Energy Ordering of Molecular Orbitals
2016-01-01
Orbitals are invaluable in providing a model of bonding in molecules or between molecules and surfaces. Most present-day methods in computational chemistry begin by calculating the molecular orbitals of the system. To what extent have these mathematical objects analogues in the real world? To shed light on this intriguing question, we employ a photoemission tomography study on monolayers of 3,4,9,10-perylene-tetracarboxylic acid dianhydride (PTCDA) grown on three Ag surfaces. The characteristic photoelectron angular distribution enables us to assign individual molecular orbitals to the emission features. When comparing the resulting energy positions to density functional calculations, we observe deviations in the energy ordering. By performing complete active space calculations (CASSCF), we can explain the experimentally observed orbital ordering, suggesting the importance of static electron correlation beyond a (semi)local approximation. On the other hand, our results also show reality and robustness of the orbital concept, thereby making molecular orbitals accessible to experimental observations. PMID:27935313
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)
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).
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.
NASA Astrophysics Data System (ADS)
Roskop, Luke; Fedorov, Dmitri G.; Gordon, Mark S.
2013-07-01
The fragment molecular orbital (FMO) method is used to model truncated portions of mesoporous silica nanoparticle (MSN) pores. The application of the FMO/RHF (restricted Hartree-Fock) method to MCM-41 type MSNs is discussed and an error analysis is given. The FMO/RHF method is shown to reliably approximate the RHF energy (error ∼0.2 kcal/mol), dipole moment (error ∼0.2 debye) and energy gradient (root mean square [RMS] error ∼0.2 × 10-3 a.u./bohr). Several FMO fragmentation schemes are employed to provide guidance for future applications to MSN models. An MSN pore model is functionalised with (phenyl)propyl substituents and the diffusion barrier for benzene passing through the pore is computed by the FMO/RHF-D method with the Grimme dispersion correction (RHF-D). For the reaction coordinates examined here, the maximum FMO/RHF-D interaction energies range from -0.3 to -5.8 kcal/mol.
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.
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.
Floating orbital molecular dynamics simulations.
Perlt, Eva; Brüssel, Marc; Kirchner, Barbara
2014-04-21
We introduce an alternative ab initio molecular dynamics simulation as a unification of Hartree-Fock molecular dynamics and the floating orbital approach. The general scheme of the floating orbital molecular dynamics method is presented. Moreover, a simple but sophisticated guess for the orbital centers is provided to reduce the number of electronic structure optimization steps at each molecular dynamics step. The conservation of total energy and angular momentum is investigated in order to validate the floating orbital molecular dynamics approach with and without application of the initial guess. Finally, a water monomer and a water dimer are simulated, and the influence of the orbital floating on certain properties like the dipole moment is investigated.
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.
Tsukamoto, Yusuke; Ikabata, Yasuhiro; Romero, Jonathan; Reyes, Andrés; Nakai, Hiromi
2016-10-05
An efficient computational method to evaluate the binding energies of many protons in large systems was developed. Proton binding energy is calculated as a corrected nuclear orbital energy using the second-order proton propagator method, which is based on nuclear orbital plus molecular orbital theory. In the present scheme, the divide-and-conquer technique was applied to utilize local molecular orbitals. This use relies on the locality of electronic relaxation after deprotonation and the electron-nucleus correlation. Numerical assessment showed reduction in computational cost without the loss of accuracy. An initial application to model a protein resulted in reasonable binding energies that were in accordance with the electrostatic environment and solvent effects.
Mapping Interaction Energies in Chorismate Mutase with the Fragment Molecular Orbital Method.
Pruitt, Spencer R; Steinmann, Casper
2017-03-02
The Claisen rearrangement of chorismate to prephenate is mapped across the entire reaction pathway using the fragment molecular orbital (FMO) method. Three basis sets (6-31G(d), cc-pVDZ, and pcseg-1) are studied to provide guidance toward obtaining high accuracy with the FMO method on such systems. Using a fragmentation scheme of one residue per fragment, the FMO method using the 6-31G(d) basis set and second-order Møller-Plesset perturbation theory (MP2) with the hybrid orbital projection fragmentation scheme provides the most reliable results across the entire reaction pathway. Calculations using the multilayer FMO method are performed and shown to be in agreement with single-layer calculations in all cases with differences of less than one kilocalorie per mole for all tested basis set combinations along the entire reaction path. The use of restricted Hartree-Fock for the lower-level layer and MP2 for the higher-level layer gives the most consistent results when using the same basis set for both layers. Pair interaction energy decomposition analysis calculations confirm that electrostatic interactions are the predominant force between three key arginine residues and chorismate and that dispersion and charge transfer interactions in the binding pocket also play a role in the local chemistry of the reaction.
Herder, Martin; Eisenreich, Fabian; Bonasera, Aurelio; Grafl, Anna; Grubert, Lutz; Pätzel, Michael; Schwarz, Jutta; Hecht, Stefan
2017-01-17
Among bistable photochromic molecules, diarylethenes (DAEs) possess the distinct feature that upon photoisomerization they undergo a large modulation of their π-electronic system, accompanied by a marked shift of the HOMO/LUMO energies and hence oxidation/reduction potentials. The electronic modulation can be utilized to remote-control charge- as well as energy-transfer processes and it can be transduced to functional entities adjacent to the DAE core, thereby regulating their properties. In order to exploit such photoswitchable systems it is important to precisely adjust the absolute position of their HOMO and LUMO levels and to maximize the extent of the photoinduced shifts of these energy levels. Here, we present a comprehensive study detailing how variation of the substitution pattern of DAE compounds, in particular using strongly electron-accepting and chemically stable trifluoromethyl groups either in the periphery or at the reactive carbon atoms, allows for the precise tuning of frontier molecular orbital levels over a broad energy range and the generation of photoinduced shifts of more than 1 eV. Furthermore, the effect of different DAE architectures on the transduction of these shifts to an adjacent functional group is discussed. Whereas substitution in the periphery of the DAE motif has only minor implications on the photochemistry, trifluoromethylation at the reactive carbon atoms strongly disturbs the isomerization efficiency. However, this can be overcome by using a nonsymmetrical substitution pattern or by combination with donor groups, rendering the resulting photoswitches attractive candidates for the construction of remote-controlled functional systems.
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.
Nozaki, Daijiro; Lücke, Andreas; Schmidt, Wolf Gero
2017-02-16
Destructive quantum interference (QI) in molecular junctions has attracted much attention in recent years. It can tune the conductance of molecular devices dramatically, which implies numerous potential applications in thermoelectric and switching applications. There are several schemes that address and rationalize QI in single molecular devices. Dimers play a particular role in this respect because the QI signal may disappear, depending on the dislocation of monomers. We derive a simple rule that governs the occurrence of QI in weakly coupled dimer stacks of both alternant and nonalternant polyaromatic hydrocarbons (PAHs) and extends the Tada-Yoshizawa scheme. Starting from the Green's function formalism combined with the molecular orbital expansion approach, it is shown that QI-induced antiresonances and their energies can be predicted from the amplitudes of the respective monomer terminal molecular orbitals. The condition is illustrated for a toy model consisting of two hydrogen molecules and applied within density functional calculations to alternant dimers of oligo(phenylene-ethynylene) and nonalternant PAHs. Minimal dimer structure modifications that require only a few millielectronvolts and lead to an energy crossing of the essentially preserved monomer orbitals are shown to result in giant conductance switching ratios.
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.
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.
Xu, Xuefei; Yang, Ke R; Truhlar, Donald G
2013-08-13
Complete-active-space self-consistent-field (CASSCF) calculations provide useful reference wave functions for configuration interaction or perturbation theory calculations of excited-state potential energy surfaces including dynamical electron correlation. However, the canonical molecular orbitals (MOs) of CASSCF calculations usually have mixed character in regions of strong interaction of two or more electronic states; therefore, they are unsuitable for diabatization using the configurational uniformity approach. Here, CASSCF diabatic MOs for phenol have been obtained by the 4-fold way, and comparison to the CASSCF canonical MOs shows that they are much smoother. Using these smooth CASSCF diabatic MOs, we performed direct diabatization calculations for the three low-lying states ((1)ππ, (1)ππ*, and (1)πσ*) and their diabatic (scalar) couplings at the dynamically correlated multiconfiguration quasidegenerate perturbation theory (MC-QDPT) level. We present calculations along the O-H stretching and C-C-O-H torsion coordinates for the nonadiabatic photodissociation of phenol to the phenoxyl radical and hydrogen atom. The seams of (1)ππ*/(1)πσ* and (1)ππ/(1)πσ* diabatic crossings are plotted as functions of these coordinates. We also present diabatization calculations for displacements along the out-of-plane ring distortion modes 16a and 16b of the phenyl group. The dominant coupling modes of the two conical intersections ((1)ππ*/(1)πσ* and (1)ππ/(1)πσ*) are discussed. The present diabatization method is confirmed to be valid even for significantly distorted ring structures by diabatization calculations along a reaction path connecting the planar equilibrium geometry of phenol to its strongly distorted prefulvenic form. The present work provides insight into the mode specificity of phenol photodissociation and shows that diabatization at the MC-QDPT level employing CASSCF diabatic MOs can be a good starting point for multidimensional dynamics
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.
Spectroscopic studies, potential energy surface and molecular orbital calculations of pramipexole
NASA Astrophysics Data System (ADS)
Muthu, S.; Uma Maheswari, J.; Srinivasan, S.; Isac paulraj, E.
2013-11-01
A systematic vibrational spectroscopic assignment and analysis of pramipexole [(S)-N6-propyl-4,5,6,7-tetrahydro-1,3-benzothiazole-2,6-diamine] has been carried out using FT-IR and FT-Raman spectral data. The vibrational analysis was aided by an electronic structure calculation based on the hybrid density functional method B3LYP using a 6-311G(d, p) and cc-pVTZ basis sets. Molecular equilibrium geometries, electronic energies, IR and Raman intensities, harmonic vibrational frequencies have been computed. The assignments are based on the experimental IR and Raman spectra, and a complete assignment of the observed spectra has been proposed. The UV-visible spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies and the maximum absorption λmax were determined by time-dependent DFT (TD-DFT) method. The geometrical parameters, vibrational frequencies and absorption wavelengths were compared with the experimental data. The complete vibrational assignments are performed on the basis of the potential energy distributions (PEDs) of the vibrational modes in terms of natural internal coordinates. The simulated FT-IR, FT-Raman, and UV spectra of the title compound have been constructed. In addition, the potential energy surface, HOMO and LUMO energies, the molecular electrostatic potential and the first-order hyperpolarizability have been computed. The magnitude of the first-order hyperpolarizability is 5 times larger than that of urea and the title compound may be a potential applicant for the development of NLO materials.
Diffractive molecular-orbital tomography
NASA Astrophysics Data System (ADS)
Zhai, Chunyang; Zhu, Xiaosong; Lan, Pengfei; Wang, Feng; He, Lixin; Shi, Wenjing; Li, Yang; Li, Min; Zhang, Qingbin; Lu, Peixiang
2017-03-01
High-order-harmonic generation in the interaction of femtosecond lasers with atoms and molecules opens the path to molecular-orbital tomography and to probe the electronic dynamics with attosecond-Ångström resolutions. Molecular-orbital tomography requires both the amplitude and phase of the high-order harmonics. Yet the measurement of phases requires sophisticated techniques and represents formidable challenges at present. Here we report a scheme, called diffractive molecular-orbital tomography, to retrieve the molecular orbital solely from the amplitude of high-order harmonics without measuring any phase information. We have applied this method to image the molecular orbitals of N2, CO2, and C2H2 . The retrieved orbital is further improved by taking account the correction of Coulomb potential. The diffractive molecular-orbital tomography scheme, removing the roadblock of phase measurement, significantly simplifies the molecular-orbital tomography procedure and paves an efficient and robust way to the imaging of more complex molecules.
Sand, Andrew M; Mazziotti, David A
2013-06-28
Different sets of molecular orbitals and the rotations connecting them are of great significance in molecular electronic structure. Most electron correlation methods depend on a reference wave function that separates the orbitals into occupied and unoccupied spaces. Energies and properties from these methods depend upon rotations between the spaces. Some electronic structure methods, such as modified coupled electron pair approximations and the recently developed parametric two-electron reduced density matrix (2-RDM) methods [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], also depend upon rotations between occupied orbitals and rotations between unoccupied orbitals. In this paper, we explore the sensitivity of the ground-state energies from the parametric 2-RDM method to rotations within the occupied space and within the unoccupied space. We discuss the theoretical origin of the rotational dependence and provide computational examples at both equilibrium and non-equilibrium geometries. We also study the effect of these rotations on the size extensivity of the parametric 2-RDM method. Computations show that the orbital rotations have a small effect upon the parametric 2-RDM energies in comparison to the energy differences observed between methodologies such as coupled cluster and parametric 2-RDM. Furthermore, while the 2-RDM method is rigorously size extensive in a local molecular orbital basis set, calculations reveal negligible deviations in nonlocal molecular orbital basis sets such as those from canonical Hartree-Fock calculations.
Visualization of Molecular Orbitals: Formaldehyde
ERIC Educational Resources Information Center
Olcott, Richard J.
1972-01-01
Describes a computer program that plots a solid" representation of molecular orbital charge density which can be used to analyze wave functions of molecules. Illustrated with diagrams for formaldehyde. (AL)
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.
NASA Astrophysics Data System (ADS)
Thirman, Jonathan; Head-Gordon, Martin
2015-08-01
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.
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.
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
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.
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.
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.
NASA Astrophysics Data System (ADS)
Baeck, Kyoung K.; Watts, John D.; Bartlett, Rodney J.
1997-09-01
Analytic coupled-cluster (CC) and many-body perturbation theory (MBPT) energy gradient methods with restricted Hartree-Fock (RHF), unrestricted Hartree-Fock (UHF), restricted open-shell Hartree-Fock (ROHF), and quasi-RHF(QRHF) reference functions are extended to permit dopping core and excited orbitals. By using the canonical property of the semicanonical ROHF orbitals and the RHF orbitals from which the QRHF reference function is constructed, it is shown that a general procedure can be established not only for RHF and UHF, but also for ROHF and QRHF reference functions. The basic theory and implementation are reported. To provide a systematic study of the trends and magnitudes of the effects of dropped molecular orbitals (MOs) on the structures, harmonic frequencies, and ir intensities, we study HCN, C2H2, CO2, HO2, and C2H4 at increasing levels of correlation and basis sets. The effects of the dropped MOs with the largest basis sets are about 0.003 Å and 0.1° in structures and about 1% on harmonic frequencies and ir intensities. The magnitude and the direction of the drop-MO effect tend to be almost constant from MBPT(2) to CCSD(T) methods. The two isomers of S3 are studied by the drop-MO-method, yielding very accurate results.
NASA Astrophysics Data System (ADS)
Charry, J.; Romero, J.; Varella, M. T. do N.; Reyes, A.
2014-05-01
We report positron binding energies (PBEs) for the 20 standard amino acids in the global minimum, hydrogen-bonded, and zwitterionic forms. The calculations are performed at the any-particle molecular-orbital (APMO) Hartree-Fock (HF), Koopmans' theorem (KT), second-order Möller-Plesset (MP2), and second-order propagator (P2) levels of theory. Our study reveals that the APMO KT and APMO P2 methods generally provide higher PBEs than the APMO HF and APMO MP2 methods, respectively, with only a fraction of the computational costs of the latter. We also discuss the impact of the choice of the positronic center on the PBEs and propose a simple and inexpensive procedure, based on the condensed Fukui functions of the parent molecules, to select the most suitable expansion center. The results reported so far indicate that APMO KT and APMO P2 methods are convenient options for a qualitative or semiquantitative analysis of positron binding in medium to large polyatomic systems.
Kubo, Hiromu; Hirose, Takashi; Matsuda, Kenji
2017-03-30
The effect of different substituents on the fluorescence properties of [5]helicene derivatives was investigated in terms of molecular orbital symmetry. Unsubstituted [5]helicene is nonemissive due to the symmetry-forbidden S1 → S0 transition. However, the fluorescence emission rate constant (kf) of [5]helicenes is efficiently increased by removing the orbital degeneracy involved in the S1 → S0 transition. As a result, we achieved a [5]helicene derivative exhibiting a high fluorescence quantum yield (Φf = 0.23) and short emission lifetime (⟨τf⟩ = 1.5 ns), which is in marked contrast to unsubstituted [5]helicene (Φf = 0.04 and ⟨τf⟩ = 26 ns).
Asada, Naoya; Fedorov, Dmitri G.; Kitaura, Kazuo; Nakanishi, Isao; Merz, Kenneth M.
2012-01-01
We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4′-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed method is shown to be efficient and accurate in the evaluation of the protein-ligand interaction energies. PMID:23050059
Simulation of Atomic and Molecular Orbitals
ERIC Educational Resources Information Center
Massey, A. G.; Massey S.
1976-01-01
Describes the use of magnets to simulate s, p, and d atomic orbitals from which a wide variety of molecular orbitals can be derived. The technique gives students an idea of molecular orbitals' shapes and stresses the importance of symmetry labels. (MLH)
NASA Astrophysics Data System (ADS)
Sato, Kota; Sugiyama, Yoko; Uchiyama, Akihiko; Iwabuchi, Susumu; Hirano, Tsuneo; Koinuma, Hideomi
1992-07-01
Successive hydrogen elimination reactions with low activation energies during the formation of a-Si:H by silane plasma chemical vapor deposition are proposed on the basis of an ab initio molecular-orbital method. The activation energy of the first step, the reaction of a dangling-bond site with an adjacent tetrahedrally coordinated silicon atom, was found to be 25.2 kcal/mol at 0 K when the zero-point vibrational energy was taken into account. The subsequent step was an exothermic process with a lower activation energy. The total process was thermodynamically much more favorable than the molecular processes by which a hydrogen atom or molecule is eliminated.
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.
NASA Astrophysics Data System (ADS)
Kobayashi, Masato
2014-02-01
The analytical gradient for the atomic-orbital-based Hartree-Fock-Bogoliubov (HFB) energy functional, the modified form of which was proposed by Staroverov and Scuseria to account for the static electron correlation [J. Chem. Phys. 117, 11107 (2002)], is derived. Interestingly, the Pulay force for the HFB energy is expressed with the same formula as that for the Hartree-Fock method. The efficiency of the present HFB energy gradient is demonstrated in the geometry optimizations of conjugated and biradical systems. The geometries optimized by using the HFB method with the appropriate factor ζ, which controls the degree of static correlation included, are found to show good agreement with those obtained by using a complete active-space self-consistent field method, although they are significantly dependent on ζ.
Kobayashi, Masato
2014-02-28
The analytical gradient for the atomic-orbital-based Hartree-Fock-Bogoliubov (HFB) energy functional, the modified form of which was proposed by Staroverov and Scuseria to account for the static electron correlation [J. Chem. Phys. 117, 11107 (2002)], is derived. Interestingly, the Pulay force for the HFB energy is expressed with the same formula as that for the Hartree-Fock method. The efficiency of the present HFB energy gradient is demonstrated in the geometry optimizations of conjugated and biradical systems. The geometries optimized by using the HFB method with the appropriate factor ζ, which controls the degree of static correlation included, are found to show good agreement with those obtained by using a complete active-space self-consistent field method, although they are significantly dependent on ζ.
Kobayashi, Masato
2014-02-28
The analytical gradient for the atomic-orbital-based Hartree–Fock–Bogoliubov (HFB) energy functional, the modified form of which was proposed by Staroverov and Scuseria to account for the static electron correlation [J. Chem. Phys. 117, 11107 (2002)], is derived. Interestingly, the Pulay force for the HFB energy is expressed with the same formula as that for the Hartree–Fock method. The efficiency of the present HFB energy gradient is demonstrated in the geometry optimizations of conjugated and biradical systems. The geometries optimized by using the HFB method with the appropriate factor ζ, which controls the degree of static correlation included, are found to show good agreement with those obtained by using a complete active-space self-consistent field method, although they are significantly dependent on ζ.
The rotational barrier in ethane: a molecular orbital study.
Quijano-Quiñones, Ramiro F; Quesadas-Rojas, Mariana; Cuevas, Gabriel; Mena-Rejón, Gonzalo J
2012-04-20
The energy change on each Occupied Molecular Orbital as a function of rotation about the C-C bond in ethane was studied using the B3LYP, mPWB95 functional and MP2 methods with different basis sets. Also, the effect of the ZPE on rotational barrier was analyzed. We have found that σ and π energies contribution stabilize a staggered conformation. The σ(s) molecular orbital stabilizes the staggered conformation while the stabilizes the eclipsed conformation and destabilize the staggered conformation. The π(z) and molecular orbitals stabilize both the eclipsed and staggered conformations, which are destabilized by the π(v) and molecular orbitals. The results show that the method of calculation has the effect of changing the behavior of the energy change in each Occupied Molecular Orbital energy as a function of the angle of rotation about the C-C bond in ethane. Finally, we found that if the molecular orbital energy contribution is deleted from the rotational energy, an inversion in conformational preference occurs.
Density functional theory for comprehensive orbital energy calculations.
Nakata, Ayako; Tsuneda, Takao
2013-08-14
This study reveals the reason core 1s orbital energies and the highest occupied molecular orbital (HOMO) energies of hydrogen and rare gas atoms are underestimated by long-range corrected (LC) density functional theory (DFT), which quantitatively reproduces the HOMO energies of other systems and the lowest unoccupied molecular orbital (LUMO) energies. Applying the pseudospectral regional (PR) self-interaction correction (SIC) drastically improved the underestimated orbital energies in LC-DFT calculations, while maintaining or improving the accuracies in the calculated valence HOMO and LUMO energies. This indicates that the self-interaction error in exchange functionals causes the underestimations of core 1s orbital energies and the HOMO energies of hydrogen and rare gas atoms in LC-DFT calculations. To clarify the reason for the improvement, the fractional occupation dependences of total electronic energies and orbital energies were examined. The calculated results clearly showed that the LC-PR functional gives almost linear dependences of total electronic energies for a slight decrease in the occupation number of core 1s orbitals, although this linear dependence disappears for significant decrease due to the shrinking of exchange self-interaction regions. It was also clarified that the PRSIC hardly affects the occupation number dependences of the total electronic energies and orbital energies for the fractional occupations of HOMOs and LUMOs. As a result, it was concluded that core orbital energies are obtained accurately by combining LC-DFT with PRSIC.
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.
Energy and the Elliptical Orbit
NASA Astrophysics Data System (ADS)
Nettles, Bill
2009-03-01
In the January 2007 issue of The Physics Teacher, Prentis, Fulton, Hesse, and Mazzino describe a laboratory exercise in which students use a geometrical analysis inspired by Newton to show that an elliptical orbit and an inverse-square law force go hand in hand. The historical, geometrical, and teamwork aspects of the exercise are useful and important. This paper presents an exercise which uses an energy/angular momentum conservation model for elliptical orbits. This exercise can be done easily by an individual student and on regular notebook-sized paper.
Orbitals and orbital energies in DFT and TDDFT
NASA Astrophysics Data System (ADS)
Baerends, Evert Jan
The status and meaning of orbitals and orbital energies in the Kohn-Sham one-electron model of DFT has been controversial, in contrast to Hartree-Fock orbitals and orbital energies. We will argue the opposite: the exact Kohn-Sham orbitals of DFT are ''better'' than HF orbitals and their orbital energies are much closer to ionization energies than HF orbital energies are. This follows from the relation between the KS potential and the wavefunction, which can be cast in the form vs =vc , kin +vH +vxchole +vresp, where each term depends on the KS orbitals and the wavefunction (the one- or two-particle density matrices). The response potential vresp (r) = ∑ j ∞|/dj(r) | 2 ρ (r) Ij - ∑ i H|/ψs , i(r) | 2 ρ (r) (-ɛi) (dj is the Dyson orbital corresponding to ion state ΨjN - 1 , ψs , i is a Kohn-Sham orbital) enables the connection between ionization energies Ii and orbital energies ɛi to be made. For virtual orbitals and orbital energies similar statements can be made: the shapes and energies of the (exact) KS orbitals are much more realistic than those of the Hartree-Fock model or hybrid functionals. The HOMO-LUMO gap in molecules is very close to the optical gap, and very different from the fundamental gap. In solids the situation is very different, which is the well-known ''KS gap problem''. Again the response potential vresp (a good approximation to it) helps to solve this problem, affording a straigtforward correction method of the KS gap to the fundamental gap.
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.
NASA Astrophysics Data System (ADS)
Azar, R. Julian; Head-Gordon, Martin
2012-01-01
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 Cs-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.
Molecular orbital imaging for partially aligned molecules
NASA Astrophysics Data System (ADS)
Qin, Meiyan; Zhu, Xiaosong
2017-01-01
We investigate molecular orbital reconstruction using high-order harmonic emissions from partially aligned molecular ensembles. By carrying out the reconstruction procedure using the harmonic sampling with or without the spectral minimum, the roles of the harmonic phase and amplitude modulation due to the partial alignment can be separately studied. It is found that with the prior knowledge of the orbital symmetry, the reconstructed result is very sensitive to the modulation of the harmonic phase for the πg orbital, while in the case of σg orbital, the reconstructed result is mainly determined by the harmonic amplitude. These results can provide an important reference for the future experiment of molecular orbital imaging.
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.)
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)
Morikami, Kenji; Itezono, Yoshiko; Nishimoto, Masahiro; Ohta, Masateru
2014-01-01
Compounds with a medium-sized flexible ring often show atropisomerism that is caused by the high-energy barriers between long-lived conformers that can be isolated and often have different biological properties to each other. In this study, the frequency of the transition between the two stable conformers, aS and aR, of thienotriazolodiazepine compounds with flexible 7-membered rings was estimated computationally by Monte Carlo (MC) simulations and validated experimentally by NMR experiments. To estimate the energy barriers for transitions as precisely as possible, the potential energy (PE) surfaces used in the MC simulations were calculated by molecular orbital (MO) methods. To accomplish the MC simulations with the MO-based PE surfaces in a practical central processing unit (CPU) time, the MO-based PE of each conformer was pre-calculated and stored before the MC simulations, and then only referred to during the MC simulations. The activation energies for transitions calculated by the MC simulations agreed well with the experimental ΔG determined by the NMR experiments. The analysis of the transition trajectories of the MC simulations revealed that the transition occurred not only through the transition states, but also through many different transition paths. Our computational methods gave us quantitative estimates of atropisomerism of the thienotriazolodiazepine compounds in a practical period of time, and the method could be applicable for other slow-dynamics phenomena that cannot be investigated by other atomistic simulations.
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.
Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet
2015-02-05
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 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.
1988-01-01
manuals, these ver- 36. R. M . Sweet, in Cephalosporins and Penicillins: sions make use oI the Broyden-Fletcher-Goldfarb- Chemistry and Biology, E . H. Flynn... Ramsden , J. Am. Chem. dure uncovered here will not occur for every SoC., 97, 1311 (1975).molule. isoed m t liely tot occur w n hey 7. M.J. S. Dewar...Clark, A Handbook of Computational Chemistry : 4, 84 (1983); M.J.S. Dewar, M . L. McKee, and H.S. A Practical Guide to Chemical Structure and Energy Rzepa
Liu, Shubin; Schauer, Cynthia K
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.
Molecular orbitals for properties and spectroscopies
NASA Astrophysics Data System (ADS)
Robert, Vincent; Domingo, Alex; Braunstein, Pierre; Danopoulos, Andreas; Monakhov, Kirill
2015-12-01
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 sp3 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 Fe2+/Fe3+ 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 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.
Unitary Optimization of Localized Molecular Orbitals.
Lehtola, Susi; Jónsson, Hannes
2013-12-10
A unified formalism and its implementation is presented for Foster-Boys, fourth moment, Pipek-Mezey, and Edmiston-Ruedenberg type localization schemes of molecular orbitals through unitary optimization of the localizing transform matrix using a recently proposed algorithm [ Abrudan ; et al. Signal Processing 2009 , 89 , 1704 ]. A conjugate gradient algorithm is used with an efficient line search method. The option of using complex valued orbitals is included. Applications to fullerenes from C20 to C100, as well as benzene and arachic acid are presented, showing the capability of the method, which has been implemented in ERKALE, an open source program for electronic structure calculations of atoms and molecules.
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.
NASA Astrophysics Data System (ADS)
Park, Hongkun; Zare, Richard N.
1996-03-01
A theoretical formalism is developed for the quantum-state-specific photoelectron angular distributions (PADs) from the direct photoionization of a diatomic molecule in which both the ionizing state and the state of the ion follow Hund's case (b) coupling. The formalism is based on the molecular-orbital decomposition of the ionization continuum and therefore fully incorporates the molecular nature of the photoelectron-ion scattering within the independent electron approximation. The resulting expression for the quantum-state-specific PADs is dependent on two distinct types of dynamical quantities, one that pertains only to the ionization continuum and the other that depends both on the ionizing state and the ionization continuum. Specifically, the electronic dipole-moment matrix element rlλ exp(iηlλ) for the ejection of a photoelectron with orbital angular momentum quantum number l making a projection λ on the internuclear axis is expressed as ΣαλŪlαλλ exp (iπτ¯αλλ) Mαλλ, where Ūλ is the electronic transformation matrix, τ¯αλλ is the scattering phase shift associated with the αλth continuum molecular orbital, and Mαλλ is the real electronic dipole-moment matrix element that connects the ionizing orbital to the αλth continuum molecular orbital. Because Ūλ and τ¯αλλ depend only on the dynamics in the ionization continuum, this formalism allows maximal exploitation of the commonality between photoionization processes from different ionizing states. It also makes possible the direct experimental investigation of scattering matrices for the photoelectron-ion scattering and thus the dynamics in the ionization continuum by studying the quantum-state-specific PADs, as illustrated in the companion article on the photoionization of NO.
An ab initio molecular orbital study of potential energy surface of the NH2+NO2 reaction
NASA Astrophysics Data System (ADS)
Mebel, A. M.; Hsu, C.-C.; Lin, M. C.; Morokuma, K.
1995-10-01
Potential energy surface of the reaction of NH2 with NO2 has been studied at the QCISD(T)/6-311G(d,p)//MP2/6-311G(d,p)+ZPC[MP2/6-311G(d,p)] and GAUSSIAN-2 (G2) levels of calculation. The reaction is shown to give three different groups of products. H2NO+NO can be produced by two different channels: (i) the barrierless association of the reactants to form H2NNO2 1, followed by the nitro-nitrite rearrangement into H2NONO 3 and the ON bond scission and (ii) the association of H2N with ONO directly forming 3 without barrier, followed by the dissociation 3. The barrier for the nitro-nitrite rearrangement at the transition state (TS) 2, 31.2 kcal/mol with respect to 1, is 20.8 kcal/mol lower than the reactants at the best G2 level. The TS 2 is found to lie significantly lower and to have much tighter structure than those previously reported. The thermodynamically most stable N2O+H2O products can be formed from 1 by the complex mechanism (iii), involving 1,3-hydrogen shift from nitrogen to oxygen, rotation of the OH bond, H shift from one oxygen to another and migration of the second H atom from N to O leading to elimination of H2O. The rate-determining step is the 1,3-H shift at TS 4 which is 12.5 kcal/mol lower than NH2+NO2, but 8.3 kcal/mol higher than the barrier for the nitro-nitrite isomerization at TS 2 at the G2 level. N2+H2O2 cannot be formed in the reaction, but several channels are shown to produce N2+2OH. All of them have as the rate-determining step the second 1,3-hydrogen shift from nitrogen to oxygen at TS 11 or 16, lying by 6.9 kcal/mol higher than NH2+NO2, and are not expected to compete with the reaction mechanisms producing H2NO+NO and N2O+H2O.
Coulomb-corrected molecular orbital tomography of nitrogen
NASA Astrophysics Data System (ADS)
Zhai, Chunyang; He, Lixin; Lan, Pengfei; Zhu, Xiaosong; Li, Yang; Wang, Feng; Shi, Wenjing; Zhang, Qingbin; Lu, Peixiang
2016-03-01
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.
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
2016-03-22
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.
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)
Sato, Kota; Honna, Hiroshi; Iwabuchi, Susumu; Hirano, Tsuneo; Koinuma, Hideomi
1994-07-01
Successive hydrogen-elimination reactions with low activation energies during the formation of a-Si:H by silane plasma chemical-vapor deposition proposed by us were studied by using a larger cluster model on the basis of an ab initio molecular-orbital method. The activation energy of the first step, the reaction of a dangling-bond site with an adjacent tetrahedrally coordinated silicon, was found to be 18.2 kcal/mol (0.79 eV) by employing a larger cluster model. The total process was also shown to be thermodynamically more favorable by using larger cluster models. Thus, the successive process is considered to play an important role in a-Si:H formation processes.
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
Energy and the Elliptical Orbit
ERIC Educational Resources Information Center
Nettles, Bill
2009-01-01
In the January 2007 issue of "The Physics Teacher," Prentis, Fulton, Hesse, and Mazzino describe a laboratory exercise in which students use a geometrical analysis inspired by Newton to show that an elliptical orbit and an inverse-square law force go hand in hand. The historical, geometrical, and teamwork aspects of the exercise are useful and…
Xiao, Shengqiang; Stuart, Andrew C; Liu, Shubin; You, Wei
2009-07-01
Fusing bithiophene units with a benzo moiety, benzo[2,1-b:3,4-b']dithiophene (BDT), was projected by theoretical calculations to lower the highest occupied molecular orbital (HOMO) energy level of the resulting polymers compared with that of the bithiophene unit, which would enhance the open circuit voltage of bulk heterojunction photovoltaic cells fabricated from BDT-based polymers blended with PCBM. The homopolymer of BDT (HMPBDT) and alternating copolymer of BDT with 2,1,3-benzothiadiazole (PBDT-BT) were therefore synthesized and fully characterized. Both the homopolymer (HMPBDT) and the copolymer (PBDT-BT) were experimentally confirmed to have low HOMO energy levels (-5.70 eV for HMPBDT and -5.34 eV for PBDT-BT). Introducing the acceptor moiety (2,1,3-benzothiadiazole) successfully lowered the optical band gap of the copolymer from 2.31 eV (HMPBDT) to 1.78 eV (PBDT-BT). Bulk heterojunction photovoltaic devices were fabricated from blends of these structurally related polymers with PBCM to investigate the photovoltaic performances. The optimized device of HMPBDT:PCBM (1:3, 180 nm) exhibited an improved open circuit voltage (V(oc)) of 0.76 V, a short circuit current (J(sc)) of 0.34 mA/cm(2), and a fill factor (FF) of 0.40, offering an overall efficiency of 0.10%. The observed large phase separation of the thin film by AFM and the large band gap were accountable for the small current. The optimized device of PBDT-BT:PCBM (1:3, 55 nm) demonstrated a better efficiency of 0.6%, with V(oc) = 0.72 V, J(sc) = 2.06 mA/cm(2), and FF = 0.42. The much improved current was attributed to the lower bandgap and better film morphology. However, the low hole mobility limited the thickness of the PBDT-BT:PCBM film, making inaccessible the thicker film which would utilize more light and enhance the current. Further improvements are expected if the mobility and film morphology can be improved by the new materials design, together with low band gap and low HOMO energy level.
Molecular Orbital Based Design Guidelines for Hypergolic Energetic Ionic Liquids
2015-01-01
Journal Article 3. DATES COVERED (From - To) October 2013- December 2013 4. TITLE AND SUBTITLE Molecular Orbital Based Design Guidelines for Hypergolic... orbitals (HOMO) of the anions for a series of ionic liquids and the lowest occupied molecular orbital (LUMO) of HNO3, and variation in the computed...code) 661-525-5657 Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std. 239.18 DOI: 10.1002/prep.201400087 Molecular Orbital Based Design
Conformation effects on the molecular orbitals of serine
NASA Astrophysics Data System (ADS)
Wang, Ke-Dong; Ma, Peng-Fei; Shan, Xu
2011-03-01
This paper calculates the five most stable conformers of serine with Hartree—Fock theory, density functional theory (B3LYP), Møller—Plesset perturbation theory (MP4(SDQ)) and electron propagation theory with the 6-311++G(2d,2p) basis set. The calculated vertical ionization energies for the valence molecular orbitals of each conformer are in agreement with the experimental data, indicating that a range of molecular conformations would coexist in an equilibrium sample. Information of the five outer valence molecular orbitals for each conformer is explored in coordinate and momentum spaces using dual space analysis to investigate the conformational processes, which are generated from the global minimum conformer Ser1 by rotation of C2-C3 (Ser4), C1-C2 (Ser5) and C1-O2 (Ser2 and Ser3). Orbitals 28a, 27a and 26a are identified as the fingerprint orbitals for all the conformational processes. Project supported by the Doctoral Research Fund of Henan Normal University, China (Grant No. 525449).
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.
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)
The Energy of Substituted Ethanes. Asymmetry Orbitals
Salem, Lionel; Hoffmann, Roald; Otto, Peter
1973-01-01
The leading terms in the energy of a general substituted ethane are derived in explicit form as a function of the torsional angle θ, the substituent electronegativities, and their mutual overlaps. The energy is found to be the sum of all four overlaps between pairs of asymmetry orbitals, and satisfies the requisite symmetry properties. PMID:16592060
Band formation in a molecular quantum well via 2D superatom orbital interactions.
Dougherty, Daniel 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 intermolecular orbital overlap in the previously unrecognized superatom character of the σ* orbital of C6F6 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.
NASA Astrophysics Data System (ADS)
Stanke, Monika; Palikot, Ewa; KÈ©dziera, Dariusz; Adamowicz, Ludwik
2016-12-01
An algorithm for calculating the first-order electronic orbit-orbit magnetic interaction correction for an electronic wave function expanded in terms of all-electron explicitly correlated molecular Gaussian (ECG) functions with shifted centers is derived and implemented. The algorithm is tested in calculations concerning the H2 molecule. It is also applied in calculations for LiH and H3+ molecular systems. The implementation completes our work on the leading relativistic correction for ECGs and paves the way for very accurate ECG calculations of ground and excited potential energy surfaces (PESs) of small molecules with two and more nuclei and two and more electrons, such as HeH-, H3+, HeH2, and LiH2+. The PESs will be used to determine rovibrational spectra of the systems.
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
2013-01-08
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.
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
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…
Jasmine, N Jeeva; Muthiah, P Thomas; Arunagiri, C; Subashini, A
2015-06-05
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.
Fragment Molecular Orbital Nonadiabatic Molecular Dynamics for Condensed Phase Systems.
Nebgen, Ben; Prezhdo, Oleg V
2016-09-15
A method for efficiently simulating nonadiabatic molecular dynamics (NAMD) of nanoscale and condensed phase systems is developed and tested. The electronic structure, including force and nonadiabatic coupling, are obtained with the fragment molecular orbital (FMO) approximation, which provides significant computational savings by splitting the system into fragments and computing electronic properties of each fragment subject to the external field due to other all other fragments. The efficiency of the developed technique is demonstrated by studying the effect of explicit solvent molecules on excited state relaxation in the Fe(CO)4 complex. The relaxation in the gas phase occurs on a 50 fs time scale, which is in excellent agreement with previously recorded femtosecond pump-probe spectroscopy. Adding a solvation shell of ethanol molecules to the simulation results in an increase in the excited state lifetime to 100 fs, in agreement with recent femtosecond X-ray spectroscopy measurements.
Field-dressed orbitals in strong-field molecular ionization
NASA Astrophysics Data System (ADS)
Siemering, Robert; Njoya, Oumarou; Weinacht, Thomas; de Vivie-Riedle, Regina
2015-10-01
We demonstrate the importance of considering the shape of field-dressed molecular orbitals in interpreting angle-dependent measures of strong-field ionization from excited states. Our calculations of angle-dependent ionization for three homologous polyatomic molecules with very similar valence orbitals show that one has to take into account the shape of the field-dressed orbitals rather than the field-free orbitals in order to rationalize the experimental measurements.
Orbital views of molecular conductance perturbed by anchor units.
Tsuji, Yuta; Staykov, Aleksandar; Yoshizawa, Kazunari
2011-04-20
Site-specific electron transport phenomena through benzene and benzenedithiol derivatives are discussed on the basis of a qualitative Hückel molecular orbital analysis for better understanding of the effect of anchoring sulfur atoms. A recent work for the orbital control of electron transport through aromatic hydrocarbons provided an important concept for the design of high-conductance connections of a molecule with anchoring atoms. In this work the origin of the frontier orbitals of benzenedithiol derivatives, the effect of the sulfur atoms on the orbitals and on the electron transport properties, and the applicability of the theoretical concept on aromatic hydrocarbons with the anchoring units are studied. The results demonstrate that the orbital view predictions are applicable to molecules perturbed by the anchoring units. The electron transport properties of benzene are found to be qualitatively consistent with those of benzenedithiol with respect to the site dependence. To verify the result of the Hückel molecular orbital calculations, fragment molecular orbital analyses with the extended Hückel molecular orbital theory and electron transport calculations with density functional theory are performed. Calculated results are in good agreement with the orbital interaction analysis. The phase, amplitude, and spatial distribution of the frontier orbitals play an essential role in the design of the electron transport properties through aromatic hydrocarbons.
Ultrafast molecular orbital imaging based on attosecond photoelectron diffraction.
Li, Yang; Qin, Meiyan; Zhu, Xiaosong; Zhang, Qingbin; Lan, Pengfei; Lu, Peixiang
2015-04-20
We present ab initio numerical study of ultrafast ionization dynamics of H(2)(+) as well as CO(2) and N(2) exposed to linearly polarized attosecond extreme ultraviolet pulses. When the molecules are aligned perpendicular to laser polarization direction, photonionization of these molecules show clear and distinguishing diffraction patterns in molecular attosecond photoelectron momentum distributions. The internuclear distances of the molecules are related to the position of the associated diffraction patterns, which can be determined with high accuracy. Moreover, the relative heights of the diffraction fringes contain fruitful information of the molecular orbital structures. We show that the diffraction spectra can be well produced using the two-center interference model. By adopting a simple inversion algorithm which takes into account the symmetry of the initial molecular orbital, we can retrieve the molecular orbital from which the electron is ionized. Our results offer possibility for imaging of molecular structure and orbitals by performing molecular attosecond photoelectron diffraction.
