VTechWorks Repository :: Browsing by Author "Crawford, T. Daniel"

Browsing by Author "Crawford, T. Daniel"

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Ab initio and Direct Quasiclassical Trajectory Study of the F + CH₄ → HF + CH₃ and F + C₂H₆ → HF + C₂H₅ Reactions
Weiss, Paula (Virginia Tech, 2007-09-25)
The reparametization of semiempirical Hamiltonians is an emerging method used in direct dynamics studies. The use of semiempirical Hamiltonians in direct dynamics studies diminishes the computational cost of trajectory calculations and negates the need for an analytical potential energy surface when performing reaction dynamics studies. The reparametization of semiempirical Hamiltonians increases the agreement with experiment and high level ab initio theory. We have chosen to create one set of new parameters that apply to two related reactions, F + CH₄ → HF + CH₃ and F + C₂H₆ → HF + C₂H₅. We have performed an electronic structure study for these reactions. The ab initio data obtained from the electronic structure study is then used as the reference for a reparametization of the PM3 Hamiltonian. The reparametization has improved the ab initio and PM3 reaction energy and potential energy surface scan agreement. This new set of parameters for PM3 (SRP-PM3) is used to perform a direct quasiclassical trajectory study of the reactions. The vibrational and rotational HF distributions calculated using SRP-PM3 are compared with experiments. We have observed an improvement in the agreement with experimental vibrational distributions but have seen no change in the rotational distributions.
Ab initio Calculations of Optical Rotation
Tam, Mary Christina (Virginia Tech, 2006-04-18)
Coupled cluster (CC) and density functional theory (DFT) are highly regarded as robust quantum chemical methods for accurately predicting a wide variety of properties, such as molecular structures, thermochemical data, vibrational spectra, etc., but there has been little focus on the theoretical prediction of optical rotation. This property, also referred to as circular birefringence, is inherent to all chiral molecules and occurs because such samples exhibit different refractive indices for left- and right- circularly polarized light. This thesis focuses on the theoretical prediction of this chiroptic property using CC and DFT quantum chemical models. Several small chiral systems have been studied, including (S)-methyloxirane, (R)-epichlorohydrin, (R)-methylthiirane, and the conformationally flexible molecules, (R)-3-chloro-1-butene and (R)-2-chlorobutane. All predicted results have been compared to recently published gas-phase cavity ringdown polarimetry data. When applicable, well-converged Gibbs free energy differences among confomers were determined using complete-basis-set extrapolations of CC energies in order to obtain Boltzmann-averaged specific rotations. The overall results indicate that the theoretical rotation is highly dependent on the choice of optimized geometry and basis set (diffuse functions are shown to be extremely important), and that there is a large difference between the CC and DFT predicted values, with DFT usually predicting magnitudes that are larger than those of coupled cluster theory.
Accurate Calculations of Molecular Properties with Explicitly Correlated Methods
Zhang, Jinmei (Virginia Tech, 2014-08-13)
Conventional correlation methods suffer from the slow convergence of electron correlation energies with respect to the size of orbital expansions. This problem is due to the fact that orbital products alone cannot describe the behavior of the exact wave function at short inter-electronic distances. Explicitly correlated methods overcome this basis set problem by including the inter-electronic distances (rij) explicitly in wave function expansions. Here, the origin of the basis set problem of conventional wave function methods is reviewed, and a short history of explicitly correlated methods is presented. The F12 methods are the focus herein, as they are the most practical explicitly correlated methods to date. Moreover, some of the key developments in modern F12 technology, which have significantly improved the efficiency and accuracy of these methods, are also reviewed. In this work, the extension of the perturbative coupled-cluster F12 method, CCSD(T)F12, developed in our group for the treatment of high-spin open-shell molecules (J. Zhang and E. F. Valeev, J. Chem. Theory Comput., 2012, 8, 3175.), is also documented. Its performance is assessed for accurate prediction of chemical reactivity. The reference data include reaction barrier heights, electronic reaction energies, atomization energies, and enthalpies of formation from the following sources: (1) the DBH24/08 database of 22 reaction barriers (Truhlar et al., J. Chem. Theory Comput., 2007, 3, 569.), (2) the HJO12 set of isogyric reaction energies (Helgaker et al., Modern Electronic Structure Theory, Wiley, Chichester, first ed., 2000.), and (3) the HEAT set of atomization energies and heats of formation (Stanton et al., J. Chem. Phys., 2004, 121, 11599.). Two types of analyses were performed, which target the two distinct uses of explicitly correlated CCSD(T) models: as a replacement for the basis-set-extrapolated CCSD(T) in highly accurate composite methods like HEAT and as a distinct model chemistry for standalone applications. Hence, (1) the basis set error of each component of the CCSD(T)F12 contribution to the chemical energy difference in question and (2) the total error of the CCSD(T)F12 model chemistry relative to the benchmark values are analyzed in detail. Two basis set families were utilized in the calculations: the standard aug-cc-p(C)VXZ (X = D, T, Q) basis sets for the conventional correlation methods and the cc-p(C)VXZ-F12 (X = D, T, Q) basis sets of Peterson and co-workers that are specifically designed for explicitly correlated methods. The conclusion is that the performance of the two families for CCSD correlation contributions (which are the only components affected by the explicitly correlated terms in our formulation) are nearly identical with triple- and quadruple-ζ quality basis sets, with some differences at the double-ζ level. Chemical accuracy (~4.18 kJ/mol) for reaction barrier heights, electronic reaction energies, atomization energies, and enthalpies of formation is attained, on average, with the aug-cc-pVDZ, aug-cc-pVTZ, cc- pCVTZ-F12/aug-cc-pCVTZ, and cc-pCVDZ-F12 basis sets, respectively, at the CCSD(T)F12 level of theory. The corresponding mean unsigned errors are 1.72 kJ/ mol, 1.5 kJ/mol, ~ 2 kJ/mol, and 2.17 kJ/mol, and the corresponding maximum unsigned errors are 4.44 kJ/mol, 3.6 kJ/mol, ~ 5 kJ/mol, and 5.75 kJ/mol. In addition to accurate energy calculations, our studies were extended to the computation of molecular properties with the MP2-F12 method, and its performance was assessed for prediction of the electric dipole and quadrupole moments of the BH, CO, H2O, and HF molecules (J. Zhang and E. F. Valeev, in preparation for submission). First, various MP2- F12 contributions to the electric dipole and quadrupole moments were analyzed. It was found that the unrelaxed one-electron density contribution is much larger than the orbital response contribution in the CABS singles correction, while both contributions are important in the MP2 correlation contribution. In contrast, the majority of the F12 correction originates from orbital response effects. In the calculations, the two basis set families, the aug-cc-pVXZ (X = D, T, Q) and cc-pVXZ-F12 (X = D, T, Q) basis sets, were also employed. The two basis set series show noticeably different performances at the double-ζ level, though the difference is smaller at triple- and quadruple-ζ levels. In general, the F12 calculations with the aug-cc- pVXZ series give better results than those with the cc-pVXZ-F12 family. In addition, the contribution of the coupling from the MP2 and F12 corrections was investigated. Although the computational cost of the F12 calculations can be significantly reduced by neglecting the coupling terms, this does increase the errors in most cases. With the MP2-F12C/aug-cc-pVDZ calculations, dipole moments close to the basis set limits can be obtained; the errors are around 0.001 a.u. For quadrupole moments, the MP2-F12C/aug-cc-pVTZ calculations can accurately approximate the MP2 basis set limits (within 0.001 a.u.).
