Relevant bibliographies by topics / Hydrogenase, hydrogen, density functional theory

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers
  5. Reports

Academic literature on the topic 'Hydrogenase, hydrogen, density functional theory'

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Published: 9 March 2023
Last updated: 10 March 2023

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Journal articles on the topic "Hydrogenase, hydrogen, density functional theory"

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Mpourmpakis, Giannis, and George E. Froudakis. "Assessing the Density Functional Theory in the Hydrogen Storage Problem." Journal of Nanoscience and Nanotechnology 8, no. 6 (June 1, 2008): 3091–96. http://dx.doi.org/10.1166/jnn.2008.107.

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A variety of high and low level ab-initio calculations have been performed to calculate hydrogen's physisorption binding energy on carbon nanotube's walls. This study focuses on the performance of several functionals on treating the H2-carbon nanotube interaction within the Density Functional Theory. Our results show that the behavior of the exchange functional in the low density region plays an important role in describing this weak van der Waals type of interaction. By comparing the binding energy values obtained on each theoretical level and interpreting the results in terms of %wt percentages of hydrogen storage using the Langmuir isotherms, we proposed possible ways to treat computationally the hydrogen storage problem within the DFT.
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Trohalaki, Steven, and Ruth Pachter. "Mechanism of Hydrogen Production in [Fe−Fe]-Hydrogenase: A Density Functional Theory Study." Energy & Fuels 21, no. 4 (July 2007): 2278–86. http://dx.doi.org/10.1021/ef060577n.

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Salam, M. Abdus, Bawadi Abdullah, and Suriati Sufian. "Hydrogenated Microstructure and Its Hydrogenation Properties: A Density Functional Theory Study." Journal of Nanomaterials 2014 (2014): 1–7. http://dx.doi.org/10.1155/2014/749804.

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The relationship between microstructure and hydrogenation properties of the mixed metals has been investigated via different spectroscopic techniques and the density functional theory (DFT). FESEM and TEM analyses demonstrated the nano-grains of Mg2NiH4and MgH2on the hydrogenated microstructure of the adsorbents that were confirmed by using XPS analysis technique. SAED pattern of hydrogenated metals attributed the polycrystalline nature of mixed metals and ensured the hydrogenation to Mg2NiH4and MgH2compounds. Flower-like rough surface of mixed metals showed high hydrogenation capacity. The density functional theory (DFT) predicted hydrogenation properties; enthalpy and entropy changes of hydrogenated microstructure of MgH2and Mg2NiH4are −62.90 kJ/mol, −158 J/mol·K and −52.78 kJ/mol, −166 J/mol·K, respectively. The investigation corresponds to the hydrogen adsorption feasibility, reversible range hydrogenation thermodynamics, and hydrogen desorption energy of 54.72 kJ/mol. DFT predicted IR band for MgH2and Mg2NiH4attributed hydrogen saturation on metal surfaces.
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Pantha, Nurapati, Asim Khaniya, and Narayan Prasad Adhikari. "Hydrogen storage on palladium adsorbed graphene: A density functional theory study." International Journal of Modern Physics B 29, no. 20 (August 5, 2015): 1550143. http://dx.doi.org/10.1142/s021797921550143x.

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We have performed density functional theory (DFT)-based first-principles calculations to study the stability, geometrical structures, and electronic properties of a single palladium (Pd) atom adsorbed graphene with reference to pristine graphene. The study also covers the adsorption properties of molecular hydrogen/s on the most stable Pd-graphene geometry by taking into account London dispersion forces in addition to the standard DFT calculations in the Quantum ESPRESSO package. From the analysis of estimated values of binding energy of Pd on different occupation sites (i.e., bridge, hollow, and top) of graphene supercells, the bridge site is found to be the most favorable one with the magnitudes of 1.114, 1.426, and 1.433 eV in 2×2, 3×3, and 4×4 supercells, respectively. The study of the electronic properties of Pd adsorbed graphene shows a bandgap of 45 meV, which can account for the breaking of the symmetry of the graphene structure. Regarding the gaseous (hydrogen) adsorption on Pd-adatom graphene, we checked the increasing number of molecular hydrogens ( H 2) from one to seven on the 3×3 supercell, and found that the adsorption energy per H 2 decreases on increasing hydrogen concentration and lies within the range of 0.998–0.151 eV.
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Toh, Pek-Lan, Syed Amir Abbas Shah Naqvi, Suh-Miin Wang, and Yao-Cong Lim. "PRISTINE AND GROUP IV DOPED BORON NITRIDE SINGLE-WALL NANOTUBES FOR HYDROGEN STORAGE: A DENSITY FUNCTIONAL THEORY COMPUTATIONAL INVESTIGATION." Jurnal Teknologi 84, no. 6 (September 25, 2022): 147–56. http://dx.doi.org/10.11113/jurnalteknologi.v84.18668.

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In this report, a density functional theory (DFT) computational approach was used to investigate the structural and electronic properties of molecular hydrogens adsorbed on single-walled boron nitride nanotubes (BNNTs) with/without doped by group IV elements, such as carbon (C), silicon (Si), and germanium (Ge) atom. The twelve hydrogen molecules (H2) were added to the outer surfaces of BNNT frameworks. Geometry optimization calculations were performed to find the local energy minima of the BNNTs nanostructures with the molecular hydrogens at the DFT/B3LYP/6-31G level of theory. By employing single-point calculations at the B3LYP/6-31G* level of theory, the equilibrium geometric structures were then utilized to find the electronic structures of hydrogen molecules adsorbed on the surfaces of BNNT frameworks. The results showed that the bond lengths of B-N are in the range of1.44 Å – 1.48 Å. The optimized distances of hydrogen molecules from the surfaces of BNNTs were predicted to be 3.1 Å – 3.2 Å. Moreover, the computed HOMO-LUMO energies of molecular hydrogens adsorbed on the surface of BNNTs are about 2.2 eV – 4.3 eV. For the surface map of HOMO, the electron density distribution of hydrogen molecules adsorbed on the surface of pristine BNNT was localized in the N-tip. While in the case of doped BNNTs, the electron densities of HOMOs were focused on the group IV elements. The B-tips on the pristine and doped BNNTs possess the major contribution to the LUMO.
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Li, Zong Sheng. "Density Functional Theory Calculations of Atomic Hydrogen Adsorption on (3, 3) Single-Wall Carbon Nanotubes with Vacancy Defects." Applied Mechanics and Materials 687-691 (November 2014): 4315–18. http://dx.doi.org/10.4028/www.scientific.net/amm.687-691.4315.