Analytic Gradients for the Effective Fragment Molecular Orbital Method.
Bertoni, Colleen; Gordon, Mark S
2016-10-11
The analytic gradient for the Coulomb, polarization, exchange-repulsion, and dispersion terms of the fully integrated effective fragment molecular orbital (EFMO) method is derived and the implementation is discussed. The derivation of the EFMO analytic gradient is more complicated than that for the effective fragment potential (EFP) gradient, because the geometry of each EFP fragment is flexible (not rigid) in the EFMO approach. The accuracy of the gradient is demonstrated by comparing the EFMO analytic gradient with the numeric gradient for several systems, and by assessing the energy conservation during an EFMO NVE ensemble molecular dynamics simulation of water molecules. In addition to facilitating accurate EFMO geometry optimizations, this allows calculations with flexible EFP fragments to be performed.
Molecular vibrational energy flow
NASA Astrophysics Data System (ADS)
Gruebele, M.; Bigwood, R.
This article reviews some recent work in molecular vibrational energy flow (IVR), with emphasis on our own computational and experimental studies. We consider the problem in various representations, and use these to develop a family of simple models which combine specific molecular properties (e.g. size, vibrational frequencies) with statistical properties of the potential energy surface and wavefunctions. This marriage of molecular detail and statistical simplification captures trends of IVR mechanisms and survival probabilities beyond the abilities of purely statistical models or the computational limitations of full ab initio approaches. Of particular interest is IVR in the intermediate time regime, where heavy-atom skeletal modes take over the IVR process from hydrogenic motions even upon X H bond excitation. Experiments and calculations on prototype heavy-atom systems show that intermediate time IVR differs in many aspects from the early stages of hydrogenic mode IVR. As a result, IVR can be coherently frozen, with potential applications to selective chemistry.
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.
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.
Charge transfer processes: the role of optimized molecular orbitals.
Meyer, Benjamin; Domingo, Alex; Krah, Tim; Robert, Vincent
2014-08-07
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.
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.
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
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.
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.
Imaging the Temporal Evolution of Molecular Orbitals during Ultrafast Dissociation
NASA Astrophysics Data System (ADS)
Sann, H.; Havermeier, T.; Müller, C.; Kim, H.-K.; Trinter, F.; Waitz, M.; Voigtsberger, J.; Sturm, F.; Bauer, T.; Wallauer, R.; Schneider, D.; Weller, M.; Goihl, C.; Tross, J.; Cole, K.; Wu, J.; Schöffler, M. S.; Schmidt-Böcking, H.; Jahnke, T.; Simon, M.; Dörner, R.
2016-12-01
We investigate the temporal evolution of molecular frame angular distributions of Auger electrons emitted during ultrafast dissociation of HCl following a resonant single-photon excitation. The electron emission pattern changes its shape from that of a molecular σ orbital to that of an atomic p state as the system evolves from a molecule into two separated atoms.
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.
Khaliullin, Rustam Z.; Head-Gordon, Martin; Bell, Alexis T.
2008-05-14
A new method based on absolutely localized molecular orbitals (ALMOs) is proposed to measure the degree of intermolecular electron density delocalization (charge transfer) in molecular complexes. ALMO charge transfer analysis (CTA) enables separation of the forward and backward charge transfer components for each pair of molecules in the system. The key feature of ALMO CTA is that all charge transfer terms have corresponding well defined energetic effects that measure the contribution of the given term to the overall energetic stabilization of the system. To simplify analysis of charge transfer effects, the concept of chemically significant complementary occupied-virtual orbital pairs (COVPs) is introduced. COVPs provide a simple description of intermolecular electron transfer effects in terms of just a few localized orbitals. ALMO CTA is applied to understand fundamental aspects of donor-acceptor interactions in borane adducts, synergic bonding in classical and nonclassical metal carbonyls, and multiple intermolecular hydrogen bonds in a complex of isocyanuric acid and melamine. These examples show that the ALMO CTA results are generally consistent with the existing conceptual description of intermolecular bonding. The results also show that charge transfer and the energy lowering due to charge transfer are not proportional to each other, and some interesting differences emerge which are discussed. Additionally, according to ALMO CTA, the amount of electron density transferred between molecules is significantly smaller than charge transfer estimated from various population analysis methods.
Khaliullin, Rustam Z; Bell, Alexis T; Head-Gordon, Martin
2008-05-14
A new method based on absolutely localized molecular orbitals (ALMOs) is proposed to measure the degree of intermolecular electron density delocalization (charge transfer) in molecular complexes. ALMO charge transfer analysis (CTA) enables separation of the forward and backward charge transfer components for each pair of molecules in the system. The key feature of ALMO CTA is that all charge transfer terms have corresponding well defined energetic effects that measure the contribution of the given term to the overall energetic stabilization of the system. To simplify analysis of charge transfer effects, the concept of chemically significant complementary occupied-virtual orbital pairs (COVPs) is introduced. COVPs provide a simple description of intermolecular electron transfer effects in terms of just a few localized orbitals. ALMO CTA is applied to understand fundamental aspects of donor-acceptor interactions in borane adducts, synergic bonding in classical and nonclassical metal carbonyls, and multiple intermolecular hydrogen bonds in a complex of isocyanuric acid and melamine. These examples show that the ALMO CTA results are generally consistent with the existing conceptual description of intermolecular bonding. The results also show that charge transfer and the energy lowering due to charge transfer are not proportional to each other, and some interesting differences emerge which are discussed. Additionally, according to ALMO CTA, the amount of electron density transferred between molecules is significantly smaller than charge transfer estimated from various population analysis methods.
NASA Astrophysics Data System (ADS)
Khaliullin, Rustam Z.; Bell, Alexis T.; Head-Gordon, Martin
2008-05-01
A new method based on absolutely localized molecular orbitals (ALMOs) is proposed to measure the degree of intermolecular electron density delocalization (charge transfer) in molecular complexes. ALMO charge transfer analysis (CTA) enables separation of the forward and backward charge transfer components for each pair of molecules in the system. The key feature of ALMO CTA is that all charge transfer terms have corresponding well defined energetic effects that measure the contribution of the given term to the overall energetic stabilization of the system. To simplify analysis of charge transfer effects, the concept of chemically significant complementary occupied-virtual orbital pairs (COVPs) is introduced. COVPs provide a simple description of intermolecular electron transfer effects in terms of just a few localized orbitals. ALMO CTA is applied to understand fundamental aspects of donor-acceptor interactions in borane adducts, synergic bonding in classical and nonclassical metal carbonyls, and multiple intermolecular hydrogen bonds in a complex of isocyanuric acid and melamine. These examples show that the ALMO CTA results are generally consistent with the existing conceptual description of intermolecular bonding. The results also show that charge transfer and the energy lowering due to charge transfer are not proportional to each other, and some interesting differences emerge which are discussed. Additionally, according to ALMO CTA, the amount of electron density transferred between molecules is significantly smaller than charge transfer estimated from various population analysis methods.
Fabbris, G.; Meyers, D.; Okamoto, J.; Pelliciari, J.; Disa, A. S.; Huang, Y.; Chen, Z. -Y.; Wu, W. B.; Chen, C. T.; Ismail-Beigi, S.; Ahn, C. H.; Walker, F. J.; Huang, D. J.; Schmitt, T.; Dean, M. P. M.
2016-09-30
We used resonant inelastic x-ray scattering to investigate the electronic origin of orbital polarization in nickelate heterostructures taking LaTiO_{3}-LaNiO_{3}-3×(LaAlO_{3}), a system with exceptionally large polarization, as a model system. Furthermore, we find that heterostructuring generates only minor changes in the Ni 3d orbital energy levels, contradicting the often-invoked picture in which changes in orbital energy levels generate orbital polarization. Instead, O K-edge x-ray absorption spectroscopy demonstrates that orbital polarization is caused by an anisotropic reconstruction of the oxygen ligand hole states. This also provides an explanation for the limited success of theoretical predictions based on tuning orbital energy levels and implies that future theories should focus on anisotropic hybridization as the most effective means to drive large changes in electronic structure and realize novel emergent phenomena.
Fabbris, G.; Meyers, D.; Okamoto, J.; ...
2016-09-30
We used resonant inelastic x-ray scattering to investigate the electronic origin of orbital polarization in nickelate heterostructures taking LaTiO3-LaNiO3-3×(LaAlO3), a system with exceptionally large polarization, as a model system. Furthermore, we find that heterostructuring generates only minor changes in the Ni 3d orbital energy levels, contradicting the often-invoked picture in which changes in orbital energy levels generate orbital polarization. Instead, O K-edge x-ray absorption spectroscopy demonstrates that orbital polarization is caused by an anisotropic reconstruction of the oxygen ligand hole states. This also provides an explanation for the limited success of theoretical predictions based on tuning orbital energy levels andmore » implies that future theories should focus on anisotropic hybridization as the most effective means to drive large changes in electronic structure and realize novel emergent phenomena.« less
Study of an orbiting tethered dumbbell system having positive orbital energy
NASA Technical Reports Server (NTRS)
Arnold, David A.
1988-01-01
For very long tethered systems the sum of the kinetic and potential energy can be positive. The system remains in a circular orbit as long as the masses remain vertically aligned. The system is unstable without constant control of the alignment. If the upper mass rotates forward in the direction of the orbital motion, the system escapes out of orbit. If the upper mass rotates backward, the system falls out of orbit and the lower mass impacts the body around which the system is orbiting.
Towards simple orbital-dependent density functionals for molecular dissociation
NASA Astrophysics Data System (ADS)
Zhang, Igor Ying; Richter, Patrick; Scheffler, Matthias
2015-03-01
Density functional theory (DFT) is one of the leading first-principles electronic-structure theories. However, molecular dissociation remains a challenge, because it requires a well-balanced description of the drastically different electronic structure at different bond lengths. One typical and well-documented case is the dissociation of both H2+ and H2, for which all popular DFT functionals fail. We start from the Bethe-Goldstone equation to propose a simple orbital-dependent correlation functional which generalizes the linear adiabatic connection approach. The resulting scheme is based on second-order perturbation theory (PT2), but includes the self-consistent coupling of electron-hole pairs, which ensures the correct H2 dissociation limit and gives a finite correlation energy for systems with a (near)-degenerate energy gap. This coupling PT2-like (CPT2) approximation delivers a significant improvement over all existing functionals for both H2 and H2+ dissociation. We will demonstrate the reason for this improvement analytically for H2 in a minimal basis.
[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).
1984-10-19
a molecular orbital approximation to the electron delocalization energy.1 8 The ASED theory is derived from the Hellmann- Feynman formula for...34 . . 4.•" " ., .7% . r .- - - . , .-. - . . _ .-.- :.- .- . v ._ . _ . " - . ’ " _ _ 12. Wheeler , B. L.; Nagasubramanian, G.; Bard, A. J
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)
Developmental AB Initio Molecular Orbital Theory
NASA Astrophysics Data System (ADS)
Blurock, Edward (Ned) Samuel
The frozen core approximation (FCA) was applied to the main group elements of the first four rows of the periodic table (i.e., through Iodine). For hydride bond lengths, the results of the FCA calculation were consistently closer to experiment. The FCA calculation assumes that the core space is complete and restricts its further optimization. The standard calculation does not have this restriction and further completion of the core space (during the optimization procedure) by valence orbitals on neighboring atoms produced shorter (compared to FCA and experiment) hydride bond lengths. A new set of two-electron integrals was developed combining the use of Rys quadrature and the axis-switch algorithm. The combined algorithm was found to be advantageous only under higher contraction. Also, it was determined that extension of the algorithm to higher angular momentum functions would yield improvement in only selected cases. The SYMGEN program, a symbolic algebra program written by the author, was used to generate and globally optimize the newly developed code. The SYMGEN program is a general program with potential uses in a variety of other coding and global optimization problems.
NASA Astrophysics Data System (ADS)
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 phenyl
Targeting Low-Energy Transfers to Low Lunar Orbit
NASA Technical Reports Server (NTRS)
Parker, Jeffrey S.; Anderson, Rodney L.
2011-01-01
A targeting scheme is presented to build trajectories from a specified Earth parking orbit to a specified low lunar orbit via a low-energy transfer and up to two maneuvers. The total transfer delta V (velocity) is characterized as a function of the Earth parking orbit inclination and the departure date for transfers to each given low lunar orbit. The transfer delta V (velocity) cost is characterized for transfers constructed to low lunar polar orbits with any longitude of ascending node and for transfers that arrive at the Moon at any given time during a month.
Intramolecular charge ordering in the multi molecular orbital system (TTM-TTP)I3
NASA Astrophysics Data System (ADS)
Bonnet, Marie-Laure; Robert, Vincent; Tsuchiizu, Masahisa; Omori, Yukiko; Suzumura, Yoshikazu
2010-06-01
Starting from the structure of the (TTM-TTP)I3 molecular-based material, we examine the characteristics of frontier molecular orbitals using ab initio (CASSCF/CASPT2) configurations interaction calculations. It is shown that the singly occupied and second-highest-occupied molecular orbitals are close to each other, i.e., this compound should be regarded as a two-orbital system. By dividing virtually the [TTM-TTP] molecule into three fragments, an effective model is constructed to rationalize the origin of this picture. In order to investigate the low-temperature, symmetry breaking experimentally observed in the crystal, the electronic distribution in a pair of [TTM-TTP] molecules is analyzed from CASPT2 calculations. Our inspection supports and explains the speculated intramolecular charge ordering which is likely to give rise to low-energy magnetic properties.
NASA Astrophysics Data System (ADS)
Balachandran, Janakiraman; Reddy, Pramod; Dunietz, Barry; Gavini, Vikram
2014-03-01
The frontier molecular orbital (FMO) reorganization and in turn on the thermopower of the aromatic molecules trapped between metal electrodes (aka molecular junctions) depends on two effects namely (1) the stabilization effect - due to the physical presence of the metal electrode atoms and (2) change in e-e interactions - due to end-group mediated charge transfer. The stabilization effect always reduces the FMO energies. The charge transfer effect increases the FMO energies in charge-gaining molecules, which in turn opposes the stabilization effect resulting in a small overall shift. However, the charge transfer effect decreases the FMO energies in charge-losing molecules, which in turn complements the stabilization effect resulting in a large overall downward shift. This hypothesis is validated by delineating the shifts due to stabilization and charge-transfer effects independently. Further we also demonstrate the generality of the hypothesis by applying it on a wide range of aromatic molecules with different length and end-groups. Finally, we also present computationally efficient strategies, based on the proposed mechanism, to quantitatively compute the FMO reorganization which in turn has potential for high throughput analysis of molecular junctions.
Schenker, Sebastian; Schneider, Christopher; Tsogoeva, Svetlana B; Clark, Timothy
2011-11-08
The performance of computationally accessible levels of calculation for the transition states of organocatalytic reaction has been assessed. Reference post-Hartree-Fock single point energy calculations were used as standards for the gas-phase Born-Oppenheimer relative energies of pairs of alternative transition states that lead to the two product enantiomers. We show that semiempirical methods cannot even be relied on to yield qualitatively correct results. The geometries (optimized, for instance, with DFT) have a large impact on the results of high-level post-HF calculations, so that it is essential to use an adequate DFT technique and basis set. DFT can yield quantitatively correct results that are consistent with post-HF calculations if functionals that consider dispersion are used. Geometries for large systems show larger errors than those for smaller ones but are treated better by functionals such as M06-2X and w97Bxd that include dispersion implicitly or explicitly. Local correlation techniques introduce errors of comparable magnitude to those given by different levels of geometry optimization. We recommend RICC2/TZVP//M06-2X/TZVP, RI-MP2/TZVP// M06-2X/TZVP, and M06-2X/TZVP// M06-2X/TZVP calculations in that order, depending on the size of the system.
Energy level alignment of catechol molecular orbitals on ZnO(1 1 2¯ 0) and TiO 2(1 1 0) surfaces
NASA Astrophysics Data System (ADS)
Rangan, Sylvie; Theisen, Jean-Patrick; Bersch, Eric; Bartynski, R. A.
2010-05-01
The occupied and unoccupied electronic structure of catechol adsorbed onto two single crystal surfaces, rutile TiO 2(1 1 0) and wurtzite ZnO(1 1 2¯ 0), have been investigated using UV-photoemission and inverse photoemission spectroscopies (UPS and IPS) in an ultra-high vacuum environment. To aid in assignment of the spectral features, model metal-bound catechol structures were calculated using a DFT approach. From these measurements, the energy alignment of the catechol-related states with respect to the substrates band edges is directly determined and is in good agreement with a direct injection process of the photoexcited electron into the substrate conduction band, resulting in the characteristic absorption properties of adsorbed catechol.
NASA Astrophysics Data System (ADS)
Yamamoto, Takashi; Tamura, Masafumi; Yakushi, Kyuya; Kato, Reizo
2016-10-01
We have carried out the complete analyses of the C=C stretching modes in the vibrational spectra in the triangular lattice of β'-Cs[Pd(dmit)2]2 in order to solve the puzzling phenomenon that the ground state is neither spin frustration nor anti-ferromagnetic state but octamerization. We found that both charge-rich and charge-poor dimers are non-centrosymmetric dimers with the inhomogeneous charges. Because the energy levels of HOMO and LUMO are interchanged due to the tight dimerization, the cooperative interaction between the inter-site Coulomb repulsions and the valence-bond formation operates within and between dimers, those which contribute to the inter-dimer and intra-dimer charge separations, respectively. Octamer is the minimal unit under both cooperative interactions. In the high-temperature phase of β'-Cs[Pd(dmit)2]2, the competition between octamerization and tetramerization is observed because of the suppression of the intra-dimer cooperative interaction. The competition between two different states indicates the degree of freedom characteristic of the molecular orbital due to the tight dimerization. The cooperative interactions of the various X[Pd(dmit)2]2 salts are quantitatively evaluated from the C=C stretching modes.
Orbital-Free Molecular Dynamics Simulations at Extreme Conditions
NASA Astrophysics Data System (ADS)
Kress, J. D.; Collins, L. A.; Ticknor, C.
2015-06-01
Large-scale molecular dynamics (MD) simulations in an orbital-free (OF) density-functional theory (DFT) formulation have been performed for pure and mixed species over a broad range of temperatures (T) and densities (ρ) that includes the warm, dense matter and high-energy density physics regimes. A finite-temperature Thomas-Fermi-Dirac form with a local-density exchange-correlation potential and a regularized electron-ion interaction represents the quantum nature of the electrons. In particular, we examine the efficacy of the OFMD approach as an effective bridge between Kohn-Sham DFT MD at low temperatures and simple, fully-ionized plasma models at high temperatures. Comparisons against intermediate-range constructions such as the Yukawa and one-component plasmas are also made. We examine the mass transport (diffusion, viscosity) properties of various systems, ranging from light to heavy elements, including lithium hydride (LiH), mixtures of LiH with uranium, mixtures of deuterium-tritium (DT) with plutonium and mixtures of DT with plastic (CH). The OFMD mass transport results have been fitted to simple functions of ρ and T suitable for use in hydrodynamics simulation codes.
NASA Astrophysics Data System (ADS)
Canning, A.; Galli, G.; Mauri, F.; De Vita, A.; Car, R.
1996-04-01
The implementation of an O( N) tight-binding molecular dynamics code on the Cray T3D parallel computer is discussed. The O( N) energy functional depends on non-orthogonal, localised orbitals and a chemical potential parameter which determines the number of electrons in the system. The localisation introduces a sparse nature to the orbital data and Hamiltonian matrix, greatly changing the coding on parallel machines compared to non-localised systems. The data distribution, communication routines and dynamic load-balancing scheme of the program are presented in detail together with the speed and scaling of the code on various homogeneous and inhomogeneous physical systems. Performance results will be presented for systems of 2048 to 32768 atoms on 32 to 512 processors. We discuss the relevance to quantum molecular dynamics simulations with localised orbitals, of techniques used for programming short-range classical molecular dynamics simulations on parallel machines. The absence of global communications and the localised nature of the orbitals makes these algorithms extremely scalable in terms of memory and speed on parallel systems with fast communications. The main aim of this article is to present in detail all the new concepts and programming techniques that localisation of the orbitals introduces which scientists, coming from a background in non-localised quantum molecular dynamics simulations, may be unfamiliar with.
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…
Huang, Ying; Rong, Chunying; Zhang, Ruiqin; Liu, Shubin
2017-01-01
Wave function theory (WFT) and density functional theory (DFT)-the two most popular solutions to electronic structure problems of atoms and molecules-share the same origin, dealing with the same subject yet using distinct methodologies. For example, molecular orbitals are artifacts in WFT, whereas in DFT, electron density plays the dominant role. One question that needs to be addressed when using these approaches to appreciate properties related to molecular structure and reactivity is if there is any link between the two. In this work, we present a piece of strong evidence addressing that very question. Using five polymeric systems as illustrative examples, we reveal that using quantities from DFT such as Shannon entropy, Fisher information, Ghosh-Berkowitz-Parr entropy, Onicescu information energy, Rényi entropy, etc., one is able to accurately evaluate orbital-related properties in WFT like frontier orbital energies and the HOMO (highest occupied molecular orbital)/LUMO (lowest unoccupied molecular orbital) gap. We verified these results at both the whole molecule level and the atoms-in-molecules level. These results provide compelling evidence suggesting that WFT and DFT are complementary to each other, both trying to comprehend the same properties of the electronic structure and molecular reactivity from different perspectives using their own characteristic vocabulary. Hence, there should be a bridge or bridges between the two approaches.
Nakata, Hiroya; Fedorov, Dmitri G
2016-12-15
The analytic gradient is derived for the frozen domain formulation of the fragment molecular orbital (FMO) method combined with the polarizable continuum model. The accuracy is tested in comparison to full FMO calculations for a representative set of systems in terms of the gradient accuracy, protein-ligand binding energies, and optimized structures. The frozen domain method reproduced geometries optimized with full FMO within 0.03-0.09 Å in terms of reduced mean square deviations, whereas a single-point gradient calculation is accelerated by the factor of 38 (Trp-cage protein in explicit solvent, PDB: 1L2Y ) and 12 (crambin, PDB: 1CRN ). The method is applied to a geometry optimization of the K-Ras protein-ligand complex (4Q03) using two domain definitions, and the optimized structures are consistent with experiment. Pair interaction analysis is used to identify residues important in binding the ligand.
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.
Field theoretic approach to dynamical orbital localization in ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Thomas, Jordan W.; Iftimie, Radu; Tuckerman, Mark E.
2004-03-01
Techniques from gauge-field theory are employed to derive an alternative formulation of the Car-Parrinello ab initio molecular-dynamics method that allows maximally localized Wannier orbitals to be generated dynamically as the calculation proceeds. In particular, the Car-Parrinello Lagrangian is mapped onto an SU(n) non-Abelian gauge-field theory and the fictitious kinetic energy in the Car-Parrinello Lagrangian is modified to yield a fully gauge-invariant form. The Dirac gauge-fixing method is then employed to derive a set of equations of motion that automatically maintain orbital locality by restricting the orbitals to remain in the “Wannier gauge.” An approximate algorithm for integrating the equations of motion that is stable and maintains orbital locality is then developed based on the exact equations of motion. It is shown in a realistic application (64 water molecules plus one hydrogen-chloride molecule in a periodic box) that orbital locality can be maintained with only a modest increase in CPU time. The ability to keep orbitals localized in an ab initio molecular-dynamics calculation is a crucial ingredient in the development of emerging linear scaling approaches.
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.
Molecular orbital theory of ballistic electron transport through molecules
NASA Astrophysics Data System (ADS)
Ernzerhof, Matthias; Rocheleau, Philippe; Goyer, Francois
2009-03-01
Electron transport through molecules occurs, for instance, in STM imaging and in conductance measurements on molecular electronic devices (MEDs). To model these phenomena, we use a non-Hermitian model Hamiltonian [1] for the description of open systems that exchange current density with their environment. We derive qualitative, molecular-orbital-based rules relating molecular structure and conductance. We show how side groups attached to molecular conductors [2] can completely suppress the conductance. We discuss interference effects in aromatic molecules [3] that can also inhibit electron transport. Rules are developed [1] for the prediction of Fano resonances. All these phenomena are explained with a molecular orbital theory [1,4] for molecules attached to macroscopic reservoirs. [1] F. Goyer, M. Ernzerhof, and M. Zhuang, JCP 126, 144104 (2007); M. Ernzerhof, JCP 127, 204709 (2007). [2] M. Ernzerhof, M. Zhuang, and P. Rocheleau, JCP 123, 134704 (2005); G. C. Solomon, D Q. Andrews, R P. Van Duyne, and M A. Ratner, JACS 130, 7788 (2008). [3] M. Ernzerhof, H. Bahmann, F. Goyer, M. Zhuang, and P. Rocheleau, JCTC 2, 1291 (2006); G. C. Solomon, D. Q. Andrews, R. P. Van Duyne, and M. A. Ratner, JCP 129, 054701 (2008). [4] B.T. Pickup, P.W. Fowler, CPL 459, 198 (2008); P. Rocheleau and M. Ernzerhof, JCP, submitted.
NASA Astrophysics Data System (ADS)
Absi, Noureddine; Hoggan, Philip
The integral bottleneck in evaluating molecular energies arises from the two-electron contributions. These are difficult and time-consuming to evaluate, especially over exponential type orbitals, used here to ensure the correct behavior of atomic orbitals. The two-center two-electron integrals are essential to describe atom pairs in molecules and distinguish those that are bound. In this work on analytical integration, it is shown that the two-center Coulomb integrals involved can be expressed as one-electron kinetic energy-like integrals. This is accomplished using the fact that the Coulomb operator is a Green's function of the Laplacian. The ensuing integrals may be further simplified by defining spectral forms for the one-electron potential satisfying Poisson's equation therein. A sum of overlap integrals with the atomic orbital energy eigenvalue as a factor is then obtained to give the Coulomb energy. This is most easily evaluated by direct integration. The orbitals involved in three and four center integrals are translated to two centers. This is discussed very briefly. The evaluation of exchange energy is a straightforward extension of this work. The summation coefficients in spectral forms are evaluated analytically from Gaunt coefficients. The Poisson method may be used to calculate Coulomb energy integrals efficiently. For a single processor, gains of CPU time for a given chemical accuracy exceed a factor of 4. This method lends itself to efficient evaluation on a parallel computer.
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.
NASA Astrophysics Data System (ADS)
Takada, Tatsuo; Hayase, Yuji; Miyake, Hiroaki; Tanaka, Yasuhiro; Yoshida, Masafumi
This paper reports an examination of hetero-space charge trapping site in cross linked polyethylene (XLPE) using Molecular Orbital calculation. We chose a simple model for polyethylene (C24H50) with one molecular of acetophenone (one of cross linking byproducts), for the examination of XLPE sample. Molecular Orbital calculation can give the microscopic information of electron energy levels, electron density distributions and electro-static potential maps for the simple molecular mode of XLPE. It is presumed that the negative hetero-space charge (electron) and positive hetero-space charge (hole) were trapped at the permanent dipole of acetophenone, and the hole carrier could move in the polyethylene chain.
2016-01-01
Diarylethene molecules are prototype molecular switches with their two isomeric forms exhibiting strikingly different conductance, while maintaining similar length. We employed low-temperature scanning tunneling microscopy (STM) to resolve the energy and the spatial extend of the molecular orbitals of the open and closed isomers when lying on a Au(111) surface. We find an intriguing difference in the extension of the respective HOMOs and a peculiar energy splitting of the formerly degenerate LUMO of the open isomer. We then lift the two isomers with the tip of the STM and measure the current through the individual molecules. By a simple analytical model of the transport, we show that the previously determined orbital characteristics are essential ingredients for the complete understanding of the transport properties. We also succeeded in switching the suspended molecules by the current, while switching the ones which are in direct contact to the surface occurs nonlocally with the help of the electric field of the tip. PMID:27775886
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.
Polarized Molecular Orbital Model Chemistry. II. The PMO Method
Zhang, Peng; Fiedler, Luke; Leverentz, Hannah R.; Truhlar, Donald G.; Gao, Jiali
2012-01-01
We present a new semiempirical molecular orbital method based on neglect of diatomic differential overlap. This method differs from previous NDDO-based methods in that we include p orbitals on hydrogen atoms to provide a more realistic modeling of polarizability. As in AM1-D and PM3-D, we also include damped dispersion. The formalism is based on the original MNDO one, but in the process of parameterization we make some specific changes to some of the functional forms. The present article is a demonstration of the capability of the new approach, and it presents a successful parametrization for compounds composed only of hydrogen and oxygen atoms, including the important case of water clusters. PMID:23378824
Low-energy lunar transfers using spatial transit orbits
NASA Astrophysics Data System (ADS)
Ren, Yuan; Shan, Jinjun
2014-03-01
This paper is concerned with natural and artificial low-energy lunar transfers in three-dimensional space. The main contribution of this paper is that the limitations of the planar manifold assumption, which is adopted in previous low-energy orbit design methods, are avoided by describing the transfer orbits with more realistic spatial transit and non-transit orbits. To start, the limitations of the previous design methods for the low-energy trajectories are highlighted, and the boundaries of the spatial transit orbits, which can enter into or escape from the potential well near the Moon through the L1 or L2 bottleneck regions of the zero velocity surface, are defined on a Poincaré section by using the necessary and sufficient condition of transition. Next, by considering the dominant gravity bodies in different orbit segments the motion near the Moon is analyzed in the Earth-Moon circular restricted three-body problem (CR3BP). For natural celestial bodies, the statistical characteristics of the lunar collision trajectories are studied. For the artificial celestial bodies, the investigation is focused on the achievable range of inclination and height of the low lunar orbit (LLO). Then, the motion between the Earth and the Moon is studied in the Earth-Moon based Sun-perturbed bicircular four-body problem (B4BP). For natural and artificial celestial bodies, the Earth-origin trajectories and the trajectories from the low Earth orbits are analyzed. Compared to the current planar manifold based design methods, the technique introduced in this paper can evaluate the lunar transfer orbits more accurately. Also, some lunar transfer trajectories which do not exist in the manifold based models can be found, and the heights and inclinations of the parking orbits around the Earth and the Moon can also be analyzed.
Proppe, Jonny; Herrmann, Carmen
2015-02-05
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.
Catastrophic failure of stored energy modules following orbital debris penetration
NASA Astrophysics Data System (ADS)
Williamsen, Joel E.; Goodwin, Charles J.
1996-10-01
The population of dangerous orbital debris particles in low Earth orbit is growing, resulting in a need for improved risk assessment and risk management of critical space station elements from this hypervelocity impact threat. The effects of micrometeoroid and orbital debris (M/OD) penetration on space station equipment can very from a local damage problem to a possible catastrophic system failure (i.e., crew or station loss). Given this possibility, a preliminary study was undertaken by Meyer Analytics and NASA-MSFC to quantify and reduce the likelihood of catastrophic failure following orbital debris penetration of two Russian supplied modules: the FGB Energy Block module and the SPP-1 gyrodyne module. Each of these modules contains stored energy in the form of chemical propellants (UDMH), high pressure tanks, or kinetic energy (gyrodynes) that may release energy and propagate damage to the rest of the space station if impacted by a sufficiently energetic orbital debris particle. The study recommended design improvements to lower these probabilities, including spall blankets around the gyrodynes to lower the probability of gyrodyne penetration and fragment damage given gyrodyne rupture.
Electrochemical Energy Storage for an Orbiting Space Station
NASA Technical Reports Server (NTRS)
Martin, R. E.
1981-01-01
The system weight of a multi hundred kilowatt fuel cell electrolysis cell energy storage system based upon alkaline electrochemical cell technology for use in a future orbiting space station in low Earth orbit (LEO) was studied. Preliminary system conceptual design, fuel cell module performance characteristics, subsystem and system weights, and overall system efficiency are identified. The impact of fuel cell module operating temperature and efficiency upon energy storage system weight is investigated. The weight of an advanced technology system featuring high strength filament wound reactant tanks and a fuel cell module employing lightweight graphite electrolyte reservoir plates is defined.
Electrochemical energy storage for an orbiting space station
NASA Astrophysics Data System (ADS)
Martin, R. E.
1981-12-01
The system weight of a multi hundred kilowatt fuel cell electrolysis cell energy storage system based upon alkaline electrochemical cell technology for use in a future orbiting space station in low Earth orbit (LEO) was studied. Preliminary system conceptual design, fuel cell module performance characteristics, subsystem and system weights, and overall system efficiency are identified. The impact of fuel cell module operating temperature and efficiency upon energy storage system weight is investigated. The weight of an advanced technology system featuring high strength filament wound reactant tanks and a fuel cell module employing lightweight graphite electrolyte reservoir plates is defined.
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.
Path Integral Molecular Dynamics for Hydrogen with Orbital-Free Density Functional Theory
NASA Astrophysics Data System (ADS)
Runge, Keith; Karasiev, Valentin; Deymier, Pierre
2014-03-01
The computational bottleneck for performing path-integral molecular dynamics (PIMD) for nuclei on a first principles electronic potential energy surface has been the speed with which forces from the electrons can be generated. Recent advances in orbital-free density functional theory (OF-DFT) not only allow for faster generation of first principles forces but also include the effects of temperature on the electron density. We will present results of calculations on hydrogen in warm dense matter conditions where the protons are described by PIMD and the electrons by OF-DFT. Work supported by U.S. Dept. of Energy, grant DE-SC0002139.
Assessment of delocalized and localized molecular orbitals through electron momentum spectroscopy
NASA Astrophysics Data System (ADS)
Liu, Yuan; Cheung, Ling-Fung; Ning, Chuan-Gang
2014-06-01
Recently, there was a hot controversy about the concept of localized orbitals, which was triggered by Grushow's work titled “Is it time to retire the hybrid atomic orbital?” [J. Chem. Educ. 88, 860 (2011)]. To clarify the issue, we assess the delocalized and localized molecular orbitals from an experimental view using electron momentum spectroscopy. The delocalized and localized molecular orbitals based on various theoretical models for CH4, NH3, and H2O are compared with the experimental momentum distributions. Our results show that the delocalized molecular orbitals rather than the localized ones can give a direct interpretation of the experimental (e, 2e) results.
Spin-orbital entangled molecular jeff states in lacunar spinel compounds.
Kim, Heung-Sik; Im, Jino; Han, Myung Joon; Jin, Hosub
2014-06-03
The entanglement of the spin and orbital degrees of freedom through the spin-orbit coupling has been actively studied in condensed matter physics. In several iridium oxide systems, the spin-orbital entangled state, identified by the effective angular momentum jeff, can host novel quantum phases. Here we show that a series of lacunar spinel compounds, GaM4X8 (M=Nb, Mo, Ta and W and X=S, Se and Te), gives rise to a molecular jeff state as a new spin-orbital composite on which the low-energy effective Hamiltonian is based. A wide range of electron correlations is accessible by tuning the bandwidth under external and/or chemical pressure, enabling us to investigate the cooperation between spin-orbit coupling and electron correlations. As illustrative examples, a two-dimensional topological insulating phase and an anisotropic spin Hamiltonian are investigated in the weak and strong coupling regimes, respectively. Our finding can provide an ideal platform for exploring jeff physics and the resulting emergent phenomena.
Jagau, Thomas-C; Krylov, Anna I
2016-02-07
The theoretical description of electronic resonances is extended beyond calculations of energies and lifetimes. We present the formalism for calculating Dyson orbitals and transition dipole moments within the equation-of-motion coupled-cluster singles and doubles method for electron-attached states augmented by a complex absorbing potential (CAP-EOM-EA-CCSD). The capabilities of the new methodology are illustrated by calculations of Dyson orbitals of various transient anions. We also present calculations of transition dipole moments between transient and stable anionic states as well as between different transient states. Dyson orbitals characterize the differences between the initial neutral and final electron-attached states without invoking the mean-field approximation. By extending the molecular-orbital description to correlated many-electron wave functions, they deliver qualitative insights into the character of resonance states. Dyson orbitals and transition moments are also needed for calculating experimental observables such as spectra and cross sections. Physically meaningful results for those quantities are obtained only in the framework of non-Hermitian quantum mechanics, e.g., in the presence of a complex absorbing potential (CAP), when studying resonances. We investigate the dependence of Dyson orbitals and transition moments on the CAP strength and illustrate how Dyson orbitals help understand the properties of metastable species and how they are affected by replacing the usual scalar product by the so-called c-product.
Jagau, Thomas-C.; Krylov, Anna I.
2016-02-07
The theoretical description of electronic resonances is extended beyond calculations of energies and lifetimes. We present the formalism for calculating Dyson orbitals and transition dipole moments within the equation-of-motion coupled-cluster singles and doubles method for electron-attached states augmented by a complex absorbing potential (CAP-EOM-EA-CCSD). The capabilities of the new methodology are illustrated by calculations of Dyson orbitals of various transient anions. We also present calculations of transition dipole moments between transient and stable anionic states as well as between different transient states. Dyson orbitals characterize the differences between the initial neutral and final electron-attached states without invoking the mean-field approximation. By extending the molecular-orbital description to correlated many-electron wave functions, they deliver qualitative insights into the character of resonance states. Dyson orbitals and transition moments are also needed for calculating experimental observables such as spectra and cross sections. Physically meaningful results for those quantities are obtained only in the framework of non-Hermitian quantum mechanics, e.g., in the presence of a complex absorbing potential (CAP), when studying resonances. We investigate the dependence of Dyson orbitals and transition moments on the CAP strength and illustrate how Dyson orbitals help understand the properties of metastable species and how they are affected by replacing the usual scalar product by the so-called c-product.
Ab initio Path Integral Molecular Dynamics Based on Fragment Molecular Orbital Method
NASA Astrophysics Data System (ADS)
Fujita, Takatoshi; Watanabe, Hirofumi; Tanaka, Shigenori
2009-10-01
We have developed an ab initio path integral molecular dynamics method based on the fragment molecular orbital method. This “FMO-PIMD” method can treat both nuclei and electrons quantum mechanically, and is useful to simulate large hydrogen-bonded systems with high accuracy. After a benchmark calculation for water monomer, water trimer and glycine pentamer have been studied using the FMO-PIMD method to investigate nuclear quantum effects on structure and molecular interactions. The applicability of the present approach is demonstrated through a number of test calculations.
Low-Energy Ballistic Transfers to Lunar Halo Orbits
NASA Technical Reports Server (NTRS)
Parker, Jeffrey S.
2009-01-01
Recent lunar missions have begun to take advantage of the benefits of low-energy ballistic transfers between the Earth and the Moon rather than implementing conventional Hohmann-like lunar transfers. Both Artemis and GRAIL plan to implement low-energy lunar transfers in the next few years. This paper explores the characteristics and potential applications of many different families of low-energy ballistic lunar transfers. The transfers presented here begin from a wide variety of different orbits at the Earth and follow several different distinct pathways to the Moon. This paper characterizes these pathways to identify desirable low-energy lunar transfers for future lunar missions.
Saju, K K; Jayadas, N H; Vidyanand, S; James, J
2011-03-01
It has been established that the adhesion of cells on to the surfaces of orthopaedic implants depends on the ability of the surfaces to accommodate protein molecules. Hydroxyapatite coating and anodizing are the most common methods to make TiAl6V4 implants (Ti) more biocompatible. In this paper Spartan 02, a molecular dynamics software, is used to analyze and predict the bonding characteristics of Extra cellular matrix protein sequence arginine-glycine-aspartic acid (RGD) on a Hyrdoxyapatite (HA) coated Ti and an anodized Ti surface based on the property of its constituent atoms, their polarity (net electrostatic charge, Qr), the energies of the molecular orbital E_HOMO (energy of the highest occupied molecular orbital), and E_LUMO (energy of the lowest unoccupied molecular orbital). The results show favourable criterion for formation of bonding between the HOMO orbital of the HA coated and anodized surfaces and LUMO orbital of the glycine strand from the RGD unit. The mechanism of bonding of individual atoms to form primary calcium oxide compounds is likely only in the case of HA coated surfaces . The surface texture of the anodized Ti with inherent porosities appear more responsible for the adsorption of proteins on to them by mechanical interlocking than the formation of any intermediate calcium oxide compounds.
Multi-Orbital Molecular Compound (TTM-TTP)I3: Effective Model and Fragment Decomposition
NASA Astrophysics Data System (ADS)
Tsuchiizu, Masahisa; Omori, Yukiko; Suzumura, Yoshikazu; Bonnet, Marie-Laure; Robert, Vincent; Ishibashi, Shoji; Seo, Hitoshi
2011-01-01
The electronic structure of the molecular compound (TTM-TTP)I3, which exhibits a peculiar intra-molecular charge ordering, has been studied using multi-configuration ab initio calculations. First we derive an effective Hubbard-type model based on the molecular orbitals (MOs) of TTM-TTP; we set up a two-orbital Hamiltonian for the two MOs near the Fermi energy and determine its full parameters: the transfer integrals, the Coulomb and exchange interactions. The tight-binding band structure obtained from these transfer integrals is consistent with the result of the direct band calculation based on density functional theory. Then, by decomposing the frontier MOs into two parts, i.e., fragments, we find that the stacked TTM-TTP molecules can be described by a two-leg ladder model, while the inter-fragment Coulomb energies are scaled to the inverse of their distances. This result indicates that the fragment picture that we proposed earlier [M.-L. Bonnet et al.: J. Chem. Phys. 132 (2010) 214705] successfully describes the low-energy properties of this compound.
P and N compensation in diamond molecular orbital theory
NASA Astrophysics Data System (ADS)
Anderson, Alfred B.; Kostadinov, Lubomir N.
1997-01-01
Cluster models and the atom superposition and electron delocalization molecular orbital theory calculations lead to an explanation for the ability of nitrogen to cause phosphorous incorporation in low pressure grown diamond films as observed recently by Cao and coworkers. The theory shows that substitutional N compensates substitutional P, creating stable P+-N- disubstitutional pairs. These ionized systems are calculated to be deep donors, which explains the absence of measurable electrical conductivity or phosphorous induced luminescence. The possibility of creating donor P defects by the annealing reaction P-N+N→P+N-N is discussed. The issues of atom size and electronegativity and their influence on donor capability are addressed. It is shown that the difference between substitutional P, a shallow donor, and substitutional N, a deep donor, is predominantly due to the larger size of P; its lower electronegativity makes a relatively small contribution.
