Steering and ro-vibrational effects on dissociative adsorption and associative desorption of H2/Pd(100)

The interaction of hydrogen with many transition metal surfaces is characterized by a coexistence of activated with non-activated paths to adsorption with a broad distribution of barrier heights. By performing six-dimensional quantum dynamical calculations using a potential energy surface derived from ab initio calculations for the system H₂/Pd(100) we show that these features of the potential energy surface lead to strong steering effects in the dissociative adsorption and associative desorption dynamics.

In particular, we focus on the coupling of the translational, rotational and vibrational degrees of freedom of the hydrogen molecule in the reaction dynamics.     

On the dynamics of H2 adsorption on the Pt(111) surface

The dynamics and kinetics of the dissociation of hydrogen over the hexagonal close packed platinum (Pt(111)) surface are investigated using Car–Parrinello molecular dynamics and static density functional theory calculations of the potential energy surfaces. The calculations model the reference energy‐resolved molecular beam experiments, considering the degrees of freedom of the catalytic surface. Two‐dimensional potential energy surfaces above the main sites on Pt(111) are determined. Combined with Car–Parrinello trajectories, they confirm the dissociative adsorption of H₂ as the only adsorption pathway on this surface at H₂ incindence energies above 5 kJ/mol. A direct determination of energy‐resolved sticking coefficients from molecular dynamics is also performed, showing an excellent agreement with the experimental data at incidence energies in the 5–30 kJ/mol range. Application of dispersion corrections does not lead to an improvement in the prediction of the H₂ sticking coefficient. The adsorption reaction rate obtained from the calculated sticking coefficients is consistent with experimentally derived literature values.     

New insights on reaction dynamics from formaldehyde photodissociation

We review the photodissociation dynamics of formaldehyde with an emphasis on recent calculations that make use of a global ab initio-based potential energy surface for the S(0) state. These calculations together with recent experiments reveal striking departures from conventional transition state theory for the formation of the molecular products H(2) + CO. The evidence for this departure is reviewed in detail by examining properties of the new potential surface and results of quasiclassical trajectory dynamics calculations using this surface. We also review very recent work on the dynamics governing the formation of radical products, H + HCO. These products can be formed on the T(1) surface as well as the S(0) one, and we present some results contrasting the dynamics on these two surfaces. This work makes use of a new semi-global ab initio-based T(1) potential energy surface.     

Atomistic simulation of the homogeneous nucleation and of the growth of N2 crystallites

We report on a computer simulation study of the early stages of the crystallization of molecular nitrogen. First, we study how homogeneous nucleation takes place in supercooled liquid N(2) for a moderate degree of supercooling. Using the umbrella sampling technique, we determine the free energy barrier of formation for a critical nucleus of N(2). We show that, in accord with Ostwald's rule of stages, the structure of the critical nucleus is predominantly that of a metastable polymorph (alpha-N(2) for the state point investigated). We then monitor the evolution of several critical nuclei through a series of unbiased molecular dynamics trajectories. The growth of N(2) crystallites is accompanied by a structural evolution toward the stable polymorph beta-N(2). The microscopic mechanism underlying this evolution qualitatively differs from that reported previously. We do not observe any dissolution or reorganization of the alpha-like core of the nucleus. On the contrary, we show that alpha-like and beta-like blocks coexist in postcritical nuclei. We relate the structural evolution to a greater adsorption rate of beta-like molecules on the surface and show that this transition actually starts well within the precritical regime. We also carefully investigate the effect of the system size on the height of the free energy barrier of nucleation and on the structure and size of the critical nucleus.     

High-dimensional quantum dynamical study of the dissociation of H2 on Pd110

We report the first six-dimensional quantum dynamical study of the dissociative adsorption of H(2) on a (110) surface. We have performed quantum coupled-channel calculations for the system H(2)/Pd(110) based on a potential energy surface (PES) that was derived from ab initio electronic structure calculations. In particular, we have focused on the effects of the corrugation and anisotropy of the PES on the H(2) dissociation probability. Our results agree well with the available experimental data for the sticking probability as a function of the initial kinetic energy and the angle of incidence. Because of the coupling between the anisotropy and corrugation of the potential energy surface our calculations predict an unusual rotational heating and a rather small rotational alignment in desorption.     

BEP relations for N2 dissociation over stepped transition metal and alloy surfaces

We present density functional theory (DFT) calculations for N2 dissociation on stepped face-centred cubic (211) surface slabs. By using the same crystal structure, the same adsorption site for atomic nitrogen, and the same transition-state bond length of N2 over a range of pure metal surfaces, a perfectly linear Br?nsted-Evans-Polanyi (BEP) relation between the transition-state potential energy and the dissociative chemisorption energy is obtained. The perfect BEP relation, which extends over 12 eV in chemisorption energy, suggests that the manifestation of BEP relations for surface reactions is a general electronic structure effect, and that geometric effects are responsible for the scatter which is normally observed around the BEP line. The BEP relation is also shown to be valid for both surface and bulk alloys. The scatter is, however, larger than for the pure elements. This can be understood as a larger geometrical variance. To analyze the accuracy of the DFT calculations a detailed convergence study is performed for several adsorbates on stepped hexagonal close-packed and face-centred cubic Ru slabs.     

