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Ondar EE, Polynski MV, Ananikov VP. Predicting 195 Pt NMR Chemical Shifts in Water-Soluble Inorganic/Organometallic Complexes with a Fast and Simple Protocol Combining Semiempirical Modeling and Machine Learning. Chemphyschem 2023:e202200940. [PMID: 36806426 DOI: 10.1002/cphc.202200940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 02/23/2023]
Abstract
Water-soluble Pt complexes are the key components in medicinal chemistry and catalysis. The well-known cisplatin family of anticancer drugs and industrial hydrosylilation catalysts are two leading examples. On the molecular level, the activity mechanisms of such complexes mostly involve changes in the Pt coordination sphere. Using 195 Pt NMR spectroscopy for operando monitoring would be a valuable tool for uncovering the activity mechanisms; however, reliable approaches for the rapid correlation of Pt complex structure with 195 Pt chemical shifts are very challenging and not available for everyday research practice. While NMR shielding is a response property, molecular 3D structure determines NMR spectra, as widely known, which allows us to build up 3D structure to 195 Pt chemical shift correlations. Accordingly, we present a new workflow for the determination of lowest-energy configurational/conformational isomers based on the GFN2-xTB semiempirical method and prediction of corresponding chemical shifts with a Machine Learning (ML) model tuned for Pt complexes. The workflow was designed for the prediction of 195 Pt chemical shifts of water-soluble Pt(II) and Pt(IV) anionic, neutral, and cationic complexes with halide, NO2 - , (di)amino, and (di)carboxylate ligands with chemical shift values ranging from -6293 to 7090 ppm. The model offered an accuracy (normalized root-mean-square deviation/RMSD) of 1.08 %/145.02 ppm on the held-out test set.
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Affiliation(s)
- Evgeniia E Ondar
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, 119991, Russia
| | - Mikhail V Polynski
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, 119991, Russia.,Scientific Technological Center of Organic and Pharmaceutical Chemistry, National Academy of Sciences, 26 Azatutyan Ave, 0014, Yerevan, Armenia
| | - Valentine P Ananikov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, 119991, Russia
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Raeker T, Jansen B, Behrens D, Hartke B. Simulations of optically switchable molecular machines for particle transport. J Comput Chem 2018; 39:1433-1443. [PMID: 29573268 DOI: 10.1002/jcc.25212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 02/27/2018] [Accepted: 02/27/2018] [Indexed: 12/22/2022]
Abstract
A promising application for design and deployment of molecular machines is nanoscale transport, driven by artificial cilia. In this contribution, we present several further steps toward this goal, beyond our first-generation artificial cilium (Raeker et al., J. Phys. Chem. A 2012, 116, 11241). Promising new azobenzene-derivatives were tested for use as cilium motors. Using a QM/MM partitioning in on-the-fly photodynamics, excited-state surface-hopping trajectories were calculated for each isomerization direction and each motor version. The methods used were reparametrized semiempirical quantum chemistry together with floating-occupation configuration interaction as the QM part and the OPLSAA-L forcefield as MM part. In addition, we simulated actual particle transport by a single cilium attached to a model surface, with varying attachment strengths and modes, and with transport targets ranging from single atoms to multi-molecule arrangements. Our results provide valuable design guidelines for cilia-driven nanoscale transport and emphasize the need to carefully select the whole setup (not just the cilium itself, but also its surface attachment and the dynamic cilium-target interaction) to achieve true transport. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Tim Raeker
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstraße 40, Kiel, D-24098, Germany
| | - Björn Jansen
- Institut für Pharmazeutische Chemie, Christian-Albrechts-Universität zu Kiel, Gutenbergstraße 76, Kiel, D-24118, Germany
| | - Dominik Behrens
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstraße 40, Kiel, D-24098, Germany
| | - Bernd Hartke
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstraße 40, Kiel, D-24098, Germany
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Rouillé G, Jäger C, Huisken F, Henning T, Czerwonka R, Theumer G, Börger C, Bauer I, Knölker HJ. Quantitative Structure-Retention Relationships for Polycyclic Aromatic Hydrocarbons and their Oligoalkynyl-Substituted Derivatives. ChemistryOpen 2017; 6:519-525. [PMID: 28794947 PMCID: PMC5542760 DOI: 10.1002/open.201700115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Indexed: 11/08/2022] Open
Abstract
Reversed‐phase high‐performance liquid chromatography (RP‐HPLC) has been carried out for a series of unsubstituted polycyclic aromatic hydrocarbons (PAHs) and the corresponding ethynyl, 1,3‐butadiynyl, and 1,3,5‐hexatriynyl derivatives. Theoretical values of the isotropic polarizability and several polarity descriptors have been computed for each compound by using semiempirical models and density functional theory (DFT), with the aim of evaluating linear functions as quantitative structure–retention relationships (QSRRs). The polarity has been described by using either the permanent electric dipole moment, the subpolarity, or a topological electronic index. Three types of partial atomic charges have been used to calculate the subpolarity and a topological index. The choice of the theoretical model, of the polarity descriptor, and of the partial atomic charges is discussed and the resulting QSRRs are compared. Calculating the retention times from the polarizability and the topological electronic index (AM1, PM3, or DFT‐B3LYP/6–31+G(d,p)) gives the best agreement with the experimental values.
