• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.817-823
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• 2003

We have performed ab initio calculation on the active site of HIV-1 protease. The FEP method was used to determine the binding free energy of four different of protonated states of HIV-1 protease with inhibitor. The structure of the active site and hole structure was taken from the X-ray crystallographic coordinates of the C₂ symmetric inhibitor A74704 protease bound. The active site was modeled with the fragment molecules of binding pocket, acetic acid/ acetate anion (Asp25, Asp125), formamide (amide bond of Thr26/Gly27, Thr126/ Gly127), and methanol as inhibitor fragment. All possibly protonated states of the active site were considered, which were diprotonated state (0, 0), monoprotonated (-1, 0),(0, -1) and diunprotonated state (-1, -1). Once the binding energy Debind, of each model was calculated, more probabilistic protonated states can be proposed from binding energy. From ab-initio results, the FEP simulations were performed for the three following mutations: Ⅰ) Asp25 … Asp125 → AspH25 … Asp125, ⅱ) Asp25 … Asp125 → Asp25 … AspH125, ⅲ) AspH25 … Asp125 → AspH25 … AspH125. The free energy difference between the four states gives the information of the more realistic protonated state of active site aspartic acid. These results provide a theoretical prediction of the protonation state of the catalytic aspartic residues for A74707 complex, and may be useful for the evaluation of potential therapeutic targets.

• Nuclear Engineering and Technology
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• v.53 no.8
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• pp.2570-2575
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• 2021

The exchange behaviors of hydrogen isotopes between protonated lithium metal compounds and deuterated water or tritiated water were investigated. The various protonated lithium metal compounds were prepared by acid treatment of lithium metal compounds with different crystal structures and metal compositions. The protonated lithium metal compounds could more effectively reduce the deuterium concentration in water compared with the corresponding pristine lithium metal compounds. The H⁺ in the protonated lithium metal compounds was speculated to be more readily exchangeable with hydrons in the aqueous solution compared with Li⁺ in the pristine lithium metal compounds, and the exchanged heavier isotopes were speculated to be more stably retained in the crystal structure compared with the light protons. When the tritiated water (157.7 kBq/kg) was reacted with the protonated lithium metal compounds, the protonated lithium manganese nickel cobalt oxide was found to adsorb and retain twice as much tritium (163.9 Bq/g) as the protonated lithium manganese oxide (69.9 Bq/g) and the protonated lithium cobalt oxide (75.1 Bq/g) in the equilibrium state.

• Bulletin of the Korean Chemical Society
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• v.18 no.6
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• pp.657-662
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• 1997

Gas-phase phenyl group migration within the protonated ketones has been studied MO theoretically using the AM1 method. The initial state structure shows relatively strong resonance delocalization of positive charge into the nonmigrating (Y) ring, while the ring migration (Z-ring) is nearly complete in the transition state. These results are reflected in the large $p^+_Z$ (<0) and $p^+_$Y (>0) values and in the predominant contribution of resonance (r) over inductive (field, f) effect, r/f ranging from 1.3 ($p^+_r$) to 1.5 ($p^+_z$). The cross-interaction constant $p_{YZ}$ is vanishingly small ($p_{YZ}$=0.03) which is in contrast to the larger magnitudes for benzilic ($p_{YZ}$=-0.48) and azibenzil ($p_{YZ}$=-0.53) rearrangement processes. The relationship found between the extent of resonance contribution in the initial state and the magnitude of $p_{YZ}$ provides strong support for the proportionality between the magnitude of $p_{YZ}$ and the change in the intensity of interaction, ${\Delta}I^{\cdot}_{YZ}$, in the activation process.

• Bulletin of the Korean Chemical Society
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• v.11 no.3
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• pp.194-200
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• 1990

Various mechanistic aspects of the A2 hydrolysis of methyl acetimidate were explored using the MNDO method. As in thecorresponding reactions of acetamide and methyl carbamate, a proton transfer pre-equilibrium exists between the N-protonated and the O-protonated tautomers, and the subsequent hydrolysis proceeds from the more stable N-protonated form. Of the two reaction pathways, the $A_{AL}2$ path is favored in the gas phase and in concentrated acid solutions, whereas the $A_{AC}2$ path is favored in less acidic solutions with a stable cationic tetrahedral intermediate formed in the rate determining step. Negative charge development on the alkoxy oxygen in the transition state suggested a rate increase with the increase in the electron withdrawing power of the alkoxy group. Calculations on the reaction processes with AM1 indicated that MNDO is more reliable in this type of work, although AM1 is better than MNDO in reproducing hydrogen bonds.

• Journal of Photoscience
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• v.9 no.2
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• pp.302-304
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• 2002

pharaonis phoborhodopsin (ppR), a photophobic sensor of haloalkaliphilic bacteria, Natronobacterium phar-aonis, has retinal as a chromophore covalently bound to Lys in G-helix via a protonated Schiff base (PSB), as is the same as bacteriorhodopsin (bR). For ppR, the corresponding counter-ion is Asp residue (Asp75) located in C-helix. Here we investigated the influence of the protonated state of this counter-ion and its location on the chromophore configuration. Under alkaline condition, the chromophore configuration of D75E mutant was analyzed by HPLC. D75E had a much larger content of 13-cis isomer: the ratio of 13-cis to all-trans was 6:4 while the wild-type had this ratio of 1 :9. On the other hand, under acidic condition where Glu was associated, D75E had no 13-cis retinal isomer. Mutants whose Asp75 was replaced by neutral amino acids (D75N and D75Q) did not contain 13-cis retinal. Furthermore, retinal isomer compositions and the change in the visible ab- sorption spectra (indicating the dissociation state of Glu75) were measured under varying pH, and these were almost the same dependencies. These results indicate that an important factor determining the 13-cis isomer content is the presence of negative charge of the counter-ion against PSB, but not the size of this residue. Com- parison between the wild-type and D75E in alkaline solutions indicates the influence of the location of the counter-ion.

