ISS EPS Orbital Replacement Unit Block Diagrams
NASA Technical Reports Server (NTRS)
Schmitz, Gregory V.
2001-01-01
The attached documents are being provided to Switching Power Magazine for information purposes. This magazine is writing a feature article on the International Space Station Electrical Power System, focusing on the switching power processors. These units include the DC-DC Converter Unit (DDCU), the Bi-directional Charge/Discharge Unit (BCDU), and the Sequential Shunt Unit (SSU). These diagrams are high-level schematics/block diagrams depicting the overall functionality of each unit.
Stability diagrams for a rigid gyrostat in a circular orbit
NASA Astrophysics Data System (ADS)
Hughes, P. C.; Golla, D. F.
1984-05-01
The dynamics of a rigid gyrostat travelling in a circular orbit are reviewed. The two torques to be balanced are the gyroscopic torque associated with the once per orbit precession of the in plane angular momentum vector, and the gravitational torque that results from the principal inertial axes not being aligned with the orbiting axes. Different methods of balancing these two torques lead to different classes of relative equilibria, viz., the cylindrical case, the conical case, the hyperbolic case, and the general case. The principal contribution is to present a large number of stability diagrams for the many different cases and subcases that arise. A large number of equilbria are, in fact, unstable. However, as shown here, they can usually be stabilized by adding a momentum wheel aligned with the pitch axis.
Basic primitives for molecular diagram sketching
2010-01-01
A collection of primitive operations for molecular diagram sketching has been developed. These primitives compose a concise set of operations which can be used to construct publication-quality 2 D coordinates for molecular structures using a bare minimum of input bandwidth. The input requirements for each primitive consist of a small number of discrete choices, which means that these primitives can be used to form the basis of a user interface which does not require an accurate pointing device. This is particularly relevant to software designed for contemporary mobile platforms. The reduction of input bandwidth is accomplished by using algorithmic methods for anticipating probable geometries during the sketching process, and by intelligent use of template grafting. The algorithms and their uses are described in detail. PMID:20923555
Fake molecular-orbital calculations
NASA Astrophysics Data System (ADS)
Harris, Frank E.; Trautwein, Alfred; Delhalle, Joseph
1980-06-01
The FAKE method of approximate molecular-orbital calculations is presented and illustrated by application to a number of molecules. The method is of the extended Huckel type but uses accurately computed kinetic-energy matrix elements and avoids scale factors of the Wolfsberg—Helmholtz type. It also includes neighbor-atom charge effects and single-center off-diagonal matrix elements. These features permit FAKE occupied-orbital energies and charge distributions to come into close agreement with corresponding ab initio quantities.
How Different Variants of Orbit Diagrams Influence Student Explanations of the Seasons
ERIC Educational Resources Information Center
Lee, Victor R.
2010-01-01
The cause of the seasons is often associated with a very particular alternative conception: That the earth's orbit around the sun is highly elongated, and the differences in distance result in variations in temperature. It has been suggested that the standard diagrams used to depict the earth's orbit may be in some way responsible for the initial…
Orbital effect of magnetic field on the Majorana phase diagram
NASA Astrophysics Data System (ADS)
Nijholt, Bas; Akhmerov, Anton R.
2016-06-01
Studies of Majorana bound states in semiconducting nanowires frequently neglect the orbital effect of a magnetic field. Systematically studying its role leads us to several conclusions for designing Majoranas in this system. Specifically, we show that for experimentally relevant parameter values the orbital effect of a magnetic field has a stronger impact on the dispersion relation than the Zeeman effect. While Majoranas do not require the presence of only one dispersion subband, we observe that the size of the Majoranas becomes unpractically large, and the band gap unpractically small, when more than one subband is filled. Since the orbital effect of a magnetic field breaks several symmetries of the Hamiltonian, it leads to the appearance of large regions in parameter space with no band gap whenever the magnetic field is not aligned with the wire axis. The reflection symmetry of the Hamiltonian with respect to the plane perpendicular to the wire axis guarantees that the wire stays gapped in the topologically nontrivial region as long as the field is aligned with the wire.
Some Observations on Molecular Orbital Theory
ERIC Educational Resources Information Center
Journal of Chemical Education, 2005
2005-01-01
A few flawed predictions in the context of homonuclear diatomic molecules are presented in order to introduce students to molecular orbital (MO) theory. A common misrepresentation of the relationship between the energy of an atomic orbital and the energy of the MO associated with the atomic orbital is illustrated.
Molecular Complexation and Phase Diagrams of Urea/PEG Mixtures
NASA Astrophysics Data System (ADS)
Fu, Guoepeng; Kyu, Thein
2014-03-01
Polyethylene glycol (PEG) and urea complexation has been known to form a stable crystal due to molecular complexation. The effect of molecular weight of PEG on the phase diagrams of its blends with urea has been explored. In the case of high molecular weight PEG8k/urea, the observed phase diagram is azeotrope, accompanied by eutectoid reactions in the submerged phases such as induced stable ``alpha'' phase crystals and metastable ``beta'' phase crystals. The metastable crystal can transform to stable crystal under a certain thermal annealing condition. However, the phase diagram of PEG1k/urea is of coexistence loop, whereas PEG400/urea exhibits eutectic character. Subsequently, the change of azeotrope to eutectic behavior with PEG molecular weight is analyzed in the context of the combined Flory-Huggins theory of liquid-liquid demixing and phase field theory of crystal solidification. Of particular interest is that only a very small urea amount (2 wt%) is needed to form a stable inclusion crystal via complexation with PEG. Potential application in lithium battery is discussed based on AC impedance spectroscopy and cyclic voltammetry. Supported by NSF-DMR 1161070.
ERIC Educational Resources Information Center
Bo¨rgel, Jonas; Campbell, Michael G.; Ritter, Tobias
2016-01-01
The presentation of d-orbital splitting diagrams for square planar transition metal complexes in textbooks and educational materials is often inconsistent and therefore confusing for students. Here we provide a concise summary of the key features of orbital splitting diagrams for square planar complexes, which we propose may be used as an updated…
Orbiting molecular-beam laboratory
NASA Technical Reports Server (NTRS)
Outlaw, R. A.; Brock, F. J.
1977-01-01
The composition of the atmosphere within the planned orbital envelope of the Space Shuttle and the velocity necessary to maintain a stable orbit within that envelope provide unique conditions for forming a high-purity, moderate energy beam (about 5 eV) of atomic oxygen. At 500 km, for example, atomic oxygen comprises approximately 90% of the atmosphere. Since the mean thermal speed of the ambient atomic oxygen is substantially less than the orbital speed, a high-purity beam can be generated by sweeping through the gas with a series of beam-forming truncated conical shells. Characteristics of the beam, including energy distribution, flux, and purity variation with orbital altitude and methods for lowering the mean energy, are presented. Gas-surface interaction experiments that have been proposed for this laboratory are also discussed.
A Simple Huckel Molecular Orbital Plotter
ERIC Educational Resources Information Center
Ramakrishnan, Raghunathan
2013-01-01
A program is described and presented to readily plot the molecular orbitals from a Huckel calculation. The main features of the program and the scope of its applicability are discussed through some example organic molecules. (Contains 2 figures.)
Moderate pressure phase diagram of methane by Molecular Dynamics simulations
NASA Astrophysics Data System (ADS)
Spanu, L.; Donadio, D.; Galli, G.
2008-12-01
By using classical and ab initio Molecular Dynamics simulations we have investigated the phase diagram of methane up to ~ 25 Gpa. The melting line of phase I (fcc) was computed in a range of pressure corresponding to the Earth's crust conditions by using classical potentials and three different approaches -free energy calculations, phase coexistence method and integration over the coexistence line. The three techniques consistently give a phase boundary in good agreement with known experimental values. The solid phases in a range of temperature between 100K and 300K were investigated using a metadynamics technique, our results providing a possible assignments of structure and explanation of existing, controversial experiments.
Molecular Electronic Terms and Molecular Orbital Configurations.
ERIC Educational Resources Information Center
Mazo, R. M.
1990-01-01
Discussed are the molecular electronic terms which can arise from a given electronic configuration. Considered are simple cases, molecular states, direct products, closed shells, and open shells. Two examples are provided. (CW)
ERIC Educational Resources Information Center
Orenha, Renato P.; Galembeck, Sérgio E.
2014-01-01
This computational experiment presents qualitative molecular orbital (QMO) and computational quantum chemistry exercises of NO, NO[superscript+], and NO[superscript-]. Initially students explore several properties of the target molecules by Lewis diagrams and the QMO theory. Then, they compare qualitative conclusions with EHT and DFT calculations…
Spin–orbit interaction mediated molecular dissociation
Kokkonen, E. Jänkälä, K.; Kettunen, J. A.; Heinäsmäki, S.; Karpenko, A.; Huttula, M.; Löytynoja, T.
2014-05-14
The effect of the spin–orbit interaction to photofragmentation is investigated in the mercury(II) bromide (HgBr{sub 2}) molecule. Changes in the fragmentation between the two spin–orbit components of Hg 5d photoionization, as well as within the molecular-field-splitted levels of these components are observed. Dissociation subsequent to photoionization is studied with synchrotron radiation and photoelectron-photoion coincidence spectroscopy. The experimental results are accompanied by relativistic ab initio analysis of the photoelectron spectrum.
Molecular diagnosis of orbital inflammatory disease.
Rosenbaum, James T; Choi, Dongseok; Wilson, David J; Grossniklaus, Hans E; Sibley, Cailin H; Harrington, Christina A; Planck, Stephen R
2015-04-01
Orbital inflammatory diseases include thyroid eye disease (TED), granulomatosis with polyangiitis (GPA), sarcoidosis, and nonspecific orbital inflammation (NSOI). Histopathological diagnosis usually relies on the clinical context and is not always definitive. Gene expression profiling provides diagnostic and therapeutic information in several malignancies, but its role in evaluating nonmalignant disease is relatively untested. We hypothesized that gene expression profiling could provide diagnostic information for NSOI. We collected formalin-fixed, paraffin-embedded orbital biopsies from 10 institutions and 83 subjects including 25 with thyroid eye disease, 25 nonspecific orbital inflammation, 20 healthy controls, 6 with granulomatosis with polyangiitis, and 7 with sarcoidosis. Tissues were divided into discovery and validation sets. Gene expression was quantified using Affymetrix U133 Plus 2.0 microarrays. A random forest statistical algorithm based on data from 39 probe sets identified controls, GPA, or TED with an average accuracy of 76% (p=0.02). Random forest analysis indicated that 52% of tissues from patients with nonspecific inflammation were consistent with a diagnosis of GPA. Molecular diagnosis by gene expression profiling will augment clinical data and histopathology in differentiating forms of orbital inflammatory disease.
NASA Astrophysics Data System (ADS)
Dauth, M.; Wiessner, M.; Feyer, V.; Schöll, A.; Puschnig, P.; Reinert, F.; Kümmel, S.
2014-10-01
Fascinating pictures that can be interpreted as showing molecular orbitals have been obtained with various imaging techniques. Among these, angle resolved photoemission spectroscopy (ARPES) has emerged as a particularly powerful method. Orbital images have been used to underline the physical credibility of the molecular orbital concept. However, from the theory of the photoemission process it is evident that imaging experiments do not show molecular orbitals, but Dyson orbitals. The latter are not eigenstates of a single-particle Hamiltonian and thus do not fit into the usual simple interpretation of electronic structure in terms of molecular orbitals. In a combined theoretical and experimental study we thus check whether a Dyson-orbital and a molecular-orbital based interpretation of ARPES lead to differences that are relevant on the experimentally observable scale. We discuss a scheme that allows for approximately calculating Dyson orbitals with moderate computational effort. Electronic relaxation is taken into account explicitly. The comparison reveals that while molecular orbitals are frequently good approximations to Dyson orbitals, a detailed understanding of photoemission intensities may require one to go beyond the molecular orbital picture. In particular we clearly observe signatures of the Dyson-orbital character for an adsorbed semiconductor molecule in ARPES spectra when these are recorded over a larger momentum range than in earlier experiments.
A Comparison of Molecular Vibrational Theory to Huckel Molecular Orbital Theory.
ERIC Educational Resources Information Center
Keeports, David
1986-01-01
Compares the similar mathematical problems of molecular vibrational calculations (at any intermediate level of sophistication) and molecular orbital calculations (at the Huckel level). Discusses how the generalizations of Huckel treatment of molecular orbitals apply to vibrational theory. (TW)
Crystal field and molecular orbital theory of MBm centres in glasses
NASA Astrophysics Data System (ADS)
Kustov, E. F.; Bulatov, L. I.; Dvoyrin, V. V.; Mashinsky, V. M.; Dianov, E. M.
2010-01-01
The spectral phenomena in optical fibres with bismuth-doped aluminosilicate glass core are explicated on the basis of a molecular orbital theory and of a Schrödinger equation solution, taking into account the exchange, spin-orbit and crystal field interactions of s, p and d electrons of M atoms (M signifies Bi, Sb, Pb, Sn, In, Te, etc) with ligand orbits of environmental B atoms (B signifies O, S, Se, etc). Energy level diagrams and selection rules of transitions between molecular orbital states of s and p electrons of MBm molecule permit us to determine the energies of the main spectral transitions of absorption and luminescent spectra and their correspondence with experimental spectra of different types of optical fibres is obtained.
ERIC Educational Resources Information Center
Tsaparlis, Georgios
1997-01-01
Investigates the impact an undergraduate quantum chemistry course has on students' knowledge and understanding of atomic orbitals, molecular orbitals, and related concepts. Analysis reveals that students do not have a clear understanding of these concepts and confuse the various atomic orbital representations. Includes some suggestions and…
Tuning molecular orbitals in molecular electronics and spintronics.
Kim, Woo Youn; Kim, Kwang S
2010-01-19
With the advance of nanotechnology, a variety of molecules, from single atoms to large-scale structures such as graphene or carbon nanotubes, have been investigated for possible use as molecular devices. Molecular orbitals (MOs) are a key ingredient in determining the transport properties of molecules, because they contain all the quantum mechanical information of molecular electronic structures and offer spatial conduction channels for electron transport. Therefore, the delicate modulation of the MOs enables us to tune the performance of electron transport through the molecule. Electric and magnetic fields are powerful and readily accessible means for that purpose. In this Account, we describe the effects of external fields on molecular electronic and spintronic devices. Quantum transport through a molecule that connects source and drain electrodes depends strongly on the alignment of molecular energy levels with respect to the chemical potentials at both electrodes. This dependence results from the energy levels being exploited in resonant tunneling processes when the molecule is weakly coupled to the electrodes in the molecular junction. Molecular energy levels can be shifted by the Stark effect of an external electric field. For a molecule with no permanent dipole moment, the polarizability is the primary factor determining the energy shift of each MO, according to the second-order Stark effect; more polarizable MOs undergo a larger energy shift. Interestingly, even a small shift may lead to a completely nontrivial result. For example, we show a magnetic on-off switching phenomenon of a molecule controlled by an electric field. If a molecule has a nonmagnetic ground state but a highly polarizable magnetic excited state with an energy slightly above the ground state, the magnetic excited state can have lower energy than the ground state under a sufficiently strong electric field. A magnetic field is normally used to control spin orientation in a ferromagnetic
Molecular orbitals for properties and spectroscopies
Robert, Vincent; Domingo, Alex; Braunstein, Pierre; Danopoulos, Andreas; Monakhov, Kirill
2015-12-31
The description and clarification of spectroscopies and properties goes through ab initio calculations. Wave function based calculations (CASSCF/CASPT2) are particularly appealing since they offer spectroscopic accuracy and means of interpretation. we performed such calculations to elucidate the origin of unusual structural changes and intramolecular electron transfer phenomenon. Based on optimized molecular orbitals and a reading of the multireference wave function, it is suggested that intimate interactions are likely to considerably modify the standard pictures. A so-called PIMA (polarization-induced metalâĹŠarene) interaction similar to the more familiar anion-π interaction is responsible for a significant deviation from sp{sup 3} geometry and an energetic stabilization of 50 kJ/mol in Cr(II) benzyl organometallic complexes. In a similar fashion, it is proposed that the energetic profile of the IVCT (inter valence charge transfer) exhibits strong similarities to the Marcus’ theory, suggesting a response behaviour of the ensemble of electrons as electron transfer occurs in Fe{sup 2+}/Fe{sup 3+} bimetallic compound. The electronic reorganization induced by the IVCT process accounts for 11.8 eV, a very large effect that reduces the transfer energy down to 0.89 eV, in very good agreement with experiments.
Molecular-orbital model for metal-sapphire interfacial strength
NASA Technical Reports Server (NTRS)
Johnson, K. H.; Pepper, S. V.
1982-01-01
Self-consistent-field X-Alpha scattered-wave cluster molecular-orbital models have been constructed for transition and noble metals (Fe, Ni, Cu, and Ag) in contact with a sapphire (Al2O3) surface. It is found that a chemical bond is established between the metal d-orbital electrons and the nonbonding 2p-orbital electrons of the oxygen anions on the Al2O3 surface. An increasing number of occupied metal-sapphire antibonding molecular orbitals explains qualitatively the observed decrease of contact shear strength through the series Fe, Ni, Cu, and Ag.
NASA Astrophysics Data System (ADS)
Dong, Dong; Zou, Xu-Bo; Guo, Guang-Can
2015-07-01
We studied the system of pure Rashba spin-orbit coupled Bose gas with an in-plane magnetic field. Based on the mean field theory, we obtained the zero temperature phase diagram of the system which exhibits three phases, plane wave (PW) phase, striped wave (SW) phase, and zero momentum (ZM) phase. It was shown that with a growing in-plane field, both SW and ZM phases will eventually turn into the PW phase. Furthermore, we adopted the Bogoliubov theory to study the excitation spectrum as well as the sound speed. Project supported by the National Natural Science Foundation of China (Grant No. 10774088).
Orbital Energy Levels in Molecular Hydrogen. A Simple Approach.
ERIC Educational Resources Information Center
Willis, Christopher J.
1988-01-01
Described are the energetics involved in the formation of molecular hydrogen using concepts that should be familiar to students beginning the study of molecular orbital theory. Emphasized are experimental data on ionization energies. Included are two-electron atomic and molecular systems. (CW)
Periodic orbits of the hydrogen molecular ion and their quantization
Duan, Y.; Yuan, J.; Bao, C.
1995-11-01
In a classical study of the hydrogen molecular ion beyond the Born-Oppenheimer approximation (BOA), we have found that segments of trajectories resemble that of the Born-Oppenheimer approximation periodic orbits. The importance of this fact to the classical understanding of chemical bonding leads us to a systematic study of the periodic orbits of the planar hydrogen molecular ion within the BOA. Besides introducing a classification scheme for periodic orbits, we discuss the convergence properties of families of periodic orbits and their bifurcation patterns according to their types. Semiclassical calculations of the density of states based on these periodic orbits yield results in agreement with the exact quantum eigenvalues of the hydrogen molecular ion system.
BetaVoid: molecular voids via beta-complexes and Voronoi diagrams.
Kim, Jae-Kwan; Cho, Youngsong; Laskowski, Roman A; Ryu, Seong Eon; Sugihara, Kokichi; Kim, Deok-Soo
2014-09-01
Molecular external structure is important for molecular function, with voids on the surface and interior being one of the most important features. Hence, recognition of molecular voids and accurate computation of their geometrical properties, such as volume, area and topology, are crucial, yet most popular algorithms are based on the crude use of sampling points and thus are approximations even with a significant amount of computation. In this article, we propose an analytic approach to the problem using the Voronoi diagram of atoms and the beta-complex. The correctness and efficiency of the proposed algorithm is mathematically proved and experimentally verified. The benchmark test clearly shows the superiority of BetaVoid to two popular programs: VOIDOO and CASTp. The proposed algorithm is implemented in the BetaVoid program which is freely available at the Voronoi Diagram Research Center (http://voronoi.hanyang.ac.kr). PMID:24677176
Local Molecular Orbitals from a Projection onto Localized Centers.
Heßelmann, Andreas
2016-06-14
A localization method for molecular orbitals is presented which exploits the locality of the eigenfunctions associated with the largest eigenvalues of the matrix representation of spatially localized functions. Local molecular orbitals are obtained by a projection of the canonical orbitals onto the set of the eigenvectors which correspond to the largest eigenvalues of these matrices. Two different types of spatially localized functions were chosen in this work, a two-parameter smooth-step-type function and the weight functions determined by a Hirshfeld partitioning of the molecular volume. It is shown that the method can provide fairly local occupied molecular orbitals if the positions of the set of local functions are set to the molecular bond centers. The method can also yield reasonably well-localized virtual molecular orbitals, but here, a sensible choice of the positions of the functions are the atomic sites and the locality then depends more strongly on the shape of the set of local functions. The method is tested for a range of polypeptide molecules in two different conformations, namely, a helical and a β-sheet conformation. Futhermore, it is shown that an adequate locality of the occupied and virtual orbitals can also be obtained for highly delocalized systems. PMID:27164445
NASA Technical Reports Server (NTRS)
Adler, David S.; Roberts, William W., Jr.
1992-01-01
Techniques which use longitude-velocity diagrams to identify molecular cloud complexes in the disk of the Galaxy are investigated by means of model Galactic disks generated from N-body cloud-particle simulations. A procedure similar to the method used to reduce the low-level emission in Galactic l-v diagrams is employed to isolate complexes of emission in the model l-v diagram (LVCs) from the 'background'clouds. The LVCs produced in this manner yield a size-line-width relationship with a slope of 0.58 and a mass spectrum with a slope of 1.55, consistent with Galactic observations. It is demonstrated that associations identified as LVCs are often chance superpositions of clouds spread out along the line of sight in the disk of the model system. This indicates that the l-v diagram cannot be used to unambiguously determine the location of molecular cloud complexes in the model Galactic disk. The modeling results also indicate that the existence of a size-line-width relationship is not a reliable indicator of the physical nature of cloud complexes, in particular, whether the complexes are gravitationally bound objects.
Tada, Tomofumi; Yoshizawa, Kazunari
2015-12-28
In this study, we report our viewpoint of single molecular conductance in terms of frontier orbitals. The orbital rule derived from orbital phase and amplitude is a powerful guideline for the qualitative understanding of molecular conductance in both theoretical and experimental studies. The essence of the orbital rule is the phase-related quantum interference, and on the basis of this rule a constructive or destructive pathway for electron transport is easily predicted. We have worked on the construction of the orbital rule for more than ten years and recently found from its application that π-stacked molecular junctions fabricated experimentally are in line with the concept for conductance-decay free junctions. We explain the orbital rule using benzene molecular junctions with the para-, meta- and ortho-connections and discuss linear π-conjugated chains and π-stacked molecular junctions with respect to their small decay factors in this manuscript.
Super-atom molecular orbital excited states of fullerenes.
Johansson, J Olof; Bohl, Elvira; Campbell, Eleanor E B
2016-09-13
Super-atom molecular orbitals are orbitals that form diffuse hydrogenic excited electronic states of fullerenes with their electron density centred at the centre of the hollow carbon cage and a significant electron density inside the cage. This is a consequence of the high symmetry and hollow structure of the molecules and distinguishes them from typical low-lying molecular Rydberg states. This review summarizes the current experimental and theoretical studies related to these exotic excited electronic states with emphasis on femtosecond photoelectron spectroscopy experiments on gas-phase fullerenes.This article is part of the themed issue 'Fullerenes: past, present and future, celebrating the 30th anniversary of Buckminster Fullerene'.
Gai, Jing-Gang; Zuo, Yuan
2012-06-01
Numerous studies suggest that two-phase morphology and thick interface are separately beneficial to the viscosity reduction and mechanical property maintainence of the matrix when normal molecular weight polymer (NMWP) is used for modification of ultrahigh molecular weight polyethylene (UHMWPE). Nevertheless, it is very difficult to obtain a UHMWPE/NMWP blend which may demonstrate both two-phase morphology and thick interface. In this work, dissipative particle dynamics simulations and Flory-Huggins theory are applied in predicting the optimum NMWP and the corresponding conditions, wherein the melt flowability of UHMWPE can be improved while its mechanical properties can also be retained. As is indicated by dissipative particle dynamics simulations and phase diagram calculated from Flory-Huggins theory, too small Flory-Huggins interaction parameter (χ) and molecular chain length of NMWP (N(NMWP)) may lead to the formation of a homogeneous phase, whereas very large interfacial tension and thin interfaces might also appear when parameters N(NMWP) and χ are too large. When these parameters are located in the metastable region of the phase diagram, however, two-phase morphology occurs and interfaces of the blends are extremely thick. Therefore, metastable state is found to be advisable for both the viscosity reduction and mechanical property improvement of the UHMWPE/NMWP blends.
Nonorthogonal molecular orbital method: single-determinant theory.
Watanabe, Yoshihiro; Matsuoka, Osamu
2014-05-28
Using the variational principle, we have derived a variant of the Adams-Gilbert equation for nonorthogonal orbitals of a single-determinant wave function, which we name the modified Adams-Gilbert equation. If we divide the molecular system into several subsystems, such as bonds, lone pairs, and residues, we can solve the equations for the subsystems one by one. Thus, this procedure has linear scaling. We have presented a practical procedure for solving the equations that is also applicable to macromolecular calculations. The numerical examples show that the procedure yields, with reasonable effort, results comparable with those of the Hartree-Fock-Roothaan method for orthogonal orbitals. To resolve the convergence difficulty in the self-consistent-field iterations, we have found that virtual molecular-orbital shifts are very effective.
Coulomb-corrected molecular orbital tomography of nitrogen
Zhai, Chunyang; He, Lixin; Lan, Pengfei; Zhu, Xiaosong; Li, Yang; Wang, Feng; Shi, Wenjing; Zhang, Qingbin; Lu, Peixiang
2016-01-01
High-order harmonic generation (HHG) from aligned molecules has provided a promising way to probe the molecular orbital with an Ångström resolution. This method, usually called molecular orbital tomography (MOT) replies on a simple assumption of the plane-wave approximation (PW), which has long been questioned due to that PW approximation is known to be valid in the keV energy region. However, the photon energy is usually no more than 100 eV in HHG. In this work, we experimentally reconstruct the highest occupied molecular orbital (HOMO) of nitrogen (N2) by using a Coulomb-corrected MOT (CCMOT) method. In our scheme, the molecular continuum states are described by a Coulomb wave function instead of the PW approximation. With CCMOT, the reconstructed orbital is demonstrated to agree well with the theoretical prediction and retain the main features of the HOMO of N2. Compared to the PW approximation method, the CCMOT shows a significant improvement in eliminating the artificial structures caused by PW approximation. PMID:27000666
Molecular orbital calculations on tumour-inhibitory aniline mustards: QSARs.
Lewis, D F
1989-02-01
1. Molecular orbital calculations by the MINDO/3 method are reported for a series of 23 para-substituted aniline mustards. 2. Quantitative structure-activity relationships are presented which show that electronic structural parameters can be related to a number of features of aniline mustard reactivity.
Frontier orbital control of molecular conductance and its switching.
Tsuji, Yuta; Hoffmann, Roald
2014-04-14
For transmission of electrons through a π system, when the Landauer theory of molecular conductance is viewed from a molecular orbital (MO) perspective, there obtains a simple perturbation theoretic dependence, due to Yoshizawa and Tada, on a) the product of the orbital coefficients at the sites of electrode attachment, and b) the MO energies. The frontier orbitals consistently and simply indicate high or low transmission, even if other orbitals may contribute. This formalism, with its consequent reinforcement and/or interference of conductance, accounts for the (previously explained) difference in direct vs. cross conjugated transmission across an ethylene, as well as the comparative ON/OFF ratios in the experimentally investigated dimethyldihydropyrene and dithienylethene-type single-molecule switches. A strong dependence of the conductance on the site of attachment of the electrodes in a π system is an immediate extrapolation; the theory then predicts that for some specified sites the switching behavior will be inverted; i.e. the "open" molecular form of the switch will be more conductive.
Local reactivity descriptors from degenerate frontier molecular orbitals
NASA Astrophysics Data System (ADS)
Martínez, Jorge
2009-08-01
Conceptual Density Functional Theory (DFT) has proposed a set of local descriptors to measure the reactivity on specific sites of a molecule, as an example dual descriptor has been successfully used in analyzing interesting systems to understand their local reactivity, however under the frozen orbital approximation (FOA), it is defined from non-degenerate frontier molecular orbitals (FMOs). In this work, the degeneration is taken into account to propose approximated expressions to obtain the dual descriptor, nucleophilic and electrophilic Fukui functions in closed-shell systems. The proposed expressions have been tested on molecules presenting degenerate FMOs.
Intracellular molecular distributions in spacecraft experiments in orbit around Earth
NASA Astrophysics Data System (ADS)
Haranas, Ioannis; Gkigkitzis, Ioannis; Zouganelis, George D.
2012-04-01
It is possible that the nucleolous inside the cell plays the role of a "gravity receptor". Furthermore, cells up to 10 μm in diameter can demonstrate some effect due to the redistribution of mitochondria or nucleolous. Effects of gravity should be present in various cell systems where larger objects such as the ribosomes move from cell to cell. In this paper we study the effects of gravity on cells. In particular, we examine the resulting intracellular molecular distribution due to Brownian motion and the ordered distribution of molecules under the action of gravity, where n0 is the number per unit volume at certain level, and n is the number per unit volume above that level. This is an experiment that takes place at a certain orbital altitude in a spacecraft in orbit around Earth, where the acceleration due to the central field is corrected for the oblateness and also the rotation of the Earth. We found that equatorial circular and elliptical orbits have the highest n/n0 ratios. This experiment takes place in circular and elliptical orbits, with eccentricities e = 0, 0.1 and involves a bacterial cell at an orbital altitude of 300 km. We found that n/n0 = 1.00299 and 1.0037 respectively, which is still a 0.6-0.7 % higher than n/n0 = 0.0996685 calculated on the surface of the Earth. Examining mitochondria in similar orbital experiments we found that equatorial orbits result to higher n/n0 ratios. In particular, we found that n/n0 = 8.38119, where an elliptical orbit of eccentricity e = 0.1 results to n/n0 = 13.8525. Both are high above 100%, signifying the importance of Brownian motion over gravity. Our results are of interest to biomedical applications. Molecular concentrations are important for various processes such as the embryogenesis, positional homeostasis and its relation to cell energy expenditure, cell torque, cell deformation, and more. These results indicate that statistical molecular distributions play an important role for the recognition of a
A Simple Demonstration of Atomic and Molecular Orbitals Using Circular Magnets
ERIC Educational Resources Information Center
Chakraborty, Maharudra; Mukhopadhyay, Subrata; Das, Ranendu Sekhar
2014-01-01
A quite simple and inexpensive technique is described here to represent the approximate shapes of atomic orbitals and the molecular orbitals formed by them following the principles of the linear combination of atomic orbitals (LCAO) method. Molecular orbitals of a few simple molecules can also be pictorially represented. Instructors can employ the…
Liu, Shubin; Schauer, Cynthia K
2015-02-01
To have a quantitative understanding about the origin of conformation stability for molecular systems is still an unaccomplished task. Frontier orbital interactions from molecular orbital theory and energy partition schemes from density functional reactivity theory are the two approaches available in the literature that can be used for this purpose. In this work, we compare the performance of these approaches for a total of 48 simple molecules. We also conduct studies to flexibly bend bond angles for water, carbon dioxide, borane, and ammonia molecules to obtain energy profiles for these systems over a wide range of conformations. We find that results from molecular orbital interactions using frontier occupied orbitals such as the highest occupied molecular orbital and its neighbors are only qualitatively, at most semi-qualitatively, trustworthy. To obtain quantitative insights into relative stability of different conformations, the energy partition approach from density functional reactivity theory is much more reliable. We also find that the electrostatic interaction is the dominant descriptor for conformational stability, and steric and quantum effects are smaller in contribution but their contributions are indispensable. Stable molecular conformations prefer to have a strong electrostatic interaction, small molecular size, and large exchange-correlation effect. This work should shed new light towards establishing a general theoretical framework for molecular stability.
Liu, Shubin E-mail: schauer@unc.edu; Schauer, Cynthia K. E-mail: schauer@unc.edu
2015-02-07
To have a quantitative understanding about the origin of conformation stability for molecular systems is still an unaccomplished task. Frontier orbital interactions from molecular orbital theory and energy partition schemes from density functional reactivity theory are the two approaches available in the literature that can be used for this purpose. In this work, we compare the performance of these approaches for a total of 48 simple molecules. We also conduct studies to flexibly bend bond angles for water, carbon dioxide, borane, and ammonia molecules to obtain energy profiles for these systems over a wide range of conformations. We find that results from molecular orbital interactions using frontier occupied orbitals such as the highest occupied molecular orbital and its neighbors are only qualitatively, at most semi-qualitatively, trustworthy. To obtain quantitative insights into relative stability of different conformations, the energy partition approach from density functional reactivity theory is much more reliable. We also find that the electrostatic interaction is the dominant descriptor for conformational stability, and steric and quantum effects are smaller in contribution but their contributions are indispensable. Stable molecular conformations prefer to have a strong electrostatic interaction, small molecular size, and large exchange-correlation effect. This work should shed new light towards establishing a general theoretical framework for molecular stability.
MOPAC manual. Sixth edition. A general molecular orbital package
NASA Astrophysics Data System (ADS)
Stewart, James J.
1990-11-01
MOPAC is a general-purpose, semi-empirical molecular orbital program for the study of chemical reactions involving molecules, ions, and linear polymers. It implements the semi-empirical Hamiltonians MNDO, AM1, PM3, and MINDO/3 and combines the calculations of vibrational spectra, thermodynamic quantities, isotopic substitution effects, time-dependent effects, and force constants in a fully integrated program. Elements parameterized at the PM3 level are H, Be, C, N, O, F, Mg, Al, Si, P, S, Cl, Zn, lja, lje, As, Br, Cd, In, Sn, Sb, Te, I, Hg, Tl, Pb, and Bi. Within the electronic part of the calculation, molecular and localized orbitals excited states up to sextets, chemical bond indices, charges, etc. are computed. Both intrinsic and dynamic reaction coordinates can be calculated. A transition-state location routine and two transition-state optimizing routines are available for studying chemical reactions.
GAUSSIAN 76: An ab initio Molecular Orbital Program
DOE R&D Accomplishments Database
Binkley, J. S.; Whiteside, R.; Hariharan, P. C.; Seeger, R.; Hehre, W. J.; Lathan, W. A.; Newton, M. D.; Ditchfield, R.; Pople, J. A.
1978-01-01
Gaussian 76 is a general-purpose computer program for ab initio Hartree-Fock molecular orbital calculations. It can handle basis sets involving s, p and d-type Gaussian functions. Certain standard sets (STO-3G, 4-31G, 6-31G*, etc.) are stored internally for easy use. Closed shell (RHF) or unrestricted open shell (UHF) wave functions can be obtained. Facilities are provided for geometry optimization to potential minima and for limited potential surface scans.
A low Earth orbit molecular beam space simulation facility
NASA Technical Reports Server (NTRS)
Cross, J. B.
1984-01-01
A brief synopsis of the low Earth orbit (LEO) satellite environment is presented including neutral and ionic species. Two ground based atomic and molecular beam instruments are described which are capable of simulating the interaction of spacecraft surfaces with the LEO environment and detecting the results of these interactions. The first detects mass spectrometrically low level fluxes of reactively and nonreactively surface scattered species as a function of scattering angle and velocity while the second ultrahigh velocity (UHV) molecular beam, laser induced fluorescence apparatus is capable of measuring chemiluminescence produced by either gas phase or gas-surface interactions. A number of proposed experiments are described.
Ikabata, Yasuhiro; Imamura, Yutaka; Nakai, Hiromi
2011-03-01
The intermolecular geometric isotope effect (GIE) in hydrogen bond A-X···B (X = H and D) is investigated theoretically using the nuclear orbital plus molecular orbital (NOMO) theory. To interpret the GIE in terms of physically meaningful energy components such as electrostatic and exchange-repulsion interactions, the reduced variational space self-consistent-field method is extended to the NOMO scheme. The intermolecular GIE is analyzed as a two-stage process: the intramolecular bond shrinkage and the intermolecular bond elongation. According to the isotopic shifts of energy components described by the NOMO/MP2 method, the intermolecular GIE is approximately interpreted as a process reducing the exchange-repulsion interaction after the decrease of electrostatic interaction. PMID:21306139
Nakai, Hiromi; Hoshino, Minoru; Miyamoto, Kaito; Hyodo, Shiaki
2005-04-22
The nuclear orbital plus molecular orbital (NOMO) theory was developed in order to determine the nonadiabatic nuclear and electronic wave functions. This study presents a formulation to remove the contamination of rotational motion as well as translational motion in the NOMO theory. We have formulated the translation- and rotation-free (TRF)-NOMO theory by introducing the TRF Hamiltonian. The principal moment of inertia, which is the denominator in the rotational Hamiltonian, is expanded in a Taylor series. The zeroth-order of the Taylor expansion corresponds to a rigid-body rotator. The first-order terms contribute the coupling between the vibration and the rotation. Hartree-Fock equations have been derived in the framework of the TRF-NOMO theory. Numerical assessments, which were preformed for H2, D2, T2, mu2 (muon dimmer), and H2O, confirmed the importance of the TRF treatment. PMID:15945666
Molecular orbital analysis of the hydrogen bonded water dimer.
Wang, Bo; Jiang, Wanrun; Dai, Xin; Gao, Yang; Wang, Zhigang; Zhang, Rui-Qin
2016-02-24
As an essential interaction in nature, hydrogen bonding plays a crucial role in many material formations and biological processes, requiring deeper understanding. Here, using density functional theory and post-Hartree-Fock methods, we reveal two hydrogen bonding molecular orbitals crossing the hydrogen-bond's O and H atoms in the water dimer. Energy decomposition analysis also shows a non-negligible contribution of the induction term. Our finding sheds light on the essential understanding of hydrogen bonding in ice, liquid water, functional materials and biological systems.
Molecular orbital analysis of the hydrogen bonded water dimer
Wang, Bo; Jiang, Wanrun; Dai, Xin; Gao, Yang; Wang, Zhigang; Zhang, Rui-Qin
2016-01-01
As an essential interaction in nature, hydrogen bonding plays a crucial role in many material formations and biological processes, requiring deeper understanding. Here, using density functional theory and post-Hartree-Fock methods, we reveal two hydrogen bonding molecular orbitals crossing the hydrogen-bond’s O and H atoms in the water dimer. Energy decomposition analysis also shows a non-negligible contribution of the induction term. Our finding sheds light on the essential understanding of hydrogen bonding in ice, liquid water, functional materials and biological systems. PMID:26905305
The activation strain model and molecular orbital theory
Wolters, Lando P; Bickelhaupt, F Matthias
2015-01-01
The activation strain model is a powerful tool for understanding reactivity, or inertness, of molecular species. This is done by relating the relative energy of a molecular complex along the reaction energy profile to the structural rigidity of the reactants and the strength of their mutual interactions: ΔE(ζ) = ΔEstrain(ζ) + ΔEint(ζ). We provide a detailed discussion of the model, and elaborate on its strong connection with molecular orbital theory. Using these approaches, a causal relationship is revealed between the properties of the reactants and their reactivity, e.g., reaction barriers and plausible reaction mechanisms. This methodology may reveal intriguing parallels between completely different types of chemical transformations. Thus, the activation strain model constitutes a unifying framework that furthers the development of cross-disciplinary concepts throughout various fields of chemistry. We illustrate the activation strain model in action with selected examples from literature. These examples demonstrate how the methodology is applied to different research questions, how results are interpreted, and how insights into one chemical phenomenon can lead to an improved understanding of another, seemingly completely different chemical process. WIREs Comput Mol Sci 2015, 5:324–343. doi: 10.1002/wcms.1221 PMID:26753009
Charge transfer processes: the role of optimized molecular orbitals.
Meyer, Benjamin; Domingo, Alex; Krah, Tim; Robert, Vincent
2014-08-01
The influence of the molecular orbitals on charge transfer (CT) reactions is analyzed through wave function-based calculations. Characteristic CT processes in the organic radical 2,5-di-tert-butyl-6-oxophenalenoxyl linked with tetrathiafulvalene and the inorganic crystalline material LaMnO3 show that changes in the inner shells must be explicitly taken into account. Such electronic reorganization can lead to a reduction of the CT vertical transition energy up to 66%. A state-specific approach accessible through an adapted CASSCF (complete active space self-consistent field) methodology is capable of reaching good agreement with the experimental spectroscopy of CT processes. A partitioning of the relaxation energy in terms of valence- and inner-shells is offered and sheds light on their relative importance. This work paves the way to the intimate description of redox reactions using quantum chemistry methods.
Molecular electric moments calculated by using natural orbital functional theory.
Mitxelena, Ion; Piris, Mario
2016-05-28
The molecular electric dipole, quadrupole, and octupole moments of a selected set of 21 spin-compensated molecules are determined employing the extended version of the Piris natural orbital functional 6 (PNOF6), using the triple-ζ Gaussian basis set with polarization functions developed by Sadlej, at the experimental geometries. The performance of the PNOF6 is established by carrying out a statistical analysis of the mean absolute errors with respect to the experiment. The calculated PNOF6 electric moments agree satisfactorily with the corresponding experimental data and are in good agreement with the values obtained by accurate ab initio methods, namely, the coupled-cluster single and doubles and multi-reference single and double excitation configuration interaction methods.
Molecular electric moments calculated by using natural orbital functional theory
NASA Astrophysics Data System (ADS)
Mitxelena, Ion; Piris, Mario
2016-05-01
The molecular electric dipole, quadrupole, and octupole moments of a selected set of 21 spin-compensated molecules are determined employing the extended version of the Piris natural orbital functional 6 (PNOF6), using the triple-ζ Gaussian basis set with polarization functions developed by Sadlej, at the experimental geometries. The performance of the PNOF6 is established by carrying out a statistical analysis of the mean absolute errors with respect to the experiment. The calculated PNOF6 electric moments agree satisfactorily with the corresponding experimental data and are in good agreement with the values obtained by accurate ab initio methods, namely, the coupled-cluster single and doubles and multi-reference single and double excitation configuration interaction methods.
Ab initio molecular simulations with numeric atom-centered orbitals
NASA Astrophysics Data System (ADS)
Blum, Volker; Gehrke, Ralf; Hanke, Felix; Havu, Paula; Havu, Ville; Ren, Xinguo; Reuter, Karsten; Scheffler, Matthias
2009-11-01
We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.
Band Formation in a Molecular Quantum Well via 2D Superatom Orbital Interactions
Dougherty, D. B.; Feng, Min; Petek, Hrvoje; Yates, John T.; Zhao, Jin
2012-12-28
By scanning tunneling microscopy and spectroscopy, we study nearly free electron band formation of the σ*lowest unoccupied molecular orbital of C₆F₆ on a Cu(111) surface. In fractal islands, the lowest unoccupied molecular orbital energy systematically stabilizes with the number of interacting near-neighbor C₆F₆ molecules. Density functional theory calculations reveal the origin of effective intermo- lecular orbital overlap in the previously unrecognized superatom character of the σ*orbital of ₆F₆ molecules. The discovery of superatom orbitals in planar molecules offers a new universal principle for effective band formation, which can be exploited in designing organic semiconductors with nearly free electron properties
van Meer, R; Gritsenko, O V; Baerends, E J
2014-10-14
In recent years, several benchmark studies on the performance of large sets of functionals in time-dependent density functional theory (TDDFT) calculations of excitation energies have been performed. The tested functionals do not approximate exact Kohn-Sham orbitals and orbital energies closely. We highlight the advantages of (close to) exact Kohn-Sham orbitals and orbital energies for a simple description, very often as just a single orbital-to-orbital transition, of molecular excitations. Benchmark calculations are performed for the statistical average of orbital potentials (SAOP) functional for the potential [J. Chem. Phys. 2000, 112, 1344; 2001, 114, 652], which approximates the true Kohn-Sham potential much better than LDA, GGA, mGGA, and hybrid potentials do. An accurate Kohn-Sham potential does not only perform satisfactorily for calculated vertical excitation energies of both valence and Rydberg transitions but also exhibits appealing properties of the KS orbitals including occupied orbital energies close to ionization energies, virtual-occupied orbital energy gaps very close to excitation energies, realistic shapes of virtual orbitals, leading to straightforward interpretation of most excitations as single orbital transitions. We stress that such advantages are completely lost in time-dependent Hartree-Fock and partly in hybrid approaches. Many excitations and excitation energies calculated with local density, generalized gradient, and hybrid functionals are spurious. There is, with an accurate KS, or even the LDA or GGA potentials, nothing problematic about the "band gap" in molecules: the HOMO-LUMO gap is close to the first excitation energy (the optical gap).
Analyzing and Interpreting NMR Spin-Spin Coupling Constants Using Molecular Orbital Calculations
ERIC Educational Resources Information Center
Autschbach, Jochen; Le Guennic, Boris
2007-01-01
Molecular orbital plots are used to analyze and interpret NMR spin-spin coupling constants, also known as J coupling constants. Students have accepted the concept of contributions to molecular properties from individual orbitals without the requirement to provide explicit equations.
ERIC Educational Resources Information Center
Johnson, Adam R.
2013-01-01
A molecular orbital (MO) diagram, especially its frontier orbitals, explains the bonding and reactivity for a chemical compound. It is therefore important for students to learn how to construct one. The traditional methods used to derive these diagrams rely on linear algebra techniques to combine ligand orbitals into symmetry-adapted linear…
[Applications of the Fragment Molecular Orbital Method in Drug Discovery].
Ishikawa, Takeshi
2016-01-01
Recently, ab initio quantum mechanical calculations have been applied to large molecules, including biomolecular systems. The fragment molecular orbital (FMO) method is one of the most efficient approaches for the quantum mechanical investigation of such molecules. In the FMO method, dividing a target molecule into small fragments reduces computational effort. The clear definition of inter-fragment interaction energy (IFIE) as an expression of total energy is another valuable feature of the FMO method because it provides the ability to analyze interactions in biomolecules. Thus, the FMO method is expected to be useful for drug discovery. This study demonstrates applications of the FMO method related to drug discovery. First, IFIE, according to FMO calculations, was used in the optimization of drug candidates for the development of anti-prion compounds. The second example involved interaction analysis of the human immunodeficiency virus type 1 (HIV-1) protease and a drug compound that used a novel analytical method for dispersion interaction, i.e., fragment interaction analysis based on LMP2 (FILM). PMID:26725679
Nakata, Hiroya; Schmidt, Michael W; Fedorov, Dmitri G; Kitaura, Kazuo; Nakamura, Shinichiro; Gordon, Mark S
2014-10-16
The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree–Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.
Nakata, Hiroya; Schmidt, Michael W; Fedorov, Dmitri G; Kitaura, Kazuo; Nakamura, Shinichiro; Gordon, Mark S
2014-10-16
The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree-Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.
Bâldea, Ioan
2014-11-14
Estimating the relative alignment between the frontier molecular orbitals (MOs) that dominates the charge transport through single-molecule junctions represents a challenge for theory. This requires approaches beyond the widely employed framework provided by the density functional theory, wherein the Kohn-Sham 'orbitals' are treated as if they were real MOs, which is not the case. In this paper, we report results obtained by means of quantum chemical calculations, including the equation-of-motion coupled-cluster singles and doubles, which is the state-of-the-art of quantum chemistry for medium-size molecules like those considered here. These theoretical results are validated against data on the MO energy offset relative to the electrodes' Fermi energy extracted from experiments for junctions based on 4,4'-bipyridine and 1,4-dicyanobenzene.
Gilbert, Kathleen M; Skawinski, William J; Misra, Milind; Paris, Kristina A; Naik, Neelam H; Buono, Ronald A; Deutsch, Howard M; Venanzi, Carol A
2004-11-01
Methylphenidate (MP) binds to the cocaine binding site on the dopamine transporter and inhibits reuptake of dopamine, but does not appear to have the same abuse potential as cocaine. This study, part of a comprehensive effort to identify a drug treatment for cocaine abuse, investigates the effect of choice of calculation technique and of solvent model on the conformational potential energy surface (PES) of MP and a rigid methylphenidate (RMP) analogue which exhibits the same dopamine transporter binding affinity as MP. Conformational analysis was carried out by the AM1 and AM1/SM5.4 semiempirical molecular orbital methods, a molecular mechanics method (Tripos force field with the dielectric set equal to that of vacuum or water) and the HF/6-31G* molecular orbital method in vacuum phase. Although all three methods differ somewhat in the local details of the PES, the general trends are the same for neutral and protonated MP. In vacuum phase, protonation has a distinctive effect in decreasing the regions of space available to the local conformational minima. Solvent has little effect on the PES of the neutral molecule and tends to stabilize the protonated species. The random search (RS) conformational analysis technique using the Tripos force field was found to be capable of locating the minima found by the molecular orbital methods using systematic grid search. This suggests that the RS/Tripos force field/vacuum phase protocol is a reasonable choice for locating the local minima of MP. However, the Tripos force field gave significantly larger phenyl ring rotational barriers than the molecular orbital methods for MP and RMP. For both the neutral and protonated cases, all three methods found the phenyl ring rotational barriers for the RMP conformers/invertamers (denoted as cte, tte, and cta) to be: cte, tte > MP > cta. Solvation has negligible effect on the phenyl ring rotational barrier of RMP. The B3LYP/6-31G* density functional method was used to calculate the
Quantum Monte Carlo study of the phase diagram of solid molecular hydrogen at extreme pressures
Drummond, N. D.; Monserrat, Bartomeu; Lloyd-Williams, Jonathan H.; Ríos, P. López; Pickard, Chris J.; Needs, R. J.
2015-01-01
Establishing the phase diagram of hydrogen is a major challenge for experimental and theoretical physics. Experiment alone cannot establish the atomic structure of solid hydrogen at high pressure, because hydrogen scatters X-rays only weakly. Instead, our understanding of the atomic structure is largely based on density functional theory (DFT). By comparing Raman spectra for low-energy structures found in DFT searches with experimental spectra, candidate atomic structures have been identified for each experimentally observed phase. Unfortunately, DFT predicts a metallic structure to be energetically favoured at a broad range of pressures up to 400 GPa, where it is known experimentally that hydrogen is non-metallic. Here we show that more advanced theoretical methods (diffusion quantum Monte Carlo calculations) find the metallic structure to be uncompetitive, and predict a phase diagram in reasonable agreement with experiment. This greatly strengthens the claim that the candidate atomic structures accurately model the experimentally observed phases. PMID:26215251
A growth diagram for plasma-assisted molecular beam epitaxy of GaN nanocolumns on Si(111)
Fernandez-Garrido, S.; Grandal, J.; Calleja, E.; Sanchez-Garcia, M. A.; Lopez-Romero, D.
2009-12-15
The morphology of GaN samples grown by plasma-assisted molecular beam epitaxy on Si(111) was systematically studied as a function of impinging Ga/N flux ratio and growth temperature (730-850 deg. C). Two different growth regimes were identified: compact and nanocolumnar. A growth diagram was established as a function of growth parameters, exhibiting the transition between growth regimes, and showing under which growth conditions GaN cannot be grown due to thermal decomposition and Ga desorption. Present results indicate that adatoms diffusion length and the actual Ga/N ratio on the growing surface are key factors to achieve nanocolumnar growth.
Polarized Molecular Orbital Model Chemistry 3. The PMO Method Extended to Organic Chemistry
Isegawa, Miho; Fiedler, Luke; Leverentz, Hannah R.; Wang, Yingjie; Nachimuthu, Santhanamoorthi; Gao, Jiali; Truhlar, Donald G.
2013-01-01
The polarized molecular orbital (PMO) method, a neglect-of-diatomic-differential-overlap (NDDO) semiempirical molecular orbital method previously parameterized for systems composed of O and H, is here extended to carbon. We modified the formalism and optimized all the parameters in the PMO Hamiltonian by using a genetic algorithm and a database containing both electrostatic and energetic properties; the new parameter set is called PMO2. The quality of the resulting predictions is compared to results obtained by previous NDDO semiempirical molecular orbital methods, both including and excluding dispersion terms. We also compare the PMO2 properties to SCC-DFTB calculations. Within the class of semiempirical molecular orbital methods, the PMO2 method is found to be especially accurate for polarizabilities, atomization energies, proton transfer energies, noncovalent complexation energies, and chemical reaction barrier heights and to have good across-the-board accuracy for a range of other properties, including dipole moments, partial atomic charges, and molecular geometries. PMID:23704835
NASA Astrophysics Data System (ADS)
Petsalakis, Ioannis D.; Theodorakopoulos, Giannoula
2012-02-01
A theoretical approach is described for the design of donor-acceptor intramolecular charge transfer (ICT) systems and for photoinduced electron transfer (PET) hybrids of fullerene, based on orbital level diagrams of the separate donor and acceptor moieties. Minimization of the HOMO-LUMO (highest occupied-lowest unoccupied orbital) gap in ICT systems, translates to a requirement for near degeneracy of the HOMO of the donor and LUMO of the acceptor, determined separately for the two moieties by density functional theory calculations. Similarly, near degeneracy of the LUMO of the donor and LUMO of the acceptor moieties would indicate the possibility of PET in the combined hybrid.
Moving Beyond the Single Center--Ways to Reinforce Molecular Orbital Theory in an Inorganic Course
ERIC Educational Resources Information Center
Cass, Marion E.; Hollingsworth, William E.
2004-01-01
It is suggested that molecular theory should be taught earlier in the inorganic chemistry curriculum even in the introductory chemistry course in order to integrate molecular orbital arguments more effectively throughout the curriculum. The method of teaching relies on having access to molecular modeling software as having access to such software…
Hoshino, Minoru; Nakai, Hiromi
2006-05-21
The translation- and rotation-free nuclear orbital plus molecular orbital (TRF-NOMO) theory was developed to determine the nonadiabatic nuclear and electronic wave functions. This study presents a formulation of TRF-NOMO second-order Moller-Plesset (MP2) perturbation and Epstein-Nesbet (EN) theory with the use of the TRF Hamiltonian. Numerical assessment of the TRF-NOMO/MP2 and EN is performed for several molecules. We confirm the importance of the elimination of translational and rotational motions in the many-body calculations. PMID:16729806
Abramo, M. C.; Caccamo, C. Costa, D.; Munaò, G.
2014-09-07
We report an atomistic molecular dynamics determination of the phase diagram of a rigid-cage model of C{sub 36}. We first show that free energies obtained via thermodynamic integrations along isotherms displaying “van der Waals loops,” are fully reproduced by those obtained via isothermal-isochoric integration encompassing only stable states. We find that a similar result also holds for isochoric paths crossing van der Waals regions of the isotherms, and for integrations extending to rather high densities where liquid-solid coexistence can be expected to occur. On such a basis we are able to map the whole phase diagram of C{sub 36}, with resulting triple point and critical temperatures about 1770 K and 2370 K, respectively. We thus predict a 600 K window of existence of a stable liquid phase. Also, at the triple point density, we find that the structural functions and the diffusion coefficient maintain a liquid-like character down to 1400–1300 K, this indicating a wide region of possible supercooling. We discuss why all these features might render possible the observation of the melting of C{sub 36} fullerite and of its liquid state, at variance with what previously experienced for C{sub 60}.
Spin-orbit coupled molecular quantum magnetism realized in inorganic solid.
Park, Sang-Youn; Do, S-H; Choi, K-Y; Kang, J-H; Jang, Dongjin; Schmidt, B; Brando, Manuel; Kim, B-H; Kim, D-H; Butch, N P; Lee, Seongsu; Park, J-H; Ji, Sungdae
2016-01-01
Molecular quantum magnetism involving an isolated spin state is of particular interest due to the characteristic quantum phenomena underlying spin qubits or molecular spintronics for quantum information devices, as demonstrated in magnetic metal-organic molecular systems, the so-called molecular magnets. Here we report the molecular quantum magnetism realized in an inorganic solid Ba3Yb2Zn5O11 with spin-orbit coupled pseudospin-½ Yb(3+) ions. The magnetization represents the magnetic quantum values of an isolated Yb4 tetrahedron with a total (pseudo)spin 0, 1 and 2. Inelastic neutron scattering results reveal that a large Dzyaloshinsky-Moriya interaction originating from strong spin-orbit coupling of Yb 4f is a key ingredient to explain magnetic excitations of the molecular magnet states. The Dzyaloshinsky-Moriya interaction allows a non-adiabatic quantum transition between avoided crossing energy levels, and also results in unexpected magnetic behaviours in conventional molecular magnets. PMID:27650796
Spin–orbit coupled molecular quantum magnetism realized in inorganic solid
Park, Sang-Youn; Do, S.-H.; Choi, K.-Y.; Kang, J.-H.; Jang, Dongjin; Schmidt, B.; Brando, Manuel; Kim, B.-H.; Kim, D.-H.; Butch, N. P.; Lee, Seongsu; Park, J.-H.; Ji, Sungdae
2016-01-01
Molecular quantum magnetism involving an isolated spin state is of particular interest due to the characteristic quantum phenomena underlying spin qubits or molecular spintronics for quantum information devices, as demonstrated in magnetic metal–organic molecular systems, the so-called molecular magnets. Here we report the molecular quantum magnetism realized in an inorganic solid Ba3Yb2Zn5O11 with spin–orbit coupled pseudospin-½ Yb3+ ions. The magnetization represents the magnetic quantum values of an isolated Yb4 tetrahedron with a total (pseudo)spin 0, 1 and 2. Inelastic neutron scattering results reveal that a large Dzyaloshinsky–Moriya interaction originating from strong spin–orbit coupling of Yb 4f is a key ingredient to explain magnetic excitations of the molecular magnet states. The Dzyaloshinsky–Moriya interaction allows a non-adiabatic quantum transition between avoided crossing energy levels, and also results in unexpected magnetic behaviours in conventional molecular magnets. PMID:27650796
Spin-orbit coupled molecular quantum magnetism realized in inorganic solid.
