scholarly journals Tracking the Amide I and αCOO− Terminal ν(C=O) Raman Bands in a Family of l-Glutamic Acid-Containing Peptide Fragments: A Raman and DFT Study

Molecules ◽  
2021 ◽  
Vol 26 (16) ◽  
pp. 4790
Author(s):  
Ashley E. Williams ◽  
Nathan I. Hammer ◽  
Ryan C. Fortenberry ◽  
Dana N. Reinemann
Keyword(s):  
Hydrogen Bonding ◽  
Charge Transfer ◽  
Density Functional ◽  
Intramolecular Charge Transfer ◽  
Solid Phase ◽  
Intramolecular Hydrogen Bonding ◽  
Peptide Fragment ◽  
Peptide Fragments ◽  
Band Position ◽  
Intramolecular Hydrogen

The E-hook of β-tubulin plays instrumental roles in cytoskeletal regulation and function. The last six C-terminal residues of the βII isotype, a peptide of amino acid sequence EGEDEA, extend from the microtubule surface and have eluded characterization with classic X-ray crystallographic techniques. The band position of the characteristic amide I vibration of small peptide fragments is heavily dependent on the length of the peptide chain, the extent of intramolecular hydrogen bonding, and the overall polarity of the fragment. The dependence of the E residue’s amide I ν(C=O) and the αCOO− terminal ν(C=O) bands on the neighboring side chain, the length of the peptide fragment, and the extent of intramolecular hydrogen bonding in the structure are investigated here via the EGEDEA peptide. The hexapeptide is broken down into fragments increasing in size from dipeptides to hexapeptides, including EG, ED, EA, EGE, EDE, DEA, EGED, EDEA, EGEDE, GEDEA, and, finally, EGEDEA, which are investigated with experimental Raman spectroscopy and density functional theory (DFT) computations to model the zwitterionic crystalline solids (in vacuo). The molecular geometries and Boltzmann sum of the simulated Raman spectra for a set of energetic minima corresponding to each peptide fragment are computed with full geometry optimizations and corresponding harmonic vibrational frequency computations at the B3LYP/6-311++G(2df,2pd) level of theory. In absence of the crystal structure, geometry sampling is performed to approximate solid phase behavior. Natural bond order (NBO) analyses are performed on each energetic minimum to quantify the magnitude of the intramolecular hydrogen bonds. The extent of the intramolecular charge transfer is dependent on the overall polarity of the fragment considered, with larger and more polar fragments exhibiting the greatest extent of intramolecular charge transfer. A steady blue shift arises when considering the amide I band position moving linearly from ED to EDE to EDEA to GEDEA and, finally, to EGEDEA. However, little variation is observed in the αCOO− ν(C=O) band position in this family of fragments.

scholarly journals NMR of Natural Products as Potential Drugs

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3763
Author(s):  
Poul Erik Hansen
Keyword(s):  
Natural Products ◽  
Hydrogen Bonding ◽  
Density Functional ◽  
Chemical Shifts ◽  
Isotope Effects ◽  
Density Functional Theory Calculations ◽  
Intramolecular Hydrogen Bonding ◽  
Chemical Equilibria ◽  
Nmr Techniques ◽  
Intramolecular Hydrogen

This review outlines methods to investigate the structure of natural products with emphasis on intramolecular hydrogen bonding, tautomerism and ionic structures using NMR techniques. The focus is on 1H chemical shifts, isotope effects on chemical shifts and diffusion ordered spectroscopy. In addition, density functional theory calculations are performed to support NMR results. The review demonstrates how hydrogen bonding may lead to specific structures and how chemical equilibria, as well as tautomeric equilibria and ionic structures, can be detected. All these features are important for biological activity and a prerequisite for correct docking experiments and future use as drugs.

Switching On/Off the Intramolecular Hydrogen Bonding of 2-Methoxyphenol Conformers: An NMR Study

2020 ◽  
Vol 73 (3) ◽  
pp. 222
Author(s):  
Frederick Backler ◽  
Feng Wang
Keyword(s):  
Hydrogen Bonding ◽  
Chemical Shift ◽  
1H Nmr ◽  
Density Functional ◽  
Point Group ◽  
Decomposition Analysis ◽  
Intramolecular Hydrogen Bonding ◽  
Group Symmetry ◽  
Energy Decomposition Analysis ◽  
Intramolecular Hydrogen

