The oblique coordinate transform, pioneered by Zùñiga and coworkers, provides an intermediate between the generic, but delocalized normal mode treatment and intuitive but constrained local mode models. Zùñiga et al. J. Phys. B: At., Mol. Opt. Phys. 52, 055101, (2019)hrough a straightforward oblique transformation, the interpretability of a local mode model can be retained while better adapting to the potential of the system. No inputs are required beyond the initial set of coordinates and the normal modes of the system. Oblique coordinates have been used to study highly excited states of systems with small numbers of degrees of freedom.Zùñiga et al. J. Phys. B: At. Mol. Opt. Phys. 53 025101 (2020)n a recent work, we extended the use of oblique coordinates to larger systems and demonstrated the benefits of such an approach.J. Chem. Phys. 159, 234108 (2023)e provide here another case study, using oblique coordinates to provide a localized model for the investigation of environmental effects on hydrogen bonding interactions, with specific application to a series of water clusters.

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Footnotes:

Zùñiga et al. J. Phys. B: At., Mol. Opt. Phys. 52, 055101, (2019)T Zùñiga et al. J. Phys. B: At. Mol. Opt. Phys. 53 025101 (2020)I J. Chem. Phys. 159, 234108 (2023)W

Diagonalization of effective (ro)vibrational Hamiltonians is a central exercise in vibrational spectroscopy. These techniques are used to solve a wide array of problems in vibrational simulations, such as resolving Fermi Resonances in VPT2 calculations^1,2, treating floppy vibrational motion in an arbitrary basis³, or constructing local-mode wavefunctions⁴, and have proven to be extremely successful. Naturally, many such procedures must truncate or approximate the interactions between vibrational modes in order to remain computationally feasible. However, this comes with a hidden danger well known to electronic structure practitioners : violation of size-extensivity and/or size-consistency. Ultimately these effects manifest as unphysical coupling between vibrational degrees of freedom that may not have meaningful interactions in a fully-coupled treatment.⁵ This presentation will discuss the origin of this phenomena, why it matters for some types of effective Hamiltonians and not for others, and what can be done about it when it does arise.
¹D. A. Matthews, J. V ázquez, and J. F. Stanton, Molecular Physics 105, 2659 (2007). ² M. Piccardo, J. Bloino, and V. Barone, International Journal of Quantum Chemistry 115, 948 (2015). ³ P. B. Changala and J. H. Baraban, The Journal of Chemical Physics 145, 174106 (2016). ⁴ E. L. Sibert, The Journal of Chemical Physics 88, 4378 (1988). ⁵ O. Christiansen, The Journal of Chemical Physics 120, 2149 (2004).

Multi-state vibronic potential energy surfaces in a quasi-diabatic basis are often expressed in terms of polynomial representations involving a complete set of normal coordinates. Polynomial representations of PESs inherently suffer from the complication of canyons, which are regions on the potential energy surface where the potential becomes unbound. If present, these regions can easily be found by running Monte-Carlo simulations on the PESs. Nonetheless, having such regions in the PES hinders our ability to obtain vibronic information using them. However, having high-order, multi-state vibronic potentials is essential for obtaining sufficiently accurate vibronic eigenvalues and eigenfunctions to understand the experimental spectral data available for à  ² E" state of the NO₃ radical¹ . In this presentation, we talk about the five state quasi-diabatic PES for NO₃ that includes the X̃  ²A₂′, à  ²E" and B̃  ²E′ states and the Jahn-Teller and pseudo-Jahn-Teller couplings, respectively within and between them. While desirable, the sixth-order polynomial representation of the vibronic Hamiltonian is riddled with canyons. We will discuss the repercussions of these canyons and ways to deal with them.

As the natural extension to the harmonic treatment, vibrational perturbation theory provides an elegant approach to exploring the effects of higher-order contributions to potentials and dipole moments on vibrational spectra. Dating back to the beginning of the 20th century, the most commonly used approach to vibrational perturbation theory develops analytic expressions for the corrections to energies and other properties. The algebraic complexity of this approach means it is usually not extended beyond second order, and furthermore it requires a specific reference coordinate set. Over the past few decades, Sibert and others have developed more flexible numerical approaches to vibrational perturbation theory. In particular, these methods allow for arbitrary coordinate choice and extension beyond second order. We provide here a complementary approach, building off of combinatoric ideas to extend analytic approaches to higher orders and generic coordinate sets. By making use of the recursive nature of perturbation theory, it is possible to not only obtain computationally efficient expressions, but also to investigate how the vibrational spectrum is affected by refinements to the underlying force fields and coordinate choice.

r0pt Figure In this talk, we present the latest version of our database cluster, which we have decided to call CaSDa24. This is a set of 10 databases, each operating independently and dedicated to a single molecule. It contains data for CH₄, C₂H₄, SF₆, CF₄, GeH₄, CH₃Cl, RuO₄, UF₆, SiF₄ and SiH₄. The relational schemas of these databases are equivalent and optimized to enable the better compromise between data retrieval and compatibility with the XSAMS (XML Schema for Atoms, Molecules and Solids) format adopted by the VAMDC project. Several of them have been updated, and others have been added in regard to our last publication in 2020. The polyad structures are reported, and the transitions are precisely described by their energy, their intensity and the full description of the lower and upper states involved in the transitions. Calculations and modeling are carried out by the XTDS/SPVIEW tandem developed in the Dijon group. All the databases are accessible online for free at the following url http://vamdc.icb.cnrs.fr.

