Ab Initio Analysis Research Articles

Speciation and Reactivity Control of Cu-Oxo Clusters via Extraframework Al in Mordenite for Methane Oxidation.

The stoichiometric conversion of methane to methanol by Cu-exchanged zeolites can be brought to highest yields by the presence of extraframework Al and high CH4 chemical potentials. Combining theory and experiments, the differences in chemical reactivity of monometallic Cu-oxo and bimetallic Cu-Al-oxo nanoclusters stabilized in zeolite mordenite (MOR) are investigated. Cu-L3 edge X-ray absorption near-edge structure (XANES), infrared (IR), and ultraviolet-visible (UV-vis) spectroscopies, in combination with CH4 oxidation activity tests, support the presence of two types of active clusters in MOR and allow quantification of the relative proportions of each type in dependence of the Cu concentration. Ab initio molecular dynamics (MD) calculations and thermodynamic analyses indicate that the superior performance of materials enriched in Cu-Al-oxo clusters is related to the activity of two μ-oxo bridges in the cluster. Replacing H2O with ethanol in the product extraction step led to the formation of ethyl methyl ether, expanding this way the applicability of these materials for the activation and functionalization of CH4. We show that competition between different ion-exchanged metal-oxo structures during the synthesis of Cu-exchanged zeolites determines the formation of active species, and this provides guidelines for the synthesis of highly active materials for CH4 activation and functionalization.

Physical, chemical and antibacterial properties of benzethonium chloride: Experimental and ab-initio analysis

The present study investigates the properties of benzethonium chloride compound using experimental analysis (NMR, FT-Raman/FTIR, TGA/DTG and DSC) and DFT method. Three molecular structures (BZT, BZT-Cl and BZT-Cl-H2O) were considered and optimized using 6–311++G** method. The computed theoretical shifts depicted an excellent matching with 13C and 1HNMR peaks, as well for FT-Raman and FTIR spectroscopic data. On the other hand, it was found that BZT-Cl compound has a higher polarizability (α) along z-direction when compared to BZT and BZT-Cl-H2O; while adding of chlorine and water molecule increase significantly the total first-order hyper-polarizability (β). The electrostatic mapping potential depicted that chlorine and water enhanced the nucleophile character. The HOMO-LUMO energies and reactivity parameters significantly change in BZT-Cl and BZT-Cl-H2O. Furthermore, the thermal analysis showed a good stability up to 160 °C. Finally, antibacterial tests against several strains demonstrated an excellent activity and a mechanism structure/activity was proposed.

Nonradiative Dynamics Induced by Vacancies in Wide-Gap III-Nitrides: Ab Initio Time-Domain Analysis.

Insightful understanding of defect properties and prevention of defect damage are among the biggest issues in the development of photoelectronic devices based on wide-gap III-nitride semiconductors. Here, we have investigated the vacancy-induced carrier nonradiative dynamics in wide-gap III-nitrides (GaN, AlN, and AlxGa1-xN) by ab initio molecular dynamics and nonadiabatic (NA) quantum dynamics simulations since the considerable defect density in epitaxy samples. E-h recombination is hardly affected by Vcation, which created shallow states near the VBM. Our findings demonstrate that VN in AlN creates defect-assisted nonradiative recombination centers and shortens the recombination time (τ) as in the Shockley-Read-Hall (SRH) model. In GaN, VN improves the NA coupling between the CBM and the VBM. Additionally, increasing x in the AlxGa1-xN alloys accelerates nonradiative recombination, which may be an important issue in further improving the IQE of high Al-content AlxGa1-xN alloys. These findings have significant implications for the improvement of wide-gap III-nitrides-based photoelectronic devices.

Proton-Tunneling Dynamics along Low-Barrier Hydrogen Bonds: A Full-Dimensional Instanton Study of 6-Hydroxy-2-formylfulvene.

