Vibrational spectroscopy for glycine adsorbed on silicon clusters: Harmonic and anharmonic calculations for models of the Si(1 0 0)-2 × 1 surface

The vibrational spectroscopy of a glycine molecule adsorbed on a silicon surface is studied computationally, using different clusters as models for the surface. Harmonic frequencies are computed using density functional theory (DFT) with the B3LYP functional. Anharmonic frequency calculations are carried out using vibrational self-consistent field (VSCF) algorithms on an improved PM3 potential energy surface. The results are compared with experiments on Glycine@Si(1 0 0)-2 × 1.

The main findings are: (1) Agreement of the computed frequencies with experiment improves with cluster size. (2) The anharmonic calculations are generally in better agreement with experiment than the harmonic ones. The improvements due to anharmonicity are most significant for hydrogenic stretching. (3) An important part of the anharmonic effects is due to anharmonic coupling between different normal modes of the system. (4) The anharmonic coupling between glycine vibrational modes is much larger than the anharmonic coupling between glycine and “phonon” (cluster) modes.

Implications of the results for surface vibrational spectroscopy are discussed.     

Influence of water on anharmonicity, stability, and vibrational energy distribution of hydrogen-bonded adducts in atmospheric reactions: case study of the OH + isoprene reaction intermediate using ab initio molecular dynamics

The effect of water on the stability and vibrational states of a hydroxy-isoprene adduct is probed through the introduction of 1-15 water molecules. It is found that when a static nuclear harmonic approximation is invoked there is a substantial red-shift of the alcohol O-H stretch (of the order of 800 cm(-1)) as a result of introduction of water. When potential energy surface sampling and associated anharmonicities are introduced through finite temperature ab initio dynamics, this hydroxy-isoprene OH stretch strongly couples with all the water vibrational modes as well as the hydroxy-isoprene OH bend modes. A new computational technique is introduced to probe the coupling between these modes. The method involves a two-dimensional, time-frequency analysis of the finite temperature vibrational properties. Such an analysis not only provides information about the modes that are coupled as a result of finite-temperature analysis, but also the temporal evolution of such coupling.     

Dynamics of a laser-irradiated adatom

The dynamics of an adsorbed atom irradiated by an I.R. laser in resonance with a single pair of states of the vibrational adbond is studied. Using a non-perturbative treatment for the laser-adbond interaction, a master equation is derived, which governs the time evolution of the populations of the laser-dressed states of the adbond. The effect of resonant heating and laser-induced desorption, as an example of a possible laser-induced surface process, is discussed.     

Taylor expansion of polymer chain dispersion relations and spectral densities to calculate thermodynamic functions

It is shown how to calculate exactly the derivatives of the dispersion relation and the spectral density for arbitrary regular polymer chains in harmonic approximation. The theory is based on a generalization of the characteristic polynomial. In the vibrational part of the free energy and other thermodynamic functions, the integral over normal modes is done approximately by Taylor expanding the density of states.Dedicated to Professor Dr. F. H. Müller.     

Optimal control in a dissipative system: vibrational excitation of CO/Cu(100) by IR pulses

The question as to whether state-selective population of molecular vibrational levels by shaped infrared laser pulses is possible in a condensed phase environment is of central importance for such diverse fields as time-resolved spectroscopy, quantum computing, or "vibrationally mediated chemistry." This question is addressed here for a model system, representing carbon monoxide adsorbed on a Cu(100) surface. Three of the six vibrational modes are considered explicitly, namely, the CO stretch vibration, the CO-surface vibration, and a frustrated translation. Optimized infrared pulses for state-selective excitation of "bright" and "dark" vibrational levels are designed by optimal control theory in the framework of a Markovian open-system density matrix approach, with energy flow to substrate electrons and phonons, phase relaxation, and finite temperature accounted for. The pulses are analyzed by their Husimi "quasiprobability" distribution in time-energy space.     

Langevin model of the temperature and hydration dependence of protein vibrational dynamics

The modification of internal vibrational modes in a protein due to intraprotein anharmonicity and solvation effects is determined by performing molecular dynamics (MD) simulations of myoglobin, analyzing them using a Langevin model of the vibrational dynamics and comparing the Langevin results to a harmonic, normal mode model of the protein in vacuum. The diagonal and off-diagonal Langevin friction matrix elements, which model the roughness of the vibrational potential energy surfaces, are determined together with the vibrational potentials of mean force from the MD trajectories at 120 K and 300 K in vacuum and in solution. The frictional properties are found to be describable using simple phenomenological functions of the mode frequency, the accessible surface area, and the intraprotein interaction (the displacement vector overlap of any given mode with the other modes in the protein). The frictional damping of a vibrational mode in vacuum is found to be directly proportional to the intraprotein interaction of the mode, whereas in solution, the friction is proportional to the accessible surface area of the mode. In vacuum, the MD frequencies are lower than those of the normal modes, indicating intramolecular anharmonic broadening of the associated potential energy surfaces. Solvation has the opposite effect, increasing the large-amplitude vibrational frequencies relative to in vacuum and thus vibrationally confining the protein atoms. Frictional damping of the low-frequency modes is highly frequency dependent. In contrast to the damping effect of the solvent, the vibrational frequency increase due to solvation is relatively temperature independent, indicating that it is primarily a structural effect. The MD-derived vibrational dynamic structure factor and density of states are well reproduced by a model in which the Langevin friction and potential of mean force parameters are applied to the harmonic normal modes.     

