. An intermediate with a bent azide moiety is identified that is pre-organised for dinitrogen release via a low-lying transition state. The photochemical decay paths on the singlet and triplet surfaces including the importance of spin-orbit coupling are discussed. We compare our findings with the processes discussed for photochemical dinitrogen activation and highlight implications for the photochemistry of azides more generally.
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Affiliation(s)
- Frederik Scherz
- Department of Chemistry, Theoretical Chemistry, TU Darmstadt Peter-Grünberg-Str. 4 64287 Darmstadt Germany
| | - Markus Bauer
- Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn Wegelerstraße 12 53115 Bonn Germany
| | - Luis I Domenianni
- Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn Wegelerstraße 12 53115 Bonn Germany
| | - Carolin Hoyer
- Institut für Chemie und Biochemie, Freie Universität Berlin Fabeckstraße 34-36 14195 Berlin Germany
| | - Jonas Schmidt
- Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn Wegelerstraße 12 53115 Bonn Germany
| | - Biprajit Sarkar
- Institute of Inorganic Chemistry, University of Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
- Institut für Chemie und Biochemie, Freie Universität Berlin Fabeckstraße 34-36 14195 Berlin Germany
| | - Peter Vöhringer
- Clausius-Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn Wegelerstraße 12 53115 Bonn Germany
| | - Vera Krewald
- Department of Chemistry, Theoretical Chemistry, TU Darmstadt Peter-Grünberg-Str. 4 64287 Darmstadt Germany
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7
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Barbosa WG, Santos-Jr CV, Andrade RB, Lucena JR, Moura RT. Bond analysis in meta- and para-substituted thiophenols: overlap descriptors, local mode analysis, and QTAIM. J Mol Model 2024; 30:139. [PMID: 38639900 DOI: 10.1007/s00894-024-05932-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/07/2024] [Indexed: 04/20/2024]
Abstract
CONTEXT This study delves into the chemical nuances of thiophenols and their derivatives through a comprehensive computational analysis, moving beyond traditional energetic perspectives such as bond dissociation enthalpy and S-H dissociation dynamics. By employing the overlap model along with its topological descriptors (OP/TOP), quantum theory of atoms in molecules (QTAIM), and local vibrational mode (LVM) theories, the research provides a deeper understanding of the S-H and C-S bonding scenarios in substituted thiophenols. The investigation follows the electron-donating capacity of S-H substituent variation with the nature and positioning of other ring substituents. Energy profile analyses indicate distinct stability differences in the cis and trans conformations of meta- and para-PhSH systems, influenced by the electron-donating strength of these substituents. The study also uncovers significant variations in S-H bond distances and descriptor values, particularly in para-substituted PhSH, reflecting the influence of electron-donating or withdrawing substituents. In contrast, alterations at the meta-position show minimal effects on C-S bond descriptors, while para-substitutions markedly influence C-S bond characteristics, demonstrating a clear correlation with the electron-donating or withdrawing capabilities of the substituents. This research sheds light on the intricate bond dynamics in aromatic systems with diverse substituents, highlighting the complex interaction between electronic effects and molecular conformation. METHODS The study employs the ω B97X-D/Def2TZVP level of theory for molecular geometries, ensuring accurate characterization of structures as true minima via analytical harmonic frequency determination. The electronic properties of S-H and C-S bonds in variously substituted thiophenols were analyzed using OP/TOP, QTAIM, and LVM methodologies. Computational processes, including conformational scans, geometry optimizations, and vibrational frequency calculations, were conducted using Gaussian 09, with ultra-fine integration grids and tight convergence criteria for the SCF procedure. Bond descriptors were computed utilizing ChemBOS, Multiwfn, and LModeA software, providing a robust and detailed examination of bond properties.