Understanding the dynamics of proton transfer along low-barrier hydrogen bonds remains an outstanding challenge of great fundamental and practical interest, reflecting the central role of quantum effects in reactions of chemical and biological importance. Here, we combine ab initio calculations with the semiclassical ring-polymer instanton method to investigate tunneling processes on the ground electronic state of 6-hydroxy-2-formylfulvene (HFF), a prototypical neutral molecule supporting low-barrier hydrogen-bonding. The results emerging from a full-dimensional ab initio instanton analysis reveal that the tunneling path does not pass through the instantaneous transition-state geometry. Instead, the tunneling process involves a multidimensional reaction coordinate with concerted reorganization of the heavy-atom skeletal framework to substantially reduce the donor-acceptor distance and drive the ensuing intramolecular proton-transfer event. The predicted tunneling-induced splittings for HFF isotopologues are in good agreement with experimental findings, leading to percentage deviations of only 20-40%. Our full-dimensional results allow us to characterize vibrational contributions along the tunneling path, highlighting the intrinsically multidimensional nature of the attendant hydron-migration dynamics.

Theoretical investigation on the structure-activity relationship for methane activation in Cu-CHA zeolite

The active sites and structure–activity relationship for methane activation over Cu-CHA were investigated by Density Functional Theory (DFT) calculations. [CuOCu]2+, [CuO2Cu]2+, [CuOH]+ and [CuO]+ were employed as possible active sites, but the Ab initio thermodynamics analysis results indicate that [CuO]+ is thermodynamically prohibitive. Methane activation in Cu-CHA proceeds through a homolytic mechanism, and the activity of Cu complexes in CH bond activation of methane follows the sequence [CuOH]+ (doublet) < [CuOCu]2+ (triplet) < [Cu2O2]2+ (triplet) in the six-member ring (6MR) and eight-member ring (8MR). In addition, the structure–activity relationship was established: The more reactive site is due to the ability to stabilize the methyl radical intermediate.

He+ +N2 Charge Transfer Reaction: An Ab initio Analysis.

An ab initio analysis on the involved potential energy surfaces is presented for the investigation of the charge transfer mechanism for the He+ +N2 system. At high collision energy, as many as seven low-lying electronic states are observed to be involved in the charge transfer mechanism. Potential energy surfaces for these low-lying electronic states have been computed in the Jacobi scattering coordinates, applying multireference configuration interaction level of theory and aug-cc-pVQZ basis sets. Asymptotes for the ground and various excited states are assigned to mark the entrance (He+ +N2 ) and charge transfer channels (He+N2 + ). Nonadiabatic coupling matrix elements and quasi-diabatic potential energy surfaces have been computed for all seven states to rationalize the available experimental data on the charge transfer processes and to facilitate dynamics studies.

Nanoarhitectonics of Inorganic-Organic Silica-Benzil Composites: Synthesis, Nanocrystal Morphology and Micro-Raman Analysis.

The synthesis of nanosized organic benzil (C6H5CO)2 crystals within the mesoporous SiO2 host matrix was investigated via X-ray diffraction, transmission electron microscopy, Raman spectroscopy, and ab initio lattice dynamics analysis. Combining these methods, we have proved that the main structural properties of benzil nanocrystals embedded into SiO2 host membranes with pore diameters of 6.0, 7.8, 9.4, and 13.0 nm are preserved compared to a bulk benzil crystal. Space confinement has an insignificant impact on the lattice vibrational properties of benzil crystals implanted into the host matrices. The ab initio lattice dynamics calculation of the phonon spectrum in the Brillouin zone center shows the mechanical and dynamical stability of benzil lattice, revealing very low optical frequency of 11 cm-1 at point Γ.

Theoretical Investigation of the Electrochemical Oxidation of H2 and CO Fuels on a Ruddlesden-Popper SrLaFeO4-δ Anode.

