New algorithms for optimizing and linking conical intersection points

In this paper we present two new algorithms to study the extended nature of the crossing seam between electronic potential energy surfaces. The first algorithm is designed to optimize conical intersection geometries: both minima and saddle points. In addition, this method will optimize conical intersection geometries using arbitrary geometrical constraints. We demonstrate its potential on different crossing seams of benzene, z-penta-3,5-dleniminium, and 1,3-butadiene. The second algorithm is designed to explicitly compute the intersection-space minimum energy coordinate. Our computations show how an intersection seam and the energy along it can be unambiguously defined. A finite region of the S0/S11,3-butadiene crossing seam has been mapped out, and a new saddle point linked with two lower-lying geometries on the sea

Analytic gradient techniques for investigating the complex-valued potential energy surfaces of electronic resonances

Electronic resonances are metastable atomic or molecular systems that can decay by electron detachment. They play an important role in biological processes such as DNA fragmentation induced by slow electrons or in interstellar reactions as in the formation of neutral molecules and molecular anions. As opposed to bound states, resonances do not correspond to discrete eigenstates of a Hermitian Hamiltonian, and therefore their theoretical description requires special methods. The complex absorbing potential (CAP) method can be used to calculate both the energy and the lifetime of a resonance as a discrete eigenstate in a non-Hermitian time-independent framework. The CAP method allows for applying well-known bound-state electronic structure methods to resonances as well. In this work, the applicability of CAP-augmented equation-of-motion coupled-cluster (CAP-EOM-CC) methods is extended for locating equilibrium structures and crossings on complex-valued potential energy surfaces of electronic resonances by introducing analytic energy gradients. The structure and energy of these points are needed for, e.g., estimating the importance of a specific dissociation route or deactivation process. The accuracy of structural parameters, vertical and adiabatic electron affinities, and resonance widths obtained with approximate methods and various diffuse basis sets is investigated. Applications of optimization methods are also presented for systems that are relevant in interstellar or biological processes. Properties of the complex-valued potential energy surfaces of anionic resonances of acrylonitrile and methacrylonitrile are connected to experimental observations. Dissociative electron attachment to chlorosubstituted ethylenes is also investigated. This can help in understanding detoxification processes of these compounds and might facilitate the exploration of DEA pathways for other halogenated molecules as well

Analytic gradient techniques for investigating the complex-valued potential energy surfaces of electronic resonances

Electronic resonances are metastable atomic or molecular systems that can decay by electron detachment. They play an important role in biological processes such as DNA fragmentation induced by slow electrons or in interstellar reactions as in the formation of neutral molecules and molecular anions. As opposed to bound states, resonances do not correspond to discrete eigenstates of a Hermitian Hamiltonian, and therefore their theoretical description requires special methods. The complex absorbing potential (CAP) method can be used to calculate both the energy and the lifetime of a resonance as a discrete eigenstate in a non-Hermitian time-independent framework. The CAP method allows for applying well-known bound-state electronic structure methods to resonances as well. In this work, the applicability of CAP-augmented equation-of-motion coupled-cluster (CAP-EOM-CC) methods is extended for locating equilibrium structures and crossings on complex-valued potential energy surfaces of electronic resonances by introducing analytic energy gradients. The structure and energy of these points are needed for, e.g., estimating the importance of a specific dissociation route or deactivation process. The accuracy of structural parameters, vertical and adiabatic electron affinities, and resonance widths obtained with approximate methods and various diffuse basis sets is investigated. Applications of optimization methods are also presented for systems that are relevant in interstellar or biological processes. Properties of the complex-valued potential energy surfaces of anionic resonances of acrylonitrile and methacrylonitrile are connected to experimental observations. Dissociative electron attachment to chlorosubstituted ethylenes is also investigated. This can help in understanding detoxification processes of these compounds and might facilitate the exploration of DEA pathways for other halogenated molecules as well

