Journal articles: 'Structure and Prototropy'

1

Cornejo, J., and M. C. Hermosin. "Structural alteration of sepiolite by dry grinding." Clay Minerals 23, no. 4 (December 1988): 391–98. http://dx.doi.org/10.1180/claymin.1988.023.4.06.

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AbstractThe effects of dry grinding on the structure of sepiolite were studied by XRD, surface area measurement, TG-DTA and IR spectroscopy techniques. The results show that the sepiolite framework is rather resistant to mechanical stress and its alteration by dry grinding occurs through three successive, overlapping processes: (i) thinning of the fibrous particles without structural alteration; (ii) distortion of the parallel units of sepiolite fibres, affecting essentially the particle surface which transforms into an amorphous protective coating; (iii) disruption of the inner structure and a prototropy effect, producing an amorphous phase with some residual order.

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2

Sheshashena Reddy, T., N. Rameshwar, B. Bhudevi, and A. Ram Reddy. "Structure dependent prototropy in 4-hydroxy-3-formylideneamino-1-methyl/phenylquinolin-2-ones." Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 73, no. 5 (September 2009): 916–21. http://dx.doi.org/10.1016/j.saa.2009.04.019.

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3

Grigg, Ronald, Jasothara Markandu, Trevor Perrior, Sivagnanasundram Surendrakumar, and William J. Warnock. "Effect of structure on tandem 1,2-prototropy-cycloaddition versus tandem cyclisation-cycloaddition reactions of oximes." Tetrahedron Letters 31, no. 4 (January 1990): 559–62. http://dx.doi.org/10.1016/0040-4039(90)87034-w.

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4

Colsch, Benoit, Annelaure Damont, Christophe Junot, François Fenaille, and Jean-Claude Tabet. "Experimental evidence that electrospray-produced sodiated lysophosphatidyl ester structures exist essentially as protonated salts." European Journal of Mass Spectrometry 25, no. 3 (March 25, 2019): 333–38. http://dx.doi.org/10.1177/1469066719838924.

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Sodiated lysoglycerophosphatidylethanolamine (LGPE) and lysoglycerophosphatidylcholine (LGPC) species dissociate under low collision energy by covalent bond cleavage resulting in product ions with either sodium retention or without sodium retention. For explaining these fragmentations, sodium chelation by heteroatoms (as charge-solvated structures) is often considered, and consequently, under keV collision conditions, sodium is “spectator” of cleavages (charge remote fragmentation). However, cleavage of such charge-solvated forms under low-energy conditions should result in sodium desolvation rather than covalent bond cleavage. In the present study, protonated salts are proposed as the main representative structures of the sodiated LGPE and LGPC forms. These structures are generated from sodiation of zwitterionic and betaine forms of LGPE and LGPC molecules, respectively. Experimental evidence to determine which structure is involved in the dissociations is provided, especially by comparing the dissociation of LGPL sodiated forms with that of sodiated polyethylene glycols. Energy-resolved mass spectrometry breakdown experiments were performed on a quadrupole time-of-flight instrument to demonstrate that both LGPE and LGPC sodiated forms exist as protonated salt structures. From such structures, proton migration by prototropy can result in different bond cleavages whereas the salt moiety remains spectator of these processes.

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Perrin, Monique, Alain Thozet, Pilar Cabildo, Rosa Ma Claramunt, Eduard Valenti, and José Elguero. "Molecular structure and tautomerism of 3,5-bis(4-methylpyrazol-1-yl)-4-methylpyrazole." Canadian Journal of Chemistry 71, no. 9 (September 1, 1993): 1443–49. http://dx.doi.org/10.1139/v93-186.

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The title compound C12N6H14, 1, crystallizes in the space group P21/n (a = 8.222(2) Å, b = 27.336(8) Å, c = 5.574(2) Å, α = 90.00°, β = 100.97(4)°, γ = 90.00°), Z = 4, d = 1.308 g cm−3. The conformation about the N—C bonds linking the pyrazole rings can be defined as EZ, with "pyridine-like" nitrogen atoms in an anti disposition [Formula: see text] and "pyridine-like" and "pyrrole-like" nitrogen atoms in a syn disposition [Formula: see text] with regard to the central pyrazole. Intermolecular hydrogen bonds between the central and the terminal pyrazole ring of configuration Z form centrosymmetric dimers. They pack in sheets nearly parallel to the (−2 3 1) plane. Its tautomerization barrier has been determined in methanol-d4; the value, 11.9 kcal mol−1, is similar to those of 3,5-dimethyl-4-chloropyrazole (12.8 kcal mol−1) and 3,5-dimethyl-4-nitropyrazole (12.1 kcalmol−1). These values together with the shape of the conformational potential surface (calculated using the AM1 Hamiltonian) suggest that, in compound 1, prototropy and rotation about the N—C bonds linking the three pyrazole rings take place simultaneously.

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Star, Alexander, Israel Goldberg, and Benzion Fuchs. "Diazadioxadecalin and salen podands and macrocycles within dynamic combinatorial virtual libraries: structure, prototropy, complexation and enantioselective catalysis." Journal of Organometallic Chemistry 630, no. 1 (July 2001): 67–77. http://dx.doi.org/10.1016/s0022-328x(01)00882-8.

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7

Szymańska, Małgorzata, and Irena Majerz. "Prototropy, Intramolecular Interactions, Electron Delocalization, and Physicochemical Properties of 1,8-dihydroxy-9-anthrone—DFT-D3 Study of Substituent Effects." Molecules 28, no. 1 (January 1, 2023): 344. http://dx.doi.org/10.3390/molecules28010344.

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1,8-dihydroxy-9-anthrone are tricyclic compounds with a ketone group in the middle ring and two hydroxyl groups substituted in the side-aromatic rings what results in formation of two intramolecular hydrogen bonds in which the oxygen atom from the ketone group is the proton acceptor. 1,8-dihydroxy-9-anthrones in which intramolecular proton transfer between C10 and CO in the middle ring occurs, can exist in a tautomeric keto-enol equilibrium. For anthralin, the most important representative of this group, this equilibrium has been studied previously, but it has not been studied for its derivatives. Substituents in the middle ring change the geometry of 1,8-dihydroxy-9-anthrones so they are also expected to affect the keto-enol equilibrium. It is also important to study the effect of intramolecular hydrogen bonds on the structure of both tautomeric forms. It was found that the nature of the substituent in the middle ring could affect the antioxidant properties of the investigated compound.

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8

Lacalli, T. C. "Prototroch structure and innervation in the trochophore larva of Phyllodoce (Polychaeta)." Canadian Journal of Zoology 64, no. 1 (January 1, 1986): 176–84. http://dx.doi.org/10.1139/z86-028.

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The prototroch and prototroch nerve in trochophores of two Phyllodoce species are described at the ultrastructural level and interpreted with reference to the observed normal behavior of larvae during swimming. The prototroch is a complex structure consisting of four tiers of cells of which the second bears the main locomotory cilia. Cells in the other tiers also have cilia but are notable chiefly for the slender processes they send to the prototroch nerve and which evidently contribute to the sheath that surrounds the nerve. Neurociliary synapses were not observed, but the prototroch arrests when the frontal organ is touched and in response to cholinergic drugs. The arrests are only partial in that the cilia continue to beat, but in a restricted register. The mechanism responsible was not identified, but several possibilities are discussed. While the capacity to arrest could be intrinsic to the main trochal cells (i.e., tier 2), the absence of obvious regions of contact between these cells and the prototroch nerve increases the likelihood that the other tiers are also involved. The arrests could in fact result simply from physical interference between the cilia of adjacent tiers. The arrest response in Phyllodoce is compared with that seen in trochal bands in other spiralian larvae.

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9

Ma, Jiani, Jan-Michael Mewes, Kyle T. Harris, Timothy M. Dore, David Lee Phillips, and Andreas Dreuw. "Unravelling the early photochemical behavior of (8-substituted-7-hydroxyquinolinyl)methyl acetates through electronic structure theory and ultrafast transient absorption spectroscopy." Physical Chemistry Chemical Physics 19, no. 2 (2017): 1089–96. http://dx.doi.org/10.1039/c6cp05499d.

