Engineering topics
Lee, Timothy J.
Publications and source records attributed to Lee, Timothy J..
Modeling the infrared cascade spectra of small PAHs: the 11.2 μm band
The profile of the 11.2 μm feature of the infrared (IR) cascade emission spectra of polycyclic aromatic hydrocarbon (PAH) molecules is investigated using a vibrational anharmonic method. Several factors are found to affect the profile including: the energy of the initially absorbed ultraviolet (UV) photon, the density of vibrational states, the anharmonic nature of the vibrational modes, the relative intensities of the vibrational modes, the rotational temperature of the molecule, and blending with nearby features. Each of these factors is explored independently and influence either the red or blue wing of the 11.2 μm feature. The majority impact solely the red wing, with the only factor altering the blue wing being the rotational temperature.
Molecular growth upon ionization of van der Waals clusters containing HCCH and HCN is a pathway to prebiotic molecules
The growth mechanisms of organic molecules in an ionizing environment such as the interstellar medium are not completely understood. Here we examine by means of ab initio molecular dynamics (AIMD) simulations and density functional theory (DFT) computations the possibility of bond formation and molecular growth upon ionization of van der Waals clusters of pure HCN clusters, and mixed clusters of HCN and HCCH, both of which are widespread in the interstellar medium. Ionization of van der Waals clusters can potentially lead to growth in low temperature and low-density environments. Our results show, that upon ionization of the pure HCN clusters, strongly bound stable structures are formed that contain N∙∙∙H bonds, and growth beyond pairwise HCN molecules is seen only in a small percentage of cases. In contrast, mixed clusters, where HCCH is preferentially ionized over HCN, can grow up to 3 or 4 units long with new carbon–carbon and carbon–nitrogen covalent bonds. Moreover, cyclic molecules formed, such as the radical cation of pyridine, which is a prebiotic molecule. The results presented here are significant as they provide a feasible pathway for molecular growth of small organic molecules containing both carbon and nitrogen in cold and relatively denser environments such as in dense molecular clouds but closer to the photo-dissociation regions, and protoplanetary disks. In the mechanism we propose, first, a neutral van der Waals cluster is formed. Once the cluster is formed it can undergo photoionization which leads to chemical reactivity without any reaction barrier.
The Production and Potential Detection of Hexamethylenetetramine-Methanol in Space
Numerous laboratory studies of astrophysical ice analogues have shown that their exposure to ionizing radiation leads to the production of large numbers of new, more complex compounds, many of which are of astrobiological interest. We show here that the irradiation of astrophysical ice analogues containing H2O, CH3OH, CO, and NH3 yields quantities of hexamethylenetetramine-methanol (hereafter HMT-methanol; C7N4H14O) that are easily detectible in the resulting organic residues. This molecule differs from simple HMT, which is known to be abundant in similar ice photolysis residues, by the replacement of a peripheral H atom with a CH2OH group. As with HMT, HMT-methanol is likely to be an amino acid precursor. HMT has tetrahedral (T(d)) symmetry, whereas HMT-methanol has C1 symmetry. We report the computed expected infrared spectra for HMT and HMT-methanol obtained using ab initio quantum chemistry methods and show that there is a good match between the observed and computed spectra for regular HMT. Since HMT-methanol lacks the high symmetry of HMT, it produces rotational transitions that could be observed at longer wavelengths, although establishing the exact positions of these transitions may be challenging. It is likely that HMT-methanol represents an abundant member of a larger family of functionalized HMT molecules that may be present in cold astrophysical environments.
Cation, Anion, and Radical Isomers of C4H4N: Computational Characterization and Implications for Astrophysical and Planetary Environments
Nitrogen-containing ions and molecules in the gas phase have been detected in non-Earth environments such as dark molecular clouds and more recently in the atmosphere of Saturn's moon Titan. These molecules may serve as precursors to larger heterocyclic structures that provide the foundation of complex biological molecules. On Titan, molecules of m/z 66 have been detected by the Cassini mission, and species of the empirical formula C 4 H 4 N may contribute to this signature. We have characterized seven isomers of C 4 H 4 N in anionic, neutral radical, and cationic states using density functional theory. Structures were optimized using the range-separated hybrid ωB97X-V with the cc-pVTZ and aug-cc-pVTZ basis sets. Anionic and radical C4H4N favor cyclic structures with aromatic and quasi-aromatic electron arrangements, respectively. Interestingly, ionization from the radical surface to the cation induces significant changes in structural stability, and the global minimum for positively charged isomers is CH 2 CCHCNH + , a pseudo-linear species reminiscent of cyanoallene. Select formation pathways to these structures from Titan's existing or postulated gas-phase species, reactions that are also relevant for other astrophysical environments, are discussed. By characterizing C 4 H 4 N isomers, we have identified energetically stable anionic, radical, and cationic structures that may be present in Titan's atmosphere and dark molecular clouds.
