Stereochemistry of Simple Molecules inside Nanotubes and Fullerenes: Unusual Behavior of Usual Systems
Abstract
:1. Introduction
2. Conformational Behavior of Ethane and Its Analogs in Nanotubes
2.1. Ethane
2.2. Propane
2.3. 2,2,3,3-Tetramethylbutane
2.4. 2,2-Dimethylpropane
2.5. Fluoroethanes
2.6. Ammonia Borane
2.7. Disilane and Digermane
3. Conformational Behavior of Other Acyclic Molecules in Nanotubes
3.1. Hydroxyborane
3.2. Diborane (4)
3.3. Dialane (4)
3.4. Hydrazine
3.5. Methanol and Methanethiol
3.6. Dimethyl Ether
4. Conformational Properties of Simple Molecules in Fullerenes
4.1. Ethane and Its Analogs
4.2. Methanethiol
5. Conformational Behavior of Saturated Cyclic Molecules inside Nanotubes and Fullerenes
5.1. Cyclohexane in Nanotubes
5.2. 1,3-Dioxane in Nanotubes
5.3. 1,3-Dioxa-2-Silacyclohexane in Nanotubes
5.4. Hexahydropyrimidin-2-One in Nanotubes
5.5. 1,3,2-Dioxaborinane in Fullerenes
6. Nitrogen Pyramidal Inversion inside Nanotubes and Fullerenes
6.1. Ammonia and Trimethylamine in Nanotubes
6.2. Piperidine inside Nanotube
6.3. Perhydro-1,3,2-Dioxazine inside Nanotubes
6.4. Ammonia and Trimethylamine in Fullerenes
7. Recognition of the R- and S-Isomers by Chiral Nanotubes
7.1. R- and S-Isomers of 1-Fluoroethanol Inside SWCNTs (4,4) and (4,1)
7.2. R- and S-Isomers of α-Alanine inside SWCNTs (n,m)
8. Relative Stability of Cis and Trans Isomers inside Nanotubes. The “Trans-Effect”
9. Conclusions
- The preferred conformation of ethane and its analogs inside nanotubes of small diameter is not the staggered, but the eclipsed form. The conformational behavior of ethane-like molecules inside fullerenes is less clear and depends on the size and chemical composition of the nanoobject.
- Hydroxyborane and diborane in endohedral clusters of nanotubes are characterized by reducing the barriers of internal rotation about the B-O and B-B bonds; in the case of dialane, the planar form—the transition state for the free molecule—becomes the minimum on the potential energy surface. A similar change in the nature of the preferred conformation is observed for hydrazine, methanol, methanethiol and dimethyl ether, together with cyclic molecules: cyclohexane, 1,3-dioxa-2-silacyclohexane and hexahydropirimidine-2-one inside nanotubes. In the case of 1,3-dioxane inside SWCNT and 1,3,2-dioxaborinane inside fullerene C60 conformational equilibrium is shifted to forms that can never be realized as a ground state for neither free molecule, nor for these species in any solvent.
- The barrier to pyramidal inversion of amines in endocomplexes varies depending on the nature of the amine and the size of the nanocavity.
- Chiral nanotubes are able to recognize molecules of enantiomers owing to increased affinity of P-SWCNT for the S-isomer and M-SWCNT for the R-form.
- SWCNTs of small diameter are able to drastically change the relative stability of cis and trans isomers in their cavity.
