Two different products from the reaction of 1-aryl-5-chloro-3-methyl-1H-pyrazole-4-carbaldehyde with cyclohexylamine when the aryl substituent is phenyl or pyridin-2-yl: hydrogen-bonded sheetsversusdimers

2015 ◽  
Vol 71 (5) ◽  
pp. 363-368 ◽  
Author(s):  
Jessica Orrego Hernandez ◽  
Jaime Portilla ◽  
Justo Cobo ◽  
Christopher Glidewell
Keyword(s):  
Hydrogen Bond ◽  
Negative Charge ◽  
Positive Charge ◽  
Molecular Type ◽  
Aryl Substituent ◽  
Centrosymmetric Dimer ◽  
Partial Positive Charge ◽  
Partial Negative Charge ◽  
Independent Molecules ◽  
Compound Ii

Cyclohexylamine reacts with 5-chloro-3-methyl-1-(pyridin-2-yl)-1H-pyrazole-4-carbaldehyde to give 5-cyclohexylamino-3-methyl-1-(pyridin-2-yl)-1H-pyrazole-4-carbaldehyde, C16H20N4O, (I), formed by nucleophilic substitution, but with 5-chloro-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde the product is (Z)-4-[(cyclohexylamino)methylidene]-3-methyl-1-phenyl-1H-pyrazol-5(4H)-one, C17H21N3O, (II), formed by condensation followed by hydrolysis. Compound (II) crystallizes withZ′ = 2, and in one of the two independent molecular types the cyclohexylamine unit is disordered over two sets of atomic sites having occupancies of 0.65 (3) and 0.35 (3). The vinylogous amide portion in each compound shows evidence of electronic polarization, such that in each the O atom carries a partial negative charge and the N atom of the cyclohexylamine portion carries a partial positive charge. The molecules of (I) contain an intramolecular N—H...N hydrogen bond, and they are linked by C—H...O hydrogen bonds to form sheets. Each of the two independent molecules of (II) contains an intramolecular N—H...O hydrogen bond and each molecular type forms a centrosymmetric dimer containing oneR22(4) ring and two inversion-relatedS(6) rings.

scholarly journals Crystal structures of three 6-aryl-2-(4-chlorobenzyl)-5-[(1H-indol-3-yl)methyl]imidazo[2,1-b][1,3,4]thiadiazoles

2020 ◽  
Vol 76 (1) ◽  
pp. 18-24
Author(s):  
Sadashivamurthy Shamanth ◽  
Kempegowda Mantelingu ◽  
Haruvegowda Kiran Kumar ◽  
Hemmige S. Yathirajan ◽  
Sabine Foro ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Three Dimensional ◽  
Asymmetric Unit ◽  
Compound I ◽  
Π Interactions ◽  
Reductive Condensation ◽  
Independent Molecules ◽  
Compound Ii

Three title compounds, namely, 2-(4-chlorobenzyl)-5-[(1H-indol-3-yl)methyl]-6-phenylimidazo[2,1-b][1,3,4]thiadiazole, C26H19ClN4S, (I), 2-(4-chlorobenzyl)-6-(4-fluorophenyl)-5-[(1H-indol-3-yl)methyl]imidazo[2,1-b][1,3,4]thiadiazole, C26H18ClFN4S, (II), and 6-(4-bromophenyl)-2-(4-chlorobenzyl)-5-[(1H-indol-3-yl)methyl]imidazo[2,1-b][1,3,4]thiadiazole, C26H18BrClN4S, (III), have been prepared using a reductive condensation of indole with the corresponding 6-aryl-2-(4-chlorobenzyl)imidazo[2,1-b][1,3,4]thiadiazole-5-carbaldehydes (aryl = phenyl, 4-fluorophenyl or 4-bromophenyl), and their crystal structures have been determined. The asymmetric unit of compound (I) consists of two independent molecules and one of the molecules exhibits disorder of the 4-chlorobenzyl substituent with occupancies 0.6289 (17) and 0.3711 (17). Each type of molecule forms a C(8) chain motif built from N—H...N hydrogen bonds, which for the fully ordered molecule is reinforced by C—H...π interactions. In compound (II), the chlorobenzyl unit is again disordered, with occupancies 0.822 (6) and 0.178 (6), and the molecules form C(8) chains similar to those in (I), reinforced by C—H...π interactions involving only the major disorder component. The chlorobenzyl unit in compound (III) is also disordered with occupancies of 0.839 (5) and 0.161 (5). The molecules are linked by a combination of one N—H...N hydrogen bond and four C—H...π interactions, forming a three-dimensional framework.

