X-ray studies of self-assembled organic monolayers grown on hydrogen-terminated Si(111)

The structure of self-assembled monolayers (SAMs) of undecylenic acid methyl ester (SAM-1) and undec-10-enoic acid 2-bromo-ethyl ester (SAM-2) grown on hydrogen-passivated Si(111) were studied by X-ray reflectivity (XRR), X-ray standing waves (XSW), X-ray fluorescence (XRF), atomic force microscopy, and X-ray photoelectron spectroscopy (XPS). The two different SAMs were grown by immersion of H-Si(111) substrates into the two different concentrated esters. UV irradiation during immersion was used to create Si dangling bond sites that act as initiators of the surface free-radical addition process that leads to film growth. The XRR structural analysis reveals that the molecules of SAM-1 and SAM-2 respectively have area densities corresponding to 50% and 57% of the density of Si(111) surface dangling bonds and produce films with less than 4 angstroms root-mean-square roughness that have layer thicknesses of 12.2 and 13.2 angstroms. Considering the molecular lengths, these thicknesses correspond to a 38 degrees and 23 degrees tilt angle for the respective molecules. For SAM-2/Si(111) samples, XRF analysis reveals a 0.58 monolayer (ML) Br total coverage. Single-crystal Bragg diffraction XSW analysis reveals (unexpectedly) that 0.48 ML of these Br atoms are at a Si(111) lattice position height that is identical to the T1 site that was previously found by XSW analysis for Br adsorbed onto Si(111) from a methanol solution and from ultrahigh vacuum. From the combined XPS, XRR, XRF, and XSW evidence, it is concluded that Br abstraction by reactive surface dangling bonds competes with olefin addition to the surface.     

Purely site-specific chemisorption and conformation of trimethylamine on Si(100)c(4 x 2)

One of the fundamental points of interest on the Si(100) surface is how the spatial localization of electron density on the buckled silicon dimer controls the site-specific reaction toward different Lewis acid and Lewis base molecules. We have investigated the adsorption of trimethylamine (TMA) on Si(100)c(4x2) using scanning tunneling microscopy (STM) at 80 K. The adsorbed TMA appears as a triangle-shaped bright protrusion in the occupied-state STM image. The triangle-shaped protrusion is ascribed to three methyl groups in the adsorbed TMA. The center of the protrusion is located on the down atom site, which indicates that the adsorption of TMA occurs only on the down dimer atom. Thus, TMA adsorption on Si(100)c(4x2) is found to be purely site-specific on the down dimer atom and can be categorized in Lewis acid-base reaction.     

Structural analysis of the reconstructed Si(001)-C surface

The atomic structure of reconstructed Si(001)c(4 x 4)-C surface has been studied by coaxial impact collision ion scattering spectroscopy. When the 100L of ethylene (C(2)H(4)) molecules have been exposed on Si(001)-(2 x 1) surface at 700 degrees C, it is found that C atoms cause the ordering of missing Si dimer defects and occupy the fourth layer of Si(001) directly below the bridge site. Our results provide the support for the previous model in which a missing dimer structure is accompanied by C incorporation into the subsurface.     

Identification of single and double sites of phosphorylation by ECD FT-ICR/MS in peptides related to the phosphorylation site domain of the myristoylated alanine-rich c kinase protein

A series of phosphorylated test peptides was studied by electron capture dissociation Fourier transform ion cyclotron resonance mass spectrometry (ECD FT-ICR MS). The extensive ECD-induced fragmentation made identification of phosphorylation sites for these peptides straightforward. The site(s) of initial phosphorylation of a synthetic peptide with a sequence identical to that of the phosphorylation site domain (PSD) of the myristoylated alanine-rich C kinase (MARCKS) protein was then determined. Despite success in analyzing fragmentation of the smaller test peptides, a unique site on the PSD for the first step of phosphorylation could not be identified because the phosphorylation reaction produced a heterogeneous mixture of products. Some molecules were phosphorylated on the serine closest to the N-terminus, and others on one of the two serines closest to the C-terminus of the peptide. Although no definitive evidence for phosphorylation on either of the remaining two serines in the PSD was found, modification there could not be ruled out by the ECD fragmentation data.     

