Femtosecond observation of benzyne intermediates in a molecular beam: Bergman rearrangement in the isolated molecule

In this communication, we report our femtosecond real-time observation of the dynamics for the three didehydrobenzene molecules (p-, m-, and o-benzyne) generated from 1,4-, 1,3-, and 1,2-dibromobenzene, respectively, in a molecular beam, by using femtosecond time-resolved mass spectrometry. The time required for the first and the second C-Br bond breakage is less than 100 fs; the benzyne molecules are produced within 100 fs and then decay with a lifetime of 400 ps or more. Density functional theory and high-level ab initio calculations are also reported herein to elucidate the energetics along the reaction path. We discuss the dynamics and possible reaction mechanisms for the disappearance of benzyne intermediates. Our effort focuses on the isolated molecule dynamics of the three isomers on the femtosecond time scale.

Progress toward chemical accuracy in the computer simulation of condensed phase reactions.

We describe a procedure for the generation of chemically accurate computer-simulation models to study chemical reactions in the condensed phase. The process involves (i) the use of a coupled semiempirical quantum and classical molecular mechanics method to represent solutes and solvent, respectively; (ii) the optimization of semiempirical quantum mechanics (QM) parameters to produce a computationally efficient and chemically accurate QM model; (iii) the calibration of a quantum/classical microsolvation model using ab initio quantum theory; and (iv) the use of statistical mechanical principles and methods to simulate, on massively parallel computers, the thermodynamic properties of chemical reactions in aqueous solution. The utility of this process is demonstrated by the calculation of the enthalpy of reaction in vacuum and free energy change in aqueous solution for a proton transfer involving methanol, methoxide, imidazole, and imidazolium, which are functional groups involved with proton transfers in many biochemical systems. An optimized semiempirical QM model is produced, which results in the calculation of heats of formation of the above chemical species to within 1.0 kcal/mol (1 kcal = 4.18 kJ) of experimental values. The use of the calibrated QM and microsolvation QM/MM (molecular mechanics) models for the simulation of a proton transfer in aqueous solution gives a calculated free energy that is within 1.0 kcal/mol (12.2 calculated vs. 12.8 experimental) of a value estimated from experimental pKa values of the reacting species.

Towards Accurate and Efficient Description of Excited States

Thesis (Ph.D.)--University of Washington, 2016-06

Developments in the Theory of X-ray Absorption and Compton Scattering.

Thesis (Ph.D.)--University of Washington, 2016-06

Comparisons of diffusive and viscous contributions to transport coefficients of light gases in single-walled carbon nanotubes

We examine here the relative importance of different contributions to transport of light gases in single walled carbon nanotubes, using methane and hydrogen as examples. Transport coefficients at 298 K are determined using molecular dynamics simulation with atomistic models of the nanotube wall, from which the diffusive and viscous contributions are resolved using a recent approach that provides an explicit expression for the latter. We also exploit an exact theory for the transport of Lennard-Jones fluids at low density considering diffuse reflection at the tube wall, thereby permitting the estimation of Maxwell coefficients for the wall reflection. It is found that reflection from the carbon nanotube wall is nearly specular, as a result of which slip flow dominates, and the viscous contribution is small in comparison, even for a tube as large as 8.1 nm in diameter. The reflection coefficient for hydrogen is 3-6 times as large as that for methane in tubes of 1.36 nm diameter, indicating less specular reflection for hydrogen and greater sensitivity to atomic detail of the surface. This reconciles results showing that transport coefficients for hydrogen and methane, obtained in simulation, are comparable in tubes of this size. With increase in adsorbate density, the reflection coefficient increases, suggesting that adsorbate interactions near the wall serve to roughen the local potential energy landscape perceived by fluid molecules.

Design strategies for controlling the molecular weight and rate using reversible addition-fragmentation chain transfer mediated living radical polymerization

Living radical polymerization has allowed complex polymer architectures to be synthesized in bulk, solution, and water. The most versatile of these techniques is reversible addition-fragmentation chain transfer (RAFT), which allows a wide range of functional and nonfunctional polymers to be made with predictable molecular weight distributions (MWDs), ranging from very narrow to quite broad. The great complexity of the RAFT mechanism and how the kinetic parameters affect the rate of polymerization and MWD are not obvious. Therefore, the aim of this article is to provide useful insights into the important kinetic parameters that control the rate of polymerization and the evolution of the MWD with conversion. We discuss how a change in the chain-transfer constant can affect the evolution of the MWD. It is shown how we can, in principle, use only one RAFT agent to obtain a poly-mer with any MWD. Retardation and inhibition are discussed in terms of (1) the leaving R group reactivity and (2) the intermediate radical termination model versus the slow fragmentation model. (c) 2005 Wiley Periodicals, Inc.