The microwave spectrum of molecular oxygen is due to the magnetic dipole (M1) and electric quadrupole (E2) transitions, as there is no electric dipole moment in O₂. In addition, there are M1 and E2 transitions which both satisfy the same selection rules and in such cases it may be difficult to decipher their individual contribution to the observed spectral line intensity. The effort to characterize the recorded spectra in terms of well defined multipole contribution is greatly facilitated by ab initio calculations which, in turn, may guide the experiment in probing various physico-chemical properties of the molecule. Furthermore, theoretical calculations are especially important when the investigated spectra cannot be described in terms of the vibrational Franck-Condon factors multiplied by the squared modulus of some permanent multipole moment. The E2 transitions in ¹⁶O₂(X³Σ⁻_g) are of this kind and in the calculations of the spectral line intensities one must account for the dependence of the O₂ quadrupole moment on the bond length. We report the ab initio calculations of the intensities of all rovibrational E2 absorption lines in ¹⁶O₂(X³Σ⁻_g). We include the vibrational overtones and hot bands for which the vibrational quantum number v ≤ 35 and the total angular momentum quantum number J ≤ 40. We account for the bond length-dependence of the quadrupole moment by using a new ab initio quadrupole moment curve for O₂(X³Σ⁻_g) and we go beyond the pure Hund's case (b) description by including the mixing of rotational states due to the effective spin-spin interaction between the two unpaired electrons in the ground-state O₂. We obtain a good agreement between our calculated line intensities and those available in the HITRAN database which, at present, includes only the (1,0) vibrational band. We therefore recommend including the calculated line intensities for the other vibrational bands in HITRAN.

The tumor suppression protein p53, negatively regulated by the ubiquitin ligase MDM2, plays a crucial role in preventing cancer. MDM2 binds p53 through the N-terminal transactivation domain of p53, inhibiting its transcription activity and promoting its degradation. This negative feedback loop maintains low p53 levels in normal cells. Disrupting the p53-MDM2 interaction is a promising approach for therapy. To explore the probable binding/unbinding pathway of p53 during the formation/dissociation of the p53-MDM2 complex, we performed a Molecular Dynamics (MD) investigation of the p53-MDM2 complex (PDB ID :1YCR). We investigated the potential of mean force (PMF) using different force fields to understand the free energy landscape of the dissociation process. Additionally, we examined p53's stability and structural dynamics as its distance from MDM2 varied. Furthermore, using computational analysis, we systematically mutated residues within the MDM2 and p53, particularly those near the binding region. This finding provides valuable insight into p53-MDM2 binding and unbinding mechanism and unveil potential mutation hotspots for targeted cancer therapies.

Polyethylene Terephthalate (PET) is the most common petroleum-derived synthetic polymer that is being used in many industries such as packaging, clothing and many more. The lack of economically feasible recycling technologies and the mismanagement of single-use PET contributed to plastic pollution. The discoveries of plastic degradation enzymes enable PET's biological recycling or upcycling to establish a circular material flow. For instance, Ideonella Sakaiensis (I.S.), which expresses dual enzymes PETase and MHETase, catalyzes PET depolymerization and converts PET into original monomers, terephthalate and ethylene glycol. However, its conversion efficiency must be improved for promising industrial use. In this regard, engineering existing enzymes or searching for novel enzymes is of timely interest. Mle046 is a promising, yet relatively less studied enzyme from a marine microbial consortium which is a homolog to MHETase with an ability to depolymerize MHET into its building blocks, TPA and EG. We report the results from ab initio Density Functional Theory, Molecular Docking and Molecular Dynamics Simulations for the characterization and engineering of Mle046. This study is based on the three-dimensional configuration obtained through homology modeling, as the experimental structure is not yet available. Multiple sequence alignment with its homologs indicates that the active sites of Mle046 remain conserved, displaying a catalytic triad consisting of SER, HIS, and ASP, similar to the known PET hydrolases. In this study, we report the possibility of improving the enzyme’s stability by adding a disulfide bond. Further, we analyze the potential metal center dynamics by ab initio Density Functional Theory. By analyzing the PET binding surface in Mle046, we will show potential mutations that will enhance PET depolymerization activity.

Plastic, a synthetic polymer renowned for its exceptional material properties, plays a pivotal role in modern life by enabling a multitude of applications. Among various types of plastics, Polyethylene terephthalate (PET), derived from petroleum, stands as the third most utilized synthetic polymer, serving industries ranging from textiles, fibers, and films to the production of single-use bottles and packaging materials. However, despite its extensive utility, the inefficient management of plastic waste poses a significant threat to both the environment and human health. Mechanical recycling plastic is an improvement over directly dumping first-use plastics in landfills, but it often yields low-grade plastics. Researchers use chemical recycling to convert plastic into original monomers to recreate the plastic with similar mechanical properties; however, processes involve harsh catalysts and solvents. Alternately, biological plastic upcycling is a promising alternative for enabling a circular economy for plastic. Plastic upcycling involves depolymerizing PET into higher-value products. PET depolymerization, supported by biocatalysts, has shown promise as a method for plastic upcycling. However, there is still a dire need for finding biocatalysts that can optimize the efficiency of PET depolymerization. Among various PET hydrolyzing enzymes, LCC demonstrates a higher conversion efficiency. However, its activity degrades after 65 degree Celsius due to the enzyme's low thermal stability. Tournier and coworkers tailored an engineered version of LCC that increases both thermal stability and degradation efficiency. In the present work, based on the results from ab initio Density Functional Theory and Molecular Dynamics simulations, we will discuss the effect of metal-site substitutions by divalent ions on the thermal stability and catalytic activity of already suggested engineered LCC configurations and its new variants.