Session X25: Structure and Spectroscopy in Chemical Physics

Live

I will discuss recent results that apply directly determined pair-natural orbitals to quantum chemistry algorithms on quantum computers (arxiv:2008.02819). The approach allows the automated construction of system-adapted orbitals through a classical surrogate model, leading to compact Hamiltonians with significantly reduced qubit requirements. Furthermore, the physical properties of the surrogate model can be exploited in the construction of low-depth quantum circuits. I will give a high level overwiev over the involved physical principles and numerical techniques, combined with more detailed illustrations on explicit examples.   

Live

DNA duplex hybridization is central to biology and nanotechnology and has been the subject of numerous studies over the past decades. Recent findings from experiment and simulation demonstrate that even small oligonucleotides (<20 bp) may undergo complex structural dynamics during hybridization. DNA hybridization is complicated by many fast structural motions, such as fraying and sliding, and therefore its investigation requires the ability to probe DNA structure across both fast (ns-µs) and slow (ms-s) timescales. Along these lines we have developed temperature-jump IR and two-dimensional IR methods that can monitor DNA interactions from nanoseconds to many seconds. We are investigating how DNA dehybridization is modulated by nucleobase sequence, chemical modifications, and nucleobase protonation. Recently, we have found that the modified nucleobases 5formyl and 5carboxylcytosine can alter DNA dehybridization with great sensitivity to solution pH. Our results provide insight into a complex interplay between sequence, chemical modification, and sequence that may tune DNA hybridization dynamics.   

Live

We report scalar-relativistic Delta-coupled-cluster (ΔCC) methods with core-valence separation (CVS) approximation^[1] to study single core ionization energies ^[2] and hetero-site double core ionization energies ^[3] for second-row elements. ΔCCSD(T) is shown to be as accurate as CVS-equation-of-motion coupled-cluster with higher quadruple excitations^[4,5] in benchmark calculations of single core ionization energies ^[2]. ΔCC methods are also capable of providing accurate double core ionization energies with remaining errors estimated to be below 0.3 eV. They appear to be promising tools to facilitate experimental studies of two-site double core-ionized states that are involved in X-ray pump/X-ray probe studies of electronic and molecular dynamics following inner shell ionization or excitation.

Reference
[1] L. S. Cederbaum, W. Domcke, and J. Schirmer, Phys. Rev. A 22, 206–222 (1980).
[2] X. Zheng and L. Cheng, J. Chem. Theory Comput. 15, 4945-4955 (2019).
[3] X. Zheng, J. Liu, G. Doumy, L. Young, and L. Cheng, J. Phys. Chem. A 124, 4413-4426 (2020).
[4] S. Coriani, and H. Koch, J. Chem. Phys. 143, 181103 (2015).
[5] J. Liu , D. Matthews, S. Coriani and L. Cheng, J. Chem. Theory Comput. 15, 1642–1651 (2019).   

Live

To compute vibrationally resolved electronic spectra at zero temperature, we recently implemented the on-the-fly ab initio extended thawed Gaussian approximation, which accounts for anharmonicity, mode-mode coupling, and Herzberg-Teller effects. Here, we generalize this method to spectra at non-zero temperature. As in thermo-field dynamics, we transform von Neumann's evolution of the coherence component of the density matrix to the Schrödinger evolution of a wavefunction in an augmented space with twice as many degrees of freedom. Due to efficiency of the thawed Gaussian approximation, this increase in dimensionality results in nearly no additional computational cost: compared to the zero-temperature version, the finite-temperature method requires no additional ab initio electronic structure calculations. The new approach allows for a clear distinction among finite-temperature, anharmonicity, and Herzberg--Teller effects on spectra. We show, on a model Morse system, the advantages of the finite-temperature thawed Gaussian approximation over the popular global harmonic methods and apply it to evaluate the symmetry-forbidden absorption spectrum of benzene, where all of the aforementioned effects contribute.
[1] J. Chem. Phys. 153, 024105 (2020). Editor's pick and featured article.   

Live

Conventional ultrafast spectroscopy requires optically dense samples such as solids or liquids. However, studying jet-cooled gas-phase molecules is more desirable for direct comparison to ab initio theory. In molecular beams, one can also study systems that do not exist in solution such as clusters and radicals. To this end, we have developed an ultrafast spectrometer based on the cavity-enhancement of frequency combs to enable transient absorption measurements in molecular beams, with a demonstrated detection limit of ΔOD = 1×10^-9/√Hz [1]. With probe pulses tunable between 450 and 700 nm, broadband ultrafast transient absorption spectra can be recorded. In this way, we can record the same observable routinely used in solution-phase studies, but now from jet-cooled molecules and clusters, enabling direct comparison of the molecular dynamics in different environments. We will discuss technical details of this novel spectrometer and ultrafast spectroscopy of chemical dynamics. For example, we will discuss proton transfer in 1-hydroxy 2-acetonaphthone and the internal conversion of salicylideneaniline in argon clusters of varying size.

