Potential Energy Diagram Research Articles

A multi-stable energy harvester: Dynamic modeling and bifurcation analysis

A theoretical investigation is conducted on the dynamic and energetic characteristics of a multi-stable bimorph cantilever energy harvester that uses magnetic attraction effect. The multi-stable energy harvester under study is composed of a bimorph cantilever beam with soft magnetic tip and two externally fixed permanent magnets that are arranged in series. With this configuration, the magnetic force and the moment that are exerted on the cantilever tip tend to be highly dependent on the magnetic field induced by the external magnets. Such an energy harvester can possess multi-stable potential functions, ranging from mono-stable to penta-stable. The mechanism that governs the formation of this multi-stability is thoroughly identified and examined thorough a bifurcation analysis performed on the system׳s equilibrium solutions. From this analysis, it is found that the transitions between these multi-stable states occur through very complicated bifurcation scenarios that include degenerate pitchfork bifurcations and mergers of pitchfork bifurcations or saddle-node bifurcations. Bifurcation set diagram is obtained, which is composed of five separate parametric regions, from mono- to penta-stability. The resulting stability map satisfactorily describes the multi-stable characteristics of the present energy harvester. In addition, the dynamic and energetic characteristics of the present multi-stable energy harvester are more thoroughly examined using its potential energy diagrams and a series of numerical simulations, and the obtained results are compared with those for the equivalent bi-stable cases.

Configuration change of NO on Cu(110) as a function of temperature.

The bonding structure of nitric oxide (NO) on Cu(110) is studied by means of scanning tunneling microscopy, reflection absorption infrared spectroscopy, and electron energy loss spectroscopy at 6-160 K. At low temperatures, the NO molecule adsorbs at the short bridge site via the N end in an upright configuration. At around 50 K, this turns into a flat configuration, in which both the N and O atoms interact with the surface. The flat configuration is characterized by the low-frequency N-O stretching mode at 855 cm(-1). The flat-lying NO flips back and forth when the temperature increases to ~80 K, and eventually dissociates at ~160 K. We propose a potential energy diagram for the conversion of NO on the surface.

Correlation between bowl-inversion energy and bowl depth in substituted sumanenes

AbstractThe correlation between the bowl-inversion energy and the bowl depth for sumanenes monosubstituted with an iodo, formyl, or nitro group was investigated experimentally and by theoretical calculations. The bowl-inversion energies of the substituted sumanenes were determined experimentally by two-dimensional NMR exchange spectroscopy measurements. Various density functional theory methods were examined for the calculation of the structure and the bowl-inversion energy of sumanene, and it was found that PBE0, ωB97XD, and M06-2X gave better fits of the experimental value than did B3LYP. The experimental value was well reproduced at these levels of theory. The bowl structures and bowl-inversion energies of monosubstituted sumanenes were therefore calculated at the ωB97XD/6-311+G(d,p) level of theory. In both the experiments and the calculations, the correlation followed the equation ΔE=acos4θ, whereais a coefficient, ΔEis the bowl-inversion energy, and cos θ is the normalized bowl depth, indicating that the bowl inversion follows a double-well potential energy diagram.

Low-Temperature Trapping of Photointermediates of the Rhodopsin E181Q Mutant.

