### Browsing by Author "Troya, Diego"

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- Ab initio and Direct Quasiclassical Trajectory Study of the F + CH₄ → HF + CH₃ and F + C₂H₆ → HF + C₂H₅ ReactionsWeiss, Paula (Virginia Tech, 2007-09-25)
Show more 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.Show more - Accurate Calculations of Molecular Properties with Explicitly Correlated MethodsZhang, Jinmei (Virginia Tech, 2014-08-13)
Show more 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.).Show more - Accurate Prediction of Chiroptical PropertiesMach, Taylor Joseph (Virginia Tech, 2014-06-16)
Show more 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.Show more - Advanced Quantum Mechanical Simulations of Circular Dichroism SpectraPearce, Kirk C. (Virginia Tech, 2022-01-27)
Show more In quantum chemistry, scientists aim to solve the time-independent Schrödinger equation by employing a variety of approximation techniques whose accuracy are typically inversely proportional to their computational cost. This problem is amplified when it comes to chiral molecules, whose stereochemical assignments and associated chiroptical properties can be incredibly sensitive to small changes in their three-dimensional structure, requiring highly accurate theoretical methods. On the other hand, due to the polynomial scaling with system size, it is sometimes impractical to apply such methods to chemical compounds of broad scientific interest, especially when a multitude of low-energy conformations have to be accounted for as well. As a result, the assignment of absolute configurations to chiral compounds remains a tedious task. However, the characterization of these compounds is something that many different scientists are significantly invested in. The ultimate goal, then, is twofold: to gain useful insight by utilizing the electronic structure methods at your disposal while simultaneously developing new approximation techniques that can be used to push the boundaries on what is currently capable in computational chemistry. Therefore, we start by applying widely accepted density functional theory methods to predict optical rotations and electronic circular dichroism for naturally occurring antiplasmodial and anticancer drug candidates. We find that by comparing the computational results directly with those obtained through experimental measurement, we can provide reliable absolute config- uraitonal assignments to a variety of chiral compounds with numerous stereogenic centers. We also present the first ever prediction of vibrational circular dichroism with second-order Møller-Plesset perturbation theory. This extension opens the door to systematically improvable correlated wave function methods that can be employed when density functional theory fails or when higher accuracy results are required.Show more - Atomic resolution tracking of nerve-agent simulant decomposition and host metal-organic framework response in real spaceTerban, Maxwell W.; Ghose, Sanjit K.; Plonka, Anna M.; Troya, Diego; Juhas, Pavol; Dinnebier, Robert E.; Mahle, John J.; Gordon, Wesley O.; Frenkel, Anatoly I. (2021-01-04)
Show more Gas capture and sequestration are valuable properties of metal-organic frameworks (MOFs) driving tremendous interest in their use as filtration materials for chemical warfare agents. Recently, the Zr-based MOF UiO-67 was shown to effectively adsorb and decompose the nerve-agent simulant, dimethyl methylphosphonate (DMMP). Understanding mechanisms of MOF-agent interaction is challenging due to the need to distinguish between the roles of the MOF framework and its particular sites for the activation and sequestration process. Here, we demonstrate the quantitative tracking of both framework and binding component structures using in situ X-ray total scattering measurements of UiO-67 under DMMP exposure, pair distribution function analysis, and theoretical calculations. The sorption and desorption of DMMP within the pores, association with linker-deficient Zr6 cores, and decomposition to irreversibly bound methyl methylphosphonate were directly observed and analyzed with atomic resolution. Metal-organic frameworks have been shown to adsorb and decompose chemical warfare agents, but their mechanism of action is not completely understood. Here the authors quantitatively track the binding and decomposition product structures of nerve-agent simulant dimethyl methylphosphonate in host UiO-67 through in situ X-ray total scattering measurements, pair distribution function analysis, and density functional theory calculations.Show more - Atomic-Level Structural Dynamics of Polyoxoniobates during DMMP DecompositionWang, Qi; Chapleski, Robert C. Jr.; Plonka, Anna M.; Gordon, Wesley O.; Guo, Weiwei; Thuy-Duong Nguyen-Phan; Sharp, Conor H.; Marinkovic, Nebojsa S.; Senanayake, Sanjaya D.; Morris, John R.; Hill, Craig L.; Troya, Diego; Frenkel, Anatoly I. (Springer Nature, 2017-04-10)
