• Bulletin of the Korean Chemical Society
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• 제16권5호
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• pp.410-416
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• 1995

The proton transfer energies of gas phase glycine and alanine and those of hydrated glycine and alanine were calculated both with Hartree-Fock and $M{\Phi}ller-Plesset$ ab initio molecular orbital (MO) calculations with 6-31G** basis set. The transition states of the proton transfer of gas phase glycine was also investigated. For zwitterions, both for glycine and alanine, the water bound to -NH3+ site stabilize the complex more compared with the water bound to -CO2-. The proton transfer energy, ΔEpt, of glycine, alanine, mono-hydrated glycine, mono-hydrated alanine, di-hydrated glycine and di-hydrated alanine were obtained as 30.78 (MP2: 22.57), 31.43, 23.99 (MP2: 17.00), 24.98, 22.87, and 25.63 kcal/mol, respectively. The activation energy for proton transfer from neutral (Nt) glycine to zwitterion (Zw) glycine, Ea, was obtained as 16.13 kcal/mol and that for reverse process, Ear, was obtained as 0.85 kcal/mol. Since the transition state of the proton transfer of gas phase glycine locate near the glycine zwitterion on the potential energy surface and the shape of the potential well of the zwitterion is shallow, the zwitterion easily changed to neutral glycine through the proton transfer.

• Bulletin of the Korean Chemical Society
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• 제14권4호
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• pp.491-496
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• 1993

A class A ${\beta}$-lactamase from Staphylococcus aureus PC1 complexed with 3R,5R-clavulanate is studied. The starting geometry for the computation is the crystal structure of the ${\beta}$-lactamase. Docking of the clavulanate to the enzyme is done exploiting the requirements of electrostatic and shape complementarity between the enzyme and clavulanate. This structure is then hydrated by water molecules and refined by energy minimization and short molecular dynamics simulation. In the energy refined structure of this complex, the carboxyl group of the clavulanate is hydrogen bonded to Lys-234, and the the carbonyl carbon atom of the clavulanate is adjacent to the $O_{\gamma}$ of Ser-70. It is found that a crystallographic water molecule initially located at the oxyanion hole, which is formed by the two -NH group of Ser-70 and Gln-237, is replaced by the carbonyl oxygen atom of the 3R,5R-clavulanate after docking and energy reginement. The crystallographic water molecules are proved to be important in ligand binding. Glu-166 residue is found to be repulsive to the binding of clavulanate, which is in agreement with experimental observation. Arg-244 residue is found to be important to the binding of clavulanate as well as to interaction with C2 side chain of the clavulanate. The electron density redistribution of the clavulanate on binding to the ${\beta}$-lactamase in studied by an ab initio quantum-mechanical calculation. A significant redistribution of electron density of the clavulanate is induced by the enzyme, toward the enzyme, toward the transition state of the enzymatic reaction.

• Bulletin of the Korean Chemical Society
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• 제21권5호
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• pp.503-509
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• 2000

The solvent effects on the relative free energies of solvation and the difference in partition coefficients (log P) for $Rb^+$ to $K^+$ mutation in several solvents have been investigated using Monte Carlo simulation (MCS) of statistical perturbation theory(SPT). In comparing the relative free energies for interconversion of one ion pair, $Rb^+$ to $K^+$, in $H_2O$(TIP4P) in this study with the relative free energies of the computer simulations and the experimental, we found that the figure in this study with the relative free energies of the computert simulations and the experimental, we found that the figure in this study is $-5.00\pm0.11$ kcal/mol and those of the computer simulations are $-5.40\pm1.9$, -5.5, and -5.4 kcal/mol. The experimental is -5.1 kcal/mol. There is good agreement among various studies, taking into account both methods used to obtain the hydration free energies and standard deviations. There is also good agreement between the calculated structural properties of this study and the simulations, ab initio and the experimental results. We have explained the deviation of the relationship between the free energy difference and the Onsager dielectric function of solvents by the electron pair donor properties of the solvents. For the $Rb^+$ and $K^+$ ion pair, the Onsager dielectric function of solvents (or solvent permittivity), donor number of solvent and the differences in solvation dominate the differences in the relative free energies of solvation and partition coefficients.