Sulfur at nickel-alumina interfaces - Molecular orbital theory
NASA Technical Reports Server (NTRS)
Hong, S. Y.; Anderson, Alfred B.; Smialek, James L.
1990-01-01
Previous studies on Al-Ni alloys containing sulfur as an impurity suggest that, when S is in the interface between a metal and an oxide scale, it weakens the chemical bonding between them. This paper investigates factors responsible for this effect, using a molecular orbital theory to predict sulfur structures and electronic properties on the Ni-Al2O3 interface. It is shown that, in absence of S, the basal plane of Al2O3 will bind strongly through the Al(3+) cation surface to Ni (111). When segregated S impurity is present on the Ni surface, there are too few interfacial AlS bonds to effect good adhesion, leading to an inhibition of the oxide scale adhesion in NiCrAl alloys.
Theoretical analysis of the density within an orbiting molecular shield
NASA Technical Reports Server (NTRS)
Hueser, J. E.; Brock, F. J.
1976-01-01
An analytical model based on the kinetic theory of a drifting Maxwellian gas is used to determine the nonequilibrium molecular density distribution within a hemispherical shell open aft with its axis parallel to its velocity. Separate numerical results are presented for the primary and secondary density distribution components due to the drifting Maxwellian gas for speed ratios between 2.5 and 10. An analysis is also made of the density component due to gas desorbed from the wall of the hemisphere, and numerical results are presented for the density distribution. It is shown that the adsorption process may be completely ignored. The results are applicable to orbital trajectories in any planet-atmosphere system and interplanetary transfer trajectories. Application to the earth's atmosphere is mentioned briefly.
Nanoscale orbital excitations and the infrared spectrum of a molecular Mott insulator: A15-Cs3C60.
Naghavi, S S; Fabrizio, M; Qin, T; Tosatti, E
2016-10-14
The quantum physics of ions and electrons behind low-energy spectra of strongly correlated molecular conductors, superconductors and Mott insulators is poorly known, yet fascinating especially in orbitally degenerate cases. The fulleride insulator Cs3C60 (A15), one such system, exhibits infrared (IR) spectra with low temperature peak features and splittings suggestive of static Jahn-Teller distortions with a breakdown of orbital symmetry in the molecular site. That is puzzling, since there is no detectable static distortion, and because the features and splittings disappear upon modest heating, which they should not. Taking advantage of the Mott-induced collapse of electronic wavefunctions from lattice-extended to nanoscale localized inside a caged molecular site, we show that the unbroken spin and orbital symmetry of the ion multiplets explains the IR spectrum without adjustable parameters. This demonstrates the importance of a fully quantum treatment of nuclear positions and orbital momenta in the Mott insulator sites, dynamically but not statically distorted. The observed demise of these features with temperature is explained by the thermal population of a multiplet term whose nuclear positions are essentially undistorted, but whose energy is very low-lying. That term is in fact a scaled-down orbital excitation analogous to that of other Mott insulators, with the same spin 1/2 as the ground state, but with a larger orbital momentum of two instead of one.
Spectroscopic signatures of molecular orbitals in transition metal oxides with a honeycomb lattice
NASA Astrophysics Data System (ADS)
Pchelkina, Z. V.; Streltsov, S. V.; Mazin, I. I.
2016-11-01
A tendency to form benzenelike molecular orbitals has recently been shown to be a common feature of the 4 d and 5 d transition metal oxides with a honeycomb lattice. This tendency competes with other interactions such as the spin-orbit coupling and Hubbard correlations and can be partially or completely suppressed. In the calculations, SrRu2O6 presents the cleanest case of well-formed molecular orbitals so far; however, direct experimental evidence for or against this proposition has been missing. In this paper, we show that combined photoemission and optical studies can be used to identify molecular orbitals in SrRu2O6 . Symmetry-driven election selection rules suppress optical transitions between certain molecular orbitals, while photoemission and inverse photoemission measurements are insensitive to them. Comparing the photoemission and optical conductivity spectra, one should be able to observe clear signatures of molecular orbitals.
NASA Astrophysics Data System (ADS)
Gao, Chang; Zhang, Shen; Kang, Wei; Wang, Cong; Zhang, Ping; He, X. T.
2016-11-01
With 6LiD as an example, we show that the applicable region of the orbital-free molecular dynamics (OFMD) method in a large temperature range is determined by the thermal ionization process of bound electrons in shell structures. The validity boundary of the OFMD method is defined roughly by the balance point of the average thermal energy of an electron and the ionization energy of the lowest localized electronic state. This theoretical proposition is based on the observation that the deviation of the OFMD method originates from its less accurate description to the charge density in partially ionized shells, as compared with the results of the extended first-principles molecular dynamics method, which well reproduces the charge density of shell structures.
NASA Astrophysics Data System (ADS)
Velasco, A. M.; Lavín, C.; Díaz-Tinoco, Manuel; Ortiz, J. V.
2017-01-01
In this work, electron-propagator methods are applied to the calculation of the ionization potential and vertical excitation energies for several Rydberg series of the CaH molecule. The present calculations cover more highly excited states than those previously reported. In particular, excitation energies for ns (n>5), np (n>5), nd (n>4) and nf Rydberg states are given. Oscillator strengths for electronic transitions involving Rydberg states of CaH, as well as photoionization cross sections for Rydberg channels, also have been determined by using the Molecular Quantum Defect Orbital approach. Good agreement has been found with the scarce comparative data that are available for oscillator strengths. To our knowledge, predictions of photoionization cross sections from the outermost orbital of CaH are made here for the first time. A Cooper minimum and mixed atomic orbital character in some of the Dyson orbitals are among the novel features of these present calculations.
Imprints of the molecular-orbital geometry on the high-harmonic ellipticity.
Qin, Meiyan; Zhu, Xiaosong; Liu, Kunlong; Zhang, Qingbin; Lu, Peixiang
2012-08-27
The influence of the orbital symmetry on the ellipticity of the high-order harmonics is investigated. It is found that the ellipticity maps have distinct shapes for the molecular orbitals with different symmetry. Our analysis shows that the feature of the harmonic ellipticity map is essentially determined by the nodal structure of the nonsymmetric orbital. The results indicate that the molecular-orbital geometry is imprinted on the ellipticity of the high-order harmonics, which invites the use of ellipticity measurements as a probe of the orbital structure for polar molecules.
NASA Astrophysics Data System (ADS)
Nakata, Hiroya; Fedorov, Dmitri G.; Yokojima, Satoshi; Kitaura, Kazuo; Nakamura, Shinichiro
2014-05-01
We developed the analytic second derivative of the energy for unrestricted Hartree-Fock based on the fragment molecular orbital (FMO) method. We formulated the second order derivative for the separated dimer approximation in both restricted and unrestricted methods, which accelerated the calculations by the factor of 9 for a radical system containing 704 atoms. The accuracy was evaluated for organic radicals in explicit solvent, in comparison to full ab initio results. The method was applied to study the change of IR absorption spectra in the tyrosine oxidation reaction for a polypeptide representing the active part of the photosynthetic reaction center.
Localization of open-shell molecular orbitals via least change from fragments to molecule
NASA Astrophysics Data System (ADS)
Li, Hongyang; Liu, Wenjian; Suo, Bingbing
2017-03-01
Both top-down and bottom-up localization schemes are proposed for constructing localized molecular orbitals (LMOs) of open-shell systems, via least change from fragments to molecule. The success of both schemes stems from (1) the primitive fragment LMOs that are local not only in space but also in energy and (2) the "conquer step" that allows arbitrary assignment of the unpaired electrons to fragments. Moreover, integral occupations are retained, so as to facilitate subsequent treatment of electron correlation and excitation.
Offenbacher, Hannes; Lüftner, Daniel; Ules, Thomas; Reinisch, Eva Maria; Koller, Georg; Puschnig, Peter; Ramsey, Michael G
2015-10-01
The frontier orbitals of molecules are the prime determinants of their chemical, optical and electronic properties. Arguably, the most direct method of addressing the (filled) frontier orbitals is ultra-violet photoemission spectroscopy (UPS). Although UPS is a mature technique from the early 1970s on, the angular distribution of the photoemitted electrons was thought to be too complex to be analysed quantitatively. Recently angle resolved UPS (ARUPS) work on conjugated molecules both, in ordered thick films and chemisorbed monolayers, has shown that the angular (momentum) distribution of the photocurrent from orbital emissions can be simply understood. The approach, based on the assumption of a plane wave final state is becoming known as orbital tomography. Here we will demonstrate, with selected examples of pentacene (5A) and sexiphenyl (6P), the potential of orbital tomography. First it will be shown how the full angular distribution of the photocurrent (momentum map) from a specific orbital is related to the real space orbital by a Fourier transform. Examples of the reconstruction of 5A orbitals will be given and the procedure for recovering the lost phase information will be outlined. We then move to examples of sexiphenyl where we interrogate the original band maps of thick sexiphenyl in the light of our understanding of orbital tomography that has developed since then. With comparison to theoretical simulations of the molecular band maps, the molecular conformation and orientation will be concluded. New results for the sexiphenyl monolayer on Al(1 1 0) will then be presented. From the band maps it will be concluded that the molecule is planarised and adopts a tilted geometry. Finally the momentum maps down to HOMO-11 will be analysed and real space orbitals reconstructed.
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.
Separated-orbit bisected energy-recovered linear accelerator
Douglas, David R.
2015-09-01
A separated-orbit bisected energy-recovered linear accelerator apparatus and method. The accelerator includes a first linac, a second linac, and a plurality of arcs of differing path lengths, including a plurality of up arcs, a plurality of downgoing arcs, and a full energy arc providing a path independent of the up arcs and downgoing arcs. The up arcs have a path length that is substantially a multiple of the RF wavelength and the full energy arc includes a path length that is substantially an odd half-integer multiple of the RF wavelength. Operation of the accelerator includes accelerating the beam utilizing the linacs and up arcs until the beam is at full energy, at full energy executing a full recirculation to the second linac using a path length that is substantially an odd half-integer of the RF wavelength, and then decelerating the beam using the linacs and downgoing arcs.
AM1 and ab initio molecular orbital study of water dimer
Dannenberg, J.J.
1988-12-01
Several structures for the water dimer, including trifurcated structures similar to the optimized AM1 geometry, have been calculated by using the MP4/6-311G** level of ab initio molecular orbital theory. The relative energies of the structures become quite close at the higher levels of calculation. The best trifurcated is only 0.2 kcal/mol higher than the optimized HF/6-31G* structure and only 0.4 kcal/mol higher than the lowest energy structure found (optimized by using AM1 with the H bond constrained to be linear). It appears likely that the potential surface of the water dimer is extremely flat. The experimental geometry, which corresponds to the minimum on the free energy surface, is likely to be dominated by entropy contributions.
Pereira, Florbela; Xiao, Kaixia; Latino, Diogo A R S; Wu, Chengcheng; Zhang, Qingyou; Aires-de-Sousa, Joao
2017-01-23
Machine learning algorithms were explored for the fast estimation of HOMO and LUMO orbital energies calculated by DFT B3LYP, on the basis of molecular descriptors exclusively based on connectivity. The whole project involved the retrieval and generation of molecular structures, quantum chemical calculations for a database with >111 000 structures, development of new molecular descriptors, and training/validation of machine learning models. Several machine learning algorithms were screened, and an applicability domain was defined based on Euclidean distances to the training set. Random forest models predicted an external test set of 9989 compounds achieving mean absolute error (MAE) up to 0.15 and 0.16 eV for the HOMO and LUMO orbitals, respectively. The impact of the quantum chemical calculation protocol was assessed with a subset of compounds. Inclusion of the orbital energy calculated by PM7 as an additional descriptor significantly improved the quality of estimations (reducing the MAE in >30%).
Overview of Molecular Line Parameters for the Orbiting Carbon Observatory
NASA Astrophysics Data System (ADS)
Brown, L.; Crisp, D.; Miller, C.; Martin-Torres, J.; Toth, R.
2009-04-01
The Orbiting Carbon Observatory, scheduled to launch early in 2009, will make spatially resolved measurements of the column averaged CO2 dry air mole fraction, XCO2, with precisions of 1 ppm to distinguish their spatial and temporal gradients of CO2. Achieving this goal requires implementation of non-Voigt line shape models, line mixing and improved molecular line parameters for near infrared absorption bands of O2 (near 760 nm), and CO2 (near 1600 and 2060 nm) . The first interval is dominated by the absorptions of the O2 A-band while the others contain strong CO2 features, as well as weak transitions of water and methane. The OCO linelist is composed of results from numerous new laboratory studies undertaken to improve experimental precisions and to characterize line mixing effects. The sources and accuracies of the new linelist for the three OCO channels1 will be described. The research described in this paper was performed at the Jet Propulsion Laboratory, California Institute of Technology, under contract with The National Aeronautics and Space Administration.
Unravelling the origin of intermolecular interactions using absolutely localized molecular orbitals.
Khaliullin, Rustam Z; Cobar, Erika A; Lochan, Rohini C; Bell, Alexis T; Head-Gordon, Martin
2007-09-13
An energy decomposition analysis (EDA) method is proposed to isolate physically relevant components of the total intermolecular interaction energies such as the contribution from interacting frozen monomer densities, the energy lowering due to polarization of the densities, and the further energy lowering due to charge-transfer effects. This method is conceptually similar to existing EDA methods such as Morokuma analysis but includes several important new features. The first is a fully self-consistent treatment of the energy lowering due to polarization, which is evaluated by a self-consistent field calculation in which the molecular orbital coefficients are constrained to be block-diagonal (absolutely localized) in the interacting molecules to prohibit charge transfer. The second new feature is the ability to separate forward and back-donation in the charge-transfer energy term using a perturbative approximation starting from the optimized block-diagonal reference. The newly proposed EDA method is used to understand the fundamental aspects of intermolecular interactions such as the degree of covalency in the hydrogen bonding in water and the contributions of forward and back-donation in synergic bonding in metal complexes. Additionally, it is demonstrated that this method can be used to identify the factors controlling the interaction of the molecular hydrogen with open metal centers in potential hydrogen storage materials and the interaction of methane with rhenium complexes.
Energy transformation in molecular electronic systems
Kasha, M.
1985-07-25
Our new optical pumping spectroscopy (steady state, and double-laser pulse) allows the production and study of the unstable rare tautomer in its ground and excited states, including picosecond dynamic studies. Molecules under study here included 7-azaindole (model for biological purines), 3-hydroxyflavone (model for plant flavones), lumichrome, and other heterocyclics. New detailed molecular mechanisms for proton transfer are derived, especially with catalytic assisting molecules. A new proton-transfer laser of extraordinary efficiency has become a side dividend, possibly worth of industrial development. The excited and highly reactive singlet molecular oxygen species /sup 1/..delta../sub g/) has proven to be ubiquitous in chemical peroxide systems and in physically excited sensitizer-oxygen systems. Hyperbaric oxygen mechanisms in biology probably involve singlet oxygen. We have undertaken a spectroscopic study of tris - dibenzoylmethane chelates of Al, Gd, Eu, and Yb trivalent ions. These chelates offer a variety of electronic behaviors, from Z-effects on ..pi..-electron spin-orbital coupling (Al, Gd) to Weissman intramolecular energy transfer to 4f mestable levels (Eu, Gd). Elegant new spectroscopic resolution at 77K permits separation of tautomeric, parasitic self-absorption, dissociation, and cage effects to be resolved. 18 refs., 4 figs.
Energy transformation in molecular electronic systems
NASA Astrophysics Data System (ADS)
Kasha, M.
1985-07-01
Our new optical pumping spectroscopy allows the production and study of the unstable rate tautomer in its ground and excited states, including picosecond dynamic studies. Molecules under study here included 7-azaindole 3-hydroxyflavone, lumichrome, and other heterocyclics. New detailed molecular mechanisms for proton transfer are derived, especially with catalytic assisting molecules. A new proton-transfer laser of extraordinary efficiency has become a side dividend, possibly worthy of industrial development. The excited and highly reactive singlet molecular oxygen species (1) DELTA sub g has proven to be ubiquitous in chemical peroxide systems and in physically excited sensitizer-oxygen systems. Hyperbaric oxygen mechanisms in biology probably involve singlet oxygen. We have undertaken a spectroscopic study of trisdibenzoylmethane chelates of Al, Gd, Eu, and Yb trivalent ions. These chelates offer a variety of electronic behaviors, from Z-effects on (PI)--electron spin-orbital coupling (Al, Gd) to Weissman intramolecular energy transfer to 4f mestable levels (Eu, Gd). Elegant new spectroscopic resolution at 77K permits separation of tautomeric, parasitic self-absorption, dissociation, and cage effects to be resolved.
Enhanced solar energy options using earth-orbiting mirrors
NASA Technical Reports Server (NTRS)
Gilbreath, W. P.; Billman, K. W.; Bowen, S. W.
1978-01-01
A system of orbiting space reflectors is described, analyzed, and shown to economically provide nearly continuous insolation to preselected ground sites, producing benefits hitherto lacking in conventional solar farms and leading to large reductions in energy costs for such installations. Free-flying planar mirrors of about 1 sq km are shown to be optimum and can be made at under 10 g/sq m of surface, thus minimizing material needs and space transportation costs. Models are developed for both the design of such mirrors and for the analysis of expected ground insolation as a function of orbital parameters, time, and site location. Various applications (agricultural, solar-electric production, weather enhancement, etc.) are described.
Habeeb, Moustafa M; Al-Attas, Amirah S; Al-Raimi, Doaa S
2015-05-05
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 589nm, 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.
NASA Astrophysics Data System (ADS)
Truong, Thanh N.; Lu, Da-hong; Lynch, Gillian C.; Liu, Yi-Ping; Melissas, Vasilios S.; Stewart, James J. P.; Steckler, Rozeanne; Garrett, Bruce C.; Isaacson, Alan D.; Gonzalez-Lafont, Angels; Rai, Sachchida N.; Hancock, Gene C.; Joseph, Tomi; Truhlar, Donald G.
1993-04-01
We present a computer program, MORATE (Molecular Orbital RATE calculations), for direct dynamics calculations of unimolecular and bimolecular rate constants of gas-phase chemical reactions involving atoms, diatoms, or polyatomic species. The potential energies, gradients, and higher derivatives of the potential are calculated whenever needed by semiempirical molecular orbital theory without the intermediary of a global or semiglobal fit. The dynamical methods used are conventional or variational transition state theory and multidimensional semiclassical approximations for tunneling and nonclassical reflection. The computer program is conveniently interfaced package consisting of the POLYRATE program, version 4.5.1, for dynamical rate calculations, and the MOPAC program, version 5.03, for semiempirical electronic structure computations. All semiempirical methods available in MOPAC, in particular MINDO/3, MNDO, AM1, and PM3, can be called on to calculate the potential and gradient. Higher derivatives of the potential are obtained by numerical derivatives of the gradient. Variational transition states are found by a one-dimensional search of generalized-transition-state dividing surfaces perpendicular to the minimum-energy path, and tunneling probabilities are evaluated by numerical quadrature.
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.
Electron-Proton and High Energy Telescopes for Solar Orbiter
NASA Astrophysics Data System (ADS)
Kulkarni, Shrinivasrao R.; Grunau, Jan; Boden, Sebastian; Steinhagen, Jan; Martin, Cesar; Wimmer-Schweingruber, Robert F.; Boettcher, Stephan; Rodríguez-Pacheco, Javier; Seimetz, Lars; Schuster, Bjoern; Kulemzin, Alexander; Wetzel, Moritz; Ravanbakhsh, Ali
2013-04-01
The Energetic Particle Detector (EPD) suite for ESA's Solar Orbiter will provide key measurements to address particle acceleration at and near the Sun. The EPD suite consists of five sensors (STEIN, SIS, EPT, LET and HET). The University of Kiel in Germany is responsible for the design, development, and build of EPT and HET which are presented here. The Electron Proton Telescope (EPT) is designed to cleanly separate and measure electrons in the energy range from 20 - 400 keV and protons from 20 - 7000 keV. The Solar Orbiter EPT electron measurements from 20 - 400 keV will cover the gap with some overlap between suprathermal electrons measured by STEIN and high energy electrons measured by HET. The proton measurements from 20 -7000 keV will cover the gap between STEIN and LET. The Electron and Proton Telescope relies on the magnet/foil-technique. The High-Energy Telescope (HET) on ESA's Solar Orbiter mission, will measure electrons from 300 keV up to about 30 MeV, protons from 10 -100 MeV, and heavy ions from ~20 to 200 MeV/nuc. Thus, HET covers the energy range which is of specific interest for studies of the space environment and will perform the measurements needed to understand the origin of high-energy events at the Sun which occasionally accelerate particles to such high energies that they can penetrate the Earth's atmosphere and be measured at ground level (ground-level events). These measurement capabilities are reached by a combination of solid-state detectors and a scintillator calorimeter which allows use of the dE/dx vs. total E technique for particle identification and energy measurement. The upper limits on energy listed above refer to particles (ions) stopping in the scintillator and careful modeling of HET properties will allow discrimination of forward/backward penetrating particles in a wider energy range. Here we present the current development status of EPT-HET units focusing on the test and calibration results obtained with the demonstration
Resolving Multiple Molecular Orbitals Using Two-Dimensional High-Harmonic Spectroscopy
NASA Astrophysics Data System (ADS)
Yun, Hyeok; Lee, Kyung-Min; Sung, Jae Hee; Kim, Kyung Taec; Kim, Hyung Taek; Nam, Chang Hee
2015-04-01
High-harmonic radiation emitted from molecules in a strong laser field contains information on molecular structure and dynamics. When multiple molecular orbitals participate in high-harmonic generation, resolving the contribution of each orbital is crucial for understanding molecular dynamics and for extending high-harmonic spectroscopy to more complicated molecules. We show that two-dimensional high-harmonic spectroscopy can resolve high-harmonic radiation emitted from the two highest-occupied molecular orbitals, HOMO and HOMO-1, of aligned molecules. By the application of an orthogonally polarized two-color laser field that consists of the fundamental and its second-harmonic fields to aligned CO2 molecules, the characteristics attributed to the two orbitals are found to be separately imprinted in odd and even harmonics. Two-dimensional high-harmonic spectroscopy may open a new route to investigate ultrafast molecular dynamics during chemical processes.
Resolving multiple molecular orbitals using two-dimensional high-harmonic spectroscopy.
Yun, Hyeok; Lee, Kyung-Min; Sung, Jae Hee; Kim, Kyung Taec; Kim, Hyung Taek; Nam, Chang Hee
2015-04-17
High-harmonic radiation emitted from molecules in a strong laser field contains information on molecular structure and dynamics. When multiple molecular orbitals participate in high-harmonic generation, resolving the contribution of each orbital is crucial for understanding molecular dynamics and for extending high-harmonic spectroscopy to more complicated molecules. We show that two-dimensional high-harmonic spectroscopy can resolve high-harmonic radiation emitted from the two highest-occupied molecular orbitals, HOMO and HOMO-1, of aligned molecules. By the application of an orthogonally polarized two-color laser field that consists of the fundamental and its second-harmonic fields to aligned CO2 molecules, the characteristics attributed to the two orbitals are found to be separately imprinted in odd and even harmonics. Two-dimensional high-harmonic spectroscopy may open a new route to investigate ultrafast molecular dynamics during chemical processes.
Nishimoto, Yoshio; Fedorov, Dmitri G
2017-03-15
The three-body fragment molecular orbital (FMO3) method is formulated for density-functional tight-binding (DFTB). The energy, analytic gradient, and Hessian are derived in the gas phase, and the energy and analytic gradient are also derived for polarizable continuum model. The accuracy of FMO3-DFTB is evaluated for five proteins, sodium cation in explicit solvent, and three isomers of polyalanine. It is shown that FMO3-DFTB is considerably more accurate than FMO2-DFTB. Molecular dynamics simulations for sodium cation in water are performed for 100 ps, yielding radial distribution functions and coordination numbers. © 2017 Wiley Periodicals, Inc.
A unified scheme for ab initio molecular orbital theory and path integral molecular dynamics
NASA Astrophysics Data System (ADS)
Shiga, Motoyuki; Tachikawa, Masanori; Miura, Shinichi
2001-11-01
We present a general approach for accurate calculation of chemical substances which treats both nuclei and electrons quantum mechanically, adopting ab initio molecular orbital theory for the electronic structure and path integral molecular dynamics for the nuclei. The present approach enables the evaluation of physical quantities dependent on the nuclear configuration as well as the electronic structure, within the framework of Born-Oppenheimer adiabatic approximation. As an application, we give the path integral formulation of electric response properties—dipole moment and polarizability, which characterize the changes both in electronic structure and nuclear configuration at a given temperature when uniform electrostatic field is present. We also demonstrate the calculation of a water molecule using the present approach and the result of temperature and isotope effects is discussed.
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…
NASA Astrophysics Data System (ADS)
Zhao, Xin; Geskin, Victor; Stadler, Robert
2017-03-01
Destructive quantum interference (DQI) in single molecule electronics is a purely quantum mechanical effect and is entirely defined by the inherent properties of the molecule in the junction such as its structure and symmetry. This definition of DQI by molecular properties alone suggests its relation to other more general concepts in chemistry as well as the possibility of deriving simple models for its understanding and molecular device design. Recently, two such models have gained a wide spread attention, where one was a graphical scheme based on visually inspecting the connectivity of the carbon sites in conjugated π systems in an atomic orbital (AO) basis and the other one puts the emphasis on the amplitudes and signs of the frontier molecular orbitals (MOs). There have been discussions on the range of applicability for these schemes, but ultimately conclusions from topological molecular Hamiltonians should not depend on whether they are drawn from an AO or a MO representation, as long as all the orbitals are taken into account. In this article, we clarify the relation between both models in terms of the zeroth order Green's function and compare their predictions for a variety of systems. From this comparison, we conclude that for a correct description of DQI from a MO perspective, it is necessary to include the contributions from all MOs rather than just those from the frontier orbitals. The cases where DQI effects can be successfully predicted within a frontier orbital approximation we show them to be limited to alternant even-membered hydrocarbons, as a direct consequence of the Coulson-Rushbrooke pairing theorem in quantum chemistry.
Optimal aeroassisted coplanar orbital transfer using an energy model
NASA Technical Reports Server (NTRS)
Halyo, Nesim; Taylor, Deborah B.
1989-01-01
The atmospheric portion of the trajectories for the aeroassisted coplanar orbit transfer was investigated. The equations of motion for the problem are expressed using reduced order model and total vehicle energy, kinetic plus potential, as the independent variable rather than time. The order reduction is achieved analytically without an approximation of the vehicle dynamics. In this model, the problem of coplanar orbit transfer is seen as one in which a given amount of energy must be transferred from the vehicle to the atmosphere during the trajectory without overheating the vehicle. An optimal control problem is posed where a linear combination of the integrated square of the heating rate and the vehicle drag is the cost function to be minimized. The necessary conditions for optimality are obtained. These result in a 4th order two-point-boundary-value problem. A parametric study of the optimal guidance trajectory in which the proportion of the heating rate term versus the drag varies is made. Simulations of the guidance trajectories are presented.
Kohut, Sviataslau V; Cuevas-Saavedra, Rogelio; Staroverov, Viktor N
2016-08-21
Ryabinkin and Staroverov [J. Chem. Phys. 141, 084107 (2014)] extended the concept of average local ionization energy (ALIE) to correlated wavefunctions by defining the generalized ALIE as Ī(r)=-∑jλj|fj(r)|(2)/ρ(r), where λj are the eigenvalues of the generalized Fock operator and fj(r) are the corresponding eigenfunctions (energy orbitals). Here we show that one can equivalently express the generalized ALIE as Ī(r)=∑kIk|dk(r)|(2)/ρ(r), where Ik are single-electron removal energies and dk(r) are the corresponding Dyson orbitals. The two expressions for Ī(r) emphasize different physical interpretations of this quantity; their equivalence enables one to calculate the ALIE at any level of ab initio theory without generating the computationally expensive Dyson orbitals.
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.
NASA Astrophysics Data System (ADS)
Deslippe, Jack; Samsonidze, Georgy; Jain, Manish; Cohen, Marvin L.; Louie, Steven G.
2013-04-01
Ab initio GW calculations are a standard method for computing the spectroscopic properties of many materials. The most computationally expensive part in conventional implementations of the method is the generation and summation over the large number of empty orbitals required to converge the electron self-energy. We propose a scheme to reduce the summation over empty states by the use of a modified static remainder approximation, which is simple to implement and yields accurate self-energies for both bulk and molecular systems requiring a small fraction of the typical number of empty orbitals.
Molecular orbital studies of gas-phase interactions between complex molecules.
Gaudreault, Roger; Whitehead, M A; van de Ven, Theo G M
2006-03-16
Describing interactions among large molecules theoretically is a challenging task. As an example, we investigated gas-phase interactions between a linear nonionic oligomer and various model compounds (cofactors), which have been reported to associate experimentally, using PM3 semiempirical molecular orbital theory. As oligomer, we studied the hexamer of poly(ethylene oxide) (PEO), and as cofactors, we studied corilagin and related compounds containing phenolic groups (R-OH). These systems are of interest because they are models for PEO/cofactor flocculation systems, used in industrial applications. The PM3 delocalized molecular orbitals (DLMO) describe the bonding between (PEO)6 and cofactors, and some of them cover the complete complex. The DLMOs which cover the traditionally considered hydrogen bonds R-OH...O or R-CH...O show a distinct "pinch", a decrease of the electron density, between the H...O atoms. Calculations of Gibbs free energy, entropy, and enthalpy show that the PEO/cofactor complexes do not form at room temperature, because the loss of entropy exceeds the increase in enthalpy. The change in enthalpy is linearly related to the change in entropy for the different complexes. Even though bond lengths, bond angles, DLMOs, and electron densities for the PEO/cofactor complexes are consistent with the definition of hydrogen bonds, the number of intermolecular R-OH...O and R-CH...O bonds does not correlate with the enthalpy of association, indicating that the bonding mechanism for these systems is the sum of many small contributions of many delocalized orbitals.
Low Energy Charged Particle Measurement by Japanese Lunar Orbiter SELENE
NASA Astrophysics Data System (ADS)
Saito, Yu.; Yokota, S.; Asamura, K.; Tanaka, T.; Mukai, T.
SELenological and ENgineering Explorer (SELENE) is a Japanese lunar orbiter that will be launched in 2007. The main purpose of this satellite is to study the origin and evolution of the Moon by means of global mapping of element abundances, mineralogical composition, and surface geographical mapping from 100 km altitude. Plasma energy Angle and Composition Experiment (PACE) is one of the scientific instruments onboard the SELENE satellite. The scientific objectives of PACE are (1) to measure the ions sputtered from the lunar surface and the lunar atmosphere, (2) to measure the magnetic anomaly on the lunar surface using two electron spectrum analyzers (ESAs) and a magnetometer onboard SELENE simultaneously as an electron reflectometer, (3) to resolve the Moon-solar wind interaction, (4) to resolve the Moon-Earth's magnetosphere interaction, and (5) to observe the Earth's magnetotail. PACE consists of four sensors: ESA-S1, ESA-S2, ion mass analyzer (IMA), and ion energy analyzer (IEA). ESA-S1 and S2 measure the three-dimensional distribution function of low energy electrons below 15 keV, while IMA and IEA measure the three-dimensional distribution function of low energy ions below 28 keV/q.
Expressions of Energy and Potential due to Orbital Polarization
NASA Astrophysics Data System (ADS)
Narita, Akira; Higuchi, Masahiko
2006-02-01
The simple and tractable representation for the LS-multiplet energy in l1l2-configuration in an atom is derived in the form of the polynomials being a function of l1\\cdotl2 which obey the recurrence formulae, and is suitable for the vector model. Moreover, it is extended to ln configurations. On a basis of the model, the definition of the orbital polarization energy is given. The more precise expressions of the energies compared to those so far proposed by Eriksson et al. are derived for the maximal spin multiplets in pn, dn, and fn. They are composed of two terms depending on -3L2/2 and n(n-2l-1). They are the exact for pn and dn, but it for fn is correct only for a ground multiplet. Other expressions are also derived as a function of L2 for fn, though more complicated. For the actual atomic and band structure calculations based on local-spin-density-approximation (LSDA), the modified expression for the energy is proposed. The potential is derived from its expression in terms of the density functional theory, and can be applied to their structure calculations.
Low-energy plasma observations at synchronous orbit
NASA Technical Reports Server (NTRS)
Lennartsson, W.; Reasoner, D. L.
1978-01-01
The University of California at San Diego Auroral Particles Experiment on the ATS 6 satellite in synchronous orbit has detected a low-energy plasma population which is separate and distinct from both the ring current and the plasma sheet populations. The density and temperature of this low-energy population are highly variable, with temperatures in the range kT = 1-30 eV and densities ranging from less than 1 per cu cm to more than 10 per cu cm. The occurrence of a dense low-energy plasma is most likely in the afternoon and dusk local time sectors, whereas n greater than 1 per cu cm is seen in the local night sector only during magnetically quiet periods. These observations suggest that this plasma is the outer zone of the plasmasphere. During magnetically active periods this low-energy plasma is often observed flowing sunward. In the dusk sector, strong sunward plasma flow is often observed for 1-2 hours prior to the onset of a substorm-associated particle injection.
NASA Astrophysics Data System (ADS)
Shiga, Motoyuki; Tachikawa, Masanori; Miura, Shinichi
2000-12-01
We present an accurate calculational scheme for many-body systems composed of electrons and nuclei, by path integral molecular dynamics technique combined with the ab initio molecular orbital theory. Based upon the scheme, the simulation of a water molecule at room temperature is demonstrated, applying all-electron calculation at the Hartree-Fock level of theory.
Pruitt, Spencer R.; Nakata, Hiroya; Nagata, Takeshi; Mayes, Maricris; Alexeev, Yuri; Fletcher, Graham D.; Fedorov, Dmitri G; Kitaura, Kazuo; Gordon, M
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 Hartree-Fock, second-order Møller-Plesset perturbation, and density functional theories. 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.
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).
Mean excitation energies for molecular ions
NASA Astrophysics Data System (ADS)
Jensen, Phillip W. K.; Sauer, Stephan P. A.; Oddershede, Jens; Sabin, John R.
2017-03-01
The essential material constant that determines the bulk of the stopping power of high energy projectiles, the mean excitation energy, is calculated for a range of smaller molecular ions using the RPA method. It is demonstrated that the mean excitation energy of both molecules and atoms increase with ionic charge. However, while the mean excitation energies of atoms also increase with atomic number, the opposite is the case for mean excitation energies for molecules and molecular ions. The origin of these effects is explained by considering the spectral representation of the excited state contributing to the mean excitation energy.
Differential neutron energy spectra measured on spacecraft low Earth orbit
Benton, E.V.; Frank, A.L.; Dudkin, E.V.; Potapov, Yu.V.; Akopova, A.B.; Melkumyan, L.V. |
1995-03-01
Two methods for measuring neutrons in the range from thermal energies to dozens of MeV were used. In the first method, alpha-particles emitted from the (sup 6) Li(n,x)T reaction are detected with the help of plastic nuclear track detectors, yielding results on thermal and resonance neutrons. Also, fission foils are used to detect fast neutrons. In the second method, fast neutrons are recorded by nuclear photographic emulsions (NPE). The results of measurements on board various satellites are presented. The neutron flux density does not appear to correlate clearly with orbital parameters. Up to 50% of neutrons are due to albedo neutrons from the atmosphere while the fluxes inside the satellites are 15-20% higher than those on the outside. Estimates show that the neutron contribution to the total equivalent radiation dose reaches 20-30%.
Differential neutron energy spectra measured on spacecraft low Earth orbit
NASA Technical Reports Server (NTRS)
Benton, E. V.; Frank, A. L.; Dudkin, E. V.; Potapov, Yu. V.; Akopova, A. B.; Melkumyan, L. V.
1995-01-01
Two methods for measuring neutrons in the range from thermal energies to dozens of MeV were used. In the first method, alpha-particles emitted from the (sup 6) Li(n.x)T reaction are detected with the help of plastic nuclear track detectors, yielding results on thermal and resonance neutrons. Also, fission foils are used to detect fast neutrons. In the second method, fast neutrons are recorded by nuclear photographic emulsions (NPE). The results of measurements on board various satellites are presented. The neutron flux density does not appear to correlate clearly with orbital parameters. Up to 50% of neutrons are due to albedo neutrons from the atmosphere while the fluxes inside the satellites are 15-20% higher than those on the outside. Estimates show that the neutron contribution to the total equivalent radiation dose reaches 20-30%.
The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds
Steinmann, Casper; Fedorov, Dmitri G.; Jensen, Jan H.
2012-01-01
We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 Å for RHF and MP2, respectively. PMID:22844433
Effects of Exchange Energy and Spin-Orbit Coupling on Bond Energies
ERIC Educational Resources Information Center
Smith, Derek W.
2004-01-01
Since chemical reactions involve the breaking and making of bonds, understanding the relative strengths of bonds is of paramount importance in the study, teaching, and practice of chemistry. Further, it is showed that free atoms having p(super n) configuration with n = 2,3, or 4 are stabilized by exchange energy, and by spin-orbit coupling for n =…
Findlater, Alexander D; Zahariev, Federico; Gordon, Mark S
2015-04-16
The local correlation "cluster-in-molecule" (CIM) method is combined with the fragment molecular orbital (FMO) method, providing a flexible, massively parallel, and near-linear scaling approach to the calculation of electron correlation energies for large molecular systems. Although the computational scaling of the CIM algorithm is already formally linear, previous knowledge of the Hartree-Fock (HF) reference wave function and subsequent localized orbitals is required; therefore, extending the CIM method to arbitrarily large systems requires the aid of low-scaling/linear-scaling approaches to HF and orbital localization. Through fragmentation, the combined FMO-CIM method linearizes the scaling, with respect to system size, of the HF reference and orbital localization calculations, achieving near-linear scaling at both the reference and electron correlation levels. For the 20-residue alanine α helix, the preliminary implementation of the FMO-CIM method captures 99.6% of the MP2 correlation energy, requiring 21% of the MP2 wall time. The new method is also applied to solvated adamantine to illustrate the multilevel capability of the FMO-CIM method.
Low Energy Charged Particle Measurement by Japanese Lunar Orbiter SELENE
NASA Astrophysics Data System (ADS)
Saito, Y.; Yokota, S.; Asamura, K.; Mukai, T.
2004-12-01
SELENE (SELenological and Engineering satellite) is a Japanese lunar orbiter that will be launched in 2006. The main purpose of this satellite is to study the origin and evolution of the moon by means of global mapping of element abundances, mineralogical composition, and surface geographical mapping from 100km altitude. PACE (Plasma energy Angle and Composition Experiment) is one of the scientific instruments onboard the SELENE satellite. PACE consists of 4 sensors: ESA (Electron Spectrum Analyzer)-S1, ESA-S2, IMA (Ion Mass Analyzer), and IEA (Ion Energy Analyzer). ESA-S1 and S2 measure three-dimensional distribution function of low energy electrons below 17keV. ESA basically employs a method of a top hat electrostatic analyzer with angular scanning deflectors at the entrance and toroidal electrodes inside. IMA and IEA measure the three-dimensional distribution function of low energy ions below 28keV/q. IMA has an ability to discriminate the ion mass with high mass resolution. IMA consists of an energy analyzer that is basically the same as ESA and an LEF (Linear Electric Field) TOF (Time Of Flight) ion mass analyzer. IEA consists of only an energy analyzer that is the same as the energy analyzer of IMA. Each sensor has hemi-spherical field of view (FOV). With two pairs of sensors ESA-S1 & IMA, and ESA-S2 & IEA, which are installed on the +Z and -Z surface of the spacecraft, three-dimensional distribution function of low energy electrons and ions are observed. The scientific objectives of PACE are 1) to measure the ions sputtered from the lunar surface and the lunar atmosphere, 2) to measure the magnetic anomaly on the lunar surface using two ESAs and a magnetometer onboard SELENE simultaneously as an electron reflectometer, 3) to resolve the moon - solar wind interaction, 4) to resolve the moon - Earth's magnetosphere interaction, and 5) to observe the Earth's magnetotail. Sputtered ions from the lunar surface will be measured for the first time. Recently, ground
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.
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.
Electron flux models for different energies at geostationary orbit
NASA Astrophysics Data System (ADS)
Boynton, R. J.; Balikhin, M. A.; Sibeck, D. G.; Walker, S. N.; Billings, S. A.; Ganushkina, N.
2016-10-01
Forecast models were derived for energetic electrons at all energy ranges sampled by the third-generation Geostationary Operational Environmental Satellites (GOES). These models were based on Multi-Input Single-Output Nonlinear Autoregressive Moving Average with Exogenous inputs methodologies. The model inputs include the solar wind velocity, density and pressure, the fraction of time that the interplanetary magnetic field (IMF) was southward, the IMF contribution of a solar wind-magnetosphere coupling function proposed by Boynton et al. (2011b), and the Dst index. As such, this study has deduced five new 1 h resolution models for the low-energy electrons measured by GOES (30-50 keV, 50-100 keV, 100-200 keV, 200-350 keV, and 350-600 keV) and extended the existing >800 keV and >2 MeV Geostationary Earth Orbit electron fluxes models to forecast at a 1 h resolution. All of these models were shown to provide accurate forecasts, with prediction efficiencies ranging between 66.9% and 82.3%.
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.
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)
Roemelt, Michael
2015-07-01
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.
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.
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.
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).
Ab initio charge, spin and orbital energy scales in LaMnO3
NASA Astrophysics Data System (ADS)
Tyer, R.; Temmerman, W. M.; Szotek, Z.; Banach, G.; Svane, A.; Petit, L.; Gehring, G. A.
2004-02-01
The first-principles SIC-LSD theory is utilized to study electronic, magnetic and orbital phenomena in LaMnO3. The correct ground state is found, which is antiferro orbitally ordered with the spin magnetic moments antiferromagnetically aligned. Jahn-Teller energies are found to be the largest energy scale. In addition, it is the Jahn-Teller interaction which is the dominant effect in realizing orbital order, and the electronic effects alone do not suffice.
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.