• Journal of Photoscience
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• v.11 no.32
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• pp.71-74
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• 2004

The macrocycle L exhibited a switch on-off behavior through the fluorescent responses by aromatic imine molecule 1 (X=H) / trifluoroacetic acid (TFA). In the 'switch on' state, it was supposed that the aromatic imine molecule 1 is in the cavity of macrocycle L and a photoinduced electron transfer (PET) from the nitrogen of azacrown part to the anthryl group is inhibited by the interaction between the aromatic imine molecule 1 and the azacrown part of macrocycle L. In the 'switch off' state, it was supposed that the protonated imine molecule 1 is induced by the continuous addition of TFA and a repulsion between the protonated azacrown part and the protonated imine molecule 1 is occurred. It was considered that this process induces the intermolecular PET from the protonated imine molecule 1 to the anthryl group of macrocycle L because of a proximity effect between the anthryl group and the protonated imine molecule 1. From the investigation of the transient emission decay curve, the macrocycle L showed three components (3.45 ns (79.72%), 0.61 ns (14.53%), and 0.10 ns (5.75%). When the imine molecule 1 was added in the macrocycle L as molar ratio=1:1, the first main component showed a little longer lifetime as 3.68 ns (82.75%) although the other two components were similar as 0.64 ns (14.28%) and 0.08 ns (2.96%). On the contrary, when the imine molecule 3 (X=C1) was added in the macrocycle L as molar ratio=l:1, all the three components were decreased such as 3.27 ns (69.83%), 0.44 ns (13.24%), and 0.06 ns (16.93%). The fluorescent pH titration of macrocycle L was carried out from pH=3 to pH=9. The macrocycle L and C $U^{2+}$- macrocycle L complex were intersected at about pH=5, while the E $u^{3+}$ -macrocycle L complex was intersected at about pH=5.5. In addtion, we investigated the fluorescence change of macrocycle L as a function of the substituent constant ($\sigma$$_{p}$$^{o}$) showing in the para-substituent with electron withdrawing groups (X=F, Cl) and electron donating groups (X=C $H_3$, OC $H_3$, N(C $H_3$)$_2$), respectively, as well as non-substituent (X=H).).ctively, as well as non-substituent (X=H).

• Bulletin of the Korean Chemical Society
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• v.19 no.9
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• pp.993-999
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• 1998

Acid catalyzed hydrolysis of 1-phenoxyethyl propionate, Ⅰ, has been studied using the PM3 method in the gas phase. The first step of the reaction is the protonation of basic sites, three different oxygens in Ⅰ, producing three protonated species Ⅱ, Ⅲ and Ⅳ. All possible reaction pathways have been studied from each protonated structure. Changes in the reaction mechanisms have also been discussed from the results obtained by varying a nucleophile from a water monomer to a water dimer to a complex between one water molecule and an intermediate product (propionic acid or phenol) produced in the preceding unimolecular dissociation processes. Minimum energy reaction pathway is 2-W among the possible pathways, in which water dimer acts as an active catalyst and therefore facilitates the formation of a six-membered cyclic transition state. Lower barrier of 2-W is ascribed to an efficient bifunctional catalytic effect of water molecules. PM3-SM3.1 single point calculations have been done at the gas-phase optimized structure (SM3.1/PM3//PM3) to compare theoretical results to those of experimental work.

• Bulletin of the Korean Chemical Society
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• v.21 no.5
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• pp.477-482
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• 2000

Phenyl group migration within protonated 1,2-diphenyl hydrazines has been studied theoretically using the semi-empirical AM1 method. This reaction proceeds through a 3-membered cyclic transition state and requires high activation energy. In the reactant, there was no resonance stabilization for the moving Z-ring, however, hammett $p_Z^+$ values are large due to the direct involvement of the Z-ring inthe reaction, and the development of a negative charge on the reaction center gives them a posifive value. In the case of the non-moving ring, $p_Y^+$ values are small and negative owing to the smaller positive charge increase in the reaction center. The cross-interaction constant, $p_YZ^+$, was obtained from the activation enthalpies, using the multipe linear regression methdo, and the interaction between two substituents, Y and Z, is examined.

• Bulletin of the Korean Chemical Society
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• v.10 no.2
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• pp.151-154
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• 1989

4-Methoxy-4-methylcyclohexa-2,5-dienone 1 in aqueous sulfuric acid underwent the normal dienone-phenol rearrangement with methyl group migration. The fact that methyl is migrating group and methoxy is remaining group can be rationalized by the stabilization of positive charge at C-4 during the transition state. Methoxy methyl dienone 1 $((H_0)_{1/2} = - 4.6)$ is less basic than 4,4-dimethylcyclohexa-2,5-dienone whose half protonation acidity is reported as - 3.15 or - 3.66. This basicity difference comes from the unstabilization of the protonated methoxy methyl dienone 1 due to the electron withdrawing inductive effect of a methoxy group.

• Journal of the Korean Chemical Society
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• v.24 no.3
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• pp.201-208
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• 1980

The CNDO/2 MO method has been used to study gas phase reactions of protonated acetaldehyde with alcohols and protonated acetic acid with alcohols respectively by optimizing state geometries. Results showed that the former is predicted to proceed by alkyl-O cleavage and the latter by acyl-O cleavage. It has also been found using eigenvector properties of reactants that the former should be a charge controlled while the latter an orbital controlled reaction. According to the calculated activation energies assuming the transition states proposed by Caserio et al., the predicted reactivity order for alcohols agreed with the experiments for the latter but the order predicted was the reverse of the experimental one for the former.