Accurate Prediction of Chiroptical Properties
Mach, Taylor Joseph (Virginia Tech, 2014-06-16)
Accurate theoretical predictions of optical rotation are of substantial utility to the chemical community enabling the determination of absolute configuration without the need for poten- tially lengthy total synthesis. The requirements for robust calculation of gas-phase optical rotation are well understood, but too expensive for routine use. In an effort to reduce this cost we have examined the performance of the LPol and ORP basis sets, created for use in density functional theory calculations of optical rotation, finding that at the coupled cluster level of theory they perform the same or better than comparably sized general basis sets that are often used. We have also examined the performance of a perturbational approach to inclusion of explicit solvent molecules in an effort to extend the calculation of response properties from the gas phase to the condensed phase. This N-body approach performs admirably for interaction energies and even dipole moments but breaks down for optical rotation, exhibiting large basis set superposition errors and requiring higher-order terms in the expansion to provide reasonable accuracy. In addition, we have begun the process of implementing a gauge invariant version of coupled cluster response properties to address the fundamentally unphysical lack of gauge invariance in coupled cluster optical rotations. Correcting this problem, which arises from the non- variational nature of the coupled cluster wavefunction, involves reformulating the response amplitude and function expressions and solving for all necessary amplitudes simultaneously.
Born-Oppenheimer Corrections Near a Renner-Teller Crossing
Herman, Mark Steven (Virginia Tech, 2008-07-03)
We perform a rigorous mathematical analysis of the bending modes of a linear triatomic molecule that exhibits the Renner-Teller effect. Assuming the potentials are smooth, we prove that the wave functions and energy levels have asymptotic expansions in powers of Îµ, where Îµ4 is the ratio of an electron mass to the mass of a nucleus. To prove the validity of the expansion, we must prove various properties of the leading order equations and their solutions. The leading order eigenvalue problem is analyzed in terms of a parameter bË , which is equivalent to the parameter originally used by Renner. For 0 < bË < 1, we prove self-adjointness of the leading order Hamiltonian, that it has purely discrete spectrum, and that its eigenfunctions and their derivatives decay exponentially. Perturbation theory and finite difference calculations suggest that the ground bending vibrational state is involved in a level crossing near bË = 0.925. We also discuss the degeneracy of the eigenvalues. Because of the crossing, the ground state is degenerate for 0 < bË < 0.925 and non-degenerate for 0.925 < bË < 1.
Computational Investigations at the Gas-Surface Interface: Organic Surface Oxidation and Hydrolysis of Chemical Warfare Agents and Simulants
Chapleski Jr, Robert Charles (Virginia Tech, 2017-04-25)
Motivated by recent experiments in gas-surface chemistry, we report our results from computational investigations of heterogeneous systems relevant to atmospheric chemistry and protection against chemical weapons. To elucidate findings of ultra-high vacuum experiments that probe the oxidation of carbon-carbon double bonds on model surfaces, we used electronic structure and QM/MM methods to study the reaction of ozone with C60-fullerene and the products of nitrate addition to a vinyl-terminated self-assembled monolayer. In the first system, we followed a reaction pathway beginning with primary ozonide formation through the formation of stable products. Theoretical vibrational spectra were used to identify a ketene product in prior experimental work. Next, through the construction of a multilayer model for the initial addition product of a nitrate radical to a chain embedded within a self-assembled monolayer, we report theoretical spectra that are consistent with experimental results. We then examined the fundamentals of the hydrolysis mechanism for nerve agents by a catalyst of interest in the development of filtration materials for chemical-warfare-agent defense. By following the gas-surface reaction pathway of the nerve agent Sarin on the Lindqvist polyoxoniobate Cs8Nb6O19, we determined that the rate-limiting step is the transfer of a proton from an adsorbed water molecule to the niobate surface, concomitant with the nucleophilic addition of the nascent hydroxide to the phosphorus atom in Sarin. Our results support a general base hydrolysis mechanism, though high product-adsorption energies suggest that thermal treatment of the system is required to fully regenerate the catalyst. We report similar mechanisms for the simulants dimethyl methylphosphonate and dimethyl chlorophosphate, though the latter may serve as a better simulant in studies of this type. Finally, an investigation of Sarin hydrolysis with solvated Cs8Nb6O19 shows an increase in the rate-limiting barrier relative to the gas-surface system, revealing the role of Cs counterions in the reaction. Then, we further increased explicit solvation to model the homogeneous solution-phase reaction, finding a different mechanism in which a water molecule adds to phosphorus in the rate-limiting step and protonation of the niobate surface occurs in a subsequent barrierless step. By examining the rate-limiting barrier for protonation, we suggest that specific base hydrolysis is also likely in the homogeneous system.