Show more Ambient pressure in situ synchrotron-based spectroscopic techniques have been correlated to illuminate atomic-level details of bond breaking and formation during the hydrolysis of a chemical warfare nerve agent simulant over a polyoxometalate catalyst. Specifically, a Cs-8[Nb6O19] polyoxoniobate catalyst has been shown to react readily with dimethyl methylphosphonate (DMMP). The atomic-level transformations of all reactant moieties, the [Nb6O19](8)-polyanion, its Cs+ counterions, and the DMMP substrate, were tracked under ambient conditions by a combination of X-ray absorption fine structure spectroscopy, Raman spectroscopy, and X-ray diffraction. Results reveal that the reaction mechanism follows general base (in contrast to specific base) hydrolysis. Together with computational results, the work demonstrates that the ultimate fate of DMMP hydrolysis at the Cs-8[Nb6O19] catalyst is strong binding of the (methyl) methylphosphonic acid ((M) MPA) product to the polyanions, which ultimately inhibits catalytic turnover.Show more - Breaking the curse of dimensionality in electronic structure methods: towards optimal utilization of the canonical polyadic decompositionPierce, Karl Martin (Virginia Tech, 2022-01-27)
Show more Despite the fact that higher-order tensors (HOTs) plague electronic structure methods and severely limits the modeling of interesting chemistry problems, introduction and application of higher-order tensor (HOT) decompositions, specifically the canonical polyadic (CP) decomposition, is fairly limited. The CP decomposition is an incredibly useful sparse tensor factorization that has the ability to disentangle all correlated modes of a tensor. However the complexities associated with CP decomposition have made its application in electronic structure methods difficult. Some of the major issues related to CP decomposition are a product of the mathematics of computing the decomposition: determining the exact CP rank is a non-polynomially hard problem, finding stationary points for rank-R approximations require non-linear optimization techniques, and inexact CP approximations can introduce a large degree of error into tensor networks. While other issues are a result of the construction of computer architectures. For example, computer processing units (CPUs) are organized in a way to maximize the efficiency of dense linear algebra and, thus, the performance of routine tensor algebra kernels, like the Khatri-Rao product, is limited. In this work, we seek to reduce the complexities associated with the CP decomposition and create a route for others to develop reduced-scaling electronic structure theory methods using the CP decomposition. In Chapter 2, we introduce the robust tensor network approximation. This approximation is a way to, in general, eliminate the leading-order error associated with approximated tensors in a network. We utilize the robust network approximation to significantly increase the accuracy of approximating density fitting (DF) integral tensors using rank-deficient CP decompositions in the particle-particle ladder (PPL) diagram of the coupled cluster method with single and double substitutions (CCSD). We show that one can produce results with negligible error in chemically relevant energy differences using a CP rank roughly the same size as the DF fitting basis; which is a significantly smaller rank requirement than found using either a nonrobust approximation or similar grid initialized CP approximations (the pseudospectral (PS) and tensor hypercontraction (THC) approximations). Introduction of the CP approximation, formally, reduces the complexity of the PPL diagram from 𝓞(N⁶) to 𝓞(N⁵) and, using the robust approximation, we are able to observe a cost reduction in CCSD calculations for systems as small as a single water molecule. In Chapter 3, we further demonstrate the utility of the robust network approximation and, in addition, we construct a scheme to optimize a grid-free CP decomposition of the order-four Coulomb integral tensor in 𝓞(N⁴) time. Using these ideas, we reduce the complexity of ten bottleneck contractions from 𝓞(N⁶) to 𝓞(N⁵) in the Laplace transform (LT) formulation of the perturbative triple, (T), correction to CCSD. We show that introducing CP into the LT (T) method with a CP rank roughly the size of the DF fitting basis reduces the cost of computing medium size molecules by a factor of about 2.5 and introduces negligible error into chemically relevant energy differences. Furthermore, we implement these low-cost algorithms using newly developed, optimized tensor algebra kernels in the massively-parallel, block-sparse TiledArray [Calvin, et. al Chemical Reviews 2021 121 (3), 1203-1231] tensor framework.Show more - Characterization of Cellulose and Chitin Thin Films and Their Interactions with Bio-based PolymersKittle, Joshua Daniel (Virginia Tech, 2012-04-02)