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10

Sergienko, V. S., V. L. Abramenko, and Yu E. Gorbunova. "Prototropic Tautomerism of Salicylideneimines. Crystal Structure of 3,5-Dichlorosalicylideneallylimine." Crystallography Reports 65, no. 1 (January 2020): 53–55. http://dx.doi.org/10.1134/s106377452001023x.

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11

Vouffo, Erik Donfack, Clovis Douanla-Meli, Angelbert Fusi Awantu, Bruno Ndjakou Lenta, Sylvère Ngouela, Etienne Tsamo, and Hartmut Laatsch. "New Metabolites From the Endophytic Fungus Cercophora samala Associated With Mitragyna inermis." Natural Product Communications 16, no. 5 (May 2021): 1934578X2110132. http://dx.doi.org/10.1177/1934578x211013220.

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Two new natural products, mitrafungidione (1) elucidated as prototrop-isomers of ( R-3-acetyl-5-ethyl-4-hydroxy-5 H-furan-2-one, and maristachone F (2a), elucidated as 5-(1-hydroxyethyl)-4-(hydroxymethyl)-3-methoxy-2-methylphenol, together with 5 known compounds have been isolated from the solid cultures of an endophytic fungus associated with Mitragyna inermis (Rubiaceae) and identified as Cercophora samala. The structures of these compounds were elucidated by detailed spectroscopic analysis and by comparison of their spectroscopic data with those reported in the literature. The absolute configuration of 1 and 2a were determined by extensive DFT calculations.

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12

Radeglia, Reiner, Jörg Andersch, and Werner Schroth. "Zum dynamischen Strukturverhalten des Dimethylamin—Kohlendioxid-Komplexes (Dimcarb) / On the Dynamic Structure Behaviour of the Dimethylamine—Carbondioxide Complex (Dimcarb)." Zeitschrift für Naturforschung B 44, no. 2 (February 1, 1989): 181–86. http://dx.doi.org/10.1515/znb-1989-0215.

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Abstract Dimcarb, a liquid distillable 1 .8 :1-dimethylamine-carbondioxide complex which can be used as a preparatively profitable dimethylamine source, displays unusual properties in view of a salt ("dimethylammonium dimethylcarbamate"). The dynamic structure behaviour has been investigated by1'H, 13C, and 15N NMR spectroscopy: At ambient temperature dimcarb underlies a rapid dimethylamine change between ammonium and carbamate functionality (⊿G ≠ about 58 kJ/mol). On further temperature decreasing prototropic interactions between dimethylammonium and dimethylamine as well as dimethylcarbamate and dimethylcarbamic acid species are additionally revealed. Timely averaged, ionic structures predominate, obviously dimethylammonium dimethylcarbamate combinations as intimate ion pairs. Involved dimethylcarbamic acid can be trapped as methylester in high yield by reaction of dimcarb with diazomethane. Moreover, the dimethylcarbamic acid trimethylsilylester, obtained from dimcarb with the aid of trimethyl-chlorosilane, affords a crystalline product by methanolysis at -78 °C. probably dimethylcarbamic acid, which decomposes above -50 °C under carbondioxide elimination and regeneration of dimcarb.

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13

Fain, V. Ya, B. E. Zaitsev, and M. A. Ryabov. "1,10-quinoid structure and prototropic amino-imine tautomerism of α-aminoanthraquinones." Russian Journal of General Chemistry 82, no. 9 (September 2012): 1558–66. http://dx.doi.org/10.1134/s1070363212090186.

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14

Kubicki, Maciej. "Two tautomers in one crystal: 4(5)-nitro-5(4)-methoxyimidazole." Acta Crystallographica Section B Structural Science 60, no. 2 (March 18, 2004): 191–96. http://dx.doi.org/10.1107/s0108768104003179.

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The case of prototropic annular tautomerism in an imidazole derivative has been found. The crystal structure contains a 50:50 mixture of two tautomers: 4-nitro-5-methoxyimidazole and 5-nitro-4-methoxyimidazole. The X-ray experiment actually shows the superposition of these compounds; it appears as if the structure is centrosymmetric and the N—H hydrogen atoms are disordered over two ring N atoms. Owing to the hydrogen-bond pattern, the values of their site occupation factors have to be exactly equal to 1/2. The molecules are connected into a three-dimensional network by means of N—H...N and C—H...O hydrogen bonds.

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15

Szabo, Jan, and Gerhard Maas. "Derivatives of the Triaminoguanidinium Ion, 2. Prototropic Tautomerism, Crystal and Molecular Structure of N,N´,N´´-Tris(propan- 2-iminyl)guanidine [1, 2]." Zeitschrift für Naturforschung B 68, no. 3 (March 1, 2013): 207–13. http://dx.doi.org/10.5560/znb.2013-3023.

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The title compound, C10H20N6 (2), was prepared from N,N´,N´´-triaminoguanidinium chloride. Solvent- and temperature-dependent 1H NMR spectra indicating prototropic tautomerism were observed in solution. The crystal and molecular structure was determined by X-ray diffraction analysis. The compound crystallizes in the hexagonal space group P63/m. The molecules lie on crystallographic mirror planes parallel to the a,b plane, which are separated from each other by 3:37 Å . The threefold crystallographic symmetry of the molecules is due to disorder with positional averaging of individual molecules.

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16

Jameh-Bozorghi, Saeed, Zahra Javanshir, and D. Nori Shargh. "Prototropic and metallotropic migration of isolobal fragments on indol rings. Theoretical study and NBO analysis." JOURNAL OF ADVANCES IN CHEMISTRY 5, no. 1 (April 29, 2009): 614–25. http://dx.doi.org/10.24297/jac.v5i1.942.

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Molecular structures, energies, NBO analysis and sigmatropic behaviour of 1-Indenyl(dihydro)borane (1) and 1-Indenyl-threecarbonylcobalt(I) (2) were investigated using DFT and ab initio molecular orbital methods. In these compounds BH2 and Co(CO)3 fragments areisolobal. The Results of calculations using B3LYP, HF and MP2methods [Basis set 6-311+G**] showed that -BH2 and -Co(CO)3 had similar behaviour in sigmatropic shifts. Prototropic shifts in compounds 1 and 2 have similar mechanisms too. Results showed that metallotrotropic shift is faster than Prototrpic shift in compounds 1 and 2. The activation energies (Ea) of Prototropic shift in compounds 1 and 2 are 18.83 and 17.38 kcal.mol-1. These energies are higher than -BH2 shifts in compound 1 (10.11 kcal.mol-1) or migration of -Co(CO)3 fragment in compound 2 (12.39 kcal.mol-1). Lower amount of activation energy in borotropic shift and cobalt`s fragment shift show that rotation of boron and cobalt on the indol ring can happen in the ambient temperature. Calculation results revealed that migration of proton and Co(CO)3 was carried out via suprafacial[1,2]-sigmatropic mechanism while -BH2 shift took place via antrafacial [1,3]-rearangment.

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17

Markova, M. V., I. V. Tatarinova, O. A. Tarasova, K. A. Apatrsin, V. V. Kireeva, and B. A. Trofimov. "Cationic copolymerisation of cholesterol vinyl ether with N-allenylpyrrolidone; a route to pharmacologically promising oligomers." Доклады Академии наук 485, no. 6 (May 24, 2019): 697–700. http://dx.doi.org/10.31857/s0869-56524856697-700.

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Cationic copolymerization of cholesterol vinyl ether with N-allenylpyrrolidone yielded co-oligomers with molecular mass of 1200-2100. The polymerization of N-allenylpyrrolidone involves both 1,2- and 2,3-positions of the allenyl substituent to give four types of units as a result of prototropic isomerization of the initially formed structures. In the developed method, the composition of co-oligomers can be controlled and, hence, their hydrophilic/hydrophobic balance, solubility, and membranotropic properties can also be controlled to change the potential biological activity of the products.

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18

Ashniev, German A., Sergey N. Petrov, Stanislav N. Iablokov, and Dmitry A. Rodionov. "Genomics-Based Reconstruction and Predictive Profiling of Amino Acid Biosynthesis in the Human Gut Microbiome." Microorganisms 10, no. 4 (March 30, 2022): 740. http://dx.doi.org/10.3390/microorganisms10040740.