Monosodium glutamate in its anhydrous and monohydrate form: differentiation by Raman spectroscopies and density functional calculations

Monosodium glutamate (MSG), a common flavor enhancer, is detected in aqueous solutions by Raman and surface-enhanced Raman (SERS) spectroscopies at the micromolar level. The presence of different species, such as protonated and unprotonated MSG, is demonstrated by concentration and pH dependent Raman and SERS experiments. In particular, the symmetric bending modes of the amino group and the stretching modes of the carboxy moiety are employed as marker bands. The protonation of the NH(2) group at acidic pH values, for example, is detected in the Raman spectra. From the measured SERS spectra, a strong chemical interaction of MSG with the colloidal particles is deduced and a geometry of MSG adsorbed on the silver surface is proposed. In order to assign the observed Raman bands, calculations employing density functional theory (DFT) were performed. The calculated geometries, harmonic vibrational wavenumbers and Raman scattering activities for both MSG forms are in good agreement with experimental data. The set of theoretical data enables a complete vibrational assignment of the experimentally detected Raman spectra and the differentiation between the anhydrous and monohydrate forms of MSG.     

Two bonding configurations of acetylene on Si(001)-(2 x 1): a combined high-resolution electron energy loss spectroscopy and density functional theory study

Two coexisting adsorption states of molecularly adsorbed acetylene on the Si(001)-(2 x 1) surface have been identified by a combined study based on the high-resolution electron energy loss spectroscopy and density functional computations. Seven possible adsorbate-substrate structures are considered theoretically including their full vibrational analysis. Based on a significantly enhanced experimental resolution, the assignment of 15 C2H2- and C2D2-derived vibrational modes identifies a dominant di-sigma bonded molecule adsorbed on top of a single Si-Si dimer. Additionally there is clear evidence for a second minority species which is di-sigma bonded between two Si-Si dimers within the same dimer row (end-bridge geometry). The possible symmetries of the adsorbate complexes are discussed based on the specular and off-specular vibrational measurements. They suggest lower than ideal C(2v) and C(s) symmetries for on-top and end-bridge species, respectively. At low coverages the symmetry reductions might be lifted.     

Vibrational relaxation in simulated two-dimensional infrared spectra of two amide modes in solution

Two-dimensional infrared spectroscopy is capable of following the transfer of vibrational energy between modes in real time. We develop a method to include vibrational relaxation in simulations of two-dimensional infrared spectra at finite temperature. The method takes into account the correlated fluctuations that occur in the frequencies of the vibrational states and in the coupling between them as a result of interaction with the environment. The fluctuations influence the two-dimensional infrared line shape and cause vibrational relaxation during the waiting time, which is included using second-order perturbation theory. The method is demonstrated by applying it to the amide-I and amide-II modes in N-methylacetamide in heavy water. Stochastic information on the fluctuations is obtained from a molecular dynamics trajectory, which is converted to time dependent frequencies and couplings with a map from a density functional calculation. Solvent dynamics with the same frequency as the energy gap between the two amide modes lead to efficient relaxation between amide-I and amide-II on a 560 fs time scale. We show that the cross peak intensity in the two-dimensional infrared spectrum provides a good measure for the vibrational relaxation.     

The effects of electron-hole pair coupling on the infrared laser-controlled vibrational excitation of NO on Au(111)

In this work, we present theoretical simulations of laser-driven vibrational control of NO adsorbed on a gold surface. Our goal is to tailor laser pulses to selectively excite specific modes and vibrational eigenstates, as well as to favor photodesorption of the adsorbed molecule. To this end, various control schemes and algorithms are applied. For adsorbates at metallic surfaces, the creation of electron-hole pairs in the substrate is known to play a dominant role in the transfer of energy from the system to the surroundings. These nonadiabatic couplings are included perturbatively in our reduced density matrix simulations using a generalization of the state-resolved position-dependent anharmonic rate model we recently introduced. An extension of the reduced density matrix is also proposed to provide a sound model for photodesorption in dissipative systems.     

