Biomedical subjects

Shyi-Long Lee

Publications and source records attributed to Shyi-Long Lee.

5 recordsLinked to original sources

PubMed2005

Theoretical studies on nonlinear optical properties of formaldehyde oligomers by ab initio and density functional theory methods.

The first and second hyperpolarizability beta and gamma are obtained for formaldehyde oligomers (H2CO)n (n = 1-7) using computational methods. We have used the finite field (FF) approach and hyperpolarizability density analysis (HDA) to predict the microscopic first and second nonlinear hyperpolarizability of the formaldehyde oligomers. The spatial contributions of electrons to the hyperpolarizability by using plots of HDA are presented. It has been found from the numerical stability checking of the hyperpolarizability calculations that the calculated values by FF method are more stable than those by HDA approach. The values of beta are zero when n is even as the molecule possesses centrosymmetry, and when n is odd, the differences among beta values are not clear. The gamma values are increased with increase in n.

Computer Simulation↗

PubMed2005

Hydrogen-bond interaction in 1:1 complexes of tetrahydrofuran with water, hydrogen fluoride, and ammonia: a theoretical study.

Ab initio and density-functional theory electronic structure calculations have been performed for the 1:1 complexes of tetrahydrofuran with water, hydrogen fluoride, and ammonia. Upon hydrogen bonding with H2O and HF, the structure of tetrahydrofuran (THF) remains relatively unchanged with the exception of THF sites involved in hydrogen-bonding interaction. But the similar findings are not true, upon hydrogen bonded with NH3, where the C2 symmetry of THF changed. The hydrogen-bonding strength for the 1:1 complexes of THF with water, HF, and NH3 is found to be in the order HF>H2O>NH3, which is well characterized by the order in bond angles O2H15F14, O2H16O14, and O2H15N14 closer to linearity, respectively, and the redshifted of stretching frequencies of upsilon(FH), upsilon(OH), and upsilon(NH), respectively. This work is an attempt to provide important predictions and to aid in future experimental and theoretical studies towards the understanding of such hydrogen-bonded van der Waals systems.

Journal Article↗

PubMed2005

A density functional theory study for the hydrogen-bonded nucleic acid base pair: cytosine dimer.

Theoretical investigation for the geometric and energetic properties, rotational constants, harmonic vibrational frequencies, and binding energies of nucleic acid base pair, cytosine dimer, are carried out by using the density functional theory method. The dimer structures resulting from both the keto and the enol (cis/trans) tautomers are investigated in the present study. Various isomers are considered to find the stable structures of the cytosine dimer. The planar cytosine dimer, K-K3 with C2h symmetry, resulting from nonplanar keto tautomers, is found to be thermodynamically most stable out of the four different stable isomers and having the highest binding energy value, 19.51 kcal/mol (including basis set superposition error correction). The vibrational frequency analysis also suggests a red shift of 367.97 cm(-1) for the hydrogen-bonding K-K3 symmetric dimer with two hydrogen bond lengths, each of length 1.913 angstroms. Moreover, charge distribution (ChelpG charges), Laplacian electronic density distribution, and the dimerization equilibrium for the most stable dimer, K-K3, have also been investigated using the same method and the basis set.

Base Pairing↗

PubMed2004

A computational study of microsolvation effect on ethylene glycol by density functional method.

This study focuses on the conformational analysis of ethylene glycol-(water)n (n=1-3) complex by using density functional theory method and the basis set 6-311++G*. Different conformers are reported and the basis set superposition error corrected total energy is -306.767 5171, -383.221 3135, and -459.694 1528 for lowest energy conformer with 1, 2, and 3 water molecules, respectively, with corresponding binding energy -7.75, -15.43, and -36.28 kcal/mol. On applying many-body analysis it has been found that relaxation energy, two-body, three-body energy have significant contribution to the binding energy for ethylene glycol-(water)3 complex whereas four-body energies are negligible. The most stable conformers of ethylene glycol-(water)n complex are the cyclic structures in which water molecules bridge between the two hydroxyl group of ethylene glycol.

Journal Article↗

PubMed2004

Many-body interaction in glycine-(water)3 complex using density functional theory method.

Various configurations were investigated to find the most stable structures of glycine-(water)3 complex. Five different optimized conformers of glycine-(water)3 complex are obtained from density functional theory calculations using 6-311++G* basis set. Relaxation energy and many body interaction energies (two, three, and four body) are also calculated for these conformers. Out of the five conformers, the most stable conformer has the BSSE corrected total energy -513.917 967 7 Hartree and binding energy -27.28 Kcal/mol. It has been found that the relaxation energies, two body energies and three body energies have significant contribution to the total binding energy whereas four body energies are very small. The chemical hardness and chemical potential also confirmed the stability of the conformer having lowest total energy.

Algorithms↗