Indirect adsorbate-adsorbate interactions mediated through the surface electronic structure of the Si(100) surface

Indirect adsorbate-adsorbate interactions between adsorbed ammonia (NH3) molecules on the Si(100) surface are investigated using density functional theory. Two different nonlocal effects mediated through the surface electronic structure are observed: "poisoning" and hydrogen bonding. We find that adsorbed NH3 "poisons" adsorption of NH3 on neighboring Si dimers on the same side of the dimer row whereas neighboring NH2(a) groups favor this configuration. Adsorption of NH3 involves charge transfer to the surface that localizes on neighboring Si dimer atoms, preventing adsorption of NH3 at these sites. These indirect interactions are similar to Friedel-type interactions observed on metal surfaces with an estimated range of less than 7.8 A on the Si(100) surface. These interactions may be manipulated to construct local ordering of the adsorbates on the surface.     

Quantum Chemical Study of Water Adsorption on the Surfaces of SrTiO3 Nanotubes

We have studied the adsorption of water molecules on the inner and outer surfaces of nanotubes generated by rolling (001) layers of SrTiO₃ cubic crystals. The stability and the atomic and electronic structures of the adsorbed layers are determined by using hybrid density functional theory. The absorption energy and the preferred adsorbate structure are essentially governed by the nature of the surface of the nanotube. Dissociative adsorption prevails on the outer nanotube surfaces. The stability of the adsorbed layers on the inner surfaces is related to the possibility of the formation of hydrogen bonds between water molecules and surface oxygen atoms, and depends on the surface curvature. The presence of water molecules on the inner surface of the nanotubes leads to an increase of the electronic band gap. Externally TiO₂‐terminated nanotubes could be used for the photocatalytic decomposition of water by ultraviolet radiation.     

Transformation from chemisorption to physisorption with tube diameter and gas concentration: computational studies on NH3 adsorption in BN nanotubes

Using first-principles computations, we studied NH3 adsorption on a series of zigzag (n,0) single-walled BN nanotubes (BNNTs) and the effect of gas coverage. Tube diameter and NH3 coverage play important roles on the tube-NH3 interaction. Chemisorption of a single NH3 molecule on top of B site is energetically preferable for all the tubes studied, but the adsorption energy decreases sharply with increasing tube diameter, and then gradually approaches the value for NH3 physisorption on BN graphene layer. On the sidewall of (10,0) BNNT, NH3 molecules prefer to pair arrangement on top of B and N atoms opposite in the same hexagon. At low coverages, NH3 molecules are partly chemically bound to BNNTs. With the increase of NH3 coverage, hydrogen bonds form between the adsorbed NH3 molecules or between the NH3 molecules and N atoms in BNNTs. When the coverage reaches 25%, the chemisorption of NH3 transforms to physisorption completely. NH3 adsorption does not modify the overall band structures of BNNTs, irrespective of NH3 coverage, but the band gap is narrowed due to the NH3-tube coupling and tube deformation.     

NO双分子和二聚体与Cu2作用的理论计算

采用密度泛函理论(DFT)中的B3LYP方法，在Lanl2DZ基组下，对NO双分子和二聚体与铜原子簇相互作用的结构进行了研究. 结果表明，NO可以在铜表面相邻的两个铜原子上形成稳定的双分子吸附和二聚体吸附，而在双分子吸附形式中NO以氮原子吸附在铜上的构型最稳定，且顶点吸附的稳定性不如非顶点吸附形式.在二聚体吸附形式中， N－N键被加强，而N－O键被削弱的程度大于双分子吸附形式，说明二聚体的形成有利于NO在金属铜表面的直接分解.同时电荷布居分析表明，单重态的二聚体与铜作用时，铜原子上的平均电荷达到0.66 e,说明在这种吸附形式中铜被离子化的倾向较大，而且这种吸附形式最有利于NO的分解.这些结果说明NO经二聚体形式在铜表面直接催化分解是可行的.     