Crown ethers at the aqueous solution-air interface: 1. Assignments and surface spectroscopy

The surface of aqueous solutions of 4-Nitro Benzo-15-Crown-5 (NB15C5) and Benzo-15-Crown-5 (B15C5) has been studied using the surface sensitive technique vibrational sum frequency spectroscopy (VSFS). The NO, CN, COC and CH vibrational modes of these compounds at the air-water interface as well as OH vibrational modes of the surface water hydrating this compound have been targeted in order to obtain molecular information about arrangement and conformation of the adsorbed crown ether molecules at the air-water interface. The CH(2) vibrational modes of crown ethers have been identified and found to be split due to interaction with ether oxygen. The spectra provide evidence for the existence of a protonated crown complex moiety at the surface leading to the appearance of strongly ordered water species. The interfacial water species are influenced by the resulting charged interface and by the strong Zundel polarizability due to tunneling of the proton species between equivalent sites within the crown ring.     

CN在 Pt(100)表面吸附的密度泛函研究

采用密度泛函方法,以原子簇Pt14为模拟表面,对CN自由基分子在Pt(100)表面上不同吸附位的吸附情况进行了研究.结果表明,CN分子吸附在Pt(100)面上时,通过原子C垂直吸附在表面顶位是其最佳吸附方式,CN键振动频率明显发生蓝移,与实验事实相吻合;而在桥位及四方穴位吸附时CN键振动频率均发生红移.吸附前后,CN分子的σ、π电子与底物间的电荷转移的差异决定了CN键振动频率的不同变化.     

Small Al clusters on the Cu(111) surface: Atomic relaxation and vibrational properties

The relaxation and vibrational properties of both Al clusters and the (111) surface of a copper sub-strate were studied using the interatomic interaction potentials obtained in a tight-binding approximation. The presence of small aluminum clusters led to modification of the vibrational states of the substrate, a shift of the Rayleigh mode, and excitation of new Z-polarized modes. Hybridized modes localized on the cluster adatoms and the neighboring atoms of the substrate were found in the phonon spectrum. The localized dipole-active modes of the cluster and their strong hybridization with vibrations of the substrate points to desorption stability of the tri- and heptaatomic clusters.     

Chemical imaging of single 4,7,12,15-tetrakis[2.2]paracyclophane by spatially resolved vibrational spectroscopy

Single 4,7,12,15-tetrakis[2.2]paracyclophane were deposited on NiAl(110) surface at 11 K. Two adsorbed species with large and small conductivities were detected by the scanning tunneling microscope (STM). Their vibrational properties were investigated by inelastic electron tunneling spectroscopy (IETS) with the STM. Five vibrational modes were observed for the species with the larger conductivity. The spatially resolved vibrational images for the modes show striking differences, depending on the coupling of the vibrations localized on different functional groups within the molecule to the electronic states of the molecule. The vibrational modes are assigned on the basis of ab initio calculations. No IETS signal is resolved from the species with the small conductivity.     

Wettability of tri-block copolymer coated hydrophobic surfaces Predictions and measurements

Hydrophobic surfaces with adsorbed tri-block copolymers are wetted by oil in spite of the hydrophilic buoy groups of the block copolymer that are present near the surface. The effect of the buoy group length of the adsorbed molecules on the wettability of hydrophobic surfaces is studied by contact angle measurements and by computer modelling.

The computer model predicts an increase in interfacial free energy with increasing buoy group length for equilibrium adsorption of block copolymer from water. Molecules with large buoy groups occupy more lateral space; therefore the “bare” surface gets more exposed and the anchor groups contribute less to the interfacial free energy which thus increases with the buoy group length.

The calculations showed that the variation of the interaction parameter between solvent and buoy group hardly influences the interfacial free energy. In contrast the interaction parameter between solvent and surface influences the interfacial free energy to a large extent because the oil/surface interactions have a lower energetic value as compared to water/surface interactions and therefore the interfacial free energy is lower than in water. The interfacial free energy varies slightly with increasing buoy group length, depending on the value chosen for the solvent/surface interaction parameter.

Advancing and receding contact angles of hexadecane, sunflower oil and hydrolysate (partly hydrolysed sunflower oil) were measured on hydrophobic surfaces. All oil/water contact angles were small, indicating a hydrophobic apolar surface character. It was found that, for oils with a “good” interaction with the surface (hexadecane and sunflower oil), the contact angle has a minimum value at a certain buoy group length. For hydrolysate (less-strong interaction with the surface) the contact angle decreases monotonically with increasing buoy group length. The results for hexadecane, sunflower oil and hydrolysate are in reasonable agreement with the model predictions. The effect of increasing buoy group length is weak; both decreasing and increasing angles are found, depending on the type of oil used.     

