Damian A. Mooney

Denaturation of hen egg white lysozyme in electromagnetic fields: A molecular dynamics study

Nonequilibrium molecular dynamics simulations of hen egg white lysozyme have been performed in the canonical ensemble at 298 K in the presence of external electromagnetic fields of varying intensity in the microwave to far-infrared frequency range. Significant nonthermal field effects were noted, such as marked changes in the proteins secondary structure which led to accelerated incipient local denaturation relative to zero-field conditions. This occurred primarily as a consequence of alignment of the proteins total dipole moment with the external field, although the enhanced molecular mobility and dipolar alignment of water molecules is influential on sidechain motion in solvent-exposed regions. The applied field intensity was found to be highly influential on the extent of denaturation in the frequency range studied, and 0.25-0.5 V Arms-1 fields were found to induce initial denaturation to a comparable extent to thermal denaturation in the 400 to 500 K range. In subsequent zero-field simulations following exposure to the e/m field, the extent of perturbation from the native fold and the degree of residual dipolar alignment were found to be influential on incipient folding.

A New Mechanism for Penetrant Diffusion in Amorphous Polymers: Molecular Dynamics Simulations of Phenol Diffusion in Bisphenol-A-polycarbonate

Atomistic molecular dynamics simulations are performed to analyze the diffusion of phenol molecules in a bisphenol-A-polycarbonate melt in the zero concentration limit for the temperature range from 500 K to 640 K. The transition from a hopping diffusion to a continuous diffusion is observed. Visualization of the diffusion process reveals a strong coupling between the polymer dynamics, i.e., size and shape fluctuations of the pore space and the hopping of the penetrant. Proper equilibration of the melt has been ensured by application of a novel multiscale simulation approach.

Molecular modeling of thermo-responsive hydrogels: observation of lower critical solution temperature

Stimuli-sensitive hydrogels offer enormous potential as ‘intelligent’ drug delivery vehicles, i.e. ones which are targeted and responsive to symptomatic needs. In particular, temperature sensitive hydrogels exhibit a dramatic, but well defined, volume phase transition (lower critical solution temperature (LCST)), which depending upon the hydrogel, results in either an expansion or shrinkage of the hydrogel. The exact mechanism of the LCST is not fully understood, weakening the ability to design devices a priori. Here, molecular simulation techniques are used to model the hydrogel poly (N-isopropyl acrylamide) (PNIPAM) above, below and at the LCST to probe the molecular level mechanisms governing its origin and transport mechanisms within the hydrogel under NPT ensembles.

Hydrogen bond perturbation in hen egg white lysozyme by external electromagnetic fields: A nonequilibrium molecular dynamics study

Nonequilibrium molecular dynamics simulations of a charge-neutral mutant of hen egg white lysozyme have been performed at 300 K and 1 bar in the presence of external microwave fields (2.45 to 100 GHz) of an rms electric field intensity of 0.05 V Å(-1). A systematic study was carried out of the distributions of persistence times and energies of each intraprotein hydrogen bond in between breakage and reformation, in addition to overall persistence over 20 ns simulations, vis-á-vis equilibrium, zero-field conditions. It was found that localized translational motion for formally charged residues led to greater disruption of associated hydrogen bonds, although induced rotational motion of strongly dipolar residues also led to a degree of hydrogen bond perturbation. These effects were most apparent in the solvent exposed exterior of hen egg white lysozyme, in which the intraprotein hydrogen bonds tend to be weaker.

Very Different Responses to Electromagnetic Fields in Binary Ionic Liquid-Water Solutions

The thermal and nonthermal effects of electromagnetic fields in the microwave to far-infrared frequency on binary mixtures of dimethylimidazolium hexafluorophosphate salts and water have been investigated by means of nonequilibrium molecular dynamics simulation. Significant alterations in dipole alignment, thermal response, and molecular mobility were found vis-a-vis zero-field conditions for mixtures of varying composition. Results indicate that ionic liquids respond most significantly to frequencies much lower than that of water in terms of both heating and nonthermal responses of dipole alignment and molecular mobility, and this was rationalized in terms of dipole moment magnitudes, rotational inertia, and translational field response.

