Ab Initio Molecular Calculations Research Articles

Size-Dependent Formation of an Ion Pair in HSO4-(H2O) n: A Molecular Model for Probing the Microsolvation of Acid Dissociation.

With a p Ka of 2.0, HSO4- is not a strong acid as its dissociation percentage is only ∼10% in a solution of 1 M. However, our ab initio molecular dynamics and density functional theory calculations show that acid dissociation in the hydrate clusters, HSO4-(H2O) n, is quite facile at moderate sizes. It starts at around n = 12 and is completed by n = 16 when the energetics becomes very favorable. The dissociation explains the significant broadening at n = 16 in the S═O stretching region of the previously reported infrared photodissociation spectra for HSO4-(H2O) n as the solvation shell is tightened around the sulfate dianion and the proton. More importantly, HSO4-(H2O) n should provide an ideal model to probe the molecular details involved in an acid dissociation process.

The experimental and theoretical insights towards the CO induced Pd-Graphene and their multifunctional energy conversion applications

Here, CO gas environment has been used for reduction of graphene oxide (GO) and Pd precursor for preparation of varieties of Pd Nanostructures (PdNSs) with different shapes, size and surface morphologies on graphene support (RG-PdNSs). The extensive ab-initio Molecular Dynamics (MD) simulations and electronic structure calculations have been carried to get theoretical insight for the reduction process of GO by CO. The reduction of GO by CO as observed in experiment are confirmed by ab-initio MD snapshots at different time steps, energetic of the process and the Partial Density of States character of O2p orbital of GO before and after interaction with CO. The discrete states in the Partial Density of States of O2p orbital after CO attack indicates detachment of O from GO. The as-prepared RG-PdNSs are thoroughly characterized by different techniques. The simulation reveals the change in electronic properties from semi-metallic in pristine graphene to metallic due to the attachment of Pd in RG-PdNSs. The electrocatalytic activity of the as-synthesized nanostructures has been investigated toward the multi-functional energy conversion applications, the methanol oxidation reaction, formic acid oxidation reaction and oxygen reduction reaction. The RG-PdNSs exhibit excellent electrocatalytic performance compared to that of unsupported PdNSs and commercial Pd/C.

Unexpected chemistry from the homogeneous thermal decomposition of acetylene: An ab initio study

The formation of the aromatic ring during the formation of polycyclic aromatic hydrocarbons (PAHs) remains controversial and the experimental evidence is still lacking. Moreover, the formation mechanism of benzene from acetylene in the gas phase has also puzzled organic chemists for decades. Here, ab initio molecular dynamics simulations and electronic structure calculations provide compelling evidence for an unexpected competitive reaction pathway in which the aromatic ring is formed through successive additions of vinylidene. Moreover, no collisions cause bond dissociation of the acetylene molecule during the formation of benzene in this work. This study reveals the key role for the vinylidene carbene and determines the lifetime of vinylidene.

Exploring a Novel Atomic Layer with Extremely Low Lattice Thermal Conductivity: ZnPSe3 and Its Thermoelectrics

We survey the thermodynamic stabilities and properties, electronic transports, and thermoelectric possibilities of two-dimensional (2D) ZnPS3 and ZnPSe3, belonging to transition-metal phosphorus trichalcogenides, by employing the first-principles electronic structure calculation. Our first-principles calculation accompanying ab initio molecular dynamics and phonon calculation predicts that a single-layer (1L-) ZnPSe3 would be thermodynamically stable; in addition, electron and hole mobilities of 1L-ZnPSe3 amount to ∼440 and ∼400 cm2 V–1 s–1, respectively, which are comparable to 1L-MoS2. More interestingly, the lattice thermal conductivity of 1L-ZnPSe3 is found to be lower than any other 2D material, which could reach the lowest, i.e., ∼0.13 W m–1 K–1 at room temperature. In contrast, the thermoelectric figure of merit of the pristine 1L-ZnPSe3 is just ∼0.8 under optimal condition. Nevertheless, this is a very promising indication for a thermoelectric application of 1L-ZnPSe3 because other elements to det...

