This chapter presents an overview of the components of the dynamical nucleation theory effective fragment potential (DNTEFP) model, the use of the DNTEFP for the representative molecular systems of atmospheric importance, and implementation and performance of these methods using two-level parallelism on high performance computers. In DNTEFP, several important concepts are combined to facilitate the computation of the evaporation rates—dynamical nucleation theory Monte Carlo (DNTMC), the effective fragment potential, and two-level parallelism. The chapter presents a brief introduction to each of the concepts to acclimate the reader to the ideas. The chapter also presents the results of the use of the DNTEFP method to study several chemical systems. Next, it discusses an assessment of the performance of the software. The investigated chemical systems are representative of different types of calculations that can be performed using the DNTEFP method—homogeneous water clusters, heterogeneous water clusters with ions, and homogeneous dehydrated systems.

Biomass recalcitrance, the resistance of cellulosic biomass to degradation, is due in part to the stability of the hydrogen bond network and stacking forces between the polysaccharide chains in cellulose microfibers. The fragment molecular orbital (FMO) method at the correlated Møller-Plesset second order perturbation level of theory was used on a model of the crystalline cellulose Iα core with a total of 144 glucose units. These computations show that the intersheet chain interactions are stronger than the intrasheet chain interactions for the crystalline structure, while they are more similar to each other for a relaxed structure. An FMO chain pair interaction energy decomposition analysis for both the crystal and relaxed structures reveals an intricate interplay between electrostatic, dispersion, charge transfer, and exchange repulsion effects. The role of the primary alcohol groups in stabilizing the interchain hydrogen bond network in the inner sheet of the crystal and relaxed structures of cellulose Iα, where edge effects are absent, was analyzed. The maximum attractive intrasheet interaction is observed for the GT-TG residue pair with one intrasheet hydrogen bond, suggesting that the relative orientation of the residues is as important as the hydrogen bond network in strengthening the interaction between the residues.

A fundamental understanding of the intermolecular forces that bind polysaccharide chains together in cellulose is crucial for designing efficient methods to overcome the recalcitrance of lignocellulosic biomass to hydrolysis. Because the characteristic time and length scales for the degradation of cellulose by enzymatic hydrolysis or chemical pretreatment span orders of magnitude, it is important to closely integrate the molecular models used at each scale so that, ultimately, one may switch seamlessly between quantum, atomistic, and coarse-grained descriptions of the system. As a step towards that goal, four multiscale coarse-grained models for polysaccharide chains in a cellulose-Iα microfiber are considered. Using the force matching method, effective coarse-grained forces are derived from all-atom trajectories. Performance of the coarse-grained models is evaluated by comparing the intrachain radial distribution functions with those obtained using the all-atom reference data. The all-atom simulation reveals a double peak in the radial distribution function for sites within each glucose residue that arises from the distinct conformations sampled by the primary alcohol group in the glucose residues. The three-site and four-site coarse-grained models have sufficient degrees of freedom to predict this double peak while the one-site and two-site models do not. This is the first time that coarse-grained models have been shown to reproduce such subtle, yet important, molecular features in a polysaccharide chain. The relative orientations between glucose residues along the polysaccharide chain are evaluated and it is found that the four-site coarse-grained model is best at reproducing the glucose-glucose conformations observed in the all-atom simulation. The success of the four-site coarse-grained model underscores the importance of decoupling the pyranose ring from the oxygen atom in the glycosidic bond when developing all-atom to coarse-grained mapping schemes for polysaccharides.

Cellulosic ethanol production is a two-stage process that involves the hydrolysis of cellulose to form simple sugars and the fermentation of these sugars to ethanol. Hydrolysis of cellulose is the rate-limiting step, and there is a great need to characterize the process with numerical simulations to better understand the complex mechanisms involved. The ultimate goal is to generate accurate coarse-grained molecular models that are capable of predicting the structure of lignocellulose before and after pretreatment so that subsequent ab initio calculations can be performed to probe the degradation pathways. As a first step toward that goal, the force-matching method is used to derive coarse-grained models for β-d-glucose molecules in aqueous solution. Using the same reference, an all-atom molecular dynamics simulation trajectory, two sets of three- and six-site coarse-grained models of β-d-glucose are developed using two definitions of the coarse-grained center site location: center of mass (CG-CM) and geometric center (CG-GC). The performance of these coarse-grained models is evaluated by comparing the coarse-grained predictions for bond-length distributions and radial distribution functions to those obtained from the all-atom reference simulation. The six-site coarse-grained models retain more structural details than the three-site coarse-grained models. Comparison between center site definitions shows that CG-CM models generally predict local ordering better, while CG-GC models predict long-range structure better.