Three active-site components in rhodopsin play a key role in the stability and function of the protein: 1) the counter-ion residues which stabilize the protonated Schiff base, 2) water molecules, and 3) the hydrogen-bonding network. The ionizable residue Glu-181, which is involved in an extended hydrogen-bonding network with Ser-186, Tyr-268, Tyr-192, and key water molecules within the active site of rhodopsin, has been shown to be involved in a complex counter-ion switch mechanism with Glu-113 during the photobleaching sequence of the protein. Herein, we examine the photobleaching sequence of the E181Q rhodopsin mutant by using cryogenic UV-visible spectroscopy to further elucidate the role of Glu-181 during photoactivation of the protein. We find that lower temperatures are required to trap the early photostationary states of the E181Q mutant compared to native rhodopsin. Additionally, a Blue Shifted Intermediate (BSI, λmax = 498 nm, 100 K) is observed after the formation of E181Q Bathorhodopsin (Batho, λmax = 556 nm, 10 K) but prior to formation of E181Q Lumirhodopsin (Lumi, λmax = 506 nm, 220 K). A potential energy diagram of the observed photointermediates suggests the E181Q Batho intermediate has an enthalpy value 7.99 KJ/mol higher than E181Q BSI, whereas in rhodopsin, the BSI is 10.02 KJ/mol higher in enthalpy than Batho. Thus, the Batho to BSI transition is enthalpically driven in E181Q and entropically driven in native rhodopsin. We conclude that the substitution of Glu-181 with Gln-181 results in a significant perturbation of the hydrogen-bonding network within the active site of rhodopsin. In addition, the removal of a key electrostatic interaction between the chromophore and the protein destabilizes the protein in both the dark state and Batho intermediate conformations while having a stabilizing effect on the BSI conformation. The observed destabilization upon this substitution further supports that Glu-181 is negatively charged in the early intermediates of the photobleaching sequence of rhodopsin.

The ab initio and potential energy curve of SiF2(1A1)

The ab initio configuration interaction method and coupled-cluster theory have been used to optimize the possible ground-state structures of SiF2. The method QCISD/6-311G(2df) is most suitable for the calculation of SiF2 by comparing the experimental value and the calculated value; and the calculated equilibrium structure, harmonic frequency, dissociation energy, force-constant are in good agreement with the experimental data. The potential energy functions of SiF2 have been derived from the many-body expansion theory. In the symmetry of stretching vibration and rotation potential energy diagram of SiF2, there is a saddle point in the reaction kinetics SiF+F→SiF2. A stable SiF2 molecule could be formed when F atom with an energy surpassing 4.38 eV. These are completely reported so far as we know for the first time. In addition, it is found that a stable SiF2 molecule could be formed through two equivalent channels of SiF+F→SiF2. And the reaction is endothermic with a threshold energy.

Computational studies on the thermal decomposition of the CH2FOCHFO radical

Theoretical studies have been carried out on the kinetics and thermochemistry of the thermal decomposition of the CH2FOCHFO radical formed during the photo-oxidation of CH2FOCH2F (HFE-152E) using the dual-level method of obtaining the optimised structure at DFT(M06-2X)/6-311++G(d,p) followed by a single-point energy calculation at the G3 level of theory. The rate constant for different reaction channels involved during the decomposition processes of CH2FOCHFO is evaluated at 298 K and 1 atm using canonical transition-state theory. The results point out that the C–H bond scission is the dominant path involving an energy barrier of 9.5 kcal mol−1 determined at the G3 level of theory. A potential energy diagram is constructed and the results are compared with the data available from the literature for a structurally similar molecule.

Catalytic properties of extraframework iron-containing species in ZSM-5 for N2O decomposition

The reactivity of mononuclear and binuclear iron-containing complexes in ZSM-5 zeolite for catalytic N2O decomposition has been investigated by periodic DFT calculations and microkinetic modeling. On mononuclear sites, the activation of a first N2O molecule is favorable. The rate of catalytic N2O decomposition over Fe2+ and [FeIIIO]+ sites is very low because of the very high barriers (>180kJ/mol) for the activation of the second N2O molecule necessary to complete the catalytic cycle by O2 formation. The catalytic cycles for N2O decomposition over binuclear [FeII(μ-O)FeII]2+ and [FeIII(μ-O2)FeIII]2+ species are interconnected. The catalytic cycle involves the interconversion of these species upon dissociation of N2O on the former complex. As the coordination of reactive Fe centers changes along the reaction coordinate, there are changes in the spin state of the complexes, which affect the overall potential energy diagram. These changes in spin multiplicities facilitate O2 formation and desorption steps. Based on the DFT-computed potential energy diagrams, microkinetic model simulations were carried out to predict reaction rates and kinetic parameters. The rate of O2 formation is much higher on binuclear sites than on mononuclear sites. For mononuclear sites, the apparent activation energy is ∼180kJ/mol, close to the barrier for dissociating a second N2O molecule. It is consistent with first-order behavior with respect to the partial pressure of N2O. Binuclear sites display much higher reactivity. At low temperature, O2 desorption is rate controlling, whereas at higher temperatures, the rate is controlled by the two N2O dissociation reactions on [FeII(μ-O)FeII]2+ and [FeIII(μ-O)2FeIII]2+. This leads to first-order behavior with respect to N2O. An alternative path involving N2O adsorption and dissociation on [OFe(μ-O)2Fe]2+ is energetically favorable but does not contribute to the catalytic cycle because O2 desorption from the [OFe(μ-O)2Fe]2+ intermediate is preferred over the activation of a third N2O molecule due to entropic reasons.

