Mechanism for the deamination of ammeline, guanine, and their analogues

Uddin, Kabir M.; Henry, David J.; Alrawashdeh, Ahmad I.; Warburton, Peter L.; Poirier, Raymond A.

doi:10.1007/s11224-017-0941-z

Cited by 11 publications

(15 citation statements)

References 27 publications

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“…The changes in structure during the reaction are accompanied by changes in the charges and the electrostatic interactions modify the geometry on several key atoms in the substrates. In our previous work, we found that the positive charge on C 2 for AMN and Gua is greater in the TS than in the reactants, while the oxygen atoms of the water molecules exhibit relatively little change in charge across the various systems upon forming six‐ and eight‐membered cyclic conformations in the TSs. The negative charges on atoms C 5 and C 6 in TS 2 for unsaturated 1‐mCyct (8) are smaller in magnitude than for saturated 1‐mDHCyt (12), which is linked to p‐electron delocalization in the ring that lowers the activation energy compared to 1‐mCyt (Figure and Table ).…”

Section: Resultssupporting

confidence: 93%

“…Analysis of the frontier MO energies shows there is a correlation between the energy of the HOMO and LUMO for the transition state structures and E a . The polarizability of the C 4 N 3 and C 5 C 6 bonds can be explained by noting that the antibonding molecular orbitals of the p-system is resonance mixed with the bonding orbitals as shown below: is consistent with our previous work, [45] we found that the N 7 ─C 2 ─N 3 bond angle in TS 1 of AMN is 116.7 while the slightly larger angle F I G U R E 4 Maps of electrostatic potential (0.04 electrons bohr −3 ) (red = electron-rich, blue = electron-deficient) for 1-mCyt (TS 2 ) and 1-mDHCyt (TS 2 ) selected transition structures for six-membered TSs in Gua (117.4 ) indicates that C 2 is nearly trigonal planar (sp 2 hybridization). Nevertheless, the activation energies are similar for both cases.…”

Section: Thermodynamic and Kinetic Propertiessupporting

confidence: 89%

“…In summary, a comprehensive mechanistic investigation for the deamination of amidine and nucleobases derivatives involves three water molecules has been conducted, which is in a good trend with our previous studies [27,32,33,38,45] on similar systems as shown in Figure 6.…”

Section: Thermodynamic and Kinetic Propertiessupporting

confidence: 82%

“…This facilitates minor distortion of the electron cloud of the structurally similar active sites in both 1‐mCyt and 1‐mDCyt systems. This is consistent with our previous work, we found that the N 7 ─C 2 ─N 3 bond angle in TS 1 of AMN is 116.7° while the slightly larger angle in Gua (117.4°) indicates that C 2 is nearly trigonal planar (sp 2 hybridization). Nevertheless, the activation energies are similar for both cases.…”

Section: Resultsmentioning

confidence: 99%

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Hydrolytic deamination reactions of amidine and nucleobase derivatives

Uddin

Alrawashdeh

Henry

et al. 2019

Int J of Quantum Chemistry

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Amidines share the same N C─N building framework with many essential biochemical substances. In this work, we present a comparative mechanistic study on the deamination reactions of 19 amidine and nucleobase derivatives by the use of density functional theory. All the computations are performed at the B3LYP/6-31G(d,p) level in the gas phase and with the polarizable continuum model (PCM). Mechanisms of 2-and 3-step pathways including six-or eight-membered ring transition states were explored. Our results show that the overall activation energies for the deamination of amidine derivatives are close to those of nucleobase derivatives of the saturated C5─C6 bond, and lower than those of nucleobase derivatives of the unsaturated C5─C6 bond, while purine derivatives have the highest activation energies among all the derivatives studied. The 3-step mechanism gives results that are more consistent with the available experimental data than the 2-step mechanism. Based on the results of our current and previous work, we believe that the 3-step mechanism is the most likely mechanism for the hydrolytic deamination reactions of amidine and nucleobase derivatives.

