Molecular basis for inner kinetochore configuration through RWD domain-peptide interactions
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Schmitzberger, Florian↗
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Theoretical Study of the Electronic Spectra of a Polycyclic Aromatic Hydrocarbon, Naphthalene, and its Derivatives
In order to preselect possible candidates for the origin of diffuse interstellar bands observed, semiempirical quantum mechanical method INDO/S was applied to the optical spectra of neutral, cationic, and anionic states of naphthalene and its hydrogen abstraction and addition derivatives. Comparison with experiment shows that the spectra of naphthalene and its ions were reliably predicted. The configuration interaction calculations with single-electron excitations provided reasonable excited state wavefunctions compared to ab initio calculations that included higher excitations. The degree of similarity of the predicted spectra of the hydrogen abstraction and derivatives to those of naphthalene and ions depends largely on the similarity of the it electron configurations. For the hydrogen addition derivatives, very little resemblance of the predicted spectra to naphthalene was found because of the disruption of the aromatic conjugation system. The relevance of these calculations to astrophysical issues is discussed within the context of these polycyclic aromatic hydrocarbon models. Comparing the calculated electronic energies to the Diffuse Interstellar Bands (DIBs), a list of possible candidates of naphthalene derivatives is established which provides selected candidates for a definitive test through laboratory studies.
Du, Ping↗
Theoretical calculations on the electron absorption spectra of selected Polycyclic Aromatic Hydrocarbons (PAH) and derivatives
As a theoretical component of the joint effort with the laboratory of Dr. Lou Allamandola to search for potential candidates for interstellar organic carbon compound that are responsible for the visible diffuse interstellar absorption bands (DIB's), quantum mechanical calculations were performed on the electron absorption spectra of selected polycyclic aromatic hydrocarbons (PAH) and derivatives. In the completed project, 15 different species of naphthalene, its hydrogen abstraction and addition derivatives, and corresponding cations and anions were studied. Using semiempirical quantum mechanical method INDO/S, the ground electronic state of each species was evaluated with restricted Hartree-Fock scheme and limited configuration interaction. The lowest energy spin state for each species was used for electron absorption calculations. Results indicate that these calculations are accurate enough to reproduce the spectra of naphthalene cation and anion observed in neon matrix. The spectral pattern of the hydrogen abstraction and addition derivatives predicted based on these results indicate that the electron configuration of the pi orbitals of these species is the dominant determinant. A combined list of 19 absorptions calculated from 4500 A to 10,400 A were compiled and suggested as potential candidates that are relevant for the DIB's absorptions. Continued studies on pyrene and derivatives revealed the ground state symmetries and multiplicities of its neutral, anionic, and cationic species. Spectral calculations show that the cation (B(sub 3g)-2) and the anion (A(sub u)-2) are more likely to have low energy absorptions in the regions between 10 kK and 20 kK, similar to naphthalene. These absorptions, together with those to be determined from the hydrogen abstraction and addition derivatives of pyrene, can be used to provide additional candidates and suggest experimental work in the search for interstellar compounds that are responsible for DIB's.
Du, Ping↗
Atomistic and phase field simulations of three dimensional interactions of {$10\bar12$} twins with grain boundaries in Mg: twin transmission and dislocation emission
In polycrystals, the interaction of dislocations and twins with grain boundaries (GBs) plays a role in hardening and formability during plastic deformation. While dislocation-GB interactions are relatively well-understood, twin-GB interactions remain mostly unknown. In this work, an approach using molecular dynamics and phase-field simulations is followed to study the forward and lateral interactions between {$10\bar12$} twins and tilt grain boundaries in Mg. Molecular dynamics results show that the resolved shear stress on slip/twinning modes of the neighboring grain, not the geometric alignment, is the dominant factor in determining the outcome of the twin-GB interactions. For some lateral interaction configurations, as the misorientation angle increases, the resolved shear stress on the same {$10\bar12$} twin variant of the neighboring grain reduces while it increases for slip or I 2 stacking fault emissions or other twin modes such as {$11\bar12$} and {$10\bar11$}, explaining why twin transmission is not seen at high misorientation angles. Furthermore, lateral and forward interactions of the twin with tilt grain boundaries whose misorientation axes are normal to the coherent twin boundary show significantly different outcomes. For the forward interaction, the twin is absorbed and stacking faults are emitted when interacting for low misorientation angles (up to 30°) while the lateral interaction results in twin transmission, nucleation of a {$11\bar12$} twin, and emission of I 2 stacking faults. Finally, comparisons between twin interactions with symmetric and asymmetric tilt GBs with different GB structures show similar outcomes.