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The human gut microbiota (HGM) have an impact on host health and disease. Amino acids are building blocks of proteins and peptides, also serving as precursors of many essential metabolites including nucleotides, cofactors, etc. Many HGM community members are unable to synthesize some amino acids (auxotrophs), while other members possess complete biosynthetic pathways for these nutrients (prototrophs). Metabolite exchange between auxotrophs and prototrophs affects microbial community structure. Previous studies of amino acid biosynthetic phenotypes were limited to model species or narrow taxonomic groups of bacteria. We analyzed over 2800 genomes representing 823 cultured HGM species with the aim to reconstruct biosynthetic pathways for proteinogenic amino acids. The genome context analysis of incomplete pathway variants allowed us to identify new potential enzyme variants in amino acid biosynthetic pathways. We further classified the studied organisms with respect to their pathway variants and inferred their prototrophic vs. auxotrophic phenotypes. A cross-species comparison was applied to assess the extent of conservation of the assigned phenotypes at distinct taxonomic levels. The obtained reference collection of binary metabolic phenotypes was used for predictive metabolic profiling of HGM samples from several large metagenomic datasets. The established approach for metabolic phenotype profiling will be useful for prediction of overall metabolic properties, interactions, and responses of HGM microbiomes as a function of dietary variations, dysbiosis and other perturbations.

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Secrieru, Alina, Susy Lopes, Maria L. S. Cristiano, and Rui Fausto. "Structure and IR Spectra of 3(5)-Aminopyrazoles and UV-Induced Tautomerization in Argon Matrix." Molecules 26, no. 14 (July 15, 2021): 4299. http://dx.doi.org/10.3390/molecules26144299.

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The prototropic tautomerism in 3(5)-aminopyrazoles was investigated by matrix isolation infrared (IR) spectroscopy, supported by DFT(B3LYP)/6-311++G(d,p) calculations. In consonance with the experimental data, the calculations predict tautomer 3-aminopyrazole (3AP) to be more stable than the 5-aminopyrazole (5AP) tautomer (calculated energy difference: 10.7 kJ mol−1; Gibbs free energy difference: 9.8 kJ mol−1). The obtained matrix isolation IR spectra (in both argon and xenon matrices) were interpreted, and the observed bands were assigned to the tautomeric forms with help of vibrational calculations carried out at both harmonic and anharmonic levels. The matrix-isolated compound (in argon matrix) was then subjected to in situ broadband UV irradiation (λ > 235 nm), and the UV-induced transformations were followed by IR spectroscopy. Phototautomerization of the 3AP tautomer into the 5AP form was observed as the strongly prevalent reaction.

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20

Nikitina, Polina A., Tatiana Yu Koldaeva, Vitaly S. Mityanov, Vladimir S. Miroshnikov, Elizaveta I. Basanova, and Valery P. Perevalov. "Prototropic Tautomerism and Some Features of the IR Spectra of 2-(3-Chromenyl)-1-hydroxyimidazoles." Australian Journal of Chemistry 72, no. 9 (2019): 699. http://dx.doi.org/10.1071/ch19222.

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Prototropic tautomerism of 2-(3-chromenyl)-1-hydroxyimidazoles with various substituents in the chromenyl moiety (1-hydroxyimidazole – imidazole N-oxide) was studied by means of 1H NMR and IR spectroscopies. It was demonstrated that in d6-DMSO solution, the substituents in the chromenyl ring have no influence on the equilibrium shift: the prevalence of the N-oxide tautomeric form is caused by the possibility of stabilization of the planar structure with the help of the carbonyl group in position 5 of the imidazole ring. In contrast, in the solid state the general effect of the chromenyl substituent in position 2 of imidazole plays the leading role. The increase in general electron-withdrawing effect of the chromenyl moiety leads to the prevalence of the imidazole N-oxide tautomer.

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21

Kühn, Christiane, R. Beckert, U. W. Grummt, C. Käpplinger, and E. Birckner. "1,4,5,8-Tetraazafulvalene – Darstellung schwefelhaltiger Derivate und Zuordnung des Chromophors / 1,4,5,8-Tetraazafulvalenes – Synthesis of Sulfur-Containing Derivatives and Classification of the Chromophor." Zeitschrift für Naturforschung B 59, no. 4 (April 1, 2004): 406–13. http://dx.doi.org/10.1515/znb-2004-0408.

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Abstract In order to obtain sulfur-containing tetraazafulvalenes the derivatives 1 - 3 were cross-coupled with different types of acetylenes via palladium-catalyzed reactions. Starting from the tetrabromoaryl derivative 3a, four bromine atoms could be replaced by 2-ethynylthiophene. Under analogous conditions, the methylsulfanyl esters 7 -11 could be obtained by employing 4-ethynylbenzoic acid 4-(methylsulfanyl)butylester 6. Lipoic acid could be integrated into tetraazafulvalenes successfully in a two step reaction. First, the Sonogashira coupling method yielded the compound 12 possessing two (4-anilino)ethynyl residues which were then condensed with lipoic acid to give derivative 13. Whereas the NMR data suggest the predominance of prototropic form A, UV/vis spectra of the deeply colored tetraazafulvalenes are in favor with structure B rather than with structure A. DFT calculations at the B3LYP/6-31G(d) level showed that tautomeric form B is about 60 kJ/mol more stable than A. In addition, time-dependent density functional theory calculations support the substructure of two crossed diazaheptamethinemerocyanines.

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22

Szemik-Hojniak, A., T. Glowiak, I. Deperasinska, and A. Puszko. "Crystal structure and spectral considerations of 5-methyl-2-nitraminopyridine N-oxide." Canadian Journal of Chemistry 80, no. 9 (September 1, 2002): 1242–51. http://dx.doi.org/10.1139/v02-142.

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The crystal structure of 5-methyl-2-nitraminopyridine N-oxide (5M) has been determined and its electronic absorption spectra in the solution have been investigated. In the solid, two monomeric proton-transferred (PT) units of 5M are perpendicularly located in the crystal lattice. They are connected by two intermolecular hydrogen bonds of different strength (O-H···N 2.647(3) and 2.695(3) Å). In the gas phase the same relative arrangement of both 5M (PT) monomers has been found. As results from semiempirical PM3-CI calculations (1214), the prototropic amino (H) [Formula: see text] imino (PT) equilibrium may occur in the solution. Assignment of experimental absorption bands to the calculated transition energies of both forms of 5M reveals that hydrogen bonded 5M (PT) dimers are dominant in cyclohexane while imino (PT) monomers seem to prevail in acetonitrile solution. The different character of electronic transitions and different relative arrangement of both monomers in amino (H) than in imino (PT) dimers are responsible for very low oscillator strengths and dipole moments of the former.Key words: crystal structure, methylated nitraminopyridine N-oxides, semiempirical PM3-CI computations, intermolecular hydrogen bonding.

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23

O'Connell, K. F., Y. Surdin-Kerjan, and R. E. Baker. "Role of the Saccharomyces cerevisiae general regulatory factor CP1 in methionine biosynthetic gene transcription." Molecular and Cellular Biology 15, no. 4 (April 1995): 1879–88. http://dx.doi.org/10.1128/mcb.15.4.1879.

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Saccharomyces cerevisiae general regulatory factor CP1 (encoded by the gene CEP1) is required for optimal chromosome segregation and methionine prototrophy. MET16-CYC1-lacZ reporter constructs were used to show that MET16 5'-flanking DNA contains a CP1-dependent upstream activation sequence (UAS). Activity of the UAS required an intact CP1-binding site, and the effects of cis-acting mutations on CP1 binding and UAS activity correlated. In most respects, MET16-CYC1-lacZ reporter gene expression mirrored that of chromosomal MET16; however, the endogenous gene was found to be activated in response to amino acid starvation (general control). The latter mechanism was both GCN4 and CP1 dependent. MET25 was also found to be activated by GCN4, albeit weakly. More importantly, MET25 transcription was strongly CP1 dependent in gcn4 backgrounds. The modulation of MET gene expression by GCN4 can explain discrepancies in the literature regarding CP1 dependence of MET gene transcription. Lastly, micrococcal nuclease digestion and indirect end labeling were used to analyze the chromatin structure of the MET16 locus in wild-type and cep1 cells. The results indicated that CP1 plays no major role in configuring chromatin structure in this region, although localized CP1-specific differences in nuclease sensitivity were detected.

