Dielectric susceptibility of dipolar molecular liquids by ab initio molecular dynamics: application to liquid HCl

Enhancing the microbial advanced oxidation of P-nitrophenol in sediment through accelerating extracellular respiration with electrical stimulation

Microbial advanced oxidation, a fundamental process for pollutant degradation in nature, is limited in efficiency by the weak respiration of indigenous microorganisms. In this study, an electric field was employed to enhance microbial respiration and facilitate the microbial advanced oxidation of p-nitrophenol (PNP) in simulated wetlands with alternation of anaerobic and aerobic conditions. With intermittent air aeration, an electric field of 0.8 V promoted extracellular electron transfer to increase Fe2+ generation through dissimilatory iron reduction and the production of hydroxyl radicals (•OH) through Fenton-like reactions. As a result, the PNP removal rate of the electrically-stimulated group was higher than that of the control (72.15 % vs 46.88 %). Multiple lines of evidence demonstrated that the electrically-induced polarization of respiratory enzymes expedited proton-coupled electron transfer within the respiratory chain to accelerate microbial advanced oxidation of PNP. The polarization of respiratory enzymes with the electric field hastened proton outflow to increase cell membrane potential for adenosine triphosphate (ATP) generation, which enhanced intracellular electron transportation to benefit reactive oxygen species generation. This study provided a new method to enhance microelectrochemical remediation of the contaminant in wetlands via the combination of intermittent air aeration.

Biological Self-Assembled Transmembrane Electron Conduits for High-Efficiency Ammonia Production in Microbial Electrosynthesis

Usually, CymA is irreplaceable as the electron transport hub in Shewanella oneidensis MR-1 bidirectional electron transfer. In this work, biologically self-assembled FeS nanoparticles construct an artificial electron transfer route and implement electron transfer from extracellular into periplasmic space without CymA involvement, which present similar properties to type IV pili. Bacteria are wired up into a network, and more electron transfer conduits are activated by self-assembled transmembrane FeS nanoparticles (electron conduits), thereby substantially enhancing the ammonia production. In this study, we achieved an average NH4+-N production rate of 391.8 μg·h-1·L reactor-1 with the selectivity of 98.0% and cathode efficiency of 65.4%. Additionally, the amide group in the protein-like substances located in the outer membrane was first found to be able to transfer electrons from extracellular into intracellular with c-type cytochromes. Our work provides a new viewpoint that contributes to a better understanding of the interconnections between semiconductor materials and bacteria and inspires the exploration of new electron transfer chain components.

Electromotive force induced by dynamic magnetic field electrically polarized sediment to aggravate methane emission

As a primary driving force of global methane production, methanogens like other living organisms are exposed to an environment filled with dynamic electromagnetic waves, which might induce electromotive force (EMF) to potentially influence the metabolism of methanogens. However, no reports have been found on the effects of the induced electromotive force on methane production. In this study, we found that exposure to a dynamic magnetic field enhanced bio-methanogenesis via the induced electromotive force. When exposed to a dynamic magnetic field with 0.20 to 0.40 mT of intensity, the methane emission of the sediments increased by 41.71%. The respiration of methanogens and bacteria was accelerated by the EMF, as the ratios of F420H2/F420 and NAD+/NADH of the sediment increased by 44.12% and 55.56%, respectively. The respiratory enzymes in respiration chains might be polarized with the EMF to accelerate the proton-coupled electron transfer to enhance microbial metabolism. Together with the enriched exoelectrogens and electrotrophic methanogens, as well as the increased sediment electro-activities, this study indicated that the EMF could enhance the electron exchange among extracellular respiratory microorganisms to increase the methane emission from sediments.

Reason for the increased electroactivity of extracellular polymeric substances with electrical stimulation: Structural change of α-helix peptide of protein