Adsorption of hydrogen molecules on the platinum-doped boron nitride nanotubes

Adsorption of hydrogen molecules on platinum-doped single-walled zigzag (8,0) boron nitride (BN) nanotube is investigated using the density-functional theory. The Pt atom tends to occupy the axial bridge site of the BN tube with the highest binding energy of -0.91 eV. Upon Pt doping, several occupied and unoccupied impurity states are induced, which reduces the band gap of the pristine BN nanotube. Upon hydrogen adsorption on Pt-doped BN nanotube, the first hydrogen molecule can be chemically adsorbed on the Pt-doped BN nanotube without crossing any energy barrier, whereas the second hydrogen molecule has to overcome a small energy barrier of 0.019 eV. At least up to two hydrogen molecules can be chemically adsorbed on a single Pt atom supported by the BN nanotube, with the average adsorption energy of -0.365 eV. Upon hydrogen adsorption on a Pt-dimer-doped BN nanotube, the formation of the Pt dimer not only weakens the interaction between the Pt cluster and the BN nanotube but also reduces the average adsorption energy of hydrogen molecules. These calculation results can be useful in the assessment of metal-doped BN nanotubes as potential hydrogen storage media.     

Insights into hydrogen atom adsorption on and the electrochemical properties of nitrogen-substituted carbon materials

The nitrogen substitution in carbon materials is investigated theoretically using the density functional theory method. Our calculations show that nitrogen substitution decreases the hydrogen adsorption energy if hydrogen atoms are adsorbed on both nitrogen atoms and the neighboring carbon atoms. On the contrary, the hydrogen adsorption energy can be increased if hydrogen atoms are adsorbed only on the neighboring carbon atoms. The reason can be explained by the electronic structures analysis of N-substituted graphene sheets. Nitrogen substitution reduces the pi electron conjugation and increases the HOMO energy of a graphene sheet, and the nitrogen atom is not stable due to its 3-valent character. This raises an interesting research topic on the optimization of the N-substitution degree, and is important to many applications such as hydrogen storage and the tokamaks device. The electronic structure studies also explain well why nitrogen substitution increases the capacitance but decreases the electron conductivity of carbon electrodes as was experimentally observed in our experiments on the supercapacitor.     

Interaction of glycine with isolated hydroxyl groups at the silica surface: first principles B3LYP periodic simulation

The adsorption of a glycine molecule on a model silica surface terminated by an isolated hydroxyl group has been studied ab initio using a double-zeta polarized Gaussian basis set, the hybrid B3LYP functional, and a full periodic treatment of the silica surface/glycine system. The hydroxylated silica surface has been simulated using either a 2D slab or a single polymer strand cut out from the (001) surface of an all-silica edingtonite. A number of B3LYP-optimized structures have been found by docking glycine on the silica surface exploiting all possible hydrogen bond patterns. Whereas glycine is generally adsorbed in its neutral form, two structures show glycine adsorbed as a zwitterion, the surface playing the role of a "solid solvent" whereas intrastrand hydrogen bond cooperativity stabilizes the zwitterions. The adsorbed zwitterionic structures are no longer formed at a lower glycine coverage as simulated by enlarging the unit cell so as to break intrastrand hydrogen bonds, showing the importance of H-bond cooperativity in stabilizing the zwitterionic forms. Each structure has been characterized by computing its harmonic vibrational spectrum at the Gamma point, which also allowed us to calculate the free energy of adsorption. The experimental infrared features of chemical-vapor-deposited glycine on a silica surface are in agreement with those computed for glycine adsorbed in its neutral form and engaging three hydrogen bonds with the surface silanols, two of them involving the C=O bond and one originating from the glycine OH group. The NH(2) group plays only a minor role as a weak hydrogen bond donor.     

钇对石墨烯储氢性能的影响

应用基于密度泛函理论的第一性原理方法研究过渡金属钇（Y）修饰对石墨烯储氢性能的影响。考虑Y原子在石墨烯上易形成团簇,采用B原子掺杂有效阻止了团簇形成。通过模拟计算得到的改性体系稳定、储氢性能优异,可吸附6个H₂分子,平均吸附能范围为-0.539到-0.655 eV （per H₂）,理论上满足理想的氢吸附能范围。经Bader电荷初步计算和基于Y/B/graphene （G）体系吸附H₂分子的电子态密度及电荷差分密度图分析得,Y原子与石墨烯间通过电荷转移产生结合,与H₂分子则发生典型的Kubas型相互作用。Y原子改变了H₂分子与石墨烯基的电荷分布,成为连接两者电子云的桥梁,从而增强了H₂分子的吸附能。改性石墨烯体系吸附的均为氢分子,有利于在环境温度和压力条件下进行循环控制,是具有良好发展前景的储氢材料之一。     

