• Bulletin of the Korean Chemical Society
• /
• v.9 no.3
• /
• pp.117-121
• /
• 1988

The molecular interaction and geometrical optimization of Cr$(CO)_5\;and\;Ni(CO)_3$ units have been studied for phosphinidene complex by means of extended Huckel calculations. The results were compared with those of ab initio calculations and found to be in qualitative agreement. Geometrical optimization of HPCr$(CO)_5\;(1)\;and\;HPNi(CO)_3$ (2) gave the values R = 2.36 ${\AA}$, ${\theta}$ = $111.5^{\circ}$, and ${\phi}$ = $45^{\circ}$for 1, and R = 2.37 ${\AA}$, ${\theta}$= $120^{\circ}$, and ${\phi}$ = $58^{\circ}$for 2. It is found that the low rotational barriers for 1(0.46 kcal $mol^{-1}$) and 2(0.12 kcal $mol^{-1}$) would be accompanied by the free rotation, in spite of the fact that both 1 and 2 adopt staggered conformations.

• Bulletin of the Korean Chemical Society
• /
• v.4 no.3
• /
• pp.133-139
• /
• 1983

To understand the importance of Y-base adjacent to the anticodon stabilizing codon-anticodon interaction, a study has been undertaken for the model compound involving the interaction between Y-base and anticodon as well as the participation of water molecule by calculating the conformational free energy using an empirical potential function. We restrict our analysis to sites directly associated with Y-base by varying only the backbone torsion angles of Y-base. The hydration and $Mg^{+2}$ binding effects on the conformational stability of Y-base are calculated and discussed. The free Y-base is proved to be less stable than the hydrated one. The free energy change due to the hydration of Y-base amounts to -119.5 kcal/mole, in which the conformational energy change is -142.4 kcal/mole and the configurational entropy change is -76.9 e. u. It is found that the water molecules bound to Y-base and $Mg^{+2}$ contribute to the conformation of Y-base dominantly.

• Bulletin of the Korean Chemical Society
• /
• v.21 no.10
• /
• pp.1035-1038
• /
• 2000

Vibrational properties of dopamine neutral species in powder state have been studied by means of the normal mode analysis based on the force constants obtained from the density functional calculation at B3LYP level and the results of Fourier trans form Raman and infrared spectroscopic measurements. Ab initio calculation at MP2 level shows that the trans conformer of dopamine has higher electronic energy about 1.4 kcal/mol than those of the gauche+ and the gauche-conformers, and two gauche conformers have almost the same energies. Free energies calculated at HF and B3LYP levels show very similar values for three conformers within 0.3 kcal/mol. Empirical force field has been constructed from force constants of three conformers, and refined upon ex-perimental Raman spectrum of dopamine to rigorous values. The major species of dopamine neutral base in the powder state is considered a trans conformer as shown in the crystallographic study of dopamine cationic salt.

• Bulletin of the Korean Chemical Society
• /
• v.18 no.10
• /
• pp.1076-1082
• /
• 1997

The infrared, Raman, and jet-cooled laser-induced fluorescence excitation spectra of 1,2,3,4-tetrahydronaphthalene have been recorded and analyzed. The observed vibrations have been assigned to understand the conformational behaviors in its electronic ground (S0) and excited (S1) states. Ab initio at the HF/6-31G** level and molecular mechanics (MM3) force field calculations have been carried out to generate the complete normal mode frequencies of the molecule in its S0 state. The vibrational frequencies calculated from the ab initio method show a better agreement with the observed infrared and Raman frequencies than those calculated from the MM3 method. In several cases, the normal mode calculations were very helpful to clarify some ambiguities of previous assignments. In addition, the ring inversion process between two twisted conformers of 1,2,3,4-tetrahydronaphthalene has been reexamined utilizing ab initio calculation. The results show that the ring inversion energy is in the range of 3.7-4.3 kcal/mol which is higher than the previously reported AM1 value of 2.1 kcal/mol.

• Bulletin of the Korean Chemical Society
• /
• v.17 no.12
• /
• pp.1149-1153
• /
• 1996

Ab initio and extended Huckel calculations were carried out on the isomers of trans-RhCl(η2-C2H2)(PH3)2 (1). Due to π-back donation in 1 complex, the rotational energy barrier of alkyne ligand is computed to be in the range of 18.6-25.2 kcal/mol at MP4 levels. The optimized hydrido-alkynyl complex (2) at ab initio level has the distorted trigonal bipyramidal structure. Vinylidene complex (3) is computed to be more stable than 1 complex by 17.1 kcal/mol at MP4//MP2 level. The stabilities of isomers show similar trend at the various level calculations, that is, EHT, MP4//HF, and MP4//MP2 levels. The optimized geometries at ab initio level are in reasonable agreement with experimental data. A detailed account of the bonding in each isomers (1-3) have been carried out in terms of orbital analyses.