Park, Sang-Youn; Do, S-H; Choi, K-Y; Kang, J-H; Jang, Dongjin; Schmidt, B; Brando, Manuel; Kim, B-H; Kim, D-H; Butch, N P; Lee, Seongsu; Park, J-H; Ji, Sungdae
2016-09-21
Molecular quantum magnetism involving an isolated spin state is of particular interest due to the characteristic quantum phenomena underlying spin qubits or molecular spintronics for quantum information devices, as demonstrated in magnetic metal-organic molecular systems, the so-called molecular magnets. Here we report the molecular quantum magnetism realized in an inorganic solid Ba3Yb2Zn5O11 with spin-orbit coupled pseudospin-½ Yb(3+) ions. The magnetization represents the magnetic quantum values of an isolated Yb4 tetrahedron with a total (pseudo)spin 0, 1 and 2. Inelastic neutron scattering results reveal that a large Dzyaloshinsky-Moriya interaction originating from strong spin-orbit coupling of Yb 4f is a key ingredient to explain magnetic excitations of the molecular magnet states. The Dzyaloshinsky-Moriya interaction allows a non-adiabatic quantum transition between avoided crossing energy levels, and also results in unexpected magnetic behaviours in conventional molecular magnets.
Spin-orbit coupled molecular quantum magnetism realized in inorganic solid
NASA Astrophysics Data System (ADS)
Park, Sang-Youn; Do, S.-H.; Choi, K.-Y.; Kang, J.-H.; Jang, Dongjin; Schmidt, B.; Brando, Manuel; Kim, B.-H.; Kim, D.-H.; Butch, N. P.; Lee, Seongsu; Park, J.-H.; Ji, Sungdae
2016-09-01
Molecular quantum magnetism involving an isolated spin state is of particular interest due to the characteristic quantum phenomena underlying spin qubits or molecular spintronics for quantum information devices, as demonstrated in magnetic metal-organic molecular systems, the so-called molecular magnets. Here we report the molecular quantum magnetism realized in an inorganic solid Ba3Yb2Zn5O11 with spin-orbit coupled pseudospin-1/2 Yb3+ ions. The magnetization represents the magnetic quantum values of an isolated Yb4 tetrahedron with a total (pseudo)spin 0, 1 and 2. Inelastic neutron scattering results reveal that a large Dzyaloshinsky-Moriya interaction originating from strong spin-orbit coupling of Yb 4f is a key ingredient to explain magnetic excitations of the molecular magnet states. The Dzyaloshinsky-Moriya interaction allows a non-adiabatic quantum transition between avoided crossing energy levels, and also results in unexpected magnetic behaviours in conventional molecular magnets.
A comprehensive diagram to grow InAlN alloys by plasma-assisted molecular beam epitaxy
Fernandez-Garrido, S.; Gacevic, Z.; Calleja, E.
2008-11-10
Indium incorporation and surface morphology of InAlN layers grown on (0001) GaN by plasma-assisted molecular beam epitaxy were investigated as a function of the impinging In flux and the substrate temperature in the 450-610 deg. C range. In incorporation was found to decrease with substrate temperature due to thermal decomposition of the growing layer, while for a given temperature it increased with the impinging In flux until stoichiometry was reached at the growth front. The InN losses during growth followed an Arrhenius behavior characterized by an activation energy of 2.0 eV. A growth diagram highly instrumental to identify optimum growth conditions was established.
Hoshino, Minoru; Nishizawa, Hiroaki; Nakai, Hiromi
2011-07-14
The present study proposes a rigorous non-Born-Oppenheimer theory combining between the explicitly correlated Gaussian (ECG) method and the nuclear orbital plus molecular orbital (NOMO) method. The new method, called ECG-NOMO, adopts the ECG functions between the electronic and nuclear coordinates and, therefore, is capable of describing the nucleus-electron correlation effect accurately. The basic formalism of the ECG-NOMO method is close to the NOMO method, which starts with the Hartree-Fock type equations for NOs and MOs. The present method requires more computational cost than the original NOMO method. However, its cost is significantly smaller than that of the ECG method. The numerical tests was performed for hydrogen-like atoms (H-Ne(9+)) and dihydrogen cations (H(2)(+), D(2)(+) and T(2)(+)), and clarified that the ECG-NOMO method shows the sufficient accuracy. PMID:21766929
Solution of multi-center molecular integrals of Slater-type orbitals
NASA Technical Reports Server (NTRS)
Tai, H.
1989-01-01
The troublesome multi-center molecular integrals of Slater-type orbitals (STO) in molecular physics calculations can be evaluated by using the Fourier transform and proper coupling of the two center exchange integrals. A numerical integration procedure is then readily rendered to the final expression in which the integrand consists of well known special functions of arguments containing the geometrical arrangement of the nuclear centers and the exponents of the atomic orbitals. A practical procedure was devised for the calculation of a general multi-center molecular integrals coupling arbitrary Slater-type orbitals. Symmetry relations and asymptotic conditions are discussed. Explicit expressions of three-center one-electron nuclear-attraction integrals and four-center two-electron repulsion integrals for STO of principal quantum number n=2 are listed. A few numerical results are given for the purpose of comparison.
Liu, Xiaojing; Sun, Xin; Xu, Xijin; Sun, Ping
2015-01-01
By using atomic force microscopy, birth and spread has proved to be the primary growth mechanism for L-prolinium phosphate (LPP). The phenomenon of newly formed islands expanding to the edge of the preceding terrace was observed. The optimized molecular structure and the molecular properties were calculated by density functional theory method. Natural bond orbital analysis was carried out to demonstrate the various inter and intramolecular interactions that are responsible for the stabilization of LPP leading to high NLO activity. Molecular electrostatic potential, frontier molecular orbital analysis and thermodynamic properties were investigated to get a better insight of the molecular properties. Global and local reactivity descriptors were computed to predict the reactivity and reactive sites on the molecules. Non-linear optical (NLO) properties such as the total dipole moment (μ) and first order hyperopolarizability (β) were also calculated to predict NLO behavior.
NASA Astrophysics Data System (ADS)
Hanson, Robert M.
2003-06-01
ORBITAL requires the following software, which is available for free download from the Internet: Netscape Navigator, version 4.75 or higher, or Microsoft Internet Explorer, version 5.0 or higher; Chime Plug-in, version compatible with your OS and browser (available from MDL).
Terazulene Isomers: Polarity Change of OFETs through Molecular Orbital Distribution Contrast.
Yamaguchi, Yuji; Takubo, Maki; Ogawa, Keisuke; Nakayama, Ken-Ichi; Koganezawa, Tomoyuki; Katagiri, Hiroshi
2016-09-01
Intermolecular orbital coupling is fundamentally important to organic semiconductor performance. Recently, we reported that 2,6':2',6″-terazulene (TAz1) exhibited excellent performance as an n-type organic field-effect transistor (OFET) via molecular orbital distribution control. To validate and develop this concept, here we present three other terazulene regioisomers, which have three azulene molecules connected at the 2- or 6-position along the long axis of the azulene, thus constructing a linear expanded π-conjugation system: 2,2':6',2″-terazulene (TAz2), 2,2':6',6″-terazulene (TAz3), and 6,2':6',6″-terazulene (TAz4). TAz2 and TAz3 exhibit ambipolar characteristics; TAz4 exhibits clear n-type transistor behavior as an OFET. The lowest unoccupied molecular orbitals (LUMOs) of all terazulenes are fully delocalized over the entire molecule. In contrast, the highest occupied molecular orbitals (HOMOs) of TAz2 and TAz3 are delocalized over the 2,2'-biazulene units; the HOMOs of TAz4 are localized at one end of the azulene unit. These findings confirm that terazulene isomers which are simple hydrocarbon compounds are versatile materials with a tunable-polarity FET characteristic that depends on the direction of the azulene unit and the related contrast of the molecular orbital distribution in the terazulene backbone. PMID:27511286
Molecular orbital ordering in titania and the associated semiconducting behavior
Park, Joseph; Ok, Kyung-Chul; Park, Jin-Seong; Du Ahn, Byung; Hun Lee, Je; Park, Jae-Woo; Chung, Kwun-Bum
2011-10-03
RF-sputtered TiO{sub x} layers were thermally treated and the associated thin-film transistor properties were studied. X-ray diffraction and x-ray absorption spectroscopy analyses indicate that as-grown amorphous TiO{sub x} films crystallize to anatase at temperatures above 450 deg. C in air. Thin-film transistors incorporating anatase active layers exhibit n-type behavior, with field effect mobility values near 0.11 cm{sup 2}/Vs when annealed at 550 deg. C. Such a phenomenon is suggested to originate from the ordering of Ti 3d orbitals upon crystallization, and the mobility enhancement at higher annealing temperatures may be attributed to the reduced grain boundary scattering of carriers by virtue of enlarged average grain size.
Fragmented Molecular Orbital with Diffusion Monte Carlo for large molecular systems
NASA Astrophysics Data System (ADS)
Benali, Anouar; Pruitt, Spencer R.; Fedorov, Dmitri G.
Performing accurate quantum mechanics (QM) calculations on larger and larger systems, while maintaining a high level of accuracy is an ongoing effort in many ab initio fields. Many different attempts have been made to develop highly scalable and accurate methods. The fragment molecular orbital (FMO) method is an ab initio method capable of taking advantage of modern supercomputers, such as the Blue Gene Q system Mira at the Argonne National Laboratory Leadership Computing Facility (ALCF). FMO is based on dividing molecules into fragments and performing ab initio calculations on fragments, their dimers and, optionally, trimers. This decomposition makes it possible to perform QM calculations of real size biological molecules. In contrast to many other fragment-based methods, the effect of the environment is rigorously accounted for by computing the electrostatic potential (ESP) due to remaining fragments that are not explicitly included in a given monomer, dimer, or trimer calculation. The use of highly accurate levels of theory, such as Diffusion Monte Carlo (DMC-QMC), in conjunction with FMO allows for the goal of highly scalable and accurate all electron calculations demonstrated in this study, on a variety of relevant systems (H2O)[3-6] and protein using GAMESS and QMCPACK.
Norris, Scott A; Samela, Juha; Bukonte, Laura; Backman, Marie; Djurabekova, Flyura; Nordlund, Kai; Madi, Charbel S; Brenner, Michael P; Aziz, Michael J
2011-01-01
Energetic particle irradiation can cause surface ultra-smoothening, self-organized nanoscale pattern formation or degradation of the structural integrity of nuclear reactor components. A fundamental understanding of the mechanisms governing the selection among these outcomes has been elusive. Here we predict the mechanism governing the transition from pattern formation to flatness using only parameter-free molecular dynamics simulations of single-ion impacts as input into a multiscale analysis, obtaining good agreement with experiment. Our results overturn the paradigm attributing these phenomena to the removal of target atoms via sputter erosion: the mechanism dominating both stability and instability is the impact-induced redistribution of target atoms that are not sputtered away, with erosive effects being essentially irrelevant. We discuss the potential implications for the formation of a mysterious nanoscale topography, leading to surface degradation, of tungsten plasma-facing fusion reactor walls. Consideration of impact-induced redistribution processes may lead to a new design criterion for stability under irradiation.
Pruitt, Spencer R; Nakata, Hiroya; Nagata, Takeshi; Mayes, Maricris; Alexeev, Yuri; Fletcher, Graham; Fedorov, Dmitri G; Kitaura, Kazuo; Gordon, Mark S
2016-04-12
The analytic first derivative with respect to nuclear coordinates is formulated and implemented in the framework of the three-body fragment molecular orbital (FMO) method. The gradient has been derived and implemented for restricted second-order Møller-Plesset perturbation theory, as well as for both restricted and unrestricted Hartree-Fock and density functional theory. The importance of the three-body fully analytic gradient is illustrated through the failure of the two-body FMO method during molecular dynamics simulations of a small water cluster. The parallel implementation of the fragment molecular orbital method, its parallel efficiency, and its scalability on the Blue Gene/Q architecture up to 262,144 CPU cores are also discussed.
NASA Technical Reports Server (NTRS)
Luther, George W., III
1987-01-01
In this paper, molecular orbital theory is used to explain a heterogeneous reaction mechanism for both pyrite oxidation and reduction. The mechanism demonstrates that the oxidation of FeS2 by Fe(3+) may occur as a result of three important criteria: (1) the presence of a suitable oxidant having a vacant orbital (in case of liquid phase) or site (solid phase) to bind to the FeS2 via sulfur; (2) the initial formation of a persulfido (disulfide) bridge between FeS2 and the oxidant, and (3) an electron transfer from a pi(asterisk) orbital in S2(2-) to a pi or pi(asterisk) orbital of the oxidant.
Fratesi, Guido; Lanzilotto, Valeria; Stranges, Stefano; Alagia, Michele; Brivio, Gian Paolo; Floreano, Luca
2014-07-28
We made use of synchrotron radiation to perform near edge X-ray absorption fine structure spectroscopy, NEXAFS, at the carbon K-edge of perylene and perylene-tetracarboxylic-diimide, PTCDI. Reference spectra measured for isolated molecules in the gas phase are compared with polarization dependent NEXAFS spectra measured on highly oriented thin films in order to study the symmetry of the molecular orbitals. The molecular overlayers are grown onto the rutile TiO2(110) surface for which the large anisotropic corrugation effectively drives the molecular orientation, while its dielectric nature prevents the rehybridization of the molecular orbitals. We employed density functional theory, DFT, calculations to disentangle the contribution of specific carbon atoms to the molecular density of states. Numerical simulations correctly predict the observed NEXAFS azimuthal dichroism of the σ* resonances above the ionization threshold, from which we determine the full geometric orientation of the overlayer molecules. A discrepancy observed for the spectral contribution of the imide carbon atom to the calculated unoccupied molecular orbitals has been explained in terms of initial state effects, as determined by Hartree-Fock corrections and in full agreement with the corresponding shift of the C 1s core level measured by X-ray photoelectron spectroscopy, XPS.
Martay, Hugo E. L.; England, Duncan G.; McCabe, David J.; Walmsley, Ian A.
2011-04-15
The complexity of ultrafast molecular photoionization presents an obstacle to the modeling of pump-probe experiments. Here, a simple optimized model of atomic rubidium is combined with a molecular dynamics model to predict quantitatively the results of a pump-probe experiment in which long-range rubidium dimers are first excited, then ionized after a variable delay. The method is illustrated by the outline of two proposed feasible experiments and the calculation of their outcomes. Both of these proposals use Feshbach {sup 87}Rb{sub 2} molecules. We show that long-range molecular pump-probe experiments should observe spin-orbit precession given a suitable pump pulse, and that the associated high-frequency beat signal in the ionization probability decays after a few tens of picoseconds. If the molecule was to be excited to only a single fine-structure state, then a low-frequency oscillation in the internuclear separation would be detectable through the time-dependent ionization cross section, giving a mechanism that would enable observation of coherent vibrational motion in this molecule.
Inversion of strong-field photoelectron spectra for molecular orbital imaging
NASA Astrophysics Data System (ADS)
Puthumpally-Joseph, R.; Viau-Trudel, J.; Peters, M.; Nguyen-Dang, T. T.; Atabek, O.; Charron, E.
2016-08-01
Imaging structures at the molecular level is a developing interdisciplinary research field that spans the boundaries of physics and chemistry. High-spatial-resolution images of molecules can be obtained with photons or ultrafast electrons. In addition, images of valence molecular orbitals can be extracted via tomographic techniques based on the coherent extreme UV radiation emitted by a molecular gas exposed to an intense ultrashort infrared laser pulse. In this paper, we demonstrate that similar information can be obtained by inverting energy-resolved photoelectron spectra using a simplified analytical model.
Tan, Aaron; Sadat, Seid; Reddy, Pramod
2010-01-08
We report an experimental technique that concurrently measures the Seebeck coefficient and the current-voltage (I-V) characteristics of a molecular junction to determine the identity and the effective energetic separation of the molecular orbital closest to the electrodes’ Fermi level. Junctions created by contacting a gold-coated atomic force microscope tip with a monolayer of molecules assembled on a gold substrate were found to have a Seebeck coefficient of (+16.9±1.4) μV/K. This positive value unambiguously shows that the highest occupied molecular orbital (HOMO) dominates charge transport. Further, by analyzing the (I-V) characteristics, the HOMO level is estimated to be ~ 0.69 eV with respect to the Fermi level.
Orbital redistribution in molecular nanostructures mediated by metal-organic bonds.
Yang, Zechao; Corso, Martina; Robles, Roberto; Lotze, Christian; Fitzner, Roland; Mena-Osteritz, Elena; Bäuerle, Peter; Franke, Katharina J; Pascual, Jose I
2014-10-28
Dicyanovinyl-quinquethiophene (DCV5T-Me2) is a prototype conjugated oligomer for highly efficient organic solar cells. This class of oligothiophenes are built up by an electron-rich donor (D) backbone and terminal electron-deficient acceptor (A) moieties. Here, we investigated its structural and electronic properties when it is adsorbed on a Au(111) surface using low temperature scanning tunneling microscopy/spectroscopy (STM/STS) and atomic force microscopy (AFM). We find that DCV5T-Me2 self-assembles in extended chains, stabilized by intercalated Au atoms. The effect of metal-ligand hybridization with Au adatoms causes an energetic downshift of the DCV5T-Me2 lowest unoccupied molecular orbital (LUMO) with respect to the uncoordinated molecules on the surface. The asymmetric coordination of a gold atom to only one molecular end group leads to an asymmetric localization of the LUMO and LUMO+1 states at opposite sides. Using model density functional theory (DFT) calculations, we explain such orbital reshaping as a consequence of linear combinations of the original LUMO and LUMO+1 orbitals, mixed by the attachment of a bridging Au adatom. Our study shows that the alignment of molecular orbitals and their distribution within individual molecules can be modified by contacting them to metal atoms in specific sites.
Atomlike, Hollow-Core–Bound Molecular Orbitals of C₆₀
Feng, Min; Zhao, Jin; Petek, Hrvoje
2008-04-17
The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The atomic electron orbitals that underlie molecular bonding originate from the central Coulomb potential of the atomic core. We used scanning tunneling microscopy and density functional theory to explore the relation between the nearly spherical shape and unoccupied electronic structure of buckminsterfullerene (C60) molecules adsorbed on copper surfaces. Besides the known p* antibonding molecular orbitals of the carbon-atom framework, above 3.5 electron volts we found atomlike orbitals bound to the core of the hollow C60 cage. These “superatom” states hybridize like the s and p orbitals of hydrogen and alkali atoms into diatomic molecule-like dimers and free-electron bands of one-dimensional wires and two-dimensional quantum wells in C60 aggregates. We attribute the superatom states to the central potential binding an electron to its screening charge, a property expected for hollow-shell molecules derived from layered materials.
A Frontier Molecular Orbital determination of the active sites on dispersed metal catalysts
Augustine, R.L.; Lahanas, K.M.
1992-11-01
An angular overlap calculation has been used to determine the s, p and d orbital energy levels of the different types of surface sites present on a dispersed metal catalysts. The basis for these calculations is the reported finding that a large number of catalyzed reactions take place on single atom active sites on the metal surface. Thus, these sites can be considered as surface complexes made up of the central active atom surrounded by near-neighbor metal atom ``ligands`` with localized surface orbitals perturbed only by these ``ligands``. These ``complexes`` are based on a twelve coordinate species with the ``ligands`` attached to the t{sub 2g} orbitals and the coordinate axes coincident with the direction of the e{sub g} orbitals on the central atom. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.
A Frontier Molecular Orbital determination of the active sites on dispersed metal catalysts
Augustine, R.L.; Lahanas, K.M.
1992-01-01
An angular overlap calculation has been used to determine the s, p and d orbital energy levels of the different types of surface sites present on a dispersed metal catalysts. The basis for these calculations is the reported finding that a large number of catalyzed reactions take place on single atom active sites on the metal surface. Thus, these sites can be considered as surface complexes made up of the central active atom surrounded by near-neighbor metal atom ligands'' with localized surface orbitals perturbed only by these ligands''. These complexes'' are based on a twelve coordinate species with the ligands'' attached to the t{sub 2g} orbitals and the coordinate axes coincident with the direction of the e{sub g} orbitals on the central atom. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.
Fluorination-dependent molecular orbital occupancy in ring-shaped perfluorocarbons.
Brandenburg, Tim; Petit, Tristan; Neubauer, Antje; Atak, Kaan; Nagasaka, Masanari; Golnak, Ronny; Kosugi, Nobuhiro; Aziz, Emad F
2015-07-28
Perfluorocarbons are a family of molecules consisting mainly of carbon and fluorine atoms. They have interesting chemical properties and have diverse applications in biomedicine, physical chemistry and polymer science. In this work, carbon K-edge absorption and emission spectra of liquid decalin are presented and compared to perfluorodecalin. A comprehensive picture of the electronic structure of decalin is provided based on soft X-ray absorption and emission spectroscopies. Experimental data are compared to theoretical time-dependent density functional theory for the hydrocarbon, the perfluorocarbon and the stepwise fluorinated derivatives. We observed a molecular orbital change from unoccupied to occupied orbitals for perfluorodecalin, which was induced through the fluorination process.
Orbital Analysis of Molecular Optical Activity Based on Configuration Rotatory Strength.
Caricato, Marco
2015-04-14
We present a method to analyze the origin of molecular optical activity in terms of orbital contributions and rotatory strength in configuration space. The method uses quantities already available at completion of standard linear-response calculations of specific rotation and requires minimal manipulation. Preliminary application to (1S,4S)-norborne-none and (P)-2,3-pentadiene shows that only a few orbitals (6 and 4, respectively) contribute significantly to the specific rotation and can be used directly for a qualitative interpretation of this fundamental property.
NASA Astrophysics Data System (ADS)
Kruijssen, J. M. Diederik; Dale, James E.; Longmore, Steven N.
2015-02-01
We recently proposed that the star-forming potential of dense molecular clouds in the Central Molecular Zone (CMZ, i.e. the central few 100 pc) of the Milky Way is intimately linked to their orbital dynamics, potentially giving rise to an absolute-time sequence of star-forming clouds. In this paper, we present an orbital model for the gas stream(s) observed in the CMZ. The model is obtained by integrating orbits in the empirically constrained gravitational potential and represents a good fit (χ _red^2=2.0) to the observed position-velocity distribution of dense (n > several 103 cm-3) gas, reproducing all of its key properties. The orbit is also consistent with observational constraints not included in the fitting process, such as the 3D space velocities of Sgr B2 and the Arches and Quintuplet clusters. It differs from previous, parametric models in several respects: (1) the orbit is open rather than closed due to the extended mass distribution in the CMZ, (2) its orbital velocity (100-200 km s-1) is twice as high as in previous models, and (3) Sgr A* coincides with the focus of the (eccentric) orbit rather than being offset. Our orbital solution supports the recently proposed scenario in which the dust ridge between G0.253+0.016 (`the Brick') and Sgr B2 represents an absolute-time sequence of star-forming clouds, of which the condensation was triggered by the tidal compression during their most recent pericentre passage. We position the clouds on a common timeline and find that their pericentre passages occurred 0.30-0.74 Myr ago. Given their short free-fall times (tff ˜ 0.34 Myr), the quiescent cloud G0.253+0.016 and the vigorously star-forming complex Sgr B2 are separated by a single free-fall time of evolution, implying that star formation proceeds rapidly once collapse has been initiated. We provide the complete orbital solution, as well as several quantitative predictions of our model (e.g. proper motions and the positions of star formation `hotspots'). The
Proppe, Jonny; Herrmann, Carmen
2015-02-01
Common trends in communication through molecular bridges are ubiquitous in chemistry, such as the frequently observed exponential decay of conductance/electron transport and of exchange spin coupling with increasing bridge length, or the increased communication through a bridge upon closing a diarylethene photoswitch. For antiferromagnetically coupled diradicals in which two equivalent spin centers are connected by a closed-shell bridge, the molecular orbitals (MOs) whose energy splitting dominates the coupling strength are similar in shape to the MOs of the dithiolated bridges, which in turn can be used to rationalize conductance. Therefore, it appears reasonable to expect the observed common property trends to result from common orbital trends. We illustrate based on a set of model compounds that this assumption is not true, and that common property trends result from either different pairs of orbitals being involved, or from orbital energies not being the dominant contribution to property trends. For substituent effects, an effective modification of the π system can make a comparison difficult.
Attia, Ali Kamal; Souaya, Eglal R.; Soliman, Ethar A.
2015-01-01
Purpose: Thermal analysis techniques have been used to study the thermal behavior of dapoxetine and vardenafil hydrochlorides and confirmed using semi-empirical molecular orbital calculations. Methods: Thermogravimetric analysis, derivative thermogravimetry, differential thermal analysis and differential scanning calorimetry were used to determine the thermal behavior and purity of the drugs under investigation. Thermodynamic parameters such as activation energy, enthalpy, entropy and Gibbs free energy were calculated. Results: Thermal behavior of DAP and VAR were confirmed using by semi-empirical molecular orbital calculations. The purity values were found to be 99.97% and 99.95% for dapoxetine and vardenafil hydrochlorides, respectively. The purity of dapoxetine and vardenafil hydrochlorides is similar to that found by reported methods according to DSC data. Conclusion: Thermal analysis justifies its application in quality control of pharmaceutical compounds due to its simplicity, sensitivity and low operational costs. PMID:26819925
NASA Technical Reports Server (NTRS)
Romere, P. O.
1982-01-01
A proposed configuration for a Space Operations Center is presented in its eight stages of buildup. The on orbit aerodynamic force and moment characteristics were calculated for each stage based upon free molecular flow theory. Calculation of the aerodynamic characteristics was accomplished through the use of an orbital aerodynamic computer program, and the computation method is described with respect to the free molecular theory used. The aerodynamic characteristics are presented in tabulated form for each buildup stage at angles of attack from 0 to 360 degrees and roll angles from -60 to +60 degrees. The reference altitude is 490 kilometers, however, the data should be applicable for altitudes below 490 kilometers down to approximately 185 kilometers.
Mulholland, J.A.; Mukherjee, J.; Wornat, M.J.; Sarofim, A.F.; Rutledge, G.C. . Dept. of Chemical Engineering)
1993-08-01
The pyrolysis of pure anthracene at temperatures between 1,200 and 1,500 K produced all six bianthryl isomers whose relative yields appear to be related to steric factors. To evaluate the hypothesis that thermodynamic factors govern the product distribution of bianthryls in this system, the relative enthalpies and entropies of biaryl isomers were estimated by molecular orbital modeling, using the semiempirical AM1 (Austin Model 1). Computational analysis of several isomer sets demonstrates that the relative stabilities of a large number of biaryl isomers are determined largely by steric interactions caused by structural features defined as bays, coves, and fjords. These steric factors affect both the degree of biaryl twist in the preferred conformation and the freedom of internal rotation. Molecular orbital modeling supports the hypothesis that a thermodynamic distribution of bianthryl isomers is produced by anthracene pyrolysis.
Imoto, Hideo; Saito, Taro; Adachi, Hirohiko
1995-04-26
Discrete variational-{Chi}{alpha} molecular orbital methods were applied to octahedral cluster complexes, [Mo{sub 6}X{sub 8}-(PH{sub 3}){sub 6}](X = S and Se). This structure is of interest due to its role in superconductivity of Chevrel plates. Level energies are discussed and factors contributing to their separations are categorized. Agreement with empirical XPS data is excellent.
Sherman, David M.
1986-01-01
A molecular orbital description, based on spin-unrestricted X??-scattered wave calculations, is given for the electronic structures of mixed valence iron oxides and silicates. The cluster calculations show that electron hopping and optical intervalence charge-transger result from weak FeFe bonding across shared edges of FeO6 coordination polyhedra. In agreement with Zener's double exchange model, FeFe bonding is found to stabilize ferromagnetic coupling between Fe2+ and Fe3+ cations. ?? 1986.
Mass transport properties of Pu/DT mixtures from orbital free molecular dynamics simulations
Kress, Joel David; Ticknor, Christopher; Collins, Lee A.
2015-09-16
Mass transport properties (shear viscosity and diffusion coefficients) for Pu/DT mixtures were calculated with Orbital Free Molecular Dynamics (OFMD). The results were fitted to simple functions of mass density (for ρ=10.4 to 62.4 g/cm^{3}) and temperature (for T=100 up to 3,000 eV) for Pu/DT mixtures consisting of 100/0, 25/75, 50/50, and 75/25 by number.
Simoncini, David; Nakata, Hiroya; Ogata, Koji; Nakamura, Shinichiro; Zhang, Kam Yj
2015-02-01
Protein structure prediction directly from sequences is a very challenging problem in computational biology. One of the most successful approaches employs stochastic conformational sampling to search an empirically derived energy function landscape for the global energy minimum state. Due to the errors in the empirically derived energy function, the lowest energy conformation may not be the best model. We have evaluated the use of energy calculated by the fragment molecular orbital method (FMO energy) to assess the quality of predicted models and its ability to identify the best model among an ensemble of predicted models. The fragment molecular orbital method implemented in GAMESS was used to calculate the FMO energy of predicted models. When tested on eight protein targets, we found that the model ranking based on FMO energies is better than that based on empirically derived energies when there is sufficient diversity among these models. This model diversity can be estimated prior to the FMO energy calculations. Our result demonstrates that the FMO energy calculated by the fragment molecular orbital method is a practical and promising measure for the assessment of protein model quality and the selection of the best protein model among many generated.
Orbit crowding of molecular gas at a bar-spiral arm transition zone in M83
NASA Technical Reports Server (NTRS)
Kenney, Jeffrey D. P.; Lord, Steven D.
1991-01-01
The southwestern bar-spiral arm transition zone in M83 is been studied in CO, H-alpha, H I, red light, and the radio continuum. A massive molecular gas complex in the heart of the transition zone is composed or two principal components which have the morphology and kinematics expected from orbit crowding, where gas on highly elliptical orbits form the bar region converges with gas on more circular orbits from the spiral arm region. Three mechanisms for the origin of the orbit crowding are investigated, and it is proposed that the crowding is due primarily to density wave streaming motions caused by the bar and spiral arms. The inner CO component is partially coincident with a region of highly polarized radio continuum emission which precedes the H-alpha spiral arm by 15-25 arcsec, indicating that it lies on or just downstream from a shock front. This suggests that the bar gas approaching the transition zone is shocked and explains the ridge of dense gas seen upstream from the spiral arm.
Molecular-orbital-free algorithm for excited states in time-dependent perturbation theory.
Lucero, Melissa J; Niklasson, Anders M N; Tretiak, Sergei; Challacombe, Matt
2008-08-14
A nonlinear conjugate gradient optimization scheme is used to obtain excitation energies within the random phase approximation (RPA). The solutions to the RPA eigenvalue equation are located through a variational characterization using a modified Thouless functional, which is based upon an asymmetric Rayleigh quotient, in an orthogonalized atomic orbital representation. In this way, the computational bottleneck of calculating molecular orbitals is avoided. The variational space is reduced to the physically-relevant transitions by projections. The feasibility of an RPA implementation scaling linearly with system size N is investigated by monitoring convergence behavior with respect to the quality of initial guess and sensitivity to noise under thresholding, both for well- and ill-conditioned problems. The molecular-orbital-free algorithm is found to be robust and computationally efficient, providing a first step toward large-scale, reduced complexity calculations of time-dependent optical properties and linear response. The algorithm is extensible to other forms of time-dependent perturbation theory including, but not limited to, time-dependent density functional theory. PMID:18715058
Néel, Nicolas; Lattelais, Marie; Bocquet, Marie-Laure; Kröger, Jörg
2016-02-23
Single-molecule chemistry with a scanning tunneling microscope has preponderantly been performed on metal surfaces. The molecule-metal hybridization, however, is often detrimental to genuine molecular properties and obscures their changes upon chemical reactions. We used graphene on Ir(111) to reduce the coupling between Ir(111) and adsorbed phthalocyanine molecules. By local electron injection from the tip of a scanning tunneling microscope the two pyrrolic H atoms were removed from single phthalocyanines. The detachment of the H atom pair induced a strong modification of the molecular electronic structure, albeit with no change in the adsorption geometry. Spectra and maps of the differential conductance combined with density functional calculations unveiled the entire depopulation of the highest occupied molecular orbital upon H abstraction. Occupied π states of intact molecules are proposed to be emptied via intramolecular electron transfer to dangling σ states of H-free N atoms.
NASA Technical Reports Server (NTRS)
Richmond, R. G.; Kelso, R. M.
1980-01-01
A concern has arisen regarding the emissive distribution of water molecules from the shuttle orbiter flash evaporator system (FES). The role of the orbiter fuselage and elevon in affecting molecular scattering distributions was nuclear. The effect of these components were evaluated. Molecular distributions of the water vapor effluents from the FE were measured. These data were compared with analytically predicted values and the resulting implications were calculated.
Yamazaki, Masakazu; Horio, Takuya; Kishimoto, Naoki; Ohno, Koichi
2007-03-15
Although the outer shapes of molecular orbitals (MO's) are of great importance in many phenomena, they have been difficult to be probed by experiments. Here we show that metastable helium (He{sup *}) atoms can sensitively probe the outer properties of molecules and that an electron spectroscopic technique using velocity-selected He{sup *} atoms in combination with classical trajectory simulations leads to a consistent determination of MO functions and the molecular surface. MO functions composed of linear combinations of atomic orbital functions were fitted to the observed collision energy dependences of partial ionization cross sections (CEDPICS). The obtained CEDPICS MO functions were compared with conventionally available Hartree-Fock, Kohn-Sham, and Dyson orbitals.
In vitro and in vivo imaging of ultra-high-molecular-weight polyethylene orbital implants.
Olszycki, Marek; Kozakiewicz, Marcin; Elgalal, Marcin; Majos, Agata; Stefanczyk, Ludomir
2015-01-01
The aim of this study is to compare magnetic resonance imaging (MRI) with computed tomography (CT) for visualization of an orbital alloplastic prosthesis made of ultra-high-molecular-weight polyethylene (UHMW-PE) both in vitro and in vivo. A study of 15 test implants from UHMW-PE visualized in vitro in CT and MRI and an in vivo visualization in a patient who suffered from orbital injury and underwent reconstructive surgery is presented. The postsurgery MRI showed the UHMW-PE material clearly, with no significant artifacts. The surrounding tissues could be satisfactorily evaluated. The CT scans did not present the graft material. Both techniques were sufficient tools for in vitro evaluation of the shape and measurement of the prosthesis.
In vitro and in vivo imaging of ultra-high-molecular-weight polyethylene orbital implants.
Olszycki, Marek; Kozakiewicz, Marcin; Elgalal, Marcin; Majos, Agata; Stefanczyk, Ludomir
2015-01-01
The aim of this study is to compare magnetic resonance imaging (MRI) with computed tomography (CT) for visualization of an orbital alloplastic prosthesis made of ultra-high-molecular-weight polyethylene (UHMW-PE) both in vitro and in vivo. A study of 15 test implants from UHMW-PE visualized in vitro in CT and MRI and an in vivo visualization in a patient who suffered from orbital injury and underwent reconstructive surgery is presented. The postsurgery MRI showed the UHMW-PE material clearly, with no significant artifacts. The surrounding tissues could be satisfactorily evaluated. The CT scans did not present the graft material. Both techniques were sufficient tools for in vitro evaluation of the shape and measurement of the prosthesis. PMID:25830408
NASA Astrophysics Data System (ADS)
Chaston, Scot
1999-02-01
Thermodynamic data such as equilibrium constants, standard cell potentials, molar enthalpies of formation, and standard entropies of substances can be a very useful basis for an organized presentation of knowledge in diverse areas of applied chemistry. Thermodynamic data can become particularly useful when incorporated into thermodynamic diagrams that are designed to be easy to recall, to serve as a basis for reconstructing previous knowledge, and to determine whether reactions can occur exergonically or only with the help of an external energy source. Few students in our chemistry-based courses would want to acquire the depth of knowledge or rigor of professional thermodynamicists. But they should nevertheless learn how to make good use of thermodynamic data in their professional occupations that span the chemical, biological, environmental, and medical laboratory fields. This article discusses examples of three thermodynamic diagrams that have been developed for this purpose. They are the thermodynamic energy account (TEA), the total entropy scale, and the thermodynamic scale diagrams. These diagrams help in the teaching and learning of thermodynamics by bringing the imagination into the process of developing a better understanding of abstract thermodynamic functions, and by allowing the reader to keep track of specialist thermodynamic discourses in the literature.
DETECTION OF A MOLECULAR DISK ORBITING THE NEARBY, 'OLD', CLASSICAL T TAURI STAR MP MUSCAE
Kastner, Joel H.; Sacco, G. G.; Hily-Blant, Pierry; Forveille, Thierry; Zuckerman, B.
2010-11-10
We have used the Atacama Pathfinder Experiment 12 m telescope to detect circumstellar CO emission from MP Muscae (MP Mus; K1 IVe), a nearby (D {approx} 100 pc), actively accreting, {approx}7 Myr old pre-main-sequence (pre-MS) star. The CO emission line profile measured for MP Mus is indicative of an orbiting disk with radius {approx}120 AU, assuming that the central star mass is 1.2 M {sub sun} and the disk inclination is i {approx} 30{sup 0}. The inferred disk molecular gas mass is {approx}3 M {sub +}. MP Mus thereby joins TW Hya and V4046 Sgr as the only late-type (low-mass), pre-MS star systems within {approx}100 pc of Earth that are known to retain orbiting, molecular disks. We also report the nondetection (with the Institut de Radio Astronomie Millimetrique 30 m telescope) of CO emission from another 10 nearby (D {approx_lt} 100 pc), dusty, young (age {approx}10-100 Myr) field stars of spectral type A-G. We discuss the implications of these results for the timescales for stellar and Jovian planet accretion from, and dissipation of, molecular disks around young stars.
Fedorov, Dmitri G; Kitaura, Kazuo
2009-11-01
We have examined the role of the exchange in describing the electrostatic potential in the fragment molecular orbital method and showed that it should be included in the total Fock matrix to obtain an accurate one-electron spectrum; however, adding it to the Fock matrices of individual fragments and pairs leads to very large errors. For the error analysis we have used the virial theorem; numerical tests have been performed for solvated phenol at the Hartree-Fock level with the 6-31G( *) and 6-311G( * *) basis sets.
Fragment molecular orbital calculation using the RI-MP2 method
NASA Astrophysics Data System (ADS)
Ishikawa, Takeshi; Kuwata, Kazuo
2009-05-01
The resolution of the identity second-order Møller-Plesset perturbation theory (RI-MP2) was introduced into the fragment molecular orbital (FMO) method, where the program of the RI-MP2 method was newly developed. After some test calculations with a small peptide, the performance of the RI-MP2 method with the FMO scheme was demonstrated for two biomolecular systems: the human immunodeficiency virus type 1 protease with the lopinavir molecule, and the prion protein with the GN8 molecule. These calculations showed the great advantage of FMO calculations using the RI-MP2 method over ordinary FMO calculations.
Radical damage in lipids investigated with the fragment molecular orbital method
NASA Astrophysics Data System (ADS)
Green, Mandy C.; Nakata, Hiroya; Fedorov, Dmitri G.; Slipchenko, Lyudmila V.
2016-05-01
To quantify the thermodynamics for hydrogen abstraction lipids, the fragment molecular orbital method (FMO) is used to calculate structures and energies of the reactants and products. The analytic second derivative is developed for the open-shell Hartree-Fock formulation of FMO and used to calculate zero point energy corrections. The accuracy of FMO is evaluated for a lipid model and the errors in reaction energies are found not to exceed 0.5 kcal/mol. The reaction energies determined for multiple sites in two lipids are used to discuss likely sites and pathways of radical initiation in membranes.
Construction of the Fock Matrix on a Grid-Based Molecular Orbital Basis Using GPGPUs.
Losilla, Sergio A; Watson, Mark A; Aspuru-Guzik, Alán; Sundholm, Dage
2015-05-12
We present a GPGPU implementation of the construction of the Fock matrix in the molecular orbital basis using the fully numerical, grid-based bubbles representation. For a test set of molecules containing up to 90 electrons, the total Hartree-Fock energies obtained from reference GTO-based calculations are reproduced within 10(-4) Eh to 10(-8) Eh for most of the molecules studied. Despite the very large number of arithmetic operations involved, the high performance obtained made the calculations possible on a single Nvidia Tesla K40 GPGPU card.
Fedorov, Dmitri G; Kitaura, Kazuo
2009-11-01
We have examined the role of the exchange in describing the electrostatic potential in the fragment molecular orbital method and showed that it should be included in the total Fock matrix to obtain an accurate one-electron spectrum; however, adding it to the Fock matrices of individual fragments and pairs leads to very large errors. For the error analysis we have used the virial theorem; numerical tests have been performed for solvated phenol at the Hartree-Fock level with the 6-31G( *) and 6-311G( * *) basis sets. PMID:19894991
NASA Astrophysics Data System (ADS)
Sawada, Toshihiko; Fedorov, Dmitri G.; Kitaura, Kazuo
The fragment molecular orbital method (FMO) was applied to the geometry optimization of several heparin oligosaccharides at the RHF/6-31(+)G(d) level combined with the polarizable continuum model (PCM). For comparison, GLYCAM force field optimization in explicit solvent was also conducted. Good accuracy of FMO was demonstrated in comparison to ab initio at the MP2/PCM level. The interaction analysis was conducted using the pair interaction energy decomposition analysis (PIEDA), and the role of hydrogen bonding and solvent was elucidated in the helix formation of heparin in solution. Content:text/plain; charset="UTF-8"
NASA Astrophysics Data System (ADS)
Watanabe, Hirofumi; Okiyama, Yoshio; Nakano, Tatsuya; Tanaka, Shigenori
2010-11-01
We developed FMO-PB method, which incorporates solvation effects into the Fragment Molecular Orbital calculation with the Poisson-Boltzmann equation. This method retains good accuracy in energy calculations with reduced computational time. We calculated the solvation free energies for polyalanines, Alpha-1 peptide, tryptophan cage, and complex of estrogen receptor and 17 β-estradiol to show the applicability of this method for practical systems. From the calculated results, it has been confirmed that the FMO-PB method is useful for large biomolecules in solution. We also discussed the electric charges which are used in solving the Poisson-Boltzmann equation.
Counterpoise-corrected interaction energy analysis based on the fragment molecular orbital scheme
NASA Astrophysics Data System (ADS)
Okiyama, Yoshio; Fukuzawa, Kaori; Yamada, Haruka; Mochizuki, Yuji; Nakano, Tatsuya; Tanaka, Shigenori
2011-06-01
Basis set superposition error (BSSE) correction with counterpoise (CP) procedure under the environmental electrostatic potential is newly introduced to interfragment interaction energy (IFIE), which is important for interaction analysis in the fragment molecular orbital method. The CP correction for IFIE is applied to a stacked dimer of base pair and a protein-ligand complex of estrogen receptor and 17β-estradiol with scaled third-order Møller-Plesset perturbation theory. The BSSEs amount to about quarter of IFIE for hydrogen-bonding and electrostatic interactions and half or even more for dispersion interactions. Estimation of IFIE with the CP correction is therefore preferred for the quantitative discussion.
NASA Astrophysics Data System (ADS)
Djorgovski, S.; Murdin, P.
2000-11-01
Initially introduced as a way to demonstrate the expansion of the universe, and subsequently to determine the expansion rate (the HUBBLE CONSTANT H0), the Hubble diagram is one of the classical cosmological tests. It is a plot of apparent fluxes (usually expressed as magnitudes) of some types of objects at cosmological distances, against their REDSHIFTS. It is used as a tool to measure the glob...
Miyamoto, Kaito; Hoshino, Minoru; Nakai, Hiromi
2006-11-01
The translation- and rotation-free nuclear orbital plus molecular orbital (TRF-NOMO) theory was developed to determine nonadiabatic nuclear and electronic wave functions. This study implemented a computational program for the TRF-NOMO method including first-order rotational terms, which corresponds to rovibronic coupling. Numerical assessments of first-order TRF-NOMO Hartree-Fock as well as second-order Møller-Plesset perturbation methods were carried out for several small molecules. The first-order contributions give small corrections in energy. Thus, we confirm that the approximate zeroth-order treatment is sufficient for eliminating the rotational contamination. PMID:26627025
A Simple Molecular Orbital Treatment of the Barrier to Internal Rotation in the Ethane Molecule
NASA Astrophysics Data System (ADS)
Smith, Derek W.
1998-07-01
The origin of the barrier to internal rotation in the ethane molecule is explored in terms of elementary molecular orbital (MO) considerations. Emphasis is placed on the antibonding effect, i.e. the result that an antibonding MO is more destabilized than its bonding counterpart is stabilized, relative to the parent atomic orbitals (AOs). It is shown that, in the case of two equivalent AOs, this effect is approximately proportional to the square of the overlap integral. By constructing the ethane Mos from those of two methyl fragments, it is shown that the most important orbital energy changes consequent upon rotation about the C-C bond can be expressed in terms of the antibonding effect arising from the filled twofold-degenerate p-bonding and -antibonding MOs. This can be reduced to the dependence on the rotation angle of the vicinal H-H overlap integrals, which are calculated explicitly, showing that the antibonding effect is minimised in the staggered conformation. A letter from Lawrence J. Sacks in our April 2000 issue addresses the above.
Direct study of eos mixing laws through an orbital-free-molecular-dynamics point of view
NASA Astrophysics Data System (ADS)
Lambert, Flavien; Danel, Jean-Francois; Kazandjian, Luc; Clerouin, Jean
2008-04-01
We have investigated eos mixing rules by an approach coupling consistently molecular dynamics for the nuclei and orbital free density functional theory for the electronic fluid. This framework allowed us to study, without mixing approximation, mixtures in the hot and dense regime -- ie a plasma strongly coupled and partially degenerated --, regime relevant for inertial confinement fusion. Several mixtures borrowed from this field have been examined in order to both present the method and check the validity of eos mixing rules commonly used in hydrodynamics simulations. [1] F. Lambert, J. Clerouin, J.-F. Danel, L. Kazandjian, and G. Zerah. Direct verification of mixing rules in the hot and dense regime. Phys. Rev. E, 2007. Submitted. [2] F. Lambert, J. Clerouin, and S. Mazevet. Structural and dynamical properties of hot dense matter by a Thomas-Fermi-Dirac molecular dynamics. Europhysics Lett., 75(5):681--687, 2006.
Liquid Be, Ca and Ba. An orbital-free ab-initio molecular dynamics study
Rio, B. G. del; González, L. E.
2015-08-17
Several static and dynamic properties of liquid beryllium (l-Be), liquid calcium (l-Ca) and liquid barium (l-Ba) near their triple point have been evaluated by the orbital-free ab initio molecular dynamics method (OF-AIMD), where the interaction between valence electrons and ions is described by means of local pseudopotentials. These local pseudopotentials used were constructed through a force-matching process with those obtained from a Kohn-Sham ab initio molecular dynamics study (KS-AIMD) of a reduced system with non-local pseudopotentials. The calculated static structures show good agreement with the available experimental data, including an asymmetric second peak in the structure factor which has been linked to the existence of a marked icosahedral short-range order in the liquid. As for the dynamic properties, we obtain collective density excitations whose associated dispersion relations exhibit a positive dispersion.
ERIC Educational Resources Information Center
Ruddick, Kristie R.; Parrill, Abby L.; Petersen, Richard L.
2012-01-01
In this study, a computational molecular orbital theory experiment was implemented in a first-semester honors general chemistry course. Students used the GAMESS (General Atomic and Molecular Electronic Structure System) quantum mechanical software (as implemented in ChemBio3D) to optimize the geometry for various small molecules. Extended Huckel…
NASA Astrophysics Data System (ADS)
Bauer, C.; Bauduin, P.; Dufrêche, J. F.; Zemb, T.; Diat, O.
2012-11-01
We consider the class of surfactants called "extractants" since they specifically interact with some cations and are used in liquid-liquid separation processes. We review here features of water-poor reverse micelles in water/oil/ extractant systems as determined by combined structural studies including small angle scattering techniques on absolute scale. Origins of instabilities, liquid-liquid separation as well as emulsification failure are detected. Phase diagrams contain the same multi-phase domains as classical microemulsions, but special unusual features appear due to the high spontaneous curvature directed towards the polar cores of aggregates as well as rigidity of the film made by extracting molecules.
Quantum Monte Carlo Method for Heavy Atomic and Molecular Systems with Spin-Orbit Interactions
NASA Astrophysics Data System (ADS)
Melton, Cody; Mitas, Lubos
We present a new quantum Monte Carlo (QMC) method that can treat spin-orbit and other types of spin-depentent interactions explicitly. It is based on generalization of the fixed-phase and projection of the nonlocal operators with spinor trial wave functions. For testing the method we calculate several atomic and molecular systems such as Bi, W, Pb, PbH and PbO, some of them with both large- and small-core pseudopotentials. We validate the quality of the results against other correlated methods such as configuration interaction in two-component formalism. We find excellent agreement with extrapolated values for the total energies and we are able to reliably reproduce experimental values of excitation energies, electron affinity and molecular binding. We show that in order to obtain the agreement with experimental values the explicit inclusion of the spin-orbit interactions is crucial. U.S. D.O.E. grant de-sc0012314 and NERSC Contract No. DE-AC02-05CH11231.
Orbital alignment at the internal interface of arylthiol functionalized CdSe molecular hybrids
Li, Zhi; Schlaf, Rudy; Mazzio, Katherine A.; Okamoto, Ken; Luscombe, Christine K.
2015-04-21
Organic-inorganic nanoparticle molecular hybrid materials are interesting candidates for improving exciton separation in organic solar cells. The orbital alignment at the internal interface of cadmium selenide (ArS-CdSe) hybrid materials functionalized with covalently attached arylthiolate moieties was investigated through X-ray photoemission spectroscopy (XPS) and ultraviolet photoemission spectroscopy (UPS). A physisorbed interface between arylthiol (ArSH) ligands and CdSe nanoparticles was also investigated for comparison. This interface was created via a multi-step thin film deposition procedure in-vacuo, where the surface was characterized after each experimental step. This enabled the direct comparison of ArSH/CdSe interfaces produced via physisorption and ArS-CdSe covalently attached hybrid materials, which rely on a chemical reaction for their synthesis. All material depositions were performed using an electrospray deposition, which enabled the direct injection of solution-originating molecular species into the vacuum system. This method allows XPS and UPS measurements to be performed immediately after deposition without exposure to the atmosphere. Transmission electron microscopy was used to determine the morphology and particle size of the deposited materials. Ultraviolet-visible spectroscopy was used to estimate the optical band gap of the CdSe nanoparticles and the HOMO-LUMO gap of the ArSH ligands. These experiments showed that hybridization via covalent bonds results in an orbital realignment at the ArSH/CdSe interface in comparison to the physisorbed interface. The orbital alignment within the hybrid caused a favorable electron injection barrier, which likely facilitates exciton-dissociation while preventing charge-recombination.
Chen, Ji; Ren, Xinguo; Li, Xin-Zheng; Alfè, Dario; Wang, Enge
2014-07-14
The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.
Genoni, Alessandro
2013-07-01
Following the X-ray constrained wave function approach proposed by Jayatilaka, we have devised a new technique that allows to extract molecular orbitals strictly localized on small molecular fragments from sets of experimental X-ray structure factors amplitudes. Since the novel strategy enables to obtain electron distributions that have quantum mechanical features and that can be easily interpreted in terms of traditional chemical concepts, the method can be also considered as a new useful tool for the determination and the analysis of charge densities from high-resolution X-ray experiments. In this paper, we describe in detail the theory of the new technique, which, in comparison to our preliminary work, has been improved both treating the effects of isotropic secondary extinctions and introducing a new protocol to halt the fitting procedure against the experimental X-ray scattering data. The performances of the novel strategy have been studied both in function of the basis-sets flexibility and in function of the quality of the considered crystallographic data. The tests performed on four different systems (α-glycine, l-cysteine, (aminomethyl)phosphonic acid and N-(trifluoromethyl)formamide) have shown that the achievement of good statistical agreements with the experimental measures mainly depends on the quality of the crystal structures (i.e., geometry positions and thermal parameters) used in the X-ray constrained calculations. Finally, given the reliable transferability of the obtained Extremely Localized Molecular Orbitals (ELMOs), we envisage to exploit the novel approach to construct new ELMOs databases suited to the development of linear-scaling methods for the refinement of macromolecular crystal structures.
Govindasamy, P; Gunasekaran, S; Srinivasan, S
2014-09-15
The Fourier transform infrared (FT-IR) and FT-Raman spectra of 2-acetoxybenzoic acid (2ABA), a painkiller agent were recorded in the region 4000-450 cm(-1) and 5000-50 cm(-1) respectively. Hartree Fock (HF) and Density functional theory (DFT) methods have been used to determine its optimized geometrical parameter, atomic charges, and vibrational wavenumbers and intensity of the vibrational bands of the title molecule. The computed vibrational wave numbers were compared with the FT-IR and FT-Raman experimental data. The computational calculations were done at HF and DFT/B3LYP level with 6-311++G(d,p) basis set. The complete vibrational assignments were performed on the basis of the potential energy distribution (PED) analysis. The Mulliken charges, UV-Visible spectral analysis and HOMO-LUMO energy gap have been calculated and reported. The B3LYP method of calculated parameters is a good complement with the experimental findings. The thermodynamic properties like entropy, heat capacity and zero vibrational energy have been calculated and discussed. The electrostatic potential (ESP) contour surface and molecular electrostatic potential (MESP) of the molecule were constructed.
NASA Astrophysics Data System (ADS)
Blackstone, Christopher C.; Sanov, Andrei
2016-06-01
Using the generalized model for photodetachment of electrons from mixed-character molecular orbitals, we gain insight into the nature of the HOMO of HO2- by treating it as a coherent superpostion of one p- and one d-type atomic orbital. Fitting the pd model function to the ab initio calculated HOMO of HO2- yields a fractional d-character, γp, of 0.979. The modeled curve of the anisotropy parameter, β, as a function of electron kinetic energy for a pd-type mixed character orbital is matched to the experimental data.
Ghasemi, A S; Mashhadban, F; Hoseini-Alfatemi, S M; Sharifi-Rad, J
2015-12-24
Today the use of nanotubes (CNTs) is widely spread a versatile vector for drug delivery that can officiate as a platform for transporting a variety of bioactive molecules, such as drugs. In the present study, the interaction between the nanotube and anticancer drugs is investigated. Density functional theory (DFT) calculations were using the Gauss view and the complexes were optimized by B3LYP method using B3LYP/6-31G (d, p) and B3LYP/6-311++G (d, p) basis set in the gas phase and water solution at 298.15K. The calculated hikes' occupied molecular orbital (HOMO) and the lowest unoccupied (LUMO) energies Show that charge transfer occurs within the molecule. Furthermore, the effects of interactions on the natural bond orbital analysis (NBO) have been used to a deeper investigation into the studied compounds. These factors compete against each other to determine the adsorption behavior of the tube computer simulation is seen to be capable to optimize anticancer drug design. This review article mainly concentrates on the different protocols of loading anticancer drugs onto CNTs as well as how to control the anticancer drug release and cancer treatment.
