Effective Detection of Phenylalanine Using Pyridine Based Sensor.

Pyridine based organic molecule as probe has been synthesized for the detection of phenylalanine (PA) biomarker. The synthesized probe is characterized by H and C NMR and mass spectroscopic studies. The photophysical properties for the probe has recorded by colorimetric and fluorimetric techniques.

Development of Optical Biosensor for the Detection of Glutamine in Human Biofluids Using Merocyanine Dye.

Merocyanine dye based fluorescent organic compound has been synthesized for the detection of glutamine. The probe showed remarkable fluorescent intensity with glutamine through ICT (Intermolecular Charge Transfer Mechanism). Hence, it is tested for the detection of glutamine using colorimetric and fluorimetric techniques in physiological and neutral pH (7.

Eco-Friendly Sustainable Poly(benzoxazine--urethane) with Room-Temperature-Assisted Self-Healing Based on Supramolecular Interactions.

This work is an attempt to develop bio-based eco-friendly poly(benzoxazine--urethane) [poly(U--CDL-aee)] materials using cardanol-based benzoxazines (CDL) and hexamethylene diisocyanate (HMDI) to check their self-healing ability and thermal properties. CDL monomers were synthesized using cardanol, amino ethoxyethanol (aee) or 3-aminopropanol (3-ap), and paraformaldehyde through the Mannich reaction. Later, CDL-aee or CDL-3-ap monomers were copolymerized with a urethane precursor (HMDI), followed by ring-opening polymerization through thermal curing.

Atomistic simulation on flavonoids derivatives as potential inhibitors of bacterial gyrase of .

The bacterial DNA gyrase is an attractive target to identify the novel antibacterial agents. The flavonoid derivatives possess various biological activities such as antimicrobial, anti-inflammatory and anticancer activities. The aim of present study is to identify the potential molecule from flavonoid derivatives against using atomistic simulation namely Molecular Docking, Quantum Chemical and Molecular Dynamics.

Rationally designed imidazole derivative as colorimetric and fluorometric sensor for selective, qualitative and quantitative cyanide ion detection in real time samples.

A new imidazole derivative of 1,2-diaminoanthraquinone and fluorene-2-carboxaldehyde was designed as a sensor B2 to selectively detect the cyanide (CN) ion through colorimetric and/or fluorometric methods. The photochemical characterizations of sensor B2 were tested using absorption and emission spectral studies in CHCN-HO (8:2) semi-aqueous medium. An excited state proton transfer process (ESIPT) was proved by theoretical and spectral studies.

Highly Selective and Sensitive Colorimetric and Fluorimetric Sensor for Cu.

A newly designed fluorescent and colorimetric probe was synthesized and selective detection of cu was successful in aqueous medium. The design strategy exhibited strongly fluorescent when binding with cu based on the change in structure between spirocyclic to a non-cyclic form of rhodamine based dye. The UV visible spectra of probe (6GS2) exhibited three absorption peaks at 229, 309 and 530 nm respectively.

On the misincorporation of nucleotides opposite mutagenic cyclic 1,N-propanoguanine: A computational investigation.

The misincorporation properties of exocyclic DNA adduct, cyclic 1,N-propanoguanine with nucleobases have been investigated using DFT and DFT-D methods. Number of possible and stable mispairing conformations of cyclic 1,N-propanoguanine with A,T,G and C have been considered for our investigation. The single point energy calculations have been carried out at the M06/6-311++G**, ωB97XD/6-311++G** and MP2/6-311++G** levels on corresponding optimized geometries.

Intramolecular hydroarylation of aryl propargyl ethers catalyzed by indium: the mechanism of the reaction and identifying the catalytic species.

The mechanism and regioselectivity of the intramolecular hydroarylation of phenyl propargyl ether catalyzed by indium in gas and solvent phases were investigated by means of the density functional theory method. The computed results revealed that the reaction proceeds through initial π-coordination of the propargyl moiety to the catalyst, which triggers the nucleophilic attack of the phenyl ring via an exo- or endo-dig pathway in a Friedel-Crafts type mechanism. Calculation results obtained employing InI2(+) as the possible catalyst show similar activation energies for the 5-exo-dig and 6-endo-dig pathways.