Development of Reaction Discovery Tools in Photochemistry and Condensed Phases

Photochemistry obeys different rules than ground-state chemistry and by doing so opens avenues for synthesis and materials properties. However, the different rules of photochemistry make understanding the fine details of photochemical reactions difficult. Computational chemistry can provide the details for understanding photochemical reactions, but the field of computational photochemistry is still new, and many techniques developed for ground-state reactions are not directly applicable to photochemical reactions. As a result, many photochemical mechanisms are not understood, and this hinders the rational design and synthesis of new photochemistry. To address this need, this thesis develops techniques to search for and study photochemical reactions. Chapter 2 and 3 develop methods to calculate photochemical reactions in gas- and condensed-phases via minimum energy reaction paths. First, Chapter 2 develops a method to search the molecular 3N-6 space for photochemical reactions. This space, although vast, is not chaotic and can be efficiently searched using a concept familiar to chemists: breaking and adding bonds and driving angles and torsions. Furthermore, this procedure can be automated to predict new chemistry not previously identified by experiments. Chapter 3 furthers this research by leveraging the concept of molecules to enable the computational study of reactions in large multi-molecular systems like crystals. Specifically, the use of a new coordinate system involving translational and rotational coordinates allows decoupling of the coordinate systems of the individual molecules, which is necessary for the efficient algebra. Importantly, these methods are general, they can be used to study single molecules and crystals, and much in between. These methods are demonstrated on complex chemical problems including the isomerization pathways of ethylene and stilbene (Chapter 2), the photocycloaddition of butadiene (Chapter 2), the rotation of a crystalline gyroscope (Chapter 3), the bicycle pedal rotation of cis,cis-diphenylbutadiene (Chapter 4), and the mechanism of a reversible photoacid (Chapter 5). These problems have value in understanding the processes of vision, optomechanics, and high-energy materials, and through their xx study much needed insight is gained that can be useful for designing new syntheses and materials. Furthermore, the new computational methods open the possibility for many future investigations. The results of Chapter 2 find a novel roaming-atom and hula-twist isomerization pathway and use automated reaction discovery tools to identify a missing butadiene photoproduct and why the [4+2] cycloaddition is forbidden. The results of Chapter 3 and 4 build on Chapter 2 by including the influence of a steric environment. Chapter 3 demonstrates by application to a molecular gyroscope that extreme long-range correlated motion can be captured with GSM, and Chapter 4 details how the one-bond flip and hula-twist mechanisms are suppressed by the crystal cavity, the nature of the seam space in steric environments, and the features of the bicycle pedal mechanism. For example, the bicycle pedals rotate through the passageway in the adjacent monomers. However, the models do not capture the quantitative activation barriers and more work is needed. Finally, Chapter 5 provides the ultrafast details of how the photoacid isomerizes and ring-closes with experimental and computational evidence. Unfortunately, quantitative calculation of pKa cannot be provided with the computations employed herein. In summary, this thesis provides an advancement in the knowledge of photochemical mechanisms that can be used for the development of new syntheses and offers new tools with capacity to study complex photochemical problems.PHDChemistryUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/163005/1/craldaz_1.pd

Relation between molecular structure and ultrafast photoreactivity with application to molecular switches