Revealing the Size Effect of Platinum Cocatalyst for Photocatalytic Hydrogen Evolution on TiO2 Support: A DFT Study

In heterogeneous catalysis metal particle morphology and size can influence markedly the activity, both in heat-driven and in electro-photocatalytic conditions. Because of the intimate coupling between the photoelectron transfer and the surface catalytic reaction, it has been challenging to determine the optimal metal particle size in photocatalytic reactions. Here, we utilize ab initio molecular dynamics and hybrid density functional theory calculations to reveal the size-dependent activity of photocatalytic hydrogen evolution reaction (HER) over Pt/TiO2 photocatalysts. By supporting four different Pt particles Pt5, Pt8, Pt13, and Pt19 on anatase TiO2(101), we determine the optimal geometries, the electronic structures, the photoelectron-transfer efficiency, and the surface hydrogen coupling reaction activity of these composite materials. We demonstrate that very small Pt clusters with less than two atomic layers are efficient photoelectron collectors from TiO2 bulk due to their low highest occupied mole...

Theoretical Investigation of the Structural Stabilities of Ceria Surfaces and Supported Metal Nanocluster in Vapor and Aqueous Phases

In the present work, the stabilities of three low-index ceria (CeO2) surfaces, that is, (111), (110), and (100) in vapor and aqueous phases were studied using ab initio molecular dynamics (AIMD) simulations and density functional theory calculations. On the basis of the calculated Gibbs surface free energies, the morphology and exposed surface structures of the CeO2 nanoparticle were predicted using the Wulff construction principle. It is found that the partially hydroxylated (111) and (100) are two major surface structures of the CeO2 nanoparticle in the vapor phase at ambient temperature. As the temperature increases, the fully dehydrated (111) surface becomes the most dominant structure. However, in the aqueous phase, the exposed surface of the CeO2 nanoparticle is dominated by the hydroxylated (110) structure. The morphology and stability of a cuboctahedron Pt13 nanocluster supported on CeO2 surfaces in both gas and aqueous phases were further investigated. Because of the strong metal–support interact...

Hydrogen-free defects in hydrogenated black TiO2.

Black anatase TiO2 has surprisingly enhanced solar energy harvesting efficiency and electrical conductivity, which makes it a promising material in a wide range of energy and environmental applications. Several experimental and theoretical studies have successfully revealed the mechanisms of band gap reduction by surface hydrogenation of anatase TiO2. However, recent experimental evidence suggests the existence of bulk point defects that yield infrared (∼1.0 eV) photoabsorption and high conductivity of black anatase TiO2. In the current study, using a combination of ab initio molecular dynamics simulations and electronic structure calculations, we successfully explain the physical properties, metallicity, and infrared/microwave absorption (i.e., black color) of highly reduced anatase TiO2 crystal in a hydrogenated state with a newly found pair defect (Tii-VO)4+. Hydrogen atoms in the bulk are unnecessary to understand the observed properties.

Two-dimensional semiconductors ZrNCl and HfNCl: Stability, electric transport, and thermoelectric properties

Searching for novel two-dimensional (2D) semiconducting materials is a challenging issue. We investigate novel 2D semiconductors ZrNCl and HfNCl which would be isolated to single layers from van der Waals layered bulk materials, i.e., ternary transition-metal nitride halides. Their isolations are unquestionably supported through an investigation of their cleavage energies as well as their thermodynamic stability based on the ab initio molecular dynamics and phonon dispersion calculations. Strain engineering is found to be available for both single-layer (1L) ZrNCl and 1L-HfNCl, where a transition from an indirect to direct band gap is attained under a tensile strain. It is also found that 1L-ZrNCl has an excellent electron mobility of about 1.2 × 103 cm2 V−1 s−1, which is significantly higher than that of 1L-MoS2. Lastly, it is indicated that these systems have good thermoelectric properties, i.e., high Seebeck coefficient and high power factor. With these findings, 1L-ZrNCl and 1L-HfNCl would be novel promising 2D materials for a wide range of optoelectronic and thermoelectric applications.