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24

Zhang, Chong, Xiaohui Zhang, Zhengying Yao, Yaping Lu, Fengxia Lu, and Zhaoxin Lu. "A new method for multiple gene inactivations in Bacillus subtilis 168, producing a strain free of selectable markers." Canadian Journal of Microbiology 57, no. 5 (May 2011): 427–36. http://dx.doi.org/10.1139/w11-035.

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This study describes a novel method for repeated gene inactivation in Bacillus subtilis 168. A B. subtilis strain (BS-PS) that is conditionally auxotrophic for lysine was obtained by replacing the PlysA promoter with the Pspac promoter. The homologous recombination integration vector PLC-T was constructed to contain lacI, which encodes a Pspac promoter repressor, and the chloromycetin resistance gene. Target genes were manipulated by generating an insertion sequence with two homologous arms and the target gene in PLC-T to create a specific integrating vector. Integration into the BS-PS chromosome occurred by a single crossover at either of the two homologous arms. The resulting transitional strain (BS-PS-PI) was chloromycetin resistant and lysine auxotrophic and had an unstable genome structure because of the duplication. Excision of lacI and chloromycetin resistance gene was achieved by a second single crossover at the duplication. Recovery of a lysine prototroph functioned as counter-selection and was identified by PCR. In this work, we inactivated nprE and aprE, two protease genes secreted by B. subtilis 168 free of selectable markers.

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25

Stewart, Ross, and S. J. Gumbley. "Synthesis, base strength, and prototropic behaviour of a number of alkyllumazines." Canadian Journal of Chemistry 63, no. 12 (December 1, 1985): 3290–93. http://dx.doi.org/10.1139/v85-544.

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A number of lumazines and 5-deazalumazines containing a methyl group at C-7 have been prepared, their pKBH+ values determined, and measurements made of the rates at which the hydrogen atoms of their 7-methyl groups undergo isotopic exchange in aqueous sulfuric acid. The presence of an alkyl group at N-8 in the protonated forms of these compounds activates the neighbouring methyl group at C-7; the effect is considerably larger than that previously observed for a methyl group at C-6, which is the other neighbouring position. The comparison of methyl and hydrogen at N-8 can be made only for the acid-catalyzed reaction because the structures of the neutral compounds, which take part in the base-catalyzed reaction, are not analogous.

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26

Sydorenko, Ivan, Serhii Holota, Andrii Lozynskyi, Yulian Konechnyi, Volodymyr Horishny, Andriy Karkhut, Svyatoslav Polovkovych, Olexandr Karpenko, and Roman Lesyk. "2-(Cyclopropylamino)-5-(4-methoxybenzylidene)thiazol-4(5H)-one." Molbank 2022, no. 4 (October 31, 2022): M1478. http://dx.doi.org/10.3390/m1478.

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Multicomponent reactions effectively contribute to modern organic and medicinal chemistry. 4-Thiazolidinone core and cyclopropyl moiety are important structural motifs for design of potential biologically active molecules. In the present paper, the convenient step-economy and cost-effective synthesis of 2-(cyclopropylamino)-5-(4-methoxybenzylidene)thiazol-4(5H)-one (2) is described based on the application of the MCR methodology. The proposed approach includes direct one-pot interaction of 2-thioxothiazolidin-4-one (rhodanine), 4-methoxybenzaldehyde with cyclopropylamine which was used in 10% excess compare to other reagents. The structure of synthesized compound 2 was confirmed using 1H, 13C, 2D NMR, LC-MS, IR and UV spectra. The presence of prototropic amino/imino tautomerism for synthesized compound 2 was observed based on spectral analysis data. Screening of antimicrobial activity against 12 strains of Gram-positive and Gram-negative bacteria, as well as yeasts, was performed for synthesized derivative 2.

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27

Amado, Patrícia S. M., Inês C. C. Costa, José A. Paixão, Ricardo F. Mendes, Sofia Cortes, and Maria L. S. Cristiano. "Synthesis, Structure and Antileishmanial Evaluation of Endoperoxide–Pyrazole Hybrids." Molecules 27, no. 17 (August 24, 2022): 5401. http://dx.doi.org/10.3390/molecules27175401.

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Leishmaniases are among the most impacting neglected tropical diseases. In attempts to repurpose antimalarial drugs or candidates, it was found that selected 1,2,4-trioxanes, 1,2,4,5-tetraoxanes, and pyrazole-containing chemotypes demonstrated activity against Leishmania parasites. This study reports the synthesis and structure of trioxolane–pyrazole (OZ1, OZ2) and tetraoxane–pyrazole (T1, T2) hybrids obtained from the reaction of 3(5)-aminopyrazole with endoperoxide-containing building blocks. Interestingly, only the endocyclic amine of 3(5)-aminopyrazole was found to act as nucleophile for amide coupling. However, the fate of the reaction was influenced by prototropic tautomerism of the pyrazole heterocycle, yielding 3- and 5-aminopyrazole containing hybrids which were characterized by different techniques, including X-ray crystallography. The compounds were evaluated for in vitro antileishmanial activity against promastigotes of L. tropica and L. infantum, and for cytotoxicity against THP-1 cells. Selected compounds were also evaluated against intramacrophage amastigote forms of L. infantum. Trioxolane–pyrazole hybrids OZ1 and OZ2 exhibited some activity against Leishmania promastigotes, while tetraoxane–pyrazole hybrids proved inactive, most likely due to solubility issues. Eight salt forms, specifically tosylate, mesylate, and hydrochloride salts, were then prepared to improve the solubility of the corresponding peroxide hybrids and were uniformly tested. Biological evaluations in promastigotes showed that the compound OZ1•HCl was the most active against both strains of Leishmania. Such finding was corroborated by the results obtained in assessments of the L. infantum amastigote susceptibility. It is noteworthy that the salt forms of the endoperoxide–pyrazole hybrids displayed a broader spectrum of action, showing activity in both strains of Leishmania. Our preliminary biological findings encourage further optimization of peroxide–pyrazole hybrids to identify a promising antileishmanial lead.

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Banks, G. R., and S. Y. Taylor. "Cloning of the PYR3 gene of Ustilago maydis and its use in DNA transformation." Molecular and Cellular Biology 8, no. 12 (December 1988): 5417–24. http://dx.doi.org/10.1128/mcb.8.12.5417-5424.1988.

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The Ustilago maydis PYR3 gene encoding dihydroorotase activity was cloned by direct complementation of Escherichia coli pyrC mutations. PYR3 transformants of E. coli pyrC mutants expressed homologous transcripts of a variety of sizes and regained dihydroorotase activity. PYR3 also complemented Saccharomyces cerevisiae ura4 mutations, and again multiple transcripts were expressed in transformants, and enzyme activity was regained. A 1.25-kilobase poly(rA)+ PYR3 transcript was detected in U. maydis itself. Linear DNA carrying the PYR3 gene transformed a U. maydis pyr3-1 pyrimidine auxotroph to prototrophy. Hybridization analysis revealed that three different types of transformants could be generated, depending on the structure of the transforming DNA used. The first type involved exchange of chromosomal mutant gene sequences with the cloned wild-type plasmid sequences. A second type had integrated linear transforming DNA at the chromosomal PYR3 locus, probably via a single crossover event. The third type had integrated transforming DNA sequences at multiple sites in the U. maydis genome. In the last two types, tandemly reiterated copies of the transforming DNA were found to have been integrated. All three types had lost the sensitivity of the parental pyr3-1 mutant to UV irradiation. They had also regained dihydroorotase activity, although its level did not correlate with the PYR3 gene copy number.

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29

Banks, G. R., and S. Y. Taylor. "Cloning of the PYR3 gene of Ustilago maydis and its use in DNA transformation." Molecular and Cellular Biology 8, no. 12 (December 1988): 5417–24. http://dx.doi.org/10.1128/mcb.8.12.5417.