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In this paper, we have employed density functional theory (DFT) to investigate the adsorption mechanisms of atomic hydrogens on the sidewalls of (3, 3) single-wall carbon nanotubes (CNTs) which have vacancy defects. All the calculations were performed using the generalized gradient approximation (GGA) with the Perdew, Burke and Ernzerhof (PBE) correlation functional.Our results show that hydrogen atoms can chemically adsorb on the defective nanotube. Bonding energy of per hydrogen atom decreases with the number of adsorbed hydrogen atoms. The hydrogen atoms will enhance the electrical conductivity of the (3, 3) nanotube. Besides one hydrogen atom adsorbing on the nanotube with a vacancy defect (MVD), hydrogen atoms move towards the MVD of the nanotube.
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Agrawal, Aruna Goenka, Maurice van Gastel, Wolfgang Gärtner, and Wolfgang Lubitz. "Hydrogen Bonding Affects the [NiFe] Active Site ofDesulfovibriovulgarisMiyazaki F Hydrogenase: A Hyperfine Sublevel Correlation Spectroscopy and Density Functional Theory Study." Journal of Physical Chemistry B 110, no. 15 (April 2006): 8142–50. http://dx.doi.org/10.1021/jp0573902.

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Unsal, E., F. Iyikanat, H. Sahin, and R. T. Senger. "Hydrogenated derivatives of hexacoordinated metallic Cu2Si monolayer." RSC Advances 8, no. 70 (2018): 39976–82. http://dx.doi.org/10.1039/c8ra07824f.

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Herein, we carried out first-principles calculations based on density functional theory to investigate the effects of surface functionalization with hydrogen atoms on structural, dynamical and electronic properties of Cu2Si monolayer.
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Sunnardianto, Gagus Ketut, Intan Ayu Larasati, Farid Triawan, and Ammar M. Aamer. "Effect of charge on graphene vacancy for hydrogen storage application." MATEC Web of Conferences 197 (2018): 04001. http://dx.doi.org/10.1051/matecconf/201819704001.

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We investigated the effect of charge to the interaction between a hydrogen molecule and a hydrogenated vacancy V11 in graphene surface based on density functional theory calculation. V11 is graphene mono-vacancy with two hydrogen atoms adsorbed at the edge of vacancy. The hydrogen molecule physisorbed on deformed V11 is shown to dissociate producing a known stable vacancy V211, in which two carbon atoms are mono-hydrogenated and another is di-hydrogenated at the edge of the vacancy. We found that additional electron charge to the system could influence the reaction pathways and reduced the energy barrier for dissociation adsorption and desorption process provides a basic understanding in the mechanism of hydrogenation processes on graphene vacancy for hydrogen storage aplication.
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Chettri, B., P. K. Patra, Sunita Srivastava, Lalhriatzuala, Lalthakimi Zadeng, and D. P. Rai. "Electronic Properties of Hydrogenated Hexagonal Boron Nitride (h-BN): DFT Study." Senhri Journal of Multidisciplinary Studies 4, no. 2 (December 28, 2019): 72–79. http://dx.doi.org/10.36110/sjms.2019.04.02.008.

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In this work, we have constructed the hydrogenated hexagonal boron nitride (h-BN) by placing hydrogen atom at different surface sites. The possibility of hydrogen adsorption on the BN surface has been estimated by calculating the adsorption energy. The electronic properties were calculated for different hydrogenated BNs. The theoretical calculation was based on the Density Functional Theory (DFT). The electron-exchange energy was treated within the most conventional functional called generalized gradient approximation. The calculated band gap of pure BN is 3.80 eV. The adsorption of two H-atoms at two symmetrical sites of B and N sites reduces the band gap value to 3.5 eV. However, in all other combination the systems show dispersed band at the Fermi level exhibiting conducting behavior. Moreover, from the analysis of band structure and Density Of States we can conclude that, the hydrogenation tunes the band gap of hexagonal boron nitride.
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Dissertations / Theses on the topic "Hydrogenase, hydrogen, density functional theory"

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GRECO, CLAUDIO. "A DFT and QM/MM Investigation on Models Related to the [FeFe]-Hydrogenase Active Site." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2007. http://hdl.handle.net/10281/45775.