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Affiliation(s)
- Willis G Barbosa
- Department of Chemistry, State University of Paraiba, Campina Grande, 58429-500, PB, Brazil
| | - Carlos V Santos-Jr
- Department of Chemistry, Federal University of Paraiba, João Pessoa, 58051-970, PB, Brazil
| | - Railton B Andrade
- Department of Chemistry, State University of Paraiba, Campina Grande, 58429-500, PB, Brazil
| | - Juracy R Lucena
- Department of Chemistry, State University of Paraiba, Campina Grande, 58429-500, PB, Brazil
| | - Renaldo T Moura
- Department of Chemistry and Physics, Center of Agrarian Sciences, Federal University of Paraiba, Areia, 58397-000, PB, Brazil.
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, 75275, USA.
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8
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Nyagilo VO, Mallojjala SC, Hirschi JS. Transition State Analysis of Key Steps in Dual Photoredox-Cobalt-Catalyzed Elimination of Alkyl Bromides. ACS Catal 2024; 14:4683-4689. [PMID: 39211423 PMCID: PMC11361288 DOI: 10.1021/acscatal.3c06324] [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] [Indexed: 09/04/2024]
Abstract
A combination of inter- and intramolecular 13C kinetic isotope effects and density functional theory analysis is used to evaluate the key mechanistic events of sequentially operating catalytic cycles in the dual photoredox-cobalt-catalyzed elimination of alkyl bromides. The results point to a mechanism proceeding via irreversible halogen-atom transfer (XAT) from the alkyl halide, resulting in an alkyl radical, which undergoes hydrogen-atom transfer (HAT) to a Co(II) intermediate to deliver the product olefin. Alternative pathways involving nucleophilic substitution by a Co(I) species and by β-hydride elimination are discounted based on the poor agreement of experimental and predicted 13C KIEs. This mechanistic understanding is used to evaluate the origins of regioselectivity in the elimination step for an unsymmetrical alkyl halide catalyzed by electronically and sterically distinct cobaloxime catalysts. This study represents the experimental validation of the key features of the transition state structure of XAT by α-aminoalkyl radicals, an important class of atom transfer reactions that generate carbon-centered radicals from alkyl and aryl halides. Furthermore, it illustrates the power of 13C KIEs in probing complex mechanisms in metallaphotoredox catalysis.
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Affiliation(s)
- Victor O Nyagilo
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
| | | | - Jennifer S Hirschi
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
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9
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Pawlędzio S, Ziemniak M, Trzybiński D, Arhangelskis M, Makal A, Woźniak K. Influence of N-protonation on electronic properties of acridine derivatives by quantum crystallography. RSC Adv 2024; 14:5340-5350. [PMID: 38348299 PMCID: PMC10859733 DOI: 10.1039/d3ra08081a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 01/30/2024] [Indexed: 02/15/2024] Open
Abstract
Applications of 9-aminoacridine (9aa) and its derivatives span fields such as chemistry, biology, and medicine, including anticancer and antimicrobial activities. Protonation of such molecules can alter their bioavailability as weakly basic drugs like aminoacridines exhibit reduced solubility at high pH levels potentially limiting their effectiveness in patients with elevated gastric pH. In this study, we analyse the influence of protonation on the electronic characteristics of the molecular organic crystals of 9-aminoacridine. The application of quantum crystallography, including aspherical atom refinement, has enriched the depiction of electron density in the studied systems and non-covalent interactions, providing more details than previous studies. Our experimental results, combined with a topological analysis of the electron density and its Laplacian, provided detailed descriptions of how protonation changes the electron density distribution around the amine group and water molecule, concurrently decreasing the electron density at bond critical points of N/O-H bonds. Protonation also alters the molecular architecture of the systems under investigation. This is reflected in different proportions of the N⋯H and O⋯H intermolecular contacts for the neutral and protonated forms. Periodic DFT calculations of the cohesive energies of the crystal lattice, as well as computed interaction energies between molecules in the crystal, confirm that protonation stabilises the crystal structure due to a positive synergy between strong halogen and hydrogen bonds. Our findings highlight the potential of quantum crystallography in predicting crystal structure properties and point to its possible applications in developing new formulations for poorly soluble drugs.
