Engineering topics
Lee, Timothy J.
Publications and source records attributed to Lee, Timothy J..
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.
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.
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.
Excited Vibrational Level Rotational Constants for SiC2: A Sensitive Molecular Diagnostic for Astrophysical Conditions
Silacyclopropynylidene, SiC2, is a known and highly abundant circumstellar molecule. Its spectrum has been established as a major component of lines observed toward the carbon-rich star IRC +10216 (CW Leonis). It has been detected in its low-lying v(sub 3) = 1 and 2 vibrational states as well as in various isotopic compositions. Increasing sensitivity and spatial resolution will enable many more emission or absorption lines to be detected. In order to detect new molecular species, unassigned lines of known species must be identified. This work uses established ab initio quartic force fields to produce data necessary for this classification of lines related to SiC2. Agreement between the theoretical vibrational frequencies and known rotational and spectroscopic constants is quite good, as good as 5 cm(exp -1) and 3 MHz, respectively in some cases. Additionally, experimentally unknown vibrational frequencies and rotational constants are provided for the first overtones and combination bands in addition to 3(sub v3), the second overtone of the low-lying antisymmetric stretch/carbide rotation mode. Frequencies of v(sub 3) = 3 low-J rotational transitions of the main isotopic species are also estimated from published data for v(sub 3) ≤ 2. Further, we determine rotational and centrifugal distortion parameters for which in most cases vibrational effects due to the v(sub 3) mode were reduced to first, and in several cases also to second order. These values may approximate equilibrium values better than the ground state values. The data produced herein will aid in the experimental and observational characterization of this known astromolecule in order to identify some of the unassigned lines for a known entity.
Energy and Spectroscopic Characterization of the Isomers of C4H3-, C6H3-, and C6H5-
Organic and inorganic molecules, neutral and ions have been observed in the interstellar medium. A few anions of organic molecules have also been observed recently. The Cassini spacecraft in the upper atmosphere of Titan has observed anions of large organic molecules. In this project we have studied the physical and spectroscopic properties of C4H3-, C6H3-, and C6H5-. We have optimized the geometrical structures of all low-lying isomers of the anions, calculated rotational, and harmonic vibrational frequencies of the anions mentioned above using the B3LYP density functional along with the augmented correlation consistent polar valence triple zeta (aug-cc-pVTZ) basis set. We have found many low-lying isomers on the potential energy surface of these anions.
Vibrational Frequencies and Spectroscopic Constants for 1(sup 3)A' HNC and 1(sup 3)A' HOC+ from High-Accuracy Quartic Force Fields
The spectroscopic constants and vibrational frequencies for the 1(sup 3)A' states of HNC, DNC, HOC+, and DOC+ are computed and discussed in this work. The reliable CcCR quartic force field based on high-level coupled cluster ab initio quantum chemical computations is exclusively utilized to provide the anharmonic potential. Then, second order vibrational perturbation theory and vibrational configuration interaction methods are employed to treat the nuclear Schroedinger equation. Second-order perturbation theory is also employed to provide spectroscopic data for all molecules examined. The relationship between these molecules and the corresponding 1(sup 3)A' HCN and HCO+ isomers is further developed here. These data are applicable to laboratory studies involving formation of HNC and HOC+ as well as astronomical observations of chemically active astrophysical environments.
Highly Accurate Potential Energy Surface, Dipole Moment Surface, Rovibrational Energy Levels, and Infrared Line List for (32)S(16)O2 up to 8000 cm(exp -1)
A purely ab initio potential energy surface (PES) was refined with selected (32)S(16)O2 HITRAN data. Compared to HITRAN, the root-mean-squares error (RMS) error for all J=0-80 rovibrational energy levels computed on the refined PES (denoted Ames-1) is 0.013 cm(exp -1). Combined with a CCSD(T)/aug-cc-pV(Q+d)Z dipole moment surface (DMS), an infrared (IR) line list (denoted Ames-296K) has been computed at 296K and covers up to 8,000 cm(exp -1). Compared to the HITRAN and CDMS databases, the intensity agreement for most vibrational bands is better than 85-90%. Our predictions for (34)S(16)O2 band origins, higher energy (32)S(16)O2 band origins and missing (32)S(16)O2 IR bands have been verified by most recent experiments and available HITRAN data. We conclude that the Ames-1 PES is able to predict (32/34)S(16)O2 band origins below 5500 cm(exp -1) with 0.01-0.03 cm(exp -1) uncertainties, and the Ames-296K line list provides continuous, reliable and accurate IR simulations. The Ka-dependence of both line position and line intensity errors is discussed. The line list will greatly facilitate SO2 IR spectral experimental analysis, as well as elimination of SO2 lines in high-resolution astronomical observations.
