Strong-field ionization and AC-Stark shifted Rydberg states in OCS

We present theoretical results for intensity-dependent above-threshold ionization (ATI) spectra from oriented OCS molecules probed by intense femtosecond laser pulses with wavelengths of 800 and 400 nm. The calculations were performed using the time-dependent Schroodinger equation within the single-active-electron approximation and including multielectron polarization effects. The results are in qualitative agreement with experimental data [Yu et al., J. Phys. B: At. Mol. Opt. Phys. 50, 235602 (2017)]. In particular, characteristic features in the ATI spectra which correspond to resonant multiphoton ionization via highly-excited Rydberg states are captured by the theory.Comment: 3 figure

Ionization of 1D and 3D oriented asymmetric top molecules by intense circularly polarized femtosecond laser pulses

We present a combined experimental and theoretical study on strong-field ionization of a three-dimensionally oriented asymmetric top molecule, benzonitrile (C$_7$H$_5$N), by circularly polarized, nonresonant femtosecond laser pulses. Prior to the interaction with the strong field, the molecules are quantum-state selected using a deflector, and 3-dimensionally (3D) aligned and oriented adiabatically using an elliptically polarized laser pulse in combination with a static electric field. A characteristic splitting in the molecular frame photoelectron momentum distribution reveals the position of the nodal planes of the molecular orbitals from which ionization occurs. The experimental results are supported by a theoretical tunneling model that includes and quantifies the splitting in the momentum distribution. The focus of the present article is to understand strong-field ionization from 3D-oriented asymmetric top molecules, in particular the suppression of electron emission in nodal planes of molecular orbitals. In the preceding article [Dimitrovski et al., Phys. Rev. A 83, 023405 (2011)] the focus is to understand the strong-field ionization of one-dimensionally-oriented polar molecules, in particular asymmetries in the emission direction of the photoelectrons.Comment: 12 pages, 9 figure

Lineshape Models in Inner-shell Photoelectron Spectra of Free Molecules and Clusters

Investigating the nature of molecules and clusters is of paramount importance for our understanding of the composition and the properties of matter. X-ray photoelectron spectroscopy is one of the most powerful techniques for obtaining information at the fundamental level about molecules and clusters. Our interest in this particular kind of spectroscopy derives from its ability to probe individual atoms in a molecule and their chemical surrounding. Experimental core-level photoelectron spectra show great complexity, even for simple molecules. Hence, developing theoretical lineshapes to model and interpret experimental spectra is necessary. This thesis is devoted to the development of novel theoretical methods for modeling x-ray photoelectron spectra of molecules and clusters. It also demonstrates how these models can be used as means of extracting chemical information from experimental spectra. In this thesis, the carbon 1s photoelectron spectrum of gas-phase ethanol has been investigated by calculations, and found to be significantly influenced by the presence of a conformational equilibrium. Furthermore, theoretical models have been used to analyze inner-shell photoelectron spectra of clusters made up of either argon, methane, or methanol molecules. With the help of these models we have been able to interpret the experimental spectra in terms of chemical shifts, vibrations, and the chemical surrounding of atoms (molecules) in the cluster. The results are very interesting and will, hopefully, contribute to the development of the current understanding of the structures and properties of clusters

Formation and Growth of Clusters of Sulfur Dioxide

Formation and growth of neutral SO2 clusters is investigated in an adiabatic-expansion setup by means of sulfur 2p (S2p) photoelectron spectroscopy and theoretical modeling. The shift in S2p ionization energy between the cluster and a single molecule, i.e., IE(cluster)-IE(monomer), is recorded and used to monitor the mean cluster size over a wide range of expansion conditions. The produced clusters were shown to fall into two different size regimes. Comparison between theoretical simulations and experimental observations suggests that while the smallest clusters belong to the ultrafine particle mode and have a liquid-like structure, the larger clusters belong to the accumulation mode of fine particles and possibly have a frozen cluster core. The transition between the two size/structure regimes occurs over a narrow interval in expansion conditions and may possibly reflect a change in growth mechanism from monomer addition to growth by cluster-cluster collisions

Evaluating the Physicochemical Properties–Activity Relationship and Discovering New 1,2-Dihydropyridine Derivatives as Promising Inhibitors for PIM1-Kinase: Evidence from Principal Component Analysis, Molecular Docking, and Molecular Dynamics Studies

In this study, we evaluated the physicochemical properties related to the previously reported anticancer activity of a dataset comprising thirty 1,2-dihydropyridine derivatives. We utilized Principal Component Analysis (PCA) to identify the most significant influencing factors. The PCA analysis showed that the first two principal components accounted for 59.91% of the total variance, indicating a strong correlation between the molecules and specific descriptors. Among the 239 descriptors analyzed, 18 were positively correlated with anticancer activity, clustering with the 12 most active compounds based on their IC50 values. Six of these variables—LogP, Csp3, b_1rotN, LogS, TPSA, and lip_don—are related to drug-likeness potential. Thus, we then ranked the 12 compounds according to these six variables and excluded those violating the drug-likeness criteria, resulting in a shortlist of nine compounds. Next, we investigated the binding affinity of these nine shortlisted compounds with the use of molecular docking towards the PIM-1 Kinase enzyme (PDB: 2OBJ), which is overexpressed in various cancer cells. Compound 6 exhibited the best docking score among the docked compounds, with a docking score of −11.77 kcal/mol, compared to −12.08 kcal/mol for the reference PIM-1 kinase inhibitor, 6-(5-bromo-2-hydroxyphenyl)-2-oxo-4-phenyl-1,2-dihydropyridine-3-carbonitrile. To discover new PIM-1 kinase inhibitors, we designed nine novel compounds featuring hybrid structures of compound 6 and the reference inhibitor. Among these, compound 31 displayed the best binding affinity, with a docking score of −13.11 kcal/mol. Additionally, we performed PubChem database mining using the structure of compound 6 and the similarity search tool, identifying 16 structurally related compounds with various reported biological properties. Among these, compound 52 exhibited the best binding affinity, with a docking score of −13.03 kcal/mol. Finally, molecular dynamics (MD) studies were conducted to confirm the stability of the protein–ligand complexes obtained from docking the studied compounds to PIM-1 kinase, validating the potential of these compounds as PIM-1 kinase inhibitors