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Organics, Volume 5, Issue 2 (June 2024) – 6 articles

Cover Story (view full-size image): Polyether amines are versatile compounds characterized by a flexible structure of polyoxypropylene and polyoxyethylene backbones with amine groups at each end. This study demonstrates the innovative use of polyether amine as a recyclable catalyst for the aerobic oxidation of thiophenols, leading to the synthesis of disulfides. In contrast to known methods for thiol oxidation, this polyether amine-based catalytic process eliminates the need for expensive stoichiometric oxidants and minimizes the formation of over-oxidized by-products. A remarkable yield of over 96% was achieved for all 16 test substrates, encompassing a diverse range of functional groups under catalytic aerobic oxidation conditions, using just 0.5% of polyether amine as the catalyst. View this paper
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49 pages, 7257 KiB  
Review
Architecture of Molecular Logic Gates: From Design to Application as Optical Detection Devices
by Gleiston G. Dias and Francielly T. Souto
Organics 2024, 5(2), 114-162; https://doi.org/10.3390/org5020008 - 6 Jun 2024
Cited by 2 | Viewed by 1745
Abstract
Three decades after A. P. de Silva’s seminal paper introduced the concept of logic gates at the molecular level, the field of molecular logic gates (MLGs) has witnessed significant advancements. MLGs are devices designed to perform logical operations, utilizing one or more physical [...] Read more.
Three decades after A. P. de Silva’s seminal paper introduced the concept of logic gates at the molecular level, the field of molecular logic gates (MLGs) has witnessed significant advancements. MLGs are devices designed to perform logical operations, utilizing one or more physical or chemical stimulus signals (inputs) to generate an output response. Notably, MLGs have found diverse applications, with optical detection of analytes emerging as a notable evolution of traditional chemosensors. Organic synthesis methods are pivotal in crafting molecular architectures tailored as optical devices capable of analyte detection through logical functions. This review delves into the fundamental aspects and physical–chemical properties of MLGs, with a particular emphasis on synthetic strategies driving their design. Full article
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Figure 1

Figure 1
<p>Examples of chromophores/fluorophores, which are usually used as building blocks for constructing optical devices.</p>
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<p>Receptors based on association with the design of chemosensors.</p>
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<p>Summary of constructing (<b>a</b>) donor–acceptor, (<b>b</b>) donor–acceptor–donor, and (<b>c</b>) acceptor–donor–acceptor configurations.</p>
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<p>Symbolic representation of logic gates and their corresponding truth tables built from values of inputs and outputs.</p>
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<p>Structure of the first MLG <b>102</b>, reported by Prasanna de Silva et al. [<a href="#B11-organics-05-00008" class="html-bibr">11</a>].</p>
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<p>General representation of (<b>a</b>) a chemosensor building strategy and strategies for building chemodosimeters, considering: (<b>a</b>) the covalent bond of the analyte with the chemodosimeter inducing an optical response, (<b>b</b>) the analyte binding to the chemodosimeter and catalyzing a chemical reaction and (<b>c</b>) the reaction of the analyte with the chemodosimeter capable of cleaving part of the molecule.</p>
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<p>Generic representation of the ESIPT process and its prevention by basic and metallic species in case of analyte detection.</p>
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<p>Receptor functions can detect analyte molecules by forming a covalent bond.</p>