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In the present thesis, a theoretical investigation is described regarding hydroge- nases - enzymes that are able to catalyze the reversible oxidation of molecular hydrogen: H2 2H+ + 2e− . Such a very simple reaction could have fundamen- tal importance for the possible future development of a hydrogen-based econ- omy. However, the current approaches for molecular hydrogen oxidation imply the use of very expensive platinum-containing catalysts, while H2 production at industrial level still depends on hydrocarbons. In this framework, hydrogenases represent a model for the development of new-generation catalysts, as they con- tain only inexpensive transition metal cofactors (iron and/or nickel ions) and are able to evolve hydrogen directly from acidic aqueous solutions supplied with a convenient source of electrons. The present work deals with the characterization of a specific class of hydro- genases, termed [FeFe]-hydrogenases. These enzymes contain in their active site a peculiar Fe6 S6 cluster - the so-called H-cluster - which can be ideally subdi- vided in two distinct portions: a classical Fe4 S4 moiety, and a Fe2 S2 subcluster (commonly termed [2Fe]H ) bearing CO and CN− ligands; these subclusters are linked to each other through the sulphur atom of a cysteine residue. The two iron atoms of the binuclear sub-site are termed proximal (Fep ) or distal (Fed ), de- pending on their positions with respect to the Fe4 S4 moiety. Notably one of the carbonyl groups included in the [2Fe]H subsite bridges the Fep and Fed centers, and it moves to a semibridging position when the enzyme is in its completely reduced form. The coordination environment of the iron ions included in the binuclear cluster is completed by a bidentate ligand which has been proposed to correspond either to a di(thiomethyl)amine (DTMA) or to a propanedithiolate (PDT) residue. Direct metal-hydrogen interaction at the binuclear sub-site is required for the enzymatic activity of [FeFe]-hydrogenases; however, there is still some debate about the way in which the interaction takes place, and about the catalytic mechanism leading to H2 splitting/formation. In fact, despite the large number of theoretical and experimental investigations carried out to clarify the catalytic mechanism of [FeFe]-hydrogenases, a direct comparison between the two more plausible routes for dihydrogen evolution/oxidation - i.e. a path involving the formation of metal-bound terminal hydrides, as opposed to a route that implies the presence of a hydride bridging Fep and Fed - was still lacking. Such study has then been carried out in our laboratories, using computational models of the H-cluster binuclear subsite in the context of a Density Functional Theory (DFT) representation; this work is presented in Chapter 2. It turns out that H2 formation can take place according to reaction pathways that imply initial protonation of the Fe(I)-Fe(I) form of [2Fe]H , leading to a formal Fe(II)-Fe(II) hydride species, subsequent monoelectron reduction to an Fe(II)-Fe(I) species, further protonation, and H2 release. A comparison of pathways involving either the initial protonation of Fed or protonation of the Fep -Fed bond shows also that the former pathway is characterized by smaller activation barriers, as well as a downhill free-energy profile, suggesting that it could be the H2 production pathway operative in the enzyme. The next chapter in the present thesis is devoted to the characterization of CO-mediated enzyme inhibition; indeed, the enzyme active site is able to bind exogenous carbon monoxide, and such an interaction impairs the catalytic process of H2 production/oxidation. Experimental and computational studies have converged towards the assignment of a Fe(I)Fe(II) state to the CO-inhibited binuclear sub-cluster, while there is still much debate about the disposition of CO and CN− ligands around Fed in this form. Our analysis is carried out us- ing a hybrid quantum mechanical/molecular mechanical (QM/MM) approach; this means that an all-atom model of the enzyme is used for studying different geometrical configurations of the active site. This allows us to show that the protein environment surrounding the H-cluster plays a crucial role in influenc- ing the mechanism of CO-inhibition; as a result, the CO-inhibited H-cluster is expected to be characterized by a terminal CO ligand trans to the μ-CO group on Fed . A QM/MM approach is also used in order to unravel key issues regarding the activation of the enzyme from its completely oxidized inactive state (Hox inact , an enzyme form in which the [2Fe]H subcluster attains the Fe(II)Fe(II) redox state), and the influence of the protein environment on the structural and cat- alytic properties of the H-cluster (see Chapter 4). Our results show that, in Hox inact , a water molecule is bound to Fed . The computed QM/MM energy values for water binding to the diferrous subsite are in fact over 17 kcal mol−1 ; however, the affinity towards water decreases by one order of magnitude af- ter a one-electron reduction of Hox inact , thus leading to release of coordinated water from the H-cluster. The investigation of a catalytic cycle of the [FeFe]- hydrogenase that implies formation of a terminal hydride ion and a DTMA molecule acting as acid/base catalyst indicates that all steps have reasonable reaction energies, and that the influence of the protein on the thermodynamic profile of H2 production catalysis is not negligible; QM/MM results show that the interactions between the Fe2 S2 subsite and the protein environment could give place to structural rearrangements of the H-cluster functional for catalysis, provided that the bidentate ligand that bridges the iron atoms in the binuclear subsite is actually a DTMA residue. In the last two studies included in the present thesis (Chapter 5 and Chapter 6), DFT investigations are presented regarding the characterization of two syn- thetic model complexes that represent structural and functional model of the [2Fe]H cluster: Fe2 (S2 C3 H6 )(CO)6 and (S2 C3 H6 )[Fe2 (CO)5 P(NC4 H8 )3 ]. Both of them are known to be able to catalyze proton reduction in an electrochemical cell, but the details of the electrocatalytic mechanisms leading to H2 produc- tion needed clarification. As for Fe2 (S2 C3 H6 )(CO)6 (a), it is showed that, in the early stages of the catalytic cycle, a neutral μ-H adduct is formed; mono-electron reduction and subsequent protonation can give rise to a diprotonated neutral species (a-μH-SH), which is characterized by a μ-H group, a protonated sulfur atom and a CO group bridging the two iron centers, in agreement with experi- mental IR data indicating the formation of a long-lived μ-CO species. H2 release from a-μH-SH and its less stable isomer a-H2 is kinetically unfavourable, while the corresponding monoanionic compounds (a-μH-SH− and a-H2 − ) are more reactive in terms of dihydrogen evolution, in agreement with experimental data. As far as (S2 C3 H6 )[Fe2 (CO)5 P(NC4 H8 )3 ] (A) is concerned, experimental results have suggested that the presence of the electron donor P(NC4 H8 )3 ligand in A could favour the formation of a μ-CO species similar to that observed in the enzymatic cluster. However, insight into the structural features of key catalytic intermediates deriving from reduction and protonation of A was still lacking. Thus, in Chapter 6 we present results obtained using Density Functional Theory to evaluate structures, relative stabilities and spectroscopic properties of several species relevant for the electrocatalytic H2 evolving process. The results enable us to unravel the structure of the μ-CO complex ex- perimentally detected after monoelectronic reduction of A. Moreover, we show that the introduction of the large electron-donor ligand P(NC4 H8 )3 in the bio- mimetic complex does not favour the stabilization of terminal-hydride adducts, which are expected to be very reactive in terms of H2 production. The comparison of our findings with previous theoretical and experimental results obtained on similar model complexes suggests that the introduction of an electron donor ligand as good as P(NC4 H8 )3 , but less sterically demanding, could represent a better choice to facilitate the formation of μ-CO complexes more closely resembling the structure of the enzymatic cluster.
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Lockett, Lani Victoria. "Gas-Phase Photoelectron Spectroscopy and Computational Studies of [FeFe]-Hydrogenase Inspired-Catalysts for Hydrogen Production." Diss., The University of Arizona, 2009. http://hdl.handle.net/10150/193874.