International Journal of Quantum ChemistryVolume 111, Issue 13 p. 3280-3283 Perspective: The RASPT2 Method Perspective on “The restricted active space self-consistent-field method, implemented with a split-graph unitary group approach” Mark S. Gordon, Corresponding Author Mark S. Gordon mgordon@iastate.edu Department of Chemistry and Ames Laboratory, Iowa State University, Ames, IA 50011Department of Chemistry and Ames Laboratory, Iowa State University, Ames, IA 50011Search for more papers by this authorLuke Roskop, Luke Roskop Department of Chemistry and Ames Laboratory, Iowa State University, Ames, IA 50011Search for more papers by this authorAjitha Devarajan, Ajitha Devarajan Department of Chemistry and Ames Laboratory, Iowa State University, Ames, IA 50011Search for more papers by this author Mark S. Gordon, Corresponding Author Mark S. Gordon mgordon@iastate.edu Department of Chemistry and Ames Laboratory, Iowa State University, Ames, IA 50011Department of Chemistry and Ames Laboratory, Iowa State University, Ames, IA 50011Search for more papers by this authorLuke Roskop, Luke Roskop Department of Chemistry and Ames Laboratory, Iowa State University, Ames, IA 50011Search for more papers by this authorAjitha Devarajan, Ajitha Devarajan Department of Chemistry and Ames Laboratory, Iowa State University, Ames, IA 50011Search for more papers by this author First published: 18 January 2011 https://doi.org/10.1002/qua.23017Citations: 4Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Citing Literature Volume111, Issue13Special Issue: A Celebration of the Scientific Achievements of Björn O. Roos5 November 2011Pages 3280-3283 RelatedInformation

In this work, the dynamical nucleation theory (DNT) model using the ab initio based effective fragment potential (EFP) is implemented for evaluating the evaporation rate constant and molecular properties of molecular clusters. Predicting the nucleation rates of aerosol particles in different chemical environments is a key step toward understanding the dynamics of complex aerosol chemistry. Therefore, molecular scale models of nanoclusters are required to understand the macroscopic nucleation process. On the basis of variational transition state theory, DNT provides an efficient approach to predict nucleation kinetics. While most DNT Monte Carlo simulations use analytic potentials to model critical sized clusters, or use ab initio potentials to model very small clusters, the DNTEFP Monte Carlo method presented here can treat up to critical sized clusters using the effective fragment potential (EFP), a rigorous nonempirical intermolecular model potential based on ab initio electronic structure theory calculations, improvable in a systematic manner. The DNTEFP method is applied to study the evaporation rates, energetics, and structure factors of multicomponent clusters containing water and isoprene. The most probable topology of the transition state characterizing the evaporation of one water molecule from a water hexamer at 243 K is predicted to be a conformer that contains six hydrogen bonds, with a topology that corresponds to two water molecules stacked on top of a quadrangular (H(2)O)(4) cluster. For the water hexamer in the presence of isoprene, an increase in the cluster size and a 3-fold increase in the evaporation rate are predicted relative to the reaction in which one water molecule evaporates from a water hexamer cluster.

We report the implementation of a frequency-dependent two-component relativistic density functional theory method based on the zeroth order regular approximation (ZORA) for computations of complex linear response of molecules including spin-orbit coupling. The implementation is based on Slater-type atomic orbital basis functions and makes extensive use of density fitting techniques. The complex response is obtained by applying damping in the computations. The method is validated by computations of the real and imaginary part of the static and dynamic polarizability of group 12 atoms, of a number of heavy-atom diatomic molecules, of a range of two- and three-dimensional gold clusters, and of group 8 oxides and metallocenes. Simulated spectra--a plot of extinction coefficient as a function of frequency--obtained from the isotropic imaginary polarizability are compared to broadened spectra obtained from two-component ZORA excitation energies and oscillator strengths.

