Physical analysis of aspirin in different phases and states using density functional theory.

This study analyzed the aspirin molecule (C9H8O4) using Density Functional Theory (DFT) on Gaussian 09W software. First, the structure of aspirin was optimized using the DFT method with the B3LYP functional and the 6-311+G (d,p) basis set. A global reactivity study was employed to understand the reactivity of aspirin in gas and solvent water for both anion and neutral states. To understand the involvement of orbitals in chemical stability and electron conductivity, we calculated the HOMO-LUMO. The thermodynamic function of a molecule was understood using thermochemistry. Molecular Electrostatic Potential (MEP) was employed to understand the physiochemical properties of aspirin. We observed the Mulliken atomic charge to calculate the atomic charge of aspirin. Finally, the title molecule's UV-Vis, FTIR, and Raman spectra are analyzed and compared with the experimental data.

Identification of potent inhibitors of HDAC2 from herbal products for the treatment of colon cancer: Molecular docking, molecular dynamics simulation, MM/GBSA calculations, DFT studies, and pharmacokinetic analysis.

The histone deacetylase 2 (HDAC2), an enzyme involved in gene regulation, is a potent drug target for the treatment of colon cancer. Phytocompounds having anticancer properties show the ability to interact with HDAC2 enzyme. Among the compounds, docking scores of caffeic acid (CA) and p-coumaric acid (pCA) with HDAC2 showed good binding efficacy of -5.46 kcal/mol and -5.16 kcal/mol, respectively, with small inhibition constants. The higher binding efficacy of CA compared to pCA can be credited to the presence of an extra oxygen atom in the CA molecule, which forms an additional hydrogen bond with Tyr297. The HDAC2 in complex with these molecules was found to be stable by analyzing RMSD, RMSF, Rg, and SASA values obtained through MD simulations. Furthermore, CA and pCA exhibited low MM/GBSA free energies of -16.32 ± 2.62 kcal/mol and -17.01 ± 2.87 kcal/mol, respectively. The HOMO and LUMO energy gaps, dipole moments, global reactivity descriptor values, and MEP surfaces showed the reactivity of the molecules. The favourable physicochemical and pharmacokinetic properties, along with absence of toxicity of the molecules determined using ADMET analysis, suggested both the acids to be regarded as effective drugs in the treatment of colon cancer.

Molecular simulation, vibrational spectroscopy and global reactivity descriptors of pseudoephedrine molecule in different phases and states.

The ground state molecular energy, vibrational frequencies and HOMO-LUMO analysis of the title compound have been calculated with density functional theory in the B3LYP/6-311 + G (d,p) basis set using Gaussian 09 W software. The FT-IR spectrum of pseudoephedrine has been computed in the gas phase and in the presence of solvent water both in neutral and anionic structures. The TED assignments of the vibrational spectra have been assigned in the selected intense region. On isotopic substitution of carbon atoms, the shifting of frequencies is distinctly observed. The reported values and HOMO-LUMO mappings reveal the possibility of different charge transfers occurring within the molecule. A MEP map is depicted and the Mulliken atomic charge is also calculated. The UV-Vis spectra have been illustrated and explained from the frontier molecular orbitals using a TD-DFT approach.

Quantum chemical calculations of nicotine and caffeine molecule in gas phase and solvent using DFT methods.

In this study, the molecular structures of nicotine and caffeine molecule have been generated using the 6-311++G(d,p) basis set in the DFT/B3LYP method. The molecules were optimized on the same basis set and their minimum stable energy was calculated. The HOMO-LUMO energies were calculated to establish the kinetic stability and chemical reactivity of the chosen compounds. The variation of energy and its gap were closely studied for both nicotine and caffeine in the presence of solvent water as well. Similarly, vibrational spectroscopy was studied at the most prominent region in both gas phase and solvent water with their respective TED assignments. The shifting of frequency clearly indicates the impact of solvent water and isotopic substitution of carbon atoms.

Echo dephasing and heat capacity from constrained and unconstrained dynamics of triiodothyronine nuclear receptor protein.

The objective of this study is to observe the echo feature curves, vibrational dephasing, and heat capacity of a protein-hormone system taking thyroid hormone receptor-beta (THR-ß) as an example. Constrained and unconstrained molecular dynamics simulations are performed by implementing the theory of velocity reassignments to probe the phase coherent state in terms of echo pulses. The constrained vibrations are incorporated by adjusting rigid bonds to all hydrogen atoms with an integrator parameter of 2 fs/step in order to reduce the degrees of freedom whereas 1 fs/step is used in the free vibrations of the atomic cluster. The nature of temperature auto-correlation functions changes so that echo feature curves also show a distinct nature in the cases of constrained and unconstrained vibrations. There is a large variation in kinetic temperature and internal potential energy in the echo time zone. The temperature rate of change of internal potential energy is the main contributor to the heat capacity of the native state protein-hormone system. The heat capacity of proteins estimated from this technique is in good agreement with the values from experiments. This study shows that triiodothyronine (T3) hormone makes some differences in heat capacity upon binding to the THR-ß ligand binding domain (LBD). The physical properties of unliganded THR-ß and T3-bound THR-ß LBD in the cases of constrained and unconstrained dynamics are observed distinctly under the effect of anharmonicity on the phase coherent state of normal modes and the dephasing time lies in a range of 0.6-0.8 ps when the systems are perturbed suddenly.

Calculated vibrational properties of pigments in protein binding sites.

FTIR difference spectroscopy is widely used to probe molecular bonding interactions of protein-bound electron transfer cofactors. The technique is particularly attractive because it provides information on both neutral and radical cofactor states. Such dual information is not easily obtainable using other techniques. Although FTIR difference spectroscopy has been used to study cofactors in biological protein complexes, in nearly all cases interpretation of the spectra has been purely qualitative. Virtually no computational work has been undertaken in an attempt to model the spectra. To address this problem we have developed the use of ONIOM (our own N-layered integrated molecular Orbital + Molecular mechanics package) (quantum mechanical:molecular mechanics) methods to calculate FTIR difference spectra associated with protein-bound cofactors. As a specific example showing the utility of the approach we have calculated isotope edited FTIR difference spectra associated with unlabeled and labeled ubiquinones in the Q(A) binding site in Rhodobacter sphaeroides photosynthetic reaction centers. The calculated spectra are in remarkable agreement with experiment. Such agreement cannot be obtained by considering ubiquinone molecules in the gas phase or in solution. A calculation including the protein environment is required. The ONIOM calculated spectra agree well with experiment but indicate a very different interpretation of the experimental data compared to that proposed previously. In particular the calculations do not predict that one of the carbonyl groups of Q(A) is very strongly hydrogen bonded. We show that a computational-based interpretation of FTIR difference spectra associated with protein-bound cofactors is now possible. This approach will be applicable to FTIR studies of many cofactor-containing proteins.