• Bulletin of the Korean Chemical Society
• /
• v.19 no.5
• /
• pp.557-560
• /
• 1998

The structures and energies for the intramolecular rearrangement in $d^8-MCl(PH_3)_2$(HC≡CPh), M=Rh and Ir, complexes were studied by ab initio method at the Hartree-Fock and MP2 levels of theory. Three transition states in two pathways were optimized and characterized by frequency calculations. The activation energies for the process of π-type complex 1 to hydrido-alkynyl 2 have been computed to be relatively low 6.97 and 21.33 kcal/mol at MP2 level for Rh and Ir metals, respectively. However, the activation energies for a 1,2-hydrogen shift via t.s.3 have been computed to be high 50.83 and 60.05 kcal/mol for Rh and Ir metals.

• Bulletin of the Korean Chemical Society
• /
• v.20 no.5
• /
• pp.559-566
• /
• 1999

Gas-phase alkylations of delocalized ambident anions, Y---CH---X- where X, Y=CH2, O, or S, have been investigated theoretically at the MP2/6-31+G*//MP2/6-31+G* and QCISD/6-31+G*//MP2/6-31+G* lev-els. O-and S-alkylations (X=O and S) are more favored kinetically by ΔE^≠ = 4.6 and 9.8 kcal mol-1 than the respective C-alkylations even though they are thermodynamically less favored by 22.4 and 6.0 kcal mol-1 respectively. It was found that the transition structures for the C-alkylations are imbalanced due to the endoergic rehybridi-zation of the carbon center from sp2 to sp3 which leads to premature bond contraction of the C-Y bond and delayed bond stretching of the C-X bond. In the O-, or S-alkylation, such endoergic process is not required since the σ-lone pair on O or S is involved in the initial stage of alkylation. The imbalanced TSs for the C-alkylation are accompanied by higher intrinsic barriers and deformation energies.

• Bulletin of the Korean Chemical Society
• /
• v.15 no.8
• /
• pp.658-662
• /
• 1994

Ab initio and extended Huckel calculations have been applied to discuss the electronic structure, ring inversion barrier, and geometry of the $Cp_2TiS_3$ compound. The deformation of four membered ring in the planar geometry is originated from a second-order Jahn-Teller distortion due to the small energy gap between HOMO and LUMO on the basis of extended Huckel calculations. The puckered $C_s$ geometry is stabilized by the interaction of the $x^2-y^2$ metal orbital with the hybrid orbital in sulfur. Ab initio calculations have been carried out to explore the ring inversion process for the model $Cl_2TiS_3$ compound. We have optimized $C_s$ and $C_{2v}$ structures of the model compound at the RHF level. The energy barriers for the ring inversion are sensitive to the used basis set. With 4-31$G^*$ for the Cl and S ligands, the barriers are computed to be 8.41 kcal/mol at MP2 and 8.02 kcal/mol at MP4 level.

• Bulletin of the Korean Chemical Society
• /
• v.10 no.3
• /
• pp.247-250
• /
• 1989

The molecular structure of cyclobutylmethyl ketone (c-$C_4H_7COCH_3$) has been investigated by molecular mechanics II (MM2). For the monosubstituted cyclobutane there are two possible ring conformations, the equatorial and axial form, but for the cyclobutylmethyl ketone the equatorial form is predominant conformation. For the $COCH_3$ moiety there are two stable orientations which are the equatorial-gauche and the equatorial-trans form. The equatorial-gauche form where the C = O bond is nearly eclipsing (torsional angle ${\angle}C4-C3-C2-O10=14.5^{\circ}$) one of the ${\alpha}$C-C bonds of the four-membered ring was preferred conformer with steric energy of 13.37 kcal/mol. The equatorial-trans form where the C = O bond is nearly eclipsing (${\angle}C4-C3-C2-O10=145.0^{\circ}$) the ${\alpha}$ C-H bond of the four-membered ring was less stable conformer with steric energy of 15.40 kcal/mol.

• Applied Chemistry for Engineering
• /
• v.33 no.4
• /
• pp.425-430
• /
• 2022

L-alanine (LA, as an amino acid residue) pentamer model was used to investigate changes in the dihedral angle, intramolecular hydrogen bonding and formation energies during structural optimization. LA pentamers having four conformation types [𝛽: 𝜑/𝜓=t-/t+, 𝛼: 𝜑/𝜓=g-/g-, PP_II: 𝜑/𝜓=g-/t+ and P-like: 𝜑/𝜓= g-/g+] were carried out by quantum chemical calculations (QCC) [B3LYP/6-31G(d,p)]. In LA, 𝛽, 𝛼, and P-like types did not change by optimization, having an intra-molecular hydrogen bond: NH⋯OC (H-bond), and PP_II types in the absence of H-bond were transformed into P-like at the designated 𝜓 of 140°, and to 𝛽 at that of 160° or 175°. P-like and 𝛼 were about 0.5 kcal/mol/mu more stable than 𝛽. In order to understand the processes of the transformations, the changes of 𝜑/𝜓, distances of NH-OC (d_NH/CO) and formation energies (𝜟E, kcal/mol/mu) were examined.