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.

scholarly journals Density Functional Studies on Secondary Amides: Role of Steric Factors in Cis/Trans Isomerization

Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2455 ◽  
Author(s):  
Balmukund Thakkar ◽  
John Svendsen ◽  
Richard Engh
Keyword(s):  
Density Functional ◽  
Amide Bond ◽  
Steric Effects ◽  
Amide Bonds ◽  
Functional Studies ◽  
Bond Rotation ◽  
Trans Isomerization ◽  
Wide Range ◽  
Potential Applications ◽  
Secondary Amides

Cis/trans isomerization of amide bonds is a key step in a wide range of biological and synthetic processes. Occurring through C-N amide bond rotation, it also coincides with the activation of amides in enzymatic hydrolysis. In recently described QM studies of cis/trans isomerization in secondary amides using density functional methods, we highlighted that a peptidic prototype, such as glycylglycine methyl ester, can suitably represent the isomerization and complexities arising out of a larger molecular backbone, and can serve as the primary scaffold for model structures with different substitution patterns in order to assess and compare the steric effect of the substitution patterns. Here, we describe our theoretical assessment of such steric effects using tert-butyl as a representative bulky substitution. We analyze the geometries and relative stabilities of both trans and cis isomers, and effects on the cis/trans isomerization barrier. We also use the additivity principle to calculate absolute steric effects with a gradual increase in bulk. The study establishes that bulky substitutions significantly destabilize cis isomers and also increases the isomerization barrier, thereby synergistically hindering the cis/trans isomerization of secondary amides. These results provide a basis for the rationalization of kinetic and thermodynamic properties of peptides with potential applications in synthetic and medicinal chemistry.

scholarly journals An ab-initio study of pyrrole and imidazole arylamides

2013 ◽  
Vol 78 (11) ◽  
pp. 1789-1795
Author(s):  
Ara Abramyan ◽  
Zhiwei Liu ◽  
Vojislava Pophristic
Keyword(s):  
Dna Binding ◽  
Force Field ◽  
Dna Sequences ◽  
Density Functional ◽  
Md Simulations ◽  
Building Blocks ◽  
Amide Bond ◽  
Amide Bonds ◽  
Force Field Parameters ◽  
Arylamide Foldamers

Arylamide foldamers have been shown to have a number of biological and medicinal applications. For example, a class of pyrrole-imidazole polyamide foldamers is capable of binding specific DNA sequences and preventing development of various gene disorders, most importantly cancer. Molecular dynamics (MD) simulations can provide crucial details in understanding the atomic level events related to foldamer/DNA binding. An important first step in the accurate simulation of these foldamer/DNA systems is the reparametrization of force field parameters for torsion around the aryl-amide bonds. Here we highlight our Density Functional Theory (DFT) potential energy profiles and derived force field parameters for four aryl-amide bond types for the pyrrole and imidazole building blocks extensively used in foldamer design for the DNA-binding polyamides. These results contribute to developing of computational tools for an appropriate molecular modeling of pyrrole-imidazole polyamide/DNA binding, and provide an insight into the chemical factors that influence the flexibility of the pyrrole-imidazole polyamides, and their binding to DNA.

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.

scholarly journals Catalyzed Ethanol Chemical Looping Gasification Mechanism on the Perfect and Reduced Fe2O3 Surfaces

Energies ◽  
2021 ◽  
Vol 14 (6) ◽  
pp. 1663
Author(s):  
Laixing Luo ◽  
Xing Zheng ◽  
Jianye Wang ◽  
Wu Qin ◽  
Xianbin Xiao ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Reaction Mechanism ◽  
Density Functional ◽  
Oxygen Carrier ◽  
Catalytic Decomposition ◽  
Density Functional Theory Calculations ◽  
Chemical Looping ◽  
Functional Theory ◽  
Barrier Energy ◽  
Gasification Technology

Biomass chemical looping gasification (CLG) is a novel gasification technology for hydrogen production, where the oxygen carrier (OC) transfers lattice oxygen to catalytically oxidize fuel into syngas. However, the OC is gradually reduced, showing different reaction activities in the CLG process. Fully understanding the CLG reaction mechanism of fuel molecules on perfect and reduced OC surfaces is necessary, for which the CLG of ethanol using Fe2O3 as the OC was introduced as the probe reaction to perform density functional theory calculations to reveal the decomposition mechanism of ethanol into the synthesis gas (including H2, CH4, ethylene, formaldehyde, acetaldehyde, and CO) on perfect and reduced Fe2O3(001) surfaces. When Fe2O3(001) is reduced to FeO0.375(001), the calculated barrier energy decreases and then increases again, suggesting that the reduction state around FeO(001) favors the catalytic decomposition of ethanol to produce hydrogen, which proves that the degree of reduction has an important effect on the CLG reaction.

