Recent theoretical developments permit the prediction of 1H, 13C, 15N, and 19F nuclear magnetic resonance chemical shifts in proteins and offer new ways of analyzing secondary and tertiary structure as well as for probing protein electrostatics. For 13C, phi, psi torsion angles dominate shielding for C alpha and C beta, but the addition of hydrogen bonding and electrostatics gives even better a...

A new method is proposed for constant pH molecular dynamics (MD), employing generalized Born (GB) electrostatics. Protonation states are modeled with different charge sets, and titrating residues sample a Boltzmann distribution of protonation states as the simulation progresses, using Monte Carlo sampling based on GB-derived energies. The method is applied to four different crystal structures o...

The coupled motion of electrons and protons occurs in many proteins. Using appropriate tools for calculation, the three-dimensional protein structure can show how each protein modulates the observed electron and proton transfer reactions. Some of the assumptions and limitations involved in calculations that rely on continuum electrostatics to calculate the energy of charges in proteins are outl...

Conventional wisdom suggests that decreasing dimensions of dielectric materials (e.g., thickness of a film) should yield increasing capacitance. However, the quantum capacitance and the so-called "dead-layer" effect often conspire to decrease the capacitance of extremely small nanostructures, which is in sharp contrast to what is expected from classical electrostatics. Very recently, first-prin...

Experiments were carried out in a pilot-scale pulverized coal combustor at the Energy and Environmental Research Center (EERC) burning a Powder River Basin (PRB) subbituminous coal. A scanning mobility particle sizer (SMPS) and an electrical low-pressure impactor (ELPI) were used to measure the particle size distributions (PSDs) in the range of 17 nm to 10 microm at the inlet and outlet of the ...

Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions is dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computational methods for calculating these interactions can provide very powerful to...

Salt formation is an effective method of improving physicochemical properties of acidic and basic drugs. The selection of a salt form most suitable for drug development requires a well-designed screening strategy to ensure various issues are addressed in the early development stages. Triboelectrification of pharmaceutical powders may cause problems during processing such as segregation of compo...

Ionic detergent micelles have the capacity to solubilize organic substrates, interact selectively with counterions, repel coions, exhibit partial “dissociation” of the counterions, grow in size with added salt, affect the position of chemical equilibria, accelerate or inhibit the rates of chemical reactions, modulate photochemical reactivity and determine the dynamics of diffusion or neardiffus...

Poisson-Boltzmann (PB) theory is the classic approach to soft matter electrostatics and has been applied to numerous physical chemistry and biophysics problems. Its essential limitations are in its neglect of correlation effects and fluid structure. Recently, several theoretical insights have allowed the formulation of approaches that go beyond PB theory in a systematic way. In this topical rev...

The mechanics of DNA at length scales of few hundred nanometers is described by a fluctuating elastic rod model. In this paper we couple the fluctuating rod model with a variational method for describing plectonemes to unravel the mechanics of some recent single molecule experiments. We are able to reproduce some features seen in these experiments which analyze plectoneme formation in DNA under...