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%. In addition, a blueshift of about 45 cm-1 is seen in the vibrational frequency distribution of interfacial water molecules compared to that of the bulk. Furthermore, the dynamics of water molecules beyond the topmost molecular layer was found to be rather similar to that of bulk water.

Vibrational dynamics and spectroscopy of water at porous g-C3N4 and C2N 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. Vibrational spectroscopy can answer some of these questions. In this work, the vibrational dynamics and spectroscopy of deuterated water molecules (D2O) mimicking dense water layers at room temperature on the surfaces of two different C/N-based materials with different N content and pore size, namely graphitic C3N4 (g-C3N4) and C2N, are studied using ab initio molecular dynamics (AIMD). In particular, time-dependent vibrational sum frequency generation (TD-vSFG) spectra of the OD modes and also time-averaged vSFG spectra and OD frequency distributions are computed. This allows us to distinguish "free" (dangling) OD bonds from OD bonds that are bound in a H-bonded water network or at the surface - with subtle differences between the two surfaces and also to a pure water/air interface. It is found that the temporal decay of OD modes is very similar on both surfaces with a correlation time near 4 ps. In contrast, TD-vSFG spectra reveal that the interconversion time from "bonded" to "free" OD bonds is about 8 ps for water on C2N and thus twice as long as for g-C3N4, demonstrating a propensity of the former material to stabilize bonded OD bonds.

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. This multiprotein system is the sole pathway for [Fe-S] cluster biogenesis in mycobacteria during oxidative stress and Fe starvation. Although metal toxicity and metal starvation are components of host immunity, correlation of metal stress to Mtu SufB intein splicing is missing till date. Current study examines the splicing and N-terminal cleavage reactions of Mtu SufB precursor protein in presence of micronutrient metal ions like Zn+2, Cu+2, and Fe+3/+2. A known intein splicing inhibitor Pt+4 was also tested to support its proposed role as an anti-TB agent. Mtu SufB precursor protein exhibited significant attenuation of splicing and N-terminal cleavage reactions across different concentration ranges for Pt+4, Cu+2, Zn+2, while Fe+3 interaction resulted in precursor accumulation. UV-Vis spectroscopy, inductively coupled plasma-optical emission spectroscopy (ICP-OES), Tryptophan fluorescence assay, and dynamic light scattering (DLS) techniques analyzed metal-protein interaction. Mutagenesis experiments and Ellman's assay identified plausible metal co-ordination sites within Mtu SufB protein. Analyzing the metal effect on Mtu SufB splicing may provide elemental information about the fate of mycobacterial infection, and a probable mechanism to attenuate intracellular survival of Mtu. Current research hints at the host regulatory mechanism on SufB splicing in its native environment and a likely target for developing next-generation anti-TB drugs.

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 (D2O) using ab initio 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-1 whereas the overall vibrational dynamics get slower with the relaxation time constant to be around 4.9 ps. Thus we infer that the local hydrogen bond network tends to reorganize in the presence of an external field with an increase in local structural order as evident from the overall slower vibrational dynamics and reduced molar entropy.

Conservation Tillage and Waste Crop Residue Based Zinc Fortification in Rice and Wheat under Reclaimed Sodic Soils: Progress toward Nutrient Circularity and Sustainability.

Nearly 50% of the population across the globe is at risk of malnutrition with respect to zinc (Zn) in areas where a cereal based dietary system dominates. The present study estimated daily Zn intake in humans through field experiments in reclaimed sodic soil, utilizing waste crop residue (CR) in conservation tillage where CR played a vital role in enhancing Zn uptake in rice and wheat grains. Zn dynamics, its bioavailability, interaction with soil properties, and plausible contribution in dietary intake were studied extensively to supplement the research. A higher mobility factor (2.70%) and plant available Zn resulted in its higher uptake in rice (58.2 mg kg-1) and wheat (67.2 mg kg-1) under zero tillage in rice followed by zero tillage in wheat where CR was retained on the surface (ZTR-ZTW+CR). Daily Zn intake was found to be maximum (0.651 mg kg-1 day-1) under ZTR-ZTW+CR, demonstrating zinc sufficiency. Thus, this study may help in formulating actionable policies for combating both nutritional security and environmental hazards due to CR burning.

