Investigation of the host-guest complexation between 4-sulfocalix[4]arene and nedaplatin for potential use in drug delivery

NASA Astrophysics Data System (ADS)

Fahmy, Sherif Ashraf; Ponte, Fortuna; Abd El-Rahman, Mohamed K.; Russo, Nino; Sicilia, Emilia; Shoeib, Tamer

2018-03-01

Macromolecules including macrocyclic species have been reported to have the potential to encapsulate biologically active compounds such as drugs through host-guest complexation to increase their solubility, stability and bioavailability. In this paper the first experimental and theoretical investigation of the complexation between nedaplatin, a second generation antineoplastic drug, and p-4-sulfocalix[4]arene, a macromolecule possessing a bipolar amphiphilic structure with good biocompatibility and relatively low haemolytic toxicity for potential use as a drug delivery system is presented. Data from 1H NMR, UV, Job's plot analysis, HPLC and DFT calculations are detailed and suggest the formation of a 1:1 complex. The stability constant of the complex was experimentally estimated to be 3.6 × 104 M- 1 and 2.1 × 104 M- 1 which correspond to values of - 6.2 and - 5.9 kcal mol- 1, respectively for the free energy of complexation while the interaction free energy is calculated to be - 4.9 kcal mol- 1. The formed species is shown to be stabilised in solution through hydrogen bonding between the host and the guest which may allow for this strategy to be effective for potential use in drug delivery.

A benchmark for reaction coordinates in the transition path ensemble

PubMed Central

2016-01-01

The molecular mechanism of a reaction is embedded in its transition path ensemble, the complete collection of reactive trajectories. Utilizing the information in the transition path ensemble alone, we developed a novel metric, which we termed the emergent potential energy, for distinguishing reaction coordinates from the bath modes. The emergent potential energy can be understood as the average energy cost for making a displacement of a coordinate in the transition path ensemble. Where displacing a bath mode invokes essentially no cost, it costs significantly to move the reaction coordinate. Based on some general assumptions of the behaviors of reaction and bath coordinates in the transition path ensemble, we proved theoretically with statistical mechanics that the emergent potential energy could serve as a benchmark of reaction coordinates and demonstrated its effectiveness by applying it to a prototypical system of biomolecular dynamics. Using the emergent potential energy as guidance, we developed a committor-free and intuition-independent method for identifying reaction coordinates in complex systems. We expect this method to be applicable to a wide range of reaction processes in complex biomolecular systems. PMID:27059559

Energy absorption capabilities of complex thin walled structures

NASA Astrophysics Data System (ADS)

Tarlochan, F.; AlKhatib, Sami

2017-10-01

Thin walled structures have been used in the area of energy absorption during an event of a crash. A lot of work has been done on tubular structures. Due to limitation of manufacturing process, complex geometries were dismissed as potential solutions. With the advancement in metal additive manufacturing, complex geometries can be realized. As a motivation, the objective of this study is to investigate computationally the crash performance of complex tubular structures. Five designs were considered. In was found that complex geometries have better crashworthiness performance than standard tubular structures used currently.

New Rh 2 (II,II) Complexes for Solar Energy Applications: Panchromatic Absorption and Excited-State Reactivity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whittemore, Tyler J.; Sayre, Hannah J.; Xue, Congcong

In this work, the new heteroleptic paddlewheel complexes cis-[Rh 2(μ-form) 2(μ-np) 2][BF 4] 2, where form = p-ditolylformamidinate (DTolF) or p-difluorobenzylformamidinate (F-form) and np = 1,8-napthyridyine, and cis-Rh 2(μ-form) 2(μ-npCOO) 2 (npCOO – = 1,8-naphthyridine-2-carboxylate), were synthesized and characterized. The complexes absorb strongly throughout the ultraviolet (λ max = 300 nm, ε = 20 300 M –1 cm –1) and visible regions (λ max = 640 nm ε = 3500 M –1 cm –1), making them potentially useful new dyes with panchromatic light absorption for solar energy conversion applications. Ultrafast and nanosecond transient absorption and time-resolved infrared spectroscopies were usedmore » to characterize the identity and dynamics of the excited states, where singlet and triplet Rh 2/form-to-naphthyridine, metal/ligand-to-ligand charge-transfer (ML-LCT) excited states were observed in all four complexes. The npCOO – complexes exhibit red-shifted absorption profiles extending into the near-IR and undergo photoinitiated electron transfer to generate reduced methyl viologen, a species that persists in the presence of a sacrificial donor. The energy of the triplet excited state of each complex was estimated from energy-transfer quenching experiments using a series of organic triplet donors (E( 3ππ*) from 1.83 to 0.78 eV). The singlet reduction (+0.6 V vs Ag/AgCl) potentials, and singlet and triplet oxidation potentials (-1.1 and -0.5 V vs Ag/AgCl, respectively) were determined. Finally, based on the excited-state lifetimes and redox properties, these complexes represent a new class of light absorbers with potential application as dyes for charge injection into semiconductor solar cells and in sensitizer-catalyst assemblies for photocatalysis that operate with irradiation from the ultraviolet to ~800 nm.« less

New Rh 2 (II,II) Complexes for Solar Energy Applications: Panchromatic Absorption and Excited-State Reactivity

DOE PAGES

Whittemore, Tyler J.; Sayre, Hannah J.; Xue, Congcong; ...

2017-10-04

In this work, the new heteroleptic paddlewheel complexes cis-[Rh 2(μ-form) 2(μ-np) 2][BF 4] 2, where form = p-ditolylformamidinate (DTolF) or p-difluorobenzylformamidinate (F-form) and np = 1,8-napthyridyine, and cis-Rh 2(μ-form) 2(μ-npCOO) 2 (npCOO – = 1,8-naphthyridine-2-carboxylate), were synthesized and characterized. The complexes absorb strongly throughout the ultraviolet (λ max = 300 nm, ε = 20 300 M –1 cm –1) and visible regions (λ max = 640 nm ε = 3500 M –1 cm –1), making them potentially useful new dyes with panchromatic light absorption for solar energy conversion applications. Ultrafast and nanosecond transient absorption and time-resolved infrared spectroscopies were usedmore » to characterize the identity and dynamics of the excited states, where singlet and triplet Rh 2/form-to-naphthyridine, metal/ligand-to-ligand charge-transfer (ML-LCT) excited states were observed in all four complexes. The npCOO – complexes exhibit red-shifted absorption profiles extending into the near-IR and undergo photoinitiated electron transfer to generate reduced methyl viologen, a species that persists in the presence of a sacrificial donor. The energy of the triplet excited state of each complex was estimated from energy-transfer quenching experiments using a series of organic triplet donors (E( 3ππ*) from 1.83 to 0.78 eV). The singlet reduction (+0.6 V vs Ag/AgCl) potentials, and singlet and triplet oxidation potentials (-1.1 and -0.5 V vs Ag/AgCl, respectively) were determined. Finally, based on the excited-state lifetimes and redox properties, these complexes represent a new class of light absorbers with potential application as dyes for charge injection into semiconductor solar cells and in sensitizer-catalyst assemblies for photocatalysis that operate with irradiation from the ultraviolet to ~800 nm.« less

Selective Co-Encapsulation Inside an M6 L4 Cage.

PubMed

Leenders, Stefan H A M; Becker, René; Kumpulainen, Tatu; de Bruin, Bas; Sawada, Tomohisa; Kato, Taito; Fujita, Makoto; Reek, Joost N H

2016-10-17

There is broad interest in molecular encapsulation as such systems can be utilized to stabilize guests, facilitate reactions inside a cavity, or give rise to energy-transfer processes in a confined space. Detailed understanding of encapsulation events is required to facilitate functional molecular encapsulation. In this contribution, it is demonstrated that Ir and Rh-Cp-type metal complexes can be encapsulated inside a self-assembled M 6 L 4 metallocage only in the presence of an aromatic compound as a second guest. The individual guests are not encapsulated, suggesting that only the pair of guests can fill the void of the cage. Hence, selective co-encapsulation is observed. This principle is demonstrated by co-encapsulation of a variety of combinations of metal complexes and aromatic guests, leading to several ternary complexes. These experiments demonstrate that the efficiency of formation of the ternary complexes depends on the individual components. Moreover, selective exchange of the components is possible, leading to formation of the most favorable complex. Besides the obvious size effect, a charge-transfer interaction may also contribute to this effect. Charge-transfer bands are clearly observed by UV/Vis spectrophotometry. A change in the oxidation potential of the encapsulated electron donor also leads to a shift in the charge-transfer energy bands. As expected, metal complexes with a higher oxidation potential give rise to a higher charge-transfer energy and a larger hypsochromic shift in the UV/Vis spectrum. These subtle energy differences may potentially be used to control the binding and reactivity of the complexes bound in a confined space. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory

NASA Astrophysics Data System (ADS)

Mrugalla, Florian; Kast, Stefan M.

2016-09-01

Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems.

Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory.

PubMed

Mrugalla, Florian; Kast, Stefan M

2016-09-01

Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems.

Safety management of complex research operations

NASA Technical Reports Server (NTRS)

Brown, W. J.

1981-01-01

Complex research and technology operations present many varied potential hazards which must be addressed in a disciplined independent safety review and approval process. The research and technology effort at the Lewis Research Center is divided into programmatic areas of aeronautics, space and energy. Potential hazards vary from high energy fuels to hydrocarbon fuels, high pressure systems to high voltage systems, toxic chemicals to radioactive materials and high speed rotating machinery to high powered lasers. A Safety Permit System presently covers about 600 potentially hazardous operations. The Safety Management Program described in this paper is believed to be a major factor in maintaining an excellent safety record at the Lewis Research Center.

Complexes of a Zn-metalloenzyme binding site with hydroxamate-containing ligands. A case for detailed benchmarkings of polarizable molecular mechanics/dynamics potentials when the experimental binding structure is unknown.

PubMed

Gresh, Nohad; Perahia, David; de Courcy, Benoit; Foret, Johanna; Roux, Céline; El-Khoury, Lea; Piquemal, Jean-Philip; Salmon, Laurent

2016-12-15

Zn-metalloproteins are a major class of targets for drug design. They constitute a demanding testing ground for polarizable molecular mechanics/dynamics aimed at extending the realm of quantum chemistry (QC) to very long-duration molecular dynamics (MD). The reliability of such procedures needs to be demonstrated upon comparing the relative stabilities of competing candidate complexes of inhibitors with the recognition site stabilized in the course of MD. This could be necessary when no information is available regarding the experimental structure of the inhibitor-protein complex. Thus, this study bears on the phosphomannose isomerase (PMI) enzyme, considered as a potential therapeutic target for the treatment of several bacterial and parasitic diseases. We consider its complexes with 5-phospho-d-arabinonohydroxamate and three analog ligands differing by the number and location of their hydroxyl groups. We evaluate the energy accuracy expectable from a polarizable molecular mechanics procedure, SIBFA. This is done by comparisons with ab initio quantum-chemistry (QC) calculations in the following cases: (a) the complexes of the four ligands in three distinct structures extracted from the entire PMI-ligand energy-minimized structures, and totaling up to 264 atoms; (b) the solvation energies of several energy-minimized complexes of each ligand with a shell of 64 water molecules; (c) the conformational energy differences of each ligand in different conformations characterized in the course of energy-minimizations; and (d) the continuum solvation energies of the ligands in different conformations. The agreements with the QC results appear convincing. On these bases, we discuss the prospects of applying the procedure to ligand-macromolecule recognition problems. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

A new ab initio potential energy surface for the collisional excitation of HCN by para- and ortho-H{sub 2}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Denis-Alpizar, Otoniel, E-mail: otonieldenisalpizar@gmail.com; Departamento de Física, Universidad de Matanzas, Matanzas 40100; Kalugina, Yulia

We present a new four-dimensional potential energy surface for the collisional excitation of HCN by H{sub 2}. Ab initio calculations of the HCN–H{sub 2} van der Waals complex, considering both molecules as rigid rotors, were carried out at the explicitly correlated coupled cluster with single, double, and perturbative triple excitations [CCSD(T)-F12a] level of theory using an augmented correlation-consistent triple zeta (aVTZ) basis set. The equilibrium structure is linear HCN–H{sub 2} with the nitrogen pointing towards H{sub 2} at an intermolecular separation of 7.20 a{sub 0}. The corresponding well depth is −195.20 cm{sup −1}. A secondary minimum of −183.59 cm{sup −1}more » was found for a T-shape configuration with the H of HCN pointing to the center of mass of H{sub 2}. We also determine the rovibrational energy levels of the HCN–para-H{sub 2} and HCN–ortho-H{sub 2} complexes. The calculated dissociation energies for the para and ortho complexes are 37.79 cm{sup −1} and 60.26 cm{sup −1}, respectively. The calculated ro-vibrational transitions in the HCN–H{sub 2} complex are found to agree by more than 0.5% with the available experimental data, confirming the accuracy of the potential energy surface.« less

Pyruvate dehydrogenase complex and nicotinamide nucleotide transhydrogenase constitute an energy consuming redox circuit

PubMed Central

Fisher-Wellman, Kelsey H.; Lin, Chien-Te; Ryan, Terence E.; Reese, Lauren R.; Gilliam, Laura A. A.; Cathey, Brook L.; Lark, Daniel S.; Smith, Cody D.; Muoio, Deborah M.; Neufer, P. Darrell

2015-01-01

SUMMARY Cellular proteins rely on reversible redox reactions to establish and maintain biological structure and function. How redox catabolic (NAD+:NADH) and anabolic (NADP+:NADPH) processes integrate during metabolism to maintain cellular redox homeostasis however is unknown. The present work identifies a continuously cycling, mitochondrial membrane potential-dependent redox circuit between the pyruvate dehydrogenase complex (PDHC) and nicotinamide nucleotide transhydrogenase (NNT). PDHC is shown to produce H2O2 in relation to reducing pressure within the complex. The H2O2 produced however is effectively masked by a continuously cycling redox circuit that links, via glutathione/thioredoxin, to NNT, which catalyzes the regeneration of NADPH from NADH at the expense of the mitochondrial membrane potential. The net effect is an automatic fine tuning of NNT-mediated energy expenditure to metabolic balance at the level of PDHC. In mitochondria, genetic or pharmacological disruptions in the PDHC-NNT redox circuit negate counterbalance changes in energy expenditure. At the whole animal level, mice lacking functional NNT (C57BL/6J) are characterized by lower energy expenditure rates, consistent with their well known susceptibility to diet-induced obesity. These findings suggest the integration of redox sensing of metabolic balance with compensatory changes in energy expenditure provides a potential mechanism by which cellular redox homeostasis is maintained and body weight is defended during periods of positive and negative energy balance. PMID:25643703

Chirality of weakly bound complexes: The potential energy surfaces for the hydrogen-peroxide−noble-gas interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roncaratti, L. F., E-mail: lz@fis.unb.br; Leal, L. A.; Silva, G. M. de

2014-10-07

We consider the analytical representation of the potential energy surfaces of relevance for the intermolecular dynamics of weakly bound complexes of chiral molecules. In this paper we study the H{sub 2}O{sub 2}−Ng (Ng=He, Ne, Ar, Kr, and Xe) systems providing the radial and the angular dependence of the potential energy surface on the relative position of the Ng atom. We accomplish this by introducing an analytical representation which is able to fit the ab initio energies of these complexes in a wide range of geometries. Our analysis sheds light on the role that the enantiomeric forms and the symmetry ofmore » the H{sub 2}O{sub 2} molecule play on the resulting barriers and equilibrium geometries. The proposed theoretical framework is useful to study the dynamics of the H{sub 2}O{sub 2} molecule, or other systems involving O–O and S–S bonds, interacting by non-covalent forces with atoms or molecules and to understand how the relative orientation of the O–H bonds changes along collisional events that may lead to a hydrogen bond formation or even to selectivity in chemical reactions.« less

Hydrogen incorporation into BN fullerene-like nanostructures: A first-principles study

NASA Astrophysics Data System (ADS)

Ganji, M. D.; Abbaszadeh, B.; Ahaz, B.

2011-10-01

We performed density functional theory calculations to investigate the possibility of formation of endohedrally H@(BN) n-fullerene ( n: 24, 36, 60) and H@C 60 complexes for potential applications in solid-state quantum-computers. Spin-polarized approach within the generalized gradient approximation with the Perdew-Burke-Ernzerhof functional was used for the total energies and structural relaxation calculations. The calculated binding energies show that H atom being incorporated into B 60N 60 nanocage can form most stable complexes while the B 24N 24 and C 60 nanocages might form unstable complex with positive binding energy. We have also examined the penetration of an H atom into the respective nanocages and the calculated barrier energies indicate that the H atom prefers to penetrate into the B 24N 24 and B 60N 60 nanocages with barrier energy of about 0.47 eV (10.84 kcal/mol). Furthermore the binding characteristic is rationalized by analyzing the electronic structures. Our findings reveal that the B 60N 60 nanocage has fascinating potential application in future solid-state quantum-computers.

The CO 2 with dimethylamine reaction: ab initio predicted vibrational spectra

NASA Astrophysics Data System (ADS)

Jamróz, M. H.; Dobrowolski, J. Cz.; Borowiak, M. A.

1999-05-01

The IR spectra of CO 2, dimethylamine (DMA), (DMA) 2 dimers, DMA⋯CO 2 (2 : 1) complex, dimethylcarbamic acid (DMCA), DMCA⋯DMA (1 : 1) complex, DMCA -, and DMA(H) + were calculated at the B3PW91/6-31G** level. Potential energy distribution (PED) was calculated for predicted spectra to form basis for elucidation of experimental IR data. The stabilisation energy of the studied complexes was corrected by counterpoise method.

Second order Møller-Plesset and coupled cluster singles and doubles methods with complex basis functions for resonances in electron-molecule scattering

DOE PAGES

White, Alec F.; Epifanovsky, Evgeny; McCurdy, C. William; ...

