• 한국생물물리학회:학술대회논문집
• /
• 한국생물물리학회 2003년도 정기총회 및 학술발표회
• /
• pp.73-73
• /
• 2003

We report here the results on N-acetyl-N'-methylamide of alanine (Ac-Ala-NHMe) calculated using the ab initio molecular orbital method with the self-consistent reaction field (SCRF) theory at the HF level with the 6-3l+G(d) basis set to investigate the conformational preference of alanine depending on the backbone torsion angles $\square$ and$\square$ in the gas phase, chloroform, and water. There are seven local minima (LM) in the gas phase and two additional LM are found in chloroform and water. These two additional LM A (an $\square$-helical structure) and F (a polyproline structure) are stabilized only in solutions. In the gas phase, the lowest LM is the conformation C with a C$\sub$7/ intramolecular hydrogen bond and the relative conformational energies range from 0.3 to 6.0 ㎉/mol. In chloroform, the lowest LM is the conformation E (an extended structure) and the relative conformational energies range from 0.7 to 4.9 ㎉/mol. In particular, we identified 14 possible transition states connecting between seven LM in the gas phase. The search for transition states probable in chloroform and water is now in progress.

• 한국생물물리학회:학술대회논문집
• /
• 한국생물물리학회 2003년도 정기총회 및 학술발표회
• /
• pp.74-74
• /
• 2003

We report here the results on N-acetyl-N'-methylamide of oxazolidine (Ac-Oxa-NHMe) calculated using the ab initio molecular orbital method with the self-consistent reaction field (SCRF) theory at the HF level of theory with the 6-3l+G(d) basis set. The displacement of the $\square$-CH$_2$ group in proline ring by oxygen atom has affected the structure of proline, cis$\^$∼/ trans equilibrium, and rotational barrier. The up-puckered structure is found to be prevalent for the trans conformers of the Oxa amide. The higher cis populations of the Oxa amide can be interpreted due to the longer distance between the acetyl methyl group and the 5-methylene group of the ring for the trans conformer of the Oxa amide than that of the Pro amide. The changes in charge of the prolyl nitrogen and the decrease in electron overlap of the C$\^$∼/ N bond for TS structures seem to play a role in lowering rotational barriers of the Oxa amide compared to that of the Pro amide. The calculated preferences for cis conformers in the order of Oxa > Pro amides and for trans-to-cis rotational barriers in the order of Pro > Oxa amide in water are consistent with experimental results on Oxa-containing peptides. The pertinent distance between the prolyl nitrogen and the N$\^$∼/ H amide group to form a hydrogen bond might indicate that this intramolecular hydrogen bond could contribute in stabilizing the TS structures of Oxa and Pro amides and play a role in prolyl isomerization.

• Genomics & Informatics
• /
• 제9권1호
• /
• pp.39-43
• /
• 2011

MicroRNAs (miRNAs) are recently discovered small RNA molecules usually resulting in translational repression and gene silencing. Despite the fact that specific cloning of small RNA's is a method in practice, computational identification of miRNA's has been a major focus recent days, since is a rapid process following AB initio and sequence alignment methods. Here we developed new software called MiRPI that aims to identify the highly conserved miRNAs without any mismatches from given fasta formatted gene sequences by using non-repeated miRNA dataset of the user's interest. The new window embedded with the software is used to identify the targets for inputted mature miRNAs in the mRNA sequences. Also MiRPI is designed to measure the precursor miRNA statistics, majorly focusing the Adjusted Minimum Folding free Energy (AMFE) and Minimum Folding free Energy Index (MFEI), the most important parameters in miRNA confirmation. MiRPI is developed by PERL (Practical Extraction and Report Language) and Tk (Tool kit widgets) scripting languages. It is user friendly, portable offline software that works in all windows OS, sized to 3 MB.

• Bulletin of the Korean Chemical Society
• /
• 제25권6호
• /
• pp.819-822
• /
• 2004

Protonation constants of calix[4]-cyclen-benzo-crown-6, L in 1X$10^{-2}$ M $Bu_4NCF_3SO_3$ in 40% $CH_2Cl_2/CH_3OH$ at $25^{\circ}C$ determined by potentiometric titration are log $K_1$ = 10.91, log $K_2$ = 10.30, log $K_3$ = 6.24 and log $K_4$ = 2.55. Stability constants for the receptor L complexes with Cu(II) and Zn(II) in 1X$10^{-2}$ M $Bu_4NCF_3SO_3$ in 40% $CH_2Cl_2/CH_3OH$ at $25^{\circ}C$ were determined by UV-VIS spectrometric titration. Stability constants of the CuL and ZnL complexes as log $\beta$ are 4.37 and 3.45, respectively. Stabilization energies for protonations of receptor L, derived from ab initio Hartree-Fock method with 6-31G basis set, are ${\Delta}E_1$ = -290.1, ${\Delta}E_2$ = -205.0, ${\Delta}E_3$ = -124.9 and ${\Delta}E_4$ = -26.9 kcal/mol and complexation energy of ZnL complex is -370.3 kcal/mol.

