Fixed-node diffusion Monte Carlo shows promise for modeling reaction thermochemistry of hydrocarbon-based radicals.

Reliable thermodynamic and kinetic properties of free radical polymerization reactions are essential for synthesizing both primary polymeric materials and specialty polymers. The computational generation of these data from quantum chemistry requires a time-efficient method capable of capturing the essential physics. One such method, fixed-node diffusion Monte Carlo (FN-DMC) (using single Slater-Jastrow trial wavefunctions), has demonstrated the capability to recover 90%-95% of missing dynamic correlation energy for typical systems. In this study, methyl radical addition to ethylene serves as a simple model to test FN-DMC's ability to calculate enthalpies of reaction and activation energies with different time steps, antisymmetric trial wavefunctions, basis set sizes, and effective core potentials. The FN-DMC computational protocol thus defined for methyl radical addition to ethylene is subsequently benchmarked against Weizmann-1 and experimental reaction enthalpies from Lin et al.'s test set of 21 radical addition and 28 hydrogen abstraction enthalpies. Our findings reveal that FN-DMC consistently generates reaction enthalpies with chemical accuracy, exhibiting mean absolute deviation of 3.5(7) and 1.4(8) kJ/mol from the Weizmann-1 reference for radical addition and hydrogen abstraction reactions, respectively. Given its favorable computational scaling and high degree of parallelizability, we, therefore, recommend more comprehensive testing of FN-DMC with effective core potentials to address more extensive and intricate polymerization reactions and reactions with other radicals.

Structure factor lineshape model gives approximate nanoscale size of polar aggregates in the ionic liquid N-methyl-N-propylpyrrolidinium bis(trifluoromethylsulfonyl)imide.

A Lorentzian lineshape model is developed and tested for the charge alternation peak in X-ray structure factors calculated from MD simulations for N-methyl-N-propylpyrrolidinium bis(trifluoromethylsulfonyl)imide. Applying the model to published, experimental X-ray scattering data reproduces calculated cation-cation and anion-anion distances within 6% and implies that half of ionic aggregates are larger than 12.7 Å.

Temperature Dependence of Static Structure Factor Peak Intensities for a Pyrrolidinium-Based Ionic Liquid.

Static structure factors ( S( q)) for many ionic liquids show low-wavenumber peaks whose intensities increase with increasing temperature. The greater peak intensities might seem to imply increasing intermediate-range order with increasing temperature. Molecular dynamics (MD) simulations for a representative ionic liquid, 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide (C4C1pyrrTFSI), were used to calculate S( q) and partial S( q) (cation-cation, anion-anion, and cation-anion) at 298, 363, and 500 K. S( q) and partial S( q) were further decomposed into positive and negative components (which each indicate structural ordering) by separately summing positive and negative Fourier transform summands. Increasing temperature causes the negative components of each partial S( q) to decrease in magnitude more than the positive components, causing the total S( q) to increase in magnitude. Thus, structural ordering with periodicities corresponding to observed peaks in S( q) does not increase but instead decoheres with increasing temperature, even though S( q) peak heights increase. Fourier transform summands also show where in real space the positive and negative component contributions to S( q) change when the temperature increases. This new, detailed analysis based on Fourier transform summands comprising S( q) argues for great caution when interpreting S( q) intensities and highlights the value of simulations as a complement to X-ray (or neutron) scattering experiments.

Distinguishing the Protonation State of the Histidine Ligand to the Oxidized Iron-Sulfur Cluster from the MitoNEET Family of Proteins.

The iron-sulfur cluster located in the recently discovered human mitoNEET protein (and related proteins) is structurally similar to the more well-known ferredoxin and Rieske clusters. Although its biological function is uncertain, the iron-sulfur cluster in mitoNEET has been proposed to undergo proton-coupled electron transfer involving the histidine ligand to the cluster. The cluster is also released from the protein at low pH. This contribution reports density functional calculations to model the structures, vibrations, and Heisenberg coupling constants (J) for high-spin (HS), broken symmetry (BS) singlet, and extended broken symmetry (EBS) singlet states of the oxidized iron-sulfur cluster from mitoNEET. This work suggests that J values or 15 N isotopic frequency shifts may provide methods for determining experimentally whether the histidine ligand to the oxidized iron-sulfur cluster in human mitoNEET and mitoNEET-related proteins is protonated or deprotonated.

Distinguishing Protonation States of Histidine Ligands to the Oxidized Rieske Iron-Sulfur Cluster through (15) N Vibrational Frequency Shifts.