2017-06-21

The method of complex basis functions is applied to molecular resonances at correlated levels of theory. Møller-Plesset perturbation theory at second order and equation-of-motion electron attachment coupled-cluster singles and doubles (EOM-EA-CCSD) methods based on a non-Hermitian self-consistent-field reference are used to compute accurate Siegert energies for shape resonances in small molecules including N 2 - , CO - , CO 2 - , and CH 2 O - . Analytic continuation of complex θ-trajectories is used to compute Siegert energies, and the θ-trajectories of energy differences are found to yield more consistent results than those of total energies.more » Furthermore, the ability of such methods to accurately compute complex potential energy surfaces is investigated, and the possibility of using EOM-EA-CCSD for Feshbach resonances is explored in the context of e-helium scattering.« less

Second order Møller-Plesset and coupled cluster singles and doubles methods with complex basis functions for resonances in electron-molecule scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Alec F.; Epifanovsky, Evgeny; McCurdy, C. William

The method of complex basis functions is applied to molecular resonances at correlated levels of theory. Møller-Plesset perturbation theory at second order and equation-of-motion electron attachment coupled-cluster singles and doubles (EOM-EA-CCSD) methods based on a non-Hermitian self-consistent-field reference are used to compute accurate Siegert energies for shape resonances in small molecules including N 2 - , CO - , CO 2 - , and CH 2 O - . Analytic continuation of complex θ-trajectories is used to compute Siegert energies, and the θ-trajectories of energy differences are found to yield more consistent results than those of total energies.more » Furthermore, the ability of such methods to accurately compute complex potential energy surfaces is investigated, and the possibility of using EOM-EA-CCSD for Feshbach resonances is explored in the context of e-helium scattering.« less

Chiral Nucleon-Nucleus Potentials at N3LO

NASA Astrophysics Data System (ADS)

Finelli, Paolo; Vorabbi, Matteo; Giusti, Carlotta

2018-03-01

Elastic scattering is probably one of the most relevant tools to study nuclear interactions. In this contribution we study the domain of applicability of microscopic two-body chiral potentials in the construction of an optical potential. A microscopic complex optical potential is derived and tested performing calculations on 16O at different energies. Good agreement with empirical data is obtained if a Lippmann-Schwinger cutoff at relatively high energies (above 500 MeV) is employed.

Energy minimization for self-organized structure formation and actuation

NASA Astrophysics Data System (ADS)

Kofod, Guggi; Wirges, Werner; Paajanen, Mika; Bauer, Siegfried

2007-02-01

An approach for creating complex structures with embedded actuation in planar manufacturing steps is presented. Self-organization and energy minimization are central to this approach, illustrated with a model based on minimization of the hyperelastic free energy strain function of a stretched elastomer and the bending elastic energy of a plastic frame. A tulip-shaped gripper structure illustrates the technological potential of the approach. Advantages are simplicity of manufacture, complexity of final structures, and the ease with which any electroactive material can be exploited as means of actuation.

Metastable Autoionizing States of Molecules and Radicals in Highly Energetic Environment

DTIC Science & Technology

2016-03-22

electronic states. The specific aims are to develop and calibrate complex-scaled equation-of-motion coupled cluster (cs-EOM- CC ) and CAP (complex...absorbing potential) augmented EOM- CC methods. We have implemented and benchmarked cs-EOM-CCSD and CAP- augmented EOM-CCSD methods for excitation energies...motion coupled cluster (cs-EOM- CC ) and CAP (complex absorbing potential) augmented EOM- CC methods. We have implemented and benchmarked cs-EOM-CCSD and

Dynamical importance of van der Waals saddle and excited potential surface in C(1D)+D2 complex-forming reaction

PubMed Central

Shen, Zhitao; Ma, Haitao; Zhang, Chunfang; Fu, Mingkai; Wu, Yanan; Bian, Wensheng; Cao, Jianwei

2017-01-01

Encouraged by recent advances in revealing significant effects of van der Waals wells on reaction dynamics, many people assume that van der Waals wells are inevitable in chemical reactions. Here we find that the weak long-range forces cause van der Waals saddles in the prototypical C(1D)+D2 complex-forming reaction that have very different dynamical effects from van der Waals wells at low collision energies. Accurate quantum dynamics calculations on our highly accurate ab initio potential energy surfaces with van der Waals saddles yield cross-sections in close agreement with crossed-beam experiments, whereas the same calculations on an earlier surface with van der Waals wells produce much smaller cross-sections at low energies. Further trajectory calculations reveal that the van der Waals saddle leads to a torsion then sideways insertion reaction mechanism, whereas the well suppresses reactivity. Quantum diffraction oscillations and sharp resonances are also predicted based on our ground- and excited-state potential energy surfaces. PMID:28094253

Investigating protein-protein interaction surfaces using a reduced stereochemical and electrostatic model.

PubMed

Warwicker, J

1989-03-20

A method of calculating the electrostatic potential energy between two molecules, using finite difference potential, is presented. A reduced charge set is used so that the interaction energy can be calculated as the two static molecules explore their full six-dimensional configurational space. The energies are contoured over surfaces fixed to each molecule with an interactive computer graphics program. For two crystal structures (trypsin-trypsin inhibitor and anti-lysozyme Fab-lysozyme), it is found that the complex corresponds to highly favourable interacting regions in the contour plots. These matches arise from a small number of protruding basic residues interacting with enhanced negative potential in each case. The redox pair cytochrome c peroxidase-cytochrome c exhibits an extensive favourably interacting surface within which a possible electron transfer complex may be defined by an increased electrostatic complementarity, but a decreased electrostatic energy. A possible substrate transfer configuration for the glycolytic enzyme pair glyceraldehyde phosphate dehydrogenase-phosphoglycerate kinase is presented.

Critical coupling and coherent perfect absorption for ranges of energies due to a complex gain and loss symmetric system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hasan, Mohammad, E-mail: mohammadhasan786@gmail.com; Ghatak, Ananya, E-mail: gananya04@gmail.com; Mandal, Bhabani Prasad, E-mail: bhabani.mandal@gmail.com

2014-05-15

We consider a non-Hermitian medium with a gain and loss symmetric, exponentially damped potential distribution to demonstrate different scattering features analytically. The condition for critical coupling (CC) for unidirectional wave and coherent perfect absorption (CPA) for bidirectional waves are obtained analytically for this system. The energy points at which total absorption occurs are shown to be the spectral singular points for the time reversed system. The possible energies at which CC occurs for left and right incidence are different. We further obtain periodic intervals with increasing periodicity of energy for CC and CPA to occur in this system. -- Highlights:more » •Energy ranges for CC and CPA are obtained explicitly for complex WS potential. •Analytical conditions for CC and CPA for PT symmetric WS potential are obtained. •Conditions for left and right CC are shown to be different. •Conditions for CC and CPA are shown to be that of SS for the time reversed system. •Our model shows the great flexibility of frequencies for CC and CPA.« less

Anion-π aromatic neutral tweezers complexes: are they stable in polar solvents?

PubMed

Sánchez-Lozano, Marta; Otero, Nicolás; Hermida-Ramón, Jose M; Estévez, Carlos M; Mandado, Marcos

2011-03-17

The impact of the solvent environment on the stabilization of the complexes formed by fluorine (T-F) and cyanide (T-CN) substituted tweezers with halide anions has been investigated theoretically. The study was carried out using computational methodologies based on density functional theory (DFT) and symmetry adapted perturbation theory (SAPT). Interaction energies were obtained at the M05-2X/6-31+G* level. The obtained results show a large stability of the complexes in solvents with large dielectric constant and prove the suitability of these molecular tweezers as potential hosts for anion recognition in solution. A detailed analysis of the effects of the solvent on the electron withdrawing ability of the substituents and its influence on the complex stability has been performed. In particular, the interaction energy in solution was split up into intermonomer and solvent-complex terms. In turn, the intermonomer interaction energy was partitioned into electrostatic, exchange, and polarization terms. Polar resonance structures in T-CN complexes are favored by polar solvents, giving rise to a stabilization of the intermonomer interaction, the opposite is found for T-F complexes. The solvent-complex energy increases with the polarity of the solvent in T-CN complexes, nonetheless the energy reaches a maximum and then decreases slowly in T-F complexes. An electron density analysis was also performed before and after complexation, providing an explanation to the trends followed by the interaction energies and their different components in solution.

Charge-transfer mechanism for electrophilic aromatic nitration and nitrosation via the convergence of (ab initio) molecular-orbital and Marcus-Hush theories with experiments.

PubMed

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.

A full-dimensional ab initio potential energy surface and rovibrational energies of the Ar–HF complex

NASA Astrophysics Data System (ADS)

Huang, Jing; Zhou, Yanzi; Xie, Daiqian

2018-04-01

We report a new full-dimensional ab initio potential energy surface for the Ar-HF van der Waals complex at the level of coupled-cluster singles and doubles with noniterative inclusion of connected triples levels [CCSD(T)] using augmented correlation-consistent quintuple-zeta basis set (aV5Z) plus bond functions. Full counterpoise correction was employed to correct the basis-set superposition error. The hypersurface was fitted using artificial neural network method with a root mean square error of 0.1085 cm-1 for more than 8000 ab initio points. The complex was found to prefer a linear Ar-H-F equilibrium structure. The three-dimensional discrete variable representation method and the Lanczos propagation algorithm were then employed to calculate the rovibrational states without separating inter- and intra- molecular nuclear motions. The calculated vibrational energies of Ar-HF differ from the experiment values within about 1 cm-1 on the first four HF vibrational states, and the predicted pure rotational energies on (0000) and (1000) vibrational states are deviated from the observed value by about 1%, which shows the accuracy of our new PES.

The structure of the NO(X (2)Pi)-N(2) complex: A joint experimental-theoretical study.

PubMed

Wen, B; Meyer, H; Kłos, J

2010-04-21

We report the first measurement of the spectrum of the NO-N(2) complex in the region of the first vibrational NO overtone transition. The origin band of the complex is blueshifted by 0.30 cm(-1) from the corresponding NO monomer frequency. The observed spectrum consists of three bands assigned to the origin band, the excitation of one quantum of z-axis rotation and one associated hot band. The spacing of the bands and the rotational structure indicate a T-shaped vibrationally averaged structure with the NO molecule forming the top of the T. These findings are confirmed by high level ab initio calculations of the potential energy surfaces in planar symmetry. The deepest minimum is found for a T-shaped geometry on the A(")-surface. As a result the sum potential also has the global minimum for this structure. The different potential surfaces show several additional local minima at slightly higher energies indicating that the complex most likely will perform large amplitude motion even in its ground vibrational state. Nevertheless, as suggested by the measured spectra, the complex must, on average, spend a substantial amount of time near the T-shaped configuration.

The Marketability of Integrated Energy/Utility Systems: A Guide to the Dollar Savings Potential in Integrated Energy/Utility Systems; for Campuses, Medical Complexes, and Communities; Architect/Engineers, Industrial and Power Plant Owners; Suppliers; and Constructors.

ERIC Educational Resources Information Center

Coxe, Edwin F.; Hill, David E.

This publication acquaints the prospective marketplace with the potential and underlying logic of the Integrated Utility System (IUS) concept. This system holds promise for educational and medical institutions seeking to reduce their energy costs. The generic IUS concept is described and how it can be incorporated into existing heating and…

Energetics analysis of interstitial loops in single-phase concentrated solid-solution alloys

NASA Astrophysics Data System (ADS)

Wang, Xin-Xin; Niu, Liang-Liang; Wang, Shaoqing

2018-04-01

Systematic energetics analysis on the shape preference, relative stability and radiation-induced segregation of interstitial loops in nickel-containing single-phase concentrated solid-solution alloys have been conducted using atomistic simulations. It is shown that the perfect loops prefer rhombus shape for its low potential energy, while the Frank faulted loops favor ellipse for its low potential energy and the possible large configurational entropy. The decrease of stacking fault energy with increasing compositional complexity provides the energetic driving force for the formation of faulted loops, which, in conjunction with the kinetic factors, explains the experimental observation that the fraction of faulted loops rises with increasing compositional complexity. Notably, the kinetics is primarily responsible for the absence of faulted loops in nickel-cobalt with a very low stacking fault energy. We further demonstrate that the simultaneous nickel enrichment and iron/chromium depletion on interstitial loops can be fully accounted for by their energetics.

Machine Learning Estimates of Natural Product Conformational Energies

PubMed Central

Rupp, Matthias; Bauer, Matthias R.; Wilcken, Rainer; Lange, Andreas; Reutlinger, Michael; Boeckler, Frank M.; Schneider, Gisbert

2014-01-01

Machine learning has been used for estimation of potential energy surfaces to speed up molecular dynamics simulations of small systems. We demonstrate that this approach is feasible for significantly larger, structurally complex molecules, taking the natural product Archazolid A, a potent inhibitor of vacuolar-type ATPase, from the myxobacterium Archangium gephyra as an example. Our model estimates energies of new conformations by exploiting information from previous calculations via Gaussian process regression. Predictive variance is used to assess whether a conformation is in the interpolation region, allowing a controlled trade-off between prediction accuracy and computational speed-up. For energies of relaxed conformations at the density functional level of theory (implicit solvent, DFT/BLYP-disp3/def2-TZVP), mean absolute errors of less than 1 kcal/mol were achieved. The study demonstrates that predictive machine learning models can be developed for structurally complex, pharmaceutically relevant compounds, potentially enabling considerable speed-ups in simulations of larger molecular structures. PMID:24453952

Safety management of complex research operators

NASA Technical Reports Server (NTRS)

Brown, W. J.

1981-01-01

Complex research and technology operations present varied potential hazards which are addressed in a disciplined, independent safety review and approval process. Potential hazards vary from high energy fuels to hydrocarbon fuels, high pressure systems to high voltage systems, toxic chemicals to radioactive materials and high speed rotating machinery to high powered lasers. A Safety Permit System presently covers about 600 potentially hazardous operations. The Safety Management Program described is believed to be a major factor in maintaining an excellent safety record.

Self-organized minimum-energy structures for dielectric elastomer actuators

NASA Astrophysics Data System (ADS)

Kofod, G.; Paajanen, M.; Bauer, S.

2006-11-01

When a stretched elastomer is laminated to a flat plastic frame, a complex shape is formed, which is termed a minimum-energy structure. It is shown how self-organized structures can be applied in the development of actuators with complex, out-of-plane actuationmodes. This unusual concept is then demonstrated in the case of dielectric elastomer actuators. Among advantages of this approach are the simplicity in manufacturing, the potential complexity and sophistication of the manufactured structures, and the general benefits of the concept when applied to other electro-mechanically active materials.

Study of charge transfer complexes of menadione (vitamin K 3) with a series of anilines

NASA Astrophysics Data System (ADS)

Pal, Purnendu; Saha, Avijit; Mukherjee, Asok K.; Mukherjee, Dulal C.

2004-01-01

Menadione (vitamin K 3) has been shown to form charge transfer complexes with N, N-dimethyl aniline, N, N-dimethyl p-toluidine and N, N-dimethyl m-toluidine in CCl 4 medium. The CT transition energies are well correlated with the ionisation potentials of the anilines. The formation constants of the complexes have been determined at a number of temperatures from which the enthalpies and entropies of formation have been obtained. The formation constants exhibit a very good linear free energy relationship (Hammett) at all the temperatures studied.

Using Hyperfine Electron Paramagnetic Resonance Spectroscopy to Define the Proton-Coupled Electron Transfer Reaction at Fe-S Cluster N2 in Respiratory Complex I.

PubMed

Le Breton, Nolwenn; Wright, John J; Jones, Andrew J Y; Salvadori, Enrico; Bridges, Hannah R; Hirst, Judy; Roessler, Maxie M

2017-11-15

Energy-transducing respiratory complex I (NADH:ubiquinone oxidoreductase) is one of the largest and most complicated enzymes in mammalian cells. Here, we used hyperfine electron paramagnetic resonance (EPR) spectroscopic methods, combined with site-directed mutagenesis, to determine the mechanism of a single proton-coupled electron transfer reaction at one of eight iron-sulfur clusters in complex I, [4Fe-4S] cluster N2. N2 is the terminal cluster of the enzyme's intramolecular electron-transfer chain and the electron donor to ubiquinone. Because of its position and pH-dependent reduction potential, N2 has long been considered a candidate for the elusive "energy-coupling" site in complex I at which energy generated by the redox reaction is used to initiate proton translocation. Here, we used hyperfine sublevel correlation (HYSCORE) spectroscopy, including relaxation-filtered hyperfine and single-matched resonance transfer (SMART) HYSCORE, to detect two weakly coupled exchangeable protons near N2. We assign the larger coupling with A( 1 H) = [-3.0, -3.0, 8.7] MHz to the exchangeable proton of a conserved histidine and conclude that the histidine is hydrogen-bonded to N2, tuning its reduction potential. The histidine protonation state responds to the cluster oxidation state, but the two are not coupled sufficiently strongly to catalyze a stoichiometric and efficient energy transduction reaction. We thus exclude cluster N2, despite its proton-coupled electron transfer chemistry, as the energy-coupling site in complex I. Our work demonstrates the capability of pulse EPR methods for providing detailed information on the properties of individual protons in even the most challenging of energy-converting enzymes.

Quantum mechanical characterization of the He4ICl weakly bound complex.

PubMed

Valdés, Álvaro; Prosmiti, Rita

2013-08-15

Vibrational calculations are performed for the 12-dimensional He4ICl van der Waals complex using the multiconfiguration time-dependent Hartree (MCTDH) method. The potential energy surface of the cluster is represented as a sum of the triatomic He-ICl ab initio parametrized terms plus the He-He interactions. The topology of the potential presents higher anisotropy compared to the one with a homonuclear dopant, and this is clearly reflected in the structure and energetics of the low-lying conformers of the system. In order to take advantage of the MCTDH method, natural potential fits are employed for the potential energy operator, and also, a mode combination scheme is introduced in order to speed up the computations. Zero-point energy, binding energies, and vibrationally averaged structures of different isomers of the He4ICl cluster are obtained. The present results predict that the (3,1,0) structure, involving three He atoms in the near T-shaped and one He atom in the linear configurations, to be the most stable one in accord with recent experimental findings. Comparisons with previous theoretical and experimental data are presented, and the stability of the high-order conformers is discussed in connection with the multiple minima (global and local) of the underlying potential surface.

Calculations of the free energy of interaction of the c-Fos-c-Jun coiled coil: effects of the solvation model and the inclusion of polarization effects.

PubMed

Zuo, Zhili; Gandhi, Neha S; Mancera, Ricardo L

2010-12-27

The leucine zipper region of activator protein-1 (AP-1) comprises the c-Jun and c-Fos proteins and constitutes a well-known coiled coil protein-protein interaction motif. We have used molecular dynamics (MD) simulations in conjunction with the molecular mechanics/Poisson-Boltzmann generalized-Born surface area [MM/PB(GB)SA] methods to predict the free energy of interaction of these proteins. In particular, the influence of the choice of solvation model, protein force field, and water potential on the stability and dynamic properties of the c-Fos-c-Jun complex were investigated. Use of the AMBER polarizable force field ff02 in combination with the polarizable POL3 water potential was found to result in increased stability of the c-Fos-c-Jun complex. MM/PB(GB)SA calculations revealed that MD simulations using the POL3 water potential give the lowest predicted free energies of interaction compared to other nonpolarizable water potentials. In addition, the calculated absolute free energy of binding was predicted to be closest to the experimental value using the MM/GBSA method with independent MD simulation trajectories using the POL3 water potential and the polarizable ff02 force field, while all other binding affinities were overestimated.