Funding
Conflicts of Interest
Abbreviations
SWCNTs | single-walled carbon nanotubes |
PES | potential energy surface |
TS | transition state |
DFT | density functional theory |
HF | Hartree–Fock |
PBE | Perdew–Burke–Ernzerhof |
O | Mulliken bond order |
HOMO | high occupied molecular orbital |
LUMO | low unoccupied molecular orbital |
C | conformation of chair form |
Tw | conformation of twist form |
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Form | ΔG≠298 (kcal/mol) | rC–C (Å) | OC–C | Charge |
---|---|---|---|---|
C2H6 | ||||
Staggered Eclipsed | 0 2.5 | 1.531 1.544 | 1.02 1.00 | 0 0 |
C2H6@(4,4)-closed | ||||
Staggered Eclipsed | 0.6 0 | 1.495 1.499 | 0.80 0.78 | −0.54 −0.57 |
C2H6@(6,0)-short | ||||
Staggered Eclipsed | 2.0 0 | 1.431 1.429 | 0.51 0.53 | 0.72 0.73 |
C2H6@(6,0)-long | ||||
Staggered Eclipsed | 1.7 0 | 1.434 1.432 | 0.49 0.50 | 0.40 0.48 |
C2H6@(6,0)-CBN | ||||
Staggered Eclipsed | 0.9 0 | 1.449 1.449 | 0.66 0.66 | −1.16 −1.22 |
Form | ΔG≠298 (kcal/mol) | rC–C (Å) | OC–C | Charge | Reference |
---|---|---|---|---|---|
C2H5F | |||||
Staggered Eclipsed | 0 3.1 (exp. 3.31) | 1.514 1.530 | 1.03 1.01 | 0 0 | [94,139,140] |
C2H5F@(4,4) | |||||
Staggered Eclipsed | 0.8 0 | 1.487 1.485 | 0.68 0.73 | −0.19 −0.16 | [140] |
C2H5F@(5,5) | |||||
Staggered Eclipsed | 0 2.4 | 1.508 1.522 | 0.96 0.97 | −0.41 −0.40 | [140] |
CH3−CF3 | |||||
Staggered Eclipsed | 0 2.7 (exp. 3.17) | 1.507 1.521 | 1.01 1.01 | 0 0 | [139,141,142] |
CH3−CF3@(4,4) | |||||
Staggered Eclipsed | 1.2 0 | 1.505 1.518 | 0.94 0.92 | −0.22 −0.20 | [142] |
CH3−CF3@(5,5) | |||||
Staggered Eclipsed | 0 2.0 | 1.501 1.513 | 0.99 0.98 | −0.27 −0.26 | [142] |
CF3−CF3 | |||||
Staggered Eclipsed | 0 4.5 (exp. 4.30) | 1.565 1.600 | 0.88 0.88 | 0 0 | [139,143] |
CF3−CF3@(5,5) | |||||
Staggered Eclipsed | 2.3 0 | 1.562 1.587 | 0.88 0.86 | −0.15 −0.16 | [143] |
CF3−CF3@(6,6) | |||||
Staggered Eclipsed | 0 4.2 | 1.539 1.572 | 0.89 0.87 | −0.13 −0.13 | [143] |
Cluster; ΔG≠298 (kcal/mol) 1 | rC–C (Å) 1 | O 1 | Charge | Reference |
---|---|---|---|---|
C2H6@C60; 3.3 (2,5) | 1.465 (1.531) | 1.12 (1.00) | −0.47 | [196] |
C2F6@C60; 15.1 (4,6) | 1.374 (1.565) | 0.86 (0.88) | 0.20 | [197,198] |
C2F6@C12B24N24; 6.5 | 1.405 | 0.83 | 0.46 | [198] |
C2F6@B36N24; 8.2 | 1.464 | 0.86 | 0.48 | [198] |
C2F6@C80; 7.2 | 1.477 | 0.89 | −0.27 | [197,198] |
C2F6@C14B33N33; 10.0 | 1.493 | 0.90 | 0.15 | [198] |