Optimum conditions for adsorptive storage

The storage of gases in porous adsorbents, such as activated carbon and carbon nanotubes, is examined here thermodynamically from a systems viewpoint, considering the entire adsorption-desorption cycle. The results provide concrete objective criteria to guide the search for the Holy Grail adsorbent, for which the adsorptive delivery is maximized. It is shown that, for ambient temperature storage of hydrogen and delivery between 30 and 1.5 bar pressure, for the optimum adsorbent the adsorption enthalpy change is 15.1 kJ/mol. For carbons, for which the average enthalpy change is typically 5.8 kJ/mol, an optimum operating temperature of about 115 K is predicted. For methane, an optimum enthalpy change of 18.8 kJ/mol is found, with the optimum temperature for carbons being 254 K. It is also demonstrated that for maximum delivery of the gas the optimum adsorbent must be homogeneous, and that introduction of heterogeneity, such as by ball milling, irradiation, and other means, can only provide small increases in physisorption-related delivery for hydrogen. For methane, heterogeneity is always detrimental, at any value of average adsorption enthalpy change. These results are confirmed with the help of experimental data from the literature, as well as extensive Monte Carlo simulations conducted here using slit pore models of activated carbons as well as atomistic models of carbon nanotubes. The simulations also demonstrate that carbon nanotubes offer little or no advantage over activated carbons in terms of enhanced delivery, when used as storage media for either hydrogen or methane.

The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions

The effect of the box shape on the dynamic behavior of proteins simulated under periodic boundary conditions is evaluated. In particular, the influence of simulation boxes defined by the near-densest lattice packing (NDLP) in conjunction with rotational constraints is compared to that of standard box types without these constraints. Three different proteins of varying size, shape, and secondary structure content were examined in the study. The statistical significance of differences in RMSD, radius of gyration, solvent-accessible surface, number of hydrogen bonds, and secondary structure content between proteins, box types, and the application or not of rotational constraints has been assessed. Furthermore, the differences in the collective modes for each protein between different boxes and the application or not of rotational constraints have been examined. In total 105 simulations were performed, and the results compared using a three-way multivariate analysis of variance (MANOVA) for properties derived from the trajectories and a three-way univariate analysis of variance (ANOVA) for collective modes. It is shown that application of roto-translational constraints does not have a statistically significant effect on the results obtained from the different simulations. However, the choice of simulation box was found to have a small (5-10%), but statistically significant effect on the behavior of two of the three proteins included in the study. (c) 2005 Wiley Periodicals, Inc.

Optimization of slitlike carbon nanopores for storage of hythane fuel at ambient temperatures

Carbons with slitlike pores can serve as effective host materials for storage of hythane fuel, a bridge between the petrol combustion and hydrogen fuel cells. We have used grand canonical Monte Carlo simulation for the modeling of the hydrogen and methane mixture storage at 293 K and pressure of methane and hydrogen mixture up to 2 MPa. We have found that these pores serve as efficient vessels for the storage of hythane fuel near ambient temperatures and low pressures. We find that, for carbons having optimized slitlike pores of size H congruent to 7 angstrom ( pore width that can accommodate one adsorbed methane layer), and bulk hydrogen mole fraction >= 0.9, the volumetric stored energy exceeds the 2010 target of 5.4 MJ dm(-3) established by the U. S. FreedomCAR Partnership. At the same condition, the content of hydrogen in slitlike carbon pores is congruent to 7% by energy. Thus, we have obtained the composition corresponding to hythane fuel in carbon nanospaces with greatly enhanced volumetric energy in comparison to the traditional compression method. We proposed the simple system with added extra container filled with pure free/adsorbed methane for adjusting the composition of the desorbed mixture as needed during delivery. Our simulation results indicate that light slit pore carbon nanomaterials with optimized parameters are suitable filling vessels for storage of hythane fuel. The proposed simple system consisting of main vessel with physisorbed hythane fuel, and an extra container filled with pure free/adsorbed methane will be particularly suitable for combustion of hythane fuel in buses and passenger cars near ambient temperatures and low pressures.

