Journal articles: '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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Kaduk, James A., Amy M. Gindhart, and Thomas N. Blanton. "Crystal structures of two polymorphs of alclometasone dipropionate, C28H37ClO7." Powder Diffraction 35, no. 1 (January 15, 2020): 45–52. http://dx.doi.org/10.1017/s0885715619000940.

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The crystal structures of two forms of alclometasone dipropionate have been solved and refined using a single synchrotron X-ray powder diffraction pattern and optimized using density functional techniques. Both forms crystallize in the space group P212121 (#19) with Z = 4. The lattice parameters of Form 1 are a = 10.44805(7), b = 14.68762(8), c = 17.31713(9) Å, and V = 2657.44(2) Å3, and those of Form 2 are a = 10.69019(13), b = 14.66136(23), c = 17.17602(23) Å, and V = 2692.05(5) Å3. Both density functional theory and molecular mechanics optimizations indicate that Form 2 is lower in energy, but the differences are within the expected uncertainties of such calculations. In both forms, the only traditional hydrogen bond is between the hydroxyl group and the ketone in the steroid A ring. The chlorine atom acts as an acceptor in two intramolecular C–H⋯Cl hydrogen bonds involving ring hydrogens, as well as in an intermolecular hydrogen bond involving a methyl group. There are several C–H⋯O hydrogen bonds, mainly to ketone oxygens, but also to the hydroxyl group and an ether oxygen. The powder patterns have been submitted to ICDD for inclusion in the Powder Diffraction File™.

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Ferrante, Francesco, Antonio Prestianni, Marco Bertini, and Dario Duca. "H2 Transformations on Graphene Supported Palladium Cluster: DFT-MD Simulations and NEB Calculations." Catalysts 10, no. 11 (November 12, 2020): 1306. http://dx.doi.org/10.3390/catal10111306.

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Molecular dynamics simulations based on density functional theory were employed to investigate the fate of a hydrogen molecule shot with different kinetic energy toward a hydrogenated palladium cluster anchored on the vacant site of a defective graphene sheet. Hits resulting in H2 adsorption occur until the cluster is fully saturated. The influence of H content over Pd with respect to atomic hydrogen spillover onto graphene was investigated. Calculated energy barriers of ca. 1.6 eV for H-spillover suggest that the investigated Pd/graphene system is a good candidate for hydrogen storage.

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Deka, Ajanta. "Structure and Reverse Hydrogen Spillover in Mononuclear Au0 and AuI Complexes Bonded to Faujasite Zeolite: A Density Functional Study." Journal of Catalysts 2013 (May 25, 2013): 1–5. http://dx.doi.org/10.1155/2013/467846.

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We have studied the structure of mononuclear gold supported on acidic form of faujasite zeolite in two oxidation states, namely, 0 and +1, using density functional theory. The binding of the gold monomer to the zeolite support is stronger in the oxidation state +1 than in the oxidation state 0. For the oxidation state 0, the hydrogenated clusters AuH/(2H)-FAU, AuH2/H-FAU generated by stepwise reverse hydrogen spillover from bridging OH groups of zeolite are energetically preferred over the Au/(3H)-FAU structure. Reverse hydrogen spillover of all the three acidic protons from the zeolite to the Au monomer did not lead to a stable structure. The calculated reverse hydrogen spillover energy per hydrogen atom for zeolite supported AuH and AuH2 clusters are −10.2 and −5.1 kJ/mol, respectively, in the oxidation state 0, while in the oxidation state +1 it is 20.9 kJ/mol for zeolite supported Au+H cluster.

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Folga, E., and T. Ziegler. "A theoretical study on the activation of hydrogen–hydrogen and hydrogen–alkyl bonds by electron-poor early transition metals." Canadian Journal of Chemistry 70, no. 2 (February 1, 1992): 333–42. http://dx.doi.org/10.1139/v92-047.

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A theoretical study has been carried out on four σ-bond metathesis reactions mediated by the electron-poor lutetium metal centre. The four processes include hydrogen exchange, X2Lu-H + D2 → X2Lu-D + HD (1), and hydrogenolysis X2Lu-CH3 + H2 → Cl2Lu-H + CH4 (2), in which a H—H bond is activated, as well as methane exchange, X2Lu-CH3 + CH4 → X2Lu-CH3 + CH4 (3), and methylation, Cl2Lu-H + CH4 → X2Lu-CH3 + H2 (4), in which a C—H bond is activated. The [Formula: see text] fragment employed in a number of experimental studies was modelled by Cl2Lu and all calculations were based on approximate Density Functional Theory (DFT). The study combined methods from quantum mechanics and statistical mechanics to obtain enthalpies and entropies of activation as well as transition state structures. All four processes were found to have an ordered four-centre transition state with negative entropies of activation given by ΔS≠ = −109(1), −124(2), −131 (3), and −134(4)&nbspJ mol−1 K−1 at T = 298.15 K. The Gibb's free energies of activation, ΔG≠(= ΔH≠ − TΔS≠) were calculated as ΔG≠ = 81.6 (1), 126.0 (2), 136.7 (3), and 130.6 (4) kJ mol−1 at T = 298.15 K. The calculated trends in ΔG≠ are consistent with the observed order of reactivity for σ-bond metathesis reactions between R—H and M—R′ bonds: R = R′ = H >> R = H, R′ = CH3 > R = R′ = CH3. The decrease in the reaction rate is related to the different abilities of the 1s hydrogen orbital and the [Formula: see text] methyl orbital to stabilize the four-centre transition state. Thus, the spherical 1s hydrogen orbital is better able to overlap fully with orbitals on adjacent centres than the directional [Formula: see text] orbital. As a consequence, the electronic barrier is seen to increase from the hydrogen exchange reaction towards the hydrogenolysis and methane exchange processes as one or two hydrogens, respectively, are replaced by methyl groups in the four-centre transition state. Keywords: Density Functional Theory, C—H activation, metathesis, hydrogenolysis, H—H activation.

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Hu, Jutao, Huahai Shen, Ming Jiang, Hengfeng Gong, Haiyan Xiao, Zijiang Liu, Guangai Sun, and Xiaotao Zu. "A DFT Study of Hydrogen Storage in High-Entropy Alloy TiZrHfScMo." Nanomaterials 9, no. 3 (March 20, 2019): 461. http://dx.doi.org/10.3390/nano9030461.