C2F6@B47N33; 7.6 | 1.507 | 0.92 | 0.15 | [198] |
C2Cl6@C80; 43.5 (13,8) | 1.431 (1.590) | 0.98 (1.06) | −0.22 | [199] |
C5H12@C60; 10.7 (3,8) | 1.366 (1.539) | 0.86 (1.00) | 2.07 | [200] |
C5H12@C80; 8.3 | 1.459 | 0.86 | −1.27 | [200] |
H3B←NH3@C60; 4.4 (2,0) | 1.522 (1.652) | 0.43 (0.65) | −0.71 | [201] |
H3B←NH3@C12B24N24; 1.5 | 1.544 | 0.54 | −0.79 | [201] |
H3B←NH3@B36N24; 2.3 | 1.558 | 0.48 | −0.22 | [201] |
H3B←NH3@C70; 2.1 | 1.595 | 0.62 | −0.90 | [201] |
H3B←NH3@B41N29; 1.8 | 1.610 | 0.72 | −0.11 | [201] |
H3B←NH3@C80; 1.8 | 1.601 | 0.58 | −0.64 | [201] |
H3B←NH3@C14B33N33; 1.1 | 1.605 | 0.57 | −0.11 | [201] |
H3B←NH3@B47N33; 1.6 | 1.618 | 0.64 | −0.06 | [201] |
Si2H6@Si60; 1.0 (1,3) | 2.351 (3.355) | 0.97 (1.00) | −0.12 | [202] |
Si2H6@C80; 2.4 | 2.184 | 1.52 | −1.16 | [202] |
Si2H6@B47N33; 1.6 | 2.252 | 1.08 | 0.01 | [202] |
Object | ΔG2980 (ΔG298≠), kcal/mol | Electric Charge |
---|---|---|
(5,5) | 0 | 0 |
P,M(5,1) 1 | 5.9 | 0 |
P,M(5,2) 1 | 16.1 | 0 |
S-C3H7NO2 (A) | 0 | 0 |
S-C3H7NO2 (B) 2 | (3.1) | 0 |
S-C3H7NO2 (D) 2 | (2.7) | 0 |
R,S-C3H7NO2@(5,5) 3 | 13.9 | −0.69 |
S-C3H7NO2@M(5,1) 3 | 12.3 | −0.69 |
S-C3H7NO2@P(5,1) 3 | 12.1 | −0.67 |
R-C3H7NO2@M(5,1) 3 | 12.1 | −0.67 |
R-C3H7NO2@P(5,1) 3 | 12.3 | −0.69 |
S-C3H7NO2@M(5,2) 3 | 4.6 | −0.64 |
S-C3H7NO2@P(5,2) | 0 | −0.67 |
R-C3H7NO2@M(5,2) 3 | 0.1 | −0.67 |
R-C3H7NO2@P(5,2) 3 | 4.7 | −0.65 |
Object | ΔG2980, kcal/mol | OX=X | Charge |
---|---|---|---|
CHF=CHF, cis- trans- | 0 0.6 | 1.78 1.77 | 0 0 |
FN=NF, cis- trans- | 0 3.4 | 1.76 1.66 | 0 0 |
CHF=CHF@(4,4), cis- trans- | 26.2 0 | 1.32 1.44 | 0.46 0.52 |
CHF=CHF@(6,6), cis- trans- | 0.9 0 | 1.72 1.73 | −0.16 −0.17 |
FN=NF@(4,4), cis- trans- | 27.4 0 | 1.46 1.73 | −0.36 −0.36 |
FN=NF@(6,6), cis- trans- | 0 3.8 | 1.71 1.69 | −0.03 −0.004 |
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Kuznetsov, V. Stereochemistry of Simple Molecules inside Nanotubes and Fullerenes: Unusual Behavior of Usual Systems. Molecules 2020, 25, 2437. https://doi.org/10.3390/molecules25102437
Kuznetsov V. Stereochemistry of Simple Molecules inside Nanotubes and Fullerenes: Unusual Behavior of Usual Systems. Molecules. 2020; 25(10):2437. https://doi.org/10.3390/molecules25102437
Chicago/Turabian StyleKuznetsov, Valerij. 2020. "Stereochemistry of Simple Molecules inside Nanotubes and Fullerenes: Unusual Behavior of Usual Systems" Molecules 25, no. 10: 2437. https://doi.org/10.3390/molecules25102437