The electrochemical oxidation of H2 and CO fuels have been investigated on the Ruddlesden-Popper layered perovskite SrLaFeO4-δ (SLF) under anodic solid oxide fuel cell conditions using periodic density functional theory and microkinetic modeling techniques. Two distinct FeO2-plane-terminated surface models differing in terms of the underlying rock salt layer (SrO or LaO) are used to identify the active site and limiting factors for the electro-oxidation of H2, CO, and syngas fuels. Microkinetic modeling predicted an order of magnitude higher turnover frequency for the electro-oxidation of H2 compared to CO for SLF at short-circuit conditions. The surface model with an underlying SrO layer was found to be more active with respect to H2 oxidation than the LaO-based surface model. At an operating voltage of less than 0.7 V, surface H2O/CO2 formation was found to be the key rate-limiting step, and the surface H2O/CO2 desorption was the key charge transfer step. In contrast, the bulk oxygen migration process was found to affect the overall rate at high cell voltage conditions above 0.9 V. In the presence of syngas fuel, the overall electrochemical activity is derived mainly from H2 electro-oxidation and CO2 is chemically shifted to CO via the reverse water-gas shift reaction. Substitutional doping of a surface Fe atom with Co, Ni, and Mn revealed that the H2 electro-oxidation activity of FeO2-plane terminated anodes with an underlying LaO rock salt layer can be improved with dopant introduction, with Co yielding a three orders of magnitude higher activity relative to the undoped LaO surface model. Constrained ab initio thermodynamic analysis furthermore suggested that the SLF anodes are resistant toward sulfur poisoning both in the presence and absence of dopants. Our findings reflect the role of various elements in controlling the fuel oxidation activity of SLF anodes that could aid the development of new Ruddlesden-Popper phase materials for fuel cell applications.

Ab-initio analysis of Li adsorption on boron doped armchair silicon carbide nanoribbon for lithium ion batteries (LIBs)

It is well known that the electrochemical storage capacity of anode materials can be modified by the doping of heteroatom. Here, first-principles approach is used to investigate the adsorption energy (Eads), open circuit voltage (OCV), and storage capacity of boron co-doped armchair silicon carbide anode (B-ASiCNR) material for Li ion battery. When B atoms are doped at the center of the armchair silicon carbide nanoribbon (ASiCNR), new energy states emerge and it results in Fermi-Level shift towards the valence band. The binding strength of a single Li atom is significantly higher in B-ASiCNR because of B atom doping. The open circuit voltage decreases from 3.76 V to 2.34 V when Li atoms adsorbed from first hexagonal position to all hole position of the substrate. Calculations reveal that the storage capacity of B-ASiCNR reached to the maximum value of 836 mAhg−1 when all hole positions are adsorbed by Li atoms. Calculated Eads, OCV, storage capacity suggest that the B-ASiCNR can be used as future anode materials for Li ion battery.

New insights into the mechanism of reactive adsorption desulfurization on Ni/ZnO catalysts: Theoretical evidence showing the existence of interfacial sulfur transfer pathway and the essential role of hydrogen

As well known in the petroleum industry and academia, Ni/ZnO catalysts have excellent desulfurization performance. However, the sulfur transfer mechanism of reactive adsorption desulfurization (RADS) that occurs on Ni/ZnO catalysts remains controversial. Herein, a periodic Ni nanorod supported on ZnO slab was built to represent the Ni/ZnO system, and density functional theory calculations were performed to study the sulfur transfer process and the role of H2 within the process. The results elucidate that the direct solid-state diffusion of S from Ni to interfacial oxygen vacancies (Ov) is more favorable than the hydrogenation of S to SH/H2S on Ni and the subsequent H2S desorption, and accordingly, H2O is produced on Ni rather than on ZnO. Ab initio thermodynamics analysis shows that the hydrogen atmosphere applied in preparing Ni/ZnO catalysts greatly promotes the Ov formation on ZnO surface, which accounts for the presence of interfacial Ov in freshly prepared catalysts. Under RADS condition, hydrogenation of interfacial O atoms to form O−H groups facilitates the reverse spillover of these lattice O atoms from ZnO to Ni, accompanied with the interfacial Ov generation. In contrast to the classic S transfer mechanism via H2S, the present work clearly demonstrates that the interfacial S transfer is a feasible reaction pathway in the RADS mechanism. More importantly, the existence of interfacial Ov is an essential prerequisite for this interfacial S diffusion, and H2 plays a key role in facilitating the Ov formation.