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<p>(<b>a</b>) Generic representation of copper-catalyzed azide-alkyne cycloaddition (CuAAC) to afford 1,4-disubstituted 1,2,3-triazoles and (<b>b</b>) their application as sensors; (<b>c</b>) Representation of coupling reactions in obtaining and modifying optical detection devices.</p>
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<p>Chemosensor prepared by Ghosh et al. [<a href="#B249-organics-05-00008" class="html-bibr">249</a>]. (<b>a</b>) Synthetic route adopted by the authors. (<b>b</b>) The interaction mechanism between compound <b>30</b> and acetate anion and (<b>c</b>) the detection of Al<sup>3+</sup> by 30 involving the ESIPT phenomenon and isomerization of the CH–N bond.</p>
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<p>(<b>a</b>) Synthetic route of chemosensor <b>61</b>. (<b>b</b>) Sensing mechanism of chemosensor based on displacement assay for detection of Zn<sup>2+</sup> and PPi, presented by Mawai et al. [<a href="#B251-organics-05-00008" class="html-bibr">251</a>].</p>
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<p>Chromoreagent prepared by Nedeljko et al. [<a href="#B252-organics-05-00008" class="html-bibr">252</a>] for detection of biogenic amines.</p>
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<p>(<b>a</b>) Synthesis of phenanthro[9,10-<span class="html-italic">d</span>]imidazole <b>73</b> described by Bhaumik et al. [<a href="#B256-organics-05-00008" class="html-bibr">256</a>]. (<b>b</b>) Interaction of HO<sup>−</sup> and F<sup>−</sup> with NH in <b>74</b>. (<b>c</b>) Interaction with Fe<sup>2+</sup> in <b>75</b>.</p>
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<p>Synthesis of 1,6-bis[(<span class="html-italic">N</span>,<span class="html-italic">N</span>-<span class="html-italic">p</span>-(R)-diphenylamino)phenyl]pyrenes (<b>82</b>–<b>86</b>) proposed by Kim et al. [<a href="#B257-organics-05-00008" class="html-bibr">257</a>].</p>
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<p>(<b>a</b>) Synthetic route for preparation of compounds <b>89</b> and <b>91</b>. (<b>b</b>) Reaction of compound <b>91</b> with CN<sup>–</sup>, generating the phenolate <b>92</b>, proposed by Souto et al. [<a href="#B260-organics-05-00008" class="html-bibr">260</a>].</p>
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<p>(<b>a</b>) Synthesis of the D–A system <b>98</b> reported by Song et al. (<b>b</b>) Sensing mechanism of Cys detection [<a href="#B267-organics-05-00008" class="html-bibr">267</a>].</p>
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<p>(<b>a</b>) The synthetic route for obtaining chemosensor <b>109</b>, proposed by Li et al. [<a href="#B290-organics-05-00008" class="html-bibr">290</a>]; (<b>b</b>) GSH, Cys, and Hcy structures and adducts (<b>112</b>–<b>114</b>) formed between them and the chemosensor <b>109</b>.</p>
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<p>The sensing mechanism of compound <b>115</b> and acetate anion, according to Noushija et al. [<a href="#B294-organics-05-00008" class="html-bibr">294</a>].</p>
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<p>(<b>a</b>) Synthetic route to obtain compounds <b>121</b> and <b>122</b> based on crown ether development by Gauci et al. [<a href="#B295-organics-05-00008" class="html-bibr">295</a>]; (<b>b</b>) Corresponding truth table and (<b>c</b>) MLG diagram.</p>
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<p>(<b>a</b>) Synthesis of compounds <b>128</b> and <b>129</b> described by Fang et al. [<a href="#B297-organics-05-00008" class="html-bibr">297</a>]; (<b>b</b>) Truth table for NAND logic and (<b>c</b>) the corresponding diagram.</p>
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<p>(<b>a</b>) MLG rhodamine-6G-based (<b>135</b>) described by Bai et al. [<a href="#B300-organics-05-00008" class="html-bibr">300</a>]; (<b>b</b>) Sensing mechanism for detection of Hg<sup>2+</sup> and I<sup>−</sup>; (<b>c</b>) Truth table and (<b>d</b>) the corresponding diagram.</p>
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<p>(<b>a</b>) Molecular logic gate <b>140</b> for detection of Hg<sup>2+</sup> described by Kumar et al. [<a href="#B303-organics-05-00008" class="html-bibr">303</a>]; (<b>b</b>) The sensing mechanism and (<b>c</b>) corresponding truth table and (<b>d</b>) diagram.</p>
