• Bulletin of the Korean Chemical Society
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• v.33 no.6
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• pp.1913-1918
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• 2012

The nitramine explosives with $-NH_2$ and -F groups were optimized to obtain their molecular geometries and electronic structures at DFT-B3LYP/6-31+G(d) level. The theoretical molecular density (${\rho}$), heat of formation (HOF), detonation velocity ($D$) and detonation pressure ($P$), estimated using Kamlet-Jacobs equations, showed that the detonation properties of these compounds were excellent. Based on the frequencies scaled by 0.96 and the principle of statistic thermodynamics, the thermodynamic properties were evaluated, which were respectively related with the temperature. The simulation results reveal that 1,3,5,7-tetranitro-1,3,5,7-tetrazocan-2-amine (molecule B1) performs similarly to the famous explosive HMX, and 2-fluoro-1,3,5-trinitro-1,3,5-triazinane (molecule C1) and 2-fluoro-1,3,5,7-tetranitro-1,3,5,7-tetrazocane (molecule D1) outperform HMX. According to the quantitative standard of energetics and stability as an HEDC (high energy density compound), molecules C1 and D1 essentially satisfy this requirement. These results provide basic information for molecular design of novel high energetic density compounds.

• Bulletin of the Korean Chemical Society
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• v.34 no.10
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• pp.3093-3097
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• 2013

The synthesis, X-ray crystallography, spectroscopic (IR, UV-vis), and electrochemical properties of the title compound, $[H_3O][Cr(dipic)_2][H_3O^+.Cl^-]$ (1), ($H_2dipic$ = 2,6-pyridinedicarboxylic acid), are reported. This complex crystallizes in the monoclinic space group Cc with a = 14.9006(10) ${\AA}$, b = 12.2114(8) ${\AA}$, c = 8.6337(6) ${\AA}$, ${\alpha}=90.00^{\circ}$, ${\beta}=92.7460(10)^{\circ}$, ${\gamma}=90.00^{\circ}$, and V = 1569.16(18) ${\AA}^3$ with Z = 4. The hydrogen bonding and noncovalent interactions play roles in the stabilization of the structure. In order to gain a better understanding of the most important geometrical parameters in the structure of the complex, atoms in molecules (AIM) method at B3LYP/6-31G level of theory has been employed.

• Bulletin of the Korean Chemical Society
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• v.27 no.1
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• pp.39-43
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• 2006

The relaxed torsional potential of a liquid crystalline polymer containing an ester functional group in a mesogenic unit (hereafter 12-4 oligomer) has been calculated with the ab initio self-consistent-field using 6-31G$^*$ basis set. GIAO^{13}C NMR chemical shifts also have been calculated at the B3LYP/6-31G$^*$ level of theory for each conformational structure obtained from torsional potential calculation. The results show that the phenyl ring-ester linkages are coplanar with the dihedral angle of about 0$^{\circ}$ and the ring-ring linkages in the biphenyl groups are tilted with the dihedral angle of around 43-44$^{\circ}$ in the lowest energy conformer. The biphenyl ring has a comparatively lower energy barrier of internal rotation potential in the ring-ring than that of phenyl ring-ester. The ^{13}C chemical shifts of carbonyl carbons were found to move to upfield due to $\pi$ -conjugation with phenyl ring and slightly affected about 0.5 ppm by dihedral angle of the ring-ring linkage.

• Bulletin of the Korean Chemical Society
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• v.33 no.8
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• pp.2711-2718
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• 2012

The alkylation of the ambident enolates of a methyl glycinate Schiff base with ethyl chloride was studied at B3LYP and MP2 levels with $6-31+G^*$ basis set. The free (E)-enolates and (Z)-enolate are similar in energy and geometry. The transition states for the alkylation of the free (E)/(Z)-enolate with ethyl chloride have similar energy barriers of ~13 kcal/mol. However, with a lithium ion, the (E)-enolate behaves as an ambident enolate and makes a cyclic lithium-complex in bidentate pattern which is more stable by 11-23 kcal/mol than the (Z)-enolate-lithium complexes. And the TS for the alkylation of (E)-enolate-lithium complex coordinated with one methyl ether is lower in energy than those from (Z)-enolate-lithium complexes by 4.3-7.3 kcal/mol. Further solvation model (SCRF-CPCM) and reaction coordinate (IRC) were studied. This theoretical study suggests that the alkylation of ambident enolates proceeds with stable cyclic bidentate complexes in the presence of metal ion and solvent.

• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.6-13
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• 2015

이 연구는 초기 지구의 대기 환경에서 유기화합물(glycine)이 합성되는 실험(Urey-Miller 실험)에서의 반응 경로를 Deterministic한 방법의 중간체 sampling 방법으로 반응 네트워크를 구성하고 Yen's알고리즘으로 네트워크 내의 최단경로를 제시함으로써 반응물과 생성물이 결정되어 있을 때 최소한의 화학적 직관만을 이용하여 제시하는 것이 목표이다. 이 연구 결과는 2014년도 Nature Chemistry에 발표된 다른 방법론을 적용하여 제시된 Urey-Miller reaction path와 비교해 어떠한 반응이 상대적으로 더 타당한 경로를 제시했을지 알아보았다. 이 연구에서 나온 reaction path에서의 중간체들에 대해 GAMESS를 이용한 B3LYP/6-31g(d,p) DFT계산을 수행하였다. 결과를 분석해보면서 어떤 부분이 부족하며 이 연구에 적용한 방법론을 어떻게 발전시켜나가야 더 나은 결과를 얻을 수 있을지를 함께 고려해 보았다.

• Bulletin of the Korean Chemical Society
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• v.33 no.2
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• pp.641-646
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• 2012

We used the hybrid density-functional (B3LYP/6-31G(d,p)) method to analyze the substitution patterns of $C_{20}H_{18}X_2$ derivatives (X = F, Cl, Br, or OH) obtained as disubstituted $C_{20}H_{20}$ cages. Our results suggest that the cis-1 regioisomers (1,2-dihalo derivatives) are less stable than the trans-1 regioisomers (1,20-dihalo derivatives), whereas in the case of the dihydroxy derivatives, the cis-1 regioisomer is more stable than the trans-1 regioisomer. This implies that in the dihalo-induced strain cages of $C_{20}H_{18}X_2$, the strain effect would affect the relative energies, while in the dihydroxide, the hydrogen bonds have a stronger effect on the relative energies in cis-1 regioisomer than the strain effect do. Thus this supports the experimental result in which the bisvicinal tetrol was of particular preparative-synthetic interest as a substitute for the lacking bisvicinal tetrabromide. Further, the topologies of the HOMO and LUMO characteristics of all $C_{20}H_{18}Cl_2$ and $C_{20}H_{18}Br_2$ regioisomers with the same symmetry are same, but they are different from those of $C_{20}H_{18}F_2$ and $C_{20}H_{18}(OH)_2$. This indicates that the five regioisomers of each $C_{20}H_{20}$ disubstituted derivative will have an entirely different set of characteristic chemical reactions.

• Bulletin of the Korean Chemical Society
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• v.31 no.10
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• pp.2903-2908
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• 2010

Protein S-nitrosation is common in cells under nitrosative stress. In order to model proteins with S-nitrosocysteine (CysSNO) residues, we first developed an Amber force field for S-nitrosoethanethiol (EtSNO) and then transferred it to CysSNO. Partial atomic charges for EtSNO and CysSNO were obtained by a restrained electrostatic potential approach to be compatible with the Amber-99 force field. The force field parameters for bonds and angles in EtSNO were obtained from a generalized Amber force field (GAFF) by running the Antechamber module of the Amber software package. The GAFF parameters for the CC-SN and CS-NO dihedrals were not accurate and thus determined anew. The CC-SN and CS-NO torsional energy profiles of EtSNO were calculated quantum mechanically at the level of B3LYP/cc-pVTZ//HF/6-$31G^*$. Torsional force constants were obtained by fitting the theoretical torsional energies with those obtained from molecular mechanics energy minimization. These parameters for EtSNO reproduced, to a reasonable accuracy, the corresponding torsional energy profiles of the capped tripeptide ACE-CysSNO-NME as well as their structures obtained from quantum mechanical geometry optimization. A molecular dynamics simulation of myoglobin with a CysSNO residue produced a well-behaved trajectory demonstrating that the parameters may be used in modeling other S-nitrosated proteins.

