Surface-adsorbed Molecules Research Articles

Chemical Analysis of Complex Surface-Adsorbed Molecules and Their Reactions by Means of Cluster-Induced Desorption/Ionization Mass Spectrometry.

Desorption/ionization induced by neutral SO2 clusters (DINeC) is used for mass spectrometry (MS) of surface-adsorbed molecules. The method is shown to be a surface-sensitive analysis tool capable of detecting molecular adsorbates in a wide range of molecular weights as well as their reactions on surfaces, which are otherwise difficult to access. Two different surface/adsorbate systems prepared by means of electrospray ion beam deposition (ES-IBD) were investigated: For the peptide angiotensin II on gold, intact molecules were desorbed from the surface when deposited by soft landing ES-IBD. By comparison to the well-controlled amount of substance deposited by ES-IBD, the sensitivity of DINeC-MS was shown to be on the order of 0.1% of a monolayer coverage, corresponding to femtomoles of analyte. Depending on deposition and sample conditions, the original state of charge of the molecules could be retrieved. Reaction of the adsorbed molecules both with surface atoms as well as with coadsorbed D2O was monitored. Rhodamine 6G was also desorbed as an intact molecule when deposited with kinetic energies below 50 eV. For higher deposition energy, fragmentation of the dye molecules was observed by means of DINeC-MS.

Effect of Adsorbed Water Molecules on Light Harvesting and Electron Injection Processes in Dye-Sensitized Nanocrystalline TiO2 Films

We studied the effects of adsorbed water molecules on light harvesting and electron injection processes in nanocrystalline TiO2 films sensitized with Ru-complex dyes. We found that the absorption spectra of adsorbed dyes containing SCN groups were sensitive to humidity (that is, the dyes exhibited vapochromism) and that the absorption spectra of dyes adsorbed on nanocrystalline films differed slightly from the spectra of the same dyes adsorbed on TiO2 single crystals, suggesting that the orientation of the dye molecules on the surface was affected by surface-adsorbed water molecules. The dynamics of electron injection from the excited dye molecules into the TiO2 were studied by transient absorption spectroscopy. Transient absorption signal intensities decreased with decreasing humidity, indicating that electron injection efficiency was reduced by loss of water molecules from the surface. IR spectroscopy indicated that only a small amount of physisorbed water was lost upon drying, and the use of an indicator dye showed that the proton concentration around the dye molecules on the surface was markedly increased by drying. On the basis of these findings, we discuss possible mechanisms for the vapochromism and for the reduction in electron injection efficiency caused by the loss of water molecules from the surface.

Calculations of Oxygen Adsorption-Induced Surface Reconstruction and Oxide Formation on Cu(100)

The energetics and kinetics of the missing-row reconstruction (MRR) and missing-row island formation on the Cu(100) surface are investigated using density functional theory calculations. We find that copper ejection from the c(2 × 2) surface is made energetically possible by the presence of surface-adsorbed O2 molecules. The barrier for MRR formation via this ejection mechanism is calculated to be 0.96 eV, consistent with the experimentally observed formation temperature of 400 K. The reaction pathways between Cu and O2 result in the formation of Cu–O chains on the c(2 × 2) surface, which can grow from the −O–Cu–O– trimer at least up to the −Cu–O–Cu–O–Cu– pentamer. Remarkably, these chains can both diffuse rapidly and change their orientation on the surface, allowing them to assemble into longer Cu–O chains. Facile diffusion of the Cu–O chains occurs via a collective mechanism which limits the number of broken Cu–O bonds. Perpendicular to the Cu–O rows, the chains hop first at one end and then the other. ...

Studying Water Hydrogen-Bonding Network near the Lipid Multibilayer with Multiple IR Probes.