Computational Studies of Protonated Cyclic Ethers and Benzylic Organolithium Compounds
Deora, Nipa (Virginia Tech, 2010-05-10)
Protonated epoxides feature prominently in organic chemistry as reactive intermediates. Gas-phase calculations studying the structure and ring-opening energetics of protonated ethylene oxide, propylene oxide and 2-methyl-1,2-epoxypropane were performed at the B3LYP and MP2 levels (both with the 6-311++G** basis set). Structural analyses were performed for 10 protonated epoxides using B3LYP, MP2, and CCSD/6-311++G** calculations. Protonated 2-methyl-1,2-epoxypropane was the most problematic species studied, where relative to CCSD, B3LYP consistently overestimates the C2-O bond length. The difficulty for DFT methods in modeling the protonated isobutylene oxide is due to the weakness of this C2-O bond. Protonated epoxides featuring more symmetrical charge distribution and cyclic homologues featuring less ring strain are treated with greater accuracy by B3LYP. Ion-pair separation (IPS) of THF-solvated fluorenyl, diphenylmethyl, and trityl lithium was studied computationally. Minimum-energy equilibrium geometries of explicit mono, bis and tris-solvated contact ion pairs (CIPs) and tetrakis-sovlated solvent separated ion pair (SSIPs) were modeled at B3LYP/6-31G*. Associative transition structures linking the tris-solvated CIPs and tetrakis-solvated SIPs were also located. In vacuum, B3LYP/6-31G* ΔHIPS values are 6-8 kcal/mol less exothermic than the experimentally-determined values in THF solution. Incorporation of secondary solvation in the form of Onsager and PCM single-point calculations showed an increase in exothermicity of IPS. Application of a continuum solvation model (Onsager) during optimization at the B3LYP/6-31G* level of theory produced significant changes in the Cα-Li contact distances in the SSIPs. An increase in of ion pair separation exothermicity was observed upon using both PCM and Onsager solvation models, highlighting the importance of both explicit and implicit solvation in modeling of ion pair separation.
Computational Study of the Properties and Stabilities of Endohedral Metallofullerenes
Fuhrer, Timothy J. (Virginia Tech, 2013-04-23)
The chemistry of fullerenes, which are a class of carbon allotropes that can be prepared by vaporization of graphite in an electric arc in a low pressure atmosphere,1 has become a topic of much experimental and theoretical study over the past 25 years. Herein we present a series of theoretical studies related to recently discovered or studied endohedral metallofullerenes (EMF) and a theory as to the selective stability of certain isomers of EMFs. Computational treatments of the anions of C80 and C94 are presented and compared in an effort to gain an understanding and predictive model for which isomers of each cage size EMF will be most stable. A model is proposed in which the pentagons of fullerene anions are seen as charge localization centers that repel one another, making the pyracyclene bonding motif much more unstable for fullerene anions than for fullerene neutral cages. Computational treatments are also presented for two newly discovered EMFs, Y2C2@C92 and Gd2@C79N. Y2C2@C92 is reported to exhibit a previously undiscovered mode of internal cluster rotation, while Gd2@C79N is shown to have unusual stability for an azofullerene with a large spin quantum number (15/2). Finally, computational techniques are employed to predict the thermodynamic feasibility of a chemical reaction replacing one metal atom in a trimetallic-nitride template (TNT) endohedral metallofullerene with different metal atom. At least two of these are predicted to be thermodynamically practical.
Coupled-Cluster Methods for Large Molecular Systems Through Massive Parallelism and Reduced-Scaling Approaches
Peng, Chong (Virginia Tech, 2018-05-02)
Accurate correlated electronic structure methods involve a significant amount of computations and can be only employed to small molecular systems. For example, the coupled-cluster singles, doubles, and perturbative triples model (CCSD(T)), which is known as the ``gold standard" of quantum chemistry for its accuracy, usually can treat molecules with 20-30 atoms. To extend the reach of accurate correlated electronic structure methods to larger molecular systems, we work towards two directions: parallel computing and reduced-cost/scaling approaches. Parallel computing can utilize more computational resources to handle systems that demand more substantial computational efforts. Reduced-cost/scaling approaches, which introduce approximations to the existing electronic structure methods, can significantly reduce the amount of computation and storage requirements. In this work, we introduce a new distributed-memory massively parallel implementation of standard and explicitly correlated (F12) coupled-cluster singles and doubles (CCSD) with canonical bigO{N^6} computational complexity ( C. Peng, J. A. Calvin, F. Pavov{s}evi'c, J. Zhang, and E. F. Valeev, textit{J. Phys. Chem. A} 2016, textbf{120}, 10231.), based on the TiledArray tensor framework. Excellent strong scaling is demonstrated on a multi-core shared-memory computer, a commodity distributed-memory computer, and a national-scale supercomputer. We also present a distributed-memory implementation of the density-fitting (DF) based CCSD(T) method. (C. Peng, J. A. Calvin, and E. F. Valeev, textit{in preparation for submission}) An improved parallel DF-CCSD is presented utilizing lazy evaluation for tensors with more than two unoccupied indices, which makes the DF-CCSD storage requirements always smaller than those of the non-iterative triples correction (T). Excellent strong scaling is observed on both shared-memory and distributed-memory computers equipped with conventional Intel Xeon processors and the Intel Xeon Phi (Knights Landing) processors. With the new implementation, the CCSD(T) energies can be evaluated for systems containing 200 electrons and 1000 basis functions in a few days using a small size commodity cluster, with even more massive computations possible on leadership-class computing resources. The inclusion of F12 correction to the CCSD(T) method makes it converge to basis set limit much more rapidly. The large-scale parallel explicitly correlated coupled-cluster program makes the accurate estimation of the coupled-cluster basis set limit for molecules with 20 or more atoms a routine. Thus, it can be used rigorously to test the emerging reduced-scaling coupled-cluster approaches. Moreover, we extend the pair natural orbital (PNO) approach to excited states through the equation-of-motion coupled cluster singles and doubles (EOM-CCSD) method. (C. Peng, M. C. Clement, and E. F. Valeev, textit{submitted}) We simulate the PNO-EOM-CCSD method using an existing massively parallel canonical EOM-CCSD program. We propose the use of state-averaged PNOs, which are generated from the average of the pair density of excited states, to span the PNO space of all the excited states. The doubles amplitudes in the CIS(D) method are used to compute the state-averaged pair density of excited states. The issue of incorrect states in the state-averaged pair density, caused by an energy reordering of excited states between the CIS(D) and EOM-CCSD, is resolved by simply computing more states than desired. We find that with a truncation threshold of $10^{-7}$, the truncation error for the excitation energy is already below 0.02 eV for the systems tested, while the average number of PNOs is reduced to 50-70 per pair. The accuracy of the PNO-EOM-CCSD method on local, Rydberg and charge transfer states is also investigated.
