Chemistry Commons^™

Modelling Terrestrial And Potential Extraterrestrial Photopigments Via Density Functional Theory, Dorothea Illner

Theses and Dissertations

In the search for extraterrestrial life, biosignatures play a crucial role in identifying its putative traces. A commonly known and robust biosignature is the Vegetation Red Edge (VRE), which can be described as a sharp increase of reflectance observed from a planet and stems from the light absorption of photopigments in specific regions in the electromagnetic spectrum. For Earth, this VRE is known to occur around 700 nm, however, if the photopigments absorb light in different regions and have different structures the VRE could experience a wavelenght shift.

In this work, Chlorophyll a and a potential photopigment precursor called Phot0 …

Preparation Of Methanediamine (Ch2(Nh2)2)—A Precursor To Nucleobases In The Interstellar Medium, Joshua H. Marks, Jia Wang, Ryan C. Fortenberry, Ralf I. Kaiser

Faculty and Student Publications

Although methanediamine (CH2(NH2)2) has historically been the subject of theoretical scrutiny, it has never been isolated to date. Here, we report the preparation of methanediamine (CH2(NH2)2)—the simplest diamine. Low-temperature interstellar analog ices composed of ammonia and methylamine were exposed to energetic electrons which act as proxies for secondary electrons produced in the track of galactic cosmic rays. These experimental conditions, which simulate the conditions within cold molecular clouds, . result in radical formation and initiate aminomethyl (ĊH2NH2) and amino (NH2) radical chemistry. Exploiting tunable photoionization reflectron time-of-flight mass spectrometry (PI-ReToF-MS) to make isomer-specific assignments, methanediamine was identified in the gas …

The Spectral Features And Detectability Of Small, Cyclic Silicon Carbide Clusters, Christopher M. Sehring, C. Zachary Palmer, Brent R. Westbrook, Ryan C. Fortenberry

Faculty and Student Publications

Rovibrational spectral data for several tetra-atomic silicon carbide clusters (TASCCs) are computed in this work using a CCSD(T)-F12b/cc-pCVTZ-F12 quartic force field. Accurate theoretical spectroscopic data may facilitate the observation of TASCCs in the interstellar medium which may lead to a more complete understanding of how the smallest silicon carbide (SiC) solids are formed. Such processes are essential for understanding SiC dust grain formation. Due to SiC dust prevalence in the interstellar medium, this may also shed light on subsequent planetary formation. Rhomboidal Si2C2 is shown here to have a notably intense (247 km mol−1) anharmonic vibrational frequency at 988.1 cm−1 …

Theoretical Spectra And Energetics For C-C3hc2h, L-C5h2, And Bipyramidal D3h C5h2, Alexandria G. Watrous, Brent R. Westbrook, Ryan C. Fortenberry

Faculty and Student Publications

The recent astronomical detection of c-C3HC2H and l-C5H2 has led to increased interest in C5H2 isomers and their relative stability. The present work provides the first complete list of anharmonic vibrational spectral data with infrared intensities for three such isomers as well as including the first set of rotational data for the bipyramidal C5H2 isomer allowing for these molecules to serve as potential tracers of interstellar carbon. All three isomers have fundamental vibrational frequencies with at least one notably intense fundamental frequency. The l-C5H2 isomer has, by far, the highest intensities out of the three isomers at 2076.3 cm−1 (738 …

State-To-State Rate Coefficients For Hcs+In Rotationally Inelastic Collisions With H2at Low Temperatures, Otoniel Denis-Alpizar, Ernesto Quintas-Sánchez, Richard Dawes

Chemistry Faculty Research & Creative Works

HCS⁺ ions have been detected in several regions of the interstellar medium (ISM), but an accurate determination of the chemical-physical conditions in the molecular clouds where this molecule is observed requires detailed knowledge of the collisional rate coefficients with the most common colliders in those environments. In this work, we study the dynamics of rotationally inelastic collisions of HCS⁺ + H₂ at low temperature, and report, for the first time, a set of rate coefficients for this system. We used a recently developed potential energy surface for the HCS⁺-H₂ van der Waals complex and …

Computational Investigations Into Astrochemical Inorganic Oxides, Ammonia Borane, And Genetic Algorithms, E. Michael Valencia

