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The hybridized nitrogen atom in amines possesses a lone pair of electrons and is bound to three substituents with a bond angle of around 108°, which is less than the tetrahedral angle of 109.5°. However, the C–N–H bond angle is slightly larger at 112°, with a carbon–nitrogen bond length of 147 pm. This carbon–nitrogen bond length of of amines is longer than the carbon–oxygen bond of alcohols (143 pm) but shorter than alkanes’...
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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
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A type of Lewis acid-base chemistry involves the formation of a complex ion (or a coordination complex) comprising a central atom, typically a transition metal cation, surrounded by ions or molecules called ligands. These ligands can be neutral molecules like H2O or NH3, or ions such as CN− or OH−. Often, the ligands act as Lewis bases, donating a pair of electrons to the central atom. These types of Lewis acid-base reactions are examples of a broad subdiscipline called coordination...
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The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
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Conformational Analysis of Neutral and Ionic Arginine Forms Using DFT Methods.

Fulya Çağlar1,2, Gözde Aksoy3, Cenk Selçuki1,3

  • 1Department of Health Bioinformatics, Institute of Health Sciences, Ege University, 35040 Bornova, Izmir, Turkey.

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Summary

Arginine (Arg) conformers were investigated using density functional theory (DFT). New stable Arg conformers were identified in both aqueous and gas phases, advancing our understanding of this essential amino acid.

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Area of Science:

  • Biochemistry
  • Computational Chemistry

Background:

  • Arginine (Arg) is an essential amino acid crucial for protein charge balance and function.
  • Its guanidino side chain influences protein folding, solubility, and interactions.
  • A comprehensive understanding of all Arg forms and their roles is lacking.

Purpose of the Study:

  • To investigate all possible conformers of various arginine forms.
  • To utilize density functional theory (DFT) for analysis in both aqueous and gas phases.
  • To identify novel stable conformers and understand their structural and energetic properties.

Main Methods:

  • Conformational analysis using Spartan'16 software.
  • Geometry optimization via DFT with ωB97XD and B3LYP functionals and 6-311++G-(d,p) basis set.
  • Reoptimization using MP2/6-311++G-(d,p) and frequency analysis to verify stability.

Main Results:

  • New stable conformers for arginine were identified in vacuum and aqueous environments.
  • Some zwitterionic and cationic Arg forms were found to be unstable, converting to other forms.
  • Previously unreported conformations of cationic Arg were calculated.

Conclusions:

  • The study provides new insights into the structural diversity of arginine conformers.
  • DFT calculations reveal the stability and transformations of different Arg ionic forms.
  • This research contributes to a more complete understanding of arginine's role in biological systems.