Cui, Ganglong; Fang, Weihai; Yang, Weitao
2010-01-14
Time-dependent density functional theory (TDDFT) has broad application in the study of electronic response, excitation and transport. To extend such application to large and complex systems, we develop a reformulation of TDDFT equations in terms of non-orthogonal localized molecular orbitals (NOLMOs). NOLMO is the most localized representation of electronic degrees of freedom and has been used in ground state calculations. In atomic orbital (AO) representation, the sparsity of NOLMO is transferred to the coefficient matrix of molecular orbitals (MOs). Its novel use in TDDFT here leads to a very simple form of time propagation equations which can be solved with linear-scaling effort. We have tested the method for several long-chain saturated and conjugated molecular systems within the self-consistent charge density-functional tight-binding method (SCC-DFTB) and demonstrated its accuracy. This opens up pathways for TDDFT applications to large bio- and nano-systems.
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.
Potential energy hypersurface and molecular flexibility
NASA Astrophysics Data System (ADS)
Koča, Jaroslav
1993-02-01
The molecular flexibility phenomenon is discussed from the conformational potential energy(hyper) surface (PES) point of view. Flexibility is considered as a product of three terms: thermodynamic, kinetic and geometrical. Several expressions characterizing absolute and relative molecular flexibility are introduced, depending on a subspace studied of the entire conformational space, energy level E of PES as well as absolute temperature. Results obtained by programs DAISY, CICADA and PANIC in conjunction with molecular mechanics program MMX for flexibility analysis of isopentane, 2,2-dimethylpentane and isohexane molecules are introduced.
Sulphur hexaflouride: low energy (e,2e) experiments and molecular three-body distorted wave theory
NASA Astrophysics Data System (ADS)
Nixon, Kate L.; Murray, Andrew J.; Chaluvadi, H.; Ning, C. G.; Colgan, James; Madison, Don H.
2016-10-01
Experimental and theoretical triple differential ionisation cross-sections (TDCSs) are presented for the highest occupied molecular orbital of sulphur hexafluoride. These measurements were performed in the low energy regime, with outgoing electron energies ranging from 5 to 40 eV in a coplanar geometry, and with energies of 10 and 20 eV in a perpendicular geometry. Complementary theoretical predictions of the TDCS were calculated using the molecular three-body distorted wave formalism. Calculations were performed using a proper average over molecular orientations as well as the orientation-averaged molecular orbital approximation. This more sophisticated model was found to be in closer agreement with the experimental data, however neither model accurately predicts the TDCS over all geometries and energies.
Properties of hot dense plasmas by Orbital-Free Molecular Dynamics
NASA Astrophysics Data System (ADS)
Clerouin, Jean
2011-10-01
During the last decade DFT calculations have been successfully applied to the WDM regime. To overcome the limitations of DFT in temperature and density we propose to return to the very basis of DFT by using an ``only on the density'' formulation of the electronic kinetic energy, essentially captured by the finite temperature formulation of the Thomas-Fermi theory. High temperatures (up to few KeV) and high densities (up to 10 ×ρ0) systems can be addressed by orbital free molecular dynamics simulations (OFMD) at the expense of a fine description of atomic properties such as binding properties. Thanks to an efficient numerical scheme, up to thousands of particles can be propagated giving accurate static and dynamical properties without any assumptions on the ionization state or on the screening of interactions. Simulations of hydrogen and iron up to 5 keV and boron up to 10 times the normal density were performed. Very dissymmetrical mixtures can be also treated without difficulties. More recently, this method has been applied to hydrogen at high density (up to 160 g/cc) and high temperature (up to 1 KeV) to generate long trajectories for a later computation of the thermal conductivity with classical DFT. This method bridges the gap between quantum and classical molecular dynamics in the field of hot-dense plasmas and could be also used as a platform to include more physics such as nuclear reactions or interaction with a radiative field.
Terazulene Isomers: Polarity Change of OFETs through Molecular Orbital Distribution Contrast.
Yamaguchi, Yuji; Takubo, Maki; Ogawa, Keisuke; Nakayama, Ken-Ichi; Koganezawa, Tomoyuki; Katagiri, Hiroshi
2016-09-07
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.
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.
NASA Technical Reports Server (NTRS)
Billman, Kenneth W.; Gilbreath, William P.; Bowen, Stuart W.
1978-01-01
A system of orbiting, large-area, low mass density reflector satellites which provide nearly continuous solar energy to a world-distributed set of conversion sites is examined under the criteria for any potential new energy system: technical feasibility, significant and renewable energy impact, economic feasibility and social/political acceptability. Although many technical issues need further study, reasonable advances in space technology appear sufficient to implement the system. The enhanced insolation is shown to greatly improve the economic competitiveness of solar-electric generation to circa 1995 fossil/nuclear alternatives. The system is shown to have the potential for supplying a significant fraction of future domestic and world energy needs. Finally, the environmental and social issues, including a means for financing such a large shift to a world solar energy dependence, is addressed.
Molecular Motion and Energy Migration in Polymers.
1985-06-01
A EDUUNI MAR 8 STOK ISEXHASTED " LOAN, 0 - LO 00 MOLECULAR MOTION AND ENERGY MIGRATION IN POLYMERS Professor David Phillips June 1985 US Army...and Energy Migration in Final Technical Report Polymers 6. PERFORMING ORG. REPORT NUMBER 7. AUTHOR(s) 8. CONTRACT OR GRANT NUMBER(s) Professor David...acenaphthylene, poly(diacetylenes),4h,4’ - diphenylene diphenyl vinylene, energy transfer, migration, segmental motion, rotational relaxation. 20. ABSTRACT
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…
Low-energy physics of three-orbital impurity model with Kanamori interaction
NASA Astrophysics Data System (ADS)
Horvat, Alen; Žitko, Rok; Mravlje, Jernej
2016-10-01
We discuss the low-energy physics of the three-orbital Anderson impurity model with the Coulomb interaction term of the Kanamori form which has orbital SO(3) and spin SU(2) symmetry and describes systems with partially occupied t2 g shells. We focus on the case with two electrons in the impurity that is relevant to Hund's metals. Using the Schrieffer-Wolff transformation we derive an effective Kondo model with couplings between the bulk and impurity electrons expressed in terms of spin, orbital, and orbital quadrupole operators. The bare spin-spin Kondo interaction is much smaller than the orbit-orbit and spin-orbital couplings or is even ferromagnetic. Furthermore, the perturbative scaling equations indicate faster renormalization of the couplings related to orbital degrees of freedom compared to spin degrees of freedom. Both mechanisms lead to a slow screening of the local spin moment. The model thus behaves similarly to the related quantum impurity problem with a larger SU(3) orbital symmetry (Dworin-Narath interaction) where this was first observed. We find that the two problems actually describe the same low-energy physics since the SU(3) symmetry is dynamically established through the renormalization of the splittings between the orbital and quadrupole coupling constants to zero. The perturbative renormalization group results are corroborated with the numerical-renormalization group (NRG) calculations. The dependence of spin Kondo temperatures and orbital Kondo temperatures as a function of interaction parameters, the hybridization, and the impurity occupancy is calculated and discussed.
A Molecular Orbital Study of Atmospherically Important Species.
1983-06-01
from the OH to the H2 0 upon formation of the hydrogen bond. The electron density is transferred to the oxygen and terminal hydrogen of the water ...Method," J. Chem. Phys., 52, 3362-3368, 1970. • -o . ..-.. . -34- 48. Chipman, D.M. "Effect of Molecular Geometry on the Electron Affinity of Water ...34 J. Phvs. Chem., 82, 1080-1083, 1978. 49. Benedict, W.S., N. Gailar, and E.K. Plvler, "Rotation-Vibration Spectra of Deuteriated Water Vapor," J. Chem
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.
Velasco, A M; Pitarch-Ruiz, J; Sánchez de Merás, Alfredo M J; Sánchez-Marín, J; Martin, I
2006-03-28
Vertical excitation energies as well as related absolute photoabsorption oscillator strength data are very scarce in the literature for methane. In this study, we have characterized the three existing series of low-lying Rydberg states of CH4 by computing coupled cluster linear response (CCLR) vertical excitation energies together with oscillator strengths in the molecular-adapted quantum defect orbital formalism from a distorted Cs geometry selected on the basis of outer valence green function calculations. The present work provides a wide range of data of excitation energies and absolute oscillator strengths which correspond to the Rydberg series converging to the three lower ionization potential values of the distorted methane molecule, in energy regions for which experimentally measured data appear to be unavailable.
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.
Echegaray, Eleonora; Cárdenas, Carlos; Rabi, Sandra; Rabi, Nataly; Lee, Sungmin; Zadeh, Farnaz Heidar; Toro-Labbe, Alejandro; Anderson, James S M; Ayers, Paul W
2013-07-01
In our quest to explore molecules with chemically significant regions where the Fukui function is negative, we explored reactions where the frontier orbital that indicates the sites for electrophilic attack is not the highest occupied molecular orbital. The highest occupied molecular orbital (HOMO) controls the location of the regions where the Fukui function is negative, supporting the postulate that negative values of the Fukui function are associated with orbital relaxation effects and nodal surfaces of the frontier orbitals. Significant negative values for the condensed Fukui function, however, were not observed.
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.
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…
Internal kink stabilization by high-energy ions with nonstandard orbits
NASA Astrophysics Data System (ADS)
Porcelli, F.; Stankiewicz, R.; Berk, H. L.; Zhang, Y. Z.
1992-10-01
A generalized energy principle that takes into account the nonstandard, potato-shaped particle orbits of high-energy ions in the central region of a tokamak is derived. It is shown that, in the limit of zero orbit width, this energy principle reduces to the one formulated by Van Dam et al. [Phys. Fluids 25, 1349 (1982)]. The modification of hot particle stabilization theory when such orbit effects are important is investigated. In particular, a model distribution function is chosen to describe high-energy trapped ions produced by ion cyclotron resonant frequency (ICRF) heating applied near the axis of a tokamak. Standard banana orbit theory predicts that, for fixed total stored energy of energetic particles peaked about the magnetic axis, the stabilizing influence on internal kink modes is inversely proportional to the spatial spread of the hot particles. However, this scaling saturates when the spatial spread of the distribution function approaches the width of a typical nonstandard orbit. Hence, ICRF heating is most efficient in producing stabilization when the heating zone is comparable to the orbit width, while the tendency to stabilize does not improve if the heating zone is narrower than the orbit width. Further, it is shown that, if particle orbits can extend close to the q=1 surface, the tendency for stabilization is inhibited.
NASA Astrophysics Data System (ADS)
Jitrik, Oliverio; Bunge, Carlos F.
2005-07-01
Transition probabilities have been computed using a variational many-electron theory [R. Jáuregui, C.F. Bunge, E. Ley-Koo, Phys. Rev. A 55 (1997) 1781] incorporating positive-energy and negative-energy orbitals without ambiguities, and absolutely free from variational collapse. The results agree with experiment and with other calculations based on the no-pair Hamiltonian where ad hoc negative-energy orbitals occur in first-order corrections to the wave functions.
NASA Astrophysics Data System (ADS)
Hafner, P.; Habitz, P.; Ishikawa, Y.; Wechsel-Trakowski, E.; Schwarz, W. H. E.
1981-06-01
Calculations on ground and valence-excited states of Au +2, Tl 2 and Pb 2, and on the ground states of HgCl 2, PbCl 2 and PbH 2 have teen performed within the Kramers-restricteu self-consistent-field approach using a quasi-relativitistic model-potential hamiltonian. The influence of spin—orbit coupling on molecular orbitals, bond energies and geometries is discussed.
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.
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.
Rotational Doppler Effect: A Probe for Molecular Orbitals Anisotropy.
Miao, Quan; Travnikova, Oksana; Gel'mukhanov, Faris; Kimberg, Victor; Sun, Yu-Ping; Thomas, T Darrah; Nicolas, Christophe; Patanen, Minna; Miron, Catalin
2015-05-07
The vibrationally resolved X-ray photoelectron spectra of X2Σg+(3σg−1) and B2Σu+(2σu−1) states of N2+ were recorded for different photon energies and orientations of the polarization vector. Clear dependencies of the spectral line widths on the X-ray polarization as well as on the symmetry of the final electronic states are observed. Contrary to the translational Doppler, the rotational Doppler broadening is sensitive to the photoelectron emission anisotropy. On the basis of theoretical modeling, we suggest that the different rotational Doppler broadenings observed for gerade and ungerade final states result from a Young's double-slit interference phenomenon.
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.
Vibrational energy transfer in shocked molecular crystals.
Hooper, Joe
2010-01-07
We consider the process of establishing thermal equilibrium behind an ideal shock front in molecular crystals and its possible role in initiating chemical reaction at high shock pressures. A new theory of equilibration via multiphonon energy transfer is developed to treat the scattering of shock-induced phonons into internal molecular vibrations. Simple analytic forms are derived for the change in this energy transfer at different Hugoniot end states following shock compression. The total time required for thermal equilibration is found to be an order of magnitude or faster than proposed in previous work; in materials representative of explosive molecular crystals, equilibration is predicted to occur within a few picoseconds following the passage of an ideal shock wave. Recent molecular dynamics calculations are consistent with these time scales. The possibility of defect-induced temperature localization due purely to nonequilibrium phonon processes is studied by means of a simple model of the strain field around an inhomogeneity. The specific case of immobile straight dislocations is studied, and a region of enhanced energy transfer on the order of 5 nm is found. Due to the rapid establishment of thermal equilibrium, these regions are unrelated to the shock sensitivity of a material but may allow temperature localization at high shock pressures. Results also suggest that if any decomposition due to molecular collisions is occurring within the shock front itself, these collisions are not enhanced by any nonequilibrium thermal state.
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.
NASA Astrophysics Data System (ADS)
Petersen, Ingo; Henkel, Jost; Lein, Manfred
2015-03-01
Strong-field ionization of aligned diatomic and polyatomic molecules such as O2, N2, C2H4, and others in circularly polarized laser fields is investigated theoretically. By calculating the emission-angle-resolved lateral width of the momentum distribution perpendicular to the polarization plane, we show that nodal planes in molecular orbitals are directly imprinted on the angular dependence of the width. We demonstrate that orbital symmetries can be distinguished with the information obtained by observing the lateral width in addition to the angular distributions.
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
Energy Functional Based on Natural Orbitals and Occupancies for Static Properties of Nuclei
Lacroix, Denis
2009-08-26
The possibility to use functionals of occupation numbers and natural orbitals for interacting fermions is discussed as an alternative to multi-reference energy density functional method. An illustration based on the two-level Lipkin model is discussed.
Investigation of the energy dependence of the orbital light curve in LS 5039
NASA Astrophysics Data System (ADS)
Chang, Z.; Zhang, S.; Ji, L.; Chen, Y. P.; Kretschmar, P.; Kuulkers, E.; Collmar, W.; Liu, C. Z.
2016-11-01
LS 5039 is so far the best-studied γ-ray binary system at multiwavelength energies. A time-resolved study of its spectral energy distribution (SED) shows that above 1 keV its power output is changing along its binary orbit as well as being a function of energy. To disentangle the energy dependence of the power output as a function of orbital phase, we investigated in detail the orbital light curves as derived with different telescopes at different energy bands. We analysed the data from all existing International Gamma-Ray Astrophysics Laboratory (INTEGRAL)/INTEGRAL on-board Imager/INTEGRAL Soft Gamma-Ray Imager observations of the source and generated the most up-to-date orbital light curves at hard X-ray energies. In the γ-ray band, we carried out orbital phase-resolved analysis of Fermi-Large Area Telescope (LAT) data between 30 MeV and 10 GeV in five different energy bands. We found that, at ≲100 MeV and ≳1 TeV the peak of the γ-ray emission is near orbital phase 0.7, while between ˜100 MeV and ˜1 GeV it moves close to orbital phase 1.0 in an orbital anticlockwise manner. This result suggests that the transition region in the SED at soft γ-rays (below a hundred MeV) is related to the orbital phase interval of 0.5-1.0 but not to the one of 0.0-0.5, when the compact object is `behind' its companion. Another interesting result is that between 3 and 20 GeV no orbital modulation is found, although Fermi-LAT significantly (˜18σ) detects LS 5039. This is consistent with the fact that at these energies, the contributions to the overall emission from the inferior conjunction phase region (INFC, orbital phase 0.45-0.9) and from the superior conjunction phase region (orbital phase 0.9-0.45) are equal in strength. At TeV energies the power output is again dominant in the INFC region and the flux peak occurs at phase ˜0.7.
Development of Molecular Electrocatalysts for Energy Storage
DuBois, Daniel L.
2014-02-20
Molecular electrocatalysts can play an important role in energy storage and utilization reactions needed for intermittent renewable energy sources. This manuscript describes three general themes that our laboratories have found useful in the development of molecular electrocatalysts for reduction of CO_{2} to CO and for H_{2} oxidation and production. The first theme involves a conceptual partitioning of catalysts into first, second, and outer coordination spheres. This is illustrated with the design of electrocatalysts for CO_{2 }reduction to CO using first and second coordination spheres and for H_{2} production catalysts using all three coordination spheres. The second theme focuses on the development of thermodynamic models that can be used to design catalysts to avoid high energy and low energy intermediates. In this research, new approaches to the measurement of thermodynamic hydride donor and acceptor abilities of transition metal complexes were developed. Combining this information with other thermodynamic information such as pKa values and redox potentials led to more complete thermodynamic descriptions of transition metal hydride, dihydride, and related species. Relationships extracted from this information were then used to develop models that are powerful tools for predicting and understanding the relative free energies of intermediates in catalytic reactions. The third theme is the control of proton movement during electrochemical fuel generation and utilization reactions. This research involves the incorporation of pendant amines in the second coordination sphere that can facilitate H-H bond heterolysis and heteroformation, intramolecular and intermolecular proton transfer steps, and the coupling of proton and electron transfer steps. Studies also indicate an important role for outer coordination sphere in the delivery of protons to the second coordination sphere. Understanding these proton transfer reactions and their
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.
Prabavathi, N; Senthil Nayaki, N; Venkatram Reddy, B
2015-02-05
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).
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.
Molecularly Engineered Energy Materials, an Energy Frontier Research Center
Ozolins, Vidvuds
2016-09-28
Molecularly Engineered Energy Materials (MEEM) was established as an interdisciplinary cutting-edge UCLA-based research center uniquely equipped to attack the challenge of rationally designing, synthesizing and testing revolutionary new energy materials. Our mission was to achieve transformational improvements in the performance of materials via controlling the nano-and mesoscale structure using selectively designed, earth-abundant, inexpensive molecular building blocks. MEEM has focused on materials that are inherently abundant, can be easily assembled from intelligently designed building blocks (molecules, nanoparticles), and have the potential to deliver transformative economic benefits in comparison with the current crystalline-and polycrystalline-based energy technologies. MEEM addressed basic science issues related to the fundamental mechanisms of carrier generation, energy conversion, as well as transport and storage of charge and mass in tunable, architectonically complex materials. Fundamental understanding of these processes will enable rational design, efficient synthesis and effective deployment of novel three-dimensional material architectures for energy applications. Three interrelated research directions were initially identified where these novel architectures hold great promise for high-reward research: solar energy generation, electrochemical energy storage, and materials for CO_{2} capture. Of these, the first two remained throughout the project performance period, while carbon capture was been phased out in consultation and with approval from BES program manager.
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.
Effect of vacuum processing on outgassing within an orbiting molecular shield
NASA Technical Reports Server (NTRS)
Outlaw, R. A.
1982-01-01
The limiting hydrogen number density in an orbiting molecular shield is highly dependent on the outgassing rates from the materials of construction for the shield, experimental apparatus, and other hardware contained within the shield. Ordinary degassing temperatures used for ultrahigh vacuum studies (less than 450 C) are not sufficient to process metals so that the contribution to the number density within the shield due to outgassing is less than the theoretically attainable level (approximately 200 per cu. cm). Pure aluminum and type 347 stainless steel were studied as candidate shield materials. Measurements of their hydrogen concentration and diffusion coefficients were made, and the effects of high temperature vacuum processing (greater than 600 C) on their resulting outgassing rates was determined. The densities in a molecular shield due to the outgassing from either metal were substantially less ( 0.003) than the density due to the ambient atomic hydrogen flux at an orbital altitude of 500 km.
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.
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
Molecular orbital view of the electronic coupling between two metal nanoparticles
Troparevsky, Claudia; Zhao, Ke; Xiao, Di; Eguiluz, Adolfo G; Zhang, Zhenyu
2010-01-01
The electronic coupling between metal nanoparticles is responsible for intriguing new phenomena observed when the particles are near touching contact, which is exemplified by recent investigations of nanoparticle dimers. However, little is known about the role of the molecular orbitals of the nanoparticle dimers. The expectation is that the physics and chemistry of the system must be reflected in the orbitals that control the bonding at touching contact. This expectation is borne out in the present investigation in which we present a comprehensive theoretical study based on density-functional theory of the electronic coupling between two silver nanoparticles. We explain our findings by studying the molecular orbitals of the dimers as a function of the separation and relative orientation between the nanoparticles. We show that as the nanoparticles approach each other a bond-forming step takes place, and that the strength of the hybridization is a key element to determine various properties of the system. We find that the relative orientation between the nanoparticles plays an important role in determining the strength of the coupling which can be visualized by the spatial distribution of the highest occupied molecular orbitals. Moreover, the strength of the coupling will in turn determine the ease of their transition to the nonlinear dielectric-response regime. This effect allows for the tunability of the electronic coupling and magnetic moment of the dimer. Our findings are essential for understanding and tailoring desired physical and chemical properties of closely aggregated nanoparticles relevant for applications such as surface-enhanced Raman scattering and quantum transport in molecular devices.
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.
Molecular orbital calculations on atomic structures of Si-based covalent amorphous ceramics
Matsunaga, K.; Matsubara, H.
1999-07-01
The authors have performed ab-initio Hartree-Fock molecular orbital calculations of local atomic structures and chemical bonding states in Si-N covalent amorphous ceramics. Solute elements such as boron, carbon and oxygen were considered in the Si-N network, and the bonding characteristics around the solute elements were analyzed. When a nitrogen atom is substituted by a carbon atom, it was found that Si-C bonds reinforce the Si-N network due to strong covalency.
Learning molecular energies using localized graph kernels
NASA Astrophysics Data System (ADS)
Ferré, Grégoire; Haut, Terry; Barros, Kipton
2017-03-01
Recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturally incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. We benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules.
A molecular orbital rationalization of ligand effects in N2 activation.
Ariafard, Alireza; Brookes, Nigel J; Stranger, Robert; Yates, Brian F
2008-01-01
Molecular orbital theory has been used to study a series of [(micro-N2){ML3}2] complexes as models for dinitrogen activation, with M=Mo, Ta, W, Re and L=NH2, PH2, AsH2, SbH2 and N(BH2)2. The main aims of this study have been to provide a thorough electronic analysis of the complexes and to extend previous work involving molecular orbital analyses. Molecular orbital diagrams have been used to rationalize why for L=NH2 ligand rotation is important for the singlet state but not the triplet, to confirm the effect of ligand pi donation, and to rationalize the importance of the metal d-electron configuration. The outcomes of this study will assist with a more in-depth understanding of the electronic basis for N2 activation and allow clearer predictions to be made about the structure and multiplicity of systems involved in transition-metal catalysis.
Ab initio derivation of multi-orbital extended Hubbard model for molecular crystals
NASA Astrophysics Data System (ADS)
Tsuchiizu, Masahisa; Omori, Yukiko; Suzumura, Yoshikazu; Bonnet, Marie-Laure; Robert, Vincent
2012-01-01
From configuration interaction (CI) ab initio calculations, we derive an effective two-orbital extended Hubbard model based on the gerade (g) and ungerade (u) molecular orbitals (MOs) of the charge-transfer molecular conductor (TTM-TTP)I3 and the single-component molecular conductor [Au(tmdt)2]. First, by focusing on the isolated molecule, we determine the parameters for the model Hamiltonian so as to reproduce the CI Hamiltonian matrix. Next, we extend the analysis to two neighboring molecule pairs in the crystal and we perform similar calculations to evaluate the inter-molecular interactions. From the resulting tight-binding parameters, we analyze the band structure to confirm that two bands overlap and mix in together, supporting the multi-band feature. Furthermore, using a fragment decomposition, we derive the effective model based on the fragment MOs and show that the staking TTM-TTP molecules can be described by the zig-zag two-leg ladder with the inter-molecular transfer integral being larger than the intra-fragment transfer integral within the molecule. The inter-site interactions between the fragments follow a Coulomb law, supporting the fragment decomposition strategy.
Yamaguchi, Yuji; Ogawa, Keisuke; Nakayama, Ken-Ichi; Ohba, Yoshihiro; Katagiri, Hiroshi
2013-12-26
We present herein a linear expanded π-conjugation system comprising azulene units: 2,6':2',6″-terazulene. This simple hydrocarbon exhibits excellent n-type transistor performance with an electron mobility of up to 0.29 cm(2) V(-1) s(-1). The lowest unoccupied molecular orbital (LUMO) is well distributed over the entire molecule, whereas the highest occupied molecular orbital (HOMO) is localized at one end. These findings indicate a disadvantage of hole carrier transport and an advantage of n-type-specific transport behavior. This system presents an unconventional concept: polarity control of OFET by molecular orbital distribution control.
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.
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.
Angular-overlap calculation of the Jahn-Teller stabilization energie for f-orbital degeneracies
Warren, K.D.
1980-03-01
The angular-overlap model is applied to the calculation of the linear Jahn-Teller coupling constants for f-orbital degeneracies. The MX/sub 6/, O/sub h/, chromophore is treated as representative of the highest symmetry commonly occurring in the lanthanide and actinide series, and it is shown that, even when spin-orbit effects are taken into account, 5f orbital degeneracies may lead to significant Jahn-Teller stabilization energies. The operation of this effect for F/sup 1/ GAMMA/sub 8/ states is considered. 2 tables.
Molecular quantum magnetism with strong spin-orbit coupling in inorganic solid Ba3Yb2Zn5O11
NASA Astrophysics Data System (ADS)
Park, Sang-Youn; Ji, Sungdae; Park, Jae-Hoon; Do, Seunghwan; Choi, Kwang-Yong; Jang, Dongjin; Schmidt, Burkhard; Brando, Manuel; Butch, Nicholas
The molecular magnet, assembly of finite number of spins which are isolated from environment, is a model system to study the quantum information process such as the qubit or spintronic devices. In past decades, the molecular magnet has been mostly realized in organic material, however, it has difficulty synthesizing materials or controlling their properties, meanwhile tremendous endeavors to search inorganic molecular magnet are continuing. Here, we propose Ba3Yb2Zn5O11 as a candidate of inorganic molecular magnet. This material consists of an alternating 3D-array of small and large tetrahedron containing antiferromagnetically coupled four pseudospin-1/2 Yb ions, and magnetic properties are described by an isolated tetrahedron without long-range magnetic ordering. Inelastic neutron scattering measurement with external magnetic field reveals that extraordinarily huge Dzyaloshinsky-Moriya (DM) interaction originating from strong spin-orbit coupling in Yb isospin is the key to explain energy level of tetrahedron in addition to Heisenberg exchange interaction and Zeeman effect. Magnetization measurement shows the Landau-Zener transition between avoided crossing levels caused by DM interaction.
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.
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.
Methods of performing downhole operations using orbital vibrator energy sources
Cole, Jack H.; Weinberg, David M.; Wilson, Dennis R.
2004-02-17
Methods of performing down hole operations in a wellbore. A vibrational source is positioned within a tubular member such that an annulus is formed between the vibrational source and an interior surface of the tubular member. A fluid medium, such as high bulk modulus drilling mud, is disposed within the annulus. The vibrational source forms a fluid coupling with the tubular member through the fluid medium to transfer vibrational energy to the tubular member. The vibrational energy may be used, for example, to free a stuck tubular, consolidate a cement slurry and/or detect voids within a cement slurry prior to the curing thereof.
Analytic energy gradients in closed-shell coupled-cluster theory with spin-orbit coupling.
Wang, Fan; Gauss, Jürgen
2008-11-07
Gradients in closed-shell coupled-cluster (CC) theory with spin-orbit coupling included in the post Hartree-Fock treatment have been implemented at the CC singles and doubles (CCSD) level and at the CCSD level augmented by a perturbative treatment of triple excitations [CCSD(T)]. The additional computational effort required in analytic energy-gradient calculations is roughly the same as that for ground-state energy calculations in the case of CCSD, and it is about twice in the case of CCSD(T) calculations. The structures, harmonic frequencies, and dipole moments of some heavy-element compounds have been calculated using the present analytic energy-gradient techniques including spin-orbit coupling. The results show that spin-orbit coupling can have a significant influence on both the equilibrium structure and the harmonic vibrational frequencies and that its inclusion is essential to obtain reliable and accurate estimates for geometrical parameters of heavy-element compounds.
Scalable Quantum Simulation of Molecular Energies
NASA Astrophysics Data System (ADS)
O'Malley, P. J. J.; Babbush, R.; Kivlichan, I. D.; Romero, J.; McClean, J. R.; Barends, R.; Kelly, J.; Roushan, P.; Tranter, A.; Ding, N.; Campbell, B.; Chen, Y.; Chen, Z.; Chiaro, B.; Dunsworth, A.; Fowler, A. G.; Jeffrey, E.; Lucero, E.; Megrant, A.; Mutus, J. Y.; Neeley, M.; Neill, C.; Quintana, C.; Sank, D.; Vainsencher, A.; Wenner, J.; White, T. C.; Coveney, P. V.; Love, P. J.; Neven, H.; Aspuru-Guzik, A.; Martinis, J. M.
2016-07-01
We report the first electronic structure calculation performed on a quantum computer without exponentially costly precompilation. We use a programmable array of superconducting qubits to compute the energy surface of molecular hydrogen using two distinct quantum algorithms. First, we experimentally execute the unitary coupled cluster method using the variational quantum eigensolver. Our efficient implementation predicts the correct dissociation energy to within chemical accuracy of the numerically exact result. Second, we experimentally demonstrate the canonical quantum algorithm for chemistry, which consists of Trotterization and quantum phase estimation. We compare the experimental performance of these approaches to show clear evidence that the variational quantum eigensolver is robust to certain errors. This error tolerance inspires hope that variational quantum simulations of classically intractable molecules may be viable in the near future.
Suresh, S; Gunasekaran, S; Srinivasan, S
2014-05-05
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.
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.
Monthly Variations of Low-Energy Ballistic Transfers to Lunar Halo Orbits
NASA Technical Reports Server (NTRS)
Parker, Jeffrey S.
2010-01-01
The characteristics of low-energy transfers between the Earth and Moon vary from one month to the next largely due to the Earth's and Moon's non-circular, non-coplanar orbits in the solar system. This paper characterizes those monthly variations as it explores the trade space of low-energy lunar transfers across many months. Mission designers may use knowledge of these variations to swiftly design desirable low-energy lunar transfers in any given month.
Effect of the orbital debris environment on the high-energy Van Allen proton belt
NASA Technical Reports Server (NTRS)
Konradi, Andrei
1988-01-01
The lifetimes of high-energy (greater than 55 MeV) protons in the Van Allen radiation belt are calculated, assuming that in time the protons will collide with and be absorbed by particulate orbiting material. The calculations are based on the NASA/DoD Civil Needs Database for orbital debris (Gaines, 1966) and moderate assumptions of future space traffic. It is found that the lifetimes of high-energy protons below 1500 km will decrease, leading to a noticeable redution in their fluxes.
NASA Astrophysics Data System (ADS)
Hohenstein, Edward G.
2016-11-01
The floating occupation molecular orbital complete active space configuration interaction (FOMO-CASCI) method is quite promising for the study of nonadiabatic processes. Use of this method directly in nonadiabatic dynamics simulations has been limited by the lack of available first-order nonadiabatic coupling vectors. Here, an analytic formulation of these derivative coupling vectors is presented for FOMO-CASCI wavefunctions using a simple Lagrangian-based approach. The derivative coupling vectors are applied in the optimization of minimum energy conical intersections of an aqueously solvated model compound for the chromophore of the green fluorescent protein (including 100 water molecules). The computational cost of the FOMO-CASCI derivative coupling vector is shown to scale quadratically, O ( N 2 ) , with system size and is applied to systems with up to 1000 atoms.
Hohenstein, Edward G
2016-11-07
The floating occupation molecular orbital complete active space configuration interaction (FOMO-CASCI) method is quite promising for the study of nonadiabatic processes. Use of this method directly in nonadiabatic dynamics simulations has been limited by the lack of available first-order nonadiabatic coupling vectors. Here, an analytic formulation of these derivative coupling vectors is presented for FOMO-CASCI wavefunctions using a simple Lagrangian-based approach. The derivative coupling vectors are applied in the optimization of minimum energy conical intersections of an aqueously solvated model compound for the chromophore of the green fluorescent protein (including 100 water molecules). The computational cost of the FOMO-CASCI derivative coupling vector is shown to scale quadratically, O(N(2)), with system size and is applied to systems with up to 1000 atoms.
An ab initio molecular orbital study of the reaction NH 2+NO → H 2+N 2O
NASA Astrophysics Data System (ADS)
Baker, Lane A.; Su, Shujun
1998-03-01
Potential energy surface of the reaction NH 2+NO → H 2+N 2O has been studied at several high levels of ab initio molecular orbital theory. The reaction pathway involves initially the formation without a barrier of a twisted non-planar H 2N-NO nitrosamine intermediate, and a C s symmetry transition state, followed by a dihydrogen H 2 elimination to form the products. The reaction path bifurcates before the transition state. At MP4(SDTQ)/6-311G(2d,p)//CASSCF/6-31G(d,p) level of theory, the reaction barrier for this path is found to be +33.7 kcal/mol.
Molecular-Orbital Basis for Superconductivity in High- and Low-Dimensional Metals.
1982-09-24
between 150A and 50A, respectively. [5,6] Similar increases of Tc with decreasing grain size have be-n measured for evaporated aluminum thin films . [69,70...momentum h/F F = h/2d (2) and kinetic energy (the Fermi energy) 2m 2 2 F /2m = h2/8md2 (3) On the other hand, within each layer-orbital component of...potential can be written in the form (30), which Weisskopf views as being contained in a "long thin tube" of length z and diameter d while acting only
NASA Astrophysics Data System (ADS)
Li, Shaowei; Yuan, Dingwang; Yu, Arthur; Czap, Gregory; Wu, Ruqian; Ho, W.
2015-05-01
A hydrogen molecule can diffuse freely on the surface and be trapped above an adsorbed molecule within the junction of a scanning tunneling microscope. The trapped dihydrogen exhibits the properties of a free rotor. Here we show that the intermolecular interaction between dihydrogen and Mg-porphyrin (MgP) can be visualized by imaging j =0 to 2 rotational excitation of dihydrogen. The interaction leads to a weakened H-H bond and modest electron donation from the dihydrogen to the lowest unoccupied molecular orbital of MgP, a process similarly observed for the interaction between dihydrogen and an adsorbed Au atom.
Development of minimized mixing molecular orbital method for designing organic ferromagnets.
Zhu, Xun; Aoki, Yuriko
2015-06-15
Predicting the high spin stability of organic radicals correctly for designing organic ferromagnets remains a significant challenge. We have developed a method with an index (L(min)) for predicting the high spin stability of conjugated organic radicals at the restricted open-shell Hartree-Fock level. Unitary transformations were performed for localizing the coefficients of nonbonding molecular orbitals, and subsequently the localized coefficients were used to calculate L(min) that indicates the high spin stability of conjugated organic radicals. This method can be combined with the elongation method to treat huge high spin open-shell systems. Thus, this method is useful for designing organic ferromagnets.
Multicenter molecular integrals for Slater orbitals of higher principal quantum numbers
NASA Technical Reports Server (NTRS)
Tai, H.
1989-01-01
As was shown earlier by Tai (1979), by using the Fourier-transform technique and properly coupling a pair of two-center exchange integrals, the multicenter molecular integrals can be cast into a simple expression upon which numerical procedures can be directly applied. In this paper, the procedure of Tai is extended to integrals involving orbitals with arbitrarily higher principal quantum number. The derivation is outlined, and the explicit expressions are presented for a three-center nuclear attraction integral and a four-center two-electron Coulomb repulsion integral of arbitrary higher states.
Earth-to-Moon low energy transfers targeting L1 hyperbolic transit orbits.
Topputo, Francesco; Vasile, Massimiliano; Bernelli-Zazzera, Franco
2005-12-01
In the frame of the lunar exploration, numerous future space missions will require maximization of payload mass, and simultaneously achieving reasonable transfer times. To fulfill this request, low energy non-Keplerian orbits could be used to reach the Moon instead of high energetic transfers. The low energy solutions can be separated into two main categories depending on the nature of the trajectory approaching the Moon: low energy transit orbits that approach the Moon from the interior equilibrium point L(1) and weak stability boundary transfers that reach the Moon after passing through L(2). This paper proposes an alternative way to exploit the opportunities offered by L(1) transit orbits for the design of Earth-Moon transfers. First, in a neighborhood of the L(1) point, the three-body dynamics is linearized and written in normal form; then the entire family of nonlinear transit orbits is obtained by selecting the appropriate nontrivial amplitudes associated with the hyperbolic part. The L(1)-Earth arc is close to a 5:2 resonant orbit with the Moon, whose perturbations cause the apogee to rise. In a second step, two selected low altitude parking orbits around the Earth and the Moon are linked with the transit orbit by means of two three-body Lambert arcs, solutions of two two-point boundary value problems. The resulting Earth-to-Moon trajectories prove to be very efficient in the Moon captured arc and save approximately 100 m/sec in Deltav cost when compared to the Hohmann transfer. Furthermore, such solutions demonstrate that Moon capture could be obtained in the frame of the Earth-Moon R3BP neglecting the presence of the Sun.
Molecular orbital predictions of the vibrational frequencies of some molecular ions
NASA Technical Reports Server (NTRS)
Defrees, D. J.; Mclean, A. D.
1985-01-01
The initial detections of IR vibration-rotation bands in polyatomic molecular ions by recent spectroscopic advances were guided by ab initio prediction of vibrational frequencies. The present calculations predict the vibrational frequencies of additional ions which are candidates for laboratory analysis. Neutral molecule vibrational frequencies were computed at three levels of theory and then compared with experimental data; the effect of scaling was also investigated, in order to determine how accurately vibrational frequencies could be predicted. For 92 percent of the frequencies examined, the relatively simple HF/6-31G theory's vibrational frequencies were within 100/cm of experimental values, with a mean absolute error of 49/cm. On this basis, the frequencies of 30 molecular ions (many possessing astrophysical significance) were computed.
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.
Spin-orbit force, recoil corrections, and possible BB¯* and DD¯* molecular states
NASA Astrophysics Data System (ADS)
Zhao, Lu; Ma, Li; Zhu, Shi-Lin
2014-05-01
In the framework of the one-boson exchange model, we have calculated the effective potentials between two heavy mesons BB¯* and DD¯* from the t- and u-channel π-, η-, ρ-, ω-, and σ-meson exchanges with four kinds of quantum number: I=0, JPC=1++; I =0, JPC=1+-; I =1, JPC=1++; I =1, JPC=1+-. We keep the recoil corrections to the BB¯* and DD¯* systems up to O(1/M2). The spin-orbit force appears at O(/1M), which turns out to be important for the very loosely bound molecular states. Our numerical results show that the momentum-related corrections are unfavorable to the formation of the molecular states in the I =0, JPC=1++ and I =1, JPC=1+- channels in the DD¯* system.
Detecting dark energy in orbit: The cosmological chameleon
Brax, Philippe; Davis, Anne-Christine; Khoury, Justin; Weltman, Amanda
2004-12-15
We show that the chameleon scalar field can drive the current phase of cosmic acceleration for a large class of scalar potentials that are also consistent with local tests of gravity. These provide explicit realizations of a quintessence model where the quintessence scalar field couples directly to baryons and dark matter with gravitational strength. We analyze the cosmological evolution of the chameleon field and show the existence of an attractor solution with the chameleon following the minimum of its effective potential. For a wide range of initial conditions, spanning many orders of magnitude in initial chameleon energy density, the attractor is reached before nucleosynthesis. Surprisingly, the range of allowed initial conditions leading to a successful cosmology is wider than in normal quintessence. We discuss applications to the cyclic model of the universe and show how the chameleon mechanism weakens some of the constraints on cyclic potentials.
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.
CSR Interaction for a 2D Energy-Chirped Bunch on a General Orbit
Rui Li
2009-05-01
When an electron bunch with initial linear energy chirp traverses a bunch compression chicane, the bunch interacts with itself via coherent synchrotron radiation (CSR) and space charge force. The effective longitudinal CSR force for such kind of 2D bunch on a circular orbit has been analyzed earlier [1]. In this paper, we present the analytical results of the effective longitudinal CSR force for a 2D energy-chirped bunch going through a general orbit, which includes the entrance and exit of a circular orbit. In particular, we will show the behavior of the force in the last bend of a chicane when the bunch is under extreme compression. This is the condition when bifurcation of bunch phase space occurs in many CSR measurements. [1] R. Li, Phys. Rev. ST Accel. Beams 11, 024401 (2008)
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
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…
Tawa, G.J.; Pratt, L.R.; Martin, R.L.
1996-12-31
We present a method for computing the electrostatic component of the solvation free energy, {Delta}G{sup el}, of a solute molecule in the presence of solvent modeled as a dielectric continuum. The method is based on an integral form of Poisson`s equation which is solved to obtain a distribution of induced polarization charge at the solute-solvent dielectric interface. The solution of Poisson`s equation is obtained by application of a boundary element procedure. The method is tested by comparing its predictions of {Delta}G{sup el} to exact values for several model problems. The method is then used in a variety of contexts to assess its qualitative prediction ability. It is first combined with a molecular mechanics treatment of the solute to evaluate the effects of aqueous solvent on the conformational equilibria of several small molecules of interest-these are N-methyl acetamide and alanine dipeptide. For both molecules dielectric continuum solvation predicts torsional free energies of solvation that are in accord with other more complete treatments of solvation. The method is then combined with ab initio and semi-empirical molecular orbital theory for the solute. Self consistent reaction field calculations (SCRF) are performed to evaluate the correlation is in general very good. Relative agreement with experiment is best for ions where electrostatics predominate and worst for non-polar neutral molecules were electrostatics are minor. Semi-empirical configuration interaction SCRF calculations are also performed in the presence of solvent in order to determine ground-to-excited state absorption energy shifts for formaldehyde and indole mine ground-to-excited state absorption energy shifts for formaldehyde and indole when placed in water. We find a rough correlation between transition energy shifts and the dipole moments of the initial and final states involved in the transition.