Construction of adiabatic vis-á-vis quasi-diabatic surfaces of He+ + CO system for the investigation of charge transfer reaction

The charge transfer process, He+ + CO → He + CO+, is one of the often-seen events in high energy collisions that correspond to typical solar wind conditions. At MRCI/aug-cc-pVQZ level of theory, an elaborate ab initio analysis involving the lowest nine electronic states for the system has been conducted to identify and investigate the involved potential energy surfaces for the charge transfer process. The reaction is caused by non-adiabatic interactions among all the nine electronic states. The nonadiabatic couplings and the associated quasi-diabatic surfaces have also been computed using ab initio procedure. The strength of the non-adiabatic couplings corroborates the experimental findings on different probable charge transfer channels.

Synthesis and analysis of novel catecholic ligands as inhibitors of catechol-O-methyltransferase

l-DOPA, a dopamine precursor, is commonly used as a treatment for patients with conditions such as Parkinson’s disease. This therapeutic l-DOPA, as well as the dopamine derived from l-DOPA, can be deactivated via metabolism by catechol-O-methyltransferase (COMT). Targeted inhibition of COMT prolongs the effectiveness of l-DOPA and dopamine, resulting in a net increase in pharmacological efficiency of the treatment strategy. Following the completion of a previous ab initio computational analysis of 6-substituted dopamine derivatives, several novel catecholic ligands with a previously unexplored neutral tail functionality were synthesized in good yields and their structures were confirmed. The ability of the catecholic nitriles and 6-substituted dopamine analogues to inhibit COMT was tested. The nitrile derivatives inhibited COMT most effectively, in agreement with our previous computational work. pKa values were used to further examine the factors involved with the inhibition and molecular docking studies were performed to support the ab initio and experimental work. The nitrile derivatives with a nitro substituent show the most promise as inhibitors, confirming that both the neutral tail and the electron withdrawing group are essential on this class of inhibitors.

Molecular Bridge Engineering for Tuning Quantum Electronic Transport and Anisotropy in Nanoporous Graphene

Recent advances on surface-assisted synthesis have demonstrated that arrays of nanometer wide graphene nanoribbons can be laterally coupled with atomic precision to give rise to a highly anisotropic nanoporous graphene structure. Electronically, this graphene nanoarchitecture can be conceived as a set of weakly coupled semiconducting 1D nanochannels with electron propagation characterized by substantial interchannel quantum interferences. Here, we report the synthesis of a new nanoporous graphene structure where the interribbon electronic coupling can be controlled by the different degrees of freedom provided by phenylene bridges that couple the conducting channels. This versatility arises from the multiplicity of phenylene cross-coupling configurations, which provides a robust chemical knob, and from the interphenyl twist angle that acts as a fine-tunable knob. The twist angle is significantly altered by the interaction with the substrate, as confirmed by a combined bond-resolved scanning tunneling microscopy (STM) and ab initio analysis, and should accordingly be addressable by other external stimuli. Electron propagation simulations demonstrate the capability of either switching on/off or modulating the interribbon coupling by the corresponding use of the chemical or the conformational knob. Molecular bridges therefore emerge as efficient tools to engineer quantum transport and anisotropy in carbon-based 2D nanoarchitectures.