Photoinduced ultrafast isomerizations are fundamental reactions in photochemistry and photobiology. This thesis aims for an understanding of the generic forces driving these reactions and a theoretical approach is set up, able to handle realistic systems, whose fast relaxation is mediated by conical intersections. The main focus is on the development of strategies for the prediction and accelerated optimization of conical intersections and their application to artificial compounds with promising physicochemical properties for technical applications as molecular switches. All calculations are based on advanced quantum chemical methods and mixed quantum-classical dynamics. In the first part of this thesis the two-electron two-orbital theory by Michl and Bonacic-Koutecky used in its original formulation to rationalize the structure of conical intersections in charged polyene systems is extended by including the interactions of the active pair of electrons with the remaining closed-shell electrons that are present in any realistic system. A set of conditions, called resonance and heterosymmetry conditions, for the formation of conical intersections in multielectronic systems are derived and verified by calculations on the basic units ethylene, cis-butadiene and 1,3-cyclohexadiene at various geometries and functionalizational patterns. The quantitative results help to understand the role of geometrical deformations and substituent effects for the formation of conical intersections and to derive rules of thumb for their qualitative prediction in arbitrary polyenes. An extension of the rules of thumb to conical intersection seams is formulated. The strategy pursued is to divide the molecular system into basic units and into functional groups. Each unit and its intersection space are treated independently, thereby reducing the dimensionality of the search space compared to the complete molecule. Subsequently, the interconnectivity of the intersection spaces of the different units is determined and an initial guess for the complete seam is constructed. This guess is then fed into a quantum chemistry package to finalize the optimization. The strategy is demonstrated for two multi-functionalized systems, hemithioindigo-hemistilbene and trifluoromethyl-pyrrolylfulgide. In the second part of this thesis state-of-the-art quantum chemical calculations and time-resolved transient and infrared spectroscopy are used to reconstruct the complex multi-channel isomerization mechanisms of hemithioindigo-hemistilbene and trifluoromethyl-indolylfulgide. Both the cis-trans isomerization in hemithioindigo-hemistilbene and the electrocyclic ring closure/opening in indolylfulgide are characterized by a charge transfer in the excited state. The ability of each system to stabilize this charge transfer is essential for the returning to the ground state. The relaxation to the ground state through extended regions of the seam is found to be the decisive step determining the reaction speed and the quantum yield. In the last part of this thesis mixed quantum-classical dynamics simulations at multi-configurational perturbation theory (MS-CASPT2) level, using Tully's fewest switches surface hopping approach, are performed to study the ultrafast photoreactivity of 1,3-cyclohexadiene in the gas-phase. For this purpose a numerical routine for the efficient calculation of non-adiabatic couplings at MS-CASPT2 level is presented. The major part of the excited molecules are found to circumvent the 1B2/2A1 conical intersection and reach the conical intersection seam between the excited state and the ground state instantaneuosly. Time constants for the evolution of the wavepacket on the bright 1B2-state, the relaxation into the 2A1-state and the return to the ground state are extracted. It is demonstrated that the accessibility of the conical intersection seam depends on its energetic and spatial relation to the minimum energy path, as well as on the momentum which is accumulated during relaxation on the excited state potential energy surface

Oxidation of methionine residues in protein pharmaceuticals

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2004.Includes bibliographical references (p. 171-189).(cont.) of free methionine. Therefore, the environments surrounding different methionine sites in G-CSF mainly provide spatial restriction to the access to the solvent but do not affect oxidation in a specific manner, consistent with the good correlation between 2SWCN's and the rates of oxidation. A comprehensive picture of oxidation is thus developed. It allows an accurate prediction of protein oxidation, and provides a rationale for developing strategies to control oxidation, such as modulating protein conformation via adding excipients. This knowledge could aid in developing in a more rational manner solvent formulations that protect therapeutic proteins against oxidation.Oxidation of the amino acid methionine by peroxides in aqueous formulations of proteins is a critical issue in the development of therapeutic products. It must be controlled so that therapeutic proteins can maintain their activity. In addition, oxidized therapeutics are undesirable due to their possible immunogenetic effects. An understanding of the mechanism and the factors that influence the reactivity of different methionine sites toward oxidation is therefore important. In this thesis, computational methods are applied and developed to address these problems. First, a mechanism by which peroxides oxidize the sulfur atom of methionine is developed. The rate-limiting step was found to be the breaking of the O-O bond of H₂O₂ and the formation of the S-O bond during which significant charge separation is developed. The charge separation can be stabilized via specific interactions such as hydrogen bonding with surrounding water molecules. This "water-mediated" mechanism of oxidation is consistent with experimental data such as those on activation energies of oxidation and pH dependence of the rates of oxidation. Based on the "water-mediated" mechanism, a structural property, average 2-shell water coordination number (2SWCN), has been shown to correlate well to the rates of oxidation of different methionine groups in Granulocyte Colony-Stimulating Factor (G-CSF) and in a Human Parathyroid hormone fragment (hPTH(1-34)). Including the dynamics of protein and water molecules in an explicit manner was found to be important for such correlation. Via combined quantum mechanical and molecular mechanical free energy simulations, the activation free energies of the oxidation of methionine residues in G-CSF are found to be equivalent to the values for the oxidationby Jhih-Wei Chu.Ph.D