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 Plasmodium species are yet to be understood during these infections of varied pathology and severity. An untargeted metabolomics approach utilizing the liquid chromatography-mass spectrometry platform has been used to identify the affected host metabolic pathways and associated metabolites in the serum of murine malaria models with uncomplicated malaria, hyperparasitemia, and experimental cerebral malaria. We report that mice with malaria share similar metabolic attributes like higher levels of bile acids, bile pigments, and steroid hormones that have been reported for human malaria infections. Moreover, in severe malaria, upregulated levels of metabolites like phenylalanine, histidine, valine, pipecolate, ornithine, and pantothenate, with decreased levels of arginine and hippurate, were observed. Metabolites of sphingolipid metabolism were upregulated in experimental cerebral malaria. Higher levels of 20-hydroxy-leukotriene B4 and epoxyoctadecamonoenoic acids were found in uncomplicated malaria, with lower levels observed for experimental cerebral malaria. Our study provides insights into host biology during different pathological stages of malaria disease and would be useful for the selection of animal models for evaluating diagnostic and therapeutic interventions against malaria. The raw data files are available via MetaboLights with the identifier MTBLS4387.

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). Although it follows a canonical intein splicing pathway, distinct features are added by extein residues present in the active site. Sequence analysis identified two conserved histidines in the N-extein region; His-5 and His-38. Kinetic analyses of His-5Ala and His-38Ala SufB mutants exhibited significant reductions in splicing and cleavage rates relative to the SufB wildtype (WT) precursor protein. Structural analysis and molecular dynamics (MD) simulations suggested that Mtu SufB displays a unique mechanism where two remote histidines work concurrently to facilitate N-terminal cleavage reaction. His-38 is stabilized by the solvent-exposed His-5, and can impact N-S acyl shift by direct interaction with the catalytic Cys1. Development of inteins as biotechnological tools or as pathogen-specific novel antimicrobial targets requires a more complete understanding of such unexpected roles of conserved extein residues in protein splicing.

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. falciparum heat-shock protein 40, PF11_0034, that localizes to the cytoplasmic side of J-dots and interacts with the erythrocyte cytoskeleton, and therefore named eCiJp (erythrocyte cytoskeleton-interacting J protein). Recombinant eCiJp binds to the human heat-shock protein 70 HsHSPA1 and promotes its ATPase activity. In addition, eCiJp could suppress protein aggregation. Our data suggest that eCiJp recruits HsHSPA1 to the host erythrocyte cytoskeleton, where it may become involved in remodeling of the erythrocyte cytoskeleton and/or folding of exported parasite proteins.

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.

Gold Nanoparticles Augment N-Terminal Cleavage and Splicing Reactions in Mycobacterium tuberculosis 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. This is the first study to show the effect of nanoparticles (NPs) on protein splicing. We found that gold nanoparticles (AuNPs) of various sizes can increase the splicing efficiency by more than 50% and the N-terminal cleavage efficiency by more than 45% in Mycobacterium tuberculosis SufB precursor protein. This study provides an effective strategy for engineering splicing-enhanced intein platforms. UV-vis absorption spectroscopy, isothermal titration calorimetry (ITC), and transmission electron microscopy (TEM) confirmed AuNP interaction with the native protein. Quantum mechanics/molecular mechanics (QM/MM) analysis suggested a significant reduction in the energy barrier at the N-terminal cleavage site in the presence of gold atom, strengthening our experimental evidence on heightened the N-terminal cleavage reaction. The encouraging observation of enhanced N-terminal cleavage and splicing reaction can have potential implementations from developing a rapid drug delivery system to designing a contemporary protein purification system.

"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. The spectrum henceforth obtained captures the signatures of hydrogen bond stretching, bending, as well as low-frequency librational modes.

