Dissociation Constants of Weak Acids from ab Initio Molecular Dynamics Using Metadynamics: Influence of the Inductive Effect and Hydrogen Bonding on pK(a) Values

The theoretical estimation of the dissociation constant, or pK(a), of weak acids continues to be a challenging field. Here, we show that ab initio CarParrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free-energy profile of the dissociation reaction provide reasonable estimates of the pK(a) value. Water molecules, sufficient to complete the three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. The free-energy profiles exhibit two distinct minima corresponding to the dissociated and neutral states of the acid, and the difference in their values provides the estimate for pK(a). We show for a series of organic acids that CPMD simulations in conjunction with metadynamics can provide reasonable estimates of pK(a) values. The acids investigated were aliphatic carboxylic acids, chlorine-substituted carboxylic acids, cis- and trans-butenedioic acid, and the isomers of hydroxybenzoic acid. These systems were chosen to highlight that the procedure could correctly account for the influence of the inductive effect as well as hydrogen bonding on pK(a) values of weak organic acids. In both situations, the CPMD metadynamics procedure faithfully reproduces the experimentally observed trend and the magnitudes of the pK(a) values.

Structure, dynamics and thermodynamics of single-file water under confinement: effects of polarizability of water molecules

Various structural, dynamic and thermodynamic properties of water molecules confined in single-wall carbon nanotubes (CNTs) are investigated using both polarizable and non-polarizable water models. The inclusion of polarizability quantitatively affects the nature of hydrogen bonding, which governs many properties of confined water molecules. Polarizable water leads to tighter hydrogen bonding and makes the distance between neighboring water molecules shorter than that for non-polarizable water. Stronger hydrogen bonding also decreases the rotational entropy and makes the diffusion constant smaller than in TIP3P and TIP3PM water models. The reorientational dynamics of the water molecules is governed by a jump mechanism, the barrier for the jump being highest for the polarizable water model. Our results highlight the role of polarizability in governing the dynamics of confined water and demonstrate that the inclusion of polarizability is necessary to obtain agreement with the results of ab initio simulations for the distributions of waiting and jump times. The SPC/E water model is found to predict various water properties in close agreement with the results of polarizable water models with much lower computational costs.

Mapping Post-translational Modifications of Mammalian Testicular Specific Histone Variant TH2B in Tetraploid and Haploid Germ Cells and Their Implications on the Dynamics of Nucleosome Structure

Histones regulate a variety of chromatin templated events by their post-translational modifications (PTMs). Although there are extensive reports on the PTMs of canonical histones, the information on the histone variants remains very scanty. Here, we report the identification of different PTMs, such as acetylation, methylation, and phosphorylation of a major mammalian histone variant TH2B. Our mass spectrometric analysis has led to the identification of both conserved and unique modifications across tetraploid spermatocytes and haploid spermatids. We have also computationally derived the 3-dimensional model of a TH2B containing nucleosome in order to study the spatial orientation of the PTMs identified and their effect on nucleosome stability and DNA binding potential. From our nucleosome model, it is evident that substititution of specific amino acid residues in TH2B results in both differential histone-DNA and histone-histone contacts. Furthermore, we have also observed that acetylation on the N-terminal tail of TH2B weakens the interactions with the DNA. These results provide direct evidence that, similar to somatic H2B, the testis specific histone TH2B also undergoes multiple PTMs, suggesting the possibility of chromatin regulation by such covalent modifications in mammalian male germ cells.