Single layers and multilayers of GaN and AlN in square-octagon structure: Stability, electronic properties, and functionalization

Further to planar single-layer hexagonal structures, GaN and AlN can also form free-standing, single-layer structures constructed from squares and octagons. We performed an extensive analysis of dynamical and thermal stability of these structures in terms of ab initio finite-temperature molecular dynamics and phonon calculations together with the analysis of Raman and infrared active modes. These single-layer square-octagon structures of GaN and AlN display directional mechanical properties and have wide, indirect fundamental band gaps, which are smaller than their hexagonal counterparts. These density functional theory band gaps, however, increase and become wider upon correction. Under uniaxial and biaxial tensile strain, the fundamental band gaps decrease and can be closed. The electronic and magnetic properties of these single-layer structures can be modified by adsorption of various adatoms, or by creating neutral cation-anion vacancies. The single-layer structures attain magnetic moment by selected adatoms and neutral vacancies. In particular, localized gap states are strongly dependent on the type of vacancy. The energetics, binding, and resulting electronic structure of bilayer, trilayer, and three-dimensional (3D) layered structures constructed by stacking the single layers are affected by vertical chemical bonds between adjacent layers. In addition to van der Waals interaction, these weak vertical bonds induce buckling in planar geometry and enhance their binding, leading to the formation of stable 3D layered structures. In this respect, these multilayers are intermediate between van der Waals solids and wurtzite crystals, offering a wide range of tunability.

Decomposition of the Experimental Raman and Infrared Spectra of Acidic Water into Proton, Special Pair, and Counterion Contributions.

Textbooks describe excess protons in liquid water as hydronium (H3O+) ions, although their true structure remains lively debated. To address this question, we have combined Raman and infrared (IR) multivariate curve resolution spectroscopy with ab initio molecular dynamics and anharmonic vibrational spectroscopic calculations. Our results are used to resolve, for the first time, the vibrational spectra of hydrated protons and counterions and reveal that there is little ion-pairing below 2 M. Moreover, we find that isolated excess protons are strongly IR active and nearly Raman inactive (with vibrational frequencies of ∼1500 ± 500 cm-1), while flanking water OH vibrations are both IR and Raman active (with higher frequencies of ∼2500 ± 500 cm-1). The emerging picture is consistent with Georg Zundel's seminal work, as well as recent ultrafast dynamics studies, leading to the conclusion that protons in liquid water are primarily hydrated by two flanking water molecules, with a broad range of proton hydrogen bond lengths and asymmetries.

Use of Crystal Structure Informatics for Defining the Conformational Space Needed for Predicting Crystal Structures of Pharmaceutical Molecules.

Determining the range of conformations that a flexible pharmaceutical-like molecule could plausibly adopt in a crystal structure is a key to successful crystal structure prediction (CSP) studies. We aim to use conformational information from the crystal structures in the Cambridge Structural Database (CSD) to facilitate this task. The conformations produced by the CSD Conformer Generator are reduced in number by considering the underlying rotamer distributions, an analysis of changes in molecular shape, and a minimal number of molecular ab initio calculations. This method is tested for five pharmaceutical-like molecules where an extensive CSP study has already been performed. The CSD informatics-derived set of crystal structure searches generates almost all the low-energy crystal structures previously found, including all experimental structures. The workflow effectively combines information on individual torsion angles and then eliminates the combinations that are too high in energy to be found in the solid state, reducing the resources needed to cover the solid-state conformational space of a molecule. This provides insights into how the low-energy solid-state and isolated-molecule conformations are related to the properties of the individual flexible torsion angles.

Manipulating the Magnetic Moment of Palladium Clusters by Adsorption and Dissociation of Molecular Hydrogen

There is a sizable probability for the dissociation of H2 deposited at low energy on palladium clusters supported on graphene. This is accompanied by a total or partial quenching of the magnetic moment of the cluster, and we have investigated the interplay between these two processes: magnetization change and molecular dissociation. For this purpose, the density functional formalism has been used, in the form of ab initio molecular dynamics simulations and static calculations. Two different cluster sizes have been investigated, Pd6 and Pd13, and the conclusion is that the size of the Pd cluster has a strong influence on the sequence of these two processes. The effect of H2 dissociation is to reduce the magnetic moments of both clusters by about 2 μB, resulting in unpolarized Pd6 on the one hand and Pd13 with a magnetic moment of 2 μB on the other. In the case of Pd6, the quenching of the magnetic moment occurs immediately after the dissociation of the H2 molecule. In contrast, the quenching of the magneti...

