The local vibrational mode theory originally introduced by Konkoli and Cremer has become over the past years a versatile tool for extracting important chemical information, hidden in vibrational spectroscopy data caused by the delocalized nature of normal vibrational modes in polyatomic molecules.[1,2]

After a short introduction of the theoretical background and description how local vibrational modes are derived from fundamental vibrational normal modes, we will present three recent examples, elucidating how our tool can help finding answers to open vibrational spectroscopy questions: (i) metal-ligand bonding in heme proteins, such as myoglobin and neuroglobin; (ii) disentanglement of DNA normal modes; and (iii) hydrogen bonding in water clusters and ice.

Finally, we will present the open-source local mode program LModeA which can easily be applied after a routine quantum chemical calculation of vibrational frequencies but also to measured vibrational frequencies, with moderate computational costs.

References: 1. Feature Article: The Local Vibrational Mode Theory and Its Place in the Vibrational Spectroscopy Arena, E. Kraka, M. Quintano, H. W. La Force, J. J. Antonio and M. Freindorf, J. Phys. Chem. A, 126, 8781 (2022) 2. Decoding chemical information from vibrational spectroscopy data: Local vibrational mode theory. E. Kraka, W. Zou, and Y. Tao, WIREs: Comput. Mol. Sci., e1480 (2020)

Beyond their central roles in some enzymes and proteins, chiral organometallic complexes have potential applications in synthetic drugs, as biomarkers or in catalysis for instance. Their structural characterization can help rationalize their activity, including their bioactivity and toxicology. Experimentally, a key role is played by vibrational spectroscopies like IR and Raman scattering, with a more comprehensive picture achieved by the use of their chiroptical counterparts, respectively vibrational circular dichroism (VCD) and Raman optical activity (ROA).[1] Because of the complexity of the signal, the interpretation of chiral spectra needs to be assisted by computations. r0pt Figure However, chiral spectroscopies are characterized by a higher sensitivity and low-intensity spectra (typically 4-5 orders of magnitude lower than the non-chiral ones), so standard protocols rooted into the density functional theory within the harmonic-oscillator approximation can be insufficient. A straightforward path of improvement is the inclusion of anharmonicity, but the typical size of organometallic compounds is generally too large even for relatively cheap methods such as the second-order vibrational perturbation theory (VPT2). On the other hand, a full anharmonic treatment may be unnecessary to investigate probe vibrations or specific spectral regions. Indeed, a model system can be built by considering the anharmonic contributions only for a subset of relevant modes without loss of accuracy. In this contribution, we will discuss how this can be done and analyze the potential pitfalls. Finally, we will show how computations can be used to provide new visual insights on the local origin of the observed bands.[2]

We recently developed an implementation of vibrational perturbation theory (VPT) based on the approach described by Sakurai in which the perturbation theory calculations are performed numerically using linear algebra approaches. This has been incorporated in the PyVibPTn codes. Advantages that are realized by this approach include flexibility with respect to the coordinates used to expand the Hamiltonian and in the identification of possible resonance interactions. Specifically, in PyVibPTn resonances are identified based on the size of corrections to the wave function from higher-order terms in the Hamiltonian. This approach has the advantage over the Martin test, which focuses on corrections to the energies from the first order corrections to the Hamiltonian, in that our approach treats the first and second order corrections to the Hamiltonian in a more balanced manner. It also allows us to identify resonance interactions that have large effects on the intensities or other properties, while having only small impacts on the energies. This implementation of VPT has been used in several studies of vibrational spectra. These include an analysis of the IR-cryo-SEVI spectra of vyonxide in collaboration with the Neumark group. In this study, the vynoxide ion is excited to states with one quantum of excitation in the CO or CH stretching vibration prior to electron photodetachment. We also describe how VPT was used to reassess the assignment of the vibrational spectrum of H⁺(C₂H₄). Additionally, we use VPT to obtain insights into the origins of IR intensity for transitions by decomposing the transition moment into contributions from higher order terms in the expansions of the potential and dipole moment surfaces.

