L. Senthilkumar

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.

An experimental and theoretical study of the kinetics of the reaction between 3-hydroxy-3-methyl-2-butanone and OH radicals

Absolute experimental and theoretical rate constants are determined for the first time for the reaction of 3-hydroxy-3-methyl-2-butanone (3H3M2B) with OH radicals as a function of temperature. Experimental studies were carried out over the temperature range of 277 to 353 K and the pressure range of 5 to 80 Torr, by using a cryogenically cooled cell coupled to the PLP-LIF technique. OH radicals were generated for the first time from the photodissociation of the reactant 3H3M2B at 266 nm and the OH formation yield in 3H3M2B photolysis at 266 nm was measured under our experimental conditions. In addition, the reaction of 3H3M2B with OH radicals was studied theoretically by using the Density Functional Theory (DFT) method under three hydrogen abstraction pathways. According to these calculations, H-atom abstraction occurs more favourably from the methyl group adjacent to the hydroxyl group with a small barrier height. The calculated theoretical rate constants are in good agreement with the experimental data over the temperature range of 278 to 1000 K. No significant temperature dependence can be observed although a very slight effect was observed within the error bars.

Degradation of methyl salicylate through Cl initiated atmospheric oxidation – a theoretical study

In the present study, a possible reaction mechanism for the degradation through Cl initiated atmospheric oxidation of methyl salicylate (MeSA) was studied using density functional theory at B3LYP and M06-2X levels of theory with 6-311++G(d,p) basis set. The degradation occurred through an abstraction process at the meta position of MeSA along the entire reaction path. The barrier height values indicated that the reaction of the benzoate radical of MeSA and NO was a favourable route for degradation, which was thermodynamically exothermic and exergonic in nature. The lifetime calculations indicated a short life span for MeSA at 1.14 days. The rate constant values displayed good Arrhenius character with respect to temperature. The activation hardness predicted a rapid reaction between MeSA and NO. The HOMO and LUMO values along with their plot indicated that the NO radical and benzene ring in the MeSA were highly reactive. Topological analysis revealed that during the reaction the interaction between reactants was covalent in nature.

Density functional theory investigation of cocaine water complexes

Twenty cocaine–water complexes were studied using density functional theory (DFT) B3LYP/6-311++G** level to understand their geometries, energies, vibrational frequencies, charge transfer and topological parameters. Among the 20 complexes, 12 are neutral and eight are protonated in the cocaine-water complexes. Based on the interaction energy, the protonated complexes are more stable than the neutral complexes. In both complexes, the most stable structure involves the hydrogen bond with water at nitrogen atom in the tropane ring and C = O groups in methyl ester. Carbonyl groups in benzoyl and methyl ester is the most reactive site in both forms and it is responsible for the stability order. The calculated topological results show that the interactions involved in the hydrogen bond are electrostatic dominant. Natural bond orbital (NBO) analysis confirms the presence of hydrogen bond and it supports the stability order. Atoms in molecules (AIM) and NBO analysis confirms the C-H · · · O hydrogen bonds formed between the cocaine-water complexes are blue shifted in nature.

Influence of metal ions (Zn2+, Cu2+, Ca2+, Mg2+ and Na+) on the water coordinated neutral and zwitterionic L-histidine dimer

The interaction of metal cations with mono hydrated, neutral and zwitterionic histidine dimer complexes are studied using the density functional theory (DFT-B3LYP) method in both gas and liquid phase. It is found that the metal interaction with histidine is governed by two types of bonds (I) N–Mn+ (Mn+ = Zn2+, Cu2+, Ca2+, Mg2+ and Na+), O–Mn+ bonds and (II) N⋯H–O and N–H⋯O hydrogen bonds. For both the liquid and gas phase, the coordination of metals with the nitrogen atom is strong in neutral systems, whereas the coordination with the oxygen atom is strong in the zwitterions systems. Among all the metal ions considered, the Cu2+ ion strongly coordinates with both the neutral and the zwitterionic forms of histidine dimer. AIM analysis indicates that the N–Mn+, O–Mn+ and hydrogen bonds are partially covalent and electrostatic in nature. The enthalpy of the reaction indicates that the reaction is energetically favoured and exothermic in nature. For all the metal complexes, pKa values decrease with the increase in hydrogen bond strength. Redox potential is high for the zwitterionic complex because of the transfer of electrons from the carboxylic group to amine moiety in all the metal complexes. From the MD calculations, we find that the backbone Mg2+ substituted complexes are stabilized around 0.9 nm, while for the other metal ions it is more than 1.0 nm. Kirkwoods potential indicates the presence of antiparallel dipole–dipole interactions.

Spectroscopic investigations and hydrogen bond interactions of 8-aza analogues of xanthine, theophylline and caffeine: a theoretical study

