Hydration effects on the reaction with an open-shell transition state: QM/MM-ER study for the dehydration reaction of alcohol in hot water

Takahashi, Hideaki; Miki, Fumihiro; Ohno, Hajime; Kishi, Ryohei; Ohta, Suguru; Furukawa, Shunsuke; Nakano, Masayoshi

doi:10.1007/s10910-009-9544-2

Cited by 8 publications

(9 citation statements)

References 32 publications

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“…HDO(H 2 O) 6 , to explore the possibility of the water-assisted pathway. [37][38][39][40][41] At the second stage we calculated the free energy landscape with respect to three collective variables (CV), d, f and n, which are found to characterize the reaction in the first stage; d = r 28 À r 27 is the difference in bond distances between C 2 -O 8 and C 2 -O 7 atoms, f is the dihedral angle with respect to the O 7 -C 2 -C 3 -C 4 atoms, and n = n 7 is the hydrogen coordination number of the O 7 atom (see Fig. 2 and eqn (1) below for the definitions of atomic numbering and the coordination number).…”

Section: Methodsmentioning

confidence: 99%

The reaction mechanism of polyalcohol dehydration in hot pressurized water

Ruiz-Barragan

Ribas‐Ariño

Shiga

2016

Phys. Chem. Chem. Phys.

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The use of high-temperature liquid water (HTW) as a reaction medium is a very promising technology in the field of green chemistry. In order to fully exploit this technology, it is crucial to unravel the reaction mechanisms of the processes carried out in HTW. In this work, the reaction mechanism of 2,5-hexanediol dehydration in HTW has been studied by means of three different ab initio simulations: the string method, metadynamics and molecular dynamics in real time. It is found that the whole reaction involving protonation, bond exchange and deprotonation occurs in a single step without a stable intermediate. The hydrogen bonded network of the surrounding water has a vital role in assisting an efficient proton relay at the beginning and at the end of the reaction. It is confirmed that the reaction is energetically most favorable in the S2 pathway with an estimated barrier of 36 kcal mol, which explains the high stereoselectivity and the reaction rate observed in experiment. The mechanistic insights provided by our study are relevant for a prominent class of reactions in the context of sustainable biomass processing, namely dehydration reactions of polyalcohol molecules.

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Section: Methodsmentioning

confidence: 99%

The reaction mechanism of polyalcohol dehydration in hot pressurized water

Ruiz-Barragan

Ribas‐Ariño

Shiga

2016

Phys. Chem. Chem. Phys.

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“…It should be mentioned that the mechanism of dehydration reactions of dialcohols or glycerol in HTW has been investigated in previous computational works using different simulation techniques. 32,48,49 However, this is the first computational work dealing with selectivity issues when both five-membered and six-membered cyclic ethers can be formed.…”

Section: Introductionmentioning

confidence: 99%

“…In the present study, we carried out first-principles molecular dynamics simulations in the condensed phase (under the same conditions as described in the experiment by Shirai and co-workers) combined with several enhanced sampling techniques with the goal of establishing the mechanism of PTO dehydration in HTW and elucidating the origin of its selectivity. It should be mentioned that the mechanism of dehydration reactions of dialcohols or glycerol in HTW has been investigated in previous computational works using different simulation techniques. ,, However, this is the first computational work dealing with selectivity issues when both five-membered and six-membered cyclic ethers can be formed.…”

Section: Introductionmentioning

confidence: 99%

Understanding Competition of Polyalcohol Dehydration Reactions in Hot Water

et al. 2019

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Dehydration of biomass-derived polyalcohols has recently drawn attention in green chemistry as a prototype of selective reactions controllable in hot water or hot carbonated water, without any use of organic solvents or metal catalysts. Here we report a free energy analysis based on first-principles metadynamics and blue-moon ensemble simulations to understand the mechanism of competing intramolecular dehydration reactions of 1,2,5-pentanetriol (PTO) in hot acidic water. The simulations consistently predict that the most dominant mechanism is the proton-assisted S N 2 process where the protonation of the hydroxyl group by water and the CO bond breaking and formation occurs in a single step. However the free energy barriers are different between the reaction paths: those leading to five membered ether products, tetrahydrofurfuryl alcohol (THFA), are few kcal/mol lower than those leading to six membered ether products, 3-hydroxytetrahydropyran (3-HTHP). A slight difference is seen in the timing of the protonation of the hydroxyl group of THFA and 3-HTHP on their reaction pathways. The detailed mechanism found from the simulations shows how the reaction paths are selective in hot water and why the reaction rates are accelerated in acidic environments, thus giving a clear explanation of experimental findings for a broad class of competing dehydration processes of polyalcohols.

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“…In the following section, we provide an outline for the QM/MM-ER method. We refer the readers to previous papers − or reviews − for more details.…”

Section: Methodsmentioning

confidence: 99%

Drastic Compensation of Electronic and Solvation Effects on ATP Hydrolysis Revealed through Large-Scale QM/MM Simulations Combined with a Theory of Solutions

et al. 2017

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Hydrolysis of adenosine triphosphate (ATP) is the "energy source" for a variety of biochemical processes. In the present work, we address key features of ATP hydrolysis: the relatively moderate value (about -10 kcal/mol) of the standard free energy, ΔG, of reaction and the insensitivity of ΔG to the number of excess electrons on ATP. We conducted quantum mechanical/molecular mechanical simulation combined with the energy-representation theory of solutions to analyze the electronic-state and solvation contributions to ΔG. It was revealed that the electronic-state contribution in ΔG is largely negative (favorable) upon hydrolysis, due to the reduction of electrostatic repulsion accompanying the breakage of the P-O bond. In contrast, the solvation effect was found to be strongly more favorable on the reactant side. Thus, we showed that a drastic compensation of the two opposite effects takes place, leading to the modest value of ΔG at each number of excess electrons examined. The computational analyses were also conducted for pyrophosphate ions (PPi), and the parallelism between the ATP and PPi hydrolyses was confirmed. Classical molecular dynamics simulation was further carried out to discuss the effect of the solvent environment; the insensitivity of ΔG to the number of excess electrons was seen to hold in solvent water and ethanol.

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Hydration effects on the reaction with an open-shell transition state: QM/MM-ER study for the dehydration reaction of alcohol in hot water

Cited by 8 publications

References 32 publications

The reaction mechanism of polyalcohol dehydration in hot pressurized water

The reaction mechanism of polyalcohol dehydration in hot pressurized water

Understanding Competition of Polyalcohol Dehydration Reactions in Hot Water

Drastic Compensation of Electronic and Solvation Effects on ATP Hydrolysis Revealed through Large-Scale QM/MM Simulations Combined with a Theory of Solutions

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