Reaction of Dimethyl Ether with Hydroxyl Radicals: Kinetic Isotope Effect and Prereactive Complex Formation

The kinetic isotope effect of the reactions OH + CH3OCH3 (DME) and OH + CD3OCD3 (DME-d6) was experimentally and theoretically studied. Experiments were carried out in a slow-flow reactor at pressures between 5 and 21 bar (helium as bath gas) with production of OH by laser flash photolysis of HNO3 and time-resolved detection of OH by laser-induced fluorescence. The temperature dependences of the rate coefficients obtained can be described by the following modified Arrhenius expressions: k(OH+DME) = (4.5 ± 1.3) × 10(-16) (T/K)(1.48) exp(66.6 K/T) cm(3) s(-1) (T = 292-650 K, P = 5.9-20.9 bar) and k(OH+DME-d6) = (7.3 ± 2.2) × 10(-23) (T/K)(3.57) exp(759.8 K/T) cm(3) s(-1) (T = 387-554 K, P = 13.0-20.4 bar). A pressure dependence of the rate coefficients was not observed. The agreement of our experimental results for k(OH+DME) with values from other authors is very good, and from a fit to all available literature data, we derived the following modified Arrhenius expression, which reproduces the values obtained in the temperature range T = 230-1500 K at pressures between 30 mbar and 21 bar to better than within ±20%: k(OH+DME) = 8.45 × 10(-18) (T/K)(2.07) exp(262.2 K/T) cm(3) s(-1). For k(OH+DME-d6), to the best of our knowledge, this is the first experimental study. For the analysis of the reaction pathway and the kinetic isotope effect, potential energy diagrams were calculated by using three different quantum chemical methods: (I) CCSD(T)/cc-pV(T,Q)Z//MP2/6-311G(d,p), (II) CCSD(T)/cc-pV(T,Q)Z//CCSD/cc-pVDZ, and (III) CBS-QB3. In all three cases, the reaction is predicted to proceed via a prereaction OH-ether complex with subsequent intramolecular hydrogen abstraction and dissociation to give the methoxymethyl radical and water. Overall rate coefficients were calculated by assuming a thermal equilibrium between the reactants and the prereaction complex and by calculating the rate coefficients of the hydrogen abstraction step from canonical transition state theory. The results based on the molecular data from methods (I) and (II) showed a satisfactory agreement with the experimental values, which indicates that the pre-equilibrium assumption is reasonable under our conditions. In the case of method (III), the isotope effect was significantly underpredicted. The reason for this discrepancy was identified in a fundamentally differing reaction coordinate. Obviously, the B3LYP functional applied in method (III) for geometry and frequency calculations is inadequate to describe such systems, which is in line with earlier findings of other authors.

DFT study of mercury adsorption on α-Fe2O3 surface: Role of oxygen

First-principle calculations based on density functional theory were performed to investigate the micro-mechanism of Hg0 adsorption on α-Fe2O3 (001) surface in the presence of O2. Considering O2 is more easily adsorbed on α-Fe2O3 than Hg0, this paper investigated Hg0 adsorption on O2 embedded α-Fe2O3 (001) surface to clarify the effect of O2 on the capture of mercury by α-Fe2O3. Theoretical calculations indicate that O2 dissociates in two steps on the surface, leaving one O atom to interact with a surface Fe atom. Hg0 adsorption on O/α-Fe2O3 (001) surface belongs to weak chemisorption, and the potential energy diagram is provided. Additionally, the study of coverage shows that O atom coverage has a huge impact on Hg0 adsorption. The adsorption mechanism of Hg0 on the surface changes from weak chemisorption into stronger chemisorption as the O coverage increases from 0.25 to 1mL, with the largest adsorption energy of −268.1kJ/mol.