Why many semiempirical molecular orbital theories fail for liquid water and how to fix them.
Welborn, Matthew; Chen, Jiahao; Wang, Lee-Ping; Van Voorhis, Troy
2015-05-05
Water is an extremely important liquid for chemistry and the search for more accurate force fields for liquid water continues unabated. Neglect of diatomic differential overlap (NDDO) molecular orbital methods provide and intriguing generalization of classical force fields in this regard because they can account both for bond breaking and electronic polarization of molecules. However, we show that most standard NDDO methods fail for water because they give an incorrect description of hydrogen bonding, water's key structural feature. Using force matching, we design a reparameterized NDDO model and find that it qualitatively reproduces the experimental radial distribution function of water, as well as various monomer, dimer, and bulk properties that PM6 does not. This suggests that the apparent limitations of NDDO models are primarily due to poor parameterization and not to the NDDO approximations themselves. Finally, we identify the physical parameters that most influence the condensed phase properties. These results help to elucidate the chemistry that a semiempirical molecular orbital picture of water must capture. We conclude that properly parameterized NDDO models could be useful for simulations that require electronically detailed explicit solvent, including the calculation of redox potentials and simulation of charge transfer and photochemistry.
The use of invariant manifolds for transfers between unstable periodic orbits of different energies
NASA Astrophysics Data System (ADS)
Davis, Kathryn E.; Anderson, Rodney L.; Scheeres, Daniel J.; Born, George H.
2010-08-01
Techniques from dynamical systems theory have been applied to the construction of transfers between unstable periodic orbits that have different energies. Invariant manifolds, trajectories that asymptotically depart or approach unstable periodic orbits, are used to connect the initial and final orbits. The transfer asymptotically departs the initial orbit on a trajectory contained within the initial orbit’s unstable manifold and later asymptotically approaches the final orbit on a trajectory contained within the stable manifold of the final orbit. The manifold trajectories are connected by the execution of impulsive maneuvers. Two-body parameters dictate the selection of the individual manifold trajectories used to construct efficient transfers. A bounding sphere centered on the secondary, with a radius less than the sphere of influence of the secondary, is used to study the manifold trajectories. A two-body parameter, κ, is computed within the bounding sphere, where the gravitational effects of the secondary dominate. The parameter κ is defined as the sum of two quantities: the difference in the normalized angular momentum vectors and eccentricity vectors between a point on the unstable manifold and a point on the stable manifold. It is numerically demonstrated that as the κ parameter decreases, the total cost to complete the transfer decreases. Preliminary results indicate that this method of constructing transfers produces a significant cost savings over methods that do not employ the use of invariant manifolds.
Orbital alignment at the internal interface of arylthiol functionalized CdSe molecular hybrids
NASA Astrophysics Data System (ADS)
Li, Zhi; Mazzio, Katherine A.; Okamoto, Ken; Luscombe, Christine K.; Schlaf, Rudy
2015-04-01
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.
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.
Kamei, Noriyasu; Kikuchi, Shingo; Takeda-Morishita, Mariko; Terasawa, Yoshiaki; Yasuda, Akihito; Yamamoto, Shuichi; Ida, Nobuo; Nishio, Reiji; Takayama, Kozo
2013-02-01
Our recent work has shown that the intestinal absorption of insulin can be improved significantly by coadministration of cell-penetrating peptides (CPPs), especially penetratin. However, a relatively high dose of penetratin is required to adequately stimulate the intestinal absorption of insulin. Therefore, in this study, we sought to determine the CPP that most effectively enhanced intestinal insulin absorption. An in situ loop absorption study using 26 penetratin analogues suggested that the chain length, hydrophobicity, and amphipathicity of the CPPs, as well as their basicity, contribute to their absorption-enhancing efficiency. Moreover, a molecular orbital method with self-organizing maps (SOMs) classification suggested that multiple factors, including the molecular weight, basicity, the lowest unoccupied molecular orbital energy, absolute hardness, and chemical potential of CPPs, are associated with their effects on intestinal insulin absorption. Furthermore, the new CPPs proposed by SOM clustering had a marked capacity to interact with insulin, and their ability to enhance insulin absorption was much stronger than that of the original penetratin. Therefore, the peptide sequence that optimally enhances intestinal insulin absorption could be defined by SOM with the molecular orbital method, and our present work emphasizes the utility of such methodologies in the development of effective drug delivery systems.
Energy structure of non-hydrogen-like impurities in quantum wells without spin-orbit coupling
Romanov, K. S. Averkiev, N. S.
2012-06-15
Hole states localized at an acceptor in a quantum well formed of a semiconductor with cubic symmetry without spin-orbit coupling (the symmetry {Gamma}{sub 15}) are considered. It is shown that the triply degenerate level is split, and the energies of the levels are calculated as functions of the well width.
Regenerative fuel cell energy storage system for a low Earth orbit space station
Martin, R.E.; Garow, J.; Michaels, K.B.
1984-08-01
Results of a study to define the characteristics of a regenerative fuel cell energy storage system for a large space station operating in low earth orbit (LEO) are presented. The regenerative fuel cell system employs an alkaline electrolyte fuel cell with the option of employing either an alkaline or a solid polymer electrolyte electrolyzer.
Effect of the orbital debris environment on the high-energy van allen proton belt.
Konradi, A
1988-12-02
Orbital debris in the near-Earth environment has reached a number density sufficient for a significant collisional interaction with some of the long-lived high-energy protons in the radiation belt. As a result of a continuing buildup of a shell of man-made debris, the lifetimes of high-energy protons whose trajectories remain below 1500 kilometers will decrease to the point where in the next decades we can expect a noticeable reduction in their fluxes.
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.
Genoni, Alessandro
2013-07-09
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.
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
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.
Nguyen Lan, Tran; Kananenka, Alexei A; Zgid, Dominika
2016-10-11
We present a detailed discussion of the self-energy embedding theory (SEET), which is a quantum embedding scheme allowing us to describe a chosen subsystem very accurately while keeping the description of the environment at a lower level. We apply SEET to molecular examples where our chosen subsystem is made out of a set of strongly correlated orbitals while the weakly correlated orbitals constitute an environment. Consequently, a highly accurate method is used to calculate the self-energy for the system, while a lower-level method is employed to find the self-energy for the environment. Such a self-energy separation is very general, and to make the SEET procedure applicable to multiple systems, a detailed and practical procedure for the evaluation of the system and environment self-energy is necessary. We list all of the intricacies for one of the possible procedures while focusing our discussion on many practical implementation aspects such as the choice of best orbital basis, impurity solver, and many steps necessary to reach chemical accuracy. Finally, on a set of carefully chosen molecular examples, we demonstrate that SEET, which is a controlled, systematically improvable Green's function method, can be as accurate as established wave function quantum chemistry methods.
IMAGING THE MOLECULAR DISK ORBITING THE TWIN YOUNG SUNS OF V4046 Sgr
Rodriguez, David R.; Kastner, Joel H.; Wilner, David; Qi, Chunhua E-mail: jhk@cis.rit.ed E-mail: cqi@cfa.harvard.ed
2010-09-10
We have imaged the disk surrounding the nearby (D {approx} 73 pc), {approx}12 Myr, classical T Tauri binary system V4046 Sgr with the Submillimeter Array (SMA) at an angular resolution of {approx}2''. We detect a rotating disk in {sup 12}CO(2-1) and {sup 13}CO(2-1) emission and resolve the continuum emission at 1.3 mm. We infer disk gas and dust masses of {approx}110 and {approx}40 Earth masses, respectively. Fits to a power-law disk model indicate that the molecular disk extends to {approx}370 AU and is viewed at an inclination of between {approx}33{sup 0} and {approx}39{sup 0} for dynamical stellar masses ranging from 1.8 M {sub sun} down to 1.5 M {sub sun} (the range of the total mass previously determined for the central, 2.4 day spectroscopic binary). This range of disk inclination is consistent with that assumed in deducing the central binary mass (i.e., 35{sup 0}), suggesting that the V4046 Sgr binary system and its circumbinary, molecular disk are coplanar. In light of the system's age and binarity, the presence of an extensive molecular disk orbiting V4046 Sgr provides constraints on the timescales of processes related to Jovian planet formation and demonstrates that circumbinary Jovian planets potentially could form around close binary systems.
Arun, K. G.; Iyer, Bala R.; Qusailah, Moh'd S. S.
2008-03-15
The instantaneous contributions to the third post-Newtonian (3PN) gravitational wave luminosity from the inspiral phase of a binary system of compact objects moving in a quasi-elliptical orbit is computed using the multipolar post-Minkowskian wave generation formalism. The necessary inputs for this calculation include the 3PN accurate mass quadrupole moment for general orbits and the mass octupole and current quadrupole moments at 2PN. Using the recently obtained 3PN quasi-Keplerian representation of elliptical orbits, the flux is averaged over the binary's orbit. Supplementing this by the important hereditary contributions arising from tails, tails of tails, and tails-squared terms calculated in a previous paper, the complete 3PN energy flux is obtained. The final result presented in this paper would be needed for the construction of ready-to-use templates for binaries moving on noncircular orbits, a plausible class of sources not only for the space-based detectors like LISA but also for the ground-based ones.
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.
Extension of the PDDG/PM3 Semiempirical Molecular Orbital Method to Sulfur, Silicon, and Phosphorus
Tubert-Brohman, Ivan; Guimarães, Cristiano Ruch Werneck; Jorgensen, William L.
2008-01-01
The PDDG/PM3 semiempirical molecular orbital method has been parameterized for molecules, ions, and complexes containing sulfur; the mean absolute error (MAE) for heats of formation, ΔHf, of 6.4 kcal/mol is 35 − 40 % smaller than for PM3, AM1, and MNDO/d. For completeness, parameterization was also carried out for silicon and phosphorous. For 144 silicon-containing molecules, the ΔHf MAE for PDDG/PM3, PM3, and AM1 is 11 − 12 kcal/mol, while MNDO/d yields 9.4 kcal/mol. For the limited set of 43 phosphorus-containing molecules, MNDO/d also yields the best results followed by PDDG/PM3, AM1, and PM3. The benefits of the d-orbitals in MNDO/d for hypervalent compounds are apparent for silicon and phosphorous, while they are masked in the larger dataset for sulfur by large errors for branched compounds. Overall, for 1480 molecules, ions, and complexes containing the elements H, C, N, O, F, Si, P, S, Cl, Br, and I, the MAEs in kcal/mol for ΔHf are 6.5 (PDDG/PM3), 8.7 (PM3), 10.3 (MNDO/d), 10.8 (AM1), and 19.8 (MNDO). PMID:19011692
Rakhmilevitch, David; Sarkar, Soumyajit; Bitton, Ora; Kronik, Leeor; Tal, Oren
2016-03-09
Molecular junctions based on ferromagnetic electrodes allow the study of electronic spin transport near the limit of spintronics miniaturization. However, these junctions reveal moderate magnetoresistance that is sensitive to the orbital structure at their ferromagnet-molecule interfaces. The key structural parameters that should be controlled in order to gain high magnetoresistance have not been established, despite their importance for efficient manipulation of spin transport at the nanoscale. Here, we show that single-molecule junctions based on nickel electrodes and benzene molecules can yield a significant anisotropic magnetoresistance of up to ∼200% near the conductance quantum G0. The measured magnetoresistance is mechanically tuned by changing the distance between the electrodes, revealing a nonmonotonic response to junction elongation. These findings are ascribed with the aid of first-principles calculations to variations in the metal-molecule orientation that can be adjusted to obtain highly spin-selective orbital hybridization. Our results demonstrate the important role of geometrical considerations in determining the spin transport properties of metal-molecule interfaces.
Orbital-free molecular dynamics simulations of transport properties in dense-plasma uranium
NASA Astrophysics Data System (ADS)
Kress, J. D.; Cohen, James S.; Kilcrease, D. P.; Horner, D. A.; Collins, L. A.
2011-09-01
We have calculated the self-diffusion coefficients and shear viscosity of dense-plasma uranium using orbital-free molecular dynamics (OFMD) at the Thomas-Fermi-Dirac level. The transport properties of uranium in this regime have not previously been investigated experimentally or theoretically. The OFMD calculations were performed for temperatures from 50 to 5000 eV and densities from ambient to 10 times compressed. The results are compared with the one-component-plasma (OCP) model, using effective charges given by the average-atom code INFERNO and by the regularization procedure from the OFMD method. The latter generally showed better agreement with the OFMD for viscosity and the former for diffusion. A Stokes-Einstein relationship of the OFMD viscosities and diffusion coefficients is found to hold fairly well with a constant of 0.075 ± 0.10, while the OCP/INFERNO model yields 0.13 ± 0.10.
Molecular orbital study of the bond-valence sum rule using Lewis-electron pair theory.
Mohri, Fumihito
2003-04-01
The bond-valence sum rule has been examined by molecular-orbital methods related to spin-coupling matrix theory [Okada & Fueno (1976). Bull. Chem. Soc. Jpn, 49, 1524-1530], to give a new formulation of the Lewis-electron pair concept. It is shown that the 'pair-coupling population' between atoms M and X exhibits the same behaviour as the bond valence between them. A quantum chemical definition for bond valence is proposed and successfully applied to Al(2)Cl(6), Te(4)Cl(16) and Al(2)Be(3)(SiO(3))(6) (beryl). Using an alternative bond-valence definition it is shown that for oxides the bond valence can possibly be taken as the double pair-coupling population.
Spin-orbit coupling effects on the molecular structure of Thallium(I)formiate
NASA Astrophysics Data System (ADS)
Berger, Raphael J. F.
2017-03-01
While scalar relativistic effects on molecular structures have been described for ample compounds both experimentally and theoretically, not much is known about the influence of non-scalar relativistic effects like spin-orbit-coupling (SOC) on geometric structure parameters of free molecules. 'Fully-relativistic' optimizations based on four-component DFT calculations on thallium(I)hydride (TlH) and thallium(I)formiate (Tl[O2CH]) are presented. In TlH at 4c-PBE0/VTZ level of theory SOC shortens re(Tl-H) by 0.008 Å (from 1.882 Å to 1.874 Å (exp.: 1.872 Å)). In Tl[O2CH] (C2v symmetry) SOC shortens re(Tl⋯O) by 0.006 Å (from 2.446 Å to 2.440 Å).
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.
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.
Steinmann, Casper; Fedorov, Dmitri G; Jensen, Jan H
2013-01-01
We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be [Formula: see text] kcal mol(-1) for MP2/cc-pVDZ and [Formula: see text] for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively.
Molecular orbital studies of enzyme activity: catalytic mechanism of serine proteinases.
Scheiner, S; Lipscomb, W N
1976-01-01
The catalytic activity of the serine proteinases is studied using molecular orbital methods on a model of the enzyme-substrate complex. A mechanism is employed in which Ser-195, upon donating a proton to the His-57-Asp-102 dyad, attacks the substrate to form the tetrahedral intermediate. As His-57 then donates a proton to the leaving group, the intermediate decomposes to the acyl enzyme. An analogous process takes place during deacylation, as a water molecule takes the place of Ser-195 as the nucleophile. The motility of the histidine is found to be an important factor in both steps. An attempt is made to include the effects of those atoms not explicitly included in the calculations and to compare the reaction rate of the proposed mechanism with that of the uncatalyzed hydrolysis. This mechanism is found to be in good agreement with structural and kinetic data. PMID:1061145
Steinmann, Casper; Fedorov, Dmitri G.; Jensen, Jan H.
2013-01-01
We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be kcal mol−1 for MP2/cc-pVDZ and for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively. PMID:23593259
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.
Arulmozhiraja, Sundaram; Matsuo, Naoya; Ishitsubo, Erika; Okazaki, Seiji; Shimano, Hitoshi
2016-01-01
Dipeptidyl peptidase IV (DPP-4) enzyme is responsible for the degradation of incretins that stimulates insulin secretion and hence inhibition of DPP-4 becomes an established approach for the treatment of type 2 diabetics. We studied the interaction between DPP-4 and its inhibitor drugs (sitagliptin 1, linagliptin 2, alogliptin 3, and teneligliptin 4) quantitatively by using fragment molecular orbital calculations at the RI-MP2/cc-pVDZ level to analyze the inhibitory activities of the drugs. Apart from having common interactions with key residues, inhibitors encompassing the DPP-4 active site extensively interact widely with the hydrophobic pocket by their hydrophobic inhibitor moieties. The cumulative hydrophobic interaction becomes stronger for these inhibitors and hence linagliptin and teneligliptin have larger interaction energies, and consequently higher inhibitory activities, than their alogliptin and sitagliptin counterparts. Though effective interaction for both 2 and 3 is at S2' subsite, 2 has a stronger binding to this subsite interacting with Trp629 and Tyr547 than 3 does. The presence of triazolopiperazine and piperazine moiety in 1 and 4, respectively, provides the interaction to the S2 extensive subsite; however, the latter’s superior inhibitory activity is not only due to a relatively tighter binding to the S2 extensive subsite, but also due to the interactions to the S1 subsite. The calculated hydrophobic interfragment interaction energies correlate well with the experimental binding affinities (KD) and inhibitory activities (IC50) of the DPP-4 inhibitors. PMID:27832184
Scheiner, S; Kleier, D A; Lipscomb, W N
1975-01-01
The charge relay ststem and its role in the acylation of serine proteinases is studied using the partial retention of diatomic differential overlap (PRDDO) technique to perform approximate ab initio molecular orbital calculations on a model of the enzyme-substrate complex. The aspartate in the charge relay system is seen to act as the ultimate proton acceptor during the charging of the serine nucleophile. A projection of the potential energy surface is obtained in a subspace corresponding to this charge transfer and to the coupled motions of active site residues and the substrate. These results together with extended basis set results for cruder models suggest that a concerted transfer of protons from Ser-195 to His-57 and from His-57 to Asp-102 occurs with an energy barrier of 20-25 kcal/mole (84-105 kJ/mole). The subsequent nucleophilic attack on the scissile peptide linkage by the charged serine is then seen to proceed energetically downhill to the tetrahedral intermediate. The formation of the tetrahedral intermediate from the Michaelis complex is calculated to be nearly thermoneutral. PMID:1058476
Mahalakshmi, G; Balachandran, V
2014-10-15
The FT-IR and FT-Raman spectra of 4-Aminomethylpiperidine have been recorded using Perkin Elmer Spectrophotometer and Nexus 670 spectrophotometer. The equilibrium geometrical parameters, various bonding features, the vibrational wavenumbers, the infrared intensities and the Raman scattering activities were calculated using Hartree-Fock and density functional method (B3LYP) with 6-311+G(d,p) basis set. Detailed interpretations of the vibrational spectra have been carried out with the aid of the normal coordinate analysis. The spectroscopic and natural bonds orbital (NBO) analysis confirms the occurrence of intra molecular hydrogen bonds, electron delocalization and steric effects. The changes in electron density in the global minimum and in the energy of hyperconjugative interactions of 4-Aminomethylpiperidine (4AMP) were calculated. The theoretical UV-Visible spectrum of the compound was computed in the region 200-400nm by time-dependent TD-DFT approach. The calculated HOMO and LUMO energies show that charge transfer occur within the molecule. The dipole moment (μ) and polarizability (α), anisotropy polarizability (Δα) and hyperpolarizability (β) of the molecule have been reported.
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.
Prospects for ultrahigh-energy particle observation based on the lunar orbital LORD space experiment
NASA Astrophysics Data System (ADS)
Ryabov, V. A.; Chechin, V. A.; Gusev, G. A.; Maung, K. T.
2016-08-01
The problem of searching for highest-energy cosmic rays and neutrinos in the Universe is reviewed. Possibilities for using the radio method for detecting particles of energies above the GZK cut-off are analyzed. The method is based on the registration of coherent radio emission produced by cascades of most energetic particles in radio-transparent lunar regolith. The Luna-Resurs Orbiter space mission to be launched in the near future (2020) involves the Lunar Orbital Radio Detector (LORD). The design of the LORD space instrument and its scientific potentialities for registration of low-intense cosmic ray particle fluxes of energies above the GZK cut-off up to 1024eV are discussed. The designed LORD module (including the antenna, amplification, and data-acquisition systems) now is under construction. Exposure and capabilities of the LORD space experiment for detection of ultrahigh-energy cosmic rays and neutrinos have been compared with those for well-known current and proposed experiments. The LORD space experiment will make it possible to obtain important information on the highest-energy particles in the Universe, to verify modern models for the origin and the propagation of ultrahigh-energy cosmic rays and neutrinos.
Liu, Shubin; Pedersen, Lee G.
2009-01-01
An effective approach of estimating molecular pKa values from simple density functional calculations is proposed in this work. Both the molecular electrostatic potential (MEP) at the nucleus of the acidic atom and the sum of valence natural atomic orbitals are employed for three categories of compounds, amines and anilines, carbonyl acids and alcohols, and sulfonic acids and thiols. A strong correlation between experimental pKa values and each of these two quantities for each of the three categories has been discovered. Moreover, if the MEP is subtracted by the isolated atomic MEP for each category of compounds, we observe a single unique linear relationship between the resultant MEP difference and experimental pKa data of amines, anilines, carbonyl acids, alcohols, sulfonic acids, thiols, and their substituents. These results can generally be utilized to simultaneously estimate pKa values at multiple sites with a single calculation for either relatively small molecules in drug design or amino acids in proteins and macromolecules. PMID:19317439
Nagata, Takeshi; Fedorov, Dmitri G; Sawada, Toshihiko; Kitaura, Kazuo
2012-09-13
Based on the proposed new expression of the polarization energy for the fragment molecular orbital (FMO) method interfaced with effective fragment potentials (EFPs), we develop an analysis of the solute(FMO)-solvent(EFP) interactions by defining individual fragment contributions for both solute and solvent. The obtained components are compared to all-electron calculations where water is treated as FMO fragments in the pair interaction energy decomposition analysis. The new energy expression is shown to be accurate, and the developed energy analysis is applied to the solvated griffithsin-carbohydrate complex. The details of the ligand recognition are revealed in the context with their interplay with the solvent effects. Tyr residue fragments are shown to reduce the desolvation penalty for Asp, which strongly binds the ligand.
NASA Technical Reports Server (NTRS)
Almlof, Jan; Taylor, Peter R.
1990-01-01
A recently proposed scheme for using natural orbitals from atomic configuration interaction 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 outermost 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 sets.
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.
Geng, Hua; Niu, Yingli; Peng, Qian; Shuai, Zhigang; Coropceanu, Veaceslav; Brédas, Jean-Luc
2011-09-14
Chemical substitutions are powerful molecular design tools to enhance the performance of organic semiconductors, for instance, to improve solubility, intermolecular stacking, or film quality. However, at the microscopic level, substitutions in general tend to increase the molecular reorganization energy and thus decrease the intrinsic charge-carrier mobility. Through density functional theory calculations, we elucidate strategies that could be followed to reduce the reorganization energy upon chemical substitution. Specific examples are given here for hole-transport materials including indolo-carbazoles and several triarylamine derivatives. Through decomposition of the total reorganization energy into the internal coordinate space, we are able to identify the molecular segment that provides the most important contributions to the reorganization energy. It is found that when substitution reduces (enhances) the amplitude of the relevant frontier molecular orbital in that segment, the total reorganization energy decreases (increases). In particular, chlorination at appropriate positions can significantly reduce the reorganization energy. Several other substituents are shown to play a similar role, to a greater or lesser extent.
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…
Yao, Bin; Zhou, Yue; Ye, Xichong; Wang, Rong; Zhang, Jie; Wan, Xinhua
2017-04-03
An electron-deficient star-shaped molecule based on anthraquinone imide was synthesized and characterized. It showed high electron accommodating capacity and strong electron-withdrawing ability with a low-lying lowest unoccupied molecular orbital (LUMO) of -4.10 eV. In addition, it exhibited panchromatic electrochromism attributed to the simultaneous presence of π*-π* transitions and intervalence charge transfer (IV-CT) upon one-electron reduction, and revealed long-term stability in electron gain and loss due to the proper LUMO energy level and ordered intermolecular assembly.
Opitz, Andreas
2017-04-05
Planar organic heterojunctions are widely used in photovoltaic cells, light-emitting diodes, and bilayer field-effect transistors. The energy level alignment in the devices plays an important role in obtaining the aspired gap arrangement. Additionally, the π-orbital overlap between the involved molecules defines e.g. the charge-separation efficiency in solar cells due to charge-transfer effects. To account for both aspects, direct/inverse photoemission spectroscopy and near edge x-ray absorption fine structure spectroscopy were used to determine the energy level landscape and the molecular orientation at prototypical planar organic heterojunctions. The combined experimental approach results in a comprehensive model for the electronic and morphological characteristics of the interface between the two investigated molecular semiconductors. Following an introduction on heterojunctions used in devices and on energy levels of organic materials, the energy level alignment of planar organic heterojunctions will be discussed. The observed energy landscape is always determined by the individual arrangement between the energy levels of the molecules and the work function of the electrode. This might result in contact doping due to Fermi level pinning at the electrode for donor/acceptor heterojunctions, which also improves the solar cell efficiency. This pinning behaviour can be observed across an unpinned interlayer and results in charge accumulation at the donor/acceptor interface, depending on the transport levels of the respective organic semiconductors. Moreover, molecular orientation will affect the energy levels because of the anisotropy in ionisation energy and electron affinity and is influenced by the structural compatibility of the involved molecules at the heterojunction. High structural compatibility leads to π-orbital stacking between different molecules at a heterojunction, which is of additional interest for photovoltaic active interfaces and for ground
NASA Astrophysics Data System (ADS)
Opitz, Andreas
2017-04-01
Planar organic heterojunctions are widely used in photovoltaic cells, light-emitting diodes, and bilayer field-effect transistors. The energy level alignment in the devices plays an important role in obtaining the aspired gap arrangement. Additionally, the π-orbital overlap between the involved molecules defines e.g. the charge-separation efficiency in solar cells due to charge-transfer effects. To account for both aspects, direct/inverse photoemission spectroscopy and near edge x-ray absorption fine structure spectroscopy were used to determine the energy level landscape and the molecular orientation at prototypical planar organic heterojunctions. The combined experimental approach results in a comprehensive model for the electronic and morphological characteristics of the interface between the two investigated molecular semiconductors. Following an introduction on heterojunctions used in devices and on energy levels of organic materials, the energy level alignment of planar organic heterojunctions will be discussed. The observed energy landscape is always determined by the individual arrangement between the energy levels of the molecules and the work function of the electrode. This might result in contact doping due to Fermi level pinning at the electrode for donor/acceptor heterojunctions, which also improves the solar cell efficiency. This pinning behaviour can be observed across an unpinned interlayer and results in charge accumulation at the donor/acceptor interface, depending on the transport levels of the respective organic semiconductors. Moreover, molecular orientation will affect the energy levels because of the anisotropy in ionisation energy and electron affinity and is influenced by the structural compatibility of the involved molecules at the heterojunction. High structural compatibility leads to π-orbital stacking between different molecules at a heterojunction, which is of additional interest for photovoltaic active interfaces and for ground
Ferenczy, György G
2013-04-05
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.
NASA Astrophysics Data System (ADS)
Jung, Jaewoon; Re, Suyong; Sugita, Yuji; Ten-no, Seiichiro
2013-01-01
The nudged elastic band (NEB) and string methods are widely used to obtain the reaction path of chemical reactions and phase transitions. In these methods, however, it is difficult to define an accurate Lagrangian to generate the conservative forces. On the other hand, the constrained optimization with locally updated planes (CO-LUP) scheme defines target function properly and suitable for micro-iteration optimizations in quantum mechanical/molecular mechanical (QM/MM) systems, which uses the efficient second order QM optimization. However, the method does have problems of inaccurate estimation of reactions and inappropriate accumulation of images around the energy minimum. We introduce three modifications into the CO-LUP scheme to overcome these problems: (1) An improved tangent estimation of the reaction path, which is used in the NEB method, (2) redistribution of images using an energy-weighted interpolation before updating local tangents, and (3) reduction of the number of constraints, in particular translation/rotation constraints, for improved convergence. First, we test the method on the isomerization of alanine dipeptide without QM/MM calculation, showing that the method is comparable to the string method both in accuracy and efficiency. Next, we apply the method for defining the reaction paths of the rearrangement reaction catalyzed by chorismate mutase (CM) and of the phosphoryl transfer reaction catalyzed by cAMP-dependent protein kinase (PKA) using generalized hybrid orbital QM/MM calculations. The reaction energy barrier of CM is in high agreement with the experimental value. The path of PKA reveals that the enzyme reaction is associative and there is a late transfer of the substrate proton to Asp 166, which is in agreement with the recently published result using the NEB method.
Linear Energy Transfer (LET) spectra of cosmic radiation in low Earth orbit
Parnell, T.A.; Watts, J.W. Jr.; Akopova, A.B.; Magradze, N.V.; Dudkin, V.E.; Kovalev, E.E.; Potapov, Yu.V.; Benton, E.V.; Frank, A.L.; Benton, E.R. ||
1995-03-01
Integral linear energy transfer (LET) spectra of cosmic radiation (CR) particles were measured on five Cosmos series spacecraft in low Earth orbit (LEO). Particular emphasis is placed on results of the Cosmos 1887 biosatellite which carried a set of joint U.S.S.R.-U.S.A. radiation experiments involving passive detectors that included thermoluminescent detectors (TLD`s), plastic nuclear track detectors (PNTD`s), fission foils, nuclear photo-emulsions, etc. which were located both inside and outside the spacecraft. Measured LET spectra are compared with those theoretically calculated. Results show that there is some dependence of LET spectra on orbital parameters. The results are used to estimate the CR quality factor (QF) for the COSMOS 1887 mission.
Linear Energy Transfer (LET) spectra of cosmic radiation in low Earth orbit
NASA Technical Reports Server (NTRS)
Parnell, T. A.; Watts, J. W., Jr.; Akopova, A. B.; Magradze, N. V.; Dudkin, V. E.; Kovalev, E. E.; Potapov, Yu. V.; Benton, E. V.; Frank, A. L.; Benton, E. R.
1995-01-01
Integral linear energy transfer (LET) spectra of cosmic radiation (CR) particles were measured on five Cosmos series spacecraft in low Earth orbit (LEO). Particular emphasis is placed on results of the Cosmos 1887 biosatellite which carried a set of joint U.S.S.R.-U.S.A. radiation experiments involving passive detectors that included thermoluminescent detectors (TLD's), plastic nuclear track detectors (PNTD's), fission foils, nuclear photo-emulsions, etc. which were located both inside and outside the spacecraft. Measured LET spectra are compared with those theoretically calculated. Results show that there is some dependence of LET spectra on orbital parameters. The results are used to estimate the CR quality factor (QF) for the COSMOS 1887 mission.
Dynamic kinetic energy potential for orbital-free density functional theory.
Neuhauser, Daniel; Pistinner, Shlomo; Coomar, Arunima; Zhang, Xu; Lu, Gang
2011-04-14
A dynamic kinetic energy potential (DKEP) is developed for time-dependent orbital-free (TDOF) density function theory applications. This potential is constructed to affect only the dynamical (ω ≠ 0) response of an orbital-free electronic system. It aims at making the orbital-free simulation respond in the same way as that of a noninteracting homogenous electron gas (HEG), as required by a correct kinetic energy, therefore enabling extension of the success of orbital-free density functional theory in the static case (e.g., for embedding and description of processes in bulk materials) to dynamic processes. The potential is constructed by expansions of terms, each of which necessitates only simple time evolution (concurrent with the TDOF evolution) and a spatial convolution at each time-step. With 14 such terms a good fit is obtained to the response of the HEG at a large range of frequencies, wavevectors, and densities. The method is demonstrated for simple jellium spheres, approximating Na(9)(+) and Na(65)(+) clusters. It is applicable both to small and large (even ultralarge) excitations and the results converge (i.e., do not blow up) as a function of time. An extension to iterative frequency-resolved extraction is briefly outlined, as well as possibly numerically simpler expansions. The approach could also be extended to fit, instead of the HEG susceptibility, either an experimental susceptibility or a theoretically derived one for a non-HEG system. The DKEP potential should be a powerful tool for embedding a dynamical system described by a more accurate method (such as time-dependent density functional theory, TDDFT) in a large background described by TDOF with a DKEP potential. The type of expansions used and envisioned should be useful for other approaches, such as memory functionals in TDDFT. Finally, an appendix details the formal connection between TDOF and TDDFT.
Observation of ultrahigh-energy cosmic rays and neutrinos from lunar orbit: LORD space experiment
NASA Astrophysics Data System (ADS)
Ryabov, Vladimir; Chechin, Valery; Gusev, German
The problem of detecting highest-energy cosmic rays and neutrinos in the Universe is reviewed. Nowadays, there becomes clear that observation of these particles requires approaches based on novel principles. Projects based on orbital radio detectors for particles of energies above the CZK cut-off are discussed. We imply the registration of coherent Cherenkov radio emission produced by cascades of most energetic particles in radio-transparent lunar regolith. The Luna-Glob space mission proposed for launching in the near future involves the Lunar Orbital Radio Detector (LORD). The feasibility of LORD space instrument to detect radio signals from cascades initiated by ultrahigh-energy particles interacting with lunar regolith is examined. The comprehensive Monte Carlo calculations were carried out within the energy range of 10 (20) -10 (25) eV with the account for physical properties of the Moon such as its density, the lunar-regolith radiation length, the radio-wave absorption length, the refraction index, and the orbital altitude of a lunar satellite. We may expect that the LORD space experiment will surpass in its apertures and capabilities the majority of well-known current and proposed experiments dealing with the detection of both ultrahigh-energy cosmic rays and neutrinos. The design of the LORD space instrument and its scientific potentialities in registration of low-intense cosmic-ray particle fluxes above the GZK cut-off up to 10 (25) eV is discussed as well. The designed LORD module (including an antenna system, amplifiers, and a data acquisition system) now is under construction. The LORD space experiment will make it possible to obtain important information on the highest-energy particles in the Universe, to verify modern models for the origin and the propagation of ultrahigh-energy cosmic rays and neutrinos. Successful completion of the LORD experiment will permit to consider the next step of the program, namely, a multi-satellite lunar systems to
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)
Blum, Volker
This talk describes recent advances of a general, efficient, accurate all-electron electronic theory approach based on numeric atom-centered orbitals; emphasis is placed on developments related to materials for energy conversion and their discovery. For total energies and electron band structures, we show that the overall accuracy is on par with the best benchmark quality codes for materials, but scalable to large system sizes (1,000s of atoms) and amenable to both periodic and non-periodic simulations. A recent localized resolution-of-identity approach for the Coulomb operator enables O (N) hybrid functional based descriptions of the electronic structure of non-periodic and periodic systems, shown for supercell sizes up to 1,000 atoms; the same approach yields accurate results for many-body perturbation theory as well. For molecular systems, we also show how many-body perturbation theory for charged and neutral quasiparticle excitation energies can be efficiently yet accurately applied using basis sets of computationally manageable size. Finally, the talk highlights applications to the electronic structure of hybrid organic-inorganic perovskite materials, as well as to graphene-based substrates for possible future transition metal compound based electrocatalyst materials. All methods described here are part of the FHI-aims code. VB gratefully acknowledges contributions by numerous collaborators at Duke University, Fritz Haber Institute Berlin, TU Munich, USTC Hefei, Aalto University, and many others around the globe.
Low-energy structures in strong field ionization revealed by quantum orbits.
Yan, Tian-Min; Popruzhenko, S V; Vrakking, M J J; Bauer, D
2010-12-17
Experiments on atoms in intense laser pulses and the corresponding exact ab initio solutions of the time-dependent Schrödinger equation (TDSE) yield photoelectron spectra with low-energy features that are not reproduced by the otherwise successful work horse of strong field laser physics: the "strong field approximation" (SFA). In the semiclassical limit, the SFA possesses an appealing interpretation in terms of interfering quantum trajectories. It is shown that a conceptually simple extension towards the inclusion of Coulomb effects yields very good agreement with exact TDSE results. Moreover, the Coulomb quantum orbits allow for a physically intuitive interpretation and detailed analysis of all low-energy features in the semiclassical regime, in particular, the recently discovered "low-energy structure" [C. I. Blaga, Nature Phys. 5, 335 (2009) and W. Quan, Phys. Rev. Lett. 103, 093001 (2009).
Characterising the energy deposition events produced by trapped protons in low earth orbit.
Brackenbush, L W; Braby, L A; Anderson, G A
1989-01-01
Men and equipment in space vehicles in low earth orbit are exposed to a wide variety of radiations, but the majority of the dose is due to trapped protons, which have energies of the order of 100 MeV and are low LET particles. These high energy particles produce nuclear fragmentation with high LET secondaries that may be responsible for a significant fraction of dose equivalent. In order to understand better the biological effectiveness of this radiation environment, a portable tissue equivalent proportional counter spectrometer has been developed that automatically records the distribution of energy in a small tissue-like site as a function of time. This instrument weighs about 700 g and will be flown on a number of future space shuttle flights.
Russian measurements of neutron energy spectra on the Mir orbital station.
Lyagushin, V I; Dudkin, V E; Potapov, Y V; Sevastianov, V D
2001-06-01
Results of the experiments on neutron energy spectra measurements within broad energy range from 5 x 10(-7) to 2 x 10(2) MeV aboard the Mir orbital station and equivalent neutron dose estimation are presented. Four measurement techniques were used during the experiments. The shape of spectra and their absolute values are in good agreement. According to those experiments, an equivalent neutron dose depends upon effective shielding thickness and spacecraft mass. The neutron dose mentioned is comparable with that of ionizing radiation. Neutron flux levels measured aboard the Mir station have shown that a neutron spectrometer involving broad energy range will be used within the radiation monitoring systems in manned space flights.
Molecular Slater Integrals for Electronic Energy Calculations
2010-10-15
Facultad de Ciencias . Departamento de Quı́mica Fı́sica Aplicada. C-XIV. Abstract The algorithms for computing molecular integrals with Slater functions...and propulsion sciences research programs. This extension requires a thorough revision on the performance of the algorithms currently available and
NASA Astrophysics Data System (ADS)
Litvinyuk, I. V.; Zheng, Y.; Brion, C. E.
2000-11-01
The electron binding energy spectrum and valence orbital electron momentum density distributions of amantadine (1-aminoadamantane), an important anti-viral and anti-Parkinsonian drug, have been measured by electron momentum spectroscopy. Theoretical momentum distributions, calculated at the 6-311++G** and AUG-CC-PVTZ levels within the target Hartree-Fock and also the target Kohn-Sham density functional theory approximations, show good agreement with the experimental results. The results for amantadine are also compared with those for the parent molecule, adamantane, reported earlier (Chem. Phys. 253 (2000) 41). Based on the comparison tentative assignments of the valence region ionization bands of amantadine have been made.
Cardona, Claudia M; Li, Wei; Kaifer, Angel E; Stockdale, David; Bazan, Guillermo C
2011-05-24
Narrow bandgap conjugated polymers in combination with fullerene acceptors are under intense investigation in the field of organic photovoltaics (OPVs). The open circuit voltage, and thereby the power conversion efficiency, of the devices is related to the offset of the frontier orbital energy levels of the donor and acceptor components, which are widely determined by cyclic voltammetry. Inconsistencies have appeared in the use of the ferrocenium/ferrocene (Fc + /Fc) redox couple, as well as the values used for the absolute potentials of standard electrodes, which can complicate the comparison of materials properties and determination of structure/property relationships.
Regenerative Hydrogen-oxygen Fuel Cell-electrolyzer Systems for Orbital Energy Storage
NASA Technical Reports Server (NTRS)
Sheibley, D. W.
1984-01-01
Fuel cells have found application in space since Gemini. Over the years technology advances have been factored into the mainstream hardware programs. Performance levels and service lives have been gradually improving. More recently, the storage application for fuel cell-electrolyzer combinations are receiving considerable emphasis. The regenerative system application described here is part of a NASA Fuel Cell Program which was developed to advance the fuel cell and electrolyzer technology required to satisfy the identified power generation and energy storage need of the Agency for space transportation and orbital applications to the year 2000.
Improvements on the minimax algorithm for the Laplace transformation of orbital energy denominators
Helmich-Paris, Benjamin Visscher, Lucas
2016-09-15
We present a robust and non-heuristic algorithm that finds all extremum points of the error distribution function of numerically Laplace-transformed orbital energy denominators. The extremum point search is one of the two key steps for finding the minimax approximation. If pre-tabulation of initial guesses is supposed to be avoided, strategies for a sufficiently robust algorithm have not been discussed so far. We compare our non-heuristic approach with a bracketing and bisection algorithm and demonstrate that 3 times less function evaluations are required altogether when applying it to typical non-relativistic and relativistic quantum chemical systems.
Localization of energy on the molecular scale
Lindenberg, K.; Brown, D.W.
1997-12-31
We discuss the spontaneous localization of vibrational energy in translationally invariant anharmonic chains at finite temperatures. In addition to the familiar energy-driven coherent mechanisms, which are rapidly degraded by thermal fluctuations, we identify the entropy-driven phenomenon we call {open_quotes}stochastic localization{close_quotes}, within which we include a number of characteristics of soft anharmonic oscillators in thermal equilibrium. Principal among these are a tendency for soft oscillators to spend more time at higher energies than comparable harmonic oscillators, and for high-energy fluctuations in soft oscillators to persist for longer times than lower-energy fluctuations, leading to a tendency for energy fluctuations to be organized into {open_quotes}bursts{close_quotes} separated by intervals of relative quiet. We illustrate the effects of stochastic localization on a bistable impurity embedded in a chain of soft oscillators by comparing it to an impurity embedded in a harmonic chain. Effects on transition rates at a given system energy can be quite dramatic.
Spin-orbit configuration interaction calculation of the potential energy curves of iodine oxide
Roszak, S.; Krauss, M.; Alekseyev, A.B.; Liebermann, H.P.; Buenker, R.J.