Carbon Footprints: The Wittig Reaction

Reactions ◽  
2011 ◽  
Author(s):  
Peter Atkins
Keyword(s):  
Wittig Reaction ◽  
Negative Charge ◽  
Positive Charge ◽  
Carbon Chain ◽  
Hydroxide Ion ◽  
Carbon Footprints ◽  
Proper Nouns ◽  
Partial Negative Charge ◽  
Growing Network ◽  
Positive Ion

As a molecular architect working on an atomic construction site you need to be able to build up the carbon skeleton of your project, not merely decorate it with foreign atoms. There are dozens of different ways of doing that, and in this and the next section I shall introduce you to just two of them to give you a taste of what is available. A secondary point is that throughout chemistry you will find reactions denoted by proper nouns, recognizing the chemists who have invented or developed them. One example is that of the ‘Wittig reaction’, which is named after the German chemist Georg Wittig (1897–1987; Nobel Prize 1979). The reaction is used to replace the oxygen atom of a CO group in a molecule by a carbon atom, so that what starts out as decoration becomes part of a growing network of carbon atoms. You need to know that phosphine, PH3, 1, the phosphorus cousin of ammonia, NH3, is a base (Reaction 2). When it accepts a proton it becomes the ion PH4+. The H atoms in that ion can be replaced with other groups of atoms. A replacement that will be of interest is when three of the H atoms have been replaced by benzene rings and the remaining H atom has been replaced by –CH3. The resulting ion is 2. In the presence of a base, such as the hydroxide ion, OH–, the –CH3 group can be induced to release one of its protons, so the positive ion becomes the neutral molecule, 3. Note that there is a partial positive charge on the P atom and a partial negative charge on the C atom of the CH2 group. The presence of that partial negative charge suggests that the species could act as a nucleophile (Reaction 15), a seeker out of positive charge, with the CH2 group the charge-seeking head of the missile. Let’s watch what happens when 3 attacks a molecule with a CO group, specifically 4: perhaps you want to sprout a carbon chain out from the ring and intend to begin by replacing the O atom with a C atom.

scholarly journals Crystal structures ofN-(4-chlorophenyl)-2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]acetamide andN-(3-chlorophenyl)-2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]acetamide

2017 ◽  
Vol 73 (4) ◽  
pp. 467-471 ◽  
Author(s):  
S. Subasri ◽  
Timiri Ajay Kumar ◽  
Barij Nayan Sinha ◽  
Venkatesan Jayaprakash ◽  
Vijayan Viswanathan ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Benzene Ring ◽  
Three Dimensional ◽  
Pyrimidine Ring ◽  
Dimensional Structure ◽  
Asymmetric Unit ◽  
Independent Molecules ◽  
Compound Ii ◽  
Ring Motif

The title compounds, C12H12ClN5OS, (I), and C12H12ClN5OS, (II), are 2-[(diaminopyrimidin-2-yl)sulfanyl]acetamides. Compound (II), crystallizes with two independent molecules (AandB) in the asymmetric unit. In each of the molecules, in both (I) and (II), an intramolecular N—H...N hydrogen bond forms anS(7) ring motif. The pyrimidine ring is inclined to the benzene ring by 42.25 (14)° in (I), and by 59.70 (16) and 62.18 (15)° in moleculesAandB, respectively, of compound (II). In the crystal of (I), molecules are linked by pairs of N—H...N hydrogen bonds, forming inversion dimers with anR22(8) ring motif. The dimers are linkedviabifurcated N—H...O and C—H...O hydrogen bonds, forming corrugated layers parallel to theacplane. In the crystal of (II), theAmolecules are linked through N—H...O and N—H...Cl hydrogen bonds, forming layers parallel to (100). TheBmolecules are also linked by N—H...O and N—H...Cl hydrogen bonds, also forming layers parallel to (100). The parallel layers ofAandBmolecules are linkedviaN—H...N hydrogen bonds, forming a three-dimensional structure.

scholarly journals The crystal structures of 6′-(4-chlorophenyl)- and 6′-(4-methoxyphenyl)-6a′-nitro-6a′,6b′,7′,9′,10′,12a′-hexahydro-2H,6′H,8′H-spiro[acenaphthylene-1,12′-chromeno[3,4-a]indolizin]-2-one

2019 ◽  
Vol 75 (2) ◽  
pp. 218-222 ◽  
Author(s):  
S. Syed Abuthahir ◽  
M. NizamMohideen ◽  
V. Viswanathan ◽  
D. Velmurugan ◽  
J. Nagasivarao
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Supramolecular Structure ◽  
Three Dimensional ◽  
Asymmetric Unit ◽  
Π Interactions ◽  
Independent Molecules ◽  
Intramolecular Hydrogen ◽  
Compound Ii ◽  
Ring Motif