Ab Initio Molecular Dynamic Simulations on Pd Clusters Confined in UiO-66-NH2

The thermodynamically stable metal organic framework UiO-66-NH2 has experimentally been demonstrated as an ideal platform to isolate metal clusters within its nanocages; however, the electronic structures and the dynamics of the encapsulated metal clusters are still unclear. Ab initio molecular dynamics simulations combined with density functional theory-based methods were employed to search the stable structures of Pdn@UiO-66-NH2 composites, and their electronic properties were analyzed in detail. We found that the thermodynamics of the composites are highly correlated with charge transfer between the Pdn cluster and the UiO-66-NH2 framework, as well as the deformation energy of the framework. In addition, both ab initio molecular dynamics simulations and density functional theory calculations show that the small Pd clusters can easily diffuse into the tetrahedral cage of UiO-66-NH2 from the octahedral cage through the window connecting these two types of cages, with a small energy barrier.

Proton-Promoted Electron Transfer in Photocatalysis: Key Step for Photocatalytic Hydrogen Evolution on Metal/Titania Composites

Metal cocatalysts are widely utilized for enhancing photocatalytic conversion. In TiO2-based photocatalysts, a wide range of metals dispersed on TiO2 surfaces were observed to be effective for photocatalytic hydrogen production. To clarify the metal/oxide synergistic effect in photocatalysis and the insensitivity of photoactivity on metal types, here we investigate the mechanism of electron transfer from semiconductor to the cocatalyst by using ab initio molecular dynamics and hybrid density functional theory calculations. By determining the optimal geometry of a Pt13 subnano cluster on anatase TiO2(101) and quantifying the electron transfer energetics, we find that the electron transfer from oxide to the metal cluster is significantly boosted (exothermic by more than 0.3 eV) by the adsorption of proton on the metal cluster, which is otherwise endothermic without the presence of proton. This cooperative effect between oxide, subnano metal cluster, and adsorbed proton is rationalized from electronic struct...

Nanostructured Bulk-Heterojunction Solar Cells Based on Amorphous Carbon

Amorphous carbon (a-C) has the potential to provide properties important to solar photovoltaics that are comparable to those of silicon-based materials with further advantages such as low cost, solution processing, air stability, and higher thermal resistance. We employ accurate computational approaches to explore and understand active layers based on bulk heterojunctions containing a-C. Our results show that interfaces with a-C and other carbon nanostructures could enable successful electron and hole extraction as well as reduced sources for carrier recombination. Ab initio molecular dynamics and density functional theory calculations are carried out for a large statistical set of interfaces between a-C structures of different densities and either carbon nanotubes or fullerenes. We show that the energy alignment at such interfaces can be widely tuned as a function of a-C density, doping chemistry, or nanostructure size to obtain type-II heterostructures and that the optical properties of such interfaces ...

Full atomistic reaction mechanism with kinetics for CO reduction on Cu(100) from ab initio molecular dynamics free-energy calculations at 298 K

A critical step toward the rational design of new catalysts that achieve selective and efficient reduction of CO2 to specific hydrocarbons and oxygenates is to determine the detailed reaction mechanism including kinetics and product selectivity as a function of pH and applied potential for known systems. To accomplish this, we apply ab initio molecular metadynamics simulations (AIMμD) for the water/Cu(100) system with five layers of the explicit solvent under a potential of -0.59 V [reversible hydrogen electrode (RHE)] at pH 7 and compare with experiment. From these free-energy calculations, we determined the kinetics and pathways for major products (ethylene and methane) and minor products (ethanol, glyoxal, glycolaldehyde, ethylene glycol, acetaldehyde, ethane, and methanol). For an applied potential (U) greater than -0.6 V (RHE) ethylene, the major product, is produced via the Eley-Rideal (ER) mechanism using H2O + e- The rate-determining step (RDS) is C-C coupling of two CO, with ΔG‡ = 0.69 eV. For an applied potential less than -0.60 V (RHE), the rate of ethylene formation decreases, mainly due to the loss of CO surface sites, which are replaced by H*. The reappearance of C2H4 along with CH4 at U less than -0.85 V arises from *CHO formation produced via an ER process of H* with nonadsorbed CO (a unique result). This *CHO is the common intermediate for the formation of both CH4 and C2H4 These results suggest that, to obtain hydrocarbon products selectively and efficiency at pH 7, we need to increase the CO concentration by changing the solvent or alloying the surface.