Adsorption of 40 low molecular weight drugs on pristine and fluorinated C60 fullerenes: Ab initio, statistical and neural networks analysis

Loading of 40 small drugs molecules with molecular weights in 47–210 g/mol range consisted of H, C, N, O, F, S elements on C60, C60F2 and C60F48 fullerenes are studied with the density functional theory. Adsorption energies as well as deformation energies of fullerenes and drugs are calculated. The C60F2 is recognized as the most active drugs adsorbent. Mean adsorption energies averaged over all considered drugs are 0.41, 0.59 and 0.54 eV with standard deviations of 0.10, 0.09 and 0.14 eV for C60, C60F2 and C60F48 fullerenes, respectively. Mean energies of drug-induced deformations of C60, C60F2 and C60F48 are 8.6, 12.0 and 16.6 meV, respectively. Multilinear regressions and neural networks were proposed for prediction of adsorption energies based on dipole moments and frontier molecular orbitals of the drugs. Achievable accuracy of such predictions is about 0.1 eV. Altretamine antibiotic is recognized as the notable drug possessing extremely high binding energies about 1 eV with fullerenes. Infrared spectral shifts due to its loading on fullerene carriers are calculated.

Current transmission pathways in potassium intercalated graphene

Carbon-based conductors are the focus of considerable research investigating the material roles and transport mechanisms which determine current transmission performance. Ab initio analysis of the potassium–graphene system suggests that neither material constituent should be cast in a subordinate current transmission role. When the dopant density is low, the potassium atoms perform a conventional doping function, improving the conductivity of the current carrying carbon substrate via charge transfer. As the doping density increases, the potassium atoms begin to form a second transmission pathway, complimenting the carbon substrate pathway and contributing to the net current transport. At the highest modeled dopant density, corresponding to the well known KC8 structure studied in various experiments, the potassium atoms form a parallel and nominally independent current transmission network, whose contribution to electron transport approximately matches that of the underlying graphene. Consistent with published experimental data on doped nanowires, the modeling results show that conductivity is a sensitive function of potassium concentration. The sensitivity is due to an internal state transition, not subject to direct experimental measurement, which strongly influences nanocomposite conductor performance.

Dissecting amide-I vibrations in histidine dipeptide

The amide-I vibrational characteristics and conformational preferences of the model compound - histidine dipeptide (Ac-His-NHCH3, HISD) in gas phase and solution have been revealed with the help of ab initio calculations and wavefunction analyses. The Gibbs free energy surfaces (FESs) of solvated HISD were smoothed by solvent effect to exhibit different structural populations concerning various external environments. It was shown that the most stable conformations of HISD in CHCl3 and gas phase are C7eq, while those in DMSO and water are β and PPII, respectively. Compared with ALAD, the number of accessible conformational states on these FESs was predicted to be reduced due to the steric effect of imidazole group. The two amide-I normal modes of HISD were found to have intrinsically secondary structural dependencies, and be sensitive to surrounding environments. The average amide-Ia frequencies of HISD isomers in these environments were predicted to be almost the same as those of ALAD, while the amide-Ib mean frequencies were estimated to be lower than ALAD due to the intramolecular interactions between the imidazole group and amino-terminal amide unit. The good linear correlations between amide-I frequencies and the atomic electrostatic potentials (ESPs) of amide groups were also found to interpret the solvent-induced amide-I frequency shifts of HISD at the electronic structure level. These results allow us to gain a deep understanding of amide-I vibrations of HISD, and would be helpful for the site-specific conformational monitoring and spectral interpretation of solvated polypeptides.

