• Bulletin of the Korean Chemical Society
• /
• v.29 no.3
• /
• pp.627-640
• /
• 2008

The geometrical structures, atomic charges, and relative energies of tetracoordinated Pd complexes [PdCl3Z (Z = Cl-, Br-, OH?-, H2O, NH3, PH3), PdCl2Z2 (Z = Br-, OH?-, H2O, NH3, PH3), PdZ?2X (Z = Cl-, OH?-, H2O, NH3, PH3; X = oxalate, O2-?CCO2-), and PdZ2Y (Z = Cl?-, OH?-, H2O, NH3, PH3; Y = succinate, CO2-?CHCHCO2-?)] and the ligand exchange reactions of the Pd complexes were investigated using the ab initio second order Mller-Plesset perturbation (MP2) and Density Functional Theory (DFT) methods. The geometrical characteristics of the tetracoordinated Pd(II) complexes with mono- and bidentate ligands, the effects of the atomic charges for the charged and uncharged ligands, the (dz2-p ) interactions between the dz2-orbital of Pd(II) and the p -orbital of bidentates, and the relative stabilities between the isomers of PdCl2Z2 and PdZ2Y were investigated in detail. The potential energy surfaces for the ligand exchange reactions used for the conversions of {[PdCl2(NH3)2] + H2O} to {[PdCl(NH3)2(H2O)]+ + Cl?-?} and {[PdCl2(PH3)2] + H2O} to {[PdCl(PH3)2(H2O)]+ + Cl?-?]} were investigated. The geometrical structure variations, molecular orbital variations (HOMO and LUMO), and relative stabilities for the ligand exchange processes were also examined quantitatively.

• Polymer(Korea)
• /
• v.30 no.6
• /
• pp.453-463
• /
• 2006

Molecular simulation is an exceptionally useful method for predicting self-assembled structures in various macromolecular systems, enlightening the origins of many interesting molecular events such as protein folding, polymer micellization, and ordering of molten block copolymer. The length scales of those events ranges widely from sub-nanometer scale to micron-scale or to even larger, which is the main obstacle to simulate all the events in an ab initio principle. In order to detour this major obstacle in the molecular simulation approach, a molecular model can be rebuilt by sacrificing some unimportant molecular details, based on two different perspectives with respect to the resolution of model. These two perspectives are generally referred to as 'atomistic' and 'mesoscopit'. This paper reviews various simulation methods for macromolecular self-assembly in both atomistic and mesoscopic perspectives.

• Nuclear Engineering and Technology
• /
• v.55 no.4
• /
• pp.1280-1286
• /
• 2023

MgF₂ as a moderator material has been extensively used in the beam shaping assembly (BSA) that plays an important role in the boron neutron capture therapy (BNCT). Regarded as important for applications, the thermal neutron scattering data of MgF₂ were calculated, based on the phonon expansion model. The structural properties of MgF₂ were researched by the VASP code based on the ab-initio methods. The PHONOPY code was employed to calculate the phonon density of states. Furthermore, the NJOY code was used to calculate the thermal neutron scattering data of MgF₂. The calculated inelastic cross sections plus absorption cross sections are in agreement with the available experimental data. The neutron transport in the BSA has been simulated by using a hybrid Monte-Carlo-Deterministic code NECP-MCX. The results indicated that compared with the calculation of the free gas model, the thermal neutron flux and epithermal neutron flux at the BSA exit port calculated by using the thermal neutron scattering data of MgF₂ were reduced by 27.7% and 8.2%, respectively.

• Journal of the Institute of Electronics Engineers of Korea SD
• /
• v.41 no.6
• /
• pp.25-31
• /
• 2004

In this paper, we introduce kinetic Monte Carlo (kMC) methods for simulating diffusion process in nano-scale device fabrication. At first, we review kMC theory and backgrounds and give a simple point defect diffusion process modeling in thermal annealing after ion (electron) implantation into Si crystalline substrate to help understand kinetic Monte Carlo methods. kMC is a kind of Monte Carlo but can simulate time evolution of diffusion process through Poisson probabilistic process. In kMC diffusion process, instead of. solving differential reaction-diffusion equations via conventional finite difference or element methods, it is based on a series of chemical reaction (between atoms and/or defects) or diffusion events according to event rates of all possible events. Every event has its own event rate and time evolution of semiconductor diffusion process is directly simulated. Those event rates can be derived either directly from molecular dynamics (MD) or first-principles (ab-initio) calculations, or from experimental data.