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<p>(<b>a</b>) Molecular logic gate <b>145</b> for detection of K<sup>+</sup> and Zn<sup>2+</sup> described by Li et al. [<a href="#B304-organics-05-00008" class="html-bibr">304</a>] and (<b>b</b>) the corresponding truth table and (<b>c</b>) diagram associated.</p>
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<p>(<b>a</b>) Synthesis of <b>151</b> proposed by Guo et al. [<a href="#B305-organics-05-00008" class="html-bibr">305</a>]; (<b>b</b>) Sensing mechanism for Zn<sup>2+</sup> and (<b>c</b>) logical interpretation.</p>
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<p>(<b>a</b>) Synthesis of compound <b>158</b> and functionalized material <b>159</b>, produced by Souto and Machado; (<b>b</b>) The truth table of INHIBIT-type and (<b>c</b>) IMPLICATION-type logic [<a href="#B306-organics-05-00008" class="html-bibr">306</a>].</p>
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<p>(<b>a</b>) Synthetic route of MLG <b>164</b>–<b>166</b> described by Sharma et al.; (<b>b</b>) IMPLICATION logic gate and (<b>c</b>) the corresponding truth table [<a href="#B235-organics-05-00008" class="html-bibr">235</a>].</p>
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<p>(<b>a</b>) The synthetic route for <b>168</b> proposed by Thipathy et al. [<a href="#B307-organics-05-00008" class="html-bibr">307</a>]; (<b>b</b>) Sensing mechanism for detecting Hg<sup>2+</sup> and fluoride; (<b>c</b>) Corresponding truth table and (<b>d</b>) logic diagram.</p>
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<p>Lab-on-a-molecule <b>172</b> proposed by Scerri et al. and the truth table corresponding to an AND-type gate with three inputs [<a href="#B317-organics-05-00008" class="html-bibr">317</a>].</p>
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<p>(<b>a</b>) Synthesis of rotaxane <b>178</b> reported by Li et al. [<a href="#B326-organics-05-00008" class="html-bibr">326</a>]; (<b>b</b>) Corresponding truth table and (<b>c</b>) diagram.</p>
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<p>(<b>a</b>) Structures proposed by Klein et al. for [2]Rotaxane <b>186</b>, (<b>b</b>) Sensing mechanism of <b>186</b> with HBF<sub>4</sub> and HCl; (<b>c</b>) The truth table of <b>186</b> corresponds to an AND-type molecular logic gate [<a href="#B327-organics-05-00008" class="html-bibr">327</a>].</p>
Full article ">Scheme 26
<p>(<b>a</b>) Synthesis of polymeric system <b>193</b> proposed by Bai et al.; (<b>b</b>) Sensing mechanism for recognition of Al<sup>3+</sup> and EDTA; (<b>c</b>) Molecular logic gate system and (<b>d</b>) truth table Al<sup>3+</sup> [<a href="#B328-organics-05-00008" class="html-bibr">328</a>].</p>
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<p>(<b>a</b>) The polymerization reaction of <b>199</b> presented by Zhou et al.; (<b>b</b>) AND gate identified and (<b>c</b>) corresponding truth table [<a href="#B329-organics-05-00008" class="html-bibr">329</a>].</p>
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3 pages, 161 KiB  
Editorial
Special Issue “Progress in Synthesis and Applications of Phosphorus-Containing Compounds”
by Tomasz K. Olszewski
Organics 2024, 5(2), 111-113; https://doi.org/10.3390/org5020007 - 27 May 2024
Viewed by 739
Abstract
Organophosphorus compounds, due to their interesting physicochemical properties, have found wide applications in many important areas of the chemical industry, such as the synthesis of utility chemicals [...] Full article
40 pages, 29528 KiB  
Review
How Much Potential Do Nucleoside Analogs Offer to Combat Human Corona Viruses?
by Włodzimierz Buchowicz and Mariola Koszytkowska-Stawińska
Organics 2024, 5(2), 71-110; https://doi.org/10.3390/org5020006 - 8 May 2024
Viewed by 1482
Abstract
Nucleoside analogs (NAs) have been extensively examined as plausible antiviral agents in recent years, in particular since the outbreak of the global pandemic of COVID-19 in 2019. In this review, the structures and antiviral properties of over 450 NAs are collected according to [...] Read more.
