Genetic Algorithm Driven Force Field Parameterization for Molten Alkali-Metal Carbonate and Hydroxide Salts.

Molten alkali-metal carbonates and hydroxides play important roles in the molten carbonate fuel cell and in Earth's geochemistry. Molecular simulations allow us to study these systems at extreme conditions without the need for difficult experimentation. Using a genetic algorithm to fit ab intio molecular dynamics-computed densities and radial distribution functions, as well as experimental enthalpies of formation, we derive new classical force fields able to accurately predict liquid chemical potentials. These fitting properties were chosen to ensure accurate liquid phase structure and energetics. Although the predicted dynamics is slow when compared to experiments, in general the trends in dynamic properties across different systems still hold true. In addition, these newly parametrized force fields can be extended to the molten carbonate-hydroxide mixtures by using standard combining rules.

Pair-distribution-function guided optimization of fingerprints for atom-centered neural network potentials.

Atom-centered neural network (ANN) potentials have shown promise in computational simulations and are recognized as both efficient and sufficiently accurate to describe systems involving bond formation and breaking. A key step in the development of ANN potentials is to represent atomic coordinates as suitable inputs for a neural network, commonly described as fingerprints. The accuracy and efficiency of the ANN potentials depend strongly on the selection of these fingerprints. Here, we propose an optimization strategy of atomic fingerprints to improve the performance of ANN potentials. Specifically, a set of fingerprints is optimized to fit a set of pre-selected template functions in the f*g space, where f and g are the fingerprint and the pair distribution function for each type of interatomic interaction (e.g., a pair or 3-body). With such an optimization strategy, we have developed an ANN potential for the Pd13H2 nanoparticle system that exhibits a significant improvement to the one based upon standard template functions. We further demonstrate that the ANN potential can be used with the adaptive kinetic Monte Carlo method, which has strict requirements for the smoothness of the potential. The algorithm proposed here facilitates the development of better ANN potentials, which can broaden their application in computational simulations.

Small Pore Aluminosilicate EMM-37: Synthesis and Structure Determination Using Continuous Rotation Electron Diffraction.

A new aluminosilicate zeolite, denoted EMM-37, with a 3D small pore channel system, has been synthesized using a diquaternary ammonium molecule as the structure directing agent (SDA) and metakaolin as the aluminum source. The structures of both as-made and calcined forms of EMM-37 were solved and refined using continuous rotation electron diffraction (cRED) data. cRED is a powerful method for the collection of 3D electron diffraction data from submicron- and nanosized crystals, which allows for successful solution and refinement of complex structures in symmetry as low as P1̅.

Adaptive kinetic Monte Carlo simulations of surface segregation in PdAu nanoparticles.

Surface segregation in bimetallic nanoparticles (NPs) is critically important for their catalytic activity because the activity is largely determined by the surface composition. Little, however, is known about the atomic scale mechanisms and kinetics of surface segregation. One reason is that it is hard to resolve atomic rearrangements experimentally. It is also difficult to model surface segregation at the atomic scale because the atomic rearrangements can take place on time scales of seconds or minutes - much longer than can be modeled with molecular dynamics. Here we use the adaptive kinetic Monte Carlo (AKMC) method to model the segregation dynamics in PdAu NPs over experimentally relevant time scales, and reveal the origin of kinetic stability of the core@shell and random alloy NPs at the atomic level. Our focus on PdAu NPs is motivated by experimental work showing that both core@shell and random alloy PdAu NPs with diameters of less than 2 nm are stable, indicating that one of these structures must be metastable and kinetically trapped. Our simulations show that both the Au@Pd and the PdAu random alloy NPs are metastable and kinetically trapped below 400 K over time scales of hours. These AKMC simulations provide insight into the energy landscape of the two NP structures, and the diffusion mechanisms that lead to segregation. In the core-shell NP, surface segregation occurs primarily on the (100) facet through both a vacancy-mediated and a concerted mechanism. The system becomes kinetically trapped when all corner sites in the core of the NP are occupied by Pd atoms. Higher energy barriers are required for further segregation, so that the metastable NP has a partially alloyed shell. In contrast, surface segregation in the random alloy PdAu NP is suppressed because the random alloy NP has reduced strain as compared to the Au@Pd NP, and the segregation mechanisms in the alloy require more elastic energy for exchange of Pd and Au and between the surface and subsurface.