Electroactivity is an important parameter to assess the ability of the extracellular polymeric substance (EPS) of microorganisms to participate in extracellular respiration. Many reports have found that the electroactivity of microbial sludge could be enhanced with electrical stimulation, but the reason remains unclear. The results of this study showed that the current generation of the three microbial electrolysis cells increased by 1.27-1.76 times during 49 days of electrical stimulation, but the typical electroactive microorganisms were not enriched. Meanwhile, the capacitance and conductivity of EPS of sludge after the electrical stimulation increased by 1.32-1.83 times and 1.27-1.32 times, respectively. In-situ FTIR analysis indicated that the electrical stimulation could lead to the polarization of amide groups in the protein, likely affecting the protein structure related to the electroactivity. Accordingly, the dipole moment of the α-helix peptide of protein of sludge increased from 220 D to 280 D after the electrical stimulation, which was conducive to electron transfer in the α-helix peptide. Moreover, the vertical ionization potential and E_LUMO-E_HOMO energy gap of the C-terminal in the α-helix peptide decreased from 4.43 eV to 4.10 eV and 0.41 eV to 0.24 eV, respectively, which indicated that the α-helix was easier to serve as the electron transfer site of electron hopping. These results meant that the enhancement of the dipole moment of the α-helix peptide unchoked the electron transfer chain of the protein, which was the main reason for the increased electroactivity of EPS protein.

Applying Dynamic Magnetic Field To Promote Anaerobic Digestion via Enhancing the Electron Transfer of a Microbial Respiration Chain

Electrochemical methods have been reported to strengthen anaerobic digestion, but the continuous electrical power supply and the complicated electrode installed inside the digester have restricted it from practical use. In this study, a dynamic magnetic field (DMF) was placed outside a digester to induce an electromotive force to electrically promote anaerobic digestion. With the applied DMF, an electromotive force of 0.14 mV was generated in the anaerobic sludge, and a 65.02% methane increment was obtained from the anaerobic digestion of waste-activated sludge. Experiments on each stage of anaerobic digestion showed that acidification and methanogenesis that involve electron transfer of respiration chains were promoted with the DMF, while solubilization and hydrolysis less related to respiration chains were not enhanced. Further analysis indicated that the induced electromotive force polarized the protein-like substances in the sludge to increase the conductivity and capacitance of the sludge. Electrotrophic methanogens (Methanothrix) and exoelectrogens (Exiguobacterium) were enriched with DMF. The kinetic isotope effect test confirmed that electron transfer was accelerated with DMF. Consistently, the concentration ratio of co-enzymes (NADH/NAD⁺ and F₄₂₀H₂/F₄₂₀₎ that reflects the electron exchange with respiration chains significantly increased. Applying the DMF seemed a more accessible strategy to electrically strengthen anaerobic digestion.

Electro-polarization of protein-like substances accelerates trans-cell-wall electron transfer in microbial extracellular respiration

Electrical stimulation has been used to strengthen microbial extracellular electron transfer (EET), however, the deep-seated reasons remain unclear. Here we reported that Bacillus subtilis, a typical gram-positive bacterium capable of extracellular respiration, obtained a higher EET capacity after the electrical domestication. After the electrical domestication, the current generated by the EET of B. subtilis was 23.4-fold that of the control group without pre-domestication. Multiple lines of evidence in bacterial cells of B. subtilis, their cell walls, and a model tripeptide indicated that the polarization of amide groups after the electrical stimulation forwarded the H-bonds recombination and radical generation of protein-like substances to develop extracellular electron transfer via the proton-coupled pattern. The improved electrochemical properties of protein-like substances benefited the trans-cell-wall electron transfer and strengthen extracellular respiration. This study was the first exploration to promote microbial extracellular respiration by improving the electrochemical properties of protein-like substances in cell envelopes.

Extracellular electron uptake for CO2 fixation by Rhodopseudomonas palustris during electro-cultivation in darkness

As a vital part of the global carbon cycle, photosynthesis helps in fixing CO₂ to produce diverse biomass. However, over-reliance on optical density results in inadequate photosynthesis under limited light sources. The coupling of extracellular respiration and photosynthetic chain via the quinone pool provides a possibility for electrically driven photosynthesis in darkness, which is not well understood. In this study, CO₂ fixation of photosynthetic bacteria Rhodopseudomonas palustris was enhanced in the dark via extracellular electron uptake from the electrode at -0.4 V. The copy number of R. palustris increased by 35 folds during 28 days of operation, accompanied by the increase of ATP content, NADH/NAD⁺, and NADPH/NADP⁺ of cells. Especially, the activity of Rubisco, the key enzyme of the Calvin cycle, increased by 28 % during electro-cultivation. Accordingly, the electrochemical activity of R. palustris was found to increase, which might be attributed to the structural modification of protein-like substances due to the enhanced proton-coupled electron transfer (PCET) process in electro-cultivation, which was further confirmed by in situ Fourier transform infrared spectroscopy and kinetic isotope effect tests. This study indicated that extracellular respiration could be electrostimulated via PCET to maintain photosynthesis in R. palustris in the dark.