Nucleoside analogs (NAs) have been extensively examined as plausible antiviral agents in recent years, in particular since the outbreak of the global pandemic of COVID-19 in 2019. In this review, the structures and antiviral properties of over 450 NAs are collected according to the type of virus, namely SARS-CoV, SARS-CoV-2, MERS-CoV, HCoV-OC43, HCoV-229E, and HCoV-NL63. The activity of the NAs against HCoV-related enzymes is also presented. Selected studies dealing with the mode of action of the NAs are discussed in detail. The repurposing of known NAs appears to be the most extensively investigated scientific approach towards efficacious anti-HCoV agents. The recently reported de novo-designed NAs seem to open up additional approaches to new drug candidates. Full article
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Figure 1

Figure 1
<p>NAs with well-recognized activity and modes of action against HCoVs. (<b>A</b>) RNA chain terminators, including those acting with a dual mechanism of action (remdesivir, islatravir, AT-527, and bemnifosbuvir) [<a href="#B26-organics-05-00006" class="html-bibr">26</a>]. (<b>B</b>) NAs causing lethal mutagenesis. (<b>C</b>) NAs inhibiting viral methyltransferases.</p>
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12 pages, 3310 KiB  
Article
Innovative Application of Polyether Amine as a Recyclable Catalyst in Aerobic Thiophenol Oxidation
by Lingxia Chen, Junyu Li, Ke Ni, Xinshu Qin, Lijun Wang, Jiaman Hou, Chao Wang, Xuan Li, Minlong Wang and Jie An
Organics 2024, 5(2), 59-70; https://doi.org/10.3390/org5020005 - 26 Apr 2024
Cited by 1 | Viewed by 1022
Abstract
Polyether amines are versatile compounds characterized by a flexible structure, consisting of polyoxypropylene and polyoxyethylene as the backbone, with amine groups at each end. They have widespread applications in various industrial processes and daily life. Despite their versatility, the utilization of polyether amines [...] Read more.
Polyether amines are versatile compounds characterized by a flexible structure, consisting of polyoxypropylene and polyoxyethylene as the backbone, with amine groups at each end. They have widespread applications in various industrial processes and daily life. Despite their versatility, the utilization of polyether amines as base catalysts is rare. In this study, one kind of three-arm polyether amine 1 was employed as an environmentally friendly, cost-effective catalyst for the aerobic oxidation of thiophenols, leading to the synthesis of disulfides. The oxidative coupling of thiols serves as a fundamental pathway for the production of disulfides, which are vital in both chemical and biological processes. In contrast to known methods for thiol oxidation, this polyether amine-based catalytic process eliminates the need for expensive stoichiometric oxidants and minimizes the formation of over-oxidized by-products. Using a mere 0.5 mol % of the polyether amine 1 as the catalyst, a remarkable > 96% yield was achieved for all 16 tested substrates, encompassing a diverse range of functional groups, under the catalytic aerobic oxidation conditions. Furthermore, it is noteworthy that over 90% of the polyether amine catalyst can be efficiently recovered for reuse without loss of activity, making this a sustainable and cost-effective catalytic approach. Full article
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Figure 1

Figure 1
<p>Selected examples of polymer catalysts in organic synthesis.</p>
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<p>Selected applications of disulfides.</p>
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<p>Polyether-amine-<b>1</b>-catalyzed aerobic oxidation of thiophenols to disulfides. Reaction conditions: thiols (0.5 mmol), polyether amine <b>1</b> (0.5 mol %), CH<sub>3</sub>CN, under O<sub>2</sub>, r.t., 16 h.</p>
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<p>The study of the interaction between the thiol and the polyether amine <b>1</b>. <sup>a</sup> “Reaction mixture” refers to the reaction mixture for mechanistic investigation.</p>
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<p>The catalyzed aerobic oxidation of thiophenols.</p>
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<p>50 mmol-scale reaction.</p>
