This document summarizes research on glycine molecules confined inside fullerene cages. The researchers used density functional theory to optimize molecular geometries and electronic structures of glycine in different confinement environments. They found that confinement led to variations in bond lengths and angles compared to isolated glycine. Specifically, one conformer of glycine was observed to change into a zwitterion structure inside one cage due to proton transfer. Overall, confinement had notable impacts on the molecular structure of glycine.

1. ENDOHEDRAL BIO-MOLECULES
Date: 29, April, 2022 Central
University
of Jammu
Department of Chemistry
and Chemical Sciences.
Zeeshan Nazir 3940319

2. Table of Contents
• Structure of Glycine (gly)
• Confined structures
• Effect of Confinement on bond length
• Effect of Confinement on bond angle
• Confined vs Isolated Glycine
2

3. Structure of Glycine
Grey = Carbon
Red = Oxygen
Blue = Nitrogen
White = Hydrogen
Image reference: https://pubchem.ncbi.nlm.nih.gov/compound/Glycine
3
Animation reference: https://pubchem.ncbi.nlm.nih.gov/compound/Glycine

4. Molecular geometries and electronic structures were optimised using DFT theory.
Method: M06-2X
Basis set: 6-311G (d,p)
“To handle dispersion effects correctly.”

5. 5
A
Image reference: M. Shahamirian,S.M.Azami 1

6. 6
B
Image reference: M. Shahamirian,S.M.Azami 1

7. 7
C
Image reference: M. Shahamirian,S.M.Azami 1

8. 8
D
Image reference: M. Shahamirian,S.M.Azami 1

9. 9
E
Image reference: M. Shahamirian,S.M.Azami 1

10. Variations in bond lengths (Å)
10
Arelaxed Aconfined Brelaxed Bconfined Crelaxed Cconfined Drelaxed Dconfined Erelaxed Econfined
rN-H 1.01 0.97 1.01 1.00 1.01 1.00 1.01 0.97 1.01 1.00
rC-H 1.09 1.04 1.09 1.04 1.09 1.04 1.09 1.04 1.10 1.04
rO-H 0.98 1.01 0.97 0.96 0.98 - 0.97 0.96 0.96 0.96
rC-N 1.46 1.43 1.45 1.42 1.46 1.43 1.45 1.43 1.44 1.42
rC-C 1.53 1.40 1.52 1.39 1.53 1.43 1.51 1.39 1.53 1.39
rC=O 1.19 1.17 1.20 1.18 1.19 1.21 1.20 1.18 1.19 1.17
rC-O 1.33 1.29 1.35 1.28 1.33 1.21 1.34 1.27 1.35 1.17
M. Shahamirian,S.M.Azami, Encapsulation of glycine inside C60 fullerene: Impact of confinement 1

11. Variations in bond angles (◦
)
11
Arelaxed Aconfined Brelaxed Bconfined Crelaxed Cconfined Drelaxed Dconfined Erelaxed Econfined
∠HNH 107.67 109.26 105.97 106.15 107.67 111.10 108.32 109.09 105.13 103.92
∠HCH 107.21 109.26 105.67 120.92 107.21 121.46 106.79 121.05 106.23 118.69
∠NCC 111.01 88.54 118.24 89.44 111.01 88.08 109.64 85.54 114.80 90.33
∠OCO 123.61 123.48 122.76 122.37 123.61 128.26 123.19 123.33 120.87 121.38
∠HOC 105.89 96.17 106.55 103.53 105.89 - 107.03 103.16 110.33 107.62
M. Shahamirian,S.M.Azami, Encapsulation of glycine inside C60 fullerene: Impact of confinement 1

12. Unusual behaviour of ‘C’ conformer
12
Dramatic decrease in C-O bond length (1.33 Å to 1.21 Å)
Unusual increase in OCO bond angle (123.60 to 128.260 )
Reason being: glycine (C) changes to zwitter-ion upon confinement
By proton transfer from hydroxyl towards amino group
Changing hybridisation of O-atom to SP2 from SP3
Unusual Increase in C=O bond length (1.19 Å to 1.21 Å)

13. Exohedral vs Isolated/ Relaxed
13
Aisolated AOS Bisolated BOS Cisolated COS Disolated DOS Eisolated EOS
rN-H 1.01 1.02 1.01 1.02 1.01 1.02 1.09 1.02 1.01 1.03
rC-H 1.09 1.09 1.09 1.11 1.09 1.10 0.97 1.09 1.01 1.1
rO-H 0.98 0.99 0.97 - 0.98 0.98 1.45 1.04 1.10 1.01
rC-N 1.46 1.48 1.45 1.46 1.46 1.47 1.51 1.49 0.96 1.49
rC-C 1.53 1.54 1.52 1.52 1.53 1.54 1.20 1.56 1.44 1.54
rC=O 1.19 1.21 1.20 1.21 1.19 1.44 1.34 1.22 1.53 1.22
rC-O 1.33 - 1.35 1.35 1.33 1.38 1.01 1.35 1.19 1.36
OS: Reported structure of glycine in other systems
AOS reference 2 BOS reference 2 EOS reference
4
DOS reference
3
COS reference 2

14. References
1. M. Shahamirian, S.M. Azami, Encapsulation of glycine inside C60 fullerene: Impact of confinement, Physics
2019, 383, 36, 126004.
2. Y. Hang Hu, E. Ruckenstein, Complexes of a bio-molecule and a C60 cage, J. Mol. Struct., Theochem 2008, 850,
67–71.
3. A. de Leon, A.F. Jalbout, V.A. Basiuk, Fullerene–amino acid interactions. A theoretical study, Chem. Phys.
Lett. 2008, 452, 306–314.
4. A. de Leon, A.F. Jalbout, V.A. Basiuk, SWNT–amino acid interactions: a theoretical study, Chem. Phys. Lett.
2008, 457, 185–190.
14

15. ?
Thank you so much!
15

16. Special thanks to Dr. T K Roy (Sir)
Linkedin.com/ZeeshanNazir
Slideshare.net/ZeeshanNazir17
16