• Proceeding of EDISON Challenge
• /
• 2014.03a
• /
• pp.141-155
• /
• 2014

Peptide bond hydrolysis는 세포 내외의 생화학반응에 있어서 핵심이다. 하지만 amide Hydrolysis Mechanism은 아직 명확하게 규명되지 않았다. pH가 중성인 물에서의 비 촉매 가수분해가 발생하는 몇몇 실험적 증거가 있지만, 해당 반응 매커니즘은 4 가지(non-assisted concerted, non-assisted step-wise, assisted concerted, assisted step-wise)로 여전히 논란이 있다. 이번 연구에서는, Formamide의 가능한 Hydrolysis Mechanism을 자세히 연구해보고자 한다. 먼저, Ab-initio 계산을 통해 4가지 반응 메커니즘의 다시 한번 확인하고, quantum chemical calculations과 quantum mechanical molecular dynamic이 결합된 (QMMD) simulation을 통하여 water solvent에서의 반응 메커니즘의 에너지관계를 규명하였다. 결론적으로 아직 계산이 끝나지 않은 supported concerted mechanism을 제외한 모든 계산에서 non-supported, supported 두 system 모두에서 step-wise가 일어나기 쉬웠고, non-supported 보다 supported mechanism이 선호됨을 보였다. Intermediate인 amino-gem-diol의 수용액 상에서 안정화 또한 나타났다. 이는 Ab-initio 계산만 통해서는 정확하게 산출할 수 없는 엔트로피의 영향을 잘 보여준다.

• Bulletin of the Korean Chemical Society
• /
• v.32 no.5
• /
• pp.1539-1542
• /
• 2011

The aminolysis of O-methyl S-aryl thiocarbonates with benzylamines are studied in acetonitrile at -45.0$^{\circ}C$. The ${\beta}_X$(${\beta}_{nuc}$) values are in the range 0.62-0.80 with a negative cross-interaction constant, ${\rho}_{XZ}$ = -0.42, which are interpreted to indicate a concerted mechanism. The kinetic isotope effects involving deuterated benzylamine nucleophiles ($XC_6H_4CH_2ND_2$) are large, $k_H/k_D$ = 1.29-1.75, suggesting that the N-H(D) bond is partially broken in the transition state by forming a hydrogen-bonded four-center cyclic structure. The concerted mechanism is enforced by the strong push provided by the MeO group which enhances the nucleofugalities of both benzylamine and arenethiolate from the putative zwitterionic tetrahedral intermediate.

• Bulletin of the Korean Chemical Society
• /
• v.32 no.1
• /
• pp.137-140
• /
• 2011

The aminolysis reactions of phenyl N-benzyl thiocarbamate with benzylamines in acetonitrile at $50.0^{\circ}C$ are investigated. The reactions are first order in both the amine and the substrate. Under amine excess, pseudo-first coefficient ($k_{obs}$) are obtained, plot of $k_{obs}$ vs free amine concentration are linear. The signs of ${\rho}_{XZ}$ (< 0) are consistent with concerted mechanism. Moreover, the variations of $\rho_X$ and $\rho_Z$ with respect to the sustituent in the substrate and large ${\rho}_{XZ}$ value indicate that the reactions proceed concerted mechanism. The normal kinetic isotope effects ($k_H/k_D$ = 1.3 ~ 1.5) involving deuterated benzylamine nucleophiles suggest a hydrogen-bonded, four-centered-type transition state. The activation parameters, ${\Delta}H^\ddagger$ and ${\Delta}S^\ddagger$, are consistent with this transition state structure.

• Bulletin of the Korean Chemical Society
• /
• v.35 no.7
• /
• pp.2081-2085
• /
• 2014

Second-order rate constants ($k_N$) have been measured spectrophotometrically for the reactions of phenyl 2- pyridyl carbonate (6) with a series of cyclic secondary amines in MeCN at $25.0{\pm}0.1^{\circ}C$. The Br${\o}$nsted-type plot for the reaction of 6 is linear with ${\beta}_{nuc}$ = 0.54, which is typical for reactions reported previously to proceed through a concerted mechanism. Substrate 6 is over $10^3$ times more reactive than 2-pyridyl benzoate (5), although the reactions of 6 and 5 proceed through the same mechanism. A combination of steric hindrance, inductive effect and resonance contribution is responsible for the kinetic results. The reactions of 6 and 5 proceed through a cyclic transition state (TS) in which H-bonding interactions increase the nucleofugality of the leaving group (i.e., 2-pyridiniumoxide). The enhanced nucleofugality forces the reactions of 6 and 5 to proceed through a concerted mechanism. In contrast, the corresponding reaction of 4-nitrophenyl 2-pyridyl carbonate (7) proceeds through a stepwise mechanism with quantitative liberation of 4-nitrophenoxide ion as the leaving group, indicating that replacement of the 4-nitrophenoxy group in 7 by the PhO group in 6 changes the reaction mechanism (i.e., from a stepwise mechanism to a concerted pathway) as well as the leaving group (i.e., from 4-nitrophenoxide to 2-pyridiniumoxide). The strong electron-withdrawing ability of the 4-nitrophenoxy group in 7 inhibits formation of a H-bonded cyclic TS. The presence or absence of a H-bonded cyclic TS governs the reaction mechanism (i.e., a concerted or stepwise mechanism) as well as the leaving group (i.e., 2-pyridiniumoxide or 4-nitrophenoxide).