• Journal of the Korean Chemical Society
• /
• v.39 no.7
• /
• pp.564-571
• /
• 1995

5-Amino-2H-1,2,4-thiadiazoline-3-one has been prepared from 2-thiobiuret through a oxidative cyclization under basic hydrogen peroxide condition. Lactam-lactim tautomerism of 5-amino-2H-1,2,4-thiadiazoline-3-one has been examined by spectroscopic methods and ab initio molecular orbital calculation. These results were shown that 5-amino-2H-1,2,4-thiadiazoline-3-one exists as lactam form. Reaction conditions for alkylating 5-amino-2H-1,2,4-thiadiazoline-3-one with alkyl halides in the presence of various bases were studied in DMF and $H_2O$-THF two phase system. $Li_2CO_3$ base in DMF method gave best result in this investigation. The alkylation has been taken place at N-2 position. The identification of the product is confirmed by spectral data of IR, $^1H$ NMR and $^13C$ NMR and the comparison of authentic sample, 5-amino-2-methyl-1,2,4-thiadiazolidine-3-one, obtained from the oxidative cyclization of 5-methyl-2-thiobiuret.

• Journal of the Korean Chemical Society
• /
• v.59 no.3
• /
• pp.209-214
• /
• 2015

The formation of complexes between SO₂ and acetic acid was studied theoretically. The ab initio and DFT calculations were performed with MP2 and B3LYP methods using 6-311++G(d,p), aug-cc-pVDZ and aug-cc-pVTZ basis sets. Six stable complexes were identified, and three stable bidentate complexes, C1, C2 and C3, were formed between SO₂ and syn-acetic acid, which is more stable form of acetic acid. Anti-acetic acid also form three complexes, C4, C5 and C6, with SO₂. C4 is bidentate and C5, C6 are monodentate complexes, which are less stable. The most stable complex, C1 has S⋯O=C and O⋯H-O interactions, and the S⋯O and O⋯H distances are less than the sum of van der Waals radii. The vibrational frequencies of complexes were calculated and were compared with those of monomers. The frequency shifts after formation of complex were found, and the overall pattern of frequency shifts relative to monomers is similar among the six complexes.

• Bulletin of the Korean Chemical Society
• /
• v.27 no.9
• /
• pp.1405-1417
• /
• 2006

The geometrical structures, potential energy surfaces, and energetics for the ligand exchange reactions of tetracoordinated platinum $(PtY_2L_2\;:\;Y,\;L=Cl^-,\;OH^-,\;OH_2,\;NH_3)$ complexes in the ligand-solvent interaction systems were investigated using the ab initio Hartree-Fock (HF) and Density Functional Theory (DFT) methods. The potential energy surfaces for the ligand exchange reactions used for the conversions of $(PtCl_4\;+\;H_2O)^{^\ast_\ast}\;to\;[PtCl_3(H_2O)\;+\;Cl^-]$ and $[Pt(NH_3)_2Cl_2\;+\;H_2O]$$[Pt(NH_3)_2Cl_2\;+\;H_2O]$ to $[Pt(NH_3)_2Cl(H_2O)\;+\;Cl^-] $ were investigated in detail. For these two exchange reactions, the transition states $([PtY_2L_2{\cdot}{\cdot}{\cdot}L^\prime])^{^\ast_\ast} $ correspond to complexes such as $(PtCl_4{\cdot}{\cdot}{\cdot}H_2O)^{^\ast_\ast}$ and $[Pt(NH_3)_2Cl_2{\cdot}{\cdot}{\cdot}H_2O]^{^\ast_\ast}$, respectively. In the transition state, $([PtCl_4{\cdot}{\cdot}{\cdot}H_2O]^{^\ast_\ast}$ and $[Pt(NH_3)_2Cl_2{\cdot}{\cdot}{\cdot}H_2O]]^{^\ast_\ast})$ have a kind of 6-membered $(Pt-Cl{\cdot}{\cdot}{\cdot}HOH{\cdot}{\cdot}{\cdot}Cl)$ and $(Pt-OH{\cdot}{\cdot}{\cdot}Cl{\cdot}{\cdot}{\cdot}HN)$ interactions, respectively, wherein a central Pt(II) metal directly combines with a leaving $Cl^-$ and an entering $H_2O$. Simultaneously, the entering $H_2O$ interacts with a leaving $Cl^-$. No vertical one metal-ligand interactions $([PtY_2L_2{\cdot}{\cdot}{\cdot}L^\prime]) $ are found at the axial positions of the square planar $(PtY_2L_2)$ complexes, which were formed via a vertically associative mechanism leading to $D_{3h}$ or $C_{2v}$-transition state symmetry. The geometrical structure variations, molecular orbital variations (HOMO and LUMO), and relative stabilities for the ligand exchange processes are also examined quantitatively. Schematic diagrams for the dissociation reactions of {PtCl4(H2O)n(n=2,4)} into {$PtCl_3(H_2O)_{(n-2)}\;+\;Cl^-(H_2O)_2$} and the binding energies {$PtCl_4(H_2O)_n$(n = 1-5)} of $PtCl_4$ with water molecules are drawn.

