• Transactions on Electrical and Electronic Materials
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• v.17 no.1
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• pp.29-32
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• 2016

Using the various exchange-correlation functionals, such as LDA, GGA-PBE, GGA-PBEsol and GGA-AM05 functionals, first principle studies were conducted to determine the structures of paraelectric and ferroelectric PbTiO₃. Based on the structures determined by the various functionals, the piezoelectric properties of PbTiO₃ are predicted under the density-functional perturbation theory (DFPT). The present prediction with the various GGA functionals are closer to the experimental findings compared to the LDA values. The present DFT calculations using the GGA-PBEsol functional estimate the experimental data more reasonably than the conventional LDA and GGA fucntionals. The GGA-AM05 functional also predicts the experimental data as well as the GGA-PBEsol. The piezoelectric tensor calculated with PBEsol is relatively insensitive to pressure.

• Bulletin of the Korean Chemical Society
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• v.19 no.12
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• pp.1314-1319
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• 1998

Electronic structures and properties of the organometallic precursors [Me2AlNHR]2 (R =Me, iPr, and tBu) have been calculated by the semiempirical (ASED-MO, MNDO, AM1 and PM3) methods. Optimized structures obtained from the MNDO, AM1, and PM3 calculations indicate that the N-C bond lengths are considerably affected by the change of the R groups bonded to nitrogen, but the bond lengths of the Al-N and Al-C bonds are little affected. This result is useful in explaining the experimental results for the elimination of the R groups bonded to nitrogen, and could serve as a guide in designing an optimum precursor for the AlN thin film formation.

• Bulletin of the Korean Chemical Society
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• v.11 no.3
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• pp.194-200
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• 1990

Various mechanistic aspects of the A2 hydrolysis of methyl acetimidate were explored using the MNDO method. As in thecorresponding reactions of acetamide and methyl carbamate, a proton transfer pre-equilibrium exists between the N-protonated and the O-protonated tautomers, and the subsequent hydrolysis proceeds from the more stable N-protonated form. Of the two reaction pathways, the $A_{AL}2$ path is favored in the gas phase and in concentrated acid solutions, whereas the $A_{AC}2$ path is favored in less acidic solutions with a stable cationic tetrahedral intermediate formed in the rate determining step. Negative charge development on the alkoxy oxygen in the transition state suggested a rate increase with the increase in the electron withdrawing power of the alkoxy group. Calculations on the reaction processes with AM1 indicated that MNDO is more reliable in this type of work, although AM1 is better than MNDO in reproducing hydrogen bonds.

• Journal of the Korean Chemical Society
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• v.48 no.2
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• pp.123-128
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• 2004

Quantum chemical quantities, enthalpy of formation(${\Delta}H_f$), HOMO and LUMO energy, and dipole moment(${\mu}_D$) were acquired by AM1, PM3, and ZINDO/1 methods for polyamines and imidazole derivatives. The investigation of the inhibitory activity on some Ni(II) complexes with polyamines and imidazole derivatives is performed by ZINDO/1 calculations. It was found that experimental inhibitory activity(IA) appeared when the value of net charge and enthalpy of formation were over 0.03 and -300 eV, respectively for Ni(II) complexes. These results showed that the Ni(II) complexes have exception on the following very unstable compounds: square pyramidal [Ni(dpt)(tn)])]$^{2+}$(dpt=3,3'-diaminodipropylamine)(tn=1,3-diaminopropane) and distorted tetrahedral [Ni(N-PropIm))$_2$(NCS))$_2$](N-PropIm=N-Propylimidazole).

• Bulletin of the Korean Chemical Society
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• v.24 no.11
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• pp.1649-1654
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• 2003

We have investigated substituent effect on the stabilization energies, and nucleus-independent chemical shifts of pentafulvalenes and on the electronic structures of the corresponding polypentafulvalenes to design environmentally stable semiconductive or conductive polymers. Geometrical optimizations of the molecules were carried out at the density functional level of theory with B3LYP hybrid functional and 6-311+G(d) basis set. Stabilization energies were estimated using isodesmic and homodesmotic reactions. As a criterion of aromaticity nucleus-independent chemical shifts of the molecules were computed using GIAO approach. For the polymers the geometrical parameters were optimized through AM1 band calculations and the electronic structures were obtained through modified extended Huckel band calculations. It is found that strong electronwithdrawing substituents increase isodesmic and homodesmotic stabilization energies of pentafulvalene, though it does not increase the aromaticity. Nitro-substituted pentafulvalene is estimated to have stabilization energy as much as azulene. However, substitution either with electron-donating groups or with electronwithdrawing groups does not significantly affect the electronic structures of polypentafulvalene and poly (vinylenedioxypentafulvalene).

• Bulletin of the Korean Chemical Society
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• v.18 no.6
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• pp.573-578
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• 1997

Ion fragmentations of fatty acids such as stearic acid, palmitic acid, myristic acid, and lauric acid were studied using mass spectrometry and semiempirical calculations. The mass spectra of fatty acids showed the distributions of CH₃(CH₂)$_n^+$ and $[(CH_2)_nCO_2H]^+$ fragment ions. The relative ion abundance distributions of $[(CH_2)_nCO_2H]^+$ showed the local maxima at n=6, 10, and 14. The local maximum phenomena were also found in the mass spectra of methyl stearate but not in those of normal alcohols. These local maxima could be explained not by heats of reaction for fragmentation but by the cyclic structures of the molecular ions. The AM1 semiempirical calculations for fatty acids clearly show that the linear structures are more favorable than the cyclic ones for neutral molecules while the cyclic structures are more favorable than the linear ones for ionic molecules. The distances between carboxyl group and methylene of the cylic structures of ionized fatty acids were calculated. The methylene carbons with n=6, 10, and 14 were closer to the carboxyl group than adjacent ones.