2000-04-06
An ab initio configuration interaction (CI) study including spin-orbit coupling is carried out for the ground and excited states of the IO radical by employing relativistic effective core potentials. The computed spectroscopic constants are in good agreement with available experimental data, with some tendency to underestimate the strength of bonding. The first excited state, a{sup 4}{Sigma}{sup {minus}}, which has not yet been observed experimentally, is predicted to be bound by 30.1 kJ/mol and to have a significantly larger equilibrium distance than the ground state. It is split by spin-orbit interaction into 1/2 and 3/2 components, with the 1/2 component being the lower one with a calculated spin-orbit splitting of 210 cm{sup {minus}1}. The most interesting state in the low-energy IO spectrum, A{sub 1}{sup 2}{Pi}{sub 3/2}, is shown to be predissociated due to interaction with a number of repulsive electronic states. Predissociation of the A{sup 1}, {nu}{prime} = 0, 1 vibrational levels is attributed to a fairly weak spin-orbit coupling with the {sup 2}{Delta}{sub 3/2} state, while rotationally dependent predissociation of the {nu}{prime} = 2 level is explained by the coupling with the 1/2(III) state having mainly {sup 2}{Sigma}{sup {minus}} character. Strong predissociation of the {nu}{prime} {ge} 4 levels is attributed to interaction with the higher-lying {Omega} = 3/2 states, with predominantly {sup 4}{Sigma}{sup +} and {sup 4}{Delta} origin.
The Space Shuttle Orbiter molecular environment induced by the supplemental flash evaporator system
NASA Technical Reports Server (NTRS)
Ehlers, H. K. F.
1985-01-01
The water vapor environment of the Space Shuttle Orbiter induced by the supplemental flash evaporator during the on-orbit flight phase has been analyzed based on Space II model predictions and orbital flight measurements. Model data of local density, column density, and return flux are presented. Results of return flux measurements with a mass spectrometer during STS-2 and of direct flux measurements during STS-4 are discussed and compared with model predictions.
Potential energy surface for C2H4I2+ dissociation including spin-orbit effects
Siebert, Matthew R.; Aquino, Adelia J.; De Jong, Wibe A.; Granucci, Giovanni; Hase, William L.
2012-10-24
Previous experiments [Baer, et al. J. Phys. Chem. A 116, 2833 (2012)] have studied the dissociation of 1,2-diiodoethane radical cation (C2H4I2+•) and found a one-dimensional distribution of translational energy; an odd finding considering most product relative translational energy distributions are two-dimensional. The goal of this study is to obtain an accurate understanding of the potential energy surface (PES) topology for the unimolecular decomposition reaction C2H4I2+• - C2H4I+ + I•. This is done through comparison of many single-reference electronic structure methods, coupled-cluster single point (energy) calculations, and multi-reference calculations used to quantify spin-orbit (SO) coupling effects. We find that the structure of the C2H4I2+• reactant has a substantial effect on the role of SO coupling on the reaction energy. Both the BHandH and MP2 theories with an ECP/6-31++G** basis set, and without SO coupling corrections, provide accurate models for the reaction energetics. MP2 theory gives an unsymmetric structure with different C-I bond lengths, resulting in a SO energy for C2H4I2+• similar to that for the product I-atom and a negligible SO correction to the reaction energy. In contrast, DFT gives a symmetric structure for C2H4I2+•, similar to that of the neutral C2H4I2 parent, resulting in a substantial SO correction and increasing the reaction energy by 6.0-6.5 kcal/mol. Also, we find that for this system single point energy calculations are inaccurate, since a small change in geometry can lead to a large change in energy.
Whitenack, Daniel L; Wasserman, Adam
2012-04-28
Aspects of density functional resonance theory (DFRT) [D. L. Whitenack and A. Wasserman, Phys. Rev. Lett. 107, 163002 (2011)], a recently developed complex-scaled version of ground-state density functional theory (DFT), are studied in detail. The asymptotic behavior of the complex density function is related to the complex resonance energy and system's threshold energy, and the function's local oscillatory behavior is connected with preferential directions of electron decay. Practical considerations for implementation of the theory are addressed including sensitivity to the complex-scaling parameter, θ. In Kohn-Sham DFRT, it is shown that almost all θ-dependence in the calculated energies and lifetimes can be extinguished via use of a proper basis set or fine grid. The highest occupied Kohn-Sham orbital energy and lifetime are related to physical affinity and width, and the threshold energy of the Kohn-Sham system is shown to be equal to the threshold energy of the interacting system shifted by a well-defined functional. Finally, various complex-scaling conditions are derived which relate the functionals of ground-state DFT to those of DFRT via proper scaling factors and a non-Hermitian coupling-constant system.
Energy Band and Josephson Dynamics of Spin-Orbit Coupled Bose-Einstein Condensates
NASA Astrophysics Data System (ADS)
Zhang, Xin; Yu, Zi-Fa; Xue, Ju-Kui
2015-10-01
We theoretically investigate the energy band structure and Josephson dynamics of a spin-orbit coupled Bose-Einstein condensate in a double-well potential. We study the energy band structure and the corresponding tunneling dynamics of the system by properly adjusting the SO coupling, Raman coupling, Zeeman field and atomic interactions. The coupled effects of SO coupling, Raman coupling, Zeeman field and atomic interactions lead to the appearance of complex energy band structure including the loop structure. Particularly, the emergence of the loop structure in energy band also depends on SO coupling, Raman coupling, Zeeman field and atomic interactions. Correspondingly, the Josephson dynamics of the system are strongly related to the energy band structure. Especially, the emergence of the loop structure results in complex tunneling dynamics, including suppression-revival transitions and self-trapping of atoms transfer between two spin states and two wells. This engineering provides a possible means for studying energy level and corresponding dynamics of two-species SO coupled BECs. Supported by the National Natural Science Foundation of China under Grant Nos. 11274255 and 11305132, by Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20136203110001, by the Natural Science Foundation of Gansu province under Grant No. 2011GS04358, and by Creation of Science and Technology of Northwest Normal University under Grant Nos. NWNU-KJCXGC-03-48, NWNU-LKQN-12-12
Sirjoosingh, Andrew; Pak, Michael V; Swalina, Chet; Hammes-Schiffer, Sharon
2013-07-21
In the application of the nuclear-electronic orbital (NEO) method to positronic systems, all electrons and the positron are treated quantum mechanically on the same level. Explicit electron-positron correlation can be included using Gaussian-type geminal functions within the variational self-consistent-field procedure. In this paper, we apply the recently developed reduced explicitly correlated Hartree-Fock (RXCHF) approach to positronic molecular systems. In the application of RXCHF to positronic systems, only a single electronic orbital is explicitly correlated to the positronic orbital. We apply NEO-RXCHF to three systems: positron-lithium, lithium positride, and positron-lithium hydride. For all three of these systems, the RXCHF approach provides accurate two-photon annihilation rates, average contact densities, electronic and positronic single-particle densities, and electron-positron contact densities. Moreover, the RXCHF approach is significantly more accurate than the original XCHF approach, in which all electronic orbitals are explicitly correlated to the positronic orbital in the same manner, because the RXCHF wavefunction is optimized to produce a highly accurate description of the short-ranged electron-positron interaction that dictates the annihilation rates and other local properties. Furthermore, RXCHF methods that neglect or approximate the electronic exchange interactions between the geminal-coupled electronic orbital and the regular electronic orbitals lead to virtually identical annihilation rates and densities as the fully antisymmetric RXCHF method but offer substantial advantages in computational tractability. Thus, NEO-RXCHF is a promising, computationally practical approach for studying larger positron-containing systems.
Surface Immobilization of Molecular Electrocatalysts for Energy Conversions.
Bullock, Morris; Das, Atanu K; Appel, Aaron M
2017-02-08
Electrocatalysts are critically important for a secure energy future, as they facilitate the conversion between electrical and chemical energy. Molecular catalysts offer precise control of structure that enables understanding of structure-reactivity relationships, which can be difficult to achieve with heterogeneous catalysts. Molecular electrocatalysts can be immobilized on surfaces by covalent bonds or through non-covalent interactions. Advantages of surface immobilization include the need for less catalyst, avoidance of bimolecular decomposition pathways, and easier determination of catalyst lifetime. This mini-review highlights surface immobilization of molecular electrocatalysts for reduction of O2, oxidation of H2O, production of H2, and reduction of CO2.
Alkaline regenerative fuel cell energy storage system for manned orbital satellites
NASA Technical Reports Server (NTRS)
Martin, R. E.; Gitlow, B.; Sheibley, D. W.
1982-01-01
It is pointed out that the alkaline regenerative fuel cell system represents a highly efficient, lightweight, reliable approach for providing energy storage in an orbiting satellite. In addition to its energy storage function, the system can supply hydrogen and oxygen for attitude control of the satellite and for life support. A summary is presented of the results to date obtained in connection with the NASA-sponsored fuel cell technology advancement program, giving particular attention to the requirements of the alkaline regenerative fuel cell and the low-earth mission. Attention is given to system design guidelines, weight considerations, gold-platinum cathode cell performance, matrix development, the electrolyte reservoir plate, and the cyclical load profile tests.
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…
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.
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 C(2)H(3) 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 C(2)H(3) 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.
Nondynamical correlation energy in model molecular systems
NASA Astrophysics Data System (ADS)
Chojnacki, Henryk
The hypersurfaces for the deprotonation processes have been studied at the nonempirical level for H3O+, NH+4, PH+4, and H3S+ cations within their correlation consistent basis set. The potential energy curves were calculated and nondynamical correlation energies analyzed. We have found that the restricted Hartree-Fock wavefunction leads to the improper dissociation limit and, in the three latest cases requires multireference description. We conclude that these systems may be treated as a good models for interpretation of the proton transfer mechanism as well as for testing one-determinantal or multireference cases.
Kimizuka, Nobuo; Yanai, Nobuhiro; Morikawa, Masa-Aki
2016-11-29
The self-assembly of functional molecules into ordered molecular assemblies and the fulfillment of potentials unique to their nanotomesoscopic structures have been one of the central challenges in chemistry. This Feature Article provides an overview of recent progress in the field of molecular self-assembly with the focus on the triplet-triplet annihilation-based photon upconversion (TTA-UC) and supramolecular storage of photon energy. On the basis of the integration of molecular self-assembly and photon energy harvesting, triplet energy migration-based TTA-UC has been achieved in varied molecular systems. Interestingly, some molecular self-assemblies dispersed in solution or organogels revealed oxygen barrier properties, which allowed TTA-UC even under aerated conditions. The elements of molecular self-assembly were also introduced to the field of molecular solar thermal fuel, where reversible photoliquefaction of ionic crystals to ionic liquids was found to double the molecular storage capacity with the simultaneous pursuit of switching ionic conductivity. A future prospect in terms of innovating molecular self-assembly toward molecular systems chemistry is also discussed.
Molecular Beam Studies of Low Energy Reactions.
1983-03-31
COMPLETING PORN . REPORT NUMBER 1 2. GOVT ACCESSION NO. S. RECIPIENT’S CATALOG NUMBER A D A Oaq J- 4. TITLE (And Subtitle) . TYPE OF REPORT & PERIOD COVERED...Gatlinburg, Tenn . in 1981. 2+ c) Studies were made of the charge transfer reaction Ar + Ar 4 2+ Ar + Ar at relative energies from 2 to 1000 eV. Reasons for
NASA Astrophysics Data System (ADS)
DiLabio, Gino A.; Christiansen, Phillip A.
1998-05-01
The spin-orbit energy contributions to the ground state potential energy curves for the main group hydrides, TIH through AtH are estimated by differencing multireference, single promotion, configuration interaction (MRS-CI) energies with and without the spin-orbit operator. The spin-orbit contributions are then summed into the energies determined at the λ-s MRSD-CI level (both single and double promotions). The agreement between the resultant curves and those obtained using intermediate coupling MRSD-CI is within 1.2 kcal/mol over a range of internuclear separations. This suggests that, contrary to previous arguments, spin-orbit coupling and correlation energies are very nearly separable for the main group hydride ground states. Furthermore, the computational effort expended by this separate evaluation is up to 12 times less than that for a comparable intermediate coupling CI. The analysis of some properties of these hydrides indicates that bond length shifts due to spin-orbit coupling are small (0.03 Å) while harmonic vibrational frequencies decrease by up to 9%. Dissociation energies are predicted to change considerably in the presence of the operator in agreement with previous findings.
Hydration Free Energies of Molecular Ions from Theory and Simulation.
Misin, Maksim; Fedorov, Maxim V; Palmer, David S
2016-02-11
We present a theoretical/computational framework for accurate calculation of hydration free energies of ionized molecular species. The method is based on a molecular theory, 3D-RISM, combined with a recently developed pressure correction (PC+). The 3D-RISM/PC+ model can provide ∼3 kcal/mol hydration free energy accuracy for a large variety of ionic compounds, provided that the Galvani potential of water is taken into account. The results are compared with direct atomistic simulations. Several methodological aspects of hydration free energy calculations for charged species are discussed.
NASA Technical Reports Server (NTRS)
Throckmorton, D. A.
1982-01-01
Temperatures measured at the aerodynamic surface of the Orbiter's thermal protection system (TPS), and calorimeter measurements, are used to determine heating rates to the TPS surface during atmospheric entry. On the Orbiter leeside, where convective heating rates are low, it is possible that a significant portion of the total energy input may result from solar radiation, and for the wing, cross radiation from the hot (relatively) Orbiter fuselage. In order to account for the potential impact of these sources, values of solar- and cross-radiation heat transfer are computed, based upon vehicle trajectory and attitude information and measured surface temperatures. Leeside heat-transfer data from the STS-2 mission are presented, and the significance of solar radiation and fuselage-to-wing cross-radiation contributions to total energy input to Orbiter leeside surfaces is assessed.
Energy Transformation in Molecular Electronic Systems
Kasha, Michael
1999-05-17
This laboratory has developed many new ideas and methods in the electronic spectroscopy of molecules. This report covers the contract period 1993-1995. A number of the projects were completed in 1996, and those papers are included in the report. The DOE contract was terminated at the end of 1995 owing to a reorganizational change eliminating nationally the projects under the Office of Health and Environmental Research, U. S. Department of Energy.
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).
NASA Astrophysics Data System (ADS)
Werner, Hans-Joachim
2016-11-01
The accuracy of multipole approximations for distant pair energies in local second-order Møller-Plesset perturbation theory (LMP2) as introduced by Hetzer et al. [Chem. Phys. Lett. 290, 143 (1998)] is investigated for three chemical reactions involving molecules with up to 92 atoms. Various iterative and non-iterative approaches are compared, using different energy thresholds for distant pair selection. It is demonstrated that the simple non-iterative dipole-dipole approximation, which has been used in several recent pair natural orbitals (PNO)-LMP2 and PNO-LCCSD (local coupled-cluster with singles and doubles) methods, may underestimate the distant pair energies by up to 50% and can lead to significant errors in relative energies, unless very tight thresholds are used. The accuracy can be much improved by including higher multipole orders and by optimizing the distant pair amplitudes iteratively along with all other amplitudes. A new approach is presented in which very small special PNO domains for distant pairs are used in the iterative approach. This reduces the number of distant pair amplitudes by 3 orders of magnitude and keeps the additional computational effort for the iterative optimization of distant pair amplitudes minimal.
Werner, Hans-Joachim
2016-11-28
The accuracy of multipole approximations for distant pair energies in local second-order Møller-Plesset perturbation theory (LMP2) as introduced by Hetzer et al. [Chem. Phys. Lett. 290, 143 (1998)] is investigated for three chemical reactions involving molecules with up to 92 atoms. Various iterative and non-iterative approaches are compared, using different energy thresholds for distant pair selection. It is demonstrated that the simple non-iterative dipole-dipole approximation, which has been used in several recent pair natural orbitals (PNO)-LMP2 and PNO-LCCSD (local coupled-cluster with singles and doubles) methods, may underestimate the distant pair energies by up to 50% and can lead to significant errors in relative energies, unless very tight thresholds are used. The accuracy can be much improved by including higher multipole orders and by optimizing the distant pair amplitudes iteratively along with all other amplitudes. A new approach is presented in which very small special PNO domains for distant pairs are used in the iterative approach. This reduces the number of distant pair amplitudes by 3 orders of magnitude and keeps the additional computational effort for the iterative optimization of distant pair amplitudes minimal.
Exact formulas for multipole moments using Slater-type molecular orbitals
NASA Technical Reports Server (NTRS)
Jones, H. W.
1986-01-01
A triple infinite sum of formulas expressed as an expansion in Legendre polynomials is generated by use of computer algebra to represent the potential from the midpoint of two Slater-type orbitals; the charge density that determines the potential is given as the product of the two orbitals. An example using 1s orbitals shows that only a few terms are needed to obtain four-figure accuracy. Exact formulas are obtained for multipole moments by means of a careful study of expanded formulas, allowing an 'extrapolation to infinity'. This Loewdin alpha-function approach augmented by using a C matrix to characterize Slater-type orbitals can be readily generalized to all cases.
Low Molecular Weight Norbornadiene Derivatives for Molecular Solar-Thermal Energy Storage.
Quant, Maria; Lennartson, Anders; Dreos, Ambra; Kuisma, Mikael; Erhart, Paul; Börjesson, Karl; Moth-Poulsen, Kasper
2016-09-05
Molecular solar-thermal energy storage systems are based on molecular switches that reversibly convert solar energy into chemical energy. Herein, we report the synthesis, characterization, and computational evaluation of a series of low molecular weight (193-260 g mol(-1) ) norbornadiene-quadricyclane systems. The molecules feature cyano acceptor and ethynyl-substituted aromatic donor groups, leading to a good match with solar irradiation, quantitative photo-thermal conversion between the norbornadiene and quadricyclane, as well as high energy storage densities (396-629 kJ kg(-1) ). The spectroscopic properties and energy storage capability have been further evaluated through density functional theory calculations, which indicate that the ethynyl moiety plays a critical role in obtaining the high oscillator strengths seen for these molecules.
Low Molecular Weight Norbornadiene Derivatives for Molecular Solar‐Thermal Energy Storage
Quant, Maria; Lennartson, Anders; Dreos, Ambra; Kuisma, Mikael; Erhart, Paul; Börjesson, Karl
2016-01-01
Abstract Molecular solar‐thermal energy storage systems are based on molecular switches that reversibly convert solar energy into chemical energy. Herein, we report the synthesis, characterization, and computational evaluation of a series of low molecular weight (193–260 g mol−1) norbornadiene–quadricyclane systems. The molecules feature cyano acceptor and ethynyl‐substituted aromatic donor groups, leading to a good match with solar irradiation, quantitative photo‐thermal conversion between the norbornadiene and quadricyclane, as well as high energy storage densities (396–629 kJ kg−1). The spectroscopic properties and energy storage capability have been further evaluated through density functional theory calculations, which indicate that the ethynyl moiety plays a critical role in obtaining the high oscillator strengths seen for these molecules. PMID:27492997
Collisions near Kerr black holes: lower limit of energy between orbiting and incoming particles
NASA Astrophysics Data System (ADS)
Rutkowski, Mieszko
2017-01-01
In our paper we investigate the lower limit of collisional energy of test particles near the Kerr black hole. In particular we examine the minimal Lorentz factor between the freely falling particles and the particles orbiting around a black hole. We consider collisions on the innermost stable circular orbit and examine near-extreme case, where collisions take place near an event horizon. By fine-tuning the particles' angular momentum, the Lorentz factor of the collision can always be minimized to a value dependent on the black hole's spin. We identified that this minimal value is always less than 2√{2}-1/√{3} and more than √{12}-1/√{6} (the limits are the values for an extreme Kerr and Schwarzschild, respectively). It implies that this kind of collisions of compact objects are expected to be highly energetic near supermassive black holes. In addition, we show that an interaction between black hole's and particle's spins has an influence on minimal Lorentz factor. This contribution is nonnegligible for near-extreme black holes. We also discuss the relation between our results and sci-fi movie Interstellar.
Energy Aspects of Thermal Molecular Switching: Molecular Thermal Hysteresis of Helicene Oligomers.
Shigeno, Masanori; Kushida, Yo; Yamaguchi, Masahiko
2015-07-20
Molecular switching is a phenomenon by which a molecule reversibly changes its structure and state in response to external stimuli or energy. Herein, molecular switching is discussed from thermodynamic and kinetic aspects in terms of energy supply with an emphasis on the thermal switching exhibited by helicene oligomers. It includes the inversion of relative thermodynamic stability induced by temperature changes and molecular thermal hysteresis in a closed system. The thermal phenomenon associated with the oligomers involves population/concentration changes between metastable states under nonequilibrium thermodynamic control.
Suresh, S; Gunasekaran, S; Srinivasan, S
2015-03-05
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.
Hay, P.J.; Wadt, W.R.
1985-01-01
Ab initio effective core potentials (ECP's) have been generated to replace the innermost core electron for third-row (K--Au), fourth-row (Rb--Ag), and fifth-row (Cs--Au) atoms. The outermost core orbitals: corresponding to the ns/sup 2/np/sup 6/ configuration for the three rows here: are not replaced by the ECP but are treated on an equal footing with the nd, (n+1)s and (n+1)p valence orbitals. These ECP's have been derived for use in molecular calculations where these outer core orbitals need to be treated explicitly rather than to be replaced by an ECP. The ECP's for the forth and fifth rows also incorporate the mass--velocity and Darwin relativistic effects into the potentials. Analytic fits to the potentials are presented for use in multicenter integral evaluation. Gaussian orbital valence basis sets are developed for the (3s, 3p, 3d, 4s, 4p), (4s, 4p, 4d, 5s, 5p), and (5s, 5p, 5d, 6s, 6p) ortibals of the three respective rows.
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.
Dynamics of Finite Energy Airy Beams Carrying Orbital Angular Momentum in Multilevel Atomic Vapors
NASA Astrophysics Data System (ADS)
Wu, Zhenkun; Wang, Shun; Hu, Weifei; Gu, Yuzong
2016-10-01
We numerically investigate the dynamics of inward circular finite-energy Airy beams carrying different orbital angular momentum (OAM) numbers in a close-Λ three-level atomic vapor with the electromagnetically induced transparency (EIT) window. We report that due to the EIT induced by the microwave field, the transverse intensity distribution properties of Airy beam can be feasibly manipulated and modulated through adjusting OAM numbers l and the frequency detuning, as well as the propagation distance, in the multi-level atomic systems. What's more, the rotation of the beam also can be observed with different positions in atomic ensembles. The investigation may provide a useful tool for studying particle manipulation, signal processing and propagation in graded-index (GRIN) fibers.
Antihydrogen-hydrogen elastic scattering at thermal energies using an atomic-orbital technique
Sinha, Prabal K.; Chaudhuri, Puspitapallab; Ghosh, A.S.
2003-05-01
In view of the recent interest in the trapping of antihydrogen atom H(bar sign), at very low temperatures, H-bar-H scattering has been investigated at low incident energies using a close-coupling model with the basis set H-bar(1s,2s,2p-bar)+H(1s,2s,2p-bar). The predicted s-wave elastic phase shifts, scattering length, and effective range are in a good agreement with the other recent predictions of Jonsell et al. and of Armour and Chamberlain. The results indicate that the atomic orbital expansion model is suitable to study the H-bar-H scattering at ultracold temperatures.
Generation of High-Energy Photons with Large Orbital Angular Momentum by Compton Backscattering
NASA Astrophysics Data System (ADS)
Jentschura, U. D.; Serbo, V. G.
2011-01-01
Usually, photons are described by plane waves with a definite 4-momentum. In addition to plane-wave photons, “twisted photons” have recently entered the field of modern laser optics; these are coherent superpositions of plane waves with a defined projection ℏm of the orbital angular momentum onto the propagation axis, where m is an integer. In this Letter, we show that it is possible to produce high-energy twisted photons by Compton backscattering of twisted laser photons off ultrarelativistic electrons. Such photons may be of interest for experiments related to the excitation and disintegration of atoms and nuclei, and for studying the photoeffect and pair production off nuclei in previously unexplored experimental regimes.
Wang, Weihua; Ji, Yongfei; Zhang, Hui; Zhao, Aidi; Wang, Bing; Yang, Jinlong; Hou, J G
2012-08-28
It has been a long-term desire to fabricate hybrid silicon-molecular devices by taking advantages of organic molecules and the existing silicon-based technology. However, one of the challenging tasks is to design applicable functions on the basis of the intrinsic properties of the molecules, as well as the silicon substrates. Here we demonstrate a silicon-molecular system that produces negative differential resistance (NDR) by making use of the well-defined intrinsic surface-states of the Si (111)-√3 × √3-Ag (R3-Ag/Si) surface and the molecular orbital of cobalt(II)-phthalocyanine (CoPc) molecules. From our experimental results obtained using scanning tunneling microscopy/spectroscopy, we find that NDR robustly appears at the Co(2+) ion centers of the CoPc molecules, independent of the adsorption configuration of the CoPc molecules and irrespective of doping type and doping concentration of the silicon substrates. Joint with first principle calculations, we conclude that NDR is originated from the resonance between the intrinsic surface-state band S(1) of the R3-Ag/Si surface and the localized unoccupied Co(2+)d(z(2)) orbital of the adsorbed CoPc molecules. We expect that such a mechanism can be generally used in other silicon-molecular systems.
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.
Energy dissipation in an adaptive molecular circuit
NASA Astrophysics Data System (ADS)
Wang, Shou-Wen; Lan, Yueheng; Tang, Lei-Han
2015-07-01
The ability to monitor nutrient and other environmental conditions with high sensitivity is crucial for cell growth and survival. Sensory adaptation allows a cell to recover its sensitivity after a transient response to a shift in the strength of extracellular stimulus. The working principles of adaptation have been established previously based on rate equations which do not consider fluctuations in a thermal environment. Recently, Lan et al (2012 Nat. Phys. 8 422-8) performed a detailed analysis of a stochastic model for the Escherichia coli sensory network. They showed that accurate adaptation is possible only when the system operates in a nonequilibrium steady-state (NESS). They further proposed an energy-speed-accuracy (ESA) trade-off relation. We present here analytic results on the NESS of the model through a mapping to a one-dimensional birth-death process. An exact expression for the entropy production rate is also derived. Based on these results, we are able to discuss the ESA relation in a more general setting. Our study suggests that the adaptation error can be reduced exponentially as the methylation range increases. Finally, we show that a nonequilibrium phase transition exists in the infinite methylation range limit, despite the fact that the model contains only two discrete variables.
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.
The contribution of low-energy protons to the total on-orbit SEU rate
Dodds, Nathaniel Anson; Martinez, Marino J.; Dodd, Paul E.; ...
2015-11-10
Low- and high-energy proton experimental data and error rate predictions are presented for many bulk Si and SOI circuits from the 20-90 nm technology nodes to quantify how much low-energy protons (LEPs) can contribute to the total on-orbit single-event upset (SEU) rate. Every effort was made to predict LEP error rates that are conservatively high; even secondary protons generated in the spacecraft shielding have been included in the analysis. Across all the environments and circuits investigated, and when operating within 10% of the nominal operating voltage, LEPs were found to increase the total SEU rate to up to 4.3 timesmore » as high as it would have been in the absence of LEPs. Therefore, the best approach to account for LEP effects may be to calculate the total error rate from high-energy protons and heavy ions, and then multiply it by a safety margin of 5. If that error rate can be tolerated then our findings suggest that it is justified to waive LEP tests in certain situations. Trends were observed in the LEP angular responses of the circuits tested. As a result, grazing angles were the worst case for the SOI circuits, whereas the worst-case angle was at or near normal incidence for the bulk circuits.« less
The contribution of low-energy protons to the total on-orbit SEU rate
Dodds, Nathaniel Anson; Martinez, Marino J.; Dodd, Paul E.; Shaneyfelt, Marty R.; Sexton, Frederick W.; Black, Jeffrey D.; Lee, David S.; Swanson, Scot E.; Bhuva, B. L.; Warren, K. M.; Reed, R. A.; Trippe, J.; Sierawski, B. D.; Weller, R. A.; Mahatme, N.; Gaspard, N.; Assis, T.; Austin, R.; Massengill, L. M.; Swift, G.; Wirthlin, M.; Cannon, M.; Liu, R.; Chen, L.; Kelly, A. T.; Marshall, P.; Trinczek, M.; Blackmore, E. W.; Wen, S. -J.; Wong, R.; Narasimham, B.; Pellish, J. A.; Puchner, H.; Weeden-Wright, S. L.
2015-11-10
Low- and high-energy proton experimental data and error rate predictions are presented for many bulk Si and SOI circuits from the 20-90 nm technology nodes to quantify how much low-energy protons (LEPs) can contribute to the total on-orbit single-event upset (SEU) rate. Every effort was made to predict LEP error rates that are conservatively high; even secondary protons generated in the spacecraft shielding have been included in the analysis. Across all the environments and circuits investigated, and when operating within 10% of the nominal operating voltage, LEPs were found to increase the total SEU rate to up to 4.3 times as high as it would have been in the absence of LEPs. Therefore, the best approach to account for LEP effects may be to calculate the total error rate from high-energy protons and heavy ions, and then multiply it by a safety margin of 5. If that error rate can be tolerated then our findings suggest that it is justified to waive LEP tests in certain situations. Trends were observed in the LEP angular responses of the circuits tested. As a result, grazing angles were the worst case for the SOI circuits, whereas the worst-case angle was at or near normal incidence for the bulk circuits.
Molecular dynamics simulation of threshold displacement energies in zircon
Moreira, Pedro A.; Devanathan, Ramaswami; Yu, Jianguo; Weber, William J.
2009-10-15
Molecular-dynamics simulations were used to examine the displacement threshold energy (Ed) surface for Zr, Si and O in zircon using two different interatomic potentials. For each sublattice, the simulation was repeated from different initial conditions to estimate the uncertainty in the calculated value of Ed. The displacement threshold energies vary considerably with crystallographic direction and sublattice. The average displacement energy calculated with a recently developed transferable potential is about 120 and 60 eV for cations and anions, respectively. The oxygen displacement energy shows good agreement with experimental estimates in ceramics.
Study on Properties of Energy Spectra of the Molecular Crystals
NASA Astrophysics Data System (ADS)
Pang, Xiao-Feng; Chen, Xiang-Rong
The energy-spectra of nonlinear vibration of molecular crystals such as acetanilide have been calculated by using discrete nonlinear Schrödinger equation appropriate to the systems, containing various interactions. The energy levels including higher excited states are basically consistent with experimental values obtained by infrared absorption and Raman scattering in acetanilide. We further give the features of distribution of the energy-spectra for the acetanilide. Using the energy spectra we also explained well experimental results obtained by Careri et al..
Electron energy-loss spectra in molecular fluorine
NASA Technical Reports Server (NTRS)
Nishimura, H.; Cartwright, D. C.; Trajmar, S.
1979-01-01
Electron energy-loss spectra in molecular fluorine, for energy losses from 0 to 17.0 eV, have been taken at incident electron energies of 30, 50, and 90 eV and scattering angles from 5 to 140 deg. Features in the spectra above 11.5 eV energy loss agree well with the assignments recently made from optical spectroscopy. Excitations of many of the eleven repulsive valence excited electronic states are observed and their location correlates reasonably well with recent theoretical results. Several of these excitations have been observed for the first time and four features, for which there are no identifications, appear in the spectra.
State-to-state dynamics of molecular energy transfer
Gentry, W.R.; Giese, C.F.
1993-12-01
The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.
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
2016-08-09
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.
Öberg, H; Brinck, T
2016-06-01
The importance of key residues to the activity of the cAMP-dependent protein kinase catalyzed phosphoryl transfer and to the stabilization of the transition state of the reaction has been investigated by means of the fragment molecular orbital (FMO) method. To evaluate the accuracy of the method and its capability of fragmenting covalent bonds, we have compared stabilization energies due to the interactions between individual residues and the reaction center to results obtained with the differential transition state stabilization method (Szarek, et al., J. Phys. Chem. B, 2008, 112, 11819-11826) and observe, despite a size difference in the fragment describing the reaction center, near-quantitative agreement. We have also computed deletion energies to investigate the effect of virtual deletion of key residues on the activation energy. These results are consistent with the stabilization energies and yield additional information as they clearly capture the effect of secondary interactions, i.e. interactions in the second coordination layer of the reaction center. We find that using FMO to calculate deletion energies is a powerful and time efficient approach to analyze the importance of key residues to the activity of an enzyme catalyzed reaction.
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.
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
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.
Photoswitchable Molecular Rings for Solar-Thermal Energy Storage.
Durgun, E; Grossman, Jeffrey C
2013-03-21
Solar-thermal fuels reversibly store solar energy in the chemical bonds of molecules by photoconversion, and can release this stored energy in the form of heat upon activation. Many conventional photoswichable molecules could be considered as solar thermal fuels, although they suffer from low energy density or short lifetime in the photoinduced high-energy metastable state, rendering their practical use unfeasible. We present a new approach to the design of chemistries for solar thermal fuel applications, wherein well-known photoswitchable molecules are connected by different linker agents to form molecular rings. This approach allows for a significant increase in both the amount of stored energy per molecule and the stability of the fuels. Our results suggest a range of possibilities for tuning the energy density and thermal stability as a function of the type of the photoswitchable molecule, the ring size, or the type of linkers.
A molecularly based theory for electron transfer reorganization energy.
Zhuang, Bilin; Wang, Zhen-Gang
2015-12-14
Using field-theoretic techniques, we develop a molecularly based dipolar self-consistent-field theory (DSCFT) for charge solvation in pure solvents under equilibrium and nonequilibrium conditions and apply it to the reorganization energy of electron transfer reactions. The DSCFT uses a set of molecular parameters, such as the solvent molecule's permanent dipole moment and polarizability, thus avoiding approximations that are inherent in treating the solvent as a linear dielectric medium. A simple, analytical expression for the free energy is obtained in terms of the equilibrium and nonequilibrium electrostatic potential profiles and electric susceptibilities, which are obtained by solving a set of self-consistent equations. With no adjustable parameters, the DSCFT predicts activation energies and reorganization energies in good agreement with previous experiments and calculations for the electron transfer between metallic ions. Because the DSCFT is able to describe the properties of the solvent in the immediate vicinity of the charges, it is unnecessary to distinguish between the inner-sphere and outer-sphere solvent molecules in the calculation of the reorganization energy as in previous work. Furthermore, examining the nonequilibrium free energy surfaces of electron transfer, we find that the nonequilibrium free energy is well approximated by a double parabola for self-exchange reactions, but the curvature of the nonequilibrium free energy surface depends on the charges of the electron-transferring species, contrary to the prediction by the linear dielectric theory.
A molecularly based theory for electron transfer reorganization energy
Zhuang, Bilin; Wang, Zhen-Gang
2015-12-14
Using field-theoretic techniques, we develop a molecularly based dipolar self-consistent-field theory (DSCFT) for charge solvation in pure solvents under equilibrium and nonequilibrium conditions and apply it to the reorganization energy of electron transfer reactions. The DSCFT uses a set of molecular parameters, such as the solvent molecule’s permanent dipole moment and polarizability, thus avoiding approximations that are inherent in treating the solvent as a linear dielectric medium. A simple, analytical expression for the free energy is obtained in terms of the equilibrium and nonequilibrium electrostatic potential profiles and electric susceptibilities, which are obtained by solving a set of self-consistent equations. With no adjustable parameters, the DSCFT predicts activation energies and reorganization energies in good agreement with previous experiments and calculations for the electron transfer between metallic ions. Because the DSCFT is able to describe the properties of the solvent in the immediate vicinity of the charges, it is unnecessary to distinguish between the inner-sphere and outer-sphere solvent molecules in the calculation of the reorganization energy as in previous work. Furthermore, examining the nonequilibrium free energy surfaces of electron transfer, we find that the nonequilibrium free energy is well approximated by a double parabola for self-exchange reactions, but the curvature of the nonequilibrium free energy surface depends on the charges of the electron-transferring species, contrary to the prediction by the linear dielectric theory.
Calculation of molecular free energies in classical potentials
NASA Astrophysics Data System (ADS)
Farhi, Asaf; Singh, Bipin
2016-02-01
Free energies of molecules can be calculated by quantum chemistry computations or by normal mode classical calculations. However, the first can be computationally impractical for large molecules and the second is based on the assumption of harmonic dynamics. We present a novel, accurate and complete calculation of molecular free energies in standard classical potentials. In this method we transform the molecule by relaxing potential terms which depend on the coordinates of a group of atoms in that molecule and calculate the free energy difference associated with the transformation. Then, since the transformed molecule can be treated as non-interacting systems, the free energy associated with these atoms is analytically or numerically calculated. This two-step calculation can be applied to calculate free energies of molecules or free energy difference between (possibly large) molecules in a general environment. We demonstrate the method in free energy calculations for methanethiol and butane molecules in vacuum and solvent. We suggest the potential application of free energy calculation of chemical reactions in classical molecular simulations.
A pair natural orbital implementation of the coupled cluster model CC2 for excitation energies.
Helmich, Benjamin; Hättig, Christof
2013-08-28
We demonstrate how to extend the pair natural orbital (PNO) methodology for excited states, presented in a previous work for the perturbative doubles correction to configuration interaction singles (CIS(D)), to iterative coupled cluster methods such as the approximate singles and doubles model CC2. The original O(N(5)) scaling of the PNO construction is reduced by using orbital-specific virtuals (OSVs) as an intermediate step without spoiling the initial accuracy of the PNO method. Furthermore, a slower error convergence for charge-transfer states is analyzed and resolved by a numerical Laplace transformation during the PNO construction, so that an equally accurate treatment of local and charge-transfer excitations is achieved. With state-specific truncated PNO expansions, the eigenvalue problem is solved by combining the Davidson algorithm with deflation to project out roots that have already been determined and an automated refresh with a generation of new PNOs to achieve self-consistency of the PNO space. For a large test set, we found that truncation errors for PNO-CC2 excitation energies are only slightly larger than for PNO-CIS(D). The computational efficiency of PNO-CC2 is demonstrated for a large organic dye, where a reduction of the doubles space by a factor of more than 1000 is obtained compared to the canonical calculation. A compression of the doubles space by a factor 30 is achieved by a unified OSV space only. Moreover, calculations with the still preliminary PNO-CC2 implementation on a series of glycine oligomers revealed an early break even point with a canonical RI-CC2 implementation between 100 and 300 basis functions.
A pair natural orbital implementation of the coupled cluster model CC2 for excitation energies
NASA Astrophysics Data System (ADS)
Helmich, Benjamin; Hättig, Christof
2013-08-01
We demonstrate how to extend the pair natural orbital (PNO) methodology for excited states, presented in a previous work for the perturbative doubles correction to configuration interaction singles (CIS(D)), to iterative coupled cluster methods such as the approximate singles and doubles model CC2. The original O(N^5) scaling of the PNO construction is reduced by using orbital-specific virtuals (OSVs) as an intermediate step without spoiling the initial accuracy of the PNO method. Furthermore, a slower error convergence for charge-transfer states is analyzed and resolved by a numerical Laplace transformation during the PNO construction, so that an equally accurate treatment of local and charge-transfer excitations is achieved. With state-specific truncated PNO expansions, the eigenvalue problem is solved by combining the Davidson algorithm with deflation to project out roots that have already been determined and an automated refresh with a generation of new PNOs to achieve self-consistency of the PNO space. For a large test set, we found that truncation errors for PNO-CC2 excitation energies are only slightly larger than for PNO-CIS(D). The computational efficiency of PNO-CC2 is demonstrated for a large organic dye, where a reduction of the doubles space by a factor of more than 1000 is obtained compared to the canonical calculation. A compression of the doubles space by a factor 30 is achieved by a unified OSV space only. Moreover, calculations with the still preliminary PNO-CC2 implementation on a series of glycine oligomers revealed an early break even point with a canonical RI-CC2 implementation between 100 and 300 basis functions.
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.
Molecular ion sources for low energy semiconductor ion implantation (invited)
NASA Astrophysics Data System (ADS)
Hershcovitch, A.; Gushenets, V. I.; Seleznev, D. N.; Bugaev, A. S.; Dugin, S.; Oks, E. M.; Kulevoy, T. V.; Alexeyenko, O.; Kozlov, A.; Kropachev, G. N.; Kuibeda, R. P.; Minaev, S.; Vizir, A.; Yushkov, G. Yu.
2016-02-01
Smaller semiconductors require shallow, low energy ion implantation, resulting space charge effects, which reduced beam currents and production rates. To increase production rates, molecular ions are used. Boron and phosphorous (or arsenic) implantation is needed for P-type and N-type semiconductors, respectively. Carborane, which is the most stable molecular boron ion leaves unacceptable carbon residue on extraction grids. A self-cleaning carborane acid compound (C4H12B10O4) was synthesized and utilized in the ITEP Bernas ion source resulting in large carborane ion output, without carbon residue. Pure gaseous processes are desired to enable rapid switch among ion species. Molecular phosphorous was generated by introducing phosphine in dissociators via 4PH3 = P4 + 6H2; generated molecular phosphorous in a pure gaseous process was then injected into the HCEI Calutron-Bernas ion source, from which P4+ ion beams were extracted. Results from devices and some additional concepts are described.
Molecular ion sources for low energy semiconductor ion implantation (invited).
Hershcovitch, A; Gushenets, V I; Seleznev, D N; Bugaev, A S; Dugin, S; Oks, E M; Kulevoy, T V; Alexeyenko, O; Kozlov, A; Kropachev, G N; Kuibeda, R P; Minaev, S; Vizir, A; Yushkov, G Yu
2016-02-01
Smaller semiconductors require shallow, low energy ion implantation, resulting space charge effects, which reduced beam currents and production rates. To increase production rates, molecular ions are used. Boron and phosphorous (or arsenic) implantation is needed for P-type and N-type semiconductors, respectively. Carborane, which is the most stable molecular boron ion leaves unacceptable carbon residue on extraction grids. A self-cleaning carborane acid compound (C4H12B10O4) was synthesized and utilized in the ITEP Bernas ion source resulting in large carborane ion output, without carbon residue. Pure gaseous processes are desired to enable rapid switch among ion species. Molecular phosphorous was generated by introducing phosphine in dissociators via 4PH3 = P4 + 6H2; generated molecular phosphorous in a pure gaseous process was then injected into the HCEI Calutron-Bernas ion source, from which P4(+) ion beams were extracted. Results from devices and some additional concepts are described.