Two-dimensional pentacene:3,4,9,10-perylenetetracarboxylic dianhydride supramolecular chiral networks on Ag(111)

Self-assembly of the binary molecular system of pentacene and 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) on Ag(111) has been investigated by low-temperature scanning tunneling microscopy, molecular dynamics (MD), and density functional theory (DFT) calculations. Well-ordered two-dimensional (2D) pentacene:PTCDA supramolecular chiral networks are observed to form on Ag(111). The 2D chiral network formation is controlled by the strong interfacial interaction between adsorbed molecules and the underlying Ag(111), as revealed by MD and DFT calculations. The registry effect locks the adsorbed pentacene and PTCDA molecules into specific adsorption sites due to the corrugation of the potential energy surface. The 2D supramolecular networks are further constrained through the directional CO...H-C multiple intermolecular hydrogen bonding between the anhydride groups of PTCDA and the peripheral aromatic hydrogen atoms of the neighboring pentacene molecules.     

Reaction scheme of ammonia synthesis in the ECR plasmas

The reaction scheme of ammonia synthesis in the ECR plasma apparatus teas investigated from both identifications of the species in the plasmas and the adsorbed species on the surface of a steel substrate placed in the plasmas. The adsorbed species were considerably different when different kinds of plasmas are used. NH, species were adsorbed on the steel substrate surface in the nitrogen-hydrogen plasma, and N₂ molecules were adsorbed in the nitrogen plasma. By the application of a negative bias potential on the substrate, the adsorption of N atom or Fe-N bond formation was identified on the steel substrate surface. When the stainless steel wall of the chamber was covered with aluminum foil, the yield of NH,, radicals, which were on both the substrate and in the plasma, decreased. By exposure of the substrate, on which N₂ molecules or N atoms adsorbed, to the hydrogen plasma, N₂ and N disappeared from the steel substrate surface, forming ammonia. Moreover, the adsorption of NH,, radicals disappeared when the stainless steel wall surface was covered with aluminum foil. Thus, the surface of the stainless steel wall acts as a catalyst in ammonia formation. The formation of ammonia in the nitrogen-hydrogen ECR plasma, in which the steel substrate served as the catalyst, is not only through the dissociative adsorption of excited nitrogen molecules but also through the dissociative adsorption of nitrogen molecular ions.     

Properties of copper (fluoro-)phthalocyanine layers deposited on epitaxial graphene

We investigate the atomic structure and electronic properties of monolayers of copper phthalocyanines (CuPc) deposited on epitaxial graphene substrate. We focus in particular on hexadecafluorophthalocyanine (F(16)CuPc), using both theoretical and experimental (scanning tunneling microscopy - STM) studies. For the individual CuPc and F(16)CuPc molecules, we calculated the electronic and optical properties using density functional theory (DFT) and time-dependent DFT and found a red-shift in the absorption peaks of F(16)CuPc relative to those of CuPc. In F(16)CuPc, the electronic wavefunctions are more polarized toward the electronegative fluorine atoms and away from the Cu atom at the center of the molecule. When adsorbed on graphene, the molecules lie flat and form closely packed patterns: F(16)CuPc forms a hexagonal pattern with two well-ordered alternating α and β stripes while CuPc arranges into a square lattice. The competition between molecule-substrate and intermolecular van der Waals interactions plays a crucial role in establishing the molecular patterns leading to tunable electron transfer from graphene to the molecules. This transfer is controlled by the layer thickness of, or the applied voltage on, epitaxial graphene resulting in selective F(16)CuPc adsorption, as observed in STM experiments. In addition, phthalocyanine adsorption modifies the electronic structure of the underlying graphene substrate introducing intensity smoothing in the range of 2-3 eV below the Dirac point (E(D)) and a small peak in the density of states at ～0.4 eV above E(D).     