[1] M. A. R. Reber, Y. Chen, and T. K. Allison, Optica 3, 311 (2016).   

Live

Simple molecules like carbon monoxide (CO) and carbon dioxide (CO₂) is ubiquitous in our atmosphere and plays important roles in the life cycle and the greenhouse effect. I will present our recent results showing excited state dynamics of these molecules through femtosecond (fs) pump-probe spectroscopy. Photoexcitation from a 35 fs pump laser impulsively transfers CO₂ from the X → A state, preparing a bending vibrational wavepacket that influences its dissociation. Using mass spectrometry, we report changes in the fragmentation pattern as a function of time delay between the pump and probe laser pulses that reflect the vibrational motion. At well-defined time delays the dissociation oscillates between observable CO⁺ and O₂⁺ fragments. Strong-field excitation is also applied to drive the Coulomb explosion of small gas-phase molecules such as formic acid, where multiply charged ions are observed. Potential energy curves are calculated and confirm the existence of a metastable states for COⁿ⁺, n ≤ 3. Kinetic energy release measurements for the ions are consistent with our molecular dynamics simulations.   

Live

As demonstrated in spectroscopic studies of 1,3-dioxole (1,3-DO) and 1,3-benzodioxole (1,3-BDO), analysis of the ring-puckering potential energy function (PEF) of a “pseudo-four-membered ring” molecule can provide insight into understanding the magnitude of the anomeric effect. In this study ab initio computations have been utilized to calculate the PEFs for 1,3-BO and 1,3-BDO and ten related molecules containing sulfur and selenium atoms and possessing the anomeric effect. The potential energy parameters derived for the PEFs directly provide a comparison of the relative magnitudes of the anomeric effect for molecules possessing OCO, OCS, OCSe, SCS, SCSe, and SeCSe linkages. The torsional potential energies produced by the anomeric effect for these linkages were estimated to range from 5.97 down to 1.91 kcal/mole. The ab initio calculations also yielded the structural parameters, barriers to planarity, and ring-puckering angles for each of the twelve molecules studied. Improved PEFs for 1,3-DO and 1,3-BDO were also calculated. The calculations also support the conclusion that the relatively low barrier to planarity of 1,3-BDO results from competitive interactions between its benzene ring and the oxygen atom p orbitals.   

Live

Vibrational circular dichroism (VCD) is an effective technique to study the characteristic amide-I vibrational mode of peptides and thus determine their secondary structures. However, the structure-spectrum relationship for the VCD spectra of peptides is yet to be established. Theoretical modeling has been playing an important role in connecting the peptide structures to their infrared (IR) spectra, and in this work, we aim at achieving a similar goal for the amide-I VCD spectra of peptides by developing a mixed quantum/classical approach.

We devise an ab-initio based scheme to compute the transition magnetic dipole moment, a key quantity in simulating VCD, based on small model systems such as N-methylacetamide. We then validate the new method by comparing the computed VCD spectra of several representative peptides with well-defined secondary structures including α-helix, β-hairpin, and 3₁₀-helix to their experimental spectra. The analyses of the molecular dynamics simulations and the simulated VCD spectra shed light on the molecular origins of some observed VCD spectral features.   

Live

Rare-earth (RE) ions, such as Dysprosium, have well-defined luminescent properties studied successfully using glass structures typically in oxide form, such as Dy₂O₃. Using the technique of photoluminescence, with an Argon-Ion Laser for excitation, the spectral emission can be collected with a standard GaAs detector and the dominant electronic transitions examined to determine their suitability for applications in solid-state lasers or light-emitting devices. Few literature studies exist on photoluminescence of the powder form of pure Dy₂O₃ powder, which is more practical for light emitting devices. Using our previous research on these pure oxides as a control sample for this project, a collaborative project was undertaken to sinter new samples where sulfur is incorporated at various levels into the structure of the pure Dysprosium oxide samples as Dy₂O_(3-x)S_x, where x-values vary from 0-3, in an attempt to enhance their photoluminescence. Exact levels of dopant incorporated into the samples were determined from a differential analysis of X-Ray diffraction data. A corresponding differential comparison of the photoluminescence emission spectra from the samples exhibits clear enhancement of selected luminescence peaks as the actual S content (x-value) increases.   

Live

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, also known as coenzyme B12, has an adenosyl upper ligand and dimethylbenzimidazole lower ligand. The photochemistry of AdoCbl is important due to its central role in the CarH photoreceptor. 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 different molecule-fixed directions. Extensive time-resolved XANES data have been collected on this molecule in both water and ethylene glycol solvent. In order to assign specific spectral changes to structural changes in the AdoCbl, the XANES spectra must be simulated for comparison with the experimental XANES difference spectrum. We use the finite difference method near edge structure method (FDMNES) to simulate the ground and excited state spectra. FDMNES allows for systematic examination of the rotations, bond-lengthening, and other manipulations needed to reproduce the experimental XANES data.   