A critical difference between living and nonliving is the existence of cell membranes, and hydration of membrane surface is a prerequisite for structural stability and various functions such as absorption/desorption of drugs, proteins, and ions. Therefore, a molecular level understanding of water structure and dynamics near the membrane is important to perceive the role of water in such a biologically relevant environment. In our recent paper [ J. Phys. Chem. Lett. 2016 , 7 , 741 ] on the IR pump-probe study of the OD stretch mode of HDO near lipid multibilayers, we have observed two different vibrational lifetime components of OD stretch mode in the phospholipid multibilayer systems. The faster component (0.6 ps) is associated with OD groups interacting with the phosphate moiety of the lipid, while the slower component (1.9 ps) is due to choline-associated water molecules that are close to bulklike water. Here, we additionally use hydrazoic acid (HN3) as another IR probe of which frequency is highly sensitive to its local H-bonding water density. Interestingly, we found that the vibrational lifetime of the asymmetric azido stretch mode of HN3 in the lipid multibilayer system is similar to that in neat water, whereas its orientational relaxation is a bit slower than that in bulk water. This indicates that due to the tight packing of lipid molecules, particularly the head parts, in the gel phase, HN3 molecules mostly stay near the choline group of lipid and interact with water molecules in the vicinity of choline groups. This suggests that membrane surface-adsorbed molecules such as hydrophilic drug molecules may interact with choline-associated water molecules, when the membrane is in the gel phase, instead of phosphate-associated water molecules.

Role of limited hydrogen and flow interval on the growth of single crystal to continuous graphene by low-pressure chemical vapor deposition

A method for defect-free large crystallite graphene growth remains unknown despite much research effort. In this work, we discuss the role of flow duration of H2 gas for the production of graphene as per requirement and production at a minimum flow rate considering the safety issue of hydrogen utilization. The copper substrate used for growth was treated for different time intervals (0 to 35 min) in H2 flow prior to growth. Structural and chemical changes occurring in the copper substrate surface were probed by grazing incidence x-ray diffraction and x-ray photoelectron spectroscopy. The results were correlated with the Raman spectroscopy data, which can quantify the quality of graphene. With increasing H2 flow interval, secondary nucleation sites were observed and growth favored few-layer graphene structures. The surface-adsorbed oxygen molecules and its conversion to an OH terminated surface with increasing hydrogen flow interval was found to be a key factor in enhancing nucleation density. The Stranski–Krastanov type of nucleation was observed for samples grown with different time intervals of H2 treatment, except 5 min of H2 flow prior to growth for which the Volmer–Weber type of growth favored monolayer graphene crystallite growth.

Adsorption of Ferrocene on Carbon Nanotubes, Graphene, and Activated Carbon

Ferrocene could be adsorbed on activated carbon, carbon nanotube surfaces, graphite, and graphene in the absence of a solvent at room temperature in spite of its high melting point (174 °C). In each case only monolayers formed via self-adsorption and the transition to surplus polycrystalline material was abrupt, with no multiple layers occurring. Variable-temperature multinuclear solid-state NMR spectroscopy was applied to study the mobilities of the surface-adsorbed ferrocene molecules. It has been demonstrated that on favorable supports the major anisotropic interactions that usually broaden the solid-state NMR signals of polycrystalline and amorphous materials were reduced or completely eliminated due to the mobility of the adsorbed ferrocene. In favorable cases the chemical shift anisotropy (CSA) and the dipolar and quadrupolar interactions were reduced to a degree that allowed the recording of the spectra of the solid materials on a conventional solution NMR spectrometer.

Structure and Dynamics of Water/Methanol Mixtures at Hydroxylated Silica Interfaces Relevant to Chromatography.

The spectroscopy and dynamics of water/methanol (MeOH) mixtures at hydroxylated silica surfaces is investigated from atomistic simulations. The particular focus is on how the structural dynamics of MeOH changes when comparing surface-bound and MeOH in the bulk. From analyzing the frequency frequency correlation functions it is found that the dynamics on the picosecond time scale differs by almost a factor of two. While the relaxation time is 2.0 ps for MeOH in the bulk solvent it is considerably slowed-down to 3.5 ps for surface-bound MeOH. Surface-adsorbed MeOH molecules reside there for several nanoseconds and their H-bonds are strongly oriented towards the surface-OH groups. These results are of particular relevance for chromatographic systems where the solvent may play a central role in their function. The present simulations suggest that surface-sensitive spectroscopic techniques should be useful in better characterizing such heterogeneous systems and provide detailed insight into solvent dynamics and structure relevant in chromatographic applications.