On Complex Nuclei Energetics in LENR

NASA Astrophysics Data System (ADS)

Miley, George H.; Hora, Heinz

2005-03-01

Swimming Electron Layer (SEL) theory plus fission of ``complex nuclei'' were proposed earlier to explain reaction products observed in electrolysis with multi-layer thin-film metallic electrodesootnotetext1.G.H. Miley, and J.A. Patterson, J. New Energy, Vol. 1, pp.11-15, (1996).. SEL was then extended to treat gas-diffusion driven transmutation experimentsootnotetextG. H. Miley and H. Hora, ``Nuclear Reactions in Solids,'' APS DNP Mtg., East Lansing, MI, Oct (2002).. It is also consistent with measured charged-particle emission during thin-film electrolysis and x-ray emission during plasma bombardment experimentsootnotetextA. Karabut, ``X-ray emission in high-current glow discharge,'' Proc., ICCF-9, Beijing China, May (2002).. The binding energy per complex nucleon can be estimated by an energy balance combined with identification of products for each complex e.g. complexes of A 39 have ˜ 0.05 MeV/Nucleon, etc, in thin film electrolysis. Energies in gas diffusion experiments are lower due to the reduced trap site potential at the multi-atom surface. In the case of x-ray emission, complexes involve subsurface defect center traps, giving only a few keV/Nucleon, consistent with experiments^3.

Unconventional Superconductivity in Luttinger Semimetals: Theory of Complex Tensor Order and the Emergence of the Uniaxial Nematic State

NASA Astrophysics Data System (ADS)

Boettcher, Igor; Herbut, Igor F.

2018-02-01

We investigate unconventional superconductivity in three-dimensional electronic systems with the chemical potential close to a quadratic band touching point in the band dispersion. Short-range interactions can lead to d -wave superconductivity, described by a complex tensor order parameter. We elucidate the general structure of the corresponding Ginzburg-Landau free energy and apply these concepts to the case of an isotropic band touching point. For a vanishing chemical potential, the ground state of the system is given by the superconductor analogue of the uniaxial nematic state, which features line nodes in the excitation spectrum of quasiparticles. In contrast to the theory of real tensor order in liquid crystals, however, the ground state is selected here by the sextic terms in the free energy. At a finite chemical potential, the nematic state has an additional instability at weak coupling and low temperatures. In particular, the one-loop coefficients in the free energy indicate that at weak coupling genuinely complex orders, which break time-reversal symmetry, are energetically favored. We relate our analysis to recent measurements in the half-Heusler compound YPtBi and discuss the role of cubic crystal symmetry.

Character of intermolecular interaction in pyridine-argon complex: Ab initio potential energy surface, internal dynamics, and interrelations between SAPT energy components.

PubMed

Makarewicz, Jan; Shirkov, Leonid

2016-05-28

The pyridine-Ar (PAr) van der Waals (vdW) complex is studied using a high level ab initio method. Its structure, binding energy, and intermolecular vibrational states are determined from the analytical potential energy surface constructed from interaction energy (IE) values computed at the coupled cluster level of theory with single, double, and perturbatively included triple excitations with the augmented correlation consistent polarized valence double-ζ (aug-cc-pVDZ) basis set complemented by midbond functions. The structure of the complex at its global minimum with Ar at a distance of 3.509 Å from the pyridine plane and shifted by 0.218 Å from the center of mass towards nitrogen agrees well with the corresponding equilibrium structure derived previously from the rotational spectrum of PAr. The PAr binding energy De of 392 cm(-1) is close to that of 387 cm(-1) calculated earlier at the same ab initio level for the prototypical benzene-Ar (BAr) complex. However, under an extension of the basis set, De for PAr becomes slightly lower than De for BAr. The ab initio vdW vibrational energy levels allow us to estimate the reliability of the methods for the determination of the vdW fundamentals from the rotational spectra. To disclose the character of the intermolecular interaction in PAr, the symmetry-adapted perturbation theory (SAPT) is employed for the analysis of different physical contributions to IE. It is found that SAPT components of IE can be approximately expressed in the binding region by only two of them: the exchange repulsion and dispersion energy. The total induction effect is negligible. The interrelations between various SAPT components found for PAr are fulfilled for a few other complexes involving aromatic molecules and Ar or Ne, which indicates that they are valid for all rare gas (Rg) atoms and aromatics.

The analytical transfer matrix method for PT-symmetric complex potential

NASA Astrophysics Data System (ADS)

Naceri, Leila; Hammou, Amine B.

2017-07-01

We have extended the analytical transfer matrix (ATM) method to solve quantum mechanical bound state problems with complex PT-symmetric potentials. Our work focuses on a class of models studied by Bender and Jones, we calculate the energy eigenvalues, discuss the critical values of g and compare the results with those obtained from other methods such as exact numerical computation and WKB approximation method.

Nonlinear network model analysis of vibrational energy transfer and localisation in the Fenna-Matthews-Olson complex

NASA Astrophysics Data System (ADS)

Morgan, Sarah E.; Cole, Daniel J.; Chin, Alex W.

2016-11-01

Collective protein modes are expected to be important for facilitating energy transfer in the Fenna-Matthews-Olson (FMO) complex of photosynthetic green sulphur bacteria, however to date little work has focussed on the microscopic details of these vibrations. The nonlinear network model (NNM) provides a computationally inexpensive approach to studying vibrational modes at the microscopic level in large protein structures, whilst incorporating anharmonicity in the inter-residue interactions which can influence protein dynamics. We apply the NNM to the entire trimeric FMO complex and find evidence for the existence of nonlinear discrete breather modes. These modes tend to transfer energy to the highly connected core pigments, potentially opening up alternative excitation energy transfer routes through their influence on pigment properties. Incorporating localised modes based on these discrete breathers in the optical spectra calculations for FMO using ab initio site energies and excitonic couplings can substantially improve their agreement with experimental results.

Intermolecular configurations dominated by quadrupole-quadrupole electrostatic interactions: explicit correlation treatment of the five-dimensional potential energy surface and infrared spectra for the CO-N2 complex.

PubMed

Liu, Jing-Min; Zhai, Yu; Zhang, Xiao-Long; Li, Hui

2018-01-17

A thorough understanding of the intermolecular configurations of van der Waals complexes is a great challenge due to their weak interactions, floppiness and anharmonic nature. Although high-resolution microwave or infrared spectroscopy provides one of the most direct and precise pieces of experimental evidence, the origin and key role in determining such intermolecular configurations of a van der Waals system strongly depend on its highly accurate potential energy surface (PES) and a detailed analysis of its ro-vibrational wavefunctions. Here, a new five-dimensional potential energy surface for the van der Waals complex of CO-N 2 which explicitly incorporates the dependence on the stretch coordinate of the CO monomer is generated using the explicitly correlated couple cluster (CCSD(T)-F12) method in conjunction with a large basis set. Analytic four-dimensional PESs are obtained by the least-squares fitting of vibrationally averaged interaction energies for v = 0 and v = 1 to the Morse/Long-Range potential mode (V MLR ). These fits to 7966 points have root-mean-square deviations (RMSD) of 0.131 cm -1 and 0.129 cm -1 for v = 0 and v = 1, respectively, with only 315 parameters. Energy decomposition analysis is carried out, and it reveals that the dominant factor in controlling intermolecular configurations is quadrupole-quadrupole electrostatic interactions. Moreover, the rovibrational levels and wave functions are obtained for the first time. The predicted infrared transitions and intensities for the ortho-N 2 -CO complex as well as the calculated energy levels for para-N 2 -CO are in good agreement with the available experimental data with RMSD discrepancies smaller than 0.068 cm -1 . The calculated infrared band origin shift associated with the fundamental band frequency of CO is -0.721 cm -1 for ortho-N 2 -CO which is in excellent agreement with the experimental value of -0.739 cm -1 . The agreement with experimental values validates the high quality of the PESs and enhances our confidence to explain the observed mystery lines around 2163 cm -1 .

Analysis of Immune Complex Structure by Statistical Mechanics and Light Scattering Techniques.

NASA Astrophysics Data System (ADS)

Busch, Nathan Adams

1995-01-01

The size and structure of immune complexes determine their behavior in the immune system. The chemical physics of the complex formation is not well understood; this is due in part to inadequate characterization of the proteins involved, and in part by lack of sufficiently well developed theoretical techniques. Understanding the complex formation will permit rational design of strategies for inhibiting tissue deposition of the complexes. A statistical mechanical model of the proteins based upon the theory of associating fluids was developed. The multipole electrostatic potential for each protein used in this study was characterized for net protein charge, dipole moment magnitude, and dipole moment direction. The binding sites, between the model antigen and antibodies, were characterized for their net surface area, energy, and position relative to the dipole moment of the protein. The equilibrium binding graphs generated with the protein statistical mechanical model compares favorably with experimental data obtained from radioimmunoassay results. The isothermal compressibility predicted by the model agrees with results obtained from dynamic light scattering. The statistical mechanics model was used to investigate association between the model antigen and selected pairs of antibodies. It was found that, in accordance to expectations from thermodynamic arguments, the highest total binding energy yielded complex distributions which were skewed to higher complex size. From examination of the simulated formation of ring structures from linear chain complexes, and from the joint shape probability surfaces, it was found that ring configurations were formed by the "folding" of linear chains until the ends are within binding distance. By comparing the single antigen/two antibody system which differ only in their respective binding site locations, it was found that binding site location influences complex size and shape distributions only when ring formation occurs. The internal potential energy of a ring complex is considerably less than that of the non-associating system; therefore the ring complexes are quite stable and show no evidence of breaking, and collapsing into smaller complexes. The ring formation will occur only in systems where the total free energy of each complex may be minimized. Thus, ring formation will occur even though entropically unfavorable conformations result if the total free energy can be minimized by doing so.

Pyruvate dehydrogenase complex and nicotinamide nucleotide transhydrogenase constitute an energy-consuming redox circuit.

PubMed

Fisher-Wellman, Kelsey H; Lin, Chien-Te; Ryan, Terence E; Reese, Lauren R; Gilliam, Laura A A; Cathey, Brook L; Lark, Daniel S; Smith, Cody D; Muoio, Deborah M; Neufer, P Darrell

2015-04-15

Cellular proteins rely on reversible redox reactions to establish and maintain biological structure and function. How redox catabolic (NAD+/NADH) and anabolic (NADP+/NADPH) processes integrate during metabolism to maintain cellular redox homoeostasis, however, is unknown. The present work identifies a continuously cycling mitochondrial membrane potential (ΔΨm)-dependent redox circuit between the pyruvate dehydrogenase complex (PDHC) and nicotinamide nucleotide transhydrogenase (NNT). PDHC is shown to produce H2O2 in relation to reducing pressure within the complex. The H2O2 produced, however, is effectively masked by a continuously cycling redox circuit that links, via glutathione/thioredoxin, to NNT, which catalyses the regeneration of NADPH from NADH at the expense of ΔΨm. The net effect is an automatic fine-tuning of NNT-mediated energy expenditure to metabolic balance at the level of PDHC. In mitochondria, genetic or pharmacological disruptions in the PDHC-NNT redox circuit negate counterbalance changes in energy expenditure. At the whole animal level, mice lacking functional NNT (C57BL/6J) are characterized by lower energy-expenditure rates, consistent with their well-known susceptibility to diet-induced obesity. These findings suggest the integration of redox sensing of metabolic balance with compensatory changes in energy expenditure provides a potential mechanism by which cellular redox homoeostasis is maintained and body weight is defended during periods of positive and negative energy balance.

Optimizing energy functions for protein-protein interface design.

PubMed

Sharabi, Oz; Yanover, Chen; Dekel, Ayelet; Shifman, Julia M

2011-01-15

Protein design methods have been originally developed for the design of monomeric proteins. When applied to the more challenging task of protein–protein complex design, these methods yield suboptimal results. In particular, they often fail to recapitulate favorable hydrogen bonds and electrostatic interactions across the interface. In this work, we aim to improve the energy function of the protein design program ORBIT to better account for binding interactions between proteins. By using the advanced machine learning framework of conditional random fields, we optimize the relative importance of all the terms in the energy function, attempting to reproduce the native side-chain conformations in protein–protein interfaces. We evaluate the performance of several optimized energy functions, each describes the van der Waals interactions using a different potential. In comparison with the original energy function, our best energy function (a) incorporates a much “softer” repulsive van der Waals potential, suitable for the discrete rotameric representation of amino acid side chains; (b) does not penalize burial of polar atoms, reflecting the frequent occurrence of polar buried residues in protein–protein interfaces; and (c) significantly up-weights the electrostatic term, attesting to the high importance of these interactions for protein–protein complex formation. Using this energy function considerably improves side chain placement accuracy for interface residues in a large test set of protein–protein complexes. Moreover, the optimized energy function recovers the native sequences of protein–protein interface at a higher rate than the default function and performs substantially better in predicting changes in free energy of binding due to mutations.

An Energetic Concept of Habitability for the Deep Subsurface

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.

2006-01-01

Universally, life must be characterized by a characteristic level of order and complexity. In the most general sense, habitability could then be defined as the set of factors required to allow the creation and maintenance of molecular complexity. These factors are: chemical raw materials; energy with which to assemble those materials into complex molecules and sustain the resultant state of complexity; a solvent that allows the interaction of complex molecules, promotes tertiary structure, and permits compartmentalization; and environmental conditions that permit the assembly and maintenance of complex molecules. On Earth, these general requirements correspond to the major biogenic elements C, H, O, N, P, S; chemical or light energy; the solvent water; and specific ranges of temperature, pH, radiation, ionic strength, and so forth, which have thus far been determined on and exclusively empirical basis. Importantly, while the complete absence of any of these factors ensures uninhabitable conditions, the mere presence of all four does not guarantee habitability. In each case - even that of water - it is a question of degree. This question can be couched in quantitative terms by considering the impact of each of these factors on cellular energy balance. More "extreme" conditions (e.g., high temperature, high or low pH, etc.), lower water activity, and low concentrations of nutrients incur or have potential to be addressed by increased investment of energy on the part of the cell. This must be balanced by energy conservation in the cell, noting that biochemical, mass transport, and abiotic chemical limitations intervene between environmental energy availability and biological energy capture. Similarly, lower boundary conditions are emplaced on useful environmental energy yields by the "quantized" nature of biological energy conservation, and upper boundary conditions are emplaced by energy levels or fluxes that are destructive with respect to complexity. This energetic framework, with boundary conditions supplied by the specifics of the biochemistry in question, offers a generalized, yet quantitative means of assessing the habitability of any system with respect to complex life.

A computational study of the CO dissociation in cyclopentadienyl ruthenium complexes relevant to the racemization of alcohols.

PubMed

Stewart, Beverly; Nyhlen, Jonas; Martín-Matute, Belén; Bäckvall, Jan-E; Privalov, Timofei

2013-01-28

The formation of an active 16-electron ruthenium sec-alkoxide complex via loss of the CO ligand is an important step in the mechanism of the racemization of sec-alcohols by (η(5)-Ph(5)C(5))Ru(CO)(2)X ruthenium complexes with X = Cl and O(t)Bu. Here we show with accurate DFT calculations the potential energy profile of the CO dissociation pathway for a series of relevant (η(5)-Ph(5)C(5))Ru(CO)(2)X complexes, where X = Cl, O(t)Bu, H and COO(t)Bu. We have found that the CO dissociation energy increases in the following order: O(t)Bu (lowest), Cl, COO(t)Bu and H (highest). Using the distance between ruthenium and C(CO), r = Ru-C(CO), as a constraint, and by optimizing all other degrees of freedom for a range of Ru-CO distances, we obtained relative energies, ΔE(r) and geometries of a sufficient number of transient structures with the elongated Ru-CO bond up to r = 3.4 Å. Our calculations provide a quantitative understanding of the CO ligand dissociation in (η(5)-Ph(5)C(5))Ru(CO)(2)Cl and (η(5)-Ph(5)C(5))Ru(CO)(2)(O(t)Bu) complexes, which is relevant to the mechanism of their catalytic activity in the racemization of alcohols. We recently reported that exchange of the CO ligand by isotopically labeled (13)CO in the Ru-O(t)Bu complex occurs twenty times faster than that in the Ru-Cl complex. This corresponds to a difference of 1.8 kcal mol(-1) in the CO dissociation energy (at room temperature). This is in very good agreement with the calculated difference between the two potential energy curves for Ru-O(t)Bu and Ru-Cl complexes, which is about 1.8-2 kcal mol(-1) around the corresponding transition states of the CO dissociation. The calculated difference in the total energy for CO dissociation in (η(5)-Ph(5)C(5))Ru(CO)(2)X complexes is related to the stabilization provided by the X group in the final 16-electron complexes, which are formed via product-like transition states. In addition to the calculated transition states of CO dissociation in Ru-O(t)Bu and Ru-Cl complexes, the calculated transient structures with the elongated Ru-CO bond provide insight into how the geometry of the ruthenium complex with a potent heteroatom donor group (X) gradually changes when one of the COs is dissociating.

Dinuclear polypyridylruthenium(II) complexes: flow cytometry studies of their accumulation in bacteria and the effect on the bacterial membrane.

PubMed

Li, Fangfei; Feterl, Marshall; Warner, Jeffrey M; Keene, F Richard; Collins, J Grant

2013-12-01

To determine the energy dependency of and the contribution of the membrane potential to the cellular accumulation of the dinuclear complexes [{Ru(phen)2}2{μ-bbn}](4+) (Rubbn) and the mononuclear complexes [Ru(Me4phen)3](2+) and [Ru(phen)2(bb7)](2+) in Staphylococcus aureus and Escherichia coli, and to examine their effect on the bacterial membrane. The accumulation of the ruthenium complexes in bacteria was determined using flow cytometry at a range of temperatures. The cellular accumulation of the ruthenium complexes was also determined in cells that had been incubated with the metal complexes in the presence or absence of metabolic stimulators or inhibitors and/or commercial dyes to determine the membrane potential or membrane permeability. The accumulation of ruthenium complexes in the two bacterial strains was shown to increase with increasing incubation temperature, with the relative increase in accumulation greater with E. coli, particularly for Rubb12 and Rubb16. No decrease in accumulation was observed for Rubb12 in ATP-inhibited cells. While carbonyl cyanide m-chlorophenyl hydrazone (CCCP) did depolarize the cell membrane, no reduction in the accumulation of Rubb12 was observed; however, all ruthenium complexes, when incubated with S. aureus at concentrations twice their MIC, depolarized the membrane to a similar extent to CCCP. Except for the mononuclear complex [Ru(Me4phen)3](2+), incubation of any of the other ruthenium complexes allowed a greater quantity of the membrane-impermeable dye TO-PRO-3 to be taken up by S. aureus. The results indicate that the potential new antimicrobial Rubbn complexes enter the cell in an energy-independent manner, depolarize the cell membrane and significantly permeabilize the cellular membrane.