Ionic liquids in external electric and electromagnetic fields: a molecular dynamics study

The non-thermal effects of external electric and electromagnetic fields in the microwave to far-infrared frequency range and at (r.m.s.) electric field intensities of 10−3 to 0.25 V/År.m.s. on neat salts of 1,3-dimethyl-imidazolium hexafluorophosphate ([dmim][PF6]) and 1-butyl-3-methyl-imidazolium hexafluorophosphate ([bmim][PF6]) have been investigated by means of non-equilibrium molecular dynamics simulation. Significant alterations in molecular mobility were found vis-à-vis zero-field conditions. Using Green–Kubo and transient time correlation function analysis, the electrical conductivity of these ionic liquids has been estimated. The results indicate that ionic liquids respond most significantly to frequencies much lower than those of smaller polar solvents such as water, although the mechanism of the field response is almost exclusively translational.

Electromagnetic field effects on binary dimethylimidazolium-based ionic liquid/water solutions

The non-thermal effects of electromagnetic fields in the microwave to far-infrared frequency on neat dimethylimidazolium chloride and triflate salts and their binary mixtures with water have been investigated by means of non-equilibrium molecular dynamics simulation. Significant alterations in dipole alignment and molecular mobility were found vis-à-vis zero-field conditions for mixtures of varying composition. Results indicate that the dimethylimidazolium and triflate ions respond most significantly to frequencies much lower than that of water in terms of dipole alignment and molecular mobility, and this was rationalized. in terms of dipole moment magnitudes, rotational inertia and translational field response.

Mechanism of atmospheric CO2 fixation in the cavities of a dinuclear cryptate.

Using density functional theory (DFT) methods, we have investigated two possible mechanisms for atmospheric CO(2) fixation in the cavity of the dinuclear zinc(II) octa-azacryptate, and the subsequent reaction with methanol whereby this latter reaction transforms the (essentially) chemically inert CO(2) into useful products. The first mechanism (I) was proposed by Chen et al. [Chem.-Asian J. 2007, 2, 710], and involves the attachment of one CO(2) molecule onto the hydroxyl-cryptate form, resulting in the formation of a bicarbonate-cryptate species and subsequent reaction with one methanol molecule. In addition, we suggest another mechanism that is initiated via the attachment of a methanol molecule onto one of the Zn-centers, yielding a methoxy-cryptate species. The product is used to activate a CO(2) molecule and generate a methoxycarbonate-cryptate. The energy profiles of both mechanisms were determined, and we conclude that, while both mechanisms are energetically feasible, free energy profiles suggest that the scheme proposed by Chen et al. is most likely.

Effects of external electromagnetic fields on the conformational sampling of a short alanine peptide

Non‐equilibrium molecular dynamics simulations of a solvated 21‐residue polyalanine (A21) peptide, featuring a high propensity for helix formation, have been performed at 300 K and 1 bar in the presence of external electromagnetic (e/m) fields in the microwave region (2.45 GHz) and an r.m.s. electric field intensity range of 0.01–0.05 V/Å. To investigate how the field presence affects transitions between the conformational states of a protein, we report 16 independent 40 ns‐trajectories of A21 starting from both extended and fully folded states. We observe folding‐behavior of the peptide consistent with prior simulation and experimental studies. The peptide displays a natural tendency to form stable elements of secondary structure which are stabilized by tertiary interactions with proximate regions of the peptide. Consistent with our earlier work, the presence of external e/m fields disrupts this behavior, involving a mechanism of localized dipolar alignment which serves to enhance intra‐protein perturbations in hydrogen bonds (English, et al., J. Chem. Phys. 2010, 133, 091105), leading to more frequent transitions between shorter‐lifetime states.

Hybrid density functional theory description of N- and C-doping of NiO.

The large intrinsic bandgap of NiO hinders its potential application as a photocatalyst under visible-light irradiation. In this study, we have performed first-principles screened exchange hybrid density functional theory with the HSE06 functional calculations of N- and C-doped NiO to investigate the effect of doping on the electronic structure of NiO. C-doping at an oxygen site induces gap states due to the dopant, the positions of which suggest that the top of the valence band is made up primarily of C 2p-derived states with some Ni 3d contributions, and the lowest-energy empty state is in the middle of the gap. This leads to an effective bandgap of 1.7 eV, which is of potential interest for photocatalytic applications. N-doping induces comparatively little dopant-Ni 3d interactions, but results in similar positions of dopant-induced states, i.e., the top of the valence band is made up of dopant 2p states and the lowest unoccupied state is the empty gap state derived from the dopant, leading to bandgap narrowing. With the hybrid density functional theory (DFT) results available, we discuss issues with the DFT corrected for on-site Coulomb description of these systems.