应用理论计算研究MCM-22分子筛相邻酸性位上乙烯和苯的吸附

应用ONIOM计算方法研究了MCM-22分子筛超笼12元环上存在两个酸性位时的酸强度及其与骨架铝之间距离的关系,并研究了乙烯和苯分子吸附的规律.计算采用52T簇模型和B3LYP/6-31G**/MNDO方法.结果表明,存在两个酸性位且两个骨架铝之间间隔1个骨架硅时,酸强度比孤立的酸性位明显降低;当间隔的硅原子数增加时,酸强度呈上升趋势,间隔3个以上骨架硅时,其酸强度与孤立的酸性位几乎没有差别.对于乙烯的吸附,当两个骨架铝之间间隔1~4个骨架硅时,其吸附能几乎没有差别(31~35 kJ/mol);对于苯的吸附,当两个骨架铝之间间隔1个骨架硅时,其吸附能有所提高,因为两个桥羟基同时对苯分子产生氢键吸附作用.当两个骨架铝之间的距离增大时,苯的吸附能几乎相同(21~29 kJ/mol).若两个乙烯分子或苯分子同时吸附在双酸性位上,其吸附能与单个分子在孤立酸性位吸附时几乎没有差别.应用自然键轨道计算分析了吸附配合物的电子结构,进一步探明了乙烯和苯在分子筛酸性位上吸附的本质.     

Angle-resolved photoelectron measurements on the 2p orbitals of Si in SiF4 and Si(CH3)4 in the gas phase

Angle-resolved photoelectron measurements have been carried out on the 2p orbital of Si in the gas-phase molecules SiF₄ and Si(CH₃)₄ as a function of energy from 3 to 45 eV above the ionization threshold. From these data the angular distribution parameter, β, has been obtained. Below a photoelectron energy of 15 eV the angular distribution parameter for these two molecules differ by as much as 0.4 units. The differences in the behavior of β near threshold for the two molecules is attributed to the different molecular environment of the silicon atom. To test this idea, calculations have been made on β for neutral and charged atomic silicon.     

Eu/RG absorption and excitation spectroscopy in the solid rare gases: state dependence of crystal field splitting and Jahn-Teller coupling

Absorption spectroscopy recorded for annealed samples of matrix-isolated atomic europium reveals a pair of thermally stable sites in Ar and Kr while a single site exists in Xe. Plots of the matrix shifts of the visible s → p bands versus host polarizability, allowed the association of the single site in Xe and the blue sites in Ar and Kr. On the basis of the similar ground state bond lengths expected for the Eu-rare gas (RG) diatomics and the known Na-RG molecules, the blue sites are attributed to Eu occupancy in the smaller tetra-vacancy while the red sites are proposed to arise from hexa-vacancy sites. Both sites are of cubic symmetry, consistent with the pronounced Jahn-Teller structure present on the y(8)P ← a(8)S(7/2) transition for these bands in the three hosts studied. Site-selective excitation spectroscopy has been used to reanalyze complex absorption spectra previously published by Jakob et al. [Phys. Lett. A 57, 67 (1976)] for the near-UV f → d transitions. On the basis that a pair of thermally stable sites exist in solid argon, the occurrence of crystal field splitting has been identified to occur for the J ≥ 5/2 level of the (8)P state when isolated in these two sites with cubic symmetry. From a detailed lineshape analysis, the magnitude of the crystal field splittings on the J = 5/2 level in Ar is found to be 105 and 123 cm(-1) for the red and blue sites, respectively.     

Diffusion by chemical bond hopping of single O2 and H on Si(111)-7×7 surfaces

Using a variable temperature STM to trace in detail the path of single particle movement, it is possible to derive diffusion parameters of individual atoms and molecules on solid surfaces as well as to probe the mechanisms. Below ˜370 °C, O₂ molecules adsorb on Si(111)-7×7 surfaces at the top site of Si-adatoms as bright image spots. An O₂ molecule can hop between two adatom sites within the half unit cell it adsorbs via two rest-atom sites. Above this temperature, it can either hop out of the half cell, or can go through other reaction pathways. In contrast, for H atoms, the adsorption sites are rest-atom sites. An H atom darkens the rest-atom in filled state image, but the surrounding adatoms will appear brighter because of a reverse charge transfer. Above ˜280 °C, it can hop to a neighbor rest atom site within the half cell via an adatom site. The adatom in the short lived intermediate state appears darker because of the saturation of its dangling bond. Above ˜340 °C, it can hop out of the half cell via two adatom sites. Thus diffusion of H and O₂ on this surface is achieved by hopping of chemical bonds via intermediate states. We have also derived site and pathway-specific activation energies and frequency factors and the potential energy curves for the hopping of O₂ and H on Si(111)-7×7 surfaces.     

