Changes In Charge Distribution Research Articles

Temporal Changes of Charge Distribution in High Density Self-aligned Si-based Quantum Dots as Evaluated by AFM/KFM

Temporal Changes of Charge Distribution in High Density Self-aligned Si-based Quantum Dots as Evaluated by AFM/KFM

Solvent Effects on Electronically Excited States Using the Conductor-Like Screening Model and the Second-Order Correlated Method ADC(2).

The conductor-like screening model (COSMO) is used to treat solvent effects on excited states within a correlated method based on the algebraic-diagrammatic construction through second-order ADC(2). The origin of solvent effects is revisited, and it is pointed out that two types of contributions have to be considered. One effect is due to the change of the solute's charge distribution after excitation, which triggers a reorganization of the solvent. Initially, only the electronic degrees of freedom adapt to the new charge distribution (nonequilibrium case); for sufficiently long-lived states, the reorientation of the solvent molecules contributes, as well (equilibrium case). The second effect is the coupling of the transition densities to the fast (purely electronic) response of the solvent molecules, which can be viewed as excitonic coupling between solute and solvent molecules. This interaction is also responsible for the screening of excitonic couplings between spatially separated chromophores. While most previous implementations of comparable continuum solvation models only include either of both effects, we argue that both contributions should be taken into account. Both effects can significantly influence the excitation energy and excited state properties of the solute, as exemplified for the π-π* and n-π* excitations of acrolein, and no a priori reason exists to neglect either. The implementation is also tested for the excitonic coupling of the ethene dimer where linear response contributions are indispensable for recovering the screening effects due to the solvent. Example applications to larger cases are provided, too. We discuss the excitonic coupling in a linked dyad consisting of two perylene-tetracarboxy-diimide chromophores, and the solvent effects on an intramolecular charge-transfer state of 4-(N,N-dimethylamino)benzonitrile.

Ras and GTPase-activating protein (GAP) drive GTP into a precatalytic state as revealed by combining FTIR and biomolecular simulations

Members of the Ras superfamily regulate many cellular processes. They are down-regulated by a GTPase reaction in which GTP is cleaved into GDP and P(i) by nucleophilic attack of a water molecule. Ras proteins accelerate GTP hydrolysis by a factor of 10(5) compared to GTP in water. GTPase-activating proteins (GAPs) accelerate hydrolysis by another factor of 10(5) compared to Ras alone. Oncogenic mutations in Ras and GAPs slow GTP hydrolysis and are a factor in many cancers. Here, we elucidate in detail how this remarkable catalysis is brought about. We refined the protein-bound GTP structure and protein-induced charge shifts within GTP beyond the current resolution of X-ray structural models by combining quantum mechanics and molecular mechanics simulations with time-resolved Fourier-transform infrared spectroscopy. The simulations were validated by comparing experimental and theoretical IR difference spectra. The reactant structure of GTP is destabilized by Ras via a conformational change from a staggered to an eclipsed position of the nonbridging oxygen atoms of the γ- relative to the β-phosphates and the further rotation of the nonbridging oxygen atoms of α- relative to the β- and γ-phosphates by GAP. Further, the γ-phosphate becomes more positive although two of its oxygen atoms remain negative. This facilitates the nucleophilic attack by the water oxygen at the phosphate and proton transfer to the oxygen. Detailed changes in geometry and charge distribution in the ligand below the resolution of X-ray structure analysis are important for catalysis. Such high resolution appears crucial for the understanding of enzyme catalysis.

Changes in Charge Distribution, Molecular Volume, Accessible Surface Area and Electronic Structure along the Reaction Coordinate for a Carbocationic Triple Shift Rearrangement of Relevance to Diterpene Biosynthesis

The nature of the recently described "triple shift" rearrangement of a biologically relevant carbocation (computed in the absence of a surrounding enzyme) is characterized by examining the evolution of charge distribution, molecular volume, accessible surface area, and multicenter bonding indices along its reaction coordinate. Implications for interaction of the rearranging carbocation with a terpene synthase active site are discussed.