Zhou, Xin
1998-11-30
Photoemission intensities from the molecular orbitals of c(2x2)CO/Pt(111) over a wide photon energy range were measured and analyzed by the same methods developed for structural studies using core levels. The 4{sigma} orbital center of gravity is found to be concentrated between the C and O atoms, while that of the 5{sigma} orbital lies between the C atom and the Pt surface. The C 1s photoelectron diffraction was used to determine the adsorption geometry. The earlier ambiguity that multiple scattering is needed to correctly model a {chi} curve while single scattering is sufficient for understanding major peaks in the ARPEFS-FTS is clarified by studying the clean Ni(111) surface. In the normal emission case, several different combinations of scattering events have similar path length differences (PLDs), and can either cancel each other or enhance the corresponding FT peak. In the off-normal case the degeneracy is greatly reduced due to the lower degree of symmetry. In normal emission AR PEFS, up to third order multiple scattering is needed to describe fully both the {chi} curve and its FT spectrum. To improve the spectral resolution in the ARPEFS-FT analysis, several new spectral analysis methods are introduced. With both autocorrelation autoregression (ACAR) and autocorrelation eigenvector (ACE), we can produce a reliable power spectrum by following the order-closing procedure. The best spectra are usually obtained when the autocorrelation sequence is computed with lags up to half the data range. A simple way of determining surface adsorption sites is proposed as follows: First use a single scattering cluster for possible adsorption sites to construct the geometrical PLDs from the strong backscattering events; then compare these PLDs with those obtained from the ARPEFS-FT analysis of the experimental data. After the preferred adsorption site is determined, fine tune the interlayer distances according to the positional R-factor.
Molecular Orbital Simulations of Metal 1s2p Resonant Inelastic X-ray Scattering.
Guo, Meiyuan; Källman, Erik; Sørensen, Lasse Kragh; Delcey, Mickaël G; Pinjari, Rahul V; Lundberg, Marcus
2016-07-28
For first-row transition metals, high-resolution 3d electronic structure information can be obtained using resonant inelastic X-ray scattering (RIXS). In the hard X-ray region, a K pre-edge (1s→3d) excitation can be followed by monitoring the dipole-allowed Kα (2p→1s) or Kβ (3p→1s) emission, processes labeled 1s2p or 1s3p RIXS. Here the restricted active space (RAS) approach, which is a molecular orbital method, is used for the first time to study hard X-ray RIXS processes. This is achieved by including the two sets of core orbitals in different partitions of the active space. Transition intensities are calculated using both first- and second-order expansions of the wave vector, including, but not limited to, electric dipoles and quadrupoles. The accuracy of the approach is tested for 1s2p RIXS of iron hexacyanides [Fe(CN)6](n-) in ferrous and ferric oxidation states. RAS simulations accurately describe the multiplet structures and the role of 2p and 3d spin-orbit coupling on energies and selection rules. Compared to experiment, relative energies of the two [Fe(CN)6](3-) resonances deviate by 0.2 eV in both incident energy and energy transfer directions, and multiplet splittings in [Fe(CN)6](4-) are reproduced within 0.1 eV. These values are similar to what can be expected for valence excitations. The development opens the modeling of hard X-ray scattering processes for both solution catalysts and enzymatic systems. PMID:27398775
Danel, J.-F.; Blottiau, P.; Kazandjian, L.; Piron, R.; Torrent, M.
2014-10-15
The applicability of quantum molecular dynamics to the calculation of the equation of state of a dense plasma is limited at high temperature by computational cost. Orbital-free molecular dynamics, based on a semiclassical approximation and possibly on a gradient correction, is a simulation method available at high temperature. For a high-Z element such as lutetium, we examine how orbital-free molecular dynamics applied to the equation of state of a dense plasma can be regarded as the limit of quantum molecular dynamics at high temperature. For the normal mass density and twice the normal mass density, we show that the pressures calculated with the quantum approach converge monotonically towards those calculated with the orbital-free approach; we observe a faster convergence when the orbital-free approach includes the gradient correction. We propose a method to obtain an equation of state reproducing quantum molecular dynamics results up to high temperatures where this approach cannot be directly implemented. With the results already obtained for low-Z plasmas, the present study opens the way for reproducing the quantum molecular dynamics pressure for all elements up to high temperatures.
Predicting the solid solubility limit in high-entropy alloys using the molecular orbital approach
NASA Astrophysics Data System (ADS)
Sheikh, Saad; Klement, Uta; Guo, Sheng
2015-11-01
High-entropy alloys (HEAs) are currently at the research frontier of metallic materials. Understanding the solid solubility limit in HEAs, such a highly concentrated multicomponent alloy system, is scientifically intriguing. It is also technically important to achieve desirable mechanical properties by controlling the formation of topologically or geometrically closed packed phases. Previous approaches to describe the solid solubilities in HEAs could not accurately locate the solubility limit and have to utilize at least two parameters. Here, we propose to use a single parameter, the average energy of d-orbital levels, Md, to predict the solid solubility limit in HEAs. It is found that Md can satisfactorily describe the solid solubilities in fcc structured HEAs containing 3 d transition metals, and also in bcc structured HEAs. This finding will greatly simplify the alloys design and lends more flexibility to control the mechanical properties of HEAs. When 4 d transition metals are alloyed, Md alone cannot describe the solid solubility limit in fcc structured HEAs, due to the large increase of the bond strength that can be gauged by the bond order, Bo. The potential opportunities and challenges with applying the molecular orbital approach to HEAs are discussed.
Molecular orbital studies in oxidation: Sulfate formation and metal-metal oxide adhesion
NASA Technical Reports Server (NTRS)
Anderson, A. B.
1985-01-01
The chemical mechanisms for sulfate formation from sodium chloride and sulfur trioxide, which is a product of jet fuel combustion was determined. Molten sodium sulfate leads to hot corrosion of the protective oxide layers on turbine blades. How yttrium dopants in nidkel-aluminum alloys used in turbine blades reduce the spalling rate of protective alumina films and enhance their adhesion was also determined. Two other fulfate mechanisms were deduced and structure of carbon monoxide on a clean chronium and clean platinum-titanium alloys surfaces was determined. All studies were by use of the atom superposition and electron delocalization molecular orbital (ASED-MO) theory. Seven studies were completed. Their titles and abstracts are given.
Nakata, Hiroya; Fedorov, Dmitri G; Nagata, Takeshi; Kitaura, Kazuo; Nakamura, Shinichiro
2015-07-14
The fully analytic first and second derivatives of the energy in the frozen domain formulation of the fragment molecular orbital (FMO) were developed and applied to locate transition states and determine vibrational contributions to free energies. The development is focused on the frozen domain with dimers (FDD) model. The intrinsic reaction coordinate method was interfaced with FMO. Simulations of IR and Raman spectra were enabled using FMO/FDD by developing the calculation of intensities. The accuracy is evaluated for S(N)2 reactions in explicit solvent, and for the free binding energies of a protein-ligand complex of the Trp cage protein (PDB: 1L2Y ). FMO/FDD is applied to study the keto-enol tautomeric reaction of phosphoglycolohydroxamic acid and the triosephosphate isomerase (PDB: 7TIM ), and the role of amino acid residue fragments in the reaction is discussed.
Tognetti, Vincent; Morell, Christophe; Ayers, Paul W; Joubert, Laurent; Chermette, Henry
2013-09-14
In this paper, we introduce new local descriptors in the framework of Conceptual Density Functional Theory. They can be considered as an extension of the dual descriptor [Morell et al., J. Phys. Chem. A, 2005, 109, 205]. These indices are particularly suited for the discrimination between electrophilic and nucleophilic sites inside a molecule. They are computed using the densities of the electronic excited states, giving a picture of the polarization of the electron density induced by the approach of a reactant. Links with the linear-response function are discussed, and the first examples of applications are given, highlighting how these new descriptors can be used in practice for reactivity studies. It has been found that this extension of the dual descriptor can handle tricky cases, such as nitrobenzene or isoquinoline, for which Frontier Molecular Orbital Theory fails.
NASA Astrophysics Data System (ADS)
Chakraborty, Debajit; Karasiev, Valentin; Trickey, Samuel
Aluminum is frequently used in warm-dense matter (WDM) experiments. However, experimental diagnostic limitations make computational exploration of the Al liquid-vapor transition important. The elevated temperaure and low-density make ab initio molecular dynamics (AIMD) with Kohn-Sham (KS) density functional theory (DFT) searches for the divergent compressibility extremely time consuming. Orbital free DFT (OFDFT) in principle is a cost-effective alternative. Here we report on calculations utilizing the PROFESS@QuantumEspresso interface to explore suitable pseudo-potentials, the limitations of our wholly constraint-based VT84F non-ineracting free-energy functional as exposed in the low-density regime, and possible extensions or extrapolations via tunable non-interacting free energy functionals. Work supported by U.S. Dept. of Energy, Grant DE-SC0002139.
Yuan, Wenjuan E-mail: luojunkink@126.com; Yang, Hongping; Zhu, Jing; Luo, Jun E-mail: luojunkink@126.com
2015-11-15
Defects are capable of modulating various properties of graphene, and thus controlling defects is useful in the development of graphene-based devices. Here we present first-principles calculations, which reveal a new avenue for defect engineering of graphene: the modulation by defects on the highest occupied molecular orbital (HOMO) energy of a charged monolayer graphene quantum dot (GQD) is discriminative. When the charge of a GQD increases its HOMO energy also increases. Importantly, when the GQD contains one particular class of defects its HOMO energy is sometimes higher and sometimes lower than that of the corresponding GQD without any defects, but when the GQD contains another class of defects its HOMO energy is always higher or lower than that of the corresponding intact GQD as its excess charge reaches a critical value. This discriminative modulation could allow defect engineering to control secondary electron ejection in graphene, leading to a new way to develop graphene-based devices.
Oxygen evolution on a SrFeO3 anode - Mechanistic considerations from molecular orbital theory
NASA Technical Reports Server (NTRS)
Mehandru, S. P.; Anderson, Alfred B.
1989-01-01
Various pathways proposed in the literature for the evolution of O2 in electrochemical oxidations are explored using the atom superposition and electron delocalization molecular orbital (ASED-MO) theory and the cluster models of the SrFeO3 surface as a prototype material. Calculations indicate that oxygen atoms can be easily formed on the (100) surface as well as on the edge cation sites of a SrFeO3 anode by the discharge of OH(-), followed by its deprotonation and electron transfer to the electrode. The O atoms can form O2 on the edge and corner sites, where the Fe(4+) is coordinated to four and three bulk oxygen anions, respectively. The calculations strongly disfavor mechanisms involving coupling of oxygen atoms adsorbed on different cations as well as a mechanism featuring an ozone intermediate.
NASA Astrophysics Data System (ADS)
Collado, J. R. Alvarez
A previous self-consistent field molecular orbital method, able to describe systems having a large number of unpaired electrons, n, is reviewed and improved. This method is applied to the study of paramagnetism in large (1,000-16,000 atoms) zigzag carbon nanotubes, represented by their n values. The computational scheme is based on the Hückel neglect differential overlap approach. It is shown that dependence of n on the semiempirical parameters is very small, and so they can be removed from the calculation. Enhancement of the paramagnetism (increase of n), by use of a strong external magnetic field, is also studied. Finally, the dependence of the Fermi one-electron potential energies and the spin atomic densities on both the parameters and the shape of the nanotubes is analyzed.0
NASA Astrophysics Data System (ADS)
Safouhi, Hassan; Hoggan, Philip
2003-01-01
This review on molecular integrals for large electronic systems (MILES) places the problem of analytical integration over exponential-type orbitals (ETOs) in a historical context. After reference to the pioneering work, particularly by Barnett, Shavitt and Yoshimine, it focuses on recent progress towards rapid and accurate analytic solutions of MILES over ETOs. Software such as the hydrogenlike wavefunction package Alchemy by Yoshimine and collaborators is described. The review focuses on convergence acceleration of these highly oscillatory integrals and in particular it highlights suitable nonlinear transformations. Work by Levin and Sidi is described and applied to MILES. A step by step description of progress in the use of nonlinear transformation methods to obtain efficient codes is provided. The recent approach developed by Safouhi is also presented. The current state of the art in this field is summarized to show that ab initio analytical work over ETOs is now a viable option.
Analytic second derivatives of the energy in the fragment molecular orbital method.
Nakata, Hiroya; Nagata, Takeshi; Fedorov, Dmitri G; Yokojima, Satoshi; Kitaura, Kazuo; Nakamura, Shinichiro
2013-04-28
We developed the analytic second derivatives of the energy for the fragment molecular orbital (FMO) method. First we derived the analytic expressions and then introduced some approximations related to the first and second order coupled perturbed Hartree-Fock equations. We developed a parallel program for the FMO Hessian with approximations in GAMESS and used it to calculate infrared (IR) spectra and Gibbs free energies and to locate the transition states in SN2 reactions. The accuracy of the Hessian is demonstrated in comparison to ab initio results for polypeptides and a water cluster. By using the two residues per fragment division, we achieved the accuracy of 3 cm(-1) in the reduced mean square deviation of vibrational frequencies from ab initio for all three polyalanine isomers, while the zero point energy had the error not exceeding 0.3 kcal/mol. The role of the secondary structure on IR spectra, zero point energies, and Gibbs free energies is discussed.
Analytic second derivatives of the energy in the fragment molecular orbital method
NASA Astrophysics Data System (ADS)
Nakata, Hiroya; Nagata, Takeshi; Fedorov, Dmitri G.; Yokojima, Satoshi; Kitaura, Kazuo; Nakamura, Shinichiro
2013-04-01
We developed the analytic second derivatives of the energy for the fragment molecular orbital (FMO) method. First we derived the analytic expressions and then introduced some approximations related to the first and second order coupled perturbed Hartree-Fock equations. We developed a parallel program for the FMO Hessian with approximations in GAMESS and used it to calculate infrared (IR) spectra and Gibbs free energies and to locate the transition states in SN2 reactions. The accuracy of the Hessian is demonstrated in comparison to ab initio results for polypeptides and a water cluster. By using the two residues per fragment division, we achieved the accuracy of 3 cm-1 in the reduced mean square deviation of vibrational frequencies from ab initio for all three polyalanine isomers, while the zero point energy had the error not exceeding 0.3 kcal/mol. The role of the secondary structure on IR spectra, zero point energies, and Gibbs free energies is discussed.
Ab initio molecular orbital calculations of the vibrational frequencies of XY4/sup -n/ anions
NASA Astrophysics Data System (ADS)
Curtiss, L. A.; Nichols, R.
The vibrational frequencies of a seris of XY4/sup -n/ anions (BeF4(-2), BF4(-), AlF4(-), MgCl4(-2), and AlCl4(-)) have been calculated by ab initio molecular orbital theory using the 3-21G and 6-31G* basis sets. The predicted harmonic frequencies are for the most part in good agreement with the observed frequencies of these anions in molten alkali halide mixtures. At the 3-21G basis set level the average difference between the observed and predicted frequencies is 12% while at the 6-31G* basis set level the average difference is 6%. Calculations of this type may be helpful in predicting the vibrational frequencies of other anions in molten salts.
Li, Xiao-Hong; Mei, Zheng; Zhang, Xian-Zhou
2014-01-24
The vibrational frequencies of acetophenone thiosemicarbazone in the ground state have been calculated using density functional method (B3LYP) with 6-31G(d), 6-31G(d,p) and 6-311++G(d,p) basis sets. The analysis of natural bond orbital was also performed. The IR spectra were obtained and interpreted by means of potential energies distributions (PEDs) using MOLVIB program. In addition, the results show that there exist N-H…N and N-H…S hydrogen bonds in the title compound, which play a major role in stabilizing the molecule and are confirmed by the natural bond orbital analysis. The predicted NLO properties show that the title compound is a good candidate as second-order NLO material. In addition, the frontier molecular orbitals were analyzed and the crystal structure obtained by molecular mechanics belongs to the Pbca space group, with lattice parameters Z=8, a=16.0735 Å, b=7.1719 Å, c=7.8725 Å, ρ=0.808 g/cm(3).
ERIC Educational Resources Information Center
Halkides, Christopher J.
2013-01-01
In this activity, students manipulate three-dimensional molecular models of the Ala-Ala-Ala tripeptide, where Ala is alanine. They rotate bonds to show that the pairs of dihedral angles phi = 0 degrees, psi = 180 degrees, and phi = 0 degrees, psi = 0 degrees lead to unfavorable interactions among the main chain atoms of the tripeptide. This…
Molecular Binding in Post-Kohn-Sham Orbital-Free DFT.
Borgoo, Alex; Green, James A; Tozer, David J
2014-12-01
Molecular binding in post-Kohn-Sham orbital-free DFT is investigated, using noninteracting kinetic energy functionals that satisfy the uniform electron gas condition and which are inhomogeneous under density scaling. A parameter is introduced that quantifies binding, and a series of functionals are determined from fits to near-exact effective homogeneities and/or Kohn-Sham noninteracting kinetic energies. These are then used to investigate the relationship between binding and the accuracy of the effective homogeneity and noninteracting kinetic energy at the equilibrium geometry. For a series of 11 molecules, the binding broadly improves as the effective homogeneity improves, although the extent to which it improves is dependent on the accuracy of the noninteracting kinetic energy; optimal binding appears to require both to be accurate simultaneously. The use of a Thomas-Fermi-von Weizsäcker form, augmented with a second gradient correction, goes some way toward achieving this, exhibiting molecular binding on average. The findings are discussed in terms of the noninteracting kinetic potential and the Hellmann-Feynman theorem. The extent to which the functionals can reproduce the system-dependence of the near-exact effective homogeneity is quantified, and potential energy curves are presented for selected molecules. The study provides impetus for including density scaling homogeneity considerations in the design of noninteracting kinetic energy functionals. PMID:26583217
NASA Technical Reports Server (NTRS)
Almloef, Jan; Taylor, Peter R.
1989-01-01
A recently proposed scheme for using natural orbitals from atomic configuration interaction (CI) wave functions as a basis set for linear combination of atomic orbitals (LCAO) calculations is extended for the calculation of molecular properties. For one-electron properties like multipole moments, which are determined largely by the outermost regions of the molecular wave function, it is necessary to increase the flexibility of the basis in these regions. This is most easily done by uncontracting the outmost Gaussian primitives, and/or by adding diffuse primitives. A similar approach can be employed for the calculation of polarizabilities. Properties which are not dominated by the long-range part of the wave function, such as spectroscopic constants or electric field gradients at the nucleus, can generally be treated satisfactorily with the original atomic natural orbital (ANO) sets.
NASA Astrophysics Data System (ADS)
Habeeb, Moustafa M.; Al-Attas, Amirah S.; Al-Raimi, Doaa S.
2015-05-01
Charge transfer (CT) interaction between 3,5-dimethylpyrazole (DMP) with the π-acceptor 2,3-dichloro-5,6-dicyano-p-benzoquinon (DDQ) has been investigated spectrophotometrically in acetonitrile (AN). Simultaneous reddish brown color has been observed upon mixing donor with acceptor solutions attributing to CT complex formation. The electronic spectra of the formed complex exhibited multi-charge transfer bands at 429, 447, 506, 542 and 589 nm, respectively. Job's method of continuous variations and spectrophotometric titration methods confirmed the formation of the studied complex in 1:2 ratio between DMP and DDQ. Benesi-Hildebrand equation has been applied to calculate the stability constant of the formed complex where it recorded high value supporting formation of stable complex. Molecular orbital calculations using MM2 method and GAMESS (General Atomic and Molecular Electronic Structure System) interface computations as a package of ChemBio3D Ultra12 software were carried out for more analysis of the formed complex in the gas phase. The computational analysis included energy minimisation, stabilisation energy, molecular geometry, Mullikan charges, molecular electrostatic potential (MEP) surfaces of reactants and complex as well as characterization of the higher occupied molecular orbitals (HOMO) and lower unoccupied molecular orbitals (LUMO) surfaces of the complex. A good consistency between experimental and theoretical results has been recorded.
Ewen, Pascal R; Sanning, Jan; Koch, Tobias; Doltsinis, Nikos L; Strassert, Cristian A; Wegner, Daniel
2014-01-01
The improvement of molecular electronic devices such as organic light-emitting diodes requires fundamental knowledge about the structural and electronic properties of the employed molecules as well as their interactions with neighboring molecules or interfaces. We show that highly resolved scanning tunneling microscopy (STM) and spectroscopy (STS) are powerful tools to correlate the electronic properties of phosphorescent complexes (i.e., triplet emitters) with their molecular structure as well as the local environment around a single molecule. We used spectroscopic mapping to visualize several occupied and unoccupied molecular frontier orbitals of Pt(II) complexes adsorbed on Au(111). The analysis showed that the molecules exhibit a peculiar localized strong hybridization that leads to partial depopulation of a dz² orbital, while the ligand orbitals are almost unchanged. We further found that substitution of functional groups at well-defined positions can alter specific molecular orbitals without influencing the others. The results open a path toward the tailored design of electronic and optical properties of triplet emitters by smart ligand substitution, which may improve the performance of future OLED devices.
Ewen, Pascal R; Sanning, Jan; Koch, Tobias; Doltsinis, Nikos L
2014-01-01
Summary The improvement of molecular electronic devices such as organic light-emitting diodes requires fundamental knowledge about the structural and electronic properties of the employed molecules as well as their interactions with neighboring molecules or interfaces. We show that highly resolved scanning tunneling microscopy (STM) and spectroscopy (STS) are powerful tools to correlate the electronic properties of phosphorescent complexes (i.e., triplet emitters) with their molecular structure as well as the local environment around a single molecule. We used spectroscopic mapping to visualize several occupied and unoccupied molecular frontier orbitals of Pt(II) complexes adsorbed on Au(111). The analysis showed that the molecules exhibit a peculiar localized strong hybridization that leads to partial depopulation of a dz² orbital, while the ligand orbitals are almost unchanged. We further found that substitution of functional groups at well-defined positions can alter specific molecular orbitals without influencing the others. The results open a path toward the tailored design of electronic and optical properties of triplet emitters by smart ligand substitution, which may improve the performance of future OLED devices. PMID:25551053
ERIC Educational Resources Information Center
Litofsky, Joshua; Viswanathan, Rama
2015-01-01
Matrix diagonalization, the key technique at the heart of modern computational chemistry for the numerical solution of the Schrödinger equation, can be easily introduced in the physical chemistry curriculum in a pedagogical context using simple Hückel molecular orbital theory for p bonding in molecules. We present details and results of…
Matus, Myrna H; Garza, Jorge; Galván, Marcelo
2004-06-01
In order to study the Kohn-Sham frontier molecular orbital energies in the complete basis limit, a comparative study between localized functions and plane waves, obtained with the local density approximation exchange-correlation functional is made. The analyzed systems are ethylene and butadiene, since they are theoretical and experimentally well characterized. The localized basis sets used are those developed by Dunning. For the plane-waves method, the pseudopotential approximation is employed. The results obtained by the localized basis sets suggest that it is possible to get an estimation of the orbital energies in the limit of the complete basis set, when the basis set size is large. It is shown that the frontier molecular orbital energies and the energy gaps obtained with plane waves are similar to those obtained with a large localized basis set, when the size of the supercell and the plane-wave expansion have been appropriately calibrated.
NASA Astrophysics Data System (ADS)
Mok, Michelle; Burghardt, Wesley; Ellison, Christopher; Torkelson, John
2009-03-01
Traditionally, phase transitions of block copolymers could only be tuned through molecular weight and relative block length. Here, we introduce comonomer sequence design through gradient compositions as a means of further manipulating phase diagram boundaries. In such gradient copolymers, the reduced repulsion between chain segments allows access to phase transitions even at high molecular weights (MW). Rheological and x-ray scattering studies were performed to study the impact of comonomer sequence on phase behavior in styrene/n-butyl acrylate (S/nBA) systems. In S/nBA block copolymers, only upper critical ordering behavior was observed. In contrast, by using a gradient architecture of higher MW we observed both upper and lower ordering transitions similar to those seen in very weakly segregating S/n-butyl methacrylate block copolymers, where such dual ordering transitions were first detected by Russell et al. This is the first study to access a miscibility gap in gradient copolymers. Access to such behavior is very rare in blends and block copolymers, limited to low MW and/or very weakly segregating systems.
Nakata, Hiroya; Nishimoto, Yoshio; Fedorov, Dmitri G
2016-07-28
The analytic second derivative of the energy is developed for the fragment molecular orbital (FMO) method combined with density-functional tight-binding (DFTB), enabling simulations of infrared and Raman spectra of large molecular systems. The accuracy of the method is established in comparison to full DFTB without fragmentation for a set of representative systems. The performance of the FMO-DFTB Hessian is discussed for molecular systems containing up to 10 041 atoms. The method is applied to the study of the binding of α-cyclodextrin to polyethylene glycol, and the calculated IR spectrum of an epoxy amine oligomer reproduces experiment reasonably well. PMID:27475354
NASA Astrophysics Data System (ADS)
Nakata, Hiroya; Nishimoto, Yoshio; Fedorov, Dmitri G.
2016-07-01
The analytic second derivative of the energy is developed for the fragment molecular orbital (FMO) method combined with density-functional tight-binding (DFTB), enabling simulations of infrared and Raman spectra of large molecular systems. The accuracy of the method is established in comparison to full DFTB without fragmentation for a set of representative systems. The performance of the FMO-DFTB Hessian is discussed for molecular systems containing up to 10 041 atoms. The method is applied to the study of the binding of α-cyclodextrin to polyethylene glycol, and the calculated IR spectrum of an epoxy amine oligomer reproduces experiment reasonably well.
NASA Astrophysics Data System (ADS)
Okamoto, Akisumi; Yano, Atsushi; Nomura, Kazuya; Higai, Shin'ichi; Kurita, Noriyuki
2013-07-01
Aggregation of amyloid β-proteins (Aβ) plays a key role in the mechanism of molecular pathogenesis of Alzheimer’s disease (AD). It is known that full-length Aβ(1-42) is more prone to aggregation than Aβ(1-40). We here search stable conformations of solvated Aβ(1-42) monomer by replica exchange molecular dynamics simulations based on classical force fields, and the most stable conformation is determined from the total energies evaluated by the ab initio fragment molecular orbital (FMO) calculations. In addition, based on the FMO results, the amino acid residues of Aβ(1-42) contributing to the stabilization of the monomer are highlighted.
Wyrick, Jonathan; Bartels, Ludwig; Einstein, T. L.
2015-03-14
We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species’ diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system.
NASA Astrophysics Data System (ADS)
Wyrick, Jonathan; Einstein, T. L.; Bartels, Ludwig
2015-03-01
We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species' diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system.
Wyrick, Jonathan; Einstein, T L; Bartels, Ludwig
2015-03-14
We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species' diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system.
Krah, Tim; Ben Amor, Nadia; Maynau, Daniel; Berger, J A; Robert, Vincent
2014-07-01
Based on localized molecular orbitals, the proposed method reduces large configuration interaction (CI) spaces while maintaining agreement with reference values. Our strategy concentrates the numerical effort on physically pertinent CI-contributions and is to be considered as a tool to tackle large systems including numerous open-shells. To show the efficiency of our method we consider two 4-electron parent systems. First, we illustrate our approach by describing the van der Waals interactions in the (H2)2 system. By systematically including local correlation, dispersion and charge transfer mechanisms, we show that 90% of the reference full CI dissociation energy of the H2 dimer is reproduced using only 3% of the full CI space. Second, the conformational cis/trans rotation barrier of the butadiene molecule is remarkably reproduced (97% of the reference value) with less than 1% of the reference space. This work paves the way to numerical strategies which afford the electronic structure determination of large open-shell systems avoiding the exponential limitation. At the same time, a physical analysis of the contents of the wave function is offered.
Cahill, Katharine J; Johnson, Richard P
2013-03-01
Polar bimolecular reactions often begin as charge-transfer complexes and may proceed with a high degree of electron transfer character. Frontier molecular orbital (FMO) theory is predicated in part on this concept. We have developed an electron transfer model (ETM) in which we systematically transfer one electron between reactants and then use density functional methods to model the resultant radical or radical ion intermediates. Sites of higher reactivity are revealed by a composite spin density map (SDM) of odd electron character on the electron density surface, assuming that a new two-electron bond would occur preferentially at these sites. ETM correctly predicts regio- and stereoselectivity for a broad array of reactions, including Diels-Alder, dipolar and ketene cycloadditions, Birch reduction, many types of nucleophilic additions, and electrophilic addition to aromatic rings and polyenes. Conformational analysis of radical ions is often necessary to predict reaction stereochemistry. The electronic and geometric changes due to one-electron oxidation or reduction parallel the reaction coordinate for electrophilic or nucleophilic addition, respectively. The effect is more dramatic for one-electron reduction.
Analytic Gradient for Density Functional Theory Based on the Fragment Molecular Orbital Method.
Brorsen, Kurt R; Zahariev, Federico; Nakata, Hiroya; Fedorov, Dmitri G; Gordon, Mark S
2014-12-01
The equations for the response terms for the fragment molecular orbital (FMO) method interfaced with the density functional theory (DFT) gradient are derived and implemented. Compared to the previous FMO-DFT gradient, which lacks response terms, the FMO-DFT analytic gradient has improved accuracy for a variety of functionals, when compared to numerical gradients. The FMO-DFT gradient agrees with the fully ab initio DFT gradient in which no fragmentation is performed, while reducing the nonlinear scaling associated with standard DFT. Solving for the response terms requires the solution of the coupled perturbed Kohn-Sham (CPKS) equations, where the CPKS equations are solved through a decoupled Z-vector procedure called the self-consistent Z-vector method. FMO-DFT is a nonvariational method and the FMO-DFT gradient is unique compared to standard DFT gradients in that the FMO-DFT gradient requires terms from both DFT and time-dependent density functional theory (TDDFT) theories.
Tokuda, Kana; Watanabe, Chiduru; Okiyama, Yoshio; Mochizuki, Yuji; Fukuzawa, Kaori; Komeiji, Yuto
2016-09-01
The fragment molecular orbital (FMO) method was applied to quantum chemical calculations of neuramic acid, the natural substrate of the influenza virus neuraminidase, and two of its competitive inhibitors, Oseltamivir (Tamiful(®)) and Zanamivir (Relenza(®)), to investigate their hydrated structures and energetics. Each of the three ligands was immersed in an explicit water solvent, geometry-optimized by classical MM and QM/MM methods, and subjected to FMO calculations with 2-, 3-, and 4-body corrections under several fragmentation options. The important findings were that QM/MM optimization was preferable to obtain reliable hydrated structures of the ligands, that the 3-body correction was important for quantitative evaluation of the solvation energy, and that the dehydration effect was most remarkable near the hydrophobic sections of the ligands. In addition, the hydration energy calculated by the explicit solvent was compared with the hydration free energy calculated by the implicit solvent via the Poisson-Boltzmann equation, and the two showed a fairly good correlation. These findings will serve as useful information for rapid drug design. PMID:27611645
NASA Astrophysics Data System (ADS)
Kubicki, J. D.; Heaney, P. J.
2002-12-01
Researchers recently have made the discovery that hypercoordinate Si-sorbitol complexes will readily form in biologically relevant fluids, and they have reported the first evidence for a transient organosilicon complex generated within the life cycle of an organism. These interpretations are based upon peak assignments of Si-29 NMR spectra that invoke Si-polyol complexes with Si in five- and six-fold coordination states. However, ab initio analyses of the proposed organosilicon structures do not reproduce the experimentally observed chemical shifts. We have successfully modeled one of the observed Si-29 chemical shifts with a 5-fold Si-disorbitol complex involving 5-membered ring configurations (i.e., Si-O-C-C-O), which yielded Si-29 chemical shifts that closely matched the observed values in the -100 to -102 ppm range. Likewise, Si-29 NMR peaks near -144 ppm were well fit by a model in which a 6-fold Si was complexed to three sorbitol molecules in a 5-membered ring configuration. The ability to simulate observed NMR signals using molecular orbital calculations provides strong support for the controversial role of hypercoordinate organosilicon species in the uptake and transport of silica by biological systems. The existence of such complexes in turn may explain other puzzles in Si biogeochemistry, such as the persistence of monomeric silica in concentrated biological fluids and the biofractionation of Si isotopes and Ge.
Stan, Raluca-Maria; Gaina, Roxana; Enachescu, Cristian E-mail: radu.tanasa@uaic.ro; Stancu, Alexandru; Tanasa, Radu E-mail: radu.tanasa@uaic.ro; Bronisz, Robert
2015-05-07
In this paper, we analyze two types of hysteresis in spin crossover molecular magnets compounds in the framework of the First Order Reversal Curve (FORC) method. The switching between the two stable states in these compounds is accompanied by hysteresis phenomena if the intermolecular interactions are higher than a threshold. We have measured the static thermal hysteresis (TH) and the kinetic light induced thermal hysteresis (LITH) major loops and FORCs for the polycrystalline Fe(II) spin crossover compound [Fe{sub 1−x}Zn{sub x}(bbtr){sub 3}](ClO{sub 4}){sub 2} (bbtr = 1,4-di(1,2,3-triazol-1-yl)butane), either in a pure state (x = 0) or doped with Zn ions (x = 0.33) considering different sweeping rates. Here, we use this method not only to infer the domains distribution but also to disentangle between kinetic and static components of the LITH and to estimate the changes in the intermolecular interactions introduced by dopants. We also determined the qualitative relationship between FORC distributions measured for TH and LITH.
NASA Astrophysics Data System (ADS)
Drake, Kyle; Bonacum, Jason; Zhang, Guo-Ping
2014-03-01
The molecular structure of Buckminster fullerene (C60) allows for electron delocalization in all of the pi-bonding electrons of the molecule. This coupled with the symmetry of the molecule allows for the formation of super-atomic molecular orbitals (SAMOs) similar to those observed in aluminum clusters. The SAMOs behave as if the molecule that they belong to is a single atom. We compute the eigenstates of C60 compulationally using density functional theory (DFT) and a grid mesh. Using larger radii also allows us to accurately describe SAMOs and test the convergence of our data. The results are interesting because for the first time, we can show the true converged super atomic orbitals in C60. Indiana State University SURE Program, Department of Energy, Indiana State University Department of Physics, and Indiana State University Center for Student Creativity and Research.
NASA Astrophysics Data System (ADS)
Philipp, Dean Michael
Methodology is discussed for mixed ab initio quantum mechanics/molecular mechanics modeling of systems where the quantum mechanics (QM) and molecular mechanics (MM) regions are within the same molecule. The ab initio QM calculations are at the restricted Hartree-Fock level using the pseudospectral method of the Jaguar program while the MM part is treated with the OPLS force fields implemented in the IMPACT program. The interface between the QM and MM regions, in particular, is elaborated upon, as it is dealt with by ``breaking'' bonds at the boundaries and using Boys-localized orbitals found from model molecules in place of the bonds. These orbitals are kept frozen during QM calculations. The mixed modeling presented here can be used for single point energy calculations and geometry optimizations. Results from tests of the method to find relative conformational energies and geometries of alanine tetrapeptides are presented along with comparisons to pure QM and pure MM calculations.
Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet
2015-02-01
In this study, 5-iodosalicylic acid (5-ISA, C7H5IO3) is structurally characterized by FT-IR, FT-Raman, NMR and UV spectroscopies. There are eight conformers, Cn, n=1-8 for this molecule therefore the molecular geometry for these eight conformers in the ground state are calculated by using the ab-initio density functional theory (DFT) B3LYP method approach with the aug-cc-pVDZ-PP basis set for iodine and the aug-cc-pVDZ basis set for the other elements. The computational results identified that the most stable conformer of 5-ISA is the C1 form. The vibrational spectra are calculated DFT method invoking the same basis sets and fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method with PQS program. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (COOP or OPDOS) diagrams analysis for C1 conformer were calculated using the same method. The energy and oscillator strength are calculated by time-dependent density functional theory (TD-DFT) results complement with the experimental findings. Besides, charge transfer occurring in the molecule between HOMO and LUMO energies, frontier energy gap, molecular electrostatic potential (MEP) are calculated and presented. The NMR chemical shifts ((1)H and (13)C) spectra are recorded and calculated using the gauge independent atomic orbital (GIAO) method. Mulliken atomic charges of the title molecule are also calculated, interpreted and compared with salicylic acid. The optimized bond lengths, bond angles and calculated NMR and UV, vibrational wavenumbers showed the best agreement with the experimental results. PMID:25448933
Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet
2015-02-01
In this study, 5-iodosalicylic acid (5-ISA, C7H5IO3) is structurally characterized by FT-IR, FT-Raman, NMR and UV spectroscopies. There are eight conformers, Cn, n=1-8 for this molecule therefore the molecular geometry for these eight conformers in the ground state are calculated by using the ab-initio density functional theory (DFT) B3LYP method approach with the aug-cc-pVDZ-PP basis set for iodine and the aug-cc-pVDZ basis set for the other elements. The computational results identified that the most stable conformer of 5-ISA is the C1 form. The vibrational spectra are calculated DFT method invoking the same basis sets and fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method with PQS program. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (COOP or OPDOS) diagrams analysis for C1 conformer were calculated using the same method. The energy and oscillator strength are calculated by time-dependent density functional theory (TD-DFT) results complement with the experimental findings. Besides, charge transfer occurring in the molecule between HOMO and LUMO energies, frontier energy gap, molecular electrostatic potential (MEP) are calculated and presented. The NMR chemical shifts ((1)H and (13)C) spectra are recorded and calculated using the gauge independent atomic orbital (GIAO) method. Mulliken atomic charges of the title molecule are also calculated, interpreted and compared with salicylic acid. The optimized bond lengths, bond angles and calculated NMR and UV, vibrational wavenumbers showed the best agreement with the experimental results.
NASA Astrophysics Data System (ADS)
Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet
2015-02-01
In this study, 5-iodosalicylic acid (5-ISA, C7H5IO3) is structurally characterized by FT-IR, FT-Raman, NMR and UV spectroscopies. There are eight conformers, Cn, n = 1-8 for this molecule therefore the molecular geometry for these eight conformers in the ground state are calculated by using the ab-initio density functional theory (DFT) B3LYP method approach with the aug-cc-pVDZ-PP basis set for iodine and the aug-cc-pVDZ basis set for the other elements. The computational results identified that the most stable conformer of 5-ISA is the C1 form. The vibrational spectra are calculated DFT method invoking the same basis sets and fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method with PQS program. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (COOP or OPDOS) diagrams analysis for C1 conformer were calculated using the same method. The energy and oscillator strength are calculated by time-dependent density functional theory (TD-DFT) results complement with the experimental findings. Besides, charge transfer occurring in the molecule between HOMO and LUMO energies, frontier energy gap, molecular electrostatic potential (MEP) are calculated and presented. The NMR chemical shifts (1H and 13C) spectra are recorded and calculated using the gauge independent atomic orbital (GIAO) method. Mulliken atomic charges of the title molecule are also calculated, interpreted and compared with salicylic acid. The optimized bond lengths, bond angles and calculated NMR and UV, vibrational wavenumbers showed the best agreement with the experimental results.
Pharmacophore Modeling for Anti-Chagas Drug Design Using the Fragment Molecular Orbital Method
Ohno, Kazuki; Orita, Masaya; Inoue, Masayuki; Shiba, Tomoo; Harada, Shigeharu; Honma, Teruki; Balogun, Emmanuel Oluwadare; da Rocha, Josmar Rodrigues; Montanari, Carlos Alberto; Kita, Kiyoshi; Sekijima, Masakazu
2015-01-01
Background Chagas disease, caused by the parasite Trypanosoma cruzi, is a neglected tropical disease that causes severe human health problems. To develop a new chemotherapeutic agent for the treatment of Chagas disease, we predicted a pharmacophore model for T. cruzi dihydroorotate dehydrogenase (TcDHODH) by fragment molecular orbital (FMO) calculation for orotate, oxonate, and 43 orotate derivatives. Methodology/Principal Findings Intermolecular interactions in the complexes of TcDHODH with orotate, oxonate, and 43 orotate derivatives were analyzed by FMO calculation at the MP2/6-31G level. The results indicated that the orotate moiety, which is the base fragment of these compounds, interacts with the Lys43, Asn67, and Asn194 residues of TcDHODH and the cofactor flavin mononucleotide (FMN), whereas functional groups introduced at the orotate 5-position strongly interact with the Lys214 residue. Conclusions/Significance FMO-based interaction energy analyses revealed a pharmacophore model for TcDHODH inhibitor. Hydrogen bond acceptor pharmacophores correspond to Lys43 and Lys214, hydrogen bond donor and acceptor pharmacophores correspond to Asn67 and Asn194, and the aromatic ring pharmacophore corresponds to FMN, which shows important characteristics of compounds that inhibit TcDHODH. In addition, the Lys214 residue is not conserved between TcDHODH and human DHODH. Our analysis suggests that these orotate derivatives should preferentially bind to TcDHODH, increasing their selectivity. Our results obtained by pharmacophore modeling provides insight into the structural requirements for the design of TcDHODH inhibitors and their development as new anti-Chagas drugs. PMID:25961853
Using the fragment molecular orbital method to investigate agonist-orexin-2 receptor interactions.
Heifetz, Alexander; Aldeghi, Matteo; Chudyk, Ewa I; Fedorov, Dmitri G; Bodkin, Mike J; Biggin, Philip C
2016-04-15
The understanding of binding interactions between any protein and a small molecule plays a key role in the rationalization of affinity and selectivity and is essential for an efficient structure-based drug discovery (SBDD) process. Clearly, to begin SBDD, a structure is needed, and although there has been fantastic progress in solving G-protein-coupled receptor (GPCR) crystal structures, the process remains quite slow and is not currently feasible for every GPCR or GPCR-ligand complex. This situation significantly limits the ability of X-ray crystallography to impact the drug discovery process for GPCR targets in 'real-time' and hence there is still a need for other practical and cost-efficient alternatives. We present here an approach that integrates our previously described hierarchical GPCR modelling protocol (HGMP) and the fragment molecular orbital (FMO) quantum mechanics (QM) method to explore the interactions and selectivity of the human orexin-2 receptor (OX2R) and its recently discovered nonpeptidic agonists. HGMP generates a 3D model of GPCR structures and its complexes with small molecules by applying a set of computational methods. FMO allowsab initioapproaches to be applied to systems that conventional QM methods would find challenging. The key advantage of FMO is that it can reveal information on the individual contribution and chemical nature of each residue and water molecule to the ligand binding that normally would be difficult to detect without QM. We illustrate how the combination of both techniques provides a practical and efficient approach that can be used to analyse the existing structure-function relationships (SAR) and to drive forward SBDD in a real-world example for which there is no crystal structure of the complex available.
ERIC Educational Resources Information Center
Bridgeman, Adam J.; Schmidt, Timothy W.; Young, Nigel A.
2013-01-01
The stretching modes of ML[subscript "x"] complexes have the same symmetry as the atomic orbitals on M that are used to form its s bonds. In the exercise suggested here, the atomic orbitals are used to derive the form of the stretching modes without the need for formal group theory. The analogy allows students to help understand many…
Roemelt, Michael
2015-07-28
Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctions are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method.
NASA Astrophysics Data System (ADS)
Ferl, Robert J.; Zupanska, Agata; Spinale, April; Reed, David; Manning-Roach, Susan; Guerra, George; Cox, David R.; Paul, Anna-Lisa
2011-07-01
Molecular biology experiments on the International Space Station (ISS) continue to face challenges of sample harvesting and sample return to earth for post flight analysis; however, the use of Kennedy Space Center Fixation Tubes filled with RNALater has proven to be a robust solution to many of these challenges. While it is clear that one direction of future spaceflight experimentation may be towards enhanced on-orbit analytical capabilities, the rapid progress of earth-bound analytical capacity dictates that facile return of molecular biology samples from the ISS will continue to be a mainstay of space life sciences research and flight operations. In this paper we present a case study of the successful performance of KFTs and RNALater over a broad set of operational conditions of ascent configuration, on-orbit experiment use, on-orbit storage and sample return configurations that are unique to ISS current operations and constraints. We also provide observations on performance limits and discuss deployment opportunities and scenarios that are consistent with continued successful ISS molecular biology experimentation.
Direct observation of molecular orbitals in an individual single-molecule magnet Mn12 on Bi(111).
Sun, Kai; Park, Kyungwha; Xie, Jiale; Luo, Jiyong; Yuan, Hongkuan; Xiong, Zuhong; Wang, Junzhong; Xue, Qikun
2013-08-27
Single-molecule nanomagnets have unique quantum properties, and their potential applications require characterization and accessibility of individual single-molecule magnets on various substrates. We develop a gentle tip-deposition method to bring individual prototype single-molecule magnets, manganese-12-acetate (Mn12) molecules, onto the semimetallic Bi(111) surface without linker molecules, using low-temperature scanning tunneling microscopy. We are able to identify both the almost flat-lying and side-lying orientations of Mn12 molecules at 4.5 K. Energy-resolved spectroscopic mapping enables the first observation of several molecular orbitals of individual Mn12 molecules in real space, which is consistent with density functional theory calculations. Both experimental and theoretical results suggest that an energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the almost flat-lying Mn12 is only 40% of such a gap for an isolated (free) Mn12 molecule, which is caused by charge transfer from the metallic surface states of Bi to the Mn12. Despite the reduction of this gap, STM images show that the local lattices of Bi(111) covered with Mn12 remain essentially intact, indicating that Mn12-Bi interactions are not strong. Our findings open an avenue to address directly the local structural and electronic properties of individual single-molecule magnets on solid substrates.
NASA Astrophysics Data System (ADS)
Riquelme, D.; Amo-Baladrón, M. A.; Martín-Pintado, J.; Mauersberger, R.; Martín, S.; Bronfman, L.
2013-01-01
Context. It is well known that the kinetic temperatures, Tkin, of the molecular clouds in the Galactic center region are higher than in typical disk clouds. However, the Tkin of the molecular complexes found at higher latitudes towards the giant molecular loops in the central region of the Galaxy is so far unknown. The gas of these high-latitude molecular clouds (hereafter referred to as "halo clouds") is located in a region where the gas in the disk may interact with the gas in the halo in the Galactic center region. Aims: To derive Tkin in the molecular clouds at high latitude and understand the physical process responsible for the heating of the molecular gas both in the central molecular zone (the concentration of molecular gas in the inner ~500 pc) and in the giant molecular loops. Methods: We measured the metastable inversion transitions of NH3 from (J,K) = (1,1) to (6,6) toward six positions selected throughout the Galactic central disk and halo. We used rotational diagrams and large velocity gradient (LVG) modeling to estimate the kinetic temperatures toward all the sources. We also observed other molecules like SiO, HNCO, CS, C34S, C18O, and 13CO, to derive the densities and to trace different physical processes (shocks, photodissociation, dense gas) expected to dominate the heating of the molecular gas. Results: We derive for the first time Tkin of the high-latitude clouds interacting with the disk in the Galactic center region. We find high rotational temperatures in all the observed positions. We derive two kinetic temperature components (~150 K and ~40 K) for the positions in the central molecular zone, and only the warm kinetic temperature component for the clouds toward the giant molecular loops. The fractional abundances derived from the different molecules suggest that shocks provide the main heating mechanism throughout the Galactic center, also at high latitudes. Appendices A and B are available in electronic form at http://www.aanda.org
NASA Astrophysics Data System (ADS)
Palii, Andrei; Tsukerblat, Boris; Clemente-Juan, Juan Modesto; Coronado, Eugenio
This review article is a first attempt to give a systematic and comprehensive description (in the framework of the unified theoretical approach) of the exchange interactions in polynuclear systems based on orbitally degenerate metal ions in the context of their relevance to the modern molecular magnetism. Interest in these systems is related to the fundamental problems of magnetism and at the same time steered by a number of impressive potential applications of molecular magnets, like high-density memory storage units, nanoscale qubits, spintronics and photoswitchable devices. In the presence of orbital degeneracy, the conventional spin Hamiltonian (Heisenberg-Dirac-van Vleck model) becomes inapplicable even as an approximation. The central component of this review article constitutes the concept of orbitally-dependent exchange interaction between metal ions possessing unquenched orbital angular momenta. We present a rigorous procedure of derivation of the kinetic exchange Hamiltonian for a pair of orbitally degenerate transition metal ions that is expressed in terms of the orbital matrices and spin operators. The microscopic background reveals the interrelations between the parameters of the Hamiltonian and the internal parameters of the system including all relevant transfer integrals and fundamental intracenter interactions. The developed formalism integrated with the irreducible tensor operator (ITO) technique makes it possible to describe the exchange coupling and all relevant interactions (crystal fields, spin-orbit (SO) and Zeeman couplings) in terms of the ITOs of the full spherical group, and in this way to develop anunified and efficient computational tool. The orbitally-dependent exchange was shown to lead to an anomalously strong magnetic anisotropy that can be considered as a main physical manifestation of the unquenched orbital angular momentum in metal clusters of orbitally-degenerate ions. The theoretical background is illustrated by the following
Pinjari, Rahul V; Delcey, Mickaël G; Guo, Meiyuan; Odelius, Michael; Lundberg, Marcus
2014-09-28
The metal L-edge (2p → 3d) X-ray absorption spectra are affected by a number of different interactions: electron-electron repulsion, spin-orbit coupling, and charge transfer between metal and ligands, which makes the simulation of spectra challenging. The core restricted active space (RAS) method is an accurate and flexible approach that can be used to calculate X-ray spectra of a wide range of medium-sized systems without any symmetry constraints. Here, the applicability of the method is tested in detail by simulating three ferric (3d(5)) model systems with well-known electronic structure, viz., atomic Fe(3+), high-spin [FeCl6](3-) with ligand donor bonding, and low-spin [Fe(CN)6](3-) that also has metal backbonding. For these systems, the performance of the core RAS method, which does not require any system-dependent parameters, is comparable to that of the commonly used semi-empirical charge-transfer multiplet model. It handles orbitally degenerate ground states, accurately describes metal-ligand interactions, and includes both single and multiple excitations. The results are sensitive to the choice of orbitals in the active space and this sensitivity can be used to assign spectral features. A method has also been developed to analyze the calculated X-ray spectra using a chemically intuitive molecular orbital picture.
Phipps, M J S; Fox, T; Tautermann, C S; Skylaris, C-K
2016-07-12
We report the development and implementation of an energy decomposition analysis (EDA) scheme in the ONETEP linear-scaling electronic structure package. Our approach is hybrid as it combines the localized molecular orbital EDA (Su, P.; Li, H. J. Chem. Phys., 2009, 131, 014102) and the absolutely localized molecular orbital EDA (Khaliullin, R. Z.; et al. J. Phys. Chem. A, 2007, 111, 8753-8765) to partition the intermolecular interaction energy into chemically distinct components (electrostatic, exchange, correlation, Pauli repulsion, polarization, and charge transfer). Limitations shared in EDA approaches such as the issue of basis set dependence in polarization and charge transfer are discussed, and a remedy to this problem is proposed that exploits the strictly localized property of the ONETEP orbitals. Our method is validated on a range of complexes with interactions relevant to drug design. We demonstrate the capabilities for large-scale calculations with our approach on complexes of thrombin with an inhibitor comprised of up to 4975 atoms. Given the capability of ONETEP for large-scale calculations, such as on entire proteins, we expect that our EDA scheme can be applied in a large range of biomolecular problems, especially in the context of drug design.
Heifetz, Alexander; Chudyk, Ewa I; Gleave, Laura; Aldeghi, Matteo; Cherezov, Vadim; Fedorov, Dmitri G; Biggin, Philip C; Bodkin, Mike J
2016-01-25
Our interpretation of ligand-protein interactions is often informed by high-resolution structures, which represent the cornerstone of structure-based drug design. However, visual inspection and molecular mechanics approaches cannot explain the full complexity of molecular interactions. Quantum Mechanics approaches are often too computationally expensive, but one method, Fragment Molecular Orbital (FMO), offers an excellent compromise and has the potential to reveal key interactions that would otherwise be hard to detect. To illustrate this, we have applied the FMO method to 18 Class A GPCR-ligand crystal structures, representing different branches of the GPCR genome. Our work reveals key interactions that are often omitted from structure-based descriptions, including hydrophobic interactions, nonclassical hydrogen bonds, and the involvement of backbone atoms. This approach provides a more comprehensive picture of receptor-ligand interactions than is currently used and should prove useful for evaluation of the chemical nature of ligand binding and to support structure-based drug design.
Liquid Water through Density-Functional Molecular Dynamics: Plane-Wave vs Atomic-Orbital Basis Sets.
Miceli, Giacomo; Hutter, Jürg; Pasquarello, Alfredo
2016-08-01
We determine and compare structural, dynamical, and electronic properties of liquid water at near ambient conditions through density-functional molecular dynamics simulations, when using either plane-wave or atomic-orbital basis sets. In both frameworks, the electronic structure and the atomic forces are self-consistently determined within the same theoretical scheme based on a nonlocal density functional accounting for van der Waals interactions. The overall properties of liquid water achieved within the two frameworks are in excellent agreement with each other. Thus, our study supports that implementations with plane-wave or atomic-orbital basis sets yield equivalent results and can be used indiscriminately in study of liquid water or aqueous solutions.
NASA Technical Reports Server (NTRS)
Roberts, W. W., Jr.; Stewart, G. R.
1987-01-01
The different roles played by orbital dynamics and dissipative cloud-cloud collisions in the formation of giant molecular clouds (GMCs) in a global spiral structure are investigated. The interstellar medium (ISM) is simulated by a system of particles, representing clouds, which orbit in a spiral-perturbed, galactic gravitational field. The overall magnitude and width of the global cloud density distribution in spiral arms is very similar in the collisional and collisionless simulations. The results suggest that the assumed number density and size distribution of clouds and the details of individual cloud-cloud collisions have relatively little effect on these features. Dissipative cloud-cloud collisions play an important steadying role for the cloud system's global spiral structure. Dissipative cloud-cloud collisions also damp the relative velocity dispersion of clouds in massive associations and thereby aid in the effective assembling of GMC-like complexes.
Liquid Water through Density-Functional Molecular Dynamics: Plane-Wave vs Atomic-Orbital Basis Sets.
Miceli, Giacomo; Hutter, Jürg; Pasquarello, Alfredo
2016-08-01
We determine and compare structural, dynamical, and electronic properties of liquid water at near ambient conditions through density-functional molecular dynamics simulations, when using either plane-wave or atomic-orbital basis sets. In both frameworks, the electronic structure and the atomic forces are self-consistently determined within the same theoretical scheme based on a nonlocal density functional accounting for van der Waals interactions. The overall properties of liquid water achieved within the two frameworks are in excellent agreement with each other. Thus, our study supports that implementations with plane-wave or atomic-orbital basis sets yield equivalent results and can be used indiscriminately in study of liquid water or aqueous solutions. PMID:27434607
NASA Astrophysics Data System (ADS)
Chen, Mohan; Xia, Junchao; Huang, Chen; Dieterich, Johannes M.; Hung, Linda; Shin, Ilgyou; Carter, Emily A.
2015-05-01
Orbital-free density functional theory (OFDFT) is a linear-scaling first-principles quantum mechanics method used to calculate the ground-state energy of a given system. Here we present a new version of PRinceton Orbital-Free Electronic Structure Software (PROFESS) with new features. First, PROFESS 3.0 provides a set of new kinetic energy density functionals (KEDFs) which are designed to model semiconductors or transition metals. Specifically, PROFESS 3.0 includes the Huang-Carter (HC) KEDF [1], a density decomposition method with fixed localized electronic density [2], the Wang-Govind-Carter (WGC) decomposition KEDF [3], and the Enhanced von Weizsäcker (EvW)-WGC KEDF [4]. Other major new functions are included, such as molecular dynamics with different statistical mechanical ensembles and spin-polarized density optimizers.
ERIC Educational Resources Information Center
Kimmins, Dovie L.; Winters, J. Jeremy
2015-01-01
Two perspectives of the term "Venn diagram" reflect the typical differences in the uses of Venn diagrams in the subject areas of mathematics and language arts. These differences are subtle; nevertheless, they can potentially be confusing. In language arts, the circles in a Venn diagram typically represent things that can be compared and…
ERIC Educational Resources Information Center
Gillespie, Ronald J.; And Others
1996-01-01
Presents an alternative approach to bonding and geometry--the electron domain model--which avoids some of the problems with the conventional approach. Discusses difficulties with the orbital model at the introductory level, electron spin and the Pauli exclusion principle, electron pair domains, nonequivalent domains, multiple bonds, and origins…
Molecular orbital (SCF-Xα-SW) theory of metal-metal charge transfer processes in minerals
Sherman, David M.
1987-01-01
Electronic transitions between the Fe-Fe bonding and Fe-Fe antibonding orbitals results in the optically-induced intervalence charge transfer bands observed in the electronic spectra of mixed valence minerals. Such transitions are predicted to be polarized along the metal-metal bond direction, in agreement with experimental observations.
Balachandran, V; Karunakaran, V
2014-06-01
The FT-IR (4000-400cm(-)(1)) and FT-Raman spectra (3500-100cm(-)(1)) of 2,3,4,5,6-pentafluorophenylacetic acid (PAA) have been recorded. Density functional theory calculation with LSDA/6-31+G(d,p) and B3LYP/6-31+G(d,p) basis sets have been used to determine ground state molecular geometries (bond lengths and bond angles), harmonic vibrational frequencies, infrared intensities, Raman intensities and bonding features of the title compound. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field (SQMFF) methodology. The first order hyperpolarizability (β0) and related properties (β, α0 and Δα) of PAA are calculated using B3LYP/6-31+G(d,p) method on the finite-field approach. The calculated first hyperpolarizability shows that the molecule is an attractive molecule for future applications in non-linear optics. The stability of molecule has been analyzed by using NBO analysis. The calculated HOMO and LUMO energies show that charge transfer occurs within this molecule. Mulliken population analysis on atomic charges is also calculated. Thermodynamic properties (heat capacity, enthalpy, Gibb's free energy and entropy) of the title compound at different temperatures were calculated.
