Nicholas Dimakis

Elucidating the Ionomer-Electrified Metal Interface

The competitive adsorption of Nafion functional groups induce complex potential dependencies (Stark tuning) of vibrational modes of CO adsorbed (CO(ads)) on the Pt of operating fuel cell electrodes. Operando infrared (IR) spectroscopy, polarization modulated IR spectroscopy (PM-IRRAS) of Pt-Nafion interfaces, and attenuated total reflectance IR spectroscopy of bulk Nafion were correlated by density functional theory (DFT) calculated spectra to elucidate Nafion functional group coadsorption responsible for the Stark tuning of CO(ads) on high surface area fuel cell electrodes. The DFT calculations and observed spectra suggest that the side-chain CF3, CF2 groups (i.e., of the backbone and side chain) and the SO3(-) are ordered by the platinum surface. A model of the Nafion-Pt interface with appropriate dihedral and native bond angles, consistent with experimental and calculated spectra, suggest direct adsorption of the CF3 and SO3(-) functional groups on Pt. Such adsorption partially orders the Nafion backbone and/or side-chain CF2 groups relative to the Pt surface. The coadsorption of CF3 is further supported by Mulliken partial charge calculations: The CF3 fluorine atoms have the highest average charge among all types of Nafion fluorine atoms and are second only to the sulfonate oxygen atoms.

Zinc cysteine active sites of metalloproteins: A density functional theory and x-ray absorption fine structure study

Density functional theory (DFT) and x-ray absorption fine structure (XAFS) spectroscopy are complementary tools for the biophysical study of active sites in metalloproteins. DFT is used to compute XAFS multiple scattering Debye Waller factors, which are then employed in genetic algorithm-based fitting process to obtain a global fit to the XAFS in the space of fitting parameters. Zn-Cys sites, which serve important functions as transcriptional switches in Zn finger proteins and matrix metalloproteinases, previously have proven intractable by this method; here these limitations are removed. In this work we evaluate optimal DFT nonlocal functionals and basis sets for determining optimal geometries and vibrational densities of states of mixed ligation Zn(His)(4-n)(Cys)(n) sites. Theoretical results are compared to experimental XAFS measurements and Raman spectra from the literature and tabulated for use.

Vanadium Pentoxide Nanobelt-Reduced Graphene Oxide Nanosheet Composites as High-Performance Pseudocapacitive Electrodes: ac Impedance Spectroscopy Data Modeling and Theoretical Calculations

Graphene nanosheets and graphene nanoribbons, G combined with vanadium pentoxide (VO) nanobelts (VNBs) and VNBs forming GVNB composites with varying compositions were synthesized via a one-step low temperature facile hydrothermal decomposition method as high-performance electrochemical pseudocapacitive electrodes. VNBs from vanadium pentoxides (VO) are formed in the presence of graphene oxide (GO), a mild oxidant, which transforms into reduced GO (rGOHT), assisting in enhancing the electronic conductivity coupled with the mechanical robustness of VNBs. From electron microscopy, surface sensitive spectroscopy and other complementary structural characterization, hydrothermally-produced rGO nanosheets/nanoribbons are decorated with and inserted within the VNBs’ layered crystal structure, which further confirmed the enhanced electronic conductivity of VNBs. Following the electrochemical properties of GVNBs being investigated, the specific capacitance Csp is determined from cyclic voltammetry (CV) with a varying scan rate and galvanostatic charging-discharging (V–t) profiles with varying current density. The rGO-rich composite V1G3 (i.e., VO/GO = 1:3) showed superior specific capacitance followed by VO-rich composite V3G1 (VO/GO = 3:1), as compared to V1G1 (VO/GO = 1:1) composite, besides the constituents, i.e., rGO, rGOHT and VNBs. Composites V1G3 and V3G1 also showed excellent cyclic stability and a capacitance retention of >80% after 500 cycles at the highest specific current density. Furthermore, by performing extensive simulations and modeling of electrochemical impedance spectroscopy data, we determined various circuit parameters, including charge transfer and solution resistance, double layer and low frequency capacitance, Warburg impedance and the constant phase element. The detailed analyses provided greater insights into physical-chemical processes occurring at the electrode-electrolyte interface and highlighted the comparative performance of thin heterogeneous composite electrodes. We attribute the superior performance to the open graphene topological network being beneficial to available ion diffusion sites and the faster transport kinetics having a larger accessible geometric surface area and synergistic integration with optimal nanostructured VO loading. Computational simulations via periodic density functional theory (DFT) with and without V2O5 adatoms on graphene sheets are also performed. These calculations determine the total and partial electronic density of state (DOS) in the vicinity of the Fermi level (i.e., higher electroactive sites), in turn complementing the experimental results toward surface/interfacial charge transfer on heterogeneous electrodes.