The Rieske [2Fe-2S] cluster is a vital component of many oxidoreductases, including mitochondrial cytochrome bc1; its chloroplast equivalent, cytochrome b6f; one class of dioxygenases; and arsenite oxidase. The Rieske cluster acts as an electron shuttle and its reduction is believed to couple with protonation of one of the cluster's His ligands. In cytochromes bc1 and b6f, for example, the Rieske cluster acts as the first electron acceptor in a modified Q cycle. The protonation states of the cluster's His ligands determine its ability to accept a proton and possibly an electron through a hydrogen bond to the electron carrier, ubiquinol. Experimental determination of the protonation states of a Rieske cluster's two His ligands by NMR spectroscopy is difficult, due to the close proximity of the two paramagnetic iron atoms of the cluster. Therefore, this work reports density functional calculations and proposes that difference vibrational spectroscopy with (15) N isotopic substitution may be used to assign the protonation states of the His ligands of the oxidized Rieske [2Fe-2S] complex.

Harmonic vibrational frequencies: scale factors for pure, hybrid, hybrid meta, and double-hybrid functionals in conjunction with correlation consistent basis sets.

Scale factors for (a) low (<1000 cm(-1)) and high harmonic vibrational frequencies, (b) thermal contributions to enthalpy and entropy, and (c) zero-point vibrational energies have been determined for five hybrid functionals (B3P86, B3PW91, PBE1PBE, BH&HLYP, MPW1K), five pure functionals (BLYP, BPW91, PBEPBE, HCTH93, and BP86), four hybrid meta functionals (M05, M05-2X, M06, and M06-2X) and one double-hybrid functional (B2GP-PLYP) in combination with the correlation consistent basis sets [cc-pVnZ and aug-cc-pVnZ, n = D(2),T(3),Q(4)]. Calculations for vibrational frequencies were carried out on 41 organic molecules and an additional set of 22 small molecules was used for the zero-point vibrational energy scale factors. Before scaling, approximately 25% of the calculated frequencies were within 3% of experimental frequencies. Upon application of the derived scale factors, nearly 90% of the calculated frequencies deviated less than 3% from the experimental frequencies for all of the functionals when the augmented correlation consistent basis sets were used.

Vibrational spectroscopy of secondary amine salts: 1. Assignment of NH(2)(+) stretching frequencies in crystalline phases.

The NH(2)(+) stretching modes of secondary amine salts have been previously studied, but the band assignments are inconsistent between the various studies. This paper assigns characteristic NH(2)(+) group frequencies between approximately 2500 and 2400 cm(-1). Crystal structures of four diamine salts are reported here. Vibrational frequencies were calculated with the B3LYP hybrid Hartree-Fock/density functional method and the 6-31G(d) split-valence plus polarization basis set, and the results are in agreement with the experimental frequencies. Deuterium dilution experiments result in a group of sharply featured bands between the NH(2)(+) and the ND(2)(+) stretching bands. These bands, located between 2200 and 2100 cm(-1), are attributed to modes that contain contributions from coupled N-H and N-D stretching motions.

Pressure Annealing as a Complement to Temperature Annealing To Find Low-Energy Structures of Oligomeric Molecules.

Finding the lowest-energy geometry of a molecule or collection of molecules is a fundamental challenge of modern computational chemistry and is closely related to the more general problem of optimizing a function. Temperature annealing, popularly called simulated annealing, is a powerful and commonly used technique, but it is not well suited to conformational sampling of long, oligomeric molecules. A method is presented herein that incorporates pressure as an optimization parameter to complement temperature annealing, and several tests of its effectiveness are described. Bayesian statistical analysis shows that pressure-temperature annealing confers no advantage in control simulations of Lennard-Jones particles, but it yields lower-energy structures than pure temperature annealing with significant credibility for two model polyethers, monoglyme (CH3OCH2CH2OCH3) and tetraglyme [CH3(OCH2CH2)4OCH3].

The vibrational spectrum of the secondary electron acceptor, A1, in photosystem I.

Photosystem I (PSI) is a multisubunit protein complex which carries out light-induced, transmembrane charge separation in oxygenic photosynthesis. In PSI, the electron-transfer pathway consists of chlorophyll and phylloquinone molecules, as well as iron-sulfur clusters. There are two phylloquinone molecules, which are located in structurally symmetric positions in the reaction center. It has been proposed that both phylloquinone molecules are active as the A1 secondary electron acceptor in bidirectional electron-transfer reactions. The PSI A1 acceptors are of interest because they have the lowest reduction potential of any quinone found in nature. In this work using light-induced FT-IR spectroscopy, isotope-edited spectra are presented, which attribute vibrational bands to the carbonyl stretching vibrations of A1 and A1- and the quinoid ring stretching vibration of A1. Bands are assigned by comparison with hybrid Hartee-Fock density functional calculations, which predict vibrational frequencies, amplitudes, and isotope shifts for the phylloquinone singlet and radical anion states. The results are consistent with an environmental interaction increasing the frequency of the singlet CO vibration and decreasing the frequency of the anion radical CO vibration, relative to model compounds. This environmental interaction may be the asymmetric hydrogen bond to A1/A1-, electrostatic interactions with charged amino acid side chains, or a pi-pi interaction with the indole ring of a nearby tryptophan. Such differential effects on the structure of A1 and A1- may be associated with a destabilization of the anion radical. These studies give novel information concerning the effect of the protein matrix on the PSI electron-transfer cofactor.