First principle calculations study of AlN surface terminal structure evolution under different conditions

The surface structure and properties of aluminum nitride (AlN) play an important role in many applications. Using the first principle calculations method, we analyzed the surface terminal structure of AlN and its evolution under different conditions by determining the surface energy, adsorption energy, and evaporation energy of the Al and N terminals on the AlN(0001) surface. Our results show that the reason why the N terminal is less stable than the Al terminal is not only because of its high surface energy but also because its adsorption performance is extremely sensitive to the adsorption position. The surface N atoms combine to form N₂ molecules that escape during the evaporation process at high temperature. After surface N atoms escape, the AlN surface structure reconstitutes to form a hexagonal closest packing (HCP)–like structure, and the energy barrier for the reconstructing process is 3.2 eV. This shows that the structure and form of the AlN(0001) terminals depend on the environmental conditions.     

Oxidation of Anatase TiO2(001) (1×4) Surface

Anatase TiO₂(001) surface arouses lots of research interests since it is believed to be the most reactive surface. However, recent STM measurements showed that except the defect sites, anatase TiO₂(001) (1×4) reconstructed surface is inert to H₂O adsorption. It was indicated that oxidation could be the reason which induces the inert surface reactivity. Therefore, it is strongly motivated to understand the oxidation structures as well as the oxidation process on this surface. In this work, based on first principles calculations, we investigated the oxidized structures and processes of TiO₂ anatase (001) surface with (1×4) reconstruction. We have discovered two kinds of oxidized structures through the molecular adsorption and dissociated adsorption with different oxidation ratio. To understand the oxidation process, we studied the reaction barrier of oxidation process. We conclude the stability of different oxidized structures with different oxidation ratio by comparing the free energy of the system as a function of oxygen chemical potential. Based on that, a first-principles-based phase diagram of the low-energy oxidized surface structures is provided. The effects of the lattice stress are also studied. Results show that the oxidized structure and oxidation ratio strongly depend on the temperature and pressure. The lattice stress also plays an important role.     

Theoretical study of hydrogen dissociative adsorption on the Cu(110) surface

We have calculated the six-dimensional (6D) potential energy surface for H2 in front of a frozen Cu(110) surface using density functional theory for 22 H2-surface configurations and the corrugation reducing procedure to interpolate between them. We carry out classical trajectory calculations on the dissociative adsorption process and find excellent agreement with measurements. We find that it is of prominent importance to account for the rovibrational state distribution in the incident H2 beam. A straightforward analysis leads to the conclusion that the motion along the surface does not play an appreciable role in the dynamics whereas the dynamical role of molecular rotation is crucial. The latter fact precludes any interpretation of dissociation in terms of a static concept such as "barrier distributions."     

Six-dimensional quantum dynamics of H2 dissociative adsorption on the Pt(211) stepped surface

Results of experimental studies, and theoretical calculations utilizing classical trajectories, have shown that dissociation of H2 on the Pt(211) stepped surface is enhanced at low energies by a molecular trapping mechanism. Because quantum effects can play a large role at the low energies and long lifetimes that characterize molecular trapping, we have undertaken quantum dynamics calculations for this system, the first to treat all molecular degrees of freedom of a gas molecule reacting on a stepped metallic surface. The calculations show that molecular trapping persists in the quantum system, but only at much lower energies than experimentally seen, pointing to possible deficiencies in the potential energy surface. Classical and quasiclassical trajectory calculations on the same potential provide a reasonable picture of reaction overall, but many of the finer details are inaccurate, and certain classical reaction mechanisms are entirely invalid. We conclude that some skepticism should be shown toward any classical study for which long-lived trapping states play a role.     