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Affiliation(s)
- Sylwia Pawlędzio
- Neutron Scattering Division, Oak Ridge National Laboratory Oak Ridge TN 37831 USA
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-093 Warszawa Poland
| | - Marcin Ziemniak
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-093 Warszawa Poland
| | - Damian Trzybiński
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-093 Warszawa Poland
| | - Mihails Arhangelskis
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-093 Warszawa Poland
| | - Anna Makal
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-093 Warszawa Poland
| | - Krzysztof Woźniak
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-093 Warszawa Poland
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10
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Meng EC, Goddard TD, Pettersen EF, Couch GS, Pearson ZJ, Morris JH, Ferrin TE. UCSF ChimeraX: Tools for structure building and analysis. Protein Sci 2023; 32:e4792. [PMID: 37774136 PMCID: PMC10588335 DOI: 10.1002/pro.4792] [Citation(s) in RCA: 352] [Impact Index Per Article: 352.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/20/2023] [Accepted: 09/23/2023] [Indexed: 10/01/2023]
Abstract
Advances in computational tools for atomic model building are leading to accurate models of large molecular assemblies seen in electron microscopy, often at challenging resolutions of 3-4 Å. We describe new methods in the UCSF ChimeraX molecular modeling package that take advantage of machine-learning structure predictions, provide likelihood-based fitting in maps, and compute per-residue scores to identify modeling errors. Additional model-building tools assist analysis of mutations, post-translational modifications, and interactions with ligands. We present the latest ChimeraX model-building capabilities, including several community-developed extensions. ChimeraX is available free of charge for noncommercial use at https://www.rbvi.ucsf.edu/chimerax.
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Affiliation(s)
- Elaine C. Meng
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Thomas D. Goddard
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Eric F. Pettersen
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Greg S. Couch
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Zach J. Pearson
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - John H. Morris
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Thomas E. Ferrin
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCaliforniaUSA
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11
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Daniels BS, Hou X, Corio SA, Weissman LM, Dong VM, Hirschi JS, Nie S. Copper-Phosphido Catalysis: Enantioselective Addition of Phosphines to Cyclopropenes. Angew Chem Int Ed Engl 2023; 62:e202306511. [PMID: 37332088 PMCID: PMC11365472 DOI: 10.1002/anie.202306511] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/15/2023] [Accepted: 06/15/2023] [Indexed: 06/20/2023]
Abstract
We describe a copper catalyst that promotes the addition of phosphines to cyclopropenes at ambient temperature. A range of cyclopropylphosphines bearing different steric and electronic properties can now be accessed in high yields and enantioselectivities. Enrichment of phosphorus stereocenters is also demonstrated via a Dynamic Kinetic Asymmetric Transformation (DyKAT) process. A combined experimental and theoretical mechanistic study supports an elementary step featuring insertion of a CuI -phosphido into a carbon-carbon double bond. Density functional theory calculations reveal migratory insertion as the rate- and stereo-determining step, followed by a syn-protodemetalation.
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Affiliation(s)
- Brian S Daniels
- Department of Chemistry, University of California, Irvine, 92697, Irvine, CA, USA
| | - Xintong Hou
- Department of Chemistry, University of California, Irvine, 92697, Irvine, CA, USA
| | - Stephanie A Corio
- Department of Chemistry, Binghamton University, 13902, Binghamton, NY, USA
| | - Lindsey M Weissman
- Department of Chemistry, Binghamton University, 13902, Binghamton, NY, USA
| | - Vy M Dong
- Department of Chemistry, University of California, Irvine, 92697, Irvine, CA, USA
| | - Jennifer S Hirschi
- Department of Chemistry, Binghamton University, 13902, Binghamton, NY, USA
| | - Shaozhen Nie
- Department of Medicinal Chemistry, GSK, 1250 S. Collegeville Rd, 19426, Collegeville, PA, USA