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The Ustilago maydis PYR3 gene encoding dihydroorotase activity was cloned by direct complementation of Escherichia coli pyrC mutations. PYR3 transformants of E. coli pyrC mutants expressed homologous transcripts of a variety of sizes and regained dihydroorotase activity. PYR3 also complemented Saccharomyces cerevisiae ura4 mutations, and again multiple transcripts were expressed in transformants, and enzyme activity was regained. A 1.25-kilobase poly(rA)+ PYR3 transcript was detected in U. maydis itself. Linear DNA carrying the PYR3 gene transformed a U. maydis pyr3-1 pyrimidine auxotroph to prototrophy. Hybridization analysis revealed that three different types of transformants could be generated, depending on the structure of the transforming DNA used. The first type involved exchange of chromosomal mutant gene sequences with the cloned wild-type plasmid sequences. A second type had integrated linear transforming DNA at the chromosomal PYR3 locus, probably via a single crossover event. The third type had integrated transforming DNA sequences at multiple sites in the U. maydis genome. In the last two types, tandemly reiterated copies of the transforming DNA were found to have been integrated. All three types had lost the sensitivity of the parental pyr3-1 mutant to UV irradiation. They had also regained dihydroorotase activity, although its level did not correlate with the PYR3 gene copy number.

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30

Kosar Kirca, Basak, Gonca Ozdemir Tarı, Cıgdem Albayrak Kastas, Mustafa Odabasoglu, and Orhan Buyukgungor. "Crystal structure, spectral characterization, molecular modeling studies and structural effects of the proton transfer process for (E)-5-methoxy-2-[(3,4-dimethylphenylimino) methyl]phenol." Macedonian Journal of Chemistry and Chemical Engineering 36, no. 2 (December 20, 2017): 265. http://dx.doi.org/10.20450/mjcce.2017.1295.

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The main purpose of this study is to characterize a new organic material, (E)-5-methoxy-2-[(3,4-dimethylphenylimino)methyl]phenol, which was synthesized and grown as a single crystal. The molecular structure and spectroscopic properties of the ortho-hydroxy Schiff base compound were determined by X-ray diffraction analysis, Fourier-transform infrared (FT-IR), ultraviolet-visible (UV-Vis) and nuclear magnetic resonance (NMR) spectroscopy techniques, experimentally and computationally with density functional theory (DFT) calculations. X-ray and UV-Vis studies show that the compound exists in an OH tautomeric form in the solid and solvent media. The gas phase geometry optimizations of two possible forms of the title compound, resulting from the prototropic tautomerism, were obtained using DFT calculations at the B3LYP/6-311G+(d,p) level of theory. A relaxed potential energy surface (PES) scan was performed based on the optimized geometry of the OH tautomeric form by varying the redundant internal coordinate, the O-H bond distance. According to the PES scan process, the molecular geometry is strongly affected by the intramolecular proton transfer. The calculated first hyperpolarizability indicates that the compound could be a good material for non-linear optical applications.

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31

Okouchi, S., K. Yamanaka, Y. Ishihara, T. Yanaka, and H. Uedaira. "Relationship between water qualities and treatments in the ultra pure water production system." Water Science and Technology 30, no. 10 (November 1, 1994): 237–41. http://dx.doi.org/10.2166/wst.1994.0533.

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In an ultra pure water (UPW) production system which can satisfy the water qualities for 4 megabit DRAM, the changes in water qualities from a tap water (58.4 mg/dm3 as CaCO3 hardness) as a raw water to UPW were followed from the view of the micro-structure and microdynamic behavior of water molecules with increasing of the water purity by a complex permittivity and 17O-NMR measurements, as well as measurements of resistivity, density, and so on. The dielectric relaxation time and spin-lattice relaxation time of 17O nuclei related to the microdynamic behavior of water molecules indicated a trace change between the tap water and UPW. However, the dielectric parameter α which characterizes a symmetric distribution of relaxation times was gradually lowered with increasing of the water purity. The relationship between the half-width of 17O magnetic resonance and pH gave the rate constants for the prototropic charge migration in water. The difference of α and density between the tap water and UPW became a measure of water purity.

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Krishnamurthy, Mannam, Karthik A. Iyer, and Sneh K. Dogra. "Electronic structure of quinoxaline-2,3(1H,4H)dione and its prototropic species in the ground and excited singlet states." Journal of Photochemistry 38 (June 1987): 277–87. http://dx.doi.org/10.1016/0047-2670(87)87023-5.

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Shagun, V. A., V. F. Sidorkin, V. A. Usov, and M. G. Voronkov. "Quantum-chemical study of the structure and prototropic conversions of 2-methyl-1,3-bishetero derivatives of indene and indan." Bulletin of the Academy of Sciences of the USSR Division of Chemical Science 35, no. 5 (May 1986): 1019–22. http://dx.doi.org/10.1007/bf00955371.

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34

Brovarets’, Ol’ha O., and Dmytro M. Hovorun. "A new era of the prototropic tautomerism of the quercetin molecule: A QM/QTAIM computational advances." Journal of Biomolecular Structure and Dynamics 38, no. 16 (December 16, 2019): 4774–800. http://dx.doi.org/10.1080/07391102.2019.1691660.

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35

Barczak, A. J., J. Zhao, K. D. Pruitt, and R. L. Last. "5-Fluoroindole resistance identifies tryptophan synthase beta subunit mutants in Arabidopsis thaliana." Genetics 140, no. 1 (May 1, 1995): 303–13. http://dx.doi.org/10.1093/genetics/140.1.303.

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Abstract A study of the biochemical genetics of the Arabidopsis thaliana tryptophan synthase beta subunit was initiated by characterization of mutants resistant to the inhibitor 5-fluoroindole. Thirteen recessive mutations were recovered that are allelic to trp2-1, a mutation in the more highly expressed of duplicate tryptophan synthase beta subunit genes (TSB1). Ten of these mutations (trp2-2 through trp2-11) cause a tryptophan requirement (auxotrophs), whereas three (trp2-100 through trp2-102) remain tryptophan prototrophs. The mutations cause a variety of changes in tryptophan synthase beta expression. For example, two mutations (trp2-5 and trp2-8) cause dramatically reduced accumulation of TSB mRNA and immunologically detectable protein, whereas trp2-10 is associated with increased mRNA and protein. A correlation exists between the quantity of mutant beta and wild-type alpha subunit levels in the trp2 mutant plants, suggesting that the synthesis of these proteins is coordinated or that the quantity or structure of the beta subunit influences the stability of the alpha protein. The level of immunologically detectable anthranilate synthase alpha subunit protein is increased in the trp2 mutants, suggesting the possibility of regulation of anthranilate synthase levels in response to tryptophan limitation.

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Rak, Janusz, Jerzy Blazejowski, and Randy J. Zauhar. "Theoretical studies on the prototropic tautomerism, structure, and features of acridine and 9-acridinamine free bases and their protonated forms." Journal of Organic Chemistry 57, no. 13 (June 1992): 3720–25. http://dx.doi.org/10.1021/jo00039a039.

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37

Fofanova, Elizaveta. "Dimorphilus gyrociliatus (Annelida: Dinophiliformia) Dwarf Male Nervous System Represents a Common Pattern for Lophotrochozoa." Biology 11, no. 11 (November 17, 2022): 1674. http://dx.doi.org/10.3390/biology11111674.

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Dinophiliformia is a newly revealed clade within Annelida that is a sister group to Pleistoannelida. Dimorphilus gyrociliatus is a representative of this clade that has fascinated scientists with its high degree of sexual dimorphism. Both males and females are small, worm-like creatures that have specific ciliary structures: anterior ventral, posterior ventral, and dorsal ciliary fields in males, and prototroch, metatroch, and ventral ciliary fields in females. There are data on the morphology and development of the nervous system in Oweniidae, Sipunculida, Pleistoannelida, and even Dinophiliformia. However, data on the neuromorphology and development of D. gyrociliatus dwarf males are limited. Here, we present data on the distribution of cilia, sensory neurons, and the 5-HT-like immunoreactive system in 3D reconstructions and cross-sections. Immunochemical labeling with anti-acetylated tubulin and anti-5-HT antibodies and confocal microscopy were used to visualize the ciliary structures and neurons. The male has three ciliary fields: anterior ventral, posterior ventral, and dorsal. These include frontal ganglia, five commissures, two ventral and two dorsal bundles, and penial nerves. A total of fifty-seven neurons and only five 5-HT-like immunoreactive cells were described. Although the sensory neurons were not 5-HT-like immunoreactive, they had 5-HT innervation, which may indicate the role of 5-HT in perception. There may be homology between male and female ciliary structures. The dwarf male of D. gyrociliatus may have a reduced apical organ consisting of two sensory neurons and a 5-HT-like immunoreactive cell.