Computational analysis of the proton translocation from Asp96 to schiff base in bacteriorhodopsin

The potential energy change during the M --> N process in bacteriorhodopsin has been evaluated by ab initio quantum chemical and advanced quantum chemical calculations following molecular dynamics (MD) simulations. Many previous experimental studies have suggested that the proton transfer from Asp96 to the Schiff base occurs under the following two conditions: (1) the hydrogen bond between Thr46 and Asp96 breaks and Thr46 is detached from Asp96 and (2) a stable chain of four water molecules spans an area from Asp96 --> Schiff base. In this work, we successfully reproduced the proton-transfer process occurring under these two conditions by molecular dynamics and quantum chemical calculations. The quantum chemical computation revealed that the proton transfer from Asp96 to Shiff base occurs in two-step reactions via an intermediate in which an H(3)O(+) appears around Ala215. The activation energy for the proton transfer in the first reaction was calculated to be 9.7 kcal/mol, which enables fast and efficient proton pump action. Further QM/MM (quantum mechanical/molecular mechanical) and FMO (fragment molecular orbital) calculations revealed that the potential energy change during the proton transfer is tightly regulated by the composition and the geometry of the surrounding amino acid residues of bacteriorhodopsin. Here, we report in detail the Asp96 --> Schiff base proton translocation mechanism of bacteriorhodopsin. Additionally, we discuss the effectiveness of combining quantum chemical calculations with truncated cluster models followed by advanced quantum chemical calculations applied to a whole protein to elucidate its reaction mechanism.     

Searching the "biologically relevant"conformation of dopamine: a computational approach

We report here an exhaustive and complete conformational study on the conformational potential energy hypersurface (PEHS) of dopamine (DA) interacting with the dopamine D2 receptor (D2-DR). A reduced 3D model for the binding pocket of the human D2-DR was constructed on the basis of the theoretical model structure of bacteriorhodopsin. In our reduced model system, only 13 amino acids were included to perform the quantum mechanics calculations. To obtain the different complexes of DA/D2-DR, we combined semiempirical (PM6), DFT (B3LYP/6-31G(d)), and QTAIM calculations. The molecular flexibility of DA interacting with the D2-DR was evaluated from potential energy surfaces and potential energy curves. A comparative study between the molecular flexibility of DA in the gas phase and at D2-DR was carried out. In addition, several molecular dynamics simulations were carried out to evaluate the molecular flexibility of the different complexes obtained. Our results allow us to postulate the complexes of type A as the "biologically relevant conformations" of DA. In addition, the theoretical calculations reported here suggested that a mechanistic stepwise process takes place for DA in which the protonated nitrogen group (in any conformation) acts as the anchoring portion, and this process is followed by a rapid rearrangement of the conformation allowing the interaction of the catecholic OH groups.     

The role of molecular rotation in activated dissociative adsorption on metal surfaces

The role of molecular rotation in dissociative adsorption of H2 on the activated NiAl(110) metal surface is systematically investigated by means of classical dynamics calculations performed on ab initio six-dimensional potential energy surfaces. The calculations show that molecules rotate abruptly when they are close to the surface and that this rotation allows the molecules to adopt the orientation that is more convenient for dissociation (i.e., nearly parallel to the surface). Also, in reactive sectors of the NiAl(110) unit cell, there is an "angular threshold" below which molecules cannot dissociate. This angular threshold goes down as the incidence energy increases, which explains the rise of the dissociation probability and the fact that it reaches a value close to 1 at incidence energies of the order of 2 eV. The fact that switching on molecular rotation favors dissociation establishes a competition between dissociation and rotational excitation of reflected molecules above the dissociation threshold. Measurements on rotational excitation might thus bring indirect evidence on the dissociation dynamics. Sample calculations for nonactivated Pd(111) and activated Cu(110) metal surfaces suggest that some of these conclusions may be of general validity.     

Separation of gas mixtures using a range of zeolite membranes: a molecular-dynamics study

Gas separation efficiencies of three zeolite membranes (Faujasite, MFI, and Chabazite) have been examined using the method of molecular dynamics. Our investigation has allowed us to study the effects of pore size and structure, state conditions, and compositions on the permeation of two binary gas mixtures, O(2)N(2) and CO(2)N(2). We have found that for the mixture components with similar sizes and adsorption characteristics, such as O(2)N(2), small-pore zeolites are not suited for separations, and this result is explicable at the molecular level. For mixture components with differing adsorption behavior, such as CO(2)N(2), separation is mainly governed by adsorption and small-pore zeolites separate such gases quite efficiently. When selective adsorption takes place, we have found that, for species with low adsorption, the permeation rate is low, even if the diffusion rate is quite high. Our results further indicate that loading (adsorption) dominates the separation of gas mixtures in small-pore zeolites, such as MFI and Chabazite. For larger-pore zeolites such as Faujasite, diffusion rates do have some effect on gas mixture separation, although adsorption continues to be important. Finally, our simulations using existing intermolecular potential models have replicated all known experimental results for these systems. This shows that molecular simulations could serve as a useful screening tool to determine the suitability of a membrane for potential separation applications.     

