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At least 127 records · Page 7

Formation of Carbon Nanotube Based Gears: Quantum Chemistry and Molecular Mechanics Study of the Electrophilic Addition of o-Benzyne to Fullerenes, Graphene, and Nanotubes

Considerable progress has been made in recent years in chemical functionalization of fullerene molecules. In some cases, the predominant reaction products are different from those obtained (using the same reactants) from polycyclic aromatic hydrocarbons (PAHs). One such example is the cycloaddition of o-benzyne to C60. It is well established that benzyne adds across one of the rings in naphthalene, anthracene and other PAHs forming the [2+4] cycloaddition product (benzobicyclo[2.2.2.]-octatriene with naphthalene and triptycene with anthracene). However, Hoke et al demonstrated that the only reaction path for o-benzyne with C60 leads to the [2+2] cycloaddition product in which benzyne adds across one of the interpentagonal bonds (forming a cyclobutene ring in the process). Either reaction product results in a loss of aromaticity and distortion of the PAH or fullerene substrate, and in a loss of strain in the benzyne. It is not clear, however, why different products are preferred in these cases. In the current paper, we consider the stability of benzyne-nanotube adducts and the ability of Brenner's potential energy model to describe the structure and stability of these adducts. The Brenner potential has been widely used for describing diamondoid and graphitic carbon. Recently it has also been used for molecular mechanics and molecular dynamics simulations of fullerenes and nanotubes. However, it has not been tested for the case of functionalized fullerenes (especially with highly strained geometries). We use the Brenner potential for our companion nanogear simulations and believe that it should be calibrated to insure that those simulations are physically reasonable. In the present work, Density Functional theory (DFT) calculations are used to determine the preferred geometric structures and energetics for this calibration. The DFT method is a kind of ab initio quantum chemistry method for determining the electronic structure of molecules. For a given basis set expansion, it is comparable in accuracy to the MP2 method (better than Hartree Fock, but less accurate than more extensive electron correlation methods such as MP4 or CCSD). However, for systems with large numbers of basis functions it more efficient than any other methods that include electron correlation effects. In this presentation we show the results of DFT calculations for the reaction of benzyne with naphthalene, C60, and nanotube models. We compare energies for [2+2] and [2+4] cycloaddition products. The preferred products for the naphthalene and C60 reactions have been determined by experiment and, thus, these cases serve as a validation of our quantum chemical approach. We also compare the DFT and Brenner potential results. Finally we can predict the likelihood of reaction between benzyne and nanotubes.

Jaffe, Richard↗

Low-energy electron scattering from CO. 2: Ab-initio study using the frame-transformation theory

The Wigner-Eisenbud R matrix method has been combined with the frame transformation theory to study electron scattering from molecular systems. The R matrix, calculated at the boundary point of the molecular core radius, has been transformed to the space frame in order to continue the solution of the scattering equations in the outer region where rotational motion of the nuclei is taken into account. This procedure has been applied to a model calculation of thermal energy electron scattering from CO.

Chandra, N.↗

Macromolecular recognition: Structural aspects of the origin of the genetic system

Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of evolution of life. Using computational and modeling techniques and guided by analogies from present day systems we, seek to understand the emergence of genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. In one possible scenario, the RNA enzymatic reaction plays a key role in the emergence of the self-replicating and offers a clue to the onset of enzymatic catalysis prior to the existence of the protein biosynthetic machinery. Our ultimate goal is to propose a simple RNA segment which contains the specificity and catalytic activity of the contemporary RNA enzyme and which could emerge in a primordial chemical environment. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation have been studied. Another important aspect of this reaction is the identity of the functional groups which are essential for the acid base catalysis. The structural characteristics of the target helices, particularly a possible role of G center dot T pair, is under examination by molecular dynamics (MD) simulation technique. Modeling of the ancestral aminoacyl-tRNA synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. Assuming that the catalytic function evolved before the elements of specific recognition of a particular amino acid, we are exploring the minimal structural requirements for the catalysis of tRNA aminoacylation. The molecular modeling system SYBYL was used for this study based on the high resolution crystallographic structures of the present day tyrosyl-adenylate:tyrRS and tRNA(Gln): ATP:glnRS complexes. The trinucleotide CCA of the 3'-end tRNA is placed into the active site pocket of tyrRS, based on the scheme of interaction between tRNA(Gln) and glnRS, and upon the stereochemistry of the tyrRS:tRNA:Tyr-AMP transition state. This provides a model of the non-specific recognition of a tRNA's 3'-end by an aRS, which might be similar to that of the ancestral aRS's. In the next step, modeling of the rest of the acceptor stem of tRNA (Tyr) with tyrRS is carried out.