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Section: Resultssupporting

confidence: 93%

Section: Thermodynamic and Kinetic Propertiessupporting

confidence: 89%

Section: Thermodynamic and Kinetic Propertiessupporting

confidence: 82%

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

Hydrolytic deamination reactions of amidine and nucleobase derivatives

Uddin

Alrawashdeh

Henry

et al. 2019

Int J of Quantum Chemistry

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“…In recent years, the deamination of ammeline has been studied in detail by means of DFT calculations , . Understanding of this reaction is of great interest in view of the aforementioned hydrolysis of melamine, which is thought to be the cause for the formation of melamine cyanurate complexes from melamine contaminated foodstuff.…”

Section: Introductionmentioning

confidence: 99%

Ammelinium Sulfate Monohydrate and Ammelinium Sulfate Cyanuric Acid – Synthesis and Structural Characterization

Kessler¹,

Schnick²

2019

Zeitschrift anorg allge chemie

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Two ionic carbon nitride type compounds containing the ammelinium cation, ammelinium sulfate cyanuric acid (6C3N5H6O+·3SO42–·1⅔C3N3H3O3·H2O) (1) and ammelinium sulfate monohydrate (2C3N5H6O+·SO42–·H2O) (2) were synthesized through hydrolysis of melam (C6N11H9) in diluted sulfuric acid. 1 crystallizes in hexagonal space group P63 (no. 173) with lattice parameters of a = 14.642(3), c = 13.113(4), and Z = 2. The structure is comprised of protonated ammelinium ions and neutral cyanuric acid molecules, which form a layered structure, as well as sulfate ions that span through these layers. 2 crystallizes in the triclinic space group P1 with lattice parameters of a = 7.404(3), b = 9.673(4), c = 10.040(4), α = 91.098(15), β = 109.884(10), γ = 92.567(13), and Z = 2. As for 1, the ammelinium rings form layers with the sulfate ions located in between. In both structures, no extended hydrogen bond networks between the respective triazine‐based molecules are formed. Instead, single molecules or small building blocks occur isolated and interact primarily with sulfate anions. Compound 1, which was obtained phase pure, was further investigated by FTIR spectroscopy, solid‐state NMR spectroscopy and powder X‐ray diffractometry.

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New insight into the substituent effects on the hydrolytic deamination of saturated and unsaturated cytosine

Uddin

Islam

et al. 2022

Int J of Quantum Chemistry

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Ab initio calculations were carried out to understand the effect of electron donating groups (EDG) and electron withdrawing groups (EWG) at the C5 position of cytosine (Cyt) and saturated cytosine (H2Cyt) of the deamination reaction. Geometries of the reactants, transition states, intermediates, and products were fully optimized at the B3LYP/6‐31G(d,p) level in the gas phase as this level of theory has been found to agree very well with G3 theories. Activation energies, enthalpies, and Gibbs energies of activation along with the thermodynamic properties (ΔE, ΔH, and ΔG) of each reaction were calculated. A plot of the Gibbs energies of activation (ΔG‡) for C5 substituted Cyt and H2Cyt against the Hammett σ‐constants reveal a good linear relationship. In general, both EDG and EWG substituents at the C5 position in Cyt results in higher ΔG‡ and lower σ values compared to those of H2Cyt deamination reactions. C5 alkyl substituents (H, CH3, CH2CH3, CH2CH2CH3) increase ΔG‡ values for Cyt, while the same substituents decrease ΔG‡ values for H2Cyt which is likely due to steric effects. However, the Hammett σ‐constants were found to decrease at the C5 position of cytosine (Cyt) and saturated cytosine (H2Cyt) on the deamination reaction. Both ΔG‡ and σ values decrease for the substituents Cl and Br in the Cyt reaction, while ΔG‡ values increase and σ decrease in the H2Cyt reaction. This may be due to high polarizability of bromine which results in a greater stabilization of the transition state in the case of bromine compared to chlorine. Regardless of the substituent at C5, the positive charge on C4 is greater in the TS compared to the reactant complex for both the Cyt and H2Cyt. Moreover, as the charges on C4 in the TS increase compared to reactant, ΔG‡ also increase for the C5 alkyl substituents (H, CH3, CH2CH3, CH2CH2CH3) in Cyt, while ΔG‡ decrease in H2Cyt. In addition, analysis of the frontier MO energies for the transition state structures shows that there is a correlation between the energy of the HOMO–LUMO gap and activation energies.

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Mechanism for the deamination of ammeline, guanine, and their analogues

Cited by 11 publications

References 27 publications

Hydrolytic deamination reactions of amidine and nucleobase derivatives

Hydrolytic deamination reactions of amidine and nucleobase derivatives

Ammelinium Sulfate Monohydrate and Ammelinium Sulfate Cyanuric Acid – Synthesis and Structural Characterization

New insight into the substituent effects on the hydrolytic deamination of saturated and unsaturated cytosine

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