Thermal processing as a means to prepare durable, submicron thickness ionomer films for study by transmission infrared spectroscopy.

A high temperature solution processing method was adapted to prepare durable, freestanding, submicrometer thickness films for transmission infrared spectroscopy studies of ionomer membrane. The materials retain structural integrity following cleaning and ion-exchange steps in boiling solutions, similar to a commercial fuel cell membrane. Unlike commercial membrane, which typically has thicknesses of >25 μm, the structural properties of the submicrometer thickness materials can be probed in mid-infrared spectral measurements with the use of transmission sampling. Relative to the infrared attenuated total reflection (ATR) technique, transmission measurements can sample ionomer membrane materials more uniformly and suffer less distortion from optical effects. Spectra are reported for thermally processed Nafion and related perfluoroalkyl ionomer materials containing phosphonate and phosphinate moieties substituted for the sulfonate end group on the side chain. Band assignments for complex or unexpected features are aided by density functional theory (DFT) calculations.

Carbon monoxide adsorption on platinum-osmium and platinum-ruthenium-osmium mixed nanoparticles.

Density functional calculations (DFT) on carbon monoxide (CO) adsorbed on platinum, platinum-osmium, and platinum-ruthenium-osmium nanoclusters are used to elucidate changes on the adsorbate internal bond and the carbon-metal bond, as platinum is alloyed with osmium and ruthenium atoms. The relative strengths of the adsorbate internal bond and the carbon-metal bond upon alloying, which are related to the DFT calculated C-O and C-Pt stretching frequencies, respectively, cannot be explained by the traditional 5σ-donation/2π*-back-donation theoretical model. Using a modified π-attraction σ-repulsion mechanism, we ascribe the strength of the CO adsorbate internal bond to changes in the polarization of the adsorbate-substrate hybrid orbitals towards carbon. The strength of the carbon-metal bond is quantitatively related to the CO contribution to the adsorbate-substrate hybrid orbitals and the sp and d populations of adsorbing platinum atom. This work complements prior work on corresponding slabs using periodic DFT. Similarities and differences between cluster and periodic DFT calculations are discussed.

Single and multiple scattering XAFS Debye-Waller factors for crystalline materials using periodic Density Functional Theory

We present an accurate and efficient technique for calculating thermal X-ray absorption fine structure (XAFS) Debye-Waller factors (DWFs) applicable to crystalline materials. Using Density Functional Theory on a 3×3×3 supercell pattern of MnO structure, under the nonlocal hybrid B3LYP functional paired with Gaussian local basis sets, we obtain the normal mode eigenfrequencies and eigenvectors; these parameters are in turn used to calculate single and multiple scattering XAFS DWFs. The DWFs obtained via this technique are temperature dependent expressions and can be used to substantially reduce the number of fitting parameters, when experimental spectra are fitted with a hypothetical structure. The size of the supercell size limits the R-space range that these parameters could be used. Therefore corresponding DWFs for paths outside of this range are calculated using the correlated Debye model. Our method is compared with prior cluster calculations and with corresponding values obtained from fitting experimental XAFS spectra on manganosite with simulated spectra.

Verification of a distortion in the microstructure of GaN detected by EXAFS using ab initio density functional theory calculations

X-ray absorption fine structure (XAFS) measurements on a series of epitaxially grown GaN samples have shown a distortion in the microstructure of GaN. More specifically the central N atom is 4-fold coordinated but the four Ga atoms are not equidistant. It has been shown that 2.9 to 3.5 of them (depending on the growth conditions) are found in the expected from XRD distance of 1.94 A and the remaining are at a distance longer by approximately 15%. Second derivative calculation of the conformation energy using the Density Functional Theory (DFT) is used to investigate if the symmetric GaN cluster as given by XRD is the most energetically favorable configuration and if not which distorted structure corresponds to the most energetically favorable one. A very good agreement between DFT results and experimental XAFS spectra has been found. Generalization this technique to other dislocated clusters is also discussed.