Computing Rotational, Rovibrational, and Vibrational Spectra for Astronomical Observations: High Accuracy Line Lists for High Temperatures, Limited Line Lists for Biosignature Molecules, and PAH Emission Spectra
Over the last several years, our group has been involved in developing approaches to compute highly accurate spectroscopic constants and vibrational frequencies for small transient molecules that may be used in the interpretation and assignment of high-resolution laboratory experiments as well as high-resolution astronomical spectra. Additionally, we have used the computed spectroscopic constants to simulate purely rotational and rovibrational spectra so that these may be compared directly with high- resolution astronomical observations, and we have worked on developing approaches that can be applied to much larger molecules, such as PAHs, where we can explicitly determine an harmonic corrections to vibrational modes as well as take into account intensity sharing due to resonances. Another part of our work in spectroscopic signatures involves computing highly accurate line lists for common molecules, such as CO2, SO2, and NH3, which occur in many astrophysical environments, including the atmospheres of exoplanets, and often need to have their lines identified in high- resolution observations in order to determine which lines are due to other molecules. In order to characterize the atmospheres of hot exoplanets, these line lists need to be very accurate and extend to very high energies. I will discuss our latest work in these areas of astrochemical spectroscopy research.
Fully anharmonic infrared cascade spectra of polycyclic aromatic hydrocarbons
The infrared (IR) emission of polycyclic aromatic hydrocarbons (PAHs) permeates our universe; astronomers have detected the IR signatures of PAHs around many interstellar objects. The IR emission of interstellar PAHs differs from their emission as seen under conditions on Earth as they emit through a collisionless cascade down through their excited vibrational states from high internal energies. The difficulty in reproducing interstellar conditions in the laboratory results in a reliance on theoretical techniques. However, the size and complexity of PAHs require careful consideration when producing the theoretical spectra. In this work, we outline the theoretical methods necessary to lead to fully theoretical IR cascade spectra of PAHs including: an anharmonic second order vibrational perturbation theory treatment, the inclusion of Fermi resonances through polyads, and the calculation of anharmonic temperature band shifts and broadenings (including resonances) through a Wang-Landau approach. We also suggest a simplified scheme to calculate vibrational emission spectra that retain the essential characteristics of the full IR cascade treatment and can directly transform low temperature absorption spectra in IR cascade spectra. Finally, we show that past astronomical models were in error in assuming a 15 cm -1 correction was needed to account for anharmonic emission effects.
Anharmonicity and the infrared emission spectrum of highly excited polycyclic aromatic hydrocarbons
Infrared (IR) spectroscopy is a powerful tool to study molecules in space. A key issue in such analyses is understanding the effect that temperature and anharmonicity have on different vibrational bands, and thus interpreting the IR spectra for molecules under various conditions. We combined second order vibrational perturbation theory and the Wang-Landau random walk technique to produce accurate IR spectra of highly excited polycyclic aromatic hydrocarbons. We fully incorporated anharmonic effects, such as resonances, overtones, combination bands, and temperature effects. The results are validated against experimental results for the pyrene molecule (C 16 H 10 ). Finally, in terms of positions, widths, and relative intensities of the vibrational bands, our calculated spectra are in excellent agreement with gas-phase experimental data.
The Failure of Correlation to Describe Out-of-Plane Carbon=Carbon Bending
Carbon-carbon multiply bonded systems are improperly described with standard correlation methods and basis sets. For computations of vibrational modes, the out-of- plane bends can be reported as imaginary at worst or simply too low at best. Utilizing the simplest of aromatic structures (cyclopropenylidene) and various levels of theory, this work diagnoses this known behavior for the first time. A combined 1-particle and n-particle basis set effect conspire to produce these non-physical results. When moving from sp2 to sp3 hybridization in the carbon atoms, the larger number of basis functions overcorrects the energy. This is exacerbated by correlation methods. These allow for occupation of the π and π∗ orbitals in the expanded wave function that combine with the hydrogen s orbitals. As a result, the improperly described space can be further and non-physically stabilized by post-Hartree-Fock correlation. This represents a fundamental problem with at least Hartree-Fock based methods of all flavors in describing carbon. Beyond being a flaw in quantum chemical theory, other repercussions will be present in computations regarding spectroscopy as well as energy and environmental studies where highly-accurate hydrocabon vibrational transitions or thermochemical data are needed.