Krieger, Christine C; Gershengorn, Marvin C
2014-02-01
Excess production of hyaluronan (hyaluronic acid [HA]) in the retro-orbital space is a major component of Graves' ophthalmopathy, and regulation of HA production by orbital cells is a major research area. In most previous studies, HA was measured by ELISAs that used HA-binding proteins for detection and rooster comb HA as standards. We show that the binding efficiency of HA-binding protein in the ELISA is a function of HA polymer size. Using gel electrophoresis, we show that HA secreted from orbital cells is primarily comprised of polymers more than 500 000. We modified a commercially available ELISA by using 1 million molecular weight HA as standard to accurately measure HA of this size. We demonstrated that IL-1β-stimulated HA secretion is at least 2-fold greater than previously reported, and activation of the TSH receptor by an activating antibody M22 from a patient with Graves' disease led to more than 3-fold increase in HA production in both fibroblasts/preadipocytes and adipocytes. These effects were not consistently detected with the commercial ELISA using rooster comb HA as standard and suggest that fibroblasts/preadipocytes may play a more prominent role in HA remodeling in Graves' ophthalmopathy than previously appreciated.
NASA Technical Reports Server (NTRS)
Lo, M.
1998-01-01
The invariant manifolds associated with the outer planets are extremely large objects in phase space. They are trajectories in the ecliptic which intersect one another. This enables a low energy single impulse transfer between the planets which requries several orbital periods.
Design of low-energy transfer from lunar orbit to asteroid in the Sun-Earth-Moon system
NASA Astrophysics Data System (ADS)
Wang, Ya-Min; Qiao, Dong; Cui, Ping-Yuan
2014-12-01
Asteroid exploration trajectories which start from a lunar orbit are investigated in this work. It is assumed that the probe departs from lunar orbit and returns to the vicinity of Earth, then escapes from the Earth by performing a perigee maneuver. A low-energy transfer in Sun-Earth-Moon system is adopted. First, the feasible region of low-energy transfer from lunar orbit to perigee within 5 000km height above the Earth surface in Sun-Earth-Moon system is calculated and analyzed. Three transfer types are found, i.e., large maneuver and fast transfers, small maneuver and fast transfers, and disordered and slow transfers. Most of feasibility trajectories belong to the first two types. Then, the low-energy trajectory leg from lunar orbit to perigee and a heliocentric trajectory leg from perigee to asteroid are patched by a perigee maneuver. The optimal full-transfer trajectory is obtained by exploiting the differential evolution algorithm. Finally, taking 4179 Toutatis asteroid as the target, some low-energy transfer trajectories are obtained and analyzed.
Zarycz, Natalia; Aucar, Gustavo A
2012-02-02
NMR J-coupling calculations at the second-order of polarization propagator approach, SOPPA, are among the most reliable. They include a high percentage of the total electron correlation effects in saturated and unsaturated molecular systems. Furthermore, J-couplings are quite sensitive to the whole electronic molecular framework. We present in this article the first study of all three response mechanisms, Fermi contact, FC, spin-dipolar, SD and paramagnetic spin-orbital, PSO, for J-couplings with occupied localized molecular orbitals at the SOPPA level of approach. Even though SOPPA results are not invariant under unitary transformations, the difference between results obtained with canonical and localized molecular orbitals, LMOs, are small enough to permit its application with confidence. The following small-size saturated and unsaturated compounds were analyzed: CH(4), CH(3)F, C(2)H(6), NH(3), C(2)H(4), CH(2)NH, H(2)C═CHF, and FHC═CHF. The local character of the FC mechanism that appears in J-couplings of these molecular models is shown through the analysis of contributions from LMOs. The importance of including the electron correlation on the engaged bonding orbitals for one-bond couplings is emphasized. Almost all electron correlation effects are included in such orbitals. Interesting findings were the large contributions by s-type LMOs to the C-H and C-C J-couplings; they are responsible for the variation of (1)J(C-C) when going from ethane to ethene and to 1,2-difluoroethene. The previously proposed hyperconjugative transfer mechanism has been tested. Among other tests we found the difference anti-syn of one-bond (1)J(C-H) in imine as due to both the corresponding σ(C-H) and the lone-pair, LP, contribution. Geminal and vicinal J-couplings were also analyzed. Our findings are in accord with a previous work by Pople and Bothner-by, who considered results taken from calculations or empirical data. For all geminal couplings the pattern of J-couplings, like
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.
Generalized Potential Energy Finite Elements for Modeling Molecular Nanostructures.
Chatzieleftheriou, Stavros; Adendorff, Matthew R; Lagaros, Nikos D
2016-10-24
The potential energy of molecules and nanostructures is commonly calculated in the molecular mechanics formalism by superimposing bonded and nonbonded atomic energy terms, i.e. bonds between two atoms, bond angles involving three atoms, dihedral angles involving four atoms, nonbonded terms expressing the Coulomb and Lennard-Jones interactions, etc. In this work a new, generalized numerical simulation is presented for studying the mechanical behavior of three-dimensional nanostructures at the atomic scale. The energy gradient and Hessian matrix of such assemblies are usually computed numerically; a potential energy finite element model is proposed herein where these two components are expressed analytically. In particular, generalized finite elements are developed that express the interactions among atoms in a manner equivalent to that invoked in simulations performed based on the molecular dynamics method. Thus, the global tangent stiffness matrix for any nanostructure is formed as an assembly of the generalized finite elements and is directly equivalent to the Hessian matrix of the potential energy. The advantages of the proposed model are identified in terms of both accuracy and computational efficiency. In the case of popular force fields (e.g., CHARMM), the computation of the Hessian matrix by implementing the proposed method is of the same order as that of the gradient. This analysis can be used to minimize the potential energy of molecular systems under nodal loads in order to derive constitutive laws for molecular systems where the entropy and solvent effects are neglected and can be approximated as solids, such as double stranded DNA nanostructures. In this context, the sequence dependent stretch modulus for some typical base pairs step is calculated.
1991-01-01
codes can be made available to the Orbital Debris Spacecraft Breakup Modeling Program through technology transfer. This will reduce duplication...conserve scarce R&D funds, and provide a head start to orbital debris breakup modeling efforts. This paper highlights results from those LTH-5 activities...which will be of most interest to those involved with orbital debris generation and the effects of debris on spacecraft. The attached bibliography
Collision Induced Dissociation and Energy Transfer in Molecular Hydroge
NASA Astrophysics Data System (ADS)
Mandy, Margot E.
2006-06-01
Molecular hydrogen is a significant constituent in giant molecular clouds in the interstellar medium. Shocks in these clouds are associated with star formation. The cooling of the shocks is governed by competition of collisional energy transfer and dissociation with radiative cooling by quadrupole emission. Thus a detailed understanding of collisional behaviour of molecular hydrogen is needed. Work in this group has examined energy transfer and dissociation in molecular energy transfer as the result of collisions with H, D, He, and H2. Using quasiclassical trajectories and chemically accurate ab initio potentials state-to-state rate coefficients have been determined. The uncertainties of the cross sections are propagated rigourously to give uncertainties of the rate coefficients and the rate coefficients are parameterized as a function of temperature. Comparisons with quantum calculations are discussed and the proposed website is described.This work was supported by a grant from the Natural Sciences and Engineering Research Council of Canada. The calculations were carried out using the high performance computing facility jointly supported by the Canadian Foundation for Innovation, the British Columbia Knowledge Development Fund, and Silicon Graphics at the University of Northern British Columbia.
NASA Astrophysics Data System (ADS)
Liu, Zhenfei; Neaton, Jeffrey B.
In quantum transport calculations, transmission functions of molecular junctions, as well as spectral functions of metal-organic interfaces, often feature peaks originating from molecular resonances. These resonance peaks are often assumed to be Lorentzian, with an energy-independent broadening function Γ. However, in the general case, the wide-band-limit breaks down, and the Lorentzian approximation is no longer valid. Here, we develop a new energy-dependent broadening function Γ (E) , based on diagonalization of non-Hermitian matrices within a non-equilbrium Green's function (NEGF) formalism. As defined, Γ (E) can describe resonances of non-Lorentzian nature and can be decomposed into components associated with the left and right leads, respectively; and it is particularly useful in understanding transport properties in terms of molecular orbitals in asymmetric junctions. We compute this quantity via an ab initio NEGF approach based on density functional theory and illustrate its utility with several junctions of experimental relevance, including recent work on rectification in Au-graphite junctions. This work is supported by the DOE, and computational resources are provided by NERSC.
Porchelvi, E Elamurugu; Muthu, S
2015-01-05
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).
Nishimoto, Yoshio; Nakata, Hiroya; Fedorov, Dmitri G; Irle, Stephan
2015-12-17
The fully analytic gradient is developed for density-functional tight-binding (DFTB) combined with the fragment molecular orbital (FMO) method (FMO-DFTB). The response terms arising from the coupling of the electronic state to the embedding potential are derived, and the gradient accuracy is demonstrated on water clusters and a polypeptide. The radial distribution functions (RDFs) obtained with FMO-DFTB are found to be similar to those from conventional DFTB, while the computational cost is greatly reduced; for 256 water molecules one molecular dynamics (MD) step takes 73.26 and 0.68 s with full DFTB and FMO-DFTB, respectively, showing a speed-up factor of 108. FMO-DFTB/MD is applied to 100 ps MD simulations of liquid hydrogen halides and is found to reproduce experimental RDFs reasonably well.
NASA Astrophysics Data System (ADS)
Buhl, Margaret Linn
The electronic properties of trinuclear iron, tetranuclear iron butterfly, iron-cobalt, and iron-copper clusters have been studied experimentally at 78K by the Mossbauer effect and theoretically by Fenske-Hall molecular orbital calculations. The Mossbauer effect isomer shift is very sensitive to the differences in the iron s-electron densities in these clusters and, as expected, decreases as the sum of the iron 4s Mulliken population and the Clementi and Raimondi effective nuclear charge increases. The molecular orbital wave functions and the Mulliken atomic charges are used to calculate the electric field gradient at the metal nuclei and the iron Mossbauer effect quadrupole splittings. The valence contribution was found to be the major component of the electric field gradient in all the clusters studied. In general the calculated value of Delta E_ {Q} is larger than the observed value, as a result of neglect of the valence Sternheimer factor, R. The metal charge depends upon its electronegativity and upon the nature of its Lewis base ligands. The carbonyl ligand carbon charge becomes more positive as the metal electronegativity increases. The oxygen charge becomes more negative as the anionic cluster charge increases, and in so doing, yields the maximum anionic charge separation. The electronic properties of the terminal carbonyl ligands are similar to those of carbon monoxide, whereas the electronic properties of the bridging carbonyl ligands are similar to those of the carbonyl group found in aldehydes and ketones.
Stagner, Anna M; Jakobiec, Frederick A; Fay, Aaron
Synovial sarcoma is a soft-tissue sarcoma of the extremities developing in young adults that has rarely been reported in the orbit. Synovial sarcoma is associated with a unique translocation, resulting in an SYT-SSX fusion gene. We analyze 7 published periocular cases, together with the current one, to gain a better appreciation of the features of the tumor in this location and to compare the findings with those derived from nonophthalmic studies. An inferior orbital mass developed in a 31-year-old woman after experiencing periorbital and hemifacial pain for more than a decade. Radiographically, the mass was circumscribed and displayed coarse internal calcifications. A large but subtotal excision with histopathologic examination disclosed a primitive tumor composed of spindled and ovoid cells. Immunohistochemistry demonstrated positivity for nuclear transducin-like enhancer of split 1 and membranous CD99, typical for synovial sarcoma. Fluorescence in situ hybridization identified a (X,18) translocation in the tumor cells. The patient underwent postoperative adjuvant proton beam radiotherapy with a good response that has been maintained during 1 year of follow-up. Orbital soft-tissue tumors of all types are increasingly identified by their distinctive genetic signatures that offer more specificity than standard immunohistochemical tests.
Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.
Cawkwell, M J; Niklasson, Anders M N
2012-10-07
Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces.
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.
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)
Liu, Chao-Fei; JuzeliÅ«nas, Gediminas; Liu, W. M.
2017-02-01
Atomic-molecular Bose-Einstein condensates (BECs) offer brand new opportunities to revolutionize quantum gases and probe the variation of fundamental constants with unprecedented sensitivity. The recent realization of spin-orbit coupling (SOC) in BECs provides a new platform for exploring completely new phenomena unrealizable elsewhere. In this study, we find a way of creating a Rashba-Dresselhaus SOC in atomic-molecular BECs by combining the spin-dependent photoassociation and Raman coupling, which can control the formation and distribution of a different type of topological excitation—carbon-dioxide-like skyrmion. This skyrmion is formed by two half-skyrmions of molecular BECs coupling with one skyrmion of atomic BECs, where the two half-skyrmions locate at both sides of one skyrmion. Carbon-dioxide-like skyrmion can be detected by measuring the vortices structures using the time-of-flight absorption imaging technique in real experiments. Furthermore, we find that SOC can effectively change the occurrence of the Chern number in k space, which causes the creation of topological spin textures from some separated carbon-dioxide-like monomers each with topological charge -2 to a polymer chain of the skyrmions. This work helps in creating dual SOC atomic-molecular BECs and opens avenues to manipulate topological excitations.
NASA Astrophysics Data System (ADS)
Sun, Rui; Granucci, Giovanni; Paul, Amit K.; Siebert, Matthew; Liang, Hongliang J.; Cheong, Grace; Hase, William L.; Persico, Maurizio
2015-03-01
Quantum mechanical (QM) + molecular mechanics (MM) models are developed to represent potential energy surfaces (PESs) for the HBr+ + CO2 → Br + HOCO+ reaction with HBr+ in the 2Π3/2 and 2Π1/2 spin-orbit states. The QM component is the spin-free PES and spin-orbit coupling for each state is represented by a MM-like analytic potential fit to spin-orbit electronic structure calculations. Coupled-cluster single double and perturbative triple excitation (CCSD(T)) calculations are performed to obtain "benchmark" reaction energies without spin-orbit coupling. With zero-point energies removed, the "experimental" reaction energy is 44 ± 5 meV for HBr+(2Π3/2) + CO2 → Br(2P3/2) + HOCO+, while the CCSD(T) value with spin-orbit effects included is 87 meV. Electronic structure calculations were performed to determine properties of the BrHOCO+ reaction intermediate and [HBr⋯OCO]+ van der Waals intermediate. The results of different electronic structure methods were compared with those obtained with CCSD(T), and UMP2/cc-pVTZ/PP was found to be a practical and accurate QM method to use in QM/MM direct dynamics simulations. The spin-orbit coupling calculations show that the spin-free QM PES gives a quite good representation of the shape of the PES originated by 2Π3/2HBr+. This is also the case for the reactant region of the PES for 2Π1/2 HBr+, but spin-orbit coupling effects are important for the exit-channel region of this PES. A MM model was developed to represent these effects, which were combined with the spin-free QM PES.
Sun, Rui; Granucci, Giovanni; Paul, Amit K; Siebert, Matthew; Liang, Hongliang J; Cheong, Grace; Hase, William L; Persico, Maurizio
2015-03-14
Quantum mechanical (QM) + molecular mechanics (MM) models are developed to represent potential energy surfaces (PESs) for the HBr(+) + CO2 → Br + HOCO(+) reaction with HBr(+) in the (2)Π3/2 and (2)Π1/2 spin-orbit states. The QM component is the spin-free PES and spin-orbit coupling for each state is represented by a MM-like analytic potential fit to spin-orbit electronic structure calculations. Coupled-cluster single double and perturbative triple excitation (CCSD(T)) calculations are performed to obtain "benchmark" reaction energies without spin-orbit coupling. With zero-point energies removed, the "experimental" reaction energy is 44 ± 5 meV for HBr(+)((2)Π3/2) + CO2 → Br((2)P3/2) + HOCO(+), while the CCSD(T) value with spin-orbit effects included is 87 meV. Electronic structure calculations were performed to determine properties of the BrHOCO(+) reaction intermediate and [HBr⋯OCO](+) van der Waals intermediate. The results of different electronic structure methods were compared with those obtained with CCSD(T), and UMP2/cc-pVTZ/PP was found to be a practical and accurate QM method to use in QM/MM direct dynamics simulations. The spin-orbit coupling calculations show that the spin-free QM PES gives a quite good representation of the shape of the PES originated by (2)Π3/2HBr(+). This is also the case for the reactant region of the PES for (2)Π1/2 HBr(+), but spin-orbit coupling effects are important for the exit-channel region of this PES. A MM model was developed to represent these effects, which were combined with the spin-free QM PES.
Suzuki, I. H.; Kono, Y.; Ikeda, A.; Nagaoka, S.; Ouchi, T.; Ueda, K.; Takahashi, O.; Higuchi, I.; Tamenori, Y.
2010-10-15
Spectator resonant Auger-electron spectra have been measured in the Si 1s photoexcitation region of SiF{sub 4} using an electron spectroscopic technique combined with undulator radiation. A transition with the highest intensity in the total ion yield spectrum, which comes from excitation of a 1s electron into the 6t{sub 2} valence orbital, generates resonant Auger decays in which the excited electron remains predominantly in the valence orbital or is partly shaken up into a high-lying Rydberg orbital. The higher-lying peak generated through excitation into Rydberg orbitals induces resonant Auger decays in which the excited Rydberg electron is partly shaken up to a higher-lying Rydberg orbital or shaken down to a lower-lying valence molecular orbital. These findings exhibit a clear disentanglement effect among excited orbitals which are smeared out in the 1s electron excitation spectrum.
A Spectroscopic Search for Molecular Emission due to the Planets Orbiting 51 Peg and UPS And
NASA Astrophysics Data System (ADS)
Deming, D.; Bjoraker, G.; Wiedemann, G.
1997-12-01
We have calculated synthetic infrared (2-5 micron) spectra for the planets orbiting 51 Pegasus and Upsilon Andromeda. Our calculations assume these are gas-giant planets, wherein planetary methane absorbs stellar near-infrared flux, forming a hot planetary stratosphere. The planetary spectrum consists of emission in methane and carbon monoxide lines, which may be detectable superposed on the spectrum of the parent star. We describe the results of preliminary observations designed to detect these very weak features in the stellar spectra.
Free energy landscape and molecular pathways of gas hydrate nucleation
NASA Astrophysics Data System (ADS)
Bi, Yuanfei; Porras, Anna; Li, Tianshu
2016-12-01
Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), pB histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the pB histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.
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.
Song, Lingchun; Mo, Yirong; Gao, Jiali
2009-01-01
An effective Hamiltonian mixed molecular orbital and valence bond (EH-MOVB) method is described to obtain an accurate potential energy surface for chemical reactions. Building upon previous results on the construction of diabatic and adiabatic potential surfaces using ab initio MOVB theory, we introduce a diabatic-coupling scaling factor to uniformly scale the ab initio off-diagonal matrix element H(12) such that the computed energy of reaction from the EH-MOVB method is in agreement with the target value. The scaling factor is very close to unity, resulting in minimal alteration of the potential energy surface of the original MOVB model. Furthermore, the relative energy between the reactant and product diabatic states in the EH-MOVB method can be improved to match the experimental energy of reaction. A key ingredient in the EH-MOVB theory is that the off-diagonal matrix elements are functions of all degrees of freedom of the system and the overlap matrix is explicitly evaluated. The EH-MOVB method has been applied to the nucleophilic substitution reaction between hydrosulfide and chloromethane to illustrate the methodology and the results were matched to reproduce the results from ab initio valence bond self-consistent valence bond (VBSCF) calculations. The diabatic coupling (the off-diagonal matrix element in the generalized secular equation) has small variations along the minimum energy reaction path in the EH-MOVB model, whereas it shows a maximum value at the transition state and has nearly zero values in the regions of the ion-dipole complexes from VBSCF calculations. The difference in the diabatic coupling stabilization is attributed to the large overlap integral in the computationally efficient MOVB method.
NASA Astrophysics Data System (ADS)
Liu, Qihang; Zhang, Xiuwen; Waugh, J. A.; Dessau, D. S.; Zunger, Alex
2016-09-01
Associated with spin-orbit coupling (SOC) and inversion symmetry breaking, Rashba spin polarization opens an avenue for spintronic applications that was previously limited to ordinary magnets. However, spin-polarization effects in actual Rashba systems are far more complicated than what conventional single-orbital models would suggest. By studying via density functional theory and a multiorbital k .p model a three-dimensional bulk Rashba system (free of complications by surface effects), BiTeI, we find that the physical origin of the leading spin-polarization effects is SOC-induced hybridization between spin and multiple orbitals, especially those with nonzero orbital angular momenta. In this framework we establish a general understanding of the orbital mapping, common to the surface of topological insulators and the Rashba system. Consequently, the intrinsic mechanism of various spin-polarization effects—which pertain to all Rashba systems, even those with global inversion symmetry—is understood as a manifestation of the orbital textures. This finding suggests a route for designing high-spin-polarization materials by considering the atomic-orbital content.
NASA Technical Reports Server (NTRS)
1978-01-01
The costs and benefits of existing/planned systems, new propulsion concepts, and adaptations of existing/planned systems (as supported by Orbiter interface requirements and operations requirements) were quantified. Scenarios of these propulsion approaches were established which accommodate the low energy regime as defined by the new low energy payload mission model. These scenarios were screened on a cost and then a benefits basis. A propulsion approach comprising existing/planned systems and a new propulsion concept were selected as the most cost effective approach to accommodate the model payloads and the low energy regime they represent. Key cost drivers and sensitivity trends were identified. All costs were derived in 1977 dollars.
Energy versus free-energy conservation in first-principles molecular dynamics
NASA Astrophysics Data System (ADS)
Wentzcovitch, Renata M.; Martins, José Luís; Allen, Philip B.
1992-05-01
In applying first-principles molecular dynamics to metals, a fictitious temperature is usefully assigned to the electronic (Fermi-Dirac) occupation functions. This avoids instabilities associated with fluctuations in these occupations during the minimization of the energy density functional. Because these occupations vary with the ionic motion, they give rise to an extra contribution in addition to the usual Hellmann-Feynman forces. If this extra force is omitted, energy is not conserved. We point out, however, that ionic kinetic energy plus electronic free energy is conserved, and argue that this yields a sensible and realistic conservative dynamics.
Monte Carlo simulation of energy deposition by low-energy electrons in molecular hydrogen
NASA Technical Reports Server (NTRS)
Heaps, M. G.; Furman, D. R.; Green, A. E. S.
1975-01-01
A set of detailed atomic cross sections has been used to obtain the spatial deposition of energy by 1-20-eV electrons in molecular hydrogen by a Monte Carlo simulation of the actual trajectories. The energy deposition curve (energy per distance traversed) is quite peaked in the forward direction about the entry point for electrons with energies above the threshold of the electronic states, but the peak decreases and broadens noticeably as the electron energy decreases below 10 eV (threshold for the lowest excitable electronic state of H2). The curve also assumes a very symmetrical shape for energies below 10 eV, indicating the increasing importance of elastic collisions in determining the shape of the curve, although not the mode of energy deposition.
The properties of gamma-radiation and high-energy neutron fluxes in "MIR" station orbit.
Bogomolov, A V; Bogomolov, V V; Denisov, Yu I; Logachev, Yu I; Svertilov, S I; Kudryavtsev, M I; Lyagushin, V I; Ershova, T V
2002-10-01
The study of radiation background components in the near-Earth space is very important for different branches of space research, in particular for space dosimetry and for the planning of gamma-astronomy experiments. Detailed information on the neutral components (gamma-quanta, neutrons) of background radiation was obtained during the Grif-1 experiment onboard Mir orbital station (OS). The measurements of fluxes of 0.05-50 MeV gamma-quanta and >30 MeV neutrons with a large area instrument (approximately 250 cm2 for gamma-quanta, approximately 30 cm2 for neutrons) as well as corresponding charged particle measurements (0.4-1.5 MeV electrons, 1-200 MeV protons) were made during this experiment. The background components induced by the station's own radiation as well as the albedo gamma-rays from the Earth's atmosphere were revealed as the result of data analysis for about 600 h of observation. A mathematical model describing the latitude and energy dependences of atmospheric albedo gamma-rays as well as of those of gamma-quanta produced in the material of the station due to cosmic ray interactions was developed. An analytical approximation of the spectrum of induced gamma-rays from radioactive isotopes stored in the station and instrument's materials is presented. The dynamics of gamma-quantum background fluxes during the geomagnetic disturbances of January 10-11, 1997 are discussed. An analytical representation of the latitude dependence of the integral flux of neutrons with >30 MeV is given.
NASA Astrophysics Data System (ADS)
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.
Zobač, Vladimír; Lewis, James P; Abad, Enrique; Mendieta-Moreno, Jesús I; Hapala, Prokop; Jelínek, Pavel; Ortega, José
2015-05-08
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.
NASA Astrophysics Data System (ADS)
Pederzoli, Marek; Pittner, Jiří
2017-03-01
We present surface hopping dynamics on potential energy surfaces resulting from the spin-orbit splitting, i.e., surfaces corresponding to the eigenstates of the total electronic Hamiltonian including the spin-orbit coupling. In this approach, difficulties arise because of random phases of degenerate eigenvectors and possibility of crossings of the resulting mixed states. Our implementation solves these problems and allows propagation of the coefficients both in the representation of the spin free Hamiltonian and directly in the "diagonal representation" of the mixed states. We also provide a detailed discussion of the state crossing and point out several peculiarities that were not mentioned in the previous literature. We also incorporate the effect of the environment via the quantum mechanics/molecular mechanics approach. As a test case, we apply our methodology to deactivation of thiophene and selenophene in the gas phase, ethanol solution, and bulk liquid phase. First, 100 trajectories without spin-orbit coupling have been calculated for thiophene starting both in S1 and S2 states. A subset of 32 initial conditions starting in the S2 state was then used for gas phase simulations with spin-orbit coupling utilizing the 3-step integrator of SHARC, our implementation of the 3-step propagator in Newton-X and two new "one-step" approaches. Subsequently, we carried out simulations in ethanol solution and bulk liquid phase for both thiophene and selenophene. For both molecules, the deactivation of the S2 state proceeds via the ring opening pathway. The total population of triplet states reaches around 15% and 40% after 80 fs for thiophene and selenophene, respectively. However, it only begins growing after the ring opening is initiated; hence, the triplet states do not directly contribute to the deactivation mechanism. For thiophene, the resulting deactivation lifetime of the S2 state was 68 fs in the gas phase, 76 fs in ethanol solution, and 78 fs in the liquid phase
Park, Young Ran; Kim, Hyeong Jin; Hong, Young Joon E-mail: yjhong@sejong.ac.kr; Im, Sungjin; Shin, Koo E-mail: yjhong@sejong.ac.kr; Seo, Sunae; Choi, Won Kook
2016-01-11
We report the tailoring of the electronic structure of poly(N-vinylcarbazole) (PVK) using a mixture layer of polyaniline:poly(p-styrenesulfonic acid) (PANI:PSS) in organic multilayer PVK/PANI:PSS/poly(3,4-ethylenedioxythiophene):PSS heterojunctions. The overall electronic structure of the PVK overlayer was systematically down-shifted while the work function of PANI:PSS increased as a function of the PSS-to-PANI weight ratio for the ratio range from 1 to 11 in the PANI:PSS film. The down-shift in the highest occupied molecular orbital of PVK markedly reduced the hole injection barrier from PVK to quantum-dot (QD) layers in QD-light emitting diode (QD-LED) structures, resulting in superior electrical and electroluminescent characteristics for QD-LEDs. The influences of PANI:PSS thickness on the electronic structure of PVK and the performance of QD-LEDs are also discussed.
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)
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.
Tachikawa, Masanori; Kita, Yukiumi; Buenker, Robert J
2011-02-21
Characteristic features of the positron binding structure of some nitrile (-CN functional group) species such as acetonitrile, cyanoacetylene, acrylonitrile, and propionitrile are discussed with the configuration interaction scheme of multi-component molecular orbital calculations. This method can take the electron-positron correlation contribution into account through single electronic-single positronic excitation configurations. Our PA value of acetonitrile with the electronic 6-31++G(2df,2pd) and positronic [15s15p3d2f1g] basis set is calculated as 4.96 mhartree, which agrees to within 25% with the recent experimental value of 6.6 mhartree by Danielson et al. [Phys. Rev. Lett., 2010, 104, 233201]. Our PA values of acrylonitrile and propionitrile (5.70 and 6.04 mhartree) are the largest among these species, which is consistent with the relatively large dipole moments of the latter two systems.
Use of excess solar array power by regenerative fuel cell energy storage systems in low earth orbit
Hoberecht, M.A.; Green, R.D.
1997-12-31
Regenerative Fuel Cells (RFC`s) are a competing energy storage system technology for a number of low-earth-orbit applications. The system is comprised of an electrolyzer which utilizes solar array power to convert water into hydrogen and oxygen reactants, a fuel cell that recombines the reactants back into water and produces power during eclipse, and associated controls and reactant storage. Round-trip electrical efficiencies of RFC systems are typically lower than competing battery energy storage systems. This results in larger solar arrays for the same application, with inherent drag, mass, and cost penalties. However, the increase in solar array size can be limited, if not totally eliminated, because of the ability of RFC systems to use excess solar array power. For this paper, the International Space Station (ISS) application was chosen for evaluation and comparison of battery and RFC energy storage systems. This selection was based on the authors` familiarity with the ISS design and the availability of a detailed in-house computer model specific to the ISS electrical power system (SPACE). Combined altitude and orientation effects, seasonal variations, and beginning-of-life solar array performance were examined for individual orbits at and above specified reference points. Charging characteristics of the battery system were also investigated. The evaluation allowed a comparison of the solar array size required with the existing battery energy storage system to the projected solar array size required with a possible RFC system. The results of the examination indicated that no increase in solar array size would be necessary for the ISS if outfitted with a RFC energy storage system, in spite of the lower round-trip electrical efficiency. For orbits with a minimum of excess power, the battery energy storage system used only 73% of the available solar array power as compared to 100% usage for a RFC system. The usage by the battery system was far less for the orbits
Energy conservation in molecular dynamics simulations of classical systems.
Toxvaerd, Søren; Heilmann, Ole J; Dyre, Jeppe C
2012-06-14
Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete "Verlet" algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence of a "shadow Hamiltonian" H [S. Toxvaerd, Phys. Rev. E 50, 2271 (1994)], i.e., a Hamiltonian close to the original H with the property that the discrete positions of the Verlet algorithm for H lie on the analytic trajectories of H. The shadow Hamiltonian can be obtained from H by an asymptotic expansion in the time step length. Here we use the first non-trivial term in this expansion to obtain an improved estimate of the discrete values of the energy. The investigation is performed for a representative system with Lennard-Jones pair interactions. The simulations show that inclusion of this term reduces the standard deviation of the energy fluctuations by a factor of 100 for typical values of the time step length. Simulations further show that the energy is conserved for at least one hundred million time steps provided the potential and its first four derivatives are continuous at the cutoff. Finally, we show analytically as well as numerically that energy conservation is not sensitive to round-off errors.
Forces on nuclei moving on autoionizing molecular potential energy surfaces.
Moiseyev, Nimrod
2017-01-14
Autoionization of molecular systems occurs in diatomic molecules and in small biochemical systems. Quantum chemistry packages enable calculation of complex potential energy surfaces (CPESs). The imaginary part of the CPES is associated with the autoionization decay rate, which is a function of the molecular structure. Molecular dynamics simulations, within the framework of the Born-Oppenheimer approximation, require the definition of a force field. The ability to calculate the forces on the nuclei in bio-systems when autoionization takes place seems to rely on an understanding of radiative damages in RNA and DNA arising from the release of slow moving electrons which have long de Broglie wavelengths. This work addresses calculation of the real forces on the nuclei moving on the CPES. By using the transformation of the time-dependent Schrödinger equation, previously used by Madelung, we proved that the classical forces on nuclei moving on the CPES correlated with the gradient of the real part of the CPES. It was proved that the force on the nuclei of the metastable molecules is time independent although the probability to detect metastable molecules exponentially decays. The classical force is obtained from the transformed Schrödinger equation when ℏ=0 and the Schrödinger equation is reduced to the classical (Newtonian) equations of motion. The forces on the nuclei regardless on what potential energy surface they move (parent CPES or product real PESs) vary in time due to the autoionization process.
Selective excitation, relaxation, and energy channeling in molecular systems
Rhodes, W.C.
1993-08-01
Research involves theoretical studies of response, relaxation, and correlated motion in time-dependent behavior of large molecular systems ranging from polyatomic molecules to protein molecules in their natural environment. Underlying theme is subsystem modulation dynamics. Main idea is that quantum mechanical correlations between components of a system develop with time, playing a major role in determining the balance between coherent and dissipative forces. Central theme is interplay of coherence and dissipation in determining the nature of dynamic structuring and energy flow in molecular transformation mechanisms. Subsystem equations of motion are being developed to show how nonlinear, dissipative dynamics of a particular subsystem arise from correlated interactions with the rest of the system (substituent groups, solvent, lattice modes, etc.); one consequence is resonance structures and networks. Quantum dynamics and thermodynamics are being applied to understand control and energy transfer mechanisms in biological functions of protein molecules; these mechanisms are both global and local. Besides the above theory, the research deals with phenomenological aspects of molecular systems.
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.
Molecular ion sources for low energy semiconductor ion implantation (invited)
Hershcovitch, A.; Gushenets, V. I.; Bugaev, A. S.; Oks, E. M.; Vizir, A.; Yushkov, G. Yu.; Seleznev, D. N.; Kulevoy, T. V.; Kozlov, A.; Kropachev, G. N.; Kuibeda, R. P.; Minaev, S.; Dugin, S.; Alexeyenko, O.
2016-02-15
Smaller semiconductors require shallow, low energy ion implantation, resulting space charge effects, which reduced beam currents and production rates. To increase production rates, molecular ions are used. Boron and phosphorous (or arsenic) implantation is needed for P-type and N-type semiconductors, respectively. Carborane, which is the most stable molecular boron ion leaves unacceptable carbon residue on extraction grids. A self-cleaning carborane acid compound (C{sub 4}H{sub 12}B{sub 10}O{sub 4}) was synthesized and utilized in the ITEP Bernas ion source resulting in large carborane ion output, without carbon residue. Pure gaseous processes are desired to enable rapid switch among ion species. Molecular phosphorous was generated by introducing phosphine in dissociators via 4PH{sub 3} = P{sub 4} + 6H{sub 2}; generated molecular phosphorous in a pure gaseous process was then injected into the HCEI Calutron-Bernas ion source, from which P{sub 4}{sup +} ion beams were extracted. Results from devices and some additional concepts are described.
NASA Astrophysics Data System (ADS)
Ayyappan, S.; Sundaraganesan, N.; Aroulmoji, V.; Murano, E.; Sebastian, S.
2010-09-01
The FT-IR and FT-Raman spectral studies of the Methotrexate (MTX) were carried out. The equilibrium geometry, various bonding features and harmonic vibrational frequencies of MTX have been investigated with the help of B3LYP density functional theory (DFT) using 6-31G(d) as basis set. Detailed analysis of the vibrational spectra has been made with the aid of theoretically predicted vibrational frequencies. The vibrational analysis confirms the differently acting ring modes, steric repulsion, conjugation and back-donation. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) results complement with the experimental findings. The calculated HOMO and LUMO energies show that charge transfer occur within the molecule. Good correlations between the experimental 1H and 13C NMR chemical shifts in DMSO solution and calculated GIAO shielding tensors were found.
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.
Photochemical energy conversion: from molecular dyads to solar cells.
Durrant, James R; Haque, Saif A; Palomares, Emilio
2006-08-21
Photochemical approaches to solar energy conversion are currently making rapid progress, increasing not only academic but also commercial interest in molecular-based photovoltaic solar cells. This progress has been achieved not only by increased understanding of the physics and physical chemistry of device function but also through advances in chemical and materials synthesis and processing, which now allows the design and fabrication of increasingly sophisticated device structures organised on the nanometer length scale. In this feature article, we review some progress in this field, focusing in particular upon the electron-transfer dynamics which underlie the function of dye-sensitised, nanocrystalline solar cells. The article starts by building upon the parallels between the function of such devices and the function of simple donor/acceptor molecular systems in solution. We then go on to discuss the optimisation of device function, and in particular the use of self-assembly-based strategies to control interfacial electron-transfer kinetics.
Electronic excitation of molecular hydrogen by low-energy electrons
NASA Astrophysics Data System (ADS)
Hargreaves, Leigh
2016-09-01
Molecular hydrogen is the most abundant element in the universe, particularly in interstellar plasmas such as atmospheres of gas giant planets and stars. Electron collision data for hydrogen is critical to interpreting the spectroscopy of interstellar objects, as well as being of applied value for modelling technological plasmas. Hydrogen is also fundamentally interesting, as while highly accurate wave functions for this simple molecule are available, providing an accurate, ab initio, treatment the collision dynamics has proven challenging, on account of the need to have a complete description of channel coupling and polarization effects. To date, no single theoretical approach has been able to replicate experimental results across all transitions and incident energies, while the experimental database that is available is far from complete and not all available measurements are in satisfactory agreement. In this talk, we present differential and integral cross section measurements for electronic excitation cross sections for molecular hydrogen by low-energy electron impact. The data were measured at incident energies below 20eV, using a well-tested crossed beam apparatus and employing a moveable gas source approach to ensure that background contributions to the scattering are accurately accounted for. These measurements are compared with new theoretical results employing the convergent close coupling approach.
Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation
NASA Astrophysics Data System (ADS)
Polyak, Iakov; Benighaus, Tobias; Boulanger, Eliot; Thiel, Walter
2013-08-01
The dual Hamiltonian free energy perturbation (DH-FEP) method is designed for accurate and efficient evaluation of the free energy profile of chemical reactions in quantum mechanical/molecular mechanical (QM/MM) calculations. In contrast to existing QM/MM FEP variants, the QM region is not kept frozen during sampling, but all degrees of freedom except for the reaction coordinate are sampled. In the DH-FEP scheme, the sampling is done by semiempirical QM/MM molecular dynamics (MD), while the perturbation energy differences are evaluated from high-level QM/MM single-point calculations at regular intervals, skipping a pre-defined number of MD sampling steps. After validating our method using an analytic model potential with an exactly known solution, we report a QM/MM DH-FEP study of the enzymatic reaction catalyzed by chorismate mutase. We suggest guidelines for QM/MM DH-FEP calculations and default values for the required computational parameters. In the case of chorismate mutase, we apply the DH-FEP approach in combination with a single one-dimensional reaction coordinate and with a two-dimensional collective coordinate (two individual distances), with superior results for the latter choice.
NASA Astrophysics Data System (ADS)
O'Brien, James F.; Haworth, Daniel T.
2001-01-01
A student exercise employing semiempirical molecular orbital calculations in the area of organometallic chemistry is presented. PM3 level calculations are applied to the ground-state structures of C6H6)Cr(CO)3 and (B3N3H6)Cr(CO)3. The calculations are generally successful in computing the known features of the ground-state structures. Comparison of the geometries computed for free and complexed C6H6 and B3N3H6 allow discussion of the reasons for the changes observed. The structures of the transition states for rotation of the rings with respect to Cr(CO)3 are also computed. These results permit calculation of the activation energies for the ring rotations. The activation energies computed at the PM3 level are 0.4 and 18.3 kcal/mol for (C6H6)Cr(CO)3 and (B3N3H6)Cr(CO)3, respectively. These results highlight the differences between the two molecules. Students are encouraged to comment on structural changes in the rings, on the phenomenon of ring rotation in these systems and others such as ferrocene, on the question of the aromaticity of the borazine ring, and on the effect of p back-bonding on the positions of the carbonyl stretching bands in the both complexes.
Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm
NASA Technical Reports Server (NTRS)
Darve, Eric; Wilson, Micahel A.; Pohorille, Andrew
2000-01-01
One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous
Infrared spectroscopy of molecular ions in selected rotational and spin-orbit states
NASA Astrophysics Data System (ADS)
Jacovella, U.; Agner, J. A.; Schmutz, H.; Deiglmayr, J.; Merkt, F.
2016-07-01
First results are presented obtained with an experimental setup developed to record IR spectra of rotationally state-selected ions. The method we use is a state-selective version of a method developed by Schlemmer et al. [Int. J. Mass Spectrom. 185, 589 (1999); J. Chem. Phys. 117, 2068 (2002)] to record IR spectra of ions. Ions are produced in specific rotational levels using mass-analyzed-threshold-ionization spectroscopy. The state-selected ions generated by pulsed-field ionization of Rydberg states of high principal quantum number (n ≈ 200) are extracted toward an octupole ion guide containing a neutral target gas. Prior to entering the octupole, the ions are excited by an IR laser. The target gas is chosen so that only excited ions react to form product ions. These product ions are detected mass selectively as a function of the IR laser wavenumber. To illustrate this method, we present IR spectra of C 2 H2 + in selected rotational levels of the 2Πu,3/2 and 2Πu,1/2 spin-orbit components of the vibronic ground state.
Arun, K. G.; Iyer, Bala R.; Qusailah, Moh'd S. S.
2008-03-15
The far-zone flux of energy contains hereditary (tail) contributions that depend on the entire past history of the source. Using the multipolar post-Minkowskian wave generation formalism, we propose and implement a semianalytical method in the frequency domain to compute these contributions from the inspiral phase of a binary system of compact objects moving in quasi-elliptical orbits up to third post-Newtonian (3PN) order. The method explicitly uses the quasi-Keplerian representation of elliptical orbits at 1PN order and exploits the doubly periodic nature of the motion to average the 3PN fluxes over the binary's orbit. Together with the instantaneous (nontail) contributions evaluated in a companion paper, it provides crucial inputs for the construction of ready-to-use templates for compact binaries moving on quasi-elliptic orbits, an interesting class of sources for the ground-based gravitational-wave detectors such as LIGO and Virgo, as well as space-based detectors like LISA.