Using Force Matching To Determine Reactive Force Fields for Water under Extreme Thermodynamic Conditions.

We present a method for the creation of classical force fields for water under dissociative thermodynamic conditions by force matching to molecular dynamics trajectories from Kohn-Sham density functional theory (DFT). We apply our method to liquid water under dissociative conditions, where molecular lifetimes are less than 1 ps, and superionic water, where hydrogen ions diffuse at liquid-like rates through an oxygen lattice. We find that, in general, our new models are capable of accurately reproducing the structural and dynamic properties computed from DFT, as well as the molecular concentrations and lifetimes. Overall, our force-matching approach presents a relatively simple way to create classical reactive force fields for a single thermodynamic state point that largely retains the accuracy of DFT while having the potential to access experimental time and length scales.

Using force-matched potentials to improve the accuracy of density functional tight binding for reactive conditions.

We show that force matching can be used to determine accurate empirical repulsive energies for the density functional tight binding method (DFTB) for chemical reactivity in condensed phases. Our approach yields improved results over previous parametrizations for molten liquid carbon and a phenolic polymer under combustion conditions. The method we present here allows for predictions of chemical properties over longer time periods than accessible via Kohn-Sham density functional theory while retaining its accuracy.

A fixed-node diffusion Monte Carlo study of the 1,2,3-tridehydrobenzene triradical.

The electronic structure of 1,2,3-tridehydrobenzene was investigated using quantum Monte Carlo methods. The radical contains two low-lying electronic states that are nearly degenerate adiabatically (within 2 kcal/mol separation), according to previous coupled cluster calculations. We performed Diffusion Monte Carlo (DMC) calculations starting from Multi-Reference Configuration Interaction (MRCI) trial wavefunctions, with a complete active space (CAS) containing 9 electrons in 9 orbitals, CAS(9,9). Our converged DMC results are in close agreement with the best coupled-cluster results, and further strengthen the assignment of a (2)A1 ground state.

Molecular recognition of aromatic rings by flavin: electrostatics and dispersion determine ring positioning above isoalloxazine.

Aromatic stacking interactions between isoalloxazine (ISA) of flavin and three prototypical aromatics (benzene, pyridine, chlorobenzene) were investigated using electronic structure calculations with Monte Carlo simulated annealing. The Effective Fragment Potential (EFP) method was used to locate the low-energy equilibrium configurations for the three dimer systems. These structures were further characterized through DFT (M06-2X) and MP2 calculations. One equilibrium configuration exists for ISA-benzene; characterizing the stacked dimer surface revealed a steep, single-welled potential that funnels benzene directly between rings II and III, positioning a substituent hydrogen adjacent to the redox-active N5. ISA-pyridine and ISA-chlorobenzene minimum-energy structures contain the aromatic ring in very similar position to that in ISA-benzene. However, the added rotational degree of freedom leads to two distinct binding motifs, having approximately antiparallel or parallel dipole moment alignment with ISA. The existence of the latter binding configuration was unexpected but is explained by the shape of the ISA electrostatic potential. Dispersion is the primary noncovalent interaction driving the positioning of aromatic rings above ISA, while electrostatics determine the orientation in dipole-containing substituted benzenes. The interplay of these interactions can be used to tune molecular recognition properties of synthetic redox cofactors, including positioning desired functional groups adjacent to the redox-active N5.

Comparison and analysis of zinc and cobalt-based systems as catalytic entities for the hydration of carbon dioxide.