Rein, Robert↗

Molecular Modeling and Experimental Investigations of Nonlinear Optical Compounds Monosubstituted Derivatives of Dicyanovinylbenzene

A search for potential nonlinear optical compounds was performed using the Cambridge Structure Database and molecular modeling. We investigated a series of monosubstituted derivatives of dicyanovinylbenzene, since the nonlinear optical (NLO) properties of such derivatives (o-methoxy-dicyanovinylbenzene, DIVA) were studied earlier. The molecular geometry of these compounds was investigated with x-ray analysis and discussed along with the results of molecular mechanics and ab initio quantum chemical calculations. The influence of crystal packing on the planarity of the molecules of this series has been revealed. Two new compounds from the series studied, ortho-F and para-Cl-dicyanovinylbenzene, according to powder measurements, were found to be NLO compounds in the crystal state about 10 times more active than urea. The peculiarities of crystal structure formation in the framework of balance between van der Waals and electrostatic interactions have been discussed. The crystal shape of DIVA and two new NLO compounds have been calculated on the basis of the known crystal structure.

Timofeeva, Tatiana V.↗

Heats of Segregation of BCC Binaries from Ab Initio and Quantum Approximate Calculations

We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.

Good, Brian S.↗

Recommended Direct Simulation Monte Carlo Collision Model Parameters for Reacting Methane Flows

While hydrocarbon combustion and gas-surface interactions have been simulated for a variety of applications in continuum solvers, such processes have been rarely investigated in Direct Simulation Monte Carlo (DSMC). Thus Variable Hard/Soft Sphere (VHS/VSS)collision parameters are not available for most molecules of interest in the decomposition of methane, a significant pyrolysis gas product and potential atmospheric species for Titan re-entries. As these properties are essential for accurate modeling of gas transport and thermochemical effects, a method must be devised to compute them for use in DSMC. In this study, the methodology outlined in Stephani et al is utilized to compute the VHS/VSS parameters by fitting the Ω(1,1)and Ω(2,2) collision integrals [1]. These collision integrals are typically computed from intermolecular potentials and are used in CFD simulations to calculate transport properties such as viscosity, thermal conductivity, and diffusion. This approach ensures consistency between micro-scale collisions and macro-scale transport properties. To produce the necessary collision integrals needed for the fitting routine, we utilize the method described by Laricchiuta et al, where collision integrals are computed based on the constituent particles’ polarizability and effective electron number [2].Preliminary computations of pure-species Ω(1,1)and Ω(2,2)collision integrals produced from the coupled approach of Stephani et al and Laricchiuta et al for methane show good agreement with those computed via available ab-initio Potential Energy Surface Computations, as seen in Figure 1. Above 300K, no more than 12% deviation is observed between the two results over the temperature range of the fitted PES data [3].Current results of this study include full collision-specificVSS transport properties for a complex-species mixture involving major byproducts of pure methane decomposition. Targeted final results will include a comprehensive list of VSS parameters relevant toDSMC simulations of Titan atmospheric entry, based on the reduced kinetic model of Savajano et al [4].

M R Gosma↗

Ab initio calculation of infrared intensities for the linear isoelectronic series HCN, HNC, CO, HCO/+/, and HOC/+/

Ab initio infrared intensities and dipole moment derivatives expressed in atomic polar tensor form are calculated using the 4-31 and 6-31G(double asterisk) basis sets for the isoelectronic HCN, HNC, CO, HCO(+), and HOC(+) series of molecules. The calculated atomic polar tensors are analyzed in terms of the charge-charge flux-overlap model, which is found to be useful in explaining some of the trends observed in the dipole moment derivatives for this series of molecules. A detailed examination of the dipole moment derivatives for the structural isomers indicates some of the ways in which experimental atomic polar tensors for one isomer should be modified to predict infrared intensities for the other isomer. The absolute intensities calculated for the HCO(+) and HOC(+) ions are believed to be accurate to within a factor of 2 and thus should be useful in astrophysical applications.