Honors Theses

The formulations of quantum mechanics in the early 1900s were exciting theoretical discoveries, but were not practical to apply until the advent of computers and the subsequent computational methods in 1951. With the introduction of tractable simplifications, procedures such as Hartree-Fock allowed for determination of properties of non-trivial systems. Presently, huge leads of computational power have allowed for extremely precise, quantitative work that can be applied to the human body, synthesis, or even astrochemical processes. This thesis presents works concerning 1) the history of quantum mechanics; 2) a brief primer on computational chemistry and its methods; 3) inorganic oxides in …

Spectral Signatures Of Hydrogen Thioperoxide (Hosh) And Hydrogen Persulfide (Hssh): Possible Molecular Sulfur Sinks In The Dense Ism, Charles Z. Palmer, Ryan C. Fortenberry, Joseph S. Francisco

Faculty and Student Publications

For decades, sulfur has remained underdetected in molecular form within the dense interstellar medium (ISM), and somewhere a molecular sulfur sink exists where it may be hiding. With the discovery of hydrogen peroxide (HOOH) in the ISM in 2011, a natural starting point may be found in sulfur-bearing analogs that are chemically similar to HOOH: hydrogen thioperoxide (HOSH) and hydrogen persulfide (HSSH). The present theoretical study couples the accuracy in the anharmonic fundamental vibrational frequencies from the explicitly correlated coupled cluster theory with the accurate rotational constants provided by canonical high-level coupled cluster theory to produce rovibrational spectra for use …

Valence-, Dipole-And Quadropole-Bound Electronically Excited States Of Closed-Shell Anions Formed By Deprotonation Of Cyano-And Ethynyl-Disubstituted Polycyclic Aromatic Hydrocarbons, Marie E. Strauss, Taylor J. Santaloci, Ryan C. Fortenberry

Faculty and Student Publications

Dicyano-functionalized benzene and naphthalene anion derivatives exhibit a relatively rich population of electronically excited states in stark contrast to many assumptions regarding the photophysics of anions in general. The present work has quantum chemically analyzed the potential electronically excited states of closed-shell anions created by replacing hydrogen atoms with valence-bound lone pairs in benzene and naphthalene difunctionalized with combinations of-CN and-C2H. Dicyanobenzene anion derivatives can exhibit dipole-bound excited states as long as the cyano groups are not in para position to one another. This also extends to cyanoethynylbenzene anions as well as deprotonated dicyano-and cyanoethynylnaphthalene anion derivatives. Diethynyl functionalization is …

Synthesis Of Methanediol [Ch2(Oh)2]: The Simplest Geminal Diol, Cheng Zhu, N. Fabian Kleimeier, Andrew M. Turner, Santosh K. Singh, Ryan C. Fortenberry, Ralf I. Kaiser

Faculty and Student Publications

Geminal diols—organic molecules carrying two hydroxyl groups at the same carbon atom—have been recognized as key reactive intermediates by the physical (organic) chemistry and atmospheric science communities as fundamental transients in the aerosol cycle and in the atmospheric ozonolysis reaction sequence. Anticipating short lifetimes and their tendency to fragment to water plus the aldehyde or ketone, free geminal diols represent one of the most elusive classes of organic reactive intermediates. Here, we afford an exceptional glance into the preparation of the previously elusive methanediol [CH2(OH)2] transient—the simplest geminal diol—via energetic processing of low-temperature methanol–oxygen ices. Methanediol was identified in the …

Inelastic, Exchange, And Reactive Processes In Rovibrationally Excited Collisions Of Hd With H, Boyi Zhou, Benhui Yang, Balakrishnan Naduvalath, B. K. Kendrick, Maodu Chen, P. C. Stancil

Chemistry and Biochemistry Faculty Research

The HD molecule is an important coolant in early universe chemistry models and a tracer of H2 in star-forming regions. Rate coefficients for collisional excitation and de-excitation of HD rotational and vibrational levels form important ingredients in astrophysical models. While collisions with He, H2, and H are the most important, available data for H + HD collisions are largely limited to temperatures less than 1000 K for the vibrational ground state, low-lying rotational levels of the v = 1 HD vibrational level, or computed without reactive contributions. Here, through explicit quantum scattering calculations, we report extensive data for rovibrational transitions …

Computational Investigation Of Stellar Cooling, Noble Gas Nucleation, And Organic Molecular Spectra, Jax Dallas

