Session N02: Structure and Spectroscopy of Molecules and Clusters

Using Ultrafast XANES and FDMNES Simulations to Examine the Photochemistry of Adenosylcobalamin

Adenosylcobalamin (AdoCbl) is a member of the cobalamin family, a class of molecules that feature a cobalt center with a corrin ring and upper and lower ligands.  Adenosylcobalamin has an adenosyl upper ligand and dimethylbenzimidazole lower ligand.  The photochemistry of AdoCbl is important due to its central role in the CarH photoreceptor, found in bacterial species such as M. xanthus.  Time-resolved X-ray absorption near-edge structure (XANES) is a method of examining the excited states of molecules, with the capability of studying structural change.  The use of polarization selection allows for the deconvolution of structural change in molecule-fixed directions.  Extensive time-resolved XANES data have been collected on AdoCbl in varying solvents.  In order to assign specific spectral changes to structural changes in the AdoCbl, the XANES spectra must be simulated for comparison with the experimental difference spectra.  We use a method called the finite difference method near-edge structure (FDMNES) to simulate the ground and excited state spectra.  FDMNES allows for systematic examination of the structural manipulations needed to reproduce the experimental XANES data.  These simulations permit the identification of sequential structural changes.   

Determining the X-ray absorption signatures of Ga(I) and Ga(III) in molecular complexes and crystals

Ga-based heterogeneous catalysts are the basis for commercial propane dehydroaromatization and can potentially replace Pt- and Cr-based ones in propane dehydrogenation. Based on experimental and theoretical studies, the proposed Ga active sites have a variety of coordination environments and oxidations states. To understand this diversity, we have studied the Ga K-edge XANES of compounds with well-known structures using StoBe, CASTEP and FEFF simulations. We find that for a series of Ga(III) molecular compounds, the position of the intense white line (WL) is modulated by two main factors: 1) Changing the local coordination environment from O to C atoms shifts the position of the empty p-state involved in the WL to higher energies, and 2) variations in the nearest-neighbor distance change the screening of the core-hole and its ionization energy. We also studied well-defined molecular and crystalline Ga(I) compounds to understand how their much more intense observed WL compares to those of compounds containing Ga(III) sites. We find that the increase in WL intensity originates from the presence of not just one empty p-like state, but either two or three of them, depending on the structure of the compounds. This change in intensity could be used to differentiate between oxidation states under realistic reaction conditions.   

Single Molecule Optical Rectification Spectroscopy and Microscopy

Rectification effect is known as the emergence of DC signal due to the existence of an AC signal. It has been widely observed in the systems that have nonlinear I-V response. Rectification current generated by AC bias modulation of frequency range between kHz and THz has been observed on single molecules study with Scanning Tunneling Microscope (STM). However, the rectification signal of single molecules induced by light from near infrared to visible frequency range has not been observed due to the significant tunneling gap oscillation caused by thermal fluctuation from amplitude modulation of light. We apply synchronized tunneling gap modulation to compensate this thermal fluctuation and measure the rectification spectra of a single pyrrolidine molecule adsorbed on a Cu(001) surface irradiated with 780 nm CW light. Our finding indicates a competition between tip enhanced Raman excitation and inelastic electron tunneling excitation of the vibration modes of single molecules.   

CW THz rectification spectroscopy of single molecules in STM tunneling junction

We report rectification spectra obtained for single molecules in the STM junction induced by a frequency-tunable, continuous-wave (CW) THz laser. By focusing the THz beam into the tip-substrate junction of an 8K-STM, we observed rectification current at DC biases where the I-V curve exhibits nonlinearity. The rectification spectra over a single molecule exhibit line shape similar to those obtained by the inelastic electron tunneling spectroscopy (IETS) and provide an alternative way of measuring vibrational modes in a single molecule. Two different methods are proposed for the calibration of THz nearfield at the tip-substrate junction. Variation of the voltage drop induced by the CW THz field across the STM junction was not observed in the measured range of the tip-substrate gap.   