First principle and ReaxFF molecular dynamics investigations of formaldehyde dissociation on Fe(100) surface

Detailed formaldehyde adsorption and dissociation reactions on Fe(100) surface were studied using first principle calculations and molecular dynamics (MD) simulations, and results were compared with available experimental data. The study includes formaldehyde, formyl radical (HCO), and CO adsorption and dissociation energy calculations on the surface, adsorbate vibrational frequency calculations, density of states analysis of clean and adsorbed surfaces, complete potential energy diagram construction from formaldehyde to atomic carbon (C), hydrogen (H), and oxygen (O), simulation of formaldehyde adsorption and dissociation reaction on the surface using reactive force field, ReaxFF MD, and reaction rate calculations of adsorbates using transition state theory (TST). Formaldehyde and HCO were adsorbed most strongly at the hollow (fourfold) site. Adsorption energies ranged from -22.9 to -33.9 kcal/mol for formaldehyde, and from -44.3 to -66.3 kcal/mol for HCO, depending on adsorption sites and molecular direction. The dissociation energies were investigated for the dissociation paths: formaldehyde → HCO + H, HCO → H + CO, and CO → C + O, and the calculated energies were 11.0, 4.1, and 26.3 kcal/mol, respectively. ReaxFF MD simulation results were compared with experimental surface analysis using high resolution electron energy loss spectrometry (HREELS) and TST based reaction rates. ReaxFF simulation showed less reactivity than HREELS observation at 310 and 523 K. ReaxFF simulation showed more reactivity than the TST based rate for formaldehyde dissociation and less reactivity than TST based rate for HCO dissociation at 523 K. TST-based rates are consistent with HREELS observation.

On the Origin of the Methyl Radical Loss from Deprotonated Ferulic and Isoferulic Acids: Electronic Excitation of a Transient Structure

Formation of radical fragments from even-electron ions is an exception to the "even-electron rule". In this work, ferulic acid (FA) and isoferulic acid (IFA) were used as the model compounds to probe the fragmentation mechanisms and the isomeric effects on homolytic cleavage. Elimination of methyl radical and CO2 are the two competing reactions observed in the CID-MS of [FA - H](-) and [IFA - H](-), of which losing methyl radical violates the "even-electron rule". The relative intensity of their product ions is significantly different, and thereby the two isomeric compounds can be differentiated by tandem MS. Theoretical calculations indicate that both the singlet-triplet gap and the excitation energy decrease in the transient structures, as the breaking C-O bond is lengthened. The methyl radical elimination has been rationalized as the intramolecular electronic excitation of a transient structure with an elongating C-O bond. The potential energy diagrams, completed by the addition of the energy barrier of the radical elimination, have provided a reasonable explanation of the different CID-MS behaviors of [FA - H](-) and [IFA - H](-).

Temperature dependence of negative bias under illumination stress and recovery in amorphous indium gallium zinc oxide thin film transistors

We have investigated the temperature dependence of negative bias under illumination stress and recovery. The transfer characteristics exhibits a non-rigid shift towards negative gate voltages. For both stress and recovery, the voltage shift in deep depletion is twice that in accumulation. The results support the mechanism we previously proposed, which is creation and annealing of a double donor, likely to be an oxygen vacancy. The time dependence of stress and recovery can be fitted to stretched exponentials. Both processes are thermally activated with activation energies 1.06 eV and 1.25 eV for stress and recovery, respectively. A potential energy diagram is proposed to explain the results.

The ab initio potential energy curve of HNO(1A’)

The ab initio coupled-cluster theory and the configuration interaction method have been used to optimize the possible ground state structures of NH, NO and HNO. The potential energy functions of HNO have been derived from the many-body expansion theory. In the symmetric stretching vibration and rotation potential energy diagram of HNO, there are saddle points in reaction kinetics O+NH→HNO, H+NO→HNO, N+HO→HNO, when O, H, N atoms with the energies surpassing 1.153 eV, 1.683 eV, 2.216 eV respectively, a stable HNO molecule could be formed. These are reported for the first time so for as we know. In addition, It is reported that the position of HNO’s isomer in the curve and the energy of transition from HNO to HON are also determined.