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In recent years, high-entropy alloys have been proposed as potential hydrogen storage materials. Despite a number of experimental efforts, there is a lack of theoretical understanding regarding the hydrogen absorption behavior of high-entropy alloys. In this work, the hydrogen storage properties of a new TiZrHfScMo high-entropy alloy are investigated. This material is synthesized successfully, and its structure is characterized as body-centered cubic. Based on density functional theory, the lattice constant, formation enthalpy, binding energy, and electronic properties of hydrogenated TiZrHfScMo are all calculated. The calculations reveal that the process of hydrogenation is an exothermic process, and the bonding between the hydrogen and metal elements are of covalent character. In the hydrogenated TiZrHfScMo, the Ti and Sc atoms lose electrons and Mo atoms gain electrons. As the H content increases, the <Ti–H> bonding is weakened, and the <Hf–H> and <Mo–H> bonding are strengthened. Our calculations demonstrate that the TiZrHfScMo high-entropy alloy is a promising hydrogen storage material, and different alloy elements play different roles in the hydrogen absorption process.

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Mehdi Aghaei, Sadegh, and Irene Calizo. "Density Functional Theory Study on Energy Band Gap of Armchair Silicene Nanoribbons with Periodic Nanoholes." MRS Advances 1, no. 22 (2016): 1613–18. http://dx.doi.org/10.1557/adv.2016.123.

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ABSTRACTIn this study, density functional theory (DFT) is employed to investigate the electronic properties of armchair silicene nanoribbons perforated with periodic nanoholes (ASiNRPNHs). The dangling bonds of armchair silicene nanoribbons (ASiNR) are passivated by mono- (:H) or di-hydrogen (:2H) atoms. Our results show that the ASiNRs can be categorized into three groups based on their width: W = 3P − 1, 3P, and 3P + 1, P is an integer. The band gap value order changes from “EG (3P − 1) < EG (3P) < EG (3P + 1)” to “EG (3P + 1) < EG (3P − 1) < EG (3P)” when edge hydrogenation varies from mono- to di-hydrogenated. The energy band gap values for ASiNRPNHs depend on the nanoribbons width and the repeat periodicity of the nanoholes. The band gap value of ASiNRPNHs is larger than that of pristine ASiNRs when repeat periodicity is even, while it is smaller than that of pristine ASiNRs when repeat periodicity is odd. In general, the value of energy band gap for ASiNRPNHs:2H is larger than that of ASiNRPNHs:H. So a band gap as large as 0.92 eV is achievable with ASiNRPNHs of width 12 and repeat periodicity of 2. Furthermore, creating periodic nanoholes near the edge of the nanoribbons cause a larger band gap due to a strong quantum confinement effect.

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Kusakabe, Koichi. "SIMULATION OF NANOSCALE ETCHING FOR NANOTUBE AND GRAPHENE DEVICES." MRS Proceedings 1451 (2012): 21–24. http://dx.doi.org/10.1557/opl.2012.850.

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ABSTRACTIn order to find an efficient method to etch nano-carbon materials by hydrogenation in a controlled manner, we have studied hydrogen-atom adsorption on various deformed nanotubes using computer simulations based on the density-functional theory. The nanotube with an atomic lack is compared to a deformed tube with the Stone-Wales defect and a twisted tube wall. Similar to the known experimental etching condition for graphene, an atomic lack is effective to accumulate hydrogen atoms around the defect. Compared to the flat graphene, however, nanotube walls with curvature allow on-top adsorption of a hydrogen atom and selectivity in the hydrogenated site becomes worse. To achieve a controlled etching process, usage of a tungsten tip which realizes focused hydrogenation is proposed for natotubes and curved graphene.

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Liu, Feng Bin, Jia Dao Wang, Da Rong Chen, and Bing Liu. "Ab Initio Study of Hydrogen Desorption from Hydrogenated Diamond (100) Surface." Solid State Phenomena 121-123 (March 2007): 1119–24. http://dx.doi.org/10.4028/www.scientific.net/ssp.121-123.1119.

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By means of the density functional theory on the basis of generalized gradient approximation, the reaction paths of the dehydrogenation from the diamond (100) surface was deduced due to the reaction heat. Moreover, the most stable structure of the hydride diamond (100) surface was obtained. The results indicate that the dehydrogenation is easier to take place at the same C-C dimer and forms the parallel geometries. The parallel 1×1:1.5H, 2×1:H and parallel 2×1:0.5H are the intermediate products during the hydrogen desorption process, while, 2×1:H is the most stable structure of the hydride diamond (100) surfaces. The calculated reaction heat is in accordance with the experimental results.

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Surawatanawong, Panida, Jesse W. Tye, Marcetta Y. Darensbourg, and Michael B. Hall. "Mechanism of electrocatalytic hydrogen production by a di-iron model of iron–iron hydrogenase: A density functional theory study of proton dissociation constants and electrode reduction potentials." Dalton Transactions 39, no. 12 (2010): 3093. http://dx.doi.org/10.1039/b925262b.

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Pamungkas, Mauludi Ariesto, Husain, Achmad Kafi Shobirin, Tri Sugiono, and Masruroh Masruroh. "The Electronic Structure of Ga-Doped Hydrogen-Passivated Germanene: First Principle Study." Key Engineering Materials 833 (March 2020): 157–61. http://dx.doi.org/10.4028/www.scientific.net/kem.833.157.

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Germanene, which has the same structure as graphene, is an exciting novel 2D functionalized material that controls its band gap using functionalization. The effects of the Ga atom and hydrogen atoms on the structure of Ga-doped H-passivated germanene were investigated with a density functional theory (DFT) calculation. H-passivated germanene has a direct gap of 2.10 eV. Opening the band gap in the H-passivated germanene is due to transition from sp2 to sp3 orbital. Adsorption of the Ga adatom on H-site decrease the band gap to 1.38 eV. No interaction between Ga atoms and Hydrogen atoms was observed. Hence, their effects on the band structure of hydrogenated graphene were independent of each other. Our results suggest that hydrogen passivation combined with adsorption of the Ga adatoms could effectively control the band gap of germanene.

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Grocholska, Paulina, Marta Kowalska, Robert Wieczorek, and Remigiusz Bąchor. "A Non-Covalent Dimer Formation of Quaternary Ammonium Cation with Unusual Charge Neutralization in Electrospray-Ionization Mass Spectrometry." Molecules 26, no. 19 (September 28, 2021): 5868. http://dx.doi.org/10.3390/molecules26195868.