Zhang Shichang
2010-05-15
Nonlinear model and simulation technique of the interaction and energy transfer between a fast wave and a large-orbit relativistic electron beam in a coaxial electrostatic wiggler are presented. Unlike the situations in a magnetostatic-wiggler free-electron laser (MWFEL) and in an electron cyclotron maser (ECM), the electrostatic potential of the electrons plays an important role and participates in the energy exchange between the wave and the electron beam. Compared to MWFEL and ECM, the coaxial electrostatic-wiggler configuration has a distinguishing peculiarity that besides the electron-beam's kinetic energy, its electrostatic potential energy can be effectively transferred to the fast wave. Simulation shows that wave could be amplified with ultrahigh gain by extracting both the kinetic energy and electrostatic potential energy of the electron beam.
Wang, Z. H.; Zheng, Q.; Wang, Xiaoguang; Li, Yong
2016-01-01
We study the energy-level crossing behavior in a two-dimensional quantum well with the Rashba and Dresselhaus spin-orbit couplings (SOCs). By mapping the SOC Hamiltonian onto an anisotropic Rabi model, we obtain the approximate ground state and its quantum Fisher information (QFI) via performing a unitary transformation. We find that the energy-level crossing can occur in the quantum well system within the available parameters rather than in cavity and circuit quantum eletrodynamics systems. Furthermore, the influence of two kinds of SOCs on the QFI is investigated and an intuitive explanation from the viewpoint of the stationary perturbation theory is given. PMID:26931762
Wang, Z H; Zheng, Q; Wang, Xiaoguang; Li, Yong
2016-03-02
We study the energy-level crossing behavior in a two-dimensional quantum well with the Rashba and Dresselhaus spin-orbit couplings (SOCs). By mapping the SOC Hamiltonian onto an anisotropic Rabi model, we obtain the approximate ground state and its quantum Fisher information (QFI) via performing a unitary transformation. We find that the energy-level crossing can occur in the quantum well system within the available parameters rather than in cavity and circuit quantum eletrodynamics systems. Furthermore, the influence of two kinds of SOCs on the QFI is investigated and an intuitive explanation from the viewpoint of the stationary perturbation theory is given.
Liu, Zheng-Fang; Wu, Qing-Ping E-mail: aixichen@ecjtu.jx.cn; Chen, Ai-Xi E-mail: aixichen@ecjtu.jx.cn; Xiao, Xian-Bo; Liu, Nian-Hua
2014-05-28
We investigate the possibility of spin polarization in graphene. The result shows that a spin energy gap can be opened in the presence of both spin-orbit coupling and strain. We find that high spin polarization with large spin-polarized current is achieved in the spin energy gap. However, only one of the two modulations is present, no spin polarization can be generated. So the combination of the two modulations provides a way to design tunable spin polarization without need for a magnetic element or an external magnetic field.
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.
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; Sauer, Stephan P A; Provasi, Patricio F
2014-10-21
We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the (1)J(C-H) coupling constant of CH4 using a decomposition into contributions from localized molecular orbitals and compare with the (1)J(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.
Electronic Structure and Lubrication Properties of MoS2: a Qualitative Molecular Orbital Approach
1990-03-21
ELEMENT NO. NO. NO. ACCESSION NO. 11 TITLE (Include Security Classification) Electronic Structure and Lubrication Properties of MoS2 : A Qualitative...assign peaks in t~e’ valence-level photoelectron spectrum (VLPS) and the electron energy loss spectrum of MoS2 (0001) and to interpret the effects of ion...energy levels in the MO diagram. Variations in crystal lattice spacing within sputter-deposited MoS2 films are explained in terms of electron density
NASA Technical Reports Server (NTRS)
1978-01-01
A payload mission model covering 129 launches, was examined and compared against the space transportation system shuttle standard orbit inclinations and a shuttle launch site implementation schedule. Based on this examination and comparison, a set of six reference missions were defined in terms of spacecraft weight and velocity requirements to deliver the payload from a 296 km circular Shuttle standard orbit to the spacecraft's planned orbit. Payload characteristics and requirements representative of the model payloads included in the regime bounded by each of the six reference missions were determined. A set of launch cost envelopes were developed and defined based on the characteristics of existing/planned Shuttle upper stages and expendable launch systems in terms of launch cost and velocity delivered. These six reference missions were used to define the requirements for the candidate propulsion modes which were developed and screened to determine the propulsion approaches for conceptual design.
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.
Lyu, Yan; Fang, Yuan; Miao, Qingqing; Zhen, Xu; Ding, Dan; Pu, Kanyi
2016-04-26
Optical theranostic nanoagents that seamlessly and synergistically integrate light-generated signals with photothermal or photodynamic therapy can provide opportunities for cost-effective precision medicine, while the potential for clinical translation requires them to have good biocompatibility and high imaging/therapy performance. We herein report an intraparticle molecular orbital engineering approach to simultaneously enhance photoacoustic brightness and photothermal therapy efficacy of semiconducting polymer nanoparticles (SPNs) for in vivo imaging and treatment of cancer. The theranostic SPNs have a binary optical component nanostructure, wherein a near-infrared absorbing semiconducting polymer and an ultrasmall carbon dot (fullerene) interact with each other to induce photoinduced electron transfer upon light irradiation. Such an intraparticle optoelectronic interaction augments heat generation and consequently enhances the photoacoustic signal and maximum photothermal temperature of SPNs by 2.6- and 1.3-fold, respectively. With the use of the amplified SPN as the theranostic nanoagent, it permits enhanced photoacoustic imaging and photothermal ablation of tumor in living mice. Our study thus not only introduces a category of purely organic optical theranostics but also highlights a molecular guideline to amplify the effectiveness of light-intensive imaging and therapeutic nanosystems.
NASA Astrophysics Data System (ADS)
An, Zhenlian; Kamezawa, Chihiro; Hirai, Masaaki; Kusaka, Masahiko; Iwami, Motohiro
2002-12-01
A systematic study of the valence band structure of Cu3Si has been performed by soft X-ray emission spectroscopy and a first-principle molecular orbital calculation using the discrete-variational (DV)-Xα cluster model. The existence of Cu 4s, 4p states in the valence band and their important contributions to the valence band as that of Cu 3d are indicated together with previously reported ones. The high-binding energy peak in the Si L2,3 emission spectrum is considered to originate mainly from the Si-Si 3s bonding state but also have a certain contribution of Si 3s bonding state with Cu 4s, 4p. On the other hand, the low-binding energy peaks in the Si L2,3 emission band are attributed to both the antibonding states of Si 3s and the bonding states of Si 3d with Cu 4s, 4p and Cu 3d. The bonding states of Si 3s with Cu 4s, 4p and Cu 3d are expected to exist in the lower part of the valence band for η\\prime-Cu3Si on the basis of the theoretical calculations. As for Si p states, the high-binding energy peak and the low-binding energy peak in the Si Kβ emission spectrum should be attributed to the Si 3p bonding state and antibonding state with Cu 3d and Cu 4s, 4p, respectively, according to the theoretical calculations. A comparison is made between experimental spectra and theoretical density of states.
Optimal composition of atomic orbital basis sets for recovering static correlation energies.
Wallace, Andrew J; Crittenden, Deborah L
2014-03-20
Static correlation energies (Estat) are calculated in a range of basis sets for a chemically diverse collection of atoms and molecules. The reliability of a basis set in capturing Estat is assessed according to the following: mean and maximum absolute deviations from near-exact Estat estimates, monotonic convergence to the complete basis set limit, and ability to capture Estat accurately independent of changes in geometry, molecular size, and electronic configuration. Within the polarization and correlation-consistent basis set series, triple-ζ basis sets are the smallest that can reliably capture Estat. The cc-pVTZ basis set performs particularly well, recovering Estat to chemical accuracy for all atoms and molecules in our data set. A series of customized basis sets are constructed by stripping polarization functions from, and swapping polarization functions among, existing basis sets. Basis sets without polarization functions are incapable of accurately recovering Estat. Basis sets with a near-complete set of s, p, and d functions can approach chemical accuracy in maximum absolute error. However, this may be achieved at lower computational cost by using a well balanced triple-ζ basis set including f functions, along with a smaller number of s, p, and d functions. Recommended basis sets for calculating Estat with increasing accuracy at increasing computational cost are 6-311G(2d,2p), cc-pVTZ, and cc-pVQZ stripped of g functions.
Superintermolecular orbitals in the C60-pentacene complex
NASA Astrophysics Data System (ADS)
Zhang, G. P.; Gardner, A.; Latta, T.; Drake, K.; Bai, Y. H.
2016-12-01
We report a group of unusually big molecular orbitals in the C60-pentacene complex. Our first-principles density-functional calculation shows that these orbitals are very delocalized and cover both C60 and pentacene, which we call superintermolecular orbitals (SIMOs). Their spatial extension can reach 1 nm or larger. Optically, SIMOs are dark. Different from ordinary unoccupied molecular orbitals, SIMOs have a very weak Coulomb and exchange interaction. Their energy levels are very similar to the native superatomic molecular orbitals in C60and can be approximately characterized by orbital angular momentum quantum numbers. They have a distinctive spatial preference. These features fit the key characters of charge-generation states that channel initially bound electrons and holes into free-charge carriers. Thus, our finding is important for C60-pentacene photovoltaics.
Molecular understanding of mutagenicity using potential energy methods
Broyde, S.; Shapiro, R.
1992-07-01
Our objective, has been to elucidate on a molecular level, at atomic resolution, the structures of DNAs modified by 2-aminofluorene and its N-acetyl derivative, 2-acetylaminofluorene (AAF). The underlying hypothesis is that DNA replicates with reduced fidelity when its normal right-handed B-structure is altered, and one result is a higher mutation rate. This change in structure may occur normally at a low incidence, for example by the formation of hairpin loops in appropriate sequences, but it may be enhanced greatly after covalent modification by a mutagenic substance. We use computational methods and have been able to incorporate the first data from NMR studies in our calculations. Computational approaches are important because x-ray and spectroscopic studies have not succeeded in producing atomic resolution views of mutagen and carcinogen-oligonucleotide adducts. The specific methods that we employ are minimized potential energy calculations using the torsion angle space molecular mechanics program DUPLEX to yield static views. Molecular dynamics simulations, with full solvent and salt, of the important static structures are carried out with the program AMBER; this yields mobile views in a medium that mimics the natural aqueous environment of the cell as well as can be done with current available computing resources.
Zhou, Miao; Ming, Wenmei; Liu, Zheng; ...
2014-11-19
For potential applications in spintronics and quantum computing, it is desirable to place a quantum spin Hall insulator [i.e., a 2D topological insulator (TI)] on a substrate while maintaining a large energy gap. Here, we demonstrate a unique approach to create the large-gap 2D TI state on a semiconductor surface, based on first-principles calculations and effective Hamiltonian analysis. We show that when heavy elements with strong spin orbit coupling (SOC) such as Bi and Pb atoms are deposited on a patterned H-Si(111) surface into a hexagonal lattice, they exhibit a 2D TI state with a large energy gap of ≥0.5more » eV. The TI state arises from an intriguing substrate orbital filtering effect that selects a suitable orbital composition around the Fermi level, so that the system can be matched onto a four-band effective model Hamiltonian. Furthermore, it is found that within this model, the SOC gap does not increase monotonically with the increasing strength of SOC. These interesting results may shed new light in future design and fabrication of large-gap topological quantum states.« less
Zhou, Miao; Ming, Wenmei; Liu, Zheng; Wang, Zhengfei; Yao, Yugui; Liu, Feng
2014-11-19
For potential applications in spintronics and quantum computing, it is desirable to place a quantum spin Hall insulator [i.e., a 2D topological insulator (TI)] on a substrate while maintaining a large energy gap. Here, we demonstrate a unique approach to create the large-gap 2D TI state on a semiconductor surface, based on first-principles calculations and effective Hamiltonian analysis. We show that when heavy elements with strong spin orbit coupling (SOC) such as Bi and Pb atoms are deposited on a patterned H-Si(111) surface into a hexagonal lattice, they exhibit a 2D TI state with a large energy gap of ≥0.5 eV. The TI state arises from an intriguing substrate orbital filtering effect that selects a suitable orbital composition around the Fermi level, so that the system can be matched onto a four-band effective model Hamiltonian. Furthermore, it is found that within this model, the SOC gap does not increase monotonically with the increasing strength of SOC. These interesting results may shed new light in future design and fabrication of large-gap topological quantum states.
NASA Astrophysics Data System (ADS)
Lüchow, Arne; Fink, Reinhold F.
2000-11-01
While the diffusion quantum Monte Carlo method (DQMC) is capable, in principle, of calculating exact ground state energies, in practice the fixed-node (FN) approximation leads to node location errors which make FN-DQMC energies upper bounds. It is shown that the node location error can be reduced systematically and without prohibitive increase of computer time requirements by using nodes derived from pair natural orbital CI wave functions (PNO-CI). The reduction is demonstrated for the N atom and the molecules N2 and H2O. With the DQMC/PNOCI method, we obtain a variational energy of -109.520(3) H for the N2 molecule and -76.429(1) H for the ground state of the water molecule which is only 22 and 9 mH above the estimated nonrelativistic ground state energy, respectively.
M + Ng potential energy curves including spin-orbit coupling for M = K, Rb, Cs and Ng = He, Ne, Ar.
Blank, L; Weeks, David E; Kedziora, Gary S
2012-03-28
The X(2)Σ(1/2)(+), A(2)Π(1∕2), A(2)Π(3∕2), and B(2)Σ(1/2)(+) potential energy curves and associated dipole matrix elements are computed for M + Ng at the spin-orbit multi-reference configuration interaction level, where M = K, Rb, Cs and Ng = He, Ne, Ar. Dissociation energies and equilibrium positions for all minima are identified and corresponding vibrational energy levels are computed. Difference potentials are used together with the quasistatic approximation to estimate the position of satellite peaks of collisionally broadened D2 lines. The comparison of potential energy curves for different alkali atom and noble gas atom combinations is facilitated by using the same level of theory for all nine M + Ng pairs.
Pogni, Rebecca; Basosi, Riccardo; Donati, Alessandro; Rossi, Claudio; Sabadini, Luciano; Rollo, Libertario; Lorenzini, Sauro; Gelli, Renata; Marcolongo, Roberto
1995-01-01
rates of neutral, zwitterionic and anionic piroxicam, in DMSO solution are explained by the thermal equilibrium between the three most stable structures of the three forms, thus confirming the high quality of the force field. The EPR spectrum of [CuII(Pir)2(DMF)2] (DMSO/GLY, 2:1, v/v, 298 and 110 K) agrees with a N2O2+O2 pseudo-octahedral coordination geometry. The EPR spectrum of [CuII(Pir)2·0.5DMF agrees with a pseudo-tetrahedral coordination geometry. The parameters extracted from the room temperature spectra of the solution phases are in agreement with the data reported for powder and frozen solutions. The extended-Hückel calculations on minimum energy structures of [CuII(Pir)2(DMF)2] and [CuII(Pir)2] (square planar) revealed that the HOMOs have a relevant character of dx2−y2. On the other hand the HOMO of a computer generated structure for [CuII(Pir)2] (pseudo-tetrahedral) has a relevant character of dxy atomic orbital. A dxy orbital is better suited to allow a dπ-pπ interaction to the O2- anion. Therefore this work shows that the anti-inflammatory activity of piroxicam could be due in part to the formation of [CuII(Pir)2] chelates, which can exert a SOD-like activity. PMID:18472745
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.
Camera for detection of cosmic rays of energy more than 10 Eev on the ISS orbit
NASA Astrophysics Data System (ADS)
Garipov, G. K.; Khrenov, B. A.; Nikitsky, V. P.; Panasyuk, M. I.; Saprykin, O. A.; Sholokhov, A. V.; Syromyatnikov, V. S.
1998-06-01
Concept of the EHE CR observation from the ISS orbit is discussed. A design of the camera at the Russian segment of the ISS comprising a large area (60 m2) parabolic mirror with a photo multiplier pixel retina in its focal plane is described.
Nodular Fasciitis of the Orbit: A Case Report Confirmed by Molecular Cytogenetic Analysis.
Anzeljc, Andrew J; Oliveira, Andre M; Grossniklaus, Hans E; Kim, Hee Joon; Hayek, Brent
2016-02-12
Nodular fasciitis is a benign fibroblastic proliferation typically found in the subcutaneous tissue or superficial fascia of the extremities that is often confused for malignancy. These lesions rarely occur on the eyelids and ocular adnexa and are seldom analyzed by ophthalmic pathologists. USP6 gene rearrangement has been recently demonstrated in nodular fasciitis and this rearrangement may lead to the formation of a fusion gene MYH9-USP6 in some cases. Herein, the authors describe a 38-year-old woman with a 6-month history of a progressively enlarging mass beneath her right medial upper eyelid. Histopathologic analysis of the excisional biopsy confirmed classic features of nodular fasciitis. Molecular cytogenetic analysis revealed a rearrangement of the USP6 locus, confirming the diagnosis of benign nodular fasciitis.
NASA Technical Reports Server (NTRS)
Zweibel, Ellen G.; Mckee, Christopher F.
1995-01-01
Molecular clouds are observed to be partially supported by turbulent pressure. The kinetic energy of the turbulence is directly measurable, but the potential energy, which consists of magnetic, thermal, and gravitational potential energy, is largly unseen. We have extended previous results on equipartition between kinetic and potential energy to show that it is likely to be a very good approximation in molecular clouds. We have used two separate approaches to demonstrate this result: For small-amplitude perturbations of a static equilibrium, we have used the energy principle analysis of Bernstein et al. (1958); this derivation applies to perturbations of arbitary wavelength. To treat perturbations of a nonstatic equilibrium, we have used the Lagrangian analysis of Dewar (1970); this analysis applies only to short-wavelength perturbations. Both analysis assume conservation of energy. Wave damping has only a small effect on equipartition if the wave frequency is small compared to the neutral-ion collision frequency; for the particular case we considered, radiative losses have no effect on equipartition. These results are then incorporated in a simple way into analyses of cloud equilibrium and global stability. We discuss the effect of Alfvenic turbulence on the Jeans mass and show that it has little effect on the magnetic critical mass.
NASA Astrophysics Data System (ADS)
Fujimori, A.; Minami, F.; Tsuda, N.
1980-10-01
Electronic energy bands have been calculated for CeH2 and CeH3 using the augmented-plane-wave method and have been fitted by the linear-combination-of-atomic-orbitals interpolation scheme. The partial densities of states and the numbers of electrons on atomic orbitals indicate that hydrogen in CeH2 is almost anionlike. When going from CeH2 to CeH3, shallow bonding levels are found to form between the third hydrogen state and conduction electrons of CeH2, other features of CeH2 being little affected by it. Thus the rare-earth dihydrides are regarded as ionic compounds similar to the saline-element dihydrides except for the presence of d-like conduction electrons.
Iuchi, Satoru Koga, Nobuaki
2014-01-14
With the aim of exploring excited state dynamics, a model electronic Hamiltonian for several low-lying d−d states of [Fe(bpy){sub 3}]{sup 2+} complex [S. Iuchi, J. Chem. Phys. 136, 064519 (2012)] is refined using density-functional theory calculations of singlet, triplet, and quintet states as benchmarks. Spin−orbit coupling elements are also evaluated within the framework of the model Hamiltonian. The accuracy of the developed model Hamiltonian is determined by examining potential energies and spin−orbit couplings at surface crossing regions between different spin states. Insights into the potential energy surfaces around surface crossing regions are also provided through molecular dynamics simulations. The results demonstrate that the constructed model Hamiltonian can be used for studies on the d−d excited state dynamics of [Fe(bpy){sub 3}]{sup 2+}.
Zhang, R L; Qi, D X; Wang, D L; Li, J; Peng, R W; Huang, R S; Wang, Mu
2013-02-01
In this work, we theoretically investigate the spin-split energy bands of electrons and spin-polarized transport in two-dimensional (2D) spin-orbit lateral superlattices (SOLSLs), where the square rods with Rashba spin-orbit coupling (SOC) are distributed periodically by applying gate voltages on the semiconductor. Within the Landauer framework of ballistic transport, the energy bands, the electrical conductance, the spin polarization and the spin-dependent electronic charge distributions have been calculated. It is found that the energy minibands are formed and the energy levels are split up by the Rashba SOC. As a result, the spin-polarized conductance is obtained even in the absence of external magnetic fields and magnetic materials. Meanwhile, the spin polarization can approach high values in the SOLSLs by manipulating the strength of SOC. Furthermore, the spin-dependent electronic charge distributions have been obtained, which present a clear picture of spin-polarized conductance. Our investigations have the potential applications in spin-based quantum devices and semiconductor spintronics.
NASA Technical Reports Server (NTRS)
Bagus, P. S.; Bauschlicher, C. W., Jr.; Nelin, C. J.; Laskowski, B. C.; Seel, M.
1984-01-01
The interaction of CO with Cu5, Ni5, and Al4 are treated as model systems for molecular adsorption on metal surfaces. The effect of the use of pseudopotentials for the metal atoms is studied by considering three types of clusters. In the first case, all of the metal electrons are explicitly included in the wave function; an all electron (AE) treatment. In the second case, the metal atom which directly interacts with the CO is described by AE but the remaining metal atoms include a pseudopotential for their core electrons. Finally, in the third case, all of the metal atoms in the cluster have a pseudopotential treatment for the core electrons. The AE cluster results are taken as reference values for the two pseudopotential treatments. The mixed cluster results are in excellent agreement with those of the all AE clusters; however, the results for the all pseudopotential cluster of Ni5CO or of Cu5CO are qualitatively different. The pseudopotential treatment for all of the metal atoms often leads to results that contain serious errors and it is not a reliable approach.
Zhang, Huaiyu; Danovich, David; Wu, Wei; Braïda, Benoît; Hiberty, Philippe C; Shaik, Sason
2014-06-10
The charge-shift bonding (CSB) concept was originally discovered through valence bond (VB) calculations. Later, CSB was found to have signatures in atoms-in-molecules and electron-localization-function and in experimental electron density measurements. However, the CSB concept has never been derived from a molecular orbital (MO)-based theory. We now provide a proof of principle that an MO-based approach enables one to derive the CSB family alongside the distinctly different classical family of covalent bonds. In this bridging energy decomposition analysis, the covalent-ionic resonance energy, RECS, of a bond is extracted by cloning an MO-based purely covalent reference state, which is a constrained two-configuration wave function. The energy gap between this reference state and the variational TCSCF ground state yields numerical values for RECS, which correlate with the values obtained at the VBSCF level. This simple MO-based method, which only takes care of static electron correlation, is already sufficient for distinguishing the classical covalent or polar-covalent bonds from charge-shift bonds. The equivalence of the VB and MO-based methods is further demonstrated when both methods are augmented by dynamic correlation. Thus, it is shown from both MO and VB perspectives that the bonding in the CSB family does not arise from electron correlation. Considering that the existence of the CSB family is associated also with quite a few experimental observations that we already reviewed ( Shaik , S. , Danovich , D. , Wu , W. , and Hiberty , P. C. Nat. Chem. , 2009 , 1 , 443 - 449 ), the new bonding concept has passed by now two stringent tests. This derivation, on the one hand, supports the new concept and on the other, it creates bridges between the two main theories of electronic structure.
Ab initio molecular dynamics calculations of ion hydration free energies.
Leung, Kevin; Rempe, Susan B; von Lilienfeld, O Anatole
2009-05-28
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li(+), Cl(-), and Ag(+) ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (DeltaG(hyd)) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model phi predictions. The sums of Li(+)/Cl(-) and Ag(+)/Cl(-) AIMD DeltaG(hyd), which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag(+)+Ni(+)-->Ag+Ni(2+) in water. The predictions for this reaction suggest that existing estimates of DeltaG(hyd) for unstable radiolysis intermediates such as Ni(+) may need to be extensively revised.
Boda, Aalu Kumar, D. Sanjeev; Chatterjee, Ashok; Mukhopadhyay, Soma
2015-06-24
The ground state energy of a hydrogenic D{sup 0} complex trapped in a three-dimensional GaAs quantum dot with Gaussian confinement is calculated variationally incorporating the effect of Rashba spin-orbit interaction. The results are obtained as a function of the quantum dot size and the Rashba spin-orbit interaction. The results show that the Rashba interaction reduces the ground state energy of the system.
Deakyne, C.A. ); Liebman, J.F. ); Frenking, G. ); Koch, W. )
1990-03-22
MP4/6-311G(2df,2pd)//MP2/6-31G{sup **} and MPn/6-31G{sup **}//ClD/6-31G{sup **} (n = 2-4) calculations have been carried out for HeF{sup +}, NeF{sup +}, ArF{sup +}, ArH{sup +}, HCl, HCl{sup +}, ClF, Cl{sub 2}, HF, HF{sup +}, F{sub 2}, H{sub 2}, and H{sub 2}{sup +}. Structures, vibrational frequencies, ionization potentials, reaction enthalpies, and triplet vs singlet energies (for HeF{sup +}, NeF{sup +}, and ArF{sup +}) have been examined. The reactions considered include hydrogenolysis and bond dissociation reactions.
Relative Photoionization Cross Sections of Super-Atom Molecular Orbitals (SAMOs) in C60.
Bohl, Elvira; Sokół, Katarzyna P; Mignolet, Benoit; Thompson, James O F; Johansson, J Olof; Remacle, Francoise; Campbell, Eleanor E B
2015-11-25
The electronic structure and photoinduced dynamics of fullerenes, especially C60, is of great interest because these molecules are model systems for more complex molecules and nanomaterials. In this work we have used Rydberg Fingerprint Spectroscopy to determine the relative ionization intensities from excited SAMO (Rydberg-like) states in C60 as a function of laser wavelength. The relative ionization intensities are then compared to the ratio of the photoionization widths of the Rydberg-like states, computed in time-dependent density functional theory (TD-DFT). The agreement is remarkably good when the same photon order is required to energetically access the excited states. This illustrates the predictive potential of quantum chemistry for studying photoionization of large, complex molecules as well as confirming the assumption that is often made concerning the multiphoton excitation and rapid energy redistribution in the fullerenes.
NASA Astrophysics Data System (ADS)
Schwarzer, D.; Kutne, P.; Schröder, C.; Troe, J.
2004-07-01
Intramolecular vibrational energy flow in excited bridged azulene-anthracene compounds is investigated by time-resolved pump-probe laser spectroscopy. The bridges consist of molecular chains and are of the type (CH2)m with m up to 6 as well as (CH2OCH2)n (n=1,2) and CH2SCH2. After light absorption into the azulene S1 band and subsequent fast internal conversion, excited molecules are formed where the vibrational energy is localized at the azulene side. The vibrational energy transfer through the molecular bridge to the anthracene side and, finally, to the surrounding medium is followed by probing the red edge of the azulene S3 absorption band at 300 nm and/or the anthracene S1 absorption band at 400 nm. In order to separate the time scales for intramolecular and intermolecular energy transfer, most of the experiments were performed in supercritical xenon where vibrational energy transfer to the bath is comparably slow. The intramolecular equilibration proceeds in two steps. About 15%-20% of the excitation energy leaves the azulene side within a short period of 300 fs. This component accompanies the intramolecular vibrational energy redistribution (IVR) within the azulene chromophore and it is caused by dephasing of normal modes contributing to the initial local excitation of the azulene side and extending over large parts of the molecule. Later, IVR in the whole molecule takes place transferring vibrational energy from the azulene through the bridge to the anthracene side and thereby leading to microcanonical equilibrium. The corresponding time constants τIVR for short bridges increase with the chain length. For longer bridges consisting of more than three elements, however, τIVR is constant at around 4-5 ps. Comparison with molecular dynamics simulations suggests that the coupling of these chains to the two chromophores limits the rate of intramolecular vibrational energy transfer. Inside the bridges the energy transport is essentially ballistic and, therefore
Spin-orbit coupling effect on quantum hall ferromagnets with vanishing zeeman energy
Fal'ko; Iordanskii
2000-01-03
We present the phase diagram of a ferromagnetic nu = 2N+1 quantum Hall liquid in a narrow quantum well with vanishing single-particle Zeeman splitting, varepsilon(Z), and a pronounced spin-orbit coupling. Upon decreasing varepsilon(Z) the spin-polarization field of a liquid takes, first, the easy-axis configuration, followed by the formation of a helical state which affects the transport and NMR properties of a liquid and the form of topological defects in it.
Ab initio molecular orbital study of Fe{sub 2}C1{sub 6} and FeA1C1{sub 6}.
Scholz, G.; Curtiss, L. A.; Humboldt Univ. zu Berlin
2000-07-24
Ab initio molecular orbital theory was used to determine the equilibrium structure and vibrational frequencies of Fe{sub 2}Cl{sub 6} and FeAlCl{sub 6}. The equilibrium structure the Fe{sub 2}Cl{sub 6} dimer has D{sub 2h} symmetry with a planar arrangement of the four membered {l_brace}FeCl{sub br}FeCl{sub br}{r_brace} ring, similar to the Al{sub 2}Cl{sub 6} dimer. The calculated bond distances and vibrational frequencies are in good agreement with experiment. The potential energy surface for the puckering of the {l_brace}FeCl{sub br}FeCl{sub br}{r_brace} ring is extremely flat. This prevents an unambiguous assignment of either D{sub 2h} or C{sub 2v} symmetry to the Fe{sub 2}Cl{sub 6}structure in electron diffraction measurements. The FeAlCl{sub 6} molecule is found to have a C{sub 2v} structure similar to Fe{sub 2}Cl{sub 6} with vibrational frequencies in good agreement with experiment.
NASA Technical Reports Server (NTRS)
1978-01-01
Cost effective approaches for placing automated payloads into circular and elliptical orbits using energy requirements significantly lower than that provided by the smallest, currently planned shuttle upper stage, SSUS-D, were investigated. Launch costs were derived using both NASA existing/planned launch approaches as well as new propulsion concepts meeting low-energy regime requirements. Candidate new propulsion approaches considered were solid (tandem, cluster, and controlled), solid/liquid combinations and all-liquid stages. Results show that the most economical way to deliver the 129 low energy payloads is basically with a new modular, short liquid bipropellant stage system for the large majority of the payloads. For the remainder of the payloads, use the shuttle with integral OMS and the Scout form for a few specialized payloads until the Shuttle becomes operational.
Janzen, Daron E.; Burand, Michael W.; Ewbank, Paul C.; Pappenfus, Ted M.; Higuchi, Hiroyuki; da Silva, Demetrio A.; Young, Victor G.; Bredas, Jean-Luc; Mann, Kent R.
2010-11-16
A series of new quinodimethane-substituted terthiophene and quaterthiophene oligomers has been investigated for comparison with a previously studied quinoid oligothiophene that has demonstrated high mobilities and ambipolar transport behavior in thin-film transistor devices. Each new quinoidal thiophene derivative shows a reversible one-electron oxidation between 0.85 and 1.32 V, a quasi-reversible one-electron second oxidation between 1.37 and 1.96 V, and a reversible two-electron reduction between -0.05 and -0.23 V. The solution UV-vis-NIR spectrum of each compound is dominated by an intense epsilon congruent with 100,000 M{sup -1} cm{sup -1} low energy pi-pi transition that has a lambda(max) ranging between 648 and 790 nm. All X-ray crystal structures exhibit very planar quinoidal backbones and short intermolecular pi-stacking distances (3.335-3.492 A). Structures exhibit a single pi-stacking distance with parallel cofacial stacking (sulfur atoms of equivalent rings pointed in the same direction) or with alternating distances and antiparallel cofacial stacking (sulfur atoms of equivalent rings pointed in the opposite direction). Examples of the layered and herringbone-packing motifs are observed for both the parallel and the antiparallel cofacial stacking. Analysis of the X-ray structures and molecular orbital calculations indicates that all of these compounds have one-dimensional electronic band structures as a result of the pi-stacking. For structures with a unique pi-stacking distance, a simple geometric overlap parameter calculated from the shape of the molecule and the slip from perfect registry in the pi-stack correlates well with the transfer integrals (t) calculated using molecular orbital theory. The calculated valence (633 meV) and conduction (834 meV) bandwidths for a quinoid quaterthiophene structure are similar to those calculated for the benchmark pentacene and indicate that both hole and electron mobilities could be significant.
NASA Astrophysics Data System (ADS)
Bernard, Laura; Blanchet, Luc; Bohé, Alejandro; Faye, Guillaume; Marsat, Sylvain
2017-02-01
In this paper, we revisit and complete our preceding work on the Fokker Lagrangian describing the dynamics of compact binary systems at the fourth post-Newtonian (4PN) order in harmonic coordinates. We clarify the impact of the nonlocal character of the Fokker Lagrangian or the associated Hamiltonian on both the conserved energy and the relativistic periastron precession for circular orbits. We show that the nonlocality of the action, due to the presence of the tail effect at the 4PN order, gives rise to an extra contribution to the conserved integral of energy with respect to the Hamiltonian computed on shell, which was not taken into account in our previous work. We also provide a direct derivation of the periastron advance by taking carefully into account this nonlocality. We then argue that the infrared (IR) divergences in the calculation of the gravitational part of the action are problematic, which motivates us to introduce a second ambiguity parameter, in addition to the one already assumed previously. After fixing these two ambiguity parameters by requiring that the conserved energy and the relativistic periastron precession for circular orbits be in agreement with numerical and analytical gravitational self-force calculations, valid in the limiting case of small mass ratio, we find that our resulting Lagrangian is physically equivalent to the one obtained in the ADM Hamiltonian approach.
Zhou, Fangfang; Liu, Ruirui; Tang, Jia; Li, Ping; Cui, Yahui; Zhang, Houyu
2016-01-01
The nature and strength of intermolecular Se⋯N interaction between selenium-containing compounds HSeX (X = CH3, NH2, CF3, OCH3, CN, OH, NO2, Cl, F), and NH3 have been investigated at the MP2/aug-cc-pVDZ level. The Se⋯N interaction is found to be dependent on the substituent groups, which greatly affect the positive electrostatic potential of Se atoms and the accepting electron ability of X-Se σ(∗) antibonding orbital. Energy decomposition of the Se ⋯N interaction reveals that electrostatic and induction forces are comparable in the weak-bonded complexes and induction becomes more significant in the complexes with strong electron-withdrawing substituents. Natural bond orbital (NBO) analysis indicates that the primary source of the induction is the electron transfer from the N lone pair to the X-Se σ(∗) antibonding orbital. The geometry of the complex and the interaction directionality of NH3 to X-Se bond can be regarded as a consequence of the exchange-repulsion. The topological analysis on the electron density reveals the nature of closed-shell interaction in these X-Se⋯N contacts. The Se⋯N interaction in the complexes with the strong electron-withdrawing substituent has a partly covalent character.
Molecular conductance at finite voltage: bias driven evolution of Kohn-Sham-orbitals
NASA Astrophysics Data System (ADS)
Koentopp, Max; Evers, Ferdinand; Burke, Kieron
2006-03-01
Ground state density functional theory calculations yield the exact electron density if the exact exchange-correlation functional is employed. The evolution of the equilibrium density with parametric changes in the Hamiltonian, e.g. realized by a change in the electrostatic potential, can provide crucial information about transport properties, like the Coulomb blockade. To test our ideas, we perform model calculations using the quantum chemistry package TURBOMOLE for a diode molecule, which exhibits the structure of a double quantum dot and has been investigated experimentally [1]. In particular, we explain the origin of the characteristic peak structure in the differential conductance. Our results are consistent with the interpretation that the stepwise increase of the conductance occurs when the number of occupied levels of one of the dots, that have an energy above the lowest unoccupied level of the other dot, increases by one.[1] M. Elbing, R. Ochs, M. Koentopp, M. Fischer, C. von Hänisch, F. Weigend, F. Evers, H. Weber, M. Mayor, Proc. Nat. Acad. Sci. USA 102, 8815 (2005).
A perovskite oxide optimized for oxygen evolution catalysis from molecular orbital principles.
Suntivich, Jin; May, Kevin J; Gasteiger, Hubert A; Goodenough, John B; Shao-Horn, Yang
2011-12-09
The efficiency of many energy storage technologies, such as rechargeable metal-air batteries and hydrogen production from water splitting, is limited by the slow kinetics of the oxygen evolution reaction (OER). We found that Ba(0.5)Sr(0.5)Co(0.8)Fe(0.2)O(3-δ) (BSCF) catalyzes the OER with intrinsic activity that is at least an order of magnitude higher than that of the state-of-the-art iridium oxide catalyst in alkaline media. The high activity of BSCF was predicted from a design principle established by systematic examination of more than 10 transition metal oxides, which showed that the intrinsic OER activity exhibits a volcano-shaped dependence on the occupancy of the 3d electron with an e(g) symmetry of surface transition metal cations in an oxide. The peak OER activity was predicted to be at an e(g) occupancy close to unity, with high covalency of transition metal-oxygen bonds.
Mechanism of hydroxyl radical generation from a silica surface: molecular orbital calculations.
Narayanasamy, Jayakumar; Kubicki, James D
2005-11-24
The interaction of an H(2)O molecule with cluster models of fractured silica surfaces was studied by means of quantum mechanical calculations. Two clusters representing homolytic cleavage (triple bond Si(*) and triple bond SiO(*)) and two representing heterolytic cleavage (triple bond Si(+) and triple bond Si-O(-)) of silica surfaces were modeled. Vibrational frequencies of the reactants and products of these silica surfaces reacting with H(2)O have been calculated and compare favorably with experiment. Comparisons of the Gibbs free and potential energies for the model ionic and radical states were made, and the radical pair of sites was predicted to be more stable by approximately -70 to -85 kJ/mol, depending on the computational methodology. These calculations suggest that when silica is fractured in a vacuum homolytic cleavage is favored. Reaction pathways were investigated for these four model surface sites interacting with H(2)O. The reaction of H(2)O with triple bond SiO(*) was predicted to generate OH(*). Rate constants for these reactions were also calculated and predict a rapid equibrium for the reaction triple bond SiO(*) + H(2)O --> triple bond SiOH + OH(*). Stability of a finite number of triple bond SiO(*) sites at equilibrium in the above reaction with H(2)O was also predicted, which implies a long-term ability of silica surfaces to produce OH(*) radicals if the sites of the broken bonds do not repolymerize to form siloxane groups.
Exploring the free energy surface using ab initio molecular dynamics
Samanta, Amit; Morales, Miguel A.; Schwegler, Eric
2016-04-22
Efficient exploration of the configuration space and identification of metastable structures are challenging from both computational as well as algorithmic perspectives. Here, we extend the recently proposed orderparameter aided temperature accelerated sampling schemes to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways within the framework of density functional theory based molecular dynamics. The sampling method is applied to explore the relevant parts of the configuration space in prototypical materials SiO_{2} and Ti to identify the different metastable structures corresponding to different phases in these materials. In addition, we use the string method in collective variables to study the melting pathways in the high pressure cotunnite phase of SiO_{2} and the hcp to fcc phase transition in Ti.
Exploring the free energy surface using ab initio molecular dynamics
Samanta, Amit; Morales, Miguel A.; Schwegler, Eric
2016-04-22
Efficient exploration of the configuration space and identification of metastable structures are challenging from both computational as well as algorithmic perspectives. Here, we extend the recently proposed orderparameter aided temperature accelerated sampling schemes to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways within the framework of density functional theory based molecular dynamics. The sampling method is applied to explore the relevant parts of the configuration space in prototypical materials SiO2 and Ti to identify the different metastable structures corresponding to different phases in these materials. In addition, we use the string method inmore » collective variables to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hcp to fcc phase transition in Ti.« less
NASA Astrophysics Data System (ADS)
Patra, Moumita; Maiti, Santanu K.
2016-12-01
In the present work we investigate the behavior of all three components of persistent spin current in a quasi-periodic Fibonacci ring subjected to Rashba and Dresselhaus spin-orbit interactions. Analogous to persistent charge current in a conducting ring where electrons gain a Berry phase in presence of magnetic flux, spin Berry phase is associated during the motion of electrons in presence of a spin-orbit field which is responsible for the generation of spin current. The interplay between two spin-orbit fields along with quasi-periodic Fibonacci sequence on persistent spin current is described elaborately, and from our analysis, we can estimate the strength of any one of two spin-orbit couplings together with on-site energy, provided the other is known.
Footprinting molecular electrostatic potential surfaces for calculation of solvation energies.
Calero, Christian Solis; Farwer, Jochen; Gardiner, Eleanor J; Hunter, Christopher A; Mackey, Mark; Scuderi, Serena; Thompson, Stuart; Vinter, Jeremy G
2013-11-07
A liquid is composed of an ensemble of molecules that populate a large number of different states, so calculation of the solvation energy of a molecule in solution requires a method for summing the interactions with the environment over all of these states. The surface site interaction model for the properties of liquids at equilibrium (SSIMPLE) simplifies the surface of a molecule to a discrete number of specific interaction sites (SSIPs). The thermodynamic properties of these interaction sites can be characterised experimentally, for example, through measurement of association constants for the formation of simple complexes that feature a single H-bonding interaction. Correlation of experimentally determined solution phase H-bond parameters with gas phase ab initio calculations of maxima and minima on molecular electrostatic potential surfaces (MEPS) provides a method for converting gas phase calculations on isolated molecules to parameters that can be used to estimate solution phase interaction free energies. This approach has been generalised using a footprinting technique that converts an MEPS into a discrete set of SSIPs (each described by a polar interaction parameter, εi). These SSIPs represent the molecular recognition properties of the entire surface of the molecule. For example, water is described by four SSIPs, two H-bond donor sites and two H-bond acceptor sites. A liquid mixture is described as an ensemble of SSIPs that represent the components of the mixture at appropriate concentrations. Individual SSIPs are assumed to be independent, so speciation of SSIP contacts can be calculated based on properties of the individual SSIP interactions, which are given by the sum of a polar (εiεj) and a non-polar (E(vdW)) interaction term. Results are presented for calculation the free energies of transfer of a range of organic molecules from the pure liquid into water, from the pure liquid into n-hexadecane, from n-hexadecane into water, from n-octanol into
NASA Technical Reports Server (NTRS)
Semones, Edward; Leitgab, Martin
2016-01-01
The ISS-RAD instrument was activated on ISS on February 1st, 2016. Integrated in ISS-RAD, the Fast Neutron Detector (FND) performs, for the first time on ISS, routine and precise direct neutron measurements between 0.5 and 8 MeV. Preliminary results for neutron dose equivalent and neutron flux energy distributions from online/on-board algorithms and offline ground analyses will be shown, along with comparisons to simulated data and previously measured neutron spectral data. On-orbit data quality and pre-launch analysis validation results will be discussed as well.