• Bulletin of the Korean Chemical Society
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• 제20권9호
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• pp.1067-1072
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• 1999

Structures of unprotonated [(NH3)n+(n = 1-6)] and protonated [NH4+(NH3)n-1(n = 1-6)] ammonia cluster cations have been optimized with ab initio Hartree-Fock (HF) and second-order MФller-Plesset (MP2)/6-31+G ** levels and the harmonic vibrational frequencies have also been evaluated. In unprotonated cluster cations, NH3+ forms as a central core of the first ammonia solvation shell. In protonated cluster cations, NH4+ forms as a central core. In unprotonated dimer and trimer cations, there are two types of isomers (hydrogen-bonded and head-to-head interactions). In both cluster cations, the hydrogen-bonded isomers are more stable. In the hydrogen-bonded dimer cation, the proton transfer reaction takes place from (NH3-HN+H2) to (NH4+-NH2). But in the other unprotonated cluster cations, the proton transfer does not take place. In unprotonated pentamer and hexamer, a NH3+ core has both interactions in a complex. On the other hand, in unprotonated tetramer a core has only the hydrogen-bonded type combined with neutral ammonia molecules. With increasing cluster cation size, the bond lengths [R(NN)] between two nitrogen atoms and the distances [R(N ...H)] of the hydrogen-bond increase reg-ularly. In the calculated infra-red absorption bands for ammonia cluster cations, the characteristic peaks of the bridged NH vibration of the hydrogen-bonded clusters appear near 2500 cm-1 . With increasing size, the peaks shift from 2306 cm-1 to 2780 cm-1 .

• Bulletin of the Korean Chemical Society
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• 제20권10호
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• pp.1177-1180
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• 1999

The ab initio SCF MO and density functional theory (DFT) studies are carried out on the electrophilic (1a) and electron transfer (1b) addition reactions to the vinyl double bond of aryl vinyl sulfides and ethers. In the electrophilic addition processes, a double bond shift from C3 = C4 to X = C3 occurs with occupation number (1.97) close to the normal two. Due to this shift direct conjugation between the cationic center, X = S or O, and the para electron-donor substituent becomes impossible so that the reaction energies (or log K) are correlated with σ rather than σ+. By contrast, radical cation formation leads to delocalization of the SOMO, a lone-pair πorbital on X, with four major resonance structures in which cationic charge as well as spin density is delocalized over C4 , X and C7 atoms. As a result, partial πbonds are formed over C1 -X and C3 - C4 with occupation numbers (0.82) lower than one. In two of the cannonical structures, III(Ⅹ) and III(X+), direct conjugation between the cationic center, X, and the para substituent is achieved so that a better correlation with σ+ rather than σis obtained. The SCF MO energies at the HF/3-21G* and HF/6-31G* levels lead to very much inferior Hammett correlations in the σ/ σ+ diagnostic criterion. In contrast, the ρvalues evaluated with the DFT energies can give reliable diagnostic distinction between the two addition mechanisms.

• Bulletin of the Korean Chemical Society
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• 제20권11호
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• pp.1281-1287
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• 1999

The low-lying electronic states of diazirine and 3,3'-dimethyldiazirine have been studied by high level ab initio quantum chemical methods. The equilibrium geometries of the ground state and the first excited singlet and triplet states have been optimized using the Hartree-Fock (HF) and complete active space SCF (CASSCF) methods, as well as using the Møller-Plesset second order perturbation (MP2) theory and the single configuration interaction (CIS) theory. It was found that the first excited singlet state is of 1 B1 symmetry resulting from the n- π* transition, while the first excited triplet state is of 3 B2 symmetry resulting from the π- π* transition. The harmonic vibrational frequencies have been calculated at the optimized geometry of each electronic state, and the scaled frequencies have been compared with the experimental frequencies available. The adiabatic and vertical transition energies from the ground electronic state to the low-lying electronic states have been estimated by means of multireference methods based on the CASSCF wavefunctions, i.e., the multiconfigurational quasidegenerate second order perturbation (MCQDPT2) theory and the CASSCF second-order configuration interaction (CASSCF-SOCI) theory. The vertical transition energies have also been calculated by the CIS method for comparison. The computed transition energies, particularly by MCQDPT2, agree well with the experimental observations, and the electronic structures of the molecules have been discussed, particularly in light of the controversy over the existence of the so-called second electronic state.

