In this work we address two problems in computational chemistry relevant to biomolecular modeling. In the first project, we consider the conformer space of melatonin as a a representative example of “real-life” flexible biomolecules. Geometries for all 52 unique conformers are optimized using spin-component scaled MP2, and then relative energies are obtained at the CCSD (T) level near the complete basis set limit. These are then used to validate a variety of DFT methods with and without empirical dispersion corrections, as well as some lower-level ab initio methods. Basis set convergence is found to be relatively slow due to internal C-H…O and C-H…N contacts. Absent dispersion corrections, many DFT functionals will transpose the two lowest conformers. Dispersion corrections resolve the problem for most functionals. Double hybrids yield particularly good performance, as does MP2.5. In the second project, we propose a simple DFT-based diagnostic for nondynamical correlation effects. Aλ= (1-TAE [ΧλC]/TAE[XC])/λ where TAE is the total atomization energy, XC the “pure” DFT exchange-correlation functional, and ΧλC the corresponding hybrid with 100λ% HF-type exchange. The diagnostic is a good predictor for sensitivity of energetics to the level of theory, unlike most of the wavefunction-based diagnostics. For GGA functionals, Aλ values approaching unity indicate severe non-dynamical correlation. The diagnostic is only weakly sensitive to the basis set (beyond polarized double zeta) and can be applied to problems beyond practical reach of wavefunction ab-initio methods required for other diagnostics.
One of the central concerns of computational chemistry is that of efficiency (i.e. the development of methodologies which will yield increased accuracy of prediction without requiring additional computational resources – RAM, disk space, computing time). Though the equations of quantum mechanics are known, the solutions to these equations often require a great deal of computing power. This dissertation primarily concerns the theme of improved computational efficiency (i.e. the achievement of greater accuracy with reduced computational cost). Improvements in the efficiency of computational chemistry are explored first in terms of the correlation consistent composite approach (ccCA). The ccCA methodology was modified and this enhanced ccCA methodology was tested against the diverse G3/05 set of 454 energetic properties. As computational efficiency improves, molecules of increasing size may be studied and this dissertation explored the issues (differential correlation and size extensivity effects) associated with obtaining chemically accurate (within 1 kcal mol-1) enthalpies of formation for hydrocarbon molecules of escalating size. Two applied projects are also described; these projects concerned the theoretical prediction of a novel rare gas compound, FKrOH, and the mechanism of human glutathione synthetase’s (hGS) negative cooperativity. The final work examined the prospect for the parameterization of the modified embedded atom method (MEAM) potential using first principles calculations of dimer and trimer energies of nickel and carbon systems. This method of parameterization holds promise for increasing the accuracy of simulations for bulk properties within the field of materials science.
Computational chemistry has led to the greater understanding of the molecular world, from the interaction of molecules, to the composition of molecular species and materials. Of the families of computational chemistry approaches available, the main families of electronic structure methods that are capable of accurate and/or reliable predictions of energetic, structural, and spectroscopic properties are ab initio methods and density functional theory (DFT). The focus of this dissertation is to improve the accuracy of predictions and computational efficiency (with respect to memory, disk space, and computer processing time) of some computational chemistry methods, which, in turn, can extend the size of molecule that can be addressed, and, for other methods, DFT, in particular, gain greater insight into which DFT methods are more reliable than others. Much, though not all, of the focus of this dissertation is upon transition metal species – species for which much less method development has been targeted or insight about method performance has been well established. The ab initio approach that has been targeted in this work is the correlation consistent composite approach (ccCA), which has proven to be a robust, ab initio computational method for main group and first row transition metal-containing molecules yielding, on average, accurate thermodynamic properties, i.e., within 1 kcal/mol of experiment for main group species and within 3 kcal/mol of experiment for first row transition metal molecules. In order to make ccCA applicable to systems containing any element from the periodic table, development of the method for second row transition metals and heavier elements, including lower p-block (5p and 6p) elements was pursued. The resulting method, the relativistic pseudopotential variant of ccCA (rp-ccCA), and its application are detailed for second row transition metals and lower p-block elements. Because of the computational cost of ab initio methods, DFT is a popular choice …
Greater understanding and accurate predictions of structural, thermochemical, and spectroscopic properties of chemical compounds is critical for the advancements of not only basic science, but also in applications needed for the growth and health of the U.S. economy. This dissertation includes new ab initio composite approaches to predict accurate energetics of lanthanide-containing compounds including relativistic effects, and optimization of parameters for semi-empirical methods for transition metals. Studies of properties and energetics of chemical compounds through various computational methods are also the focus of this research, including the C-O bond cleavage of dimethyl ether by transition metal ions, the study of thermochemical and structural properties of small silicon containing compounds with the Multi-Reference correlation consistent Composite Approach, the development of a composite method for heavy element systems, spectroscopic of compounds containing noble gases and metals (ArxZn and ArxAg+ where x = 1, 2), and the effects due to Basis Set Superposition Error (BSSE) on these van der Waals complexes.