A DFT investigation on the mechanism for the formation of Zn(NCO)2(NH3)2

The mechanism for the formation of Zn(NCO)2(NH3)2 in the process of urea methanolysis is investigated by using density functional theory(DFT). Two paths have been proposed and simulated to investigate the formation process. For path 1, two urea molecules are adsorbed on the ZnO surface. Then, two surface-adsorbed urea molecules dissociate from the surface accompanied by the breakage of ZnO bonds, followed by the Zn(NCO)2(NH3)2 formation after NH3 combination to the Zn(NCO)2 complex. For path 2, two molecules of HNCO and NH3 are formed after a urea self-dissociation process. Then, the four molecules are adsorbed on the ZnO surface and form the product Zn(NCO)2(NH3)2 and H2O. Comparing the exothermic data and the highest energy barrier of the two paths, path 1 release more energy and its highest energy barrier is 3.7kcal/mol lower than that in path 2. In conclusion, path 1 is a more favorable way for the formation of Zn(NCO)2(NH3)2 complex.

Effect of Water Adsorption on the Photoluminescence of Silicon Quantum Dots.

The optical properties of silicon quantum dots (Si QDs) are strongly influenced by circumjacent surface-adsorbed molecules, which would highly affect their applications; however, water, as the ubiquitous environment, has not received enough attention yet. We employed the time-dependent density functional calculations to investigate the water effect of photoluminescence (PL) spectra for Si QDs. In contrast with the absorption spectra, PL spectra exhibit distinct characteristics. For Si32H38, PL presents the single maximum in the dry and humid environment, while the emission spectrum displays a dual-band fluorescence spectroscopy in the low-humidity environment. This phenomenon is also observed in the larger Si QDs. The distinct character in spectroscopy is dominated by the stretching of the Si-Si bond, which could be explained by the self-trapped exciton model. Our results shed light on the Si-water interaction that is important for the development of optical devices based on Si-coated surfaces.

Imprint Control of BaTiO3 Thin Films via Chemically Induced Surface Polarization Pinning.

Surface-adsorbed polar molecules can significantly alter the ferroelectric properties of oxide thin films. Thus, fundamental understanding and controlling the effect of surface adsorbates are crucial for the implementation of ferroelectric thin film devices, such as ferroelectric tunnel junctions. Herein, we report an imprint control of BaTiO3 (BTO) thin films by chemically induced surface polarization pinning in the top few atomic layers of the water-exposed BTO films. Our studies based on synchrotron X-ray scattering and coherent Bragg rod analysis demonstrate that the chemically induced surface polarization is not switchable but reduces the polarization imprint and improves the bistability of ferroelectric phase in BTO tunnel junctions. We conclude that the chemical treatment of ferroelectric thin films with polar molecules may serve as a simple yet powerful strategy to enhance functional properties of ferroelectric tunnel junctions for their practical applications.

Relaxation dynamics of surface-adsorbed water molecules in nanoporous silica probed by terahertz spectroscopy

Relaxation dynamics of an exclusively adsorbed water molecule in mesoporous silica MCM-41-S was studied by using terahertz spectroscopy. With the temperature controlled from 0 to 50 °C, we observed strongly frequency- and temperature-dependent dielectric relaxation responses, implying that, unlike ice, surface-adsorbed water molecules retained flourishing picosecond dynamics. Based on the Debye relaxation model, a relaxation time constant was found to increase from 1.77 to 4.83 ps when the water molecule was cooled from 50 to 0 °C. An activation energy of ∼15 kJ/mol, which was in close agreement with a hydrogen-bonding energy, was further extracted from the Arrhenius analysis. Combined with previous molecular dynamics simulations, our results indicate that the reorientation relaxation originated from the “flip-flop” rotation of a three hydrogen-bonded surface-adsorbed water molecule.