The Role of Magnesium for Geometry and Charge in GTP Hydrolysis, Revealed by Quantum Mechanics/Molecular Mechanics Simulations

The coordination of the magnesium ion in proteins by triphosphates plays an important role in catalytic hydrolysis of GTP or ATP, either in signal transduction or energy conversion. For example, in Ras the magnesium ion contributes to the catalysis of GTP hydrolysis. The cleavage of GTP to GDP and Pi in Ras switches off cellular signaling. We analyzed GTP hydrolysis in water, Ras, and Ras·Ras-GTPase-activating protein using quantum mechanics/molecular mechanics simulations. By comparison of the theoretical IR-difference spectra for magnesium ion coordinated triphosphate to experimental ones, the simulations are validated. We elucidated thereby how the magnesium ion contributes to catalysis. It provides a temporary storage for the electrons taken from the triphosphate and it returns them after bond cleavage and Pi release back to the diphosphate. Furthermore, the Ras·Mg2+ complex forces the triphosphate into a stretched conformation in which the β- and γ-phosphates are coordinated in a bidentate manner. In this conformation, the triphosphate elongates the bond, which has to be cleaved during hydrolysis. Furthermore, the γ-phosphate adopts a more planar structure, driving the conformation of the molecule closer to the hydrolysis transition state. GTPase-activating protein enhances these changes in GTP conformation and charge distribution via the intruding arginine finger.

Comparison of experimental tests and theory for a rectangular two-channel dielectric wakefield accelerator structure

Experimental results are reported for test beam acceleration and deflection in a two-channel, cm-scale, rectangular dielectric-lined wakefield accelerator structure energized by a 14-MeV drive beam. The dominant waveguide mode of the structure is at $\ensuremath{\sim}30\text{ }\text{ }\mathrm{GHz}$, and the structure is configured to exhibit a high transformer ratio ($\ensuremath{\sim}12\ensuremath{\mathbin:}1$). Accelerated bunches in the narrow secondary channel of the structure are continuously energized via Cherenkov radiation that is emitted by a drive bunch moving in the wider primary channel. Observed energy gains and losses, transverse deflections, and changes in the test bunch charge distribution compare favorably with predictions of theory.

Comprehensive understanding of size‐, shape‐, and composition‐dependent polarizabilities of SimCn (m, n = 1–4) clusters

AbstractWe performed a comprehensive study of the size‐, shape‐, and composition‐dependent polarizabilities of SimCn (m, n = 1–4) clusters on the basis of the density‐functional‐based coupled perturbed Hartree–Fock calculations. We found better correlations between the polarizabilities and both the binding energies (Eb) and change in charge distribution (Δq) than the energy gaps. The α values exhibit overall decreasing and increasing trends with increases in the Eb and Δq values, respectively. For isomers with the same Eb values and different polarizabilities, Δq can well explain the difference in polarizabilities. The π‐electron delocalization effect is the best factor for understanding the shape‐dependence. For a given m/n value, the linear clusters have an obviously larger polarizability than both the prolate and compact clusters, irrespective of the cluster size. We fit a quantitative expression [α = A − (A − B) × exp(−k(m/n))] to describe the composition‐dependent polarizabilities. © 2012 Wiley Periodicals, Inc.

Thermalization time of noble metal nanoparticles: effects of the electron density profile

The lack of d-electron screening in the s-electron spill-out region at the surface of Ag nanoparticles increases the electron-electron interaction in this region compared to the bulk. Therefore when comparing the electron-electron interaction contribution to the thermalization time of nanoparticles of varying radius, smaller particles thermalize faster due to the increased surface to bulk ratio. One aspect which has not been addressed is the effect of the spatial distribution of charge at the surface of the nanoparticle. In this work it is shown that the size dependence of the thermalization time is very sensitive to the surface density profile. The electron thermalization time of conduction electrons in noble metal nanoparticles as a function of the radius is calculated. The sensitivity of the scattering rate to the spatial distribution of charge at the surface of the nanostructure is analyzed using several model surface profiles. The change in surface charge distribution via charging or coating of the nanospheres is shown to be a tool for control and probing of the ultra-fast electron-electron dynamics in metallic nanoparticles.

Direct Measurement of the Protein Response to an Electrostatic Perturbation that Mimics the Catalytic Cycle in Ketosteroid Isomerase

electrostatic perturbation that simulates the charge displacement that occurs along the KSI catalytic reaction coordinate. Photoexcitation of a fluorescent analog (coumarin 183) of the reaction intermediate mimics the change in charge distribution that occurs between the reactant and intermediate state in the steroid substrate of KSI. We measured the electrostatic response and angular dynamics of four probe dipoles in the enzyme active site by monitoring the time-resolved changes in the vibrational absorbance (IR) spectrum of a spectator thiocyanate moiety (a quantitative sensor of changes in electric field) placed at four different locations in and around the active site, using polarization-dependent transient vibrational Stark spectroscopy. The four different dipoles in the active site remain immobile and do not align to the changes in the substrate electric field. These results indicate that the active site of KSI is preorganized with respect to functionally relevant changes in electric fields.