Quantum mechanistic insights on aryl propargyl ether Claisen rearrangement.

The mechanism of aryl propargyl ether Claisen rearrangement in gas and solvent phase was investigated using DFT methods. Solvent phase calculations are carried out using N,N-diethylaniline as a solvent in the PCM model. The most favorable pathways involve a [3,3]-sigmatropic reaction followed by proton transfer in the first two steps and then deprotonation or [1,5]-sigmatropic reaction.

Spectroscopic probe on N-H⋯N, N-H⋯O and controversial C-H⋯O contact in A-T base pair: a DFT study.

DNA base pair A-T has been investigated by IR and NMR spectroscopy using DFT methods. The results have been analyzed in terms of infrared vibrational frequencies and (1)H NMR chemical shifts. Different types of interactions N-H⋯N, N-H⋯O and C-H⋯O types have been investigated in DNA base pairs.

Stability computations for isomers of La@C(n) (n = 72, 74, 76).

Density-functional theory calculations are presented for low-energy La@C₇₂, La@C₇₄ and La@C₇₆ isomers with IPR (isolated pentagon rule) and non-IPR cages. The relative isomeric production yields at high temperatures are evaluated using the calculated terms, and the relationships to observations are discussed.

Correlation between substituent constants and hyperpolarizabilities for di-substituted trans-azobenzenes.

Nonlinear optical properties of a series of disubstituted trans-azobenzenes were studied. The structures were fully optimized by B3LYP/6-31+G* and both static polarizabilities and hyperpolarizabilities were then calculated by the derivative method. In order to show the relationships between dipole moments, (hyper)polarizabilities and the structures, three kinds of substituent constants were applied to correlate with both ground state dipole moment and hyperpolarizabilities.

Quantum mechanical calculations for the misincorporation of nucleotides opposite mutagenic 3,N4-ethenocytosine.

The ubiquitous nature and persistence of exocyclic DNA adducts suggest their involvement as initiators of carcinogenesis. We have investigated the misincorporation properties of the exocyclic DNA adduct, 3,N(4)-ethenocytosine, using DFT and DFT-D methods. Computational investigations have been carried out by using the B3LYP, M062X, and wB97XD methods with the 6-31+G* basis set to determine the hydrogen bonding strengths, binding energy, and physical parameters.

Computational investigation on microsolvation of the osmolyte glycine betaine [GB (H(2)O)(1-7)].

The preferential interactions of glycine betaine (GB) with solvent components and the effect of solvent on its stability have been examined. In particular, the microsolvation of organic osmolyte and widely important osmoprotectant in nature as glycine betaine has been reported by using M06 method. A number of configurations (b(X) (a-z)) of the clusters for one to seven water molecules (× = 1-7) have been considered for the microsolvation.

Cooperativity effects in linear formaldehyde oligomers using density functional theory calculations.

This work reports hydrogen bonding interaction in linear formaldehyde oligomers using density functional theory method. Many-body analysis technique has been used to study the various interactions in these oligomers and to obtain % contributions from individual many-body energy terms to the binding energies of these oligomers. Co-operativity effects are studied using different indicators viz.

Verification of DFT-predicted hydrogen storage capacity of VC3H3 complex using molecular dynamics simulations.

Density functional theory (DFT) and Fourth-order Möller-Plesset (MP4) perturbation theory calculations are performed to examine the possibility of hydrogen storage in V-capped VC(3)H(3) complex. Stability of bare and H(2) molecules adsorbed V-capped VC(3)H(3) complex is verified using DFT and MP4 method. Thermo-chemistry calculations are carried out to estimate the Gibbs free corrected averaged H(2) adsorption energy which reveals whether H(2) adsorption on V-capped VC(3)H(3) complex is energetically favorable, at different temperatures.