Ab initio studies of the Rg–NO{sup +}(X{sup 1}Σ{sup +}) van der Waals complexes (Rg = He, Ne, Ar, Kr, and Xe)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orek, Cahit; Bulut, Niyazi, E-mail: jklos@umd.edu, E-mail: francois.lique@univ-lehavre.fr, E-mail: bulut-niyazi@yahoo.com; Kłos, Jacek, E-mail: jklos@umd.edu, E-mail: francois.lique@univ-lehavre.fr, E-mail: bulut-niyazi@yahoo.com

2016-05-28

We used the explicitly correlated variant of the coupled clusters method with single, double, and noniterative triple excitations [CCSD(T)-F12] to compute two-dimensional potential energy surfaces of van der Waals complexes formed by rare gas atoms (Rg) and NO{sup +}(X{sup 1}Σ{sup +}) cations. We used the correlation-consistent, triple-zeta (cc-pVTZ-F12) atomic basis sets, and for Kr and Xe rare gases, we employed corresponding pseudopotential cc-pVTZ-PP-F12 atomic basis sets. These basis sets were additionally augmented with mid-bond functions. The complexes are all of skewed T-shape type with Rg atom being closer to the N-side. Using analytical representation of the potentials, we have estimatedmore » zero-point energy corrected dissociation energies from anharmonic calculations with BOUND program and also from the harmonic approximation. The binding energies increase with the polarization of the Rg atom in series from He to Xe and are 196 cm{sup −1}, 360 cm{sup −1}, 1024 cm{sup −1}, 1434 cm{sup −1}, and 2141 cm{sup −1}, respectively. Their corresponding dissociation energies are 132 cm{sup −1}, 300 cm{sup −1}, 927 cm{sup −1}, 1320 cm{sup −1}, and 1994 cm{sup −1} for the complexes with He to Xe, respectively. We find good agreement with previous theoretical and experimental results. The harmonic vibrational frequencies were calculated for the bending and stretching modes of the Rg–NO{sup +} complexes.« less

Resonances for Symmetric Two-Barrier Potentials

ERIC Educational Resources Information Center

Fernandez, Francisco M.

2011-01-01

We describe a method for the accurate calculation of bound-state and resonance energies for one-dimensional potentials. We calculate the shape resonances for symmetric two-barrier potentials and compare them with those coming from the Siegert approximation, the complex scaling method and the box-stabilization method. A comparison of the…

Vibrational spectroscopic investigation of the gold complexation within the cascade structure of phosphorus-containing dendrimer.

PubMed

Furer, V L; Vandyukov, A E; Majoral, J P; Caminade, A M; Gottis, S; Laurent, R; Kovalenko, V I

2018-05-29

The interaction of the phosphoric dendrimer with gold was performed by means of vibrational spectroscopy and quantum chemistry. Stable complexes are formed with a PN-PS linkage, whereas with an isolated PS bond this does not occur. The change in geometric parameters and delocalization of electric charge under the influence of gold was discovered. The classification of bands in the experimental vibrational spectra of the dendrimer and its complex was carried out. HOMO of molecule of the dendrimer is localized on the SPNP linkage, whereas the LUMO is located on the terminal group. In the SPNP linkage there is a noticeable delocalization of the charge which leads to a change in the reactivity of this group. Interaction energy was estimated as the difference between the energies of the complex and the energies of the molecules of the dendrimer G' 0 and two molecules AuCl and is equal to 25.2 eV. The ionization energy IE and electron affinity EA for AuCl are higher than for dendrimer, therefore, when the complex is formed, these quantities increases. Chemical potential and the electrophilicity index in the complex also increases. Copyright © 2018 Elsevier B.V. All rights reserved.

New chemical sources of energy: A theoretical study

NASA Astrophysics Data System (ADS)

Chaban, Galina

The research presented in this dissertation employs methods of quantum chemistry for the search of highly energetic chemical compounds that can have applications as possible energy sources. The areas of research include: (1) improvement of orbital optimization methods for different types of wavefunctions which leads to substantial savings of computer time and memory; (2) predicting new high energy isomers for singlet and triplet states of Nsb3F and their kinetic stability with respect to isomerisation and dissociation reactions; (3) estimation of minimum energy reaction paths for dissociation reactions of high energy isomers of Nsb2Osb2 including potential energy barriers and minimum energy crossing points between the closest singlet and triplet states; (4) investigation of thermodynamic and kinetic stability of Van der Waals complexes M-Hsb2 (M = Li, Be, B, C, Na, Mg, Al, Si) that can play an important role in improvement of energetic properties of hydrogen based rocket fuels; (5) mapping of the potential energy surface for AlHsb2 compound in the region of crossing between sp2Bsb2 and sp2Asb1 electronic states and predicting the kinetic stability of Al complex, which suggests that Al may be among the promising candidates for inclusion into solid hydrogen for the purpose of energy storage.

Modeling energy expenditure in children and adolescents using quantile regression

USDA-ARS?s Scientific Manuscript database

Advanced mathematical models have the potential to capture the complex metabolic and physiological processes that result in energy expenditure (EE). Study objective is to apply quantile regression (QR) to predict EE and determine quantile-dependent variation in covariate effects in nonobese and obes...

Lattice thermal conductivity of multi-component alloys

DOE PAGES

Caro, Magdalena; Béland, Laurent K.; Samolyuk, German D.; ...

2015-06-12

High entropy alloys (HEA) have unique properties including the potential to be radiation tolerant. These materials with extreme disorder could resist damage because disorder, stabilized by entropy, is the equilibrium thermodynamic state. Disorder also reduces electron and phonon conductivity keeping the damage energy longer at the deposition locations, eventually favoring defect recombination. In the short time-scales related to thermal spikes induced by collision cascades, phonons become the relevant energy carrier. In this paper, we perform a systematic study of phonon thermal conductivity in multiple component solid solutions represented by Lennard-Jones (LJ) potentials. We explore the conditions that minimize phonon meanmore » free path via extreme alloy complexity, by varying the composition and the elements (differing in mass, atomic radii, and cohesive energy). We show that alloy complexity can be tailored to modify the scattering mechanisms that control energy transport in the phonon subsystem. Finally, our analysis provides a qualitative guidance for the selection criteria used in the design of HEA alloys with low phonon thermal conductivity.« less

Computed Potential Energy Surfaces and Minimum Energy Pathway for Chemical Reactions

NASA Technical Reports Server (NTRS)

Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

1994-01-01

Computed potential energy surfaces are often required for computation of such observables as rate constants as a function of temperature, product branching ratios, and other detailed properties. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method with the Dunning correlation consistent basis sets to obtain accurate energetics, gives useful results for a number of chemically important systems. Applications to complex reactions leading to NO and soot formation in hydrocarbon combustion are discussed.

Oxidovanadium(IV) complexes involving dehydroacetic acid and β-diketones of bioinorganic and medicinal relevance: Their synthesis, characterization, thermal behavior and DFT aspects

NASA Astrophysics Data System (ADS)

Maurya, R. C.; Malik, B. A.; Mir, J. M.; Vishwakarma, P. K.

2015-03-01

Six new mixed-ligand complexes of oxidovanadium(IV) of the general composition [VO(dha)(L)(H2O)], where dhaH = dehydroacetic acid, LH = β-diketones, viz., acetoacetanilide (aaaH), o-acetoacetotoluidide (o-aatdH), o-acetoacetanisidide (o-aansH), acetylacetone (acacH), methyl acetoacetate (macacH) or ethyl acetoacetate (eacacH) have been synthesized by the reaction of VOSO4ṡ5H2O and the ligands given above in aqueous-ethanol medium. The resulting complexes have been characterized on the basis of elemental analyses, vanadium determination, molar conductance and magnetic measurements, mass spectrometry, thermogravimetric analysis, infrared and electron spin resonance spectral studies. The thermal decomposition processes of two representative complexes are discussed and the order of reaction (n) and the activation energy (Ea) for the particular decomposition steps have been calculated from thermogravimetric (TG) curve. Geometry optimizations were performed with the Gaussian 09 software package by using density functional theory (DFT) methods with Becke-3-Lee-Yang-Parr (B3LYP) hybrid exchange-correlation functional and the standard LANL2 MB basis set for dhaH and its complex [VO(dha)(acac)(H2O)]. Molecular surface electrostatic potentials (MSEP), vibrational frequency calculations, bond lengths, bond angles, dihedral angles, natural population analysis and calculations of molecular energies, HOMO and LUMO were made. No imaginary frequency was found in the optimized model compounds and hence ensures that the molecule is in the lowest point of the potential energy surface, that is, a energy minimum. Finally calculated results were applied to simulated Infrared spectra of the title compound which show good agreement with observed spectra. Based on experimental and theoretical data, suitable trans-octahedral structures have been proposed for these complexes.

Ab initio molecular orbital calculations on the associated complexes of lithium cyanide with ammonia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohandas, P.; Shivaglal, M.C.; Chandrasekhar, J.

Ab initio molecular orbital (MO) calculations with the 3-21G and 6-31G basis sets are carried out on a series of complexes of NH{sub 3} with Li{sup +}, C{triple_bond}N{sup -}, LiCN, and its isomer LiNC. The BSSE-corrected interaction energies, geometrical parameters, internal force constants, and harmonic vibrational frequencies are evaluated for 15 species. Complexes with trifurcated (C{sub 3v}) structures are calculated to be saddle points on the potential energy surfaces and have one imaginary frequency each. Calculated energies, geometrical parameters, internal force constants, and harmonic vibrational frequencies of the various species considered are discussed in terms of the nature of associationmore » of LiCN with ammonia. The vibrational frequencies of the relevant complexed species are compared with the experimental frequencies reported earlier for solutions of lithium cyanide in liquid ammonia. 40 refs., 1 fig., 4 tabs.« less

Structural basis for energy transduction by respiratory alternative complex III.

PubMed

Sousa, Joana S; Calisto, Filipa; Langer, Julian D; Mills, Deryck J; Refojo, Patrícia N; Teixeira, Miguel; Kühlbrandt, Werner; Vonck, Janet; Pereira, Manuela M

2018-04-30

Electron transfer in respiratory chains generates the electrochemical potential that serves as energy source for the cell. Prokaryotes can use a wide range of electron donors and acceptors and may have alternative complexes performing the same catalytic reactions as the mitochondrial complexes. This is the case for the alternative complex III (ACIII), a quinol:cytochrome c/HiPIP oxidoreductase. In order to understand the catalytic mechanism of this respiratory enzyme, we determined the structure of ACIII from Rhodothermus marinus at 3.9 Å resolution by single-particle cryo-electron microscopy. ACIII presents a so-far unique structure, for which we establish the arrangement of the cofactors (four iron-sulfur clusters and six c-type hemes) and propose the location of the quinol-binding site and the presence of two putative proton pathways in the membrane. Altogether, this structure provides insights into a mechanism for energy transduction and introduces ACIII as a redox-driven proton pump.

Quantum dynamics study on the binding of a positron to vibrationally excited states of hydrogen cyanide molecule

NASA Astrophysics Data System (ADS)

Takayanagi, Toshiyuki; Suzuki, Kento; Yoshida, Takahiko; Kita, Yukiumi; Tachikawa, Masanori

2017-05-01

We present computational results of vibrationally enhanced positron annihilation in the e+ + HCN/DCN collisions within a local complex potential model. Vibrationally elastic and inelastic cross sections and effective annihilation rates were calculated by solving a time-dependent complex-potential Schrödinger equation under the ab initio potential energy surface for the positron attached HCN molecule, [HCN; e+], with multi-component configuration interaction level (Kita and Tachikawa, 2014). We discuss the effect of vibrational excitation on the positron affinities from the obtained vibrational resonance features.

Theoretical studies for the rates and kinetic isotope effects of the excited-state double proton transfer in the 1:1 7-azaindole:H2O complex using variational transition state theory including multidimensional tunneling.

PubMed

Duong, My Phu Thi; Kim, Yongho

2010-03-18

Variational transition state theory calculations including multidimensional tunneling (VTST/MT) for excited-state tautomerization in the 1:1 7-azaindole:H(2)O complex were performed. Electronic structures and energies for reactant, product, transition state, and potential energy curves along the reaction coordinate were computed at the CASSCF(10,9)/6-31G(d,p) level of theory. The potential energies were corrected by second-order multireference perturbation theory to take the dynamic electron correlation into consideration. The final potential energy curves along the reaction coordinate were generated at the MRPT2//CASSCF(10,9)/6-31G(d,p) level. Two protons in the excited-state tautomerization are transferred concertedly, albeit asynchronously. The position of the variational transition state is very different from the conventional transition state, and is highly dependent on isotopic substitution. Rate constants were calculated using VTST/MT, and were on the order of 10(-6) s(-1) at room temperature. The HH/DD kinetic isotope effects are consistent with experimental observations; consideration of both tunneling and variational effects was essential to predict the experimental values correctly.

Investigations of the Rg-BrCl (Rg = He, Ne, Ar, Kr, Xe) binary van der Waals complexes: ab initio intermolecular potential energy surfaces, vibrational states and predicted pure rotational transition frequencies

NASA Astrophysics Data System (ADS)

Li, Song; Zheng, Rui; Chen, Shan-Jun; Chen, Yan; Chen, Peng

2017-03-01

The intermolecular potential energy surfaces (PESs) of the ground electronic state for the Rg-BrCl (Rg = He, Ne, Ar, Kr, Xe) van der Waals complexes have been constructed by using the coupled-cluster method in combination with the augmented quadruple-zeta correlation-consistent basis sets supplemented with an additional set of bond functions. The features of the anisotropic PESs for these complexes are remarkably similar, which are characterized by three minima and two saddle points between them. The global minimum corresponds to a collinear Rg-Br-Cl configuration. Two local minima, correlate with an anti-linear Rg-Cl-Br geometry and a nearly T-shaped structure, can also be located on each PES. The quantum bound state calculations enable us to investigate intermolecular vibrational states and rotational energy levels of the complexes. The transition frequencies are predicted and are fitted to obtain their corresponding spectroscopic constants. In general, the periodic trends are observed for this complex family. Comparisons with available experimental data for the collinear isomer of Ar-BrCl demonstrate reliability of our theoretical predictions, and our results for the other two isomers of Ar-BrCl as well as for other members of the complex family are also anticipated to be trustable. Except for the collinear isomer of Ar-BrCl, the data presented in this paper would be beneficial to improve our knowledge for these experimentally unknown species.

Dark gap solitons in exciton-polariton condensates in a periodic potential.

PubMed

Cheng, Szu-Cheng; Chen, Ting-Wei

2018-03-01

We show that dark spatial gap solitons can occur inside the band gap of an exciton-polariton condensate (EPC) in a one-dimensional periodic potential. The energy dispersions of an EPC loaded into a periodic potential show a band-gap structure. Using the effective-mass model of the complex Gross-Pitaevskii equation with pump and dissipation in an EPC in a periodic potential, dark gap solitons are demonstrated near the minimum energy points of the band center and band edge of the first and second bands, respectively. The excitation energies of dark gap solitons are below these minimum points and fall into the band gap. The spatial width of a dark gap soliton becomes smaller as the pump power is increased.

Dark gap solitons in exciton-polariton condensates in a periodic potential

NASA Astrophysics Data System (ADS)

Cheng, Szu-Cheng; Chen, Ting-Wei

2018-03-01

We show that dark spatial gap solitons can occur inside the band gap of an exciton-polariton condensate (EPC) in a one-dimensional periodic potential. The energy dispersions of an EPC loaded into a periodic potential show a band-gap structure. Using the effective-mass model of the complex Gross-Pitaevskii equation with pump and dissipation in an EPC in a periodic potential, dark gap solitons are demonstrated near the minimum energy points of the band center and band edge of the first and second bands, respectively. The excitation energies of dark gap solitons are below these minimum points and fall into the band gap. The spatial width of a dark gap soliton becomes smaller as the pump power is increased.

A new approach to the renewable energy-growth nexus: evidence from the USA.

PubMed

Gozgor, Giray

2018-06-01

The climate change is one of the leading problems in the today's world. The rise of the renewable energy meets the sustainable growth objectives since it can decelerate the climate change. For this purpose, this paper investigates the relationship between the renewable energy consumption and the economic growth in the United States (USA). Theoretically, the paper constructs the growth model that captures the effects of the economic complexity indicator as a measure of capabilities and productivity for exporting the "complex" (high value-added) products. Empirically, the paper uses the Autoregressive Distributed Lag (ARDL) estimations and observes that both the economic complexity and the renewable energy consumption lead to a higher rate of economic growth in the USA for the period from 1965 to 2016. The paper also discusses the potential policy implications of the results for achieving the sustainable growth objectives.

Energy and energy gradient matrix elements with N-particle explicitly correlated complex Gaussian basis functions with L =1

NASA Astrophysics Data System (ADS)

Bubin, Sergiy; Adamowicz, Ludwik

2008-03-01

In this work we consider explicitly correlated complex Gaussian basis functions for expanding the wave function of an N-particle system with the L =1 total orbital angular momentum. We derive analytical expressions for various matrix elements with these basis functions including the overlap, kinetic energy, and potential energy (Coulomb interaction) matrix elements, as well as matrix elements of other quantities. The derivatives of the overlap, kinetic, and potential energy integrals with respect to the Gaussian exponential parameters are also derived and used to calculate the energy gradient. All the derivations are performed using the formalism of the matrix differential calculus that facilitates a way of expressing the integrals in an elegant matrix form, which is convenient for the theoretical analysis and the computer implementation. The new method is tested in calculations of two systems: the lowest P state of the beryllium atom and the bound P state of the positronium molecule (with the negative parity). Both calculations yielded new, lowest-to-date, variational upper bounds, while the number of basis functions used was significantly smaller than in previous studies. It was possible to accomplish this due to the use of the analytic energy gradient in the minimization of the variational energy.

Energy and energy gradient matrix elements with N-particle explicitly correlated complex Gaussian basis functions with L=1.

PubMed

Bubin, Sergiy; Adamowicz, Ludwik

2008-03-21

In this work we consider explicitly correlated complex Gaussian basis functions for expanding the wave function of an N-particle system with the L=1 total orbital angular momentum. We derive analytical expressions for various matrix elements with these basis functions including the overlap, kinetic energy, and potential energy (Coulomb interaction) matrix elements, as well as matrix elements of other quantities. The derivatives of the overlap, kinetic, and potential energy integrals with respect to the Gaussian exponential parameters are also derived and used to calculate the energy gradient. All the derivations are performed using the formalism of the matrix differential calculus that facilitates a way of expressing the integrals in an elegant matrix form, which is convenient for the theoretical analysis and the computer implementation. The new method is tested in calculations of two systems: the lowest P state of the beryllium atom and the bound P state of the positronium molecule (with the negative parity). Both calculations yielded new, lowest-to-date, variational upper bounds, while the number of basis functions used was significantly smaller than in previous studies. It was possible to accomplish this due to the use of the analytic energy gradient in the minimization of the variational energy.

