A computational investigation of anomeric effects in piperidine rings bearing fluoro and trifluor... more A computational investigation of anomeric effects in piperidine rings bearing fluoro and trifluoromethyl substituents shows for both compounds the most pronounced evidence of the anomeric effect, as expressed as hyperconjugative delocalization of the nitrogen lone pair, in structures with the substituent in the axial position and the N–H bond in the equatorial position. This structure is the lowest-energy structure in the fluoro case but not in the trifluoromethyl case where there is an increased axial penalty associated with the CF3 group. The anomeric effect is characterized via geometrical evidence, natural bond orbital analysis, electrostatic effects, and energetic criteria. Computational results from a variety of levels of theory are presented including CCSD(T) with complete basis set extrapolation, B2PLYP-D, ωB97XD, B97-D, M06-2X, B3LYP, and MP2 allowing for a comparison of performance. The CCSD(T)/CBS results are very well represented by either B2PLYP-D or ωB97XD with moderate to large basis sets (aug-cc-pVTZ or aug-cc-pVDZ). Hyperconjugation, electrostatic effects, and steric effects play a role in the relative energetic ordering of the isomers considered.
Despite the success of AlphaFold2 (AF2), it is unclear how AF2 models accommodate for ligand bind... more Despite the success of AlphaFold2 (AF2), it is unclear how AF2 models accommodate for ligand binding. Here, we start with a protein sequence from Acidimicrobiaceae TMED77 (T7RdhA) with potential for catalyzing the degradation of per- and polyfluoroalkyl substances (PFASs). AF2 models and experiments identified T7RdhA as a corrinoid iron-sulfur protein (CoFeSP) which uses a norpseudo-cobalamin (BVQ) cofactor and two [4Fe4S] iron-sulfur clusters (SF4) for catalysis. Docking and molecular dynamics simulations suggest that T7RdhA uses perfluorooctanoic acetate (PFOA) as a substrate, supporting the reported defluorination activity of its homolog, A6RdhA. We showed that AF2 provides processual (dynamic) predictions for the binding pockets of ligands (cofactors and/or substrates). Because the pLDDT scores provided by AF2 reflect the protein native states in complex with ligands as the evolutionary constraints, the Evoformer network of AF2 predicts protein structures and residue flexibility...
Detailed physical and mechanical characterization of the matrix as well as the interphases of pol... more Detailed physical and mechanical characterization of the matrix as well as the interphases of polymer matrix composites can lead to a more complete understanding of failure mechanisms in polymer matrix composite (PMC). This study illustrates mechanical damage of polymers in both the bulk, as well as around the interphase region through integrated computation & experimentation approach. We have developed a quantum mechanics-molecular dynamics framework, which has enabled the prediction of bond scission under load, creation of intermittent free radicals, and exploration of the potential energy surface for possible secondary reactions immediately following bond scission. In parallel, we have conducted experiments with epoxy systems with varying molecular weight and cross-linker density at different load conditions to benchmark the simulation findings of the chemical species present on fracture surfaces of the polymer. In order to evaluate experimentally molecular level effects of mecha...
Author Institution: Chemical Sciences and Engineering Division, Argonne National Laboratory, Argo... more Author Institution: Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL, 60439; High Performance Technologies, Inc., 2435 5th St., WPAFB, Ohio, 45433
Ab initio molecular dynamics was used to estimate the response to constant imposed strain on a sh... more Ab initio molecular dynamics was used to estimate the response to constant imposed strain on a short polyethylene (PE) chain and a radical chain with a removed hydrogen atom. Two independent types of simulations were run. In the first case, the chains were strained by expanding a periodic cell, restraining the length but allowing the internal degrees of freedom to reach equilibrium. From these simulations, the average force on the chain was computed, and the resulting force was integrated to determine the Helmholtz free energy for chain stretching. In the second set of simulations, chains were constrained to various lengths, while a bond was restrained at various bond lengths using umbrella sampling. This provided free energy of bond scission for various chain strains. The sum of the two free energy functions results in an approximation of the free energy of chain scission under various strains and gives a realistic and new picture of the effect of chain strain on bond breaking. Uni...