AbstractThe structure, spectral properties and the hydrogen bond interactions of 8-aza analogues of xanthine, theophylline and caffeine have been studied by using quantum chemical methods. The time-dependent density functional theory (TD-DFT) and the singly excited configuration interaction (CIS) methods are employed to optimize the excited state geometries of isolated 8-azaxanthine, 8-azatheophylline tautomers and 8-azacaffeine in both the gas and solvent phases. The solvent phase calculations are performed using the polarizable continuum model (PCM). The absorption and emission spectra are calculated using the time-dependent density functional theory (TD-DFT) method. The results from the TD-DFT calculations reveal that the excitation spectra are red shifted relative to absorption in aqueous medium. These changes in the transition energies are qualitatively comparable to the experimental data. The examination of molecular orbital reveals that the molecules with a small H→L energy gap possess maximum absorption and emission wavelength. The relative stability and hydrogen bonded interactions of mono and heptahydrated 8-azaxanthine, 8-azatheophylline tautomers and 8-azacaffeine have been studied using the density functional theory (DFT) and Møller Plesset perturbation theory (MP2) implementing the 6-311++G(d,p) basis set. The formation of strong N-H…O bond has resulted in the highest interaction energy among the monohydrates. Hydration does not show any significant impact on the stability of heptahydrated complexes. The atoms in molecule (AIM) and natural bonding orbital (NBO) analyses have been performed to elucidate the nature of the hydrogen bond interactions in these complexes. FigureAbsorption and emission spectra of 8-aza analogues of xanthine, theophylline and caffeine in methanol medium

Metal-interacted histidine dimer: an ETS-NOCV and XANES study

We have analyzed the metal coordination in a histidine dimer, hydrated with a water molecule, based on the extended transition state scheme with the theory of natural orbitals for chemical valence (ETS-NOCV). Metal interaction weakens and strengthens the CO and C–N bonds respectively, which indicates σ bond formation between the metal and the ligand. Frequency analysis reveals CO bond exhibits a red shift, which confirms that the π-back donation of electrons takes place through this bond. From the ETS-NOCV analysis, the electrostatic term is dominant over the orbital term. NOCV analysis indicates that the switching of bond strength between C–N bond and CO bond in neutral and zwitterionic systems respectively is due to the amount of back donation in TM2+–N and TM2+–O bonds (TM2+ = Cu, Zn, Ca, Mg). K-edge XANES spectra for the metal indicates that oxidation state of Zn and Ca increases while for Cu and Mg it decreases. Oxygen K-edge spectra indicate that metals like zinc and copper back-donate the electrons largely to ligands.

Structure and NLO properties of halogen (F, Cl) substituted formic acid dimers.

In this work, using ab initio and density functional theory (DFT) methods halogen substituted formic acid (FA) dimer is studied. The dimer stability is due to the hydrogen bonds, either conventional (OH⋯O, OH⋯F, OH⋯Cl) or non-conventional (CH⋯O, CH⋯F, CH⋯Cl). Among all the dimers, trans-trans form is more stable than the trans-cis, and cis-cis form. Basis set extrapolated counterpoise corrected interaction energy results for the FA dimer are in excellent agreement with BSSE corrected MP2 interaction energy. Symmetry Adopted Perturbation Theory (SAPT) analysis reveals that the electrostatic effect plays a dominant role in stabilization among the dimers with maximum interaction energy. Chlorine substituted FA dimer has high hyperpolarizability, which makes them excellent candidate for nonlinear optical materials (NLO). The halogen substituted formic acid dimers have higher stability and polarizability value than the unsubstituted formic acid dimer. The hyperpolarizability values depend on the geometrical structures of halogenated formic acid dimers than the type of hydrogen bonds. The small excitation energy and HOMO-LUMO gap in the halogenated formic acid dimer has led to the strong nonlinear optical response. The depolarization ratio and Rayleigh scattering increases in formic acid dimer after the halogen atom substitution.

Elucidation of Binding Mechanism of Photodynamic Therapeutic Agent Toluidine Blue O with Chicken Egg White Lysozyme by Spectroscopic and Molecular Dynamics Studies

The nature of binding mechanism of toluidine blue O (TBO) with chicken egg white lysozyme was studied comprehensively by various spectroscopic and computational methods. Both steady state and time‐resolved fluorescence studies unambiguously point to the prevalence of static quenching mechanism in lysozyme–TBO system. Thermodynamic parameters revealed that the association of TBO with lysozyme was a spontaneous process in which hydrophobic and hydrogen bond interactions played a pivotal role in the binding process. The secondary and tertiary conformational changes of lysozyme in the presence of TBO were unraveled using absorption, Fourier transform infrared spectroscopy (FT‐IR) and circular dichroism (CD) techniques. Molecular docking studies of lysozyme–TBO system substantiated the findings of site marker experiment and revealed TBO adjacent to Trp‐63 and Trp‐108 residues of lysozyme. Molecular dynamics (MD) simulation studies of lysozyme–TBO system indicate a stable and effective complexation of TBO with lysozyme. It is hoped that the results presented here will enable further understanding of TBO toxicity.

Effect of alkyl chain on the NLO property of nonylphenol isomers: a DFT study

Density functional theory (DFT) method was employed to study the nonlinear optical (NLO) response of the nonylphenol isomers with different alkyl substituents (methyl, ethyl, propyl, and isopropyl). The linear alkyl chain (hyperpolarizability, βT) and alkyl group aggregation (Hyper Rayleigh scattering hyperpolarizability, βHRS) in nonylphenol isomer has a strong positive influence on the NLO property. Among all the substituents, the methyl dominated alkyl chain nonylphenol isomers are strong NLO materials due to their large polarizability and hyperpolarizability values compared to that of urea/phenol. The absorption spectra obtained from TD-DFT study suggest that the absorption bands are shifted towards the UV–Vis region, dominated by π–π* transitions. The C–H···π intramolecular interactions are a blue shift in nature; however, their function and influence on the NLO property is insignificant. The Rayleigh scattering is dominant for methyl and ethyl substituent, while in the Rayleigh activity is controlled by the natural light.Graphical abstract