In nature, the zinc metalloenzyme carbonic anhydrase II (CAII) efficiently catalyzes the conversion of carbon dioxide (CO2) to bicarbonate under physiological conditions. Many research efforts have been directed towards the development of small molecule mimetics that can facilitate this process and thus have a beneficial environmental impact, but these efforts have met very limited success. Herein, we undertook quantum mechanical calculations of four mimetics, 1,5,9-triazacyclododedacane, 1,4,7,10-tetraazacyclododedacane, tris(4,5-dimethyl-2-imidazolyl)phosphine, and tris(2-benzimidazolylmethyl)amine, in their complexed form either with the Zn(2+) or the Co(2+) ion and studied their reaction coordinate for CO2 hydration. These calculations demonstrated that the ability of the complex to maintain a tetrahedral geometry and bind bicarbonate in a unidentate manner were vital for the hydration reaction to proceed favorably. Furthermore, these calculations show that the catalytic activity of the examined zinc complexes was insensitive to coordination states for zinc, while coordination states above four were found to have an unfavorable effect on product release for the cobalt counterparts.

Computational Analysis of a Zn-Bound Tris(imidazolyl) Calix[6]arene Aqua Complex: Toward Incorporating Second-Coordination Sphere Effects into Carbonic Anhydrase Biomimetics.

Molecular dynamics simulations and quantum-mechanical calculations were performed to characterize a supramolecular tris(imidazolyl) calix[6]arene Zn(2+) aqua complex, as a biomimetic model for the catalyzed hydration of carbon dioxide to bicarbonate, H2O + CO2 → H(+) + HCO3(-). On the basis of potential-of-mean-force (PMF) calculations, stable conformations had distorted 3-fold symmetry and supported either one or zero encapsulated water molecules. The conformation with an encapsulated water molecule is calculated to be lower in free energy than the conformation with an empty cavity (ΔG = 1.2 kcal/mol) and is the calculated free-energy minimum in solution. CO2 molecule partitioning into the cavity is shown to be very facile, proceeding with a barrier of 1.6 kcal/mol from a weak encounter complex which stabilizes the species by about 1.0 kcal/mol. The stabilization energy of CO2 is calculated to be larger than that of H2O (ΔΔG = 1.4 kcal/mol), suggesting that the complex will preferentially encapsulate CO2 in solution. In contrast, the PMF for a bicarbonate anion entering the cavity is calculated to be repulsive in all nonbonding regions of the cavity, due to the diameter of the calix[6]arene walls. Geometry optimization of the Zn-bound hydroxide complex with an encapsulated CO2 molecule showed that multiple noncovalent interactions direct the reactants into optimal position for nucleophilic addition to occur. The calixarene complex is a structural mimic of the hydrophilic/hydrophobic divide in the enzyme, providing a functional effect for CO2 addition in the catalytic cycle. The results show that Zn-binding calix[6]arene scaffolds can be potential synthetic biomimetics for CO2 hydration catalysis, both in terms of preferentially encapsulating CO2 from solution and by spatially fixing the reactive species inside the cavity.

Toward a small molecule, biomimetic carbonic anhydrase model: theoretical and experimental investigations of a panel of zinc(II) aza-macrocyclic catalysts.

A panel of five zinc-chelated aza-macrocycle ligands and their ability to catalyze the hydration of carbon dioxide to bicarbonate, H(2)O + CO(2) → H(+) + HCO(3)(­), was investigated using quantum-mechanical methods and stopped-flow experiments. The key intermediates in the reaction coordinate were optimized using the M06-2X density functional with aug-cc-pVTZ basis set. Activation energies for the first step in the catalytic cycle, nucleophilic CO(2) addition, were calculated from gas-phase optimized transition-state geometries. The computationally derived trend in activation energies was found to not correspond with the experimentally observed rates. However, activation energies for the second, bicarbonate release step, which were estimated using calculated bond dissociation energies, provided good agreement with the observed trend in rate constants. Thus, the joint theoretical and experimental results provide evidence that bicarbonate release, not CO(2) addition, may be the rate-limiting step in CO(2) hydration by zinc complexes of aza-macrocyclic ligands. pH-independent rate constants were found to increase with decreasing Lewis acidity of the ligand-Zn complex, and the trend in rate constants was correlated with molecular properties of the ligands. It is suggested that tuning catalytic efficiency through the first coordination shell of Zn(2+) ligands is predominantly a balance between increasing charge-donating character of the ligand and maintaining the catalytically relevant pK(a) below the operating pH.

