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Gozem, Samer

Publications and source records attributed to Gozem, Samer.

6 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Teaching Nonradiative Transitions with MATLAB and Python

Nonradiative transitions are changes in energy states of atoms, ions, or molecules that do not involve the emission or absorption of photons. Despite their importance in understanding luminescent properties and photochemical reaction mechanisms, nonradiative transitions are rarely given more than a qualitative overview in undergraduate and even graduate physical chemistry curricula. To supplement the coverage of nonradiative transition topics, we provide here a set of active learning exercises to help students develop an intuitive understanding of the factors that determine the rate of nonradiative transitions. Here, we start by outlining the theoretical background through the formulations of the Franck–Condon factor and its relation to the rate of nonradiative transition. We then introduce three teaching modules, with associated MATLAB and Python codes, to explore how (1) the excited state nuclear displacement, (2) the electronic energy gap between excited and ground state and (3) the excited/ground state vibrational mode frequencies affect the magnitude of the Franck–Condon factor and thereby the rate of nonradiative transitions. The wave function overlap plots that accompany all teaching modules provide direct visualization of the effect of input parameters on the magnitude of Franck–Condon overlap integral.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

How Aqueous Solvation Impacts the Frequencies and Intensities of Infrared Absorption Bands in Flavin: The Quest for a Suitable Solvent Model

FTIR spectroscopy accompanied by quantum chemical simulations can reveal important information about molecular structure and intermolecular interactions in the condensed phase. Simulations typically account for the solvent either through cluster quantum mechanical (QM) models, polarizable continuum models (PCM), or hybrid quantum mechanical/molecular mechanical (QM/MM) models. Recently, we studied the effect of aqueous solvent interactions on the vibrational frequencies of lumiflavin, a minimal flavin model, using cluster QM and PCM models. Those models successfully reproduced the relative frequencies of four prominent stretching modes of flavin’s isoalloxazine ring in the diagnostic 1450–1750 cm−1 range but poorly reproduced the relative band intensities. Here, we extend our studies on this system and account for solvation through a series of increasingly sophisticated models. Only by combining elements of QM clusters, QM/MM, and PCM approaches do we obtain an improved agreement with the experiment. The study sheds light more generally on factors that can impact the computed frequencies and intensities of IR bands in solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

The effect of hydrogen-bonding on flavin’s infrared absorption spectrum

Cluster and continuum solvation computational models are employed to model the effect of hydrogen bonding interactions on the vibrational modes of lumiflavin. Calculated spectra were compared to experimental Fourier-transform infrared (FTIR) spectra in the diagnostic 1450–1800 cm –1 range, where intense V C=C , V C=N , V C 2 =O , and V C 4 =O stretching modes of flavin’s isoalloxazine ring are found. Local mode analysis is used to describe the strength of hydrogen-bonding in cluster models. The computations indicate that V C=C and V C=N mode frequencies are relatively insensitive to intermolecular interactions while the V C 2 =O and V C 4 =O modes are sensitive to direct (and also indirect for V C 2 =O ) hydrogen-bonding interactions. Although flavin is neutral, basis sets without the diffuse functions provide incorrect relative frequencies and intensities. The 6-31+G* basis set is found to be adequate for this system, and there is limited benefit to considering larger basis sets. Calculated vibrational mode frequencies agree with experimentally determined frequencies in solution when cluster models with multiple water molecules are used. Accurate simulation of relative FTIR band intensities, on the other hand, requires a continuum (or possibly quantum mechanical/molecular mechanical) model that accounts for long-range electrostatic effects. Lastly, an experimental peak at ca. 1624 cm –1 that is typically assigned to the V C 2 =O vibrational stretching mode has a complicated shape that suggests multiple underlying contributions. Our calculations show that this band has contributions from both the C 6 –C 7 and C 2 = O stretching vibrations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

The ezSpectra suite: An easy‐to‐use toolkit for spectroscopy modeling

Abstract A molecule's spectrum encodes information about its structure and electronic properties. It is a unique fingerprint that can serve as a molecular ID. Quantum chemistry calculations provide key ingredients for interpreting spectra, but modeling the spectra rarely ends there; it requires additional steps that entail combined treatments of electronic and nuclear degrees of freedom and account for specifics of the experimental setup (light energy, polarization, averaging over molecular orientations, temperature, etc.). This Software Focus article describes the ezSpectra suite, which currently comprises two stand‐alone open‐source codes: ezFCF and ezDyson . ezFCF calculates Franck–Condon factors, which yield vibrational progressions for polyatomic molecules, within the double‐harmonic approximation. ezDyson calculates absolute cross‐sections for photodetachment/photoionization processes and photoelectron angular distributions using Dyson orbitals computed by a quantum chemistry program. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Theoretical and Physical Chemistry > Spectroscopy Software > Simulation Methods

Gozem, Samer↗