• Journal of Microbiology and Biotechnology
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• v.17 no.7
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• pp.1098-1105
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• 2007

Quantum mechanical and molecular dynamics simulation analysis has been performed on the model system for CALB (Candida antarctica lipase B) with esters to study the reaction mechanism and conformational preference of catalytic hydrolysis and the esterification reaction. Using quantum mechanical analysis, the ping-pong bi-bi mechanism was applied and energies and 3-dimensional binding configurations of the whole reaction pathways were calculated. Further molecular dynamics simulation analysis was performed on the basis of the transition state obtained from quantum mechanical study to observe the effect of structures of the substrates. Calculation results using substrates of different chain length and chiral configurations were compared for conformational preference. The calculated results showed very small influence on chain length, whereas chiral conformation showed big differences. Calculated results from molecular modeling studies have been compared qualitatively with the experimental data using racemic mixtures of (${\pm}$)-cis-4-acetamido-cyclopent-2-ene-1-ethyl acetate as substrates.

• 한국정보디스플레이학회:학술대회논문집
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• 2008.10a
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• pp.1049-1052
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• 2008

We developed novel molecular dynamics and quantum chemical molecular dynamics simulators for the design of MgO protecting layer in plasma display panel. These simulators were applied to the investigations on the destruction processes of the MgO protecting layer as well as the evaluation of its second electron emission ability. From the simulation results, we successfully proposed new guidelines for MgO protecting layer with high durability and high second electron emission ability.

• Proceedings of the Korean Nuclear Society Conference
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• 2005.05a
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• pp.455-456
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• 2005

• Interaction and multiscale mechanics
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• v.1 no.2
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• pp.303-315
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• 2008

In this paper, thermodynamical properties of crystalline silicon under strain are calculated using classical molecular dynamics (MD) simulations based on the Tersoff interatomic potential. The Helmholtz free energy of the silicon crystal under strain is calculated by using the ensemble method developed by Frenkel and Ladd (1984). To account for quantum corrections under strain in the classical MD simulations, we propose an approach where the quantum corrections to the internal energy and the Helmholtz free energy are obtained by using the corresponding energy deviation between the classical and quantum harmonic oscillators. We calculate the variation of thermodynamic properties with temperature and strain and compare them with results obtained by using the quasi-harmonic model in the reciprocal space.

• Membrane Journal
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• v.30 no.4
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• pp.242-251
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• 2020

Computer simulation tools mainly used for polymer materials and polymeric membranes are divided into various fields depending on the size of the object to be simulated and the time to be simulated. The computer simulations introduced in this review are classified into three categories: Quantum mechanics (QM), molecular dynamics (MD), and mesoscale modeling, which are mainly used in computational material chemistry. The computer simulation used in polymer research has different research target for each kind of computational simulation. Quantum mechanics deals with microscopic phenomena such as molecules, atoms, and electrons to study small-sized phenomena, molecular dynamics calculates the movement of atoms and molecules calculated by Newton's equation of motion when a potential or force of is given, and mesoscale simulation is a study to determine macroscopically by reducing the computation time with large molecules by forming beads by grouping atoms together. In this review, various computer simulation programs mainly used for polymers and polymeric membranes divided into the three types classified above will be introduced according to each feature and field of use.

• Proceedings of the Korean Vacuum Society Conference
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• 2010.08a
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• pp.93-93
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• 2010

In this talk, I will introduce a reactive force field (ReaxFF) molecular dynamics (MD) simulation. In contrast to common MD simulations with empirical FFs, we can predict chemical reactions (bond breaking and formation) in large scale systems with the ReaxFF simulation where all of the ReaxFF parameters are from quantum mechanical calculations such as density functional theory to provide high accuracy. Accordingly, the ReaxFF simulation provides both accuracy of quantum mechanical calculations and description of large scale systems of atomistic simulations at the same time. Here, I will first discuss a theory in the ReaxFF including the differences from other empirical FFs, and then show several applications for studying chemical reactions of SiHx radicals on Si surfaces, which is an important issue in Si process.

• 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.

• Coupled systems mechanics
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• v.3 no.4
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• pp.329-344
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• 2014

In this work, quantum molecular dynamics simulations (QMD) are preformed to study the hydrogen molecules in three types of carbon nanostructures, $C_{60}$ fullerene, (5,5) and (9,0) carbon nanotubes and graphene layers. Interactions between hydrogen and the nanostructures is of importance to understand hydrogen storage for the development of hydrogen economy. The QMD method overcomes the difficulties with empirical interatomic potentials to model the interaction among hydrogen and carbon atoms in the confined geometry. In QMD, the interatomic forces are calculated by solving the Schrodinger's equation with the density functional theory (DFT) formulation, and the positions of the atomic nucleus are calculated with the Newton's second law in accordance with the Born-Oppenheimer approximation. It is found that the number of hydrogen atoms that is less than 58 can be stored in the $C_{60}$ fullerene. With larger carbon fullerenes, more hydrogen may be stored. For hydrogen molecules passing though the fullerene, a particular orientation is required to obtain least energy barrier. For carbon nanotubes and graphene, adsorption may adhere hydrogen atoms to carbon atoms. In addition, hydrogen molecules can also be stored inside the nanotubes or between the adjacent layers in graphite, multi-layer graphene.

• Proceedings of the Korean Society for Noise and Vibration Engineering Conference
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• 2008.11a
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• pp.668-669
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• 2008

In this paper, we introduce various coarse-grained elastic network modeling (ENM) techniques as a novel computational method for simulating atomic scale dynamics in macromolecules including DNA, RNA, protein, and polymer. In ENM, a system is modeled as a spring network among representative atoms in which each linear elastic spring is well designed to replace both bonded and nonbonded interactions among atoms in the sense of quantum mechanics. Based on this simplified system, a harmonic Hookean potential is defined and used for not only calculating intrinsic vibration modes of a given system, but also predicting its anharmonic conformational change, both of which are strongly related with its functional features. Various nano and bio applications of ENM such as fracture mechanics of nanocomposite and protein dynamics show that ENM is one of promising tools for simulating atomic scale dynamics in a more effective and efficient way comparing to the traditional molecular dynamics simulation.

• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.797-801
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• 2003

One of the largest challenges for quantum chemistry today is to obtain accurate results for large complex molecular systems, and a variety of approaches have been proposed recently toward this goal. We have developed the ONIOM method, an onion skin-like multi-level method, combining different levels of quantum chemical methods as well as molecular mechanics method. We have been applying the method to many different large systems, including thermochemistry, homogeneous catalysis, stereoselectivity in organic synthesis, solution chemistry, fullerenes and nanochemistry, and biomolecular systems. The method has recently been combined with the polarizable continuum model (ONIOM-PCM), and was also extended for molecular dynamics simulation of solution (ONIOM-XS). In the present article the recent progress in various applications of ONIOM and other electronic structure methods to problems of homogeneous catalyses and nanochemistry is reviewed. Topics include 1. bond energies in large molecular systems, 2. organometallic reactions and homogeneous catalysis, 3. structure, reactivity and bond energies of large organic molecules including fullerenes and nanotubes, and 4. biomolecular structure and enzymatic reaction mechanisms.