Related papers: Ligand Discrimination in Myoglobin from Linear-Sca…

We carry out a first-principles atomistic study of the electronic mechanisms of ligand binding and discrimination in the myoglobin protein. Electronic correlation effects are taken into account using one of the most advanced methods…

Although ligand-binding sites in many proteins contain a high number density of charged side chains that can polarize small organic molecules and influence binding, the magnitude of this effect has not been studied in many systems. Here, we…

Despite its widespread use, the predictive accuracy of density functional theory (DFT) is hampered by delocalization errors, especially for correlated systems such as transition-metal complexes. Two complementary tuning strategies have been…

The diffusional dynamics and vibrational spectroscopy of molecular hydrogen (H$_2$) in myoglobin (Mb) is characterized. Hydrogen has been implicated in a number of physiologically relevant processes, including cellular aging or…

Approximate density functional theory (DFT) suffers from many-electron self- interaction error, otherwise known as delocalization error, that may be diagnosed and then corrected through elimination of the deviation from exact piecewise…

Accurate treatment of amide resonance is important in electronic structure calculation of protein, for Resonance-Assisted Hydrogen Bonding in the hydrogen bonded chains of backbone amides of protein secondary structures such as beta sheets…

Although DNA is often bent in vivo, it is unclear how DNA-bending forces modulate DNA-protein binding affinity. Here, we report how a range of DNA-bending forces modulates the binding of the Integration Host Factor (IHF) protein to various…

Density functional theory $(DFT)$ studies show that doping of $3d TM$ atoms into $Mg_4^{0,+} (TMMg_3^{0,+})$ can alter the endothermic nature of molecular hydrogen adsorption on bare $Mg_4^{0,+}$. $H_2$ adsorption on $TMMg_3^{0,+}$ clusters…

We present a probabilistic approach to water-water hydrogen bonding that allows one to obtain an analytic expression for the number of bonds per water molecule as a function of both its distance to a hydrophobic particle and hydrophobe…

This study investigates the photocatalytic nitrogen fixation on a cation-doped surface (Bi$_{x}$M$_{y}$)$_2$MoO$_6$ where (M = Fe, La, Yb) in both the orthorhombic and monoclinic configurations using a density functional theory (DFT)…

Hemoglobin (Hgb) forms tetramers (dimerized dimers), which enhance its globular stability and may also facilitate small gas molecule transport, as shown by recent all-atom Newtonian solvated simulations. Hydropathic bioinformatic scaling…

Prediction of protein-ligand binding affinity is a major goal in drug discovery. Generally, free energy gap is calculated between two states (e.g., ligand binding and unbinding). The energy gap implicitly includes the effects of changes in…

Approximate semi-local density functional theory (DFT) is known to underestimate surface formation energies yet paradoxically overbind adsorbates on catalytic transition-metal oxide surfaces due to delocalization error. The low-cost DFT+U…

In the physiology of oxygen-hemoglobin binding, an important role is played by the influence of $\text{H}^+$ and $\text{CO}_2$ on the affinity of hemoglobin for $\text{O}_2$. Here we extend the allosteric model of hemoglobin to include…

A theoretical model for the effect of water hydrogen bonding on the thermodynamics of hydrophobic hydration is proposed as a combination of the classical density functional theory with the recently developed probabilistic approach to water…

Modifying the optoelectronic properties of nanostructured materials through introduction of dopant atoms has attracted intense interest. Nevertheless, the approaches employed are often trial and error, preventing rational design. We…

We utilize a multiscale modeling framework to study the effect of shape, size and ligand composition on the efficacy of binding of a ligand-coated-particle to a substrate functionalized with the target receptors. First, we show how…

While density functional theory (DFT) is widely applied for its combination of cost and accuracy, corrections (e.g., DFT+U) that improve it are often needed to tackle correlated transition-metal chemistry. In principle, the functional form…

Metallization and dissociation are key transformations in diatomic molecules at high densities particularly significant for modeling giant planets. Using X-ray absorption spectroscopy and atomistic modeling, we demonstrate that in halogens,…

The prototypical Hydrogen bond in water dimer and Hydrogen bonds in the protonated water dimer, in other small molecules, in water cyclic clusters, and in ice, covering a wide range of bond strengths, are theoretically investigated by…