Calculation of Proton Affinities Using Density Functional Procedures:  A Critical Study

Chandra, Asit K.; Goursot, Annick

doi:10.1021/jp9603750

Cited by 65 publications

(42 citation statements)

References 30 publications

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“…To investigate the energetics and relative stabilities of the two tautomers, we have calculated the difference in the free energies (

Δ G_{gas}, Δ G_{pcm}, Δ G_{actsite}

) of the ketoenamine and enolimine forms of PLP‐SER and PLP‐LYS aldimines where

Δ G = G_{enol} - G_{keto},

and the results are included in Table for the BLYP and B3LYP functionals. We have also calculated the proton affinities of the two tautomers . The proton affinity (PA) for a reaction B + H + –> BH + is calculated as

PA = - Δ E_{el} - Δ (ZPVE),

where,

Δ E_{el}

= [E(BH + ) – E(B)] is the difference in ground‐state electronic energies of the protonated and unprotonated forms of the base (B).…”

Section: Resultsmentioning

confidence: 99%

Free energy landscapes of prototropic tautomerism in pyridoxal 5′‐phosphate schiff bases at the active site of an enzyme in aqueous medium

Soniya

Chandra

2018

J Comput Chem

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We have performed hybrid quantum-classical metadynamics simulations and quantum chemical calculations to investigate the free energy landscapes of intramolecular proton transfer and associated tautomeric equilibrium in pyridoxal 5 '-phosphate (PLP) Schiff Bases, namely the internal and external aldimines, at the active site of serine hydroxymethyltransferase (SHMT) enzyme in aqueous medium. It is important to determine the relative stability of the two tautomers (ketoenamine and enolimine) of the PLP aldimines to study the catalytic activity of the concerned enzyme. Both the internal PLP aldimine (PLP-LYS) and the external PLP aldimine (PLP-SER) of SHMT are found to have a higher stability for the ketoenamine tautomer over the enolimine form. The higher stability of the ketoenamine tautomer can be attributed to the more number of favorable interactions of the ketoenamine form with its surroundings at the active site of the enzyme. The ketoenamine is found to be stabilized by about 2.5 kcal/mol in the PLP-LYS internal aldimine, while this stabilization is about 6.7 kcal/mol for the PLP-SER external aldimine at the active site of the enzyme compared to the corresponding enolimine forms. The interactions faced by the PLP aldimines at the active site pocket determine the relative dominance of the tautomers and could possibly alter the tautomeric shift in different PLP dependent enzymes. © 2018 Wiley Periodicals, Inc.

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“…To investigate the energetics and relative stabilities of the two tautomers, we have calculated the difference in the free energies (

Δ G_{gas}, Δ G_{pcm}, Δ G_{actsite}

) of the ketoenamine and enolimine forms of PLP‐SER and PLP‐LYS aldimines where

Δ G = G_{enol} - G_{keto},

PA = - Δ E_{el} - Δ (ZPVE),

where,

Δ E_{el}

= [E(BH + ) – E(B)] is the difference in ground‐state electronic energies of the protonated and unprotonated forms of the base (B).…”

Section: Resultsmentioning

confidence: 99%

Free energy landscapes of prototropic tautomerism in pyridoxal 5′‐phosphate schiff bases at the active site of an enzyme in aqueous medium

Soniya

Chandra

2018

J Comput Chem

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“…78 Domalski et al [74] Ϫ108. 57 Chao 28 Chase [73] Ϫ108. 53 Marsh et al [75] (2g) Determined using the HEAT model chemistry [85].…”

Section: Methodsmentioning

confidence: 99%

“…The results of selected previous attempts to determine the PA 33, 36, 48–61 and EF 62–75 of H 2 CO are summarized in Tables I and II, respectively. The most recent PA values are in reasonably good agreement though the drift from the early measured and evaluated values is quite notable.…”