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. The instantaneous fluctuations in frequencies of local OD stretch modes are calculated using time-series analysis of the simulated trajectories. The third-order polarization and intensities of three pulse photon-echo are calculated from ab initio simulations. The timescales of vibrational spectral diffusion are determined from the frequency time correlation functions (FTCF) and short-time slope of three pulse photon echo (S3PE) calculated within the second-order cumulant and Condon approximations. It is found that under ambient conditions, the rate of vibrational spectral diffusion becomes slower with increase in ionic concentration. Decay of S3PE calculated for different systems give timescales, which are in close agreement with those of FTCF and also with the results of experimental time-dependent vibrational spectroscopic experiments. © 2019 Wiley Periodicals, Inc.

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. The slope of the 3-pulse photon echo is determined within the cumulant and Condon approximations. Although the trend found at the low temperature is slightly non-Arrhenius, the barrier for hydrogen bond rearrangement is found to be around 4.2 kcal mol-1 from all the metrics considered here. It is in good agreement with the hydrogen bond energy determined from different experiments and theoretical studies. Based on the findings, a strong correlation between the vibrational spectral diffusion timescale and hydrogen bond dynamics is identified, which gets even more pronounced at low temperatures. Spatio-temporal correlations between frequency fluctuations and the local hydrogen bond network are also explored.

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. Although the static structural features are not altered in any significant manner, the translational, rotational, and vibrational dynamics are found to show noticeable slowing down. The diffusion coefficient of urea is found to be three times lower than that of bulk water molecules. Similarly, orientational relaxation of water molecules in the solvation shell of urea is found to be about 5.0 ps which is significantly higher than the average value of 3.8 ps found for all water molecules. The vibrational dynamics is investigated through calculations of frequency-time correlation function (FTCF), joint frequency probability, and frequency-structure correlation functions. The timescale of vibrational spectral diffusion as determined from FTCF is found to be 2.7 ps which is higher than the known calculated timescale of ∼2 ps for spectral diffusion of pure water for similar levels of calculations. The third-order polarization and the corresponding vibrational echo intensity of OD modes are calculated within the Condon and second-order cumulant approximations. The timescales of loss of correlation in the vibrational echo spectrum are calculated from the time dependence of the slope of the 3-pulse photon echo (S3PE) function. The timescales obtained from S3PE are found to be in agreement with the FTCF. The slowing down of vibrational, translational, and rotational dynamics means that urea affects the properties of water from a dynamical perspective.

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. Further, we also employ a simple model based on energy flux through the donor-acceptor water pairs to quantify the extent of the local hydrogen-bond network reorganization. Most importantly, we report a linear relationship between the OH stretch frequency and the charge and energy transfer through donor-acceptor water pairs. We demonstrate that the vibrational frequency fluctuations, which are used to determine third-order non-linear spectroscopic observables like the short-time slope of three pulse photon echo, can be used as an analog of the fluctuations in the hydrogen-bond strength and charge-transfer. The timescales obtained from our hydrogen-bond strength correlation and charge-transfer correlation decay are in excellent agreement with the computed frequency-time correlation function, as well as with recent vibrational echo experiments.

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-1 but also to an acceleration of the vibrational dynamics by as much as 30%. In addition, quantum fluctuations also entail a significantly faster decay of correlation in the initial diffusive regime, which is in agreement with recent vibrational echo experiments.

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-1. Kinetic compensation effect was established using a large number of kinetic parameters reported in the literature for pyrolysis of different lignins. The time evolution of the major functional groups in the pyrolysate was analyzed using in situ Fourier transform infrared spectroscopy. Maximum production of the volatiles occurred around 10-12s. A clear transformation of guaiacols to phenol, catechol and their derivatives, and aromatic hydrocarbons was observed with increasing temperature. The plausible reaction steps involved in various transformations are discussed.

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. In the current work, we have employed the method of ab initio molecular dynamics simulation to calculate the spectral observables of vibrational echo and two-dimensional infrared (2D-IR) spectroscopy of liquid water at room temperature under Condon and cumulant approximations. The time scales extracted from the temporal decay of the frequency-time correlation function (FTCF), short-time slope of three pulse photon echo (SP3E), dynamic line width (DLW), and the slope of nodal line of 2D-IR spectra are found to be in reasonably close agreement with each other which reinforces the assertion that signatures of FTCF can be captured using three pulse photon echo and 2D-IR spectroscopy.