Vitrimers hold great promise as adaptive materials capable of shape reconfigurability, welding, a... more Vitrimers hold great promise as adaptive materials capable of shape reconfigurability, welding, and self-healing due to dynamic covalent reactions occurring above the vitrimer transition temperatur...
The core part of the program system COLUMBUS allows highly efficient calculations using variation... more The core part of the program system COLUMBUS allows highly efficient calculations using variational multireference (MR) methods in the framework of configuration interaction with single and double excitations (MR-CISD) and averaged quadratic coupled-cluster calculations (MR-AQCC), based on uncontracted sets of configurations and the graphical unitary group approach (GUGA). The availability of analytic MR-CISD and MR-AQCC energy gradients and analytic nonadiabatic couplings for MR-CISD enables exciting applications including, e.g., investigations of π-conjugated biradicaloid compounds, calculations of multitudes of excited states, development of diabatization procedures, and furnishing the electronic structure information for on-the-fly surface nonadiabatic dynamics. With fully variational uncontracted spin-orbit MRCI, COLUMBUS provides a unique possibility of performing high-level calculations on compounds containing heavy atoms up to lanthanides and actinides. Crucial for carrying ...
Analytic gradients of electronic eigenvalues require one calculation per nuclear geometry, compar... more Analytic gradients of electronic eigenvalues require one calculation per nuclear geometry, compared to at least 3n + 1 calculations for finite difference methods, where n is the number of nuclei. Analytic nonadiabatic derivative coupling terms (DCTs), which are calculated in a similar fashion, are used to remove nondiagonal contributions to the kinetic energy operator, leading to more accurate nuclear dynamics calculations than those that employ the Born-Oppenheimer approximation, i.e., that assume off-diagonal contributions are zero. The current methods and underpinnings for calculating both of these quantities, gradients and DCTs, for the State-Averaged MultiReference Configuration Interaction with Singles and Doubles (MRCI-SD) wavefunctions in COLUMBUS are reviewed. Before this work, these methods were not available for wavefunctions of a relativistic MRCI-SD Hamiltonian. Calculation of these terms is critical in successfully modeling the dynamics of systems that depend on transi...
Density functional theory (DFT) is used to establish the ground-state structure of the self-trapp... more Density functional theory (DFT) is used to establish the ground-state structure of the self-trapped hole (STH) in KH<sub>2</sub>PO<sub>4</sub> crystals. The STHs in this nonlinear optical material are free small polarons, a fundamental intrinsic point defect. They are produced with ionizing radiation in the low-temperature orthorhombic structure of KH<sub>2</sub>PO<sub>4</sub> and are only stable (i.e., long-lived) below approximately 70 K. A large 129-atom cluster, K<sub>19</sub>H<sub>40</sub>P<sub>14</sub>O<sub>56</sub>, is constructed to model the self-trapped hole. The ωB97XD functional with the 6-31+G* basis set is used and geometry optimization is performed. Our results show that two of the oxygen ions in a PO<sub>4</sub> unit relax toward each other and equally share the hole. These two oxygen ions do not initially have close hydrogen neighbors. This equal sharing of the hole is related to the presence of isolated, slightly distorted, PO<sub>4</sub> units and is significantly different from the small-polaron behavior often observed in other oxide crystals where the hole is localized on only one oxygen ion. The computational results provide a detailed description of the lattice relaxation occurring during formation of the self-trapped hole. Characteristic spectral features of this defect are a larger hyperfine interaction with one <sup>31</sup>P nucleus and equal, but smaller, hyperfine interactions with two <sup>1</sup>H nuclei. The computed values for these isotropic and anisotropic hyperfine coupling constants are in excellent agreement with results obtained from electron paramagnetic resonance (EPR) experiments.
