On Prototropy and Bond Length Alternation in Neutral and Ionized Pyrimidine Bases and Their Model Azines in Vacuo
Abstract
:1. Introduction
2. Principles of Prototropic Equilibria
3. Quantum-Chemical Methods Applied to Tautomeric Nucleobases in Vacuo
4. Geometry-Based HOMED Index
5. Complete Prototropic Mixtures for Title Compounds
5.1. Monosubstituted Azines
5.2. Disubstituted Pyrimidine Bases
6. Internal Effects of Functional Groups on Isomer-Stability
6.1. Intramolecular Interactions between Endo and Exo Groups
6.2. Transmission of N-Endo Effects to Tautomeric Sites
6.3. Effects of Additional Exo OH and NH2 Groups
6.4. N-Endo Effects on Tautomeric Preferences
7. Alternation of Bond Lengths in Tautomers–Rotamers of Pyrimidine Bases and Their Models
8. Ionization Effects on Prototropy and Electron Delocalization in Mono- and Disubstituted Derivatives
8.1. Parent Compounds
8.2. Monosubstituted Azines
8.3. Disubstituted Pyrimidine Bases
9. Conclusions
10. General Remarks for Future Theoretical Investigations on Tautomeric Systems
Supplementary Materials
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Equilibria | Name of Conversion |
---|---|
>CH–C(=O)– >C=C(–OH)– | keto-enol |
>CH–C(=N–)– >C=C(–NH–)– | imine-enamine |
–NH–C(=N–)– –N=C(–NH–)– | imine-amine (amidine) |
–NH–C(=O)– –N=C(–OH)– | amide-iminol |
N-Endo Effects (δG) a | |||||||||
---|---|---|---|---|---|---|---|---|---|
Conformational Isomers about C–OH | Configurational Isomers about C=NH | ||||||||
Tautomer | 2-Position | Tautomer | 4-Position | Tautomer | 2-Position | Tautomer | 4-Position | ||
U b | C c | U b | iC d | iC d | C c | ||||
17 | 9.6 | 9.1, 10.0 | 18 | 6.7 | 6.8, 6.0 | 18 | 6.2, 7.0 | 17 | 4.3, 3.4 |
37 | 7.4 | 7.4, 7.4 | 38 | 2.5 | 2.2, 3.3 | 38 | 7.5, 6.6 | 37 | 2.8, 2.8 |
57 | 1.6 | 0.9, 1.7 | 58 | 7.5 | 8.0, 7.0 | 58 | 0.6, 0.4 | 57 | 5.1, 4.3 |
78 | 1.1, 0.0 | 0.7 | 78 | 5.3, 4.2 | 4.4 | 13 | 1.3 | 13 | 1.7 |
35 | 5.1 | 35 | 0.4 |
Azine | Isomer | δG | Azine | Isomer | δG | Azine | Isomer | δG |
---|---|---|---|---|---|---|---|---|
2HOPY | c | 6.7 | 2APY | c1 | 2.3 | 4APY | b2/d1 | 1.4 |
2HOPY | d | 6.9 | 2APY | c2 | 6.3 | 2APM | c | 9.9 |
4HOPY | b/d | 0.8 | 2APY | d1 | 2.0 | 4APM | d1 | 3.8 |
2HOPM | c | 8.4 | 2APY | d2 | 6.8 | 4APM | d2 | 8.6 |
4HOPM | d | 7.8 | 4APY | b1/d2 | 2.2 |
Model | Additional | Pyrimidine | δG | ||
---|---|---|---|---|---|
Compound | Exo Group | Base | N1H Isomer | N3H Isomer | C5H Isomer |
4HOPM | 2-OH | U | −1.4 | −0.2 | −4.7 |
4APM | 2-OH | C | −0.6 | −0.2 | −2.3 |
2HOPM | 4-OH | U | −2.5 | 6.4 | −4.4 |
2APM | 4-OH | iC | −2.2 | 5.9 | −5.3 |
4HOPM | 2-NH2 | iC | 3.4 | 2.9 | −7.7 |
2HOPM | 4-NH2 | C | −2.3 | 4.7 | −4.7 |
(a) Mono-hydroxy derivatives | |||||||||
Derivative | Isomer amount (xi in %) a | Ref. | |||||||
a1 | a2 | b | c | d | |||||
Phenol | 100 | 4·10−15 | 4·10−15 | 4·10−15 | [18] | ||||
2HOPY | 18 | 3·10−3 | 82 | 3·10−16 | 1·10−16 | [49] | |||
4HOPY | 88 | 1·10−11 | 12 | 1·10−11 | [49] | ||||
2HOPM | 81 | 19 | 8·10−17 | 19 | [49] | ||||
4HOPM | 3 | 5·10−4 | 97 | 2·10−5 | 4·10−18 | [49] | |||
(b) Mono-amino derivatives | |||||||||
Compound | Isomer amount (xi in %) a | Ref. | |||||||
a | b1 | b2 | c1 | c2 | d1 | d2 | |||
Aniline | 100 | 1·10−19 | 4·10−18 | 1·10−19 | [22] | ||||
2APY | 100 | 6·10−11 | 6·10−9 | 8·10−20 | 9·10−23 | 6·10−21 | 2·10−24 | [58] | |
4APY | 100 | 5·10−21 | 1·10−20 | 9·10−11 | 1·10−20 | 5·10−21 | [58] | ||
2APM | 100 | 9·10−19 | 2·10−13 | 3·10−28 | 2·10−13 | 9·10−19 | [59] | ||
4APM | 100 | 1·10−10 | 2·10−8 | 5·10−12 | 6·10−15 | 2·10−24 | 1·10−25 | [60] |
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Raczyńska, E.D. On Prototropy and Bond Length Alternation in Neutral and Ionized Pyrimidine Bases and Their Model Azines in Vacuo. Molecules 2023, 28, 7282. https://doi.org/10.3390/molecules28217282
Raczyńska ED. On Prototropy and Bond Length Alternation in Neutral and Ionized Pyrimidine Bases and Their Model Azines in Vacuo. Molecules. 2023; 28(21):7282. https://doi.org/10.3390/molecules28217282
Chicago/Turabian StyleRaczyńska, Ewa Daniela. 2023. "On Prototropy and Bond Length Alternation in Neutral and Ionized Pyrimidine Bases and Their Model Azines in Vacuo" Molecules 28, no. 21: 7282. https://doi.org/10.3390/molecules28217282