• 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.

• 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.

• 대한화학회지
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• 제56권6호
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• pp.669-672
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• 2012

Classical molecular dynamics (MD) simulations using a scaled OSS2 potential originally derived from ab initio calculations are used to study the radial distribution functions of water. The original OSS2 water potential is shown to represent a glassy or an ice at ambient temperature, but the diffusion coefficient increases on increasing the temperature of the system or decreasing the density. This suggests scaling the OSS2 potential. The O-O, O-H, and H-H radial distribution functions and the corresponding coordination numbers for the scaled OSS2 potential, obtained by MD simulation, are in good agreement with the experiment results and calculations for the SPC/E water potential over a range of temperatures.

• 한국표면공학회:학술대회논문집
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• 한국표면공학회 2016년도 추계학술대회 논문집
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• pp.97-97
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• 2016

Development of advanced Li-ion battery cells with high durability is critical for safe operation, especially in applications to electric vehicles and portable electronic devices. Understanding fundamental mechanism on the formation of a solid-electrolyte interphase (SEI) layer, which plays a substantial role in the electrochemical stability of the Li-ion battery, in a cathode was rarely reported unlike in an anode. Using first-principles density functional theory (DFT) calculations and ab-initio molecular dynamic (AIMD) simulations we demonstrate atomic-level process on the generation of the SEI layer at the interface of a carbonate-based electrolyte and a spinel $LiMn_2O_4$ cathode. To accomplish the object we calculate the energy band alignment between the work function of the cathode and frontier orbitals of the electrolyte. We figure out that a proton abstraction from the carbonate-based electrolyte is a critical step for the initiation of an SEI layer formation. Our results can provide a design concept for stable Li-ion batteries by optimizing electrolytes to form proper SEI layers.

• Advances in nano research
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• 제1권3호
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• pp.133-151
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• 2013

The availability of advanced nanotechnological methodologies (experimental and theoretical) has widened the investigation of biological/organic matter in interaction with substrates. Minerals are good candidates as substrates because they may present a wide variety of physico-chemical properties and surface nanostructures that can be used to actively condense and manipulate the biomolecules. Scanning Probe Microscopy (SPM) is one of the best suited techniques used to investigate at a single molecule level the surface interactions. In addition, the recent availability of high performance computing has increased the possibility to study quantum mechanically the interaction phenomena extending the number of atoms involved in the simulation. In the present paper, firstly we will briefly introduce new SPM technological developments and applications to investigate mineral surfaces and mineral-biomolecule interaction, then we will present results on the specific RNA-mineral interaction and recent basics and applicative achievements in the field of the interactions between other fundamental biological molecules and mineral surfaces from both an experimental and theoretical point of view.

• 한국표면공학회지
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• 제56권6호
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• pp.427-436
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• 2023

In the industry, it is recognized that human activities significantly lead to a large amount of wastewater, mainly due to the increased use of water and energy. As a result, the growing field of wastewater resource technology is getting more attention. The common technology for hydrogen production, water electrolysis, requires purified water, leading to the need for desalination and reprocessing. However, producing hydrogen directly from wastewater could be a more cost-effective option compared to traditional methods. To achieve this, a series of first-principle computational simulations were conducted to assess how waste nutrient ions affect standard electrolysis catalysts. This study focused on understanding the adsorption mechanisms of byproducts related to the oxygen evolution reaction (OER) in anion exchange membrane (AEM) electrolysis, using Co₃O₄ as a typical non-precious metal catalyst. At the same time, efforts were made to develop a comprehensive free energy prediction model for more accurate predictions of OER results.

• Journal of Photoscience
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• 제9권2호
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• pp.51-54
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• 2002

We propose a novel mechanism (Twist Sharing Mechanism) for the cis-trans photoisomerization of rhodopsin, based on the molecular dynamics (MD) simulation study. New things devised in our simulations are (1) the adoption of Mt. Fuji potentials in the excited state for twisting of the three bonds C9=C10, C11=C12 and C13=14 which are modeled using the detailed ab initio quantum chemical calculations and (2) to use the rhodopsin structure which was resolved recently by the X-ray crystallographic study. As a result, we found the followings: Due to the intramolecular steric hindrance between 20-methyl and 10-H in the retinal chromophore, the C12-C13 and C10-C11 bonds are considerably twisted counterclockwise in rhodopsin, allowing only counterclockwise rotation of the C11 =C12 in the excited state. The movement of 19-methyl in rhodopsin is blocked by the surrounding three amino acids, Thr 118, Met 207 and Tyr 268, prohibiting the rotation of C9=C10. As a result only all-trans form of the chromophore is obtainable as a photoproduct. At the 90$^{\circ}$ twisting of C11=C12 in the course of photoisomerization, twisting energies of the other bonds amount to about 20 kcal/mol. If the transition state for the thermal isomerization is assumed to be similar to this structure, the activation energy for the thermal isomerization around C11=C12'in rhodopsin is elevated by about 20 kcal/mol and the thermal isomerization rate is decelerated by 10$\^$-14/ times than that of the retinal chromophore in solution, protecting photosignal from the thermal noise.

• 폴리머
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• 제30권6호
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• pp.453-463
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• 2006

분자 모델에 의한 전산 모사는 단백질 접힘, 미셀화, 블록공중합체의 규칙구조화 등 다양한 고분자 계의 자기조립 현상을 예측하거나 그 조립 메커니즘을 밝히는 데 특별히 유용한 연구방법이다. 자기조립 현상은 분자 수, 분자 크기 등, 계의 속성에 따라 나노미터 이하의 현상으로부터 마이크론이나 그 이상의 길이 스케일의 현상까지 조립 구조의 길이 스케일이 매우 광범위하기 때문에 다양한 계의 모든 조립 현상을 양자역학적 방법과 같은 궁극의 근본원칙에 의해 모사하는 것은 현실적인 시간 내에서 불가능하다. 이러한 문제들을 해결하기 위해 계를 기술하는 과정에서 필요 이상으로 세밀한 표현을 생략하여 모델을 다른 관점에서 재구성하는 방법이 있는데 재구성된 모델은 그 관점에 따라 크게 '원자 수준'의 모델과 '메조 스케일 수준'의 모델로 분류할 수 있다. 본 총론에서는 고분자 자기조립 현상과 관련하여 이 두 가지 관점에 따른 모델과 모사 방법들에 대해 살펴보고자 한다.