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38

Nori-Shargh, Davood, Hossein Aghabozorgh, Karim Zare, Mohammad Reza Talei, Bavil Olyai, and Saeed Jameh-Bozorghi. "Ab Initio Study of Structures, Metallotropic 1,2-Shifts and Prototropic 1,2-Shifts of Cyclopentadienyl(trimethyl)silane, -germane and -stannane." Phosphorus, Sulfur, and Silicon and the Related Elements 178, no. 2 (February 1, 2003): 341–51. http://dx.doi.org/10.1080/10426500307946.

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39

Strathmann, Richard R. "Multiple origins of feeding head larvae by the Early Cambrian." Canadian Journal of Zoology 98, no. 12 (December 2020): 761–76. http://dx.doi.org/10.1139/cjz-2019-0284.

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In many animals the head develops early, most of the body axis later. A larva composed mostly of the developing front end therefore can attain mobility and feeding earlier in development. Fossils, functional morphology, and inferred homologies indicate that feeding head larvae existed by the Early Cambrian in members of three major clades of animals: ecdysozoans, lophotrochozoans, and deuterostomes. Some of these early larval feeding mechanisms were also those of juveniles and adults (the lophophore of brachiopod larvae and possibly the ciliary band of the dipleurula of hemichordates and echinoderms); some were derived from structures that previously had other functions (appendages of the nauplius). Trochophores that swim with a preoral band of cilia, the prototroch, originated before divergence of annelids and molluscs, but evidence of larval growth and thus a prototrochal role in feeding is lacking for molluscs until the Ordovician. Feeding larvae that definitely originated much later, as in insects, teleost fish, and amphibians, develop all or nearly all of what will become the adult body axis before they begin feeding. On present evidence, head larvae, including feeding head larvae, evolved multiple times early in the evolution of bilaterian animals and never since.

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Griffiths, A. J. F., X. Yang, F. J. Debets, and Y. Wei. "Plasmids in natural populations of Neurospora." Canadian Journal of Botany 73, S1 (December 31, 1995): 186–92. http://dx.doi.org/10.1139/b95-244.

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Eukaryotic plasmids are mainly fungal. Global Neurospora populations have been surveyed and show that approximately half the isolates have one or more plasmids. There are distinct homology groups of plasmids and most groups are distributed across species. One example is also in a related genus, Gelasinospora. Most plasmids are apparently benign but several examples are virulent, killing by insertion into mtDNA. In Hawaii, one of the virulent plasmids, kalilo, might be increasing in frequency. Plasmids can be transmitted horizontally between laboratory strains by forced heterokaryosis or by transient fusion. Simulations of population transmission have shown that the linear kalilo and circular Hanalei-2 plasmids are aggressively transmitted from one compatible prototroph to another. This transmission is slowed but not necessarily eliminated by het gene incompatibility. Paternal transmission of plasmids has been demonstrated and this seems to be affected by the incompatibility genotypes of the parents. However, paternal transmission might not be through the normal trichogyne route, but by a "back-door" route possibly through maternal mycelium. There are several documented ways in which plasmids can change their structure. One novel way is by recombination between two different heterologous plasmids. These processes might be relevant to plasmid evolution. Two suppression processes have been discovered that can be used by the host to eliminate specific plasmids: a cell autonomous type, and a nonautonomous type that acts during the sexual cycle. In conclusion, plasmids are diverse and widely distributed in fungi, undoubtedly reflecting their multiple modes of transmission and structural modification. Key words: Neurospora, plasmids, mitochondria, populations, kalilo.

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Halcrow, M. A., H. R. Powell, and M. J. Duer. "Tautomerism in 3{5}-(dimethoxyphenyl)pyrazoles." Acta Crystallographica Section B Structural Science 52, no. 4 (August 1, 1996): 746–52. http://dx.doi.org/10.1107/s0108768196005204.

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The single-crystal X-ray structures of 3{5}-(2′,5′-dimethoxyphenyl)pyrazole (HI) and the hemihydrate of 3 {5}-(3/,4′-dimethoxyphenyl)pyrazole (IV) have been determined. Compound (HI) exists purely as the 5-substituted prototropomer in the crystal; the pyrazole pyrollic N—H proton is involved in a three-way hydrogen bond, involving an intramolecular contact with a methoxy oxygen donor and an intermolecular interaction to the pyridinic N atom of a neighbouring molecule, forming discrete hydrogen-bonded dimers. There is no evidence of degenerate proton transfer within the dimeric units from CPMAS 13C NMR spectroscopy, in contrast to other known pyrazoles that associate in this manner. In (IV).1/2H2O, however, the pyrrolic proton is disordered over both N(1) and N(2) via hydrogen bonding to the solvate water molecule. CPMAS 13C NMR spectroscopy shows that the prototropic disorder in (IV).1/2H2O is static at temperatures up to 370 K. Solution 1H and 13C NMR data in DMSO-d 6 show that for both (HI) and (IV) the 3- and 5-substituted tautomeric forms are similarly populated in this solvent, suggesting both that the intramolecular hydrogen bond in (HI) has been disrupted and that the two tautomers of (HI) and (IV) are close in energy.

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42

Wollesen, Tim, Sonia Victoria Rodríguez Monje, André Luiz de Oliveira, and Andreas Wanninger. "Staggered Hox expression is more widespread among molluscs than previously appreciated." Proceedings of the Royal Society B: Biological Sciences 285, no. 1888 (October 10, 2018): 20181513. http://dx.doi.org/10.1098/rspb.2018.1513.

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Hox genes are expressed along the anterior–posterior body axis in a colinear fashion in the majority of bilaterians. Contrary to polyplacophorans, a group of aculiferan molluscs with conserved ancestral molluscan features, gastropods and cephalopods deviate from this pattern by expressing Hox genes in distinct morphological structures and not in a staggered fashion. Among conchiferans, scaphopods exhibit many similarities with gastropods, cephalopods and bivalves, however, the molecular developmental underpinnings of these similar traits remain unknown. We investigated Hox gene expression in developmental stages of the scaphopod Antalis entalis to elucidate whether these genes are involved in patterning morphological traits shared by their kin conchiferans. Scaphopod Hox genes are predominantly expressed in the foot and mantle but also in the central nervous system. Surprisingly, the scaphopod mid-stage trochophore exhibits a near-to staggered expression of all nine Hox genes identified. Temporal colinearity was not found and early-stage and late-stage trochophores, as well as postmetamorphic individuals, do not show any apparent traces of staggered expression. In these stages, Hox genes are expressed in distinct morphological structures such as the cerebral and pedal ganglia and in the shell field of early-stage trochophores. Interestingly, a re-evaluation of previously published data on early-stage cephalopod embryos and of the gastropod pre-torsional veliger shows that these developmental stages exhibit traces of staggered Hox expression. Considering our results and all gene expression and genomic data available for molluscs as well as other bilaterians, we suggest a last common molluscan ancestor with colinear Hox expression in predominantly ectodermal tissues along the anterior–posterior axis. Subsequently, certain Hox genes have been co-opted into the patterning process of distinct structures (apical organ or prototroch) in conchiferans.

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43

Chirkova, Zhanna V., Sergey I. Filimonov, and Igor G. Abramov. "SYNTHESIS OF BENZOFURAN-5,6-DICARBONITRILES ANNELATED WITH PYRAZOLE CYCLE." IZVESTIYA VYSSHIKH UCHEBNYKH ZAVEDENIY KHIMIYA KHIMICHESKAYA TEKHNOLOGIYA 60, no. 6 (July 19, 2017): 45. http://dx.doi.org/10.6060/tcct.2017606.5576.

