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Boiko DA, Arkhipova DM, Ananikov VP. Recognition of Molecular Structure of Phosphonium Salts from the Visual Appearance of Material with Deep Learning Can Reveal Subtle Homologs. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2403423. [PMID: 39254289 DOI: 10.1002/smll.202403423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/31/2024] [Indexed: 09/11/2024]
Abstract
Determining molecular structures is foundational in chemistry and biology. The notion of discerning molecular structures simply from the visual appearance of a material remained almost unthinkable until the advent of machine learning. This paper introduces a pioneering approach bridging the visual appearance of materials (both at the micro- and nanostructural levels) with traditional chemical structure analysis methods. Quaternary phosphonium salts are opted as the model compounds, given their significant roles in diverse chemical and medicinal fields and their ability to form homologs with only minute intermolecular variances. This research results in the successful creation of a neural network model capable of recognizing molecular structures from visual electron microscopy images of the material. The performance of the model is evaluated and related to the chemical nature of the studied chemicals. Additionally, unsupervised domain transfer is tested as a method to use the resulting model on optical microscopy images, as well as test models trained on optical images directly. The robustness of the method is further tested using a complex system of phosphonium salt mixtures. To the best of the authors' knowledge, this study offers the first evidence of the feasibility of discerning nearly indistinguishable molecular structures.
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Affiliation(s)
- Daniil A Boiko
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow, 119991, Russia
| | - Daria M Arkhipova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow, 119991, Russia
| | - Valentine P Ananikov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow, 119991, Russia
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Arkhipova DM, Ermolaev VV, Baembitova GR, Samigullina AI, Lyubina AP, Voloshina AD. Oxygen-Containing Quaternary Phosphonium Salts (oxy-QPSs): Synthesis, Properties, and Cellulose Dissolution. Polymers (Basel) 2023; 15:4097. [PMID: 37896340 PMCID: PMC10611013 DOI: 10.3390/polym15204097] [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: 08/28/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
In the present study, the synthesis of oxygen-containing quaternary phosphonium salts (oxy-QPSs) was described. Within this work, structure-property relationships of oxy-QPSs were estimated by systematic analysis of physical-chemical properties. The influence of the oxygen-containing substituent was examined by comparing the properties of oxy-QPSs in homology series as well as with phosphonium analog-included alkyl side chains. The crystal structure analysis showed that the oxygen introduction influences the conformation of the side chain of the oxy-QPS. It was found that oxy-QPSs, using an aprotic co-solvent, dimethylsulfoxide (DMSO), can dissolve microcrystalline cellulose. The cellulose dissolution in oxy-QPSs appeared to be dependent on the functional group in the cation and anion nature. For the selected conditions, dissolution of up to 5 wt% of cellulose was observed. The antimicrobial activity of oxy-QPSs under study was expected to be low. The biocompatibility of oxy-QPSs with fermentative microbes was tested on non-pathogenic Saccharomyces cerevisiae, Lactobacillus plantarum, and Bacillus subtilis. This reliably allows one to safely address the combined biomass destruction and enzyme hydrolysis processes in one pot.
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Affiliation(s)
- Daria M. Arkhipova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia;
| | - Vadim V. Ermolaev
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan 420088, Russia; (V.V.E.); (G.R.B.); (A.P.L.); (A.D.V.)
| | - Gulnaz R. Baembitova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan 420088, Russia; (V.V.E.); (G.R.B.); (A.P.L.); (A.D.V.)
| | - Aida I. Samigullina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia;
| | - Anna P. Lyubina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan 420088, Russia; (V.V.E.); (G.R.B.); (A.P.L.); (A.D.V.)
| | - Alexandra D. Voloshina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan 420088, Russia; (V.V.E.); (G.R.B.); (A.P.L.); (A.D.V.)
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Conductive Mediators in Oxidation Based on Ferrocene Functionalized Phosphonium Ionic Liquids. Int J Mol Sci 2022; 23:ijms232415534. [PMID: 36555177 PMCID: PMC9779220 DOI: 10.3390/ijms232415534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Herein, the synthesis of ferrocene-containing salts is presented. Acylation of ferrocene (Fc) according to the Friedel-Crafts method led to ω-bromoacyl ferrocenes. The ω-bromoacyl ferrocenes were subsequently introduced to quaternization reaction with tri-tert-butyl phosphine, which resulted in phosphonium salts. Obtained phosphonium salts were characterized by physical methods. The electrochemical properties of phosphonium salts were studied by cyclic voltammetry (CV). It was found that the replacement of n-butyl fragments at the phosphorus atom by tert-butyl leads to a more anodic potential shift. In contrast to isolobal structures Fc-C(O)(CH2)nP+(n-Bu)3X- and Fc-(CH2)n+1P+(n-Bu)3X-, the CV curves of Fc-C(O)(CH2)nP+(t-Bu)3X- and Fc-(CH2)n+1P+(t-Bu)3X- did not show a large discrepancy between forward and reverse currents. The transformation of the C=O groups to CH2 fragments had a significant effect on the electrochemical properties of ferrocene salts, the oxidation potential of which is close to that of pure ferrocene.