A Theoretical Study of the Interaction of Hydrogen and Oxygen with Palladium or Gold Adsorbed on Pyridine‐Like Nitrogen‐Doped Graphene

The interaction of H₂ and O₂ molecules in the presence of nitrogen‐doped graphene decorated with either a palladium or gold atom was investigated by using density functional theory. It was found that two hydrogen molecules were adsorbed on the palladium atom. The interaction of these adsorbed hydrogen molecules with two oxygen molecules generates two hydrogen peroxide molecules first through a Eley–Rideal mechanism and then through a Langmuir–Hinshelwood mechanism. The barrier energies for this reaction were small; therefore, we expect that this process may occur spontaneously at room temperature. In the case of gold, a single hydrogen molecule is adsorbed and dissociated on the metal atom. The interaction of the dissociated hydrogen molecule on the surface with one oxygen molecule generates a water molecule. The competitive adsorption between oxygen and hydrogen molecules slightly favors oxygen adsorption.     

Computational studies of boron‐ and nitrogen‐doped single‐walled carbon nanotubes as potential sensor materials of hydrogen halide molecules HX (X = F,Cl, Br)

Potential applicability of undoped, B‐, and N‐doped carbon nanotubes (CNTs) for elaboration of the working materials of gas sensors of hydrogen halide molecules HX (X = F, Cl, Br) is analyzed in computational studies of molecular adsorption on the CNTs surfaces. Density Functional Theory (DFT)‐based geometry‐optimized calculations of the electronic structure of undoped, B‐, and N‐doped CNTs of (3,3) and (5,5) chiralities with adsorbed HX (X = F, Cl, Br) molecules are performed within molecular cluster approach. Relaxed geometries, binding energies between the adsorbates and the nanotubes, charge states of the adsorbates and the electronic wave function contours are calculated and analyzed in the context of gas sensing applications. Obtained results are supplemented by calculations of adsorption of hydrogen halides on B(N)‐doped graphene sheets which are considered as model approximation for large‐diameter CNTs. It is found that the B‐doped CNTs are perspective for elaboration of sensing materials for detection of HCl and HBr molecules. The undoped and the N‐doped CNTs are predicted to be less suitable materials for detection of hydrogen halide gases HX (X = F, Cl, Br). © 2015 Wiley Periodicals, Inc.     

Co-adsorption of water and hydrogen on Ni(111)

We have studied the surface coverage dependence of the co-adsorption of D and D(2)O on the Ni(111) surface under UHV conditions. We use detailed temperature-programmed desorption studies and high resolution electron energy loss spectroscopy to show how pre-covering the surface with various amounts of D affects adsorption and desorption of D(2)O. Our results show that the effects of co-adsorption are strongly dependent on D-coverage. In the deuterium pre-coverage range of 0-0.3 ML, adsorption of deuterium leaves a fraction of the available surface area bare for D(2)O adsorption, which shows no significant changes compared to adsorption on the bare surface. Our data indicate phase segregation of hydrogen and water into islands. At low post-coverages, D(2)O forms a two-phase system on the remaining bare surface that shows zero-order desorption kinetics. This two phase system likely consists of a 2-D solid phase of extended islands of hexamer rings and a 2-D water gas phase. Increasing the water post-dose leads at first to 'freezing' of the 2-D gas and is followed by formation of ordered, multilayered water islands in-between the deuterium islands. For deuterium pre-coverages between 0.3 and 0.5 ML, our data may be interpreted that the water hexamer ring structure, (D(2)O)(6), required for the formation of an ordered multilayer, does not form anymore. Instead, more disordered linear and branched chains of water molecules grow in-between the extended, hydrophobic deuterium islands. These deuterium islands have a D-atom density in agreement with a (2x2)-2D structure. The disordered water structures adsorbed in-between form nucleation sites for growth of 3-D water structures. Loss of regular lateral hydrogen bonding and weakened interaction with the substrate reduces the binding energy of water significantly in this regime and results in lowering of the desorption temperature. At deuterium pre-coverages greater than 0.5 ML, the saturated (2x2)-2D structure mixes with (1x1)-1D patches. The mixed structures are also hydrophobic. On such surfaces, submonolayer doses of water lead to formation of 3-D water structures well before wetting the entire hydrogen-covered surface.     