A simplified electrospray ionization source based on electrostatic field induction for mass spectrometric analysis of droplet samples

A simplified electrospray ionization source based on electrostatic field induction is introduced in this paper. The electrostatic field induced spray ionization, termed EFISI, is easily performed using a needle electrode and a capillary, and it does not require heat, gas, a syringe pump or any other equipment. A high voltage is applied to a needle electrode which does not contact the sample. The capillary is used as a sample spray emitter without any electrical contact or tip modification. As only a 1 μL sample droplet is needed for analysis with no or little pretreatment, the EFISI source is particularly suitable for the mass spectrometric analysis of microlitre volume samples. The change of charge distribution in the droplet solution, by the induction of an external electrostatic field from the needle electrode, is proposed to be the main cause of ion formation. We demonstrate its feasibility for the characterization of a wide range of organic compounds and biomolecules in pure solutions or complex matrices. The influence of sample capillary length and droplet solvent composition on the ionization process are also discussed.

Electrochemical potential of Microgramma vaccinifolia rhizome lectin

This work reports the isolation of Microgramma vaccinifolia rhizome lectin (MvRL) and the determination of electrochemical potentials of MvRL in the presence of Ca2+, Mg2+ and human type O erythrocytes. MvRL showed the highest specific hemagglutinating activity with human type O erythrocytes and showed a single polypeptide band of 17kDa on SDS-PAGE. MvRL hemagglutinating activity was neutralized after dialysis with EDTA, and addition of Ca2+ and Mg2+ restored the activity. Electrochemical potentials of MvRL in the presence of 100mM Ca2+ (882mV) and 60mMMg2+ (1051mV) were higher (p<0.05) than in the presence of only 0.15M NaCl (247mV), indicating that the electrochemical system was sensitive to structural and physico-chemical changes promoted by these ions. MvRL potential did not change in the presence of type O erythrocytes. The electrochemical system was able to detect changes in electrochemical potentials of MvRL promoted by Ca2+ and Mg2+, even in a complex environment (human serum supplemented with 40 and 60mM of these ions). The study reveals that the stimulatory effect of Ca2+ and Mg2+ on hemagglutinating activity may be linked to conformational change and/or alterations in surface charge distribution of MvRL.

Sulfur-doped zinc oxide (ZnO) Nanostars: Synthesis and simulation of growth mechanism

We present a bottom-up synthesis, spectroscopic characterization, and ab initio simulations of star-shaped hexagonal zinc oxide (ZnO) nanowires. The ZnO nanostructures were synthesized by a low-temperature hydrothermal growth method. The cross-section of the ZnO nanowires transformed from a hexagon to a hexagram when sulfur dopants from thiourea [SC(NH2)2] were added into the growth solution, but no transformation occurred when urea (OC(NH2)2) was added. Comparison of the X-ray photoemission and photoluminescence spectra of undoped and sulfur-doped ZnO confirmed that sulfur is responsible for the novel morphology. Large-scale theoretical calculations were conducted to understand the role of sulfur doping in the growth process. The ab initio simulations demonstrated that the addition of sulfur causes a local change in charge distribution that is stronger at the vertices than at the edges, leading to the observed transformation from hexagon to hexagram nanostructures. Open image in new window

Direct measurement of the protein response to an electrostatic perturbation that mimics the catalytic cycle in ketosteroid isomerase

Understanding how electric fields and their fluctuations in the active site of enzymes affect efficient catalysis represents a critical objective of biochemical research. We have directly measured the dynamics of the electric field in the active site of a highly proficient enzyme, Δ(5)-3-ketosteroid isomerase (KSI), in response to a sudden electrostatic perturbation that simulates the charge displacement that occurs along the KSI catalytic reaction coordinate. Photoexcitation of a fluorescent analog (coumarin 183) of the reaction intermediate mimics the change in charge distribution that occurs between the reactant and intermediate state in the steroid substrate of KSI. We measured the electrostatic response and angular dynamics of four probe dipoles in the enzyme active site by monitoring the time-resolved changes in the vibrational absorbance (IR) spectrum of a spectator thiocyanate moiety (a quantitative sensor of changes in electric field) placed at four different locations in and around the active site, using polarization-dependent transient vibrational Stark spectroscopy. The four different dipoles in the active site remain immobile and do not align to the changes in the substrate electric field. These results indicate that the active site of KSI is preorganized with respect to functionally relevant changes in electric fields.