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Specific and nonspecific non-covalent molecular association of biomolecules is characteristic for electrospray-ionization mass spectrometry analysis of biomolecules. Understanding the interaction between two associated molecules is of significance not only from the biological point of view but also gas phase analysis by mass spectrometry. Here we reported a formation of non-covalent dimer of quaternary ammonium denatonium cation with +1 charge detected in the positive ion mode electrospray ionization mass spectrometry analysis of denatonium benzoate. Hydrogen deuterium exchange of amide and carbon-bonded hydrogens revealed that charge neutralization of one denatonium cation is the consequence of amide hydrogen dissociation. DFT (Density Functional Theory) calculations proved high thermodynamic stable of formed dimer stabilized by the short and strong N..H-N hydrogen bond. The signal intensity of the peak characterizing non-covalent dimer is low intensity and does not depend on the sample concentration. Additionally, dimer observation was found to be instrument-dependent. The current investigation is the first experimental and theoretical study on the quaternary ammonium ions dimer. Thus the present study has great significance for understanding the structures of the biomolecules as well as materials.

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ANSARI, R., M. MIRNEZHAD, and H. ROUHI. "MECHANICAL PROPERTIES OF CHIRAL SILICON CARBIDE NANOTUBES UNDER HYDROGEN ADSORPTION: A MOLECULAR MECHANICS APPROACH." Nano 09, no. 04 (June 2014): 1450043. http://dx.doi.org/10.1142/s179329201450043x.

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This paper investigates the mechanical properties of hydrogenated silicon carbide nanotubes ( H - SiCNTs ) using a molecular mechanics model in conjunction with the density functional theory (DFT). Analytical expressions presented in this study can be employed for nanotubes with different chiralities. Four different positions of adsorptions are considered in this paper and it is shown that the most stable state happens when hydrogen atoms are adsorbed on silicon and carbon atoms at the two opposite sides of hexagonal phase of silicon carbide. This paper will contribute to future research on similar studies of H - SiCNTs in the specific area as the force constants used in the molecular mechanics models regarding the hydrogen adsorption are proposed. Also, the mechanical properties and atomic structure of hydrogenated silicon carbide ( H - SiC ) sheet for different states of adsorption are determined using the DFT. The results for bending stiffness of H - SiC sheets indicate the isotropic behavior of these materials.

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Proks, Vladimír, and Miroslav Holík. "Modeling Substituent-Dependence of the Twist and Shielding in a Series of 4-Substituted N-(4-Nitrobenzylidene)anilines." Collection of Czechoslovak Chemical Communications 69, no. 8 (2004): 1566–76. http://dx.doi.org/10.1135/cccc20041566.

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A series of 15 4-substituted N-(4-nitrobenzylidene)anilines was synthesized and studied by 1H NMR spectroscopy. Their ab initio calculated geometries and the shielding as expressed by aromatic ring currents were used in correlation analysis. The geometries were fully optimized using density functional theory B3LYP/6-311G** approaches. For the determination of the ring current contribution to the shielding of azomethine hydrogens Hα was used direct ab initio calculation of the chemical shielding in a model system. Experimental chemical shift values free of these contributions were successfully correlated with increments ap of chemical shift for monosubstituted benzenes. In the same manner, the contribution of the anisotropy of C=N double bond to Hm hydrogen were calculated and values of the Hm chemical shift free of this contribution were successfully correlated with increments of chemical shift am.

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McGhee, Joseph, and Vihar P. Georgiev. "Simulation Study of Surface Transfer Doping of Hydrogenated Diamond by MoO3 and V2O5 Metal Oxides." Micromachines 11, no. 4 (April 20, 2020): 433. http://dx.doi.org/10.3390/mi11040433.

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In this work, we investigate the surface transfer doping process that is induced between hydrogen-terminated (100) diamond and the metal oxides, MoO3 and V2O5, through simulation using a semi-empirical Density Functional Theory (DFT) method. DFT was used to calculate the band structure and charge transfer process between these oxide materials and hydrogen terminated diamond. Analysis of the band structures, density of states, Mulliken charges, adsorption energies and position of the Valence Band Minima (VBM) and Conduction Band Minima (CBM) energy levels shows that both oxides act as electron acceptors and inject holes into the diamond structure. Hence, those metal oxides can be described as p-type doping materials for the diamond. Additionally, our work suggests that by depositing appropriate metal oxides in an oxygen rich atmosphere or using metal oxides with high stochiometric ration between oxygen and metal atoms could lead to an increase of the charge transfer between the diamond and oxide, leading to enhanced surface transfer doping.

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Miranda, A., J. L. Cuevas, A. E. Ramos, and Miguel Cruz-Irisson. "Effects of Morphology on the Electronic Properties of Hydrogenated Silicon Carbide Nanowires." Journal of Nano Research 5 (February 2009): 161–67. http://dx.doi.org/10.4028/www.scientific.net/jnanor.5.161.

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The effects on the electronic band structure of hydrogenated cubic silicon carbide (-SiC) nanowires of changes in the diameter and morphology are studied using a semiempirical sp3s* tight-binding approach applied to a supercell model. The results of the calculation of the electronic band structure and electronic density of states obtained are compared with those calculated by density functional theory within local density approximation only for the bulk of -SiC. As boundary conditions, we passivated all the Si and C dangling bonds with hydrogen atoms. The results show that although surface morphology modifies the band gap, the change is more systematic with the thickness variation. The energy band gap increases with decreasing diameter in all cases because of quantum confinement, but the scaling is dependent on the morphology (cross-section) of the -SiC nanowires. Finally, the calculations show a consistent asymptotical behavior to the crystalline limit when the width of the wires enlarges.

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BELELLI, PATRICIA G., and NORBERTO J. CASTELLANI. "A THEORETICAL STUDY OF UNSATURATED OLEFIN HYDROGENATION AND ISOMERIZATION ON Pd(111)." Surface Review and Letters 15, no. 03 (June 2008): 249–59. http://dx.doi.org/10.1142/s0218625x08011329.