Conference Proceedings of the Society for Experimental Mechanics Series, 2016
There is limited experimental evidence that fracture nucleation in polymers includes a small numb... more There is limited experimental evidence that fracture nucleation in polymers includes a small number of covalent bond scissions followed by rapid void growth by chemo-mechanical processes. Generalized criteria for predicting such bond scission, then, would help anticipate fracture in polymer matrix composites. Strain states at incipient bond scission for thermoset resins in plane stress are here predicted by atomistic simulation. Several cured epoxy systems were examined, each having a different chain length. For biaxial extension and a portion of the shearing regime, scission occurs at a critical value of the larger principal strain. This value increases with increasing chain length. The corresponding dilatation is largest for biaxial extension and decreases to nearly zero for pure shear. Results are compared with strain invariants at fracture measured from experiments in which polymer matrix composites having various ply stacking sequences were loaded to rupture.
Electron transfer (ET) through oxidized (QOPV) and reduced-protonated (HQOPV) forms of oligo(phen... more Electron transfer (ET) through oxidized (QOPV) and reduced-protonated (HQOPV) forms of oligo(phenylene vinylene) quinone placed between two gold electrodes in the absence and presence of external water molecules is calculated using density functional theory with a ...
Miniaturization of electronic devices to the level of single molecules requires detailed understa... more Miniaturization of electronic devices to the level of single molecules requires detailed understanding of the mechanisms of their operation. One of the questions here is the identification of the role of structural alterations in charge separation and stabilization in photoactive complexes. To address this question, we calculate optimized molecular and electronic structures, and optical and vibrational spectra of l,l′‐dimethyl 4,4′‐bipyridinium—bis tetraphenylborate PQ(BPh4)2 complex ab initio using density functional theory approach and compare them with the experimentally observed UV–Vis and Raman spectra of the molecules in solid‐state films. The results indicate that the association of PQ and BPh4 leads to the formation of an internally ionized structure that is accompanied by the structural reorganization of both PQ (the twisting of pyridinium rings) and BPh4 (phenyl rings rotation) moieties. The quanta of light do not seem to be directly involved in the formation of this ioniz...
We have used a second-order perturbation treatment of the Dirac–Coulomb–Hartree–Fock method to es... more We have used a second-order perturbation treatment of the Dirac–Coulomb–Hartree–Fock method to estimate relativistic contributions to energies in the G2/97 test set. The one-electron relativistic effect on atomization energies of molecules containing first- and second-row atoms nearly always reduces binding. When the relativistic corrections are included in G3 theory and assessed on the G2/97 test set, there is little change in overall performance.
Stationary direct perturbation theory is used to calculate a scalar relativistic correction to th... more Stationary direct perturbation theory is used to calculate a scalar relativistic correction to the species in the G3/99 test set. We observe that the relativistic energy almost always reduces atomization energies, electron affinities, and ionization potentials. Exceptions occur when s orbitals play a predominant role in the energy differences between reactants and products. The scalar relativistic energy, when added to G3 theory and the empirical parameters are reoptimized, gives slightly worse agreement with experiment.
Gaussian-3 (G3) theory is extended to molecules containing the third-row nontransition elements K... more Gaussian-3 (G3) theory is extended to molecules containing the third-row nontransition elements K, Ca, Ga–Kr. Basis sets compatible with those used in G3 theory for molecules containing first- and second-row atoms have been derived. The G3 average absolute deviation from experiment for a set of 47 test reactions containing these elements is 0.94 kcal/mol. This is a substantial improvement over Gaussian-2 theory, which has an average absolute deviation of 1.43 kcal/mol for the same set. Variations of G3 theory are also presented that are based on reduced orders of perturbation theory. These variations also show similar improvement over the corresponding G2 methods. The use of scaling parameters in G3 theory for the third row was investigated and found to perform nearly as well as use of the higher level correction. In addition, these methods are evaluated on a set of molecules containing K and Ca for which the experimental data are not accurate enough for them to be included in the t...