Evaluation of non-reductive β-elimination/Michael addition for glycosylation site determination in mucin-like O-glycopeptides

Investigation of site-specific protein O-glycosylation remains a formidable task in post-translational modification-centred proteomics. In particular, the determination of O-glycosylated amino acids in mucin-like glycopeptides lags far behind the techniques for phosphorylation site and N-glycosylation site identification, for which well-established enrichment techniques are available. The present work investigated β-elimination of mucin-like O-glycopeptides with a mild alkylamine base and concomitant Michael-type addition using 2-mercaptoethanol as nucleophile applied to synthetic GalNAcylated O-glycopeptides as well as exoglycosidase-treated endogenous peptides isolated from human blood plasma. This strategy permits O-glycosylated sites to be unambiguously localized, even in multiple-glycosylated peptides. Peptides covalently modified with the glycan surrogate exhibit excellent backbone fragmentation in MS/MS due to their stability during CID.     

Photofragmentation of SiF4 upon Si 2p and F 1s core excitation: cation and anion yield spectroscopy

We have studied the fragmentation dynamics of core-excited SiF4 by means of soft-x-ray photoexcitation and partial positive and negative ion yield measurements around the Si L2,3-shell and F K-shell ionization thresholds. All detectable ionic fragments are reported and we observe significant differences between the various partial ion yields near the Si 2p threshold. The differences are similar to our previous results from CH3Cl showing more extended fragmentation in correspondence to transitions to Rydberg states. At variance with smaller systems, we observe negative ion production in the shape resonance region. This can be related to the possibility in a relatively large system to dissipate positive charge over several channels.     

Dissociation dynamics of positive-ion and negative-ion fragments of gaseous and condensed Si(CH(3))(2)Cl(2) via Si 2p, Cl 2p, and Cl 1s core-level excitations

The state-selective positive-ion and negative-ion dissociation pathways of gaseous and condensed Si(CH(3))(2)Cl(2) following Cl 2p, Cl 1s, and Si 2p core-level excitations have been characterized. The excitations to a specific antibonding state (15a(1) (*) state) of gaseous Si(CH(3))(2)Cl(2) at the Cl 2p, Cl 1s, and Si 2p edges produce significant enhancement of fragment ions. This ion enhancement at specific core-excited states correlates closely with the ion kinetic energy distribution. The results deduced from ion kinetic energy distribution are consistent with results of quantum-chemical calculations on Si(CH(3))(2)Cl(2) using the ADF package. The Cl(-) desorption yields for Si(CH(3))(2)Cl(2)Si(100) at approximately 90 K are notably enhanced at the 15a(1) (*) resonance at both Cl 2p and Si 2p edges. The resonant enhancement of Cl(-) yield occurs through the formation of highly excited states of the adsorbed molecules. These results provide insight into the state-selective ionic fragmentation of molecules via core-level excitation.     

Theoretical investigation of the mechanisms for the reaction of fused tricyclic dimetallenes containing highly strained E═E (E = C, Si, Ge, Sn, and Pb) double bonds

The potential energy surfaces for the reactions of fused tricyclic dimetallenes that feature a highly strained E═E double bond, Rea-E═E, where E = C, Si, Ge, Sn, and Pb, were studied using density functional theory (B3LYP/LANL2DZ). Three types of chemical reactions (i.e., a self-isomerization reaction, a [2 + 2] cycloaddition with a ketone and a methanol 1,2-addition reaction) were used to determine the reactivity of the Rea-E═E molecules. The theoretical findings reveal that the smaller the singlet-triplet splitting of the Rea-E═E, the lower are its activation barriers and, in turn, the more rapid are its chemical reactions with other chemical molecules. Theoretical observations suggest that the relative reactivity increases in the following order: C═C ? Si═Si < Ge═Ge < Sn═Sn < Pb═Pb. Namely, the smaller the atomic weight of the group 14 atom (E), the smaller is the atomic radius of E and the more stable is its fused tricyclic Rea-E═E to chemical reaction. It is thus predicted that the fused tricyclic Rea-C═C and Rea-Si═Si molecules should be stable and readily synthesized and isolated at room temperature. The computational results show good agreement with the available experimental observations. The theoretical results obtained from this work allow a number of predictions to be made.     