Classical trajectory studies of gas phase reaction dynamics and kinetics using ab initio potential energy surfaces

NASA Technical Reports Server (NTRS)

Jaffe, Richard L.; Pattengill, Merle D.; Schwenke, David W.

1989-01-01

Strategies for constructing global potential energy surfaces from a limited number of accurate ab initio electronic energy calculations are discussed. Generally, these data are concentrated in small regions of configuration space (e.g., in the vicinity of saddle points and energy minima) and difficulties arise in generating a potential function that is globally well-behaved. Efficient computer codes for carrying out classical trajectory calculations on vector and parallel processors are also described. Illustrations are given from recent work on the following chemical systems: Ca + HF yields CaF + H, H + H + H2 yields H2 + H2, N + O2 yields NO + O and O + N2 yields NO + N. The dynamics and kinetics of metathesis, dissociation, recombination, energy transfer and complex formation processes will be discussed.

Tongluo Xingnao Effervescent Tablet preserves mitochondrial energy metabolism and attenuates cognition deficits in APPswe/PS1De9 mice.

PubMed

Dai, Yuan; Ma, Tao; Ren, Xiangyi; Wei, Jiangping; Fu, Wenjun; Ma, Yuntong; Xu, Shijun; Zhang, Zhanjun

2016-09-06

Tongluo Xingnao Effervescent Tablet (TXET), a traditional Chinese herbal formula composed of Ligusticum chuanxiong hor, Scutellaria baicalensis Georgi and Angelica sinensis, has been widely used to treat Alzheimer's disease (AD) and related dementias for decades in China. In the present study, we investigated the effects of TXET on mitochondrial function, energy metabolism and cognitive amelioration in the APPswe/PS1De9 transgenetic mouse model of AD. The energy charge and phosphocreatine, activity of the mitochondrial electron transport chain complexes, mitochondrial membrane potential, activity of Na(+)-K(+) ATPase and the expression levels of Bcl-2 and Bax in the brains were measured, respectively. TXET exhibits significant protection on mitochondrial function and energy supply in addition to ameliorating cognitive decline in APPswe/PS1De9 mice. TXET rescues mitochondrial function by increasing the mitochondrial membrane potential, energy charge levels, activity of respiratory chain complexes and Na(+)-K(+) ATPase activity. These findings suggest that TXET may attenuate cognition impairment through the restoration of mitochondrial function and energy metabolism in the brains in APPswe/PS1De9 mice. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Voltage clustering in redox-active ligand complexes: mitigating electronic communication through choice of metal ion

DOE PAGES

Zarkesh, Ryan A.; Ichimura, Andrew S.; Monson, Todd C.; ...

2016-02-01

We used the redox-active bis(imino)acenapthene (BIAN) ligand to synthesize homoleptic aluminum, chromium, and gallium complexes of the general formula (BIAN) 3M. The resulting compounds were characterized using X-ray crystallography, NMR, EPR, magnetic susceptibility and cyclic voltammetry measurements and modeled using both DFT and ab initio wavefunction calculations to compare the orbital contributions of main group elements and transition metals in ligand-based redox events. Ultimately, complexes of this type have the potential to improve the energy density and electrolyte stability of grid-scale energy storage technologies, such as redox flow batteries, through thermodynamically-clustered redox events.

A decision support model for improving a multi-family housing complex based on CO2 emission from electricity consumption.

PubMed

Hong, Taehoon; Koo, Choongwan; Kim, Hyunjoong

2012-12-15

The number of deteriorated multi-family housing complexes in South Korea continues to rise, and consequently their electricity consumption is also increasing. This needs to be addressed as part of the nation's efforts to reduce energy consumption. The objective of this research was to develop a decision support model for determining the need to improve multi-family housing complexes. In this research, 1664 cases located in Seoul were selected for model development. The research team collected the characteristics and electricity energy consumption data of these projects in 2009-2010. The following were carried out in this research: (i) using the Decision Tree, multi-family housing complexes were clustered based on their electricity energy consumption; (ii) using Case-Based Reasoning, similar cases were retrieved from the same cluster; and (iii) using a combination of Multiple Regression Analysis, Artificial Neural Network, and Genetic Algorithm, the prediction performance of the developed model was improved. The results of this research can be used as follows: (i) as basic research data for continuously managing several energy consumption data of multi-family housing complexes; (ii) as advanced research data for predicting energy consumption based on the project characteristics; (iii) as practical research data for selecting the most optimal multi-family housing complex with the most potential in terms of energy savings; and (iv) as consistent and objective criteria for incentives and penalties. Copyright © 2012 Elsevier Ltd. All rights reserved.

Molecular orbital study of some eight-coordinate sulfur chelate complexes of molybdenum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perkins, P.G.; Schultz, F.A.

1983-03-30

A number of molybdenum complexes involving the formal oxidation states Mo(IV) and Mo(V) have been studied by a self-consistent-field molecular orbital technique. All the complexes were of dodecahedral geometry and had eight sulfurs chelated to the central metal atom. In all, a series of five tetrakis complexes was studied, including the ligands dithiocarbamate (dtc), thioxanthate (txn), 1,1-dicyano-2,2-ethylenedithiolate (i-mnt), 1-cyano-1-carbethoxy-2,2-ethylenedithiolate (ced), and 1,1-dicarbethoxy-2,2-ethylenedithiolate (ded). The 4d orbitals were included on molybdenum, and the empty 3d levels on all sulfur atoms. The results show that the highest occupied molecular orbital in each case has over 90% metal d/sub xy/ character. Further, themore » energy of this orbital is linearly related to the reversible half-wave potentials for Mo(IV) ..-->.. Mo(V) and Mo(V) ..-->.. Mo(VI) oxidations of the complexes. A further irreversible oxidation observed experimentally also is closely related to the calculated energy levels. Relationships between the calculated results and Mo 3d/sub 5///sub 2/ X-ray photoelectron binding energies, EPR parameters, and charge-transfer absorption energies are discussed. Electrochemical and spectroscopic properties of these MoS/sub 8/ complexes can be understood in terms of a manifold of orbital energies that retain approximately constant spacings between one another and that move up or down in absolute energy in response to the charge donated or withdrawn by the ligands.« less

Control of C-H Bond Activation by Mo-Oxo Complexes: pKa or Bond Dissociation Free Energy (BDFE)?

PubMed

Nazemi, Azadeh; Cundari, Thomas R

2017-10-16

A density functional theory (DFT) study (BMK/6-31+G(d)) was initiated to investigate the activation of benzylic carbon-hydrogen bonds by a molybdenum-oxo complex with a potentially redox noninnocent supporting ligand-a simple mimic of the active species of the enzyme ethylbenzene dehydrogenase (EBDH)-through deprotonation (C-H bond heterolysis) or hydrogen atom abstraction (C-H bond homolysis) routes. Activation free-energy barriers for neutral and anionic Mo-oxo complexes were high, but lower for anionic complexes than neutral complexes. Interesting trends as a function of substituents were observed that indicated significant H δ+ character in the transition states (TS), which was further supported by the preference for [2 + 2] addition over HAA for most complexes. Hence, it was hypothesized that C-H activation by these EBDH mimics is controlled more by the pK a than by the bond dissociation free energy of the C-H bond being activated. Therefore, the results suggest promising pathways for designing more efficient and selective catalysts for hydrocarbon oxidation based on EBDH active-site mimics.

Effects of oxidants and reductants on the efficiency of excitation transfer in green photosynthetic bacteria

NASA Technical Reports Server (NTRS)

Wang, J.; Brune, D. C.; Blankenship, R. E.

1990-01-01

The efficiency of energy transfer in chlorosome antennas in the green sulfur bacteria Chlorobium vibrioforme and Chlorobium limicola was found to be highly sensitive to the redox potential of the suspension. Energy transfer efficiencies were measured by comparing the absorption spectrum of the bacteriochlorophyll c or d pigments in the chlorosome to the excitation spectrum for fluorescence arising from the chlorosome baseplate and membrane-bound antenna complexes. The efficiency of energy transfer approaches 100% at low redox potentials induced by addition of sodium dithionite or other strong reductants, and is lowered to 10-20% under aerobic conditions or after addition of a variety of membrane-permeable oxidizing agents. The redox effect on energy transfer is observed in whole cells, isolated membranes and purified chlorosomes, indicating that the modulation of energy transfer efficiency arises within the antenna complexes and is not directly mediated by the redox state of the reaction center. It is proposed that chlorosomes contain a component that acts as a highly quenching center in its oxidized state, but is an inefficient quencher when reduced by endogenous or exogenous reductants. This effect may be a control mechanism that prevents cellular damage resulting from reaction of oxygen with reduced low-potential electron acceptors found in the green sulfur bacteria. The redox modulation effect is not observed in the green gliding bacterium Chloroflexus aurantiacus, which contains chlorosomes but does not contain low-potential electron acceptors.

Genetic Diversity and Genome Complexity of Sugarcane

USDA-ARS?s Scientific Manuscript database

Sugarcane (Saccharum spp.) as a C4 plant, is one of the most efficient crops in converting solar energy into chemical energy. Sugarcane cultivar improvement programs have not yet systematically utilized the most of the genetic sources of yield potential and resistance to stresses that may exist in t...

First Principles Dynamics and Coarse-Grained Characterization of Photoisomerization in Complex Environments

ERIC Educational Resources Information Center

Virshup, Aaron Michael

2009-01-01

Photoisomerization of conjugated systems is a common pathway for photomechanical energy conversion in biological chromophores. Such reactions are mediated by conical intersections (CIs)--points of degeneracy between different potential energy surfaces, which efficiently funnel population between electronic states. There are many examples of a…

Potential of mean force for human lysozyme camelid vhh hl6 antibody interaction studies

NASA Astrophysics Data System (ADS)

Wang, Yeng-Tseng; Liao, Jun-Min; Chen, Cheng-Lung; Su, Zhi-Yuan; Chen, Chang-Hung; Hu, Jeu-Jiun

2008-04-01

Calculating antigen-antibody interaction energies is crucial for understanding antigen-antibody associations in immunology. To shed further light into this equation, we study a separation of human lysozyme-camelid vhh hl6 antibody (cAb-HuL6) complex. The c-terminal end-to-end stretching of the lysozyme-antibody complex structures have been studied using potential of mean force (PMF) calculations based on molecular dynamics (MD) and explicit water model. For the lysozyme-antibody complex, there are six important intermediates in the c-terminal extensions process. Inclusion of our simulations may help to understand the binding mechanics of lysozyme-cAb-HuL6 antibody complex.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hormain, Laureline; Monnerville, Maurice, E-mail: maurice.monnerville@univ-lille1.fr; Toubin, Céline

The chlorine/water interface is of crucial importance in the context of atmospheric chemistry. Modeling the structure and dynamics at this interface requires an accurate description of the interaction potential energy surfaces. We propose here an analytical intermolecular potential that reproduces the interaction between the Cl{sub 2} molecule and a water molecule. Our functional form is fitted to a set of high level ab initio data using the coupled-cluster single double (triple)/aug-cc-p-VTZ level of electronic structure theory for the Cl{sub 2} − H{sub 2}O complex. The potential fitted to reproduce the three minima structures of 1:1 complex is validated by themore » comparison of ab initio results of Cl{sub 2} interacting with an increasing number of water molecules. Finally, the model potential is used to study the physisorption of Cl{sub 2} on a perfectly ordered hexagonal ice slab. The calculated adsorption energy, in the range 0.27 eV, shows a good agreement with previous experimental results.« less

Neural network potential for Al-Mg-Si alloys

NASA Astrophysics Data System (ADS)

Kobayashi, Ryo; Giofré, Daniele; Junge, Till; Ceriotti, Michele; Curtin, William A.

2017-10-01

The 6000 series Al alloys, which include a few percent of Mg and Si, are important in automotive and aviation industries because of their low weight, as compared to steels, and the fact their strength can be greatly improved through engineered precipitation. To enable atomistic-level simulations of both the processing and performance of this important alloy system, a neural network (NN) potential for the ternary Al-Mg-Si has been created. Training of the NN uses an extensive database of properties computed using first-principles density functional theory, including complex precipitate phases in this alloy. The NN potential accurately reproduces most of the pure Al properties relevant to the mechanical behavior as well as heat of solution, solute-solute, and solute-vacancy interaction energies, and formation energies of small solute clusters and precipitates that are required for modeling the early stage of precipitation and mechanical strengthening. This success not only enables future detailed studies of Al-Mg-Si but also highlights the ability of NN methods to generate useful potentials in complex alloy systems.

Modeling the Energy Use of a Connected and Automated Transportation System (Poster)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gonder, J.; Brown, A.

Early research points to large potential impacts of connected and automated vehicles (CAVs) on transportation energy use - dramatic savings, increased use, or anything in between. Due to a lack of suitable data and integrated modeling tools to explore these complex future systems, analyses to date have relied on simple combinations of isolated effects. This poster proposes a framework for modeling the potential energy implications from increasing penetration of CAV technologies and for assessing technology and policy options to steer them toward favorable energy outcomes. Current CAV modeling challenges include estimating behavior change, understanding potential vehicle-to-vehicle interactions, and assessing trafficmore » flow and vehicle use under different automation scenarios. To bridge these gaps and develop a picture of potential future automated systems, NREL is integrating existing modeling capabilities with additional tools and data inputs to create a more fully integrated CAV assessment toolkit.« less

Intermolecular interaction in nucleobases and dimethyl sulfoxide/water molecules: A DFT, NBO, AIM and NCI analysis.

PubMed

Venkataramanan, Natarajan Sathiyamoorthy; Suvitha, Ambigapathy; Kawazoe, Yoshiyuki

2017-11-01

This study aims to cast light on the physico-chemical nature and energetics of interactions between the nucleobases and water/DMSO molecules which occurs through the non-conventional CH⋯O/N-H bonds using a comprehensive quantum-chemical approach. The computed interaction energies do not show any appreciable change for all the nucleobase-solvent complexes, conforming the experimental findings on the hydration enthalpies. Compared to water, DMSO form complexes with high interaction energies. The quantitative molecular electrostatic potentials display a charge transfer during the complexation. NBO analysis shows the nucleobase-DMSO complexes, have higher stabilization energy values than the nucleobase-water complexes. AIM analysis illustrates that the in the nucleobase-DMSO complexes, SO⋯H-N type interaction have strongest hydrogen bond strength with high E HB values. Furthermore, the Laplacian of electron density and total electron density were negative indicating the partial covalent nature of bonding in these systems, while the other bonds are classified as noncovalent interactions. EDA analysis indicates, the electrostatic interaction is more pronounced in the case of nucleobase-water complexes, while the dispersion contribution is more dominant in nucleobase-DMSO complexes. NCI-RDG analysis proves the existence of strong hydrogen bonding in nucleobase-DMSO complex, which supports the AIM results. Copyright © 2017 Elsevier Inc. All rights reserved.

Investigations of the Rg-BrCl (Rg=He, Ne, Ar, Kr, Xe) binary van der Waals complexes: ab initio intermolecular potential energy surfaces, vibrational states and predicted pure rotational transition frequencies.

PubMed

Li, Song; Zheng, Rui; Chen, Shan-Jun; Chen, Yan; Chen, Peng

2017-03-05

The intermolecular potential energy surfaces (PESs) of the ground electronic state for the Rg-BrCl (Rg=He, Ne, Ar, Kr, Xe) van der Waals complexes have been constructed by using the coupled-cluster method in combination with the augmented quadruple-zeta correlation-consistent basis sets supplemented with an additional set of bond functions. The features of the anisotropic PESs for these complexes are remarkably similar, which are characterized by three minima and two saddle points between them. The global minimum corresponds to a collinear Rg-Br-Cl configuration. Two local minima, correlate with an anti-linear Rg-Cl-Br geometry and a nearly T-shaped structure, can also be located on each PES. The quantum bound state calculations enable us to investigate intermolecular vibrational states and rotational energy levels of the complexes. The transition frequencies are predicted and are fitted to obtain their corresponding spectroscopic constants. In general, the periodic trends are observed for this complex family. Comparisons with available experimental data for the collinear isomer of Ar-BrCl demonstrate reliability of our theoretical predictions, and our results for the other two isomers of Ar-BrCl as well as for other members of the complex family are also anticipated to be trustable. Except for the collinear isomer of Ar-BrCl, the data presented in this paper would be beneficial to improve our knowledge for these experimentally unknown species. Copyright © 2016 Elsevier B.V. All rights reserved.

Explicit correlation treatment of the six-dimensional potential energy surface and predicted infrared spectra for OCS-H2

NASA Astrophysics Data System (ADS)

Liu, Jing-Min; Zhai, Yu; Li, Hui

2017-07-01

An effective six-dimensional ab initio potential energy surface (PES) for H2-OCS which explicitly includes the intramolecular stretch normal modes of carbonyl sulfide (OCS) is presented. The electronic structure computations are carried out using the explicitly correlated coupled cluster [CCSD(T)-F12] method with the augmented correlation-consistent aug-cc-pVTZ basis set, and the accuracy is critically tested by performing a series of benchmark calculations. Analytic four-dimensional PESs are obtained by least-squares fitting vibrationally averaged interaction energies to the Morse/long-range potential model. These fits to 13 485 points have a root-mean-square deviation (RMSD) of 0.16 cm-1. The combined radial discrete variable representation/angular finite basis representation method and the Lanczos algorithm were employed to evaluate the rovibrational energy levels for five isotopic species of the OCS-hydrogen complexes. The predicted transition frequencies and intensities based on the resulting vibrationally averaged PESs are in good agreement with the available experimental values, whose RMSDs are smaller than 0.004 cm-1 for five different species of OCS-hydrogen complexes. The calculated infrared band origin shifts for all five species of OCS-hydrogen complexes are only 0.03 cm-1 smaller than the corresponding experimental values. These validate the high quality of our PESs which can be used for modeling OCS doped in hydrogen clusters to further study quantum solution and microscopic superfluidity. In addition, the analytic coordinate transformation functions between isotopologues are also derived due to the center of mass shifting of different isotope substitutes.

