scholarly journals Amide Activation in Ground and Excited States

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2859 ◽  
Author(s):  
Ervin Kovács ◽  
Balázs Rózsa ◽  
Attila Csomos ◽  
Imre Csizmadia ◽  
Zoltán Mucsi
Keyword(s):  
Excited States ◽  
Amide Group ◽  
Amide Bond ◽  
Acyl Transfer ◽  
Biological Processes ◽  
Protein Splicing ◽  
Amide Bonds ◽  
Simple Quantum ◽  
Chemical Character ◽  
The Stability

Not all amide bonds are created equally. The purpose of the present paper is the reinterpretation of the amide group by means of two concepts: amidicity and carbonylicity. These concepts are meant to provide a new viewpoint in defining the stability and reactivity of amides. With the help of simple quantum-chemical calculations, practicing chemists can easily predict the outcome of a desired process. The main benefit of the concepts is their simplicity. They provide intuitive, but quasi-thermodynamic data, making them a practical rule of thumb for routine use. In the current paper we demonstrate the performance of our methods to describe the chemical character of an amide bond strength and the way of its activation methods. Examples include transamidation, acyl transfer and amide reductions. Also, the method is highly capable for simple interpretation of mechanisms for biological processes, such as protein splicing and drug mechanisms. Finally, we demonstrate how these methods can provide information about photo-activation of amides, through the examples of two caged neurotransmitter derivatives.

scholarly journals Quantum-mechanical hydration plays critical role in the stability of firefly oxyluciferin isomers: State-of-the-art calculations of the excited states

2020 ◽  
Vol 153 (20) ◽  
pp. 201103
Author(s):  
Yoshifumi Noguchi ◽  
Miyabi Hiyama ◽  
Motoyuki Shiga ◽  
Hidefumi Akiyama ◽  
Osamu Sugino
Keyword(s):  
Excited States ◽  
State Of The Art ◽  
Critical Role ◽  
Quantum Mechanical ◽  
The Stability

scholarly journals Engineering motile aqueous phase-separated droplets via liposome stabilisation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shaobin Zhang ◽  
Claudia Contini ◽  
James W. Hindley ◽  
Guido Bolognesi ◽  
Yuval Elani ◽  
...  
Keyword(s):  
Aqueous Phase ◽  
Marangoni Effect ◽  
Living Systems ◽  
Biological Processes ◽  
Biological Applications ◽  
Emulsion System ◽  
Biotechnological Potential ◽  
New Directions ◽  
Directional Motion ◽  
The Stability

AbstractThere are increasing efforts to engineer functional compartments that mimic cellular behaviours from the bottom-up. One behaviour that is receiving particular attention is motility, due to its biotechnological potential and ubiquity in living systems. Many existing platforms make use of the Marangoni effect to achieve motion in water/oil (w/o) droplet systems. However, most of these systems are unsuitable for biological applications due to biocompatibility issues caused by the presence of oil phases. Here we report a biocompatible all aqueous (w/w) PEG/dextran Pickering-like emulsion system consisting of liposome-stabilised cell-sized droplets, where the stability can be easily tuned by adjusting liposome composition and concentration. We demonstrate that the compartments are capable of negative chemotaxis: these droplets can respond to a PEG/dextran polymer gradient through directional motion down to the gradient. The biocompatibility, motility and partitioning abilities of this droplet system offers new directions to pursue research in motion-related biological processes.

scholarly journals 1,2,3-Triazoles as Biomimetics in Peptide Science

Molecules ◽  
2021 ◽  
Vol 26 (10) ◽  
pp. 2937
Author(s):  
Naima Agouram ◽  
El Mestafa El Hadrami ◽  
Abdeslem Bentama
Keyword(s):  
Enzymatic Degradation ◽  
Triazole Ring ◽  
Biologically Active ◽  
Amide Bond ◽  
Biologically Relevant ◽  
Amide Bonds ◽  
Natural Peptides ◽  
Mimicking Peptides ◽  
Chemical Mediators