In the title compounds, C32H25ClN2O4 (I) and C33H28N2O5 (II), the six-membered pyran and piperidine rings adopt envelope and chair conformations, respectively. The five-membered pyrrolidine rings adopt twist conformations. Compound (II) crystallizes with two independent molecules (A and B) in the asymmetric unit. In all three molecules there is a C—H...O intramolecular hydrogen bond present enclosing an S(7) ring motif. In (I), both oxygen atoms of the nitro group are disordered, while in (II) the methoxybenzene group is disordered in molecule B. The geometries were regularized by soft restraints. In the crystal of (I), molecules are linked by C—H...O hydrogen bonds, forming chains along [010]. The chains are linked by C—H...Cl hydrogen bonds, forming layers parallel to (10\overline{1}). Within the layer there are C—H...π interactions present. In the crystal of (II), the A and B molecules are linked via C—H...O hydrogen bonds, forming a square four-membered A–B–A–B unit. These units are linked by a number of C—H...π interactions, forming a three-dimensional supramolecular structure.

A Hydrogen Bond Between Linear Tetrapyrrole and Conserved Aspartate Causes the Far-Red Shifted Absorption of Phytochrome Photoreceptors

2020 ◽  
Author(s):  
Egle Maximowitsch ◽  
Tatiana Domratcheva
Keyword(s):  
Hydrogen Bond ◽  
Light Adaptation ◽  
Positive Charge ◽  
Pyrrole Ring ◽  
Md Simulations ◽  
Spectral Shift ◽  
Specific Domain ◽  
Study Guides ◽  
Rational Engineering ◽  
Tuning Mechanism

Photoswitching of phytochrome photoreceptors between red-absorbing (Pr) and far-red absorbing (Pfr) states triggers light adaptation of plants, bacteria and other organisms. Using quantum chemistry, we elucidate the color-tuning mechanism of phytochromes and identify the origin of the Pfr-state red-shifted spectrum. Spectral variations are explained by resonance interactions of the protonated linear tetrapyrrole chromophore. In particular, hydrogen bonding of pyrrole ring D with the strictly conserved aspartate shifts the positive charge towards ring D thereby inducing the red spectral shift. Our MD simulations demonstrate that formation of the ring D–aspartate hydrogen bond depends on interactions between the chromophore binding domain (CBD) and phytochrome specific domain (PHY). Our study guides rational engineering of fluorescent phytochromes with a far-red shifted spectrum.

scholarly journals Zerumbone Inhibits Helicobacter pylori Urease Activity

Molecules ◽  
2021 ◽  
Vol 26 (9) ◽  
pp. 2663
Author(s):  
Hyun Jun Woo ◽  
Ji Yeong Yang ◽  
Pyeongjae Lee ◽  
Jong-Bae Kim ◽  
Sa-Hyun Kim
Keyword(s):  
Helicobacter Pylori ◽  
Carbon Atom ◽  
Natural Compound ◽  
Urease Activity ◽  
Negative Charge ◽  
Positive Charge ◽  
Gastric Epithelium ◽  
Functional Inhibition ◽  
Electrical Gradient ◽  
H Pylori

Helicobacter pylori (H. pylori) produces urease in order to improve its settlement and growth in the human gastric epithelium. Urease inhibitors likely represent potentially powerful therapeutics for treating H. pylori; however, their instability and toxicity have proven problematic in human clinical trials. In this study, we investigate the ability of a natural compound extracted from Zingiber zerumbet Smith, zerumbone, to inhibit the urease activity of H. pylori by formation of urease dimers, trimers, or tetramers. As an oxygen atom possesses stronger electronegativity than the first carbon atom bonded to it, in the zerumbone structure, the neighboring second carbon atom shows a relatively negative charge (δ−) and the next carbon atom shows a positive charge (δ+), sequentially. Due to this electrical gradient, it is possible that H. pylori urease with its negative charges (such as thiol radicals) might bind to the β-position carbon of zerumbone. Our results show that zerumbone dimerized, trimerized, or tetramerized with both H. pylori urease A and urease B molecules, and that this formation of complex inhibited H. pylori urease activity. Although zerumbone did not affect either gene transcription or the protein expression of urease A and urease B, our study demonstrated that zerumbone could effectively dimerize with both urease molecules and caused significant functional inhibition of urease activity. In short, our findings suggest that zerumbone may be an effective H. pylori urease inhibitor that may be suitable for therapeutic use in humans.

scholarly journals Methyl 1-allyl-4-hydroxy-2,2-dioxo-1H-2λ6,1-benzothiazine-3-carboxylate