Hydrated pyrene anions are model systems for microsolvation and hydrogen bonded (H-bonded) networks on charged graphene like materials. Tandem mass spectrometry was employed to collect mass selected messenger-tag and photodissociation infrared (IR) spectra. Photodissociation spectra of cold cluster anions of the form C₁₆H₁₀⁻·(H₂O)_n·Ar₂ (n=1-4) losing Argon upon irradiation are compared to spectra of warmer C₁₆H₁₀⁻·(H₂O)_n (n=1-4) cluster anions. Structural and dynamic information about the H-bond network is encoded in OH stretching frequencies. Experimental IR spectra are compared to density functional theory calculations, and various cluster geometries are predicted. Generally, water molecules form H-bonds with other water molecules and with the excess charge in pyrene’s π-system. These binding motifs are compared to the ones found on anionic hydrated naphthalene clusters.1. B.J. Knurr, C.L. Adams, and J.M. Weber, Infrared Spectroscopy of Hydrated Naphthalene Cluster Anions. J. Chem. Phys. 137 (2012) 104303.html:<hr /><h3>Footnotes: 1. B.J. Knurr, C.L. Adams, and J.M. Weber, Infrared Spectroscopy of Hydrated Naphthalene Cluster Anions. J. Chem. Phys. 137 (2012) 104303.

The intermolecular forces that govern water-hydrocarbon interactions have profound effects in interfacial phenomena, like wetting, and large-scale applications to issues like water security through water desalination with two-dimensional membranesS. Strong; J.D. Eaves. The dynamics of water in porous two-dimensional crystals. J. Phys. Chem. B 2017, 121, 189-207 I will discuss our work on building dynamical methods and water models to describe and interpret the vibrational spectroscopy of anionic water-polycyclic aromatic hydrocarbon (PAH) clusters which act as a minimal model for aqueous-carbon interfaces. Even in a small system of one water with a charged PAH, there is significant complexity, including non-Gaussian fluctuations and ergodicity-breaking at low temperatures. Systematically accounting for these effects leads to semi-quantitative agreement between theoretical predictions and experimental measurements for the IR spectrum in the OH stretching region.

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Footnotes:

S. Strong; J.D. Eaves. The dynamics of water in porous two-dimensional crystals. J. Phys. Chem. B 2017, 121, 189-207.

Synthesis of 2-((2-aminopyridin-3-yl)methylene)-N-phenylhydrazinecarbothioamide (APHB) was attempted. Elemental analysis and NMR spectra were used to ascertain its formation. Torsional potential energy scans, for all the rotating bonds were made to get approximate initial values of dihedral angles. FT-IR, FT Raman, and UV-Vis spectra were measured for APHB. Their anticancer activity was determined experimentally, for human carcinoma cell lines pertaining to liver, colorectal, and lung. Barrier heights, around six rotating bonds in APHB were computed. Optimized structure parameters, general valence force field, harmonic vibrational fundamentals, potential energy distribution, infrared and Raman intensities, frontier molecular orbital (FMO) parameters, NLO behaviour, and NBO characteristics were determined using DFT/B3LYP/6-311++G(d,p) level of theory. TD-DFT was used to compute absorption maxima (λ _max) of electronic transitions for the molecule in DMSO-d₆ solvent. Frontier molecular orbitals were used to understand origin of UV-Vis spectrum and chemical reactivity of the molecule. Good agreement was found between measured and computed structure parameters, IR, Raman and UV-Vis spectra. The rms error between experimental and theoretical vibrational frequencies was 9.5 cm⁻¹, for APHB. All vibrational fundamentals were assigned unambiguously. The computations demonstrated that the molecule was good for NLO applications, which was substantiated by NBO analysis. Existence of bifurcated intramolecular hydrogen bond was predicted for APHB.