Rogers, J. D.↗

Boost-phase discrimination research activities

Theoretical research in two areas was performed. The aerothermodynamics research focused on the hard-body and rocket plume flows. Analytical real gas models to describe finite rate chemistry were developed and incorporated into the three-dimensional flow codes. New numerical algorithms capable of treating multi-species reacting gas equations and treating flows with large gradients were also developed. The computational chemistry research focused on the determination of spectral radiative intensity factors, transport properties and reaction rates. Ab initio solutions to the Schrodinger equation provided potential energy curves transition moments (radiative probabilities and strengths) and potential energy surfaces. These surfaces were then coupled with classical particle reactive trajectories to compute reaction cross-sections and rates.

Cooper, David M.↗

Molecular Modeling and Experimental Study of Nonlinear Optical Compounds: Mono-Substituted Derivatives of Dicyanovinylbenzene

A search for potential nonlinear optical (NLO) compounds has been performed using the Cambridge Structural Database and molecular modeling. We have studied a series of mono-substituted derivatives of dicyanovinylbenzene as the NLO properties of one of its derivatives (o-methoxy-dicyanovinylbenzene, DIVA) were described earlier. The molecular geometry in the series of the compounds studied was investigated with an X- ray analysis and discussed along with results of molecular mechanics and ab initio quantum chemical calculations. The influence of crystal packing on the molecular planarity has been revealed. Two new compounds from the series studied were found to be active for second harmonic generation (SHG) in the powder. The measurements of SHG efficiency have shown that the o-F- and p-Cl-derivatives of dicyanovinylbenzene are about 10 and 20- times more active than urea, respectively. The peculiarities of crystal structure formation in the framework of balance between the van der Waals and electrostatic interactions have been discussed. The crystal morphology of DIVA and two new SHG-active compounds have been calculated on the basis of their known crystal structures.

Timofeeva, Tatyana V.↗

Modeling the interaction Between Ethylene Diamine and Water Films on the Surface of a Carbon Nanotube

It has been observed that a carbon nanotube (CNT) AFM tip coated with ethylene diamine (EDA) penetrates the liquid water-air interface more easily than an uncoated nanotube tip. The EDA coating remains intact through repeated cycles of dipping and removal. In order to understand the physical basis for this observation, we use ab initio quantum chemistry calculations to study the EDA-CNT-water interaction and to parameterize a force field describing this system. Molecular dynamics (MD) simulations are carried out for EDA-water mixtures and an EDA-coated carbon nanotube immmed in water. These simulations are similar to our earlier MD study that characterized the CNT-water interface. The attractive CNT-EDA and CNT-water interactions arise primarily from van der Waals forces, and the EDA-EDA, EDA-water and water-water interactions are mainly due to hydrogen bond formation. The binding energ of single EDA molecule to the nanotube is nearly three times larger than the corresponding value found for water (4.3 versus 1.5 kcal mol, respectively). The EDA molecules readily stick to and diffuse along the CNT surface. As a resulf mixing of the EDA and water films does not occur on the timescale of the MD simulations. The EDA film reduces the hydrophobicity of the nanotube surface and acts like a prototypical surfactant in stabilizing the suspension of carbon nanotubes in water. For this presentation, we use the MD simulations to determine how the presence of the carbon nanotube surface perturbs the properties of EDA-water mixtures.

Jaffe, Richard L.↗

Conformational properties, torsional potential, and vibrational force field for methacryloyl fluoride - An ab initio investigation

The structure, torsional potentials, vibrational spectra, and harmonic force fields for s-cis and s-trans isomers of methacryloyl fluoride are examined to understand the conformational properties of the molecules and their relationship to macroscopic polymer properties. The structure is found to be in good agreement with experiment. It is shown by calculations that the energy difference between the cis and the transisomers is less than 1 kcal/mol at both the split valence and the split valence polarized levels, with the trans form favored. Analysis of the torsional potentials indicates that a rigid rotor model provides a reasonable description of the motion of the COF group in the molecule. The torsional barrier to interconvert the s-trans to the s-cis form is found to be 7.0 kcal/mol. A fit of the data to a three-term Fourier series shows that it is possible to reproduce the experimentally derived barrier, even though a direct determination indicates that the barrier is higher.