Exploring High School Students' Perceptions of Solar Energy and Solar Cells

ERIC Educational Resources Information Center

Kishore, Padmini; Kisiel, James

2013-01-01

Although studies examining student understanding of key concepts are common throughout the science education literature, few have examined science concepts linked to conservation or environmental issues such as global warming and alternative energy. How students make sense of these complex concepts has the potential to influence their role as…

Computed Potential Energy Surfaces and Minimum Energy Pathways for Chemical Reactions

NASA Technical Reports Server (NTRS)

Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

1994-01-01

Computed potential energy surfaces are often required for computation of such parameters as rate constants as a function of temperature, product branching ratios, and other detailed properties. For some dynamics methods, global potential energy surfaces are required. In this case, it is necessary to obtain the energy at a complete sampling of all the possible arrangements of the nuclei, which are energetically accessible, and then a fitting function must be obtained to interpolate between the computed points. In other cases, characterization of the stationary points and the reaction pathway connecting them is sufficient. These properties may be readily obtained using analytical derivative methods. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method to obtain accurate energetics, gives usefull results for a number of chemically important systems. The talk will focus on a number of applications including global potential energy surfaces, H + O2, H + N2, O(3p) + H2, and reaction pathways for complex reactions, including reactions leading to NO and soot formation in hydrocarbon combustion.

Energetic contribution potential of building-integrated photovoltaics on airports in warm climates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruether, Ricardo; LABSOLAR - Laboratorio de Energia Solar, UFSC - Universidade Federal de Santa Catarina, Caixa Postal 476, Florianopolis, SC 88040-900; Braun, Priscila

2009-10-15

Especially in warm climates, a considerable fraction of the electricity demand in commercial buildings is due to the intensive use of air-conditioning systems. Airport buildings in sunny and warm regions present a perfect match between energy demand and solar resource availability. Airport buildings are also typically large and horizontal, isolated and free of shading, and have a great potential for the integration of solar photovoltaic (PV) systems. In this work, we assess the potential impact in energy demand reduction at the Florianopolis International Airport in Brazil (27 S, 48 W) with the use of building-integrated photovoltaic (BIPV) systems. We analysemore » the building's hourly energy consumption and solar irradiation data, to assess the match between energy demand and potential generation, and we estimate the PV power necessary to supply both the total amount and fractions of the annual energy demand. Our results show that the integration of PV systems on airport buildings in warm climates can supply the entire electric power consumption of an airport complex, in line with the general concept of a zero-energy building (ZEB). (author)« less

Complex trajectories in a classical periodic potential

NASA Astrophysics Data System (ADS)

Anderson, Alexander G.; Bender, Carl M.

2012-11-01

This paper examines the complex trajectories of a classical particle in the potential V(x) = -cos (x). Almost all the trajectories describe a particle that hops from one well to another in an erratic fashion. However, it is shown analytically that there are two special classes of trajectories x(t) determined only by the energy of the particle and not by the initial position of the particle. The first class consists of periodic trajectories; that is, trajectories that return to their initial position x(0) after some real time T. The second class consists of trajectories for which there exists a real time T such that x(t + T) = x(t) ± 2π. These two classes of classical trajectories are analogous to valence and conduction bands in quantum mechanics, where the quantum particle either remains localized or else tunnels resonantly (conducts) through a crystal lattice. These two special types of trajectories are associated with sets of energies of measure 0. For other energies, it is shown that for long times the average velocity of the particle becomes a fractal-like function of energy.

Dynamics and Novel Mechanisms of SN2 Reactions on ab Initio Analytical Potential Energy Surfaces.

PubMed

Szabó, István; Czakó, Gábor

2017-11-30

We describe a novel theoretical approach to the bimolecular nucleophilic substitution (S N 2) reactions that is based on analytical potential energy surfaces (PESs) obtained by fitting a few tens of thousands high-level ab initio energy points. These PESs allow computing millions of quasi-classical trajectories thereby providing unprecedented statistical accuracy for S N 2 reactions, as well as performing high-dimensional quantum dynamics computations. We developed full-dimensional ab initio PESs for the F - + CH 3 Y [Y = F, Cl, I] systems, which describe the direct and indirect, complex-forming Walden-inversion, the frontside attack, and the new double-inversion pathways as well as the proton-transfer channels. Reaction dynamics simulations on the new PESs revealed (a) a novel double-inversion S N 2 mechanism, (b) frontside complex formation, (c) the dynamics of proton transfer, (d) vibrational and rotational mode specificity, (e) mode-specific product vibrational distributions, (f) agreement between classical and quantum dynamics, (g) good agreement with measured scattering angle and product internal energy distributions, and (h) significant leaving group effect in accord with experiments.

Symmetry blockade and its breakdown in energy equipartition of square graphene resonators

NASA Astrophysics Data System (ADS)

Wang, Yisen; Zhu, Zhigang; Zhang, Yong; Huang, Liang

2018-03-01

The interaction between flexural modes due to nonlinear potentials is critical to heat conductivity and mechanical vibration of two dimensional materials such as graphene. Much effort has been devoted to understanding the underlying mechanism. In this paper, we examine solely the out-of-plane flexural modes and identify their energy flow pathway during the equipartition process. In particular, the modes are grouped into four classes by their distinct symmetries. The couplings are significantly larger within a class than between classes, forming symmetry blockades. As a result, the energy first flows to the modes in the same symmetry class. Breakdown of the symmetry blockade, i.e., inter-class energy flow, starts when the displacement profile becomes complex and the inter-class couplings bear nonneglectable values. The equipartition time follows the stretched exponential law and survives in the thermodynamic limit. These results bring fundamental understandings to the Fermi-Pasta-Ulam problem in two dimensional systems with complex potentials and reveal clearly the physical picture of dynamical interactions between the flexural modes, which will be crucial to the understanding of their contribution in high thermal conductivity and mechanism of energy dissipation that may intrinsically limit the quality factor of the resonator.

DYNECHARM++: a toolkit to simulate coherent interactions of high-energy charged particles in complex structures

NASA Astrophysics Data System (ADS)

Bagli, Enrico; Guidi, Vincenzo

2013-08-01

A toolkit for the simulation of coherent interactions between high-energy charged particles and complex crystal structures, called DYNECHARM++ has been developed. The code has been written in C++ language taking advantage of this object-oriented programing method. The code is capable to evaluating the electrical characteristics of complex atomic structures and to simulate and track the particle trajectory within them. Calculation method of electrical characteristics based on their expansion in Fourier series has been adopted. Two different approaches to simulate the interaction have been adopted, relying on the full integration of particle trajectories under the continuum potential approximation and on the definition of cross-sections of coherent processes. Finally, the code has proved to reproduce experimental results and to simulate interaction of charged particles with complex structures.

Simultaneous realization of Hg2+ sensing, magnetic resonance imaging and upconversion luminescence in vitro and in vivo bioimaging based on hollow mesoporous silica coated UCNPs and ruthenium complex

NASA Astrophysics Data System (ADS)

Ge, Xiaoqian; Sun, Lining; Ma, Binbin; Jin, Di; Dong, Liang; Shi, Liyi; Li, Nan; Chen, Haige; Huang, Wei

2015-08-01

We have constructed a multifunctional nanoprobe with sensing and imaging properties by using hollow mesoporous silica coated upconversion nanoparticles (UCNPs) and Hg2+ responsive ruthenium (Ru) complex. The Ru complex was loaded into the hollow mesoporous silica and the UCNPs acted as an energy donor, transferring luminescence energy to the Ru complex. Furthermore, polyethylenimine (PEI) was assembled on the surface of mesoporous silica to achieve better hydrophilic and bio-compatibility. Upon addition of Hg2+, a blue shift of the absorption peak of the Ru complex is observed and the energy transfer process between the UCNPs and the Ru complex was blocked, resulting in an increase of the green emission intensity of the UCNPs. The un-changed 801 nm emission of the nanoprobe was used as an internal standard reference and the detection limit of Hg2+ was determined to be 0.16 μM for this nanoprobe in aqueous solution. In addition, based on the low cytotoxicity as studied by CCK-8 assay, the nanoprobe was successfully applied for cell imaging and small animal imaging. Furthermore, when doped with Gd3+ ions, the nanoprobe was successfully applied to in vivo magnetic resonance imaging (MRI) of Kunming mice, which demonstrates its potential as a MRI positive-contrast agent. Therefore, the method and results may provide more exciting opportunities to afford nanoprobes with multimodal bioimaging and multifunctional applications.We have constructed a multifunctional nanoprobe with sensing and imaging properties by using hollow mesoporous silica coated upconversion nanoparticles (UCNPs) and Hg2+ responsive ruthenium (Ru) complex. The Ru complex was loaded into the hollow mesoporous silica and the UCNPs acted as an energy donor, transferring luminescence energy to the Ru complex. Furthermore, polyethylenimine (PEI) was assembled on the surface of mesoporous silica to achieve better hydrophilic and bio-compatibility. Upon addition of Hg2+, a blue shift of the absorption peak of the Ru complex is observed and the energy transfer process between the UCNPs and the Ru complex was blocked, resulting in an increase of the green emission intensity of the UCNPs. The un-changed 801 nm emission of the nanoprobe was used as an internal standard reference and the detection limit of Hg2+ was determined to be 0.16 μM for this nanoprobe in aqueous solution. In addition, based on the low cytotoxicity as studied by CCK-8 assay, the nanoprobe was successfully applied for cell imaging and small animal imaging. Furthermore, when doped with Gd3+ ions, the nanoprobe was successfully applied to in vivo magnetic resonance imaging (MRI) of Kunming mice, which demonstrates its potential as a MRI positive-contrast agent. Therefore, the method and results may provide more exciting opportunities to afford nanoprobes with multimodal bioimaging and multifunctional applications. Electronic supplementary information (ESI) available: DLS of Ru-UCNPs@HmSiO2-PEI in water. The zeta potential. The XRD patterns. EDX spectrum of Ru-UCNPs@HmSiO2-PEI. FT-IR spectra. N2 adsorption-desorption isotherm and pore size distribution. The investigation of the stability of Ru-UCNPs@HmSiO2-PEI. TG curves. UV/Vis absorption spectra of Ru complex at different concentrations. The sensitivity test of Ru-UCNPs@HmSiO2-PEI towards Hg2+. Cell viabilities of HeLa cells incubated with Ru-UCNPs@HmSiO2-PEI. See DOI: 10.1039/c5nr04006j

Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.

PubMed

Rappoport, Dmitrij; Galvin, Cooper J; Zubarev, Dmitry Yu; Aspuru-Guzik, Alán

2014-03-11

While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles.

Unraveling the Nature of Chemical Reactivity of Complex Systems

DTIC Science & Technology

2009-01-13

28 J. Zhou, J. J. Lin, W. Shiu, and K. Liu, J. Chem. Phys. 119, 4997 2003. 29 S. C. Althorpe, F. Fernandez - Alonso , B. D. Bean, J. D. Ayers, A. E...Truhlar DG, Espinosa- Garcia J (2000) Potential energy surface, thermal, and state-selected rate coefficients, and kinetic isotope effects for Cl CH43...HCl CH3. J Chem Phys 112:9375–9389. 22. Rangel C, Navarrete M, Corchado JC, Espinosa- Garcia J (2006) Potential energy surface, kinetics, and

DOE Office of Scientific and Technical Information (OSTI.GOV)

Croft, J. F. E.; Makrides, C.; Li, M.

A fundamental question in the study of chemical reactions is how reactions proceed at a collision energy close to absolute zero. This question is no longer hypothetical: quantum degenerate gases of atoms and molecules can now be created at temperatures lower than a few tens of nanokelvin. Here we consider the benchmark ultracold reaction between, the most-celebrated ultracold molecule, KRb and K. We map out an accurate ab initio ground-state potential energy surface of the K 2Rb complex in full dimensionality and report numerically-exact quantum-mechanical reaction dynamics. The distribution of rotationally resolved rates is shown to be Poissonian. An analysismore » of the hyperspherical adiabatic potential curves explains this statistical character revealing a chaotic distribution for the short-range collision complex that plays a key role in governing the reaction outcome.« less

All-Atom Four-Body Knowledge-Based Statistical Potentials to Distinguish Native Protein Structures from Nonnative Folds

PubMed Central

2017-01-01

Recent advances in understanding protein folding have benefitted from coarse-grained representations of protein structures. Empirical energy functions derived from these techniques occasionally succeed in distinguishing native structures from their corresponding ensembles of nonnative folds or decoys which display varying degrees of structural dissimilarity to the native proteins. Here we utilized atomic coordinates of single protein chains, comprising a large diverse training set, to develop and evaluate twelve all-atom four-body statistical potentials obtained by exploring alternative values for a pair of inherent parameters. Delaunay tessellation was performed on the atomic coordinates of each protein to objectively identify all quadruplets of interacting atoms, and atomic potentials were generated via statistical analysis of the data and implementation of the inverted Boltzmann principle. Our potentials were evaluated using benchmarking datasets from Decoys-‘R'-Us, and comparisons were made with twelve other physics- and knowledge-based potentials. Ranking 3rd, our best potential tied CHARMM19 and surpassed AMBER force field potentials. We illustrate how a generalized version of our potential can be used to empirically calculate binding energies for target-ligand complexes, using HIV-1 protease-inhibitor complexes for a practical application. The combined results suggest an accurate and efficient atomic four-body statistical potential for protein structure prediction and assessment. PMID:29119109

Cost-Effective Method for Free-Energy Minimization in Complex Systems with Elaborated Ab Initio Potentials.

PubMed

Bistafa, Carlos; Kitamura, Yukichi; Martins-Costa, Marilia T C; Nagaoka, Masataka; Ruiz-López, Manuel F

2018-06-12

We describe a method to locate stationary points in the free-energy hypersurface of complex molecular systems using high-level correlated ab initio potentials. In this work, we assume a combined QM/MM description of the system although generalization to full ab initio potentials or other theoretical schemes is straightforward. The free-energy gradient (FEG) is obtained as the mean force acting on relevant nuclei using a dual level strategy. First, a statistical simulation is carried out using an appropriate, low-level quantum mechanical force-field. Free-energy perturbation (FEP) theory is then used to obtain the free-energy derivatives for the target, high-level quantum mechanical force-field. We show that this composite FEG-FEP approach is able to reproduce the results of a standard free-energy minimization procedure with high accuracy, while simultaneously allowing for a drastic reduction of both computational and wall-clock time. The method has been applied to study the structure of the water molecule in liquid water at the QCISD/aug-cc-pVTZ level of theory, using the sampling from QM/MM molecular dynamics simulations at the B3LYP/6-311+G(d,p) level. The obtained values for the geometrical parameters and for the dipole moment of the water molecule are within the experimental error, and they also display an excellent agreement when compared to other theoretical estimations. The developed methodology represents therefore an important step toward the accurate determination of the mechanism, kinetics, and thermodynamic properties of processes in solution, in enzymes, and in other disordered chemical systems using state-of-the-art ab initio potentials.

The role of inertial fusion energy in the energy marketplace of the 21st century and beyond

NASA Astrophysics Data System (ADS)

John Perkins, L.

The viability of inertial fusion in the 21st century and beyond will be determined by its ultimate cost, complexity, and development path relative to other competing, long term, primary energy sources. We examine this potential marketplace in terms of projections for population growth, energy demands, competing fuel sources and environmental constraints (CO 2), and show that the two competitors for inertial fusion energy (IFE) in the medium and long term are methane gas hydrates and advanced, breeder fission; both have potential fuel reserves that will last for thousands of years. Relative to other classes of fusion concepts, we argue that the single largest advantage of the inertial route is the perception by future customers that the IFE fusion power core could achieve credible capacity factors, a result of its relative simplicity, the decoupling of the driver and reactor chamber, and the potential to employ thick liquid walls. In particular, we show that the size, cost and complexity of the IFE reactor chamber is little different to a fission reactor vessel of the same thermal power. Therefore, relative to fission, because of IFE's tangible advantages in safety, environment, waste disposal, fuel supply and proliferation, our research in advanced targets and innovative drivers can lead to a certain, reduced-size driver at which future utility executives will be indifferent to the choice of an advanced fission plant or an advanced IFE power plant; from this point on, we have a competitive commercial product. Finally, given that the major potential customer for energy in the next century is the present developing world, we put the case for future IFE "reservations" which could be viable propositions providing sufficient reliability and redundancy can be realized for each modular reactor unit.

Strong CH/O interactions between polycyclic aromatic hydrocarbons and water: Influence of aromatic system size.

PubMed

Veljković, Dušan Ž

2018-03-01

Energies of CH/O interactions between water molecule and polycyclic aromatic hydrocarbons with a different number of aromatic rings were calculated using ab initio calculations at MP2/cc-PVTZ level. Results show that an additional aromatic ring in structure of polycyclic aromatic hydrocarbons significantly strengthens CH/O interactions. Calculated interaction energies in optimized structures of the most stable tetracene/water complex is -2.27 kcal/mol, anthracene/water is -2.13 kcal/mol and naphthalene/water is -1.97 kcal/mol. These interactions are stronger than CH/O contacts in benzene/water complex (-1.44 kcal/mol) while CH/O contacts in tetracene/water complex are even stronger than CH/O contacts in pyridine/water complexes (-2.21 kcal/mol). Electrostatic potential maps for different polycyclic aromatic hydrocarbons were calculated and used to explain trends in the energies of interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

Mechanistic insights into energy conservation by flavin-based electron bifurcation.

PubMed

Lubner, Carolyn E; Jennings, David P; Mulder, David W; Schut, Gerrit J; Zadvornyy, Oleg A; Hoben, John P; Tokmina-Lukaszewska, Monika; Berry, Luke; Nguyen, Diep M; Lipscomb, Gina L; Bothner, Brian; Jones, Anne K; Miller, Anne-Frances; King, Paul W; Adams, Michael W W; Peters, John W

2017-06-01

The recently realized biochemical phenomenon of energy conservation through electron bifurcation provides biology with an elegant means to maximize utilization of metabolic energy. The mechanism of coordinated coupling of exergonic and endergonic oxidation-reduction reactions by a single enzyme complex has been elucidated through optical and paramagnetic spectroscopic studies revealing unprecedented features. Pairs of electrons are bifurcated over more than 1 volt of electrochemical potential by generating a low-potential, highly energetic, unstable flavin semiquinone and directing electron flow to an iron-sulfur cluster with a highly negative potential to overcome the barrier of the endergonic half reaction. The unprecedented range of thermodynamic driving force that is generated by flavin-based electron bifurcation accounts for unique chemical reactions that are catalyzed by these enzymes.

Theory after experiment on sensing mechanism of a newly developed sensor molecule: Converging or diverging?

NASA Astrophysics Data System (ADS)

Paul, Suvendu; Karar, Monaj; Das, Biswajit; Mallick, Arabinda; Majumdar, Tapas

2017-12-01

Fluoride ion sensing mechanism of 3,3‧-bis(indolyl)-4-chlorophenylmethane has been analyzed with density functional and time-dependent density functional theories. Extensive theoretical calculations on molecular geometry & energy, charge distribution, orbital energies & electronic distribution, minima on potential energy surface confirmed strong hydrogen bonded sensor-anion complex with incomplete proton transfer in S0. In S1, strong hydrogen bonding extended towards complete ESDPT. The distinct and single minima on the PES of the sensor-anion complex for both ground and first singlet excited states confirmed the concerted proton transfer mechanism. Present study well reproduced the experimental spectroscopic data and provided ESDPT as probable fluoride sensing mechanism.