• Corrosion Science and Technology
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• v.21 no.1
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• pp.32-40
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• 2022

The o-Vanillin - Glutamine Schiff base [2-Hydroxy-3-Methoxy BenzylidineCarbomyl) -2-Butanoic Acid] was examined for low carbon steel corrosion inhibition in acid media. Weight loss studies were carried out at three different temperatures to determine the inhibition efficiency (IE). Electrochemical impedance spectroscopy revealed that the charge transfer resistance controlled the corrosion reaction and Tafel polarization indicated that the Schiff base acts as mixed mode of inhibitor. SEM images were recorded for the surface morphology of the low carbon steel surface. DFT studies revealed corrosion control mechanisms using quantum chemical parameters such as E_HOMO, E_LUMO, energy gap (∆E), chemical Hardness (η), chemical Softness (σ), Electronegativity (χ), and the fraction of electron transferred (∆N), which is calculated using Gaussian software 09. The gas-phase geometry was fully optimized in the Density Functional Theory (DFT/B3LYP-6-31G (d)).The DFT results are in good agreement with the experimental results. All the results proved that the Schiff Base (2-Hydroxy-3-Metoxy BenzylidineCarbomyl) -2-Butanoic is a suitable alternative for corrosion inhibition of low carbon steel in acid media.

• Bulletin of the Korean Chemical Society
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• v.34 no.4
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• pp.1232-1236
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• 2013

The Cu cation binding sites of $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex have been investigated to explain the $[Cu{\cdot}DNA]$ biological activity caused by the Cu association to DNA. The structure of $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex was investigated by electrospray ionization mass spectrometry (ESI-MS). The fragmentation patterns of $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex were analyzed by MS/MS spectra. In the MS/MS spectra of $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex, three fragment ions were observed with the loss of d(CpG), {d(CpG) + Cyt}, and {d(CpG) + Cyt + dR}. The Cu cation binds to d(CpG) mainly by substituting the $H^+$ of phosphate group. Simultaneously, the Cu cation prefers to bind to a guanine base rather than a cytosine base. Five possible geometries were considered in the attempt to optimize the $[Cu(I){\cdot}d(CpG){\cdot}d(CpG)-2H]^{-1}$ complex structure. The ab initio calculations were performed at B3LYP/6-31G(d) level.

• Bulletin of the Korean Chemical Society
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• v.23 no.2
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• pp.253-261
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• 2002

Vibrational properties of ferrocyanide complex ion, $[Fe(CN)_6]^{4-}$ , have been studied based on the force constants obtained from the density functional calculations at B3LYP/$6-31G^{\ast\ast}$ level by means of the normal mode analysis using new bond angle and linear angle internal coordinates recently developed. Vibrations of ferrocyanide were manipulated by twenty-three symmetry force constants. The angled bending deformations of C-Fe-C, the linear bending deformations of Fe-C${\equiv}$N and the stretching vibrations of Fe-C have been quantitatively assigned to the calculated frequencies. The force constants in the internal coordinates employed in the modified Urey-Bradley type potential were evaluated on the density functional force field applied, and better interaction force constants in the internal coordinates have been proposed. The valence force constants in the general quadratic valence force field were also given. The stretch-stretch interaction and stretch-bending interaction constants are not sensitive to the geometrical displacement in the valence force field.