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The work presented in this dissertation focuses on the [FeFe]-hydrogenase active site as inspiration for the design and synthesis of complexes capable of the electrocatalytic generation of molecular hydrogen from protons and electrons. The majority of work discussed uses gas-phase photoelectron spectroscopy (PES) and density functional theory (DFT) to probe and analyze the bonding and electron distribution in potential catalysts. These two techniques are also used to explore the nature of cyanide as a ligand, due to its presence and unknown role in these enzymes. This dissertation begins with the study of (η⁵-C₅H₅)Fe(CO)₂X (FpX) and (η⁵- C₅Me₅)Fe(CO)₂X (Fp*X) complexes where X = H⁻, Cl⁻, and CN⁻ to assess and compare their π-accepting abilities, which is contradicted in the literature. The shifts in ionization energies measured by PES provide a measure of the relative bonding effects. The results indicate cyanide is, overall, a weak π-acceptor, and the σ- and π-donor interactions are important to understanding the chemistry. The molecule [(μ-ortho-C₆H₄S₂)][Fe(CO)₃]₂ was examined, in part due to the delocalized π-orbitals of the C₆H₄S₂ ligand, which could facilitate the redox chemistry necessary for catalysis. Computations show that upon ionization, the complex adopts a semi-bridging carbonyl; termed “rotated structure”. The reorganization energy of this geometry change was determined, which may provide understanding of how the active site in the enzyme enables electron transfer to achieve this catalysis. Next complexes of the form (μ-SCH₂XCH₂S)[Fe(CO)₃]₂, where X=CH₂, O, NH, ᵗBuN, MeN, were explored in order to provide insight to the unknown atom at the central bridging position of the alkyl chain in the [FeFe]-hydrogenase enzyme. The likelihood of a rotated cationic structure is also shown, with reorganization energy values similar to that seen for [(μ-ortho-C₆H₄S₂)][Fe(CO)₃]₂. The final chapter explores the replacement of selenium for sulfur in (μ- X(CH₂)₃X)[Fe(CO)₃]₂ and (μ-X(CH₂)₂CH(CH₃)X)[Fe(CO)₃]₂, where X is either sulfur or selenium. The PES data show destabilization of the selenium complex ionizations compared to the sulfur complexes and a lower reorganization energy was calculated. The computed HOMO-LUMO gap energy for the selenium-based complex is roughly 0.17 eV smaller than for the sulfur analogs, which may indicate a lower reduction potential is needed.
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Sakamoto, Takahiro. "Relationships between Gas-Phase Ionization Energies and Solution-Phase Oxidation Potentials: Applications to the Electrocatalytic Production of Hydrogen from Weak Acids." Diss., The University of Arizona, 2010. http://hdl.handle.net/10150/194534.