Low Temperature STM Studies of Single Rare-Earth Molecules on Surfaces

Rare-earth metals are important for many technological applications from catalysis, emission, energy up-conversion to quantum information science. Local environment of rare-earth metals play vital role in their applications and engineering of electronic, and magnetic structures of rare-earth systems are of great interest. One of the best options to control the environment of rare-earth ions is to place them in molecular scaffolds where the ligands not only protect them but also can be used to modify their electronic and magnetic properties. Here, we have developed a variety of rare-earth based molecular systems that can be deposited onto materials surfaces intact under ultrahigh vacuum environment. Atomic level characterizations of structural and electronic properties of individual rare-earth molecular systems are performed with a low temperature ultrahigh vacuum scanning tunneling microscope (UHV-LT-STM) capable of single molecule tunneling spectroscopy and controlled manipulation of atoms/molecules on surfaces. dI/dV tunneling spectroscopy, and spectroscopic mapping of single molecules containing caged Eu, La, Lu, and Tb rare-earth metals adsorbed on metal surfaces such as Au(111) and Cu(111) reveal the energy gaps of highest occupied and lowest unoccupied molecular orbitals (HOMO-LUMO) as well as the spatial locations of electronic states within the molecules. The experimental measurements are corroborated by density functional theory calculations to understand their electronic states.   

Chiral Rare-Earth Molecular Clusters

Molecules containing rare-earth ions attract great attention due to their high technological applications, and molecular clusters formed by rare-earth molecules are of interest to explore for potential applications.  Here, we form molecular clusters of La(pcam)3 with quantized sizes composed of 2, 4, and 6 molecules as well as long molecular chains on Au(111) surface. Low temperature scanning tunneling microscopy studies reveal chiral nature of these rare-earth molecular clusters. Mechanical properties of the molecular clusters are investigated with scanning tunneling microscope manipulation as well as imaging using a high bias. We find that all the chiral clusters adsorbed on Au(111) are extremely stable. The electronic structures of the chiral rare-earth molecular clusters are also investigated at the atomic scale using dI/dV tunneling spectroscopy and spectroscopic mapping, which reveal a slight change in the electronic states between pairs of molecules forming the clusters. We propose that such chiral molecular clusters composed of different rare-earth metals may be useful for catalytic, and spintronic applications.   

Two-Dimensional Metal-Organic Frameworks of Rare-Earth Molecular Systems on Surfaces

Metal organic frameworks (MOF) involving rare-earth ions may play important roles in potential applications. Both molecular scaffold and ordered arrangement of rare-earth atoms can contribute to the electronic and magnetic properties of the MOF. Here, we form two-dimensional MOFs of rare-earth based molecular systems on Au(111) surface and their electronic and structural properties are investigated with scanning tunneling microscopy (STM) and tunneling spectroscopy methods in ultrahigh vacuum environment at low temperatures. STM images reveal that both Eu and Tb based molecules form an ordered arrangement of ring like structures composed of 12 molecules each. These molecular rings then form a hexagonal lattice on Au(111) surface. A careful analysis reveals that the molecules are arranged in either left or right-handed stacking and thus the 2-D MOF structure as a whole is chiral. Single point tunneling spectroscopy and spectroscopic mapping of the MOFs are performed at sub-molecular resolution and reveal spatially varying electronic structure within the MOFs. The formation of chiral 2-D MOFs using rare-earth based molecular systems on materials surfaces may pave the way to incorporate them for solid state applications.   

Benchmarking vibrational probe molecules: Dissecting the nitrile spectral response in isolated reporters

We use cryogenic infrared vibrational predissociation spectroscopy of isolated, nitrile-containing vibrational probe molecules to provide benchmarks for the probe molecule spectral response. Popular probes, such as paracyanophenylalanine, and other nitrile-containing molecules are manipulated in solution to modify conformation and charge state prior to extraction and isolation using electrospray ionization and He buffer gas cooling to ~10 K. The vibrational spectra of the cold, He- or H2-tagged molecules are collected in a linear predissociation regime and interpreted with the aid of electronic structure calculations. The results provide insight into the intrinsic spectral response of isolated nitrile vibrational reporters decoupled from solvent effects.