Natural peptides are an important class of chemical mediators, essential for most vital processes. What limits the potential of the use of peptides as drugs is their low bioavailability and enzymatic degradation in vivo. To overcome this limitation, the development of new molecules mimicking peptides is of great importance for the development of new biologically active molecules. Therefore, replacing the amide bond in a peptide with a heterocyclic bioisostere, such as the 1,2,3-triazole ring, can be considered an effective solution for the synthesis of biologically relevant peptidomimetics. These 1,2,3-triazoles may have an interesting biological activity, because they behave as rigid link units, which can mimic the electronic properties of amide bonds and show bioisosteric effects. Additionally, triazole can be used as a linker moiety to link peptides to other functional groups.

Correlation of the solid-state reactivities of racemic 2,4(6)-di-O-benzoyl-myo-inositol 1,3,5-orthoformate and its 4,4′-bipyridine cocrystal with their crystal structures

2014 ◽  
Vol 70 (11) ◽  
pp. 1040-1045 ◽  
Author(s):  
Majid I. Tamboli ◽  
Vir Bahadur ◽  
Rajesh G. Gonnade ◽  
Mysore S. Shashidhar
Keyword(s):  
Solid State ◽  
Self Assembly ◽  
Transfer Reaction ◽  
Acyl Transfer ◽  
Transfer Reactions ◽  
Group Transfer ◽  
Hydrogen Bonding Interactions ◽  
Benzoyl Group ◽  
The Stability ◽  
Group Migration

Racemic 2,4(6)-di-O-benzoyl-myo-inositol 1,3,5-orthoformate, C21H18O8,(1), shows a very efficient intermolecular benzoyl-group migration reaction in its crystals. However, the presence of 4,4′-bipyridine molecules in its cocrystal, C21H18O8·C10H8N2,(1)·BP, inhibits the intermolecular benzoyl-group transfer reaction. In(1), molecules are assembled around the crystallographic twofold screw axis (baxis) to form a helical self-assembly through conventional O—H...O hydrogen-bonding interactions. This helical association places the reactive C6-O-benzoyl group (electrophile, El) and the C4-hydroxy group (nucleophile, Nu) in proximity, with a preorganized El...Nu geometry favourable for the acyl transfer reaction. In the cocrystal(1)·BP, the dibenzoate and bipyridine molecules are arranged alternately through O—H...N interactions. The presence of the bipyridine molecules perturbs the regular helical assembly of the dibenzoate molecules and thus restricts the solid-state reactivity. Hence, unlike the parent dibenzoate crystals, the cocrystals do not exhibit benzoyl-transfer reactions. This approach is useful for increasing the stability of small molecules in the crystalline state and could find application in the design of functional solids.

scholarly journals Electronic Effect on the Molecular Motion of Aromatic Amides: Combined Studies Using VT-NMR and Quantum Calculations

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2294 ◽  
Author(s):  
Sungsoo Kim ◽  
Jungyu Kim ◽  
Jieun Kim ◽  
Daeun Won ◽  
Suk-Kyu Chang ◽  
...  
Keyword(s):  
Aromatic Compounds ◽  
Density Functional ◽  
Electronic Effect ◽  
Variable Temperature ◽  
Rotational Barrier ◽  
Amide Bond ◽  
Theoretical Research ◽  
Quantum Calculations ◽  
Amide Bonds ◽  
Barrier Energy

Rotational barrier energy studies to date have focused on the amide bond of aromatic compounds from a kinetic perspective using quantum calculations and nuclear magnetic resonance (NMR). These studies provide valuable information, not only regarding the basic conformational properties of amide bonds but also the molecular gear system, which has recently gained interest. Thus, we investigate the precise motion of the amide bonds of two aromatic compounds using an experimental rotational barrier energy estimation by NMR experiments and a theoretical evaluation of the density functional theory calculation. The theoretical potential energy surface scan method combined with the quadratic synchronous transit 3 method and consideration of additional functional group rotation with optimization and frequency calculations support the results of the variable temperature 1H NMR, with deviations of less than 1 kcal/mol. This detailed experimental and theoretical research strongly supports molecular gear motion in the aromatic amide system, and the difference in kinetic energy indicates that the electronic effect from the aromatic structure has a key role in conformational movements at different temperatures. Our study provides an enhanced basis for future amide structural dynamics research.

