• Advances in nano research
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• v.9 no.2
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• pp.69-82
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• 2020

In this paper, a new explicit analytical formula is derived for the critical buckling load of Double Walled Carbon Nanotubes (DWCNTs) embedded in Winkler elastic medium without taking into account the effects of the nonlocal parameter, which indicates the effects of the surrounding elastic matrix combined with the intertube Van der Waals (VdW) forces. Furthermore, we present a model which predicts that the critical axial buckling load embedded in Winkler, Pasternak or Kerr elastic medium under axial compression using the nonlocal Donnell shell theory, this model takes into account the effects of internal small length scale and the VdW interactions between the inner and outer nanotubes. The present model predicts that the critical axial buckling load of embedded DWCNTs is greater than that without medium under identical conditions and parameters. We can conclude that the embedded DWCNTs are less susceptible to axial buckling than those without medium.

• Journal of the Korean Chemical Society
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• v.63 no.1
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• pp.24-28
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• 2019

In this work, we discuss where the failure of Kohn-Sham Density Functional Theory (DFT) occurs in weak interactions. We have adopted density-corrected density functional calculations and dispersion correction separately to find out whether the failure is due to density-driven error or functional error. The results of Benzene Ar complex, one of the most common examples of van der Waals interactions, show that DFT calculations of van der Waals interaction suffer from functional error, rather than density-driven error. In addition, errors in DFT calculations of the S22 dataset, which contains small to relatively large (30 atoms) complexes with non-covalent interactions, are governed by functional errors.

• Advances in nano research
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• v.6 no.2
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• pp.163-182
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• 2018

Based on the Reissner mixed variational theorem (RMVT), the authors present a nonlocal Timoshenko beam theory (TBT) for the nonlinear free vibration analysis of multi-walled carbon nanotubes (MWCNT) embedded in an elastic medium. In this formulation, four different edge conditions of the embedded MWCNT are considered, two different models with regard to the van der Waals interaction between each pair of walls constituting the MWCNT are considered, and the interaction between the MWCNT and its surrounding medium is simulated using the Pasternak-type foundation. The motion equations of an individual wall and the associated boundary conditions are derived using Hamilton's principle, in which the von $K{\acute{a}}rm{\acute{a}}n$ geometrical nonlinearity is considered. Eringen's nonlocal elasticity theory is used to account for the effects of the small length scale. Variations of the lowest frequency parameters with the maximum modal deflection of the embedded MWCNT are obtained using the differential quadrature method in conjunction with a direct iterative approach.

• Journal of the Korean Society of Manufacturing Technology Engineers
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• v.24 no.4
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• pp.421-427
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• 2015

In this paper, a description is given of finite element method (FEM) simulations of the elastic bending modulus of multi-layered graphene sheets that were carried out to investigate the mechanical behavior of graphene sheets with different gap thicknesses through molecular mechanics theory. The interaction forces between layers with various gap thicknesses were considered based on the van der Waals interaction. A finite element (FE) model of a multi-layered rectangular graphene sheet was proposed with beam elements representing bonded interactions and spring elements representing non-bonded interactions between layers and between diagonally adjacent atoms. As a result, the average elastic bending modulus was predicted to be 1.13 TPa in the armchair direction and 1.18 TPa in the zigzag direction. The simulation results from this work are comparable to both experimental tests and numerical studies from the literature.

• Journal of the Korean Chemical Society
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• v.22 no.2
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• pp.86-94
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• 1978

The crystal and molecular structure of theophylline hydrochloride has been determined from X-ray data by Patterson techniques. The structure has been refined by block-diagonal least-squares and Fourier synthesis on three dimensional data. The unit cell is orthorhombic, space group $P_{na21}$, with a = 14.01, b = 11.49, c = 6.77${\AA}$, and contains four molecules. The final R value based on 743 observed reflexions is 12.2%. The intramolecular distances are similar to those in other compounds containing a purine or pyrimidine group. The molecules are nearly planar and are stacked in layers parallel to the (001)plane. The chlorine atom is coordinated to N(1) atom at a distance of 3.06${\AA}$. The structure is stabilized mainly by van der Waals interactions; however, a short N${\cdot}{\cdot}{\cdot}$Cl contact of length $3.06\AA$, which is slightly less than the expected van der Waals separation, suggest that weak charge transfer interaction may be present. The relationship between this structure and the known structures of theophylline monohydrate and caffeine monohydrate are discussed.