A computational investigation of anomeric effects in piperidine rings bearing fluoro and trifluor... more A computational investigation of anomeric effects in piperidine rings bearing fluoro and trifluoromethyl substituents shows for both compounds the most pronounced evidence of the anomeric effect, as expressed as hyperconjugative delocalization of the nitrogen lone pair, in structures with the substituent in the axial position and the N–H bond in the equatorial position. This structure is the lowest-energy structure in the fluoro case but not in the trifluoromethyl case where there is an increased axial penalty associated with the CF3 group. The anomeric effect is characterized via geometrical evidence, natural bond orbital analysis, electrostatic effects, and energetic criteria. Computational results from a variety of levels of theory are presented including CCSD(T) with complete basis set extrapolation, B2PLYP-D, ωB97XD, B97-D, M06-2X, B3LYP, and MP2 allowing for a comparison of performance. The CCSD(T)/CBS results are very well represented by either B2PLYP-D or ωB97XD with moderate to large basis sets (aug-cc-pVTZ or aug-cc-pVDZ). Hyperconjugation, electrostatic effects, and steric effects play a role in the relative energetic ordering of the isomers considered.
Despite the success of AlphaFold2 (AF2), it is unclear how AF2 models accommodate for ligand bind... more Despite the success of AlphaFold2 (AF2), it is unclear how AF2 models accommodate for ligand binding. Here, we start with a protein sequence from Acidimicrobiaceae TMED77 (T7RdhA) with potential for catalyzing the degradation of per- and polyfluoroalkyl substances (PFASs). AF2 models and experiments identified T7RdhA as a corrinoid iron-sulfur protein (CoFeSP) which uses a norpseudo-cobalamin (BVQ) cofactor and two [4Fe4S] iron-sulfur clusters (SF4) for catalysis. Docking and molecular dynamics simulations suggest that T7RdhA uses perfluorooctanoic acetate (PFOA) as a substrate, supporting the reported defluorination activity of its homolog, A6RdhA. We showed that AF2 provides processual (dynamic) predictions for the binding pockets of ligands (cofactors and/or substrates). Because the pLDDT scores provided by AF2 reflect the protein native states in complex with ligands as the evolutionary constraints, the Evoformer network of AF2 predicts protein structures and residue flexibility...
Detailed physical and mechanical characterization of the matrix as well as the interphases of pol... more Detailed physical and mechanical characterization of the matrix as well as the interphases of polymer matrix composites can lead to a more complete understanding of failure mechanisms in polymer matrix composite (PMC). This study illustrates mechanical damage of polymers in both the bulk, as well as around the interphase region through integrated computation & experimentation approach. We have developed a quantum mechanics-molecular dynamics framework, which has enabled the prediction of bond scission under load, creation of intermittent free radicals, and exploration of the potential energy surface for possible secondary reactions immediately following bond scission. In parallel, we have conducted experiments with epoxy systems with varying molecular weight and cross-linker density at different load conditions to benchmark the simulation findings of the chemical species present on fracture surfaces of the polymer. In order to evaluate experimentally molecular level effects of mecha...
Author Institution: Chemical Sciences and Engineering Division, Argonne National Laboratory, Argo... more Author Institution: Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, IL, 60439; High Performance Technologies, Inc., 2435 5th St., WPAFB, Ohio, 45433
Ab initio molecular dynamics was used to estimate the response to constant imposed strain on a sh... more Ab initio molecular dynamics was used to estimate the response to constant imposed strain on a short polyethylene (PE) chain and a radical chain with a removed hydrogen atom. Two independent types of simulations were run. In the first case, the chains were strained by expanding a periodic cell, restraining the length but allowing the internal degrees of freedom to reach equilibrium. From these simulations, the average force on the chain was computed, and the resulting force was integrated to determine the Helmholtz free energy for chain stretching. In the second set of simulations, chains were constrained to various lengths, while a bond was restrained at various bond lengths using umbrella sampling. This provided free energy of bond scission for various chain strains. The sum of the two free energy functions results in an approximation of the free energy of chain scission under various strains and gives a realistic and new picture of the effect of chain strain on bond breaking. Uni...
