• Bulletin of the Korean Chemical Society
• /
• 제24권6호
• /
• pp.712-716
• /
• 2003

The semi-diabatic potential energy surfaces (PESs) of the excited states of polyatomic molecules can be constructed for use in ab initio molecular dynamics (AIMD) studies by relying on the continuity of the electronic energy, oscillator strength, and spherical extent of an excited state along with first derivatives of these quantities as computed by using the equation-of-motion coupled-cluster (EOM-CC) method. The semidiabatic PESs of both the π → $π^*$ valence excited state and the 3s-type Rydberg state of ethylene are presented and discussed in this paper, in conjunction with some of the AIMD results we obtained for these states.

• EDISON SW 활용 경진대회 논문집
• /
• 제3회(2014년)
• /
• pp.425-429
• /
• 2014

Half-metallic nanostructure is highly applicable in the field of Spintronics and electronic device technology. We examine the electronic properties of a ferrocene-based nanowire as a possible candidate for a half-metallic nanostructure using VASP and SIESTA. Ferrocene-based nanowire shows high stability in both binding energy simulation and molecular dynamics (MD) simulation. The density of states (DOS) and the projected DOS of the ferrocene-based nanowire indicate that one-dimensional clustering of ferrocene molecules can be explained because of p-d orbital hybridization between iron and carbon. Half-metallic property and energy dispersion at the Fermi level due to one-dimensional structure is also observed from the DOS results.

• Computers and Concrete
• /
• 제33권3호
• /
• pp.325-340
• /
• 2024

The growing demands for sustainable and high-performance construction materials necessitate a deep understanding of their physicochemical properties by that of these heterogeneities. This paper presents a comprehensive review of the state-of-the-art hierarchical multiscale modeling approach aimed at predicting the intricate physicochemical characteristics of construction materials. Emphasizing the heterogeneity inherent in these materials, the review briefly introduces single-scale analyses, including the ab initio method, molecular dynamics, and micromechanics, through a scale-bridging technique. Herein, the limitations of these models are also overviewed by that of effectively scale-bridging methods of length or time scales. The hierarchical multiscale model demonstrates these physicochemical properties considering chemical reactions, material defects from nano to macro scale, microscopic properties, and their influence on macroscopic events. Thereby, hierarchical multiscale modeling can facilitate the efficient design and development of next-generation construction.

• Bulletin of the Korean Chemical Society
• /
• 제32권2호
• /
• pp.510-514
• /
• 2011

Photodissociation dynamics of allyl alcohol ($H_2C$=CH-$CH_2OH$) has been investigated at 205 - 213 nm along the UV absorption band by measuring rotationally-resolved laser-induced fluorescence spectra of OH radicals. Observed energy partitioning of the available energy among products at all photon energies investigated was similar and the barrier energy for OH production is about 574.7 kJ/mol from the OH yield measurements. The potential energy surfaces for the $S_0$, $T_1$, and $S_1$ excited states along the dissociation coordinate were obtained by ab initio quantum chemical calculations. The observed energy partitioning was successfully modeled by the "barrier-impulsive model" with the reverse barrier and the geometry obtained by the calculated potential energy surfaces. The dissociation takes place on the $T_1$ excited state potential energy surface with an energy barrier in the exit channel and a large portion of the photon energy is distributed in the internal degrees of freedom of the polyatomic products.

• Bulletin of the Korean Chemical Society
• /
• 제20권8호
• /
• pp.948-952
• /
• 1999

Electrophilic substitutions on β-position of 2,5-dimethyl pyrrole have been investigated theoretically. The electron donating methyl groups enrich electron densities on C-3, C-4 positions and π* interactions with methyl groups substituted on C-2 and C-5 positions pushed up the HOMO level of the pyrroles consequently induce rapid substitutions on C-3, C-4 sites. Substitution of phenylsulfonyl group on nitrogen stabilized LUMO levels through weak π bonding interactions. Unexpected deoxidation reaction underwent on the sulfonyl group substituted at C-3 position. The structures were solved by X-ray crystallography. Meanwhile, gas phase HF/6-31G* and density functional method (B3LYP/6-31G*) calculations gave favorable energies for 1-phenylsulfinyl pyrrole (6) over 3-phenylsulfinyl pyrrole (5) by 3.6-4.7 kcal/mol which is contrary to the experimental result. However the methods involve the effects of molecular polarizability and solvent, molecular dynamics (MD) and ab-initio self consistent reaction field (SCRF) calculations showed same trend as experiments. According to MD calculations, compound 5 is more stable than compound 6 by 4.15 kcal/mol and the SCRF, HF/6-31G* calculations gave more stable energy value for structure 5 than 6 by 0.03 kcal/mol.

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

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

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

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

• 대한전자공학회논문지SD
• /
• 제41권6호
• /
• pp.25-31
• /
• 2004

본 논문에서는 나노 스케일 확산 공정 모사를 위한 방법으로 동력학적 몬테칼로(kinetic Monte Carlo)를 소개하고자 한다. 먼저 동력학적 몬테칼로의 이론과 배경을 살펴보고 실제적인 이해를 돕기 위하여 실리콘 기판에 이온(전자) 주입 후 열처리과정에서 일어나는 점결함의 확산을 동력학적 몬테칼로를 이용하여 모사하는 간단한 예를 보여주고 있다. 동력학적 몬테칼로는 몬테칼로의 일종이지만 기존의 몬테칼로에서 구현하지 못하였던 물리적인 시간을 포아송 확률 과정을 통하여 구현하였다. 동력학적 몬테칼로 확산 공정 모사에서는 연속 확산 미분 방정식의 해를 구하는 기존의 유한 요소 수치 해석적 방법과 달리원자 상호간 혹은 원자와 결함 또는 결함들 간의 화학적 반응과 입자들의 확산 과정을 포아송 확률 과정에 따라 일어나는 화학적 반응, 입자들의 확산 사건의 연속으로 본다. 사건마다 고유의 사건 발생 확률을 갖고 이 사건 발생 확률에 따라 일어나는 확률적 사건의 연속적 발생으로 실제의 반도체 확산 공정을 시간에 따라 직접적으로 모사할 수 있다. 입자들 간의 화학적 반응 사건 확률과 입자들의 확산 공정에 필요한 확률적 인자들은 분자 동역학, 양자 역학적 계산, 흑은 실험으로 얻어진다.