• Journal of the Korea Computer Graphics Society
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• v.18 no.3
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• pp.1-7
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• 2012

In this paper, we propose a method to compute the interface between protein molecules. When a molecules is represented as a set of spheres with van der Waals radii, the distance from a spatial point p to the molecule corresponds to the distance from p to the closet sphere. The molecular interface is composed of equi-distant points from two molecules. Our algorithm decomposes the space into a set of voxels, and then constructs a voxel map by storing the information of spheres intersecting each voxel. By using the voxel map, we compute the distance between a point and the molecule. We also use GPU for the parallel processing, and efficiently approximate the interface of a pair of molecules.

• Applied Chemistry for Engineering
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• v.4 no.2
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• pp.409-415
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• 1993

A potential function is applied to a hydrogen bonded system such as O-H---O and is slightly modified to provide a good understanding of a range of data. The use of this model requires a knowledge of terms describing the Van der Waals repulsion and the electrostatic interaction and the determination of these terms form the equilibrium conditions is described. Using this simple model, it will be shown that the relationship between the frequency shift and enthalpy of hydrogen bond formation is predicted to be linear and this is in reasonable agreement with experimental results in the literature.

• Macromolecular Research
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• v.16 no.4
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• pp.320-328
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• 2008

We established a thermodynamic framework of group contribution method based on modified double lattice (MDL) model. The proposed model included the long-range interaction contribution caused by the Coulomb electrostatic forces, the middle-range interaction contribution from the indirect effects of the charge interactions and the short-range interaction from modified double lattice model. The group contribution method explained the combinatorial energy contribution responsible for the revised Flory-Huggins entropy of mixing, the van der Waals energy contribution from dispersion, the polar force, and the specific energy contribution from hydrogen bonding. We showed the solvent activities of various polymer solution systems in comparison with theoretical predictions based on experimental data. The proposed model gave a very good agreement with the experimental data.

• Bulletin of the Korean Chemical Society
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• v.16 no.12
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• pp.1193-1203
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• 1995

In this work, we focused on the setup of the tools for the analysis of the final rotational state distribution of photofragments in vibrational predissociations of triatomic van der Waals molecules A-B2. We found that reflection principle used for the direct photodissociation processes can also be applied to find out the final rotational state distributions for indirect photodissociation processes. The quantity which represents the strength of rovibrational coupling between the quasi-bound state and the final state is reflected into the mirror of the classical angular momentum function, instead of the initial state before light absorption used in the reflection principle of direct processes. The sign change in the first derivative of the interaction potential with respect to the bond distance of B2 is found to be the source of the binodal structures in the final rotational distributions of photofragments in the model system studied in this work. In MQDT analysis, short range eigenchannel basis functions were found to be localized in angle, in the previous work [Lee, C.W. Bull. Korean Chem. Soc. 1995, 16, 957.] and may be called angle functions. Angle functions enjoy simple geometrical structures which have simple functional relations with the final state distributions of photofragments. Two processes take place along the angle functions which resemble the quasi-bound state and dominate over other processes. Two such angle functions are found to be not only localized angularly but also localized either one of ends of B2 in motions along the bond of B2. These dominating photodissociation processes, however, cancel each other. This cancellation causes photodissociation to depend sensitively on the interaction potential at other angles than the dominant one. Part of potential surface where much larger torque exists can now play an important role in photodissociation. MQDT also enables us to see which processes play important roles after cancellation. This is done by examining the amounts of time delayed by asymptotic eigenchannels.

• BMB Reports
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• v.28 no.4
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• pp.363-367
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• 1995

E. coli methionyl-tRNA synthetase is one of the class I tRNA synthetases. The Tryptophane residue at the position 461 located in the C-terminal domain of the enzyme is a key amino acid for the interaction with the anticodon of $tRNA^{Met}$. W461 was replaced with other amino acids to determine the chemical requirement for the interaction with the anticodon of $tRNA^{Met}$. Saturation mutagenesis at the position 461 generated a total of 12 substitution mutants of methionyl-tRNA synthetase. All the mutants showed the same in vivo stability as the wild-type enzyme, suggesting that the amino acid substitutions did not cause severe conformational change of the protein The mutants containing tyrosine, phenylalanine, histidine and cysteine substitutions showed in vivo activity while all the other mutants did not. The comparison of the in vitro aminoacylation activities of these mutants showed that aromatic ring structure, Van der Waals volume and hydrogen bond potential of the amino acid residue at the position 461 are the major determinants for the interaction with the anticodon of $tRNA^{Met}$.