Laskowski, B. C.↗

Chromospheric heating by acoustic shocks - A confrontation of GHRS observations of Alpha Tauri (K5 III) with ab initio calculations

We compare ab initio calculations of semiforbidden C II line profiles near 2325 A with recently published observations of the inactive red giant Alpha Tau (K5 III) obtained using the GHRS on board the Hubble Space Telescope. Our one-dimensional, time-dependent calculations assume that the chromosphere is heated by stochastic acoustic shocks generated by photospheric convection. We calculate various models using results from traditional (mixing length) convection zone calculations as input to hydrodynamical models. The semiforbidden C II line profiles and ratios provide sensitive diagnostics of chromospheric velocity fields, electron densities, and temperatures. We identify major differences between observed and computed line profiles which are related to basic gas dynamics and which are probably not due to technical modeling restrictions. If the GHRS observations are representative of chromospheric conditions at all epochs, then one (or more) of our model assumptions must be incorrect. Several possibilities are examined. We predict time variability of semiforbidden C II lines for comparison with observations. Based upon data from the IUE archives, we argue that photospheric motions associated with supergranulation or global pulsation modes are unimportant in heating the chromosphere of Alpha Tau.

Judge, P. G.↗

Anisotropic Nanomechanics of Boron Nitride Nanotubes: Nanostructured "Skin" Effect

The stiffness and plasticity of boron nitride nanotubes are investigated using generalized tight-binding molecular dynamics and ab-initio total energy methods. Due to boron-nitride BN bond buckling effects, compressed zigzag BN nanotubes are found to undergo novel anisotropic strain release followed by anisotropic plastic buckling. The strain is preferentially released towards N atoms in the rotated BN bonds. The tubes buckle anisotropically towards only one end when uniaxially compressed from both. A "skin-effect" model of smart nanocomposite materials is proposed which will localize the structural damage towards the 'skin' or surface side of the material.

Srivastava, Deepak↗

Ab Initio and Improved Empirical Potentials for the Calculation of the Anharmonic Vibrational States and Intramolecular Mode Coupling of N-Methylacetamide

The second-order Moller-Plesset ab initio electronic structure method is used to compute points for the anharmonic mode-coupled potential energy surface of N-methylacetamide (NMA) in the trans(sub ct) configuration, including all degrees of freedom. The vibrational states and the spectroscopy are directly computed from this potential surface using the Correlation Corrected Vibrational Self-Consistent Field (CC-VSCF) method. The results are compared with CC-VSCF calculations using both the standard and improved empirical Amber-like force fields and available low temperature experimental matrix data. Analysis of our calculated spectroscopic results show that: (1) The excellent agreement between the ab initio CC-VSCF calculated frequencies and the experimental data suggest that the computed anharmonic potentials for N-methylacetamide are of a very high quality; (2) For most transitions, the vibrational frequencies obtained from the ab initio CC-VSCF method are superior to those obtained using the empirical CC-VSCF methods, when compared with experimental data. However, the improved empirical force field yields better agreement with the experimental frequencies as compared with a standard AMBER-type force field; (3) The empirical force field in particular overestimates anharmonic couplings for the amide-2 mode, the methyl asymmetric bending modes, the out-of-plane methyl bending modes, and the methyl distortions; (4) Disagreement between the ab initio and empirical anharmonic couplings is greater than the disagreement between the frequencies, and thus the anharmonic part of the empirical potential seems to be less accurate than the harmonic contribution;and (5) Both the empirical and ab initio CC-VSCF calculations predict a negligible anharmonic coupling between the amide-1 and other internal modes. The implication of this is that the intramolecular energy flow between the amide-1 and the other internal modes may be smaller than anticipated. These results may have important implications for the anharmonic force fields of peptides, for which N-methylacetamide is a model.