Vibrational probe molecules are popularly employed to provide spectroscopic readouts of local electrostatic environments in phenomena including bulk solvation dynamics, interfacial proton transfer, and enzyme catalysis. A range of these molecules has been developed, allowing investigators to exploit absorption-free "windows" in the infrared spectrum to ease measurement. However, in the condensed phase it is often a challenge to separate the components of the reporter's response arising from external factors, such as local electric fields or hydrogen bonding, from those due to intrinsic factors such as molecular electrostatic potential or reporter isomerization.   

Vibrational many-body perturbation theory for molecules and solids

The second-order Green's function method for anharmonic crystals has been applied to an infinite, periodic chain of polyethylene taking into account up to quartic force constants. The frequency-independent approximation to the Dyson self-energy gives rise to numerous divergent resonances, which are fortuitous. Instead, solving the Dyson equation self- consistently with a frequency-dependent self-energy resists divergences from resonances or zero-frequency acoustic vibrations. The calculated anharmonic phonon dispersion, which nonetheless displays many true resonances, and anharmonic phonon density of states furnish hitherto unknown details that explain smaller features of observed vibrational spectra.   

Anharmonic Vibrational Spectra of Molecular Dimers via Vibrational Perturbation Theory and Hindered Rotor Models

Accurate vibrational frequencies are crucial for the modeling of vibrational spectra and the calculation of free energies at finite temperatures. The anharmonic nature of individual normal modes as well as the coupling between modes can be captured by second-order vibrational perturbation theory (VPT2), which is mainly used to to describe (semi)-rigid isolated molecules. Herein, we assess the quality of VPT2 for intermolecular interactions utilizing a diverse set of small molecular dimers, which are held together by van der Waals dispersion interactions alone or also by intermolecular hydrogen bonds. Problematic large-amplitude motions like inter-/intramolecular rotations are described by hindered rotor models. First, we showcase the accuracy of this anharmonic approach by comparing our spectra obtained at the "gold standard" CCSD(T) level with available reference data. Then, we benchmark the quality of several density functionals in comparison to the CCSD(T) results. Later on, this approach can also be utilized for calculating anharmonic vibrational spectra of periodic molecular crystals via embedding methods.   

Search for long lasting electronic coherence using on-the-fly ab initio semiclassical dynamics

Using a combination of high-level ab initio electronic structure methods with efficient on-the-fly semiclassical evaluation of nuclear dynamics, we performed a massive scan of small polyatomic molecules searching for a long lasting oscillatory dynamics of the electron density triggered by the outer-valence ionization. We observed that in most of the studied molecules, the sudden removal of an electron from the system either does not lead to the appearance of the electronic coherence, or the created coherences become damped by the nuclear rearrangement on a time scale of a few femtoseconds. However, we report several so far unexplored molecules with the electronic coherences lasting up to 10~fs which can be good candidates for experimental studies. In addition, we present the full-dimensional simulations of the electronic coherences coupled to nuclear motion in several molecules which were studied previously only in the fixed nuclei approximation.   

On-the-fly ab initio semiclassical evaluation of electronic coherences in polyatomic molecules reveals a simple mechanism of decoherence

Irradiation of a molecular system by an intense laser field can trigger dynamics of both electronic and nuclear subsystems. The lighter electrons usually move on much faster, attosecond timescale but the slow nuclear rearrangement damps ultrafast electronic oscillations, leading to the decoherence of the electronic dynamics within a few femtoseconds. We show that a simple, single-trajectory semiclassical scheme can evaluate the electronic coherence time in polyatomic molecules accurately by demonstrating an excellent agreement with full-dimensional quantum calculations. In contrast to numerical quantum methods, the semiclassical one reveals the physical mechanism of decoherence beyond the general blame on nuclear motion. In the propiolic acid, the rate of decoherence and the large deviation from the static frequency of electronic oscillations are quantitatively described with just two semiclassical parameters—the phase space distance and signed area between the trajectories moving on two electronic surfaces. Because it evaluates the electronic structure on the fly, the semiclassical technique avoids the "curse of dimensionality" and should be useful for preselecting molecules for experimental studies.   