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<p>Mechanism of polyether-amine-<b>1</b>-catalyzed aerobic oxidation of thiophenols.</p>
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13 pages, 3086 KiB  
Article
Synthesis of Novel Trisubstituted Olefin-Type Probe Molecules Containing N-Heterocycles and Their Application in Detection of Malononitrile
by Zhao-Hua Chen, Shi-Wei Yu, Wen-Jin Xu, Miao-Xin Li, Yong Zeng, Si-Wei Deng, Jian-Yun Lin and Zhao-Yang Wang
Organics 2024, 5(2), 46-58; https://doi.org/10.3390/org5020004 - 2 Apr 2024
Cited by 3 | Viewed by 1144
Abstract
Recently, the construction of the trisubstituted olefin-type probe molecules has elicited the attention of many researchers. However, the synthesis of the trisubstituted olefin-type probes containing two N-heterocycles simultaneously has been rarely reported. In this study, starting from the inexpensive mucobromic acid 1 [...] Read more.
Recently, the construction of the trisubstituted olefin-type probe molecules has elicited the attention of many researchers. However, the synthesis of the trisubstituted olefin-type probes containing two N-heterocycles simultaneously has been rarely reported. In this study, starting from the inexpensive mucobromic acid 1 and N-heterocyclic compound 2, we first utilized a simple one-step reaction to synthesize a series of trisubstituted olefin-type compounds 3 simultaneously bearing with the structure of two N-heterocyclic rings in the absence of transition metal catalysts with a yield of 62–86%. The optimal reaction conditions were systematically explored, and the structure of the obtained compounds 3 were well characterized with 1H NMR, 13C NMR, X-ray single-crystal and HR-MS. The preliminary observation showed that, in the presence of base, mucobromic acid 1 reacts as its ring-opening structure, and the successive nucleophilic substitution reaction and Michael addition reaction can generate the target product 3. Considering that the aldehyde group in the molecular structure of the trisubstituted olefin-type compounds 3 may react with malononitrile, we carried out some relevant investigations so as to realize the visual detection of malononitrile. Interestingly, among the products, compounds 3a3c can be prepared in portable test strips through a simple process and used to achieve the naked-eye detection of malononitrile in environmental systems as designed. Full article
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Graphical abstract

Graphical abstract
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<p>The HR-MS spectrum of compound <b>3c</b>.</p>
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<p>The crystal structure of <b>3c</b> (<b>CCDC</b>: 2308049).</p>
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<p>The colour changes of the test strips of compounds <b>3a</b>–<b>3f</b> in the environment of malononitrile (10<sup>−1</sup> M).</p>
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<p>The colour changes of the test strips of compounds <b>3a</b>–<b>3c</b> in the environment of malononitrile (10<sup>−3</sup> M).</p>
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<p>The synthesis route of a <span class="html-italic">N</span>-heterocyclic molecule probe for PA from mucobromic acid <b>1</b> and the structure of the reaction intermediate.</p>
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<p>Synthesis route of target compounds <b>3a</b>–<b>3f</b>.</p>
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<p>The plausible reaction mechanism of the compound <b>3c</b>.</p>
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14 pages, 4465 KiB  
Article
Supramolecular Catalysis with Chiral Mono- and Bis-(Thio)Urea-Derivatives
by Veronica Iuliano, Paolo Della Sala, Carmen Talotta, Margherita De Rosa, Carmine Gaeta, Placido Neri and Annunziata Soriente
Organics 2024, 5(2), 32-45; https://doi.org/10.3390/org5020003 - 26 Mar 2024
Viewed by 853
Abstract
Chiral mono- and bis-(thio)urea supramolecular organocatalysts were studied in the enantioselective vinylogous addition reaction of 2-trimethylsilyloxyfuran (TMSOF) to carbonylic compounds; the corresponding chiral γ-hydroxymethyl-butenolides are obtained in good yields and with high enantiomeric excesses. The catalyst structure, as well as the reaction conditions, [...] Read more.