VTST/MT studies of the catalytic mechanism of C-H activation by transition metal complexes with [Cu2(μ-O2)], [Fe2(μ-O2)] and Fe(IV)-O cores based on DFT potential energy surfaces.

PubMed

Kim, Yongho; Mai, Binh Khanh; Park, Sumin

2017-04-01

High-valent Cu and Fe species, which are generated from dioxygen activation in metalloenzymes, carry out the functionalization of strong C-H bonds. Understanding the atomic details of the catalytic mechanism has long been one of the main objectives of bioinorganic chemistry. Large H/D kinetic isotope effects (KIEs) were observed in the C-H activation by high-valent non-heme Cu or Fe complexes in enzymes and their synthetic models. The H/D KIE depends significantly on the transition state properties, such as structure, energies, frequencies, and shape of the potential energy surface, when the tunneling effect is large. Therefore, theoretical predictions of kinetic parameters such as rate constants and KIEs can provide a reliable link between atomic-level quantum mechanical mechanisms and experiments. The accurate prediction of the tunneling effect is essential to reproduce the kinetic parameters. The rate constants and HD/KIE have been calculated using the variational transition-state theory including multidimensional tunneling based on DFT potential energy surfaces along the reaction coordinate. Excellent agreement was observed between the predicted and experimental results, which assures the validity of the DFT potential energy surfaces and, therefore, the proposed atomic-level mechanisms. The [Cu 2 (μ-O) 2 ], [Fe 2 (μ-O) 2 ], and Fe(IV)-oxo species were employed for C-H activation, and their role as catalysts was discussed at an atomic level.

Computational design of enzyme-ligand binding using a combined energy function and deterministic sequence optimization algorithm.

PubMed

Tian, Ye; Huang, Xiaoqiang; Zhu, Yushan

2015-08-01

Enzyme amino-acid sequences at ligand-binding interfaces are evolutionarily optimized for reactions, and the natural conformation of an enzyme-ligand complex must have a low free energy relative to alternative conformations in native-like or non-native sequences. Based on this assumption, a combined energy function was developed for enzyme design and then evaluated by recapitulating native enzyme sequences at ligand-binding interfaces for 10 enzyme-ligand complexes. In this energy function, the electrostatic interaction between polar or charged atoms at buried interfaces is described by an explicitly orientation-dependent hydrogen-bonding potential and a pairwise-decomposable generalized Born model based on the general side chain in the protein design framework. The energy function is augmented with a pairwise surface-area based hydrophobic contribution for nonpolar atom burial. Using this function, on average, 78% of the amino acids at ligand-binding sites were predicted correctly in the minimum-energy sequences, whereas 84% were predicted correctly in the most-similar sequences, which were selected from the top 20 sequences for each enzyme-ligand complex. Hydrogen bonds at the enzyme-ligand binding interfaces in the 10 complexes were usually recovered with the correct geometries. The binding energies calculated using the combined energy function helped to discriminate the active sequences from a pool of alternative sequences that were generated by repeatedly solving a series of mixed-integer linear programming problems for sequence selection with increasing integer cuts.

Comment on 'Supersymmetry, PT-symmetry and spectral bifurcation'

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bagchi, B., E-mail: bbagchi123@rediffmail.com; Quesne, C., E-mail: cquesne@ulb.ac.be

2011-02-15

We demonstrate that the recent paper by Abhinav and Panigrahi entitled 'Supersymmetry, PT-symmetry and spectral bifurcation' [K. Abhinav, P.K. Panigrahi, Ann. Phys. 325 (2010) 1198], which considers two different types of superpotentials for the PT-symmetric complexified Scarf II potential, fails to take into account the invariance under the exchange of its coupling parameters. As a result, they miss the important point that for unbroken PT-symmetry this potential indeed has two series of real energy eigenvalues, to which one can associate two different superpotentials. This fact was first pointed out by the present authors during the study of complex potentials havingmore » a complex sl(2) potential algebra.« less

Repulsive nature of optical potentials for high-energy heavy-ion scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Furumoto, T.; Sakuragi, Y.; Yamamoto, Y.

2010-10-15

The recent works by the present authors predicted that the real part of heavy-ion optical potentials changes its character from attraction to repulsion around the incident energy per nucleon E/A=200-300 MeV on the basis of the complex G-matrix interaction and the double-folding model (DFM) and revealed that the three-body force plays an important role there. In the present paper, we have precisely analyzed the energy dependence of the calculated DFM potentials and its relation to the elastic-scattering angular distributions in detail in the case of the {sup 12}C+{sup 12}C system in the energy range of E/A=100-400 MeV. The tensor forcemore » contributes substantially to the energy dependence of the real part of the DFM potentials and plays an important role to lower the attractive-to-repulsive transition energy. The nearside and farside (N/F) decompositions of the elastic-scattering amplitudes clarify the close relation between the attractive-to-repulsive transition of the potentials and the characteristic evolution of the calculated angular distributions with the increase of the incident energy. Based on the present analysis, we propose experimental measurements for the predicted strong diffraction phenomena of the elastic-scattering angular distribution caused by the N/F interference around the attractive-to-repulsive transition energy together with the reduced diffractions below and above the transition energy.« less

Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics.

PubMed

Galvelis, Raimondas; Sugita, Yuji

2017-06-13

The free energy calculations of complex chemical and biological systems with molecular dynamics (MD) are inefficient due to multiple local minima separated by high-energy barriers. The minima can be escaped using an enhanced sampling method such as metadynamics, which apply bias (i.e., importance sampling) along a set of collective variables (CV), but the maximum number of CVs (or dimensions) is severely limited. We propose a high-dimensional bias potential method (NN2B) based on two machine learning algorithms: the nearest neighbor density estimator (NNDE) and the artificial neural network (ANN) for the bias potential approximation. The bias potential is constructed iteratively from short biased MD simulations accounting for correlation among CVs. Our method is capable of achieving ergodic sampling and calculating free energy of polypeptides with up to 8-dimensional bias potential.

Optical potential from first principles

DOE PAGES

Rotureau, J.; Danielewicz, P.; Hagen, G.; ...

2017-02-15

Here, we develop a method to construct a microscopic optical potential from chiral interactions for nucleon-nucleus scattering. The optical potential is constructed by combining the Green’s function approach with the coupled-cluster method. To deal with the poles of the Green’s function along the real energy axis we employ a Berggren basis in the complex energy plane combined with the Lanczos method. Using this approach, we perform a proof-of-principle calculation of the optical potential for the elastic neutron scattering on 16O. For the computation of the ground-state of 16O, we use the coupled-cluster method in the singles-and-doubles approximation, while for themore » A ±1 nuclei we use particle-attached/removed equation-of-motion method truncated at two-particle-one-hole and one-particle-two-hole excitations, respectively. We verify the convergence of the optical potential and scattering phase shifts with respect to the model-space size and the number of discretized complex continuum states. We also investigate the absorptive component of the optical potential (which reflects the opening of inelastic channels) by computing its imaginary volume integral and find an almost negligible absorptive component at low-energies. To shed light on this result, we computed excited states of 16O using equation-of-motion coupled-cluster method with singles-and- doubles excitations and we found no low-lying excited states below 10 MeV. Furthermore, most excited states have a dominant two-particle-two-hole component, making higher-order particle-hole excitations necessary to achieve a precise description of these core-excited states. We conclude that the reduced absorption at low-energies can be attributed to the lack of correlations coming from the low-order cluster truncation in the employed coupled-cluster method.« less

Excited state electron and energy relays in supramolecular dinuclear complexes revealed by ultrafast optical and X-ray transient absorption spectroscopy.

PubMed

Hayes, Dugan; Kohler, Lars; Hadt, Ryan G; Zhang, Xiaoyi; Liu, Cunming; Mulfort, Karen L; Chen, Lin X

2018-01-28

The kinetics of photoinduced electron and energy transfer in a family of tetrapyridophenazine-bridged heteroleptic homo- and heterodinuclear copper(i) bis(phenanthroline)/ruthenium(ii) polypyridyl complexes were studied using ultrafast optical and multi-edge X-ray transient absorption spectroscopies. This work combines the synthesis of heterodinuclear Cu(i)-Ru(ii) analogs of the homodinuclear Cu(i)-Cu(i) targets with spectroscopic analysis and electronic structure calculations to first disentangle the dynamics at individual metal sites by taking advantage of the element and site specificity of X-ray absorption and theoretical methods. The excited state dynamical models developed for the heterodinuclear complexes are then applied to model the more challenging homodinuclear complexes. These results suggest that both intermetallic charge and energy transfer can be observed in an asymmetric dinuclear copper complex in which the ground state redox potentials of the copper sites are offset by only 310 meV. We also demonstrate the ability of several of these complexes to effectively and unidirectionally shuttle energy between different metal centers, a property that could be of great use in the design of broadly absorbing and multifunctional multimetallic photocatalysts. This work provides an important step toward developing both a fundamental conceptual picture and a practical experimental handle with which synthetic chemists, spectroscopists, and theoreticians may collaborate to engineer cheap and efficient photocatalytic materials capable of performing coulombically demanding chemical transformations.

Energy transfer between surface-immobilized light-harvesting chlorophyll a/b complex (LHCII) studied by surface plasmon field-enhanced fluorescence spectroscopy (SPFS).

PubMed

Lauterbach, Rolf; Liu, Jing; Knoll, Wolfgang; Paulsen, Harald

2010-11-16

The major light-harvesting chlorophyll a/b complex (LHCII) of the photosynthetic apparatus in green plants can be viewed as a protein scaffold binding and positioning a large number of pigment molecules that combines rapid and efficient excitation energy transfer with effective protection of its pigments from photobleaching. These properties make LHCII potentially interesting as a light harvester (or a model thereof) in photoelectronic applications. Most of such applications would require the LHCII to be immobilized on a solid surface. In a previous study we showed the immobilization of recombinant LHCII on functionalized gold surfaces via a 6-histidine tag (His tag) in the protein moiety. In this work the occurrence and efficiency of Förster energy transfer between immobilized LHCII on a functionalized surface have been analyzed by surface plasmon field-enhanced fluorescence spectroscopy (SPFS). A near-infrared dye was attached to some but not all of the LHC complexes, serving as an energy acceptor to chlorophylls. Analysis of the energy transfer from chlorophylls to this acceptor dye yielded information about the extent of intercomplex energy transfer between immobilized LHCII.

Chapter 28: Nanomaterials for Energy Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hurst, Katherine E; Luther, Joseph M; Ban, Chunmei

2017-01-02

A wide variety of nanomaterials have been applied to energy related applications, including nanofibers, nanocrystalline materials, nanoparticles, and thin film nanocoatings. Solid-state lighting offers significant advantages in energy efficiency compared to traditional lighting technologies. The potential for nanostructured solid-state lighting devices is excellent as it enjoys significant economic drivers in energy efficiency. Fuel cells convert chemical energy to electrical energy through electrochemical reactions at an anode and cathode. The conversion of biomass to fuels and chemicals offers great potential to reduce energy dependence on petroleum and reduce green house gas emissions. Batteries involve the production and storage of electrical charge,more » the transfer of cations and electrical current, each based on electrochemical reactions and chemical reactants. Battery performance relies on the complex processes and factors that affect the transport of charge in the reactants, and across the interface between the chemical phases.« less

Learning free energy landscapes using artificial neural networks.

PubMed

Sidky, Hythem; Whitmer, Jonathan K

2018-03-14

Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to varied free energy landscapes. Further, user-specified parameters are in general non-intuitive yet significantly affect the convergence rate and accuracy of the free energy estimate. Here we propose a novel method, wherein artificial neural networks (ANNs) are used to develop an adaptive biasing potential which learns free energy landscapes. We demonstrate that this method is capable of rapidly adapting to complex free energy landscapes and is not prone to boundary or oscillation problems. The method is made robust to hyperparameters and overfitting through Bayesian regularization which penalizes network weights and auto-regulates the number of effective parameters in the network. ANN sampling represents a promising innovative approach which can resolve complex free energy landscapes in less time than conventional approaches while requiring minimal user input.

Learning free energy landscapes using artificial neural networks

NASA Astrophysics Data System (ADS)

Sidky, Hythem; Whitmer, Jonathan K.

2018-03-01

Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to varied free energy landscapes. Further, user-specified parameters are in general non-intuitive yet significantly affect the convergence rate and accuracy of the free energy estimate. Here we propose a novel method, wherein artificial neural networks (ANNs) are used to develop an adaptive biasing potential which learns free energy landscapes. We demonstrate that this method is capable of rapidly adapting to complex free energy landscapes and is not prone to boundary or oscillation problems. The method is made robust to hyperparameters and overfitting through Bayesian regularization which penalizes network weights and auto-regulates the number of effective parameters in the network. ANN sampling represents a promising innovative approach which can resolve complex free energy landscapes in less time than conventional approaches while requiring minimal user input.

Some improvements in DNA interaction calculations

NASA Technical Reports Server (NTRS)

Egan, J. T.; Swissler, T. J.; Rein, R.

1974-01-01

Calculations are made on specific DNA-type complexes using refined expressions for electrostatic and polarization energies. Dispersion and repulsive terms are included in the evaluation of the total interaction energy. It is shown that the expansion of the electrostatic potential to include multipole moments up to octopole is necessary to achieve convergence of first-order energies. Polarization energies are not as sensitive to this expansion. The calculations also support the usefulness of the hard sphere model for DNA hydrogen bonds and indicate how stacking interactions are influenced by second-order energies.

Mobilizing Public Markets to Finance Renewable Energy Projects: Insights from Expert Stakeholders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schwabe, P.; Mendelsohn, M.; Mormann, F.

Financing renewable energy projects in the United States can be a complex process. Most equity investment in new renewable power production facilities is supported by tax credits and accelerated depreciation benefits, and is constrained by the pool of potential investors that can fully use these tax benefits and are willing to engage in complex financial structures. For debt financing, non-government lending has largely been provided by foreign banks that may be under future lending constraints due to economic and regulatory conditions. To discuss renewable energy financing challenges and to identify new sources of capital to the U.S. market, two roundtablemore » discussions were held with renewable energy and financing experts in April 2012. This report summarizes the key messages of those discussions and is designed to provide insights to the U.S. market and inform the international conversation on renewable energy financing innovations.« less

Role of B800 in carotenoid-bacteriochlorophyll energy and electron transfer in LH2 complexes from the purple bacterium Rhodobacter sphaeroides.

PubMed

Polívka, Tomas; Niedzwiedzki, Dariusz; Fuciman, Marcel; Sundström, Villy; Frank, Harry A

2007-06-28

The role of the B800 in energy and electron transfer in LH2 complexes has been studied using femtosecond time-resolved transient absorption spectroscopy. The B800 site was perturbed by application of lithium dodecyl sulfate (LDS), and comparison of treated and untreated LH2 complexes from Rhodobacter sphaeroides incorporating carotenoids neurosporene, spheroidene, and spheroidenone was used to explore the role of B800 in carotenoid to bacteriochlorophyll-a (BChla) energy transfer and carotenoid radical formation. Efficiencies of the S1-mediated energy transfer in the LDS-treated complexes were 86, 61, and 57% in the LH2 complexes containing neurosporene, spheroidene, and spheroidenone, respectively. Analysis of the carotenoid S1 lifetimes in solution, LDS-treated, and untreated LH2 complexes allowed determination of B800/B850 branching ratio in the S1-mediated energy transfer. It is shown that B800 is a major acceptor, as approximately 60% of the energy from the carotenoid S1 state is accepted by B800. This value is nearly independent of conjugation length of the carotenoid. In addition to its role in energy transfer, the B800 BChla is the only electron acceptor in the event of charge separation between carotenoid and BChla in LH2 complexes, which is demonstrated by prevention of carotenoid radical formation in the LDS-treated LH2 complexes. In the untreated complexes containing neurosporene and spheroidene, the carotenoid radical is formed with a time constant of 300-400 fs. Application of different excitation wavelengths and intensity dependence of the carotenoid radical formation showed that the carotenoid radical can be formed only after excitation of the S2 state of carotenoid, although the S2 state itself is not a precursor of the charge-separated state. Instead, either a hot S1 state or a charge-transfer state lying between S2 and S1 states of the carotenoid are discussed as potential precursors of the charge-separated state.

Quantum damped oscillator II: Bateman’s Hamiltonian vs. 2D parabolic potential barrier

NASA Astrophysics Data System (ADS)

Chruściński, Dariusz

2006-04-01

We show that quantum Bateman’s system which arises in the quantization of a damped harmonic oscillator is equivalent to a quantum problem with 2D parabolic potential barrier known also as 2D inverted isotropic oscillator. It turns out that this system displays the family of complex eigenvalues corresponding to the poles of analytical continuation of the resolvent operator to the complex energy plane. It is shown that this representation is more suitable than the hyperbolic one used recently by Blasone and Jizba.

Theoretical investigation of the He4Br2 conformers.

PubMed

Valdés, Álvaro; Prosmiti, Rita; Villarreal, Pablo; Delgado-Barrio, Gerardo

2012-07-05

Full dimensional quantum dynamics calculations of the three lowest isomers of the He(4)Br(2) van der Waals molecule in its ground electronic state are reported. The calculations are performed using the multiconfiguration time-dependent Hartree (MCTDH) method and a realistic potential form that includes the sum of three body ab initio coupled-cluster single double triple [CCSD(T)] He-Br(2) interactions plus the He-He and Br-Br interactions. This potential exhibits several multiple minima, with the three lowest ones lying very close in energy, just within 2 cm(-1). Such small differences are also found in the calculated binding energies of the three most stable conformers, indicating the floppiness of the system and, thus, the need of accurate potential forms and quantum full dynamics methods to treat this kind of complexes. The 12 dimensional results reported in this work present benchmark data and, thus, can serve to evaluate approximate methods aiming to describe higher order rare gas-dihalogen (N > 4) complexes. A comparison with previous studies using different potential forms and approaches to the energetics for the He(4)Br(2) cluster is also presented.

Coarse graining of NN inelastic interactions up to 3 GeV: Repulsive versus structural core

NASA Astrophysics Data System (ADS)

Fernández-Soler, P.; Ruiz Arriola, E.