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Affiliation(s)
- Gaël Rouillé
- Laboratory Astrophysics Group of the Max Planck Institute for Astronomy at the Friedrich Schiller University Jena Institute of Solid State Physics Helmholtzweg 3 07743 Jena Germany
| | - Cornelia Jäger
- Laboratory Astrophysics Group of the Max Planck Institute for Astronomy at the Friedrich Schiller University Jena Institute of Solid State Physics Helmholtzweg 3 07743 Jena Germany
| | - Friedrich Huisken
- Laboratory Astrophysics Group of the Max Planck Institute for Astronomy at the Friedrich Schiller University Jena Institute of Solid State Physics Helmholtzweg 3 07743 Jena Germany
| | - Thomas Henning
- Max Planck Institute for Astronomy Königstuhl 17 69117 Heidelberg Germany
| | - Regina Czerwonka
- Department Chemie Technische Universität Dresden Bergstrasse 66 01069 Dresden Germany
| | - Gabriele Theumer
- Department Chemie Technische Universität Dresden Bergstrasse 66 01069 Dresden Germany
| | - Carsten Börger
- Department Chemie Technische Universität Dresden Bergstrasse 66 01069 Dresden Germany
| | - Ingmar Bauer
- Department Chemie Technische Universität Dresden Bergstrasse 66 01069 Dresden Germany
| | - Hans-Joachim Knölker
- Department Chemie Technische Universität Dresden Bergstrasse 66 01069 Dresden Germany
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Caturello NAMS, Csók Z, Fernández G, Albuquerque RQ. Influence of Metal, Ligand and Solvent on Supramolecular Polymerizations with Transition-Metal Compounds: A Theoretical Study. Chemistry 2016; 22:17681-17689. [PMID: 27862391 DOI: 10.1002/chem.201603600] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Indexed: 12/28/2022]
Abstract
The nature of intermolecular interactions governing supramolecular polymerizations is very important for controlling their cooperativity. In order to address this problem, supramolecular columns made of PtII and PdII complexes of oligo(phenylene ethynylene)-based pyridine (OPE) and tetrazolylpyridine ligands (TEP) were investigated through the dispersion-corrected PM6 method. Aromatic, CH-π, M-Cl and metallophilic interactions helped stabilize the supramolecules studied, and their geometries and associated cooperativities were in excellent agreement with experimental data. The OPE ligand and/or the presence of PtII led to stronger metallophilic interactions and also to cooperative supramolecular polymerizations, which clearly suggests that metallophilic interactions are a key factor for controlling cooperativity. The results indicate that sequential monomer addition is in general less spontaneous than the combination of two larger preformed stacks. The present theoretical investigations contribute to the further understanding of the relation between the thermodynamics of supramolecular polymerizations and the nature of different synthons.