36 MATERIALS SCIENCE↗
Vibrational analysis of methyl cation—Rare gas atom complexes: CH + 3 —Rg (Rg = He, Ne, Ar, Kr)
The vibrational spectra of simple CH + 3 —Rg (Rg = He, Ne, Ar, Kr) complexes have been studied by vibrational configuration interaction theory relying on multidimensional potential energy surfaces (PESs) obtained from explicitly correlated coupled cluster calculations, CCSD(T)-F12a. In agreement with experimental results, the series of rare gas atoms leads to rather unsystematic results and indicates huge zero point vibrational energy effects for the helium complex. In order to study these sensitive complexes more consistently, we also introduce configuration averaged vibrational self-consistent field theory, which is a generalization of standard vibrational self-consistent field theory to several configurations. The vibrational spectra of the complexes are compared to that of the methyl cation, for which corrections due to scalar-relativistic effects, high-order coupled-cluster terms, e.g., quadruple excitations, and core-valence correlation have explicitly been accounted for. The occurrence of tunneling splittings for the vibrational ground-state of CH + 3 —He has been investigated on the basis of semiclassical instanton theory. Furthermore these calculations and a direct comparison of the energy profiles along the intrinsic reaction coordinates with that of the hydronium cation, H 3 O + , suggest that tunneling effects for vibrationally excited states should be very small.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Studies of aerothermal loads generated in regions of shock/shock interaction in hypersonic flow
Experimental studies were conducted to examine the aerothermal characteristics of shock/shock/boundary layer interaction regions generated by single and multiple incident shocks. The presented experimental studies were conducted over a Mach number range from 6 to 19 for a range of Reynolds numbers to obtain both laminar and turbulent interaction regions. Detailed heat transfer and pressure measurements were made for a range of interaction types and incident shock strengths over a transverse cylinder, with emphasis on the 3 and 4 type interaction regions. The measurements were compared with the simple Edney, Keyes, and Hains models for a range of interaction configurations and freestream conditions. The complex flowfields and aerothermal loads generated by multiple-shock impingement, while not generating as large peak loads, provide important test cases for code prediction. The detailed heat transfer and pressure measurements proved a good basis for evaluating the accuracy of simple prediction methods and detailed numerical solutions for laminar and transitional regions or shock/shock interactions.
Holden, Michael S.↗
I ntera C hem : Exploring Excited States in Virtual Reality with Ab Initio Interactive Molecular Dynamics
InteraChem is an ab initio interactive molecular dynamics (AI-IMD) visualizer that leverages recent advances in virtual reality hardware and software, as well as the graphical processing unit (GPU)-accelerated TeraChem electronic structure package, in order to render quantum chemistry in real time. We introduce the exploration of electronically excited states via AI-IMD using the floating occupation molecular orbital-complete active space configuration interaction method. The optimization tools in InteraChem enable identification of excited state minima as well as minimum energy conical intersections for further characterization of excited state chemistry in small- to medium-sized systems. We demonstrate that finite-temperature Hartree–Fock theory is an efficient method to perform ground state AI-IMD. InteraChem allows users to track electronic properties such as molecular orbitals and bond order in real time, resulting in an interactive visualization tool that aids in the interpretation of excited state chemistry data and makes quantum chemistry more accessible for both research and educational purposes.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Analytic Nuclear Gradients for Complete Active Space Linearized Pair-Density Functional Theory
Accurately modeling photochemical reactions is difficult due to the presence of conical intersections and locally avoided crossings, as well as the inherently multiconfigurational character of excited states. As such, one needs a multistate method that incorporates state interaction in order to accurately model the potential energy surface at all nuclear coordinates. The recently developed linearized pair-density functional theory (L-PDFT) is a multistate extension of multiconfiguration PDFT, and it has been shown to be a cost-effective post-MCSCF method (as compared to more traditional and expensive multireference many-body perturbation methods or multireference configuration interaction methods) that can accurately model potential energy surfaces in regions of strong nuclear–electronic coupling in addition to accurately predicting Franck–Condon vertical excitations. Here, in this paper, we report the derivation of analytic gradients for L-PDFT and their implementation in the PySCF-forge software, and we illustrate the utility of these gradients for predicting ground- and excited-state equilibrium geometries and adiabatic excitation energies for formaldehyde, s-trans-butadiene, phenol, and cytosine.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The dissociation energy of N2
The requirements for very accurate ab initio quantum chemical prediction of dissociation energies are examined using a detailed investigation of the nitrogen molecule. Although agreement with experiment to within 1 kcal/mol is not achieved even with the most elaborate multireference CI (configuration interaction) wave functions and largest basis sets currently feasible, it is possible to obtain agreement to within about 2 kcal/mol, or 1 percent of the dissociation energy. At this level it is necessary to account for core-valence correlation effects and to include up to h-type functions in the basis. The effect of i-type functions, the use of different reference configuration spaces, and basis set superposition error were also investigated. After discussing these results, the remaining sources of error in our best calculations are examined.