Phase Equilibria Diagrams Database
National Institute of Standards and Technology Data Gateway
SRD 31 NIST/ACerS Phase Equilibria Diagrams Database (PC database for purchase) The Phase Equilibria Diagrams Database contains commentaries and more than 21,000 diagrams for non-organic systems, including those published in all 21 hard-copy volumes produced as part of the ACerS-NIST Phase Equilibria Diagrams Program (formerly titled Phase Diagrams for Ceramists): Volumes I through XIV (blue books); Annuals 91, 92, 93; High Tc Superconductors I & II; Zirconium & Zirconia Systems; and Electronic Ceramics I. Materials covered include oxides as well as non-oxide systems such as chalcogenides and pnictides, phosphates, salt systems, and mixed systems of these classes.
Hohenstein, Edward G; Bouduban, Marine E F; Song, Chenchen; Luehr, Nathan; Ufimtsev, Ivan S; Martínez, Todd J
2015-07-01
The floating occupation molecular orbital-complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the state-averaged complete active space self-consistent field (SA-CASSCF) method. We have formulated the analytic first derivative of FOMO-CASCI in a manner that is well-suited for a highly efficient implementation using graphical processing units (GPUs). Using this implementation, we demonstrate that FOMO-CASCI gradients are of similar computational expense to configuration interaction singles (CIS) or time-dependent density functional theory (TDDFT). In contrast to CIS and TDDFT, FOMO-CASCI can describe multireference character of the electronic wavefunction. We show that FOMO-CASCI compares very favorably to SA-CASSCF in its ability to describe molecular geometries and potential energy surfaces around minimum energy conical intersections. Finally, we apply FOMO-CASCI to the excited state hydrogen transfer reaction in methyl salicylate. PMID:26156469
Hirano, Toshiyuki; Sato, Fumitoshi
2014-07-28
We used grid-free modified Cholesky decomposition (CD) to develop a density-functional-theory (DFT)-based method for calculating the canonical molecular orbitals (CMOs) of large molecules. Our method can be used to calculate standard CMOs, analytically compute exchange-correlation terms, and maximise the capacity of next-generation supercomputers. Cholesky vectors were first analytically downscaled using low-rank pivoted CD and CD with adaptive metric (CDAM). The obtained Cholesky vectors were distributed and stored on each computer node in a parallel computer, and the Coulomb, Fock exchange, and pure exchange-correlation terms were calculated by multiplying the Cholesky vectors without evaluating molecular integrals in self-consistent field iterations. Our method enables DFT and massively distributed memory parallel computers to be used in order to very efficiently calculate the CMOs of large molecules. PMID:24622472
Danel, J-F.; Kazandjian, L.; Zerah, G.
2009-06-15
A form of the linear mixing rule involving the equality of excess pressures is tested with various mole fractions and various types of orbital-free molecular dynamics simulations. For all the cases considered, this mixing rule yields, within statistical error, the pressure of a mixture of helium and iron obtained by a direct simulation. In an attempt to interpret the robustness of the mixing rule, we show that it can be derived from thermodynamic stability if the system is regarded as a mixture of independent effective average atoms. The success of the mixing rule applied with equations of state including various degrees of approximation leads us to suggest its use in the thermodynamic domain where quantum molecular dynamics can be implemented.
Hohenstein, Edward G; Bouduban, Marine E F; Song, Chenchen; Luehr, Nathan; Ufimtsev, Ivan S; Martínez, Todd J
2015-07-01
The floating occupation molecular orbital-complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the state-averaged complete active space self-consistent field (SA-CASSCF) method. We have formulated the analytic first derivative of FOMO-CASCI in a manner that is well-suited for a highly efficient implementation using graphical processing units (GPUs). Using this implementation, we demonstrate that FOMO-CASCI gradients are of similar computational expense to configuration interaction singles (CIS) or time-dependent density functional theory (TDDFT). In contrast to CIS and TDDFT, FOMO-CASCI can describe multireference character of the electronic wavefunction. We show that FOMO-CASCI compares very favorably to SA-CASSCF in its ability to describe molecular geometries and potential energy surfaces around minimum energy conical intersections. Finally, we apply FOMO-CASCI to the excited state hydrogen transfer reaction in methyl salicylate.
Koseki, Jun; Gouda, Hiroaki; Hirono, Shuichi
2016-01-01
The natural product argadin is a cyclopentapeptide chitinase inhibitor that binds to chitinase B (ChiB) from the pathogenic bacteria Serratia marcescens. N(ω)-Acetyl-L-arginine and L-aminoadipic acid of argadin form intramolecular ionic hydrogen bonds in the aromatic hydrophobic pocket of ChiB. We performed ab initio molecular orbital and density functional theory calculations to elucidate the role of this intramolecular hydrogen bonding on intermolecular interactions between argadin and ChiB. We found that argadin accrues large stabilization energies from the van der Waals dispersion interactions, such as CH-π, π-π, and π-lone pair interactions, in the aromatic hydrophobic pocket of ChiB, although intramolecular hydrogen bonding within argadin might result in loss of entropy. The intramolecular ionic hydrogen bonding formation canceled local molecular charges and provided good van der Waals interactions with surrounding aromatic residues.
Hirano, Toshiyuki; Sato, Fumitoshi
2014-07-28
We used grid-free modified Cholesky decomposition (CD) to develop a density-functional-theory (DFT)-based method for calculating the canonical molecular orbitals (CMOs) of large molecules. Our method can be used to calculate standard CMOs, analytically compute exchange-correlation terms, and maximise the capacity of next-generation supercomputers. Cholesky vectors were first analytically downscaled using low-rank pivoted CD and CD with adaptive metric (CDAM). The obtained Cholesky vectors were distributed and stored on each computer node in a parallel computer, and the Coulomb, Fock exchange, and pure exchange-correlation terms were calculated by multiplying the Cholesky vectors without evaluating molecular integrals in self-consistent field iterations. Our method enables DFT and massively distributed memory parallel computers to be used in order to very efficiently calculate the CMOs of large molecules.
Usui, Kosuke; Ando, Mikinori; Yokogawa, Daisuke; Irle, Stephan
2015-12-24
The precise control of on-off switching is essential to the design of ideal molecular sensors. To understand the switching mechanism theoretically, we selected as representative example a 9-anthryltriphenylstibonium cation, which was reported as a fluoride ion sensor. In this molecule, the first excited singlet state exhibits two minimum geometries, where one of them is emissive and the other one dark. The excited state at the geometry with bright emission is of π-π* character, whereas it is of π-σ* character at the "dark" geometry. Geometry changes in the excited state were identified by geometry optimization and partial potential energy surface (PES) mapping. We also studied Group V homologues of this molecule. A barrierless relaxation pathway after vertical excitation to the "dark" geometry was found for the Sb-containing compound on the excited-states PES, whereas barriers appear in the case of P and As. Molecular orbital analysis suggests that the σ* orbital of the antimony compound is stabilized along such relaxation and that the excited state changes its nature correspondingly. Our results indicate that the size of the central atom is crucial for the design of fluoride sensors with this ligand framework.
NASA Astrophysics Data System (ADS)
Xavier, S.; Periandy, S.; Carthigayan, K.; Sebastian, S.
2016-12-01
Vibrational spectral analysis of Diphenyl Carbonate (DPC) is carried out by using FT-IR and FT-Raman spectroscopic techniques. It is found that all vibrational modes are in the expected region. Gaussian computational calculations were performed using B3LYP method with 6-311++G (d, p) basis set. The computed geometric parameters are in good agreement with XRD data. The observation shows that the structure of the carbonate group is unsymmetrical by ∼5° due to the attachment of the two phenyl rings. The stability of the molecule arising from hyperconjugative interaction and charge delocalization are analyzed by Natural Bond Orbital (NBO) study and the results show the lone pair transition has higher stabilization energy compared to all other. The 1H and 13C NMR chemical shifts are calculated using the Gauge-Including Atomic Orbital (GIAO) method with B3LYP/6-311++G (d, p) method. The chemical shifts computed theoretically go very closer to the experimental results. A study on the electronic and optical properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies and Molecular electrostatic potential (MEP) exhibit the high reactivity nature of the molecule. The non-linear optical property of the DPC molecule predicted theoretically found to be good candidate for NLO material. TG/DTA analysis was made and decomposition of the molecule with respect to the temperature was studied. DPC having the anthelmintic activity is docked in the Hemoglobin of Fasciola hepatica protein. The DPC has been screened to antimicrobial activity and found to exhibit antibacterial effects.
Mean-Field Theory of Intra-Molecular Charge Ordering in (TTM--TTP)I3
NASA Astrophysics Data System (ADS)
Omori, Yukiko; Tsuchiizu, Masahisa; Suzumura, Yoshikazu
2011-02-01
We examine an intra-molecular charge-ordered (ICO) state in the multi-orbital molecular compound (TTM--TTP)I3 on the basis of an effective two-orbital model derived from ab initio calculations. Representing the model in terms of the fragment molecular-orbital (MO) picture, the ICO state is described as the charge disproportionation on the left and right fragment MOs. By applying the mean-field theory, the phase diagram of the ground state is obtained as a function of the inter-molecular Coulomb repulsion and the intra-molecular transfer integral. The ICO state is stabilized by large inter-fragment Coulomb interactions, and the small intra-molecular transfer energy between two fragment MOs. Furthermore, we examine the finite-temperature phase diagram. The relevance to the experimental observations in the molecular compound of (TTM--TTP)I3 is also discussed.
Gravity wave transmission diagram
NASA Astrophysics Data System (ADS)
Tomikawa, Yoshihiro
2016-07-01
A possibility of gravity wave propagation from a source region to the airglow layer around the mesopause has been discussed based on the gravity wave blocking diagram taking into account the critical level filtering alone. This paper proposes a new gravity wave transmission diagram in which both the critical level filtering and turning level reflection of gravity waves are considered. It shows a significantly different distribution of gravity wave transmissivity from the blocking diagram.
NASA Astrophysics Data System (ADS)
Sternberg, U.; Rosenberger, H.
1981-02-01
We give a short review of the gauge-invariant calculation of shielding constants and susceptibilities from the ground state wvefunction. Since the method is well suited for localizad orbitals, PC ILO bond orbitals are used for the shielding calculation of glycine and its hydrogen bonded dimer (and for testing the theory also CH 4 and C 2H 6). From these values the 1H shielding tensors are constructed in an incrementary way. The calculated data are compared with experimental results and the NH…O hydrogen bond is investigated in detail. The theory gives an anisotropy of a NH…O hydrogen bonded proton of Δσ = 28.3 ppm and a value of a NH proton without hydrogen bond of Δσ = 18.8 ppm and for the CH proton Δσ = 12.5 ppm results. When taking into account the rotation of the NH θ3 groups we find that the qualitative features of the experiment are correctly represented. For the anisotropy Δσ = -6.55 ppm and for the asymmetry η = 0.588 are obtained. The experimental values are -5.63 ppm and 0.805, respectively.
Solitary fibrous tumor of the orbit: morphological, cytogenetic and molecular features.
Cerdá-Nicolás, Miguel; Löpez-Gines, Concha; Gil-Benso, Rosario; Benito, Rafael; Pellin, Antonio; Ruiz-Saurí, Amparo; Sanchos-Garcia, Juan; Roldan, Pedro; Talamantes, Fernando; Barberá, José
2006-12-01
Solitary fibrous tumor (SFT), a benign neoplasm arising in mesenchymal structures, was initially described in the pleura but subsequently has also been documented in other locations. It is uncommon in the orbit, where it closely resembles other benign spindle-shaped mesenchymal tumors of this area such as schwannoma, meningioma or hemangiopericytoma. We present a case of orbital SFT in a 34-year-old woman. The radiological study showed the presence of an enhanced uptake lesion measuring 2 cm in major diameter. The histopathological evaluation revealed alternating cellular and hypocellular areas with spindle-shaped cells. The cellular organization displayed a broad variety of irregular morphological patterns. The neoplastic cells were intensely positive for CD34 and vimentin, while S100, epithelial membrane antigen (EMA), Caldesmon, Calretinin and WT-1 proved negative. The pericellular matrix exhibited strong positivity for CD44 and collagen IV. Scarce mitotic figures, a Ki-67 nuclear labeling index of <5%, and focal expression of p53 were also observed. Measurement of DNA content revealed a DNA index of 1, indicating a diploid peak in 95% of the tumor cells. A normal 46,XX karyotype was present. No TP53 (exons 5-8) mutations or MDM2 and CDK4 amplifications were observed. No p14(ARF), p15(INK4B) and p16(INK4A) deletions or hypermethylation were observed in this benign tumor. Following surgical resection and radiotherapy, the patient showed no tumor relapse after one year of follow-up.
NASA Astrophysics Data System (ADS)
Sk, Mahasin Alam; Chen, Yingqian; Manzhos, Sergei
2016-08-01
We report a qualitative difference in molecular band structures and frontier orbital nodal structures in DFT calculations using GGA vs. hybrid functionals and Hartree Fock in molecules used in electrochemical power sources. This can have a significant effect in applications sensitive to redox potentials and to orbital overlaps (excitations, electron transfer rates) but for which the use of hybrid functionals is impractical, such as solids or interfaces used in electrochemical energy conversion and storage technologies. We show that correct band structures and nodal structures (ordering) of frontier orbitals can be obtained by applying a Hubbard correction to selected atomic states.
Stasyuk, O A; Szatylowicz, H; Krygowski, T M; Fonseca Guerra, C
2016-04-28
The substituent effect of the amino and nitro groups on the electronic system of benzene has been investigated quantum chemically using quantitative Kohn-Sham molecular orbital theory and a corresponding energy decomposition analysis (EDA). The directionality of electrophilic substitution in aniline can accurately be explained with the amount of contribution of the 2pz orbitals on the unsubstituted carbon atoms to the highest occupied π orbital. For nitrobenzene, the molecular π orbitals cannot explain the regioselectivity of electrophilic substitution as there are two almost degenerate π orbitals with nearly the same 2pz contributions on the unsubstituted carbon atoms. The Voronoi deformation density analysis has been applied to aniline and nitrobenzene to obtain an insight into the charge rearrangements due to the substituent. This analysis method identified the orbitals involved in the C-N bond formation of the π system as the cause for the π charge accumulation at the ortho and para positions in the case of the NH2 group and the largest charge depletion at these same positions for the NO2 substituent. Furthermore, we showed that it is the repulsive interaction between the πHOMO of the phenyl radical and the πHOMO of the NH2 radical that is responsible for pushing up the πHOMO of aniline and therefore activating this π orbital of the phenyl ring towards electrophilic substitution.
Ohyama, Tatsuya; Hayakawa, Masato; Nishikawa, Shin; Kurita, Noriyuki
2011-06-01
Transcription mechanisms of gene information from DNA to mRNA are essentially controlled by regulatory proteins such as a lactose repressor (LacR) protein and ligand molecules. Biochemical experiments elucidated that a ligand binding to LacR drastically changes the mechanism controlled by LacR, although the effect of ligand binding has not been clarified at atomic and electronic levels. We here investigated the effect of ligand binding on the specific interactions between LacR and operator DNA by the molecular simulations combined with classical molecular mechanics and ab initio fragment molecular orbital methods. The results indicate that the binding of anti-inducer ligand strengthens the interaction between LacR and DNA, which is consistent with the fact that the binding of anti-inducer enhances the repression of gene transcription by LacR. It was also elucidated that hydrating water molecules existing between LacR and DNA contribute to the specific interactions between LacR and DNA. PMID:21328406
Localized and Spectroscopic Orbitals: Squirrel Ears on Water.
ERIC Educational Resources Information Center
Martin, R. Bruce
1988-01-01
Reexamines the electronic structure of water considering divergent views. Discusses several aspects of molecular orbital theory using spectroscopic molecular orbitals and localized molecular orbitals. Gives examples for determining lowest energy spectroscopic orbitals. (ML)
DFT calculations of molecular excited states using an orbital-dependent nonadiabatic exchange kernel
Ipatov, A. N.
2010-02-15
A density functional method for computing molecular excitation spectra is presented that uses a frequency-dependent kernel and takes into account the nonlocality of exchange interaction. Owing to its high numerical stability and the use of a nonadiabatic (frequency-dependent) exchange kernel, the proposed approach provides a qualitatively correct description of the asymptotic behavior of charge-transfer excitation energies.
Nishimoto, Yoshio; Fedorov, Dmitri G
2016-08-10
The energy and its analytic gradient are formulated for the fragment molecular orbital (FMO) method combined with density-functional tight-binding (DFTB) and the polarizable continuum model (PCM). The accuracy is demonstrated in comparison with unfragmented calculations and numerical gradients. The instability in the description of proteins using density functional theory (DFT) and DFTB is analyzed for both unfragmented and FMO methods. The cause of the instability is shown to be charged residues, and the problem is particularly severe in the gas phase when long-range functionals are not used. Adding solvent effects considerably increases the gap between occupied and virtual orbitals and stabilizes convergence. The pair interaction energies calculated using FMO-DFT and FMO-DFTB in solution are shown to correlate, whereas the latter method is 4840 times faster than the former for a protein consisting of 1961 atoms. The structures of five proteins (containing up to 3578 atoms) optimized using FMO-DFTB/PCM agree reasonably well with experiment.
Nishimoto, Yoshio; Fedorov, Dmitri G
2016-08-10
The energy and its analytic gradient are formulated for the fragment molecular orbital (FMO) method combined with density-functional tight-binding (DFTB) and the polarizable continuum model (PCM). The accuracy is demonstrated in comparison with unfragmented calculations and numerical gradients. The instability in the description of proteins using density functional theory (DFT) and DFTB is analyzed for both unfragmented and FMO methods. The cause of the instability is shown to be charged residues, and the problem is particularly severe in the gas phase when long-range functionals are not used. Adding solvent effects considerably increases the gap between occupied and virtual orbitals and stabilizes convergence. The pair interaction energies calculated using FMO-DFT and FMO-DFTB in solution are shown to correlate, whereas the latter method is 4840 times faster than the former for a protein consisting of 1961 atoms. The structures of five proteins (containing up to 3578 atoms) optimized using FMO-DFTB/PCM agree reasonably well with experiment. PMID:27215663
NASA Technical Reports Server (NTRS)
Defrees, D. J.; Mclean, A. D.
1986-01-01
The discovery of cyclopropenylidene in space suggests that other C3H2 isomers may be present, and a tentative detection of one such isomer, propargylene (HCCCH), has been reported. Ab initio molecular orbital theory has been used to characterize five low-lying, metastable isomers of cyclopropenylidene. Extended calculations including the electron correlation energy, show that the lowest in energy is singlet propadienylidene, followed by propargylene; the singlet and triplet of the latter are too close in energy to allow an assignment of the ground state; triplet propadienylidene is at a significantly higher energy. Rotational frequencies computed to an expected accuracy of + or - 1 -2 percent do not confirm the tentative detection of propargylene in space, although the discrepancy between theory and the observation is not so great as to unequivocally rule out this possibility.
Udagawa, Taro; Suzuki, Kimichi; Tachikawa, Masanori
2015-10-26
To analyze the H/D isotope effects on hydrogen transfer reactions in XHCHCHCHY↔XCHCHCHYH (X, Y=O, NH, or CH2 ) including the nuclear quantum effect of proton and deuteron, we propose a multicomponent molecular orbital-climbing image-nudged elastic band (MC_MO-CI-NEB) method. We obtain not only transition state structures but also minimum-energy paths (MEPs) on the MC_MO effective potential energy surface by using MC_MO-CI-NEB method. We find that nuclear quantum effect affects not only stationary-point geometries but also MEPs and electronic structures in the reactions. We clearly demonstrate the importance of including nuclear quantum effects for H/D isotope effect on rate constants (kH /kD ).
NASA Astrophysics Data System (ADS)
Tagami, Ayumu; Ishibashi, Nobuhiro; Kato, Dai-ichiro; Taguchi, Naoki; Mochizuki, Yuji; Watanabe, Hirofumi; Ito, Mika; Tanaka, Shigenori
2009-04-01
Bioluminescence spectra of firefly Luciola cruciata were theoretically analyzed on the basis of the fragment molecular orbital (FMO) method. The CIS(D) and PR-CIS(Ds) methods were employed for the calculations of emission energies of wild-type and mutant luciferase-oxyluciferin systems, and various multi-layer FMO calculations were performed changing the sizes of the luciferase protein and of the chromophore to which the excited-state calculations were applied. We have thus reproduced the experimental emission energies of wild-type and mutant luciferase systems with good accuracy, which provides useful information concerning the roles of protein environment for the color tuning of the bioluminescence spectra of firefly.
Yang, Hongping; Yam, Chi-Yung; Zhang, Aihua; Xu, Zhiping; Luo, Jun; Zhu, Jing
2015-03-21
The highest occupied molecular orbital (HOMO) energies of carbon nanotubes (CNTs) and graphene are crucial in fundamental and applied research of carbon nanomaterials, and so their modulation is desired. Our first-principles calculations reveal that the HOMO energies of CNTs and graphene can both be raised by negatively charging, and that the rate of increase of the HOMO energy of a CNT is much greater and faster than that of graphene with the same number of C atoms. This discriminative modulation holds true regardless of the number of C atoms and the CNT type, and so is universal. This work provides a new opportunity to develop all-carbon devices with CNTs and graphene as different functional elements. PMID:25692228
NASA Astrophysics Data System (ADS)
Ilieva, S.; Hadjieva, B.; Galabov, B.
1999-09-01
Ab initio molecular orbital calculations at HF/4-31G level and infrared spectroscopic data for the frequencies are applied to analyse the grouping in a series model aromatic secondary amides: formanilide; acetanilide; o-methylacetanilide; 2,6-dimethylformanilide, 2,6-dimethylacetanilide; N-benzylacetamide and N-benzylformamide. The theoretical and experimental data obtained show that the conformational state of the molecules studied is determined by the fine balance of several intramolecular factors: resonance effect between the amide group and the aromatic ring, steric interaction between various substituents around the -NH-CO- grouping in the aromatic ring, conjugation between the carbonyl bond and the nitrogen lone pair as well as direct field influences inside the amide group.
NASA Astrophysics Data System (ADS)
Kalfaoğlu, Emel; Karabulut, Bünyamin
2011-03-01
In this study, the molecular orbital coefficients and the spin Hamiltonian parameters of bis(histamine-saccharinate) copper(II) complex, [Cu(hsm) 2(sac) 2], are calculated theoretically. Two d- d transition spectra and four EPR parameters g∥,g⊥,A∥,A⊥ for the Cu(II) complex are calculated by using crystal-field theory. The calculated values are in good agreement with the experimental values. The g and A parameters have indicated that the paramagnetic centre is axially symmetric. Having the relations of g∥>g⊥>ge and A∥>A⊥ for Cu 2+ ions, it can be concluded that Cu 2+ ions are located in distorted octahedral sites (D 4h) elongated along the z-axis and that the ground state of the paramagnetic electron is d ( 2B1g state).
NASA Astrophysics Data System (ADS)
Chiosi, C.; Murdin, P.
2000-11-01
The Hertzsprung-Russell diagram (HR-diagram), pioneered independently by EJNAR HERTZSPRUNG and HENRY NORRIS RUSSELL, is a plot of the star luminosity versus the surface temperature. It stems from the basic relation for an object emitting thermal radiation as a black body: ...
Thirman, Jonathan Head-Gordon, Martin
2015-08-28
An energy decomposition analysis (EDA) of intermolecular interactions is proposed for second-order Møller–Plesset perturbation theory (MP2) based on absolutely localized molecular orbitals (ALMOs), as an extension to a previous ALMO-based EDA for self-consistent field methods. It decomposes the canonical MP2 binding energy by dividing the double excitations that contribute to the MP2 wave function into classes based on how the excitations involve different molecules. The MP2 contribution to the binding energy is decomposed into four components: frozen interaction, polarization, charge transfer, and dispersion. Charge transfer is defined by excitations that change the number of electrons on a molecule, dispersion by intermolecular excitations that do not transfer charge, and polarization and frozen interactions by intra-molecular excitations. The final two are separated by evaluations of the frozen, isolated wave functions in the presence of the other molecules, with adjustments for orbital response. Unlike previous EDAs for electron correlation methods, this one includes components for the electrostatics, which is vital as adjustment to the electrostatic behavior of the system is in some cases the dominant effect of the treatment of electron correlation. The proposed EDA is then applied to a variety of different systems to demonstrate that all proposed components behave correctly. This includes systems with one molecule and an external electric perturbation to test the separation between polarization and frozen interactions and various bimolecular systems in the equilibrium range and beyond to test the rest of the EDA. We find that it performs well on these tests. We then apply the EDA to a halogen bonded system to investigate the nature of the halogen bond.
Thirman, Jonathan; Head-Gordon, Martin
2015-08-28
An energy decomposition analysis (EDA) of intermolecular interactions is proposed for second-order Møller-Plesset perturbation theory (MP2) based on absolutely localized molecular orbitals (ALMOs), as an extension to a previous ALMO-based EDA for self-consistent field methods. It decomposes the canonical MP2 binding energy by dividing the double excitations that contribute to the MP2 wave function into classes based on how the excitations involve different molecules. The MP2 contribution to the binding energy is decomposed into four components: frozen interaction, polarization, charge transfer, and dispersion. Charge transfer is defined by excitations that change the number of electrons on a molecule, dispersion by intermolecular excitations that do not transfer charge, and polarization and frozen interactions by intra-molecular excitations. The final two are separated by evaluations of the frozen, isolated wave functions in the presence of the other molecules, with adjustments for orbital response. Unlike previous EDAs for electron correlation methods, this one includes components for the electrostatics, which is vital as adjustment to the electrostatic behavior of the system is in some cases the dominant effect of the treatment of electron correlation. The proposed EDA is then applied to a variety of different systems to demonstrate that all proposed components behave correctly. This includes systems with one molecule and an external electric perturbation to test the separation between polarization and frozen interactions and various bimolecular systems in the equilibrium range and beyond to test the rest of the EDA. We find that it performs well on these tests. We then apply the EDA to a halogen bonded system to investigate the nature of the halogen bond. PMID:26328835
Yoshida, Norio
2014-06-07
The three-dimensional reference interaction site model (3D-RISM) method was efficiently implemented in the fragment molecular orbital (FMO) method. The method is referred to as the FMO/3D-RISM method, and allows us to treat electronic structure of the whole of a macromolecule, such as a protein, as well as the solvent distribution around a solute macromolecule. The formalism of the FMO/3D-RISM method, for the computationally available form and variational expressions, are proposed in detail. A major concern leading to the implementation of the method was decreasing the computational costs involved in calculating the electrostatic potential, because the electrostatic potential is calculated on numerous grid points in three-dimensional real space in the 3D-RISM method. In this article, we propose a procedure for decreasing the computational costs involved in calculating the electrostatic potential in the FMO method framework. The strategy involved in this procedure is to evaluate the electrostatic potential and the solvated Fock matrix in different manners, depending on the distance between the solute and the solvent. The electrostatic potential is evaluated directly in the vicinity of the solute molecule by integrating the molecular orbitals of monomer fragments of the solute molecule, whereas the electrostatic potential is described as the sum of multipole interactions when an analog of the fast multipole method is used. The efficiency of our method was demonstrated by applying it to a water trimer system and three biomolecular systems. The FMO/3D-RISM calculation can be performed within a reasonable computational time, retaining the accuracy of some physical properties.
NASA Astrophysics Data System (ADS)
Pati, Ranjit; Karna, Shashi P.
2002-01-01
The dependence of electron transfer (ET) coupling element, VAB, on the length of rigid-rod-like systems consisting of bicyclo[1.1.1]pentane (BCP), cubane (CUB), and bicyclo[2.2.2]octane (BCO) monomers, has been investigated with the use of ab initio Hartree-Fock (HF) method employing Marcus-Hush two-state (TS) model. The value of VAB decreases exponentially with increase in the number of the cage units of the σ-bonded molecules. The calculated decay constant, β, shows good agreement with previously reported data. For molecular length⩾15 Å, the value of VAB becomes negligibly small, suggesting complete suppression of the through bond direct tunneling contribution to ET process.
Rodrigues, Alessandro; Olivato, Paulo R; Zukerman-Schpector, Julio; Maganhi, Stella H; Reis, Adriana K C A; Tiekink, Edward R T
2015-08-13
The X-ray single crystal analysis of isomeric ortho, meta, and para bromo-substituted α-methylsulfonyl-α-diethoxyphosphoryl acetophenones showed that this class of compound adopts synclinal (gauche) conformations for both [-P(O)(OEt)2] and [-S(O)2Me] groups, with respect to the carbonyl functional group. The phosphonate, sulfonyl, and carbonyl functional groups are joined through an intramolecular network of attractive interactions, as detected by molecular orbital calculations at the M06-2X/6-31G(d,p) level. These interactions are responsible for the more stable conformations in the gas phase, which also persist in the solid-state structures. The main structural distinction in the title compounds relates to the torsion angle of the aryl group (with respect to the carbonyl group), which gives rise to different interactions in the crystal packing, due to the different positions of the Br atom.
NASA Astrophysics Data System (ADS)
Kim, Minjae; Choi, Hong Chul; Shim, Ji Hoon; Min, B. I.
2014-03-01
We have studied correlated electronic structures and the phase diagram of electron-doped hydrocarbon molecular solids, based on the dynamical mean-field theory. We have determined the phase diagram of hydrocarbon molecular solids as functions of doping and energy parameters including the Coulomb correlation, the Hund coupling, and the molecular-orbital (MO) energy level splitting. We have found that the hydrocarbon superconductors (electron-doped picene and coronene) belong to the multi-band Fermi liquid state, while non-superconducting electron-doped pentacene belongs to the single-band state in the proximity of the metal-insulator transition. The size of the MO energy level splitting plays an important role in deriving the superconductivity of electron-doped hydrocarbon solids. The multi-band nature of hydrocarbon solids from the small MO energy level splitting boosts the superconductivity through the enhanced density of states at the Fermi level.
Conradie, Jeanet; Ghosh, Abhik
2014-05-19
The great majority of {NiNO}(10) complexes are characterized by short Ni-N(O) distances of 1.60-1.65 Å and linear NO units. Against this backdrop, the {CuNO}(10) unit in the recently reported [Cu(CH3NO2)5(NO)](2+) cation (1) has a CuNO angle of about 120° and a very long 1.96 Å Cu-N(O) bond. According to DFT calculations, metal-NO bonding in 1 consists of a single Cu(dz(2))-NO(π*) σ-interaction and essentially no metal(dπ)-NO(π*) π-bonding, which explains both the bent CuNO geometry and the long, weak Cu-N(O) bond. This σ-interaction is strongly favored by a ligand trans to the NO; indeed such a trans ligand may be critical for the existence and stability of a {CuNO}(10) unit. By contrast, {NiNO}(10) complexes exhibit a strong avoidance of such trans ligands. Thus, a five-coordinate {NiNO}(10) complex appears to favor a trigonal-bipyramidal structure with the NO in an equatorial position, as in the case of [Ni(bipy)2(NO)](+) (6). An unusual set of Ni(d)-NO(π*) orbital interactions accounts for the strongly bent NiNO geometry for this complex. PMID:24796643
NASA Astrophysics Data System (ADS)
Zarycz, M. Natalia C.; Sauer, Stephan P. A.; Provasi, Patricio F.
2014-10-01
We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the 1J(C-H) coupling constant of CH4 using a decomposition into contributions from localized molecular orbitals and compare with the 1J(N-H) coupling constant in NH3. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes—SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane.
Zarycz, M. Natalia C. Provasi, Patricio F.; Sauer, Stephan P. A.
2014-10-21
We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the {sup 1}J(C–H) coupling constant of CH{sub 4} using a decomposition into contributions from localized molecular orbitals and compare with the {sup 1}J(N–H) coupling constant in NH{sub 3}. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes—SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane.
Horn, Paul R; Mao, Yuezhi; Head-Gordon, Martin
2016-08-17
An energy decomposition analysis (EDA) separates a calculated interaction energy into as many interpretable contributions as possible; for instance, permanent and induced electrostatics, Pauli repulsions, dispersion and charge transfer. The challenge is to construct satisfactory definitions of all terms in the chemically relevant regime where fragment densities overlap, rendering unique definitions impossible. Towards this goal, we present an improved EDA for Kohn-Sham density functional theory (DFT) with properties that have previously not been simultaneously attained. Building on the absolutely localized molecular orbital (ALMO)-EDA, this second generation ALMO-EDA is variational and employs valid antisymmetric electronic wavefunctions to produce all five contributions listed above. These contributions moreover all have non-trivial complete basis set limits. We apply the EDA to the water dimer, the T-shaped and parallel-displaced benzene dimer, the p-biphthalate dimer "anti-electrostatic" hydrogen bonding complex, the biologically relevant binding of adenine and thymine in stacked and hydrogen-bonded configurations, the triply hydrogen-bonded guanine-cytosine complex, the interaction of Cl(-) with s-triazine and with the 1,3-dimethyl imidazolium cation, which is relevant to the study of ionic liquids, and the water-formaldehyde-vinyl alcohol ter-molecular radical cationic complex formed in the dissociative photoionization of glycerol. PMID:27492057
Heifetz, Alexander; Trani, Giancarlo; Aldeghi, Matteo; MacKinnon, Colin H; McEwan, Paul A; Brookfield, Frederick A; Chudyk, Ewa I; Bodkin, Mike; Pei, Zhonghua; Burch, Jason D; Ortwine, Daniel F
2016-05-12
Inhibition of inducible T-cell kinase (ITK), a nonreceptor tyrosine kinase, may represent a novel treatment for allergic asthma. In our previous reports, we described the discovery of sulfonylpyridine (SAP), benzothiazole (BZT), indazole (IND), and tetrahydroindazole (THI) series as novel ITK inhibitors and how computational tools such as dihedral scans and docking were used to support this process. X-ray crystallography and modeling were applied to provide essential insight into ITK-ligand interactions. However, "visual inspection" traditionally used for the rationalization of protein-ligand affinity cannot always explain the full complexity of the molecular interactions. The fragment molecular orbital (FMO) quantum-mechanical (QM) method provides a complete list of the interactions formed between the ligand and protein that are often omitted from traditional structure-based descriptions. FMO methodology was successfully used as part of a rational structure-based drug design effort to improve the ITK potency of high-throughput screening hits, ultimately delivering ligands with potency in the subnanomolar range.
Pals, Justin A.; Wagner, Elizabeth D.; Plewa, Michael J.
2016-01-01
Disinfection of drinking water protects public health against waterborne pathogens. However, during disinfection, toxic disinfection byproducts (DBPs) are formed. Exposure to DBPs was associated with increased risk of bladder cancer in humans. DBPs are generated at concentrations below their carcinogenic potencies; it is unclear how exposure leads to adverse health outcomes. We used computational estimates of the energy of the lowest unoccupied molecular orbital (ELUMO) to predict thiol reactivity and additive toxicity among soft electrophile DBPs. Bromoacetic acid (BAA) was identified as non-thiol-reactive, which was supported by in chemico and in vitro data. Bromoacetonitrile (BAN) and bromoacetamide (BAM) were thiol-reactive. Genotoxicity induced by these compounds was reduced by increasing the thiol pool with N-acetyl l-cysteine (NAC), while NAC had little effect on BAA. BAN and BAM shared depletion of glutathione (GSH) or cellular thiols as a molecular initiating event (MIE), whereas BAA induces toxicity through another pathway. Binary mixtures of BAM and BAN expressed a potentiating effect in genotoxicity. We found that soft electrophile DBPs could be an important predictor of common mechanism groups that demonstrated additive toxicity. In silico estimates of ELUMO could be used to identify the most relevant DBPs that are the forcing factors of the toxicity of finished drinking waters. PMID:26854864
The continuous and discrete molecular orbital x-ray bands from Xeq+ (12≤q≤29) +Zn collisions
Guo, Yipan; Yang, Zhihu; Hu, Bitao; Wang, Xiangli; Song, Zhangyong; Xu, Qiumei; Zhang, Boli; Chen, Jing; Yang, Bian; Yang, Jie
2016-01-01
In this paper, the x-ray emissions are measured by the interaction of 1500–3500 keV Xeq+ (q = 12, 15, 17, 19, 21, 23, 26 and 29) ions with Zn target. When q < 29, we observe Ll, Lα, Lβ1, Lβ2 and Lγ characteristic x-rays from Xeq+ ions and a broad M-shell molecular orbital (MO) x-ray band from the transient quasi-molecular levels. It is found that their yields quickly increase with different rates as the incident energy increases. Besides, the widths of the broad MO x-ray bands are about 0.9–1.32 keV over the energy range studied and are proportional to v1/2 (v = projectile velocity). Most remarkably, when the projectile charge state is 29, the broad x-ray band separates into several narrow discrete spectra, which was never observed before in this field. PMID:27469425
Almarza, Jorge; Rincón, Luis; Bahsas, Alí; Pinto, María Angela; Brito, Francisco
2013-02-01
Understanding of protein-urea interactions is one of the greatest challenges to modern structural protein chemistry. Based in enzyme kinetics experiments and (1)H NMR spectroscopic analysis we proposed that urea, at low concentrations, directly interacts with the protonated histidines of the active center of RNase A, following a simple model of competitive inhibition. These results were supported by theoretical analysis based on the frontier molecular orbital theory and suggest that urea might establish a favorable interaction with the cationic amino acids. Our experimental evidence and theoretical analysis indicate that the initials steps of the molecular mechanism of Urea-RNase A interaction passes through the establishment of a three center four electron adduct. Also, our results would explain the observed disruption of the (1)H NMR signals corresponding to H12 and H119 (involved in catalysis) of the RNase A studied in the presence of urea. Our interaction model of urea-amino acids (cationic) can be extended to explain the inactivation of other enzymes with cationic amino acids at the active site.
Pals, Justin A; Wagner, Elizabeth D; Plewa, Michael J
2016-03-15
Disinfection of drinking water protects public health against waterborne pathogens. However, during disinfection, toxic disinfection byproducts (DBPs) are formed. Exposure to DBPs was associated with increased risk of bladder cancer in humans. DBPs are generated at concentrations below their carcinogenic potencies; it is unclear how exposure leads to adverse health outcomes. We used computational estimates of the energy of the lowest unoccupied molecular orbital (ELUMO) to predict thiol reactivity and additive toxicity among soft electrophile DBPs. Bromoacetic acid (BAA) was identified as non-thiol-reactive, which was supported by in chemico and in vitro data. Bromoacetonitrile (BAN) and bromoacetamide (BAM) were thiol-reactive. Genotoxicity induced by these compounds was reduced by increasing the thiol pool with N-acetyl L-cysteine (NAC), while NAC had little effect on BAA. BAN and BAM shared depletion of glutathione (GSH) or cellular thiols as a molecular initiating event (MIE), whereas BAA induces toxicity through another pathway. Binary mixtures of BAM and BAN expressed a potentiating effect in genotoxicity. We found that soft electrophile DBPs could be an important predictor of common mechanism groups that demonstrated additive toxicity. In silico estimates of ELUMO could be used to identify the most relevant DBPs that are the forcing factors of the toxicity of finished drinking waters. PMID:26854864
The continuous and discrete molecular orbital x-ray bands from Xeq+ (12≤q≤29) +Zn collisions
NASA Astrophysics Data System (ADS)
Guo, Yipan; Yang, Zhihu; Hu, Bitao; Wang, Xiangli; Song, Zhangyong; Xu, Qiumei; Zhang, Boli; Chen, Jing; Yang, Bian; Yang, Jie
2016-07-01
In this paper, the x-ray emissions are measured by the interaction of 1500–3500 keV Xeq+ (q = 12, 15, 17, 19, 21, 23, 26 and 29) ions with Zn target. When q < 29, we observe Ll, Lα, Lβ1, Lβ2 and Lγ characteristic x-rays from Xeq+ ions and a broad M-shell molecular orbital (MO) x-ray band from the transient quasi-molecular levels. It is found that their yields quickly increase with different rates as the incident energy increases. Besides, the widths of the broad MO x-ray bands are about 0.9–1.32 keV over the energy range studied and are proportional to v1/2 (v = projectile velocity). Most remarkably, when the projectile charge state is 29, the broad x-ray band separates into several narrow discrete spectra, which was never observed before in this field.
Chang, Le; Ishikawa, Takeshi; Kuwata, Kazuo; Takada, Shoji
2013-05-30
Accurate computational estimate of the protein-ligand binding affinity is of central importance in rational drug design. To improve accuracy of the molecular mechanics (MM) force field (FF) for protein-ligand simulations, we use a protein-specific FF derived by the fragment molecular orbital (FMO) method and by the restrained electrostatic potential (RESP) method. Applying this FMO-RESP method to two proteins, dodecin, and lysozyme, we found that protein-specific partial charges tend to differ more significantly from the standard AMBER charges for isolated charged atoms. We did not see the dependence of partial charges on the secondary structure. Computing the binding affinities of dodecin with five ligands by MM PBSA protocol with the FMO-RESP charge set as well as with the standard AMBER charges, we found that the former gives better correlation with experimental affinities than the latter. While, for lysozyme with five ligands, both charge sets gave similar and relatively accurate estimates of binding affinities.
A Ring of C2H in the Molecular Disk Orbiting TW Hya
NASA Astrophysics Data System (ADS)
Kastner, Joel H.; Qi, Chunhua; Gorti, Uma; Hily-Blant, Pierre; Oberg, Karin; Forveille, Thierry; Andrews, Sean; Wilner, David
2015-06-01
We have used the Submillimeter Array to image, at ˜1.″5 resolution, C2H N=3\\to 2 emission from the circumstellar disk orbiting the nearby (D = 54 pc), ˜8 Myr-old, ˜0.8 {{M}⊙ } classical T Tauri star TW Hya. The SMA imaging reveals that the C2H emission exhibits a ring-like morphology. Based on a model in which the C2H column density follows a truncated radial power-law distribution, we find that the inner edge of the ring lies at ˜45 AU, and that the ring extends to at least ˜120 AU. Comparison with previous (single-dish) observations of C2H N=4\\to 3 emission indicates that the C2H molecules are subthermally excited and, hence, that the emission arises from the relatively warm (T≳ 40 K), tenuous (n\\ll {{10}7} cm-3) upper atmosphere of the disk. Based on these results and comparisons of the SMA C2H map with previous submillimeter and scattered-light imaging, we propose that the C2H emission most likely traces particularly efficient photo-destruction of small grains and/or photodesorption and photodissociation of hydrocarbons derived from grain ice mantles in the surface layers of the outer disk. The presence of a C2H ring in the TW Hya disk hence likely serves as a marker of dust grain processing and radial and vertical grain size segregation within the disk.
Energetic studies and phase diagram of thioxanthene.
Freitas, Vera L S; Monte, Manuel J S; Santos, Luís M N B F; Gomes, José R B; Ribeiro da Silva, Maria D M C
2009-11-19
The molecular stability of thioxanthene, a key species from which very important compounds with industrial relevance are derived, has been studied by a combination of several experimental techniques and computational approaches. The standard (p degrees = 0.1 MPa) molar enthalpy of formation of crystalline thioxanthene (117.4 +/- 4.1 kJ x mol(-1)) was determined from the experimental standard molar energy of combustion, in oxygen, measured by rotating-bomb combustion calorimetry at T = 298.15 K. The enthalpy of sublimation was determined by a direct method, using the vacuum drop microcalorimetric technique, and also by an indirect method, using a static apparatus, where the vapor pressures at different temperatures were measured. The latter technique was used for both crystalline and undercooled liquid samples, and the phase diagram of thioxanthene near the triple point was obtained (triple point coordinates T = 402.71 K and p = 144.7 Pa). From the two methods, a mean value for the standard (p degrees = 0.1 MPa) molar enthalpy of sublimation, at T = 298.15 K (101.3 +/- 0.8 kJ x mol(-1)), was derived. From the latter value and from the enthalpy of formation of the solid, the standard (p degrees = 0.1 MPa) enthalpy of formation of gaseous thioxanthene was calculated as 218.7 +/- 4.2 kJ x mol(-1). Standard ab initio molecular orbital calculations were performed using the G3(MP2)//B3LYP composite procedure and several homodesmotic reactions in order to derive the standard molar enthalpy of formation of thioxanthene. The ab initio results are in excellent agreement with the experimental data. PMID:19821598
Energetic studies and phase diagram of thioxanthene.
Freitas, Vera L S; Monte, Manuel J S; Santos, Luís M N B F; Gomes, José R B; Ribeiro da Silva, Maria D M C
2009-11-19
The molecular stability of thioxanthene, a key species from which very important compounds with industrial relevance are derived, has been studied by a combination of several experimental techniques and computational approaches. The standard (p degrees = 0.1 MPa) molar enthalpy of formation of crystalline thioxanthene (117.4 +/- 4.1 kJ x mol(-1)) was determined from the experimental standard molar energy of combustion, in oxygen, measured by rotating-bomb combustion calorimetry at T = 298.15 K. The enthalpy of sublimation was determined by a direct method, using the vacuum drop microcalorimetric technique, and also by an indirect method, using a static apparatus, where the vapor pressures at different temperatures were measured. The latter technique was used for both crystalline and undercooled liquid samples, and the phase diagram of thioxanthene near the triple point was obtained (triple point coordinates T = 402.71 K and p = 144.7 Pa). From the two methods, a mean value for the standard (p degrees = 0.1 MPa) molar enthalpy of sublimation, at T = 298.15 K (101.3 +/- 0.8 kJ x mol(-1)), was derived. From the latter value and from the enthalpy of formation of the solid, the standard (p degrees = 0.1 MPa) enthalpy of formation of gaseous thioxanthene was calculated as 218.7 +/- 4.2 kJ x mol(-1). Standard ab initio molecular orbital calculations were performed using the G3(MP2)//B3LYP composite procedure and several homodesmotic reactions in order to derive the standard molar enthalpy of formation of thioxanthene. The ab initio results are in excellent agreement with the experimental data.
Energetic Studies and Phase Diagram of Thioxanthene
NASA Astrophysics Data System (ADS)
Freitas, Vera L. S.; Monte, Manuel J. S.; Santos, Luís M. N. B. F.; Gomes, José R. B.; Ribeiro da Silva, Maria D. M. C.
2009-10-01
The molecular stability of thioxanthene, a key species from which very important compounds with industrial relevance are derived, has been studied by a combination of several experimental techniques and computational approaches. The standard (p° = 0.1 MPa) molar enthalpy of formation of crystalline thioxanthene (117.4 ± 4.1 kJ·mol-1) was determined from the experimental standard molar energy of combustion, in oxygen, measured by rotating-bomb combustion calorimetry at T = 298.15 K. The enthalpy of sublimation was determined by a direct method, using the vacuum drop microcalorimetric technique, and also by an indirect method, using a static apparatus, where the vapor pressures at different temperatures were measured. The latter technique was used for both crystalline and undercooled liquid samples, and the phase diagram of thioxanthene near the triple point was obtained (triple point coordinates T = 402.71 K and p = 144.7 Pa). From the two methods, a mean value for the standard (p° = 0.1 MPa) molar enthalpy of sublimation, at T = 298.15 K (101.3 ± 0.8 kJ·mol-1), was derived. From the latter value and from the enthalpy of formation of the solid, the standard (p° = 0.1 MPa) enthalpy of formation of gaseous thioxanthene was calculated as 218.7 ± 4.2 kJ·mol-1. Standard ab initio molecular orbital calculations were performed using the G3(MP2)//B3LYP composite procedure and several homodesmotic reactions in order to derive the standard molar enthalpy of formation of thioxanthene. The ab initio results are in excellent agreement with the experimental data.
Suresh, S; Gunasekaran, S; Srinivasan, S
2014-05-01
The solid phase FT-IR and FT-Raman spectra of 2-[2-[2-[(2,6-dichlorophenyl)amino]phenyl]acetyl] oxyacetic acid (Aceclofenac) have been recorded in the region 4000-400 and 4000-100 cm(-1) respectively. The optimized molecular geometry and fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method and a comparative study between Hartree Fork (HF) method 6-311++G(d,p) level basis set. The calculated harmonic vibrational frequencies were scaled and have been compared with experimental by obtained FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The time dependent DFT method employed to study its absorption energy and oscillator strength. The linear polarizability (α) and the first order hyper polarizability (β) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MESP) were also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.
NASA Astrophysics Data System (ADS)
Suresh, S.; Gunasekaran, S.; Srinivasan, S.
The solid phase FT-IR and FT-Raman spectra of 2-[2-[2-[(2,6-dichlorophenyl)amino]phenyl]acetyl] oxyacetic acid (Aceclofenac) have been recorded in the region 4000-400 and 4000-100 cm-1 respectively. The optimized molecular geometry and fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method and a comparative study between Hartree Fork (HF) method 6-311++G(d,p) level basis set. The calculated harmonic vibrational frequencies were scaled and have been compared with experimental by obtained FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The time dependent DFT method employed to study its absorption energy and oscillator strength. The linear polarizability (α) and the first order hyper polarizability (β) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MESP) were also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.
Prabavathi, N; Senthil Nayaki, N; Venkatram Reddy, B
2015-02-01
Vibrational spectral analysis of the molecules 3,6-dichloro-4-methylpyridazine (DMP) and 3,6-dichloropyridazine-4-carboxylic acid (DPC) was carried out using FT-IR and FT-Raman spectroscopic techniques. The molecular structure and vibrational spectra of DMP and DPC were obtained by the density functional theory (DFT) method, using B3LYP functional, with 6-311++G(d,p) basis set. A detailed interpretation of the Infrared and Raman spectra of the two molecules were reported based on potential energy distribution (PED). The theoretically predicted FTIR and FT-Raman spectra of the titled molecules have been simulated and were compared with the experimental spectra. Determination of electric dipole moment (μ) and hyperpolarizability β0 helps to study the non-linear optical (NLO) behavior of DMP and DPC. Stability of the molecules arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. (13)C and (1)H NMR spectra were recorded and (13)C and (1)H NMR chemical shifts of the molecules were calculated using the gauge independent atomic orbital (GIAO) method. UV-visible spectrum of the compounds was also recorded in the region 200-1100 nm and electronic properties, HOMO (Highest Occupied Molecular Orbitals) and LUMO (Lowest Unoccupied Molecular Orbitals) energies were measured by time-dependent TD-DFT approach. Charge density distribution and site of chemical reactivity of the molecule have been studied by mapping electron density isosurface with molecular electrostatic potential (MESP).
ERIC Educational Resources Information Center
Halpern, Arthur M.; Glendening, Eric D.
2013-01-01
A three-part project for students in physical chemistry, computational chemistry, or independent study is described in which they explore applications of valence bond (VB) and molecular orbital-configuration interaction (MO-CI) treatments of H[subscript 2]. Using a scientific spreadsheet, students construct potential-energy (PE) curves for several…
Engineering holographic phase diagrams
NASA Astrophysics Data System (ADS)
Chen, Jiunn-Wei; Dai, Shou-Huang; Maity, Debaprasad; Zhang, Yun-Long
2016-10-01
By introducing interacting scalar fields, we tried to engineer physically motivated holographic phase diagrams which may be interesting in the context of various known condensed matter systems. We introduce an additional scalar field in the bulk which provides a tunable parameter in the boundary theory. By exploiting the way the tuning parameter changes the effective masses of the bulk interacting scalar fields, desired phase diagrams can be engineered for the boundary order parameters dual to those scalar fields. We give a few examples of generating phase diagrams with phase boundaries which are strikingly similar to the known quantum phases at low temperature such as the superconducting phases. However, the important difference is that all the phases we have discussed are characterized by neutral order parameters. At the end, we discuss if there exists any emerging scaling symmetry associated with a quantum critical point hidden under the dome in this phase diagram.
NASA Astrophysics Data System (ADS)
Aso, N.; Ohta, K.; Ide, S.
2014-12-01
Deformation in a small volume of earth interior is expressed by a symmetric moment tensor located on a point source. The tensor contains information of characteristic directions, source amplitude, and source types such as isotropic, double-couple, or compensated-linear-vector-dipole (CLVD). Although we often assume a double couple as the source type of an earthquake, significant non-double-couple component including isotropic component is often reported for induced earthquakes and volcanic earthquakes. For discussions on source types including double-couple and non-double-couple components, it is helpful to display them using some visual diagrams. Since the information of source type has two degrees of freedom, it can be displayed onto a two-dimensional flat plane. Although the diagram developed by Hudson et al. [1989] is popular, the trace corresponding to the mechanism combined by two mechanisms is not always a smooth line. To overcome this problem, Chapman and Leaney [2012] developed a new diagram. This diagram has an advantage that a straight line passing through the center corresponds to the mechanism obtained by a combination of an arbitrary mechanism and a double-couple [Tape and Tape, 2012], but this diagram has some difficulties in use. First, it is slightly difficult to produce the diagram because of its curved shape. Second, it is also difficult to read out the ratios among isotropic, double-couple, and CLVD components, which we want to obtain from the estimated moment tensors, because they do not appear directly on the horizontal or vertical axes. In the present study, we developed another new square diagram that overcomes the difficulties of previous diagrams. This diagram is an orthogonal system of isotropic and deviatoric axes, so it is easy to get the ratios among isotropic, double-couple, and CLVD components. Our diagram has another advantage that the probability density is obtained simply from the area within the diagram if the probability density
Ferro-Costas, David; Pendás, Angel Martín; González, Leticia; Mosquera, Ricardo A
2014-05-28
We show that the use of the quantum theory of atoms in molecules (QTAIM) in electronically excited states allows expanding the knowledge that the molecular orbital (MO) framework provides about electronic rearrangements. Despite that historical prejudice seemed to preclude the use of QTAIM beyond the electronic ground state, this paper evidences that QTAIM is versatile enough to deal with excited states. As an example, the paradigmatic n → π* electronic transition of formaldehyde is analyzed. Using QTAIM, an energy partition of excited state energies into atomic and diatomic energies is carried out for the first time. This partition shows that upon electronic excitation the atoms of the CO bond experience a stabilization in their net energies, accompanied by a destabilization in their interaction, a fact which is in accordance with the idea of populating an antibonding π* MO. The associated C-O bond elongation in the nπ* state does not involve a change in the π atomic populations - as one would expect from a π* orbital - but in the σ ones. Moreover, it is also found that the nπ* state is characterized by a weaker C-O interaction energy in comparison to that in the electronic ground state. In order to strengthen this interaction, the electron-electron repulsion between C and O is reduced via a symmetry-breaking of the electron density, causing the C pyramidalization. A topological analysis based on the Laplacian of the electron density and on the electron localization function (ELF) reveals that the n → π* transition can be visualized as a rotation of 90° of the oxygen lone pairs.
Yoon, Min-Ho; Nam, Yun-Kyu; Choi, Woo-Young; Sung, Nack-Do
2007-11-01
A beta-glucosidase with the molecular mass of 160,000 Da was purified to homogeneity from cell extract of a cellulolytic bacterium, Cellulomonas uda CS1-1. The kinetic parameters (Km and Vmax) of the enzyme were determined with pNP-cellooligosccharides (DP 1-5) and cellobiose. The molecular orbital theoretical studies on the cellulolytic reactivity between the pNP-cellooligosaccharides as substrate (S) molecules and the purified beta-glucosidase (E) were conducted by applying the frontier molecular orbital (FMO) interaction theory. The results of the FMO interaction between E and S molecules verified that the first stage of the reaction was induced by exocyclic cleavage, which occurred in an electrophilic reaction based on a strong charge-controlled reaction between the highest occupied molecular orbital (HOMO) energy of the S molecule and the lowest occupied molecular orbital (LUMO) energy of the hydronium ion (H3O+), more than endocyclic cleavage, whereas a nucleophilic substitution reaction was induced by an orbital-controlled reaction between the LUMO energy of the oxonium ion (SH+) protonated to the S molecule and the HOMO energy of the H2O2 molecule. A hypothetic reaction route was proposed with the experimental results in which the enzymatic acid-catalyst hydrolysis reaction of E and S molecules would be progressed via SN1 and SN2 reactions. In addition, the quantitative structure-activity relationships (QSARs) between these kinetic parameters showed that Km has a significant correlation with hydrophobicity (logP), and specific activity has with dipole moment, respectively.
Multi-electron coincidence spectroscopy: double photoionization from molecular inner-shell orbitals
NASA Astrophysics Data System (ADS)
Lablanquie, P.; Penent, F.; Hikosaka, Y.
