Theoretical Study for Solvent Effect on the Potential Energy Surface for the Double Proton Transfer in Formic Acid Dimer and Formamidine Dimer

Lim, Jae Hyun; Lee, Eok Kyun; Kim, Yong-Ho

doi:10.1021/jp9626226

Cited by 85 publications

(75 citation statements)

References 34 publications

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“…In recent years, amidines have been widely studied in proton affinities [3] , proton transfer [4] , tautomerization [5][6][7] , and thermal unimolecular Scheme 1 decomposition processes [8] . Flinn et al [9] investigated the deamination of the simple formamidine with OH − , H 2 O, and H 3 O + using HF, MP2, QCISD, DFT/B3LYP, and even up to G1 and G2 methods.…”

Section: Introductionmentioning

confidence: 99%

Theoretical study on the hydrolysis mechanism of N,N-dimethyl-N′-(2′,3′-dideoxy-3′-thiacytidine)formamidine

Zhang

Yang

2008

Sci. China Ser. B-Chem.

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The hydrolysis mechanisms of N,N-dimethyl-N′-(2′,3′-dideoxy-3′-thiacytidine)formamidine (FA-3TC) in the gas phase and in aqueous solution were studied by use of the density functional theory B3LYP/6-31+G(d, p) method. Two possible reaction pathways in the title reaction were considered. In one pathway water attacks the C=N double bond first (path A) while in the other water attacks the C-N single bond first (path B). The calculated results indicate that the first step in both pathways is the rate-limiting process and path A is more favorable than path B in the gas phase. The effect of solvent water on the title reaction was assessed at the B3LYP/6-31+G(d, p) level of theory based on the polarizable continuum model (CPCM). In water the first mechanism (path A) is also favored.N,N-dimethyl-N′-(2′,3′-dideoxy-3′-thiacytidine)formamidine, hydrolysis, solvent effect, B3LYP, polarizable continuum model

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Section: Introductionmentioning

confidence: 99%

Theoretical study on the hydrolysis mechanism of N,N-dimethyl-N′-(2′,3′-dideoxy-3′-thiacytidine)formamidine

Zhang

Yang

2008

Sci. China Ser. B-Chem.

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“…Comparison with Fig. 29.6 shows that the symmetric dimer, namely dimeric formamidine with a D 2h transition state [43], shows the same pattern as the formic acid dimer, i.e. a transition state corresponding to synchronous transfer with tightened hydrogen bonding, despite the weakened hydrogen bonds.…”

Section: Dimeric Formic Acid and Related Dimersmentioning

confidence: 81%

“…This changes the strength of the hydrogen bonds in the order OH-N > OH-O > NH-O > NH-N. The calculated equilibrium structures and transition states for four analogs of the formic acid dimer, calculated at the DFT-B3LYP/6-31G(d,p) level [43][44][45][46], are illustrated in Fig. 29.7.…”

Section: Dimeric Formic Acid and Related Dimersmentioning

confidence: 99%

Multiple Proton Transfer: From Stepwise to Concerted

Smedarchina

Siebrand

Fernández‐Ramos

2006

Hydrogen‐Transfer Reactions

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It is well recognized that reactions involving the transfer of a proton or hydrogen atom are special in that these particles can tunnel through classically forbidden regions [1]. The wave-like properties also add a new element to reactions in which two or more protons transfer, since under appropriate conditions, they may allow the protons to move as a single particle. In this contribution we review the dynamics of such reactions [2], focusing on double proton transfer for simplicity. In particular, we probe how the motion of one proton influences that of the other and which conditions lead to weak or strong correlation between their motions. Generally speaking, no correlation results in independent transfer and weak correlation in stepwise transfer. Strengthening the correlation will ultimately lead to concerted transfer and may give rise to synchronous transfer if the transferred particles are equivalent.While proton-proton correlation is a unifying concept that allows us to classify and understand the various multiproton transfer mechanisms, it is not a quantity that is easily measured or calculated. In dealing with a specific reaction, one tends to use a simpler approach based on the search for a transition state, i.e. a configuration along the transfer path characterized by a first-order saddle point representing a vibrational force field with one imaginary frequency. More generally, the presence of two mobile particles implies that the potential energy surface contains stationary states with zero, one, or two imaginary frequencies, representing, respectively, a stable intermediate, a transition state, and a state with a secondorder saddle point.A stable intermediate roughly halfway along the trajectory implies barriers separating it from the equilibrium configurations. Such a potential favors stepwise transfer under conditions where the intermediate is thermally accessible. This basically reduces the dynamics to that appropriate for single proton transfer, but leaves open the question of how to deal with transfer at low temperature. A barrier corresponding to a single transition state, similar to that observed for single proton transfer, implies concerted transfer of the two protons. This again can Hydrogen-Transfer Reactions. Edited by be treated by the methods developed for single proton dynamics [1,3]. However, if, instead, this barrier corresponds to a second-order saddle point, it represents concerted motion along two proton coordinates. This situation does not immediately reveal the nature of the corresponding transfer process, but it drives home the point that the presence of two mobile protons allows at least two transfer mechanisms. On a potential energy surface with more than one saddle point, there will in general be multiple pathways along which the potential has a doubleminimum profile. To analyze the transfer dynamics governed by such a potential, we need an approach that goes beyond the question whether the transfer is concerted or stepwise.To elucidate the effect of proton-proton correlation...

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“…Also it has been established that amidines can form strong hydrogen-bonded complexes with itself [17,18], formic acid [19][20][21], formamide [22,23], glycinamide [24], water [21,25], and alcohols [26]. In the study of these hydrogen-bonded complexes, much attention has been paid to proton transfer, particularly multiproton transfer, because it plays an important role in the proton relay occurring in enzymatic reactions, transport phenomena in biological membrane, and DNA mutations.…”

Section: Introductionmentioning

confidence: 99%

Prediction and characterization of halogen bonds involving formamidine and its derivatives

Jiang

et al. 2015

Spectrochimica Acta Part A: Molecular and Biomolecular Spectros

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Theoretical Study for Solvent Effect on the Potential Energy Surface for the Double Proton Transfer in Formic Acid Dimer and Formamidine Dimer

Cited by 85 publications

References 34 publications

Theoretical study on the hydrolysis mechanism of N,N-dimethyl-N′-(2′,3′-dideoxy-3′-thiacytidine)formamidine

Theoretical study on the hydrolysis mechanism of N,N-dimethyl-N′-(2′,3′-dideoxy-3′-thiacytidine)formamidine

Multiple Proton Transfer: From Stepwise to Concerted

Prediction and characterization of halogen bonds involving formamidine and its derivatives

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