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The addition of hydrogen to the carbon–carbon double bond of 2-butenes adsorbed on Pd (111) was studied within the density functional theory (DFT) and using a periodic slab model. For that purpose, the Horiuti–Polanyi mechanisms for both complete hydrogenation and isomerization were considered. The hydrogenation of cis and trans-2-butene to produce butane proceeds via the formation of eclipsed and staggered-2-butyl intermediates, respectively. In both cases, a relatively high energy barrier to produce the half-hydrogenated intermediate makes the first hydrogen addition the slowest step of the reaction. The competitive production of trans-2-butene from cis-2-butene requires the conversion from the eclipsed-2-butyl to the staggered-2-butyl isomer. As the corresponding energy barrier is relatively small and because the first of these isomers is less stable than the second, an easy conversion is predicted.

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Hao, Haigang, Pengfei Lian, Juhui Gong, and Rui Gao. "Theoretical Study on the Hydrogenation Mechanisms of Model Compounds of Heavy Oil in a Plasma-Driven Catalytic System." Catalysts 8, no. 9 (September 7, 2018): 381. http://dx.doi.org/10.3390/catal8090381.

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Heavy oil will likely dominate the future energy market. Nevertheless, processing heavy oils using conventional technologies has to face the problems of high hydrogen partial pressure and catalyst deactivation. Our previous work reported a novel method to upgrade heavy oil using hydrogen non-thermal plasma under atmospheric pressure without a catalyst. However, the plasma-driven catalytic hydrogenation mechanism is still ambiguous. In this work, we investigated the intrinsic mechanism of hydrogenating heavy oil in a plasma-driven catalytic system based on density functional theory (DFT) calculations. Two model compounds, toluene and 4-ethyltoluene have been chosen to represent heavy oil, respectively; a hydrogen atom and ethyl radical have been chosen to represent the high reactivity species generated by plasma, respectively. DFT study results indicate that toluene is easily hydrogenated by hydrogen atoms, but hard to hydrocrack into benzene and methane; small radicals, like ethyl radicals, are prone to attach to the carbon atoms in aromatic rings, which is interpreted as the reason for the increased substitution index of trap oil. The present work investigated the hydrogenation mechanism of heavy oil in a plasma-driven catalytic system, both thermodynamically and kinetically.

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Jones, Paul M., Huan Tang, Yiao-Tee Hsia, Xiaoping Yan, James D. Kiely, Junwei Huang, Christopher Platt, Xiaoding Ma, Michael Stirniman, and Lang Dinh. "Atomistic Frictional Properties of the C(100)2x1-H Surface." Advances in Tribology 2013 (2013): 1–11. http://dx.doi.org/10.1155/2013/850473.

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Density functional theory- (DFT-) based ab initio calculations were used to investigate the surface-to-surface interaction and frictional behavior of two hydrogenated C(100) dimer surfaces. A monolayer of hydrogen atoms was applied to the fully relaxed C(100)2x1 surface having rows of C=C dimers with a bond length of 1.39 Å. The obtained C(100)2x1-H surfaces (C–H bond length 1.15 Å) were placed in a large vacuum space and translated toward each other. A cohesive state at a surface separation of 4.32 Å that is stabilized by approximately 0.42 eV was observed. An increase in the charge separation in the surface dimer was calculated at this separation having a 0.04 e transfer from the hydrogen atom to the carbon atom. The Mayer bond orders were calculated for the C–C and C–H bonds and were found to be 0.962 and 0.947, respectively.σC–H bonds did not change substantially from the fully separated state. A significant decrease in the electron density difference between the hydrogen atoms on opposite surfaces was seen and assigned to the effects of Pauli repulsion. The surfaces were translated relative to each other in the (100) plane, and the friction force was obtained as a function of slab spacing, which yielded a 0.157 coefficient of friction.

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Koskinen, Jere T., Mikko Koskinen, Ilpo Mutikainen, Berit Mannfors, and Hannu Elo. "Experimental and Computational Studies on Aminoguanidine Free Base, Monocation and Dication, Part I: The Crystal and Molecular Structure of Aminoguanidine Monohydrochloride and the ab Initio Structure of the Endiamine Tautomer of Aminoguanidine Free Base." Zeitschrift für Naturforschung B 51, no. 12 (December 1, 1996): 1771–78. http://dx.doi.org/10.1515/znb-1996-1215.

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The crystal and molecular structure of aminoguanidine monohydrochloride, CN4H7+.CL- in which aminonoguanidine exists in the monocation form, was determined by single-crystal X-ray diffraction. The structure of the monocation is largely similar to that of aminoguanidine dication as present in previously studied divalent salts. The monocation was found to exist in the form of the tautom er that allows strong resonance in the guanyl group. As compared to the dication, the terminal hydrazine nitrogen atom bears one hydrogen atom less. The monocation is planar, the only atoms deviating from the plane being the hydrogens attached to the terminal hydrazine nitrogen. Quantum chemical calculations on the endiamine tautomer of aminoguanidine free base as well as on aminoguanidine monocation and dication were also perform ed by using the HF and MP2 ab initio methods and also the B3- LYP and B-LYP methods based on density functional theory. On the basis of the calculations, a predicted structure of the endiamine tautom er of aminoguanidine free base is presented

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Kaduk, J. A., K. Zhong, T. N. Blanton, S. Gates-Rector, and T. G. Fawcett. "Powder X-ray diffraction of bendamustine hydrochloride monohydrate, C16H22Cl2N3O2Cl·H2O." Powder Diffraction 34, no. 1 (December 27, 2018): 74–75. http://dx.doi.org/10.1017/s0885715618000830.

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Bendamustine hydrochloride monohydrate (marketed as Treanda®) is a nitrogen mustard purine analog alkylator used in the treatment of chronic lymphocytic leukemia (CLL) and non-Hodgkin lymphomas. Commercial bendamustine hydrochloride monohydrate crystallizes in the monoclinic space group P21/c (14), with a = 4.71348(4) Å, b = 47.5325(3) Å, c = 8.97458 (5) Å, β = 96.6515(8)°, V = 1997.161(23) Å3, and Z = 4. A reduced cell search in the Cambridge Structural Database yielded a previously reported crystal structure (Allen, 2002), which did not include hydrogens (Reck, 2006). In this work, the sample was ordered from Santa Cruz Biotechnology, and analyzed as received. The room-temperature crystal structure was refined using synchrotron (λ = 0.413896 Å) powder diffraction data, density functional theory (DFT), and Rietveld refinement techniques. Hydrogen positions were included as part of the structure, and recalculated during the refinement. The diffraction data were collected on beamline BM-11 at the Advanced Photon Source, Argonne National Laboratory. Figure 1 shows the powder X-ray diffraction pattern of the compound. The pattern is included in the Powder Diffraction File as entry 00-064-1508.