2016-09-01
The interest of molecular double core holes was predicted in 1986 by Cederbaum et al who showed that their spectroscopy can be more informative than that of single core holes, especially when the holes are located at different sites in the molecule (Cederbaum et al 1986 J. Chem. Phys. 85 6513). Their experimental study of single photon formation had to wait until 2009-2010 with progress in synchrotron sources and the development of efficient multi-electron coincidence experiments based on a magnetic bottle time-of-flight spectrometer. At the same time the advent of x-ray free electron lasers opened the possibilty of creating them in a two-photon process, and motivated new theoretical studies of their properties. We will illustrate here the progress made recently in the field with a few examples, including the formation of double core holes by double core photoionization, their spectroscopy and decay paths, and the related process of simultaneous core ionization and core excitation.
Multi-electron coincidence spectroscopy: double photoionization from molecular inner-shell orbitals
NASA Astrophysics Data System (ADS)
Lablanquie, P.; Penent, F.; Hikosaka, Y.
2016-09-01
The interest of molecular double core holes was predicted in 1986 by Cederbaum et al who showed that their spectroscopy can be more informative than that of single core holes, especially when the holes are located at different sites in the molecule (Cederbaum et al 1986 J. Chem. Phys. 85 6513). Their experimental study of single photon formation had to wait until 2009–2010 with progress in synchrotron sources and the development of efficient multi-electron coincidence experiments based on a magnetic bottle time-of-flight spectrometer. At the same time the advent of x-ray free electron lasers opened the possibilty of creating them in a two-photon process, and motivated new theoretical studies of their properties. We will illustrate here the progress made recently in the field with a few examples, including the formation of double core holes by double core photoionization, their spectroscopy and decay paths, and the related process of simultaneous core ionization and core excitation.
NASA Astrophysics Data System (ADS)
Aarset, Kirsten; Hagen, Kolbjørn; Stølevik, Reidar
2001-06-01
The structure and conformational composition of 2-chlorobutane and 2-bromobutane have been studied by gas-phase electron diffraction (GED) at 25°C, together with ab initio molecular orbital calculations (HF/6-311+G(d,p)). These molecules may exist as three distinguishable conformers (G+, A, and G-). The symbols refer to anti (A) with a torsion angle Φ2(X 8-C 2-C 3-C 4) of about 180° and gauche (G+ and G-) with torsion angles Φ2(X 8-C 2-C 3-C 4) of about +60° and 300°(-60°), respectively. It was not possible; from our GED-data alone, to accurately determine the conformational composition because the distance distributions for two of the conformers (G+ and G-) are very similar. The conformational composition for 2-chlorobutane obtained from the ab initio calculations (G+ 62%, A 25% G- 13%) was found to fit the experimental data quite well. For 2-bromobutane the ab initio calculated conformational composition (G+ 58%, A 28% G- 14%) did not, however, fit the experimental data. Here a much better fit was obtained by using only 10% of the A conformer and using the relative energy for the two gauche conformers, as obtained in the ab initio molecular orbital calculations, to calculate the relative amounts of the two gauche forms (G+ 73%, A 10% G- 17%). The results for the principal distances ( rg) and angles ∠ α for the G+ conformer of 2-chlorobutane, with estimated 2 σ uncertainties, obtained from the combined GED/ab initio study are: r( C1- C2)=1.524(3) Å, r( C2- C3)=1.528(3) Å, r( C3- C4)=1.539(3) Å, r( C- Cl)=1.812(3) Å, r( C- H) ave=1.098(4) Å, ∠C 1C 2C 3=111.5(16)°, ∠C 2C 3C 4=113.3(5)°, ∠C 1C 2C1=110.4(9)°. The results for the G+ conformer of 2-bromobutane are: r( C1- C2)=1.526(4) Å, r( C2- C3)=1.530(4) Å, r( C3- C4)=1.540(4) Å, r( C- Br)=1.982(5) Å, r( C- H) ave=1.111(8) Å, ∠C 1C 2C 3=112.5(16)°, ∠C 2C 3C 4=114.6(15)°, ∠C 1C 2Br=110.1(16)°. Only average values for r(C-C), r(C-H), ∠CCC, and ∠CCH could be determined in the
Lee, Minju; Zimmermann-Steffens, Saskia G; Arey, J Samuel; Fenner, Kathrin; von Gunten, Urs
2015-08-18
Second-order rate constants (kO3) for the reaction of ozone with micropollutants are essential parameters for the assessment of micropollutant elimination efficiency during ozonation in water and wastewater treatment. Prediction models for kO3 were developed for aromatic compounds, olefins, and amines by quantum chemical molecular orbital calculations employing ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods. The kO3 values for aromatic compounds correlated well with the energy of a delocalized molecular orbital first appearing on an aromatic ring (i.e., the highest occupied molecular orbital (HOMO) or HOMO-n (n ≥ 0) when the HOMO is not located on the aromatic ring); the number of compounds tested (N) was 112, and the correlation coefficient (R(2)) values were 0.82-1.00. The kO3 values for olefins and amines correlated well with the energy of a localized molecular orbital (i.e., the natural bond orbital (NBO)) energy of the carbon-carbon π bond of olefins (N = 45, R(2) values of 0.82-0.85) and the NBO energy of the nitrogen lone-pair electrons of amines (N = 59, R(2) values of 0.81-0.83), respectively. Considering the performance of the kO3 prediction model and the computational costs, the HF/6-31G method is recommended for all aromatic groups and olefins investigated herein, whereas the HF/MIDI!, HF/6-31G*, or HF/6-311++G** methods are recommended for amines. Based on their mean absolute errors, the above models could predict kO3 within a factor of 4, on average, relative to the experimentally determined values. Overall, good correlations were also observed (R(2) values of 0.77-0.96) between kO3 predictions by quantum molecular orbital descriptors in this study and by the Hammett (σ) and Taft (σ*) constants from previously developed quantitative structure-activity relationship (QSAR) models. Hence, the quantum molecular orbital descriptors are an alternative to σ and σ*-values in QSAR applications and can also be utilized to
Lee, Minju; Zimmermann-Steffens, Saskia G; Arey, J Samuel; Fenner, Kathrin; von Gunten, Urs
2015-08-18
Second-order rate constants (kO3) for the reaction of ozone with micropollutants are essential parameters for the assessment of micropollutant elimination efficiency during ozonation in water and wastewater treatment. Prediction models for kO3 were developed for aromatic compounds, olefins, and amines by quantum chemical molecular orbital calculations employing ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods. The kO3 values for aromatic compounds correlated well with the energy of a delocalized molecular orbital first appearing on an aromatic ring (i.e., the highest occupied molecular orbital (HOMO) or HOMO-n (n ≥ 0) when the HOMO is not located on the aromatic ring); the number of compounds tested (N) was 112, and the correlation coefficient (R(2)) values were 0.82-1.00. The kO3 values for olefins and amines correlated well with the energy of a localized molecular orbital (i.e., the natural bond orbital (NBO)) energy of the carbon-carbon π bond of olefins (N = 45, R(2) values of 0.82-0.85) and the NBO energy of the nitrogen lone-pair electrons of amines (N = 59, R(2) values of 0.81-0.83), respectively. Considering the performance of the kO3 prediction model and the computational costs, the HF/6-31G method is recommended for all aromatic groups and olefins investigated herein, whereas the HF/MIDI!, HF/6-31G*, or HF/6-311++G** methods are recommended for amines. Based on their mean absolute errors, the above models could predict kO3 within a factor of 4, on average, relative to the experimentally determined values. Overall, good correlations were also observed (R(2) values of 0.77-0.96) between kO3 predictions by quantum molecular orbital descriptors in this study and by the Hammett (σ) and Taft (σ*) constants from previously developed quantitative structure-activity relationship (QSAR) models. Hence, the quantum molecular orbital descriptors are an alternative to σ and σ*-values in QSAR applications and can also be utilized to
Otsuka, Takao; Okimoto, Noriaki; Taiji, Makoto
2015-11-15
In the field of drug discovery, it is important to accurately predict the binding affinities between target proteins and drug applicant molecules. Many of the computational methods available for evaluating binding affinities have adopted molecular mechanics-based force fields, although they cannot fully describe protein-ligand interactions. A noteworthy computational method in development involves large-scale electronic structure calculations. Fragment molecular orbital (FMO) method, which is one of such large-scale calculation techniques, is applied in this study for calculating the binding energies between proteins and ligands. By testing the effects of specific FMO calculation conditions (including fragmentation size, basis sets, electron correlation, exchange-correlation functionals, and solvation effects) on the binding energies of the FK506-binding protein and 10 ligand complex molecule, we have found that the standard FMO calculation condition, FMO2-MP2/6-31G(d), is suitable for evaluating the protein-ligand interactions. The correlation coefficient between the binding energies calculated with this FMO calculation condition and experimental values is determined to be R = 0.77. Based on these results, we also propose a practical scheme for predicting binding affinities by combining the FMO method with the quantitative structure-activity relationship (QSAR) model. The results of this combined method can be directly compared with experimental binding affinities. The FMO and QSAR combined scheme shows a higher correlation with experimental data (R = 0.91). Furthermore, we propose an acceleration scheme for the binding energy calculations using a multilayer FMO method focusing on the protein-ligand interaction distance. Our acceleration scheme, which uses FMO2-HF/STO-3G:MP2/6-31G(d) at R(int) = 7.0 Å, reduces computational costs, while maintaining accuracy in the evaluation of binding energy.
NASA Astrophysics Data System (ADS)
Ishihara, Mariko; Sakagami, Hiroshi; Kawase, Masami; Motohashi, Noboru
The relationship between the cytotoxicity of N-heterocycles (13 4-trifluoromethylimidazole, 15 phenoxazine and 12 5-trifluoromethyloxazole derivatives), O-heterocycles (11 3-formylchromone and 20 coumarin derivatives) and seven vitamin K2 derivatives against eight tumor cell lines (HSC-2, HSC-3, HSC-4, T98G, HSG, HepG2, HL-60, MT-4) and a maximum of 15 chemical descriptors was investigated using CAChe Worksystem 4.9 project reader. After determination of the conformation of these compounds and approximation to the molecular form present in vivo (biomimetic) by CONFLEX5, the most stable structure was determined by CAChe Worksystem 4.9 MOPAC (PM3). The present study demonstrates the best relationship between the cytotoxic activity and molecular shape or molecular weight of these compounds. Their biological activities can be estimated by hardness and softness, and by using η-χ activity diagrams.
Bennett, L.K.; Beamer, R.L.
1986-08-01
Semi-empirical (CNDO) molecular orbital calculations, based on a previously reported ammonia-amine model system, were performed on an extended series of methyl-, ethyl-, and propylamines as models for the analgesic receptor. Methyl-, dimethyl-, and trimethylamines were chosen to represent the opiate molecules. Interatomic distances were varied within normally expected biological values. The results for the larger systems are similar to more elaborate calculations previously reported using smaller molecules. At internuclear distances of greater than 0.275 nm, the potential energy curves had two minima. At 0.2731 nm, the optimized N-N distance, the depth of the minima in the potential energy curve were not as great. Energy differences as well as population differences suggest deviation from the currently stated clastic binding theories mechanism for the analgesic response of the tertiary amines. The dimethylamine energy profile and population data indicate that the hypothesis of N-demethylated opiate as the active molecule needs further consideration and investigation. Investigation of larger systems is also indicated to develop increasingly realistic models for the analgesic response.
Nakata, Hiroya; Fedorov, Dmitri G.; Zahariev, Federico; Schmidt, Michael W.; Gordon, Mark S.; Kitaura, Kazuo; Nakamura, Shinichiro
2015-03-28
Analytic second derivatives of the energy with respect to nuclear coordinates have been developed for spin restricted density functional theory (DFT) based on the fragment molecular orbital method (FMO). The derivations were carried out for the three-body expansion (FMO3), and the two-body expressions can be obtained by neglecting the three-body corrections. Also, the restricted Hartree-Fock (RHF) Hessian for FMO3 can be obtained by neglecting the density-functional related terms. In both the FMO-RHF and FMO-DFT Hessians, certain terms with small magnitudes are neglected for computational efficiency. The accuracy of the FMO-DFT Hessian in terms of the Gibbs free energy is evaluated for a set of polypeptides and water clusters and found to be within 1 kcal/mol of the corresponding full (non-fragmented) ab initio calculation. The FMO-DFT method is also applied to transition states in S{sub N}2 reactions and for the computation of the IR and Raman spectra of a small Trp-cage protein (PDB: 1L2Y). Some computational timing analysis is also presented.
Lv, Xiaoli; Li, Zhuoxin; Li, Songyang; Luan, Guoyou; Liang, Dadong; Tang, Shanshan; Jin, Ruifa
2016-01-01
A series of perylene diimide (PDI) derivatives have been investigated at the CAM-B3LYP/6-31G(d) and the TD-B3LYP/6-31+G(d,p) levels to design solar cell acceptors with high performance in areas such as suitable frontier molecular orbital (FMO) energies to match oligo(thienylenevinylene) derivatives and improved charge transfer properties. The calculated results reveal that the substituents slightly affect the distribution patterns of FMOs for PDI-BI. The electron withdrawing group substituents decrease the FMO energies of PDI-BI, and the electron donating group substituents slightly affect the FMO energies of PDI-BI. The di-electron withdrawing group substituents can tune the FMOs of PDI-BI to be more suitable for the oligo(thienylenevinylene) derivatives. The electron withdrawing group substituents result in red shifts of absorption spectra and electron donating group substituents result in blue shifts for PDI-BI. The -CN substituent can improve the electron transport properties of PDI-BI. The -CH₃ group in different positions slightly affects the electron transport properties of PDI-BI. PMID:27187370
Nakata, Hiroya; Fedorov, Dmitri G; Zahariev, Federico; Schmidt, Michael W; Kitaura, Kazuo; Gordon, Mark S; Nakamura, Shinichiro
2015-03-28
Analytic second derivatives of the energy with respect to nuclear coordinates have been developed for spin restricted density functional theory (DFT) based on the fragment molecular orbital method (FMO). The derivations were carried out for the three-body expansion (FMO3), and the two-body expressions can be obtained by neglecting the three-body corrections. Also, the restricted Hartree-Fock (RHF) Hessian for FMO3 can be obtained by neglecting the density-functional related terms. In both the FMO-RHF and FMO-DFT Hessians, certain terms with small magnitudes are neglected for computational efficiency. The accuracy of the FMO-DFT Hessian in terms of the Gibbs free energy is evaluated for a set of polypeptides and water clusters and found to be within 1 kcal/mol of the corresponding full (non-fragmented) ab initio calculation. The FMO-DFT method is also applied to transition states in SN2 reactions and for the computation of the IR and Raman spectra of a small Trp-cage protein (PDB: 1L2Y). Some computational timing analysis is also presented.
Hitaoka, Seiji; Chuman, Hiroshi; Yoshizawa, Kazunari
2015-01-21
A binding mechanism between human matrix metalloproteinase-12 (MMP-12) and eight arylsulfone analogs having two types of carboxylic and hydroxamic acids as the most representative zinc binding group is investigated using a quantitative structure-activity relationship (QSAR) analysis based on a linear expression by representative energy terms (LERE). The LERE-QSAR analysis quantitatively reveals that the variation in the observed (experimental) inhibitory potency among the arylsulfone analogs is decisively governed by those in the intrinsic binding and dispersion interaction energies. The results show that the LERE-QSAR analysis not only can excellently reproduce the observed overall free-energy change but also can determine the contributions of representative free-energy changes. An inter-fragment interaction energy difference (IFIED) analysis based on the fragment molecular orbital (FMO) method (FMO-IFIED) leads to the identification of key residues governing the variation in the inhibitory potency as well as to the understanding of the difference between the interactions of the carboxylic and hydroxamic acid zinc binding groups. The current results that have led to the optimization of the inhibitory potency of arylsulfone analogs toward MMP-12 to be used in the treatment of chronic obstructive pulmonary disease may be useful for the development of a new potent MMP-12 inhibitor.
NASA Astrophysics Data System (ADS)
Bäppler, Stefanie A.; Plasser, Felix; Wormit, Michael; Dreuw, Andreas
2014-11-01
Exciton sizes and electron-hole binding energies, which are central properties of excited states in extended systems and crucial to the design of modern electronic devices, are readily defined within a quasiparticle framework but are quite challenging to understand in the molecular-orbital picture. The intent of this work is to bridge this gap by providing a general way of extracting the exciton wave function out of a many-body wave function obtained by a quantum chemical excited-state computation. This methodology, which is based on the one-particle transition density matrix, is implemented within the ab initio algebraic diagrammatic construction scheme for the polarization propagator and specifically the evaluation of exciton sizes, i.e., dynamic charge separation distances, is considered. A number of examples are presented. For stacked dimers it is shown that the exciton size for charge separated states corresponds to the intermolecular separation, while it only depends on the monomer size for locally excited states or Frenkel excitons. In the case of conjugated organic polymers, the tool is applied to analyze exciton structure and dynamic charge separation. Furthermore, it is discussed how the methodology may be used for the construction of a charge-transfer diagnostic for time-dependent density-functional theory.
Lv, Xiaoli; Li, Zhuoxin; Li, Songyang; Luan, Guoyou; Liang, Dadong; Tang, Shanshan; Jin, Ruifa
2016-01-01
A series of perylene diimide (PDI) derivatives have been investigated at the CAM-B3LYP/6-31G(d) and the TD-B3LYP/6-31+G(d,p) levels to design solar cell acceptors with high performance in areas such as suitable frontier molecular orbital (FMO) energies to match oligo(thienylenevinylene) derivatives and improved charge transfer properties. The calculated results reveal that the substituents slightly affect the distribution patterns of FMOs for PDI-BI. The electron withdrawing group substituents decrease the FMO energies of PDI-BI, and the electron donating group substituents slightly affect the FMO energies of PDI-BI. The di-electron withdrawing group substituents can tune the FMOs of PDI-BI to be more suitable for the oligo(thienylenevinylene) derivatives. The electron withdrawing group substituents result in red shifts of absorption spectra and electron donating group substituents result in blue shifts for PDI-BI. The –CN substituent can improve the electron transport properties of PDI-BI. The –CH3 group in different positions slightly affects the electron transport properties of PDI-BI. PMID:27187370
NASA Astrophysics Data System (ADS)
Nakata, Hiroya; Fedorov, Dmitri G.; Zahariev, Federico; Schmidt, Michael W.; Kitaura, Kazuo; Gordon, Mark S.; Nakamura, Shinichiro
2015-03-01
Analytic second derivatives of the energy with respect to nuclear coordinates have been developed for spin restricted density functional theory (DFT) based on the fragment molecular orbital method (FMO). The derivations were carried out for the three-body expansion (FMO3), and the two-body expressions can be obtained by neglecting the three-body corrections. Also, the restricted Hartree-Fock (RHF) Hessian for FMO3 can be obtained by neglecting the density-functional related terms. In both the FMO-RHF and FMO-DFT Hessians, certain terms with small magnitudes are neglected for computational efficiency. The accuracy of the FMO-DFT Hessian in terms of the Gibbs free energy is evaluated for a set of polypeptides and water clusters and found to be within 1 kcal/mol of the corresponding full (non-fragmented) ab initio calculation. The FMO-DFT method is also applied to transition states in SN2 reactions and for the computation of the IR and Raman spectra of a small Trp-cage protein (PDB: 1L2Y). Some computational timing analysis is also presented.
NASA Astrophysics Data System (ADS)
Dutkiewicz, Maria; Małecki, Jerzy
1997-10-01
The conformational equilibrium in 1,4-dimethoxybenzene (1,4-DMB) in benzene solutions has been studied. On the basis of experimental values of the nonlinear dielectric effect (NDE) parameter, electric permittivity and density, determined in this work, and applying the general statistical theory of NDE, the contributions of the syn-anti and syn-syn conformers and the electric dipole moment of the polar syn-syn conformer were calculated. The molecular orbital method (PM3) has also been applied for calculation of the dipole moments and energies of particular conformers. The results of the NDE study and PM3 calculations are consistent and they reveal the existence of two conformers ( syn-anti and syn-syn) of comparable energy values, but different values of dipole moments, and the predominance of the polar form ( syn-syn) of the mole fraction in benzene. Moreover, the energies of intermolecular interactions have been determined from the concentration dependence of linear and nonlinear polarisability.
Lv, Xiaoli; Li, Zhuoxin; Li, Songyang; Luan, Guoyou; Liang, Dadong; Tang, Shanshan; Jin, Ruifa
2016-05-13
A series of perylene diimide (PDI) derivatives have been investigated at the CAM-B3LYP/6-31G(d) and the TD-B3LYP/6-31+G(d,p) levels to design solar cell acceptors with high performance in areas such as suitable frontier molecular orbital (FMO) energies to match oligo(thienylenevinylene) derivatives and improved charge transfer properties. The calculated results reveal that the substituents slightly affect the distribution patterns of FMOs for PDI-BI. The electron withdrawing group substituents decrease the FMO energies of PDI-BI, and the electron donating group substituents slightly affect the FMO energies of PDI-BI. The di-electron withdrawing group substituents can tune the FMOs of PDI-BI to be more suitable for the oligo(thienylenevinylene) derivatives. The electron withdrawing group substituents result in red shifts of absorption spectra and electron donating group substituents result in blue shifts for PDI-BI. The -CN substituent can improve the electron transport properties of PDI-BI. The -CH₃ group in different positions slightly affects the electron transport properties of PDI-BI.
NASA Astrophysics Data System (ADS)
Proxauf, B.; Kimeswenger, S.; Öttl, S.
2014-04-01
Diagnostic diagrams of forbidden lines have been a useful tool for observers in astrophysics for many decades now. They are used to obtain information on the basic physical properties of thin gaseous nebulae. Moreover they are also the initial tool to derive thermodynamic properties of the plasma from observations to get ionization correction factors and thus to obtain proper abundances of the nebulae. Some diagnostic diagrams are in wavelengths domains which were difficult to take either due to missing wavelength coverage or low resolution of older spectrographs. Thus they were hardly used in the past. An upgrade of this useful tool is necessary because most of the diagrams were calculated using only the species involved as a single atom gas, although several are affected by well-known fluorescence mechanisms as well. Additionally the atomic data have improved up to the present time. The new diagnostic diagrams are calculated by using large grids of parameter space in the photoionization code CLOUDY. For a given basic parameter the input radiation field is varied to find the solutions with cooling-heating-equilibrium. Empirical numerical functions are fitted to provide formulas usable in e.g. data reduction pipelines. The resulting diagrams differ significantly from those used up to now and will improve the thermodynamic calculations.
Jones, Gregory; Wang, John E.
2005-06-15
To capture important physical properties of a spacetime we construct a new diagram, the card diagram, which accurately draws generalized Weyl spacetimes in arbitrary dimensions by encoding their global spacetime structure, singularities, horizons, and some aspects of causal structure including null infinity. Card diagrams draw only nontrivial directions providing a clearer picture of the geometric features of spacetimes as compared to Penrose diagrams, and can change continuously as a function of the geometric parameters. One of our main results is to describe how Weyl rods are traversable horizons and the entirety of the spacetime can be mapped out. We review Weyl techniques and as examples we systematically discuss properties of a variety of solutions including Kerr-Newman black holes, black rings, expanding bubbles, and recent spacelike-brane solutions. Families of solutions will share qualitatively similar cards. In addition we show how card diagrams not only capture information about a geometry but also its analytic continuations by providing a geometric picture of analytic continuation. Weyl techniques are generalized to higher dimensional charged solutions and applied to generate perturbations of bubble and S-brane solutions by Israel-Khan rods.
Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi
2015-07-01
In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl(-) + CH3Cl → ClCH3 + Cl(-)) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.
Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi
2015-07-07
In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein–Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple S{sub N}2 reaction (Cl{sup −} + CH{sub 3}Cl → ClCH{sub 3} + Cl{sup −}) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.
NASA Astrophysics Data System (ADS)
Edmiston, C.; Jarvie, J.; Bartleson, J.
1986-06-01
Walsh's rules correctly attribute the ``bent'' structures of H2O and NH3 to the occupation of the 1πz→3a1 HOMO not occupied in linear BeH2 and planar BH3. In Walsh's molecular orbital (MO) diagram E(3a1) decreases sharply with bending angle S. This has always been attributed incorrectly to changes in the 3a1 MO, mainly due to symmetry-allowed mixing with the LUMO, 4a*1. The forbidden bending of BeH2 and BH3 has been similarly ``explained.'' Using large-basis-set self-consistent field molecular orbital (SCF MO) ψs, we show that the integral Hellmann-Feynman theorem ΔEIHF≂ΔESCF much better than does the analogous second-order perturbation theory λE''(SE'=0 and λ=S2/2, ΔH≂SH'+λH''). ΔEIHF=<ψ0‖ΔNA‖ψ0>+<ψ0‖ ΔNA‖Δψ˜>+ΔNR≂Σni2Δ EIHFi+ΔNR, Δψ˜=(ψ/η)-ψ0, η=<ψ0‖ψ>, ΔEIHFi=<φ0i‖ ΔNA‖φ0i>+<φ0i‖ ΔNA‖Δφ˜i>, Δφ˜i=(φi/ηi)-φ0i, ηi=<φ0i‖φi>, ΔNA=ΔH-ΔNR. Both theories show a large negative <1πz‖ΔNA‖1πz> term and small <1πz‖ΔNA‖Δ1π˜z> HOMO-UMO mixing term, which is positive in ΔEIHF. The <1πz‖SH'‖3σ*g> HOMO-LUMO mixing term is small even when 3σ*g is optimized for the excited state. The ΔEIHFis and λE`is give the usual Walsh diagrams for bending of H2O and NH3, with or without MO partitioning of the nuclear repulsion change (ΔNR). However ``decoupling'' of the φ'is in ψ' makes the λE`is unreliable. The <1πz‖ΔNA‖1πz> term acts to create a large allowed barrier to inversion for H2O and CH4, but a strong ΔNR nearly destroys an otherwise large barrier for NH3. <1πz‖ΔNA‖1πz> acts to bend the linear H2O, planar NH3, and planar CH4, with HOMO-LUMO mixing being ``antibending.'' We show that understanding of MO correlation diagrams demands consideration of the ``static'' <φ0i‖ΔNA‖φ0i> terms as well as the OMO-UMO mixing terms, which has not been appreciated by earlier workers so far as we are aware.
Xiao-Hong, Li; Hong-Ling, Cui; Rui-Zhou, Zhang; Xian-Zhou, Zhang
2015-02-25
The vibrational frequencies of (E)-2-cyano-3-(3-hydroxyphenyl)acrylamide (HB-CA) in the ground state have been calculated using density functional method (B3LYP) with B3LYP/6-311++G(d,p) basis set. The analysis of natural bond orbital was also performed. The IR spectra were obtained and interpreted by means of potential energies distributions (PEDs) using MOLVIB program. In addition, the results show that there exists C-H⋯O hydrogen bond in the title compound, which is confirmed by the natural bond orbital analysis. The predicted NLO properties show that the title compound is a good candidate as nonlinear optical material. The analysis of frontier molecular orbitals shows that HB-CA has high excitation energies, good stability and high chemical hardness. The analysis of MEP map shows the negative and the positive potential sites.
NASA Astrophysics Data System (ADS)
Xiao-Hong, Li; Hong-Ling, Cui; Rui-Zhou, Zhang; Xian-Zhou, Zhang
2015-02-01
The vibrational frequencies of (E)-2-cyano-3-(3-hydroxyphenyl)acrylamide (HB-CA) in the ground state have been calculated using density functional method (B3LYP) with B3LYP/6-311++G(d,p) basis set. The analysis of natural bond orbital was also performed. The IR spectra were obtained and interpreted by means of potential energies distributions (PEDs) using MOLVIB program. In addition, the results show that there exists Csbnd H⋯O hydrogen bond in the title compound, which is confirmed by the natural bond orbital analysis. The predicted NLO properties show that the title compound is a good candidate as nonlinear optical material. The analysis of frontier molecular orbitals shows that HB-CA has high excitation energies, good stability and high chemical hardness. The analysis of MEP map shows the negative and the positive potential sites.
ERIC Educational Resources Information Center
Rosengrant, David
2011-01-01
Multiple representations are a valuable tool to help students learn and understand physics concepts. Furthermore, representations help students learn how to think and act like real scientists. These representations include: pictures, free-body diagrams, energy bar charts, electrical circuits, and, more recently, computer simulations and…
Tachikawa, Masanori
2015-12-31
To theoretically demonstrate the binding of a positron to small polarized molecules, we have calculated the vibrational averaged positron affinity (PA) values along the local vibrational contribution with the configuration interaction level of multi-component molecular orbital method. This method can take the electron-positron correlation contribution into account through single electronic - single positronic excitation configurations. The PA values are enhanced by including the local vibrational contribution from vertical PA values due to the anharmonicity of the potential.
NASA Technical Reports Server (NTRS)
McCourt, M.; Shibata, M.; McIver, J. W.; Rein, R.
1988-01-01
Recent discoveries have established the fact that RNA is capable of acting as an enzyme. In this study two different types of molecular orbital calculations, INDO and ab initio, were used in an attempt to assess the structural/functional role of the Mg2+ hydrated complex in ribozyme reactions. Preliminary studies indicate that the reaction is multistep and that the Mg2+ complex exerts a stabilizing effect on the intermediate or midpoint of the reaction.
McCourt, M; Shibata, M; McIver, J W; Rein, R
1988-01-01
Recent discoveries have established the fact that RNA is capable of acting as an enzyme. In this study two different types of molecular orbital calculations, INDO and ab initio, were used in an attempt to assess the structural/functional role of the Mg2+ hydrated complex in ribozyme reactions. Preliminary studies indicate that the reaction is multistep and that the Mg2+ complex exerts a stabilizing effect on the intermediate or midpoint of the reaction.
Clayton, A F; Coombs, M M; Henrick, K; McPartlin, M; Trotter, J
1983-12-01
Comparative X-ray crystallographic structure analyses have been carried out on seven cyclopenta[a]phenanthrenes, namely 15,16-dihydocyclopenta[a]phenanthren-17-one and its 2-, 6- and 12-methyl homologues (non-carcinogens) and the 7-and 11-methyl and 1,11-methano derivatives (carcinogens). All-valence-electron molecular-orbital calculations by the CNDO/2 method, using the crystallographic parameters, have also been executed. Charge distribution and the energies of the highest occupied molecular orbitals (HOMO) and lowest unoccupied molecular orbitals (LUMO) have been calculated. With one exception all the molecules show only small deviations from planarity, the exception being the strongly carcinogenic 11-methyl-17-ketone in which the bay-region methyl group causes out-of-plane deformation of the benzo rings of 12.5 degrees. Among the other six compounds the two carcinogens are readily differentiated by high angle strain induced by a 7-methyl group or a 1,11-methano bridge. As expected, the HOMO's of these molecules to some extent reflect their ease of chemical oxidation at the 6,7-double bond; biological oxidation is less easy to correlate probably due to spatial restrictions at the active site within the mono-oxygenase.
Tectonic discrimination diagrams revisited
NASA Astrophysics Data System (ADS)
Vermeesch, Pieter
2006-06-01
The decision boundaries of most tectonic discrimination diagrams are drawn by eye. Discriminant analysis is a statistically more rigorous way to determine the tectonic affinity of oceanic basalts based on their bulk-rock chemistry. This method was applied to a database of 756 oceanic basalts of known tectonic affinity (ocean island, mid-ocean ridge, or island arc). For each of these training data, up to 45 major, minor, and trace elements were measured. Discriminant analysis assumes multivariate normality. If the same covariance structure is shared by all the classes (i.e., tectonic affinities), the decision boundaries are linear, hence the term linear discriminant analysis (LDA). In contrast with this, quadratic discriminant analysis (QDA) allows the classes to have different covariance structures. To solve the statistical problems associated with the constant-sum constraint of geochemical data, the training data must be transformed to log-ratio space before performing a discriminant analysis. The results can be mapped back to the compositional data space using the inverse log-ratio transformation. An exhaustive exploration of 14,190 possible ternary discrimination diagrams yields the Ti-Si-Sr system as the best linear discrimination diagram and the Na-Nb-Sr system as the best quadratic discrimination diagram. The best linear and quadratic discrimination diagrams using only immobile elements are Ti-V-Sc and Ti-V-Sm, respectively. As little as 5% of the training data are misclassified by these discrimination diagrams. Testing them on a second database of 182 samples that were not part of the training data yields a more reliable estimate of future performance. Although QDA misclassifies fewer training data than LDA, the opposite is generally true for the test data. Therefore LDA is a cruder but more robust classifier than QDA. Another advantage of LDA is that it provides a powerful way to reduce the dimensionality of the multivariate geochemical data in a similar
Moreira, Rodrigo A.; Melo, Celso P. de
2014-09-28
Based on a quantum chemical valence formalism that allows the rigorous construction of best-localized molecular orbitals on specific parts of an extended system, we examined the separability of individual components of model systems relevant to the description of electron transport in molecular devices. We started by examining how to construct the maximally localized electronic density at the tip of a realistic model of a gold electrode. By varying the number of gold atoms included in the local region where to project the total electronic density, we quantitatively assess how many molecular orbitals are entirely localized in that region. We then considered a 1,4-benzene-di-thiol molecule connected to two model gold electrodes and examined how to localize the electronic density of the total system in the extended molecule, a fractional entity comprising the organic molecule plus an increasing number of the closest metal atoms. We were able to identify in a rigorous manner the existence of three physically different electronic populations, each one corresponding to a distinct set of molecular orbitals. First, there are those entirely localized in the extended molecule, then there is a second group of those completely distributed in the gold atoms external to that region, and, finally, there are those delocalized over the entire system. This latter group can be associated to the shared electronic population between the extended molecule and the rest of the system. We suggest that the treatment here presented could be useful in the theoretical analysis of the electronic transport in nanodevices whenever the use of localized molecular states are required by the physics of the specific problem, such as in cases of weak coupling and super-exchange limits.
NASA Astrophysics Data System (ADS)
Rosengrant, David
2011-01-01
Multiple representations are a valuable tool to help students learn and understand physics concepts. Furthermore, representations help students learn how to think and act like real scientists.2 These representations include: pictures, free-body diagrams,3 energy bar charts,4 electrical circuits, and, more recently, computer simulations and animations.5 However, instructors have limited choices when they want to help their students understand impulse and momentum. One of the only available options is the impulse-momentum bar chart.6 The bar charts can effectively show the magnitude of the momentum as well as help students understand conservation of momentum, but they do not easily show the actual direction. This paper highlights a new representation instructors can use to help their students with momentum and impulse—the impulse-momentum diagram (IMD).
Wilms, R Scott; Carlson, Bryan; Coons, James; Kubic, William
2008-01-01
This presentation describes the development of the proposed Process Flow Diagram (PFD) for the Tokamak Exhaust Processing System (TEP) of ITER. A brief review of design efforts leading up to the PFD is followed by a description of the hydrogen-like, air-like, and waterlike processes. Two new design values are described; the mostcommon and most-demanding design values. The proposed PFD is shown to meet specifications under the most-common and mostdemanding design values.
The Construction of Venn Diagrams.
ERIC Educational Resources Information Center
Grunbaum, Branko
1984-01-01
The study and use of "Venn diagrams" can lead to many interesting problems of a geometric, topological, or combinatorial character. The general nature of these diagrams is discussed and two new results are formulated. (JN)
NASA Astrophysics Data System (ADS)
Zhu, X. L.; Zeng, X. C.; Lei, Y. A.; Pan, B.
2004-05-01
Ab initio all-electron molecular-orbital calculations are carried out to study the structures and relative stability of low-energy silicon clusters (Sin,n=12-20). Selected geometric isomers include those predicted by Ho et al. [Nature (London) 392, 582 (1998)] based on an unbiased search with tight-binding/genetic algorithm, as well as those found by Rata et al. [Phys. Rev. Lett. 85, 546 (2000)] based on density-functional tight-binding/single-parent evolution algorithm. These geometric isomers are optimized at the Møller-Plesset (MP2) MP2/6-31G(d) level. The single-point energy at the coupled-cluster single and double substitutions (including triple excitations) [CCSD(T)] CCSD(T)/6-31G(d) level for several low-lying isomers are further computed. Harmonic vibrational frequency analysis at the MP2/6-31G(d) level of theory is also undertaken to assure that the optimized geometries are stable. For Si12-Si17 and Si19 the isomer with the lowest-energy at the CCSD(T)/6-31G(d) level is the same as that predicted by Ho et al., whereas for Si18 and Si20, the same as predicted by Rata et al. However, for Si14 and Si15, the vibrational frequency analysis indicates that the isomer with the lowest CCSD(T)/6-31G(d) single-point energy gives rise to imaginary frequencies. Small structural perturbation onto the Si14 and Si15 isomers can remove the imaginary frequencies and results in new isomers with slightly lower MP2/6-31G(d) energy; however the new isomers have a higher single-point energy at the CCSD(T)/6-31G(d) level. For most Sin (n=12-18,20) the low-lying isomers are prolate in shape, whereas for Si19 a spherical-like isomer is slightly lower in energy at the CCSD(T)/6-31G(d) level than low-lying prolate isomers.
Ab initio molecular orbital study of XO{sub 2}{sup +} (X = F, Cl, Br, I) systems
Alcami, M.; Mo, O.; Yanez, M.; Cooper, I.L.
1999-04-15
The depletion of stratospheric ozone has resulted in an increasing interest in the study of the possible reaction mechanisms responsible for its depletion. The structures and relative stabilities of the cationic forms of the halogen dioxides have been studied by means of ab initio molecular orbital calculations. For fluorine- and chlorine-containing compounds the geometries and the harmonic vibrational frequencies of all possible isomers were calculated at the QCISD/6-311+G(2d) level of theory. For bromine- and iodine-containing compounds the effective core-potential basis sets of Hay and Wadt, modified to include a set of diffuse functions and two sets of polarization functions, were employed. For all systems the final energies were obtained at the QCISD(T)/6-311+G(3df) level of theory. In addition, multiconfiguration-based methods have also been used. The relative stabilities of structures XOO{sup +} and OXO{sup +} are greatly reduced relative to those observed for the corresponding neutral species. In fact, for Cl and I derivatives, the lowest energy isomer corresponds to the symmetric OXO{sup +} open-chain species. The corresponding cyclic structures arise as local minima on the respective potential energy surfaces, but they lie much higher in energy than the OXO{sup +} open-chain form or the XOO{sup +} isomer. There are significant differences in bonding between XOO{sup +} and OXO{sup +}, the X-O interaction in OXO{sup +} being more covalent than in XOO{sup +}. There are also trends along the series that reflect the pronounced disparity between the electron affinity of F{sup +} and those of the heavier atoms of the group. FOO{sup +} species can be viewed as F({sup 2}P)-O{sub 2}{sup +} complexes, whereas XOO{sup +}(X = Br, I) species can be regarded as X{sup +}({sup 3}P)-O{sub 2} complexes. The OXO{sup +} open-chain species have an electron charge distribution similar to that of the ozone molecule, reflecting the same number of valence electrons in each case.
Contreras, Rubén H; Gotelli, Gustavo; Ducati, Lucas C; Barbosa, Thais M; Tormena, Cláudio F
2010-01-21
In this work, a new approach to studying coupling pathways for the Fermi contact term of NMR spin-spin coupling constants (SSCCs) is presented. It is based on the known form of propagating the Fermi hole through a canonical molecular orbital (CMO). It requires having an adequate spatial description of the relevant canonical molecular orbitals, which are obtained by expanding CMOs in terms of natural bond orbitals (NBOs). For detecting the relevant contributions of CMOs to a given Fermi contact (FC) pathway, the description of the FC in terms of the triplet polarization propagator (PP) is used. To appreciate the potential of this approach, dubbed FCCP-CMO (Fermi contact coupling pathways-CMO), it is applied to analyze the through-space transmission of the FC term of J(PP) SSCCs by overlap of the P lone pairs. This method can be applied using well-known quantum chemistry software without any further modification, which makes it appealing for use as a complement to SSCC measurements by NMR spectroscopy.
NASA Astrophysics Data System (ADS)
Shan, Xu; Xu, Chun-kai; Yin, Xiao-feng; Zhou, Li-xia; Xu, Ke-zun; Chen, Xiang-jun
2009-12-01
Electron momentum distributions for 4a1 orbitals of serial freon molecules CF3Cl, CF2Cl2, and CFCl3 (CFxCl4-x, x = 1-3) have been reanalyzed due to the severe discrepancies between theory and experiment in low momentum region. The tentative calculations using equilibrium geometries of molecular ions have exhibited a great improvement in agreement with the experimental data, which suggests that the molecular geometry distortion may be responsible for the observed high intensities at p < 0.5 a.u. Further analyses show that the severe discrepancies at low momentum region mainly arise from the influence of molecular geometry distortion on C-Cl bonding electron density distributions.
Correlated electronic structures and the phase diagram of hydrocarbon-based superconductors
NASA Astrophysics Data System (ADS)
Kim, Minjae; Choi, Hong Chul; Shim, Ji Hoon; Min, B. I.
2013-11-01
We have investigated correlated electronic structures and the phase diagram of electron-doped hydrocarbon molecular solids, based on the dynamical mean-field theory. We have found that the ground state of hydrocarbon-based superconductors such as electron-doped picene and coronene is a multi-band Fermi liquid, while that of non-superconducting electron-doped pentacene is a single-band Fermi liquid in the proximity of the metal-insulator transition. The size of the molecular orbital energy level splitting plays a key role in producing the superconductivity of electron-doped hydrocarbon solids. The multi-band nature of hydrocarbon solids would boost the superconductivity through the enhanced density of states at the Fermi level.
[Columbia Sensor Diagrams]. Revised
NASA Technical Reports Server (NTRS)
2003-01-01
A two dimensional graphical event sequence of the time history of relevant sensor information located in the left wing and wheel well areas of the Space Shuttle Columbia Orbiter is presented. Information contained in this graphical event sequence include: 1) Sensor location on orbiter and its associated wire bindle in X-Y plane; 2) Wire bundle routing; 3) Description of each anomalous sensor event; 4) Time annotation by (a) GMT, (b) time relative to LOS, (c) time history bar, and (d) ground track; and 5) Graphical display of temperature rise (based on delta temperature from point it is determined to be anomalous).
NASA Astrophysics Data System (ADS)
Zhong, Hanting; Feng, Xiao-Yong; Chen, Hua; Dai, Jianhui
2015-11-01
We study a twisted Hubbard tube modeling the [CrAs ]∞ structure of quasi-one-dimensional superconductors A2Cr3 As3 (A =K , Rb, Cs). The molecular-orbital bands emerging from the quasi-degenerate atomic orbitals are exactly solved. An effective Hamiltonian is derived for a region where three partially filled bands intersect the Fermi energy. The deduced local interactions among these active bands show a significant reduction compared to the original atomic interactions. The resulting three-channel Luttinger liquid shows various interaction-induced instabilities including two kinds of spin-triplet superconducting instabilities due to gapless spin excitations, with one of them being superseded by the spin-density-wave phase in the intermediate Hund's coupling regime. The implications of these results for the alkali chromium arsenides are discussed.
García-Lastra, J M; Cook, P L; Himpsel, F J; Rubio, A
2010-10-21
Porphyrins are widely used as dye molecules in solar cells. Knowing the energies of their frontier orbitals is crucial for optimizing the energy level structure of solar cells. We use near edge x-ray absorption fine structure (NEXAFS) spectroscopy to obtain the energy of the lowest unoccupied molecular orbital (LUMO) with respect to the N(1s) core level of the molecule. A systematic energy shift of the N(1s) to LUMO transition is found along a series of 3d metal octaethylporphyrins and explained by density functional theory. It is mainly due to a shift of the N(1s) level rather than a shift of the LUMO or a change in the electron-hole interaction of the core exciton.
Halasz, M.A.; Verbaarschot, J.J.; Jackson, A.D.; Shrock, R.E.; Stephanov, M.A.
1998-11-01
We analyze the phase diagram of QCD with two massless quark flavors in the space of temperature T and chemical potential of the baryon charge {mu} using available experimental knowledge of QCD, insights gained from various models, as well as general and model independent arguments including continuity, universality, and thermodynamic relations. A random matrix model is used to describe the chiral symmetry restoration phase transition at finite T and {mu}. In agreement with general arguments, this model predicts a tricritical point in the T{mu} plane. Certain critical properties at such a point are universal and can be relevant to heavy ion collision experiments. {copyright} {ital 1998} {ital The American Physical Society}
Knot probabilities in random diagrams
NASA Astrophysics Data System (ADS)
Cantarella, Jason; Chapman, Harrison; Mastin, Matt
2016-10-01
We consider a natural model of random knotting—choose a knot diagram at random from the finite set of diagrams with n crossings. We tabulate diagrams with 10 and fewer crossings and classify the diagrams by knot type, allowing us to compute exact probabilities for knots in this model. As expected, most diagrams with 10 and fewer crossings are unknots (about 78% of the roughly 1.6 billion 10 crossing diagrams). For these crossing numbers, the unknot fraction is mostly explained by the prevalence of ‘tree-like’ diagrams which are unknots for any assignment of over/under information at crossings. The data shows a roughly linear relationship between the log of knot type probability and the log of the frequency rank of the knot type, analogous to Zipf’s law for word frequency. The complete tabulation and all knot frequencies are included as supplementary data.
Wilson Loop Diagrams and Positroids
NASA Astrophysics Data System (ADS)
Agarwala, Susama; Marin-Amat, Eloi
2016-07-01
In this paper, we study a new application of the positive Grassmannian to Wilson loop diagrams (or MHV diagrams) for scattering amplitudes in N= 4 Super Yang-Mill theory (N = 4 SYM). There has been much interest in studying this theory via the positive Grassmannians using BCFW recursion. This is the first attempt to study MHV diagrams for planar Wilson loop calculations (or planar amplitudes) in terms of positive Grassmannians. We codify Wilson loop diagrams completely in terms of matroids. This allows us to apply the combinatorial tools in matroid theory used to identify positroids (non-negative Grassmannians) to Wilson loop diagrams. In doing so, we find that certain non-planar Wilson loop diagrams define positive Grassmannians. While non-planar diagrams do not have physical meaning, this finding suggests that they may have value as an algebraic tool, and deserve further investigation.
Ferenczy, György G
2013-04-01
Mixed quantum mechanics/quantum mechanics (QM/QM) and quantum mechanics/molecular mechanics (QM/MM) methods make computations feasible for extended chemical systems by separating them into subsystems that are treated at different level of sophistication. In many applications, the subsystems are covalently bound and the use of frozen localized orbitals at the boundary is a possible way to separate the subsystems and to ensure a sensible description of the electronic structure near to the boundary. A complication in these methods is that orthogonality between optimized and frozen orbitals has to be warranted and this is usually achieved by an explicit orthogonalization of the basis set to the frozen orbitals. An alternative to this approach is proposed by calculating the wave-function from the Huzinaga equation that guaranties orthogonality to the frozen orbitals without basis set orthogonalization. The theoretical background and the practical aspects of the application of the Huzinaga equation in mixed methods are discussed. Forces have been derived to perform geometry optimization with wave-functions from the Huzinaga equation. Various properties have been calculated by applying the Huzinaga equation for the central QM subsystem, representing the environment by point charges and using frozen strictly localized orbitals to connect the subsystems. It is shown that a two to three bond separation of the chemical or physical event from the frozen bonds allows a very good reproduction (typically around 1 kcal/mol) of standard Hartree-Fock-Roothaan results. The proposed scheme provides an appropriate framework for mixed QM/QM and QM/MM methods.
Ferenczy, György G
2013-04-01
The application of the local basis equation (Ferenczy and Adams, J. Chem. Phys. 2009, 130, 134108) in mixed quantum mechanics/molecular mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) methods is investigated. This equation is suitable to derive local basis nonorthogonal orbitals that minimize the energy of the system and it exhibits good convergence properties in a self-consistent field solution. These features make the equation appropriate to be used in mixed QM/MM and QM/QM methods to optimize orbitals in the field of frozen localized orbitals connecting the subsystems. Calculations performed for several properties in divers systems show that the method is robust with various choices of the frozen orbitals and frontier atom properties. With appropriate basis set assignment, it gives results equivalent with those of a related approach [G. G. Ferenczy previous paper in this issue] using the Huzinaga equation. Thus, the local basis equation can be used in mixed QM/MM methods with small size quantum subsystems to calculate properties in good agreement with reference Hartree-Fock-Roothaan results. It is shown that bond charges are not necessary when the local basis equation is applied, although they are required for the self-consistent field solution of the Huzinaga equation based method. Conversely, the deformation of the wave-function near to the boundary is observed without bond charges and this has a significant effect on deprotonation energies but a less pronounced effect when the total charge of the system is conserved. The local basis equation can also be used to define a two layer quantum system with nonorthogonal localized orbitals surrounding the central delocalized quantum subsystem.
Ferenczy, György G
2013-04-01
Mixed quantum mechanics/quantum mechanics (QM/QM) and quantum mechanics/molecular mechanics (QM/MM) methods make computations feasible for extended chemical systems by separating them into subsystems that are treated at different level of sophistication. In many applications, the subsystems are covalently bound and the use of frozen localized orbitals at the boundary is a possible way to separate the subsystems and to ensure a sensible description of the electronic structure near to the boundary. A complication in these methods is that orthogonality between optimized and frozen orbitals has to be warranted and this is usually achieved by an explicit orthogonalization of the basis set to the frozen orbitals. An alternative to this approach is proposed by calculating the wave-function from the Huzinaga equation that guaranties orthogonality to the frozen orbitals without basis set orthogonalization. The theoretical background and the practical aspects of the application of the Huzinaga equation in mixed methods are discussed. Forces have been derived to perform geometry optimization with wave-functions from the Huzinaga equation. Various properties have been calculated by applying the Huzinaga equation for the central QM subsystem, representing the environment by point charges and using frozen strictly localized orbitals to connect the subsystems. It is shown that a two to three bond separation of the chemical or physical event from the frozen bonds allows a very good reproduction (typically around 1 kcal/mol) of standard Hartree-Fock-Roothaan results. The proposed scheme provides an appropriate framework for mixed QM/QM and QM/MM methods. PMID:23281055
NASA Astrophysics Data System (ADS)
Zahedi, Ehsan
2015-05-01
The conductance and electronic transport properties of a single-molecular diode with one backbone ( 1), and two backbones in parallel ( 2) have been investigated using frontier orbital analysis, and the NEGF formalism combined with DFT. The frontier orbital analysis results demonstrate that the electron transport from one end of the studied molecules to other end is symmetrically allowed and the conductance of the molecule with two parallel backbones is more than the molecule with a single backbone. Transmission spectra study based on the NEGF-DFT of the selected molecules sandwiched between two gold (1 1 1) electrodes showed that, due to a higher coupling between the two electrodes and the molecule 2, the zero-bias conductance is more than twice that of the other molecular junction. Transmission spectra under different biases showed that the maximum constructive interference exists at the bias voltage 0.2, while in some of the biases destructive effects are observed. I- V curves showed that the rectifying directions of molecular junctions 1 and 2 are opposite.
Csaki, Csaba; Grossman, Yuval; Tanedo, Philip; Tsai, Yuhsin
2011-04-01
We present an analysis of the loop-induced magnetic dipole operator in the Randall-Sundrum model of a warped extra dimension with anarchic bulk fermions and an IR brane-localized Higgs. These operators are finite at one-loop order and we explicitly calculate the branching ratio for {mu}{yields}e{gamma} using the mixed position/momentum space formalism. The particular bound on the anarchic Yukawa and Kaluza-Klein (KK) scales can depend on the flavor structure of the anarchic matrices. It is possible for a generic model to either be ruled out or unaffected by these bounds without any fine-tuning. We quantify how these models realize this surprising behavior. We also review tree-level lepton flavor bounds in these models and show that these are on the verge of tension with the {mu}{yields}e{gamma} bounds from typical models with a 3 TeV Kaluza-Klein scale. Further, we illuminate the nature of the one-loop finiteness of these diagrams and show how to accurately determine the degree of divergence of a five-dimensional loop diagram using both the five-dimensional and KK formalism. This power counting can be obfuscated in the four-dimensional Kaluza-Klein formalism and we explicitly point out subtleties that ensure that the two formalisms agree. Finally, we remark on the existence of a perturbative regime in which these one-loop results give the dominant contribution.
NASA Astrophysics Data System (ADS)
Danel, J.-F.; Kazandjian, L.
2015-01-01
We test two isothermal-isobaric mixing rules, respectively based on excess-pressure and total-pressure equilibration, applied to the equation of state of a dense plasma. While the equation of state is generally known for pure species, that of arbitrary mixtures is not available so that the validation of accurate mixing rules, that implies resorting to first-principles simulations, is very useful. Here we consider the case of a plastic with composition C2H3 and we implement two complementary ab initio approaches adapted to the dense plasma domain: quantum molecular dynamics, limited to low temperature by its computational cost, and orbital-free molecular dynamics, that can be implemented at high temperature. The temperature and density range considered is 1-10 eV and 0.6-10 g/cm 3 for quantum molecular dynamics, and 5-1000 eV and 1-10 g/cm 3 for orbital-free molecular dynamics. Simulations for the full C2H3 mixture are the benchmark against which to assess the mixing rules, and both pressure and internal energy are compared. We find that the mixing rule based on excess-pressure equilibration is overall more accurate than that based on total-pressure equilibration; except for quantum molecular dynamics and a thermodynamic domain characterized by very low or negative excess pressures, it gives pressures which are generally within statistical error or within 1% of the exact ones. Besides, its superiority is amplified in the calculation of a principal Hugoniot.
Curtiss, L.A.
1993-04-01
The structures and energies of the molten salt vapor complexes LiAlF{sub 4} and NaAlF{sub 4} are studied using new high level ab initio molecular orbital methods. The structures are determined using Moller-Plesset perturbation theory to second-order and the total energies are determined using a recently introduced modification of Gaussian-2 (G2) theory. The total energies are used to determine relative energies of the corner-, edge-, and face-bridged structures and accurate reaction energies. The results are compared to previous theoretical and experimental studies.
Curtiss, L.A.
1993-01-01
The structures and energies of the molten salt vapor complexes LiAlF[sub 4] and NaAlF[sub 4] are studied using new high level ab initio molecular orbital methods. The structures are determined using Moller-Plesset perturbation theory to second-order and the total energies are determined using a recently introduced modification of Gaussian-2 (G2) theory. The total energies are used to determine relative energies of the corner-, edge-, and face-bridged structures and accurate reaction energies. The results are compared to previous theoretical and experimental studies.
Nakata, Hiroya; Fedorov, Dmitri G.; Yokojima, Satoshi; Kitaura, Kazuo; Sakurai, Minoru; Nakamura, Shinichiro
2014-04-14
We extended the fragment molecular orbital (FMO) method interfaced with density functional theory (DFT) into spin unrestricted formalism (UDFT) and developed energy gradients for the ground state and single point excited state energies based on time-dependent DFT. The accuracy of FMO is evaluated in comparison to the full calculations without fragmentation. Electronic excitations in solvated organic radicals and in the blue copper protein, plastocyanin (PDB code: 1BXV), are reported. The contributions of solvent molecules to the electronic excitations are analyzed in terms of the fragment polarization and quantum effects such as interfragment charge transfer.
Nakata, Hiroya; Fedorov, Dmitri G; Yokojima, Satoshi; Kitaura, Kazuo; Sakurai, Minoru; Nakamura, Shinichiro
2014-04-14
We extended the fragment molecular orbital (FMO) method interfaced with density functional theory (DFT) into spin unrestricted formalism (UDFT) and developed energy gradients for the ground state and single point excited state energies based on time-dependent DFT. The accuracy of FMO is evaluated in comparison to the full calculations without fragmentation. Electronic excitations in solvated organic radicals and in the blue copper protein, plastocyanin (PDB code: 1BXV), are reported. The contributions of solvent molecules to the electronic excitations are analyzed in terms of the fragment polarization and quantum effects such as interfragment charge transfer.
NASA Astrophysics Data System (ADS)
Yamagishi, Kenji; Yamamoto, Keiko; Yamada, Sachiko; Tokiwa, Hiroaki
2006-03-01
Fragment molecular orbital-interfragment interaction energy calculations of the vitamin D receptor (VDR)/1α,25-dihydroxyvitamin D 3 complex were utilized to assign functions of key residues of the VDR. Only one residue forms a significant interaction with the corresponding hydroxy group of the ligand, although two residues are located around each hydroxy group. The degradation of binding affinity for derivatives upon removal of a hydroxy group is closely related to the trend in the strength of the hydrogen bonds. Type II hereditary rickets due to an Arg274 point mutation is caused by the lack of the strongest hydrogen bond.