An ab initio study of the role of electronic curve crossing of benzene S-1 state in the photo dissociation dynamics of the iodobenzene and effect of fluorination is presented. Two dissociative life times observed in iodobenzene is attributed to the coupled repulsive potential energy curves of the low-lying n-sigma*, pi-sigma*, pi-pi* states. The direct channel is attributed to the alkyl like transition and the indirect channel is attributed to the mixing of the alkyl like transitions with the low lying benzene pi-pi* transitions. Fluorination of iodobenzene results in a substantial increase in the direct channel product. To analyze the possible role of electronic curve crossing of these transitions, potential energy curves of low-lying n-sigma*, pi-sigma*, pi-pi* states were studied including spin-orbit and relativistic effects using the Restricted Active Space state interaction multistate complete active space perturbation theory (RASSI-MS-CASPT2) method. Crossing behavior of spin-free and spin-orbit potential energy curves was analyzed for the role of the benzene S-1 state. Our results indicate the curve crossing region to be around 2.00-2.35 angstrom for both C6H5I and C6F5I. Analysis of effect of fluorination on the energies of states corresponding to benzene pi-pi* and n-sigma* transitions suggests an increase in the energy of benzene pi-pi* states and a decrease in the energy of the states corresponding to n-sigma* transitions. Increased spin-orbit gap, increased separation of the benzene S-1(pi-pi*) state and n-sigma* states in the region of curve crossing, lesser mixing of the pi-pi* and n-sigma* states, an order of magnitude decrease in the transition strength to the benzene singlet transition all contributed to the observed Substantial increase in the quantum yield of the direct channel product on fluorination of aryl halides. (c) 2009 Wiley Periodicals, Inc. Int J Quantum Chem 109: 1962-1974, 2009

The enzyme myeloperoxidase shows several unusual properties compared to other peroxidases, e.g. a red-shifted absorption spectrum and a peroxidase activity towards chloride. It has been suggested that this is caused by the unusual covalent links between the heme group and the surrounding protein, but whether it is caused by the two ester links to Glu-242 and Asp-94 or the sulfonium ion linkage to Met-243 is unclear. To investigate these suggestions, we have used density functional theory to study the structure, spectra, and reduction potential of 25 models of myeloperoxidase in the reduced (Fe(II)) and oxidized (Fe(III)) states, as well as in the compound I (formally Fe(V)O) and II (Fe(IV)O or Fe(IV)OH) states, using appropriate models of the linkages to the Asp, Glu, and Met residues (including the back-bone connection between Glu-242 and Met-243) in varying combinations. The calculated spectral shifts indicate that both the ester and sulfonium linkages play a role in the spectral shift. On the other hand, the sulfonium linkage seems to be mainly responsible for the high positive reduction potential for the both ferric/ferrous and compound I/II couples of myeloperoxidase.

Generalized van Vleck perturbation theory (GVVPT2) for molecular electronic structures is applied to examine the azabenzene series: benzene, pyridine, pyrazine, symmetric triazine and symmetric tetrazine. The spectra of azabenzenes are complex with large numbers of excited states at low energies comprising n --> pi* and pi --> pi* excited states and also doubly excited states of the n,n --> pi*,pi* type. The calculations are complicated due to strong correlation effects in the nitrogen lone-pair orbitals and the pi electrons. This study is the first to use GVVPT2 on conjugated systems. Comparison is made with experimental data and complete active space second-order perturbation theory, equation of motion coupled cluster and similarity transformed equation of motion coupled cluster theory data. Using polarized valence double split basis sets for benzene and pyrazine (cc-pVDZ) and pyridine (ANO-S) and polarized triple split basis sets (ANO-L) for triazine and tetrazine, the n --> pi* and pi --> pi* states are computed with an average error of 0.28 eV in comparison with available experimental data.

The ground state properties and absorption spectra of N-benzylideneaniline (NBA) have been studied at the density functional (DFT) and at the time-dependent density functional (TD-DFT) level of the theory. The equilibrium geometries of the E and Z isomers in the ground state and their vibrational frequencies have been computed. Furthermore, the excitation energies of the lowest excited singlet and triplet states and the potential energy curves along the torsion and the inversion isomerization coordinates were evaluated. The results are discussed in light of the available experimental data.