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Wang, Jianjun, Lin Li, Wentao Yang, Meng Li, Peng Guo, Bin Zhao, Linfeng Yang, Lili Fang, Bin Sun, and Yu Jia. "The Flexible Lubrication Performance of Graphene Used in Diamond Interface as a Solid Lubricant: First-Principles Calculations." Nanomaterials 9, no. 12 (December 16, 2019): 1784. http://dx.doi.org/10.3390/nano9121784.

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The interfacial friction performances of graphene covered and hydrogen-terminated diamond surfaces were investigated comparatively by first-principles calculations within density functional theory (DFT). Both systems exhibit similar excellent lubricating effects under small load, but the graphene covered interface presents small friction than that of hydrogenated system for the larger load. The calculated interfacial friction between two sheets of graphene covered diamond surface increases slowly than that of hydrogenated system in a wide range of pressure scale, and the friction difference between the two systems increases with increasing external pressure, indicating that graphene has flexible lubricating properties with high load-carrying capacity. This behavior can be attributed to the large interlayer space and a more uniform interlayer charge distribution of graphene covered diamond interface. Our investigations suggest that graphene is a promising candidate as solid lubricate used in diamond film, and are helpful for the understanding of interfacial friction properties of diamond film.

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Chapman, James, Kyoung E. Kweon, Nir Goldman, Nathan Daniel Keilbart, Tae Wook Heo, and Brandon C. Wood. "(Digital Presentation) Predicting Hydrogen Diffusivity in Amorphous Titania Using Markov Chain Kinetic Monte Carlo Simulations." ECS Meeting Abstracts MA2022-01, no. 16 (July 7, 2022): 1009. http://dx.doi.org/10.1149/ma2022-01161009mtgabs.

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Understanding hydrogen transport is vital to industries focused on discovering new materials for energy storage and corrosion mitigation. However, knowledge of the physical nature of hydrogen’s diffusion pathways is often limited, especially for materials that exhibit a multitude of phases/defect classes. These materials typically have three rate-limiting structural domains: (1) bulk (2) grain boundaries, and (3) surfaces. In this work we have chosen to study hydrogen diffusion through titania due to its importance in the aforementioned application spaces. Here, we aim to understand diffusion through titania grain boundaries, which are approximated via the amorphous phase. Density functional theory (DFT) was used to calculate thousands of activation energies of hydrogen diffusion in the amorphous phase via nudged elastic band calculations using an automated hydrogen pathway generation scheme. Amorphous structures, on the order of tens of nanometers, were generated using a machine learning force field via classical molecular dynamics (MD). Markov chains were generated using the MD-derived atomic structures as their reference. Kinetic Monte Carlo (KMC) simulations were then performed over a variety of temperatures and stoichiometries, for system sizes in the tens of nanometers, allowing us to connect directly with experimental measurements. Using our KMC simulations we can directly calculate the hydrogen diffusion constant, as a function of temperature and stoichiometry, and compare these values with those determined via experiments. We also employ a graph-based characterization scheme that can quantify the subtle differences in local hydrogen diffusion networks throughout the KMC simulation, allowing us to link local hydrogen diffusivity with structural differences within the material observed along the diffusion pathway. This work sets the stage for one to perform long time-scale and/or length-scale simulations to understand how temperature and atomic structure affect properties such as diffusivity, solubility, and permeation, and connect these values directly with experiments.

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ESRAFILI, MEHDI D., FATEMEH ELMI, and NASSER L. HADIPOUR. "DENSITY FUNCTIONAL THEORY STUDY OF BINDING ENERGIES, 7Li NUCLEAR MAGNETIC SHIELDING, AND ELECTRIC FIELD GRADIENT TENSORS ON THE SMALL CLUSTERS OF LinHm (m ≤ n ≤ 4)." Journal of Theoretical and Computational Chemistry 06, no. 04 (December 2007): 959–73. http://dx.doi.org/10.1142/s021963360700343x.

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The binding energies, geometries, 7 Li magnetic shielding, and electric field gradient tensors of hydrogenated lithium clusters, Li n H m (m ≤ n ≤ 4), were studied via density functional theory approach. We optimized the structures using B3LYP functional and 6-311++G (2d,2p) basis set. The calculated binding energies of lithium hydride clusters indicate that hydrogenation energy of Li n H m clusters decreases as the number of hydrogen atoms within the cluster increases. Our calculations also showed that for n = 4 clusters, the three-dimensional structure is more stable than the planar one. The study of the trends in the 7 Li magnetic shielding isotropy, σiso, and anisotropies, Δσ, values are explained in terms of the interplay between the electronic and geometrical effects. The variations in the 7 Li nuclear quadrupole coupling constants, χ, and their associated asymmetry parameters, ηQ, for different isomers of the lithium hydride clusters and the influence of hydrogenation on the EFG tensors are also discussed. For n = 4, we obtained a noticeable difference in the χ value from the planar to the three-dimensional structures. The atoms in molecules (AIM) analysis at the Li–H bond critical point reveals remarkably different topographical properties of the charge density and associated Laplacian fields for the planar and three-dimensional lithium hydride clusters.

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Piazza, Fabrice, Marc Monthioux, Pascal Puech, Iann C. Gerber, and Kathleen Gough. "Progress on Diamane and Diamanoid Thin Film Pressureless Synthesis." C 7, no. 1 (January 23, 2021): 9. http://dx.doi.org/10.3390/c7010009.

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Nanometer-thick and crystalline sp3-bonded carbon sheets are promising new wide band-gap semiconducting materials for electronics, photonics, and medical devices. Diamane was prepared from the exposure of bi-layer graphene to hydrogen radicals produced by the hot-filament process at low pressure and temperature. A sharp sp3-bonded carbon stretching mode was observed in ultraviolet Raman spectra at around 1344–1367 cm−1 while no sp2-bonded carbon peak was simultaneously detected. By replacing bi-layer graphene with few-layer graphene, diamanoid/graphene hybrids were formed from the partial conversion of few-layer graphene, due to the prevalent Bernal stacking sequence. Raman spectroscopy, electron diffraction, and Density Functional Theory calculations show that partial conversion generates twisted bi-layer graphene located at the interface between the upper diamanoid domain and the non-converted graphenic domain underneath. Carbon-hydrogen bonding in the basal plane of hydrogenated few-layer graphene, where carbon is bonded to a single hydrogen over an area of 150 μm2, was directly evidenced by Fourier transform infrared microscopy and the actual full hydrogenation of diamane was supported by first-principle calculations. Those results open the door to large-scale production of diamane, diamanoids, and diamanoid/graphene hybrids.