• Bulletin of the Korean Chemical Society
• /
• v.34 no.8
• /
• pp.2325-2329
• /
• 2013

Second-order rate constants $k_N$ have been measured for reactions of benzyl 2-pyridyl thionocarbonate (4b) and t-butyl 2-pyridyl thionocarbonate (5b) with a series of cyclic secondary amines in MeCN at $25.0{\pm}0.1^{\circ}C$. The $k_N$ values for the reactions of 4b and 5b have been compared with those reported previously for the corresponding reactions of benzyl 2-pyridyl carbonate (4a) and t-butyl 2-pyridyl carbonate (5a) to investigate the effect of changing the electrophilic center from C=O to C=S on reactivity and reaction mechanism. The thiono compound 4b is more reactive than its oxygen analogue 4a. The Br${\o}$nsted-type plots for the reactions of 4a and 4b are linear with ${\beta}_{nuc}=0.57$ and 0.37, respectively. The reactions of 4a were previously reported to proceed through a concerted mechanism, while those of 4b in this study have been concluded to proceed through a stepwise mechanism with formation of an intermediate being the rate-determining step on the basis of the ${\beta}_{nuc}$ value of 0.37. Enhanced polarizability upon changing the C=O in 4a by C=S has been suggested to be responsible for the reactivity order and the contrasting reaction mechanisms. In contrast, the reactivity of 5a and 5b is similar, but they are much less reactive than 4a and 4b. Furthermore, the reactions of 5a and 5b have been concluded to proceed through the same mechanism (i.e., a concerted mechanism) on the basis of linear Bronsted-type plots with ${\beta}_{nuc}=0.45$ or 0.47. It has been concluded that the strong steric hindrance exerted by the t-Bu in 5a and 5b causes a decrease in their reactivity and forces the reactions to proceed through a concerted mechanism.

• Bulletin of the Korean Chemical Society
• /
• v.33 no.10
• /
• pp.3253-3257
• /
• 2012

Second-order rate constants for the reactions of phenyl Y-substituted-phenyl carbonates 5a-g with Z-substituted-phenoxides ($k_{Z-PhO^-}$) have been measured spectrophotometrically in 80 mol % $H_2O$/20 mol % DMSO at $25.0{\pm}0.1^{\circ}C$. 4-Nitrophenyl phenyl carbonate (5e) is up to 235 times more reactive than 4-nitrophenyl benzoate (4e). The Br$\o$nsted-type plot for the reactions of 5e with Z-substituted-phenoxides is linear with ${\beta}_{nuc}=0.54$, which is typical for reactions reported previously to proceed through a concerted mechanism. Hammett plots correlated with ${\sigma}^o$ and ${\sigma}^-$ constants for the reactions of 5a-f with 4-chlorophenoxide exhibit highly scattered points. In contrast, the Yukawa-Tsuno plot results in an excellent linear correlation with ${\rho}_Y=1.51$ and r = 0.52, indicating that the leaving-group departure occurs at the rate-determining step (RDS). A stepwise mechanism, in which leaving-group departure occurs at RDS, has been excluded since the incoming 4-$ClPhO^-$ is more basic and a poorer nucleofuge than the leaving Y-substituted-phenoxides. Thus, the reaction has been concluded to proceed through a concerted mechanism. Our study has shown that the modification of the nonleaving group from benzoyl to phenyloxycarbonyl causes a change in the reaction mechanism (i.e., from a stepwise mechanism to a concerted pathway) as well as an increase in the reactivity.

• Bulletin of the Korean Chemical Society
• /
• v.30 no.10
• /
• pp.2403-2407
• /
• 2009