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The principal method for the preparation of substituted 4-formyl-1H-pyrazoles was the treatment of hydrazones of different structure with Vilsmeier-Haack reagent. However, for the heterocyclic benzofuran system this reaction is rarely used. Synthetic methods for preparation of novel substituted 3-(4-fomyl-1H-pyrazole-3-yl)-2-methylbenzofuran-5,6-dicarbonitriles and 2-(1H-pyrazole-4-yl)-benzofuran-5,6-dicarbonitriles were developed by modification of 2,3-disubstituted benzofuran-5,6-dicarbonitriles via Vilsmeier-Haack reaction. New substituted 3-(4-fomyl-1H-pyrazole-3-yl)-2-methylbenzofuran-5,6-dicarbonitriles were obtained by reacting 3-acetyl-2-methyl-1-benzofuran-5,6-dicarbonitrile with hydrochloric substituted phenylhydrazines followed by treatment with the Vilsmeier reagent formed hydrazones. A new method for the synthesis of 3-substituted 2-(1H-pyrazol-4-yl)-benzofuran-5,6-dicarbonitriles was based on condensation of aminovinylbenzofuranes with hydrazine hydrate in refluxing acetic acid. The structure of synthesized compounds was determined by data of the IR and NMR spectroscopy, including two-dimensional correlation 1H-1H spectroscopy, and mass spectrometry. The signals of cyano and formyl groups were characteristic in IR spectra; the signals of phthalonitrile protons and proton of aldehyde group - in 1H NMR spectra for 3-(4-formyl-1H-pyrazole)-2-methyl-1-benzofuran-5,6-dicarbonitriles. Also, structure of synthesized 4-formylpyrazoles is confirmed by their reaction with hydrazine hydrate to give corresponding hydrazones. The signals of NH-pronon of pyrazole ring, cyano and carbonyl groups were characteristic in IR spectra; signal broadened singlet of NH-proton of pyrazole ring, which determined to prototropic ring tautomerism of pyrazole ring, and singlets of phthalonitrile protons - in 1H NMR spectra for 3-substituted 2-(1H-pyrazol-4-yl)-benzofuran-5,6-dicarbonitriles. Development of methods for the synthesis of new 4-formylpyrazoles is an important task because the compounds exhibit various pharmacological properties: antimicrobial, anti-inflammatory, antituberculosis, antitumoral, antiparasitic, and antiviral.Forcitation:Chirkova Zh.V., Filimonov S.I., Abramov I.G. Synthesis of benzofuran-5,6-dicarbonitriles annelated with pyrazole cycle. Izv. Vyssh. Uchebn. Zaved. Khim. Khim. Tekhnol. 2017. V. 60. N 6. P. 45-51.

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Bihdan, O. A., and N. A. Alk Khalaf. "DFT-analysis of protolytic equivalents of 5-(aryl)-4-(methyl,amino)-1,2,4-triazole-3(2H)-thione." Current issues in pharmacy and medicine: science and practice 15, no. 2 (August 1, 2022): 133–39. http://dx.doi.org/10.14739/2409-2932.2022.2.254474.

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The use of modern computer methods in aspects of quantum chemistry and systematic analysis of their results give an idea of the reactivity of organic compounds, as well as to understand the essence of known experimental data, correct predictions, and quantitative estimates. Undoubtedly, theoretical calculations are useful in solving such an urgent problem of modern chemistry as prototropic equilibria and properties of substances in the gas phase, solutions, and solid-state. The aim of the work – until recently assigned to a theoretical vivification in the infusion of solvents on tautomeric equilibrium and acid-base powers і know more broadly practical stasis in the pharmaceutical industry. Materials and methods. The effect of solvation effects on tautomerism and antitropic properties of 1,2,4-triazole derivatives was studied on the example of model compounds. All calculations were performed using the Gauss-View 6.0.1 molecular link visualization program and Gaussian 98, Gaussian 03 software packages and the use of default convergence criteria. After optimizing the geometry, frequency calculations followed. Thus, the stationary structures are confirmed by checking that all ground states have only real frequencies, and all transition states have only one imaginary frequency. The same method and established basis were used to optimize the geometry. Solvation calculations were performed in the framework of continuous models (D-PCM, C-PCM, IEF-PCM, IPCM, SCIPCM) of discrete and combined models using the Hartree–Fock constraint method, the method of density functional theory B3LYP with basic sets 6-31G (d), 6-31G (d,p), 6-31G++ (d,p), cc-pVDZ, as well as semi-empirical methods in the MOPAC6 package. Results. For the first time, various quantum chemical calculations of solvated model compounds using different approaches and models, variation of the basis in non-empirical calculations, identification of the role of electronic correlation effects, method of geometry optimization, etc. were carried out within the theory of self-consistent reaction field. The main stage of this study was to compare trends in the equilibrium change in the relative stability of tautomeric forms of thione-thiol tautomerism of 1,2,4-triazole-2(3H)-thions in the gas phase and different prototropic solvents due to the possibility of using different models and calculation methods for quality predictions of the effect of solvation on the position of tautomeric equilibrium in compounds of this class. It was found that the selected various solvents according to all used quantum chemical methods and models (D-PCM, C-PCM. IEF-PCM, IPCM, SCIPCM) reduce the difference in the stability of tautomeric forms of the investigated compounds in comparison with the gas phase, while the greatest stabilizing effect is observed in the solvation of NH-tautomers derived from 1,2,4-triazole-2(3H)-thiones. Using all energy parameters (∆Etot, ∆E0, ∆H298, ∆G298) allowed to determine the effect of complexation on the relative stability of tautomeric forms of the studied compounds. The difference in the values of the energy levels of HOMO and LUMO – orbitals indicate the reactivity of the molecule and its activation energy, which indicates the chemical reactivity of the molecule to electronic transport and the manifestation of biological activity with intramolecular charge transfer. Conclusions. For the first time, complex quantum chemical calculations of thione-thiol tautomers of 5-(aryl)-4-(methyl, amino)-1,2,4-triazole-3(2H)-thiones were performed and it was found that prototropic solvents reduce the difference in all models. In the stability of tautomeric forms of the investigated compounds in comparison with the gas phase. The calculated values of electronic correlation models on the hydrogen atom make a significant contribution to the relative stability of tautomeric forms, while the use of polarization functions of quantum chemical methods on hydrogen atoms has practically no effect on the tautomeric equilibrium. From the obtained data it becomes clearer that in the gas phase and aprotic solvents the thione tautomer with the center of NH-acidity is the most stable, and the thiol tautomer of 1,2,4-triazole-3(2H)-thione predominates in the transition to polar proton-donor solvents. The obtained data indicate the possibility of conducting an electrophilic substitution reaction (eg, alkylation) in the form of an anion. The partially negative charge of the Nitrogen atoms of the 1,2,4-triazole ring promotes electrophilic addition reactions. In the thionic form, on the contrary, electrophilic substitution reactions are possible.

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Kaştaş, G., and Ç. Albayrak Kaştaş. "A Close Look at the Molecular Structure, Prototropic Behavior and Supramolecular Architecture of (E)-4-Bromo-2-[(phenylimino)methyl]-5-methoxyphenol by Spectroscopic, Crystallographic, and Computational Methods." Crystallography Reports 65, no. 3 (May 2020): 457–62. http://dx.doi.org/10.1134/s1063774520030141.

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Bax, Ben, Chun-wa Chung, and Colin Edge. "Getting the chemistry right: protonation, tautomers and the importance of H atoms in biological chemistry." Acta Crystallographica Section D Structural Biology 73, no. 2 (February 1, 2017): 131–40. http://dx.doi.org/10.1107/s2059798316020283.