A MoO2 sheet as a promising electrode material: ultrafast Li-diffusion and astonishing Li-storage capacity

The potential of MoO2 crystal as an electrode material is reported, and nanostructural MoO2 systems, including nanoparticles, nanospheres, nanobelts and nanowires, were synthesized and proved to be advanced electrode materials. A two-dimensional (2D) geometric structure represents an extreme of surface-to-volume ratio, and thus is more suitable as an electrode material in general. Stimulated by the recent fabrication of 2D MoO2, we adopted an ab initio molecular dynamics simulation and density functional theory calculation to study the stability and electrochemical properties of a MoO2 sheet. Identified by a phonon dispersion curve and potential energy curve calculations, the MoO2 sheet proved to be dynamically and thermally stable. After lithiation, similar to most promising 2D structures, we found that a Li atom can strongly adsorb on a MoO2 sheet, and the lithiated MoO2 sheet presented excellent metallic properties. Note that, compared with most promising 2D structures, we unexpectedly revealed that the diffusion barrier of the Li atom on the MoO2 sheet was much lower and the storage capacity of the MoO2 sheet was much larger. The calculated energy barrier for the diffusion of Li on the MoO2 sheet was only 75 meV, and, due to multilayer adsorption, the theoretical capacity of the MoO2 sheet can reach up to 2513 mA h g−1. Benefiting from general properties, such as strong Li-binding and excellent conductivity, and unique phenomena, such as ultrafast diffusion capacity and astonishing storage capacity, we highlight a new promising electrode material for the Li-ion battery.

Specific interactions between amyloid-β peptides in an amyloid-β hexamer with three-fold symmetry: Ab initio fragment molecular orbital calculations in water

The accumulation of amyloid-beta (Aβ) aggregates in brain contributes to the onset of Alzheimer's disease (AD). Recent structural analysis for the tissue obtained from AD patients revealed that Aβ aggregates have a single structure with three-fold symmetry. To explain why this structure possesses significant stability, we here investigated the specific interactions between Aβ peptides in the aggregate, using ab initio fragment molecular orbital calculations. The results indicate that the interactions between the Aβ peptides of the stacked Aβ pair are stronger than those between the Aβ peptides of the trimer with three-fold symmetry and that the charged amino-acids are important.

Stability of Excess Electrons Introduced by Ti Interstitial in Rutile TiO2(110) Surface

The surface chemistry of rutile TiO2(110) has long been ascribed to surface bridging oxygen vacancies (VO) and accompanying excess electrons. However, recently there has been debate whether titanium interstitials (Tiint), a subsurface defect, participates in the surface reactions of TiO2(110). We used a combination of ab initio molecular dynamics and static density functional theory calculations to systematically investigate the spatial distribution of excess electrons introduced by Tiint. We found that these excess electrons form polarons and that the most stable structure had one polaron located at the Tiint site, and the other three at second-layer Ti sites below five-coordinate Ti sites. This behavior of Tiint providing excess electrons to the near-surface region is similar to that of VO, which suggests that Tiint may contribute to the surface chemical reactions of TiO2(110).

Precision measurements and test of molecular theory in highly excited vibrational states of H2 (v=11).

Accurate EF^1varSigma ^+_g{-}X^1varSigma ^+_g transition energies in molecular hydrogen were determined for transitions originating from levels with highly excited vibrational quantum number, v = 11, in the ground electronic state. Doppler-free two-photon spectroscopy was applied on vibrationally excited hbox {H}_2^*, produced via the photodissociation of H2S, yielding transition frequencies with accuracies of 45 MHz or 0.0015 cm−1. An important improvement is the enhanced detection efficiency by resonant excitation to autoionizing 7ppi electronic Rydberg states, resulting in narrow transitions due to reduced ac-Stark effects. Using known EF level energies, the level energies of X(v = 11, J = 1, 3–5) states are derived with accuracies of typically 0.002 cm−1. These experimental values are in excellent agreement with and are more accurate than the results obtained from the most advanced ab initio molecular theory calculations including relativistic and QED contributions.