• Bulletin of the Korean Chemical Society
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• v.14 no.2
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• pp.262-265
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• 1993

Conformational free energy calculations using an empirical potential function and a hydration shell model (program CONBIO) were carried out on antifungal agent fluconazole in the unhydrated and hydrated states. The initial geometry of fluconazole was obtained from two minimized fragments of it using a molecular mechanics MMPMI and followed by minimizing with a semiempirical AM1 method. In both states, the feasible conformations were obtained from the calculations of conformational energy, conformational entropy, and hydration free energy by varying all the torsion angles of the molecule. The intramolecular hydrogen bonds of isopropyl hydroxyl hydrogen and triazole nitrogens and the structural flexibility are of significant importance in stabilizing the conformations of fluconazole in both states. Hydration is proved to be one of the essential factors in stabilizing the overall conformation in aqueous solution. Two F atoms of phenyl ring are not identified as an essential key in determining the stable conformations and may be responsible for the interaction with the receptor of fluconazole.

• Journal of the Korean Magnetic Resonance Society
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• v.26 no.1
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• pp.1-9
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• 2022

There are two distinct approaches to improving the quality of protein NMR structures during refinement: all-atom force fields and accumulated knowledge-assisted methods that include Rosetta. Mao et al. reported that, for 40 proteins, Rosetta increased the accuracies of their NMR-determined structures with respect to the X-ray crystal structures (Mao et al., J. Am. Chem. Soc. 136, 1893 (2014)). In this study, we calculated 32 structures of those studied by Mao et al. using all-atom force field and implicit solvent model, and we compared the results with those obtained from Rosetta. For a single protein, using only the experimental NOE-derived distances and backbone torsion angle restraints, 20 of the lowest energy structures were extracted as an ensemble from 100 generated structures. Restrained simulated annealing by molecular dynamics simulation searched conformational spaces with a total time step of 1-ns. The use of GPU-accelerated AMBER code allowed the calculations to be completed in hours using a single GPU computer-even for proteins larger than 20 kDa. Remarkably, statistical analyses indicated that the structures determined in this way showed overall higher accuracies to their X-ray structures compared to those refined by Rosetta (p-value < 0.01). Our data demonstrate the capability of sophisticated atomistic force fields in refining NMR structures, particularly when they are coupled with the latest GPU-based calculations. The straightforwardness of the protocol allows its use to be extended to all NMR structures.

• Nuclear Engineering and Technology
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• v.41 no.1
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• pp.99-106
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• 2009

The contents of transuranic elements ($^{237}Np$, $^{238}Pu$, $^{239}Pu$, $^{240}Pu$, $^{241}Am$, $^{244}Cm$, and $^{242}Cm$) in high-burnup spent fuel samples ($35.6{\sim}53.9\;GWd/MtU$) were determined by alpha spectrometry. Anion exchange chromatography and diethylhexyl phosphoric acid extraction chromatography were applied for the separation of these elements from the uranium matrix. The measured values of the nuclides were compared with ORIGEN-2 calculations. For plutonium, the measurements were higher than the calculations by about $2.6{\sim}32.7%$ on average according to each isotope, and those for americium and curium were also higher by about $35.9{\sim}63.1%$. However, for $^{237}Np$, the measurements were lower by about 52% on average for the samples.

• Bulletin of the Korean Chemical Society
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• v.16 no.2
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• pp.112-120
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• 1995

The conformational study on malonic acid, hydrogen malonate, malonate, malonyl methyl sulfide, and malonyl methyl sulfide anion, as the model compounds of malonyl-CoA, was carried out using the semiempirical MO methods (MNDO, AM1, and PM3) and hydration shell model. On the whole, the feasible conformations of malonic acid, hydrogen malonate, and malonate seem to be similar to each other. In malonic acid and malonate, two carboxyl groups are nearly perpendicular to the plane of the carbon skeleton, despite of different orientation of two carboxyl groups themselves. In particular, two carboxyl groups of hydrogen malonate are on the plane formed by carbon atoms with an intramolecular hydrogen bond. The calculated results on the geometry and conformation of three compounds are reasonably consistent with those of X-ray and spectroscopic experiments as well as the previous calculations. The orientation of two carbonyl groups of malonyl methyl sulfide is quite similar to that of malonic acid, but different from that of its anion. Especially, the computed probable conformations of the sulfide anion by the three methods are different from each other. The role of hydration seems not to be crucial in stabilizing the overall conformations of malonic acid, hydrogen malonate, malonate, and malonyl methyl sulfide. However, the probable conformations of the unhydrated sulfide anion obtained by the MNDO and AM1 methods become less stabilized by including hydration. The AM1 method seems to be appropriate for conformational study of malonyl-CoA and its model compounds because it does not result in the formation of too strong hydrogen bonds and significant change in conformational energy from one compound to another.