Gregurick, Susan K.↗

Empirical InfraRed Line Lists for Five SO2 Isotopologues: 32/33/34/36S16O2 and 32S18O2

Using the latest published, empirically refined potential energy surface (PES) Ames-1 and purely ab initio CCSD(T)/aug-cc-pVQZ dipole moment surface (DMS), we have computed Infrared line lists for five symmetric isotopologues of sulfur dioxide: 32S16O2 (626), 33S16O2 (636), 34S16O2 (646), 36S16O2 (666), and 32S18O2 (828). The line lists are based on J=0-80 rovibrational variational calculations with E’ ≤ 8000 cm-1. The 34S16O2 and 33S16O2 line lists are compared to the experiment-based models in the HIgh-resolution TRANsmission molecular absorption database (HITRAN2012, http://www.cfa.harvard.edu/hitran/) and the Cologne Database for Molecular Spectroscopy, CDMS (http://www.astro.uni-koeln.de/cdms/). The accuracy for computed 646 band origins is similar to what has been reported for the main isotopologue, i.e. 0.01 – 0.03 cm-1 for bands up to 5500 cm-1. For rovibrational transitions, the 646 line position and intensity deviation patterns are much simpler and more self-consistent than those of the main isotopologue 626. The discrepancies are mainly found for higher Ka/J transitions. 626 and 646 exhibit comparable line position and intensity agreement for lower Ka/J transitions. The line position deviations for the 636 purely rotational band are parallel to those of 626 and 646, while its line intensity deviations do not show branching patterns as we found in the 626 and 646 cases. Predictions for the other minor isotopologues are expected to exhibit similar accuracy. These line lists are accurate enough to provide alternatives for missing bands of 626 and the minor isotopologues. It may significantly facilitate the laboratory spectroscopic measurement and analysis, as well as to identify these isotopologues in various astrophysical environments.

Sulfur Dioxide↗

Theoretical studies of dissociative recombination

The calculation of dissociative recombination rates and cross sections over a wide temperature range by theoretical quantum chemical techniques is described. Model calculations on electron capture by diatomic ions are reported which illustrate the dependence of the rates and cross sections on electron energy, electron temperature, and vibrational temperature for three model crossings of neutral and ionic potential curves. It is shown that cross sections for recombination to the lowest vibrational level of the ion can vary by several orders of magnitude depending upon the position of the neutral and ionic potential curve crossing within the turning points of the v = 1 vibrational level. A new approach for calculating electron capture widths is reported. Ab initio calculations are described for recombination of O2(+) leading to excited O atoms.

Guberman, S. L.↗

The C4H radical and the diffuse interstellar bands. An ab initio study

An ab initio study of the low-lying electronic states of C4H has been presented where the species studied has a chi(2)sigma(+) ground state and two low lying pi states. Based on the vertical and adiabatic excitation energies between those states it is suggested that the 4428 A diffuse interstellar band is not carried by C4H. The application of the particle in a box model shows strong coincidences between the strong DIB's and predicted wavelengths of pi-pi transitions in C(2n)H series. Based on those coincidences, it is suggested the C(2n)H species as good candidates for carriers of diffuse interstellar bands.

Kolbuszewski, Marcin↗

Ab initio determination of the proton affinities of small neutral and anionic molecules

The proton affinity of a molecule in the gas phase is a fundamental measure of its basicity and is the factor controlling the course of many ion-molecule reactions. In this article, ab initio molecular orbital theory at the MP4/6-311 ++ G(3df, 3pd) level of theory is demonstrated to predict proton affinities (PA's) for small neutral and anionic bases to within 2 kcal mol-1. Furthermore, the errors are random, indicating that there are likely no systematic errors in either the experimental or theoretical PA's. Also, this level of theory is used to calibrate less sophisticated theoretical models which are suitable for larger molecules; the MP4/6-311 ++ G(2d, 2p) and MP2/6-311 ++ G(d, p) theoretical models should be particularly useful. A procedure for predicting the vibrational frequencies for anion is proposed and applied to CH3-, NH2-, OH-, and CN-.

Non-NASA Center↗