Honors Theses

Since the advent and optimization of the Hartree-Fock method, quantum chemistry has been utilized to investigate systems operating on timeframes and environments traditionally unavailable to bench-top chemistry. As computational methods have grown more robust and less time consuming, quantum chemistry has been utilized to investigate a range of fields, including the steadily growing discipline of computational astrochemistry. Through the lens of computational astrochemistry, chemistry that occurred billions of years ago can be explored with equal clarity to that which is currently happening in the cosmos. The work presented throughout this thesis is a series of investigations into different timeframes of …

Pathways To Detection Of Strongly-Bound Inorganic Species: The Vibrational And Rotational Spectral Data Of Alh2oh, Hmgoh, Alh2nh2, And Hmgnh2, Alexandria G. Watrous, Megan C. Davis, Ryan C. Fortenberry

Faculty and Student Publications

Small, inorganic hydrides are likely hiding in plain sight, waiting to be detected toward various astronomical objects. AlH2OH can form in the gas phase via a downhill pathway, and the present, high-level quantum chemical study shows that this molecule exhibits bright infrared features for anharmonic fundamentals in regions above and below that associated with polycyclic aromatic hydrocarbons. AlH2OH along with HMgOH, HMgNH2, and AlH2NH2 are also polar with AlH2OH having a 1.22 D dipole moment. AlH2OH and likely HMgOH have nearly unhindered motion of the hydroxyl group but are still strongly bonded. This could assist in gas phase synthesis, where …

Electronically Excited States Of Closed-Shell, Cyano-Functionalized Polycyclic Aromatic Hydrocarbon Anions, Taylor J. Santaloci, Ryan C. Fortenberry

Faculty and Student Publications

Few anions exhibit electronically excited states, and, if they do, the one or two possible excitations typically transpire beyond the visible spectrum into the near-infrared. These few, red-shifted electronic absorption features make anions tantalizing candidates as carriers of the diffuse interstellar bands (DIBs), a series of mostly unknown, astronomically ubiquitous absorption features documented for over a century. The recent interstellar detection of benzonitrile implies that cyano-functionalized polycyclic aromatic hydrocarbon (PAH) anions may be present in space. The presently reported quantum chemical work explores the electronic properties of deprotonated benzene, naphthalene, and anthracene anions functionalized with a single cyano group. Both …

Anharmonic Vibrational Frequencies And Spectroscopic Constants For The Detection Of Ethynol In Space, Jax D. Dallas, Brent R. Westbrook, Ryan C. Fortenberry

Faculty and Student Publications

The ethynol (HCCOH) molecule has recently been shown to be present in simulated astrochemical ices possibly linking it to molecular building blocks for interstellar complex organic molecules like amino acids. The proposed reaction mechanism suggests the simultaneous formation of both ketene and ethynol from mixed carbon monoxide/water ice in simulated interstellar conditions. Rigorous anharmonic spectral data within both the IR and microwave regions are needed for possible detection of ethynol in the interstellar medium. This study provides the first such data for this molecule from high-level quantum chemical computations where experiment is currently lacking. Ethynol has a (Formula presented.) comparable …

Untangling The Formation Of Methoxymethanol (Ch3Och2Oh) And Dimethyl Peroxide (Ch3Ooch3) In Star-Forming Regions, Cheng Zhu, Robert Frigge, Alexandre Bergantini, Ryan C. Fortenberry, Ralf I. Kaiser

Faculty and Student Publications

© 2019. The American Astronomical Society. All rights reserved.. Methoxymethanol (CH3OCH2OH) was recently detected toward the MM1 core in the high-mass star-forming region NGC 6334I. However, the underlying formation mechanisms of this complex organic molecule (COM) as well as its structural isomers ethylene glycol (HOCH2CH2OH) and the hitherto unobserved dimethyl peroxide (CH3OOCH3) are still elusive. Here, we report the very first confirmed synthesis of dimethyl peroxide - at various deuteration levels within interstellar analogous ices of D3-methanol (CD3OH) exposed to ionizing radiation at ultralow temperatures of 5 K. The discrimination of specific isomers is achieved by exploiting reflectron time-of-flight mass …

Organometallic Compounds As Carriers Of Extraterrestrial Cyanide In Primitive Meteorites, Karen E. Smith, Christopher H. House, Ricardo D. Arevalo Jr., Jason P. Dworkin, Michael P. Callahan