Role of Fluxionality and Metastable Isomers in the ORR Activity: A Case Study

Understanding the dynamic reconstruction of active sites and the fluxional behavior of subnanoclusters has become the heart of operando modeling techniques. An accurate description of catalysis phenomena extends toward incorporating the activity of thermally accessible ensembles of metastable isomers in addition to the global minima (GM). Considering the Pt13 cluster as a model catalyst for gas-phase oxygen reduction reaction (ORR), we have studied the role of metastable isomers and unravelled their distinct catalyst dynamics leading to high fluxionality. The different adsorption energetics and ORR activity featured by the metastable isomers reveal the importance of addressing the fluxional behavior of subnanoclusters. A detailed mechanistic ORR investigation provided isomers possessing an activity comparable to GM. Furthermore, a statistical ensemble representation demonstrates the substantial role of metastable isomers within 0.4 eV relative energy difference from GM, with negligible activity enhancement of isomers with high energy at 300 K. Ab initio thermodynamics-based stability analysis represents different energetics associated with the Pt13 clusters at high oxygen coverage. This study highlights the importance of exploring the role of metastable isomers in determining the cumulative catalytic activity of subnanometer clusters.

Nanointerconnect design based on edge fluorinated/hydrogenated zigzag borophene nanoribbons: an ab initio analysis.

Using an ab initio framework and non-equilibrium Green's function technique, the effect of hydrogen and fluorine atom passivation on the electronic and transport properties of borophene nanoribbons (BNRs) are explored. For zigzag edge states, we have explored all potentially stable combinations of hydrogen and fluorine passivation. Fluorine passivation leads to thermodynamically stable structures with improved stability for the increased concentration of F atoms, according to our binding energy (Eb) calculations. Furthermore, density-of-states and dispersion relation (E-k structures) computations indicate that fluorine-passivated BNRs are primarily metallic in nature. We proposed these nanostructures for their use in metal interconnects because of their increased metallicity. We have used the typical two-probe setup to calculate the critical parameters like quantum resistance (RQ), kinetic inductance (LK), and quantum capacitance (CQ) to evaluate their performance as metal interconnects. Because they have the lowest estimated values of LK = 26.1 nH μm-1, and CQ = 399 pF cm-1, the zigzag BNRs (ZBNRs) with two edge fluorinated (F-BNR-F) nanostructures may be considered as a promising candidate for nanoscale interconnect applications.

Locking water molecules via ternary O-H⋯O intramolecular hydrogen bonds in perhydroxylated closo-dodecaborate.

A multitude of applications related to perhydroxylated closo-dodecaborate B12(OH)122- in the condensed phase are inseparable from the fundamental mechanisms underlying the high water orientation selectivity based on the base B12(OH)122-. Herein, we directly compare the structural evolution of water clusters, ranging from monomer to hexamer, oriented by functional groups in the bases B12H122-, B12H11OH2- and B12(OH)122- using multiple theoretical methods. A significant revelation is made regarding B12(OH)122-: each additional water molecule is locked into the intramolecular hydrogen bond B-O-H ternary ring in an embedded form. This new pattern of water cluster growth suggests that B-(H-O)⋯H-O interactions prevail over the competition from water-hydrogen bonds (O⋯H-O), distinguishing it from the behavior observed in B12H122- and B12H11OH2- bases, in which competition arises from a mixed competing model involving dihydrogen bonds (B-H⋯H-O), conventional hydrogen bonds (B-(H-O)⋯H-O) and water hydrogen bonds (O⋯H-O). Through aqueous solvation and ab initio molecular dynamics analysis, we further demonstrate the largest water clusters in the first hydrated shell with exceptional thermodynamic stability around B12(OH)122-. These findings provide a solid scientific foundation for the design of boron cluster chemistry incorporating hydroxyl-group-modified borate salts with potential implications for various applications.

Two phases of trans-stilbene in a polystyrene matrix.

Variability in the spectral properties of solid conformations of stilbene under various external conditions still remains obscure. The photophysical properties of trans-stilbene solution in solid polystyrene glass have been studied by absorption and time-resolved fluorescence. Concentration-induced quenching has been observed for small concentrations of stilbene. At large concentrations, the spectroscopic characteristics become split between the two phases of the sample: single-molecule properties are responsible for absorption, while the micro-crystalline phase dominates in fluorescence. Ab initio and molecular dynamics analyses suggest permanent twisting of the stilbene molecular structure upon crystallization, which supports spectroscopic phase separation.