Nuclear quantum effects on the vibrational dynamics of the water-air interface.

We have applied path-integral molecular dynamics simulations to investigate the impact of nuclear quantum effects on the vibrational dynamics of water molecules at the water-air interface. The instantaneous fluctuations in the frequencies of the O-H stretch modes are calculated using the wavelet method of time series analysis, while the time scales of vibrational spectral diffusion are determined from frequency-time correlation functions and joint probability distributions. We find that the inclusion of nuclear quantum effects leads not only to a redshift in the vibrational frequency distribution by about 120 cm-1 for both the bulk and interfacial water molecules but also to an acceleration of the vibrational dynamics at the water-air interface by as much as 35%.

Vibrational dynamics and spectroscopy of water at porous g-CN and CN surfaces.

Porous graphitic materials containing nitrogen are promising catalysts for photo(electro)chemical reactions, notably water splitting, but can also serve as "molecular sieves". Nitrogen increases the hydrophilicity of the graphite parent material, among other effects. A deeper understanding of how water interacts with C- and N-containing layered materials, if and which differences exist between materials with different N content and pore size, and what the role of water dynamics is - a prerequsite for catalysis and sieving - is largely absent, however.

Metal regulation of Mycobacterium tuberculosis SufB intein splicing at the host-pathogen crossroad.

Intein sequences self-excise from precursor proteins to generate functional proteins in various organisms. Thus, regulation of intein splicing at the host-pathogen interface can determine the fate of infection by controlling generation of essential proteins in microbes. For instance, Mycobacterium tuberculosis (Mtu) SufB intein splicing is crucial for the functionality of SUF complex.

Vibrational dynamics of liquid water in an external electric field.

In our present study, we have investigated the effects of an externally applied static electric field on the vibrational dynamics of liquid water (DO) using molecular dynamics. The rate of vibrational spectral diffusion is obtained from simulated two-dimensional infrared spectra, three-pulse photon echo intensity, and frequency correlation functions and distributions. We find that the static vibrational frequency distribution undergoes a redshift of 90 cm whereas the overall vibrational dynamics get slower with the relaxation time constant to be around 4.

Comparative Analysis of Host Metabolic Alterations in Murine Malaria Models with Uncomplicated or Severe Malaria.

Malaria varies in severity, with complications ranging from uncomplicated to severe malaria. Severe malaria could be attributed to peripheral hyperparasitemia or cerebral malaria. The metabolic interactions between the host and species are yet to be understood during these infections of varied pathology and severity.

SufB intein splicing in Mycobacterium tuberculosis is influenced by two remote conserved N-extein histidines.

Inteins are auto-processing domains that implement a multistep biochemical reaction termed protein splicing, marked by cleavage and formation of peptide bonds. They excise from a precursor protein, generating a functional protein via covalent bonding of flanking exteins. We report the kinetic study of splicing and cleavage reaction in [Fe-S] cluster assembly protein SufB from Mycobacterium tuberculosis (Mtu).

Gold Nanoparticles Augment N-Terminal Cleavage and Splicing Reactions in SufB.

Protein splicing is a self-catalyzed event where the intervening sequence intein cleaves off, joining the flanking exteins together to generate a functional protein. Attempts have been made to regulate the splicing rate through variations in temperature, pH, and metals. Although metal-regulated protein splicing has been more captivating to researchers, metals were shown to only inhibit splicing reactions that confine their application.

Plasmodium falciparum HSP40 protein eCiJp traffics to the erythrocyte cytoskeleton and interacts with the human HSP70 chaperone HSPA1.

Renovation of host erythrocytes is vital for pathogenesis by Plasmodium falciparum. These changes are mediated by parasite proteins that translocate beyond the parasitophorous vacuolar membrane in an unfolded state, suggesting protein folding by chaperones is imperative for the functionality of exported proteins. We report a type IV P.

Hydrogen bond dynamics of interfacial water molecules revealed from two-dimensional vibrational sum-frequency generation spectroscopy.