Ab initio calculation of the photoelectron spectra of the hydroxycarbene diradicals.

Photoelectron spectra of the cis and trans isomers of HCOH were computed using vibrational wave functions calculated by diagonalizing the Watson Hamiltonian, including up to four mode couplings. The full-dimensional CCSD(T)/cc-pVTZ potential energy surfaces were employed in the calculation. Photoionization induces significant changes in equilibrium structures, which results in long progressions in the nu(5), nu(4), and nu(3) modes. The two isomers show progressions in different modes, which leads to qualitatively distinguishable spectra. The spectra were also calculated in the double harmonic parallel-mode (i.e, neglecting Duschinsky rotation) approximation. Calculating displacements along the normal coordinates of the cation state was found to give a better approximation to the vibrational configuration interaction spectrum; this is due to the effects of Duschinsky rotations on the vibrational wave functions.

Multiphoton ionization and dissociation of diazirine: a theoretical and experimental study.

Multiphoton ionization and dissociation processes in diazirine have been studied experimentally via 304-325 nm two-photon absorption and theoretically by using the EOM-CCSD and B3LYP methods. The electronic structure calculations identified two excited valence states and four Rydberg states in the region 4.0-8.5 eV. In one-photon excitation, the strongest absorption is to the 2(1)A(1)(3p(x) <-- n) Rydberg state, whereas in two-photon absorption at comparable energies the first photon excites the low-lying 1(1)B(2) (pi* <-- n) valence state, from which the strongest absorption is to the dissociative valence 1(1)A(2) (pi* <-- sigma(NN)) state. The diazirine ion is calculated to be rather unstable, with a binding energy of only 0.73 eV and a geometry that resembles a weakly bound CH(2)(+)...N(2) complex. In the experimental studies, resonance-enhanced multiphoton ionization (REMPI) experiments show no ions at the parent diazirine mass but only CH(2)(+) ions from dissociative photoionization. It is proposed that weak one-photon absorption to the 1(1)B(2) state is immediately followed by more efficient absorption of another photon to reach the 1(1)A(2) state from which competition between ionization and fast dissociation takes place. Strong signals of CH(+) ions are also detected and assigned to 2 + 1 REMPI via the D(2)Pi (v' = 2) <-- <-- X(2)Pi (v'' = 0) two-photon transition of CH fragments. Velocity map CH(+) images show that CH(X, v'' = 0, N'') fragments are born with substantial translational energy, indicating that they arise from absorption of two photons in diazirine. It is argued that two-photon processes via the 1(1)B(2) intermediate state are very efficient in this wavelength range, leading predominantly to dissociation of diazirine from the 1(1)A(2) state. The most likely route to CH(X) formation is isomerization to isodiazirine followed by dissociation to CH + HN(2). In agreement with other theoretical papers, we recommend revisions of the heats of formation of diazirine and diazomethane.

Effect of a heteroatom on bonding patterns and triradical stabilization energies of 2,4,6-tridehydropyridine versus 1,3,5-tridehydrobenzene.