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The transfer of electrons to and from a molecule is one of the more fundamental and important chemical processes. One such important example is the reduction-oxidation (redox) cycles in catalysts and enzymes. In the hydrogenase enzymes, adding and removing electrons is one of the key processes for generating H₂ from water molecules. Finding a direct free energy relation between the vertical ionization energies (IE(V)) measured spectroscopically by gas-phase photoelectron spectroscopy and the oxidation potentials (E(1/2)) measured thermodynamically in solution by cyclic voltammetry (CV) for molecules is an important aspect for developing effective catalysts. In this study, a series of organometallic compounds such as metallocenes were used for investigating the free energy relationships and catalysts inspired by the active sites of [FeFe]-hydrogenases enzymes were evaluated for their ability to produce H₂ from electrocatalytic reduction of weak acids. The first part of the dissertation explores metallocenes of the form (η⁵-C₅H₅)₂M (M= Fe, Ru, Os, Co, Ni) as the model for developing the free energy relation between gas phase ionization energies (IE(V)) and solution oxidation potentials (E(1/2)). It was found that computing the electronic properties of Cp₂Fe, Cp₂Ru, and Cp₂Os using VWN-Stoll and OPBE density functional theory (DFT) functional was successful with root mean square deviation (RMSD) of 0.02 eV between the experimental and calculated ionization energies. However, calculated ionization energies of Cp₂Co and Cp₂Ni were less successful with RMSD of 0.3 eV between the experimental and calculated ionization energies. Introduction of the B3LYP or M06 hybrid DFT functionals yielded much improved results (0.1 eV) over the previous combinations of DFT functional for Cp2Co and Cp2Ni. The energy relation between the two experimental measurements was established and further computational studies revealed that the solvation energy was the largest energy contribution between IE(V) and E(1/2) in the five studied metallocenes. The RMSD of the calculated oxidation potentials, after adjusting for the error in gas-phase ionization energies, was 0.09 V. The second part of the dissertation explores a series of catalysts inspired by the active sites of [FeFe]-hydrogenase enzymes; μ-(2,3-pyrazinedithiolato)diironhexacarbonyl (PzDT-cat), Fe₂(μ-X₂C₅H₈O)(CO)₆ (where X = S, Se, Te), and Fe₂(μ-1,3-SC₃H₆X)(CO)₆ (where X = Se and Te) for their ability to produce H₂ from weak acids utilizing the computational techniques and knowledge gained from the metallocene study. Even though the overall electronic perturbation from μ-(1,2-benzenedithiolato)diironhexacarbonyl (BDT-cat) to μ-(2,3-pyridinedithiolato)diironhexacarbonyl (PyDT-cat) to PzDT-cat is found to be small, the reduction potential of PzDT-cat was found to be 0.15 V less negative than that of BDT-cat resulting in less energy required for initiating electrocatalytic H₂ production over the BDT-cat and PyDT-cat. Lower reorganization energy has been achieved by substitutions of larger chalcogens at the Fe₂S₂ core. However, the electrocatalytic production of H₂ from acetic acid in acetonitrile was found to be diminished upon going from analogous S to Se to Te species. This is ascribed to the increase in the Fe–Fe bond distance with a corresponding increase in the size of the chalcogen atoms from S to Se to Te, disfavoring the formation of a carbonyl-bridged structure in the anion which is thought to be critical to the mechanism of H₂ production.
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Dogaru, Daniela. "Hydrogenase inhibition by O2 density functional theory/molecular mechanics investigation /." Cleveland, Ohio : Cleveland State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=csu1231721611.

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Thesis (Ph.D.)--Cleveland State University, 2008.
Abstract. Title from PDF t.p. (viewed on Apr. 13, 2009). Includes bibliographical references (p. 102-109). Available online via the OhioLINK ETD Center. Also available in print.
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Dogaru, Daniela. "Hydrogenase Inhibition by O2: Density Functional Theory/Molecular Mechanics Investigation." Cleveland State University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=csu1231721611.

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Guo, Zhen, and 郭臻. "Density functional theory studies of selected hydrogen bond assisted chemical reactions." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B42182335.

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Guo, Zhen. "Density functional theory studies of selected hydrogen bond assisted chemical reactions." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B42182335.

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Chohan, Urslaan. "Modelling early stages of hydrogen embrittlement and surface oxidation of iron using density functional theory." Thesis, University of Manchester, 2018. https://www.research.manchester.ac.uk/portal/en/theses/modelling-early-stages-of-hydrogen-embrittlement-and-surface-oxidation-of-iron-using-density-functional-theory(52c00a91-b779-4c0a-9dc7-688916f7bf57).html.

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In this project, I have modelled the adsorption and diffusion of hydrogen and oxygen on and through the three low-index planes of two phases of iron, namely the body-centred cubic ferromagnetic alpha iron, alpha-Fe, and face-centered cubic gamma iron phase, gamma-Fe. This was done using spin-polarised Density Functional Theory, and the minimum energy path for the diffusion calculation was derived from potential energy surfaces created from a tight 3D mesh through the crystal. It was found that oxygen and hydrogen atoms strongly chemisorb on the (110) phase. Oxygen strongly chemisorbs on alpha-Fe(110) at the quasi-threefold site, with a surface stretch ~500 cm-1 for higher coverage. The structural changes at the highest coverage (>0.5 ML) indicated the incipient formation of FeO(111) from the O-Fe(110) overlay. Studying the electronic properties of the formation of FeO(111) yields an understanding of the earliest stage of oxide formation. Hydrogen was found to strongly chemisorb on the (110) surface of alpha-Fe. The hydrogen adsorbs at the quasi-threefold site with an adsorption energy of ~3 eV/H atom and surface stretches at ~1100 cm-1 for higher coverages. The (111) surface of gamma-Fe has been found to have the highest barrier for bulk-like diffusion. The bulk-diffusion barrier for hydrogen through gamma-Fe is ~0.7 eV for the (111) surface, which is ~0.2 eV higher than the (110) surface. The presence of magnetism in the (001) surface of gamma-Fe resulted in a lowering in the bulk-like diffusion barrier, with an ~0.2 eV barrier in the ferromagnetic surface as opposed to the ~0.6 eV in the non-magnetic surface. The high barrier for the (111) surface of gamma-Fe demonstrates that producing textured austenitic steel components with this surface exposed to the hydrogen source may work to lower the hydrogen damage in these samples. The strong effect of magnetism in lowering the barrier for diffusion demonstrates the importance of avoiding ferromagnetic austenitic steel alloys in environments where hydrogen is in abundance. These results may be applied in the process of development of Gen IV fission and fusion reactors. Ferritic and austenitic steels are ideal candidates for a number of components in these reactors, such as the first wall/breeding blanket. There is an abundance of presence of hydrogen in nuclear reactors. Hydrogen may enter the metallic matrix through diffusion processes, leading to the embrittlement of these components. Additionally, oxygen is readily present in the environment, which may oxidise components. In this project, I have modelled the adsorption and diffusion of hydrogen and oxygen on and through the three low-index planes of two phases of iron, namely the body-centred cubic ferromagnetic alpha iron, alpha-Fe, and face-centered cubic gamma iron phase, gamma-Fe. This was done using spin-polarised Density Functional Theory, and the minimum energy path for the diffusion calculation was derived from potential energy surfaces created from a tight 3D mesh through the crystal. It was found that oxygen and hydrogen atoms strongly chemisorb on the (110) phase. Oxygen strongly chemisorbs on alpha-Fe(110) at the quasi-threefold site, with a surface stretch ~500 cm-1 for higher coverage. The structural changes at the highest coverage (>0.5 ML) indicated the incipient formation of FeO(111) from the O-Fe(110) overlay. Studying the electronic properties of the formation of FeO(111) yields an understanding of the earliest stage of oxide formation. Hydrogen was found to strongly chemisorb on the (110) surface of alpha-Fe. The hydrogen adsorbs at the quasi-threefold site with an adsorption energy of ~3 eV/H atom and surface stretches at ~1100 cm-1 for higher coverages. The (111) surface of gamma-Fe has been found to have the highest barrier for bulk-like diffusion. The bulk-diffusion barrier for hydrogen through gamma-Fe is ~0.7 eV for the (111) surface, which is ~0.2 eV higher than the (110) surface. The presence of magnetism in the (001) surface of gamma-Fe resulted in a lowering in the bulk-like diffusion barrier, with an ~0.2 eV barrier in the ferromagnetic surface as opposed to the ~0.6 eV in the non-magnetic surface. The high barrier for the (111) surface of gamma-Fe demonstrates that producing textured austenitic steel components with this surface exposed to the hydrogen source may work to lower the hydrogen damage in these samples. The strong effect of magnetism in lowering the barrier for diffusion demonstrates the importance of avoiding ferromagnetic austenitic steel alloys in environments where hydrogen is in abundance. These results may be applied in the process of development of Gen IV fission and fusion reactors. Ferritic and austenitic steels are ideal candidates for a number of components in these reactors, such as the first wall/breeding blanket. There is an abundance of presence of hydrogen in nuclear reactors. Hydrogen may enter the metallic matrix through diffusion processes, leading to the embrittlement of these components. Additionally, oxygen is readily present in the environment, which may oxidise components.
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Aurlien, Ragnhild. "A Density Functional Theory Study of Hydrogen Transfer and Rotational Barriers in Vitamin E-like Molecules." Thesis, Norges teknisk-naturvitenskapelige universitet, Institutt for fysikk, 2011. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-12798.