Chemistry and Biochemistry Faculty Publications and Presentations

Extraterrestrial delivery of cyanide may have been crucial for the origin of life on Earth since cyanide is involved in the abiotic synthesis of numerous organic compounds found in extant life; however, little is known about the abundance and species of cyanide present in meteorites. Here, we report cyanide abundance in a set of CM chondrites ranging from 50 ± 1 to 2472 ± 38 nmol·g⁻¹, which relates to the degree of aqueous alteration of the meteorite and indicates that parent body processing influenced cyanide abundance. Analysis of the Lewis Cliff 85311 meteorite shows that its releasable cyanide …

Fourier Transform Spectroscopy Of The C³Δ-X³Δ Transition Of Tio In Support Of Exoplanet Spectroscopy, James N. Hodges, Peter Bernath

Chemistry & Biochemistry Faculty Publications

Recent limitations in the TiO line list used in cross-correlation detection schemes have made the detection and quantification of TiO in exoplanetary atmospheres challenging. The quality of the line list appears to degrade at wavelengths shorter than 630 nm. The C³Δ-X³Δ electronic transition has strong rovibronic bands near 500 nm. In an effort to improve the line list, a spectrum of TiO in a furnace at 1950 K is analyzed, and the assigned lines of the C³Δ-X³Δ transition are fit with the N² Hamiltonian in the molecular spectrum fitting software, _{PGOPHER …}

Mixed Quantum/Classical Theory (Mqct) For Rotationally And Vibrationally Inelastic Scattering And Its Application To The Molecules Of Astrochemical Importance, Alexander Semenov

Dissertations (1934 -)

This thesis presents developments and applications of the mixed quantum/classical theory (MQCT) for inelastic scattering. In this approach, translational motion of collision partners is treated classically, while the internal degrees of freedom – rotational and/or vibrational motion – are treated quantum mechanically. Within this framework calculations of rotationally inelastic cross sections are carried out in a broad range of collision energies and results are compared against the exact full quantum data for several real systems. For CO +He, N2 + Na and H2 + He the agreement is excellent through six orders of magnitude range of cross sections values and …

Fourier Transform Spectroscopy Of The A3Π–X3Σ− Transition Of Oh+, James N. Hodges, Peter F. Bernath

Chemistry & Biochemistry Faculty Publications

The OH⁺ ion is of critical importance to the chemistry in the interstellar medium and is a prerequisite for the generation of more complex chemical species. Submillimeter and ultraviolet observations rely on high quality laboratory spectra. Recent measurements of the fundamental vibrational band and previously unanalyzed Fourier transform spectra of the near-ultraviolet A³Π-X 3Σ^- electronic spectrum, acquired at the National Solar Observatory at Kitt Peak in 1989, provide an excellent opportunity to perform a global fit of the available data. These new optical data are approximately four times more precise as compared to the previous values. …

A Quantum Astrochemical Perspective On The C-C3h Radical With Application To The Interstellar Medium, Matthew Bassett

Electronic Theses and Dissertations

The interstellar medium (ISM) has been an area of focus for astrochemists and quantum chemists for many years, with particular interest in the presence of interstellar molecules and the resulting chemical processes. The c-C3H radical has been detected in the ISM near the dark molecular cloud TMC-1. With the application of ab initio computational methods using coupled-cluster theory at the singles, doubles, and perturbative triples [CCSD(T)] level, highly accurate quartic force fields (QFFs) are constructed to define the electronic wavefunction for the inter nuclear Hamiltonian. The QFF is used to predict the equilibrium geometry and produce vibrational frequencies, rotational constants, …

Small Carbon Chains In Circumstellar Envelopes, R. J. Hargreaves, K. Hinkle, P. F. Bernath

Chemistry & Biochemistry Faculty Publications

Observations of carbon-rich circumstellar envelopes were made using the Phoenix spectrograph on the Gemini South telescope to determine the abundance of small carbon chain molecules. Vibration-rotation lines of the ν3 antisymmetric stretch of C₃ near 2040 cm^-1 (4.902 μm) have been used to determine the column density for four carbon-rich circumstellar envelopes: CRL 865, CRL 1922, CRL 2023 and IRC +10216. We additionally calculate the column density of C₅ for IRC +10216, and provide an upper limit for five more objects. An upper limit estimate for the C₇ column density is also provided for IRC+10216. A …

