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ItemFrom small to big: understanding noncovalent interactions in chemical systems from quantum mechanical models(Georgia Institute of Technology, 2009-03-23) Ringer, Ashley L.Noncovalent interactions in complex chemical systems are examined by considering model systems which capture the essential physics of the interactions and applying correlated electronic structure techniques to these systems. Noncovalent interactions are critical to understanding a host of energetic and structural properties in complex chemical systems, from base pair stacking in DNA to protein folding in organic solids. Complex chemical and biophysical systems, such as enzymes and proteins, are too large to be studied using computational techniques rigorous enough to capture the subtleties of noncovalent interactions. Thus, the larger chemical system must be truncated to a smaller model system to which rigorous methods can be applied in order to capture the essential physics of the interaction. Computational methodologies which can account for high levels of electron correlation, such as second-order perturbation theory and coupled-cluster theory, must be used. These computational techniques will be used to study several types (pi stacking, S/pi, and C-H/pi) of noncovalent interactions in two chemical contexts: biophysical systems and organic solids.
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ItemPi-pi to full ci: cation dimers and substituent effects in noncovalent interactions(Georgia Institute of Technology, 2009-01-12) Arnstein, Stephen A.The following thesis focuses on two areas of chemistry, pi-pi interactions and radical cation dimers. Approximations to the exact solution to the Schrodinger equation are investigated for these types of chemical systems with a variety of theoretical methods. The first chapter provides an introduction to the various quatum mechanical methods used in this research. The second chapter focuses specifically on pi-pi interaction. In this chapter, high quality quantum mechanical methods are used to examine how substituents tune pi-pi interactions between monosubstituted benzene dimers in parallel-displaced geometries. In addition, the role of dispersion and coulombic interactions in these systems is investigated to determine the nature of the substituent effect. In the third chapter radical cation dimers are investigated. Benchmark results with full configuration interaction (FCI) and equation-of-motion coupled-cluster for ionized systems (EOM-IP-CCSD) are presented for prototypical charge transfer species. Conclusions regarding chapters 2 and 3 are presented in the final chapter. This work may form the basis for improved approaches to rational drug design, organic optical materials, and molecular electronics.
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ItemMinimalistic Descriptions of Nondynamical Electron Correlation: From Bond-Breaking to Transition-Metal Catalysis(Georgia Institute of Technology, 2007-11-14) Sears, John StevenFrom a theoretical standpoint, the accurate description of potential energy surfaces for bond breaking and the equilibrium structures of metal-ligand catalysts are distinctly similar problems. Near degeneracies of the bonding and anti-bonding orbitals for the case of bond breaking and of the partially-filled d-orbitals for the case of metal-ligand catalyst systems lead to strong non-dynamical correlation effects. Standard methods of electronic structure theory, as a consequence of the single-reference approximation, are incapable of accurately describing the electronic structure of these seemingly different theoretical problems. The work within highlights the application of multi-reference methods, methods capable of accurately treating these near-degeneracies, for describing the bond-breaking potentials in several small molecular systems and the equilibrium structures of metal-salen catalysts. The central theme of this work is the ability of small, compact reference functions for accurately describing the strong non-dynamical correlation effects in these systems.
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ItemComputation of Molecular Properties at the Ab Initio Limit(Georgia Institute of Technology, 2007-01-16) Temelso, BerhaneThe accuracy of a quantum chemical calculation inherently depends on the ability to account for the completeness of the one- and n-particle spaces. The size of the basis set used can be systematically increased until it reaches the complete one-particle basis set limit (CBS) while the n-particle space approaches its exact full configuration interaction (FCI) limit by following a hierarchy of electron correlation methods developed over the last seventy years. If extremely high accuracy is desired, properly correcting for very small effects such as those resulting the Born-Oppenheimer approximation and the neglect of relativistic effects becomes indispensable. For a series of chemically interesting and challenging systems, we identify the limits of conventional approaches and use state-of-the-art quantum chemical methods along with large basis sets to get the “right answer for the right reasons.” First, we quantify the importance of small effects that are ignored in conventional quantum chemical calculations and manage to achieve spectroscopic accuracy (agreement of 1 cm−1 or less with experimental harmonic vibrational frequencies) for BH, CH+ and NH. We then definitively resolve the global minimum structure for Li₆ , Li₆⁺ , and Li₆- using high accuracy calculations of the binding energies, ionization potentials, electron affinities and vertical excitation spectra for the competing isomers. The same rigorous approach is used to study a series of hydrogen transfer reactions and validate the necessary parameters for the hydrogen abstraction and donation steps in the mechanosynthesis of diamondoids. Finally, in an effort to overcome the steep computational scaling of most high-level methods, a new hybrid methodology which scales as O(N⁵) but performs comparably to O(N⁶) methods is benchmarked for its performance in the equilibrium and dissociation regimes.