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A study of the antioxidant property of two vitamin E simplifications with density functional theory has been done. In one of the simplifications the phytyl tail and the methyl group on the heterocyclic ring in vitamin E is replaced by two hydrogen atoms, simplification A. In the other simplification the heterocyclic ring is replaced by two hydrogen atoms, simplification B. Three main investigations have been done; rotation of the hydroxyl group on the different isoforms of the two simplifications, hydrogen transfers from the alpha-isoform of the simplifications to three different radicals •OOH, •OOCH3, and •OOC2H5, and a rotation of the hydroxyl group with a hydrogen bond to •OOH and •OOCH3 for simplification B. The BLYP exchange correlation functional is found to underestimate hydrogen transfer energy barriers, which is improved with the B3LYP functional. This problem did not occur for the rotation of the hydroxyl group. The energy barriers for the rotation of the hydroxyl group is found to be smallest for the alpha-isoform, and simplification A gives lower rotational barriers than simplification B. Simplification A also results in smaller energy barriers for hydrogen transfers. The hydrogen transfer to •OOC2H5 with the B3LYP functional resulted in hydrogen barriers of 0,411 eV for simplification B and 0,231 eV for simplification A. Thus simplification B is found to be less reactive than simplification A, which is explained by the electron donating property of the heterocyclic ring not included in simplification B. Since simplification B is less reactive than simplification A, it is concluded to be a poorer antioxidant than simplification A, and a poor model for vitamin E.
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Edwards, Angela Celeste. "Probing the Hydrogen Bonding Interaction at the Gas-Surface Interface using Dispersion Corrected Density Functional Theory." Thesis, Virginia Tech, 2015. http://hdl.handle.net/10919/71784.

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he interactions of the chemical warfare agent sulfur mustard with amorphous silica were investigated using electronic structure calculations. In this thesis, the binding energies of sulfur mustard and mimic species used in the laboratory were calculated using density functional theory and fully ab initio calculations. The wB97XD and B97D functionals, which include functions to account for long-range dispersion interactions, were compared to experimental trends. The hydroxylated amorphous silica surface was approximated using a gas-phase silanol molecule and clusters containing a single hydroxyl moiety. Recent temperature programmed desorption experiments performed in UHV concluded that sulfur mustard and its less toxic mimics undergo molecular adsorption to amorphous silica. Hydrogen bonding can occur between surface silanol groups and either the sulfur or chlorine atom of the adsorbates, and the calculations indicate that the binding energies for the two hydrogen bond acceptors are similar. The adsorption of sulfur mustard and its mimics on silica also exhibits the presence of significant van der Waals interactions between alkyl of the adsorbates and the surface. These interactions, in combination with the formation of a hydrogen bond between a surface silanol group and the Cl or S atoms of the adsorbates, provide remarkably large binding energies.
Master of Science
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Book chapters on the topic "Hydrogenase, hydrogen, density functional theory"

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Sahni, Viraht. "Application of the Q-DFT Fully Correlated Approximation to the Hydrogen Molecule." In Quantal Density Functional Theory II, 289–302. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-540-92229-2_16.

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Prasad De, Sankar, and Ajay Misra. "Excited-State Intramolecular Proton Transfer Processes on Some Isomeric Naphthalene Derivatives: A Density Functional Theory Based Computational Study." In Hydrogen Bonding and Transfer in the Excited State, 589–608. Chichester, UK: John Wiley & Sons, Ltd, 2010. http://dx.doi.org/10.1002/9780470669143.ch26.