Chiral mono- and bis-(thio)urea supramolecular organocatalysts were studied in the enantioselective vinylogous addition reaction of 2-trimethylsilyloxyfuran (TMSOF) to carbonylic compounds; the corresponding chiral γ-hydroxymethyl-butenolides are obtained in good yields and with high enantiomeric excesses. The catalyst structure, as well as the reaction conditions, strongly influence the efficiency of the reaction. The conformational features of mono(thio)urea catalysts 2 and 3 and bis(thio)urea catalysts 7 and 8 were investigated by DFT calculations along with the structure of their complexes with benzaldehyde. Natural Bond Orbital (NBO) and Non-Covalent Interaction (NCI) calculations provided useful information concerning the activating H-bonding interactions in the complexes. Full article
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Figure 1

Figure 1
<p>(<b>a</b>) Organocatalysts <b>1–3</b>; (<b>b</b>) vinylogous aldol reaction catalyzed by urea <b>1</b>.</p>
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<p>Possible rotamers of derivatives <b>2</b> and <b>3</b>.</p>
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<p>DFT-optimized structures of the most stable rotamer of organocatalysts <b>2</b> (<b>a</b>) and <b>3</b> (<b>b</b>). N–H···N distances are also reported.</p>
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<p>Non-Covalent Interaction plots by the sign of the second Hessian eigenvalue (gradient isosurfaces (s = 0.5 a.u.) of complex <b>5@2-<span class="html-italic">trans</span>-A</b> (<b>a</b>) and <b>5@3-<span class="html-italic">cis</span>-A</b> (<b>b</b>).</p>
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<p>(<b>a</b>) Diastereoisomeric distribution (%) versus diene/aldehyde molar ratio. (<b>b</b>) Enantiomeric excess versus diene/aldehyde molar ratio.</p>
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<p>DFT-optimized structures for: (<b>a</b>) cis-cis rotamers of catalysts <b>7</b> (left side) and <b>8</b> (right side); (<b>b</b>) trans-cis rotamers of catalysts <b>7</b> (left side) and <b>8</b> (right side); (<b>c</b>) trans-trans rotamers of catalysts <b>7</b> (left side) and <b>8</b> (right side).</p>
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<p>Non-Covalent Interaction plots by the sign of the second Hessian eigenvalue (gradient isosurfaces s = 0.5 a.u.) of <b>7-<span class="html-italic">trans</span>-<span class="html-italic">trans</span></b>. Marked the C–H···S=C distances in weak C–H···S=C H-bonding interactions [<a href="#B37-organics-05-00003" class="html-bibr">37</a>].</p>
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<p>(<b>a</b>) Schematic view of the two possible aldehyde activation sites for organocatalyst <b>8</b>. DFT-optimized structures of complexes <b>5</b>@<b>8-<span class="html-italic">cis</span>-<span class="html-italic">cis</span></b> (<b>b</b>) and (<b>5</b>)<sub>2</sub>@<b>8-<span class="html-italic">cis</span>-<span class="html-italic">cis</span></b> (<b>c</b>).</p>
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<p>Non-Covalent Interaction plots by the sign of the second Hessian eigenvalue (gradient isosurfaces (s = 0.5 a.u.) for the 1:2 optimized complex of <b>8</b> with two molecules benzaldehyde <b>5</b>. Details of the H-bonding interactions are in the insets.</p>
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