ERIC Educational Resources Information Center
Magnasco, Valerio
2008-01-01
Orbital exponent optimization in the elementary ab-initio VB calculation of the ground states of H[subscript 2][superscript +], H[subscript 2], He[subscript 2][superscript +], He[subscript 2] gives a fair description of the exchange-overlap component of the interatomic interaction that is important in the bond region. Correct bond lengths and…
Cini, R; Pogni, R; Basosi, R; Donati, A; Rossi, C; Sabadini, L; Rollo, L; Lorenzini, S; Gelli, R; Marcolongo, R
1995-01-01
The oxygen radical scavenger activity (ORSA) of [Cu(II)(Pir)(2)] (HPir = Piroxicam = 4-hydroxy -2- methyl -N-2- pyridyl -2H- 1,2-benzothiazine -3- carboxamide 1,1-dioxide) was determined by chemiluminescence of samples obtained by mixing human neutrophils (from healthy subjects) and [Cu(II)(Pir)(2)(DMF)(2)] (DMF = N,N -dimethylformammide) in DMSO/GLY/PBS (2:1:2, v/v) solution (DMSO = dimethylsulfoxide, GLY = 1,2,3-propantriol, PBS = Dulbecco's buffer salt solution). The ratio of the residual radicals, for the HPir (1.02.10(-4)M) and [Cu(II)(Pir)(2)(DMF)(2)] (1.08.10(-5)M)/HPir (8.01.10-(-5)M) systems was higher than 12 (not stimulated) [excess of piroxicam was added (Cu/Pir molar ratio approximately 1:10) in order to have most of the metal complexed as bischelate]. In contrast, the ratio of residual radicals for the CuCl(2) (1.00.10(-5)M) and [Cu(II)(Pir)(2)(DMF)(2)] (1.08.10(-5)M)/Hpir (8.01.10(-5)M)system was 5. The [Cu(II)(Pir)(2)] compound is therefore a stronger radical scavenger than either HPir or CuCl(2). A molecular mechanics (MM) analysis of the gas phase structures of neutral HPir, its zwitterionic (HPir(+-)) and anionic (Pir(-)) forms, and some Cu(II)-piroxicam complexes based on X-ray structures allowed calculation of force constants. The most stable structure for HPir has a ZZZ conformation similar to that found in the Cu(II) (and Cd(II) complexes) in the solid state as well as in the gas phase. The structure is stabilized by a strong H bond which involves the N(amide)-H and O(enolic) groups. The MM simulation for the [Cu(II)(Pir)(2)(DMF)(2)] complex showed that two high repulsive intramolecular contacts exist between a pyridyl hydrogen atom of one Pir(-) molecule with the O donor of the other ligand. These interactions activate a transition toward a pseudo-tetrahedral geometry, in the case the apical ligands are removed. On refluxing a suspension of [Cu(II)(Pir)(2)(DMF)(2)] in acetone a brown microcystalline solid with the Cu(Pir)(2).0.5DMF
NASA Astrophysics Data System (ADS)
Koyama, Yuka; Ueno-Noto, Kaori; Takano, Keiko
2013-07-01
In HIV-1 infection, human antibody 2G12 is capable of recognizing the high-mannose glycans on the HIV-1 surface glycoprotein, gp120. To investigate the ligand binding mechanisms of antibody 2G12 with glycans aiming for the contribution to the medications, we carried out classical molecular dynamics (MD) simulations and ab initio fragment molecular orbital (FMO) calculations on the antibody 2G12 complex with its high-mannose ligand. We found that Mannose D1 of the ligand had the largest binding affinity with the antibody, which was well consistent with experimental reports. Furthermore, significant roles of Mannose 4 and 4‧ in the ligand binding were theoretically indicated.
Serianni, A.S.; Chipman, D.M.
1987-09-02
Ab initiao molecular orbital calculations have been conducted on four tetrofuranose anomers, ..cap alpha..- and ..beta..-D-erythrofuranose and ..cap alpha..- and ..beta..-D-threofuranose, to study the effect of ring conformation on molecular parameters (bond lengths, bond angles, bond torsions) and on total energies. Geometric optimizations of envelope and planar conformers were conducted using the STO-3G basis set; single-point calculations were also performed with the 3-21G basis set. Preferred solution conformations deduced from previous NMR studies are in good agreement with those predicted by calculation, indicating that the intrinsic structures of these furanoses dictate their preferred geometries, and that solvation by water (/sup 2/H/sub 2/O) does not appear to be a major conformational determinant. The ..beta..-D-erythro configuration, which is structurally related to the ..beta..-D-ribo configuration found in RNA, was found to have significantly different conformational behavior from the other three configurations.
Program Synthesizes UML Sequence Diagrams
NASA Technical Reports Server (NTRS)
Barry, Matthew R.; Osborne, Richard N.
2006-01-01
A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.
Feynchois:. a Feynman Diagram Generator
NASA Astrophysics Data System (ADS)
Choi, Chul-Woo; Gonsalves, Richard J.
A Feynman diagram generator, named FeynChois, is described. It provides the user with a full GUI (Graphical User Interface) environment which enables the generation diagrams automatically with several mouse operations. The diagram generator is built on an Application Programming Interface (API) called ViewableBeans which provides a framework for programming graphically representable objects. We also present a means for describing Feynman rules in a computer friendly manner using the XML (Extensible Markup Language) format.
Burakovsky, Leonid; Kress, Joel D.; Collins, Lee A.
2012-05-31
Mass transport properties for LiD-U mixtures were calculated using a pressure matching mixture rule for the mixing of LiD and of U properties simulated with Orbital Free Molecular Dynamics (OFMD). The mixing rule was checked against benchmark OFMD simulations for the fully interacting three-component (Li, D, U) system. To obtain transport coefficients for LiD-U mixtures of different (LiD){sub x}U{sub (1-x)} compositions as functions of temperature and mixture density is a tedious task. Quantum molecular dynamics (MD) simulations can be employed, as in the case LiD or U. However, due to the presence of the heavy constituent U, such simulations proceed so slowly that only a limited number of numerical data points in the (x, {rho}, T) phase space can be obtained. To finesse this difficulty, transport coefficients for a mixture can be obtained using a pressure-matching mixing rule discussed. For both LiD and U, the corresponding transport coefficients were obtained earlier from quantum molecular dynamics simulations. In these simulations, the quantum behavior of the electrons was represented using an orbital free (OF) version of density functional theory, and ions were advanced in time using classical molecular dynamics. The total pressure of the system, P = nk{sub B}T/V + P{sub e}, is the sum of the ideal gas pressure of the ions plus the electron pressure. The mass self-diffusion coefficient for species {alpha}, D{sub {alpha}}, the mutual diffusion coefficient for species {alpha} and {beta}, D{alpha}{beta}, and the shear viscosity, {eta}, are computed from the appropriate autocorrelation function. The details of similar QMD calculations on LiH are described in Ref. [1] for 0.5 eV < T < 3 eV, and in Ref. [2] for 2 eV < T < 6 eV.
Gwaltney, Steven R; Rosokha, Sergiy V; Head-Gordon, Martin; Kochi, Jay K
2003-03-19
The highly disparate rates of aromatic nitrosation and nitration, despite the very similar (electrophilic) properties of the active species: NO(+) and NO(2)(+) in Chart 1, are quantitatively reconciled. First, the thorough mappings of the potential-energy surfaces by high level (ab initio) molecular-orbital methodologies involving extensive coupled-cluster CCSD(T)/6-31G optimizations establish the intervention of two reactive intermediates in nitration (Figure 8) but only one in nitrosation (Figure 7). Second, the same distinctive topologies involving double and single potential-energy minima (Figures 6 and 5) also emerge from the semiquantitative application of the Marcus-Hush theory to the transient spectral data. Such a striking convergence from quite different theoretical approaches indicates that the molecular-orbital and Marcus-Hush (potential-energy) surfaces are conceptually interchangeable. In the resultant charge-transfer mechanism, the bimolecular interactions of arene donors with both NO(+) and NO(2)(+) spontaneously lead (barrierless) to pi-complexes in which electron transfer is concurrent with complexation. Such a pi-complex in nitration is rapidly converted to the sigma-complex, whereas this Wheland adduct in nitrosation merely represents a high energy (transition-state) structure. Marcus-Hush analysis thus demonstrates how the strongly differentiated (arene) reactivities toward NO(+) and NO(2)(+) can actually be exploited in the quantitative development of a single coherent (electron-transfer) mechanism for both aromatic nitrosation and nitration.
NASA Technical Reports Server (NTRS)
Hurlbert, Eric A.
2001-01-01
This slide presentation reviews the Space Shuttle's On-Orbit Propulsion systems: the Orbital Maneuvering System (OMS) and the Reaction Control System (RCS). The functions of each of the systems is described, and the diagrams of the systems are presented. The OMS/RCS thruster is detailed and a trade study comparison of non-toxic propellants is presented.
Ganesan, Aravindhan; Wang, Feng; Falzon, Chantal
2011-02-01
Intramolecular interactions between fragments of L-phenylalanine, i.e., phenyl and alaninyl, have been investigated using dual space analysis (DSA) quantum mechanically. Valence space photoelectron spectra (PES), orbital energy topology and correlation diagram, as well as orbital momentum distributions (MDs) of L-phenylalanine, benzene and L-alanine are studied using density functional theory methods. While fully resolved experimental PES of L-phenylalanine is not yet available, our simulated PES reproduces major features of the experimental measurement. For benzene, the simulated orbital MDs for 1e(1g) and 1a(2u) orbitals also agree well with those measured using electron momentum spectra. Our theoretical models are then applied to reveal intramolecular interactions of the species on an orbital base, using DSA. Valence orbitals of L-phenylalanine can be essentially deduced into contributions from its fragments such as phenyl and alaninyl as well as their interactions. The fragment orbitals inherit properties of their parent species in energy and shape (ie., MDs). Phenylalanine orbitals show strong bonding in the energy range of 14-20 eV, rather than outside of this region. This study presents a competent orbital based fragments-in-molecules picture in the valence space, which supports the fragment molecular orbital picture and building block principle in valence space. The optimized structures of the molecules are represented using the recently developed interactive 3D-PDF technique.
Diagonal Slices of 3D Young Diagrams in the Approach of Maya Diagrams
NASA Astrophysics Data System (ADS)
Cai, Li-Qiang; Wang, Li-Fang; Wu, Ke; Yang, Jie
2014-09-01
According to the correspondence between 2D Young diagrams and Maya diagrams and the relation between 2D and 3D Young diagrams, we construct 3D Young diagrams in the approach of Maya diagrams. Moreover, we formulate the generating function of 3D Young diagrams, which is the MacMahon function in terms of Maya diagrams.
ERIC Educational Resources Information Center
Barnum, Dennis W.
1982-01-01
Potential-pH diagrams show the domains of redoxpotential and pH in which major species are most stable. Constructing such diagrams provides students with opportunities to decide what species must be considered, search literature for equilibrium constants and free energies of formation, and practice in using the Nernst equation. (Author/JN)
NASA Astrophysics Data System (ADS)
Trautwein, A. X.; Bill, E.; Bläs, R.; Lauer, S.; Winkler, H.; Kostikas, A.
1985-04-01
The electronic structures of mononuclear Fe-S complexes with a FeIIS4 core and of binuclear Fe-Mo-S complexes containing the FeS2Mo core have been calculated by a semiempirical molecular orbital method (iterative extended Hückel theory), followed by a spin-orbit coupling calculation on the five highest occupied iron-like molecular orbitals. Fine structure and hyperfine structure tensors and parameters (g, D, E, A, and electric field gradient) have been calculated and compared with data from spin-Hamiltonian analysis of Mössbauer measurements. For the mononuclear complex anions [Fe(SPh)4]2- and [Fe(dts)2]2- it was found that Vẑẑ is negative, D positive, and that the magnetic anisotropy places the preferred direction of the hyperfine magnetic field perpendicular to the Vẑẑ direction in agreement with spin-Hamiltonian results. The similarity of parameters of [Fe(SPh)4]2- and reduced rubredoxin (Rdred) confirms the suggestion that this anion has a ground electronic state practically identical to Rdred. The complex anion [Fe(dts)2]2- shows smaller anisotropy, and due to the fact that the orbital ground state is energetically not well separated from higher states in this case a strong temperature dependence of the quadrupole splitting is observed. For the binuclear complex anions [(SPh)2FeS2MoS2]2-, [S5FeS2MoS2]2-, and [Cl2FeS2MoS2]2- it was found that d is negative and Vẑẑ is positive. A specific feature of these binuclear Fe-Mo-S complexes is that Vẑẑ is directed perpendicular to the Fe-Mo line. (This theoretical result is confirmed by single crystal Mössbauer studies on [Cl2FeS2MoS2]2-; see the following paper in this journal.) The preferred direction of the magnetic hyperfine field is close to the Vẑẑ axis. The correlation of calculated values of ρ(0) and isomer shifts for mononuclear and binuclear compounds confirms the role of MoS2-4 as a charge withdrawing ligand.
On-orbit flight control algorithm description
NASA Technical Reports Server (NTRS)
1975-01-01
Algorithms are presented for rotational and translational control of the space shuttle orbiter in the orbital mission phases, which are external tank separation, orbit insertion, on-orbit and de-orbit. The program provides a versatile control system structure while maintaining uniform communications with other programs, sensors, and control effectors by using an executive routine/functional subroutine format. Software functional requirements are described using block diagrams where feasible, and input--output tables, and the software implementation of each function is presented in equations and structured flow charts. Included are a glossary of all symbols used to define the requirements, and an appendix of supportive material.
Space Shuttle Orbiter auxiliary power unit status
NASA Technical Reports Server (NTRS)
Reck, M.; Loken, G.; Horton, J.; Lukens, W.; Scott, W.; Baughman, J.; Bauch, T.
1991-01-01
An overview of the United States Space Shuttle Orbiter APU, which provides power to the Orbiter vehicle hydraulic system, is presented. Three complete APU systems, each with its own separate fuel system, supply power to three dedicated hydraulic systems. These in turn provide power to all Orbiter vehicle critical flight functions including launch, orbit, reentry, and landing. The basic APU logic diagram is presented. The APU includes a hydrazine-powered turbine that drives a hydraulic pump and various accessories through a high-speed gearbox. The APU also features a sophisticated thermal management system designed to ensure safe and reliable operation in the various launch, orbit, reentry, and landing environments.
Space Shuttle Orbiter auxiliary power unit status
NASA Astrophysics Data System (ADS)
Reck, M.; Loken, G.; Horton, J.; Lukens, W.; Scott, W.; Baughman, J.; Bauch, T.
An overview of the United States Space Shuttle Orbiter APU, which provides power to the Orbiter vehicle hydraulic system, is presented. Three complete APU systems, each with its own separate fuel system, supply power to three dedicated hydraulic systems. These in turn provide power to all Orbiter vehicle critical flight functions including launch, orbit, reentry, and landing. The basic APU logic diagram is presented. The APU includes a hydrazine-powered turbine that drives a hydraulic pump and various accessories through a high-speed gearbox. The APU also features a sophisticated thermal management system designed to ensure safe and reliable operation in the various launch, orbit, reentry, and landing environments.
Azar, R. Julian; Head-Gordon, Martin
2012-01-14
We propose a wave function-based method for the decomposition of intermolecular interaction energies into chemically-intuitive components, isolating both mean-field- and explicit correlation-level contributions. We begin by solving the locally-projected self-consistent field for molecular interactions equations for a molecular complex, obtaining an intramolecularly polarized reference of self-consistently optimized, absolutely-localized molecular orbitals (ALMOs), determined with the constraint that each fragment MO be composed only of atomic basis functions belonging to its own fragment. As explicit inter-electronic correlation is integral to an accurate description of weak forces underlying intermolecular interaction potentials, namely, coordinated fluctuations in weakly interacting electronic densities, we add dynamical correlation to the ALMO polarized reference at the coupled-cluster singles and doubles level, accounting for explicit dispersion and charge-transfer effects, which map naturally onto the cluster operator. We demonstrate the stability of energy components with basis set extension, follow the hydrogen bond-breaking coordinate in the C{sub s}-symmetry water dimer, decompose the interaction energies of dispersion-bound rare gas dimers and other van der Waals complexes, and examine charge transfer-dominated donor-acceptor interactions in borane adducts. We compare our results with high-level calculations and experiment when possible.
Azar, R Julian; Head-Gordon, Martin
2012-01-14
We propose a wave function-based method for the decomposition of intermolecular interaction energies into chemically-intuitive components, isolating both mean-field- and explicit correlation-level contributions. We begin by solving the locally-projected self-consistent field for molecular interactions equations for a molecular complex, obtaining an intramolecularly polarized reference of self-consistently optimized, absolutely-localized molecular orbitals (ALMOs), determined with the constraint that each fragment MO be composed only of atomic basis functions belonging to its own fragment. As explicit inter-electronic correlation is integral to an accurate description of weak forces underlying intermolecular interaction potentials, namely, coordinated fluctuations in weakly interacting electronic densities, we add dynamical correlation to the ALMO polarized reference at the coupled-cluster singles and doubles level, accounting for explicit dispersion and charge-transfer effects, which map naturally onto the cluster operator. We demonstrate the stability of energy components with basis set extension, follow the hydrogen bond-breaking coordinate in the C(s)-symmetry water dimer, decompose the interaction energies of dispersion-bound rare gas dimers and other van der Waals complexes, and examine charge transfer-dominated donor-acceptor interactions in borane adducts. We compare our results with high-level calculations and experiment when possible.
Suresh, S; Gunasekaran, S; Srinivasan, S
2015-03-01
The solid phase FT-IR and FT-Raman spectra of 4-Hydroxy-2-methyl-N-(2-pyridinyl)-2H-1,2-benzothiazine-3-carboxamide-1,1-dioxide (Piroxicam) have been recorded in the region 4000-400 and 4000-100cm(-1) respectively. The molecular geometry, harmonic vibrational frequencies and bonding features of piroxicam in the ground state have been calculated by Hartree-Fock (HF) and density functional theory (DFT) methods using 6-311++G(d,p) basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimental obtained by FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of the title compound has been made on the basis of the calculated potential energy distribution (PED). The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MESP) are also performed. The linear polarizability (α) and the first order hyper polarizability (β) values of the title compound have been computed. The molecular stability arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.
NASA Astrophysics Data System (ADS)
Suresh, S.; Gunasekaran, S.; Srinivasan, S.
2015-03-01
The solid phase FT-IR and FT-Raman spectra of 4-Hydroxy-2-methyl-N-(2-pyridinyl)-2H-1,2-benzothiazine-3-carboxamide-1,1-dioxide (Piroxicam) have been recorded in the region 4000-400 and 4000-100 cm-1 respectively. The molecular geometry, harmonic vibrational frequencies and bonding features of piroxicam in the ground state have been calculated by Hartree-Fock (HF) and density functional theory (DFT) methods using 6-311++G(d,p) basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimental obtained by FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of the title compound has been made on the basis of the calculated potential energy distribution (PED). The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MESP) are also performed. The linear polarizability (α) and the first order hyper polarizability (β) values of the title compound have been computed. The molecular stability arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.
Prabavathi, N; Nilufer, A; Krishnakumar, V
2013-10-01
The FTIR and FT-Raman spectra of Isoxanthopterin have been recorded in the region 4000-450 and 4000-100 cm(-1), respectively. The optimized geometry, frequency and intensity of the vibrational bands of Isoxanthopterin were obtained by the density functional theory (DFT) using 6-311++G(d,p) basis set. The harmonic vibrational frequencies were scaled and compared with experimental values. The observed and the calculated frequencies are found to be in good agreement. The (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecule were also calculated using the gauge independent atomic orbital (GIAO) method. The UV-visible spectrum was also recorded and compared with the theoretical values. The calculated HOMO and LUMO energies show that charge transfer occurs within molecule. The first order hyperpolarizability (β0), related properties (β, α0 and Δα) and the Mulliken charges of the molecule were also computed using DFT calculations. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The results show that charge in electron density (ED) in the σ* and π* antibonding orbitals and second order delocalization energies (E2) confirms the occurrence of intramolecular charge transfer (ICT) within the molecule. Information about the charge density distribution of the molecule and its chemical reactivity has been obtained by mapping molecular electrostatic potential surface. In addition, the non-linear optical properties were discussed from the dipole moment values and excitation wavelength in the UV-visible region.
Chesky, P.T.; Hall, M.B.
1983-10-01
Gas-phase, ultraviolet photoelectron (PE) spectra and molecular orbital (MO) calculations are reported for SCo/sub 3/(CO)/sub 9/, SH/sub n-//sub 1/Fe/sub n/Co/sub 3//sub -n/(CO)/sub 9/ (n = 1-3), S/sub 2/Fe/sub 3/(CO)/sub 9/, and SH/sub 2/M/sub 3/(CO)/sub 9/ (M = Fe, Ru, Os). The first PE spectra reported for mixed-metal clusters are included in this series. As Co atoms are replaced by the isoelectronic FeH unit, the spectra show the loss of a Co band and the appearance of an Fe band. This phenomenon suggests that the d bands localize upon ionization. In a comparison with the PE spectrum of M/sub 3/(CO)/sub 12/ (M = Fe, Ru, Os), the major spectral changes for SH/sub 2/M/sub 3/(CO)/sub 9/ (M = Fe, Ru, Os) are the loss of a band corresponding to direct M-M interactions and the appearance of bands due to a mixture of energy-equivalent M-H-M and M-S interactions. The spectra also show a substantial rearrangement of the bands due to the t/sub 2g/-like electrons, which are usually considered M-CO ..pi.. bonding. An antibonding interaction between a S orbital and the t/sub 2g/-like orbitals is responsible for a unique band in the spectra which occurs at high ionization energy between the M-M bonding band and the main t/sub 2//sub g/-like band. 12 figures, 9 tables
Trachtman, Mendel; Markham, George D.; Glusker, Jenny P.; George, Philip; Bock, Charles W.
1998-08-24
The formation and properties of a wide range of metal ion monohydrates, M(n)()(+)-OH(2), where n = 1 and 2, have been studied by ab initio molecular orbital calculations at the MP2(FULL)/6-311++G//MP2(FULL)/6-311++G and CCSD(T)(FULL)/6-311++G//MP2(FULL)/6-311++G computational levels. The ions M are from groups 1A, 2A, 3A, and 4A in the second, third, and fourth periods of the periodic table and the first transition series. Structural parameters, vibrational frequencies, bonding enthalpies, orbital occupancies and energies, and atomic charge distributions are reported. Trends in these properties are correlated with the progressive occupancy of the s, p, and d orbitals. Except for K(+)-OH(2) and Ca(2+)-OH(2), the O-H bond lengths and HOH angles are greater in the hydrates than in unbound water. The M-O bond lengths decrease proceeding from group 1A --> 4A but become larger in proceeding from the second --> fourth period. The bonding enthalpies, are found to be inversely linearly dependent on the M-O bond length M(n)()(+) according to equations of the form = A + B(1/M-O) for n = 1 and n = 2. Within each monohydrate the distribution of atomic charge reveals a small but definite transfer of charge from water to the metal ion. Compared to unbound water there is, in a metal-ion-bound water complex, an increase in the electronic (negative) charge on the oxygen atom, accompanied by a (significantly) larger decrease in the electronic charge on the hydrogen atoms. The bonding of the water molecule, although electrostatic in origin, is thus more complex than a simple interaction between a point charge on the metal ion, and the water dipole.
Azhagiri, S; Jayakumar, S; Gunasekaran, S; Srinivasan, S
2014-04-24
In the present study, we made an attempt to calculate the energy gap, molecular dipole moment and first hyperpolarizability of 2-nitroaniline (2NA) and 4-methoxy-2-nitroaniline (4M2N) with a basis set 6-31G (d, p) function has been employed at density functional theory (DFT) methods. Geometry optimizations was carried out with DFT-B3LYP/6-31G (d, p), the results have revealed that intramolecular hydrogen bonding present in both the molecular system. We analyzed the energy gap, molecular dipole moment and hyperpolarizability changes due to substitution effect of the methoxy group in 2NA molecule. It is confirmed that strong electron acceptor and donor groups in a material yield higher NLO response.
Yamazaki, Masakazu; Oishi, Keiya; Nakazawa, Hiroyuki; Zhu, Chaoyuan; Takahashi, Masahiko
2015-03-13
We report a time-resolved (e, 2e) experiment on the deuterated acetone molecule in the S2 Rydberg state with a lifetime of 13.5 ps. The acetone S2 state was prepared by a 195 nm pump laser and probed with electron momentum spectroscopy using a 1.2 keV incident electron beam of 1 ps temporal width. In spite of the low data statistics as well as of the limited time resolution (±35 ps) due to velocity mismatch, the experimental results clearly demonstrate that electron momentum spectroscopy measurements of short-lived transient species are feasible, opening the door to time-resolved orbital imaging in momentum space.
NASA Astrophysics Data System (ADS)
James, C.; Pettit, G. R.; Nielsen, O. F.; Jayakumar, V. S.; Joe, I. Hubert
2008-10-01
The NIR-FT Raman and FT-IR spectral studies of the novel antineoplastic and antiangiogenesis substance comprestatin A-4 prodrug (CA4P) were carried out. The equilibrium geometry, various bonding features and harmonic vibrational frequencies of CA4P have been investigated with the help of B3LYP density functional theory (DFT) method. The most preferred cis-configuration for its bioactivity has been demonstrated on the basis of torsional potential energy surface (PES) scan studies. Stability of the molecule arising from hyperconjugative interactions leading to its bioactivity, charge delocalization and mesomeric effects have been analyzed using natural bond orbital (NBO) analysis. Detailed assignments of the vibrational spectra have been made with the aid of theoretically predicted vibrational frequencies. The optimized geometry shows near-planarity of phenyl rings and perpendicular conformation of meta substituted methoxy group. The vibrational analysis confirms the differently acting ring modes, steric repulsion, π conjugation and back-donation.
NASA Astrophysics Data System (ADS)
Sebastian, S.; Sylvestre, S.; Jayarajan, D.; Amalanathan, M.; Oudayakumar, K.; Gnanapoongothai, T.; Jayavarthanan, T.
2013-01-01
In this work, we report harmonic vibrational frequencies, molecular structure, NBO and HOMO, LUMO analysis of Umbelliferone also known as 7-hydroxycoumarin (7HC). The optimized geometric bond lengths and bond angles obtained by computation (monomer and dimmer) shows good agreement with experimental XRD data. Harmonic frequencies of 7HC were determined and analyzed by DFT utilizing 6-311+G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the help of Normal Coordinate Analysis (NCA) following the Scaled Quantum Mechanical Force Field Methodology (SQMFF). The change in electron density (ED) in the σ* and π* antibonding orbitals and stabilization energies E(2) have been calculated by Natural Bond Orbital (NBO) analysis to give clear evidence of stabilization originating in the hyperconjugation of hydrogen-bonded interaction. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) complements with the experimental findings. The simulated spectra satisfactorily coincides with the experimental spectra. Microbial activity of studied compounds was tested against Staphylococcus aureus, Streptococcus pyogenes, Bacillus subtilis, Escherichia coli, Psuedomonas aeruginosa, Klebsiella pneumoniae, Proteus mirabilis, Shigella flexneri, Salmonella typhi and Enterococcus faecalis.
Cobar, Erika A; Horn, Paul R; Bergman, Robert G; Head-Gordon, Martin
2012-11-28
Using the ωB97X-D and B3LYP density functionals, the absolutely localized molecular orbital energy decomposition method (ALMO-EDA) is applied to the water dimer through pentamer, 13-mer and 17-mer clusters. Two-body, three-body, and total interaction energies are decomposed into their component energy terms: frozen density interaction energy, polarization energy, and charge transfer energy. Charge transfer, polarization, and frozen orbital interaction energies are all found to be significant contributors to the two-body and total interaction energies; the three-body interaction energies are dominated by polarization. Each component energy term for the two-body interactions is highly dependent on the associated hydrogen bond distance. The favorability of the three-body terms associated with the 13- and 17-mer structures depends on the hydrogen-donor or hydrogen-acceptor roles played by each of the three component waters. Only small errors arise from neglect of three-body interactions without two adjacent water molecules, or beyond three-body interactions. Interesting linear correlations are identified between the contributions of charge-transfer and polarization terms to the two and three-body interactions, which permits elimination of explicit calculation of charge transfer to a good approximation.
Porchelvi, E Elamurugu; Muthu, S
2015-01-01
The thiosemicarbazone compound, Salicylaldehyde p-methylphenylthiosemicarbazone (abbreviated as SMPTSC) was synthesized and characterized by FTIR, FT-Raman and UV. Density functional (DFT) calculations have been carried out for the title compound by performing DFT level of theory using B3LYP/6-31++G(d,p) basis set. The molecular geometry and vibrational frequencies were calculated and compared with the experimental data. The detailed interpretation of the vibrational spectra has been carried out with aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology. The electronic dipole moment (μD) and the first hyperpolarizability (βtot) values of the investigated molecule were computed using density functional theory (DFT/B3LYP) with 6-311++G(d,p) basis set. The stability and charge delocalization of the molecule was studied by natural bond orbital (NBO) analysis. Thearomaticities of the phenyl rings were studied using the standard harmonic oscillator model of aromaticity (HOMA) index. Mulliken population analysis on atomic charges is also calculated. The molecule orbital contributions are studied by density of energy states (DOSs).
Scattering equations and Feynman diagrams
NASA Astrophysics Data System (ADS)
Baadsgaard, Christian; Bjerrum-Bohr, N. E. J.; Bourjaily, Jacob L.; Damgaard, Poul H.
2015-09-01
We show a direct matching between individual Feynman diagrams and integration measures in the scattering equation formalism of Cachazo, He and Yuan. The connection is most easily explained in terms of triangular graphs associated with planar Feynman diagrams in φ 3-theory. We also discuss the generalization to general scalar field theories with φ p interactions, corresponding to polygonal graphs involving vertices of order p. Finally, we describe how the same graph-theoretic language can be used to provide the precise link between individual Feynman diagrams and string theory integrands.
Sure, Rebecca; Brandenburg, Jan Gerit; Grimme, Stefan
2016-04-01
In quantum chemical computations the combination of Hartree-Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double-zeta quality is still widely used, for example, in the popular B3LYP/6-31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean-field methods. PMID:27308221
NASA Astrophysics Data System (ADS)
Gonzalez Del Rio, Beatriz; Gonzalez Tesedo, Luis Enrique
We report results of an orbital-free ab initio molecular dynamics (OF-AIMD) study of the free liquid surface of Sn at 1000 K. A key ingredient in the OF-AIMD method is the local ionic pseudopotential describing the ions-valence electrons interaction. We have developed a force-matching method to derive a local ionic pseudopotential suitable to account for a rapidly varying density system, such as in a free liquid surface. We obtain very good results for several structural properties. We have also studied the evolution of some dynamical properties when going from the central region (where the system behaves like the bulk liquid) towards the free liquid surface. We aknowledge the spanish MSI (Project FIS2012-33126) and the University of Valladolid for the provision of a PhD grant.
NASA Astrophysics Data System (ADS)
Hofto, Laura; Hofto, Meghan; Cross, Jessica; Cafiero, Mauricio
2007-09-01
Many diseases can be traced to point mutations in the DNA coding for specific enzymes. These point mutations result in the change of one amino acid residue in the enzyme. We have developed a model using simple molecular orbital calculations which can be used to quantitatively determine the change in interaction between the enzyme's active site and necessary ligands upon mutation. We have applied this model to three hydroxylase proteins: phenylalanine hydroxylase, tyrosine hydroxylase, and tryptophan hydroxylase, and we have obtained excellent correlation between our results and observed disease symptoms. Furthermore, we are able to use this agreement as a baseline to screen other mutations which may also cause onset of disease symptoms. Our focus is on systems where the binding is due largely to dispersion, which is much more difficult to model inexpensively than pure electrostatic interactions. Our calculations are run in parallel on a sixteen processor cluster of 64-bit Athlon processors.
Trout, Chad C; Tambach, T J; Kubicki, James D
2005-09-01
The aromatic carboxylic acids benzoic, salicylic and phthalic acid were used to study the interaction of soluble organics compounds with metal cations. To accomplish this, we have developed methods for studying the carboxylic acids using UV resonance Raman (UVRR) combined with molecular orbital density functional theory calculations. The pH values of the acid solutions were based on the pK(a)'s for the different acids to examine the neutral and charged species. Deprotonation of the organic acids was detectable down to 10(-4)M using UVRR (two orders of magnitude lower than previous vibrational spectroscopy studies). Limitations to decreasing the concentration lower using the current UVRR facilities are discussed. Two methods were used to calculate the optimized geometry and frequencies of the acids: explicit and continuum solvation. The frequencies from the experimental spectra were then compared to the theoretical results obtained from the two methods.
NASA Astrophysics Data System (ADS)
Trout, Chad C.; Tambach, T. J.; Kubicki, James D.
2005-09-01
The aromatic carboxylic acids benzoic, salicylic and phthalic acid were used to study the interaction of soluble organics compounds with metal cations. To accomplish this, we have developed methods for studying the carboxylic acids using UV resonance Raman (UVRR) combined with molecular orbital density functional theory calculations. The pH values of the acid solutions were based on the p Ka's for the different acids to examine the neutral and charged species. Deprotonation of the organic acids was detectable down to 10 -4 M using UVRR (two orders of magnitude lower than previous vibrational spectroscopy studies). Limitations to decreasing the concentration lower using the current UVRR facilities are discussed. Two methods were used to calculate the optimized geometry and frequencies of the acids: explicit and continuum solvation. The frequencies from the experimental spectra were then compared to the theoretical results obtained from the two methods.
Yamamoto, S. Faculty of Liberal Arts, Chukyo University, Kaizu-cho, Toyota 470-03 ); Yamaguchi, K. ); Nasu, K. )
1990-07-01
{ital Ab} {ital initio} molecular-orbital calculations for CuO{sub 6} clusters have been performed to elucidate the electronic structures of undoped and doped copper oxides, which are of current interest in relation to high-{ital T}{sub {ital c}} superconductivity. The electron correlation effects for these species are thoroughly investigated by the full-valence configuration-interaction method and the complete-active-space self-consistent-field method. The electron correlation effect is relatively simple for the {ital A}{sub {ital g}} state ({sigma} hole), whereas pair excitations and spin-flip excitations give sizable contributions to the configuration-interaction wave function for the {ital B} state (in-plane {pi} hole). Implications of these results are discussed in relation to the mechanisms of the high-{Tc} superconductivity.
Sure, Rebecca; Brandenburg, Jan Gerit; Grimme, Stefan
2016-04-01
In quantum chemical computations the combination of Hartree-Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double-zeta quality is still widely used, for example, in the popular B3LYP/6-31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean-field methods.
Sure, Rebecca; Brandenburg, Jan Gerit
2015-01-01
Abstract In quantum chemical computations the combination of Hartree–Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double‐zeta quality is still widely used, for example, in the popular B3LYP/6‐31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean‐field methods. PMID:27308221
Sherman, David M.
1990-01-01
Metal-metal charge-transfer and magnetic exchange interactions have important effects on the optical spectra, crystal chemistry, and physics of minerals. Previous molecular orbital calculations have provided insight on the nature of Fe2+-Fe3+ and Fe2+-Ti4+ charge-transfer transitions in oxides and silicates. In this work, spin-unrestricted molecular orbital calculations on (FeMnO10) clusters are used to study the nature of magnetic exchange and electron delocalization (charge transfer) associated with Fe3+-Mn2+, Fe3+-Mn3+, and Fe2+-Mn3+ interactions in oxides and silicates.
NASA Astrophysics Data System (ADS)
Bergeron, R. P.
1980-07-01
Orbital transfer vehicle propulsion options for SPS include both chemical (COTV) and electrical (EOTV) options. The proposed EOTV construction method is similar to that of the SPS and, by the addition of a transmitting antenna, may serve as a demonstration or precursor satellite option. The results of the studies led to the selection of a single stage COTV for crew and priority cargo transfer. An EOTV concept is favored for cargo transfer because of the more favorable orbital burden factor over chemical systems. The gallium arsenide solar array is favored over the silicon array because of its self annealing characteristics of radiation damage encountered during multiple transitions through the Van Allen radiation belt. Transportation system operations are depicted. A heavy lift launch vehicle (HLLV) delivers cargo and propellants to LEO, which are transferred to a dedicated EOTV by means of an intraorbit transfer vehicle (IOTV) for subsequent transfer to GEO. The space shuttle is used for crew transfer from Earth to LEO. At the LEO base, the crew module is removed from the shuttle cargo bay and mated to a COTV for transfer to GEO. Upon arrival at GEO, the SPS construction cargo is transferred from the EOTV to the SPS construction base by IOTV. Crew consumables and resupply propellants are transported to GEO by the EOTV. Transportation requirements are dominated by the vast quantity of materials to be transported to LEO and GEO.
Particles, Feynman Diagrams and All That
ERIC Educational Resources Information Center
Daniel, Michael
2006-01-01
Quantum fields are introduced in order to give students an accurate qualitative understanding of the origin of Feynman diagrams as representations of particle interactions. Elementary diagrams are combined to produce diagrams representing the main features of the Standard Model.
Theoretical phase diagrams for solid H{sub 2}
Surh, M.P.; Runge, K.J.
1993-07-01
Possible phase diagrams for solid molecular para-hydrogen in the 0-200 GPa pressure regime are constructed on the basis of ab initio calculations. Structures for the broken symmetry phase (BSP) and H-A phase have recently been proposed under the assumption that the molecules are centered on sites of a hexagonal close-packed lattice with the ideal c/a ratio, i.e., only molecular orientational and electronic changes are allowed. Symmetry considerations then dictate the simplest phase diagrams consistent with experimental observations, although the possibility of additional transitions cannot be ruled out. A simple model is introduced to describe the BSP and H-A transitions.
NASA Technical Reports Server (NTRS)
Patrick, E. L.; Earle, G. D.; Kasprzak, W. T.; Mahaffy, Paul R.
2008-01-01
From commercial origins as a molybdenum molecular beam nozzle, a ceramic nozzle of silicon carbide (SiC) was developed for space environment simulation. The nozzle is mechanically stable under extreme conditions of temperature and pressure. A heated, continuous, supersonically-expanded hydrogen beam with a 1% argon seed produced an argon beam component of nearly 4 km/s, with an argon flux exceeding 1x1014 /cm2.s. This nozzle was part of a molecular beam machine used in the Atmospheric Experiments Branch at NASA Goddard Space Flight Center to characterize the performance of the University of Texas at Dallas Ram Wind Sensor (RWS) aboard the Air Force Communications/Navigation Outage Forecasting System (C/NOFS) launched in the Spring of 2008.
The Hertzsprung-Russell Diagram.
ERIC Educational Resources Information Center
Woodrow, Janice
1991-01-01
Describes a classroom use of the Hertzsprung-Russell diagram to infer not only the properties of a star but also the star's probable stage in evolution, life span, and age of the cluster in which it is located. (ZWH)
Atemporal diagrams for quantum circuits
Griffiths, Robert B.; Wu Shengjun; Yu Li; Cohen, Scott M.
2006-05-15
A system of diagrams is introduced that allows the representation of various elements of a quantum circuit, including measurements, in a form which makes no reference to time (hence 'atemporal'). It can be used to relate quantum dynamical properties to those of entangled states (map-state duality), and suggests useful analogies, such as the inverse of an entangled ket. Diagrams clarify the role of channel kets, transition operators, dynamical operators (matrices), and Kraus rank for noisy quantum channels. Positive (semidefinite) operators are represented by diagrams with a symmetry that aids in understanding their connection with completely positive maps. The diagrams are used to analyze standard teleportation and dense coding, and for a careful study of unambiguous (conclusive) teleportation. A simple diagrammatic argument shows that a Kraus rank of 3 is impossible for a one-qubit channel modeled using a one-qubit environment in a mixed state.
NASA Astrophysics Data System (ADS)
Lau, S. S.; Liu, B. X.; Nicolet, M.-A.
1983-05-01
Interactions induced by ion irradiation are generally considered to be non-equilibrium processes, whereas phase diagrams are determined by phase equilibria. These two entities are seemingly unrelated. However, if one assumes that quasi-equilibrium conditions prevail after the prompt events, subsequent reactions are driven toward equilibrium by thermodynamical forces. Under this assumption, ion-induced reactions are related to equilibrium and therefore to phase diagrams. This relationship can be seen in the similarity that exists in thin films between reactions induced by ion irradiation and reactions induced by thermal annealing. In the latter case, phase diagrams have been used to predict the phase sequence of stable compound formation, notably so in cases of silicide formation. Ion-induced mixing not only can lead to stable compound formation, but also to metastable alloy formation. In some metal-metal systems, terminal solubilities can be greatly extended by ion mixing. In other cases, where the two constituents of the system have different crystal structures, extension of terminal solubility from both sides of the phase diagram eventually becomes structurally incompatible and a glassy (amorphous) mixture can form. The composition range where this bifurcation is likely to occur is in the two-phase regions of the phase diagram. These concepts are potentially useful guides in selecting metal pairs that from metallic glasses by ion mixing. In this report, phenomenological correlation between stable (and metastable) phase formation and phase diagram is discussed in terms of recent experimental data.
Kepler does not orbit the Earth, rather it orbits the Sun in concert with the Earth, slowly drifting away from Earth. Every 61 Earth years, Kepler and Earth will pass by each other. Throughout the ...
Percino, María Judith; Cerón, Margarita; Rodríguez, Oscar; Soriano-Moro, Guillermo; Castro, María Eugenia; Chapela, Víctor M; Siegler, Maxime A; Pérez-Gutiérrez, Enrique
2016-03-28
We report single crystal X-ray diffraction (hereafter, SCXRD) analyses of derivatives featuring the electron-donor N-ethylcarbazole or the (4-diphenylamino)phenyl moieties associated with a -CN group attached to a double bond. The compounds are (2Z)-3-(4-(diphenylamino)-phenyl)-2-(pyridin-3-yl)prop-2-enenitrile (I), (2Z)-3-(4-(diphenylamino)phenyl)-2-(pyridin-4-yl)-prop-2-enenitrile (II) and (2Z)-3-(9-ethyl-9H-carbazol-3-yl)-2-(pyridin-2-yl)enenitrile (III). SCXRD analyses reveal that I and III crystallize in the monoclinic space groups P2/c with Z' = 2 and C2/c with Z' = 1, respectively. Compound II crystallized in the orthorhombic space group Pbcn with Z' = 1. The molecular packing analysis was conducted to examine the pyridine core effect, depending on the ortho, meta- and para-positions of the nitrogen atom, with respect to the optical properties and number of independent molecules (Z'). It is found that the double bond bearing a diphenylamino moiety introduced properties to exhibit a strong π-π-interaction in the solid state. The compounds were examined to evaluate the effects of solvent polarity, the role of the molecular structure, and the molecular interactions on their self-assembly behaviors. Compound I crystallized with a cell with two conformers, anti and syn, due to interaction with solvent. DFT calculations indicated the anti and syn structures of I are energetically stable (less than 1 eV). Also electrochemical and photophysical properties of the compounds were investigated, as well as the determination of optimization calculations in gas and different solvent (chloroform, cyclohexane, methanol, ethanol, tetrahydrofuran, dichloromethane and dimethyl sulfoxide) in the Gaussian09 program. The effect of solvent by PCM method was also investigated. The frontier HOMO and LUMO energies and gap energies are reported.
Percino, María Judith; Cerón, Margarita; Rodríguez, Oscar; Soriano-Moro, Guillermo; Castro, María Eugenia; Chapela, Víctor M; Siegler, Maxime A; Pérez-Gutiérrez, Enrique
2016-01-01
We report single crystal X-ray diffraction (hereafter, SCXRD) analyses of derivatives featuring the electron-donor N-ethylcarbazole or the (4-diphenylamino)phenyl moieties associated with a -CN group attached to a double bond. The compounds are (2Z)-3-(4-(diphenylamino)-phenyl)-2-(pyridin-3-yl)prop-2-enenitrile (I), (2Z)-3-(4-(diphenylamino)phenyl)-2-(pyridin-4-yl)-prop-2-enenitrile (II) and (2Z)-3-(9-ethyl-9H-carbazol-3-yl)-2-(pyridin-2-yl)enenitrile (III). SCXRD analyses reveal that I and III crystallize in the monoclinic space groups P2/c with Z' = 2 and C2/c with Z' = 1, respectively. Compound II crystallized in the orthorhombic space group Pbcn with Z' = 1. The molecular packing analysis was conducted to examine the pyridine core effect, depending on the ortho, meta- and para-positions of the nitrogen atom, with respect to the optical properties and number of independent molecules (Z'). It is found that the double bond bearing a diphenylamino moiety introduced properties to exhibit a strong π-π-interaction in the solid state. The compounds were examined to evaluate the effects of solvent polarity, the role of the molecular structure, and the molecular interactions on their self-assembly behaviors. Compound I crystallized with a cell with two conformers, anti and syn, due to interaction with solvent. DFT calculations indicated the anti and syn structures of I are energetically stable (less than 1 eV). Also electrochemical and photophysical properties of the compounds were investigated, as well as the determination of optimization calculations in gas and different solvent (chloroform, cyclohexane, methanol, ethanol, tetrahydrofuran, dichloromethane and dimethyl sulfoxide) in the Gaussian09 program. The effect of solvent by PCM method was also investigated. The frontier HOMO and LUMO energies and gap energies are reported. PMID:27043499
The continuous and discrete molecular orbital x-ray bands from Xe(q+) (12≤q≤29) +Zn collisions.
Guo, Yipan; Yang, Zhihu; Hu, Bitao; Wang, Xiangli; Song, Zhangyong; Xu, Qiumei; Zhang, Boli; Chen, Jing; Yang, Bian; Yang, Jie
2016-01-01
In this paper, the x-ray emissions are measured by the interaction of 1500-3500 keV Xe(q+) (q = 12, 15, 17, 19, 21, 23, 26 and 29) ions with Zn target. When q < 29, we observe Ll, Lα, Lβ1, Lβ2 and Lγ characteristic x-rays from Xe(q+) ions and a broad M-shell molecular orbital (MO) x-ray band from the transient quasi-molecular levels. It is found that their yields quickly increase with different rates as the incident energy increases. Besides, the widths of the broad MO x-ray bands are about 0.9-1.32 keV over the energy range studied and are proportional to v(1/2) (v = projectile velocity). Most remarkably, when the projectile charge state is 29, the broad x-ray band separates into several narrow discrete spectra, which was never observed before in this field. PMID:27469425
NASA Astrophysics Data System (ADS)
Nataraj, A.; Balachandran, V.; Karthick, T.
2013-01-01
In this work, the vibrational spectral analysis was carried out using Raman and infrared spectroscopy in the range 4000-400 cm-1 and 3500-100 cm-1, respectively, for the 2-hydroxy-5-bromobenzaldehyde (HBB). The experimental spectra were recorded in the solid phase. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT) with the standard B3LYP/6-311G++(d,p) method and basis set. Normal co-ordinate calculations were performed with the DFT force field corrected by a recommended set of scaling factors yielding fairly good agreement between observed and calculated frequencies. Simulation of infrared and Raman spectra utilizing the results of these calculations led to excellent overall agreement with the observed spectral patterns. The complete assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The optimized geometric parameters (bond lengths and bond angles) were compared with experimental values of related compound. The stability of the molecule arising from hyper conjugative interactions and the charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The directly calculated ionization potential (IP), electron affinity (EA), electronegativity (χ), electrophilicity index (ω), hardness (η), chemical potential (μ), and first electron excitation (τ) are all correlated with the HOMO and LUMO energies with their molecular properties. These show that charge transfer occurs within the molecule. Furthermore, molecular electrostatic potential maps (MESP) of the molecule have been calculated.
Saravanan, S; Balachandran, V; Vishwanathan, K
2014-04-24
The FT-IR and FT-Raman spectra of 4-tert-butyl-3-methoxy-2,6-dinitrotoluene (musk ambrette) have been recorded in the regions 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The total energy calculations of musk ambrette were tried for the possible conformers. The molecular structure, geometry optimization, vibrational frequencies were obtained by the density functional theory (DFT) using B3LYP and LSDA method with 6-311G(d,p) basis set for the most stable conformer "C1". The complete assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes, calculated and the scaled values were compared with experimental FT-IR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The stability of the molecule arising from hyper conjugate interactions and the charge delocalization has been analyzed using bond orbital (NBO) analysis. The HOMO and LUMO energy gap reveals that the energy gap reflects the chemical activity of the molecule. The dipole moment (μ), polarizability (α), anisotropy polarizability (Δα) and first hyperpolarizability (βtot) of the molecule have been reported. The thermodynamic functions (heat capacity, entropy and enthalpy) were obtained for the range of temperature 100-1000 K. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecule has been obtained by mapping electron density isosurface with molecular electrostatic potential (MEP).
Zobač, Vladimír; Lewis, James P; Abad, Enrique; Mendieta-Moreno, Jesús I; Hapala, Prokop; Jelínek, Pavel; Ortega, José
2015-05-01
The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Firstly, to properly simulate photo-induced reactions the potential energy surfaces corresponding to excited states must be appropriately accessed; secondly, understanding the mechanisms of these processes requires the exploration of complex configurational spaces and the localization of conical intersections; finally, photo-induced reactions are probability events, that require the simulation of hundreds of trajectories to obtain the statistical information for the analysis of the reaction profiles. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code FIREBALL, suitable for the computational study of these problems. As an example of the application of this approach, we also report results on the [2 + 2] cycloaddition of ethylene with maleic anhydride and on the [2 + 2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition.
Kishi, Ryohei; Fujii, Hiroaki; Minami, Takuya; Shigeta, Yasuteru; Nakano, Masayoshi
2015-01-22
In this study, we apply the ab initio molecular orbital - configuration interaction based quantum master equation (MOQME) approach to the calculation and analysis of the dynamic first hyperpolarizabilities (β) of asymmetric π-conjugated molecules. In this approach, we construct the excited state models by the ab initio configuration interaction singles method. Then, time evolutions of system reduced density matrix ρ(t) and system polarization p(t) are calculated by the QME approach. Dynamic β in the second harmonic generation is calculated based on the nonperturbative definition of nonlinear optical susceptibility, using the frequency domain system polarization p(ω). Spatial contributions of electrons to β are analyzed based on the dynamic hyperpolarizability density map, which visualizes the second-order response of charge density oscillating with a frequency of 2ω. We apply the present method to the calculation of the dynamic β of a series of donor/acceptor substituted polyene oligomers, and then discuss the applicability of the MOQME method to the calculation and analysis of dynamic NLO properties of molecular systems.
Che, Yanke; Gross, Dustin E; Huang, Helin; Yang, Dongjiang; Yang, Xiaomei; Discekici, Emre; Xue, Zheng; Zhao, Huijun; Moore, Jeffrey S; Zang, Ling
2012-03-14
Development of simple, cost-effective, and sensitive fluorescence-based sensors for explosives implies broad applications in homeland security, military operations, and environmental and industrial safety control. However, the reported fluorescence sensory materials (e.g., polymers) usually respond to a class of analytes (e.g., nitroaromatics), rather than a single specific target. Hence, the selective detection of trace amounts of trinitrotoluene (TNT) still remains a big challenge for fluorescence-based sensors. Here we report the selective detection of TNT vapor using the nanoporous fibers fabricated by self-assembly of carbazole-based macrocyclic molecules. The nanoporosity allows for time-dependent diffusion of TNT molecules inside the material, resulting in further fluorescence quenching of the material after removal from the TNT vapor source. Under the same testing conditions, other common nitroaromatic explosives and oxidizing reagents did not demonstrate this postexposure fluorescence quenching; rather, a recovery of fluorescence was observed. The postexposure fluorescence quenching as well as the sensitivity is further enhanced by lowering the highest occupied molecular orbital (HOMO) level of the nanofiber building blocks. This in turn reduces the affinity for oxygen, thus allocating more interaction sites for TNT. Our results present a simple and novel way to achieve detection selectivity for TNT by creating nanoporosity and tuning molecular electronic structure, which when combined may be applied to other fluorescence sensor materials for selective detection of vapor analytes.
The Orbital Acceleration Research Experiment
NASA Astrophysics Data System (ADS)
Blanchard, R. C.; Hendrix, M. K.; Fox, J. C.; Thomas, D. J.; Nicholson, J.
The hardware and software of NASA's proposed Orbital Acceleration Research Experiment (OARE) are described. The OARE is to provide aerodynamic acceleration measurements along the Orbiter's principal axis in the free-molecular flow-flight regime at orbital attitude and in the transition regime during reentry. Models considering the effects of electromagnetic effects, solar radiation pressure, orbiter mass attraction, gravity gradient, orbital centripetal acceleration, out-of-orbital-plane effects, orbiter angular velocity, structural noise, mass expulsion signal sources, crew motion, and bias on acceleration are examined. The experiment contains an electrostatically balanced cylindrical proofmass accelerometer sensor with three orthogonal sensing axis outputs. The components and functions of the experimental calibration system and signal processor and control subsystem are analyzed. The development of the OARE software is discussed. The experimental equipment will be enclosed in a cover assembly that will be mounted in the Orbiter close to the center of gravity.
The Orbital Acceleration Research Experiment
NASA Technical Reports Server (NTRS)
Blanchard, R. C.; Hendrix, M. K.; Fox, J. C.; Thomas, D. J.; Nicholson, J.
1986-01-01
The hardware and software of NASA's proposed Orbital Acceleration Research Experiment (OARE) are described. The OARE is to provide aerodynamic acceleration measurements along the Orbiter's principal axis in the free-molecular flow-flight regime at orbital attitude and in the transition regime during reentry. Models considering the effects of electromagnetic effects, solar radiation pressure, orbiter mass attraction, gravity gradient, orbital centripetal acceleration, out-of-orbital-plane effects, orbiter angular velocity, structural noise, mass expulsion signal sources, crew motion, and bias on acceleration are examined. The experiment contains an electrostatically balanced cylindrical proofmass accelerometer sensor with three orthogonal sensing axis outputs. The components and functions of the experimental calibration system and signal processor and control subsystem are analyzed. The development of the OARE software is discussed. The experimental equipment will be enclosed in a cover assembly that will be mounted in the Orbiter close to the center of gravity.
Konschin, H.; Tylli, H. ); Gynther, J. ); Rouvinen, J. )
1989-01-01
The molecular structures of the benzodiazepine receptor ligands {beta}-carboline-3-carboxylic acid (BCCA), its methyl, ethyl, and propyl esters (BCCM, BCCE, and BCCP, respectively), and 3-CN-{beta}-carboline (BC-3-CN) have been investigated on a minimal basis STO-3G level of accuracy. For BCCM, BCCE, and BCCP semiempirical AM 1 calculations have also been performed. Fully optimized molecular geometries are reported. Comparisons with available experimental structures indicate that minimal basis results may have a useful predictive value. For the mobile ester side chains, a study of chosen points on the conformational surface was made. Both the STO-3G and the AM 1 results give the planar conformers is the most stable structures with small barriers to internal rotation, provided the ester side chain remains extended. The calculated STO-3G rotational barriers are higher than are the corresponding AM 1 barriers. Partial optimization, i.e., of side-chain structure parameters only, seems sufficient to map the conformational characteristics of these compounds. The orientation of the dipole moment vector and its magnitude may have consequences for possible interaction with a receptor. On the basis of the sidechain internal dynamics, the intramolecular flexibility tends to be confined to certain regions of conformational space.
NASA Astrophysics Data System (ADS)
Scherr, Rachel E.; Harrer, Benedikt W.; Close, Hunter G.; Daane, Abigail R.; DeWater, Lezlie S.; Robertson, Amy D.; Seeley, Lane; Vokos, Stamatis
2016-02-01
Energy is a crosscutting concept in science and features prominently in national science education documents. In the Next Generation Science Standards, the primary conceptual learning goal is for learners to conserve energy as they track the transfers and transformations of energy within, into, or out of the system of interest in complex physical processes. As part of tracking energy transfers among objects, learners should (i) distinguish energy from matter, including recognizing that energy flow does not uniformly align with the movement of matter, and should (ii) identify specific mechanisms by which energy is transferred among objects, such as mechanical work and thermal conduction. As part of tracking energy transformations within objects, learners should (iii) associate specific forms with specific models and indicators (e.g., kinetic energy with speed and/or coordinated motion of molecules, thermal energy with random molecular motion and/or temperature) and (iv) identify specific mechanisms by which energy is converted from one form to another, such as incandescence and metabolism. Eventually, we may hope for learners to be able to optimize systems to maximize some energy transfers and transformations and minimize others, subject to constraints based in both imputed mechanism (e.g., objects must have motion energy in order for gravitational energy to change) and the second law of thermodynamics (e.g., heating is irreversible). We hypothesize that a subsequent goal of energy learning—innovating to meet socially relevant needs—depends crucially on the extent to which these goals have been met.