Electronic structure of 2,4,6-tridehydropyridine and isoelectronic 1,3,5-tridehydrobenzene is characterized by the equation-of-motion spin-flip coupled-cluster calculations with single and double substitutions and including perturbative triple corrections. Equilibrium geometries of the three lowest electronic states, vertical and adiabatic states ordering, and triradical stabilization energies are reported for both triradicals. In 1,3,5-tridehydrobenzene, the ground (2)A(1) state is 0.016 eV below the (2)B(2) state, whereas in 2,4,6-tridehydropyridine the heteroatom reverses adiabatic state ordering bringing (2)B(2) below (2)A(1) by 0.613 eV. The adiabatic doublet-quartet gap of 2,4,6-tridehydropyridine is smaller than that of 1,3,5-tridehydrobenzene by 0.08 eV; the respective values are 1.223 and 1.302 [corrected] eV. Moreover, the heteroatom reduces bonding interactions between the C(2) and C(6) radical centers, which results in the increased stabilizing interactions between C(4) and C(2)/C(6). Triradical stabilization energies corresponding to the separation of C(4) and C(2) are 19.7 and -0.2 kcal/mol, respectively, in contrast to 2.8 kcal/mol in 1,3,5-tridehydrobenzene. Similarly weak interactions between C(2) and C(6) are also observed in 2,6-didehydropyridine resulting in a nearly zero singlet-triplet energy gap, in contrast to m-benzyne and 2,4-didehydropyridine. The total interaction energy of the three radical centers is very similar in 1,3,5-tridehydrobenzene and 2,4,6-tridehydropyridine and is 19.5 and 20.1 kcal/mol, respectively.

The theoretical prediction of infrared spectra of trans- and cis-hydroxycarbene calculated using full dimensional ab initio potential energy and dipole moment surfaces.

Accurate infrared spectra of the two hydroxycarbene isomers are computed by diagonalizing the Watson Hamiltonian including up to four mode couplings using full dimensional potential energy and dipole moment surfaces calculated at the CCSD(T)/cc-pVTZ (frozen core) and CCSD6-311G(**) (all electrons correlated) levels, respectively. Anharmonic corrections are found to be very important for these elusive higher-energy isomers of formaldehyde. Both the energy levels and intensities of stretching fundamentals and all overtone transitions are strongly affected by anharmonic couplings between the modes. The results for trans-HCOHHCOD are in excellent agreement with the recently reported IR spectra, which validates our predictions for the cis-isomers.

Vibronic structure and ion core interactions in Rydberg states of diazomethane: an experimental and theoretical investigation.

Vibronic transitions to the 21A2(3py <-- pi) Rydberg state of CH2N2, CD2N2, and CHDN2 were recorded by 2 + 1 REMPI spectroscopy, and kinetic energy distributions (eKE) of photoelectrons from ionization of selected vibronic levels were determined by velocity map imaging. Normal-mode frequencies were obtained for the 21A2(3py) Rydberg state and for the cation. Mixed levels of the 21A2(3py) and 21B1(3pz) of the three isotopologs were identified by photoelectron imaging and analyzed. The equilibrium geometries and harmonic vibrational frequencies of the electronic states of neutral diazomethane were calculated by CCSD(T)/cc-pVTZ, and B3LYP/6-311G(2df,p). The latter method was also used to calculate isotope shifts for the ground-state neutral and cation. Geometry and frequencies of the ground state of the cation were calculated by CCSD(T)/cc-pVTZ, using the unrestricted (UHF) reference. The equilibrium structures, frequencies, and isotope shifts of the 21A2(3py) and 21B1(3pz) Rydberg states were calculated by EOM-EE-CCSD/6-311(3+,+)G(2df). In all cases where comparisons with experimental results were available, the agreement between theory and experiment was very good allowing a full analysis of trends in structure and vibrational frequencies in going from the neutral species to the excited Rydberg states, 21A2(3py) and 21B1(3pz), and the cation. Although the 21A2(3py) and 21B1(3pz) states have planar C2v symmetry like the ion, they exhibit differences in geometry due to the specific interactions of the electron in the 3py and 3pz orbitals with the nuclei charge distributions of the ion core. Moreover, trends in normal-mode frequencies in the ground states of the neutral and ion and the 21A2(3py) and 21B1(3pz) Rydberg states are consistent with removing an electron from the bonding piCN-orbital, which also has an antibonding character with respect to NN. To explain the observed trends, the vibrational modes are divided into two groups that involve displacements mainly (i) along the CNN framework and (ii) in the CH2 moiety. Trends in the first group are due mostly to the effect of the lower CN and NN bond orders, whereas those in the second group are due to the interaction between the positively charged hydrogens and the Rydberg electron density, and the hybridization of the carbon. Within each group, marked differences in behavior between the in-plane and out-of-plane modes are observed.