Model calculations for the misincorporation of nucleotides opposite five-membered exocyclic DNA adduct: N(2),3-ethenoguanine.

Five-membered exocyclic DNA adducts are biologically very significant because of their potential to block DNA replication and transcription. N(2),3-Ethenoguanine (N(2,3)-εG) has been identified in the liver DNA of vinyl chloride-exposed rats as a five-membered DNA adduct. Singer et al.

Many-body energies during proton transfer in an aqueous system.

The energetics of the mechanism of proton transfer from a hydronium ion to one of the water molecules in its first solvation shell are studied using density functional theory and the Møller-Plesset perturbation (MP2) method. The potential energy surface of the proton transfer mechanism is obtained at the B3LYP and MP2 levels with the 6-311++G** basis set. Many-body analysis is applied to the proton transfer mechanism to obtain the change in relaxation energy, two-body, three-body and four-body energies when proton transfer occurs from the hydronium ion to one of the water molecules in its first solvation shell.

Interaction of serotonin and fluoxetine: toward understanding the importance of the chirality of fluoxetine (S form and R form).

The present investigation reports the importance of the S and R forms of fluoxetine, as an antidepressant with regards to the chirality taking different types of interactions associated with the neurotransmitter, serotonin. The goal of the present study is to provide predictions and to help experimental and theoretical studies toward understanding the chirality of fluoxetine in drug-ligand interaction, associated with serotonin-reuptake inhibitor drug design studies. Several different conformations for serotonin and fluoxetine complexes have been considered for quantum mechanical calculations.

Li(x)@C(60): Calculations of the encapsulation energetics and thermodynamics.

Li@C(60) and Li@C(70) can be prepared and thus, their calculations at higher levels of theory are also of interest. In the report, the computations are carried out on Li@C(60), Li(2)@C(60) and Li(3)@C(60) with the B3LYP density-functional theory treatment in the standard 3-21G and 6-31G* basis sets. The computed energetics suggests that Li(x) @C(60) species may be produced for a few small x values if the Li pressure is enhanced sufficiently.

Effect of microsolvation on zwitterionic glycine: an ab initio and density functional theory study.

The effect of microsolvation on zwitterionic glycine, considering both (-NH3(+)) as proton donor and (-COO(-)) as proton acceptor at correlated ab initio (MP2) level and density functional methods (B3LYP, PW91, MPW1PW91 and PBE) using 6-311++G** basis set has been reported. DFT methods have been employed so as to compare the performance/quality of different gradient-corrected correlation functionals (PW91, PBE), hybrid functionals (B3LYP, MPW1PW91) and to predict the near quantitative structural and vibrational properties, at reduced computational cost. B3LYP method outperforms among the different DFT methods for the computed hydrogen bond distances and found closer to the value obtained by correlated MP2 level, whereas MPW1PW91 and PBE methods shows very similar values but approximately 0.

Calculations on endohedral C74 complexes.

While empty C74 is still a rather elusive fullerene, its endohedral derivatives are well established. The report surveys computations for three of C74-based endohedrals--Ca@C74, Ba@C74, and Yb@C74. A set of six C74 cages is considered, namely one cage with isolated pentagons, three isomers with a pentagon-pentagon junction, two structures with one pair of connected pentagons, and one heptagon.

Interaction of adenine adducts with thymine: a computational study.

The existence of DNA adducts bring the danger of carcinogenesis because of mispairing with normal DNA bases. 1,N6-ethenoadenine adducts (epsilonA) and 1,N6-ethanoadenine adducts (EA) have been considered as DNA adducts to study the interaction with thymine, as DNA base. Several different stable conformers for each type of adenine adduct with thymine, [epsilonA(1)-T(I), epsilonA(2)-T(I), epsilonA(3)-T(I) and EA(1)-T(I), EA(2)-T(I), EA(3)-T(I)] and [epsilonA(1)-T(II), epsilonA(2)-T(II), epsilonA(3)-T(II) and EA(1)-T(II), EA(2)-T(II), EA(3)-T(II)], have been considered with regard to their interactions.

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.

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.