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Fradelos, Georgios, Jesse J. Lutz, Tomasz A. Wesołowski, Piotr Piecuch, and Marta Włoch. "Shifts in Excitation Energies Induced by Hydrogen Bonding: A Comparison of the Embedding and Supermolecular Time-Dependent Density Functional Theory Calculations with the Equation-of-Motion Coupled-Cluster Results." In Advances in the Theory of Quantum Systems in Chemistry and Physics, 219–48. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-2076-3_13.

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Antuch, Manuel, and Pierre Millet. "The Use of Density Functional Theory to Decipher the Electrochemical Activity of Metal Clathrochelates with Regard to the Hydrogen Evolution Reaction in the Homogeneous Phase." In Density Functional Theory. IntechOpen, 2019. http://dx.doi.org/10.5772/intechopen.80267.

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Das, R., A. Chakraborty, S. Pan, and P. K. Chattaraj. "Conceptual density functional theory (DFT) approach to all-metal aromaticity and hydrogen storage." In Compendium of Hydrogen Energy, 243–80. Elsevier, 2016. http://dx.doi.org/10.1016/b978-1-78242-362-1.00010-9.

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D. Kulkarni, Anant. "Unraveling Hydrogen Bonded Clustering with Water: Density Functional Theory Perspective." In Density Functional Theory - Recent Advances, New Perspectives and Applications [Working Title]. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.99958.

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Extensive density functional theory (DFT) studies have been compiled and additional investigation has been performed for several energetically favorable conformers of hydrogen bonded water clusters. The focus here is not to merely reviewing the literature on DFT investigations on water clusters but to understand the basic building blocks, structural patterns and trends in the energetics of the clusters during the cluster growth. The successive addition of water molecules to these clusters alters the hydrogen bonding pattern, that leads to modification in overall cluster geometry which is also reflected in the vibrational frequency shifts in simulated vibrational infra-red (IR) spectra.
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Srinivasadesikan, Venkatesan, Chitra Varadaraju, Raghunath Putikam, and Shyi-Long Lee. "Applications of Density Functional Theory on Heavy Metal Sensor and Hydrogen Evolution Reaction (HER)." In Density Functional Theory - Recent Advances, New Perspectives and Applications [Working Title]. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.99825.

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A great effort has been devoted to develop the numerical methods to solve Schrödinger equation for atoms and molecules which help to reveal the physico-chemical process and properties of various known/unknown materials. Designing the efficient probe to sense the heavy metals is a crucial process in chemistry. And, during this energy crisis, to find the effective conversion materials for water splitting is an important approach. The density functional theory (DFT) is a powerful tool to identify such materials and made great achievements in the field of heavy metal chemosensor and photocatalysis. Particularly, DFT helps to design the chemosensor for the effective sensor applications. The universe is moving towards the exhaustion of fossil fuels in a decade and so on, DFT plays a vital role to find the green energetic alternative to fossil fuel which is the Hydrogen energy. This book chapter will focus on the application of DFT deliberately on the heavy metal sensors and hydrogen evolution reaction.
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I. Grinvald, Iosif, Ivan Yu. Kalagaev, and Rostislav V. Kapustin. "The Formation Mechanism and Structure of Organic Liquids in the DFT Challenges." In Density Functional Theory - Recent Advances, New Perspectives and Applications [Working Title]. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.100429.

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In the paper the experimental and theoretical approaches to problem of organic liquids formation mechanism and its structure are reviewed. It was shown that all presented models have the advantages and disadvantages at interpretation of molecular interaction and arrangement in liquid phase. The DFT calculation in different variant of models including paired interaction hydrogen atom transfer, model of transformation and the general conclusion following from this consideration are presented.
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Teberekidis, V., and M. Sigalas. "Ab initio and Density Functional Theory Study of the Hydrogen- Bonded Pyridine-H2 S Complex." In Recent Progress in Computational Sciences and Engineering (2 vols), 1523–26. CRC Press, 2006. http://dx.doi.org/10.1201/b12066-204.

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Pottachola, Sumayya, Arifa Kaniyantavida, and Muraleedharan Karuvanthodiyil. "DFT Study of Structure and Radical Scavenging Activity of Natural Pigment Delphinidin and Derivatives." In Density Functional Theory - Recent Advances, New Perspectives and Applications [Working Title]. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.98647.

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A theoretical evaluation of the antioxidant activity of natural pigment delphinidin (1a) and derivatives 1b, 1c, 1d & 1e was performed using the DFT-B3LYP/6–311 + G (d, p) level of theory. Three potential working mechanisms, hydrogen atom transfer (HAT), stepwise electron transfer proton transfer (SET-PT), and sequential proton loss electron transfer (SPLET), have been investigated. The physiochemical parameters, including O–H bond dissociation enthalpy (BDE), ionization potential (IP), proton dissociation enthalpy (PDE), proton affinity (PA), and electron transfer enthalpy (ETE), have been calculated in the gas phase and aqueous phase. The study found that the most suitable mechanism for explaining antioxidant activity is HAT in the gas phase and SPLET in the aqueous medium in this level of theory. Spin density calculation and delocalization index of studied molecules also support the radical scavenging activity. When incorporated into natural pigment delphinidin, the gallate moiety can enhance the activity and stability of the compounds.
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Conference papers on the topic "Hydrogenase, hydrogen, density functional theory"

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Tao, Yi, Chenhan Liu, Juekuan Yang, Kedong Bi, Weiyu Chen, and Yunfei Chen. "First Principles Study of Thermal Conductance Across Cu/Graphene/Cu Nanocomposition and the Effect of Hydrogenation." In ASME 2016 5th International Conference on Micro/Nanoscale Heat and Mass Transfer. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/mnhmt2016-6318.

