Theoretical insights into C–H bond activation of methane by transition metal clusters: the role of anharmonic effects

To incorporate the anharmonicity in the vibrational free energy contribution to the configurational entropy, we evaluate the excess free energy of clusters numerically by a thermodynamic integration method with ab initio molecular dynamics (aiMD) simulation inputs.

Base pairing and stacking contributions to double stranded DNA formation

Double-strand (ds)DNA formation and dissociation are of fundamental biological importance. The negatively DNA charge influences the dsDNA stability. However, the base pairing and the stacking between neighboring bases are responsible for the sequence dependent stability of dsDNA. The stability of a dsDNA molecule can be estimated from empirical nearest-neighbor models based on contributions assigned to base pair steps along the DNA and additional parameters due to DNA termini. In efforts to separate contributions it has been concluded that base-stacking dominates dsDNA stability whereas base-pairing contributes negligibly. Using a different model for dsDNA formation we re-analyze dsDNA stability contributions and conclude that base stacking contributes already at the level of separate ssDNAs but that pairing contributions drive the dsDNA formation. The theoretical model also predicts that stability contributions of base pair steps that contain only guanine/cytosine, mixed steps and steps with only adenine/thymine follows the order 6:5:4, respectively, as expected based on the formed hydrogen bonds. The model is fully consistent with available stacking data and nearest-neighbor dsDNA parameters. It allows to assign a narrowly distributed value for the effective free energy contribution per formed hydrogen bond during dsDNA formation of −0.72 kcal·mol-1 based entirely on experimental data.

Wetting of Nematic Liquid Crystals on Crenellated Substrates: A Frank–Oseen Approach

We revisit the wetting of nematic liquid crystals in contact with crenellated substrates, studied previously using the Landau–de Gennes formalism. However, due to computational limitations, the characteristic length scales of the substrate relief considered in that study limited to less than 100 nematic correlation lengths. The current work uses an extended Frank–Oseen formalism, which includes not only the free-energy contribution due to the elastic deformations but also the surface tension contributions and, if disclinations or other orientational field singularities are present, their core contributions. Within this framework, which was successfully applied to the anchoring transitions of a nematic liquid crystal in contact with structured substrates, we extended the study to much larger length scales including the macroscopic scale. In particular, we analyzed the interfacial states and the transitions between them at the nematic–isotropic coexistence.

The mechanism and conformational changes of polybrominated diphenyl ethers to TTR by fluorescence spectroscopy, molecular simulation, and quantum chemistry

Free energy contribution of amino acid LYS (B and D chains) and PDBEs was analyzed combining quantum chemistry and molecular modeling.

TKSA-MC: A Web Server for rational mutation through the optimization of protein charge interactions

The TKSAMC is a web server which calculates protein charge-charge interactions via the Tanford-Kirkwood Surface Accessibility model with the Monte Carlo method for sampling different protein protonation states. The optimization of charge-charge interactions via directed mutations has successfully enhanced the thermal stability of different proteins and could be a key to protein engineering improvement. The server presents the electrostatic free energy contribution of each polar-charged residue to protein native state stability. The server also indicates which residues contribute to destabilizing the protein native state with positive energy and the side chain exposed to solvent. This residue is a candidate for mutation to increase protein thermostability as a function of the chosen pH condition. The web server is freely available at UNESP (São Paulo State University - DF/IBILCE): http://tksamc.df.ibilce.unesp.br.