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Gao, Min, Yong-Qi Ding, and Jia-Bi Ma. "Experimental and Theoretical Study of N2 Adsorption on Hydrogenated Y2C4H− and Dehydrogenated Y2C4− Cluster Anions at Room Temperature." International Journal of Molecular Sciences 23, no. 13 (June 23, 2022): 6976. http://dx.doi.org/10.3390/ijms23136976.

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The adsorption of atmospheric dinitrogen (N2) on transition metal sites is an important topic in chemistry, which is regarded as the prerequisite for the activation of robust N≡N bonds in biological and industrial fields. Metal hydride bonds play an important part in the adsorption of N2, while the role of hydrogen has not been comprehensively studied. Herein, we report the N2 adsorption on the well-defined Y2C4H0,1− cluster anions under mild conditions by using mass spectrometry and density functional theory calculations. The mass spectrometry results reveal that the reactivity of N2 adsorption on Y2C4H− is 50 times higher than that on Y2C4− clusters. Further analysis reveals the important role of the H atom: (1) the presence of the H atom modifies the charge distribution of the Y2C4H− anion; (2) the approach of N2 to Y2C4H− is more favorable kinetically compared to that to Y2C4−; and (3) a natural charge analysis shows that two Y atoms and one Y atom are the major electron donors in the Y2C4− and Y2C4H− anion clusters, respectively. This work provides new clues to the rational design of TM-based catalysts by efficiently doping hydrogen atoms to modulate the reactivity towards N2.

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Cuevas, Jose Luis, Miguel Ojeda Martinez, and Saravana Prakash Thirumuruganandham. "Band-Gap Engineering: Lithium Effect on the Electronic Properties of Hydrogenated 3C-SiC (1 1 0) Surfaces." Batteries 8, no. 11 (November 18, 2022): 247. http://dx.doi.org/10.3390/batteries8110247.

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Silicon carbide has structural strength, high electronic conductivity, low diffusion barrier and high storage capacity, which are suitable for engineering applications such as lithium-ion batteries, electric vehicles, uninterruptible power supplies and SiC diodes. In particular, 3C-SiC monolayers oriented along the (1 1 0) crystallographic direction that could have symmetric surfaces have been poorly studied, as have the effects of surface passivation on their physical and electronic properties. In this work, we investigate the influence of lithium on the electronic properties of hydrogenated surfaces in 3C-SiC monolayers using density functional theory. We examine the electronic properties of surfaces fully passivated with hydrogen with those of surfaces fully passivated with lithium and those with mixed passivation. Our results show that only fully hydrogenated surfaces exhibit a direct band-gap, while the full Li, CH+SiLi, and H+Lic passivations exhibit metallic behavior. The CLi+SiH, H+1LiC, and H+1LiSi passivation systems decrease the band-gap compared to the hydrogenated case and show an indirect band-gap. The formation energy of the system shows that the most stable arrangement is full-H, followed by H+1LiC, and the most unstable system is full-Li, which has a positive formation energy.

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Castellanos, P., A. Candian, J. Zhen, H. Linnartz, and A. G. G. M. Tielens. "Photoinduced polycyclic aromatic hydrocarbon dehydrogenation The competition between H- and H2-loss." Astronomy & Astrophysics 616 (August 2018): A166. http://dx.doi.org/10.1051/0004-6361/201833220.

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Polycyclic aromatic hydrocarbons (PAHs) constitute a major component of the interstellar medium carbon budget, locking up to 10–20% of the elemental carbon. Sequential fragmentation induced by energetic photons leads to the formation of new species, including fullerenes. However, the exact chemical routes involved in this process remain largely unexplored. In this work, we focus on the first photofragmentation steps, which involve the dehydrogenation of these molecules. For this, we consider a multidisciplinary approach, taking into account the results from experiments, density functional theory (DFT) calculations, and modeling using dedicated Monte-Carlo simulations. By considering the simplest isomerization pathways — i.e., hydrogen roaming along the edges of the molecule — we are able to characterize the most likely photodissociation pathways for the molecules studied here. These comprise nine PAHs with clearly different structural properties. The formation of aliphatic-like side groups is found to be critical in the first fragmentation step and, furthermore, sets the balance of the competition between H- and H2-loss. We show that the presence of trio hydrogens, especially in combination with bay regions in small PAHs plays an important part in the experimentally established variations in the odd-to-even H-atom loss ratios. In addition, we find that, as PAH size increases, H2 formation becomes dominant, and sequential hydrogen loss only plays a marginal role. We also find disagreements between experiments and calculations for large, solo containing PAHs, which need to be accounted for. In order to match theoretical and experimental results, we have modified the energy barriers and restricted the H-hopping to tertiary atoms. The formation of H2 in large PAHs upon irradiation appears to be the dominant fragmentation channel, suggesting an efficient formation path for molecular hydrogen in photodissociation regions (PDRs).

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Chen, Tao, and Aigen Li. "Synthesizing carbon nanotubes in space." Astronomy & Astrophysics 631 (October 18, 2019): A54. http://dx.doi.org/10.1051/0004-6361/201935789.

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Context. As the fourth most abundant element in the universe, carbon (C) is widespread in the interstellar medium (ISM) in various allotropic forms (e.g. fullerenes have been identified unambiguously in many astronomical environments, the presence of polycyclic aromatic hydrocarbon molecules in space has been commonly acknowledged, and presolar graphite, as well as nanodiamonds, have been identified in meteorites). As stable allotropes of these species, whether carbon nanotubes (CNTs) and their hydrogenated counterparts are also present in the ISM or not is unknown. Aims. The aim of the present works is to explore the possible routes for the formation of CNTs in the ISM and calculate their fingerprint vibrational spectral features in the infrared (IR). Methods. We studied the hydrogen-abstraction and acetylene-addition (HACA) mechanism and investigated the synthesis of nanotubes using density functional theory (DFT). The IR vibrational spectra of CNTs and hydrogenated nanotubes (HNTs), as well as their cations, were obtained with DFT. Results. We find that CNTs could be synthesized in space through a feasible formation pathway. CNTs and cationic CNTs, as well as their hydrogenated counterparts, exhibit intense vibrational transitions in the IR. Their possible presence in the ISM could be investigated by comparing the calculated vibrational spectra with astronomical observations made by the Infrared Space Observatory, Spitzer Space Telescope, and particularly the upcoming James Webb Space Telescope.