scholarly journals Investigation of Solvatomorphism and Its Photophysical Implications for Archetypal Trinuclear Au3(1-Methylimidazolate)3

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4404
Author(s):  
Shengyang Guan ◽  
David C. Mayer ◽  
Christian Jandl ◽  
Sebastian J. Weishäupl ◽  
Angela Casini ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Density Functional ◽  
Bulk Material ◽  
Variable Temperature ◽  
Active Phase ◽  
Solvent Free ◽  
X Ray Diffraction ◽  
X Ray ◽  
Aurophilic Interactions

A new solvatomorph of [Au3(1-Methylimidazolate)3] (Au3(MeIm)3)—the simplest congener of imidazolate-based Au(I) cyclic trinuclear complexes (CTCs)—has been identified and structurally characterized. Single-crystal X-ray diffraction revealed a dichloromethane solvate exhibiting remarkably short intermolecular Au⋯Au distances (3.2190(7) Å). This goes along with a dimer formation in the solid state, which is not observed in a previously reported solvent-free crystal structure. Hirshfeld analysis, in combination with density functional theory (DFT) calculations, indicates that the dimerization is generally driven by attractive aurophilic interactions, which are commonly associated with the luminescence properties of CTCs. Since Au3(MeIm)3 has previously been reported to be emissive in the solid-state, we conducted a thorough photophysical study combined with phase analysis by means of powder X-ray diffraction (PXRD), to correctly attribute the photophysically active phase of the bulk material. Interestingly, all investigated powder samples accessed via different preparation methods can be assigned to the pristine solvent-free crystal structure, showing no aurophilic interactions. Finally, the observed strong thermochromism of the solid-state material was investigated by means of variable-temperature PXRD, ruling out a significant phase transition being responsible for the drastic change of the emission properties (hypsochromic shift from 710 nm to 510 nm) when lowering the temperature down to 77 K.

scholarly journals New Volatile Perfluorinated Amidine–Carboxylate Copper(II) Complexes as Promising Precursors in CVD and FEBID Methods

Materials ◽  
2021 ◽  
Vol 14 (12) ◽  
pp. 3145
Author(s):  
Katarzyna Madajska ◽  
Iwona Barbara Szymańska
Keyword(s):  
Electron Microscopy ◽  
Mass Spectrometry ◽  
Electron Beam ◽  
Infrared Spectroscopy ◽  
Density Functional ◽  
Variable Temperature ◽  
Chemical Vapour ◽  
Thermal Decomposition Mechanism ◽  
Transmission Electron Microscopy Analysis ◽  
Reduced Pressure

In the present study, we have synthesised and characterised newly copper(II) complexes with the general formula [Cu2(NH2(NH=)CC2F5)2(µ–O2CCRF)4], where RF = CF3, C2F5, C3F7, C4F9. Infrared spectroscopy, mass spectrometry with electron ionisation (EI MS), and density-functional theory (DFT) calculations were used to confirm compounds’ composition and structure. The volatility of the compounds was studied using thermal analysis (TGA), EI MS mass spectrometry, variable temperature infrared spectroscopy (VT IR), and sublimation experiments. Research has revealed that these compounds are the source of metal carriers in the gas phase. The thermal decomposition mechanism over reduced pressure was proposed. TGA studies demonstrated that copper transfer to the gaseous phase occurs even at atmospheric pressure. Two selected complexes [Cu2(NH2(NH=)CC2F5)2(µ–O2CC2F5)4] and [Cu2(NH2(NH=)CC2F5)2(µ–O2CC3F7)4] were successful used as chemical vapour deposition precursors. Copper films were deposited with an evaporation temperature of 393 K and 453 K, respectively, and a decomposition temperature in the range of 573–633 K without the use of hydrogen. The microscopic observations made to investigate the interaction of the [Cu2(NH2(NH=)CC2F5)2(µ–O2CC2F5)4] with the electron beam showed that the ligands are completely lost under transmission electron microscopy analysis conditions (200 keV), and the final product is copper(II) fluoride. In contrast, the beam energy in scanning electron microscopy (28 keV) was insufficient to break all coordination bonds. It was shown that the Cu-O bond is more sensitive to the electron beam than the Cu-N bond.

Development of Divide‐and‐Conquer Density‐Functional Tight‐Binding Method for Theoretical Research on Li‐Ion Battery

2018 ◽  
Vol 19 (4) ◽  
pp. 746-757 ◽  
Author(s):  
Chien‐Pin Chou ◽  
Aditya Wibawa Sakti ◽  
Yoshifumi Nishimura ◽  
Hiromi Nakai
Keyword(s):  
Density Functional ◽  
Tight Binding ◽  
Divide And Conquer ◽  
Theoretical Research ◽  
Li Ion Battery ◽  
Tight Binding Method ◽  
Li Ion

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.

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