Jupiter's Great Red Spot Is Composed Of Ammonia And Phosphine, Erika Rosenberger

Natural Sciences Student Research Presentations

In Jupiter's Great Red Spot, ammonia, phosphine, and para-Hydrogen were found. The Great Red Spot is the local maximum of ammonia, the most abundant compound of the atmosphere. The abundance of ammonia in the Spot is regulated by a complex interaction between photochemistry, condensation, precipitation, and atmospheric dynamics. Ammonia is found most abundant in the regions at around 400-500 mbar when phosphine is the most abundant at 600 mbar. The photo-dissociation reaction of phosphine that occurs in the Spot helps explain why the planet Jupiter and the Great Red Spot is red. The reaction sequence proposed by scientists Prinn and …

Murchison Chondrite, Marisol Chirinos

Natural Sciences Student Research Presentations

Murchson Chondrite is a carbonaceous meteorite that fell in a small town called Murchson in Victoria, Australia, on September 28, 1969. It is believed to be one of the most primitive meteorites to fall on earth. Amino acides found in Murchison differ in structures from amino acids found on Earth. While the carbon atom in the carboxylic acid and amion group of biological terrestrial amino acids have a hydrogen atom attached to it, the Murchison's amino acids have a methyl group instead.

High­- Accuracy Quartic Force Field Calculations For The Spectroscopic Constants And Vibrational Frequencies Of 11A′ L-­C3H-­: A Possible Link To Lines Observed In The Horsehead Nebula Pdr, Ryan C. Fortenberry, Xinchuan Huang, T. D. Crawford, Timothy J. Lee

Ryan C. Fortenberry

It has been shown that rotational lines observed in the Horsehead nebula photodissociation region (PDR) are probably not caused by l-C₃H⁺, as was originally suggested. In the search for viable alternative candidate carriers, quartic force fields are employed here to provide highly accurate rotational constants, as well as fundamental vibrational frequencies, for another candidate carrier: 1¹ A' C₃H^–. The ab initio computed spectroscopic constants provided in this work are, compared to those necessary to define the observed lines, as accurate as the computed spectroscopic constants for many of the known interstellar …

Spectroscopic Constants And Vibrational Frequencies For L­-C3H+ And Isotopologues From Highly­Accurate Quartic Force Fields: The Detection Of L­-C3H+ In The Horsehead Nebula Pdr Questione, Xinchuan Huang, Ryan C. Fortenberry, Timothy J. Lee

Ryan C. Fortenberry

Very recently, molecular rotational transitions observed in the photon-dominated region of the Horsehead nebula have been attributed to l-C₃H⁺. In an effort to corroborate this finding, we employed state-of-the-art and proven high-accuracy quantum chemical techniques to compute spectroscopic constants for this cation and its isotopologues. Even though the B rotational constant from the fit of the observed spectrum and our computations agree to within 20 MHz, a typical level of accuracy, the D rotational constant differs by more than 40%, while the H rotational constant differs by three orders of magnitude. With the likely errors in …

Theoretical Electronic And Rovibrational Studies For Anions Of Interest To The Dibs, Ryan C. Fortenberry

Ryan C. Fortenberry

The dipole-bound excited state of the methylene nitrile anion (CH2CN−) has been suggested as a candidate carrier for a diffuse interstellar band (DIB) at 803.8 nm. Its corresponding radical has been detected in the interstellar medium (ISM), making the existence for the anion possible. This work applies state-of-the-art ab initio methods such as coupled cluster theory to reproduce accurately the electronic excitations for CH2CN− and the similar methylene enolate anion, CH2CHO−. This same approach has been employed to indicate that 19 other anions may possess electronically excited states, five of which are valence in nature. Concurrently, in order to assist …

On The Electronic Spectroscopy Of Closed Shell Cations Derived From Resonance Stabilized Radicals: Insights From Theory And Franck-Condon Analysis, T. P. Troy, S. H. Kable, T. W. Schmidt, Scott Reid

Chemistry Faculty Research and Publications

Context. Recent attention has been directed on closed-shell aromatic cations as potential carriers of the diffuse interstellar bands. The spectra of mass-selected, matrix-isolated benzylium, and tropylium cations were recently reported. The visible spectrum of benzylium exhibits a large Franck-Condon (FC) envelope, inconsistent with diffuse interstellar band carriers.

Aims. We perform a computational analysis of the experimentally studied benzylium spectrum before extending the methods to a range of larger, closed-shell aromatic cations to determine the potential for this class of systems as diffuse interstellar band carriers.

Methods. Density functional theory (DFT), time-dependent ((TD)DFT), and multi-configurational self-consistent field second-order perturbation theory (MRPT2) …