Recently, Fukushima reported laser-induced fluorescence of the ~B²E' - ~X²A'₂ transition from the vibrationless ~B²E' excited state of jet cooled ¹⁴NO₃ and ¹⁵NO₃ in which two beautiful series of ν₄ progressions in the ground X²A'₂ state have been identified.Fukushima, M. 2022, J. Mol. Spectrosc. 387, 111646ne of the progressions corresponds to transitions with vibrational symmetry a₁' - a₁' while the other with a₁' - e'. The former is the ordinary single-photon spontaneous emission given in Eq.(II,11) of Herzberg Vol.III, while the latter is not discussed in ordinary textbook of spectroscopy. Here I propose that the latter is due to Raman-type laser stimulated two-photon processes that were commonly observed around 1970.Freund, S.M., Oka, T. 1976, Phys. Rev. A. 13, 2178 Oka, T. 1977, Frontiers in Laser Spectroscopy, II (Proceedings, Summer School of Theoretical Physics, Les Houches), R. Balian, S. Haroche and S. Lieberman, eds., North-Holland, Amsterdam, pp. 531–569 Contrary to the previous assignments which invoke vibronic mixing between the ~B²E' and ~X²A'₂ states, the 2-photon assignment leaves the vibrational angular momentum l₄ in the ground ~X²A'₂ state a good quantum number except for the ∆l = 3 mixing. Therefore the l₄ assignment and the vibrational structure are extremely simple as reported in the Fukushima paper. The calculation using the Kramers-Heisenberg formula indicates that the laser power density indicates sufficiently high to cause the two-photon process. The perfectly normal ν₄ progression suggests strongly that the ν₃ progression is also normal. This suggests that the so-called Ässignment I" in which the intensity of the ν₃ fundamental band is higher than that of the ν₃ + ν₄ combination band is more reasonable than the Ässignment II" in which a theoretical calculation gives the ν₃ band weaker than the ν₃ + ν₄ band by a factor of 60Stanton, J.F. 2009, Mol. Phys. 107, 1059nd an experimental observation by  ∼  2000.Kawaguchi, K., Tang, J., Akikusa, N. 2021, Chem. Phys. Lett. 765, 138365html:<hr /><h3>Footnotes: Fukushima, M. 2022, J. Mol. Spectrosc. 387, 111646O Freund, S.M., Oka, T. 1976, Phys. Rev. A. 13, 2178

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Footnotes:

Stanton, J.F. 2009, Mol. Phys. 107, 1059a Kawaguchi, K., Tang, J., Akikusa, N. 2021, Chem. Phys. Lett. 765, 138365

Although the ground X̃ ¹A₁ electronic state of silylene SiH₂ is fairly well characterized,¹ fewer results are available about its first excited triplet ã ³B₁ electronic state and about its cationic species SiH − 2⁺. The ground electronic state of the latter is split into bent X̃^+ 2A₁ and linear Ã^+ 2B₁ doublet electronic states by the Renner-Teller coupling.²

Threshold photoelectron (TPE) spectroscopy has been used to obtain spectroscopic information about the cationic species SiH₂⁺ of silylene and about the first excited triplet electronic state of neutral SiH₂. The TPE spectrum, recorded at Synchrotron SOLEIL from 7.5 to 11.5 eV using VUV synchrotron radiation, displays several sharp features and was modeled using wavepacket propagation.³ ωB97XD ab initio calculations were carried out using cc-PVTZ correlation-consistent basis set functions to retrieve 3-D potential energy surfaces for the four electronic states involved in the TPE spectrum. The MCTDH method⁴ was first used to obtain the 3-D vibrational wavefunctions of the neutral species X̃ ¹A₁ and ã ³B₁ electronic states using propagation in negative imaginary time. The wavefunctions thus obtained were then time-propagated in the potential energy surfaces of the coupled electronic states of the cationic species using also MCTDH.^c, d The photoionisation cross-section was at last computed as the Fourier transform of the auto-correlation function.