Vitrimers hold great promise as adaptive materials capable of shape reconfigurability, welding, a... more Vitrimers hold great promise as adaptive materials capable of shape reconfigurability, welding, and self-healing due to dynamic covalent reactions occurring above the vitrimer transition temperatur...
The core part of the program system COLUMBUS allows highly efficient calculations using variation... more The core part of the program system COLUMBUS allows highly efficient calculations using variational multireference (MR) methods in the framework of configuration interaction with single and double excitations (MR-CISD) and averaged quadratic coupled-cluster calculations (MR-AQCC), based on uncontracted sets of configurations and the graphical unitary group approach (GUGA). The availability of analytic MR-CISD and MR-AQCC energy gradients and analytic nonadiabatic couplings for MR-CISD enables exciting applications including, e.g., investigations of π-conjugated biradicaloid compounds, calculations of multitudes of excited states, development of diabatization procedures, and furnishing the electronic structure information for on-the-fly surface nonadiabatic dynamics. With fully variational uncontracted spin-orbit MRCI, COLUMBUS provides a unique possibility of performing high-level calculations on compounds containing heavy atoms up to lanthanides and actinides. Crucial for carrying ...
Analytic gradients of electronic eigenvalues require one calculation per nuclear geometry, compar... more Analytic gradients of electronic eigenvalues require one calculation per nuclear geometry, compared to at least 3n + 1 calculations for finite difference methods, where n is the number of nuclei. Analytic nonadiabatic derivative coupling terms (DCTs), which are calculated in a similar fashion, are used to remove nondiagonal contributions to the kinetic energy operator, leading to more accurate nuclear dynamics calculations than those that employ the Born-Oppenheimer approximation, i.e., that assume off-diagonal contributions are zero. The current methods and underpinnings for calculating both of these quantities, gradients and DCTs, for the State-Averaged MultiReference Configuration Interaction with Singles and Doubles (MRCI-SD) wavefunctions in COLUMBUS are reviewed. Before this work, these methods were not available for wavefunctions of a relativistic MRCI-SD Hamiltonian. Calculation of these terms is critical in successfully modeling the dynamics of systems that depend on transi...
Density functional theory (DFT) is used to establish the ground-state structure of the self-trapp... more Density functional theory (DFT) is used to establish the ground-state structure of the self-trapped hole (STH) in KH<sub>2</sub>PO<sub>4</sub> crystals. The STHs in this nonlinear optical material are free small polarons, a fundamental intrinsic point defect. They are produced with ionizing radiation in the low-temperature orthorhombic structure of KH<sub>2</sub>PO<sub>4</sub> and are only stable (i.e., long-lived) below approximately 70 K. A large 129-atom cluster, K<sub>19</sub>H<sub>40</sub>P<sub>14</sub>O<sub>56</sub>, is constructed to model the self-trapped hole. The ωB97XD functional with the 6-31+G* basis set is used and geometry optimization is performed. Our results show that two of the oxygen ions in a PO<sub>4</sub> unit relax toward each other and equally share the hole. These two oxygen ions do not initially have close hydrogen neighbors. This equal sharing of the hole is related to the presence of isolated, slightly distorted, PO<sub>4</sub> units and is significantly different from the small-polaron behavior often observed in other oxide crystals where the hole is localized on only one oxygen ion. The computational results provide a detailed description of the lattice relaxation occurring during formation of the self-trapped hole. Characteristic spectral features of this defect are a larger hyperfine interaction with one <sup>31</sup>P nucleus and equal, but smaller, hyperfine interactions with two <sup>1</sup>H nuclei. The computed values for these isotropic and anisotropic hyperfine coupling constants are in excellent agreement with results obtained from electron paramagnetic resonance (EPR) experiments.