Direct and indirect causes of Fermi level pinning at the SiO/GaAs interface

The correlation between atomic bonding sites and the electronic structure of SiO on GaAs(001)-c(2x8)/(2x4) was investigated using scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), and density functional theory (DFT). At low coverage, STM images reveal that SiO molecules bond Si end down; this is consistent with Si being undercoordinated and O being fully coordinated in molecular SiO. At approximately 5% ML (monolayer) coverage, multiple bonding geometries were observed. To confirm the site assignments from STM images, DFT calculations were used to estimate the total adsorption energies of the different bonding geometries as a function of SiO coverage. STS measurements indicated that SiO pins the Fermi level midgap at approximately 5% ML coverage. DFT calculations reveal that the direct causes of Fermi level pinning at the SiO GaAs(001)-(2x4) interface are a result of either local charge buildups or the generation of partially filled dangling bonds on Si atoms.     

Generating 3D molecules conditional on receptor binding sites with deep generative models

The goal of structure-based drug discovery is to find small molecules that bind to a given target protein. Deep learning has been used to generate drug-like molecules with certain cheminformatic properties, but has not yet been applied to generating 3D molecules predicted to bind to proteins by sampling the conditional distribution of protein–ligand binding interactions. In this work, we describe for the first time a deep learning system for generating 3D molecular structures conditioned on a receptor binding site. We approach the problem using a conditional variational autoencoder trained on an atomic density grid representation of cross-docked protein–ligand structures. We apply atom fitting and bond inference procedures to construct valid molecular conformations from generated atomic densities. We evaluate the properties of the generated molecules and demonstrate that they change significantly when conditioned on mutated receptors. We also explore the latent space learned by our generative model using sampling and interpolation techniques. This work opens the door for end-to-end prediction of stable bioactive molecules from protein structures with deep learning.

We generate 3D molecules conditioned on receptor binding sites by training a deep generative model on protein–ligand complexes. Our model uses the conditional receptor information to make chemically relevant changes to the generated molecules.     

Some considerations on Ueff values entering the hubbard hamiltonian

One of the simplest ways to take into account correlations between electrons in solid state physics, beyond the usual one electron approximation, is to use the Hubbard Hamiltonian Although it corresponds to very severe approximations, since intersite correlations are neglected, and since the whole problem is reduced to a single parameter U, it is already very difficult to solve, and exact solutions exist in only a few cases. It is thus not desired to introduce more complications in the Hamiltonian; but it could be interesting to understand, at least qualitatively, which processes influence the value taken by parameter U. The question arises in concrete cases, such as transition metals or organic molecules; comparing experiments and approximate solutions of the Hubbard Hamiltonian has shown that, in most cases, the value of U that yields the best fit is very different from what would be expected from atomic considerations. For instance, if one wants to study correlations on atoms of type M, a pure atomic point of view would affect to U the change in energy U_at in the redox-type equation . However it seems that solid state effects play an important role and we discuss, in this paper, three of them: (i) the finite time that one electron spends on a given atom due to the delocalization of the electrons in a band (effect of β_ij which increases U relatively to U_at); (ii) the mixing of bands of different orbital character which allow two electrons not to be on the same orbital of an atom (and thus decreases U); and (iii) the existence of Coulomb repulsion between electrons on neighboring sites which reduces their effective exclusion on the same site.     

Simulating the thermal behavior and fragmentation mechanisms of exohedral and substitutional silicon-doped C60

Structures, thermal behavior, and fragmentation mechanisms of exohedral and substitutional silicon-doped C(60) containing 1-12 Si atoms are investigated by extensive molecular-dynamics simulations. A nonorthogonal tight-binding model is used to mimic the interatomic interactions in the doped fullerenes. Beginning from the minimum-energy structures, the temperature of the doped fullerenes is slowly increased until fragmentation takes place. A correlation can be established between the exohedral and substitutional structures and the corresponding fragmentation mechanisms and fragmentation temperatures. Exohedral C(60)Si(m) fullerenes fragment into two homonuclear pieces, the Si(m) cluster and the C(60) fullerene that remains intact. In contrast, the substitutional C(60-m)Si(m) heterofullerenes undergo structural transformations, including the partial unraveling of the cage, prior to fragmentation. Then, ejection of atoms or small molecules takes place from the distorted structures. The slow heating rate used, combined with long simulation runs, allows us to determine the fragmentation temperature of exohedral and substitutional Si-doped fullerenes as a function of the number of silicon atoms. Substitutional Si-doped fullerenes exhibit much higher fragmentation temperatures (1000-1500 K higher) than the exohedral fullerenes. This can be understood from the different bonding of the Si atoms in both structures.     

