Vibrations of a single adsorbed organic molecule: anharmonicity matters!

Computational vibrational spectroscopy of molecule-surface interactions: what is still difficult and what can be done about it

Interactions of molecules with solid surfaces are responsible for key functionalities for a range of currently actively pursued technologies, including heterogeneous catalysis for synthesis or decomposition of molecules, sensitization, surface...

Discrimination between hydrogen bonding and protonation in the spectra of a surface-enhanced Raman sensor

Adsorbed mercaptopyridine can sense hydrogen-bonding because the ring breathing mode has a different frequency from bare and protonated species.

Evidence for Ultralow-Energy Vibrations in Large Organic Molecules

The quantum efficiency or the rate of conversion of incident photon to free electron in photosynthesis is known to be extremely high. It has long been thought that the origin of this efficiency are molecular vibrations leading to a very fast separation of electrons and holes within the involved molecules. However, molecular vibrations are commonly in the range above 100 meV, which is too high for excitations in an ambient environment. Here, we analyze experimental spectra of single organic molecules on metal surfaces at ∼4 K, which often exhibit a pronounced dip. We show that measurements on iron(II) [tetra-(pentafluorophenyl)]porphyrin resolve this single dip at 4 K into a series of step-shaped inelastic excitations at 0.4 K. Via extensive spectral maps under applied magnetic fields and corresponding theoretical analysis we find that the dip is due to ultralow-energy vibrations of the molecular frame, typically in the range below 20 meV. The result indicates that ultralow energy vibrations in organic molecules are much more common than currently thought and may be all-pervasive for molecules above a certain size.

Vibrational Signature of a Single Water Molecule Adsorbed on Pt(111): Toward a Reliable Anharmonic Description

In this study, we present a thorough benchmarking of our direct anharmonic vibrational variation-perturbation approach for adsorbed molecules on surfaces. We then use our method to describe the vibrational structure of a water molecule adsorbed on a Pt(111) surface and compare our results with the available experimental data. By using an explicitly correlated hybrid method to describe the molecule-surface interaction, we improve on the initial periodic PBE/DZP potential energy landscape and obtain vibrational frequencies that are of near-experimental accuracy. We introduce an implementation of anharmonic z-polarized IR intensity calculation and explain the absence of antisymmetric O-H stretch in the experimental data for the adsorbed water molecule, while the symmetric O-H stretch is predicted to be visible.

Temperature effects in the vibrational spectra of self-assembled monolayers

The vibrational spectrum of a thiolate-based self-assembled monolayer fabricated by the adsorption of benzylmercaptan on a Au(111) substrate is studied using a combined experimental and theoretical approach employing infrared reflection absorption spectroscopy and density functional theory. The vibrational spectra are derived both using a finite differences approach and from ab initio molecular dynamics simulations at various temperatures. In addition, the possibility of adsorbate-induced reconstructions of the Au(111) substrate is taken into account. It turns out that the measured spectra can only be understood by taking finite temperatures into account.

Analysis of rich inelastic electron tunneling spectra: case study of terthiophene on Au(111)

Even moderately small molecules like 2,2':5',2"-terthiophene exhibit quite rich vibrational spectra. Detection and assignment of vibronic transitions of such a single adsorbed molecule in inelastic electron tunneling spectroscopy (IETS) using scanning tunneling microscopy are notoriously hampered by noise and the low efficiency of inelastic channels of typically well below 1%. We demonstrate by a thorough statistical analysis that detection of almost all predicted transitions can be determined experimentally within the energy range 0-120 meV with an estimated detection limit for the efficiency of inelastic channels of ∼0.15%. The maximum accuracy of our transition energies is 2 meV and thus smaller than the thermal broadening at 5 K. On short time scales up to some hours, that accuracy appears to be limited by tunneling current noise. The present analysis confirms earlier results which showed that IETS obeys propensity rules rather than selection rules as observed for optical transitions. Furthermore, the previous indications that anharmonic components in the interaction potentials are important for calculating properties of molecular vibrations were corroborated.

Towards Accurate Spectroscopic Identification of Species at Catalytic Surfaces: Anharmonic Vibrations of Formate on AuPt

We present a calculation of vibrational frequencies of formate on the AuPt(111) surface alloy including full anharmonicity and coupling of all six intramolecular degrees of freedom. This species is a key intermediate in methanol oxidation on this material. We use a modified version of the method of Manzhos and Carrington to compute the spectrum directly from a small number (<10,000) of DFT single-point energies, bypassing the construction of a potential energy surface. This is the first such calculation for a 4-atomic species at a surface. The spectrum is obtained using rectangular collocation and a small basis set of parameterized Hermite functions. The achievable accuracy of the order of several cm-1 corresponds to the typical experimental resolution. Using normal coordinates makes the equations simple and general and easily applicable to other systems. This calculation is doable on a PC. We predict that anharmonicity and coupling lower the fundamental frequencies by dozens of cm-1, which could affect species assignment.

Towards a scalable and accurate quantum approach for describing vibrations of molecule-metal interfaces

We present a theoretical framework for the computation of anharmonic vibrational frequencies for large systems, with a particular focus on determining adsorbate frequencies from first principles. We give a detailed account of our local implementation of the vibrational self-consistent field approach and its correlation corrections. We show that our approach is both robust, accurate and can be easily deployed on computational grids in order to provide an efficient computational tool. We also present results on the vibrational spectrum of hydrogen fluoride on pyrene, on the thiophene molecule in the gas phase, and on small neutral gold clusters.

Influence of water on the properties of an Au/Mpy/Pd metal/molecule/metal junction

The geometric and electronic structure of the metal-molecule interface in metal/molecule/metal junctions is of great interest since it affects the functionality of such units in possible nanoelectronic devices. We have investigated the interaction between water and a palladium monolayer of a Au(111)/4-mercaptopyridine/Pd junction by means of DFT calculations. A relatively strong bond between water and the palladium monolayer of the Au/Mpy/Pd complex is observed via a one-fold bond between the oxygen atom of the water molecule and a Pd atom. An isolated H(2)O molecule adsorbs preferentially in a flat-lying geometry on top of a palladium atom that is at the same time also bound to the nitrogen atom of a Mpy molecule of the underlying self-assembled monolayer. The electronic structure of these Pd atoms is considerably modified which is reflected in a reduced local density of states at the Fermi energy. At higher coverages, water can be arranged in a hexagonal ice-like bilayer structure in analogy to water on bulk metal surfaces, but with a much stronger binding which is dominated by O-Pd bonds.