Measuring the effects of reaction coordinate and electronic treatments in the QM/MM reaction dynamics of Trypanosoma cruzi trans-sialidase

The free energy of activation, as defined in transition state theory, is central to calculating reaction rates, distinguishing between mechanistic paths and elucidating the catalytic process. Computational free energies are accessible through the reaction space that is comprised of the conformational and electronic degrees of freedom orthogonal to the reaction coordinate. The overarching aim of this thesis was to address theoretical and methodological challenges facing current methods for calculating reaction free energies in glycoenzyme systems. Tractable calculations balance chemical accuracy and sampling efficiency that necessitates simplification of these complex reaction spaces through quantum mechanics/molecular mechanics partitioning and use of a semi-empirical electronic method to sample an approximated reaction coordinate. Here I directly and indirectly interrogate both the appropriate levels of sampling as well as the accuracy of the semi-empirical method required for reliable analysis of glycoenzyme reaction pathways. Free Energies from Adaptive Reaction Coordinates Forces, a method that builds the potential of mean force from multiple iterations of reactive trajectories, was used to construct reaction surfaces and volumes for the glycosylation and deglycosylation reactions comprising the T. cruzi trans-sialidase catalytic itinerary. This enzyme was chosen for the wealth of experimental data available for it built from its significance as a potential drug target against Chagas disease. Of equal importance is the identification of an elimination reaction competing with the primary transferase activity. The identification of this side reaction, that is observable only in the absence of the trans-sialidase or sialic acid acceptor, presented the opportunity to study the means by which enzymes selectivity bias in favor of a single reaction path. I therefore set out to explore the molecular details of how T. cruzi transsialidase asserts a precision and selectivity synonymous with enzyme catalysis. The chemical nature of the transition sate, formally defined as a dividing hypersurface separating the reactant and product regions of phase space, was characterized for the deglycosylation reaction. More than 40 transition state configurations were isolated from reactive trajectories, and the sialic acid substrate conformations were analyzed as well as the substrate interactions with the nucleophile and catalytic acid/base. A successful barrier crossing requires that the substrate pass through a family of E₅, ⁴H₅ and ⁶H₅ puckered conformations, all of which interact slightly differently with the enzyme. This work brings new evidence to the prevailing premise that there are several pathways from reactant to product passing through the saddle and successful product formation is not restricted to the minimum energy path. Increasing the reaction space with use of a multi-dimensional (3-D) reaction coordinate allowed simultaneous monitoring of the hitherto unexplored competition between a minor elimination reaction and the dominant displacement reaction present in both steps of the catalytic cycle. The dominant displacement reactions display lower barriers in the free energy profiles, greater sampling of favorable reactant stereoelectronic alignments and a greater number of possible transition paths leading to successful crossing reaction trajectories. The effects on the electronic degrees of freedom in reaction space were then investigated by running density functional theory reactive trajectories on the semi-empirical free energy. In order to carry out these simulations Free Energies from Adaptive Reaction Coordinates Forces was ported as a Fortran 90 library that interfaces with the NWChem molecular dynamics package. The resulting B3LYP/6-31G/CHARMM crossing trajectory provides a molecular orbital description of the glycosylation reaction. Direct investigation of the underlying potential energy functions for B3LYP/6-31G(d), B3LYP/6-31G and SCC-DFTB/MIO point to the minimal basis set as the primary limitation in using self-consistent charge density functional tight binding as the quantum mechanical model for modeling of enzymatic reactions transforming sialic acid substrates