Conference Proceedings of the Society for Experimental Mechanics Series, 2016
There is limited experimental evidence that fracture nucleation in polymers includes a small numb... more There is limited experimental evidence that fracture nucleation in polymers includes a small number of covalent bond scissions followed by rapid void growth by chemo-mechanical processes. Generalized criteria for predicting such bond scission, then, would help anticipate fracture in polymer matrix composites. Strain states at incipient bond scission for thermoset resins in plane stress are here predicted by atomistic simulation. Several cured epoxy systems were examined, each having a different chain length. For biaxial extension and a portion of the shearing regime, scission occurs at a critical value of the larger principal strain. This value increases with increasing chain length. The corresponding dilatation is largest for biaxial extension and decreases to nearly zero for pure shear. Results are compared with strain invariants at fracture measured from experiments in which polymer matrix composites having various ply stacking sequences were loaded to rupture.
Electron transfer (ET) through oxidized (QOPV) and reduced-protonated (HQOPV) forms of oligo(phen... more Electron transfer (ET) through oxidized (QOPV) and reduced-protonated (HQOPV) forms of oligo(phenylene vinylene) quinone placed between two gold electrodes in the absence and presence of external water molecules is calculated using density functional theory with a ...
Miniaturization of electronic devices to the level of single molecules requires detailed understa... more Miniaturization of electronic devices to the level of single molecules requires detailed understanding of the mechanisms of their operation. One of the questions here is the identification of the role of structural alterations in charge separation and stabilization in photoactive complexes. To address this question, we calculate optimized molecular and electronic structures, and optical and vibrational spectra of l,l′‐dimethyl 4,4′‐bipyridinium—bis tetraphenylborate PQ(BPh4)2 complex ab initio using density functional theory approach and compare them with the experimentally observed UV–Vis and Raman spectra of the molecules in solid‐state films. The results indicate that the association of PQ and BPh4 leads to the formation of an internally ionized structure that is accompanied by the structural reorganization of both PQ (the twisting of pyridinium rings) and BPh4 (phenyl rings rotation) moieties. The quanta of light do not seem to be directly involved in the formation of this ioniz...
We have used a second-order perturbation treatment of the Dirac–Coulomb–Hartree–Fock method to es... more We have used a second-order perturbation treatment of the Dirac–Coulomb–Hartree–Fock method to estimate relativistic contributions to energies in the G2/97 test set. The one-electron relativistic effect on atomization energies of molecules containing first- and second-row atoms nearly always reduces binding. When the relativistic corrections are included in G3 theory and assessed on the G2/97 test set, there is little change in overall performance.
Stationary direct perturbation theory is used to calculate a scalar relativistic correction to th... more Stationary direct perturbation theory is used to calculate a scalar relativistic correction to the species in the G3/99 test set. We observe that the relativistic energy almost always reduces atomization energies, electron affinities, and ionization potentials. Exceptions occur when s orbitals play a predominant role in the energy differences between reactants and products. The scalar relativistic energy, when added to G3 theory and the empirical parameters are reoptimized, gives slightly worse agreement with experiment.
Gaussian-3 (G3) theory is extended to molecules containing the third-row nontransition elements K... more Gaussian-3 (G3) theory is extended to molecules containing the third-row nontransition elements K, Ca, Ga–Kr. Basis sets compatible with those used in G3 theory for molecules containing first- and second-row atoms have been derived. The G3 average absolute deviation from experiment for a set of 47 test reactions containing these elements is 0.94 kcal/mol. This is a substantial improvement over Gaussian-2 theory, which has an average absolute deviation of 1.43 kcal/mol for the same set. Variations of G3 theory are also presented that are based on reduced orders of perturbation theory. These variations also show similar improvement over the corresponding G2 methods. The use of scaling parameters in G3 theory for the third row was investigated and found to perform nearly as well as use of the higher level correction. In addition, these methods are evaluated on a set of molecules containing K and Ca for which the experimental data are not accurate enough for them to be included in the t...
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Papers by Gary Kedziora