Localized Probing of Gas Molecule Adsorption Energies and Desorption Attempt Frequencies

Gas-mediated electron beam induced etching (EBIE) and deposition (EBID) can be used to measure activation energies that are interpreted as the adsorption energies of surface-adsorbed precursor molecules. However, the measured quantities often disagree with adsorption energies measured by conventional analysis techniques such as thermally programmed desorption and have anomalous dependencies on parameters such as the electron beam current used to perform EBID. Here, we use the theory of EBIE and EBID rate kinetics to explain this behavior and identify conditions under which the activation energies and the associated pre-exponential factors correspond to gas molecule adsorption energies and desorption attempt frequencies, respectively. Under these conditions, EBIE and EBID can be used as robust, nanoscale techniques for the analysis of adsorbates.

When are antifreeze proteins in solution essential for ice growth inhibition?

Antifreeze proteins (AFPs) are a widespread class of proteins that bind to ice and facilitate the survival of organisms under freezing conditions. AFPs have enormous potential in applications that require control over ice growth. However, the nature of the binding interaction between AFPs and ice remains the subject of debate. Using a microfluidics system developed in-house we previously showed that hyperactive AFP from the Tenebrio molitor beetle, TmAFP, remains bound to an ice crystal surface after exchanging the solution surrounding the ice crystal to an AFP-free solution. Furthermore, these surface-adsorbed TmAFP molecules sufficed to prevent ice growth. These experiments provided compelling evidence for the irreversible binding of hyperactive AFPs to ice. Here, we tested a moderately active type III AFP (AFPIII) from a fish in a similar microfluidics system. We found, in solution exchange experiments that the AFPIIIs were also irreversibly bound to the ice crystals. However, some crystals displayed "burst" growth during the solution exchange. AFPIII, like other moderately active fish AFPs, is unable to bind to the basal plane of an ice crystal. We showed that although moderate AFPs bound to ice irreversibly, moderate AFPs in solution were needed to inhibit ice growth from the bipyramidal crystal tips. Instead of binding to the basal plane, these AFPs minimized the basal face size by stabilizing other crystal planes that converge to form the crystal tips. Furthermore, when access of solution to the basal plane was physically blocked by the microfluidics device walls, we observed enhancement of the antifreeze activity. These findings provide direct evidence that the weak point of ice growth inhibition by fish AFPs is the basal plane, whereas insect AFPs, which can bind to the basal plane, are able to inhibit its growth and thereby increase antifreeze activity.

Athrombogenic hydrogel coatings for medical devices – Examination of biological properties

In the article the authors present hydrogel coatings prepared from polyvinylpyrrolidone (PVP) macromolecules, which are chemically bonded to polyurethane (PU) substrate. The coating is designed to improve the surface hemocompatibility of blood-contacting medical devices.The coating was characterized in terms of physical properties (swelling ratio, hydrogel density, surface morphology, coating thickness, coating durability). In order to examine surface hemocompatibility, the materials were contacted with whole human blood under arterial flow simulated conditions followed by calculation of platelet consumption and the number of platelet aggregates. Samples were also contacted with platelet-poor plasma; the number of surface-adsorbed fibrinogen molecules was measured using ELISA assay. Finally, the inflammatory reaction after implantation was assessed, using New Zealand rabbits.The designed coating is characterized by high water content and excellent durability in aqueous environment – over a 35-day period, no significant changes in coating thickness were observed. Experiments with blood proved twice the reduction in adsorption of serum-derived fibrinogen together with a moderate reduction in the number of platelet aggregates formed during the contact of the material with blood. The analysis of an inflammatory reaction after the implantation confirmed high biocompatibility of the fabricated materials – studies have shown no toxic effects of the implanted material on the surrounding animal tissues.

