P. Kolandaivel

Studies of solvent effects on conformers of glycine molecule

Abstract Conformational stability and solvent effects on selected conformers of glycine under different environment, such as polar and apolar solvents have been studied using ab initio and density functional theory (DFT) methods. The molecular geometries have been optimized using HF/6-31+G ∗ method of ab initio and B3LYP/6-31+G ∗ and B3PW91/6-31+G ∗ hybrid DFT methods. The effects of solvent on the geometrical parameters, relative stability and physical properties, such as dipole moment, etc. have been studied for the conformers of glycine.

Study of atomic and condensed atomic indices for reactive sites of molecules

In this paper, we have introduced the atomic descriptors s(f)k to determine the local reactive sites of the molecular systems during electrophilic, nucleophilic and radical attacks. The condensed Fukui function and the newly introduced condensed atomic descriptor have been calculated for six different systems, namely glycine, alanine, aniline, BH2Cl,trans-FC(O)OF andm-anisidine. The individual atomic charges (gross charge) calculated by the MPA scheme have been used to calculate the condensed Fukui functions (fk) and the newly derived condensed atomic descriptors (sf)kα at B1-DZP level of theory. We carried out the calculation using the “stockholders” charge partitioning technique (i.e., Hirshfeld population scheme). The newly derived quantity gives the same reactive sites as the condensed Fukui functions, and the complexities associated with the negative Fukui functions are removed.

Optical Absorption and Emission Properties of Fluoranthene, Benzo[k]fluoranthene, and Their Derivatives. A DFT Study

Fluoranthene and benzo[k]fluoranthene-based oligoarenes are good candidates for organic light-emitting diodes (OLEDs). In this work, the electronic structure and optical properties of fluoranthene, benzo[k]fluoranthene, and their derivatives have been studied using quantum chemical methods. The ground-state structures were optimized using the density functional theory (DFT) methods. The lowest singlet excited state was optimized using time-dependent density functional theory (TD-B3LYP) and configuration interaction singles (CIS) methods. On the basis of ground- and excited-state geometries, the absorption and emission spectra have been calculated using the TD-DFT method with a variety of exchange-correlation functionals. All the calculations were carried out in chloroform medium. The results show that the absorption and emission spectra calculated using the B3LYP functional is in good agreement with the available experimental results. Unlikely, the meta hybrid functionals such as M06HF and M062X underestimate the absorption and emission spectra of all the studied molecules. The calculated absorption and emission wavelength are more or less basis set independent. It has been observed that the substitution of an aromatic ring significantly alters the absorption and emission spectra.

Structural and Spectral Properties of 4-Bromo-1-naphthyl Chalcones: A Quantum Chemical Study

The structural and optical properties of 4-bromo-1-naphthyl chalcones (BNC) have been studied by using quantum chemical methods. The density functional theory (DFT) and the singly excited configuration interaction (CIS) methods were employed to optimize the ground and excited state geometries of unsubstituted and substituted BNC with different electron withdrawing and donating groups in both gas and solvent phases. Based on the ground and excited state geometries, the absorption and emission spectra of BNC molecules were calculated using the time-dependent density functional theory (TDDFT) method. The solvent phase calculations were performed using the polarizable continuum model (PCM). The geometrical parameters, vibrational frequencies, and relative stability of cis- and trans-isomers of unsubstituted and substituted BNC molecules have been studied. The results from the TDDFT calculations reveal that the substitution of electron withdrawing and electron donating groups affects the absorption and emission spectra of BNC.

Ab initio and DFT studies on structure and stability of aliphatic aldoxime molecules

Abstract Molecular structure and conformational stability of anti and syn conformers of some aliphatic aldoxime molecules RCHNOH (R=H, CH 3 , NH 2 , OH, F) have been studied by employing the ab initio and density functional theory (DFT) methods. The molecular geometries were optimized employing the MP2, BLYP, B3LYP levels of theory of ab initio and DFT methods implementing 6-31G ∗ basis set. The geometrical parameters of anti and syn conformers of aldoximes have been discussed in the light of lone pair electrons presented in the atoms. The maximum hardness principle was used to study the conformational stability of the oxime molecules. The role of lone pair electrons in the chemical hardness values has been studied. The Mullikan population analysis has been performed to study the stability of the bond in the oxime molecules.