The efforts of my research have led to the successful construction of several instruments that have helped expand the field of microwave spectroscopy. The classic Balle-Flygare spectrometer has been modified to include two different sets of antenna to operate in the frequency ranges 6-18 GHz and 18-26 GHz, allowing it to function for a large range without having to break vacuum. This modified FTMW instrument houses two low noise amplifiers in the vacuum chamber to allow for the LNAs to be as close to the antenna as physically possible, improving sensitivity. A new innovative Balle-Flygare type spectrometer, the efficient low frequency FTMW, was conceived and built to operate at frequencies as low as 500 MHz through the use of highly curved mirrors. This is new for FTMW techniques that normally operate at 4 GHz or higher with only a few exceptions around 2 GHz. The chirped pulse FTMW spectrometer uses horn antennas to observe spectra that span 2 GHz versus the standard 1 MHz of a cavity technique. This instrument decreases the amount of time to obtain a large spectral region of relative correct intensity molecular transitions. A Nd:YAG laser ablation apparatus was attached to the classic Balle-Flygare and chirped pulse FTMW spectrometers. This allowed the study of heavy metal containing compounds. The instruments I constructed and the techniques I used have allowed the discovery of further insights into molecular chemistry. I have seen the effects of fluorinating an alkyl halide by determining the geometry of the carbon backbone of trans-1-iodoperfluoropropane and observing a ΔJ = 3 forbidden transition caused by a strong quadrupole coupling constant on this heavy molecule. The quadrupole coupling tensors of butyronitrile, a molecule observed in space, have been improved. The nuclear quadrupole coupling tensor of difluoroiodomethane was added to a list of variably fluorinated methyl …
Advances in computing capabilities have facilitated the application of quantum mechanical methods to increasingly larger and more complex chemical systems, including weakly interacting and biologically relevant species. One such ab initio-based composite methodology, the correlation consistent composite approach (ccCA), has been shown to be reliable for the prediction of enthalpies of formation and reaction energies of main group species in the gas phase to within 1 kcal mol-1, on average, of well-established experiment, without dependence on experimental parameterization or empirical corrections. In this collection of work, ccCA has been utilized to determine the proton affinities of deoxyribonucleosides within an ONIOM framework (ONIOM-ccCA) and to predict accurate enthalpies of formation for organophosphorus compounds. Despite the complexity of these systems, ccCA is shown to result in enthalpies of formation to within ~2 kcal mol-1 of experiment and predict reliable reaction energies for systems with little to no experimental data. New applications for the ccCA method have also been introduced, expanding the utility of ccCA to solvated systems and complexes with significant noncovalent interactions. By incorporating the SMD solvation model into the ccCA formulation, the Solv-ccCA method is able to predict the pKa values of nitrogen systems to within 0.7 pKa unit (less than 1.0 kcal mol-1), overall. A hydrogen bonding constant has also been developed for use with weakly interacting dimers and small cluster compounds, resulting in ccCA interaction energies for water clusters and dimers of the S66 set to within 1.0 kcal mol-1 of well-established theoretical values.