Vibrational dynamics and structure of natural feldspars

The present study gives a contribution to the knowledge on the Na-feldspar and plagioclases, extending the database of the Raman spectra of plagioclases with different chemical compositions and structural orders. This information may be used for the future planetary explorations by “rovers”, for the investigation of ceramics nanocrystal materials and for the mineralogical phase identification in sediments. Na-feldspar and plagioclase solid solution have been investigated by Raman spectroscopy in order to determine the relationships between the vibrational changes and the plagioclase crystal chemistry and structure. We focused on the Raman micro-spectroscopy technique, being a non-destructive method, suited for contactless analysis with high spatial resolution. Chemical and structural analyses have been performed on natural samples to test the usefulness of Raman spectroscopy as a tool in the study of the pressure-induced structural deformations, the disordering processes due to change in the Al-Si distribution in the tetrahedral sites and, finally, in the determination of the anorthitic content (Anx) in plagioclase minerals. All the predicted 39 Ag Raman active modes have been identified and assigned to specific patterns of atomic vibrational motion. A detailed comparison between experimental and computed Raman spectra has been performed and previous assignments have been revised, solving some discrepancies reported in recent literature. The ab initio calculation at the hybrid HF/DFT level with the WC1LYP Hamiltonian has proven to give excellent agreement between calculated and experimentally measured Raman wavenumbers and intensities in triclinic minerals. A short digression on the 36 infrared active modes of Na-feldspar has been done too. The identification of all 39 computed Raman modes in the experimentally measured spectra of the fully ordered Na-feldspar, known as low albite, along with the detailed description of each vibrational mode, has been essential to extend the comparative analysis to the high pressure and high temperature structural forms of albite, which reflect the physical–chemical conditions of the hosting rocks. The understanding of feldspar structure response to pressure and temperature is crucial in order to constrain crustal behaviour. The compressional behaviour of the Na-feldspar has been investigated for the first time by Raman spectroscopy. The absence of phase transitions and the occurrence of two secondary compression mechanisms acting at different pressures have been confirmed. Moreover, Raman data suggest that the internal structural changes are confined to a small pressure interval, localized around 6 GPa, not spread out from 4 to 8 GPa as suggested by previous X-rays studies on elasticity. The dominant compression mechanisms act via tetrahedral tilting, while the T-O bond lengths remain nearly constant at moderate compressional regimes. At the spectroscopic level, this leads to the strong pressure dependencies of T-O-T bending modes, as found for the four modes at 478, 508, 578 and 815 cm-1. The Al-Si distribution in the tetrahedral sites affects also the Raman spectrum of Na-feldspar. In particular, peak broadening is more sensitive than peak position to changes in the degree of order. Raman spectroscopy is found to be a good probe for local ordering, in particular being sensitive to the first annealing steps, when the macroscopic order parameter is still high. Even though Raman data are scattered and there are outliers in the estimated values of the degree of order, the average peak linewidths of the Na-feldspar characteristic doublet band, labelled here as υa and υb, as a function of the order parameter Qod show interesting trends: both peak linewidths linearly increase until saturation. From Qod values lower than 0.6, peak broadening is no more affected by the Al-Si distribution. Moreover, the disordering process is found to be heterogeneous. SC-XRD and Raman data have suggested an inter-crystalline inhomogeneity of the samples, i.e., the presence of regions with different defect density on the micrometric scale. Finally, the influence of Ca-Na substitution in the plagioclase Raman spectra has been investigated. Raman spectra have been collected on a series of well characterized natural, low structural plagioclases. The variations of the Raman modes as a function of the chemical composition and the structural order have been determined. The number of the observed Raman bands at each composition gives information about the unit-cell symmetry: moving away from the C1 structures, the number of the Raman bands enhances, as the number of formula units in the unit cell increases. The modification from an “albite-like” Raman spectrum to a more “anorthite-like” spectrum occurs from sample An78 onwards, which coincides with the appearance of c reflections in the diffraction patterns of the samples. The evolution of the Raman bands υa and υb displays two changes in slope at ~An45 and ~An75: the first one occurs between e2 and e1 plagioclases, the latter separates e1 and I1 plagioclases with only b reflections in their diffraction patterns from I1 and P1 samples having b and c reflections too. The first variation represents exactly the e2→e1 phase transitions, whereas the second one corresponds in good approximation to the C1→I1 transition, which has been determined at ~An70 by previous works. The I1→P1 phase transition in the anorthite-rich side of the solid solution is not highlighted in the collected Raman spectra. Variations in peak broadening provide insights into the behaviour of the order parameter on a local scale, suggesting an increase in the structural disorder within the solid solution, as the structures have to incorporate more Al atoms to balance the change from monovalent to divalent cations. All the information acquired on these natural plagioclases has been used to produce a protocol able to give a preliminary estimation of the chemical composition of an unknown plagioclase from its Raman spectrum. Two calibration curves, one for albite-rich plagioclases and the other one for the anorthite-rich plagioclases, have been proposed by relating the peak linewidth of the most intense Raman band υa and the An content. It has been pointed out that the dependence of the composition from the linewidth can be obtained only for low structural plagioclases with a degree of order not far away from the references. The proposed tool has been tested on three mineralogical samples, two of meteoric origin and one of volcanic origin. Chemical compositions by Raman spectroscopy compare well, within an error of about 10%, with those obtained by elemental techniques. Further analyses on plagioclases with unknown composition will be necessary to validate the suggested method and introduce it as routine tool for the determination of the chemical composition from Raman data in planetary missions.

