• Bulletin of the Korean Chemical Society
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• 제28권12호
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• pp.2310-2314
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• 2007

Stable molecular conformations were calculated for the p-tert-butylcalix[4]arene crown ether bridged at the lower rim with pyridyl unit (1) in the various conformers and their potassium-ion complexes. The structures of three distinct conformations have been optimized using DFT B3LYP/6-31G(d,p) method. Relative stability of free host 1 is in following order: cone (most stable) > partial-cone > 1,3-alternate conformer. For two different kinds of complexation mode, the potassium cation in the crown-ether moiety (cr) has much better complexation efficiency than in the benzene-rings (bz) pocket for all three kinds of conformation of host molecule 1. The relative stability of complex (1+K+) in the cr-binding mode is in following order: partial-cone (most stable) ~ cone > 1,3-alternate conformer.

• Bulletin of the Korean Chemical Society
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• 제35권3호
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• pp.798-804
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• 2014

We present calculations for diglycine - $(H_2O)_n$ (n = 0-3) to examine the effects of microsolvating water on the relative stability of the zwitterionic vs. canonical forms of the dipeptide. We calculate the structures, energies and Gibbs free energies of the conformers at wB97XD/6-311++G** and MP2/aug-cc-pvdz levels of theory level of theory. We predict that microsolvation by up to three water molecules does not give thermodynamic stability of the zwitterion relative to the canonical forms. Our calculations also suggest that zwitterionic diglycine - $(H_2O)_3$ is not stable kinetically in low temperature gas phase environment.

• Bulletin of the Korean Chemical Society
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• 제23권9호
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• pp.1267-1271
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• 2002

The conformation dependences of basis set superposition errors (BSSE) for 1,2-difluoroethane (DFE) and 1,2-dimethoxyethane (DME) molecules have been estimated using counterpoise method at the Moller-Plesset second order perturbation (MP2) level of theory with various basis sets, assuming that all BSSE dependences on conformations are due to the change in CC bond. The BSSE on the energy differences between eclipsed and gauche forms of DFE are in the range of 0.2-1.2 kcal/mol and those between local minima, gauche and anti forms, are less than 0.2 kcal/mol. For the larger DME molecule, the BSSE differences between local minima are still less than 0.4 kcal/mol, but may not be ignored compared to the energy differences of 0.2-3.0 kcal/mol between conformers.

• Bulletin of the Korean Chemical Society
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• 제23권2호
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• pp.262-266
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• 2002

Computations are presented for the ortho- and para-substituted benzyl alcohol-$H_2O$ clusters. A variety of conformers are predicted, and their relative energies are compared. Binding energies of the clusters are computed, and detailed analysis is presented on the effects of substitution on the strength of the hydrogen bond in the clusters. F- and $NH_2-$ substituted clusters are studied to analyze the effects of electron-withdrawing and electron-pushing groups. In para-substituted clusters, the inductive effects are dominant, affecting the binding energies in opposite way depending on whether the hydroxyl group is proton-donating or -accepting. For ortho-substituted clusters, more direct involvement of the substituting group and the resulting geometry change of the hydrogen bond should be invoked to elucidate complicated pattern of the binding energy of the clusters.

• Bulletin of the Korean Chemical Society
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• 제35권2호
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• pp.531-538
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• 2014

The quantum mechanical properties of a series of oligo-para-phenylenes (2-11) were characterized using DFT B3LYP/6-311G(d,p) calculations. The global minimum among the various torsional conformers of an oligo-p-phenylene is calculated to be a twist conformation. A less stable planar conformation, in which all the dihedral angles in oligo-p-phenylene are restricted to be planar, has also been calculated. The total electronic energies, normal vibrational modes, Gibbs free energies, and HOMOs and LUMOs of the two different conformations (twisted and planar) of the oligo-p-phenylenes were analyzed. The energy differences between the HOMOs and LUMOs of the substrates are in accord with the maximum absorption peaks of the experimental UV spectra of 2-6. The calculated normal vibrational modes of 2-6 were comparable with their experimental IR spectra.