Intermittent voltage induced sludge polarization to enhance anaerobic digestion

Intermittent voltage supply has been reported to improve the performance of electro-assisted anaerobic digestion but has not been well understood. In this study, an intermittent voltage of 0.6 V (1 day on-1 day off) was applied in an electro-assisted anaerobic digester to explore its effects. Compared to those without the voltage, the methane yield increased nearly by 20.0%, and organic decomposition increased by 9.5% with the intermittent voltage, which was similar to those with the continuous voltage. The amide groups of the sludge protein after the electro-treatment were polarized to enhance electron transfer and electron storage of protein-like substances of the sludge. Although the voltage was supplied intermittently, the increased conductivity and capacitance of the sludge and EPS could effectively transport electrons between exoelectrogens and electrotrophs (such as Firmicutes and Methanothrix) to promote the anaerobic digestion. This study explained the essence of electrochemical enhancement of anaerobic digestion from the perspective of molecular structure, that is, the polarization of functional groups by voltage could improve the sludge electro-activity to maintain effective interspecies electron transfer in the periodic voltage supply.

Low-Frequency Dielectric Response of Tetragonal Perovskite CH3NH3PbI3

The dielectric properties of tetragonal hybrid perovskite CH₃NH₃PbI₃ are studied through molecular dynamics at a temperature of 300 K in the presence of a finite electric field. The high-frequency dielectric constant ε_∞ is found to be 4.5 along the a axis and 4.7 along the c axis. The values of the respective static dielectric constants ε₀ are 43 ± 1 and 53 ± 3, much larger than the value of ∼25 pertaining to the orthorhombic phase, in which the organic cations cannot rotate. At frequencies below 3 cm^-1, we observe a significant increase in ε₀ by ∼23 (a axis) and ∼30 (c axis) compared to a vibrational approach, which does not account for the reorientation of the molecular units. The decomposition shows that the reorientation of the organic cations accounts for an increase of only ∼10. An increase of similar size results from the displacement of the cations within the cages of the lattice. The dominant contribution is found to arise from lattice vibrations coupled to the motion of the organic cations.

Fouling-resistant biofilter of an anaerobic electrochemical membrane reactor

Membrane fouling is a considerable challenge for the stable operation of anaerobic membrane-based bioreactors. Membrane used as a cathode is a common measure to retard fouling growth in anaerobic electrochemical membrane bioreactors (AnEMBR), which; however, cannot avoid the fouling growth. Here we report a strategy using the membrane as an anode to resist membrane fouling in an AnEMBR. Although aggravating in the initial stage, the fouling on the anode membrane is gradually alleviated by the anode oxidation with enriching exoelectrogens to finally achieve a dynamic equilibrium between fouling growth and decomposition to maintain the operation stable. A mesh-like biofilter layer composed of cells with less extracellular polymeric substance (EPS) is formed on the membrane surface to lower the trans-membrane pressure and promote the interception of the anode membrane. The membrane has high electron storage and transfer capacities to accelerate the oxidation of the intercepted fouling materials, especially, the redundant EPSs of the biofilter layer.

Computing the Kirkwood g-Factor by Combining Constant Maxwell Electric Field and Electric Displacement Simulations: Application to the Dielectric Constant of Liquid Water

In his classic 1939 paper, Kirkwood linked the macroscopic dielectric constant of polar liquids to the local orientational order as measured by the g-factor (later named after him) and suggested that the corresponding dielectric constant at short-range is effectively equal to the macroscopic value just after "a distance of molecular magnitude" [ Kirkwood, J. Chem. Phys., 1939, 7, 911 ]. Here, we show a simple approach to extract the short-ranged Kirkwood g-factor from molecular dynamics (MD) simulation by superposing the outcomes of constant electric field E and constant electric displacement D simulations [ Zhang and Sprik, Phys. Rev. B: Condens. Matter Mater. Phys., 2016, 93, 144201 ]. Rather than from the notoriously slow fluctuations of the dipole moment of the full MD cell, the dielectric constant can now be estimated from dipole fluctuations at short-range, accelerating the convergence. Exploiting this feature, we computed the bulk dielectric constant of liquid water modeled in the generalized gradient approximation (PBE) to density functional theory and found it to be at least 40% larger than the experimental value.