XAFS Debye-Waller factors for deformed hemes and metal substituted hemes

We present an efficient and accurate method for calculating XAFS Debye-Waller factors for deformed active sites of hemoproteins and metal substituted hemes. Based on the Normal Coordinate Structural Decomposition scheme, the deformation of the porphyrin macrocycle is expressed as a linear combination of the normal modes of the planar species. In our approach, we identify the modes that contribute most to the deformation. Small metal-porphyrin structures which match the macrocycle structural deformation of the deformed hemoprotein site are used to calculate the Debye-Waller parameters at samples temperature. The Debye-Waller factors are directly obtained by calculating the normal mode spectrum of the corresponding metal-porphyrin structure using Density Functional Theory. Our method is tested on Ni-tetraadamantyl porphyrin and cytochrome c structures with more than 500 available scattering paths.

Charge transfer dynamical processes at graphene-transition metal oxides/electrolyte interface for energy storage: Insights from in-situ Raman spectroelectrochemistry

Hybrids consisting of supercapacitive functionalized graphene (graphene oxide; GO reduced graphene oxide; rGO multilayer graphene; MLG, electrochemically reduced GO; ErGO) and three-dimensional graphene scaffold (rGOHT; hydrothermally prepared) decorated with cobalt nanoparticles (CoNP), nanostructured cobalt (CoO and Co3O4) and manganese (MnO2) oxide polymorphs, assembled electrochemically facilitate chemically bridged interfaces with tunable properties. Since Raman spectroscopy can capture variations in structural and chemical bonding, Raman spectro-electrochemistry in operando i.e. under electrochemical environment with applied bias is employed to 1) probe graphene/metal bonding and dynamic processes, 2) monitor the spectral changes with successive redox interfacial reactions, and 3) quantify the associated parameters including type and fraction of charge transfer. The transverse optical (TO) and longitudinal optical (LO) phonons above 500 cm−1 belonging to Co3O4, CoO, MnO2 and carbon-carbon bonding occurring at 1340 cm-1, 1590 cm−1 and 2670 cm-1 belonging to D, G, and 2D bands, respectively, are analyzed with applied potential. Consistent variation in Raman band position and intensity ratio reveal structural modification, combined charge transfer due to localized orbital re-hybridization and mechanical strain, all resulting in finely tuned electronic properties. Moreover, the heterogeneous basal and edge plane sites of graphene nanosheets in conjunction with transition metal oxide ‘hybrids’ reinforce efficient surface/interfacial electron transfer and available electronic density of states near Fermi level for enhanced performance. We estimated the extent and nature (n− or p−) of charge transfer complemented with Density Functional Theory calculations affected by hydration and demonstrate the synergistic coupling between graphene nanosheets and nanoscale cobalt (and manganese) oxides for applied electrochemical applications.Hybrids consisting of supercapacitive functionalized graphene (graphene oxide; GO reduced graphene oxide; rGO multilayer graphene; MLG, electrochemically reduced GO; ErGO) and three-dimensional graphene scaffold (rGOHT; hydrothermally prepared) decorated with cobalt nanoparticles (CoNP), nanostructured cobalt (CoO and Co3O4) and manganese (MnO2) oxide polymorphs, assembled electrochemically facilitate chemically bridged interfaces with tunable properties. Since Raman spectroscopy can capture variations in structural and chemical bonding, Raman spectro-electrochemistry in operando i.e. under electrochemical environment with applied bias is employed to 1) probe graphene/metal bonding and dynamic processes, 2) monitor the spectral changes with successive redox interfacial reactions, and 3) quantify the associated parameters including type and fraction of charge transfer. The transverse optical (TO) and longitudinal optical (LO) phonons above 500 cm−1 belonging to Co3O4, CoO, MnO2 and carbon-carbon bonding oc...

Ab Initio Calculation of XAFS Debye‐Waller Factors for Crystalline Materials

A direct an accurate technique for calculating the thermal X‐ray absorption fine structure (XAFS) Debye‐Waller factors (DWF) for materials of crystalline structure is presented. Using the Density Functional Theory (DFT) under the hybrid X3LYP functional, a library of MnO spin—optimized clusters are built and their phonon spectrum properties are calculated; these properties in the form of normal mode eigenfrequencies and eigenvectors are in turn used for calculation of the single and multiple scattering XAFS DWF. DWF obtained via this technique are temperature dependent expressions and can be used to substantially reduce the number of fitting parameters when experimental spectra are fitted with a hypothetical structure without any ad hoc assumptions. Due to the high computational demand a hybrid approach of mixing the DFT calculated DWF with the correlated Debye model for inner and outer shells respectively is presented. DFT obtained DWFs are compared with corresponding values from experimental XAFS spectr...