This work focuses on finding the complete iodine and nitrogen nuclear electric quadrupole coupling tensors for fluoroiodoacetonitrile using chirped-pulse Fourier transform microwave spectroscopy. Fluoroiodoacetonitrile contains two hyperfine nuclei, iodine (I=5/2) and nitrogen (I=1) and the spectra were observed with great resolution. A total of 499 transitions were observed for this molecule. The a, b and c rotational constants were obtained. A study of chloropentafluoroacetone was also done using chirped-pulse Fourier transform microwave spectroscopy. The two chlorine isotopes for this molecule, Cl-35 and Cl-37 were observed and 326 and 170 transitions were recorded, respectively.
Computational chemistry lies at the intersection of chemistry, physics, mathematics, and computer science, and can be used to explain the behavior of atoms and molecules, as well as to augment experiment. In this work, computational chemistry methods are used to predict structural and energetic properties of small molecules, i.e. molecules with less than 60 atoms. Different aspects of computational chemistry are examined in this work. The importance of examining the converged orbitals obtained in an electronic structure calculation is explained. The ability to more completely describe the orbital space through the extrapolation of energies obtained at increasing quality of basis set is investigated with the use of the Sapporo-nZP-2012 family of basis set. The correlation consistent Composite Approach (ccCA) is utilized to compute the enthalpies of formation of a set of molecules and the accuracy is compared with the target method, CCSD(T,FC1)/aug-cc-pCV∞Z-DK. Both methodologies are able to produce computed enthalpies of formation that are typically within 1 kcal mol-1 of reliable experiment. This demonstrates that ccCA can be used instead of much more computationally intensive methods (in terms of memory, processors, and time required for a calculation) with the expectation of similar accuracy yet at a reduced computational cost. The enthalpies of formation for systems containing s-block elements have been computed using the multireference variant of ccCA (MR-ccCA), which is designed specifically for systems that require an explicit treatment of nondynamical correlation. Density functional theory (DFT) has been used for the prediction of the structural properties of a set of lanthanide trihalide molecules as well as the reaction energetics for the rearrangement of diphosphine ligands around a triosmium cluster.
The development of the semi-empirical atomistic potential called the embedded atom method (EAM) has allowed for the efficient modeling of solid-state environments, at a lower computational cost than afforded by density functional theory (DFT). This offers the capability of EAM to model the energetics of solid-state phases of varying coordination, including defects, such as vacancies and self-interstitials. This dissertation highlights the development and application of two EAMs: a Ti potential constructed with the multi-state modified embedded atom method (MS-MEAM), and a Ni potential constructed with the fragment Hamiltonian (FH) method. Both potentials exhibit flexibility in the description of different solid-states phases and applications. This dissertation also outlines two applications of DFT. First, a study of structure and stability for solid-state forms of NixCy (in which x and y are integers) is investigated using plane-wave DFT. A ground state phase for Ni2C is elucidated and compared to known and hypothesized forms of NixCy. Also, a set of correlation consistent basis sets, previously constructed using the B3LYP and BLYP density functionals, are studied. They are compared to the well-known to the correlation consistent basis sets that were constructed with higher-level ab initio methodologies through computations of enthalpies of formation and combustion enthalpies. The computational accuracy with regard to experiment is reported.