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Micellar nanocontainers based on sterically hindered cationic phosphonium amphiphiles. Russ Chem Bull 2022. [DOI: 10.1007/s11172-022-3481-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Ishikawa T, Honda A, Miyamura K. Effects of Alkyl Chain Length on the Cold Crystallization of Schiff-Base Nickel(II) Complexes. CrystEngComm 2022. [DOI: 10.1039/d2ce00305h] [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
"Cold crystallization" is the exothermic phenomenon occurring during the heating process of a supercooled liquid. Molecules that exhibit cold crystallization can be used as heat storage materials. Schiff-base nickel(II) complexes...
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Ermolaev VV, Arkhipova DM, Miluykov VA, Lyubina AP, Amerhanova SK, Kulik NV, Voloshina AD, Ananikov VP. Sterically Hindered Quaternary Phosphonium Salts (QPSs): Antimicrobial Activity and Hemolytic and Cytotoxic Properties. Int J Mol Sci 2021; 23:86. [PMID: 35008507 PMCID: PMC8744835 DOI: 10.3390/ijms23010086] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/09/2021] [Accepted: 12/19/2021] [Indexed: 02/06/2023] Open
Abstract
Structure-activity relationships are important for the design of biocides and sanitizers. During the spread of resistant strains of pathogenic microbes, insights into the correlation between structure and activity become especially significant. The most commonly used biocides are nitrogen-containing compounds; the phosphorus-containing ones have been studied to a lesser extent. In the present study, a broad range of sterically hindered quaternary phosphonium salts (QPSs) based on tri-tert-butylphosphine was tested for their activity against Gram-positive (Staphylococcus aureus, Bacillus cereus, Enterococcus faecalis) and Gram-negative (Escherichia coli, Pseudomonas aeruginosa) bacteria and fungi (Candida albicans, Trichophyton mentagrophytes var. gypseum). The cation structure was confirmed to determine their biological activity. A number of QPSs not only exhibit high activity against both Gram-positive and -negative bacteria but also possess antifungal properties. Additionally, the hemolytic and cytotoxic properties of QPSs were determined using blood and a normal liver cell line, respectively. The results show that tri-tert-butyl(n-dodecyl)phosphonium and tri-tert-butyl(n-tridecyl)phosphonium bromides exhibit both low cytotoxicity against normal human cells and high antimicrobial activity against bacteria, including methicillin-resistant strains S. aureus (MRSA). The mechanism of QPS action on microbes is discussed. Due to their high selectivity for pathogens, sterically hindered QPSs could serve as effective tunable biocides.
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Affiliation(s)
- Vadim V. Ermolaev
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov str., 8, Kazan 420088, Russia; (V.V.E.); (V.A.M.); (A.P.L.); (S.K.A.); (N.V.K.); (A.D.V.)
| | - Daria M. Arkhipova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov str., 8, Kazan 420088, Russia; (V.V.E.); (V.A.M.); (A.P.L.); (S.K.A.); (N.V.K.); (A.D.V.)
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow 119991, Russia;
| | - Vasili A. Miluykov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov str., 8, Kazan 420088, Russia; (V.V.E.); (V.A.M.); (A.P.L.); (S.K.A.); (N.V.K.); (A.D.V.)
| | - Anna P. Lyubina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov str., 8, Kazan 420088, Russia; (V.V.E.); (V.A.M.); (A.P.L.); (S.K.A.); (N.V.K.); (A.D.V.)
| | - Syumbelya K. Amerhanova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov str., 8, Kazan 420088, Russia; (V.V.E.); (V.A.M.); (A.P.L.); (S.K.A.); (N.V.K.); (A.D.V.)
| | - Natalia V. Kulik
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov str., 8, Kazan 420088, Russia; (V.V.E.); (V.A.M.); (A.P.L.); (S.K.A.); (N.V.K.); (A.D.V.)
| | - Alexandra D. Voloshina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov str., 8, Kazan 420088, Russia; (V.V.E.); (V.A.M.); (A.P.L.); (S.K.A.); (N.V.K.); (A.D.V.)
| | - Valentine P. Ananikov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect, 47, Moscow 119991, Russia;
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