A Generalized Model on the Effects of Nanoparticles on Fluorophore Fluorescence in Solution

Nanoparticles (NP) can modify fluorophore fluorescence in solution through multiple pathways that include fluorescence inner filter effect (IFE), dynamic and static quenching, surface enhancement, and fluorophore quantum yield variation associated with structural and conformational modifications induced by NP binding. The combined contribution of the latter three effects is termed the collective near-field effect because (1) they affect only fluorophore fluorescence in molecules close to the NPs, and (2) it is impossible to differentiate these effects with steady-state fluorescence measurements. A generalized model (F0corr/FNPcorr = (1 + K[NP])/(1 + K[NP]S) was developed for the determination of the NP collective near-field effect S on the fluorophore fluorescence in the surface-adsorbed molecules. The popular Stern–Volmer equation (F0corr/FNPcorr = (1 + K[NP]) used in current fluorescence studies of NP interfacial interactions is a special case of this generalized model, valid only under situations in which the surface-bound molecules are completely fluorescence inactive (S = 0). In addition, we excluded the possibility of NPs inducing significant dynamic fluorescence quenching under realistic experimental conditions on the basis of a simple back-of-the-envelope calculation. Furthermore, using an external reference fluorescence IFE correction method developed in this work, we demonstrated that gold nanoparticles (AuNPs) only slightly attenuate, but do not completely quench the fluorescence signal of the protein, bovine serum albumin (BSA), on AuNP. This result undermines the reliability of the BSA/AuNP binding constants calculated using the Stern–Volmer equation in earlier studies of BSA/AuNP interfacial interactions. The methodology and insights provided in this work should be of general importance for fluorescence study of nanoparticle interfacial interactions.

Localized conductive patterning via focused electron beam reduction of graphene oxide

We report on a method for “direct-write” conductive patterning via reduction of graphene oxide (GO) sheets using focused electron beam induced deposition (FEBID) of carbon. FEBID treatment of the intrinsically dielectric graphene oxide between two metal terminals opens up the conduction channel, thus enabling a unique capability for nanoscale conductive domain patterning in GO. An increase in FEBID electron dose results in a significant increase of the domain electrical conductivity with improving linearity of drain-source current vs. voltage dependence, indicative of a change of graphene oxide electronic properties from insulating to semiconducting. Density functional theory calculations suggest a possible mechanism underlying this experimentally observed phenomenon, as localized reduction of graphene oxide layers via interactions with highly reactive intermediates of electron-beam-assisted dissociation of surface-adsorbed hydrocarbon molecules. These findings establish an unusual route for using FEBID as nanoscale lithography and patterning technique for engineering carbon-based nanomaterials and devices with locally tailored electronic properties.

Effect of Methylation on the Nanomechanics of Double-Stranded DNA

In its physiological environment DNA is constantly exposed to mechanical stress. The nanomechanical properties of DNA influence not only its response to stress but also its interaction with proteins. Despite its crucial role in epigenetics, little is known about how methylation affects the nanomechanical properties of DNA. To investigate the impact of methylation on DNA nanomechanics, here we manipulated single molecules of chemically or enzymatically methylated DNA and compared their properties with those of non-methylated DNA. As a model we used a 3312-base-pair long sequence of lambda-phage DNA that met the criteria of a CpG island. Chemically methylated DNA was prepared with PCR containing 5-methyl-CTP in the reaction mixture. For enzymatic methylation the M.Sss.I methyltransferase was used. Single DNA molecules were mechanically manipulated with force-measuring optical tweezers in repeated stretch-relaxation cycles. Surface-adsorbed DNA molecules were studied by using atomic force microscopy (AFM). We found that the molecular contour length, bending rigidity and intrinsic stiffness were decreased in methylated DNA, pointing at structural and nanomechanical alterations. Furthermore, the cooperative overstretch transition was significantly longer in the methylated form of the molecule, suggesting that the dynamics of intramolecular rearrangements were also affected. AFM measurements of DNA molecules adsorbed to mica surface substantiated the significant reduction of molecular contour length in methylated DNA. By contrast, the apparent bending rigidity of the surface-adsorbed methylated DNA was increased, which is most likely caused by interactions between DNA and the mica surface. In sum, methylation leads to an axial compaction of the dsDNA structure, an increase in bending flexibility in the low-force regime and an increase in axial compliance at higher forces (>20pN). Conceivably, modulation of DNA structure and nanomechanics caused by methylation leads to a complex control of structural accessibility and association kinetics of DNA-binding proteins.