• Bulletin of the Korean Chemical Society
• /
• v.20 no.12
• /
• pp.1399-1408
• /
• 1999

Geometrical structures for the dimerization of (NO)₂ from (NO + NO) have been calculated using ab initio Har-tree-Fock (SCF), second-order Møller-Plesset perturbation (MP2), and coupled cluster with the single, double, and triple substitution [CCSD(T)] methods with a triple zeta plus polarization (TZP) basis set including diffuse Rydberg basis functions. The structure of (NO)₂ can be described by two interactions (N…N, N…O). One is the ONNO structure with an (N…N) interaction. In this structure, acyclic cis-ONNO with $C_{2v}$-symmetry, acyclic trans-ONNO with $C_{2h}$, and cyclic ONNO with trapezoidal structure ($C_{2v}$) are optimized at the MP2 level. The other structure is the ONON structure with an (N…O) interaction. In the structure, acyclic cis-ONON with Cs$^{-symmetry}$ and cyclic ONON of the rectangular ($C_{2h}$), square $(D_{2h})$, rhombic $(D_{2h})$, and parallelogramic $(D_{2h})$ geometries are also optimized. It is found that acyclic cis-ONNO (¹A₁) is the most stable structure and cyclic ONNO (³A₁) is the least stable. Acyclic trans-ONNO (³A₁) with an (N…N) interaction, acyclic trans-ONON and bicyclic ONON $(C_{2v})$ with (N…O) interaction, and acyclic cis- and trans-NOON with an (O…O) interaction can not be optimized at the MP2 level. Particularly, acyclic trans-ONNO with $C_{2h}$-symmetry can not be optimized at the CCSD(T) level. Meanwhile, acyclic NNOO (¹A₁, $C_s)$ and trianglic NNOO (¹A₁,$C_{2v})$ formed by the (O…N) interaction between O₂ and N₂ are optimized at the MP2 level. The binding energies and the relative energy gaps among the isomers are found to be relatively small./sec. Spiral CT scans during the arterial phase were obtained 35 seconds after the injection of contrast medium. CT findings of 78 lesions less than 4cm in diameter were correlated with angiographic findings. Results : The attenuation of lesions was high(n = 69), iso(n = 5), and low(n = 4) compared with liver parenchyma during the arterial phase of spiral CT. In lesions with high-, iso-, and low-attenuation during the arterial phase of spiral CT, hypervascularity on angiograms was found in 63 of 69(91.3%), three of five(60%), and three of four lesions(75%), respectively. Six lesions with high-attenuation on the arterial phase of spiral CT were not seen on angiography. Two iso-attenuated and one low-attenuated lesion were hypovascular on angiograms. Conclusion : The results of this study suggest that with some exceptions there was good correlation between the arterial phase of spiral CT and angiography.