Vibronic states in single molecules: C60 and C70 on ultrathin Al2O3 films

Vibronic states are observed in single C(60) and C(70) molecules by scanning tunneling microscopy. When single fullerene molecules are adsorbed on a thin layer of Al(2)O(3) grown on a NiAl(110) substrate, equally spaced features are observed in the differential conductance (dI/dV), which are clearly resolved in d(2)I/dV(2) spectra. These features are attributed to the vibronic states of the molecule. The vibronic progressions are sensitive to the molecular orientations and can have different spacings in different electronic bands of the same molecule. For C(60,) these vibronic states are associated with the intramolecular A(g) and H(g) vibrational modes. Vibronic states are not resolved in molecules adsorbed on the metal surface. However, inelastic electron tunneling spectroscopy exhibits a vibrational mode at 64 meV for C(60) and 61 meV for C(70) adsorbed on NiAl(110).     

Semiflexible polymers grafted to a solid planar substrate: changing the structure from polymer brush to "polymer bristle"

Monte Carlo simulations are presented for a coarse-grained model of polymer brushes with polymers having a varying degree of stiffness. Both linear chains and ring polymers grafted to a flat structureless non-adsorbing substrate surface are considered. Applying good solvent conditions, it is shown that with growing polymer stiffness the brush height increases significantly. The monomer density profiles for the case of ring polymers (chain length N(R) = 64) are very similar to the case of corresponding linear chains (N(L) = 32, grafting density larger by a factor of two) in the case of flexible polymers, while slight differences appear with increasing stiffness. Evidence is obtained that the chain dynamics in brushes is slowed down dramatically with increasing stiffness. Very short stiff rings (N(R) ≤ 16) behave like disks, grafted to the substrate such that the vector, perpendicular to the disk plane, is oriented parallel to the substrate surface. It is suggested that such systems can undergo phase transitions to states with liquid crystalline order.     

Effect of grafting on nanoparticle segregation in polymer/nanoparticle blends near a substrate

Nanoparticles in polymer films have shown the tendency to migrate to the substrate due to an entropic-based attractive depletion interaction between the particles and the substrate. It is also known that polymer-grafted nanoparticles show better dispersion in a polymer matrix. Here, molecular dynamics simulations are employed to study the effect of grafting on the nanoparticle segregation to the substrate. The nanoparticles were modeled as spheres and the polymers as bead-spring chains. The polymers of the grafts and the matrix are identical in nature. For a purely repulsive system, the nanoparticle density near the surface was found to decrease as the length of grafted chains and the number of grafts increased and in the bulk, the nanoparticles are well-dispersed. Whereas, in case of attractive systems with interparticle interactions on the order of thermal energy, the nanoparticles segregated to the substrate even more strongly, essentially forming clusters on the wall and in the bulk. However, due to the presence of grafted chains on the nanoparticles, the clusters formed in the bulk are structurally anisotropic. The effect of grafts on nanoparticle segregation to the surface was found to be qualitatively similar to the purely repulsive case.     

Vibrational lineshapes of adsorbates on solid surfaces

A review is presented of the current activity in vibrational spectroscopy of adsorbates on metal surfaces. A brief introduction of the representative spectroscopies is given to demonstrate the rich information contained in vibrational spectra, which are characterized by their intensity, peak position and width. Analysis of vibrational spectra enables us to gain the deep insight into not only the local character of adsorption site or geometry, but also the dynamical interaction between the adsorbates or between the adsorbate and the substrate. Some recent instructive experimental results, mostly of a CO molecule adsorbed on various metal surfaces, are accompanied by the corresponding theoretical recipe for vibrational excitation mechanisms. Wide spread experimental results of the C-O stretching frequency of CO adsorbed on metal surfaces are discussed in terms of the chemical effect involving the static and dynamic charge transfers between the chemisorbed CO and metal, and also of the electrostatic dipole-dipole interaction between the molecules. The central subject of this review is directed to the linshapes characterized by the vibrational relaxation processes of adsorbates. A simple and transparent model is introduced to show that the characteristic decay time of the correlation function for the vibrational coordinates is the key quantity to determine the spectral lineshapes. Recent experimental results focused on a search for an intrinsic broadening mechanism are reviewed in the light of the so-called T₁ (energy) and T₂ (phase) relaxation processesof the vibrational excited states of adsorbates. Those are the vibrational energy dissipation into the elementary excitation, such as phonons or electron-hole pairs in the metal substrate, and pure dephasing due to the energy exchange with the sorroundings. The change of width and frequency by varying the experimental variables, such as temperature or isotope effect, provides indispensable knowledge for the dynamical interaction between adsorbate and substrate. Besides spectroscopic studies of adsorbate vibrations, infrared stimulated desorption is chosen as a case study of surface chemical reactions activated by laser radiation. The dynamical processes of photodesorption is discussed in conjunction with infrared absorption, which is followed by its energy dissipation into substrate phonons or molecule-surface bond leading to desorption.