Subtractive 3D printing of optically active diamond structures.

Controlled fabrication of semiconductor nanostructures is an essential step in engineering of high performance photonic and optoelectronic devices. Diamond in particular has recently attracted considerable attention as a promising platform for quantum technologies, photonics and high resolution sensing applications. Here we demonstrate the fabrication of optically active, functional diamond structures using gas-mediated electron beam induced etching (EBIE). The technique achieves dry chemical etching at room temperature through the dissociation of surface-adsorbed H2O molecules by energetic electrons in a water vapor environment. Parallel processing is possible by electron flood exposure and the use of an etch mask, while high resolution, mask-free, iterative editing is demonstrated by direct write etching of inclined facets of diamond microparticles. The realized structures demonstrate the potential of EBIE for the fabrication of optically active structures in diamond.

Electronic Circular Dichroism of Surface-Adsorbed Molecules by Means of Quantum Mechanics Capacitance Molecular Mechanics

To promote a more comprehensive understanding of the influence of metal–adsorbate interaction for molecules at metallo surfaces or metallo nanoparticles in solvent environments on their electronic circular dichroism (ECD) spectra, we evaluate the application of a recently derived quantum mechanics capacitance molecular mechanics (QMCMM) model for ECD. Using helicene absorbed on gold surfaces in protic and aprotic solvents as illustration, we elucidate the detailed effects on excitation energies, transition moments, rotatory strengths, orientation dependence of ECD spectra, and the different roles of aprotic and protic solvents and the induced charge distribution patterns on the surface. These changes are decomposed in terms of surface alone, solvent alone, and combined surface–solvent influence, and furthermore into the indirect contributions by the surface-induced restructuring of the helicene. Much of the salient changes of the ECD can be rationalized to the substantial redistribution of charge at the gold surface induced by the presence of the helicene. The study indicates that through the QMCMM model the effects of a metallic surface on the circular dichroism spectra of adsorbed organic molecules can be tackled by extended QM calculations coupled to polarizability–capacitance force fields for large metallic clusters representing surfaces or nanoparticles.

Conformational distribution of surface-adsorbed fibronectin molecules explored by single molecule localization microscopy.

Adsorbed proteins that promote cell adhesion mediate the response of cells to biomaterials and scaffolds. As proteins undergo conformational changes upon surface adsorption, their functional display may be significantly affected by surface chemistry or solution conditions during the adsorption process. A high-resolution localization microscopy technique is extended here to probe the conformation of individual fibronectin (Fn) molecules at the glass-water interface under physiological buffer conditions. To map distances, four available cysteines located on the modules FnIII7 and FnIII15 of dimeric Fn were site-specifically labeled with Cy3B, and their relative positions were determined by stepwise photobleaching with nanometer precision. The four labels on single Fn molecules did not show a uniform or linear arrangement. The distances between label positions were distributed asymmetrically around 33 nm with a tail towards higher distances. Exposure of Fn to denaturing solution conditions during adsorption increased the average distances up to 43 nm for 4 M guanidinium HCl, while changing the solution conditions after the adsorption had no effect, indicating that the observed intra-molecular distances are locked-in during the adsorption process. Also surface coatings of different hydrophobicity altered the conformational distribution, shifting label distances from a median of 24 nm on hydrophilic to 49 nm on hydrophobic surfaces. These results further highlight that the conformation of macromolecules at interfaces depends on the adsorption history. While illustrated here for surface adsorbed Fn, the power of localization-based microscopy extends the repertoire of techniques to characterize biomolecules at interfaces.