• Bulletin of the Korean Chemical Society
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• v.26 no.4
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• pp.589-593
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• 2005

The solvation free energy of proton in methanol was calculated by B3LYP flavor of density functional calculations in combination with the Poisson-Boltzmann continuum solvation model. In order to check the adequacy of the computation level, the free energies of clustering in the gas phase were compared with the experimental data. The solvents were taken into account in a hybrid manner, i.e. one to five molecules of methanol were explicitly considered while other solvent molecules were represented with an implicit solvation model.

• JSTS:Journal of Semiconductor Technology and Science
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• v.14 no.4
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• pp.451-456
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• 2014

A compact model of a depletion-mode silicon-nanowire (Si-NW) pH sensor is proposed. This drain current model is obtained from the Pao-Sah integral and the continuous charge-based model, which is derived by applying the parabolic potential approximation to the Poisson's equation in the cylindrical coordinate system. The threshold-voltage shift in the drain-current model is obtained by solving the nonlinear Poisson-Boltzmann equation for the electrolyte. The simulation results obtained from the proposed drain-current model for the Si-NW field-effect transistor (SiNWFET) agree well with those of the three-dimensional (3D) device simulation, and those from the Si-NW pH sensor model also agree with the experimental data.

• Bulletin of the Korean Chemical Society
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• v.23 no.1
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• pp.27-28
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• 2002

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.75-88
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• 2014

본 연구에서는 비선형 Poisson-Boltzmann 식의 해를 구할 수 있는 웹 기반 EPBS를 이용하여 이온채널의 전하 분포와 유전률이 이온채널의 이온선택성에 미치는 영향에 대해 알아본다. 모델로 사용한 이온채널은 이온채널과 유사한 구조를 갖는 합성 단백질인 고리형 펩타이드 나노튜브와 자연계에 존재하는 Gramicidin A 이다. 계산 결과로부터 용매인 물과 단백질의 유전율 차이에 의해 이온이 이온채널을 통과할 때 반응장이 생성되며, 이는 이온과 상호작용을 통해 이온 종류에 관계없이 이온 통과를 방해하는 에너지 장벽을 형성함을 알 수 있다. 한편, 두 이온채널 부분 전하, 특히 골격에 존재하는 카르보닐기의 쌍극자 모멘트에 의해 이온채널 내부에는 0 보다 작은 정전기 퍼텐셜이 형성된다. 이온채널 내부의 총 정전기 퍼텐셜은 이온채널의 부분 전하에 의한 정전기 퍼텐셜과 유전률 차이에 의한 반응장의 합으로 나타나며, 계산 결과 0 보다 작은 값을 갖는다. 이로부터 본 연구에서 사용된 두 종류의 이온채널이 양이온에 선택성이 있음을 알 수 있다.

• Bulletin of the Korean Chemical Society
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• v.31 no.1
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• pp.168-170
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• 2010

• Bulletin of the Korean Chemical Society
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• v.31 no.10
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• pp.3013-3016
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• 2010

• Journal of Integrative Natural Science
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• v.5 no.4
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• pp.216-219
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• 2012

Structure-based drug design possibly benefit from in silico methods that precisely predict the binding affinity of small molecules to target macromolecules. There are many limitations arise from the difficulty of predicting the binding affinity of a small molecule to a biological target with the current scoring functions. There is thus a strong interest in novel methodologies based on MD simulations that claim predictions of greater accuracy than current scoring functions, helpful for a regular use designed for drug discovery in the pharmaceutical industry. Herein, we report a short review on free energy calculations using MMPBSA method a useful method in structure based drug discovery.

• Proceedings of the KSME Conference
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• 2004.11a
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• pp.1528-1533
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• 2004

A numerical investigation is made of transient evolutionary prcocess of electroosmotic flow in a two-dimensional microchannel connected to a reservoir. The channel height is very small so that two electric double layers forming on the charged surfaces are overlapped. Transient transports of ions in the electrolyte solution are computed by integrating the Nernst-Planck equation together with the Poisson equation for electric potential. The numerical results illustrate that there are two distinct transient phases. The physical mechanisms and relevant time scales for the transient evolution are described.

• Bulletin of the Korean Chemical Society
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• v.30 no.12
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• pp.2927-2929
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• 2009

The hydricities of d$^6$ metal hydride complexes in aqueous solution were calculated by using density functional theoretical (DFT) calculations coupled with a Poisson-Boltzmann (PB) solvent model. Hydricity describes the hydride donor ability of the metal-hydrogen bond, which assists in the study of the mechanism of many catalytic processes and chemical reactions that involve transition metal hydrides. The calculation scheme produced hydricity values that were in good agreement with experimental estimation. The inclusion of a water molecule as a weakly bound ligand to five-coordinate metal complexes gave an improved correlation result.

• Bulletin of the Korean Chemical Society
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• v.10 no.6
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• pp.585-591
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• 1989

The effects of the charged metal on the overall electrostatic potential profiles and the capacitances of the electrical double layer are brought out. A model with a simplified jellium and a point-charged electrolyte is utilized in the present calculations. Electrons are assumed not to penetrate electrode surface due to a strong screening of electrolyte at the interface. Electron density functions and ion density functions are obtained, which are also based upon the Poisson equation and Boltzmann equation on either side of the interface. A complete potential profile starting from bulk electrode and ending at bulk electrolyte is obtained by connecting the two potential profiles (one inside the metal electrode, the other inside the electrolyte) with proper boundary conditions. In spite of the simplicity of the model, the present model reveals the importance of the effect of the charged metal on the electrostatic potential profile and the electrical double layer capacitances. The results are discussed and compared with the predictions by Gouy Chapman theory.