Crystallization and Melting Behavior of Linear Polyethylene and Ethylene/Styrene Copolymers and Chain Length Dependence of Spherulitic Growth Rate for Poly(Ethylene Oxide) Fractions
Huang, Zhenyu (Virginia Tech, 2004-09-24)
The crystallization and melting behavior of linear polyethylene and of a series of random ethylene/styrene copolymers was investigated using a combination of classical and temperature modulated differential scanning calorimetry. In the case of linear polyethylene and low styrene content copolymers, the temporal evolutions of the melting temperature, degree of crystallinity, and excess heat capacity were studied during crystallization. The following correlations were established: 1) the evolution of the melting temperature with time parallels that of the degree of crystallinity, 2) the excess heat capacity increases linearly with the degree of crystallinity during primary crystallization, reaches a maximum during the mixed stage and decays during secondary crystallization, 3) the rates of shift of the melting temperature and decay of the excess heat capacity lead to apparent activation energies that are very similar to these reported for the crystal ac relaxation by other techniques. Strong correlations in the time domain between the secondary crystallization and the evolution of the excess heat capacity suggest that the reversible crystallization/melting phenomenon is associated with molecular events in the melt-crystal fold interfacial region. In the case of higher styrene content copolymers, the multiple melting behavior at high temperature is investigated through studies of the overall crystallization kinetics, heating rate effects and partial melting. Low melting crystals can be classified into two categories according to their melting behavior, superheating and reorganization characteristics. Low styrene content copolymers still exhibit some chain folded lamellar structure. The shift of the low melting temperature with time in this case is tentatively explained in terms of reorganization effects. Decreasing the crystallization temperature or increasing the styrene content leads to low melting crystals more akin to fringed-micelles. These crystals exhibit a lower tendency to reorganize during heating. The shift of their melting temperature with time is attributed to a decrease in the conformational entropy of the amorphous fraction as a result of constraints imposed by primary and secondary crystals. To further understand the mechanism of formation of low melting crystals, quasi-isothermal crystallization experiments were carried out using temperature modulation. The evolution of the excess heat capacity was correlated with that of the melting behavior. On the basis of these results, it is speculated that the generation of excess heat capacity at high temperature results from reversible segmental exchange on the fold surface. On the other hand, the temporal evolution of the excess heat capacity at low temperature for high styrene content copolymers is attributed to the reversible segment attachment and detachment on the lateral surface of primary crystals. The existence of different mechanisms for the generation of excess heat capacity in different temperature ranges is consistent with the observation of two temperature regimes for the degree of reversibility inferred from quasi-isothermal melting experiments. In a second project, the chain length and temperature dependences of spherulitic growth rates were studied for a series of narrow fractions of poly(ethylene oxide) with molecular weight ranging from 11 to 917 kg/mol. The crystal growth rate data spanning crystallization temperatures in regimes I and II was analyzed using the formalism of the Lauritzen-Hoffman (LH) theory. Our results are found to be in conflict with predictions from LH theory. The Kg ratio increases with molecular weight instead of remaining constant. The chain length dependence of the exponential prefactor, G0, does not follow the power law predicted by Hoffman and Miller (HM). On this basis, the simple reptation argument proposed in the HM treatment and the nucleation regime concept advanced by the LH model are questioned. We proposed that the observed I/II regime transition in growth rate data may be related to a transition in the friction coefficient, as postulated by the Brochard-de Gennnes slippage model. This mechanism is also consistent with recent calculations published by Toda in which both the rates of surface nucleation and substrate completion processes exhibit a strong temperature dependence.
Design, Syntheses, and Bioactivities of Conformationally Locked Pin1 Ground State Inhibitors
Wang, Xiaodong (Virginia Tech, 2005-03-04)
Pin1 (protein interacting with NIMA 1) is a peptidyl-prolyl isomerase involved in mitosis. As a potential anti-cancer drug target, Pin1 interacts and regulates the activity of an increasing number of cell cycle enzymes by an unknown mechanism. These cell cycle enzymes include Cdc25, Cdc27, Cyclin D1, Myt1, Wee1, NIMA, Cdc2, Plk1 and c-Myc. Recent research has revealed that Pin1 is overexpressed in a variety of cancer cell lines and Pin1 inhibitors inhibit proliferation activity of several cancer cells overexpressing Pin1. The most potent Pin1 inhibitors identified so far are in the micromolar range and no pharmacophore has been identified. In order to assist the understanding of the biological function of Pin1 using molecular probes, two amide isosteres of Ser-trans-Pro and Ser-cis-Pro dipeptides were designed and stereoselectively synthesized. The conformationally locked Ser–trans–Pro mimic, Boc-SerΨ[(E)CH=C]Pro–OH, was synthesized through the use of an Ireland-Claisen [3,3]-sigmatropic rearrangement in nine steps with 13% overall yield from a serine derivative. The Ser-cis-Pro mimic, Boc-SerΨ[(Z)CH=C]Pro–OH, was synthesized through the use of a Still-Wittig [2,3]-sigmatropic rearrangement in 11 steps with an overall yield of 20% from the same starting material. Conformationally locked peptidomimetics, including two exactly matched peptidomimetics, Ac–Phe–Phe–pSer–Ψ(E)CH=C]Pro–Arg–NH2 and Ac–Phe–Phe–pSer–Ψ[(Z)CH=C]Pro–Arg–NH2, were synthesized from these Ser-Pro isosteres using Fmoc SPPS. A protocol for in vitro Pin1 inhibition assay was established for measuring the inhibition constant for these peptidomimetics. A conformationally locked cis peptidomimetic inhibits Pin1 with a K_i of 1.7 μM, 23-fold more potent than its trans counterpart, illustrating the preference of Pin1 for a cis amide bond in its PPIase domain. The A2780 ovarian cancer cell antiproliferation activity of these peptidomimetics parallels their respective Pin1 inhibition data. This research provides a start toward more drug-like Pin1 inhibitor design. Gly–trans–Pro isosteres were synthesized using the Ireland-Claisen route. The construction of a non-peptidic (Z)-alkene library for Pin1 inhibition was attempted using the Ser-cis-Pro mimic, Boc—SerΨ[(Z)CH=C]Pro–OH as the core.