Structural behavior of monomer of SARS-CoV-2 spike protein during initial stage of adsorption on graphene

Spike glycoprotein of the SARS-CoV-2 virus and its structure play a crucial role in the infections of cells containing angiotensin-converting enzyme 2 (ACE2) as well as in the interactions of this virus with surfaces. Protection against viruses and often even their deactivation is one of the great varieties of graphene applications. The structural changes of the non-glycosylated monomer of the spike glycoprotein trimer (denoted as S-protein in this work) triggered by its adsorption onto graphene at the initial stage are investigated by means of atomistic molecular dynamics simulations. The adsorption of the S-protein happens readily during the first 10 ns. The shape of the S-protein becomes more prolate during the adsorption, but this trend, albeit less pronounced, is observed also for the freely relaxing S-protein in water. The receptor-binding domain (RBD) of the free and adsorbed S-protein manifests itself as the most rigid fragment of the whole S-protein. The adsorption even enhances the rigidity of the whole S-protein as well as its subunits. Only one residue of the RBD involved in the specific interactions with ACE2 during the cell infection is involved in the direct contact of the adsorbed S-protein with the graphene. The new intramolecular hydrogen bonds formed during the S-protein adsorption replace the S-protein-water hydrogen bonds; this trend, although less apparent, is observed also during the relaxation of the free S-protein in water. In the initial phase, the secondary structure of the RBD fragment specifically interacting with ACE2 receptor is not affected during the S-protein adsorption onto the graphene.     

Li修饰B12N12储氢行为的密度泛函理论研究

采用基于密度泛函理论(DFT)的第一性原理投影缀加波方法, 研究了Li 修饰的B₁₂N₁₂笼子的储氢行为.计算结果表明: Li 原子吸附在B₁₂N₁₂笼子的四元环和六元环相交的B－N桥位上, 相对于其它六个高对称吸附位置更稳定, B₁₂N₁₂笼子周围最多可以吸附3 个Li 原子, 最稳定的构型是三个Li 原子同时吸附在N原子顶位(Top-N site). 每个Li 原子的周围能吸附三个氢分子, 笼子外侧还可以吸附两个氢分子, 内部最多可以吸附5 个氢分子. 考虑到笼内和笼外的吸附, B₁₂N₁₂笼子总的储氢量(氢分子)达到9.1% (w).     

Enhancement of hydrogen physisorption on graphene and carbon nanotubes by Li doping

Density-functional calculations of the adsorption of molecular hydrogen on a planar graphene layer and on the external surface of a (4,4) carbon nanotube, undoped and doped with lithium, have been carried out. Hydrogen molecules are physisorbed on pure graphene and on the nanotube with binding energies about 80-90 meV/molecule. However, the binding energies increase to 160-180 meV/molecule for many adsorption configurations of the molecule near a Li atom in the doped systems. A charge-density analysis shows that the origin of the increase in binding energy is the electronic charge transfer from the Li atom to graphene and the nanotube. The results support and explain qualitatively the enhancement of the hydrogen storage capacity observed in some experiments of hydrogen adsorption on carbon nanotubes doped with alkali atoms.     

Theoretical study on singlet oxygen adsorption onto surface of graphene-like aromatic hydrocarbon molecules

Recently, graphene sheet is one of interesting systems to realize novel electronic properties. Especially, interaction between graphene and adsorbed oxygen molecule is very important to control electronic condition. In this paper, we employed some aromatic hydrocarbons as simple systems of graphene sheet and ab initio MO calculations were carried out to investigate inter-molecular interaction. It is found that not triplet but singlet O₂ molecule have potential of chemisorption onto graphene surface. From the calculated potential energy surface (PES) for distance between benzene and O₂ molecules, meta-stable structure is found at about 1.5 Å with potential barrier. In the optimized structure of its meta-stable state, structural strain can be relaxed through bending of planer benzene ring. Its energy is estimated at 70.10 kcal/mol for benzene. We also estimated the strain effects for naphthalene and pyrene molecules as larger case of graphene and they were 80.85 and 72.45 kcal/mol, respectively.