Reaction of Aromatic Peroxyl Radicals with Alkynes: A Mass Spectrometric and Computational Study Using the Distonic Radical Ion Approach

The reaction of the aromatic distonic peroxyl radical cations N-methyl pyridinium-4-peroxyl (PyrOO(.+)) and 4-(N,N,N-trimethyl ammonium)-phenyl peroxyl (AnOO(.+)), with symmetrical dialkyl alkynes 10a-c was studied in the gas phase by mass spectrometry. PyrOO(.+) and AnOO(.+) were produced through reaction of the respective distonic aryl radical cations Pyr(.+) and An(.+) with oxygen, O(2). For the reaction of Pyr(.+) with O(2) an absolute rate coefficient of k(1)=7.1×10(-12) cm(3) molecule(-1) s(-1) and a collision efficiency of 1.2% was determined at 298 K. The strongly electrophilic PyrOO(.+) reacts with 3-hexyne and 4-octyne with absolute rate coefficients of k(hexyne)=1.5×10(-10) cm(3) molecule(-1) s(-1) and k(octyne)=2.8×10(-10) cm(3) molecule(-1) s(-1), respectively, at 298 K. The reaction of both PyrOO(.+) and AnOO(.+) proceeds by radical addition to the alkyne, whereas propargylic hydrogen abstraction was observed as a very minor pathway only in the reactions involving PyrOO(.+). A major reaction pathway of the vinyl radicals 11 formed upon PyrOO(.+) addition to the alkynes involves γ-fragmentation of the peroxy O-O bond and formation of PyrO(.+). The PyrO(.+) is rapidly trapped by intermolecular hydrogen abstraction, presumably from a propargylic methylene group in the alkyne. The reaction of the less electrophilic AnOO(.+) with alkynes is considerably slower and resulted in formation of AnO(.+) as the only charged product. These findings suggest that electrophilic aromatic peroxyl radicals act as oxygen atom donors, which can be used to generate α-oxo carbenes 13 (or isomeric species) from alkynes in a single step. Besides γ-fragmentation, a number of competing unimolecular dissociative reactions also occur in vinyl radicals 11. The potential energy diagrams of these reactions were explored with density functional theory and ab initio methods, which enabled identification of the chemical structures of the most important products.

Density functional study of Hg adsorption mechanisms on α-Fe2O3 with H2S

First-principle calculations based on the density functional theory are performed to clarify the Hg0 adsorption reaction mechanism on an α-Fe2O3 surface with H2S in coal-utilizing facilities. Theoretical calculations based on the various adsorption mechanisms of H2S and Hg0 on α-Fe2O3 are performed to investigate a realistic reaction pathway. The results demonstrate that the Eley–Rideal mechanism with Hg0 adsorption on H2S/α-Fe2O3 surface is the most suitable reaction process, whereas the Mars–Maessen, Langmuir–Hinshelwood, and Eley–Rideal mechanisms with H2S adsorption on Hg0/α-Fe2O3 surface are not possible in real reaction mechanisms. In addition, the potential energy diagram of H2S dissociation on α-Fe2O3 surface is provided.

Nano‐constriction device for rapid protein preconcentration in physiological media through a balance of electrokinetic forces

We describe a methodology to steeply enhance streptavidin protein preconcentration within physiological media over that achieved by negative dielectrophoresis (NDEP) through utilizing a DC offset to the AC field at nanoscale constriction gap devices. Within devices containing approximately 50-nm constriction gaps, we find that the addition of a critical DC field offset (1.5 V/cm) to the NDEP condition (∼200 V(pp) /cm at 1 MHz) results in an exponentially enhanced extent of protein depletion across the device to cause a rapid and steeply rising degree of protein preconcentration. Under these conditions, an elliptical-shaped protein depletion zone that is extended along the device centerline axis forms instantaneously around the constrictions to result in protein preconcentration along the constriction sidewall direction. Through a potential energy diagram to describe the electrokinetic force balance across the device, we find that the potential energy barrier due to NDEP is gradually tilted upon addition of DC fields, to cause successively steeper potential wells along the sidewall direction for devices containing smaller constriction gaps. Hence, for approximately 50-nm constriction gaps at a critical DC field, the ensuing narrow and deep potential energy wells enable steep protein preconcentration, due to depletion over an exponentially enhanced extent across the device.