A schematic model for energy and charge transfer in the chlorophyll complex

A theory for simultaneous charge and energy transfer in the carotenoid-chlorophyll-a complex is presented here and discussed. The observed charge transfer process in these chloroplast complexes is reasonably explained in terms of this theory. In addition, the process leads to a mechanism to drive an electron in a lower to a higher-energy state, thus providing a mechanism for the ejection of the electron to a nearby molecule (chlorophyll) or into the environment. The observed lifetimes of the electronically excited states are in accord/agreement with the investigations of Sundstrom et al. and are in the range of pico-seconds and less. The change in electronic charge distribution in internuclear space as the system undergoes an electronic transition to a higher-energy state could, under appropriate physical conditions, lead to oscillating dipoles capable of transmitting energy from the carotenoid-chlorophylls chromophore to the reaction center by sending an electromagnetic wave (a photon) which provides a novel new mechanism for energy production. In the simplest version of the Forster–Dexter theory, the excitation energy of a donor is transferred to an acceptor and then de-excited to the ground state by fluorescence with no electron being transferred. In the process proposed herein, charge and energy both are transferred from donor to acceptor which can further de-excite by fluorescence. The charge transfer time scale involving an actual transfer of electron is in the pico-second range.

Crystal structure of the mismatch-specific thymine glycosylase domain of human methyl-CpG-binding protein MBD4

Methyl-CpG (mCpG) binding domain protein 4 (MBD4) is a member of mammalian DNA glycosylase superfamily. It contains an amino-proximal methyl-CpG binding domain (MBD) and a C-terminal mismatch-specific glycosylase domain, which is an important molecule believed to be involved in maintaining of genome stability. Herein, we determined the crystal structure of C-terminal glycosylase domain of human MBD4. And the structural alignments of other helix-hairpin-helix (HhH) DNA glycosylases show that the human MBD4 glycosylase domain has the similar active site and the catalytic mechanisms as others. But the different residues in the N-terminal of domain result in the change of charge distribution on the surface of the protein, which suggest the different roles that may relate some diseases.

Computational Study of the Properties and Reactions of Small Molecules Containing O, S, and Se

The reactions and properties of a series of chalcogen-containing compounds (CH(3))(2)X and (CH(3))(2)C═X, where X = O, S, and Se, were studied computationally at the CBS-QB3 level to examine the differences among these molecules. The reactions and properties investigated include the double bond dissociation energy, the ionization potential, the interaction energies with a series of acids including a proton, CH(3)(+), Li(+), MeLi, and MeOH, and the enolization energies of the (CH(3))(2)C═X species. The effect of substituting the O of acetamide with S or Se also was studied. The changes that result from these reactions were examined via changes in structure and changes in charge distribution using the Hirshfeld charges.

First-principles calculations of the structural, electronic and magnetic properties of BnN20−n (n = 6−18) clusters

The structures of B n N20 − n (n = 6−18), the clusters of boron nitride, are investigated by the density functional theory calculations. The structures of the obtained low-lying isomers can be described by the following six prototypes: single ring, double ring, three-ring, graphitic-like sheet, fullerene and others. B10N10 is demonstrated to be the most stable cluster against the nonstoichiometric ones. Nonzero magnetic moments, 1.999, 1.998, 2.000, 3.999 and 1.999μ B respectively, are found in five B n N20−n (n = 6, 7, 11, 12, 13) clusters. Further analysis indicates that the magnetic moment of the B6N14 cluster is mainly originated from the N atoms, while those of others are from the B atoms. The magnetic moment are finally attributed to the interesting issues of the 2p electrons due to the breaking of local symmetries, the change of coordination number, charge distribution and orbital hybridization.

Density functional theory investigation of the interaction of water withα−Al2O3andα−Fe2O3 (11̲02) surfaces: Implications for surface reactivity