Almloef, Jan↗
The dissociation energy of N2
The requirements for very accurate ab initio quantum chemical prediction of dissociation energies are examined using a detailed investigation of the nitrogen molecule. Although agreement with experiment to within 1 kcal/mol is not achieved even with the most elaborate multireference CI (configuration interaction) wave functions and largest basis sets currently feasible, it is possible to obtain agreement to within about 2 kcal/mol, or 1 percent of the dissociation energy. At this level it is necessary to account for core-valence correlation effects and to include up to h-type functions in the basis. The effect of i-type functions, the use of different reference configuration spaces, and basis set superposition error were also investigated. After discussing these results, the remaining sources of error in our best calculations are examined.
Almlof, Jan↗
The Interactions Between Nitrogen and Oxygen Molecules
Lippincott's delta-function model for atomic interactions is analyzed, both physically and mathematically, and extended, by differentiation between K- and L-shell electrons and the introduction of a variable parameter in the expression for the delta-function strength, to cover homonuclear molecules more complex than hydrogen. In addition, modifications are made which allow treatments of diatomic, heteronuclear molecules. This theory, in conjunction with a reasonably extensive study of resonance, dispersion, and configuration interaction phenomena, as well as the use of simple quantum mechanical arguments, is then applied to the N2-N2, N2-O2, and O2-O2 interactions.
Meador, Willard E., Jr.↗
System technology analysis of aeroassisted orbital transfer vehicles. Moderate lift/drag (0.75-1.5): Volume 1A, part 2: Executive summary, phase 2
Significant achievements and activities of Phase 2 of a study to assess aeroassisted orbit transfer vehicle (AOTV) system technology are summarized. Phase 2 was directed towards identification and prioritization of technology payoffs of representative space based mid lift/drag ratio (L/D) AOTV's and the cryofueled propulsion subsystem - configuration interactions. Enhancing technology areas were identified which could provide substantial transport cost reduction. These include: (1) improved lifetime of storable propellant engines; (2) avionics weight reduction; (3) external thermal protection system weight reduction; (4) decrease of uncertainties in aerodynamic and aerothermodynamic performance; electrical power subsystem weight reduction due to incorporation of advanced materials; and (6) structural shell weight reduction. Results indicated that advanced aerothermodynamic methodology and aft end configuring may provide an enlarged allowable zone for engine nozzle protrusions into the separated flow region. Payload manifesting and non-hydrogen propellant manifesting at the space station is recommended.
Source record↗
Proton decays in 16 Ne and 18 Mg and isospin-symmetry breaking in carbon isotopes and isotones
We report that proton-rich nuclei possess unique properties in the nuclear chart. Due to the presence of both continuum coupling and Coulomb interaction, phenomena such as halos, Thomas-Ehrman shift, and proton emissions can occur. Relevant experimental data are difficult to obtain, so that theoretical calculations are needed to understand nuclei at drip lines and to guide experimentalists. In particular, the 16 Ne and 18 Mg isotopes are supposed to be one-proton and/or two-proton emitting nuclei, but associated experimental data are either incomplete or even unavailable. Consequently, we performed Gamow shell model calculations of carbon isotones bearing A = 15 - 18 . Isospin-symmetry breaking occurring in carbon isotones and isotopes is also discussed. It is hereby shown that the mixed effects of continuum coupling and Coulomb interaction at drip lines generate complex patterns in isospin multiplets. Added to that, it is possible to determine the one-proton and two-proton widths of 16 Ne and 18 Mg . Obtained decay patterns are in agreement with those obtained in previous experimental and theoretical works. Moreover, to our knowledge, this is the first theoretical calculation of binding energy and partial decay widths of 18 Mg in a configuration interaction picture.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Can TDDFT Describe Excited Electronic States of Naphthol Photoacids? A Closer Look with EOM-CCSD
The 1 L b and 1 L a excited states of naphthols are characterized by using time-dependent density functional theory (TDDFT), configuration interaction with singles (CIS), and equation-of-motion coupled cluster singles and doubles (EOM-CCSD) methods. TDDFT fails dramatically at predicting the energy and ordering of the 1 L a and 1 L b excited states as observed experimentally, while EOM-CCSD accurately predicts the excited states as characterized by natural transition orbital analysis. Here, the limitations of TDDFT are attributed to the absence of correlation from doubly excited configurations as well as the inconsistent description of excited electronic states of naphthol photoacids revealed by excitation analysis based on the one-electron transition density matrix.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
On the Use of a Mixed Gaussian/Finite-Element Basis Set for the Calculation of Rydberg States
Configuration-interaction studies are reported for the Rydberg states of the helium atom using mixed Gaussian/finite-element (GTO/FE) one particle basis sets. Standard Gaussian valence basis sets are employed, like those, used extensively in quantum chemistry calculations. It is shown that the term values for high-lying Rydberg states of the helium atom can be obtained accurately (within 1 cm -1), even for a small GTO set, by augmenting the n-particle space with configurations, where orthonormalized interpolation polynomials are singly occupied.