Show more As the two most abundant natural polymers on earth, cellulose and chitin have attracted increasing attention as a source of renewable energy and functional materials. Thin films of cellulose and chitin are useful for studying interactions of these materials with other natural and synthetic molecules via techniques such as quartz crystal microbalance with dissipation monitoring (QCM-D) and surface plasmon resonance (SPR). Because of the difficulty of extracting native cellulose, regenerated cellulose (RC), sulfated nanocrystalline cellulose (SNC), and desulfated nanocrystalline cellulose (DNC) thin films are often studied in its place. In this work, QCM-D solvent exchange studies showed that water contents of RC, SNC and DNC films were proportional to the film thickness (d). Accessibility and degradation of the films was further analyzed via substrate exposure to cellulase. Cellulase adsorption onto RC films was independent of d, whereas cellulase adsorption onto SNC and DNC films increased with d. Enhanced access to guest molecules for SNC and DNC films relative to RC films revealed they are more porous. The porosity of these cellulose films aided in understanding the observed differences of xyloglucan (XG) adsorption onto their surfaces. Xyloglucan adsorption onto RC, SNC, and DNC was studied by QCM-D and SPR. The amount of adsorbed XG increased in the order RC < SNC < DNC. XG adsorption onto RC films was independent of d, whereas XG adsorption was weakly dependent upon d for SNC films and strongly dependent upon d for DNC films. However, XG adsorbed onto "monolayer" thin films of RC, SNC, and DNC in approximately the same amount. These results suggested that the morphology and surface charge of the cellulose substrate had a limited effect upon XG adsorption and that accessible surface area of the cellulose film may be the factor leading to apparent differences in XG adsorption for different surfaces. The porosity and surface charge of SNC films presented a unique opportunity to examine polyelectrolyte adsorption and subsequent dewatering of the SNC substrate. The adsorption of a series of cationically derivatized dextran (cDex) polyelectrolytes with various degrees of substitution (DS) onto SNC was studied using QCM-D and SPR. As the hydrophobic character of the cDex samples increased, the water content of the adsorbed cDex layer decreased. For cDex with the greatest hydrophobic content, nearly 50% by mass of the initial water present in the porous SNC film was removed upon cDex adsorption. This study indicated that the water content of the film could be tailored by controlling the DS and hydrophobic character of the polyelectrolyte. This work also presents the first report of smooth, homogeneous, ultrathin chitin films, opening the door to surface studies of binding interactions, adsorption kinetics, and enzymatic degradation. The chitin films were formed by spincoating trimethylsilyl chitin onto gold or silica substrates, followed by regeneration to a chitin film. The utility of these chitin films as biosensors was evident from QCM-D and SPR studies that revealed bovine serum albumin adsorbed as a monolayer.Show more - Chemical Reactivity and Regioselectivity of Trimetallic Nitride Endohedral MetallofullerenesCai, Ting (Virginia Tech, 2008-03-26)
Show more Endohedral metallofullerenes (EMF) have attracted increasing attention during past decades for their potential applications in the fields of biomedicine and nanomaterials. Trimetallic nitride template endohedral metallofullerenes (TNT EMFs) are some of the most promising fullerene-based materials (e.g., as MRI and X-ray contrast agents) because of their high yields compared to classic endohedral metallofullerenes. This dissertation addresses the chemical reactivity and regioselectivity of TNT EMFs. Based on the extraordinarily high stability of TNT EMFs relative to empty cage fullerenes and classic endohedral metallofullerenes, macroscopic quantities of high purity TNT EMFs were obtained directly from crude soot in a single facile step by using a cyclopentadiene-functionalized resin to trap the more reactive species via Diels-Alder reactions, allowing the TNT EMFs to pass through. We also developed a support-free chemical separation method of TNT EMFs from Sc- and Lu-based soot extract that makes use of the differing solubilities of unreacted TNT EMFs versus 9-methylanthracene-derivatized empty cage fullerenes. The exohedral functionalization of metallofullerenes can fine-tune their chemical and physical properties. The first N-methylpyrrolidino derivatives of TNT EMFs (Ih Sc3N@C80 and Ih Er3N@C80) were synthesized via 1,3-dipolar cycloaddition of N-methylazomethine