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Yang, Tingting, Qian Xue, Xuewei Yu, Xueqiang Qi, Rui Wu, Shun Lu, Zhengrong Gu, Jinxia Jiang, and Yao Nie. "DFT Study on Methanol Oxidation Reaction Catalyzed by PtmPdn Alloys." Coatings 12, no. 7 (June 29, 2022): 918. http://dx.doi.org/10.3390/coatings12070918.

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Pt is widely used as the catalyst for methanol oxidation reaction (MOR) in direct methanol fuel cells (DMFC). However, the high cost and limited supply of pure Pt limit the commercialization of DMFC. Herein, MOR catalyzed by variously designed Pd-doped PtmPdn was studied with the density functional theory (DFT); the PtmPdn(111) surface was chosen since it is the most stable surface among various low-index surfaces. The hydrogens in methyl groups were priorly dehydrogenated on Pt(111), followed by hydrogen in the hydroxyl group. The effects of both the ratio of Pt:Pd and the type of the alloy on the activity of PtmPdn catalysts toward MOR were also studied; both ordered and disordered PtPd with the 1:1 ratio had better catalytic activity towards MOR than other catalysts. Specifically, the disordered Pt:Pdd with the Pt:Pd ratio of 1:1 had the best activity for the relatively stronger adsorption of COH, but the lowest binding with CO and a moderate d band center. The adsorptions of both COH and CO are key steps in the MOR, since the steps of CH3OH→CH2OH→CHOH→COH have downhill energy profiles, while COH→CO is an uphill reaction. In addition, the d band centers of the surface atoms move towards the Fermi level with the increase of the Pd content; the d band can also be tuned by changing the atom arrangement. These findings can be used as rules to design high-performance catalysts for MOR.

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40

Vanka, Kumar, Zhitao Xu, and Tom Ziegler. "A combined density functional theory and molecular mechanics (QM/MM) study of single site ethylene polymerization catalyzed by [Cp{NC(t-Bu)2}TiR+] in the presence of the counterion (CH3B(C6F5)3)1." Canadian Journal of Chemistry 81, no. 11 (November 1, 2003): 1413–29. http://dx.doi.org/10.1139/v03-177.

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Calculations have been carried out to investigate the insertion of the ethylene monomer into the Tialkyl bond for the systems CpNC(t-Bu)2RTi-µ-Me-B(C6F5)3 (R = Me and Pr), using density functional theory. A validated QM/MM model was used to represent the counterion. The tertiary butyl groups in the ligands were modeled with QM/MM, with hydrogens being used as the capping atoms. Solvent effects were incorporated with single point solvent calculations done with cyclohexane (ε= 2.023) as the solvent. With R = Me (the initiation step), approach of the ethylene cis and trans to the -µ-Me bridge was considered. Insertion was found to be endothermic, with ΔHtot being 12.7 kcal/mol (cis) and 15.5 kcal/mol (trans). The propagation step was then studied for the contact ion pair CpNC(t-Bu)2PrTi-µ-Me-B(C6F5)3 (4). Different conformations of the propyl chain in 4 were considered by altering θ, the dihedral angle formed between the Cβ-Cα-Ti and the Cα-Ti-µC planes. The resting states were found to be at θ = 69° (4a), 177° (4b), and 53° (4c). A maxima was found near θ = 0° (4d). The cis and trans approaches of the ethylene monomer were considered for each of the four cases. The cis approach towards 4a and trans approach towards 4d led to insertion, with displacement of the counterion from the metal centre. The insertion barriers were found to be 17.8 kcal/mol, for the cis approach towards 4b and 16.4 kcal/mol for the trans approach towards 4d. The cis approaches towards conformers 4a and 4c showed common characteristics, with uptake barriers being higher than the subsequent insertion barriers in the two cases. Uptake barriers were 13.6 kcal/mol {TS(4a7a)} and 10.7 kcal/mol {TS(4c8a)}. The corresponding insertion barriers were 11.8 kcal/mol {TS(7a13a)} and 8.4 kcal/mol {TS(8a13a)}. The trans approaches towards conformers 4a and 4c led to insertion barriers of about 15.1 kcal/mol (lower than for the 4b and 4d cases). The cis approach towards 4d and trans approach towards 4b were found to lead to hydrogen transfer from the propyl chain to monomer, terminating the chain. Termination barriers were high greater than 19.0 kcal/mol. This suggested that ethylene insertion would be favoured over termination during the propagation step.Key words: homogeneous catalysis, counterion, initiation, propagation, termination.

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Partovi-Azar, Pouya, and Daniel Sebastiani. "Minimal Optimized Effective Potentials for Density Functional Theory Studies on Excited-State Proton Dissociation." Micromachines 12, no. 6 (June 10, 2021): 679. http://dx.doi.org/10.3390/mi12060679.

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Recently, a new method [P. Partovi-Azar and D. Sebastiani, J. Chem. Phys. 152, 064101 (2020)] was proposed to increase the efficiency of proton transfer energy calculations in density functional theory by using the T1 state with additional optimized effective potentials instead of calculations at S1. In this work, we focus on proton transfer from six prototypical photoacids to neighboring water molecules and show that the reference proton dissociation curves obtained at S1 states using time-dependent density functional theory can be reproduced with a reasonable accuracy by performing T1 calculations at density functional theory level with only one additional effective potential for the acidic hydrogens. We also find that the extra effective potentials for the acidic hydrogens neither change the nature of the T1 state nor the structural properties of solvent molecules upon transfer from the acids. The presented method is not only beneficial for theoretical studies on excited state proton transfer, but we believe that it would also be useful for studying other excited state photochemical reactions.