Thuemmel, Helmar T.↗
Understanding the anharmonic vibrational structure of the carbon dioxide dimer
Understanding the vibrational structure of the CO 2 system is important to confirm the potential energy surface and interactions in such van der Waals complexes. In this work, we use our previously developed mbCO2 potential function to explore the vibrational structure of the CO 2 monomer and dimer. The potential function has been trained to reproduce the potential energies at the CCSD(T)-F12b/aug-cc-pVTZ level of electronic structure theory. The harmonic approximation, as well as anharmonic corrections using vibrational structure theories such as vibrational self-consistent field, vibrational second-order Moller-Plesset perturbation, and vibrational configuration interaction (VCI), is applied to address the vibrational motions. We compare the vibrational results using the mbCO2 potential function with traditional electronic structure theory results and to experimental frequencies. The anharmonic results for the monomer most closely match the experimental data to within 3 cm -1 , including the Fermi dyad frequencies. The intermolecular and intramolecular dimer frequencies were treated separately and show good agreement with the most recent theoretical and experimental results from the literature. The VCI treatment of the dimer vibrational motions accounts for vibrational mixing and delocalization, such that we observe the dimer Fermi resonance phenomena, both in the intramolecular and intermolecular regions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Resonant x-ray emission across the L 3 edge of uranium compounds
A narrow bandwidth x-ray beamline and a multi-crystal von Hamos spectrometer were used to record x-ray absorption and x-ray emission (XES) across the uranium L 3 edge of UO 2 , UO 3 , Cs 2 UO 2 Cl 4 , and Cs 2 UCl 6 . Measurements were made over 17150–17250 eV with an instrumental resolution of ∼2 eV. This resolution allowed the use of Lorentzian peak fits to the L 3 N 4 and L 3 N 5 characteristic x-ray fluorescence lines that have ∼12–13 eV lifetime widths. The fluorescence yields of the four compounds display strong white lines near threshold and multiple scattering features at higher energies. The XES spectra were fit with three Lorentzians, two for the L 3 N 4 and L 3 N 5 lines and one for inelastic scattering by 2p–6d excitations and 4d–6d final states. The intensities of the white lines were largely due to the inelastic scattering component. To support the measurements, relativistic equation-of-motion coupled-cluster and restricted active space configuration interaction calculations were performed for uranium core-excitation energies in Cs 2 UO 2 Cl 4 and Cs 2 UCl 6 . These calculations with rigorous treatments of relativistic effects are shown to provide accurate uranium L 3 -edge binding energies, L 3 N 5 emission energies, as well as the energy losses in the inelastic scattering process. The measured and calculated results show variations between compounds with U(IV) oxidation states that contain 6d 0 5f 2 electrons in their ground configurations (UO 2 and Cs 2 UCl 6 ) compared with U(VI) compounds (UO 3 and Cs 2 UO 2 Cl 4 ) with empty 5f and 6d configurations.
74 ATOMIC AND MOLECULAR PHYSICS↗
Vibrational levels of a generalized Morse potential
A Generalized Morse Potential (GMP) is an extension of the Morse Potential (MP) with an additional exponential term and an additional parameter that compensate for MP’s erroneous behavior in the long range part of the interaction potential. Because of the additional term and parameter, the vibrational levels of the GMP cannot be solved analytically, unlike the case for the MP. We present several numerical approaches for solving the vibrational problem of the GMP based on Galerkin methods, namely, the Laguerre Polynomial Method (LPM), the Symmetrized LPM, and the Polynomial Expansion Method (PEM), and apply them to the vibrational levels of the homonuclear diatomic molecules B 2 , O 2 , and F 2 , for which high level theoretical near full configuration interaction (CI) electronic ground state potential energy surfaces and experimentally measured vibrational levels have been reported. Overall, the LPM produces vibrational states for the GMP that are converged to within spectroscopic accuracy of 0.01 cm –1 in between 1 and 2 orders of magnitude faster and with much fewer basis functions/grid points than the Colbert–Miller Discrete Variable Representation (CN-DVR) method for the three homonuclear diatomic molecules examined in this study.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