不同脱铝深度稀土超稳Y沸石的酸性质

用FT-IR和NH_2-TPD研究了稀土含量相同时脱铝程度不同的四种REUSY沸石的酸性质. 并对复杂羟基谱的归属进行了讨论. 同时将酸性质与骨架的Si、Al分布, 非骨架组份以及二次孔相关联, 提出浅、中度脱铝时主要脱除与超笼中HFOH相关联的Si(3Al)和Si(2Al)单元中的Al, 深度脱铝时则脱除与六方柱笼和方钠石笼中LFOH 羟基相关联的Si(1AI)中的铝和少量Si(2Al)中的铝. 另外发现, 非骨架组份使一部分HFOH羟基不能被吡啶分子接近. 而二次孔的形成使一部份LFOH 能被吡啶分子接近. 随着脱铝深度的加深, 总酸、B酸、L 酸量都减少. 但强酸和B酸的强度均相应增加.     

Electrospray ionization mass spectrometry as a tool for determination of drug binding sites to human serum albumin by noncovalent interaction

Most proteins in blood plasma bind ligands. Human serum albumin (HSA) is the main transport protein with a very high capacity for binding of endogenous and exogenous compounds in plasma. Many pharmacokinetic properties of a drug depend on the level of binding to plasma proteins. This work reports studies of noncovalent interactions by means of nanoelectrospray ionization mass spectrometry (nanoESI-MS) for determination of the specific binding of selected drug candidates to HSA. Warfarin, iopanoic acid and digitoxin were chosen as site-specific probes that bind to the main sites of HSA. Two drug candidates and two known binders to HSA were analyzed using a competitive approach. The drugs were incubated with the target protein followed by addition of site-specific probes, one at a time. The drug candidates showed predominant affinity to site I (warfarin site). Naproxen and glyburide showed affinity to both sites I and II. The advantages of nanoESI-MS for these studies are the sensitivity, the absence of labeled molecules and the short method development time.     

Synthesis of Poly(isosorbide carbonate) <Emphasis Type="Italic">via</Emphasis> Melt Polycondensation Catalyzed by Ca/SBA-15 Solid Base

Ca/SBA-15 solid bases with different Ca/Si atomic ratios were prepared by a one-pot route and employed as catalysts for the production of poly(isosorbide carbonate) (PIC) from diphenyl carbonate and isosorbide via a transesterification polymerization process. The relationship between physicochemical properties and catalytic performance for Ca/SBA-15 in this melt process was investigated by means of various characterization techniques. It was found that basic site amount and strength were responsible for this transesterification process; the weak and medium basic sites inclined to promote polycondensation reaction. It was worth noting that strong basic sites could favor the decomposition of the resultant PIC, resulting in the decrease of weight-average molecular weight (M_w) and yield, and the sample with Ca/Si atomic ratio of 0.4 exhibited the best catalytic performance, giving PIC with M_w of 4.88 × 10⁴ g/mol and T_g of 169 °C at the optimal conditions. This excellent activity can be ascribed to the presence of rich basic sites and specific basic strength on the surface of 0.4Ca/SBA-15.     

Water adsorption on a p(2x2)-Ni(111)-O surface studied by surface x-ray diffraction and infrared reflection absorption spectroscopy at 25 and 140 K

The adsorption of water molecules on an oxygen-predosed p(2x2)-Ni(111)-O surface was studied by surface x-ray diffraction and infrared reflection absorption spectroscopy (IRAS) at temperature of 25 and 140 K. Precise structures including adsorbed water, predosed oxygen, and substrate nickel atoms at these two temperatures were determined by x-ray structural analysis. It was found that water molecules adsorb on oxygen additive sites, forming a hydrogen bond at 25 K. A predosed 2x2 oxygen atom appears to accommodate one, two, or three water molecules at positions relating to threefold rotation symmetry. When the surface temperature was raised to 140 K, water molecules appear at an atop site of Ni. The distance between Ni and the oxygen atoms of a monomer water molecule was found to be 0.2241(22) nm. The adsorbed water molecule induces buckling and a lateral shift of the substrate nickel. The IRAS results provided evidence regarding the existence of two distinct adsorption sites. Water molecules in the low-temperature phase exhibit bands from both hydrogen-bonded nuOD and free OD stretchings, while those in the high-temperature phase lie flat with a molecular plane parallel to the surface.