Live

Recently, we have developed a new generation of correlation consistent effective core potentials (ccECP) for elements H-Kr. Here we expand to heavier elements, in particular, to a selected set of I, Bi, Pd, W, Ag, and Au. The chosen set is used to optimize the procedure for atoms with significant spin-orbit effects. First, we generate averaged relativistic effective potentials (AREP) that correspond to commonly used semi-local form. This AREP part follows the established techniques such as weighted atomic iso-spectrality with all-electron excitations and norm-conservation. Second, effective spin-orbit terms are generated using energy-consistency for pertinent states such as multiplet splitting and/or low-lying states using 2-component spinor formalism within a chosen CI active space. The quality of resulting spin-orbit ccECPs is assessed by carrying out fixed-phase diffusion Monte Carlo (DMC) calculations for the mentioned atomic states and comparing them with experimental values. Transferability is further tested by calculations of binding energies for the corresponding dimers using DMC and cross-checking with the experimental result.   

Live

A fundamental question in nanoscience is when and how the transition from molecular properties to the bulk behavior occurs. In particular, the convergence of the vibrational properties as a function of the diameter of fullerenes to the bulk material (i.e. graphene) remains as an unsolved challenge. Here we address this issue by studying fullerene’s vibrational density of states (VDOS) as a function of the size (going from 20→720 atoms) and its convergence to graphene’s VDOS using density functional theory. In general, a smooth convergence with the size is observed in most the regions of the VDOS, nevertheless a fundamental difference between the vibrational modes in the fullerene family and the phonon bands in graphene appears: The lack of out-of-plane optical band (ZO-modes) in fullerenes. The higher part of the ZO phonon branch is forbidden in fullerenes due to the presence of pentagonal faces, which restricts the symmetries of the vibrational modes allowed in fullerenes. The analysis and results in this work can be extrapolated to other structures containing pentagonal rings either as a closed shell structure or as pentagonal defects in graphene.   

Live

We exploit advances in cryogenic, gas-phase ion methods to capture and characterize the complexes formed by CO₂ and N₂ with Ni^I cyclam and Ni^I L-N₄Me₂. The measurements furnish key information about the mechanism of small molecule activation and provide a crucial test of electronic structure methods used to rationalize catalytic activity and guide catalyst development.

One of the most important challenges in catalysis is the transformation of N₂ and CO₂ to high value chemicals (e.g. ammonia and ethanol). In principle, the methods of organometallic chemistry can tailor transition metal complex electronic structure to drive desired product formation. However, studying the activity of reactive transition metal centers is challenging because they are inherently unstable and thus difficult to capture and characterize. We harness cryogenic gas-phase ion methods to overcome these difficulties and collect infrared spectra and small-molecule thermal binding curves. Electronic structure calculations constrained by infrared spectra offer insight into complex structure and mechanism of activation.   

Live

The Lippmann-Schwinger equation is formulated in momentum space and solved using the direct diagonalization method [1] to calculate the rovibrational energy levels of Neon, Krypton, and Xenon rare gas dimers. The inputs for our calculations are the matrix elements of diatomic interactions in momentum space, which are obtained from neon-neon, krypton-krypton, and xenon-xenon potential curves developed by Hellmann et al. [2, 3, 4]. Our numerical analysis confirms not only the rovibrational energy levels of neon, krypton, and xenon dimers predicted by other groups in configuration space but also provides an exact means for determining the full energy spectrum of shallow bound states with small energy eigenvalues for the first time.

[1] T. Sahraeian and M. R. Hadizadeh, International Journal of Quantum Chemistry 119.3, e25807 (2019).
[2] R. Hellmann et al., Molecular Physics 106.1, 133 (2008).
[3] B. J{\"a}ger et al., The Journal of Chemical Physics 144.11, 114304 (2016).
[4] R. Hellmann et al., The Journal of Chemical Physics 147.3, 034304 (2017).   

Not Participating

The attachment of low-energy secondary electrons to DNA is believed to be a major contributor to DNA damage. Theoretical calculations and dissociative electron attachment experiments predict that nucleobases are the most likely initial site of electron attachment, although the overall mechanism for attachment and subsequent bond breakage is not yet well understood. To probe the dynamics of this reductive DNA damage mechanism, we have employed femtosecond time-resolved photoelectron spectroscopy of gas-phase iodide-nucleobase and iodide-nucleobase-water clusters. A UV pump photon is used to initiate charge transfer from the iodide to the nucleobase moiety, and a UV or IR probe pulse is used to photodetach the excess electron from the photoexcited transient negative ions or the ionic photofragment dissociation products. In this way, the ultrafast photochemistry of excess electron accommodation in nucleobases and the subsequent photodissociation and relaxation pathways are monitored.