Quantum chemistry methodologies can be used to address a wide variety of chemical problems. Key to the success of quantum chemistry methodologies, however, is the selection of suitable methodologies for specific problems of interest, which often requires significant assessment. To gauge a number of methodologies, the utility of density functionals (BLYP, B97D, TPSS, M06L, PBE0, B3LYP, M06, and TPSSh) in predicting reaction energetics was examined for model studies of C-O bond activation of methoxyethane and methanol. These species provide excellent representative examples of lignin degradation via C-O bond cleavage. PBE0, which performed better than other considered DFT functionals, was used to investigate late 3d (Fe, Co, and Ni), 4d (Ru, Rh, and Pd), and 5d (Re, Os, and Ir) transition metal atom mediated Cβ -O bond activation of the β–O–4 linkage of lignin. Additionally, the impact of the choice of DFT functionals, basis sets, implicit solvation models, and layered quantum chemical methods (i.e., ONIOM, Our Own N-layered Integrated molecular Orbital and molecular Mechanics) was investigated for the prediction of pKa for a set of Ni-group metal hydrides (M = Ni, Pd, and Pt) in acetonitrile. These investigations have provided insight about the utility of a number of theoretical methods in the computation of thermodynamic properties of transition metal hydrides in solution. As single reference wavefunction methods commonly perform poorly in describing molecular systems that involve bond-breaking and forming or electronic near-degeneracies and are typically best described with computationally costly multireference wavefunction-based methods, it is imperative to a priori analyze the multireference character for molecular systems so that the proper methodology choice is applied. In this work, diagnostic criteria for assessing the multireference character of 4d transition metal-containing molecules was investigated. Four diagnostics were considered in this work, including the weight of the leading configuration of the CASSCF wavefunction, C02; T1, …
The reactions of atomic hydrogen with methanethiol and that of atomic hydrogen with carbon disulfide were studied experimentally using flash-photolysis resonance-fluorescence techniques. Rate constants were determined over a range of temperatures and pressures, and through analysis and comparison to theoretical work details of the reactions were ascertained.
The kinetics of the reaction of atomic sulfur with acetylene (S (3P) + C2H2) were investigated experimentally via the flash photolysis resonance fluorescence method, and the theoretical potential energy surface for the reaction CN + SO was modeled via the density functional and configuration interaction computational methods. Sulfur is of interest in modern chemistry due to its relevance in combustion and atmospheric chemistry, in the Claus process, in soot and diamond-film formation and in astrochemistry. Experimental conditions ranged from 295 – 1015 K and 10 – 400 Torr of argon. Pressure-dependence was shown at all experimental temperatures. The room temperature high-pressure limit second order rate constant was (2.10 ± 0.08) × 10-13 cm3 molecule-1 s-1. The Arrhenius plot of the high-pressure limit rate constants gave an Ea of (11.34 ± 0.03) kJ mol-1 and a pre-exponential factor of (2.14 ± 0.19) × 10-11 cm3 molecule-1 s-1. S (3P) + C2H2 is likely an adduct forming reaction due to pressure-dependence (also supported by a statistical mechanics analysis) which involves intersystem crossing. The potential energy surface for CN + SO was calculated at the B3LYP/6-311G(d) level and refined at the QCISD/6-311G(d) level. The PES was compared to that of the analogous reaction CN + O2. Notable energetically favorable products are NCS + O, CO + NS, and CS + NO. The completed PES will ultimately be modeled at the CCSD(T) level (extrapolated to infinite basis set limit) for theoretical reaction rate analysis (RRKM).
Carbon nanotubes (CNT) have unparalleled mechanical properties, spanning several orders of magnitude over both length and time scales. Computational and experimental results vary greatly, partly due to the multitude of variables. Coupling physics-based molecular dynamics (MD) with informatics methodologies is proposed to navigate the large problem space. The adaptive intermolecular reactive empirical bond order (AIREBO) is used to model short range, long range and torsional interactions. A powerful approach that has not been used to study CNT mechanical properties is the derivation of descriptors and quantitative structure property relationships (QSPRs). For the study of defected single-walled CNTs (SWCNT), two descriptors were identified as critical: the density of non-sp2 hybridized carbons and the density of methyl groups functionalizing the surface. It is believed that both of these descriptors can be experimentally measured, paving the way for closed-loop computational-experimental development. Informatics can facilitate discovery of hidden knowledge. Further evaluation of the critical descriptors selected for Poisson’s ratio lead to the discovery that Poisson’s ratio has strain-varying nonlinear elastic behavior. CNT effectiveness in composites is based both on intrinsic mechanical properties and interfacial load transfer. In double-walled CNTs, inter-wall bonds are surface defects that decrease the intrinsic properties but also improve load transfer. QSPRs can be used to model these inverse effects and pinpoint the optimal amount of inter-wall bonds.