Flexible protein-flexible ligand docking with disrupted velocity simulated annealing.

By docking flexible balanol to a rigid model of protein kinase A (PKA), we found that a new simulated annealing protocol termed disrupted velocity simulated annealing (DIVE-SA) outperformed the replica-exchange method and the traditional simulated annealing method in identifying the correct docking pose. In this protocol, the atomic velocities were reassigned periodically to encourage the system to sample a large conformational space. We also found that scaling potential energy surface to reduce structural transition barriers could further facilitate docking. The DIVE-SA method was then evaluated on its ability to perform flexible ligand-flexible protein docking of three ligands (balanol, a balanol analog, and ATP) to PKA. To reduce computational time and to avoid possible unphysical structural changes resulting from the use of nonoptimal force fields, a soft restrain was applied to keep the root-mean-square-deviation (RMSD) between instantaneous protein structures and a chosen reference structure small. Because the restrain was applied to the overall RMSD rather than to individual atoms, a protein could still experience relatively large conformational changes during docking. To examine the impact of applying such a restrain on docking, we constructed two semi-flexible protein models by choosing two different crystal structures as reference. Both the balanol analog and ATP were able to dock to either one of these semi-flexible protein models. On the other hand, balanol could only dock well to one of them. Further analysis indicated that the restrain on the glycine-rich loop was too strong, preventing it to adjust its structure to accommodate balanol in the binding pocket of PKA. Removing the restrain on the glycine-rich loop resulted in much better docking poses. This finding demonstrates the important role that the flexibility of the glycine-rich loop play in accepting different ligands and should profitably not be restrained in molecular docking so that more diverse ligands can be studied.

Fiber-optic infrared reflectance spectroelectrochemical studies of osmium and ruthenium nitrosyl porphyrins containing alkoxide and thiolate ligands.

We have examined the redox behavior of the osmium and ruthenium compounds (OEP)M(NO)(OEt) and (OEP)M(NO)(SEt) (OEP = octaethylporphyrinato dianion; M = Os, Ru) by cyclic voltammetry and infrared spectroelectrochemistry. The compound (OEP)Os(NO)(OEt) undergoes a single reversible oxidation process in dichloromethane. In contrast, the thiolate compound (OEP)Os(NO)(SEt) undergoes a net irreversible oxidation resulting in formal loss of the SEt ligand. Extended Hückel calculations on crystal structures of these two compounds provide insight into the nature of their HOMOs. In the case of the alkoxide compound, the HOMO is largely metal centered, with 70% of the charge located in the metal's orbital and approximately 25% on the porphyrin ring. However, the HOMO of the thiolate compound consists of a pi bonding interaction between the metal dxz orbital and the px orbital on the sulfur, and a pi antibonding interaction between the metal d orbital and a pi* orbital on NO. The redox behavior of the Ru analogues have been determined, and are compared with those of the Os compounds.

Wavelet Transforms for Determining Time-Dependent Vibrational Frequencies.

Fourier transforms of autocorrelation functions are typically used to calculate spectra and transport properties, but they require oscillations periodic in time (a stationary time series). The time-scale relation revealed by a wavelet transform (WT), on the other hand, gives a relation between time and pseudo-frequency that is used here to calculate vibrational frequencies for HONO and to detect the molecule's trans-cis conformational change in ab initio molecular dynamics simulations. Thus, the WT shows potential for giving new insights into nonstationary time series frequently encountered in chemistry and physics.

New perspectives on multiple-copy, mean-field molecular dynamics methods.

Mean-field molecular dynamics (MD) techniques are designed to improve phase-space sampling in MD simulations. Reviewed here are theoretical and practical contributions from our group, and the ideas our contributions are based upon, beginning with the original time-dependent Hartree technique, locally enhanced sampling (LES), and a new, purely classical derivation of multiple-copy, mean-field equations of motion. This view is used to provide new insights into approximations inherent in LES, as well as the basis for a recently proposed method, ensembles eXtracted from atomic coordinate transformations (the EXACT approximation).