Genest, Alexander; Woiterski, André; Krüger, Sven; Shor, Aleksey M; Rösch, Notker
2006-01-01
To validate the IMOMM (integrated molecular orbitals/molecular mechanics) method for ligand-stabilized transition metal clusters, we compare results of this combined quantum mechanical and molecular mechanical (QM/MM) approach, as implemented in the program ParaGauss (Kerdcharoen, T.; Birkenheuer, U.; Krüger, S.; Woiterski, A.; Rösch, N. Theor. Chem. Acc. 2003, 109, 285), to a full density functional (DF) treatment. For this purpose, we have chosen a model copper ethylthiolate cluster, Cu13(SCH2CH3)8 in D4h symmetry. The evaluation is based on 16 conformers of the cluster which exhibit single and bridging coordination of the ligands at the Cu13 cluster as well as various ligand orientations. For corresponding isomers, we obtained moderate deviations between QM and QM/MM results: 0.01-0.06 Å for pertinent bond lengths and up to ∼15° for bond angles. Ligand binding energies of the two approaches deviated less than 6 kcal/mol. The largest discrepancies between full DF and IMOMM results were found for isomers exhibiting short Cu-H and H-H contacts. We traced this back to the localization of different minima, reflecting the unequal performance of the DF and the force-field methods for nonbonding interactions. Thus, QM/MM results can be considered as more reliable because of the well-known limitations of standard exchange-correlation functionals for the description of nonbonding interactions for this class of systems.
Automatically Assessing Graph-Based Diagrams
ERIC Educational Resources Information Center
Thomas, Pete; Smith, Neil; Waugh, Kevin
2008-01-01
To date there has been very little work on the machine understanding of imprecise diagrams, such as diagrams drawn by students in response to assessment questions. Imprecise diagrams exhibit faults such as missing, extraneous and incorrectly formed elements. The semantics of imprecise diagrams are difficult to determine. While there have been…
Chaudret, Robin; Gresh, Nohad; Parisel, Olivier; Piquemal, Jean-Philip
2011-11-15
We have quantified the extent of the nonadditivity of the short-range exchange-repulsion energy, E(exch-rep), in several polycoordinated complexes of alkali, alkaline-earth, transition, and metal cations. This was done by performing ab initio energy decomposition analyses of interaction energies in these complexes. The magnitude of E(exch-rep(n-body, n > 2)) was found to be strongly cation-dependent, ranging from close to zero for some alkali metal complexes to about 6 kcal/mol for the hexahydrated Zn(2+) complex. In all cases, the cation-water molecules, E(exch-rep(three-body)), has been found to be the dominant contribution to many-body exchange-repulsion effects, higher order terms being negligible. As the physical basis of this effect is discussed, a three-center exponential term was introduced in the SIBFA (Sum of Interactions Between Fragments Ab initio computed) polarizable molecular mechanics procedure to model such effects. The three-body correction is added to the two-center (two-body) overlap-like formulation of the short-range repulsion contribution, E(rep), which is grounded on simplified integrals obtained from localized molecular orbital theory. The present term is computed on using mostly precomputed two-body terms and, therefore, does not increase significantly the computational cost of the method. It was shown to match closely E(three-body) in a series of test cases bearing on the complexes of Ca(2+), Zn(2+), and Hg(2+). For example, its introduction enabled to restore the correct tetrahedral versus square planar preference found from quantum chemistry calculations on the tetrahydrate of Hg(2+) and [Hg(H(2)O)(4)](2+). PMID:21793002
Goldfeld, Dahlia A; Bochevarov, Arteum D; Friesner, Richard A
2008-12-01
This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner et al., J. Chem. Phys. 125, 124107 (2006); E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006).] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT's inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G( *), 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal/mol [obtained with B3LYP/6-311++G(3df,3pd)] to 0.8 kcal/mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies.
NASA Astrophysics Data System (ADS)
Johnson, K. H.; McHenry, M. E.; Clougherty, D. P.
1991-11-01
Recently observed superconductivity at 18 K in potassium-doped fullerene, K xC 60, may be due to Cooper pairing of partially occupied icosahedral C 60 cluster t 1u (pπ) molecular orbitals, induced by cooperative dynamic Jahn-Teller coupling of these orbitals to “soft-mode” vibrations of the C 60 molecules, leading to a BCS-like mechanism. Predicted are a nonvanishing isotope effect and Tc increasing to 30 K or more with optimization of doping, and significant effects with pressure.
Voronoi Diagrams and Spring Rain
ERIC Educational Resources Information Center
Perham, Arnold E.; Perham, Faustine L.
2011-01-01
The goal of this geometry project is to use Voronoi diagrams, a powerful modeling tool across disciplines, and the integration of technology to analyze spring rainfall from rain gauge data over a region. In their investigation, students use familiar equipment from their mathematical toolbox: triangles and other polygons, circumcenters and…
Dietrick, Scott M; Iyengar, Srinivasan S
2012-12-11
A method of analysis is introduced to probe the spectral features obtained from ab initio molecular dynamics simulations. Here, the instantaneous mass-weighted velocities are projected onto irreducible representations constructed from discrete time translation groups comprising operations that invoke the time-domain symmetries (or periodic phase space orbits) reflected in the spectra. The projected velocities are decomposed using singular value decomposition (SVD) to construct a set of "modes" pertaining to a given frequency domain. These modes now include all anharmonicities, as sampled during the dynamics simulations. In this approach, the underlying motions are probed in a manner invariant with respect to coordinate transformations, operations being performed along the time axis rather than coordinate axes, making the analysis independent of choice of reference frame. The method is used to probe the underlying motions responsible for the doublet at ∼1000 cm(-1) in the vibrational spectrum of the H5O2(+), Zundel cation. The associated analysis results are confirmed by projecting the Fourier transformed velocities onto the harmonic normal mode coordinates and a set of mass-weighted, symmetrized Jacobi coordinates. It is found that the two peaks of the doublet are described and differentiated by their respective contributions from the proton transfer, water-water stretch, and water wag coordinates, as these are defined. Temperature dependent effects are also briefly noted.
Yamagishi, Kenji; Tokiwa, Hiroaki; Makishima, Makoto; Yamada, Sachiko
2010-07-01
To provide physicochemical insight into the role of each residue in the ligand-binding pocket (LBP) of the vitamin D receptor (VDR), we evaluated the energies of the interactions between the LBP residues and 1alpha,25(OH)2D3 by using an ab initio fragment molecular orbital (FMO) method at the Møller-Plesset second-order perturbation (MP2) level. This FMO-MP2 method can be used to correctly evaluate both electrostatic and van der Waals dispersion interactions, and it affords these interaction energies separately. We deduced the nature of each interaction and determined the importance of all the LBP residues involved in ligand recognition by the VDR. We previously reported the results of alanine-scanning mutational analysis (ASMA) of all 34 non-alanine residues lining the LBP of the human VDR. The theoretical results in combination with the ASMA results enabled us to assign the role of each LBP residue. We concluded that electrostatic interactions are the major determinant of the ligand-binding activity and ligand recognition specificity and that van der Waals interactions are important for protein folding and, in turn, for cofactor binding.
NASA Astrophysics Data System (ADS)
Zhang, Zhaofu; Geng, Zhaohui; Cai, Danyun; Pan, Tongxi; Chen, Yixin; Dong, Liyuan; Zhou, Tiege
2015-01-01
A first-principles calculation based on density functional theory is carried out to reveal the geometry, electronic structures and magnetic properties of hexagonal boron nitride sheets (h-BNSs) doped by 5d transitional mental atoms (Lu, Hf, Ta, W, Re, Os, Ir, Pt, Au and Hg) at boron-site (B5d) and nitrogen-site (N5d). Results of pure h-BNS, h-BNS with B vacancy (VB) and N vacancy (VN) are also given for comparison. It is shown that all the h-BNSs doped with 5d atoms possess a C3v local symmetry except for NLu and NHg which have a clear deviation. For the same 5d dopant, the binding energy of B5d is larger than that of N5d, which indicates the substitution of a 5d atom for B is preferred. The total densities of states are presented, where impurity energy levels exist. Besides, the total magnetic moments (TMMs) change regularly with the increment of the 5d atomic number. Theoretical analyses by molecular orbital under C3v symmetry explain the impurity energy levels and TMMs.
Tsuzuki, Seiji; Hayamizu, Kikuko; Seki, Shiro; Ohno, Yasutaka; Kobayashi, Yo; Miyashiro, Hajime
2008-08-14
Interactions of the lithium bis(trifluoromethylsulfonyl)amide (LiTFSA) complex with N, N-diethyl-N-methyl-N-(2-methoxyethyl) ammonium (DEME), 1-ethyl-3-methylimidazolium (EMIM) cations, neutral diethylether (DEE), and the DEMETFSA complex were studied by ab initio molecular orbital calculations. An interaction energy potential calculated for the DEME cation with the LiTFSA complex has a minimum when the Li atom has contact with the oxygen atom of DEME cation, while potentials for the EMIM cation with the LiTFSA complex are always repulsive. The MP2/6-311G**//HF/6-311G** level interaction energy calculated for the DEME cation with the LiTFSA complex was -18.4 kcal/mol. The interaction energy for the neutral DEE with the LiTFSA complex was larger (-21.1 kcal/mol). The interaction energy for the DEMETFSA complex with LiTFSA complex is greater (-23.2 kcal/mol). The electrostatic and induction interactions are the major source of the attraction in the two systems. The substantial attraction between the DEME cation and the LiTFSA complex suggests that the interaction between the Li cation and the oxygen atom of DEME cation plays important roles in determining the mobility of the Li cation in DEME-based room temperature ionic liquids.
Quantum phases of atomic Fermi gases with anisotropic spin-orbit coupling
NASA Astrophysics Data System (ADS)
Iskin, M.; Subaşı, A. L.
2011-10-01
We consider a general anisotropic spin-orbit coupling and analyze the phase diagrams of both balanced and imbalanced Fermi gases for the entire BCS-BEC evolution. In the first part, we use the self-consistent mean-field theory at zero temperature, and show that the topological structure of the ground-state phase diagrams is quite robust against the effects of anisotropy. In the second part, we go beyond the mean-field description, and investigate the effects of Gaussian fluctuations near the critical temperature. This allows us to derive the time-dependent Ginzburg-Landau theory, from which we extract the effective mass of the Cooper pairs and their critical condensation temperature in the molecular BEC limit.
Quantum phases of atomic Fermi gases with spin-orbit coupling
NASA Astrophysics Data System (ADS)
Iskin, Menderes; Subasi, Levent
2012-02-01
We consider a general anisotropic spin-orbit coupling and analyze the phase diagrams of both balanced and imbalanced Fermi gases for the entire BCS-BEC evolution. First we use the self-consistent mean-field theory at zero temperature, and show that the topological structure of the ground-state phase diagrams is quite robust against the effects of anisotropy. Then we go beyond the mean-field description, and investigate the effects of Gaussian fluctuations near the critical temperature. This allows us to derive the time-dependent Ginzburg-Landau theory, from which we extract the effective mass of the Cooper pairs and their critical condensation temperature in the molecular BEC limit.
Suresh, S; Gunasekaran, S; Srinivasan, S
2014-11-11
The solid phase FT-IR and FT-Raman spectra of 2-hydroxybenzoic acid (salicylic acid) have been recorded in the region 4000-400 and 4000-100 cm(-1) respectively. The optimized molecular geometry and fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method and a comparative study between Hartree Fork (HF) method at 6-311++G(d,p) level basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimentally obtained FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The time dependent DFT method is employed to predict its absorption energy and oscillator strength. The linear polarizability (α) and the first order hyper polarizability (β) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MEP) are also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.
NASA Astrophysics Data System (ADS)
Suresh, S.; Gunasekaran, S.; Srinivasan, S.
2014-11-01
The solid phase FT-IR and FT-Raman spectra of 2-hydroxybenzoic acid (salicylic acid) have been recorded in the region 4000-400 and 4000-100 cm-1 respectively. The optimized molecular geometry and fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method and a comparative study between Hartree Fork (HF) method at 6-311++G(d,p) level basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimentally obtained FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The time dependent DFT method is employed to predict its absorption energy and oscillator strength. The linear polarizability (α) and the first order hyper polarizability (β) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MEP) are also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.
White is green: new schematic diagrams
NASA Astrophysics Data System (ADS)
Glicksman, Hal
2002-06-01
Two new schematic diagrams are presented here that derive from the study of the value relationships of the primary colors of RGB computer and video color. The first diagram is a 'Truth Table' that presents true-false, on-off states of the three colors of RGB so that the colors are presented in the order of their brightness values. The second diagram is a triple Venn diagram based on the perception of color. This diagram is presented as an alternative to the Venn diagrams of additive and subtractive color usually used to explain color.
Orbiter Autoland reliability analysis
NASA Technical Reports Server (NTRS)
Welch, D. Phillip
1993-01-01
The Space Shuttle Orbiter is the only space reentry vehicle in which the crew is seated upright. This position presents some physiological effects requiring countermeasures to prevent a crewmember from becoming incapacitated. This also introduces a potential need for automated vehicle landing capability. Autoland is a primary procedure that was identified as a requirement for landing following and extended duration orbiter mission. This report documents the results of the reliability analysis performed on the hardware required for an automated landing. A reliability block diagram was used to evaluate system reliability. The analysis considers the manual and automated landing modes currently available on the Orbiter. (Autoland is presently a backup system only.) Results of this study indicate a +/- 36 percent probability of successfully extending a nominal mission to 30 days. Enough variations were evaluated to verify that the reliability could be altered with missions planning and procedures. If the crew is modeled as being fully capable after 30 days, the probability of a successful manual landing is comparable to that of Autoland because much of the hardware is used for both manual and automated landing modes. The analysis indicates that the reliability for the manual mode is limited by the hardware and depends greatly on crew capability. Crew capability for a successful landing after 30 days has not been determined yet.
Kar, Tapas; Liao, Meng-Sheng; Biswas, Susobhan; Sarkar, Saikat; Dey, Kamalendu; Yap, Glenn P A; Kreisel, Kevin
2006-11-01
A new octahedral chromium(III) complex having 2,2'-bipyridine as ligand system was synthesized in methanol. Single crystal X-ray diffraction analysis shows that it possesses non-stoichiometry in its anionic primary covalency. It has also been studied by elemental analyses, optical spectroscopy (UV-vis, IR) and magnetic susceptibility data. DFT calculations (with B3LYP functional and double-xi quality LANLDZ(D95V) basis set) were carried out to interpret the electronic and infrared spectra of the complex. The DFT optimized geometric structure for the complex is compared with the X-ray crystallographic data; the theory-experiment agreement is satisfactory.
How to Draw Energy Level Diagrams in Excitonic Solar Cells.
Zhu, X-Y
2014-07-01
Emerging photovoltaic devices based on molecular and nanomaterials are mostly excitonic in nature. The initial absorption of a photon in these materials creates an exciton that can subsequently dissociate in each material or at their interfaces to give charge carriers. Any attempt at mechanistic understanding of excitonic solar cells must start with drawing energy level diagrams. This seemingly elementary exercise, which is described in textbooks for inorganic solar cells, has turned out to be a difficult subject in the literature. The problem stems from conceptual confusion of single-particle energy with quasi-particle energy and the misleading practice of mixing the two on the same energy level diagram. Here, I discuss how to draw physically accurate energy diagrams in excitonic solar cells using only single-particle energies (ionization potentials and electron affinities) of both ground and optically excited states. I will briefly discuss current understanding on the electronic energy landscape responsible for efficient charge separation in excitonic solar cells.
Hero's journey in bifurcation diagram
NASA Astrophysics Data System (ADS)
Monteiro, L. H. A.; Mustaro, P. N.
2012-06-01
The hero's journey is a narrative structure identified by several authors in comparative studies on folklore and mythology. This storytelling template presents the stages of inner metamorphosis undergone by the protagonist after being called to an adventure. In a simplified version, this journey is divided into three acts separated by two crucial moments. Here we propose a discrete-time dynamical system for representing the protagonist's evolution. The suffering along the journey is taken as the control parameter of this system. The bifurcation diagram exhibits stationary, periodic and chaotic behaviors. In this diagram, there are transition from fixed point to chaos and transition from limit cycle to fixed point. We found that the values of the control parameter corresponding to these two transitions are in quantitative agreement with the two critical moments of the three-act hero's journey identified in 10 movies appearing in the list of the 200 worldwide highest-grossing films.
Quantum Dimer Model: Phase Diagrams
NASA Astrophysics Data System (ADS)
Goldstein, Garry; Chamon, Claudio; Castelnovo, Claudio
We present new theoretical analysis of the Quantum Dimer Model. We study dimer models on square, cubic and triangular lattices and we reproduce their phase diagrams (which were previously known only numerically). We show that there are several types of dimer liquids and solids. We present preliminary analysis of several other models including doped dimers and planar spin ice, and some results on the Kagome and hexagonal lattices.
NASA Astrophysics Data System (ADS)
Kalfaoğlu, Emel; Karabulut, Bünyamin
2016-09-01
Electron paramagnetic resonance (EPR) spectra of VO2+ ions in NaH2PO4·2H2O single crystal have been studied. The spin-Hamiltonian parameters and molecular orbital bonding coefficients were calculated. The angular variation of the EPR spectra shows two different VO2+ complexes. These are located in different chemical environment and each environment contains four magnetically inequivalent VO2+ sites. The crystal field around VO2+ ion is approximately axially symmetric since a strong V=O bond distorts the crystal lattice. Spin Hamiltonian parameters and molecular orbital bonding coefficients were calculated from the EPR data and the nature of bonding in the complex was discussed together.
INCONEL 718: A solidification diagram
NASA Astrophysics Data System (ADS)
Knorovsky, G. A.; Cieslak, M. J.; Headley, T. J.; Romig, A. D.; Hammetter, W. F.
1989-10-01
As part of a program studying weldability of Ni-base superalloys, results of an integrated analytical approach are used to generate a constitution diagram for INCONEL 718* in the temperature range associated with solidification. Differential thermal analysis of wrought material and optical and scanning electron microscopy, electron probe microanalysis, and analytical electron microscopy of gas tungsten arc welds are used in conjunction with solidification theory to generate data points for this diagram. The important features of the diagram are an austenite (γ)/Laves phase eutectic which occurs at ≈19.1 wt pct Nb between austenite containing ≈9.3 wt pct Nb and a Laves phase which contains ≈22.4 wt pct Nb. The distribution coefficient for Nb was found to be ≈0.5. The solidification sequence of INCONEL 718 was found to be (1) proeutectic γ, followed by (2) a γ/NbC eutectic at ≈1250°C, followed by (3) continued γ solidification, followed by (4) a γ/Laves phase eutectic at ≈1200°C. An estimate of the volume fraction eutectic is made using the Scheil solidification model, and the fraction of each phase in the eutectic is calculated via the lever rule. These are compared with experimentally determined values and found to be in good agreement.
Causal diagrams in systems epidemiology
2012-01-01
Methods of diagrammatic modelling have been greatly developed in the past two decades. Outside the context of infectious diseases, systematic use of diagrams in epidemiology has been mainly confined to the analysis of a single link: that between a disease outcome and its proximal determinant(s). Transmitted causes ("causes of causes") tend not to be systematically analysed. The infectious disease epidemiology modelling tradition models the human population in its environment, typically with the exposure-health relationship and the determinants of exposure being considered at individual and group/ecological levels, respectively. Some properties of the resulting systems are quite general, and are seen in unrelated contexts such as biochemical pathways. Confining analysis to a single link misses the opportunity to discover such properties. The structure of a causal diagram is derived from knowledge about how the world works, as well as from statistical evidence. A single diagram can be used to characterise a whole research area, not just a single analysis - although this depends on the degree of consistency of the causal relationships between different populations - and can therefore be used to integrate multiple datasets. Additional advantages of system-wide models include: the use of instrumental variables - now emerging as an important technique in epidemiology in the context of mendelian randomisation, but under-used in the exploitation of "natural experiments"; the explicit use of change models, which have advantages with respect to inferring causation; and in the detection and elucidation of feedback. PMID:22429606
Lunar Reconnaissance Orbiter FlatSat
NASA Technical Reports Server (NTRS)
Wright, Michael
2008-01-01
This viewgraph presentation reviews the use of FlatSat as a platform for use during flight integration and testing (I&T) of the Lunar Reconnaissance Orbiter (LRO). Included in the presentations are requirements for the facility, a diagram of the LRO FlatSat lab, and discussion of the operational documentation, facility scheduling, and issues and lessons learned.
Papatheodorou, G.N.; Curtiss, L.A.; Maroni, V.A.
1983-03-15
Raman spectra of gaseous NH/sub 3/:AlCl/sub 3/ and NH/sub 3/:AlBr/sub 3/ were recorded at 400 /sup 0/C. The observed Raman frequencies in combination with reported infrared frequencies for NH/sub 3/:AlCl/sub 3/ and ab initio molecular orbital calculations on NH/sub 3/:AlCl/sub 3/ and NH/sub 3/:AlF/sub 3/ were used to derive force constants for all three NH/sub 3/:AlX/sub 3/ complexes (X = F, Cl, Br) based on an adjusted valence force field (AVFF) concept. The resulting force constant calculations produced complete sets of A/sub 1/ and E mode frequencies for each complex. Statistical mechanical analyses were then performed using the A/sub 1/ and E mode frequencies together with estimated values for the torsional mode of each complex and published enthalpy data. From these analyses, the relative thermodynamic stability of each complex was determined. At 700 and 1000 K, NH/sub 3/:AlCl/sub 3/ was found to be more stable than NH/sub 3/:AlBr/sub 3/. It was further predicted that the reaction of gaseous NH/sub 3/ with solid AlF/sub 3/ to form NH/sub 3/:AlF/sub 3/ is not favored in this temperature range, which provides an explanation for the lack of success in prior efforts to produce NH/sub 3/:AlF/sub 3/.
Differential Effectiveness of Two Science Diagram Types.
ERIC Educational Resources Information Center
Holliday, William G.
Reported is an Aptitude Treatment Instruction (ATI) Study designed to evaluate the aptitude of verbal comprehension in terms of two unitary complex science diagram types: a single complex block word diagram and a single complex picture word diagram.. ATI theory and research indicate that different effective instructional treatments tend to help…
NASA Technical Reports Server (NTRS)
2005-01-01
The structure of NASA's Mars Reconnaissance Orbiter spacecraft is constructed from composite panels of carbon layers over aluminum honeycomb, lightweight yet strong. This forms a basic structure or skeleton on which the instruments, electronics, propulsion and power systems can be mounted. The propellant tank is contained in the center of the orbiter's structure. This photo was taken at Lockheed Martin Space Systems, Denver, during construction of the spacecraft.
Diagram, a Learning Environment for Initiation to Object-Oriented Modeling with UML Class Diagrams
ERIC Educational Resources Information Center
Py, Dominique; Auxepaules, Ludovic; Alonso, Mathilde
2013-01-01
This paper presents Diagram, a learning environment for object-oriented modelling (OOM) with UML class diagrams. Diagram an open environment, in which the teacher can add new exercises without constraints on the vocabulary or the size of the diagram. The interface includes methodological help, encourages self-correcting and self-monitoring, and…
Origin and use of crystallization phase diagrams.
Rupp, Bernhard
2015-03-01
Crystallization phase diagrams are frequently used to conceptualize the phase relations and also the processes taking place during the crystallization of macromolecules. While a great deal of freedom is given in crystallization phase diagrams owing to a lack of specific knowledge about the actual phase boundaries and phase equilibria, crucial fundamental features of phase diagrams can be derived from thermodynamic first principles. Consequently, there are limits to what can be reasonably displayed in a phase diagram, and imagination may start to conflict with thermodynamic realities. Here, the commonly used `crystallization phase diagrams' are derived from thermodynamic excess properties and their limitations and appropriate use is discussed.
Voronoi Diagrams Without Bounding Boxes
NASA Astrophysics Data System (ADS)
Sang, E. T. K.
2015-10-01
We present a technique for presenting geographic data in Voronoi diagrams without having to specify a bounding box. The method restricts Voronoi cells to points within a user-defined distance of the data points. The mathematical foundation of the approach is presented as well. The cell clipping method is particularly useful for presenting geographic data that is spread in an irregular way over a map, as for example the Dutch dialect data displayed in Figure 2. The automatic generation of reasonable cell boundaries also makes redundant a frequently used solution to this problem that requires data owners to specify region boundaries, as in Goebl (2010) and Nerbonne et al (2011).
New Orbits Based on Speckle Interferometry at SOAR
NASA Astrophysics Data System (ADS)
Tokovinin, Andrei
2016-11-01
The orbits of 55 visual binary stars are computed using recent speckle interferometry data from the SOAR telescope: 33 first-time orbits and 22 revisions of previous orbit calculations. The orbital periods range from 1.4–370 years, and the quality of the orbits ranges from definitive to preliminary and tentative. Most binaries consist of low-mass dwarfs and have short periods (median period 31 years). The dynamical parallaxes and masses are evaluated and compared to the Hipparcos parallaxes. Using differential speckle photometry, binary components are placed on the color–magnitude diagram. Based on observations obtained at the Southern Astrophysical Research (SOAR) telescope.
Phase Diagrams of Nuclear Pasta
NASA Astrophysics Data System (ADS)
Caplan, Matthew; Horowitz, Chuck; Berry, Don; da Silva Schneider, Andre
2016-03-01
In the inner crust of neutrons stars, where matter is near the saturation density, protons and neutrons arrange themselves into complex structures called nuclear pasta. Early theoretical work predicted a simple graduated hierarchy of pasta phases, consisting of spheres, cylinders, slabs, and uniform matter with voids. Previous work has simulated these phases with a simple classical model and has shown that the formation of these structures is dependent on the temperature, density, and proton fraction. However, previous work only studied a limited range of these parameters due to computational limitations. Thanks to recent advances in computing it is now possible to survey the structure of nuclear pasta for a larger range of parameters. By simulating nuclear pasta with constant temperature and proton fraction in an expanding simulation volume we are able to study the phase transitions in nuclear pasta, and thus produce a set of phase diagrams. We report on these phase diagrams as well as newly identified phases of nuclear pasta and discuss their implications for neutron star observables.
NASA Astrophysics Data System (ADS)
Lee, Sung Keun; Stebbins, Jonathan F.
2006-08-01
Estimation of the framework connectivity and the atomic structure of depolymerized silicate melts and glasses (NBO/T > 0) remains a difficult question in high-temperature geochemistry relevant to magmatic processes and glass science. Here, we explore the extent of disorder and the nature of polymerization in binary Ca-silicate and ternary Ca-aluminosilicate glasses with varying NBO/T (from 0 to 2.67) using O-17 NMR at two different magnetic fields of 9.4 and 14.1 T in conjunction with quantum chemical calculations. Non-random distributions among framework cations (Si and Al) are demonstrated in the variation of relative populations of oxygen sites with NBO/T. The proportion of non-bridging oxygen (NBO, Ca-O-Si) in the binary and ternary aluminosilicate glasses increases with NBO/T. While the trend is consistent with predictions from composition, the detailed fractions apparently deviate from the predicted values, suggesting further complications in the nature of polymerization. The proportion of each bridging oxygen in the glasses also varies with NBO/T. The fractions of Al-O-Si and Al-O-Al increase with increasing polymerization as CaO is replaced with Al 2O 3, while that of Si-O-Si seems to decrease, implying that activity of silica may decrease from calcium silicate to polymerized aluminosilicates (X=constant). Quantum chemical molecular orbital calculations based on density functional theory show that a silicate chain with Al-NBO (Ca-O-Al) has an energy penalty (calculated cluster energy difference) of about 108 kJ/mol compared with the cluster with Ca-O-Si, consistent with preferential depolymerization of Si-networks, reported in an earlier O-17 NMR study [Allwardt, J., Lee, S.K., Stebbins, J.F., 2003. Bonding preferences of non-bridging oxygens in calcium aluminosilicate glass: Evidence from O-17 MAS and 3QMAS NMR on calcium aluminate glass. Am. Mineral.88, 949-954]. These prominent types of non-randomness in the distributions suggest significant chemical
NASA Technical Reports Server (NTRS)
Kessler, D. J. (Compiler); Su, S. Y. (Compiler)
1985-01-01
Earth orbital debris issues and recommended future activities are discussed. The workshop addressed the areas of environment definition, hazards to spacecraft, and space object management. It concluded that orbital debris is a potential problem for future space operations. However, before recommending any major efforts to control the environment, more data are required. The most significant required data are on the population of debris smaller than 4 cm in diameter. New damage criteria are also required. When these data are obtained, they can be combined with hypervelocity data to evaluate the hazards to future spacecraft. After these hazards are understood, then techniques to control the environment can be evaluated.
Sherman, David M.
1987-01-01
A molecular orbital description, based on Xα-Scattered wave calculations on a (FeTiO10)14− cluster, is given for Fe2+ → Ti4+ charge transfer transitions in minerals. The calculated energy for the lowest Fe2+ → Ti4+ metal-metal charge transfer transition is 18040 cm−1 in reasonable agreement with energies observed in the optical spectra of Fe-Ti oxides and silicates. As in the case of Fe2+ → Fe3+ charge transfer in mixed-valence iron oxides and silicates, Fe2+ → Ti4+ charge transfer is associated with Fe-Ti bonding across shared polyhedral edges. Such bonding results from the overlap of the Fe(t 2g ) and Ti(t 2g ) 3d orbitals.
Zarycz, M Natalia C; Provasi, Patricio F
2015-02-01
The resonance-assisted hydrogen bond (HB) phenomenon has been studied theoretically by a localized molecular orbital (LMO) decomposition of the spin-spin coupling constants between atoms either involved or close to the O-H···O system of some β-diketones and their saturated counterparts. The analysis, carried out at the level of the second-order polarization propagator approximation, shows that the contributions in terms of LMO to the paramagnetic spin orbital and the spin dipolar Ramsey terms proof the importance of the delocalized π-electron structure supporting the idea of the existence of the resonance-assisted HB phenomenon phenomenon. The LMO contributions to the Fermi contact term indicate mainly the presence of the HB that may or not be linked to the π-electrons.
Hubble's diagram and cosmic expansion
NASA Astrophysics Data System (ADS)
Kirshner, Robert P.
2004-01-01
Edwin Hubble's classic article on the expanding universe appeared in PNAS in 1929 [Hubble, E. P. (1929) Proc. Natl. Acad. Sci. USA 15, 168-173]. The chief result, that a galaxy's distance is proportional to its redshift, is so well known and so deeply embedded into the language of astronomy through the Hubble diagram, the Hubble constant, Hubble's Law, and the Hubble time, that the article itself is rarely referenced. Even though Hubble's distances have a large systematic error, Hubble's velocities come chiefly from Vesto Melvin Slipher, and the interpretation in terms of the de Sitter effect is out of the mainstream of modern cosmology, this article opened the way to investigation of the expanding, evolving, and accelerating universe that engages today's burgeoning field of cosmology.
Hubble's diagram and cosmic expansion.
Kirshner, Robert P
2004-01-01
Edwin Hubble's classic article on the expanding universe appeared in PNAS in 1929 [Hubble, E. P. (1929) Proc. Natl. Acad. Sci. USA 15, 168-173]. The chief result, that a galaxy's distance is proportional to its redshift, is so well known and so deeply embedded into the language of astronomy through the Hubble diagram, the Hubble constant, Hubble's Law, and the Hubble time, that the article itself is rarely referenced. Even though Hubble's distances have a large systematic error, Hubble's velocities come chiefly from Vesto Melvin Slipher, and the interpretation in terms of the de Sitter effect is out of the mainstream of modern cosmology, this article opened the way to investigation of the expanding, evolving, and accelerating universe that engages today's burgeoning field of cosmology. PMID:14695886
Phase diagram of ammonium nitrate.
Dunuwille, Mihindra; Yoo, Choong-Shik
2013-12-01
Ammonium Nitrate (AN) is a fertilizer, yet becomes an explosive upon a small addition of chemical impurities. The origin of enhanced chemical sensitivity in impure AN (or AN mixtures) is not well understood, posing significant safety issues in using AN even today. To remedy the situation, we have carried out an extensive study to investigate the phase stability of AN and its mixtures with hexane (ANFO-AN mixed with fuel oil) and Aluminum (Ammonal) at high pressures and temperatures, using diamond anvil cells (DAC) and micro-Raman spectroscopy. The results indicate that pure AN decomposes to N2, N2O, and H2O at the onset of the melt, whereas the mixtures, ANFO and Ammonal, decompose at substantially lower temperatures. The present results also confirm the recently proposed phase IV-IV' transition above 17 GPa and provide new constraints for the melting and phase diagram of AN to 40 GPa and 400°C.
Phase diagram of ammonium nitrate
NASA Astrophysics Data System (ADS)
Dunuwille, Mihindra; Yoo, Choong-Shik
2013-12-01
Ammonium Nitrate (AN) is a fertilizer, yet becomes an explosive upon a small addition of chemical impurities. The origin of enhanced chemical sensitivity in impure AN (or AN mixtures) is not well understood, posing significant safety issues in using AN even today. To remedy the situation, we have carried out an extensive study to investigate the phase stability of AN and its mixtures with hexane (ANFO-AN mixed with fuel oil) and Aluminum (Ammonal) at high pressures and temperatures, using diamond anvil cells (DAC) and micro-Raman spectroscopy. The results indicate that pure AN decomposes to N2, N2O, and H2O at the onset of the melt, whereas the mixtures, ANFO and Ammonal, decompose at substantially lower temperatures. The present results also confirm the recently proposed phase IV-IV' transition above 17 GPa and provide new constraints for the melting and phase diagram of AN to 40 GPa and 400°C.
Hubble's diagram and cosmic expansion
Kirshner, Robert P.
2004-01-01
Edwin Hubble's classic article on the expanding universe appeared in PNAS in 1929 [Hubble, E. P. (1929) Proc. Natl. Acad. Sci. USA 15, 168–173]. The chief result, that a galaxy's distance is proportional to its redshift, is so well known and so deeply embedded into the language of astronomy through the Hubble diagram, the Hubble constant, Hubble's Law, and the Hubble time, that the article itself is rarely referenced. Even though Hubble's distances have a large systematic error, Hubble's velocities come chiefly from Vesto Melvin Slipher, and the interpretation in terms of the de Sitter effect is out of the mainstream of modern cosmology, this article opened the way to investigation of the expanding, evolving, and accelerating universe that engages today's burgeoning field of cosmology. PMID:14695886
Phase diagram of ammonium nitrate
NASA Astrophysics Data System (ADS)
Dunuwille, M.; Yoo, C. S.
2014-05-01
Ammonium Nitrate (AN) has often subjected to uses in improvised explosive devices, due to its wide availability as a fertilizer and its capability of becoming explosive with slight additions of organic and inorganic compounds. Yet, the origin of enhanced energetic properties of impure AN (or AN mixtures) is neither chemically unique nor well understood -resulting in rather catastrophic disasters in the past1 and thereby a significant burden on safety in using ammonium nitrates even today. To remedy this situation, we have carried out an extensive study to investigate the phase stability of AN at high pressure and temperature, using diamond anvil cells and micro-Raman spectroscopy. The present results confirm the recently proposed phase IV-to-IV' transition above 17 GPa2 and provide new constraints for the melting and phase diagram of AN to 40 GPa and 400 °C.
A Regime Diagram for Subduction
NASA Astrophysics Data System (ADS)
Stegman, D. R.; Farrington, R.; Capitanio, F. A.; Schellart, W. P.
2009-12-01
Regime diagrams and associated scaling relations have profoundly influenced our understanding of planetary dynamics. Previous regime diagrams characterized the regimes of stagnant-lid, small viscosity contrast, transitional, and no-convection for temperature-dependent (Moresi and Solomatov, 1995), and non-linear power law rheologies (Solomatov and Moresi, 1997) as well as stagnant-lid, sluggish-lid, and mobile-lid regimes once the finite strength of rock was considered (Moresi and Solomatov, 1998). Scalings derived from such models have been the cornerstone for parameterized models of thermal evolution of rocky planets and icy moons for the past decade. While such a theory can predict the tectonic state of a planetary body, it is still rather incomplete in regards to predicting tectonics. For example, the mobile-lid regime is unspecific as to how continuous lithospheric recycling should occur on a terrestrial planet. Towards this goal, Gerya et al., (2008) advanced a new regime diagram aiming to characterize when subduction would manifest itself as a one-sided or two-sided downwelling and either symmetric or asymmetric. Here, we present a regime diagram for the case of a single-sided, asymmetric type of subduction (most Earth-like type). Using a 3-D numerical model of a free subduction, we describe a total of 5 different styles of subduction that can possibly occur. Each style is distinguished by its upper mantle slab morphology resulting from the sinking kinematics. We provide movies to illustrate the different styles and their progressive time-evolution. In each regime, subduction is accommodated by a combination of plate advance and slab rollback, with associated motions of forward plate velocity and trench retreat, respectively. We demonstrate that the preferred subduction mode depends upon two essential controlling factors: 1) buoyancy of the downgoing plate and 2) strength of plate in resisting bending at the hinge. We propose that a variety of subduction
Phase diagrams for the blue phases of highly chiral liquid crystals
NASA Astrophysics Data System (ADS)
Bowling, Miriam B.; Collings, Peter J.; Booth, Christopher J.; Goodby, John W.
1993-11-01
Polarizing microscopy and optical-activity measurements are used to determine the phase diagram for the blue phases of chiral-racemic mixtures of terephthaloyloxy-bis-4-(2'-methylbutyl) benzoate. Contrary to an earlier report, it is the second blue phase (BP II) rather than the first blue phase (BP I) that is not stable relative to the other blue phases at high chirality. With this development, all phase diagrams for the blue phases reported to date have the same topology. Using similar data for two other highly chiral systems, it is found that a simple scaling of the temperature and chiral-fraction axes produces phase diagrams in quantitative agreement with the present results. Thus, in spite of differences in molecular structure, the number of chiral centers, and phase-transition temperatures, these three systems possess remarkably similar phase diagrams and lend evidence for a universal phase diagram for the blue phases.
Temperature‑field phase diagram of extreme magnetoresistance
NASA Astrophysics Data System (ADS)
Fallah Tafti, Fazel; Gibson, Quinn; Kushwaha, Satya; Krizan, Jason W.; Haldolaarachchige, Neel; Cava, Robert Joseph
2016-06-01
The recent discovery of extreme magnetoresistance (XMR) in LaSb introduced lanthanum monopnictides as a new platform to study this effect in the absence of broken inversion symmetry or protected linear band crossing. In this work, we report XMR in LaBi. Through a comparative study of magnetotransport effects in LaBi and LaSb, we construct a temperature‑field phase diagram with triangular shape that illustrates how a magnetic field tunes the electronic behavior in these materials. We show that the triangular phase diagram can be generalized to other topological semimetals with different crystal structures and different chemical compositions. By comparing our experimental results to band structure calculations, we suggest that XMR in LaBi and LaSb originates from a combination of compensated electron‑hole pockets and a particular orbital texture on the electron pocket. Such orbital texture is likely to be a generic feature of various topological semimetals, giving rise to their small residual resistivity at zero field and subject to strong scattering induced by a magnetic field.
Temperature-field phase diagram of extreme magnetoresistance.
Fallah Tafti, Fazel; Gibson, Quinn; Kushwaha, Satya; Krizan, Jason W; Haldolaarachchige, Neel; Cava, Robert Joseph
2016-06-21
The recent discovery of extreme magnetoresistance (XMR) in LaSb introduced lanthanum monopnictides as a new platform to study this effect in the absence of broken inversion symmetry or protected linear band crossing. In this work, we report XMR in LaBi. Through a comparative study of magnetotransport effects in LaBi and LaSb, we construct a temperature-field phase diagram with triangular shape that illustrates how a magnetic field tunes the electronic behavior in these materials. We show that the triangular phase diagram can be generalized to other topological semimetals with different crystal structures and different chemical compositions. By comparing our experimental results to band structure calculations, we suggest that XMR in LaBi and LaSb originates from a combination of compensated electron-hole pockets and a particular orbital texture on the electron pocket. Such orbital texture is likely to be a generic feature of various topological semimetals, giving rise to their small residual resistivity at zero field and subject to strong scattering induced by a magnetic field. PMID:27274081
Mathematical review on source-type diagrams
NASA Astrophysics Data System (ADS)
Aso, Naofumi; Ohta, Kazuaki; Ide, Satoshi
2016-03-01
A source-type diagram is a visualization tool used to display earthquake sources, including double-couples, compensated linear vector dipoles, and isotropic deformation. Together with recent observations of non-double-couple events in a variety of tectonic settings, it is important to be able to recognize the source type intuitively from a representative diagram. Since previous works have proposed diagrams created using a range of projections, we review these diagrams in the framework of the moment tensor eigenvalue space. For further applications, we also provide complete formulas for conversion between moment tensor representation and the coordinate system of each diagram style. Using both a global catalog and synthetic data, we discuss differences between types of diagrams and the relative effectiveness of each.
Continuation of point clouds via persistence diagrams
NASA Astrophysics Data System (ADS)
Gameiro, Marcio; Hiraoka, Yasuaki; Obayashi, Ippei
2016-11-01
In this paper, we present a mathematical and algorithmic framework for the continuation of point clouds by persistence diagrams. A key property used in the method is that the persistence map, which assigns a persistence diagram to a point cloud, is differentiable. This allows us to apply the Newton-Raphson continuation method in this setting. Given an original point cloud P, its persistence diagram D, and a target persistence diagram D‧, we gradually move from D to D‧, by successively computing intermediate point clouds until we finally find a point cloud P‧ having D‧ as its persistence diagram. Our method can be applied to a wide variety of situations in topological data analysis where it is necessary to solve an inverse problem, from persistence diagrams to point cloud data.
Zhao, Dong-Xia; Yang, Zhong-Zhi
2014-05-15
In recent years, the basic problem of understanding chemical bonding, nonbonded, and/or van der Waals interactions has been intensively debated in terms of various theoretical methods. We propose and construct the potential acting on one electron in a molecule-molecular orbital (PAEM-MO) diagram, which draws the PAEM inserted the MO energy levels with their major atomic orbital components. PAEM-MO diagram is able to show clear distinction of chemical bonding from nonbonded and/or vdW interactions. The rule for this is as follows. Along the line connecting two atoms in a molecule or a complex, the existence of chemical bonding between these two atoms needs to satisfy two conditions: (a) a critical point of PAEM exists and (b) PAEM barrier between the two atoms is lower in energy than the occupied major valence-shell bonding MO which contains in-phase atomic components (positive overlap) of the two considered atoms. In contrast to the chemical bonding, for a nonbonded interaction or van der Waals interaction between two atoms, both conditions (a) and (b) do not be satisfied at the same time. This is demonstrated and discussed by various typical cases, particularly those related to helium atom and H-H bonding in phenanthrene. There are helium bonds in HHeF and HeBeO molecules, whereas no H-H bonding in phenanthrene. The validity and limitation for this rule is demonstrated through the investigations of the curves of the PAEM barrier top and MO energies versus the internuclear distances for He2 , H2 , and He2 (+) systems. PMID:24615750
The neptunium-iron phase diagram
NASA Astrophysics Data System (ADS)
Gibson, J. K.; Haire, R. G.; Beahm, E. C.; Gensini, M. M.; Maeda, A.; Ogawa, T.
1994-08-01
The phase relations in the Np-Fe alloy system have been elucidated using differential thermal analysis. A phase diagram for this system is postulated based upon the experimental results, regular-solution model calculations, and an expected correspondence to the U-Fe and Pu-Fe diagrams. The postulated Np-Fe diagram is characterized by limited terminal solid solubilities, two intermetallic solid phases, NpFe 2 and Np 6Fe, and two eutectics.
Jasmine, N Jeeva; Muthiah, P Thomas; Arunagiri, C; Subashini, A
2015-06-01
The FT-IR, FT-Raman, (1)H, (13)C NMR and UV-Visible spectral measurements of N'-hydroxy-pyrimidine-2-carboximidamide (HPCI) and complete analysis of the observed spectra have been proposed. DFT calculation has been performed and the structural parameters of the compound was determined from the optimized geometry with 6-311+G(d,p) basis set and giving energies, harmonic vibrational frequencies and force constants. The results of the optimized molecular structure are presented and compared with the experimental. The geometric parameters, harmonic vibrational frequencies and chemical shifts were compared with the experimental data of the molecule. The title compound, C5H6N4O, is approximately planar, with an angle of 11.04 (15)°. The crystal structure is also stabilized by intermolecular N-H⋯O, N-H⋯N, O-H⋯N, C-H⋯O hydrogen bond and offset π-π stacking interactions. The influences of hydroxy and carboximidamide groups on the skeletal modes and proton chemical shifts have been investigated. Moreover, we have not only simulated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) but also determined the transition state and band gap. The kinetic, thermodynamic stability and chemical hardness of the molecule have been determined. Complete NBO analysis was also carried out to find out the intermolecular electronic interactions and their stabilization energy. The thermodynamic properties like entropies and their correlations with temperatures were also obtained from the harmonic frequencies of the optimized structure.
Moon, Jiwon; Kim, Joonghan
2016-09-29
Density functional theory (DFT) and ab initio calculations, including spin-orbit coupling (SOC), were performed to investigate the spin-orbit (SO) effect on the molecular properties of tellurium halides, TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4). SOC elongates the Te-X bond and slightly reduces the vibrational frequencies. Consideration of SOC leads to better agreement with experimental values. Møller-Plesset second-order perturbation theory (MP2) seriously underestimates the Te-X bond lengths. In contrast, B3LYP significantly overestimates them. SO-PBE0 and multireference configuration interactions with the Davidson correction (MRCI+Q), which include SOC via a state-interaction approach, give the Te-I bond length of TeI2 that matches the experimental value. On the basis of the calculated thermochemical energy and optimized molecular structure, TeI4 is unlikely to be stable. The use of PBE0 including SOC is strongly recommended for predicting the molecular properties of Te-containing compounds.
NASA Astrophysics Data System (ADS)
Datta, Dipayan; Kossmann, Simone; Neese, Frank
2016-09-01
The domain-based local pair-natural orbital coupled-cluster (DLPNO-CC) theory has recently emerged as an efficient and powerful quantum-chemical method for the calculation of energies of molecules comprised of several hundred atoms. It has been demonstrated that the DLPNO-CC approach attains the accuracy of a standard canonical coupled-cluster calculation to about 99.9% of the basis set correlation energy while realizing linear scaling of the computational cost with respect to system size. This is achieved by combining (a) localized occupied orbitals, (b) large virtual orbital correlation domains spanned by the projected atomic orbitals (PAOs), and (c) compaction of the virtual space through a truncated pair natural orbital (PNO) basis. In this paper, we report on the implementation of an analytic scheme for the calculation of the first derivatives of the DLPNO-CC energy for basis set independent perturbations within the singles and doubles approximation (DLPNO-CCSD) for closed-shell molecules. Perturbation-independent one-particle density matrices have been implemented in order to account for the response of the CC wave function to the external perturbation. Orbital-relaxation effects due to external perturbation are not taken into account in the current implementation. We investigate in detail the dependence of the computed first-order electrical properties (e.g., dipole moment) on the three major truncation parameters used in a DLPNO-CC calculation, namely, the natural orbital occupation number cutoff used for the construction of the PNOs, the weak electron-pair cutoff, and the domain size cutoff. No additional truncation parameter has been introduced for property calculation. We present benchmark calculations on dipole moments for a set of 10 molecules consisting of 20-40 atoms. We demonstrate that 98%-99% accuracy relative to the canonical CCSD results can be consistently achieved in these calculations. However, this comes with the price of tightening the
NASA Technical Reports Server (NTRS)
Greene, E. F.; Hall, R. B.; Mason, E. A.
1975-01-01
The energy threshold behavior of elastic rainbow scattering near the transition to orbiting is derived. Analysis of the energy dependence of the rainbow angle shows that the full range from high energies down to orbiting can be fitted with two parameters. Thus, measurements of the rainbow angle can give essentially only two pieces of information about the potential. For potentials of common shapes, such measurements are sensitive to regions of the potential just beyond the minimum and give information about the shape of the potential in this range. However, neither a minimum nor a point of inflection in the potential is necessary for rainbow scattering.
Symmetric Monotone Venn Diagrams with Seven Curves
NASA Astrophysics Data System (ADS)
Cao, Tao; Mamakani, Khalegh; Ruskey, Frank
An n-Venn diagram consists of n curves drawn in the plane in such a way that each of the 2 n possible intersections of the interiors and exteriors of the curves forms a connected non-empty region. A k-region in a diagram is a region that is in the interior of precisely k curves. A n-Venn diagram is symmetric if it has a point of rotation about which rotations of the plane by 2π/n radians leaves the diagram fixed; it is polar symmetric if it is symmetric and its stereographic projection about the infinite outer face is isomorphic to the projection about the innermost face. A Venn diagram is monotone if every k-region is adjacent to both some (k - 1)-region (if k > 0) and also to some k + 1 region (if k < n). A Venn diagram is simple if at most two curves intersect at any point. We prove that the "Grünbaum" encoding uniquely identifies monotone simple symmetric n-Venn diagrams and describe an algorithm that produces an exhaustive list of all of the monotone simple symmetric n-Venn diagrams. There are exactly 23 simple monotone symmetric 7-Venn diagrams, of which 6 are polar symmetric.
Seceleanu, Andreea; Szabo, I; Călugăru, M; Dudea, S M; Preda, D
2004-01-01
The purpose of this study was to point out a case with orbital venous abnormalities at the left eye, associated with varices of the legs. The clinical picture of this case was: intermittent exophthalmos, venous malformations at the level of the lids and episclera, elevated ocular pressure. All this signs reveal an abnormality at the level of venous wall, indicating a constitutional weakness of the venous system. The case was investigated by imagistic methods: ultrasound examination, Doppler -ultrasound and magnetic resonance imaging. According to the facts offered by clinical and imagistic investigation this case can be included into the first type of orbital varices, associated with secondary glaucoma provoked by an elevated episcleral venous pressure. PMID:15598045
Echography - eye orbit; Ultrasound - eye orbit; Ocular ultrasonography; Orbital ultrasonography ... eye is numbed with medicine (anesthetic drops). The ultrasound wand (transducer) is placed against the front surface ...
NASA Technical Reports Server (NTRS)
Roberts, William W., Jr.; Stewart, Glen R.
1987-01-01
The role of orbit crowding and cloud-cloud collisions in the formation of GMCs and their organization in global spiral structure is investigated. Both N-body simulations of the cloud system and a detailed analysis of individual particle orbits are used to develop a conceptual understanding of how individual clouds participate in the collective density response. Detailed comparisons are made between a representative cloud-particle simulation in which the cloud particles collide inelastically with one another and give birth to and subsequently interact with young star associations and stripped down simulations in which the cloud particles are allowed to follow ballistic orbits in the absence of cloud-cloud collisions or any star formation processes. Orbit crowding is then related to the behavior of individual particle trajectories in the galactic potential field. The conceptual picture of how GMCs are formed in the clumpy ISMs of spiral galaxies is formulated, and the results are compared in detail with those published by other authors.
Packwood, Daniel M; Oniwa, Kazuaki; Jin, Tienan; Asao, Naoki
2015-04-14
Organic crystals have unique charge transport properties that lie somewhere between delocalised band-type transport and localised hopping transport. In this paper, we use a stochastic tight-binding model to explore how dynamical disorder in organic crystals affects charge transport. By analysing the model in terms of Feynman diagrams (virtual processes), we expose the crucial role of correlated dynamical disorder to the charge transport dynamics in the model at short times in the order of a few hundred femtoseconds. Under correlated dynamical disorder, the random motions of molecules in the crystal allow for low-energy "bonding"-type interactions between neighboring molecular orbitals can persist over long periods of time. On the other hand, the dependence of charge transport on correlated dynamical disorder also tends to localize the charge, as correlated disorder cannot persist far in space. This concept of correlation may be the "missing link" for describing the intermediate regime between band transport and hopping transport that occurs in organic crystals.
Packwood, Daniel M.; Oniwa, Kazuaki; Jin, Tienan; Asao, Naoki
2015-04-14
Organic crystals have unique charge transport properties that lie somewhere between delocalised band-type transport and localised hopping transport. In this paper, we use a stochastic tight-binding model to explore how dynamical disorder in organic crystals affects charge transport. By analysing the model in terms of Feynman diagrams (virtual processes), we expose the crucial role of correlated dynamical disorder to the charge transport dynamics in the model at short times in the order of a few hundred femtoseconds. Under correlated dynamical disorder, the random motions of molecules in the crystal allow for low-energy “bonding”-type interactions between neighboring molecular orbitals can persist over long periods of time. On the other hand, the dependence of charge transport on correlated dynamical disorder also tends to localize the charge, as correlated disorder cannot persist far in space. This concept of correlation may be the “missing link” for describing the intermediate regime between band transport and hopping transport that occurs in organic crystals.
Packwood, Daniel M; Oniwa, Kazuaki; Jin, Tienan; Asao, Naoki
2015-04-14
Organic crystals have unique charge transport properties that lie somewhere between delocalised band-type transport and localised hopping transport. In this paper, we use a stochastic tight-binding model to explore how dynamical disorder in organic crystals affects charge transport. By analysing the model in terms of Feynman diagrams (virtual processes), we expose the crucial role of correlated dynamical disorder to the charge transport dynamics in the model at short times in the order of a few hundred femtoseconds. Under correlated dynamical disorder, the random motions of molecules in the crystal allow for low-energy "bonding"-type interactions between neighboring molecular orbitals can persist over long periods of time. On the other hand, the dependence of charge transport on correlated dynamical disorder also tends to localize the charge, as correlated disorder cannot persist far in space. This concept of correlation may be the "missing link" for describing the intermediate regime between band transport and hopping transport that occurs in organic crystals. PMID:25877586
Risk Mitigation for Managing On-Orbit Anomalies
NASA Technical Reports Server (NTRS)
La, Jim
2010-01-01
This slide presentation reviews strategies for managing risk mitigation that occur with anomalies in on-orbit spacecraft. It reviews the risks associated with mission operations, a diagram of the method used to manage undesirable events that occur which is a closed loop fault analysis and until corrective action is successful. It also reviews the fish bone diagram which is used if greater detail is required and aids in eliminating possible failure factors.
Phase Diagram of Ammonium Nitrate
NASA Astrophysics Data System (ADS)
Dunuwille, Mihindra; Yoo, Choong-Shik
2013-06-01
Ammonium Nitrate (AN) has often been subjected to uses in improvised explosive devices, due to its wide availability as a fertilizer and its capability of becoming explosive with slight additions of organic and inorganic compounds. Yet, the origin of enhanced energetic properties of impure AN (or AN mixtures) is neither chemically unique nor well understood - resulting in rather catastrophic disasters in the past1 and thereby a significant burden on safety, in using ammonium nitrates even today. To remedy this situation, we have carried out an extensive study to investigate the phase stability of AN, in different chemical environments, at high pressure and temperature, using diamond anvil cells and micro-Raman spectroscopy. The present results confirm the recently proposed phase IV-to-IV' transition above 15 GPa2 and provide new constraints for the melting and phase diagram of AN to 40 GPa and 673 K. The present study has been supported by the U.S. DHS under Award Number 2008-ST-061-ED0001.
Phase diagram of ammonium nitrate
Dunuwille, Mihindra; Yoo, Choong-Shik
2013-12-07
Ammonium Nitrate (AN) is a fertilizer, yet becomes an explosive upon a small addition of chemical impurities. The origin of enhanced chemical sensitivity in impure AN (or AN mixtures) is not well understood, posing significant safety issues in using AN even today. To remedy the situation, we have carried out an extensive study to investigate the phase stability of AN and its mixtures with hexane (ANFO–AN mixed with fuel oil) and Aluminum (Ammonal) at high pressures and temperatures, using diamond anvil cells (DAC) and micro-Raman spectroscopy. The results indicate that pure AN decomposes to N{sub 2}, N{sub 2}O, and H{sub 2}O at the onset of the melt, whereas the mixtures, ANFO and Ammonal, decompose at substantially lower temperatures. The present results also confirm the recently proposed phase IV-IV{sup ′} transition above 17 GPa and provide new constraints for the melting and phase diagram of AN to 40 GPa and 400°C.
Free-Body Diagrams: Necessary or Sufficient?
NASA Astrophysics Data System (ADS)
Rosengrant, David; Van Heuvelen, Alan; Etkina, Eugenia
2005-09-01
The Rutgers PAER group is working to help students develop various scientific abilities. One of the abilities is to create, understand and learn to use for qualitative reasoning and problem solving different representations of physical processes such as pictorial representations, motion diagrams, free-body diagrams, and energy bar charts. Physics education literature indicates that using multiple representations is beneficial for student understanding of physics ideas and for problem solving. We developed a special approach to construct and utilize free-body diagrams for representing physical phenomena and for problem solving. We will examine whether students draw free-body diagrams in solving problems when they know they will not receive credit for it; the consistency of their use in different conceptual areas; and if students who use free-body diagrams while solving problems in different areas of physics are more successful then those who do not.