High-Resolution IR Absorption Spectroscopy of Polycyclic Aromatic Hydrocarbons in the 3-micrometers Region: Role of Periphery
In this work we report on high-resolution IR absorption studies that provide a detailed view on how the peripheral structure of irregular polycyclic aromatic hydrocarbons (PAHs) affects the shape and position of their 3-micrometers absorption band. To this purpose we present mass-selected, high-resolution absorption spectra of cold and isolated phenanthrene, pyrene, benz[a]antracene, chrysene, triphenylene, and perylene molecules in the 2950-3150 per cm range. The experimental spectra are compared with standard harmonic calculations, and anharmonic calculations using a modified version of the SPECTRO program that incorporates a Fermi resonance treatment utilizing intensity redistribution. We show that the 3-micrometers region is dominated by the effects of anharmonicity, resulting in many more bands than would have been expected in a purely harmonic approximation. Importantly, we find that anharmonic spectra as calculated by SPECTRO are in good agreement with the experimental spectra. Together with previously reported high-resolution spectra of linear acenes, the present spectra provide us with an extensive dataset of spectra of PAHs with a varying number of aromatic rings, with geometries that range from open to highly-condensed structures, and featuring CH groups in all possible edge configurations. We discuss the astrophysical implications of the comparison of these spectra on the interpretation of the appearance of the aromatic infrared 3-micrometers band, and on features such as the two-component emission character of this band and the 3-micrometers emission plateau.
Computing Highly Accurate Spectroscopic Line Lists for Characterization of Planetary Atmospheres: CO2 and SO2 Line Lists Needed for Modeling Venus
Over the last decade, it has become apparent that the most effective approach for determining highly accurate rotational and rovibrational line lists for molecules of interest in planetary atmospheres and other astrophysical environments is through a combination of highresolution laboratory experiments coupled with state-of-the art ab initio quantum chemistry methods. The approach involves computing the most accurate potential energy surface (PES) possible using state-of-the art electronic structure methods, followed by computing rotational and rovibrational energy levels using an exact variational method to solve the nuclear Schrödinger equation. Then, reliable experimental data from high-resolution experiments is used to refine the ab initio PES in order to improve the accuracy of the computed energy levels and transition energies. From the refinement step, we have been able to achieve an accuracy of approximately 0.015 cm-1 for rovibrational transition energies, and even better for purely rotational transitions. This combined "experiment / theory" approach allows for determination of essentially a complete line list, with hundreds of millions of transitions, and having the transition energies and intensities be highly accurate. Our group has successfully applied this approach to determine highly accurate line lists for NH3, CO2 and isotopologues, and SO2 and isotopologues. Here I will report our latest results for CO2 and SO2 including all isotopologues. Comparisons to the available data in HITRAN2012 and other available databases will be shown, though we note that our line lists for SO2 are significantly more complete than any other databases. Since it is important to span a large temperature range in order to model the spectral signature of Venus as well as exoplanets, we will demonstrate how the spectra change on going from low temperatures (100 K) to higher temperatures (500 K to 1500 K).
Mechanisms for the Formations of the Thymine Under Astrophysical Conditions and Implications for the Origin of Life
Nucleobases are the carriers of the genetic information in ribonucleic acid and deoxyribonucleic acid (DNA) for all life on Earth. Their presence in meteorites clearly indicates that compounds of biological importance can form via non-biological processes in extraterrestrial environments. Recent experimental studies have shown that the pyrimidine-based nucleobases uracil and cytosine can be easily formed from the ultraviolet irradiation of pyrimidine in H2O-rich ice mixtures that simulate astrophysical processes. In contrast, thymine, which is found only in DNA, is more difficult to form under the same experimental conditions, as its formation usually requires a higher photon dose. Earlier quantum chemical studies confirmed that the reaction pathways were favorable provided that several H2O molecules surrounded the reactants. However, the present quantum chemical study shows that the formation of thymine is limited because of the inefficiency of the methylation of pyrimidine and its oxidized derivatives in an H2O ice, as supported by the laboratory studies. Our results constrain the formation of thymine in astrophysical environments and thus the inventory of organic molecules delivered to the early Earth and have implications for the role of thymine and DNA in the origin of life.
High-Resolution IR Absorption Spectroscopy of Polycyclic Aromatic Hydrocarbons: The Realm of Anharmonicity
We report on an experimental and theoretical investigation of the importance of anharmonicity in the 3 micrometers CH stretching region of Polycyclic Aromatic Hydrocarbon (PAH) molecules. We present mass-resolved, high-resolution spectra of the gas-phase cold ((is) approximately 4K) linear PAH molecules naphthalene, anthracene, and tetracene. The measured IR spectra show a surprisingly high number of strong vibrational bands. For naphthalene, the observed bands are well separated and limited by the rotational contour, revealing the band symmetries. Comparisons are made to the harmonic and anharmonic approaches of the widely used Gaussian software. We also present calculated spectra of these acenes using the computational program SPECTRO, providing anharmonic predictions enhanced with a Fermi-resonance treatment that utilizes intensity redistribution. We demonstrate that the anharmonicity of the investigated acenes is strong, dominated by Fermi resonances between the fundamental and double combination modes, with triple combination bands as possible candidates to resolve remaining discrepancies. The anharmonic spectra as calculated with SPECTRO lead to predictions of the main modes that fall within 0.5% of the experimental frequencies. The implications for the Aromatic Infrared Bands, specifically the 3-m band are discussed.