Development and Application of Coupled Cluster Ground- and Excited-State Models
Smith, Christopher Edward (Virginia Tech, 2006-04-24)
We give an overview of quantum chemical methods with a particular emphasis on the development of high-accuracy quantum chemical models. The reliability of these methods often hinges on whether enough electron correlation is included in the truncated wave function. As an example, we investigate the structures of m-benzyne and its fluorinated derivative, tetrafluoro-m-benzyne where the inclusion of triple excitations is paramount to correctly describe through-bond delocalization of the monocyclic form. At the CCSDT/6-31G** level of theory, the C1–C3 distance of the minimum energy form of m-benzyne is 2.0°A and the profile of the PES along the C1–C3 distance is that of an asymmetric, single-well, in agreement with previous density-functional theory and coupled cluster studies. In addition, the calculated CCSD(T) fundamental frequencies are in excellent agreement with the measured infrared frequencies, thus confirming the monocyclic form of m-benzyne. For tetrafluoro-m-benzyne, however, the increased eclipsing strain between the ring-external Câ X bonds stabilizes the bicyclo[3.1.0]hexatriene form: the C1–C3 distance is calculated at the CCSD(T)/cc-pVTZ level to be approximately 1.75 °A, which is in the range of elongated CC bonds. Computed harmonic vibrational frequencies compare reasonably well with the experimental neon-matrix difference spectrum and provide further evidence for the existence of a bicyclic form. We also report an extension of the coupled cluster iterative-triples model, CC3, to excited states of open-shell molecules, including radicals. We define the method for both spin-unrestricted Hartree-Fock (UHF) and spin-restricted open-shell Hartree-Fock (ROHF) reference determinants and discuss its efficient implementation in the PSI3 program package. The program is streamlined to use at most O(N7) computational steps and avoids storage of the triple-excitation amplitudes for both the ground-and excited-state calculations. The excitation-energy program makes use of a Lowdin projection formalism (comparable to that of earlier implementations) that allows computational reduction of the Davidson algorithm to only the single- and double-excitation space, but limits the calculation to only one excited state at a time. However, a root-following algorithm may be used to compute energies for multiple states of the same symmetry. Benchmark applications of the new methods to the lowest valence 2B1 state of the allyl radical, low-lying states of the CH and CO+ diatomics, and the nitromethyl radical show substantial improvement over ROHF- and UHF-based CCSD excitation energies for states with strong double-excitation character or cases suffering from significant spin contamination. For the allyl radical, CC3 adiabatic excitation energies differ from experiment by less than 0.02 eV, while for the 2Â§+ state of CH, significant errors of more than 0.4 eV remain. Finally, ground- and excited-state dipole moments are derived diagramatically and were recently developed within the PSI3 quantum chemistry package. However, convergence problems with computing the left-hand excited-state has prevented us from reporting any meaningful results. Thus, future work includes solving this convergence problem before the effects of triple excitations on one-electron properties can be reported with certainty.
The Dynamics of Gas-Surface Energy Transfer in Collisions of Rare Gases with Organic Thin Films
Day, Brian Scott (Virginia Tech, 2005-07-18)
Understanding mechanisms at the molecular level is essential for interpreting and predicting the outcome of processes in all fields of chemistry. Insight into gas-surface reaction dynamics can be gained through molecular beam scattering experiments combined with classical trajectory simulations. In particular, energy exchange and thermal accommodation in the initial collision, the first step in most chemical reactions, can be probed with these experimental and computational tools. There are many questions regarding the dynamic details that occur during the interaction time between gas molecules and organic surfaces. For example, how does interfacial structure and density affect energy transfer? What roles do intramonolayer forces and chemical identity play in the dynamics? We have approached these questions by scattering high-energy, rare gas atoms from functionalized self-assembled monolayers. We used classical trajectory simulations to investigate the atomic-level details of the scattering dynamics. We find that approximately six to ten carbon atoms are involved in impulsive collision events, which is dependent on the packing density of the alkyl chains. Moreover, the higher the packing density of the alkyl chains, the less energy is transferred to the surface on average and the less often the incident atoms come into thermal equilibrium with the surface. In addition to the purely hydrocarbon monolayers, organic surfaces with lateral hydrogen-bonding networks create more rigid collision partners than surfaces with smaller inter-chain forces, such as van der Waals forces. Finally, we find some interesting properties for organic surfaces that possess fluorinated groups. For argon scattering, energy transfer decreases with an increasing amount of surface fluorination, whereas krypton and xenon scattering transfer most energy to monolayers terminated in CF₃ groups, followed by purely hydrocarbon surfaces, and then perfluorinated surfaces.