ylides (Prato reaction). The demonstration of planar symmetry in the N-methylpyrrolidino derivatives by 13C NMR spectroscopy suggested that the reaction exclusively took place at the 5,6-ring junction. However, both 5,6-ring and 6,6 ring junction adducts were obtained when Ih Sc3N@C80 reacted with N-triphenylmethyl-5-oxazolidinone, as characterized by NMR spectroscopy and X-ray crystallography. The kinetically favored 6,6-ring junction adduct was converted to the thermodynamic product, the 5,6-ring junction adduct, upon thermal equilibration. The synthesis of pyrrolidino derivatives was also extended to two other Sc-based TNT EMFs, D5h Sc3N@C80 and Sc3N@C78. The reactivity and regioselectivity of D5h Sc3N@C80 and Sc3N@C78 were demonstrated by NMR spectroscopy, X-ray crystallography and theoretical calculations. Another type of reaction, the Bingel-Hirsch cyclopropanation was carried out with D3h Sc3N@C78 for the first time, yielding a single Cs-symmetric monoadduct and a dominant C2v-symmetric diadduct for the first time. The symmetric diadduct clearly demonstrates the remarkable regioselectivity control exerted by the encapsulated Sc3N cluster. We employed a LUMO electron density surface computational approach to predict multiadduct docking sites on the ellipsoidal fullerene cage surface. We also successfully synthesized the first derivative of a non-IPR fullerene, the diethyl malonate derivative of Sc3N@C68 by a Bingel-Hirsch reaction. The reactivity and regioselectivity of Sc3N@C68 were investigated by NMR spectroscopy and theoretical calculations.Show more - Computational and Spectroscopic Determination of Lithiated Benzylic Nitriles in THF/HMPA SolutionHarmon, Henry Jason (Virginia Tech, 2008-09-10)
Show more The synthetic utility of nitrile-stabilized carbanions as reactive intermediates for selective carbon-carbon bond formation has prompted numerous studies toward characterization of the solution structure of these nucleophiles. In hopes of eventually gaining a better understanding of the structural properties which may mediate reactivity and selectivity, researchers have designed elegant structure elucidation strategies. These studies have offered key advancements toward the characterization of these intermediates; however, contradictory evidence has hindered unambiguous structural determination—particularly for lithiated benzylic nitriles in low dielectric, ethereal media. Chapter 1 of this dissertation presents a review of the synthetic utility of metalated nitriles and the spectroscopic and computational techniques employed to characterize their solution structure. Also reviewed herein are the controversial determinations drawn from these efforts. The research and data which follow in Chapters 2 and 3 focus on resolution of the conflicting structural determinations drawn from multinuclear magnetic resonance (NMR) and vibrational (IR and Raman) spectroscopy. Employing a strategy to slow the lithium-nitrogen exchange rate in low dielectric media, new 7Li, 31P, and 15N NMR spectroscopic evidence (with support from computational modeling) lead us to amend our previous assessments and propose that lithiated arylacetonitriles adopt an aggregated triple-ion structure in THF/hexane with sub-stoichiometric HMPA. Due to the limitations of computer resources and the effect of non-linear scaling, theoretical modeling of aggregated and solvated lithiated benzylic nitriles became impractical at the 6-31+G(d) basis set. These limitations led to the use and comparative analysis of two alternative basis sets for the DFT analysis of lithiated benzylic nitrile derivatives' 6-31(+LiX)G(d) and 6-31â +â G(d). Defined upon the principal of resonance stabilization, these basis sets were constructed by application of varying levels of computational theory on a per-atom basis. By applying higher levels of theory only to the atoms most intimately involved in the electronic distribution, "accurate" replacement models for 6-31+G(d) structures were obtained with considerable savings in computational resources. This study in basis set economy is detailed fully within Chapters 4 and 5.Show more - Computational Investigations at the Gas-Surface Interface: Organic Surface Oxidation and Hydrolysis of Chemical Warfare Agents and SimulantsChapleski Jr, Robert Charles (Virginia Tech, 2017-04-25)
Show more 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.Show more - Computational Studies of Protonated Cyclic Ethers and Benzylic Organolithium CompoundsDeora, Nipa (Virginia Tech, 2010-05-10)
Show more 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.Show more - Conformational Analysis of Fluoro-, Chloro-, and Proteo-Alkene Gly-Pro and Pro-Pro Isosteres to Mimic CollagenArcoria, Paul J.; Ware, Rachel I.; Makwana, Sunny V.; Troya, Diego; Etzkorn, Felicia A. (American Chemical Society, 2021-12-30)