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Attia, Amr A. A., Alexandru Lupan, and R. Bruce King. "Tetracarbaboranes: nido structures without bridging hydrogens." Dalton Transactions 45, no. 46 (2016): 18541–51. http://dx.doi.org/10.1039/c6dt03507h.

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The structures and energetics of the tetracarbaboranes C₄B_n−4H_n (n = 6 to 13) have been investigated by density functional theory. In general, the lowest energy structures of the tetracarbaboranes C₄B_n−4H_n minimize the number of C–C polyhedral edges as well as the degrees of the carbon vertices.

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43

Быстров, В. С., and V. S. Bystrov. "Компьютерные исследования наноструктур гидроксиапатита, их особенности и свойства." Mathematical Biology and Bioinformatics 12, no. 1 (January 16, 2017): 14–54. http://dx.doi.org/10.17537/2017.12.14.

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In this review paper the main approaches to modeling the hydroxyapatite (HAP) structures and first-principle calculations of their properties, pure and with various defects, are considered. First, the HAP nano-particles (NPs) and clusters peculiarities are described using different methods: molecular mechanical and quantum mechanical, especially semi-empirical such as PM3. Both approximations used here, namely, restricted Hartee-Fock (RHF) and unrestricted Hartee-Fock (UHF), are considered. The influence of the protons (hydrogens), contained in the surrounding medium (pH), on the formation of HAP nanoparticles of various sizes and shapes is considered and discussed. Second, the HAP crystal unit cells studies are considered on the basis of a density functional theory (DFT) modelling. The main peculiarities of both phases (hexagonal and monoclinic) are considered too, including their ordered and disordered substructures. One of the important aspects of the computer modeling of HAP is to build the models and consider various structural modifications of HAP (such as, vacancies of oxygen atoms and hydroxyl OH group, hydrogen interstitials and different substitutions of atoms in HAP unit cell), which allow explicitly creating and exploring the changes in the charges of HAP and the electrical potential on the HAP surface. HAP modifications are most close to biological HAP and therefore are necessary for implant medical applications and can create and functionalize HAP surface with most adhesive properties for living cells (osteoblasts, osteoclatst). This improves the HAP implant quality. Besides, it has recently been established that oxygen vacancy in HAP influences their photo-catalytic properties. It is important for HAP usage as in environmental remediation and for bacteria inactivation. Therefore it is very important to create and investigate the oxygen vacancy models in HAP, and others defects models. In this work we review a DFT modelling and studies of HAP, both pure perfect bulk and imperfect bulk cases. Special HAP modelling approaches are used for layered slab super-cells units, which include vacuum spaces between the layered slabs forming HAP surface. To all these computer studies the first principle calculations were applied. In this review various DFT approximations are analysed for bulk and surface modified HAP. These approximations are carried out using both the local basis (local density approximation – LDA, in AIMPRO codes) and the plane-waves (generalized gradient approximation – GGA, in VASP codes). Data of all structures and models of HAP defects investigated are widely analyzed.

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Motiu, Stefan, Daniela Dogaru, and Valentin Gogonea. "Reactivation pathway of the hydrogenase H-cluster: Density functional theory study." International Journal of Quantum Chemistry 107, no. 5 (2007): 1248–52. http://dx.doi.org/10.1002/qua.21236.

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YANCEY, JEREMY A., M. A. NOVOTNY, and STEVEN R. GWALTNEY. "SMALL PURE CARBON MOLECULES WITH SMALL-WORLD NETWORKS USING DENSITY FUNCTIONAL THEORY SIMULATIONS." International Journal of Modern Physics C 20, no. 09 (September 2009): 1345–56. http://dx.doi.org/10.1142/s0129183109014412.

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The possible existence of small, pure carbon molecules based on small-world networks is addressed using density functional theory simulations. A ring of atoms with one or more small-world connections between pairs of non-nearest-neighbor sites was chosen for the network topology. The small-world connections are made with and without additional carbon atoms placed along the link. The energy per atom of these small-world carbon systems is compared with benchmark molecules such as the C 20 ring, bowl, and cage isomers, the C 60 Buckyball, monocyclic pure carbon rings ranging from C 4 to C 60, bare linear carbon chains ranging from C 2 to C 36, and various graphitic fragments without hydrogens. The results of the energy per atom for some of these small-world clusters provide an indication that such pure carbon molecules are reasonable for real world synthesis.

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Susnow, Roberta G., Anthony M. Dean, and William H. Green. "Hydrogen abstraction rates via density functional theory." Chemical Physics Letters 312, no. 2-4 (October 1999): 262–68. http://dx.doi.org/10.1016/s0009-2614(99)00912-4.

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Hamann, D. R. "H2O hydrogen bonding in density-functional theory." Physical Review B 55, no. 16 (April 15, 1997): R10157—R10160. http://dx.doi.org/10.1103/physrevb.55.r10157.

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Pan, Xiao-Yin, and Viraht Sahni. "Quantal density functional theory of the hydrogen molecule." Journal of Chemical Physics 120, no. 12 (March 22, 2004): 5642–49. http://dx.doi.org/10.1063/1.1647514.

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T, Mavromoustakos. "Spectroscopic and Computational Study of the Ugi Cinnamic Adduct NGI25." Advance Research in Organic and Inorganic Chemistry (AROIC) 3, no. 1 (February 14, 2022): 1–2. http://dx.doi.org/10.54026/aroic/1006.

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The structure assignment and conformational analysis of cinnamic derivative N-benzyl-N-(2-(cyclohexylamino)-2-oxoethyl) cinnamamide (NGI25) was carried out through Nuclear Magnetic Resonance (NMR) spectroscopy, Molecular Dynamics (MD) and Quantum Mechanics (QM), i.e., semiempirical and Density Functional Theory (DFT) calculations. Specifically, homonuclear (2D-COSY, 2D-NOESY) and heteronuclear (2D-HSQC, 2D-HMBC) spectra were obtained. Through them, the resonant values of the hydrogens and their constituent carbons were identified. After structure identification, NGI25 was subjected to computational calculations to reveal its most favorable conformations. QM, MD were in agreement with the spatial correlations that were observed in 2D-NOESY spectra.

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Xu, Hong, and Jean-Pierre Hansen. "Density-functional theory of pair correlations in metallic hydrogen." Physical Review E 57, no. 1 (January 1, 1998): 211–23. http://dx.doi.org/10.1103/physreve.57.211.

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

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