• Bulletin of the Korean Chemical Society
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• 제7권4호
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• pp.262-266
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• 1986

A multi-reference many-body perturbation theory (MRMBPT) method is critically tested in second order by comparing with the corresponding configuration interaction (CI) calculations. Excitation energies of the four-valence-electron states of transition metal atoms and ions are used for the comparison. The agreement between the second order MRMBPT and CI calculations is very reasonable, confirming the reliability of the second order MRMBPT method. The reliability of calculations with the present second order MRMBPT method was only been inferred empirically in the past since most results have been gauged by the agreement with experiment and/or with other MRMBPT calculations based upon different sets of orbitals and configuration spaces. The present MRMBPT method appears to be an efficient ab initio multi-reference method for the calculation of electron correlation effects in atoms and molecules, and it is shown how MRMBPT can be used to estimate core-core and core-valence correlation effects which are often omitted in CI calculations because too many configurations and correlating electrons are involved.

• Bulletin of the Korean Chemical Society
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• 제9권3호
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• pp.153-156
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• 1988

Ab initio calculations are performed for $ArCO_2^+$ and $ArCO_2$. Between the two configurations of $ArCO_2^+$ the orbital interactions and the higher order correlation calculations favor the T-shape, and their interaction energies are calculated to be approximately half the experimental values using 6-31G$^{\ast}$ basis set. In $ArCO_2$, the calculations qualitatively favor the T-structure, which is compatible with the experiment. However, the true interaction energy is obscured since it is within the BSSE limit at this basis set size and the correlation level. Addition of sp type diffuse functions increase the interaction energies by a considerable amount, but the BSSE estimated by CP method are responsible for the significant portion of the difference. The possible equilibrium structure of the $Ar^+-CO_2$ complex, where the charge is localized on Ar, is suggested as having a linear structure. The potential energy surface and the amount of charge transfer are shown to be sensitive to the type and balancing of basis set.

• 대한화학회지
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• 제67권5호
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• pp.333-338
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• 2023

In this study, the H₂O reaction with SiO clusters was investigated using ab initio Monte Carlo simulations and density functional theory calculations. Three chemistry models, PBE1/DGDZVP (Model 1), PBE1/DGDZVP (Si atom), and aug-cc-pVDZ (O and H atoms), (Model 2) and PBE1/aug-cc-pVDZ (Model 3), were used. The average bond lengths, as well as the relative and reaction energies, were calculated using Models 1, 2, and 3. The average bond lengths of Si-O and O-H are 1.67-1.75 Å and 0.96-0.97 Å, respectively, using Models 1, 2, and 3. The most stable structures were formed by the H transfer from an H₂O molecule except for Si₃O₃-H₂O-1 cluster. The Si₃O₃ cluster with H₂O exhibited the lowest reaction energy. In addition, the Bader charge distributions of the Si_nO_n and (SiO)_n-H₂O clusters with n = 1-7 were calculated using Model 1. We determined that the reaction sites between H₂O and the SiO clusters possessed the highest fraction of electrons.

• Genomics & Informatics
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• 제21권3호
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• pp.41.1-41.11
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• 2023

The Dengue virus M protein is a 75 amino acid polypeptide with two helical transmembranes (TM). The TM domain oligomerizes to form an ion channel, facilitating viral release from the host cells. The M protein has a critical role in the virus entry and life cycle, making it a potent drug target. The oligomerization of the monomeric protein was studied using ab initio modeling and molecular dynamics simulation in an implicit membrane environment. The representative structures obtained showed pentamer as the most stable oligomeric state, resembling an ion channel. Glutamic acid, threonine, serine, tryptophan, alanine, isoleucine form the pore-lining residues of the pentameric channel, conferring an overall negative charge to the channel with approximate length of 51.9 Å. Residue interaction analysis for M protein shows that Ala94, Leu95, Ser112, Glu124, and Phe155 are the central hub residues representing the physicochemical interactions between domains. The virtual screening with 165 different ion channel inhibitors from the ion channel library shows monovalent ion channel blockers, namely lumacaftor, glipizide, gliquidone, glisoxepide, and azelnidipine to be the inhibitors with high docking scores. Understanding the three-dimensional structure of M protein will help design therapeutics and vaccines for Dengue infection.