Vibrational sum-frequency generation (vSFG) spectroscopy allows the study of the structure and dynamics of interfacial systems. In the present work, we provide a simple recipe, based on a narrowband IR pump and broadband vSFG probe technique, to computationally obtain the two-dimensional vSFG spectrum of water molecules at the air-water interface. Using this technique, to study the time-dependent spectral evolution of hydrogen-bonded and free water molecules, we demonstrate that at the interface, the vibrational spectral dynamics of the free OH bond is faster than that of the bonded OH mode.

"On-The-Fly" Calculation of the Vibrational Sum-Frequency Generation Spectrum at the Air-Water Interface.

In the present work, we provide an electronic structure based method for the "on-the-fly" determination of vibrational sum frequency generation (v-SFG) spectra. The predictive power of this scheme is demonstrated at the air-water interface. While the instantaneous fluctuations in dipole moment are obtained using the maximally localized Wannier functions, the fluctuations in polarizability are approximated to be proportional to the second moment of Wannier functions.

Vibrational echo spectroscopy of aqueous sodium bromide solutions from first principles simulations.

A theoretical study of the time-dependent vibrational echo spectroscopy of sodium bromide solutions in deuterated water at two different concentrations of 0.5 and 5.0 M and at temperatures of 300 and 350 K is presented using the method of ab initio molecular dynamics simulations.

Urea in Water: Structure, Dynamics, and Vibrational Echo Spectroscopy from First-Principles Simulations.

Aqueous solution of urea at a concentration of 4.0 M is studied by using ab initio molecular dynamics simulation. The radial and spatial distribution functions reveal no significant disruption of the local solvent structure by urea even at such a rather high concentration.

Temperature dependence of the ultrafast vibrational echo spectroscopy of OD modes in liquid water from first principles simulations.

The rate of vibrational spectral diffusion of OD/OH stretch modes of water is known to be interconnected with the hydrogen bond rearrangement dynamics in aqueous media as found in several recent experiments and molecular simulations. In the present study, the temperature dependence of vibrational spectral diffusion of OD stretch modes in liquid water is investigated from first principles by using the method of ab initio molecular dynamics. Kinetic rates obtained from the frequency time correlation function (FTCF), the slope of the 3-pulse photon echo (S3PE) and local structure correlation functions are used in the Arrhenius equation to determine the energy barrier for hydrogen bond rearrangement in liquid water.

On the Hydrogen Bond Strength and Vibrational Spectroscopy of Liquid Water.

In the present work, we introduce two new metrics i.e. hydrogen-bond strength and charge-transfer between the donor/acceptor water molecules as a measure of hydrogen-bond rearrangement dynamics.

Nuclear quantum effects on the vibrational dynamics of liquid water.

Based on quantum-mechanical path-integral molecular dynamics simulations, the impact of nuclear quantum effects on the vibrational and hydrogen bond dynamics in liquid water is investigated. The instantaneous fluctuations in the frequencies of the O-H stretch modes are calculated using the wavelet method of time-series analysis, while the time scales of the vibrational spectral diffusion are determined from frequency-time correlation functions, joint probability distributions, and the slope of three-pulse photon echo. We find that the inclusion of nuclear quantum effects leads not only to a redshift of the vibrational frequency distribution by around 130 cm but also to an acceleration of the vibrational dynamics by as much as 30%.

Fast pyrolysis kinetics of alkali lignin: Evaluation of apparent rate parameters and product time evolution.

In this study, the apparent kinetics of fast pyrolysis of alkali lignin was evaluated by obtaining isothermal mass loss data in the timescale of 2-30s at 400-700°C in an analytical pyrolyzer. The data were analyzed using different reaction models to determine the rate constants and apparent rate parameters. First order and one dimensional diffusion models resulted in good fits with experimental data with apparent activation energy of 23kJmol.

Ultrafast Vibrational Echo Spectroscopy of Liquid Water from First-Principles Simulations.

Vibrational echo spectroscopy has become a powerful technique to study vibrational spectral diffusion in water and aqueous solutions. The dynamics of vibrational spectral diffusion is intimately related to the hydrogen bond fluctuations in liquid water and other hydrogen bonded liquids. Earlier theoretical calculations of vibrational echo spectroscopy of aqueous systems were based on classical molecular dynamics simulations involving empirical force fields of water.