The ab initio and potential energy curve of OH, OCI and HOCI(1A')

The possible ground state structures of OH, OCI and HOCI are optimized by using some methods included in Gaussian 09. Among them, the methods QCISD/6-311G(2df) and B3P86/6-311+G(2df) are the most suitable for the calculation of OH(X2) and OCI(X2) the spacings between eguilibrium nuclei ROH=0.09696 nm and ROCI=0.1569 nm, and harmonic freguencies (OH)=3745.37 cm-1 and (OCI)=892.046 cm-1 are calculated respectively. The calculation results are in good agreement with experimental results, Each potential energy curve obtained via scanning the single point energies of OH and OCI is well fit with the four-parameter Murrell-Sorbie function, according to which spectral data and force constants are deduced. The ground state of HOCI molecule is of 2A1' state, and the parameters of structure are ROH=0.0966 nm, HOCI 102.3, 1(a1)=738.69 cm-1, 2(b2)=1260.25 cm-1, De=2.24 eV with QCISD(T)/D95(df,pd). The present calculation results are in excellent agreement with the experimental values, and they are better than those given in the literature. And the force constants are calculated at the same time. The potential energy function of HOCI is derived from the many-body expansion theory. In the symmetric-stretch potential energy diagram, there is a saddle point in reaction channel H+OCI HOCI, and a stable HOCI molecule could be formed only when H atom crosses an energy barrier of 1.74 eV. However there is no clear energy barrier in the reaction channel Cl+OH HOCI, therefore a stable HOCI molecule can form easily.

Mechanism and Regioselectivity of the Electrochemical Reduction in Polychlorobiphenyls (PCBs): Kinetic Analysis for the Successive Reduction of Chlorines from Dichlorobiphenyls

The regioselective electrochemical reduction of three different dichlorobiphenyls is analyzed using quantum chemical calculations and convolution potential sweep voltammetry. The heterogeneous rate constants of C–Cl bond reductions of each of the dichlorobiphenyls are estimated. The mechanism of the electrochemical reduction is confirmed by estimating the intrinsic barrier from the experimental data on transfer coefficients as well as theoretical calculations involving bond length and potential energy diagrams. The reductions follow the Marcus–Hush quadratic activation driving force relation barring the meta-Cl of the 3,4-dichlorobiphenyl which obeys Butler–Volmer kinetics. The first electron transfer step is rapid in comparison with the bond-breaking, implying the stepwise reduction for all the dichlorobiphenyls studied here. High performance liquid chromotagraphy analysis of the products of the bulk electrolysis confirms the order of the reduction in dichlorobiphenyls viz. the ease of reduction follows ...

Evaluation of spectral line width of atoms in liquid helium

Laser induced fluorescence experiments indicate change of spectral line profiles of atoms and molecules compared to the free system when embedded under liquid helium. Based on relativistic density functional approach a model has been proposed here to estimate the width of the spectral lines embedded under liquid helium in which the central atom resides within a cluster of helium atoms. The model assumes an overall floppy motion of the liquid helium atoms due to finite temperature and subsequent determination of the width from the ab initio estimated potential energy diagram. Calculated width of the resonance lines of Rb and Cs show good agreement with available laser spectroscopic data.

Structure and potential energy functionof XF2(X=B,N) molecular ground state

Based on the Gaussian03 calculation software, QCISD method is used to optimize the possible ground-state structures of XF2(X=B,N) molecules with the different basis sets. On this basis, the resonant frequencies and force constants are calculated with the D95(df, pd) and D95+(df, pd) basis sets respectively. The potential energy functions of XF2(X=B,N) are derived from the many-body expansion theory. At the same time, according to the potential energy functions, three equivalent potential energy diagrams for the XF2(X=B,N) ground states are drawn. The potential energy surface is verified to be consistent with the three atomic molecular geometry. The structures and the features of XF2(X=B,N) can correctly reappear on the potential surface.