Characterization of the structure of RAMP1 by mutagenesis and molecular modeling

Receptor activity modifying proteins (RAMPs) are a family of single-pass transmembrane proteins that dimerize with G-protein-coupled receptors. They may alter the ligand recognition properties of the receptors (particularly for the calcitonin receptor-like receptor, CLR). Very little structural information is available about RAMPs. Here, an ab initio model has been generated for the extracellular domain of RAMP1. The disulfide bond arrangement (Cys 27-Cys82, Cys40-Cys72, and Cys 57-Cys104) was determined by site-directed mutagenesis. The secondary structure (a-helices from residues 29-51, 60-80, and 87-100) was established from a consensus of predictive routines. Using these constraints, an assemblage of 25,000 structures was constructed and these were ranked using an all-atom statistical potential. The best 1000 conformations were energy minimized. The lowest scoring model was refined by molecular dynamics simulation. To validate our strategy, the same methods were applied to three proteins of known structure; PDB:1HP8, PDB:1V54 chain H (residues 21-85), and PDB:1T0P. When compared to the crystal structures, the models had root mean-square deviations of 3.8 Å, 4.1 Å, and 4.0 Å, respectively. The model of RAMP1 suggested that Phe93, Tyr 100, and Phe101 form a binding interface for CLR, whereas Trp74 and Phe92 may interact with ligands that bind to the CLR/RAMP1 heterodimer. © 2006 by the Biophysical Society.

Dynamic complexity of chaotic transitions in high-dimensional classical dynamics:Leu-Enkephalin folding

Leu-Enkephalin in explicit water is simulated using classical molecular dynamics. A ß-turn transition is investigated by calculating the topological complexity (in the "computational mechanics" framework [J. P. Crutchfield and K. Young, Phys. Rev. Lett., 63, 105 (1989)]) of the dynamics of both the peptide and the neighbouring water molecules. The complexity of the atomic trajectories of the (relatively short) simulations used in this study reflect the degree of phase space mixing in the system. It is demonstrated that the dynamic complexity of the hydrogen atoms of the peptide and almost all of the hydrogens of the neighbouring waters exhibit a minimum precisely at the moment of the ß-turn transition. This indicates the appearance of simplified periodic patterns in the atomic motion, which could correspond to high-dimensional tori in the phase space. It is hypothesized that this behaviour is the manifestation of the effect described in the approach to molecular transitions by Komatsuzaki and Berry [T. Komatsuzaki and R.S. Berry, Adv. Chem. Phys., 123, 79 (2002)], where a "quasi-regular" dynamics at the transition is suggested. Therefore, for the first time, the less chaotic character of the folding transition in a realistic molecular system is demonstrated. © Springer-Verlag Berlin Heidelberg 2006.