Experimental and Computational Investigation of Tacrine-Based Inhibitors of Acetylcholinesterase
Williams, Larry D. (Virginia Tech, 2008-10-28)
Acetylcholinesterase (AChE) terminates cholinergic neurotransmission by catalyzing the hydrolysis of the neurotransmitter acetylcholine (ACh). Inhibition of AChE has proven an effective treatment for the memory loss exhibited by early stage Alzheimer's disease (AD) patients; four AChE inhibitors (AChEI) have been approved by the FDA for this purpose. The first AChEI approved for the palliative treatment of AD-related memory loss was 9-amino-1,2,3,4-tetrahydroacridine (tacrine). Inhibition of AChE may present either therapeutic or toxic effects depending upon the dose administered. With the goal of discovering safe and effective pesticides to control the population of Anopheles gambiae, a malaria-transmitting mosquito indigenous to Sub-Saharan Africa, the reoptimization of the tacrine pharmacophore was undertaken. Because the optimized drug would necessarily be a poor inhibitor for human AChE (hAChE), initial ligand design focused on modification to tacrine known to negatively impact the inhibition potency for hAChE. Ultimately, an AChEI was discovered, which exhibited micromolar inhibition of Anopheles gambiae AChE (AgAChE) and essentially no potency for hAChE. Two units of this lead compound were tethered through an alkyl chain to yield a nanomolar inhibitor of AgAChE that was more than 1,100-fold selective for the mosquito enzyme over hAChE. Dimerization of an active inhibitor is an effective strategy to increase the potency and selectivity of AChEI, and many examples of tacrine hetero- and homodimers complexed to AChE can be found in the RCSB Protein Data Bank (PDB). The bond formed between the exocyclic amine moiety and the heterocyclic ring system of tacrine is analogous to an amide bond when tacrine is protonated. Therefore, the rotational profile of protonated N-alkyltacrine should exhibit a conformational profile in which dihedral angles significantly out of the plane formed by the ring system are associated with high energies relative to those when the dihedral angles are nearly coplanar with the ring system. The barrier of rotation (ΔG^‡) produced by this phenomenon in two tacrine derivatives and two quinoline derivatives was experimentally determined using dynamic 1H NMR. These values were compared to density functional theory (DFT) derived values for the same phenomenon. Furthermore, since the ΔG^‡ proved to be impossible to experimentally determine for the optimal model compound for the active site portion of tacrine dimers, N-methyltacrine, the DFT method employed for modeling the ΔG^‡ of the tacrine and quinoline analogs was used to computationally derive the entire rotational conformation diagram of N-methyltacrine. The calculated values were then used to comment on the relative energies of adopting certain conformations found in the X-ray crystal structures of dimer/AChE complexes.
Explicitly correlated Green's function methods for calculating electron binding energies
Teke, Nakul Kushabhau (Virginia Tech, 2019-07-29)
Single-particle Green's function method is a direct way of calculating electron binding energy, which relies on expanding the Fock subspace in a finite single-particle basis. However, these methods suffer from slow asymptotic decay of basis set incompleteness error. An energy-dependent explicitly correlated (F12) formalism for Green's function is presented that achieves faster convergence to the basis set limit. The renormalized second-order Green's function method (NR2-F12) scales as iterative N^5 where N is the system size. These methods are tested on a set of small (O21) and medium-sized (OAM24) organic molecules. The basis set incompleteness error in ionization potential (IP) obtained from the NR2-F12 method and aug-cc-pVDZ basis for OAM24 is 0.033 eV compared to 0.067 eV for NR2 method and aug-cc-pVQZ basis. Hence, accurate electron binding energies can be calculated at a lower cost using NR2-F12 method. For aug-cc-pVDZ basis, the electron binding energies obtained from NR2-F12 are comparable to EOM-IP-CCSD method that uses a CCSD reference and scales as iterative N^6.
Explicitly Correlated Methods for Large Molecular Systems
Pavosevic, Fabijan (Virginia Tech, 2018-02-02)
Wave function based electronic structure methods have became a robust and reliable tool for the prediction and interpretation of the results of chemical experiments. However, they suffer from very steep scaling behavior with respect to an increase in the size of the system as well as very slow convergence of the correlation energy with respect to the basis set size. Thus these methods are limited to small systems of up to a dozen atoms. The first of these issues can be efficiently resolved by exploiting the local nature of electron correlation effects while the second problem is alleviated by the use of explicitly correlated R12/F12 methods. Since R12/F12 methods are central to this work, we start by reviewing their modern formulation. Next, we present the explicitly correlated second-order Mo ller-Plesset (MP2-F12) method in which all nontrivial post-mean-field steps are formulated with linear computational complexity in system size [Pavov{s}evi'c et al., {em J. Chem. Phys.} {bf 144}, 144109 (2016)]. The two key ideas are the use of pair-natural orbitals for compact representation of wave function amplitudes and the use of domain approximation to impose the block sparsity. This development utilizes the concepts for sparse representation of tensors described in the context of the DLPNO-MP2 method by Neese, Valeev and co-workers [Pinski et al., {em J. Chem. Phys.} {bf 143}, 034108 (2015)]. Novel developments reported here include the use of domains not only for the projected atomic orbitals, but also for the complementary auxiliary basis set (CABS) used to approximate the three- and four-electron integrals of the F12 theory, and a simplification of the standard B intermediate of the F12 theory that avoids computation of four-index two-electron integrals that involve two CABS indices. For quasi-1-dimensional systems (n-alkanes) the bigO{N} DLPNO-MP2-F12 method becomes less expensive than the conventional bigO{N^{5}} MP2-F12 for $n$ between 10 and 15, for double- and triple-zeta basis sets; for the largest alkane, C$_{200}$H$_{402}$, in def2-TZVP basis the observed computational complexity is $N^{sim1.6}$, largely due to the cubic cost of computing the mean-field operators. The method reproduces the canonical MP2-F12 energy with high precision: 99.9% of the canonical correlation energy is recovered with the default truncation parameters. Although its cost is significantly higher than that of DLPNO-MP2 method, the cost increase is compensated by the great reduction of the basis set error due to explicit correlation. We extend this formalism to develop a linear-scaling coupled-cluster singles and doubles with perturbative inclusion of triples and explicitly correlated geminals [Pavov{s}evi'c et al., {em J. Chem. Phys.