In the exploration of chemical systems through quantum mechanics, accurate treatment of the electron wavefunction, and the related electron density, is fundamental to extracting information concerning properties of a system. This work examines challenges in achieving accurate chemical information through manipulation of the one-electron basis set.
Copper(I) complexes have been studied through both experimental and computational means in the presented work. Overall, the work focuses on photophysical and photochemical properties of copper(I) complexes. Photophysical and photochemical properties are found to be dependent on the geometries of the copper(I) complexes. One of the geometric properties that are important for both photochemical and photophysical properties is coordination number. Coordination numbers have been observed to be dependent on both ligand size and recrystallization conditions. The complexes geometric structure, as well as the electronic effects of the coordination ligands, is shown both computationally as well as experimentally to affect the emission energies. Two-coordinate complexes are seen to have only weak emission at liquid nitrogen temperature (77 K), while at room temperature (298 K) the two-coordinate complexes are not observed to be luminescent. Three-coordinate complexes are observed to be luminescent at liquid nitrogen temperature as well as at room temperature. The three-coordinate complexes have a Y-shaped ground (S0) state that distorts towards a T-shape upon photoexcitation to the lowest lying phosphorescent state (T1). The geometric distortion is tunable by size of the coordinating ligand. Luminescence is controllable by limiting the amount of non-radiative emission. One manner by which non-radiative emission is controlled is the amount of geometric distortion that occurs as the complex undergoes photoexcitation. Bulky ligands allow for less distortion than smaller ligands, leading to higher emission energies (blue shifted energies) with higher quantum efficiency. Tuning emission and increasing quantum efficiencies can be used to create highly efficient, white emitting materials for use in white OLEDS.
Quantum chemical methods have been used to model a variety of p- and f-block chemical species to gain insight about their energetic and spectroscopic properties. As well, the studies have provided understanding about the utility of the quantum mechanical approaches employed for the third-row and lanthanide species. The multireference ab initio correlation consistent Composite Approach (MR-ccCA) was utilized to predict dissociation energies for main group third-row molecular species, achieving energies within 1 kcal mol-1 on average from those of experiment and providing the first demonstration of the utility of MR-ccCA for third-row species. Multireference perturbation theory was utilized to calculate the electronic states and dissociation energies of NdF2+, providing a good model of the Nd-F bond in NdF3 from an electronic standpoint. In further work, the states and energies of NdF+ were determined using an equation of motion coupled cluster approach and the similarities for both NdF2+ and NdF were noted. Finally, time-dependent density functional theory and the static exchange approximation for Hartree-Fock in conjunction with a fully relativistic framework were used to calculate the L3 ionization energies and electronic excitation spectra as a means of characterizing uranyl (UO22+) and the isoelectronic compounds NUO+ and UN2.
While computational chemistry methods have a wide range of applications within the set of traditional physical sciences, very little is being done in terms of expanding their usage into other areas of science where these methods can help clarify research questions. One such promising field is Forensic Science, where detailed, rapidly acquired sets of chemical data can help in decision-making at a crime scene. As part of an effort to create a database that fits these characteristics, the present work makes use of computational chemistry methods to increase the information readily available for the rapid identification and scheduling of drugs to the forensic scientist. Ab initio geometry optimizations, vibrational spectra calculations and ESI-MS fragmentation prediction of a group of common psychedelics are here presented. In addition, we describe an under development graphical user interface to perform ab initio calculations using the GAMESS software package in a more accessible manner. Results show that the set of theoretical techniques here utilized, closely approximate experimental data. Another aspect covered in this work is the implementation of a boiling point estimation method based on group contributions to generate chemical dispersion areas with the ALOHA software package. Once again, theoretical results showed to be in agreement with experimental boiling point values. A computer program written to facilitate the execution of the boiling point estimation method is also shown.