Intramolecular hydrogen bonding of 2-methoxyphenol (2-MP, guaiacol) is studied using NMR spectroscopy combined with quantum mechanical density functional theory (DFT) calculations. The hydrogen bonding of OH⋯O and HO⋯H is switched on in the conformers of anti–syn (AS, 99.64% dominance) and anti–gauche (AG), respectively, with respect to the anti–anti (AA) conformer (without either such hydrogen bonding interactions). It confirms that the 13C and 1H NMR chemical shift of AS dominates the measured NMR spectra, as the AS conformer reproduces the measurements in CDCl3 solvent (RMSD of 1.86ppm for 13C NMR and of 0.27ppm for 1H NMR). The chemical shift of hydroxyl H(1) at 5.66 pm is identified as the fingerprint of the OH(1)⋯OCH3 hydrogen bonding in AS, as it exhibits a significant deshielding from H(1) of AA (4.24ppm) and H(1) of AG (4.38ppm) without such OH(1)⋯OCH3 hydrogen bonding. The AG conformer (C1 point group symmetry) possesses a less strong hydrogen bonding of HO⋯HCH2O, with the methoxyl group out of the aromatic phenol plane. The substituent effect of AG due to the resonance interaction of methoxyl being out of plane in a concentrated solution shifts the ortho- and para-aromatic carbons, C(3)/C(5), of the AG to ~125.05/125.44ppm from the corresponding carbons in AS at 108.81/121.60ppm. The hydrogen bonding exhibits inwards reduction of IR frequency regions of AS and AG from AA. Finally, energy decomposition analysis (EDA) indicates that there is a steric energy of 45.01kcal mol−1 between the AS and AG when different intramolecular hydrogen bonding is switched on.

CONFORMATIONAL PROPERTIES AND INTRAMOLECULAR HYDROGEN BONDING OF 3-AMINO-PROPENESELENAL: AN AB INITIO AND DENSITY FUNCTIONAL THEORY STUDIES

2013 ◽  
Vol 12 (04) ◽  
pp. 1350025 ◽  
Author(s):  
HEIDAR RAISSI ◽  
FARZANEH FARZAD ◽  
SHAHIRA ESLAMDOOST ◽  
FARIBA MOLLANIA
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bonding ◽  
Molecular Orbital ◽  
Continuum Model ◽  
Density Functional ◽  
Intramolecular Hydrogen Bonding ◽  
Stationary Points ◽  
Functional Theory ◽  
Polarized Continuum Model ◽  
Intramolecular Hydrogen

In the present work a conformational analysis of 3-amino-propeneselenal (APS) was performed using several computational methods, including DFT (B3LYP), MP2 and G2MP2. Harmonic vibrational frequencies were estimated at the same levels to confirm the nature of the stationary points found and also to account for the zero point vibrational energy (ZPVE) correction. Two intramolecular hydrogen bonds (HBs) established between the polar groups were identified by the structural geometric parameters. The excited-state properties of intramolecular hydrogen bonding in hydrogen bonded systems have been investigated theoretically using the time dependent density functional theory (TDDFT) method. The influence of the solvent on the stability order of conformers and the strength of intramolecular hydrogen bonding was considered using the polarized continuum model (PCM), the self-consistent isodensity polarized continuum model (SCI-PCM) and the integral equation formalism-polarizable continuum model (IEF-PCM) methods. The "atoms in molecules" theory of Bader was used to analyze critical points and to study the nature of HB in these systems. Natural bond orbital (NBO) analysis was also performed for better understanding the nature of intramolecular interactions. The calculated the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies show that charge transfer occur within the molecule. Further verification of the obtained transition state structures were implemented via intrinsic reaction coordinate (IRC) analysis. Calculations of the 1 H NMR chemical shift at GIAO/B3LYP/6–311++G** level of theory are also presented.

Molecular Conformational Analysis, Spectroscopic Characterization, Intramolecular Hydrogen Bonding and Natural Bond Analysis of (E,Z)-2-(4- Amino-5-oxo-3-(thiophene-2-ylmethyl)-4,5-dihydro-1,2,4-triazole-1-yl)-N'- (thiophene-2-ylmethylene) Acetohydrazide

2019 ◽  
Vol 16 (3) ◽  
pp. 215-225
Author(s):  
Abdurrahman Atalay ◽  
Fatih Çelik ◽  
Yasemin Ünver ◽  
Kemal Sancak ◽  
Kamil Kaygusuz
Keyword(s):  
Hydrogen Bonding ◽  
Density Functional ◽  
Structural Parameters ◽  
Intramolecular Hydrogen Bonding ◽  
Spectroscopic Characterization ◽  
Frontier Molecular Orbital ◽  
Hydrogen Bond Interaction ◽  
Ft Ir ◽  
Intramolecular Hydrogen ◽  
Theoretical Results

The optimized structural parameters and electronic properties including frontier molecular orbital (FMO) analysis, molecular electrostatic potential and NBO charge analysis of (E,Z)-2-(4- amino-5-oxo-3-(thiophene-2-ylmethyl)-4,5-dihydro-1,2,4-triazole-1-yl)-N'-(thiophene-2-ylmethylene) acetohydrazide were investigated by using density functional theory (DFT) at B3LYP/6-311++G(d,p) level. The global reactivity parameters were evaluated in accordance with the energy values of HOMO and LUMO of each determined conformer. The molecule was experimentally characterized by means of FT-IR and NMR spectroscopic methods and also theoretically by B3LYP/6-311++G(d,p) and B3LYP/cc-pVTZ method (FT-IR and NMR, respectively). The theoretical results of spectroscopic analysis show good agreement with experimental outcomes. The natural bond orbital (NBO) analyses for studied conformers were performed at B3LYP/6-311++G(d,p) level to find hyperconjugative interactions as well as intramolecular hydrogen bond interaction. Besides, theoretical results indicate that the optimized structure of conformer E and Z possesses N‒H···N and N‒H···S weak hydrogen bonding, respectively.

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