Reading fitness landscape diagrams through HSAB concepts
NASA Astrophysics Data System (ADS)
Vigneresse, Jean-Louis
2014-10-01
Fitness landscapes are conceived as range of mountains, with local peaks and valleys. In terms of potential, such topographic variations indicate places of local instability or stability. The chemical potential, or electronegativity, its value changed of sign, carries similar information. In addition to chemical descriptors defined through hard-soft acid-base (HSAB) concepts and computed through density functional theory (DFT), the principles that rule chemical reactions allow the design of such landscape diagrams. The simplest diagram uses electrophilicity and hardness as coordinates. It allows examining the influence of maximum hardness or minimum electrophilicity principles. A third dimension is introduced within such a diagram by mapping the topography of electronegativity, polarizability or charge exchange. Introducing charge exchange during chemical reactions, or mapping a third parameter (f.i. polarizability) reinforces the information carried by a simple binary diagram. Examples of such diagrams are provided, using data from Earth Sciences, simple oxides or ligands.
NASA Astrophysics Data System (ADS)
Sumimoto, Michinori; Yokogawa, Daisuke; Komeda, Masahiro; Yamamoto, Hidetoshi; Hori, Kenji; Fujimoto, Hitoshi
2011-10-01
The molecular geometries, electronic structures, and excitation energies of NPh 3, NPh 2Me, NPhMe 2, and NMe 3, were investigated using DFT and post-Hartree Fock methods. When the structural stabilities of these compounds were compared to results obtained by using MP4(SDQ) method, it was confirmed that the optimized geometries by using MP2 method were sufficiently reliable. The excited states with large oscillator strengths consisted of transition components from the HOMO. It should be noted that the orbitals of the nitrogen atom mix with the π-orbital of the phenyl group in an anti-bonding way in the HOMO, and the orbital energy increases with this mixing. The unoccupied orbitals are generated from bonding and anti-bonding type interactions between the π-orbitals of the phenyl groups; therefore, the number of phenyl groups strongly affects the energy diagram of the compounds studied. The differences in the energy diagram cause a spectral change in these compounds in the ultraviolet region.
Michelotti, L.
1995-01-01
The past fifteen years have witnessed a remarkable development of methods for analyzing single particle orbit dynamics in accelerators. Unlike their more classic counterparts, which act upon differential equations, these methods proceed by manipulating Poincare maps directly. This attribute makes them well matched for studying accelerators whose physics is most naturally modelled in terms of maps, an observation that has been championed most vigorously by Forest. In the following sections the author sketchs a little background, explains some of the physics underlying these techniques, and discusses the best computing strategy for implementing them in conjunction with modeling accelerators.
NASA Astrophysics Data System (ADS)
Karunakaran, V.; Balachandran, V.
2013-12-01
Fourier transform infrared and Fourier transform Raman spectra of trans-3-(o-hydroxyphenyl-1-phenyl)-2-propen-1-one (or simply 2-hydroxychalcone) were recorded in the regions 4000-400 cm-1 and 3500-100 cm-1, respectively in the solid phase. The vibrational frequencies were calculated by Hartee-Fock and density functional B3LYP methods with 6-311++G(d,p) basis set, using Gaussian 09W program package. A detailed interpretation of the infrared and Raman spectra of 2-hydroxychalcone is reported. The thermodynamic functions of the title compound were also studied by the above methods and the basis set. The stability of the molecule arising from hyper conjugative interactions and accompanying charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The linear polarizability (α) and the first order hyperpolarizability (β) values of the investigated molecule have been computed using DFT quantum mechanical calculations. The HOMO and LUMO energy gap reflects the chemical activity of the molecule. The observed and calculated wave numbers are found to be in good agreement.
NASA Astrophysics Data System (ADS)
Karthick, T.; Balachandran, V.; Perumal, S.; Nataraj, A.
2013-04-01
In this work, the vibrational characteristics of 2-chloro-5-(trifluoromethyl) aniline have been investigated and both the experimental and theoretical vibrational data indicate the presence of various functional groups within the title molecule. The influence of chlorine substituent on the vibrational wavenumbers of a molecule in comparison with aniline and trifluoromethyl aniline has been discussed in detail. The density functional theoretical (DFT) computations were performed at the B3LYP/6-31++G(3df,3pd)/6-31G(3df,3pd) levels to derive the optimized geometry, vibrational wavenumbers with IR and Raman intensities. Furthermore, the molecular orbital calculations such as; natural bond orbitals (NBOs) and HOMO-LUMO energy gap and mapped molecular electrostatic potential (MEP) surfaces were also performed with the same level of DFT. The temperature dependence thermodynamic parameters of a molecule were illustrated on the basis of their correlation graphs. The detailed interpretation of the vibrational spectra has been carried out with the aid of potential energy distribution (PED) results obtained from MOLVIB program. The delocalization of electron density in various constituents of the molecule has been discussed with the aid of NBO and HOMO-LUMO energy gap analysis.
Szostak, Roman; Aubé, Jeffrey; Szostak, Michal
2015-08-21
Twisted amides containing nitrogen at the bridgehead position are attractive practical prototypes for the investigation of the electronic and structural properties of nonplanar amide linkages. Changes that occur during rotation around the N-C(O) axis in one-carbon-bridged twisted amides have been studied using ab initio molecular orbital methods. Calculations at the MP2/6-311++G(d,p) level performed on a set of one-carbon-bridged lactams, including 20 distinct scaffolds ranging from [2.2.1] to [6.3.1] ring systems, with the C═O bond on the shortest bridge indicate significant variations in structures, resonance energies, proton affinities, core ionization energies, frontier molecular orbitals, atomic charges, and infrared frequencies that reflect structural changes corresponding to the extent of resonance stabilization during rotation along the N-C(O) axis. The results are discussed in the context of resonance theory and activation of amides toward N-protonation (N-activation) by distortion. This study demonstrates that one-carbon-bridged lactams-a class of readily available, hydrolytically robust twisted amides-are ideally suited to span the whole spectrum of the amide bond distortion energy surface. Notably, this study provides a blueprint for the rational design and application of nonplanar amides in organic synthesis. The presented findings strongly support the classical amide bond resonance model in predicting the properties of nonplanar amides.
Orbital order of spinless fermions near an optical Feshbach resonance
Hauke, Philipp; Zhao, Erhai; Goyal, Krittika; Deutsch, Ivan H.; Liu, W. Vincent; Lewenstein, Maciej
2011-11-15
We study the quantum phases of a three-color Hubbard model that arises in the dynamics of the p-band orbitals of spinless fermions in an optical lattice. Strong, color-dependent interactions are induced by an optical Feshbach resonance. Starting from the microscopic scattering properties of ultracold atoms, we derive the orbital exchange constants at 1/3 filling on the cubic optical lattice. Using this, we compute the phase diagram in a Gutzwiller ansatz. We find phases with ''axial orbital order'' in which p{sub z} and p{sub x}+ip{sub y} (or p{sub x}-ip{sub y}) orbitals alternate.
Precision orbit determination at the NASA Goddard Space Flight Center
NASA Technical Reports Server (NTRS)
Putney, B.; Kolenkiewicz, R.; Smith, D.; Dunn, P.; Torrence, M. H.
1990-01-01
This paper describes the GEODYN computer program developed by the Geodynamics Branch at the NASA Goddard Space Flight Center and outlines the procedure for accurate satellite orbit and tracking-data analyses. The capabilities of the program allow the development of gravity fields as large as 90 by 90, and a complete modeling of tidal parameters. It is also feasible to numerically integrate a continuous orbit of a satellite such as Lageos for up to 12 years. The evolution of the orbit can be studied, and, by comparison with locally determined orbits, force model improvements can be made. The GEODYN flow diagrams are presented.
NASA Astrophysics Data System (ADS)
Shi, Xiaoling; Wang, Li; Zhao, Jie; Xu, Xingguang
2016-07-01
Within the effective-field theory (EFT), the compensation behaviors in molecular-based ferrimagnet A F eΙΙ F e Ι Ι Ι(C2O4)3 which is described by a mixed spin-2 (FeΙΙ) and spin-5/2 (FeΙΙΙ) ferrimagnetic Ising model on a honeycomb lattice are studied. The Glauber-type stochastic dynamic is used to describe the time evolution of the system under an oscillating magnetic field. A magnetic field dependence of the compensation temperature and a temperature dependence of compensating magnetic field are calculated and both curves agree qualitatively with experimental data. In particular, a two-compensation-points phenomenon which has been reported in the experimental work is also observed in this compound. Dynamic phase boundaries containing the compensation points are calculated. The dynamic tricritical point and critical end point exist on the phase transition lines. Comparing with previous theoretical results obtained by the mean-field theory (MFT), the effective-field theory results show a reasonable improvement over the MFT results.
NASA Astrophysics Data System (ADS)
Risaliti, G.; Lusso, E.
2015-12-01
We present a new method to test the ΛCDM cosmological model and to estimate cosmological parameters based on the nonlinear relation between the ultraviolet and X-ray luminosities of quasars. We built a data set of 1138 quasars by merging several samples from the literature with X-ray measurements at 2 keV and SDSS photometry, which was used to estimate the extinction-corrected 2500 Å flux. We obtained three main results: (1) we checked the nonlinear relation between X-ray and UV luminosities in small redshift bins up to z˜ 6, confirming that the relation holds at all redshifts with the same slope; (2) we built a Hubble diagram for quasars up to z˜ 6, which is well matched to that of supernovae in the common z = 0-1.4 redshift interval and extends the test of the cosmological model up to z˜ 6; and (3) we showed that this nonlinear relation is a powerful tool for estimating cosmological parameters. Using the present data and assuming a ΛCDM model, we obtain {{{Ω }}}M = 0.22{}-0.08+0.10 and {{{Ω }}}{{Λ }} = 0.92{}-0.30+0.18 ({{{Ω }}}M = 0.28 ± 0.04 and {{{Ω }}}{{Λ }} = 0.73 +/- 0.08 from a joint quasar-SNe fit). Much more precise measurements will be achieved with future surveys. A few thousand SDSS quasars already have serendipitous X-ray observations from Chandra or XMM-Newton, and at least 100,000 quasars with UV and X-ray data will be made available by the extended ROentgen Survey with an Imaging Telescope Array all-sky survey in a few years. The Euclid, Large Synoptic Survey Telescope, and Advanced Telescope for High ENergy Astrophysics surveys will further increase the sample size to at least several hundred thousand. Our simulations show that these samples will provide tight constraints on the cosmological parameters and will allow us to test for possible deviations from the standard model with higher precision than is possible today.
NASA Technical Reports Server (NTRS)
Hoyt, Robert (Inventor); Slostad, Jeffrey T. (Inventor); Frank, Scott (Inventor); Barnes, Ian M. (Inventor)
2016-01-01
Orbital winch having: lower and upper frames; spool having upper and lower flanges with lower flange attached to lower frame; axial tether guide mounted to upper frame; secondary slewing ring coaxial with spool and rotatably mounted to upper frame, wherein secondary slewing ring's outer surface has gearing; upper tether guide mounted to inner surface of secondary slewing ring; linear translation means having upper end mounted to upper frame and lower end mounted on lower frame; primary slewing ring rotatably mounted within linear translation means allowing translation axially between flanges, wherein primary slewing ring's outer surface has gearing; lower tether guide mounted on primary slewing ring's inner surface; pinion rod having upper end mounted to upper frame and lower end mounted to lower frame, wherein pinion rod's teeth engage primary and secondary slewing rings' outer surface teeth; and tether passing through axial, upper, and lower tether guides and winding around spool.
Shimomura, Kenta; Muramatsu, Yasuji; Denlinger, Jonathan D.; Gullikson, Eric M.
2008-10-31
We used the DV-X alpha method to analyze the high-resolution soft X-ray emission and absorption spectra in the CK region of titanium carbide (TiC). The spectral profiles of the X-ray emission and absorption can be ssuscfucelly reproduced by the occupied and unoccupied density of states (DOS ), respectively, in the C2p orbitals of the center carbon atoms in a Ti62C63 cluster model, suggesting that the center carbon atom in a large cluster model expanded to the cubic-structured 53 (= 125) atoms provides sufficient DOS for the X-ray spectral analysis of rock-salt structured metal carbides.
High pressure phase diagram of MgO
NASA Astrophysics Data System (ADS)
French, Martin; Cebulla, Daniel; Redmer, Ronald
2015-06-01
In order to improve the understanding of the interior of super-Earths (planets in the range of 1-10 Earth masses) and other exoplanets, ab inito calculations for the planetary materials and the equation of state (EOS) and phase diagram of planetary materials are needed. A typical representative is MgO, which is an abundant material in the Earth's mantle and is also expected to be important for the mantle of exoplanets as well as for the rocky cores of gas giants such as Jupiter. Using ab initio molecular dynamic simulations, we have determined the phase diagram for MgO up to 20000 K and 1.5 TPa. In particular, the transition from the solid to the molten salt has been studied using diffusion analyses and pair distribution functions. The transition from the B1 to the B2 structure in solid MgO is determined by calculating the respective free enthalpies. The phase diagram of MgO is constructed based on accurate EOS data. We compare with results from (decaying) shock and ramp compression experiments and theoretical calculations for the B1-B2 and the liquid-solid transition line.
Equations of state and phase diagrams of hydrogen isotopes
Urlin, V. D.
2013-11-15
A new form of the semiempirical equation of state proposed for the liquid phase of hydrogen isotopes is based on the assumption that its structure is formed by cells some of which contain hydrogen molecules and others contain hydrogen atoms. The values of parameters in the equations of state of the solid (molecular and atomic) phases as well as of the liquid phase of hydrogen isotopes (protium and deuterium) are determined. Phase diagrams, shock adiabats, isentropes, isotherms, and the electrical conductivity of compressed hydrogen are calculated. Comparison of the results of calculations with available experimental data in a wide pressure range demonstrates satisfactory coincidence.
The Art of Free-Body Diagrams.
ERIC Educational Resources Information Center
Puri, Avinash
1996-01-01
Discusses the difficulty of drawing free-body diagrams which only show forces exerted on a body from its neighbors. Presents three ways a body may be modeled: a particle, rigid extended, and nonrigid extended. (MKR)
Phase diagram for passive electromagnetic scatterers.
Lee, Jeng Yi; Lee, Ray-Kuang
2016-03-21
With the conservation of power, a phase diagram defined by amplitude square and phase of scattering coefficients for each spherical harmonic channel is introduced as a universal map for any passive electromagnetic scatterers. Physically allowable solutions for scattering coefficients in this diagram clearly show power competitions among scattering and absorption. It also illustrates a variety of exotic scattering or absorption phenomena, from resonant scattering, invisible cloaking, to coherent perfect absorber. With electrically small core-shell scatterers as an example, we demonstrate a systematic method to design field-controllable structures based on the allowed trajectories in this diagram. The proposed phase diagram and inverse design can provide tools to design functional electromagnetic devices. PMID:27136839
An Improved Mnemonic Diagram for Thermodynamic Relationships.
ERIC Educational Resources Information Center
Rodriguez, Joaquin; Brainard, Alan J.
1989-01-01
Considers pressure, volume, entropy, temperature, Helmholtz free energy, Gibbs free energy, enthalpy, and internal energy. Suggests the mnemonic diagram is for use with simple systems that are defined as macroscopically homogeneous, isotropic, uncharged, and chemically inert. (MVL)
Attribute Reduction Based on Property Pictorial Diagram
Wan, Qing; Wei, Ling
2014-01-01
This paper mainly studies attribute reduction which keeps the lattice structure in formal contexts based on the property pictorial diagram. Firstly, the property pictorial diagram of a formal context is defined. Based on such diagram, an attribute reduction approach of concept lattice is achieved. Then, through the relation between an original formal context and its complementary context, an attribute reduct of complementary context concept lattice is obtained, which is also based on the property pictorial diagram of the original formal context. Finally, attribute reducts in property oriented concept lattice and object oriented concept lattice can be acquired by the relations of attribute reduction between these two lattices and concept lattice of complementary context. In addition, a detailed illustrative example is presented. PMID:25247200
Time-dependent Benioff strain release diagrams
NASA Astrophysics Data System (ADS)
Frid, V.; Goldbaum, J.; Rabinovitch, A.; Bahat, D.
2011-04-01
New time-dependent Benioff strain (TDBS) release diagrams were analyzed for acoustic emission during various loading tests and for electromagnetic (EM) radiation emanating during compression and, tension, which end in failure. TDBS diagrams are Benioff diagrams that are built consecutively, each time using a greater number of events (acoustic or EM emissions) using the last event as if it were associated with the 'actual failure'. An examination of such TDBS diagrams shows that at a certain time point (this time point is denoted by the term 'alarm' time), a comparatively short interval prior to actual collapse, their decreasing part is broken by a positive 'bulge'. This 'bulge' is quantified and an algorithm proposed for its assessment. Using the alarm time and other parameters of the failure process (fall, bulge size and escalation factors, bulge slope and slope fall time), a criterion for estimating the time of the actual collapse is developed and shown to agree well with laboratory experimental results.
Veitch diagram plotter simplifies Boolean functions
NASA Technical Reports Server (NTRS)
Rubin, D. K.
1964-01-01
This device for simplifying the plotting of a Veitch diagram consists of several overlays for blocking out the unwanted squares. This method of plotting the various input combinations to a computer is used in conjunction with the Boolean functions.
Graphene as a reversible spin manipulator of molecular magnets.
Bhandary, Sumanta; Ghosh, Saurabh; Herper, Heike; Wende, Heiko; Eriksson, Olle; Sanyal, Biplab
2011-12-16
One of the primary objectives in molecular nanospintronics is to manipulate the spin states of organic molecules with a d-electron center, by suitable external means. In this Letter, we demonstrate by first principles density functional calculations, as well as second order perturbation theory, that a strain induced change of the spin state, from S=1→S=2, takes place for an iron porphyrin (FeP) molecule deposited at a divacancy site in a graphene lattice. The process is reversible in the sense that the application of tensile or compressive strains in the graphene lattice can stabilize FeP in different spin states, each with a unique saturation moment and easy axis orientation. The effect is brought about by a change in Fe-N bond length in FeP, which influences the molecular level diagram as well as the interaction between the C atoms of the graphene layer and the molecular orbitals of FeP.
Graphene as a Reversible Spin Manipulator of Molecular Magnets
NASA Astrophysics Data System (ADS)
Bhandary, Sumanta; Ghosh, Saurabh; Herper, Heike; Wende, Heiko; Eriksson, Olle; Sanyal, Biplab
2011-12-01
One of the primary objectives in molecular nanospintronics is to manipulate the spin states of organic molecules with a d-electron center, by suitable external means. In this Letter, we demonstrate by first principles density functional calculations, as well as second order perturbation theory, that a strain induced change of the spin state, from S=1→S=2, takes place for an iron porphyrin (FeP) molecule deposited at a divacancy site in a graphene lattice. The process is reversible in the sense that the application of tensile or compressive strains in the graphene lattice can stabilize FeP in different spin states, each with a unique saturation moment and easy axis orientation. The effect is brought about by a change in Fe-N bond length in FeP, which influences the molecular level diagram as well as the interaction between the C atoms of the graphene layer and the molecular orbitals of FeP.
el-Banna, H M
1978-08-01
The phase diagram of an aspirin-acetaminophen-urea system was constructed. The data obtained by the thermomicroscopic method showed that the binary systems of aspirin-acetaminophen, aspirin-urea, and acetaminophen-urea are simple eutectic mixtures with negligible formation of solid solutions or molecular compounds. The equilateral triangular phase diagram of the ternary system revealed that it forms, upon solidification, solid dispersions of the mechanical mixture type. The ternary eutectic corresponded to a composition of 60% aspirin, 20% acetaminophen, and 20% urea at 72 degrees. The method of calculating the composition finally solidified melts, lying within any area of the phase diagram, is presented. Use of the phase diagram in selecting the optimum ratio of components to enhance dissolution rates of these drugs may be possible. PMID:671247
A universal structured-design diagramer
NASA Technical Reports Server (NTRS)
1981-01-01
Program (FLOWCHARTER) generates standardized flowcharts and concordances for development and debugging of programs in any language. User describes programming-language grammar, providing syntax rules in Backus-Naur form (BNF), list of semantic rules, and set of concordance rules. Once grammar is described, user supplies only source code of program to be diagrammed. FLOWCHARTER automatically produces flow diagram and concordance. Source code for program is written for PASCAL Release 2 compiler, as distributed by University of Minnesota.
Elementary diagrams in nuclear and neutron matter
Wiringa, R.B.
1995-08-01
Variational calculations of nuclear and neutron matter are currently performed using a diagrammatic cluster expansion with the aid of nonlinear integral equations for evaluating expectation values. These are the Fermi hypernetted chain (FHNC) and single-operator chain (SOC) equations, which are a way of doing partial diagram summations to infinite order. A more complete summation can be made by adding elementary diagrams to the procedure. The simplest elementary diagrams appear at the four-body cluster level; there is one such E{sub 4} diagram in Bose systems, but 35 diagrams in Fermi systems, which gives a level of approximation called FHNC/4. We developed a novel technique for evaluating these diagrams, by computing and storing 6 three-point functions, S{sub xyz}(r{sub 12}, r{sub 13}, r{sub 23}), where xyz (= ccd, cce, ddd, dde, dee, or eee) denotes the exchange character at the vertices 1, 2, and 3. All 35 Fermi E{sub 4} diagrams can be constructed from these 6 functions and other two-point functions that are already calculated. The elementary diagrams are known to be important in some systems like liquid {sup 3}He. We expect them to be small in nuclear matter at normal density, but they might become significant at higher densities appropriate for neutron star calculations. This year we programmed the FHNC/4 contributions to the energy and tested them in a number of simple model cases, including liquid {sup 3}He and Bethe`s homework problem. We get reasonable, but not exact agreement with earlier published work. In nuclear and neutron matter with the Argonne v{sub 14} interaction these contributions are indeed small corrections at normal density and grow to only 5-10 MeV/nucleon at 5 times normal density.
Lattice and Phase Diagram in QCD
Lombardo, Maria Paola
2008-10-13
Model calculations have produced a number of very interesting expectations for the QCD Phase Diagram, and the task of a lattice calculations is to put these studies on a quantitative grounds. I will give an overview of the current status of the lattice analysis of the QCD phase diagram, from the quantitative results of mature calculations at zero and small baryochemical potential, to the exploratory studies of the colder, denser phase.
Fluctuations and the QCD phase diagram
Schaefer, B.-J.
2012-06-15
In this contribution the role of quantum fluctuations for the QCD phase diagram is discussed. This concerns in particular the importance of the matter back-reaction to the gluonic sector. The impact of these fluctuations on the location of the confinement/deconfinement and the chiral transition lines as well as their interrelation are investigated. Consequences of our findings for the size of a possible quarkyonic phase and location of a critical endpoint in the phase diagram are drawn.
NASA Astrophysics Data System (ADS)
Deleuze, M. S.; Knippenberg, S.
2006-09-01
The scope of the present work is to reconcile electron momentum spectroscopy with elementary thermodynamics, and refute conclusions drawn by Saha et al. in J. Chem. Phys. 123, 124315 (2005) regarding fingerprints of the gauche conformational isomer of 1,3-butadiene in electron momentum distributions that were experimentally inferred from gas phase (e,2e) measurements on this compound [M. J. Brunger et al., J. Chem. Phys. 108, 1859 (1998)]. Our analysis is based on thorough calculations of one-electron and shake-up ionization spectra employing one-particle Green's function theory along with the benchmark third-order algebraic diagrammatic construction [ADC(3)] scheme. Accurate spherically averaged electron momentum distributions are correspondingly computed from the related Dyson orbitals. The ionization spectra and Dyson orbital momentum distributions that were computed for the trans-conformer of 1,3-butadiene alone are amply sufficient to quantitatively unravel the shape of all available experimental (e,2e) electron momentum distributions. A comparison of theoretical ADC(3) spectra for the s-trans and gauche energy minima with inner- and outer-valence high-resolution photoelectron measurements employing a synchrotron radiation beam [D. M. P. Holland et al., J. Phys. B 29, 3091 (1996)] demonstrates that the gauche structure is incompatible with ionization experiments in high-vacuum conditions and at standard temperatures. On the other hand, outer-valence Green's function calculations on the s-trans energy minimum form and approaching basis set completeness provide highly quantitative insights, within ˜0.2eV accuracy, into the available experimental one-electron ionization energies. At last, analysis of the angular dependence of relative (e,2e) ionization intensities nicely confirms the presence of one rather intense π-2 π*+1 satellite at ˜13.1eV in the ionization spectrum of the s-trans conformer.
NASA Astrophysics Data System (ADS)
Long, Sheila Ann Thibeault
The H-H, C-H, and C-C spin-spin coupling constants were calculated by the finite-perturbation, intermediate -neglect-of-differential-overlap method using the Fermi contact interaction for benzene, naphthalene, biphenyl, anthracene, phenanthrene, and pyrene. The calculations were made using both the actual and the average molecular geometries. For all six of these molecules, the agreements between the calculated and the experimental coupling constants were comparable to those previously reported for other, predominantly smaller, molecules. The actual molecular geometries always gave the correct relative order of values for the H-H coupling constants, whereas the average molecular geometries did not always do so. The magnitudes, but not the signs, of the calculated coupling constants were sensitive to small changes in molecular geometry. The results were the best (next best) for the H-H (C-H) coupling constants. In addition the H-H, C-H, N-H, C-C, and N-C spin -spin coupling constants were calculated in a similar manner for pyridine, pyridazine, pyrimidine, pyrazine, s-triazine, quinoline, quinoxaline, phthalazine, benzo g quinoxaline, and benzo b phenazine. The agreements between the theoretical and the experimental values were comparable to those for the polycyclic aromatic hydrocarbons.
Feng, Min; Shi, Yongliang; Lin, Chungwei; Zhao, Jin; Liu, Fupin; Yang, Shangfeng; Petek, Hrvoje
2013-08-01
Energy stabilization of the superatom molecular orbitals (SAMOs) in fullerenes is investigated with the goal of involving their nearly free-electron bands in practical charge transport applications. Combining low-temperature scanning tunneling microscopy-based spectroscopic methods and density functional theory calculations on an endohedral metallofullerene La@C82, we confirm that the s-SAMO of C82 fullerene is stabilized by as much as 2 eV with respect to that of C60 by endohedral doping with the La atom. On the copper metal substrate, the s-SAMO energy is further lowered to just 1 eV above the Fermi level, making the applications of s-SAMO state in transport more plausible. We conclude that in an endohedral metallofullerene, the s-SAMO state is stabilized through the hybridization with the s-symmetry valence state of the metal atom and the stabilization energy correlates with the ionization potential of the free atom.
Josefsson, Ida; Kunnus, Kristjan; Schreck, Simon; Föhlisch, Alexander; de Groot, Frank; Wernet, Philippe; Odelius, Michael
2012-12-01
A new ab initio approach to the calculation of X-ray spectra is demonstrated. It combines a high-level quantum chemical description of the chemical interactions and local atomic multiplet effects. We show here calculated L-edge X-ray absorption (XA) and resonant inelastic X-ray scattering spectra for aqueous Ni(2+) and XA spectra for a polypyridyl iron complex. Our quantum chemical calculations on a high level of accuracy in a post-Hartree-Fock framework give excellent agreement with experiment. This opens the door to reliable and detailed information on chemical interactions and the valence electronic structure in 3d transition-metal complexes also in transient excited electronic states. As we combine a molecular-orbital description with a proper treatment of local atomic electron correlation effects, our calculations uniquely allow, in particular, identifying the influence of interatomic chemical interactions versus intra-atomic correlations in the L-edge X-ray spectra.
NASA Astrophysics Data System (ADS)
Carter, Melvin Keith
2007-04-01
Cyclic voltammogram (CV) electrochemical measurements for pyrocatechol, resorcinol, hydroquinone, pyrogallol, and gallic acid in strong alkaline solution produced observable oxidation-reduction potentials for each hydroxy group present except for resorcinol. UV absorption spectra were also observed for the diluted solutions. Semi-empirical molecular orbital computations were conducted for these molecules of C2 v point group symmetry to determine the character and energies to aid interpretation of the experimental results. CV oxidation removed a π-electron by a radiationless π-π* transition followed by an electron shift from a negative oxygen to the positive aromatic π-system indicated by an observable σ-π* transition. Simple semi-empirical computations correlated with measured excited electronic states during electron transfer.
Wang, Yang; Wu, Bohua; Zhang, Haoyang; Wei, Donghui; Tang, Mingsheng
2016-07-20
A comprehensive density functional theory (DFT) investigation has been performed to interrogate the mechanisms and stereoselectivities of the Csp(2)-Csp(3) single bond activation of cyclobutenones and their [4+2] cycloaddition reaction with imines via N-heterocyclic carbene (NHC) organocatalysis. According to our calculated results, the fundamental reaction pathway contains four steps: nucleophilic addition of NHC to cyclobutenone, C-C bond cleavage for the formation of an enolate intermediate, [4+2] cycloaddition of the enolate intermediate with isatin imine, and the elimination of the NHC catalyst. In addition, the calculated results also reveal that the second reaction step is the rate-determining step, whereas the third step is the regio- and stereo-selectivity determining step. For the regio- and stereo-selectivity determining step, all four possible attack modes were considered. The addition of the C[double bond, length as m-dash]N bond in isatin imine to the dienolate intermediate is more energy favorable than the addition of the C[double bond, length as m-dash]O bond to a dienolate intermediate. Moreover, the Re face addition of the C[double bond, length as m-dash]N bond in isatin imine to the Re face of the dienolate intermediate leading to the SS configuration N-containing product was demonstrated to be most energy favorable, which is mainly due to the stronger second-order perturbation energy value in the corresponding transition state. Furthermore, by tracking the frontier molecular orbital (FMO) changes in the rate-determining C-C bond cleavage step, we found that the reaction obeys the conservation principle of molecular orbital symmetry. We believe that the present work would provide valuable insights into this kind of reaction.
Wang, Yang; Wu, Bohua; Zhang, Haoyang; Wei, Donghui; Tang, Mingsheng
2016-07-20
A comprehensive density functional theory (DFT) investigation has been performed to interrogate the mechanisms and stereoselectivities of the Csp(2)-Csp(3) single bond activation of cyclobutenones and their [4+2] cycloaddition reaction with imines via N-heterocyclic carbene (NHC) organocatalysis. According to our calculated results, the fundamental reaction pathway contains four steps: nucleophilic addition of NHC to cyclobutenone, C-C bond cleavage for the formation of an enolate intermediate, [4+2] cycloaddition of the enolate intermediate with isatin imine, and the elimination of the NHC catalyst. In addition, the calculated results also reveal that the second reaction step is the rate-determining step, whereas the third step is the regio- and stereo-selectivity determining step. For the regio- and stereo-selectivity determining step, all four possible attack modes were considered. The addition of the C[double bond, length as m-dash]N bond in isatin imine to the dienolate intermediate is more energy favorable than the addition of the C[double bond, length as m-dash]O bond to a dienolate intermediate. Moreover, the Re face addition of the C[double bond, length as m-dash]N bond in isatin imine to the Re face of the dienolate intermediate leading to the SS configuration N-containing product was demonstrated to be most energy favorable, which is mainly due to the stronger second-order perturbation energy value in the corresponding transition state. Furthermore, by tracking the frontier molecular orbital (FMO) changes in the rate-determining C-C bond cleavage step, we found that the reaction obeys the conservation principle of molecular orbital symmetry. We believe that the present work would provide valuable insights into this kind of reaction. PMID:27400324
Shuttle Orbiter Uplink Text and Graphics System
NASA Technical Reports Server (NTRS)
Hoover, A. A.; Land, C. K.; Lipoma, P. C.
1978-01-01
This paper presents the definition of requirements for and current design of the Shuttle Orbiter Uplink Text and Graphics System (UT&GS). Beginning in early 1981, the UT&GS will support Shuttle flights by providing the capability of transmitting single-frame imagery from the ground to the orbiting Shuttle vehicle. Such imagery is in the form of maps, text, diagrams, or photographs, and is outputted on the Orbiter as a paper hard copy. Four modes of operation will be provided to minimize the time required to transmit less than full-resolution imagery. This paper discusses the considerations and complications leading to the four modes and associated resolution requirements. The paper also presents the design of the CCD array ground scanner and airborne CRT hardcopier.
Orbital period variation of the eclipsing binary system TT Herculis
NASA Astrophysics Data System (ADS)
Selam, S. O.; Albayrak, B.
2007-02-01
% New photoelectric U BV observations were obtained for the eclipsing binary TT Her at the Ankara University Observatory (AUO) and three new times of minima were calculated from these observations. The (O-C) diagram constructed for all available times of minima of TT Her exhibits a cyclic character superimposed on a quadratic variation. The quadratic character yields an orbital period decrease with a rate of dP/dt=-8.83×10-8 day yr-1 which can be attributed to the mass exchange/loss mechanism in the system. By assuming the presence of a gravitationally bound third body in the system, the analysis of the cyclic nature in the (O-C) diagram revealed a third body with a mass of 0.21 M\\sun orbiting around the eclipsing pair. The possibility of magnetic activity cycle effect as a cause for the observed cyclic variation in the (O-C) diagram was also discussed.
The Semiotic Structure of Geometry Diagrams: How Textbook Diagrams Convey Meaning
ERIC Educational Resources Information Center
Dimmel, Justin K.; Herbst, Patricio G.
2015-01-01
Geometry diagrams use the visual features of specific drawn objects to convey meaning about generic mathematical entities. We examine the semiotic structure of these visual features in two parts. One, we conduct a semiotic inquiry to conceptualize geometry diagrams as mathematical texts that comprise choices from different semiotic systems. Two,…
Yasarawan, Nuttawisit; Thipyapong, Khajadpai; Ruangpornvisuti, Vithaya
2014-06-01
Optimal structures and electronic properties of various species of 3-hydroxycoumarin (3-HCou) have been explored using density functional theory (DFT) methods under polarizable continuum model (PCM) of solvation. Electron transfer from pyrone to benzene moieties is enhanced upon deprotonation. Anionic and radical species have similar orbital-interaction characteristics but the charges in the former are distributed more uniformly. The rate of intramolecular proton transfer for the neutral species increases many folds upon excitation. The HOMO-LUMO transition with π→π* character mainly accounts for the UV absorption of most 3-HCou species in solution. The wavelengths of maximal absorption predicted using TD-DFT method are in agreement with the previous experiment. For the charged species, calculations with the range-corrected functional yield better agreement with the previous experiment. Anionic 3-HCou species shows high degrees of complexation with chromium(III) and copper(II) compared with oxovanadium(IV) and zinc(II). Either oxovanadium(IV) or zinc(II) prefers forming two isomeric complexes with comparable degrees of formation.
49 CFR 1152.10 - System diagram map.
Code of Federal Regulations, 2012 CFR
2012-10-01
... of its rail system or file only a narrative description of its lines that provides all of the... date upon which the diagram or narrative, or any amended diagram or narrative, is filed with the Board... pending before the Board on the date upon which the diagram or narrative, or any amended diagram...
49 CFR 1152.10 - System diagram map.
Code of Federal Regulations, 2013 CFR
2013-10-01
... of its rail system or file only a narrative description of its lines that provides all of the... date upon which the diagram or narrative, or any amended diagram or narrative, is filed with the Board... pending before the Board on the date upon which the diagram or narrative, or any amended diagram...
49 CFR 1152.10 - System diagram map.
Code of Federal Regulations, 2014 CFR
2014-10-01
... of its rail system or file only a narrative description of its lines that provides all of the... date upon which the diagram or narrative, or any amended diagram or narrative, is filed with the Board... pending before the Board on the date upon which the diagram or narrative, or any amended diagram...
The Use of Computational Diagrams and Nomograms in Higher Education.
ERIC Educational Resources Information Center
Brandenburg, Richard K.; Simpson, William A.
1984-01-01
The use of computational diagrams and nomographs for the calculations that frequently occur in college administration is examined. Steps in constructing a nomograph and a four-dimensional computational diagram are detailed, and uses of three- and four-dimensional diagrams are covered. Diagrams and nomographs are useful in the following cases: (1)…
49 CFR 1152.10 - System diagram map.
Code of Federal Regulations, 2011 CFR
2011-10-01
... of its rail system or file only a narrative description of its lines that provides all of the... date upon which the diagram or narrative, or any amended diagram or narrative, is filed with the Board... pending before the Board on the date upon which the diagram or narrative, or any amended diagram...
49 CFR 1152.10 - System diagram map.
Code of Federal Regulations, 2010 CFR
2010-10-01
... of its rail system or file only a narrative description of its lines that provides all of the... date upon which the diagram or narrative, or any amended diagram or narrative, is filed with the Board... pending before the Board on the date upon which the diagram or narrative, or any amended diagram...
Fishbone Diagrams: Organize Reading Content with a "Bare Bones" Strategy
ERIC Educational Resources Information Center
Clary, Renee; Wandersee, James
2010-01-01
Fishbone diagrams, also known as Ishikawa diagrams or cause-and-effect diagrams, are one of the many problem-solving tools created by Dr. Kaoru Ishikawa, a University of Tokyo professor. Part of the brilliance of Ishikawa's idea resides in the simplicity and practicality of the diagram's basic model--a fish's skeleton. This article describes how…
The Butterfly diagram leopard skin pattern
NASA Astrophysics Data System (ADS)
Ternullo, Maurizio
2011-08-01
A time-latitude diagram where spotgroups are given proportional relevance to their area is presented. The diagram reveals that the spotted area distribution is higly dishomogeneous, most of it being concentrated in few, small portions (``knots'') of the Butterfly Diagram; because of this structure, the BD may be properly described as a cluster of knots. The description, assuming that spots scatter around the ``spot mean latitude'' steadily drifting equatorward, is challenged. Indeed, spots cluster around at as many latitudes as knots; a knot may appear at either lower or higher latitudes than previous ones, in a seemingly random way; accordingly, the spot mean latitude abruptly drifts equatorward or even poleward at any knot activation, in spite of any smoothing procedure. Preliminary analyses suggest that the activity splits, in any hemisphere, into two or more distinct ``activity waves'', drifting equatorward at a rate higher than the spot zone as a whole.
Phase diagram of a truncated tetrahedral model.
Krcmar, Roman; Gendiar, Andrej; Nishino, Tomotoshi
2016-08-01
Phase diagram of a discrete counterpart of the classical Heisenberg model, the truncated tetrahedral model, is analyzed on the square lattice, when the interaction is ferromagnetic. Each spin is represented by a unit vector that can point to one of the 12 vertices of the truncated tetrahedron, which is a continuous interpolation between the tetrahedron and the octahedron. Phase diagram of the model is determined by means of the statistical analog of the entanglement entropy, which is numerically calculated by the corner transfer matrix renormalization group method. The obtained phase diagram consists of four different phases, which are separated by five transition lines. In the parameter region, where the octahedral anisotropy is dominant, a weak first-order phase transition is observed. PMID:27627273
Phase diagram of a truncated tetrahedral model
NASA Astrophysics Data System (ADS)
Krcmar, Roman; Gendiar, Andrej; Nishino, Tomotoshi
2016-08-01
Phase diagram of a discrete counterpart of the classical Heisenberg model, the truncated tetrahedral model, is analyzed on the square lattice, when the interaction is ferromagnetic. Each spin is represented by a unit vector that can point to one of the 12 vertices of the truncated tetrahedron, which is a continuous interpolation between the tetrahedron and the octahedron. Phase diagram of the model is determined by means of the statistical analog of the entanglement entropy, which is numerically calculated by the corner transfer matrix renormalization group method. The obtained phase diagram consists of four different phases, which are separated by five transition lines. In the parameter region, where the octahedral anisotropy is dominant, a weak first-order phase transition is observed.
Has Nemesis' orbit been detected?
NASA Astrophysics Data System (ADS)
Delsemme, A. H.
The orbital angular momenta of the system of young comets show a large anisotropy in a plane almost perpendicular to the ecliptic. Such an anisotropy would dissipate by orbital diffusion in a characteristic time of 10 to 30 million years. Therefore it cannot come from primordial or galactic effects and must be due to a recent impulsive event. The impulses due to fast-moving stars or molecular clouds have symmetry properties that do not introduce any anisotropy in the cometary orbits. Only a very slow massive body, with a velocity of the same order as that of the perturbed comets, can introduce a large anisotropy. This implies that it is likely to be bound to the solar system. Identification with the Nemesis proposed to explain the periodicity of the mass extinction of living species does not meet any inconsistency.
A pseudo-haptic knot diagram interface
NASA Astrophysics Data System (ADS)
Zhang, Hui; Weng, Jianguang; Hanson, Andrew J.
2011-01-01
To make progress in understanding knot theory, we will need to interact with the projected representations of mathematical knots which are of course continuous in 3D but significantly interrupted in the projective images. One way to achieve such a goal would be to design an interactive system that allows us to sketch 2D knot diagrams by taking advantage of a collision-sensing controller and explore their underlying smooth structures through a continuous motion. Recent advances of interaction techniques have been made that allow progress to be made in this direction. Pseudo-haptics that simulates haptic effects using pure visual feedback can be used to develop such an interactive system. This paper outlines one such pseudo-haptic knot diagram interface. Our interface derives from the familiar pencil-and-paper process of drawing 2D knot diagrams and provides haptic-like sensations to facilitate the creation and exploration of knot diagrams. A centerpiece of the interaction model simulates a "physically" reactive mouse cursor, which is exploited to resolve the apparent conflict between the continuous structure of the actual smooth knot and the visual discontinuities in the knot diagram representation. Another value in exploiting pseudo-haptics is that an acceleration (or deceleration) of the mouse cursor (or surface locator) can be used to indicate the slope of the curve (or surface) of whom the projective image is being explored. By exploiting these additional visual cues, we proceed to a full-featured extension to a pseudo-haptic 4D visualization system that simulates the continuous navigation on 4D objects and allows us to sense the bumps and holes in the fourth dimension. Preliminary tests of the software show that main features of the interface overcome some expected perceptual limitations in our interaction with 2D knot diagrams of 3D knots and 3D projective images of 4D mathematical objects.
Maeda, Yasuhiro; Nakajima, Yoko; Gotoh, Kana; Hotta, Yuji; Kataoka, Tomoya; Sugiyama, Naruji; Shirai, Naohiro; Ito, Tetsuya; Kimura, Kazunori
2016-01-01
Newborns are routinely screened for organic acidemias by acylcarnitine analysis. We previously reported the partial catalytic methylesterification of dicarboxylic acylcarnitines by benzenesulfonic acid moiety in the solid extraction cartridge during extraction from serum. Since the diagnosis of organic acidemias by tandem mass spectrometry is affected by the higher molecular weight of these derivatized acylcarnitines, we investigated the methylesterification conditions. The kinetic constants for the methylesterification of carboxyl groups on the acyl and carnitine sides of carnitine were 2.5 and 0.24h(-1), respectively. The physical basis underlying this difference in methylesterification rates was clarified theoretically, illustrating that methylesterification during extraction proceeds easily and must be prevented.
Maeda, Yasuhiro; Nakajima, Yoko; Gotoh, Kana; Hotta, Yuji; Kataoka, Tomoya; Sugiyama, Naruji; Shirai, Naohiro; Ito, Tetsuya; Kimura, Kazunori
2016-01-01
Newborns are routinely screened for organic acidemias by acylcarnitine analysis. We previously reported the partial catalytic methylesterification of dicarboxylic acylcarnitines by benzenesulfonic acid moiety in the solid extraction cartridge during extraction from serum. Since the diagnosis of organic acidemias by tandem mass spectrometry is affected by the higher molecular weight of these derivatized acylcarnitines, we investigated the methylesterification conditions. The kinetic constants for the methylesterification of carboxyl groups on the acyl and carnitine sides of carnitine were 2.5 and 0.24h(-1), respectively. The physical basis underlying this difference in methylesterification rates was clarified theoretically, illustrating that methylesterification during extraction proceeds easily and must be prevented. PMID:26597535
NASA Astrophysics Data System (ADS)
Dias, Marta; Carvalho, Patrícia Almeida; Mardolcar, Umesh Vinaica; Tougait, Olivier; Noël, Henri; Gonçalves, António Pereira
2014-04-01
The liquidus projection of the U-rich corner of the B-Fe-U phase diagram is proposed based on X-ray powder diffraction measurements, differential thermal analysis, and scanning electron microscopy observations complemented with energy- and wavelength-dispersive X-ray spectroscopies. Two ternary reactions in this U-rich region were observed and their approximate temperatures were established. In addition, an overview of the complete phase diagram is given, including the liquidus projection; isothermal sections at 1053 K, 1223 K, and 1373 K (780 °C, 950 °C, and 1100 °C); and a U:(Fe,B) = 1:5 isopleth.
Kimura, Takeshi; Murakami, Naoko; Suzuki, Eiichi; Furuyama, Taniyuki; Nakahodo, Tsukasa; Fujihara, Hisashi; Kobayashi, Nagao
2016-05-01
2,5-Diphenyl-3,4-dicyanothiophene (1) and phthalonitrile (2) were mixed and treated with ruthenium (III) trichloride, 4-methylpyridine, and 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) in 2-ethoxyethanol at 135°C, to produce low-symmetrical tetraazaporphyrins (TAPs) (3), (4), (5), and (6) with one to three thiophene rings. Two thiophene-annelated tetraazaporphyrins were isolated as opposite and adjacent isomers 4 and 5. The structure of 3 was determined by X-ray crystallography, showing that the thiophene ring linked at the 3,4-positions on the tetraazaporphyrin scaffold deviates from the mean plane of the four central pyrrole nitrogen atoms (N1-N3-N5-N7). Optical and electrochemical properties of the products were examined by UV-vis and magnetic circular dichroism (MCD) spectroscopy, together with cyclic voltammetry. In the (1)H NMR spectra, the signals of 4-methylpyridine coordinating to the central ruthenium atom appeared at a higher magnetic field than those of uncoordinated 4-methylpyridine itself due to the shielding effect of the TAP ring. Increasing the number of fused thiophene rings resulted in 1) lower magnetic field shifts of the signals of axially coordinated 4-methylpyridine in the (1)H NMR spectra, 2) lower energy shifts of the Q band absorption in the UV-vis spectra, and 3) decreasing (cathodic shift) of the first oxidation potentials. The structures of simplified model compounds were optimized using the DFT method with the Gaussian 09 program at the B3LYP/LANL2DZ level for the Ru atom and the B3LYP/6-31G (d, p) level for the C, H, N, and S atoms. The optimized structures were utilized to calculate the NMR shielding constants, the HOMO and LUMO orbital energies, and the electronic absorption spectra. PMID:26876817
NASA Astrophysics Data System (ADS)
Demircioğlu, Zeynep; Kaştaş, Çiğdem Albayrak; Büyükgüngör, Orhan
2015-07-01
The molecular structure and spectroscopic properties of (E)-2-((4-hydroxy-2-methylphenylimino)methyl)-3-methoxyphenol, were characterized by X-ray diffraction, FT-IR and UV-Vis spectroscopy. All of theoretical calculations and optimized geometric parameters have been calculated by using density functional theory (DFT) with hybrid method B3LYP by 6-31G(d,p) basis set. The title compound of C15H15N1O3 have been analyzed according to electronic and energetics behaviors for enol-imine and keto-amine tautomers. Both these tautomers engender six-membered ring due to intramolecular hydrogen bonded interactions. Two types of intramolecular hydrogen bonds (a) strong O-H⋯N interactions in enol-imine form and (b) N-H⋯O interactions in keto-amine form are compared particularly. The theoretical vibrational frequencies have been found in good agreement with the corresponding experimental data. A study on the electronic and optical properties, absorption wavelengths, excitation energy, dipole moment, molecular electrostatic potential (MEP) and frontier molecular orbital energies are performed using DFT method. Additionally, geometry optimizations in solvent media were performed with the same level of theory by the polarizable continuum model (PCM). The effect of solvents on the tautomeric stability has been investigated. Mulliken Population Method and natural population analysis (NPA) have been studied. NBO analysis is carried out to picture the charge transfer between the localized bonds and lone pairs. The local reactivity of the molecule has been studied using the Fukui function. NLO properties related to polarizability and hyperpolarizability are also discussed.
Zitare, Ulises; Alvarez-Paggi, Damián; Morgada, Marcos N; Abriata, Luciano A; Vila, Alejandro J; Murgida, Daniel H
2015-08-10
The Cu(A) site of cytochrome c oxidase is a redox hub that participates in rapid electron transfer at low driving forces with two redox cofactors in nearly perpendicular orientations. Spectroscopic and electrochemical characterizations performed on first and second-sphere mutants have allowed us to experimentally detect the reversible switching between two alternative electronic states that confer different directionalities to the redox reaction. Specifically, the M160H variant of a native Cu(A) shows a reversible pH transition that allows to functionally probe both states in the same protein species. Alternation between states exerts a dramatic impact on the kinetic redox parameters, thereby suggesting this effect as the mechanism underlying the efficiency and directionality of Cu(A) electron transfer in vivo. These findings may also prove useful for the development of molecular electronics.
Study flow diagrams in Cochrane systematic review updates: an adapted PRISMA flow diagram.
Stovold, Elizabeth; Beecher, Deirdre; Foxlee, Ruth; Noel-Storr, Anna
2014-05-29
Cochrane systematic reviews are conducted and reported according to rigorous standards. A study flow diagram must be included in a new review, and there is clear guidance from the PRISMA statement on how to do this. However, for a review update, there is currently no guidance on how study flow diagrams should be presented. To address this, a working group was formed to find a solution and produce guidance on how to use these diagrams in review updates.A number of different options were devised for how these flow diagrams could be used in review updates, and also in cases where multiple searches for a review or review update have been conducted. These options were circulated to the Cochrane information specialist community for consultation and feedback. Following the consultation period, the working group refined the guidance and made the recommendation that for review updates an adapted PRISMA flow diagram should be used, which includes an additional box with the number of previously included studies feeding into the total. Where multiple searches have been conducted, the results should be added together and treated as one set of results.There is no existing guidance for using study flow diagrams in review updates. Our adapted diagram is a simple and pragmatic solution for showing the flow of studies in review updates.
Novel P-T Phase Diagram of the Multiorbital Mott Insulator Sr2VO4.
Karmakar, S; Malavi, Pallavi S
2015-04-24
The electrical and optical properties of the Mott insulator Sr2VO4 are investigated under high pressure on a phase pure polycrystalline sample. The system undergoes a pressure-driven insulator to metal transition (IMT) with a crossover between 20 and 24 GPa. The effect of pressure on the thermally driven electronic changes resulting from spin-orbital ordering transitions is studied. A multiorbital analysis of the low frequency optical conductivity spectra suggests a bandwidth-controlled and orbital selective nature of the Mott IMT transition. Dramatic enhancement of the low energy spectral weight in the high pressure correlated metallic phase is explained in terms of the formation of a quasiparticle peak in the spectral function of the narrow and degenerate d(yz,zx) orbitals. Our results overall establish a novel electronic phase diagram of tetragonal Sr2VO4.
Nonverbal Poetry: Family Life-Space Diagrams.
ERIC Educational Resources Information Center
Bardill, Donald R.
2001-01-01
Examines life-space diagrams as a form of nonverbal poetry which taps personal feelings, tells a story, and characterizes a particular life situation, forming a useful therapy technique that provides a family the opportunity to examine its internal family relationships. Offers two case studies, discusses five levels of knowing and awareness, and…
Computer-Generated Diagrams for the Classroom.
ERIC Educational Resources Information Center
Carle, Mark A.; Greenslade, Thomas B., Jr.
1986-01-01
Describes 10 computer programs used to draw diagrams usually drawn on chalkboards, such as addition of three vectors, vector components, range of a projectile, lissajous figures, beats, isotherms, Snell's law, waves passing through a lens, magnetic field due to Helmholtz coils, and three curves. Several programming tips are included. (JN)
Spin wave Feynman diagram vertex computation package
NASA Astrophysics Data System (ADS)
Price, Alexander; Javernick, Philip; Datta, Trinanjan
Spin wave theory is a well-established theoretical technique that can correctly predict the physical behavior of ordered magnetic states. However, computing the effects of an interacting spin wave theory incorporating magnons involve a laborious by hand derivation of Feynman diagram vertices. The process is tedious and time consuming. Hence, to improve productivity and have another means to check the analytical calculations, we have devised a Feynman Diagram Vertex Computation package. In this talk, we will describe our research group's effort to implement a Mathematica based symbolic Feynman diagram vertex computation package that computes spin wave vertices. Utilizing the non-commutative algebra package NCAlgebra as an add-on to Mathematica, symbolic expressions for the Feynman diagram vertices of a Heisenberg quantum antiferromagnet are obtained. Our existing code reproduces the well-known expressions of a nearest neighbor square lattice Heisenberg model. We also discuss the case of a triangular lattice Heisenberg model where non collinear terms contribute to the vertex interactions.
Kaler, J.B.
1988-05-01
The evolution of various types of stars along the H-R diagram is discussed. Star birth and youth is addressed, and the events that occur due to core contraction, shell burning, and double-shell burning are described. The evolutionary courses of planetary nebulae, white dwarfs, and supernovas are examined.
Complexities of One-Component Phase Diagrams
ERIC Educational Resources Information Center
Ciccioli, Andrea; Glasser, Leslie
2011-01-01
For most materials, the solid at and near the triple-point temperature is denser than the liquid with which it is in equilibrium. However, for water and certain other materials, the densities of the phases are reversed, with the solid being less dense. The profound consequences for the appearance of the "pVT" diagram of one-component materials…
Constructing Causal Diagrams to Learn Deliberation
ERIC Educational Resources Information Center
Easterday, Matthew W.; Aleven, Vincent; Scheines, Richard; Carver, Sharon M.
2009-01-01
Policy problems like "What should we do about global warming?" are ill-defined in large part because we do not agree on a system to represent them the way we agree Algebra problems should be represented by equations. As a first step toward building a policy deliberation tutor, we investigated: (a) whether causal diagrams help students learn to…
Fog Machines, Vapors, and Phase Diagrams
ERIC Educational Resources Information Center
Vitz, Ed
2008-01-01
A series of demonstrations is described that elucidate the operation of commercial fog machines by using common laboratory equipment and supplies. The formation of fogs, or "mixing clouds", is discussed in terms of the phase diagram for water and other chemical principles. The demonstrations can be adapted for presentation suitable for elementary…
Image Attributes: A Study of Scientific Diagrams.
ERIC Educational Resources Information Center
Brunskill, Jeff; Jorgensen, Corinne
2002-01-01
Discusses advancements in imaging technology and increased user access to digital images, as well as efforts to develop adequate indexing and retrieval methods for image databases. Describes preliminary results of a study of undergraduates that explored the attributes naive subjects use to describe scientific diagrams. (Author/LRW)
Dynamic Tactile Diagram Simplification on Refreshable Displays
ERIC Educational Resources Information Center
Rastogi, Ravi; Pawluk, Dianne T. V.
2013-01-01
The increasing use of visual diagrams in educational and work environments, and even our daily lives, has created obstacles for individuals who are blind or visually impaired to "independently" access the information they represent. Although physical tactile pictures can be created to convey the visual information, it is typically a slow,…
Phase diagram of spiking neural networks
Seyed-allaei, Hamed
2015-01-01
In computer simulations of spiking neural networks, often it is assumed that every two neurons of the network are connected by a probability of 2%, 20% of neurons are inhibitory and 80% are excitatory. These common values are based on experiments, observations, and trials and errors, but here, I take a different perspective, inspired by evolution, I systematically simulate many networks, each with a different set of parameters, and then I try to figure out what makes the common values desirable. I stimulate networks with pulses and then measure their: dynamic range, dominant frequency of population activities, total duration of activities, maximum rate of population and the occurrence time of maximum rate. The results are organized in phase diagram. This phase diagram gives an insight into the space of parameters – excitatory to inhibitory ratio, sparseness of connections and synaptic weights. This phase diagram can be used to decide the parameters of a model. The phase diagrams show that networks which are configured according to the common values, have a good dynamic range in response to an impulse and their dynamic range is robust in respect to synaptic weights, and for some synaptic weights they oscillates in α or β frequencies, independent of external stimuli. PMID:25788885
NFHS Court and Field Diagram Guide.
ERIC Educational Resources Information Center
Gillis, John, Ed.
This guide contains a comprehensive collection of diagrams and specifications of playing fields and courts used in interscholastic and recreational sports, along with information on how to set up various formats of tournament drawings, how to compute golf handicaps, and how to convert metric-to-English distances. Lists are provided of national…