Zinc oxide based photocatalysis: tailoring surface-bulk structure and related interfacial charge carrier dynamics for better environmental applications

As an alternative to the gold standard TiO2 photocatalyst, the use of zinc oxide (ZnO) as a robust candidate for wastewater treatment is widespread due to its similarity in charge carrier dynamics upon bandgap excitation and the generation of reactive oxygen species in aqueous suspensions with TiO2. However, the large bandgap of ZnO, the massive charge carrier recombination, and the photoinduced corrosion-dissolution at extreme pH conditions, together with the formation of inert Zn(OH)(2) during photocatalytic reactions act as barriers for its extensive applicability. To this end, research has been intensified to improve the performance of ZnO by tailoring its surface-bulk structure and by altering its photogenerated charge transfer pathways with an intention to inhibit the surface-bulk charge carrier recombination. For the first time, the several strategies, such as tailoring the intrinsic defects, surface modification with organic compounds, doping with foreign ions, noble metal deposition, heterostructuring with other semiconductors and modification with carbon nanostructures, which have been successfully employed to improve the photoactivity and stability of ZnO are critically reviewed. Such modifications enhance the charge separation and facilitate the generation of reactive oxygenated free radicals, and also the interaction with the pollutant molecules. The synthetic route to obtain hierarchical nanostructured morphologies and study their impact on the photocatalytic performance is explained by considering the morphological influence and the defect-rich chemistry of ZnO. Finally, the crystal facet engineering of polar and non-polar facets and their relevance in photocatalysis is outlined. It is with this intention that the present review directs the further design, tailoring and tuning of the physico-chemical and optoelectronic properties of ZnO for better applications, ranging from photocatalysis to photovoltaics.

Spiral-wave dynamics in ionically realistic mathematical models for human ventricular tissue: the effects of periodic deformation

We carry out an extensive numerical study of the dynamics of spiral waves of electrical activation, in the presence of periodic deformation (PD) in two-dimensional simulation domains, in the biophysically realistic mathematical models of human ventricular tissue due to (a) ten-Tusscher and Panfilov (the TP06 model) and (b) ten-Tusscher, Noble, Noble, and Panfilov (the TNNPO4 model). We first consider simulations in cable-type domains, in which we calculate the conduction velocity theta and the wavelength lambda of a plane wave; we show that PD leads to a periodic, spatial modulation of theta and a temporally periodic modulation of lambda; both these modulations depend on the amplitude and frequency of the PD. We then examine three types of initial conditions for both TP06 and TNNPO4 models and show that the imposition of PD leads to a rich variety of spatiotemporal patterns in the transmembrane potential including states with a single rotating spiral (RS) wave, a spiral-turbulence (ST) state with a single meandering spiral, an ST state with multiple broken spirals, and a state SA in which all spirals are absorbed at the boundaries of our simulation domain. We find, for both TP06 and TNNPO4 models, that spiral-wave dynamics depends sensitively on the amplitude and frequency of PD and the initial condition. We examine how these different types of spiral-wave states can be eliminated in the presence of PD by the application of low-amplitude pulses by square- and rectangular-mesh suppression techniques. We suggest specific experiments that can test the results of our simulations.

Flux Transport Dynamos: From Kinematics to Dynamics

Over the past several decades, Flux-Transport Dynamo (FTD) models have emerged as a popular paradigm for explaining the cyclic nature of solar magnetic activity. Their defining characteristic is the key role played by the mean meridional circulation in transporting magnetic flux and thereby regulating the cycle period. Most FTD models also incorporate the so-called Babcock-Leighton (BL) mechanism in which the mean poloidal field is produced by the emergence and subsequent dispersal of bipolar active regions. This feature is well grounded in solar observations and provides a means for assimilating observed surface flows and fields into the models in order to forecast future solar activity, to identify model biases, and to clarify the underlying physical processes. Furthermore, interpreting historical sunspot records within the context of FTD models can potentially provide insight into why cycle features such as amplitude and duration vary and what causes extreme events such as Grand Minima. Though they are generally robust in a modeling sense and make good contact with observed cycle features, FTD models rely on input physics that is only partially constrained by observation and that neglects the subtleties of convective transport, convective field generation, and nonlinear feedbacks. Here we review the formulation and application of FTD models and assess our current understanding of the input physics based largely on complementary 3D MHD simulations of solar convection, dynamo action, and flux emergence.