Interactions of anticancer drugs with usual and mismatch base pairs — Density functional theory studies

The antitumor activity of a drug is associated with its molecular properties as well as its interactions with target molecules. The molecular structures of usual, mismatch base pairs and their drug (Hydroxyurea and 5-Fluorouracil) interacting complexes were studied using density functional theory methods. The two and three-body interaction energies have been used to analyze the influence of a drug on the stability of base pairs. The sharing of electron density between the interacting molecules is shown through electron density difference maps. The Atoms in Molecules theory and Natural Bond Orbital analysis have been performed to study the hydrogen bonds in the drug interacting complexes.

Ab initio study of the various isomers of C2H3NO

Abstract An ab initio quantum chemical study of the five possible isomers, trans- and cis-conformations of nitrosoethylene, 4H-1,2-oxazete, 2H-1 azirine 1-oxide and acetonitrile oxide, of C2H3NO is reported. Molecular geometries and energies have been obtained at the Hartree-Fock and second-order Moller-Plesset levels of theory. It is important to note that in both the levels of theory, acetonitrile oxide is found to be the most stable isomer among all the five structures. Atomic charges, through Mulliken and natural population analysis schemes, dipole moments, entropies and rotational constants have been calculated using the above-mentioned levels. Various basis sets, 3–21G, 6–31G, 6–31G∗∗ and 6–311G∗, have been used at the HF level of calculation and 6–31G∗ basis set has been utilized at the MP2 level of calculation. Finally, the vibrational spectra of all the five structures have been obtained using the HF/3–21G, HF/6–31G∗∗ and HF/6–31 1G∗ levels. An imaginary frequency has been found for the cis conformer of the nitrosoethylene molecule at both the HF/6–31G∗∗ and HF/6–311G∗ levels.

Microsolvation and hydrogen bond interactions in Glycine Dipeptide: Molecular dynamics and density functional theory studies

Molecular dynamics (MD) simulations were carried out to study the conformational characteristics of Glycine Dipeptide (GD) in the presence of explicit water molecules for over 10 ns with a MD time step of 2 fs. The density functional theory (DFT) methods with 6-311G** basis set have been employed to study the effects of microsolvation on the conformations of GD with 5-10 water molecules. The interaction energy with BSSE corrections and the strength of the intermolecular hydrogen bond interactions have been analyzed. The Baders Atoms in Molecules (AIM) theory has been employed to investigate H-bonding patterns in water interacting complexes. The natural bond orbital (NBO) analysis has been carried out to analyze the charge transfer between proton acceptor to the antibonding orbital of the XH bond in the hydrated complexes. NMR calculations have been carried out at B3LYP/6-311G (2d, 2p) level of theory to analyse the changes in structure and hydrogen bonding environment that occur upon solvation.

Structural Properties and Anion Binding Affinity of cyclo[(1R,3S)-γ-Acc-Gly]3 Hexapeptide

Abstract The structural and anion binding properties of all-trans cyclo[(1R,3S)-γ-Acc-Gly]3 hexapeptide [named as (TAG)3] were explored via quantum chemical studies. The (TAG)3 form complexes with F−, Cl−, and Br− ions inside the cavity exhibiting receptor like conformation. The structural arrangement of (TAG)3 upon ionic enclosure coincides well with the experimentally obtained α-γ cyclic peptide anionic complexes. A good consistency is noted between geometrical parameters and electronic effects. The concentrated LUMO sites in (TAG)3 are useful in deciding the selectivity of N-H group for strong hydrogen bond interaction with anion. This study emphasize that the minimal structural distortions would have pronounced effect over anion binding affinity. The overall structure of (TAG)3 is found to be highly rigid upon Cl− and Br− ionic enclosures. The strong association of (TAG)3 towards inorganic anions with large binding energies, in general shows the hybrid α-γ cyclic peptides as promising anion receptors.

Hydrogen-bonded complexes of serotonin with methanol and ethanol: a DFT study

Density functional theoretical studies on hydrogen-bonded complexes of serotonin with methanol/ethanol have been carried out in a systematic way. The conformational analysis led to ten stable conformers that can be either gauche or anti depending on the dihedral angle values taken by ethylamine side chain and the 5-hydroxyl group. Serotonin-molecules strongly bind with ethanol than methanol. Ethylamine side chain is the most reactive site in both methanol/ethanol complexes and it is responsible for the stability order. The topological parameters, electron density, and Laplacian of electron density show excellent correlation with the hydrogen bond length. Natural bond orbital analysis confirms C–H···O hydrogen bond formed between the serotonin–alcohol complexes to be red shift in nature except for Gph(out)anti complex both with methanol and ethanol to be blue shifted. The energy decomposition analysis reveals that strong interactions between serotonin and ethanol/methanol are due to the attractive contributions from the electrostatic component.