Are the amide bonds in N-acyl imidazoles twisted? A combined solid-state 17O NMR, crystallographic, and computational study

2015 ◽  
Vol 93 (4) ◽  
pp. 451-458 ◽  
Author(s):  
Xianqi Kong ◽  
Aaron Tang ◽  
Ruiyao Wang ◽  
Eric Ye ◽  
Victor Terskikh ◽  
...  
Keyword(s):  
Solid State ◽  
Chemical Shift ◽  
Crystal Structures ◽  
Computational Study ◽  
Chemical Shifts ◽  
Amide Bond ◽  
Chemical Shift Tensors ◽  
Amide Bonds ◽  
Bond Rotation ◽  
Quadrupole Coupling

We report synthesis of 17O-labeling and solid-state 17O NMR measurements of three N-acyl imidazoles of the type R-C(17O)-Im: R = p-methoxycinnamoyl (MCA-Im), R = 4-(dimethylamino)benzoyl (DAB-Im), and R = 2,4,6-trimethylbenzoyl (TMB-Im). Solid-state 17O NMR experiments allowed us to determine for the first time the 17O quadrupole coupling and chemical shift tensors in this class of organic compounds. We also determined the crystal structures of these compounds using single-crystal X-ray diffraction. The crystal structures show that, while the C(O)–N amide bond in DAB-Im exhibits a small twist, those in MCA-Im and TMB-Im are essentially planar. We found that, in these N-acyl imidazoles, the 17O quadrupole coupling and chemical shift tensors depend critically on the torsion angle between the conjugated acyl group and the C(O)–N amide plane. The computational results from a plane-wave DFT approach, which takes into consideration the entire crystal lattice, are in excellent agreement with the experimental solid-state 17O NMR results. Quantum chemical computations also show that the dependence of 17O NMR parameters on the Ar–C(O) bond rotation is very similar to that previously observed for the C(O)–N bond rotation in twisted amides. We conclude that one should be cautious in linking the observed NMR chemical shifts only to the twist of the C(O)–N amide bond.

Impact of N-(2-aminoethyl) Glycine Unit on Watson-Crick Base Pairs

2019 ◽  
Vol 233 (3) ◽  
pp. 449-469 ◽  
Author(s):  
Indumathi Karunakaran ◽  
Abiram Angamuthu ◽  
Praveena Gopalan
Keyword(s):  
Density Functional ◽  
Structural Parameters ◽  
Base Pairs ◽  
Functional Theory ◽  
Amide Bonds ◽  
Highest Occupied Molecular Orbital ◽  
Minimal Distortion ◽  
Stabilization Energies ◽  
The Stability ◽  
Lowest Unoccupied Molecular Orbitals

Abstract We aim to understand the structure and stability of the backbone tailored Watson-Crick base pairs, Guanine-Cytosine (GC), Adenine-Thymine (AT) and Adenine-Uracil (AU) by incorporating N-(2-aminoethyl) glycine units (linked by amide bonds) at the purine and pyrimidine sites of the nucleobases. Density functional theory (DFT) is employed in which B3LYP/6-311++G∗∗ level of theory has been used to optimize all the structures. The peptide attached base pairs are compared with the natural deoxyribose nucleic acid (DNA)/ribonucleic acid (RNA) base pairs and the calculations are carried out in both the gas and solution phases. The structural propensities of the optimized base pairs are analyzed using base pair geometries, hydrogen bond distances and stabilization energies and, compared with the standard reference data. The structural parameters were found to correlate well with the available data. The addition of peptide chain at the back bone of the DNA/RNA base pairs results only with a minimal distortion and hence does not alter the structural configuration of the base pairs. Also enhanced stability of the base pairs is spotted while adding peptidic chain at the purine site rather than the pyrimidine site of the nucleobases. The stability of the complexes is further interpreted by considering the hydrogen bonded N–H stretching frequencies of the respective base pairs. The discrimination in the interaction energies observed in both gas and solution phases are resulted due to the existence of distinct lowest unoccupied molecular orbitals (LUMO) in the solution phase. The reactivity of the base pairs is also analyzed through the in-depth examinations on the highest occupied molecular orbital (HOMO)-LUMO orbitals.