} {bf 146}, 174108 (2017)]. Even for conservative truncation levels, the method rapidly reaches near-linear complexity in realistic basis sets; e.g., an effective scaling exponent of 1.49 was obtained for n-alkanes with up to 200 carbon atoms in a def2-TZVP basis set. The robustness of the method is benchmarked against the massively parallel implementation of the conventional explicitly correlated coupled-cluster for a 20-water cluster; the total dissociation energy of the cluster ($sim$186 kcal/mol) is affected by the reduced-scaling approximations by only $sim$0.4 kcal/mol. The reduced-scaling explicitly correlated CCSD(T) method is used to examine the binding energies of several systems in the L7 benchmark data set of noncovalent interactions. Additionally, we discuss a massively parallel implementation of the Laplace transform perturbative triple correction (T) to the DF-CCSD energy within density fitting framework. This work is closely related to the work by Scuseria and co-workers [Constans et al., {em J. Chem. Phys.} {bf 113}, 10451 (2000)]. The accuracy of quadrature with respect to the number of quadrature points has been investigated on systems of the 18-water cluster, uracil dimer and pentacene dimer. In the case of the 18-water cluster, the $mu text{E}_{text{h}}$ accuracy is achieved with only 3 quadrature points. For the uracil dimer and pentacene dimer, 6 or more quadrature points are required to achieve $mu text{E}_{text{h}}$ accuracy; however, binding energy of $<$1 kcal/mol is obtained with 4 quadrature points. We observe an excellent strong scaling behavior on distributed-memory commodity cluster for the 18-water cluster. Furthermore, the Laplace transform formulation of (T) performs faster than the canonical (T) in the case of studied systems. The efficiency of the method has been furthermore tested on a DNA base-pair, a system with more than one thousand basis functions. Lastly, we discuss an explicitly correlated formalism for the second-order single-particle Green's function method (GF2-F12) that does not assume the popular diagonal approximation, and describes the energy dependence of the explicitly correlated terms [Pavov{s}evi'c et al., {em J. Chem. Phys.} {bf 147}, 121101 (2017)]. For small and medium organic molecules the basis set errors of ionization potentials of GF2-F12 are radically improved relative to GF2: the performance of GF2-F12/aug-cc-pVDZ is better than that of GF2/aug-cc-pVQZ, at a significantly lower cost.
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 photodissociation region
Fortenberry, Ryan Clifton; Huang, X. C.; Crawford, T. Daniel; Lee, T. J. (IOP Publishing Ltd., 2013-07)
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: 1(1)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 anions. Additionally, the computed D-eff for C3H is three times closer to the D deduced from the observed Horsehead nebula lines relative to l-C3H+. As a result, 1(1)A'C3H- is a more viable candidate for these observed rotational transitions. It has been previously proposed that at least C6H- may be present in the Horsehead nebular PDR formed by way of radiative attachment through its dipole-bound excited state. C3H- could form in a similar way through its dipole-bound state, but its valence excited state increases the number of relaxation pathways possible to reach the ground electronic state. In turn, the rate of formation for C3H- could be greater than the rate of its destruction. C3H- would be the seventh confirmed interstellar anion detected within the past decade and the first CnH- molecular anion with an odd n.
In Pursuit of Local Correlation for Reduced-Scaling Electronic Structure Methods in Molecules and Periodic Solids
Clement, Marjory Carolena (Virginia Tech, 2021-08-05)
Over the course of the last century, electronic structure theory (or, alternatively, computational quantum chemistry) has grown from being a fledgling field to being a "full partner with experiment" [Goddard Science 1985, 227 (4689), 917--923]. Numerous instances of theory matching experiment to very high accuracy abound, with one excellent example being the high-accuracy ab initio thermochemical data laid out in the 2004 work of Tajti and co-workers [Tajti et al. J. Chem. Phys. 2004, 121, 11599] and another being the heats of formation and molecular structures computed by Feller and co-workers in 2008 [Feller et al. J. Chem. Phys. 2008, 129, 204105]. But as the authors of both studies point out, this very high accuracy comes at a very high cost. In fact, at this point in time, electronic structure theory does not suffer from an accuracy problem (as it did in its early days) but a cost problem; or, perhaps more precisely, it suffers from an accuracy-to-cost ratio problem. We can compute electronic energies to nearly any precision we like, as long as we are willing to pay the associated cost. And just what are these high computational costs? For the purposes of this work, we are primarily concerned with the way in which the computational cost of a given method scales with the system size; for notational purposes, we will often introduce a parameter, N, that is proportional to the system size. In the case of Hartree-Fock, a one-body wavefunction-based method, the scaling is formally N⁴, and post-Hartree-Fock methods fare even worse. The coupled cluster singles, doubles, and perturbative triples method [CCSD(T)], which is frequently referred to as the "gold standard" of quantum chemistry, has an N⁷ scaling, making it inapplicable to many systems of real-world import. If highly accurate correlated wavefunction methods are to be applied to larger systems of interest, it is crucial that we reduce their computational scaling. One very successful means of doing this relies on the fact that electron correlation is fundamentally a local phenomenon, and the recognition of this fact has led to the development of numerous local implementations of conventional many-body methods. One such method, the DLPNO-CCSD(T) method, was successfully used to calculate the energy of the protein crambin [Riplinger, et al. J. Chem. Phys 2013, 139, 134101]. In the following work, we discuss how the local nature of electron correlation can be exploited, both in terms of the occupied orbitals and the unoccupied (or virtual) orbitals. In the case of the former, we highlight some of the historical developments in orbital localization before applying orbital localization robustly to infinite periodic crystalline systems [Clement, et al. 2021, Submitted to J. Chem. Theory Comput.]. In the case of the latter, we discuss a number of different ways in which the virtual space can be compressed before presenting our pioneering work in the area of iteratively-optimized pair natural orbitals ("iPNOs") [Clement, et al. J. Chem. Theory Comput. 