• Bulletin of the Korean Chemical Society
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• 제26권8호
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• pp.1229-1234
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• 2005

The conformational, configurtational behavior and the structure of N-2-(1,4-Dioxane)-N'-(4-methylbenzenesulfonyl)-O-(4-methylphenoxy) isourea 1 has been studied using DFT method. Calculations predict the imidoyl amino group of the dioxane ring prefers axial conformation and that the tosyl and tolyl groups about the C=N bond retain E configuration. The anomeric effect controls the population of dioxane ring conformers, and anomers. Intramolecular hydrogen bonds contribute to the stability of E isomers. The computational analysis of 1 complements the X-ray findings.

• Bulletin of the Korean Chemical Society
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• 제31권4호
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• pp.941-948
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• 2010

Ab initio and density functional theory methods have been employed to study all theoretically possible conformers of fluoroacetic acid. Molecular geometries and energetic of cis and trans monomers and cis dimers in gaseous phase have been obtained using HF, B3LYP and MP2 levels of theory, implementing 6-311++G(d,p) basis set. It was found that cis rotamers are more stable. In addition, it was found that in comparison with acetic acid the strength of hydrogen bonding in fluoroacetic acid decreased. The infrared spectrum frequencies and the vibrational frequency shifts are reported. Natural population and atom in molecule analysis performed to predict electrostatic interactions in the cyclic H-bonded complexes and charges. The proton transfer reaction is studied and activation energy is compared with acetic acid proton transfer reaction.

• Bulletin of the Korean Chemical Society
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• 제25권1호
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• pp.55-58
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• 2004

In this study we have performed ab initio computer simulations to investigate the conformational characteristics of the tetramethoxycalix[4]arenes (1 and 2). The structures of four types (cone, partial cone, 1,2-alternate, and 1,3-alternate) of conformers for each compound have been optimized using ab initio RHF/6-31G and 6-31$G^{**}$ methods. General trends in relative stabilities of tetramethyl ether derivatives of calix[4]arene 1 and p-tert-butylcalix[4]arene 2 are similar and decrease in following order: partial cone (most stable) > cone > 1,3-alternate > 1,2-alternate. The calculated results of the most stable conformation of partial cone structure agree with the reported NMR experimental observations.

• Bulletin of the Korean Chemical Society
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• 제18권2호
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• pp.143-149
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• 1997

We have investigated a relationship between conformational preferences of various substituents in monosubstituted cyclohexanes and pertinent torsional parameter values in molecular mechanics calculations. We have manipulated torsional parameters to supply a certain energy difference between gauche and anti conformers, and applied those parameters to monosubstituted cyclohexanes. After investigating 6 different substituents, namely Me, SiH3, F, Cl, Br, and I, MM3 calculations show that (1) the MM3 calculated A values with the current torsional parameters reproduce the available experimental values well, (2) the conformational energy difference between axial and equatorial conformations (the A value) correlates perfectly with the gauche/anti energy differences of the corresponding butane-like fragment (correlation coefficient=l.000), and (3) the A values are essentially twice as the gauche/anti energy differences (slopes=1.86-2.00). On the basis of our analysis, the A values as well as the gauche/anti energy differences are easily calibrated by an adjustment of the relevant torsional parameter. Thus, our technique for tuning the torsional parameters may be of great use in updating molecular mechanics results about conformational preferences whenever a further refinement is necessary.

• Bulletin of the Korean Chemical Society
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• 제10권4호
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• pp.368-371
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• 1989

The constrained, iterative Fourier deconvolution procedure was applied to quantitatively analyze the overlapped bands in the Raman spectra of biomolecules. When applied to Raman spectra of lysozyme and ${\alpha}$-amylase, this procedure resolved the amide Ⅰ band into five component peaks. The relative intensities of the resolved peaks can possibly provide the composition of secondary structure elements in proteins. The deconvolution procedure was also useful in monitoring the small changes in relative intensities of C-S stretching modes due to different conformers of L-methionine in aqueous solutions at different pH values. The implemented procedure is generally applicable to the problem of resolution enhancement of spectroscopic, chromatographic, and electrophoretic data.