“Calix[4]-box” cages promote the formation of amide bonds in water in the absence of coupling reagents

2018 ◽  
Vol 54 (70) ◽  
pp. 9738-9740 ◽  
Author(s):  
Wei-Xu Feng ◽  
Liya Dai ◽  
Shao-Ping Zheng ◽  
Arie van der Lee ◽  
Cheng-Yong Su ◽  
...  
Keyword(s):  
Template Synthesis ◽  
Bond Formation ◽  
Amide Bond ◽  
Coupling Reagents ◽  
Amide Bonds ◽  
Amide Bond Formation

Calix[4]box cages promote template synthesis via accelerated amide bond formation upon encapsulation in water.

Ternary Complexes in Solution, XII. Models for Biological Mixed-Ligand Complexes: 2,2′-Bipyridyl-Cu2+-Oligoglycine Systems

1972 ◽  
Vol 27 (4) ◽  
pp. 353-364 ◽  
Author(s):  
Helmut Sigel ◽  
Rolf Griesser ◽  
Bernhard Prijs
Keyword(s):  
Coordination Sphere ◽  
Ternary Complexes ◽  
Mixed Ligand ◽  
Amide Group ◽  
Amide Proton ◽  
Mixed Ligand Complexes ◽  
Apical Position ◽  
Binary Complexes ◽  
The Stability ◽  
Ph Range

The stability constants of the binary Cu2+ complexes of glycine amide, diglycine, diglycine amide, triglycine, and tetraglycine were determined, as were those of the mixed-ligand Cu2+ systems containing 2,2′-bipyridyl and one of the mentioned oligoglycines. The results evidence that all these complexes have the same structure and, therefore, the binding sites of the ligands have to be the terminal amino group and the oxygen of the neighbored amide group. The stability differences between the ternary and the binary complexes are in agreement with this interpretation. It is of interest to note that these ternary complexes are significantly more stable than expected on statistical reasons. With increasing pH, the amide groups in the binary complexes are successively deprotonated. Thus, with tetraglycine finally all three amide protons are displaced, and the amide nitrogens are bound to the square-planar coordination sphere of Cu2+. As in the Cu2+-2,2′-bipyridyl 1 : 1 complex, only two coordination positions are left for the binding of the oligoglycine, in the tenary complexes, only one amide group can be deprotonated. An increase in pH with deprotonation of other amide groups leads to a displacement of 2,2′-bipyridyl, i. e. the simple binary complexes result. No evidence could be observed for the coordination of a deprotonated amide group to an apical position of the coordination sphere of Cu2+. Additionally, while the displacement of the first amide proton in the several binary Cu2+ oligoglycine complexes occurs over a large pH range (4 to 7), the deprotonation in all the mixed-ligand complexes takes place at pH approximately 8.

scholarly journals Substituierte 2-Bromacetessigsäure-Amide als Chelatbildner

1970 ◽  
Vol 25 (12) ◽  
pp. 1382-1385 ◽  
Author(s):  
A. Kettrup ◽  
J. Abshagen
Keyword(s):  
Stability Constants ◽  
Amide Group ◽  
Ph Measurements ◽  
The Stability ◽  
Copper Chelates

The preparation of 2-bromacetoacetamides and their copper chelates is described. The stability constants of these compounds were determined by potentiometric pH-measurements. The change of stability constants by the substituents of the amide group is interpreted

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