Since the development of the correlation consistent composite approach (ccCA) in 2006, ccCA has been shown to be applicable across the periodic table, producing, on average, energetic properties (e.g., ionization potentials, electron affinities, enthalpies of formation, bond dissociation energies) within 1 kcal/mol for main group compounds. This dissertation utilizes ccCA in the investigation of several chemical systems including nitrogen-containing compounds, sulfur-containing compounds, and carbon dioxide complexes. The prediction and calculation of energetic properties (e.g., enthalpies of formation and interaction energies) of the chemical systems investigated within this dissertation has led to suggestions of novel insensitive highly energetic nitrogen-containing compounds, defined reaction mechanisms for sulfur compounds allowing for increased accuracy compared to experimental enthalpies of formation, and a quantitative structure activity relationship for altering the affinity of CO2 with substituted amine compounds. Additionally, a study is presented on the convergence of correlation energy and optimal domain criteria for local Møller–Plesset theory (LMP2).
The focus of this thesis is on C-O bonds activation by transition metal atoms. Lignin is a potential alternative energy resource, but currently is an underused biomass species because of its highly branched structure. To aid in better understanding this species, the oxidative cleavage of the Cβ-O bond in an archetypal arylglycerol β-aryl ether (β–O–4 Linkage) model compound of lignin with late 3d, 4d, and 5d metals was investigated. Methoxyethane was utilized as a model molecule to study the activation of the C-O bond. Binding enthalpies (ΔHb), enthalpy formations (ΔH) and activation enthalpies (ΔH‡) have been studied at 298K to learn the energetic properties in the C-O bond cleavage in methoxyethane. Density functional theory (DFT) has become a common choice for the transition metal containing systems. It is important to select suitable functionals for the target reactions, especially for systems with degeneracies that lead to static correlation effects. A set of 26 density functionals including eight GGA, six meta-GGA, six hybrid-GGA, and six hybrid-meta-GGA were applied in order to investigate the performance of different types of density functionals for transition metal catalyzed C-O bond cleavage. A CR-CCSD(T)/aug-cc-pVTZ was used to calibrate the performance of different density functionals.
CO2 activation and conversion mediated by transition metal (TM) catalysts were investigated. Homogeneous catalysis of the reverse water gas shift reaction CO2+H2→H2O+CO was studied as a means to reduce CO2. β-diketiminato metal models L'MI ( L' =C3N2H5-; M = first-row TMs) were considered as potential catalysts. The thermodynamics of prototypical reaction pathways were simulated using B3LYP/aug-cc-pVTZ. Results show that middle series metal complexes result in more thermodynamically favorable properties; therefore, more detailed thermodynamic and kinetic studies were carried out for Mn, Fe, and Co complexes. On the other hand, heterogeneous catalysis of the reduction of CO2 to CO was carried out on Fe, Co, Ni, and Cu surfaces, using the PBE functional. Reaction barriers were calculated using the climbing image nudged elastic band method. Late 3d and 4d transition metal ion (Fe, Co, Ni, Cu, Ru, Rh, Pd, and Ag) mediated activation of dimethyl ether was studied to investigate the intrinsic catalytic properties of metals for C-O bond cleavage. A set of density functional theory (DFT) methods (BLYP, B3LYP, M06, M06-L, B97-1, B97-D, TPSS, and PBE) with aug-cc-pVTZ basis sets was calibrated with CCSD(T)/CBS calculations on reaction energies and barriers.
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