2013 ◽  
Vol 69 (11) ◽  
pp. o1698-o1698 ◽  
Author(s):  
Svitlana V. Shishkina ◽  
Igor V. Ukrainets ◽  
Lidiya A. Petrushova
Keyword(s):  
Hydrogen Bond ◽  
Asymmetric Unit ◽  
Torsion Angles ◽  
Compound C ◽  
Two Component ◽  
Independent Molecules ◽  
Population Ratio ◽  
Intramolecular Hydrogen ◽  
Vinyl Group ◽  
Planar Fragment

There are two independent molecules in the asymmetric unit of the title compound, C13H13NO5S, in both of which the ester substituent is nearly coplanar [C—C—C—O torsion angles = 2.7 (7) and −0.8 (7)°] with the planar fragment of the bicycle due to the formation of a strong O—H...O intramolecular hydrogen bond. The vinyl group at the ring N atom is approximately orthogonal to the heterocyclic mean plane [C—N—C—C torsion angles = 103.1 (6) and 98.2 (5)°]. The refinement was performed on a two-component, non-merohedrally twinned crystal [population ratio = 0.483 (3):0.517 (3).

scholarly journals Indication of the Coronavirus Model Using a Nanowire Biosensor

Proceedings ◽  
2020 ◽  
Vol 60 (1) ◽  
pp. 50
Author(s):  
Vladimir Generalov ◽  
Olga Naumova ◽  
Dmitry Shcherbakov ◽  
Alexander Safatov ◽  
Boris Zaitsev ◽  
...  
Keyword(s):  
Field Effect ◽  
Field Effect Transistor ◽  
Negative Charge ◽  
Positive Charge ◽  
Silicon On Insulator ◽  
Nanowire Surface ◽  
Before And After ◽  
Effect Transistor ◽  
Current Value ◽  
Silicon On Insulator Technology

The presented results indicate virus-like particles of the coronavirus (CVP) using a nanowire (NW) biosensor based on silicon-on-insulator technology. In the experiment, we used suspensions of CVP and of specific antibodies to the virus. Measurements of the current value of the field-effect transistor before and after the introduction of the CVP on the surface of the nanowire were performed. Results showed antibody + CVP complexes on the phase section with the surface of the nanowire modulate the current of the field-effect transistor; CVP has an electrically positive charge on the phase section “nanowire surface-viral suspension»; antibody + CVP complexes have an electrically negative charge on the phase section “nanowire surface-viral suspension”; the sensitivity of the biosensor is made up of 10−18 M; the time display was 200–300 s.

scholarly journals 2,3-Dihydrobenz[4,5]imidazo[2,1-b]thiazole

IUCrData ◽  
2016 ◽  
Vol 1 (12) ◽  
Author(s):  
Ahmed Moussaif ◽  
Youssef Ramli ◽  
Nada Kheira Sebbar ◽  
El Mokhtar Essassi ◽  
Joel T. Mague
Keyword(s):  
Hydrogen Bond ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Thiazole Ring ◽  
Asymmetric Unit ◽  
Π Interactions ◽  
Compound C ◽  
Centroid Distance ◽  
Independent Molecules ◽  
And Inversion

The asymmetric unit of the title compound, C9H8N2S, consists of two independent molecules (AandB) differing in the conformation of the thiazole ring: twisted for moleculeAand planar for moleculeB. In the crystal, molecules stack along thecaxis in alternatingAandBlayers. Within the layers, molecules are linked by C—H...π interactions, and inversion-relatedBmolecules are linked by offset π–π interactions [inter-centroid distance = 3.716 (1) Å]. The two molecules are also linked by a C—H...N hydrogen bond, which results finally in the formation of a three-dimensional structure.

scholarly journals The mechanism of spray electrification: the waterfall effect

2016 ◽  
Author(s):  
James K. Beattie
Keyword(s):  
Negative Charge ◽  
Positive Charge ◽  
Hydrophobic Hydration ◽  
General Phenomenon ◽  
Aqueous Interfaces ◽  
Preferential Adsorption ◽  
Negative Surface ◽  
Negative Surface Charge ◽  
Low Permittivity ◽  
Net Positive Charge

Abstract. The waterfall effect describes the separation of charge by splashing at the base of a waterfall. Smaller drops that have a net negative charge are created, while larger drops and/or the bulk maintain overall charge neutrality with a net positive charge. Since it was first described by Lenard (1892) the effect has been confirmed many times, but a molecular explanation has not been available. Application of our fluctuation-correlation model of hydrophobic hydration accounts for the negative charge observed at aqueous interfaces with low permittivity materials. The negative surface charge observed in the waterfall effect is created by the preferential adsorption of hydroxide ions generated from the autolysis of water. On splashing, shear forces generate small negative drops from the surface, leaving a positive charge on the remaining large fragment. The waterfall effect is a manifestation of the general phenomenon of the negative charge at the interface between water and hydrophobic surfaces that is created by the preferential adsorption of hydroxide ions.

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