十二烷基苯磺酸钠在SiO2表面聚集的分子动力学模拟

采用分子动力学方法研究了阴离子表面活性剂十二烷基苯磺酸钠(SDBS)在无定形SiO2固体表面的吸附. 设置不同的水层厚度, 观察固液界面和气液界面吸附的差异. 模拟发现表面活性剂分子能够在短时间内吸附到SiO2表面, 受碳链和固体表面之间相互作用的影响形成表面活性剂分子层, 并依据吸附量的大小形成不同的聚集结构; 在水层足够厚的情况下, 由于有较多的表面活性剂分子吸附在固体表面,从而形成带有疏水核心的半胶束结构; 计算得到的成对势表明极性头与钠离子或水分子之间的结合或解离与二者之间的能垒有关, 解离能垒远大于结合能垒, 引起更多Na+聚集在极性头周围而只有少数Na+存在于溶液中; 无论气液还是固液界面, 极性头均伸向水相, 与水分子形成不同类型的氢键. 模拟表明, 分子动力学方法可以作为实验的一种补充, 为实验提供必要的微观结构信息.     

Adsorption and dissociation of NO on stepped Pt (533)

We present an experimental and theoretical investigation of the adsorption, desorption, and dissociation of NO on the stepped Pt (533) surface. By combining temperature programmed desorption and reflection absorption infrared spectroscopy, information about the adsorption sites at different temperatures is obtained. Surprisingly, metastable adsorption structures of NO can be produced through variation of the dosing temperature. We also show that part of the NO molecules adsorbed on the step sites dissociates around 450 K. After dissociation the N atoms can desorb either by combining with an O fragment, or with another N atom, resulting in NO and N(2). The N(2) production can be enhanced by coadsorbing CO on the surface: CO scavenges the oxygen atom, thereby suppressing associative recombinative desorption of N and O atoms. Density functional theory calculations are used to reveal the adsorption energies and vibrational frequencies of adsorbed NO as well as barriers for dissociation of NO and for diffusion of N atoms. The combined experimental results and theoretical calculations reveal that dissociation of NO is the rate limiting step in the formation of N(2).     

Interaction of isoniazid drug with the pristine and Ni-doped of (4, 4) armchair GaNNTs: a first principle study

In this research, the interaction of isoniazid drug (INH) with the pristine and Ni-doped Gallium nitride nanotubes (GaNNTs) is investigated by using density function theory. The adsorption energy, deformation energy, natural bond orbital (NBO), quantum parameters, molecular electrostatic potential (MEP) and thermodynamic parameters of all adsorption models are calculated from optimized structures. The values of adsorption energy, enthalpy and Gibbs free energy of all adsorption models are negative and all adsorption process are favorable in view of thermodynamic points. It is notable that Ni-doped decrease adsorption strength and it is not suitable for INH adsorption on the GaNNTs surface. The MEP, NBO and maximum amount of electronic charge ΔN results demonstrate that the negative potential are localized around adsorption position and the positive potential are localized around INH molecule. The calculated results indicate that the GaNNTs is a good candidate to making absorber and sensor for detecting INH drug.     

Interface tension of silica hydroxylated nanoparticle with brine: a combined experimental and molecular dynamics study

We have used molecular dynamics simulations to calculate the interfacial tension of hydroxylated SiO(2) nanoparticles under different temperatures and solutions (helium and brine with monovalent and divalent salts). In order to benchmark the atomistic model, quartz SiO(2) interfacial tension was measured based on inverse gas chromatography under He atmosphere. The experimental interfacial tension values for quartz were found between 0.512 and 0.617 N/m. Our calculated results for the interfacial tension of silica nanoparticles within helium atmosphere was 0.676 N/m, which is higher than the value found for the system containing He∕α-quartz (0.478 N/m), but it is similar to the one found for amorphous silica surface. We have also studied the interfacial tension of the nanoparticles in electrolyte aqueous solution for different types and salts concentrations (NaCl, CaCl(2), and MgCl(2)). Our calculations indicate that adsorption properties and salt solutions greatly influence the interfacial tension in an order of CaCl(2) > MgCl(2) > NaCl. This effect is due to the difference in distribution of ions in solution, which modifies the hydration and electrostatic potential of those ions near the nanoparticle.     

Six-dimensional quantum dynamics of (v=0,j=0)D2 and of (v=1,j=0)H2 scattering from Cu111

We report six-dimensional quantum dynamics calculations of the dissociative scattering of molecular hydrogen from the copper111 surface. Two potential energy surfaces are investigated and the results are compared with experiment. Our study completes the preliminary work of Somers et al. [Chem. Phys. Lett. 360, 390 (2002)] and focuses on the role of initial vibrational excitation and on isotopic effects. None of the two investigated potential energy surfaces is found satisfactory: the use of neither potential yields reaction and vibrational excitation probabilities and vibrational efficacies that are in close agreement with experiment. In addition to showing the shortcomings of existing potential energy surfaces we point out an inconsistency in the experimental fits for D2.