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In this work, the interfacial thermal conductance across Cu/graphene/Cu interfaces is investigated using the density functional theory (DFT) and the nonequilibrium Green’s function (NEGF) method. In order to study how hydrogenation of graphene affects thermal transport behaviors at the interfaces of Cu/graphene/Cu, we also analyze the interfacial thermal conductance across Cu/hydrogenated-graphene/Cu (Cu/H-graphene/Cu) with both double-sided and single-sided hydrogenated graphene. Our results show that, the interfacial thermal conductance across Cu/H-graphene/Cu interfaces is almost twice of the value across Cu/graphene/Cu interfaces. For Cu/H-graphene/Cu with double-sided hydrogenated graphene (Cu/DH-graphene/Cu), the hydrogen atoms between graphene and Cu layers provide additional thermal transport channels. While for Cu/H-graphene/Cu with single-sided hydrogenated graphene (Cu/SH-graphene/Cu), the hydrogen atoms not only provide additional thermal transport channels at the hydrogenated side of graphene, but also reduce the equilibrium separation between graphene and Cu layers at the non-hydrogenated side of graphene due to the transfer of massive electrons, which enhances the interface coupling between graphene and Cu layers. The phonon transmission shows that both double-sided and single-sided hydrogenation of graphene can increase the heat transport across the interface. Our calculation indicates that the interfacial thermal conductance of Cu/graphene/Cu nanocomposition can be improved by hydrogenation.
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Huang, Song, Zhiping Chen, and Wenqiang Su. "The Fatigue Threshold Computation of Steel in Hydrogen Environment by Shakedown Analysis." In ASME 2017 Pressure Vessels and Piping Conference. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/pvp2017-65432.

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In this paper, the fatigue threshold of steel servicing in hydrogen environment is studied by means of shakedown analysis. First of all, the application of shakedown analysis on the fatigue threshold prediction is reviewed briefly. Secondly, the classical static shakedown theorem for elasto-perfectly plastic structure is modified to take hydrogen’s effect into consideration. In the proposed method, the effect of hydrogen is described by a yield stress associated with hydrogen concentration and hydrogen content in metal is assumed to be composed of the hydrogen in lattice sites and in reversible trap sites. The effect of plastic flow on hydrogen trap density is involved in by considering the plastic strain as the function of residual stress, which is expected to result in a lower bound of the shakedown load. Finally, the fatigue threshold of a steel is computed as example. The performance of the proposed method is discussed and compared with the results from references. The results indicate that the proposed method is of validity.
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Huda, Muhammad N., Yanfa Yan, Aron Walsh, Su-Huai Wei, John A. Turner, and Mowafak M. Al-Jassim. "Delafossite-alloy photoelectrodes for PEC hydrogen production: a density functional theory study." In SPIE Solar Energy + Technology, edited by Hicham Idriss and Heli Wang. SPIE, 2010. http://dx.doi.org/10.1117/12.859947.

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Emilsson, Marie. "Hydrogen Desorption in High Pressure Phases of MgH2: a Density Functional Theory Based Study." In HYDROGEN IN MATTER: A Collection from the Papers Presented at the Second International Symposium on Hydrogen in Matter (ISOHIM). AIP, 2006. http://dx.doi.org/10.1063/1.2213073.

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Mishra, Anamika, Vineet Gupta, Poonam Tandon, Ko-Ki Kunimoto, P. M. Champion, and L. D. Ziegler. "Vibrational Spectroscopy and Density Functional Theory of Intermolecular Hydrogen Bonding in 2-Thiohydantoins." In XXII INTERNATIONAL CONFERENCE ON RAMAN SPECTROSCOPY. AIP, 2010. http://dx.doi.org/10.1063/1.3482568.

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Pambudi, Agung B., Arif Priyangga, Djoko Hartanto, and Lukman Atmaja. "Intramolecular hydrogen bond and vibrational spectroscopic study of cellulose oligosaccharide using density functional theory." In 4TH INTERNATIONAL SEMINAR ON CHEMISTRY. AIP Publishing, 2021. http://dx.doi.org/10.1063/5.0054693.

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Chapman, James, Kyoung Kweon, and Nir Goldman. "Understanding hydrogen diffusivity in amorphous titania: A combined density functional theory, machine learning, and graph theory study." In 1st Corrosion and Materials Degradation Web Conference. Basel, Switzerland: MDPI, 2021. http://dx.doi.org/10.3390/cmdwc2021-09929.

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Rezaie, Shima, Zohreh Golshan Bafghi, Negin Manavizadeh, and Ebrahim Nadimi. "Hydrogen Gas Sensing Mechanism in Zinc Oxide Nanowire and Nanotube: A Density Functional Theory Study." In 2019 27th Iranian Conference on Electrical Engineering (ICEE). IEEE, 2019. http://dx.doi.org/10.1109/iraniancee.2019.8786654.

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Jeanvoine, Y., F. Bohr, and M. F. Ruiz-López. "Study of some hydrogen bonded complexes in polar media using density functional theory and SCRF calculations." In The first European conference on computational chemistry (E.C.C.C.1). AIP, 1995. http://dx.doi.org/10.1063/1.47870.

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McGhee, Joseph, and Vihar P. Georgiev. "Electronic and Optical Properties of Hydrogen-Terminated Diamond Doped by Molybdenum Oxide: A Density Functional Theory Study." In 2020 International Conference on Numerical Simulation of Optoelectronic Devices (NUSOD). IEEE, 2020. http://dx.doi.org/10.1109/nusod49422.2020.9217662.

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Reports on the topic "Hydrogenase, hydrogen, density functional theory"

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Wendlandt, Johanna. Study of Hydrogen Bonding in Small Water Clusters with Density Functional Theory Calculations. Office of Scientific and Technical Information (OSTI), December 2005. http://dx.doi.org/10.2172/877463.

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