Show more Collagen is the most abundant human protein, with the canonical sequence (Gly-Pro-Hyp)in its triple helix region. Cis-trans isomerization of the Xaa-Pro amide has made two of these amide bonds the target of alkene replacement: the Gly-Pro and the Pro-Hyp positions. The conformations of Gly-Pro and Pro-Pro (as a Pro-Hyp model) fluoro-, chloro-, and proteo-alkene mimic models were investigated computationally to determine whether these alkenes can stabilize the polyproline type II (PPII) conformation of collagen. Second-order Møller-Plesset (MP2) calculations with various basis sets were used to perform the conformational analyses and locate stationary points. The calculation results predict that fluoro- and chloro-alkene mimics of Gly-Pro and Pro-Pro can participate in n→π* donation to stabilize PPII conformations, yet they are poor n→π* acceptors, shifting the global minima away from PPII conformations. For the proteo-alkene mimics, the lack of significant n→π* interactions and unstable PPII-like geometries explains their known destabilization of the triple helix in collagen-like peptides._{n}Show more - Coupled-Cluster Methods for Large Molecular Systems Through Massive Parallelism and Reduced-Scaling ApproachesPeng, Chong (Virginia Tech, 2018-05-02)
Show more 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.Show more - Dynamics of Atmospherically Important Triatomics in Collisions with Model Organic SurfacesLu, Jessica Weidgin (Virginia Tech, 2011-04-08)
Show more Detailed investigations of molecular collisions at the gas-surface interface provide insight into the dynamics and mechanisms of important interfacial reactions. A thorough understanding of the fundamental interactions between a gas and surface is crucial to the study of heterogeneous chemistry of atmospheric organic aerosols. In addition to changing the chemical and physical properties of the particle, reactions with oxidizing gases may alter aerosol optical properties, with implications for the regional radiation budget and climate. Molecular beams of CO₂, NO₂ and O₃ were scattered from long-chain methyl (CH₃-), hydroxyl (OH-), vinyl (H₂C=CH-) and perfluorinated (CF₃(CF₂)₈-, or F-) ω-functionalized alkanethiol self-assembled monolayers (SAMs) on gold, to explore the reaction dynamics of atmospherically important triatomics on proxies for organic aerosols. Energy exchange and thermal accommodation during the gas-surface collision, the first step of most interfacial reactions, was probed by time-of-flight techniques. The final energy distribution of the scattered molecules was measured under specular scattering conditions (θi = θf = 30°). Overall, extent of energy transfer and accommodation was found to depend on the terminal functional group of the SAM, incident energy of the triatomics, and gas-surface intermolecular forces. Reaction dynamics studies of O3 scattering from H2C=CH-SAMs revealed that oxidation of the double bond depend significantly on O₃ translational energy. Our results indicate that the room-temperature reaction follows the Langmuir-Hinshelwood mechanism, requiring accommodation prior to reaction. The measurements also show that the dynamics transition to a direct reaction for higher translational energies. Possible environmental impacts of heterogeneous reactions were probed by evaluating the change in the optical properties of laboratory-generated benzo[a]pyrene (BaP)-coated aerosols, after exposure to NO₃ and NO₂, at 532 nm and 355 nm by three aerosol analysis techniques: cavity ring-down aerosol spectroscopy (CRD-AS) at 355 nm and 532 nm, photoacoustic spectroscopy (PAS) at 532 nm, and an aerosol mass spectrometer (AMS). Heterogeneous reactions may lead to the nitration of organic-coated aerosols, which may account for atmospheric absorbance over urban areas. Developing a detailed understanding of heterogeneous reactions on atmospheric organic aerosols will help researchers to predict the fate, lifetime, and environmental impact of atmospherically important triatomics and the particles with which they collide.Show more - Efficient automated implementation of higher-order many-body methods in quantum chemistryTeke, Nakul Kushabhau (Virginia Tech, 2023-01-31)