2018, 14 (9), 4581--4589]. Concerning the iPNOs, we were able to recover significant accuracy with respect to traditional PNOs (which are unchanged throughout the course of a correlated calculation) at a comparable truncation level, indicating that our improved PNOs are, in fact, an improved representation of the coupled cluster doubles amplitudes. For example, when studying the percent errors in the absolute correlation energies of a representative sample of weakly bound dimers chosen from the S66 test suite [Řezác, et al. J. Chem. Theory Comput. 2011, 7 (8), 2427--2438], we found that our iPNO-CCSD scheme outperformed the standard PNO-CCSD scheme at every truncation threshold (τ_PNO) studied. Both PNO-based methods were compared to the canonical CCSD method, with the iPNO-CCSD method being, on average, 1.9 times better than the PNO-CCSD method at τ_PNO = 10⁻⁷ and more than an order of magnitude better for τ_PNO < 10⁻¹⁰ [Clement, et al. J. Chem. Theory Comput 2018, 14 (9), 4581--4589]. When our improved PNOs are combined with the PNO-incompleteness correction proposed by Neese and co-workers [Neese, et al. J. Chem. Phys. 2009, 130, 114108; Neese, et al. J. Chem. Phys. 2009, 131, 064103], the results are truly astounding. For a truncation threshold of τ_PNO = 10⁻⁶, the mean average absolute error in binding energy for all 66 dimers from the S66 test set was 3 times smaller when the incompleteness-corrected iPNO-CCSD method was used relative to the incompleteness-corrected PNO-CCSD method [Clement, et al. J. Chem. Theory Comput. 2018, 14 (9), 4581--4589]. In the latter half of this work, we present our implementation of a limited-memory Broyden-Fletcher-Goldfarb-Shanno (BFGS) based Pipek-Mezey Wannier function (PMWF) solver [Clement, et al. 2021 }, Submitted to J. Chem. Theory Comput.]. Although orbital localization in the context of the linear combination of atomic orbitals (LCAO) representation of periodic crystalline solids is not new [Marzari, et al. Rev. Mod. Phys. 2012, 84 (4), 1419--1475; Jònsson, et al. J. Chem. Theory Comput. 2017, 13} (2), 460--474], to our knowledge, this is the first implementation to be based on a BFGS solver. In addition, we are pleased to report that our novel BFGS-based solver is extremely robust in terms of the initial guess and the size of the history employed, with the final results and the time to solution, as measured in number of iterations required, being essentially independent of these initial choices. Furthermore, our BFGS-based solver converges much more quickly and consistently than either a steepest ascent (SA) or a non-linear conjugate gradient (CG) based solver, with this fact demonstrated for a number of 1-, 2-, and 3-dimensional systems. Armed with our real, localized Wannier functions, we are now in a position to pursue the application of local implementations of correlated many-body methods to the arena of periodic crystalline solids; a first step toward this goal will, most likely, be the study of PNOs, both conventional and iteratively-optimized, in this context.
Incremental evaluation of coupled cluster dipole polarizabilities
Friedrich, Joachim; McAlexander, Harley R.; Kumar, Ashutosh; Crawford, T. Daniel (The Royal Society of Chemistry, 2014-12-16)
In this work we present the first implementation of the incremental scheme for coupled cluster linear-response frequency-dependent dipole polarizabilities. The implementation is fully automated and makes use of the domain-specific basis set approach. The accuracy of the approach is determined on the basis of a test suite of 47 molecules and small clusters. The local approximation in the coupled cluster singles and doubles polarizability exhibits a mean error of 0.02% and a standard deviation of 0.32% when using a third-order incremental expansion. With the proposed approach, it is possible to compute polarizabilities with larger basis sets compared to the canonical implementation and thus it is possible to obtain higher total accuracy. The incremental scheme yields the smallest errors for weakly-bound and quasi-linear systems, while two- and three-dimensional (cage-like) structures exhibit somewhat larger errors as compared to the full test set.
Interfacial Characterization of Polyhedral Oligomeric Silsesquioxane (POSS) Amphiphiles and Polymer Blends: Thermodynamics, Morphology, and Rheology
Deng, Jianjun (Virginia Tech, 2005-04-18)
Over the past two decades one class of oligomers, polyhedral oligomeric silsesquioxanes (POSS), has attracted considerable attention because of their unique hybrid organic/inorganic molecular structures and nanoscopic sizes. While surface and interfacial properties may play a key role in many potential POSS applications, relatively little is actually known about the surface properties of POSS. This dissertation provides studies of the interfacial aspects of both POSS molecules and POSS/polymer blends at the air/water interface (A/W) through surface pressure-area per molecule (π-A) isotherm, Brewster angle microscopy (BAM), and interfacial stress rheometry (ISR) studies. Results for POSS Langmuir thin films at A/W show that trisilanol-POSS derivatives are a new class of amphiphiles, that exhibit multiple phase transitions in going from traditional 2D Langmuir monolayers (1 POSS molecule thick) to various 3D multilayer films upon compression. With small length/diameter ratios and bulky shapes, the monolayer phase behavior and packing states of different POSS are simpler than the traditional rod-like lipids. Meanwhile trisilanol-POSS derivatives have very different collapse behavior and multilayer organization showing strong substituent effects even though they have similar molecular sizes. While trisilanolisobutyl-POSS (TiBuP) monolayers undergo collapse around π ≈ 18 mNm⁻¹ and form various ordered or disordered solid-like 3D aggregates at different compression rates, trisilanolcyclohexyl-POSS (TCyP) monolayers collapse into trilayers via instantaneous nucleation with hemispherical edge growth around π ≈ 3.7 mNm⁻¹. ISR results reveal three different non-Newtonian flow regimes that correlate with phase transitions in the Pi-A isotherms. Further symmetric compression after trilayer formation induces TCyP thin films to self-assemble into highly ordered crystalline-like hydrophobic multilayers (≈8 POSS molecule thick) with unique rod-like morphologies, which are dramatically different from –collapsed– morphologies seen in other systems. By treating POSS derivatives as ideal nanofiller for studying confinement effects on filled polymer systems, amphiphilic poly(dimethylsiloxane) (PDMS) derivatives with different polar functional groups are studied as blends with TiBuP and octaisobutyl-POSS at A/W to resolve one of the key challenges for current nanocomposite applications: How to control nanofiller dispersion in polymer matrices? The results in this dissertation reveal that introducing polar groups into polymeric matrix polymers is a good way to control dispersion.

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