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Carlson CD, Hazrah AS, Mason D, Yang Q, Seifert NA, Xu Y. Alternating 1-Phenyl-2,2,2-Trifluoroethanol Conformational Landscape With the Addition of One Water: Conformations and Large Amplitude Motions. J Phys Chem A 2022; 126:7250-7260. [PMID: 36191084 DOI: 10.1021/acs.jpca.2c05803] [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 1:1 adduct of 1-phenyl-2,2,2-trifluoroethanol (PhTFE), a chiral fluoroalcohol, with water was investigated using chirped pulse Fourier transform microwave spectroscopy and computational methods. While PhTFE itself was predicted to have three minima, I (gauche+), II (trans), and III (gauche-), only I and II were stable and only I was observed experimentally. A systematic search of the PhTFE···H2O conformational landscape identified 110 stable minima, 14 of which are within a 15 kJ mol-1 energy window. Rotational spectra of the two PhTFE···H2O conformers along with several deuterium and 18O isotopologues were assigned, and the isotopic data were used to verify the corresponding structures. In the two observed monohydrate conformers, one contains PhTFE I where the water subunit is inserted into the existing intramolecular OH···F contact of I, and the binary adduct is stabilized by two intermolecular contacts: OH···OW and HW···F, whereas the other contains PhTFE II where the water subunit interacts with both the alcohol hydrogen and phenyl ring of II, demonstrating that interaction with water sufficiently stabilizes II for its observation in a jet expansion. Interestingly, the predicted electric dipole moment components at the identified minima deviate considerably from the experimental ones. Such deviations were analyzed in terms of dynamic effects associated with the large amplitude motions of the unbound HW. In addition, tunnelling effects associated with the exchange of the bonded and nonbonded HW were also discussed.
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Affiliation(s)
- Colton D Carlson
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Arsh S Hazrah
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Daniel Mason
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Qian Yang
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Nathan A Seifert
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.,Department of Chemistry and Chemical & Biomedical Engineering, University of New Haven, 300 Boston Post Rd, West Haven, Connecticut 06516, United States
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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Understanding the reaction mechanism of the CO2 and cyclohexene oxide copolymerization catalyzed by zinc(II) and magnesium(II) catalysts: a DFT approach. J Mol Model 2022; 28:314. [DOI: 10.1007/s00894-022-05293-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/19/2022] [Indexed: 10/14/2022]
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Duan C, Nandy A, Adamji H, Roman-Leshkov Y, Kulik HJ. Machine Learning Models Predict Calculation Outcomes with the Transferability Necessary for Computational Catalysis. J Chem Theory Comput 2022; 18:4282-4292. [PMID: 35737587 DOI: 10.1021/acs.jctc.2c00331] [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
Virtual high-throughput screening (VHTS) and machine learning (ML) have greatly accelerated the design of single-site transition-metal catalysts. VHTS of catalysts, however, is often accompanied with a high calculation failure rate and wasted computational resources due to the difficulty of simultaneously converging all mechanistically relevant reactive intermediates to expected geometries and electronic states. We demonstrate a dynamic classifier approach, i.e., a convolutional neural network that monitors geometry optimizations on the fly, and exploit its good performance and transferability in identifying geometry optimization failures for catalyst design. We show that the dynamic classifier performs well on all reactive intermediates in the representative catalytic cycle of the radical rebound mechanism for the conversion of methane to methanol despite being trained on only one reactive intermediate. The dynamic classifier also generalizes to chemically distinct intermediates and metal centers absent from the training data without loss of accuracy or model confidence. We rationalize this superior model transferability as arising from the use of electronic structure and geometric information generated on-the-fly from density functional theory calculations and the convolutional layer in the dynamic classifier. When used in combination with uncertainty quantification, the dynamic classifier saves more than half of the computational resources that would have been wasted on unsuccessful calculations for all reactive intermediates being considered.
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Affiliation(s)
- Chenru Duan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Husain Adamji
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yuriy Roman-Leshkov
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Andreola LR, Wheeler S. Importance of Favourable Non-Covalent Contacts in the Stereoselective Synthesis of Tetrasubstituted Chromanone. Org Chem Front 2022. [DOI: 10.1039/d2qo00090c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Automated transiton state (TS) structure computations for a recently reported Pd-catalysed conjugated addition of arylboronic acids to 2-substituted chromones (Chem Sci, 2020, 11, 4602) reveal unexpected conformations of the key...
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