Ames S-32 O-16 O-18 Line List for High-Resolution Experimental IR Analysis
By comparing to the most recent experimental data and spectra of the SO2 628 ν1/ν3 bands (see Ulenikov et al., JQSRT 168 (2016) 29-39), this study illustrates the reliability and accuracy of the Ames-296K SO2 line list, which is accurate enough to facilitate such high-resolution spectroscopic analysis. The SO2 628 IR line list is computed on a recently improved potential energy surface (PES) refinement, denoted Ames-Pre2, and the published purely ab initio CCSD(T)/aug-cc-pVQZ dipole moment surface. Progress has been made in both energy level convergence and rovibrational quantum number assignments agreeing with laboratory analysis models. The accuracy of the computed 628 energy levels and line list is similar to what has been achieved and reported for SO2 626 and 646, i.e. 0.01-0.03 cm(exp −1) for bands up to 5500 cm(exp −1). During the comparison, we found some discrepancies in addition to overall good agreements. The three-IR-list based feature-by-feature analysis in a 0.25 cm(exp −1) spectral window clearly demonstrates the power of the current Ames line lists with new assignments, correction of some errors, and intensity contributions from varied sources including other isotopologues. We are inclined to attribute part of detected discrepancies to an incomplete experimental analysis and missing intensity in the model. With complete line position, intensity, and rovibrational quantum numbers determined at 296 K, spectroscopic analysis is significantly facilitated especially for a spectral range exhibiting such an unusually high density of lines. The computed 628 rovibrational levels and line list are accurate enough to provide alternatives for the missing bands or suspicious assignments, as well as helpful to identify these isotopologues in various celestial environments. The next step will be to revisit the SO2 828 and 646 spectral analyses.
Electronically Excited States of Anistropically Extended Singly-Deprotonated PAH Anions
Polycyclic Aromatic Hydrocarbons (PAHs) play a significant role in the chemistry of the interstellar medium (ISM) as well as in hydrocarbon combustion. These molecules can have high levels of diversity with the inclusion of heteroatoms and the addition or removal of hydrogens to form charged or radical species. There is an abundance of data on the cationic forms of these molecules, but there have been many fewer studies on the anionic species. The present study focuses on the anionic forms of deprotonated PAHs. It has been shown in previous work that PAHs containing nitrogen heteroatoms (PANHs) have the ability to form valence excited states giving anions electronic absorption features. This work analyzes how the isoelectronic pure PAHs behave under similar structural constructions. Singly-deprotonated forms of benzene, naphthalene, anthracene, and teteracene classes are examined. None of the neutral-radicals possess dipole moments large enough to support dipole-bound excited states in their corresponding closed-shell anions. Even though the PANH anion derivatives support valence excited states for three-ringed structures, it is not until four-ringed structures of the pure PAH anion derivatives that valence excited states are exhibited. However, anisotropically-extended PAHs larger than tetracene will likely exhibit valence excited states. The relative energies for the anion isomers are very small for all of the systems in this study.
The Structure, Anharmonic Vibrational Frequencies, and Intensities of NNHNN+
A semi-global potential energy surface (PES) and quartic force field (QFF) based on fitting high-level electronic structure energies are presented to describe the structures and spectroscopic properties of NNHNN+. The equilibrium structure of NNHNN+ is linear with the proton equidistant between the two nitrogen groups and thus of D(sub ∞h) symmetry. Vibrational second-order perturbation theory (VPT2) calculations based on the QFF fails to describe the proton “rattle” motion, i.e., the antisymmetric proton stretch, due to the very flat nature of PES around the global minimum, but performs properly for other modes with sharper potential wells. Vibrational self-consistent field/virtual state configuration interaction (VSCF/VCI) calculations using a version of MULTIMODE without angular momentum terms successfully describe this motion and predict the fundamental to be at 759 cm(exp -1). This is in good agreement with the value of 746 cm(exp -1) from a fixed-node diffusion Monte Carlo calculation and the experimental Ar-tagged result of 743 cm(exp -1). Other VSCF/VCI energies are in good agreement with other experimentally reported ones. Both double-harmonic intensity and rigorous MULTIMODE intensity calculations show the proton transfer fundamental has a very strong intensity.