Second-order rate constants have been measured for two series of nucleophilic displacement reactions, i.e., reactions of 4-nitrophenyl benzoate with Z-substituted phenoxides and those of Y-substituted phenyl benzoates (1a-h) with 4-chlorophenoxide (4-ClPhO–) in 80 mol% $H_2O$/20 mol% DMSO at 25.0 ${\pm}\;0.1\;{^{\circ}C}$. The Br$\phi$nsted-type plot for reactions of 4-nitrophenyl benzoate with Z-substituted phenoxides exhibits an excellent linear correlation with ${\beta}_{nuc}$ = 0.72. Reactions of 1a-h with 4-chlorophenoxide result in also a linear Br$\phi$nsted-type plot with ${\beta}_{lg}$ = –0.62, a typical ${\beta}_{lg}$ value for a concerted mechanism. The Hammett plots correlated with ${\sigma}^o\;and\;{\sigma}^-$ constants show many scattered points for reactions of 1a-h with 4-chlorophenoxide. In contrast, the corresponding Yukawa-Tsuno plot exhibits an excellent linear correlation with $\rho_Y$ = 2.26 and r = 0.53, indicating that expulsion of the leaving group occurs at the rate-determining step (RDS) either in a concerted mechanism or in a stepwise pathway. However, a stepwise mechanism with leaving group departure being the RDS is excluded since the leaving Y-substituted phenoxide is less basic and a better nucleofuge than the incoming 4-ClPh$O^-$. Thus, the reactions have been concluded to proceed through a concerted mechanism, in which bond formation between the nucleophile and electrophilic center is more advanced than expulsion of the leaving group in the transition state on the basis of the magnitude of ${\beta}_{nuc}\;and\;{\beta}_{lg}$ values.

• Bulletin of the Korean Chemical Society
• /
• v.31 no.3
• /
• pp.689-693
• /
• 2010

Second-order rate constants ($k_{CN^-}$) have been measured for nucleophilic substitution reactions of Y-substituted phenyl benzoates (1a-r) with $CN^-$ ion in 80 mol % $H_2O$/20 mol % DMSO at $25.0{\pm}0.1^{\circ}C$. The Br${\o}$nsted-type plot is linear with ${\beta}_{1g}$ = -0.49, a typical ${\beta}_{1g}$ value for reactions reported to proceed through a concerted mechanism. Hammett plots correlated with ${\sigma}^{\circ}$ and ${\sigma}^-$ constants exhibit many scattered points. In contrast, the Yukawa-Tsuno plot for the same reaction exhibits excellent linearity with ${\rho}_Y$ = 1.37 and r = 0.34, indicating that a negative charge develops partially on the oxygen atom of the leaving aryloxide in the rate-determining step (RDS). Although two different mechanisms are plausible (i.e., a concerted mechanism and a stepwise pathway in which expulsion of the leaving group occurs at the RDS), the reaction has been concluded to proceed through a concerted mechanism on the basis of the magnitude of ${\beta}_{1g}$ and ${\rho}_Y$ values.

• Bulletin of the Korean Chemical Society
• /
• v.31 no.7
• /
• pp.2015-2018
• /
• 2010

Second-order rate constants $(k_{OH^-})$ have been measured spectrophotometrically for alkaline hydrolysis of Y-substituted phenyl phenyl carbonates (2a-j) and compared with the $k_{OH^-}$ values reported previously for the corresponding reactions of Y-substituted phenyl benzoates (1a-j). Carbonates 2a-j are 8~16 times more reactive than benzoates 1a-j. The Hammett plots correlated with $\sigma^-$ and $\sigma^o$ constants exhibit many scattered points, while the Yukawa-Tsuno plot results in excellent linear correlation with $\rho$ = 1.21 and $\gamma$ = 0.33. Thus, the reaction has been concluded to proceed through a concerted mechanism in which expulsion of the leaving group is advanced only a little. However, one cannot exclude a possibility that the current reaction proceeds through a forced concerted mechanism with a highly unstable intermediate.

• Bulletin of the Korean Chemical Society
• /
• v.33 no.8
• /
• pp.2719-2723
• /
• 2012

A kinetic study is reported for nucleophilic substitution reactions of benzyl 4-pyridyl carbonate 6 with a series of alicyclic secondary amines in MeCN. The plot of pseudo-first-order rate constant ($k_{obsd}$) vs. [amine] curves upward, which is typical for reactions reported previously to proceed through a stepwise mechanism with two intermediates (i.e., a zwitterionic tetrahedral intermediate $T^{\pm}$ and its deprotonated form $T^-$). Dissection of $k_{obsd}$ into the second- and third-order rate constants (i.e., $Kk_2$ and $Kk_3$, respectively) reveals that $Kk_3$ is significantly larger than $Kk_2$, indicating that the reactions proceed mainly through the deprotonation pathway (i.e., the $k_3$ process) in a high [amine] region. This contrasts to the recent report that the corresponding aminolysis of benzyl 2-pyridyl carbonate 5 proceeds through a forced concerted mechanism. An intramolecular H-bonding interaction was suggested to force the reactions of 5 to proceed through a concerted mechanism, since it could accelerate the rate of leaving-group expulsion (i.e., an increase in $k_2$). However, such H-bonding interaction, which could increase $k_2$, is structurally impossible for the reactions of 6. Thus, presence or absence of an intramolecular H-bonding interaction has been suggested to be responsible for the contrasting reaction mechanisms (i.e., a forced concerted mechanism for the reaction of 5 vs. a stepwise mechanism with $T^{\pm}$ and $T^-$ as intermediates for that of 6).