• Bulletin of the Korean Chemical Society
• /
• 제33권12호
• /
• pp.4079-4083
• /
• 2012

The mechanism of the cycloaddition reaction between singlet state dichlorosilylene germylidene ($Cl_2Si=Ge:$) and acetone has been investigated with B3LYP/6-$31G^*$ and B3LYP/6-$31G^{**}$ method, from the potential energy profile, we predict that the reaction has one dominant reaction pathway. The presented rule of the reaction is that the two reactants firstly form a Si-heterocyclic four-membered ring germylene through the [2+2] cycloaddition reaction. Because of the 4p unoccupied orbital of Ge atom in the Si-heterocyclic four-membered ring germylene and the ${\pi}$ orbital of acetone forming a ${\pi}{\rightarrow}p$ donor-acceptor bond, the Si-heterocyclic four-membered ring germylene further combines with acetone to form an intermediate. Because the Ge atom in the intermediate hybridizes to an $sp^3$ hybrid orbital after the transition state, then, the intermediate isomerizes to spiro-heterocyclic ring compound involving Si and Ge (P4) via a transition state.

• Bulletin of the Korean Chemical Society
• /
• 제33권6호
• /
• pp.1998-2004
• /
• 2012

We carried out DFT calculations for monohydrated sulfuric and phosphoric acids. We are interested in clusters which differ in orientation of hydrogen atoms only. Such molecular complexes are close in energy, since they lie in the vicinity of the global minimum energy structure on the flat potential energy surface. For monohydrated sulfuric acid we identified four different isomers. The monohydrated phosphoric acid forms five different conformers. These systems are difficult to study from the theoretical point of view, since binding energy differences in several cases are very small. For each structure, we calculated harmonic vibrational frequencies to be sure that if the optimized structures are at the local or global minima on the potential energy surface. The analysis of calculated -OH vibrational frequencies is useful in interpretation of infrared photodissociation spectroscopy experiments. We employed four different DFT functionals in our calculations. For each structure, we calculated binding energies, thermodynamic properties, and harmonic vibrational frequencies. Our analysis clearly shows that DFT approach is suitable for studying monohydrated inorganic acids with different hydrogen atom orientations. We carried out MP2 calculations with aug-cc-pVDZ basis set for both monohydrated acids. MP2 results serve as a benchmark for DFT calculations.

• Bulletin of the Korean Chemical Society
• /
• 제31권12호
• /
• pp.3553-3560
• /
• 2010

A new hydrazone derivative compound has been synthesized and characterized by IR, $^1H$-NMR, $^{13}C$-NMR and UV-vis. spectroscopy techniques, elemental analysis and single-crystal X-ray diffraction (XRD). The new compound crystallizes in monoclinic space group C2/c. In addition to the crystal structure from X-ray experiment, the molecular geometry, vibrational frequencies and frontier molecular orbitals analysis of the title compound in the ground state have been calculated by using the HF/6-31G(d, p), B3LYP/6-311G(d, p) and B3LYP/6-31G(d, p) methods. The computed vibrational frequencies are used to determine the types of molecular motions associated with each of the observed experimental bands. To determine conformational flexibility, molecular energy profile of (1) was obtained by semi-empirical (AM1) calculation with respect to a selected degree of torsional freedom, which was varied from $-180^{\circ}$ to $+180^{\circ}$ in steps of $10^{\circ}$. Molecular electrostatic potential of the compound was also performed by the theoretical method.

• Bulletin of the Korean Chemical Society
• /
• 제28권6호
• /
• pp.959-964
• /
• 2007

The benzene complexes with dimethyl sulfur (DMS) and fluorinated DMS (FDMS) have been investigated using ab initio calculations. The natural bond orbital (NBO) charge population on S atom varies remarkably for different conformations of DMS and FDMS, which determines the possible binding modes for their benzene complexes. The electronegative substituent at the methyl group of DMS causes a significant change in the molecular electrostatic potential around the sulfur atom and changes the interaction mode with aromatic ring. It was found that the sulfur…π interaction mode does not occur in the DMS-benzene complex, while it does in the FDMS-benzene complex. Both B3LYP and MP2 methods provide reliable structures, while the interaction energy obtained by B3LYP is unreliable.

• 대한화학회지
• /
• 제57권3호
• /
• pp.311-315
• /
• 2013

The geometry structures of hexa-coordinated [NiLX]X complexes ($X=Cl^-,\;Br^-,\;I^-$) {L = 8,9,18,19-tetrahydro-7H,17H-dibenzo[f,o] [1,5,9,13]dioxadiaza cyclohexadecine-8,18-diol} are optimized by density functional theory (DFT) using B3LYP/LANL2DZ. The calculated geometric parameters are in good agreement with the corresponding experimental values. Calculation results about these complexes show that dipole moment decreases, and the energy levels of HOMOs descend from iodo-complex to chloro-complex. The energy levels of HOMOs descend gently from iodo-complex to chloro-complex, while the energy levels of LUMOs in the present complexes are almost similar; therefore the energy gapes between HOMOs and LUMOs increased from iodo-complex to chloro-complex.

• Bulletin of the Korean Chemical Society
• /
• 제25권1호
• /
• pp.85-89
• /
• 2004

Geometrical structures of [Pd(L)$Cl_2$] with oxathia macrocycles have been calculated using ab initio secondorder Moller-Plesset (MP2) and Density Functional Theory (DFT) methods with triple zeta plus polarization (TZP) basis set level. In optimized Pd(L)$Cl_2$ complexes, Pd(II) locates at the center surrounded by a square planar array of two sulfurs on an oxathia macrocycle and two chlorides. The endo-Pd(II) complexes with an axial (Pd${\cdots}$O) interaction are more stable than the exo-Pd(II) complexes without the interaction. In the endo-Pd(II) complexes, the atomic charge of the oxygen atom moves to Pd(II) via the axial ($Pd{\cdots}$O) interaction and then, the charge transfer from Pd(II) to the S-atoms occurs stepwise via ${\pi}$-acceptors of the empty d-orbitals.