The 1,2,3-tridehydrobenzene triradical: 2B or not 2B? The answer is 2A!

The molecular and electronic structure of 1,2,3-tridehydrobenzene was investigated by a variety of computational methods. The two lowest electronic states of the triradical are the (2)B(2) and (2)A(1) doublet states characterized by different interactions of the unpaired electrons. Vertically, the two states are well separated in energy-by 4.9 and 1.4 eV, respectively. However, due to different bonding patterns, their equilibrium structures are very different and, adiabatically, the two states are nearly degenerate. The adiabatic energy gap between the (2)B(2) and (2)A(1) states is estimated to be 0.7-2.1 kcal/mol, in favor of the (2)A(1) state. Harmonic vibrational frequencies and anharmonic corrections were calculated for both states. Comparison with the three experimentally observed IR transitions supports the assignment of the (2)A(1) ground state for the triradical with a weakly bonding distance of 1.67-1.69 A between the meta radical centers.

Theoretical and experimental investigations of the electronic Rydberg states of diazomethane: assignments and state interactions.

The electronic states of diazomethane in the region 3.00-8.00 eV have been characterized by ab initio calculations, and electronic transitions in the region 6.32-7.30 eV have been examined experimentally using a combination of 2 + 1 REMPI spectroscopy and photoelectron imaging in a molecular beam. In the examined region, three Rydberg states of 3p character contribute to the transitions, 2(1)A2(3p(y) <-- pi), 2(1)B1(3p(z) <-- pi), and 3(1)A1(3p(x) <-- pi). The former two states are of mostly pure Rydberg character and exhibit a resolved K structure, whereas the 3(1)A1(3p(x) <-- pi) state is mixed with the valence 2(1)A1(pi* <-- pi) state, which is unbound and is strongly predissociative. Analyses of photoelectron kinetic energy distributions indicate that the ground vibrational level of the 2(1)B1(3p(z)) state is mixed with the 2(1)A2(3p(y)) nu(9) level, which is of B1 vibronic symmetry. The other 2(1)A2(3p(y)) vibronic states exhibit pure Rydberg character, generating ions in single vibrational levels. The photoelectron spectra of the 3(1)A1(3p(x) <-- pi) state, on the other hand, give rise to many states of the ion as a result of strong mixing with the valence state, as evidenced also in the ab initio calculations. The equilibrium geometries of the electronic states of neutral diazomethane were calculated by CCSD(T), using the cc-pVTZ basis, and by B3LYP, using the 6-311G(2df,p) basis. Geometry and frequencies of the ground state of the cation were calculated by CCSD(T)/cc-pVTZ, using the unrestricted (UHF) reference. Vertical excitation energies were calculated using EOM-CCSD/6-311(3+,+)G* at the B3LYP optimized geometry. The theoretical results show that the 2(1)A2(3p(y) <-- pi) and 2(1)B1(3p(z) <-- pi) states have geometries similar to the ion, which has C(2v) symmetry, with slight differences due to the interactions of the electron in the 3p orbital with the nuclei charge distributions. The geometry of the 3(1)A1(3p(x) <-- pi) state is quite different and has Cs symmetry. The experimental and theoretical results agree very well, both in regard to excitation energies and to vibrational modes of the ion.

Beyond vinyl: electronic structure of unsaturated propen-1-yl, propen-2-yl, 1-buten-2-yl, and trans-2-buten-2-yl hydrocarbon radicals.

Vertical excitation energies and oscillator strengths for several valence and Rydberg electronic states of vinyl, propen-1-yl, propen-2-yl, 1-buten-2-yl, and trans-2-buten-2-yl radicals are calculated using the equation-of-motion coupled cluster methods with single and double substitutions (EOM-CCSD). The ground and the lowest excited state (n <-- pi) equilibrium geometries are calculated using the CCSD(T) and EOM-SF-CCSD methods, respectively, and adiabatic excitation energies for the n <-- pi state are reported. Systematic changes in the geometries, excitation energies, and Rydberg state quantum defects within this group of radicals are discussed.