Complexity of classical dynamics of molecular systems. II. Finite statistical complexity of a water-Na+ system

The computational mechanics approach has been applied to the orientational behavior of water molecules in a molecular dynamics simulated water–Na + system. The distinctively different statistical complexity of water molecules in the bulk and in the first solvation shell of the ion is demonstrated. It is shown that the molecules undergo more complex orientational motion when surrounded by other water molecules compared to those constrained by the electric field of the ion. However the spatial coordinates of the oxygen atom shows the opposite complexity behavior in that complexity is higher for the solvation shell molecules. New information about the dynamics of water molecules in the solvation shell is provided that is additional to that given by traditional methods of analysis.

High pressure and low temperature study of ammonia borane and lithium amidoborane

Hydrogen has been considered as a potentially efficient and environmentally friendly alternative energy solution. However, one of the most important scientific and technical challenges that the "hydrogen economy" faces is the development of safe and economically viable on-board hydrogen storage for fuel cell applications, especially to the transportation sector. Ammonia borane (BH3NH 3), a solid state hydrogen storage material, possesses exceptionally high hydrogen content (19.6 wt%).However, a fairly high temperature is required to release all the hydrogen atoms, along with the emission of toxic borazine. Recently research interests are focusing on the improvement of H2 discharge from ammonia borane (AB) including lowering the dehydrogenation temperature and enhancing hydrogen release rate using different techniques. Till now the detailed information about the bonding characteristics of AB is not sufficient to understand details about its phases and structures. ^ Elemental substitution of ammonia borane produces metal amidoboranes. Introduction of metal atoms to the ammonia borane structure may alter the bonding characteristics. Lithium amidoborane is synthesized by ball milling of ammonia borane and lithium hydride. High pressure study of molecular crystal provides unique insight into the intermolecular bonding forces and phase stability. During this dissertation, Raman spectroscopic study of lithium amidoborane has been carried out at high pressure in a diamond anvil cell. It has been identified that there is no dihydrogen bond in the lithium amidoborane structure, whereas dihydrogen bond is the characteristic bond of the parent compound ammonia borane. It has also been identified that the B-H bond becomes weaker, whereas B-N and N-H bonds become stronger than those in the parent compound ammonia borane. At high pressure up to 15 GPa, Raman spectroscopic study indicates two phase transformations of lithium amidoborane, whereas synchrotron X-ray diffraction data indicates only one phase transformation of this material. ^ Pressure and temperature has a significant effect on the structural stability of ammonia borane. This dissertation explored the phase transformation behavior of ammonia borane at high pressure and low temperature using in situ Raman spectroscopy. The P-T phase boundary between the tetragonal (I4mm) and orthorhombic (Pmn21) phases of ammonia borane has been determined. The transition has a positive Clapeyron slope which indicates the transition is of exothermic in nature. Influence of nanoconfinemment on the I4mm to Pmn2 1 phase transition of ammonia borane was also investigated. Mesoporus silica scaffolds SBA-15 with pore size of ~8 nm and MCM-41 with pore size of 2.1-2.7 nm, were used to nanoconfine ammonia borane. During cooling down, the I4mm to Pmn21 phase transition was not observed in MCM-41 nanoconfined ammonia borane, whereas the SBA-15 nanocondfined ammonia borane shows the phase transition at ~195 K. Four new phases of ammonia borane were also identified at high pressure up to 15 GPa and low temperature down to 90 K.^

Interdigitating organic bilayers direct the short interlayer spacing in hybrid organic–inorganic layered vanadium oxide nanostructures

Layered metal oxides provide a single-step route to sheathed superlattices of atomic layers of a variety of inorganic materials, where the interlayer spacing and overall layered structure forms the most critical feature in the nanomaterials’ growth and application in electronics, health, and energy storage. We use a combination of computer simulations and experiments to describe the atomic-scale structure, dynamics and energetics of alkanethiol-intercalated layered vanadium oxide-based nanostructures. Molecular dynamics (MD) simulations identify the unusual substrate-constrained packing of the alkanethiol surfactant chains along each V2O5 (010) face that combines with extensive interdigitation between chains on opposing faces to maximize three-dimensional packing in the interlayer regions. The findings are supported by high resolution electron microscopy analyses of synthesized alkanethiol-intercalated vanadium oxide nanostructures, and the preference for this new interdigitated model is clarified using a large set of MD simulations. This dependency stresses the importance of organic–inorganic interactions in layered material systems, the control of which is central to technological applications of flexible hybrid nanomaterials.