Theoretical spectroscopic characterization of small interstellar anions: C2N- at the focal point

Although the existence and importance of negative molecular ions had been conjectured in the early days of astrochemistry, it was not until 2006 that the first interstellar anion, C₆H⁻, was finally detected. In the forthcoming years, several other anionic species have been soon identified in space such as C₄H⁻, C₈H⁻, C₃N⁻, C₅N⁻ and CN⁻. Assuming electron radiative attachment (REA) as their major formation route, chemical models have been successful in reproducing the observed abundances of the larger carbon-chain anions like C₈H⁻, C₆H⁻, and C₅N⁻. However, for the smallest species (e.g., CN⁻ and C₃N⁻) for which REA to their parent neutrals are theorized to very slow, notable discrepancies have soon appeared between the modeled and observed anion-to-neutral ratios. Recent laboratory studies pointed out the dominance of the (as yet unobserved) C₂N^- species as fragmentation product of larger carbonitrile anions in UV-abundant circumstellar media, thereby offering new prospects into its omnipresence in the external layers of the carbon-rich star IRC+10216. Motivated by these most recent findings and the general lack of spectral signatures of this anion, in this talk, I will discuss our most recent efforts to obtain accurate spectroscopic constants for l-C₂N^-(³Σ^-) and c-CNC(¹A₁) by means of a high-level theoretical approach. Special attention will be paid into the computation of their quartic force fields (QFFs) using state-of-the-art electronic structure composite methods followed by nuclear motion calculations. It is then expected that the new spectroscopic data here reported prompt future high-resolution laboratory and observational studies on this target molecular anion.   

Theoretical prospects for alkali intercalation of hexagonal boron nitride

Although alkali intercalation of graphite is well-known, the large bandgap of its sister compound hexagonal boron nitride would appear to preclude a similar charge-transfer-based mechanism for alkali intercalation of hBN. Recent experimental results on potassium intercalation of bulk hBN motivate a computational reassessment of possible driving forces towards alkali intercalation of this large-gap 2D material [1].

Different areal densities of potassium or sodium with and without defects in the underlying hBN layers were explored, with careful consideration of van der Waals contributions through DFT-D3 [2] or DFT-TS [3] methods. The intercalated state appears to support a 2D electron gas resident on the alkali layer with limited charge transfer. Boron vacancies strongly favor intercalation and also act to “pillar” the hBN to facilitate further alkali infiltration. Due to the reduced dimensionality and delocalized nature of the alkali-derived electron gas, significant ambiguity remains around the quantification of vdW contributions to the thermodynamic balance, expressible as a threshold areal density of hBN defects needed to drive intercalation.

References:

1. S. Okada and M. Otani , Phys. Rev. B: Condens. Matter Mater. Phys., 2010, 81, 233401

2. S. Grimme, J. Antony, S. Ehrlich, H. Krieg, J. Chem.Phys, 2010, 132, 154104

3. A. Tkatchenko, M. Scheffler, Phys. Rev. Lett., 2009, 102, 073005   

Modeling Non-Kekulé Molecules With Quantum Corrals

Non-Kekulé molecules are a largely unstudied group of molecules. These are difficult or impossible to synthesize and are challenging to model with conventional computational methods. However, artificial molecules present a unique tool to study molecular properties. Their lack of "real" bonds and the low temperature at which they are constructed makes them highly stable in any configuration they can be assembled. We have used artificial molecules to model and study the molecular properties of such systems. Here CO molecules are adsorbed onto a Cu[111] surface and arranged in quantum corrals to shape the wavefunction of the surface electrons. We present studies of a synthetic molecule that closely reproduces the electronic features of phenalenyl radical as predicted by density functional theory calculations.