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There are more H atoms than any other type of atom in an X-ray crystal structure of a protein–ligand complex, but as H atoms only have one electron they diffract X-rays weakly and are `hard to see'. The positions of many H atoms can be inferred by our chemical knowledge, and such H atoms can be added with confidence in `riding positions'. For some chemical groups, however, there is more ambiguity over the possible hydrogen placements, for example hydroxyls and groups that can exist in multiple protonation states or tautomeric forms. This ambiguity is far from rare, since about 25% of drugs have more than one tautomeric form. This paper focuses on the most common, `prototropic', tautomers, which are isomers that readily interconvert by the exchange of an H atom accompanied by the switch of a single and an adjacent double bond. Hydrogen-exchange rates and different protonation states of compounds (e.g. buffers) are also briefly discussed. The difference in heavy (non-H) atom positions between two tautomers can be small, and careful refinement of all possible tautomers may single out the likely bound ligand tautomer. Experimental methods to determine H-atom positions, such as neutron crystallography, are often technically challenging. Therefore, chemical knowledge and computational approaches are frequently used in conjugation with experimental data to deduce the bound tautomer state. Proton movement is a key feature of many enzymatic reactions, so understanding the orchestration of hydrogen/proton motion is of critical importance to biological chemistry. For example, structural studies have suggested that, just as a chemist may use heat, some enzymes use directional movement to protonate specific O atoms on phosphates to catalyse phosphotransferase reactions. To inhibit `wriggly' enzymes that use movement to effect catalysis, it may be advantageous to have inhibitors that can maintain favourable contacts by adopting different tautomers as the enzyme `wriggles'.

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Kobychev, Vladimir B., Nadezhda M. Vitkovskaya, Elena Yu Larionova, and Boris A. Trofimov. "Sulfur Versus Oxygen in Interaction with the Double Bond: AB Initio Study of Electronic Structure and Prototropic Rearrangement of 1-Methoxy-2-propene and 1-Methylthio-2-propene." Phosphorus, Sulfur, and Silicon and the Related Elements 177, no. 12 (December 1, 2002): 2931–40. http://dx.doi.org/10.1080/10426500214896.

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48

Kuz’mina, N. E., S. V. Moiseev, and A. I. Luttseva. "The Problem of Dynamic Process Manifestation in Identification of Organic Compounds by NMR Spectroscopy." Bulletin of the Scientific Centre for Expert Evaluation of Medicinal Products 10, no. 1 (February 26, 2020): 63–76. http://dx.doi.org/10.30895/1991-2919-2020-10-1-63-76.

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The number, shape and position of NMR spectral lines depend on dynamic processes, and this creates certain difficulties in identification of pharmaceutical substances by NMR spectroscopy. The aim of the paper was to study instances of manifestation of intramolecular dynamic processes that affect identification of organic compounds by NMR, and to illustrate the potential of the methods used for their reduction, as well as associated problems.Materials and methods: 1H and 13C spectra of the following pharmaceutical substances: «buserelin acetate», «valsartan», «goserelin acetate», «iopromide», «clopidogrel hydrogensulfate», «omeprazole», «proroxan», «risperidone», «triptorelin acetate», and «enalapril maleate» were used to demonstrate negative effects of dynamic processes. The spatial structures of conformers were established by 1H-1H ROESY experiments. The quantum-chemical calculation of geometric and thermodynamic characteristics of different conformers was carried out by the PM3 method, and electronic characteristics—by the AM1 method with the help of the HyperChem software.Results: the authors analysed intramolecular dynamic processes which are most commonly encountered in expert work: pyramidal inversion of nitrogen in a heterocyclic compound (risperidone, proroxan, clopidogrel), rotation of molecular fragments around the amide bond (valsartan, iopromide, enalapril), prototropic rearrangements (buserelin, goserelin, omeprazole, triptorelin). The change in exchange rates was explained from the perspective of the change in the system of intra- and intermolecular nonvalent interactions.Conclusions: the use of traditional methods for increasing the rate of dynamic processes (increasing the temperature and changing the solvent) does not always eliminate the negative effects of intramolecular transformations. Methods of smoothing the spectral manifestations of dynamic processes have limited application due to strong intramolecular nonvalent interactions which prevent the conversion of the dynamic process rate into fast exchange. Experts and manufacturers should take into account the manifestation of dynamic processes during identification of pharmaceutical substances by NMR spectroscopy.

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Garifzianova, Guzel G. "Theoretical study of the isomerization of 1-amino-4-phenylamino-9,10-anthraquinone." Butlerov Communications 60, no. 12 (December 31, 2019): 37–42. http://dx.doi.org/10.37952/roi-jbc-01/19-60-12-37.

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This paper presents the results of computer simulation of tautomeric transformations of the molecule 1-amino-4-phenylamino-9,10-anthraquinone. It is known from the literature that the presence of substituents in the 1,4-position of anthraquinone-9,10 leads to various tautomeric transformations, with a shift in the absorption maximum and the appearance of absorption bands in the red wave region in electronic spectra. Both the 1-amino-4-hydroxyanthraquinone described in the literature and the 1-amino-4-phenylamino-9,10-anthraquinone are characterized by two types of prototropic tautomerism – keto-enol and amino-imine. Quantum-chemical modeling contributes to the calculation of the relative energies of tautomers and isomers, the barriers of their interconversions, as well as finding their structural parameters. The aim of this study was to study the mechanism of the formation of tautomers during hydrogen transfer in the molecule of 1-amino-4-phenylamino-9,10-anthraquinone, as well as the formation of isomers during migration of the OH group. The calculations were performed using the Gaussian09 program. To study of various tautomers of 1-amino-4-phenylamino-9,10-anthraquinone, the B3LYP method with the def2TZV basis was used. A search was conducted for transition states during hydrogen transfer and OH group migration. The descent along the reaction path was calculated to confirm that the transition state is in the path of the desired reaction. The minima corresponding to the starting material and product were localized. The activation enthalpies of the studied reactions were calculated. Migration of the OH group in the 1-amino-4-phenylamino-9,10-anthraquinone molecule leads to the formation of 4-phenylamino-9-amino-1,10-anthraquinone. As the calculation shows, the keto-form of 1-amino-4-phenylamino-9,10-anthraquinone is energetically more profitable than all the isomers studied in this work, including the enol form. The smallest difference in total potential energies is 23.7 kJ/mol between the initial ketone form of 1-amino-4-phenylamino-9,10-anthraquinone and the last transformation structure – the 4-phenylamino-9-amino-1,10-anthraquinone molecule.

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Raczyńska, Ewa D. "Quantum-Chemical Search for Keto Tautomers of Azulenols in Vacuo and Aqueous Solution." Symmetry 13, no. 3 (March 18, 2021): 497. http://dx.doi.org/10.3390/sym13030497.

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Keto-enol prototropic conversions for carbonyl compounds and phenols have been extensively studied, and many interesting review articles and even books appeared in the last 50 years. Quite a different situation takes place for derivatives of biologically active azulene, for which only scanty information on this phenomenon can be found in the literature. In this work, quantum-chemical studies have been undertaken for symmetrically and unsymmetrically substituted azulenols (constitutional isomers of naphthols). Stabilities of two enol (OH) rotamers and all possible keto (CH) tautomers have been analyzed in the gas phase {DFT(B3LYP)/6-311+G(d,p)} and also in aqueous solution {PCM(water)//DFT(B3LYP)/6-311+G(d,p)}. Contrary to naphthols, for which the keto forms can be neglected, at least one keto isomer (C1H, C2H, and/or C3H) contributes significantly to the tautomeric mixture of each azulenol to a higher degree in vacuo (non-polar environment) than in water (polar amphoteric solvent). The highest amounts of the CH forms have been found for 2- and 5-hydroxyazulenes, and the smallest ones for 1- and 6-hydroxy derivatives. The keto tautomer(s), together with the enol rotamers, can also participate in deprotonation reaction leading to a common anion and influence its acid-base properties. The strongest acidity in vacuo exhibits 6-hydroxyazulene, and the weakest one displays 1-hydroxyazulene, but all azulenols are stronger acids than phenol and naphthols. Bond length alternation in all DFT-optimized structures has been measured using the harmonic oscillator model of electron delocalization (HOMED) index. Generally, the HOMED values decrease for the keto tautomers, particularly for the ring containing the labile proton. Even for the keto tautomers possessing energetic parameters close to those of the enol isomers, the HOMED indices are low. However, some kind of parallelism exists for the keto forms between their relative energies and HOMEDs estimated for the entire molecules.

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Journal articles on the topic 'Structure and Prototropy'

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