Voronoi dipole moments for the simulation of bulk phase vibrational spectra

Voronoi tessellation of the electron density in ab initio molecular dynamics simulations is used to calculate vibrational spectra.

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

A unified electrostatic and cavitation model for first-principles molecular dynamics in solution

The electrostatic continuum solvent model developed by [Fattebert and Gygi J. Comput. Chem. 23, 662 (2002); Int. J. Quantum Chem. 93, 139 (2003)] is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. Our model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. We apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon.

Extracting effective normal modes from equilibrium dynamics at finite temperature

A general method for obtaining effective normal modes of a molecular system from molecular dynamics simulations is presented. The method is based on a localization criterion for the Fourier transformed velocity time-correlation functions of the effective modes. For a given choice of the localization function used, the method becomes equivalent to the principal mode analysis (PMA) based on covariance matrix diagonalization. On the other hand, a proper choice of the localization function leads to a novel method with a strong analogy with the usual normal mode analysis of equilibrium structures, where the Hessian system at the minimum energy structure is replaced by the thermal averaged Hessian, although the Hessian itself is never actually calculated. This method does not introduce any extra numerical cost during the simulation and bears the same simplicity as PMA itself. It can thus be readily applied to ab initio molecular dynamics simulations. Three such examples are provided here. First we recover effective normal modes of an isolated formaldehyde molecule computed at 20 K in very good agreement with the results of a normal mode analysis performed at its equilibrium structure. We then illustrate the applicability of the method for liquid phase studies. The effective normal modes of a water molecule in liquid water and of a uracil molecule in aqueous solution can be extracted from ab initio molecular dynamics simulations of these two systems at 300 K.

Microscopic calculations of local lipid membrane permittivities and diffusion coefficients for application to electroporation analyses

Interaction of electric fields with biological systems has begun to receive considerable attention for applications that include field-assisted drug delivery, medical interventions, and genetic engineering. External fields induce the strongest effects at membranes with electroporation being a common feature. Membrane transport in this context of poration is often based on continuum approaches utilizing macroscopic parameters such as the permittivity, diffusion coefficients, and mobilities. In such modeling, field dependences, local inhomogeneities, and microscopic details are usually ignored. Here, a molecular dynamics (MD) scheme is used for a more rigorous and physically realistic evaluation of such parameters for potential application to electroporative transport model development. A suitable membrane structure containing a nanopore derived from MD analysis is used as the initial geometric configuration. Both static and frequency dependent diffusion coefficients have been evaluated. Permittivities are also calculated and shown to be dramatically non-uniform in the vicinity of membranes under high external fields. A positive feedback mechanism leading to enhanced membrane fields is discussed.

Ab initio molecular dynamics of liquid hydrogen chloride

We carried out an ab initio molecular dynamics simulation of liquid hydrogen chloride (l-HCl) at a temperature of 313 K. Comparison with inelastic neutron scattering data shows that the simulation achieves an overall good description of the structural correlations, improving significantly upon a description based on classical interaction potentials. Despite some minor differences between theory and experiment in the H-H partial structure factor, the simulation gives a description of the hydrogen bonding in impressive agreement with experiment, for both the amount and the bond-length distribution of the bonds. In the simulation, 40% of the molecules are nonbonded, while the hydrogen-bonded chains are short, principally consisting of dimers (25%) and trimers (15%). Neighboring molecules in the simulation are found to form L-shaped arrangements, like in the isolated (HCl)(2) dimer and in crystalline phases of HCl. The time correlation of the molecular-axis orientation is found to be characterized by a very short decay time (0.13 ps), consistent with the short length of the hydrogen-bonded chains. Other dynamical properties investigated in this work include the diffusion coefficient and the vibrational density of states. We evaluated the molecular dipole of the HCl molecule in the liquid using a definition based on the coupling of rotational modes to an external electric field. The average dipole moment (1.53 D) derived in this way is found to be considerably larger than for the isolated molecule (1.11 D). Our results show that the dipole moment in [script-l]-HCl undergoes large fluctuations, both in orientation and in modulus. Upon the onset of an external field, such dipole fluctuations concur to reduce the fluctuations of the dielectric response.