In the talk, the results of the rovibronic energies calculation will be reported and the experimental TPE spectrum will be compared to the theoretical one. The importance of the Renner-Teller coupling will be assessed and the vibrational temperature which best reproduces the experimental spectrum will be evaluated.

We report spectroscopic and theoretical studies of the cyclopropyl radical and cation (c-)¹. Through synchrotron VUV photoionization spectroscopy and novel spectral simulations, we establish the transition state nature of the cation, which is unstable towards ring-opening to the allyl cation. Additionally, we report preliminary results of the rotational spectroscopy of the radical, which exhibits inversion tunneling of the α-H atom through the C-C-C ring plane. The large energy difference between the allylic equilibrium geometry and the unstable cyclic configuration on the cation potential energy surface (PES) required the development of propagator-based methods that avoid the construction of cationic vibronic eigenstates to simulate the ionization spectrum². The results of our simulations, combined with high accuracy single-point ab initio calculations, compare well with new mass-selected threshold photoelectron measurements performed at the SOLEIL synchrotron, and attest to the transition state nature of the cation. Our results shed light on the most basic properties of the fundamental pericyclic reactions between allyl and cyclopropyl radicals and cations, which were among the very first systems to be studied from the perspectives of Woodward-Hoffmann rules and correlation diagrams. Additionally, we provide a qualitative explanation for the quantum mechanical effects that make the ionization transition favorable to a portion of a PES with negative curvature.

Among the most challenging aspects of spectral assignment in rotational spectroscopy are complex hyperfine coupling patterns and a flat potential energy surface with many stable conformers. Electronic structure calculations are an essential tool for predicting geometries and spectroscopic constants such as nuclear quadrupole splitting. Reliable predictions are therefore essential for a fast assignment process. Computational data for 22 weakly bound chlorine containing complexes is compared to experimental spectroscopic data from literature. The chosen methods are commonly used among rotational spectroscopists for initial theoretical screening of a target system. Ab initio methods with a large basis set are found to perform best overall in prediction both the geometry of the complex and the quadrupolar coupling with moderate computational costs. As inexpensive calculations determining equilibirum structures disregard large amplitude motions, which are often observed in weakly-bound complexes. Inacccurate geometries result in an incorrect projection of the nuclear quadrupole coupling tensor into the principle axis system. The quality of nuclear quadrupole predictions overall decreases compared to monomer studies from William Bailey’s quadrupolar coupling data set,W. C. Bailey, Calculation of Nuclear Quadrupole Coupling Constants in Gaseous State Molecule, 2019, https://nqcc.wcbailey.net/hich was focused on monomers. This study aims to expand upon Bailey’s benchmarking dataset and cautions for critical evaluation of secondary parameters obtained from electronic structure calculations.

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Footnotes:

W. C. Bailey, Calculation of Nuclear Quadrupole Coupling Constants in Gaseous State Molecule, 2019, https://nqcc.wcbailey.net/w

[12]r[20pt]7cm Figure UV-vis absorption and circular dichroism spectra play a significant role in probing excited-state molecular properties. They developed to become routine tools used in a variety of fields, such as pharmacology, chemical analysis, and environmental monitoring. With the advances of instrumentation and broader applications, spectral simulations face increasing challenges. Theoretical methods including vibrational effects have replaced cruder models based purely on electronic transitions. With a better balance of computational cost and accuracy, such simulations are becoming routine. An important aspect of vibronic simulations is the treatment of the transition dipole moments. The usual Franck-Condon approximation may not be adequate for weak or forbidden electronic transitions and the first order expansion (Herzberg-Teller, HT) term must be considered. For several organic molecules we show the importance of the HT effects for understanding the spectra. A family of porphyrin molecules not only exhibits the HT effects, but also hints at the need for higher-order terms to be included.