Show more To follow up on the unexpectedly-good performance of coupled-cluster models with approx- imate inclusion of 3-body clusters [J. Chem. Phys. 151, 064102 (2019)] we performed a more complete assessment of the 3CC method [J. Chem. Phys. 125, 204105 (2006)] for accurate computational thermochemistry in the standard HEAT framework. New spin- integrated implementation of the 3CC method applicable to closed- and open-shell systems utilizes a new automated toolchain for derivation, optimization, and evaluation of operator algebra in many-body electronic structure. We found that with a double-zeta basis set the 3CC correlation energies and their atomization energy contributions are almost always more accurate (with respect to the CCSDTQ reference) than the CCSDT model as well as the standard CCSD(T) model. The mean errors in { 3CC, CCSDT, and CCSD(T) } electronic (per valence electron) and atomization energies were {23, 69, 125} μEh/e and {0.39, 1.92, 2.57} kJ/mol, respectively. The significant and systematic reduction of the error by the 3CC method and its lower cost than CCSDT suggests it as a viable candidate for post-CCSD(T) thermochemistry application.Show more - The Efficient Computation of Field-Dependent Molecular Properties in the Frequency and Time DomainsPeyton, Benjamin Gilbert (Virginia Tech, 2022-05-31)
Show more The efficient computation of dynamic (time-dependent) molecular properties is a broad field with numerous applications in aiding molecular synthesis and design, with a particular preva- lence in spectroscopic predictions. Typical methods for computing the response of a molecu- lar system to an electromagnetic field (EMF) considers a quantum mechanical description of the molecule and a classical approximation for the EMF. Methods for describing light-matter interactions with high-accuracy electronic structure methods, such as coupled cluster (CC), are discussed, with a focus on improving the efficiency of such methods. The CC method suffers from high-degree polynomial scaling. In addition to the ground-state calculation, computing dynamic properties requires the description of sensitive excited-state effects. The cost of such methods often prohibits the accurate calculation of response prop- erties for systems of significant importance, such as large-molecule drug candidates or chiral species present in biological systems. While the literature is ripe with reduced-scaling meth- ods for CC ground-state calculations, considerably fewer approaches have been applied to excited-state properties, with even fewer still providing adequate results for realistic systems. This work presents three studies on the reduction of the cost of molecular property evalu- ations, in the hopes of closing this gap in the literature and widening the scope of current theoretical methods. There are two main ways of simulating time-dependent light-matter interactions: one may consider these effects in the frequency domain, where the response of the system to an EMF is computed directly; or, the response may be considered explicitly in the time domain, where wave function (or density) parameters can be propagated in time and examined in detail. Each methodology has unique advantages and computational bottlenecks. The first two studies focus on frequency-domain calculations, and employ fragmentation and machine- learning techniques to reduce the cost of single-molecule calculations or sets of calculations across a series of geometric conformations. The third study presents a novel application of the local correlation technique to real-time CC calculations, and highlights deficiencies and possible solutions to the approach.Show more - Energy Transfer Dynamics in Collisions of Polar and Non-polar Gases with Functionalized Self-Assembled MonolayersBennett, Megan (Virginia Tech, 2007-05-07)
Show more Molecular beam scattering experiments are used to investigate the extent of thermal accommodation of Ne, CD4, ND3, and D2O in collisions with long chain CH3, NH2, and OH terminated self-assembled monolayers (SAMs) on gold. Surface rigidity, internal degrees of freedom of the impinging gas, and potential energy surface well depths have been explored as a way to predict the outcome of a gas-surface collision. Ne is used to assess the mechanical rigidity of the SAMs. The order of rigidity is CH3 < NH2 ~ OH. The NH2 and OH terminated SAMs are more rigid due to the intermolecular hydrogen bonding structure at the gas-surface interface. Despite the hydrogen bonding nature of the NH2 and OH terminated SAMs CD4, ND3, and D2O are extensively thermally accommodated on the surfaces, therefore surface rigidity is no solely responsible for energy transfer dynamics. It was found that the number of degrees of freedom do not predict how extensively a gas will thermally accommodate on a surface capable of hydrogen bonding. A qualitative correlation between increasing potential energy well depths and the extent of thermal accommodation has been established as a result of these scattering experiments.Show more - Explicitly correlated Green's function methods for calculating electron binding energiesTeke, Nakul Kushabhau (Virginia Tech, 2019-07-29)
Show more 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.Show more - Explicitly Correlated Methods for Large Molecular SystemsPavosevic, Fabijan (Virginia Tech, 2018-02-02)
Show more 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.Show more