Absorption and fluorescence spectra of 2-R-5-phenyl-1,3,4-oxadiazoles (R = H, methyl, tert-butyl, trifluoromethyl, amino, phenyl, benzyl) were studied experimentally and by time dependent density functional theory (TDDFT) methods. In acidic media a substantial red shift is observed due to the presence of conjugate acid forms. Two conjugate acid forms (3H and 4H) are possible for unsymmetrically substituted oxadiazoles. Relative basicities of the two basic centers of oxadiazole ring at the S-0 and S-1 geometries were calculated using the local density descriptors approach. Substituent effects were studied by analyzing the electron density distribution in the ground and excited states. Analyzing the absorption spectra and local descriptors results, we predict 4H forms to be the dominant acid forms. Calculated emission peaks of 4H forms agree well with experimental observations. An abnormal red shift in the case of the 3H forms is attributed to the increased stabilization of the N-H bond in the 3H forms compared to the 4H forms.

We have studied the effect of axial ligation of chlorophyll and bacteriochlorophyll using density functional calculations. Eleven different axial ligands have been considered, including models of histidine, aspartate/glutamate, asparagine/glutamine, serine, tyrosine, methionine, water, the protein backbone, and phosphate. The native chlorophylls, as well as their cation and anion radical states and models of the reaction centres P680 and P700, have been studied and we have compared the geometries, binding energies, reduction potentials, and absorption spectra. Our results clearly show that the chlorophylls strongly prefer to be five-coordinate, in accordance with available crystal structures. The axial ligands decrease the reduction potentials, so they cannot explain the high potential of P680. They also redshift the Q band, but not enough to explain the occurrence of red chlorophylls. However, there is some relation between the axial ligands and their location in the various photosynthetic proteins. In particular, the intrinsic reduction potential of the second molecule in the electron transfer path is always lower than that of the third one, a feature that may prevent back-transfer of the electron.

Electronic factors influencing the photoluminescence properties and rates of excited state intramolecular proton transfer (ESIPT) reaction of o-hydroxy derivatives of 2,5-diphenyl-1,3,4-oxadiazole have been studied. The potential of these molecules as emissive and electron transport materials in designing improved organic light emitting diodes (OLEDs) has been studied by analyzing possible reasons for the unusually high Stokes shifts and ESIPT reaction rates. Time-dependent density functional theory (TDDFT) methods have been used to calculate the ground and excited state properties of the phototautomers that are the ESIPT reaction products. We study the relative effect of electron-withdrawing substituents on the proton-acceptor moiety and predict that the lowest ESIPT rate (1.9 x 10(11) s(-1)) is achieved with a dimethylamino substituent and that the Stokes shifts are around 11 000 cm(-1) for all three derivatives.

The photodissociation of bromoiodomethane has been investigated by spin-orbit ab initio calculations. The experimentally observed A- and B-bands and the corresponding photoproducts were assigned by multistate second-order multiconfigurational perturbation theory in conjunction with spin-orbit interaction through complete active space state interaction potential energy curves, vertical excitation energies, and oscillator strengths of low-lying excited states. The present conclusions with respect to the dissociation process in the B-band are different compared with those of previous studies. The reaction between the iso-CH(2)Br-I and iso-CH(2)I-Br species has also been studied. Finally, a set of stable excited states was identified for both isomers. These species might be of importance in the recombination process that follows the photodissociation in a solvent.

An ab initio study of the role of electronic curve crossing in the photodissociation dynamics of the alkyl halides is presented. Recent experimental studies show that curve crossing plays a deterministic role in deciding the channel of dissociation. Coupled repulsive potential energy curves of the low-lying n-sigma(*) states are studied including spin-orbit and relativistic effects. Basis set including effect of core correlation is used. Ab initio vertical excitation spectra of CH(3)I and CF(3)I are in agreement with the experimental observation. The curve crossing region is around 2.371 A for CH(3)I and CF(3)I. The potential curves of the repulsive excited states have larger slope for CF(3)I, suggesting a higher velocity and decreased intersystem crossing probability on fluorination. We also report the potential curves and the region of curve crossing for CH(3)Br and CH(3)Cl.

The interaction of small probe molecules with clusters chosen to represent Brφnsted acid sites in zeolites has been investigated using a local hard−soft acid−base approach. Condensed Fukui functions and local softness values of all the atoms of the probe molecules, namely, CH4, CO, and NH3, have been calculated, and these values are compared with that of the acidic hydrogen atoms of zeolite clusters to find out the most favorable adsorption sites. We calculated the interaction energy of the molecules using local HSAB principle, and the interaction energy values are in good agreement with the experimental results. Density functional and Hartree−Fock methods are used for the calculation of reactivity descriptors. We observed that the intermolecular interaction takes place via the atoms comparable softness values rather than via atoms of equal Fukui functions.