Section: Introductionmentioning

confidence: 99%

Proton affinity and enthalpy of formation of formaldehyde

Czakó

Nagy

Tasi

et al. 2009

Int J of Quantum Chemistry

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The proton affinity and the enthalpy of formation of the prototypical carbonyl, formaldehyde, have been determined by the first-principles composite focalpoint analysis (FPA) approach. The electronic structure computations employed the allelectron coupled-cluster method with up to single, double, triple, quadruple, and even pentuple excitations. In these computations the aug-cc-p(C)VXZ [X ϭ 2(D), 3(T), 4(Q), 5, and 6] correlation-consistent Gaussian basis sets for C and O were used in conjunction with the corresponding aug-cc-pVXZ (X ϭ 2-6) sets for H. The basis set limit values have been confirmed via explicitly correlated computations. Our FPA study supersedes previous computational work for the proton affinity and to some extent the enthalpy of formation of formaldehyde by accounting for (a) electron correlation beyond the "gold standard" CCSD(T) level; (b) the non-additivity of core electron correlation effects; (c) scalar relativity; (d) diagonal Born-Oppenheimer corrections computed at a correlated level; (e) anharmonicity of zero-point vibrational energies, based on global potential energy surfaces and variational vibrational computations; and (f) thermal corrections to enthalpies by direct summation over rovibrational energy levels. Our final proton affinities at 298.15 (0.0) K are ⌬ pa H o (H 2 CO) ϭ 711.02 (704.98) Ϯ 0.39 kJ mol Ϫ1 . Our final enthalpies of formation at 298.15 (0.0) K are ⌬ f H o (H 2 CO) ϭ Ϫ109.23 (Ϫ105.42) Ϯ 0.33 kJ mol Ϫ1 .The latter values are based on the enthalpy of the H 2 ϩ CO 3 H 2 CO reaction but supported by two further reaction schemes, H 2 O ϩ C 3 H 2 CO and 2H ϩ C ϩ O 3 H 2 CO. These values, especially ⌬ pa H o (H 2 CO), have better accuracy and considerably lower uncertainty than the best previous recommendations and thus should be employed in future studies.

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“…Protonation (B + H + → BH + ) and deprotonation (dehydrogenation) (HA − H + → A − ) reactions assume a significant role in natural science and organic chemistry, where A and B are the acidic and the basic centers, respectively. They are considered as the first step in several fundamental chemical mechanisms elucidated in the cited reference 15 . The ability of an atom or molecule in the gas phase to accept or to lose a proton can be described by calculating the proton affinity (PA), deprotonation (dehydrogenation) enthalpy, and molecular gas-phase basicity, which offer a profound understanding of the connections between the reactivity of the organic molecules, their molecular structures, and molecular stability 16 .…”

Section: Introductionmentioning

confidence: 99%

Computational study of the unimolecular and bimolecular decomposition mechanisms of propylamine

Almatarneh

Omari

Omeir

et al. 2020

Sci Rep

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A detailed computational study of the dehydrogenation reaction of trans-propylamine (trans-pA) in the gas phase has been performed using density functional method (DFT) and CBS-QB3 calculations. Different mechanistic pathways were studied for the reaction of n-propylamine. Both thermodynamic functions and activation parameters were calculated for all investigated pathways. Most of the dehydrogenation reaction mechanisms occur in a concerted step transition state as an exothermic process. the mechanisms for pathways A and B comprise two key-steps: H 2 eliminated from pA leading to the formation of allylamine that undergoes an unimolecular dissociation in the second step of the mechanism. Among these pathways, the formation of ethyl cyanide and H 2 is the most significant one (pathway B), both kinetically and thermodynamically, with an energy barrier of 416 kJ mol −1. the individual mechanisms for the pathways from c to n involve the dehydrogenation reaction of PA via hydrogen ion, ammonia ion and methyl cation. The formation of α-propylamine cation and nH 3 (pathway E) is the most favorable reaction with an activation barrier of 1 kJ mol −1. this pathway has the lowest activation energy calculated of all proposed pathways. Propylamine is of significant importance in chemistry, as it constitutes a central structure block for aliphatic amines 1. It is widely utilized as a solvent in organic synthesis, and as a finishing agent for drugs, rubber, fiber, paints, pesticides, textile and resin 2,3 , and in the generation of fungicides 4-6. Furthermore, it may very well be used as a petroleum additive and preservative. The disintegration of protonated of propylamine has attracted a noteworthy arrangement of fascination in the previous decade 7-10. This is mainly due to the way that the proton affinity and the structural difference in propylamine through protonation influences the separation items through the arrangement of protonated amines, methane, propene and hydrogen gas 11,12. Additionally, this reaction prompts the generation of various poisonous synthetic substances such as, alkyl cyanide, propylene, ethylene, nitrogen and hydrogen gases 13,14. Protonation (B + H + → BH +) and deprotonation (dehydrogenation) (HA − H + → A −) reactions assume a significant role in natural science and organic chemistry, where A and B are the acidic and the basic centers, respectively. They are considered as the first step in several fundamental chemical mechanisms elucidated in the cited reference 15. The ability of an atom or molecule in the gas phase to accept or to lose a proton can be described by calculating the proton affinity (PA), deprotonation (dehydrogenation) enthalpy, and molecular gasphase basicity, which offer a profound understanding of the connections between the reactivity of the organic molecules, their molecular structures, and molecular stability 16. The negative of the enthalpy change related to the gas-phase protonation reaction is referred to as proton affinity, while dehydrogenation energy is defined as the en...

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Calculation of Proton Affinities Using Density Functional Procedures: A Critical Study

Cited by 65 publications

References 30 publications

Free energy landscapes of prototropic tautomerism in pyridoxal 5′‐phosphate schiff bases at the active site of an enzyme in aqueous medium

Free energy landscapes of prototropic tautomerism in pyridoxal 5′‐phosphate schiff bases at the active site of an enzyme in aqueous medium

Proton affinity and enthalpy of formation of formaldehyde

Computational study of the unimolecular and bimolecular decomposition mechanisms of propylamine

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