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 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.

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.

Prediction of Giant Piezoelectric Properties in Puckered Two-Dimensional Monolayers: SiTe, GeTe, SnTe

2020 ◽  
Vol 15 (12) ◽  
pp. 1436-1441
Author(s):  
Tao Zhang ◽  
Jing Xu ◽  
Ming-Lin Li
Keyword(s):  
Density Functional ◽  
Piezoelectric Properties ◽  
Berry Phase ◽  
Group Iv ◽  
Two Dimensional ◽  
Density Functional Perturbation Theory ◽  
Wide Range ◽  
Potential Applications ◽  
Polarization Theory ◽  
2D Nanomaterials

The discovery of intrinsic piezoelectricity in two-dimensional (2D) nanomaterials (NDs) have increasingly attracted extensive interests for their potential applications in next generation piezoelectric devices. Among a wide range of 2D NDs, monolayer group IV monochalcogenides with black phosphorus like structures have been revealed to have giant piezoelectricity. In this letter, the piezoelectricity of puckered group IV monochalcogenides monolayer NDs, i.e., GeTe, SnTe, and SiTe, is first calculated by using the density functional first-principles theory. The lattice structures, band structures, and elastic properties of these puckered monolayer NDs (GeTe, SnTe, and SiTe) are evaluated based on the PBE functional. ?Berry-phase? polarization theory and density functional perturbation theory (DFPT) are respectively used for calculating the piezoelectric coefficients. It is found that all these puckered monolayer NDs (GeTe, SnTe, and SiTe) exhibit highly strong piezoelectric properties. The calculated superior piezoelectricity makes these puckered monolayer NDs promising applications in the nanoscale flexible electronic and energy transfer devices.

Intrinsic Stacking Interactions of Natural and Artificial Nucleobases

2019 ◽  
Author(s):  
Drew P. Harding ◽  
Laura J. Kingsley ◽  
Glen Spraggon ◽  
Steven Wheeler
Keyword(s):  
Gas Phase ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Molecular Descriptors ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Functional Theory ◽  
Binding Partner ◽  
Heavy Atoms ◽  
Wide Range

The intrinsic (gas-phase) stacking energies of natural and artificial nucleobases were explored using density functional theory (DFT) and correlated ab initio methods. Ranking the stacking strength of natural nucleobase dimers revealed a preference in binding partner similar to that seen from experiments, namely G > C > A > T > U. Decomposition of these interaction energies using symmetry-adapted perturbation theory (SAPT) showed that these dispersion dominated interactions are modulated by electrostatics. Artificial nucleobases showed a similar stacking preference for natural nucleobases and were also modulated by electrostatic interactions. A robust predictive multivariate model was developed that quantitively predicts the maximum stacking interaction between natural and a wide range of artificial nucleobases using molecular descriptors based on computed electrostatic potentials (ESPs) and the number of heavy atoms. This model should find utility in designing artificial nucleobase analogs that exhibit stacking interactions comparable to those of natural nucleobases. Further analysis of the descriptors in this model unveil the origin of superior stacking abilities of certain nucleobases, including cytosine and guanine.

Efficient Prediction of Structural and Electronic Properties of Hybrid 2D Materials Using DFT and Machine Learning

2018 ◽  
Author(s):  
Sherif Tawfik ◽  
Olexandr Isayev ◽  
Catherine Stampfl ◽  
Joseph Shapter ◽  
David Winkler ◽  
...  
Keyword(s):  
Machine Learning ◽  
Band Gap ◽  
Density Functional ◽  
2D Materials ◽  
Van Der Waals ◽  
Building Blocks ◽  
Machine Learning Techniques ◽  
Interlayer Distance ◽  
Computational Screening ◽  
Wide Range

Materials constructed from different van der Waals two-dimensional (2D) heterostructures offer a wide range of benefits, but these systems have been little studied because of their experimental and computational complextiy, and because of the very large number of possible combinations of 2D building blocks. The simulation of the interface between two different 2D materials is computationally challenging due to the lattice mismatch problem, which sometimes necessitates the creation of very large simulation cells for performing density-functional theory (DFT) calculations. Here we use a combination of DFT, linear regression and machine learning techniques in order to rapidly determine the interlayer distance between two different 2D heterostructures that are stacked in a bilayer heterostructure, as well as the band gap of the bilayer. Our work provides an excellent proof of concept by quickly and accurately predicting a structural property (the interlayer distance) and an electronic property (the band gap) for a large number of hybrid 2D materials. This work paves the way for rapid computational screening of the vast parameter space of van der Waals heterostructures to identify new hybrid materials with useful and interesting properties.

Electronic or steric effects: Detailed DFT investigations of titanium amino based Kaminsky type olefin catalysts

2018 ◽  
Author(s):  
Jörg Saßmannshausen
Keyword(s):  
Density Functional Theory ◽  
Strong Correlation ◽  
Density Functional ◽  
Steric Effects ◽  
Aryl Group ◽  
Functional Theory

We report detailed Density Functional Theory (DFT) investigations of a series of structurally similar titanium (IV) chelating σ-aryl catalysts. Particular attention was paid to the electronic charges of the Ti, C ipso of the substituted aryl group and the benzylic CH<sub>2</sub> and C<i><sub>ipso</sub></i> atoms. The Bader and NBO derived charges were compared with the recently reported polymerisation results by Chan. We found a strong correlation between the relative energies of one of the computed isomers and the activity of the catalyst. Neither NBO nor Bader charges could be convincingly correlated to the observed activity.

Ab initio calculation on the Optical Properties of AA- Stacked two dimensional Graphene, Silicene, Germanene, and Stanene

2018 ◽  
Vol 1 (1) ◽  
pp. 46-50
Author(s):  
Rita John ◽  
Benita Merlin
Keyword(s):  
Optical Properties ◽  
Band Structure ◽  
Density Functional ◽  
Electronic Band Structure ◽  
Complex Refractive Index ◽  
Single Layer ◽  
Generalized Gradient ◽  
Electronic Band ◽  
Wide Range ◽  
Optical Region

In this study, we have analyzed the electronic band structure and optical properties of AA-stacked bilayer graphene and its 2D analogues and compared the results with single layers. The calculations have been done using Density Functional Theory with Generalized Gradient Approximation as exchange correlation potential as in CASTEP. The study on electronic band structure shows the splitting of valence and conduction bands. A band gap of 0.342eV in graphene and an infinitesimally small gap in other 2D materials are generated. Similar to a single layer, AA-stacked bilayer materials also exhibit excellent optical properties throughout the optical region from infrared to ultraviolet. Optical properties are studied along both parallel (||) and perpendicular ( ) polarization directions. The complex dielectric function (ε) and the complex refractive index (N) are calculated. The calculated values of ε and N enable us to analyze optical absorption, reflectivity, conductivity, and the electron loss function. Inferences from the study of optical properties are presented. In general the optical properties are found to be enhanced compared to its corresponding single layer. The further study brings out greater inferences towards their direct application in the optical industry through a wide range of the optical spectrum.

Sign in / Sign up

Export Citation Format

Share Document