Anharmonic Rovibrational Calculations of Singlet Cyclic C4 Using a New Ab Initio Potential and a Quartic Force
We report a CCSD(T)/cc-pCV5Z quartic force field (QFF) and a semi-global CCSD(T)-F12b/aug-cc-pVTZ potential energy surface (PES) for singlet, cyclic C4. Vibrational fundamentals, combinations and overtones are obtained using vibrational second-order perturbation theory (VPT2) and the vibrational configurationinteraction (VCI) approach. Agreement is within 10 cm(exp −1) between the VCI calculated fundamentals on the QFF and PES using the MULTIMODE (MM) program, and VPT2 and VCI results agree for the fundamentals. The agreement between VPT2- QFF and MM-QFF results is also good for the C4 combinations and overtones. The J = 1 and J = 2 rovibrational energies are reported from both VCI (MM) on the PES and VPT2 on the QFF calculations. The spectroscopic constants of (12)C4 and two C(sub 2v)-symmetry, single (13)C-substituted isotopologues are presented, which may help identification of cyclic C4 in future experimental analyses or astronomical observations.
Rovibrational Spectroscopic Constants and Fundamental Vibrational Frequencies for Isotopologues of Cyclic and Bent Singlet HC2N isomers
Through established, highly-accurate ab initio quartic force fields (QFFs), a complete set of fundamental vibrational frequencies, rotational constants, and rovibrational coupling and centrifugal distortion constants have been determined for both the cyclic 1(sup 1) 1A' and bent 2(sup 1)A' DCCN, H(C13)CCN, HC(C-13)N, and HCC(N-15) isotopologues of HCCN. Spectroscopic constants are computed for all isotopologues using second-order vibrational perturbation theory (VPT2), and the fundamental vibrational frequencies are computed with VPT2 and vibrational configuration interaction (VCI) theory. Agreement between VPT2 and VCI results is quite good with the fundamental vibrational frequencies of the bent isomer isotopologues in accord to within a 0.1 to 3.2 / cm range. Similar accuracies are present for the cyclic isomer isotopologues. The data generated here serve as a reference for astronomical observations of these closed-shell, highly-dipolar molecules using new, high-resolution telescopes and as reference for laboratory studies where isotopic labeling may lead to elucidation of the formation mechanism for the known interstellar molecule: X 3A0 HCCN.
Protonated Nitrous Oxide, NNOH(+): Fundamental Vibrational Frequencies and Spectroscopic Constants from Quartic Force Fields
The interstellar presence of protonated nitrous oxide has been suspected for some time. Using established high-accuracy quantum chemical techniques, spectroscopic constants and fundamental vibrational frequencies are provided for the lower energy O-protonated isomer of this cation and its deuterated isotopologue. The vibrationally-averaged B0 and C0 rotational constants are within 6 MHz of their experimental values and the D(subJ) quartic distortion constants agree with experiment to within 3%. The known gas phase O−H stretch of NNOH(+) is 3330.91 cm(exp−1), and the vibrational configuration interaction computed result is 3330.9 cm(exp−1). Other spectroscopic constants are also provided, as are the rest of the fundamental vibrational frequencies for NNOH(+) and its deuterated isotopologue. This high-accuracy data should serve to better inform future observational or experimental studies of the rovibrational bands of protonated nitrous oxide in the ISM and the laboratory.