Keywords
ciliatine
conformational analysis
C–P bond
density functional theory
QTAIM
ELF
Boltzmann distribution
How to Cite
Abstract
The two smallest members of the natural aminophosphonic acid family — aminomethylphosphonic acid (AMPA) and 2-aminoethylphosphonic acid (ciliatine, AEPA) — were examined at the B3LYP/6-311++G(d,p) level. Four minima were located for AMPA and three for AEPA. The conformational spread of the C–P bond length is 0.0104 Å in AMPA and 0.0201 Å in AEPA. Boltzmann-averaged values are 1.8294 and 1.8257 Å, differing by only 0.0037 Å, whereas a comparison restricted to the anti conformers gives 0.0255 Å. QTAIM analysis of the wavefunctions yields ∇²ρ = −0.3991 a.u. and ELF = 0.7518 at the C–P bond critical point of AMPA against −0.2837 a.u. and 0.6426 for the anti- AEPA. No bond critical point is located between the amino hydrogens and the phosphonate oxygens in either molecule. The dipole moment of AEPA varies from 0.557 to 6.351 D across conformers, indicating that the conformational equilibrium is strongly solvent- dependent. The methylene spacer does not shorten the C–P bond — it opens the bond to conformational control.References
1. Andersson, M. P., & Uvdal, P. (2005). New scale factors for harmonic vibrational frequencies using the B3LYP density functional method with the triple-ζ basis set 6-311+G(d,p). The Journal of Physical Chemistry A, 109(12), 2937–2941. https://doi.org/10.1021/jp045733a
2. Bader, R. F. W. (1991). A quantum theory of molecular structure and its applications. Chemical Reviews, 91(5), 893–928. https://doi.org/10.1021/cr00005a013
3. Becke, A. D. (1993). Density-functional thermochemistry. III. The role of exact exchange. The Journal of Chemical Physics, 98(7), 5648–5652. https://doi.org/10.1063/1.464913
4. Carretta, L., Masin, R., & Zanin, G. (2022). Review of studies analysing glyphosate and aminomethylphosphonic acid (AMPA) occurrence in groundwater. Environmental Reviews, 30(1), 88–109. https://doi.org/10.1139/er-2020-0106
5. Grandcoin, A., Piel, S., & Baurès, E. (2017). AminoMethylPhosphonic acid (AMPA) in natural waters: Its sources, behavior and environmental fate. Water Research, 117, 187–197. https://doi.org/10.1016/j.watres.2017.03.055
6. Horiguchi, M., & Kandatsu, M. (1959). Isolation of 2-aminoethane phosphonic acid from rumen protozoa. Nature, 184(4690), 901–902. https://doi.org/10.1038/184901b0
7. Kittredge, J. S., & Roberts, E. (1969). A carbon–phosphorus bond in nature. Science, 164(3875), 37–42. https://doi.org/10.1126/science.164.3875.37
8. Krishnan, R., Binkley, J. S., Seeger, R., & Pople, J. A. (1980). Self-consistent molecular orbital methods. XX. A basis set for correlated wave functions. The Journal of Chemical Physics, 72(1), 650–654. https://doi.org/10.1063/1.438955
9. Lee, C., Yang, W., & Parr, R. G. (1988). Development of the Colle–Salvetti correlation-energy formula into a functional of the electron density. Physical Review B, 37(2), 785–789. https://doi.org/10.1103/PhysRevB.37.785
10. Lu, T., & Chen, F. (2012). Multiwfn: A multifunctional wavefunction analyzer. Journal of Computational Chemistry, 33(5), 580–592. https://doi.org/10.1002/jcc.22885
11. Marenich, A. V., Cramer, C. J., & Truhlar, D. G. (2009). Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. The Journal of Physical Chemistry B, 113(18), 6378–6396. https://doi.org/10.1021/jp810292n
12. Metcalf, W. W., & van der Donk, W. A. (2009). Biosynthesis of phosphonic and phosphinic acid natural products. Annual Review of Biochemistry, 78, 65–94. https://doi.org/10.1146/annurev.biochem.78.091707.100215
13. Mucha, A., Kafarski, P., & Berlicki, Ł. (2011). Remarkable potential of the α-aminophosphonate/phosphinate structural motif in medicinal chemistry. Journal of Medicinal Chemistry, 54(17), 5955–5980. https://doi.org/10.1021/jm200587f
14. Reed, A. E., Curtiss, L. A., & Weinhold, F. (1988). Intermolecular interactions from a natural bond orbital, donor–acceptor viewpoint. Chemical Reviews, 88(6), 899–926. https://doi.org/10.1021/cr00088a005
This work is licensed under a Creative Commons Attribution 4.0 International License.
Copyright (c) 2026 Sh.N. Rajabova, B.Sh. G'aniyev (Author)