Density functional theory calculations were performed in conjunction with ab initio thermodynamics, bond valence calculations, and density of states studies to investigate the chemical reactivity of \ensuremath{\alpha}-Al${}_{2}$O${}_{3}$ and \ensuremath{\alpha}-Fe${}_{2}$O${}_{3}$ $(1\overline{1}02)$ surfaces in a humid environment. Isostructural \ensuremath{\alpha}-Fe${}_{2}$O${}_{3}$ $(1\overline{1}02)$ displays a much higher degree of surface reactivity with respect to water adsorption and aqueous heavy metal ions than \ensuremath{\alpha}-Al${}_{2}$O${}_{3}$. The reason for these differences has not been fully explained. We have found that, while both metal oxides exhibit a similar stable $(1\overline{1}02)$ surface at and below room temperature, corresponding to a stoichiometric surface with the first layer of metal ions missing, the degree of hydroxylation of the surface oxygen atoms leads to differences in the atomic layer relaxation in $\ensuremath{\alpha}\ensuremath{-}{\mathrm{Al}}_{2}{\mathrm{O}}_{3}$ $(1\overline{1}02)$ compared to \ensuremath{\alpha}-Fe${}_{2}$O${}_{3}$ $(1\overline{1}02)$, which has also been confirmed previously by crystal truncation rod x-ray diffraction studies. Also in agreement with these experimental studies, we find the atomic layer spacing of the most energetically stable (1$\stackrel{\underline{}}{1}$02) ${\mathrm{Al}}_{2}{\mathrm{O}}_{3}$ surface is relatively insensitive to the inclusion of multiple layers of physisorbed water. This is in contrast to previously reported density functional theory studies of hydrated (1$\stackrel{\underline{}}{1}$02) $\ensuremath{\alpha}\ensuremath{-}{\mathrm{Fe}}_{2}{\mathrm{O}}_{3}$ surfaces, the results of which are confirmed in this work, that a monolayer of water is required for good agreement with experimental measurements of the atomic layer relaxation. These changes in atomic spacing result in changes in electron charge distributions and in Lewis and Br\o{}nsted acid/base properties of surface sites, which influence the relative reactivities of the two surfaces. However, the higher reactivity of the hydrated $(1\overline{1}02)$ surface of \ensuremath{\alpha}-Fe${}_{2}$O${}_{3}$ can be attributed mainly to the empty $d$ states of the surface Fe atoms, which exhibit a first peak at \ensuremath{\sim}1 eV above the Fermi level and act as very strong Lewis acid sites. In comparison, the empty $p$ states of Al in the hydrated $(1\overline{1}02)$ \ensuremath{\alpha}-Al${}_{2}$O${}_{3}$ surface, which are \ensuremath{\sim}5 eV above the Fermi level, should be much less reactive to potential adsorbates.

Monitoring Voltage-Dependent Charge Displacement of Shaker B-IR K+ Ion Channels Using Radio Frequency Interrogation

Here we introduce a new technique that probes voltage-dependent charge displacements of excitable membrane-bound proteins using extracellularly applied radio frequency (RF, 500 kHz) electric fields. Xenopus oocytes were used as a model cell for these experiments, and were injected with cRNA encoding Shaker B-IR (ShB-IR) K+ ion channels to express large densities of this protein in the oocyte membranes. Two-electrode voltage clamp (TEVC) was applied to command whole-cell membrane potential and to measure channel-dependent membrane currents. Simultaneously, RF electric fields were applied to perturb the membrane potential about the TEVC level and to measure voltage-dependent RF displacement currents. ShB-IR expressing oocytes showed significantly larger changes in RF displacement currents upon membrane depolarization than control oocytes. Voltage-dependent changes in RF displacement currents further increased in ShB-IR expressing oocytes after ∼120 µM Cu2+ addition to the external bath. Cu2+ is known to bind to the ShB-IR ion channel and inhibit Shaker K+ conductance, indicating that changes in the RF displacement current reported here were associated with RF vibration of the Cu2+-linked mobile domain of the ShB-IR protein. Results demonstrate the use of extracellular RF electrodes to interrogate voltage-dependent movement of charged mobile protein domains — capabilities that might enable detection of small changes in charge distribution associated with integral membrane protein conformation and/or drug–protein interactions.

Charge sharing in multi-electrode devices for deterministic doping studied by IBIC

Following a single ion strike in a semiconductor device the induced charge distribution changes rapidly with time and space. This phenomenon has important applications to the sensing of ionizing radiation with applications as diverse as deterministic doping in semiconductor devices to radiation dosimetry. We have developed a new method for the investigation of this phenomenon by using a nuclear microprobe and the technique of Ion Beam Induced Charge (IBIC) applied to a specially configured sub-100μm scale silicon device fitted with two independent surface electrodes coupled to independent data acquisition systems. The separation between the electrodes is comparable to the range of the 2MeV He ions used in our experiments. This system allows us to integrate the total charge induced in the device by summing the signals from the independent electrodes and to measure the sharing of charge between the electrodes as a function of the ion strike location as a nuclear microprobe beam is scanned over the sensitive region of the device. It was found that for a given ion strike location the charge sharing between the electrodes allowed the beam-strike location to be determined to higher precision than the probe resolution. This result has potential application to the development of a deterministic doping technique where counted ion implantation is used to fabricate devices that exploit the quantum mechanical attributes of the implanted ions.