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Affiliation(s)
| | - Zsolt Csók
- Sao Carlos Institute of Chemistry, University of Sao Paulo (USP), Sao Carlos, Brazil
| | - Gustavo Fernández
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - Rodrigo Q Albuquerque
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University (LJMU), Byrom Str. Campus, Liverpool, L3 3AF, UK.,Sao Carlos Institute of Chemistry, University of Sao Paulo (USP), Sao Carlos, Brazil
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Troć A, Gajewy J, Danikiewicz W, Kwit M. Specific Noncovalent Association of Chiral Large-Ring Hexaimines: Ion Mobility Mass Spectrometry and PM7 Study. Chemistry 2016; 22:13258-64. [PMID: 27534731 DOI: 10.1002/chem.201602515] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Indexed: 02/04/2023]
Abstract
Ion mobility mass spectrometry and PM7 semiempirical calculations are effective complementary methods to study gas phase formation of noncovalent complexes from vaselike macrocycles. The specific association of large-ring chiral hexaimines, derived from enantiomerically pure trans-1,2-diaminocyclohexane and various isophthaldehydes, is driven mostly by CH-π and π-π stacking interactions. The isotrianglimine macrocycles are prone to form two types of aggregates: tail-to-tail and head-to-head (capsule) dimers. The stability of the tail-to-tail dimers is affected by the size and electronic properties of the substituents at the C-5 position of the aromatic ring. Electron-withdrawing groups stabilize the aggregate, whereas bulky or electron-donating groups destabilize the complexes.
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Affiliation(s)
- Anna Troć
- Intitute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland.
| | - Jadwiga Gajewy
- Department of Chemistry, Adam Mickiewicz University, Umultowska 89B, 61 614, Poznań, Poland.,Wielkopolska Centre for Advanced Technologies (WCAT), Umultowska 89C, 61-614, Poznań, Poland
| | - Witold Danikiewicz
- Intitute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Marcin Kwit
- Department of Chemistry, Adam Mickiewicz University, Umultowska 89B, 61 614, Poznań, Poland. , .,Wielkopolska Centre for Advanced Technologies (WCAT), Umultowska 89C, 61-614, Poznań, Poland. ,
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Denmark SE, Wilson TW, Burk MT. Enantioselective construction of quaternary stereogenic carbon atoms by the Lewis base catalyzed additions of silyl ketene imines to aldehydes. Chemistry 2014; 20:9268-79. [PMID: 25043283 DOI: 10.1002/chem.201403342] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Indexed: 11/07/2022]
Abstract
Silyl ketene imines derived from a variety of α-branched nitriles have been developed as highly useful reagents for the construction of quaternary stereogenic centers via the aldol addition reaction. In the presence of SiCl4 and the catalytic action of a chiral phosphoramide, silyl ketene imines undergo extremely rapid and high yielding addition to a wide variety of aromatic aldehydes with excellent diastereo- and enantioselectivity. Of particular note are the high yields and selectivities obtained from electron-rich, electron-poor, and hindered aldehydes. Linear aliphatic aldehydes did react with good diastereo- and enantioselectivity in the presence of nBu4N(+)I(-), but branched aldehydes were much less reactive. Semiempirical calculations provided a rationalization of the observed diastereo- and enantioselectivity via open transitions states.
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Affiliation(s)
- Scott E Denmark
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801 (USA), Fax: (+1) 217-333-3984.
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Abstract
The current work presents a conformational evaluation of heparinase II (hepII) from Pedobacter heparinus, employing molecular dynamics (MD) simulations, in order to characterize the main features of the enzyme dynamics, as well as the role of the glycan and metal components on the protein scaffold. Accordingly, four systems were simulated, encompassing nonglycosylated hepII without structural ions, nonglycosylated hepII with Zn(2+), nonglycosylated hepII with Ca(2+), and glycosylated hepII with Zn(2+). The obtained data suggest a role for Zn(2+) in modulating the protein flexibility at specific loop regions. Such flexibility pattern is not properly maintained in the absence of such structural ion or when the ion is replaced by Ca(2+). Still, semiempirical calculations suggest more favorable interactions with Zn(2+). These events correlate with the experimentally reported inhibitory effect of calcium over hepII. Additionally, the glycan chain seems able to promote an additional stabilization on hepII dynamics. Taken together, these results improve our understanding of the structural and dynamical features of hepII, as well as atomic-level comprehension of previous experimental data.
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Affiliation(s)
- Cláudia L Fernandes
- a Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul , Av Bento Gonçalves, 9500, CP 15005, Porto , Alegre , 91500-970 , Brazil
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