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ItemHybrid Correlation Models For Bond Breaking Based On Active Space Partitioning(Georgia Institute of Technology, 2006-07-10) Bochevarov, Artem D.The work presented in this thesis is dedicated to developing inexpensive quantum-chemical models that are able to produce smooth and physically correct potential energy curves for the dissociation of single covalent bonds. It is well known that the energies produced by many ab initio theories scaling as the fifth order with the system size (for instance, second-order Moller-Plesset (MP2) and Epstein-Nesbet perturbation theories) diverge at large interatomic separations. We show that the divergent behavior of such perturbation schemes is due to a small number of terms in the energy expressions. Then, we demonstrate that the self-consistent replacement of these terms by their analogs from the coupled cluster theory (such as CCSD) allows one to redress the erroneous behavior of the perturbation theories without the damage to the overall scaling. We also investigate the accuracy of these hybrid perturbation theory-coupled cluster theories near equilibrium geometry. Judging from the computed spectroscopic constants and shapes of the potential energy curves, one such model, denoted MP2-CCSD(II) in this work, performs consistently better than the MP2 theory at essentially the same computational cost.
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ItemTheoretical Investigations of Pi-Pi and Sulfur-Pi Interactions and their Roles in Biomolecular Systems(Georgia Institute of Technology, 2005-11-28) Tauer, Anthony PhilipThe study of noncovalent interactions between aromatic rings and various functional groups is a very popular topic in current computational chemistry. The research presented in this thesis takes steps to bridge the gap between theoretical prototypes and real-world systems. The non-additive contributions to the interaction energy in stacked aromatic systems are measured by expanding the prototype benzene dimer into trimeric and tetrameric systems. We show that the three- and four-body interaction terms generally do not contribute significantly to the overall interaction energy, and that the two-body terms are essentially the same as in the isolated dimer. The sulfur-pi interaction is then studied by using the hydrogen sufide-benzene dimer as a prototype system for theoretical predictions. We obtain higly-accurate potential energy curves, as well as an interaction energy extrapolated to the complete basis set limit. Energy decomposition analysis using symmetry-adapted perturbation theory shows that the sulfur-pi interaction is primarily electrostatic in nature. These theoretical results are then compared to an analysis of real sulfur-pi contacts found by searching protein structures in the Brookhaven Protein DataBank. We find that the most frequently seen configuration does not correspond to the theoretically predicted equilibrium for sydrogen sulfide-benzene, but instead to a configuration that suggests an alkyl-pi interaction involving the carbon adjacent to the sulfur atom. We believe our findings indicate that environmental effects within proteins are altering the energetics of the sulfur-pi interaction so that other functional groups are preferred for interacting with the aromatic ring.
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ItemGeneral-Order Single-Reference and Mulit-Reference Methods in Quantum Chemistry(Georgia Institute of Technology, 2005-03-24) Abrams, Micah L.Many-body perturbation theory and coupled-cluster theory, combined with carefully constructed basis sets, can be used to accurately compute the properties of small molecules. We applied a series of methods and basis sets aimed at reaching the ab initio limit to determine the barrier to planarity for ethylene cation. For potential energy surfaces corresponding to bond dissociation, a single Slater determinant is no longer an appropriate reference, and the single-reference hierarchy breaks down. We computed full configuration interaction benchmark data for calibrating new and existing quantum chemical methods for the accurate description of potential energy surfaces. We used the data to calibrate single-reference configuration interaction, perturbation theory, and coupled-cluster theory and multi-reference configuration interaction and perturbation theory, using various types of molecular orbitals, for breaking single and multiple bonds on ground-state and excited-state surfaces. We developed a determinant-based method which generalizes the formulation of many-body wave functions and energy expectation values. We used the method to calibrate single-reference and multi-reference configuration interaction and coupled-cluster theories, using different types of molecular orbitals, for the symmetric dissociation of water. We extended the determinant-based method to work with general configuration lists, enabling us to study, for the first time, arbitrarily truncated coupled-cluster wave functions. We used this new capability to study the importance of configurations in configuration interaction and coupled-cluster wave functions at different regions of a potential energy surface.
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ItemTheoretical Investigations of pi-pi Interactions and Their Role in Molecular Recognition(Georgia Institute of Technology, 2004-07-07) Sinnokrot, Mutasem OmarNoncovalent interactions are of pivotal importance in many areas of chemistry, biology, and materials science, and the intermolecular interactions involving aromatic rings in particular, are fundamental to molecular organization and recognition processes. The work detailed in this thesis involves the application of state-of-the-art ab initio electronic structure theory methods to elucidate the nature of pi-pi interactions. The binding energies, and geometrical and orientational preferences of the simplest prototype of aromatic pi-pi interactions, the benzene dimer, are explored. We obtain the first converged values of the binding energies using highly accurate methods and large basis sets. Results from this study predict the T-shaped and parallel-displaced configurations of benzene dimer to be nearly isoenergetic. The role of substituents in tuning pi-pi interaction is investigated. By studying dimers of benzene with various monosubstituted benzenes (in the sandwich and two T-shaped configurations), we surprisingly find that all of the substituted sandwich dimers considered bind more strongly than benzene dimer. We also find that these interactions can be tuned by a modest degree of substitution. Energy decomposition analysis using symmetry-adapted perturbation theory (SAPT) reveals that models based solely on electrostatic effects will have difficulty in reliably predicting substituent effects in pi-pi interactions.