2017-07-01

The repulsive short-distance core is one of the main paradigms of nuclear physics which even seems confirmed by QCD lattice calculations. On the other hand nuclear potentials at short distances are motivated by high energy behavior where inelasticities play an important role. We analyze NN interactions up to 3 GeV in terms of simple coarse grained complex and energy dependent interactions. We discuss two possible and conflicting scenarios which share the common feature of a vanishing wave function at the core location in the particular case of S waves. We find that the optical potential with a repulsive core exhibits a strong energy dependence whereas the optical potential with the structural core is characterized by a rather adiabatic energy dependence which allows one to treat inelasticity perturbatively. We discuss the possible implications for nuclear structure calculations of both alternatives.

Complexes with Tunable Intramolecular Ferrocene to Ti(IV) Electronic Transitions: Models for Solid State Fe(II) to Ti(IV) Charge Transfer.

PubMed

Turlington, Michael D; Pienkos, Jared A; Carlton, Elizabeth S; Wroblewski, Karlee N; Myers, Alexis R; Trindle, Carl O; Altun, Zikri; Rack, Jeffrey J; Wagenknecht, Paul S

2016-03-07

Iron(II)-to-titanium(IV) metal-to-metal-charge transfer (MMCT) is important in the photosensitization of TiO2 by ferrocyanide, charge transfer in solid-state metal-oxide photocatalysts, and has been invoked to explain the blue color of sapphire, blue kyanite, and some lunar material. Herein, a series of complexes with alkynyl linkages between ferrocene (Fc) and Ti(IV) has been prepared and characterized by UV-vis spectroscopy and electrochemistry. Complexes with two ferrocene substituents include Cp2Ti(C2Fc)2, Cp*2Ti(C2Fc)2, and Cp2Ti(C4Fc)2. Complexes with a single ferrocene utilize a titanocene with a trimethylsilyl derivatized Cp ring, (TMS)Cp, and comprise the complexes (TMS)Cp2Ti(C2Fc)(C2R), where R = C6H5, p-C6H4CF3, and CF3. The complexes are compared to Cp2Ti(C2Ph)2, which lacks the second metal. Cyclic voltammetry for all complexes reveals a reversible Ti(IV/III) reduction wave and an Fe(II/III) oxidation that is irreversible for all complexes except (TMS)Cp2Ti(C2Fc)(C2CF3). All of the complexes with both Fc and Ti show an intense absorption (4000 M(-1)cm(-1) < ε < 8000 M(-1)cm(-1)) between 540 and 630 nm that is absent in complexes lacking a ferrocene donor. The energy of the absorption tracks with the difference between the Ti(IV/III) and Fe(III/II) reduction potentials, shifting to lower energy as the difference in potentials decreases. Reorganization energies, λ, have been determined using band shape analysis (2600 cm(-1) < λ < 5300 cm(-1)) and are in the range observed for other donor-acceptor complexes that have a ferrocene donor. Marcus-Hush-type analysis of the electrochemical and spectroscopic data are consistent with the assignment of the low-energy absorption as a MMCT band. TD-DFT analysis also supports this assignment. Solvatochromism is apparent for the MMCT band of all complexes, there being a bathochromic shift upon increasing polarizability of the solvent. The magnitude of the shift is dependent on both the electron density at Ti(IV) and the identity of the linker between the titanocene and the Fc. Complexes with a MMCT are photochemically stable, whereas Cp2Ti(C2Ph)2 rapidly decomposes upon photolysis.

a Theoretical Search for AN Electronic Spectrum of the He-BeO Complex

NASA Astrophysics Data System (ADS)

Gardner, Adrian; Heaven, Michael

2014-06-01

The surprisingly high dissociation energy of the He-Be bond in the He-BeO complex was first reported 25 years ago. Following which, a number of theoretical studies have investigated similar closed shell helium containing complexes. However, despite these investigations, a complex containing a strong He-X bond has thus far eluded experimental detection. In this work, potential energy surfaces of electronically excited states of the He-BeO complex have been calculated employing high level CASSCF+MRCI+Q methodologies and utilizing extended basis sets. Several excited states show strong interactions between helium and BeO lying in Franck-Condon accessible windows of electronic transitions arising from the vibrationless electronic ground state. It is hoped that the conclusions of this study will result in the observation an electronic spectrum of this long hypothesized strongly bound complex in the near future. W. Koch, J. R. Collins and G. Frenking, Chem. Phys. Lett. 1986, 132 330-333.

Spectrophotometric and spectroscopic studies of charge transfer complex of 1-Naphthylamine as an electron donor with picric acid as an electron acceptor in different polar solvents

NASA Astrophysics Data System (ADS)

Singh, Neeti; Ahmad, Afaq

2010-08-01

The charge transfer complex of 1-Naphthylamine as a donor with π-acceptor picric acid has been studied spectrophotometrically in different solvents at room temperature. The results indicate that the formation of charge transfer complex is high in less polar solvent. The stoichiometry of the complex was found to be 1:1 by straight line method. The data are analysed in terms of formation constant ( KCT), molar extinction coefficient ( ɛCT), standard free energy (Δ G o), oscillator strength ( ƒ), transition dipole moment ( μ EN), resonance energy ( R N) and ionization potential ( I D). It is concluded that the formation constant ( KCT) of the complex is found to be depends upon the nature of both electron acceptor and donor and also on the polarity of solvents. Further the charge transfer molecular complex between picric acid and 1-Naphthylamine is stabilized by hydrogen bonding.

Lowest-energy structures of (C60)nX (X=Li+,Na+,K+,Cl-) and (C60)nYCl (Y=Li,Na,K) clusters for n

PubMed

Hernández-Rojas, J; Bretón, J; Gomez Llorente, J M; Wales, D J

2004-12-22

Basin-hopping global optimization is used to find likely candidates for the lowest minima on the potential energy surface of (C(60))(n)X (X=Li(+),Na(+),K(+),Cl(-)) and (C(60))(n)YCl (Y=Li,Na,K) clusters with n

Benefits estimation framework for automated vehicle operations.

DOT National Transportation Integrated Search

2015-08-01

Automated vehicles have the potential to bring about transformative safety, mobility, energy, and environmental benefits to the surface transportation system. They are also being introduced into a complex transportation system, where second-order imp...

Teleconnections in complex human-Earth system models

NASA Astrophysics Data System (ADS)

Calvin, K. V.; Edmonds, J.

2017-12-01

Human systems and physical Earth systems are closely coupled and interact in complex ways that are sometimes surprising. This presentation discusses a few examples of system interactions. We consider the coupled energy-water-land-economy systems. We show how reductions in fossil fuel emissions are inversely coupled to land rents, food prices and deforestation. We discuss how water shortages in one part of the world is propagated to other distant parts of the world. We discuss the sensitivity of international trade patterns to energy and land systems technology and markets, and the potentially unanticipated results that can emerge.

Study of local currents in low dimension materials using complex injecting potentials

NASA Astrophysics Data System (ADS)

He, Shenglai; Covington, Cody; Varga, Kálmán

2018-04-01

A complex potential is constructed to inject electrons into the conduction band, mimicking electron currents in nanoscale systems. The injected electrons are time propagated until a steady state is reached. The local current density can then be calculated to show the path of the conducting electrons on an atomistic level. The method allows for the calculation of the current density vectors within the medium as a function of energy of the conducting electron. Using this method, we investigate the electron pathway of graphene nanoribbons in various structures, molecular junctions, and black phosphorus nanoribbons. By analyzing the current flow through the structures, we find strong dependence on the structural geometry and the energy of the injected electrons. This method may be of general use in the study of nano-electronic materials and interfaces.

Universality and chaoticity in ultracold K+KRb chemical reactions

DOE PAGES

Croft, J. F. E.; Makrides, C.; Li, M.; ...

2017-07-19

A fundamental question in the study of chemical reactions is how reactions proceed at a collision energy close to absolute zero. This question is no longer hypothetical: quantum degenerate gases of atoms and molecules can now be created at temperatures lower than a few tens of nanokelvin. Here we consider the benchmark ultracold reaction between, the most-celebrated ultracold molecule, KRb and K. We map out an accurate ab initio ground-state potential energy surface of the K 2Rb complex in full dimensionality and report numerically-exact quantum-mechanical reaction dynamics. The distribution of rotationally resolved rates is shown to be Poissonian. An analysismore » of the hyperspherical adiabatic potential curves explains this statistical character revealing a chaotic distribution for the short-range collision complex that plays a key role in governing the reaction outcome.« less

Determining the magnitude and direction of photoinduced ligand field switching in photochromic metal-organic complexes: molybdenum-tetracarbonyl spirooxazine complexes.

PubMed

Paquette, Michelle M; Patrick, Brian O; Frank, Natia L

2011-07-06

The ability to optically switch or tune the intrinsic properties of transition metals (e.g., redox potentials, emission/absorption energies, and spin states) with photochromic metal-ligand complexes is an important strategy for developing "smart" materials. We have described a methodology for using metal-carbonyl complexes as spectroscopic probes of ligand field changes associated with light-induced isomerization of photochromic ligands. Changes in ligand field between the ring-closed spirooxazine (SO) and ring-opened photomerocyanine (PMC) forms of photochromic azahomoadamantyl and indolyl phenanthroline-spirooxazine ligands are demonstrated through FT-IR, (13)C NMR, and computational studies of their molybdenum-tetracarbonyl complexes. The frontier molecular orbitals (MOs) of the SO and PMC forms differ considerably in both electron density distributions and energies. Of the multiple π* MOs in the SO and PMC forms of the ligands, the LUMO+1, a pseudo-b(1)-symmetry phenanthroline-based MO, mixes primarily with the Mo(CO)(4) fragment and provides the major pathway for Mo(d)→phen(π*) backbonding. The LUMO+1 is found to be 0.2-0.3 eV lower in energy in the SO form relative to the PMC form, suggesting that the SO form is a better π-acceptor. Light-induced isomerization of the photochromic ligands was therefore found to lead to changes in the energies of their frontier MOs, which in turn leads to changes in π-acceptor ability and ligand field strength. Ligand field changes associated with photoisomerizable ligands allow tuning of excited-state and ground-state energies that dictate energy/electron transfer, optical/electrical properties, and spin states of a metal center upon photoisomerization, positioning photochromic ligand-metal complexes as promising targets for smart materials.

Mechanistic insights into energy conservation by flavin-based electron bifurcation

DOE PAGES

Lubner, Carolyn E.; Jennings, David P.; Mulder, David W.; ...

2017-04-10

The recently realized biochemical phenomenon of energy conservation through electron bifurcation provides biology with an elegant means to maximize utilization of metabolic energy. The mechanism of coordinated coupling of exergonic and endergonic oxidation-reduction reactions by a single enzyme complex has been elucidated through optical and paramagnetic spectroscopic studies revealing unprecedented features. Pairs of electrons are bifurcated over more than 1 volt of electrochemical potential by generating a low-potential, highly energetic, unstable flavin semiquinone and directing electron flow to an iron-sulfur cluster with a highly negative potential to overcome the barrier of the endergonic half reaction. As a result, the unprecedentedmore » range of thermodynamic driving force that is generated by flavin-based electron bifurcation accounts for unique chemical reactions that are catalyzed by these enzymes.« less

Mechanistic insights into energy conservation by flavin-based electron bifurcation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lubner, Carolyn E.; Jennings, David P.; Mulder, David W.

The recently realized biochemical phenomenon of energy conservation through electron bifurcation provides biology with an elegant means to maximize utilization of metabolic energy. The mechanism of coordinated coupling of exergonic and endergonic oxidation-reduction reactions by a single enzyme complex has been elucidated through optical and paramagnetic spectroscopic studies revealing unprecedented features. Pairs of electrons are bifurcated over more than 1 volt of electrochemical potential by generating a low-potential, highly energetic, unstable flavin semiquinone and directing electron flow to an iron-sulfur cluster with a highly negative potential to overcome the barrier of the endergonic half reaction. As a result, the unprecedentedmore » range of thermodynamic driving force that is generated by flavin-based electron bifurcation accounts for unique chemical reactions that are catalyzed by these enzymes.« less

Invisible defects in complex crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Longhi, Stefano, E-mail: stefano.longhi@fisi.polimi.it; Della Valle, Giuseppe

2013-07-15

We show that invisible localized defects, i.e. defects that cannot be detected by an outside observer, can be realized in a crystal with an engineered imaginary potential at the defect site. The invisible defects are synthesized by means of supersymmetric (Darboux) transformations of an ordinary crystal using band-edge wavefunctions to construct the superpotential. The complex crystal has an entire real-valued energy spectrum and Bragg scattering is not influenced by the defects. An example of complex crystal synthesis is presented for the Mathieu potential. -- Highlights: •We show the existence of invisible localized defects in complex crystals. •They turn out tomore » be fully invisible to Bloch waves belonging to any lattice band. •An example of invisible defect is presented for a PT-symmetric Mathieu crystal.« less

Cytochrome bc1 complexes of microorganisms.

PubMed Central

Trumpower, B L

1990-01-01

The cytochrome bc1 complex is the most widely occurring electron transfer complex capable of energy transduction. Cytochrome bc1 complexes are found in the plasma membranes of phylogenetically diverse photosynthetic and respiring bacteria, and in the inner mitochondrial membrane of all eucaryotic cells. In all of these species the bc1 complex transfers electrons from a low-potential quinol to a higher-potential c-type cytochrome and links this electron transfer to proton translocation. Most bacteria also possess alternative pathways of quinol oxidation capable of circumventing the bc1 complex, but these pathways generally lack the energy-transducing, protontranslocating activity of the bc1 complex. All cytochrome bc1 complexes contain three electron transfer proteins which contain four redox prosthetic groups. These are cytochrome b, which contains two b heme groups that differ in their optical and thermodynamic properties; cytochrome c1, which contains a covalently bound c-type heme; and a 2Fe-2S iron-sulfur protein. The mechanism which links proton translocation to electron transfer through these proteins is the proton motive Q cycle, and this mechanism appears to be universal to all bc1 complexes. Experimentation is currently focused on understanding selected structure-function relationships prerequisite for these redox proteins to participate in the Q-cycle mechanism. The cytochrome bc1 complexes of mitochondria differ from those of bacteria, in that the former contain six to eight supernumerary polypeptides, in addition to the three redox proteins common to bacteria and mitochondria. These extra polypeptides are encoded in the nucleus and do not contain redox prosthetic groups. The functions of the supernumerary polypeptides of the mitochondrial bc1 complexes are generally not known and are being actively explored by genetically manipulating these proteins in Saccharomyces cerevisiae. Images PMID:2163487

Achieving DFT accuracy with a machine-learning interatomic potential: Thermomechanics and defects in bcc ferromagnetic iron

NASA Astrophysics Data System (ADS)

Dragoni, Daniele; Daff, Thomas D.; Csányi, Gábor; Marzari, Nicola

2018-01-01

We show that the Gaussian Approximation Potential (GAP) machine-learning framework can describe complex magnetic potential energy surfaces, taking ferromagnetic iron as a paradigmatic challenging case. The training database includes total energies, forces, and stresses obtained from density-functional theory in the generalized-gradient approximation, and comprises approximately 150,000 local atomic environments, ranging from pristine and defected bulk configurations to surfaces and generalized stacking faults with different crystallographic orientations. We find the structural, vibrational, and thermodynamic properties of the GAP model to be in excellent agreement with those obtained directly from first-principles electronic-structure calculations. There is good transferability to quantities, such as Peierls energy barriers, which are determined to a large extent by atomic configurations that were not part of the training set. We observe the benefit and the need of using highly converged electronic-structure calculations to sample a target potential energy surface. The end result is a systematically improvable potential that can achieve the same accuracy of density-functional theory calculations, but at a fraction of the computational cost.

A Separable Insertion Method to Calculate Atomic and Molecular Resonances on a FE-DVR Grid using Exterior Complex Scaling

NASA Astrophysics Data System (ADS)

Abeln, Brant Anthony

The study of metastable electronic resonances, anion or neutral states of finite lifetime, in molecules is an important area of research where currently no theoretical technique is generally applicable. The role of theory is to calculate both the position and width, which is proportional to the inverse of the lifetime, of these resonances and how they vary with respect to nuclear geometry in order to generate potential energy surfaces. These surfaces are the basis of time-dependent models of the molecular dynamics where the system moves towards vibrational excitation or fragmentation. Three fundamental electronic processes that can be modeled this way are dissociative electronic attachment, vibrational excitation through electronic impact and autoionization. Currently, experimental investigation into these processes is being preformed on polyatomic molecules while theoreticians continue their fifty-year-old search for robust methods to calculate them. The separable insertion method, investigated in this thesis, seeks to tackle the problem of calculating metastable resonances by using existing quantum chemistry tools along with a grid-based method employing exterior complex scaling (ECS). Modern quantum chemistry methods are extremely efficient at calculating ground and (bound) excited electronic states of atoms and molecules by utilizing Gaussian basis functions. These functions provide both a numerically fast and analytic solution to the necessary two-electron, six-dimensional integrals required in structure calculations. However, these computer programs, based on analytic Gaussian basis sets, cannot construct solutions that are not square-integrable, such as resonance wavefunctions. ECS, on the other hand, can formally calculate resonance solutions by rotating the asymptotic electronic coordinates into the complex plane. The complex Siegert energies for resonances, Eres = ER - iGamma/2 where ER is the real-valued position of the resonance and Gamma is the width of the resonance, can be found directly as an isolated pole in the complex energy plane. Unlike the straight complex scaling, ECS on the electronic coordinates overcomes the non-analytic behavior of the nuclear attraction potential, as a function of complex [special characters omitted] where the sum is over each nucleus in a molecular system. Discouragingly, the Gaussian basis functions, which are computationally well-suited for bound electronic structure, fail at forming an effective basis set for ECS due to the derivative discontinuity generated by the complex coordinate rotation and the piecewise defined contour. This thesis seeks to explore methods for implementing ECS indirectly without losing the numerical simplicity and power of Gaussian basis sets. The separable insertion method takes advantage of existing software by constructing a N2-term separable potential of the target system using Gaussian functions to be inserted into a finite-element discrete variable representation (FE-DVR) grid that implements ECS. This work reports an exhaustive investigation into this approach for calculating resonances. This thesis shows that this technique is successful at describing an anion shape resonance of a closed-shell atom or molecule in the static-exchange approximation. This method is applied to the 2P Be-, 2pig N2- and 2pi u CO2- shape resonances to calculate their complex Seigert energies. Additionally, many details on the exact construction of the separable potential and of the expansion basis are explored. The future work considers methods for faster convergence of the resonance energy, moving beyond the static-exchange approximation and applying this technique to polyatomic systems of interest.

Quantum chemical studies on hypothetical Fischer type Mo(CO)5[C(OEt)Me] and Mo(CO)5[C(OMe)Et] carbene complexes

NASA Astrophysics Data System (ADS)

Gövdeli, Nezafet; Karakaş, Duran

2018-07-01

Quantum chemical calculations at B3LYP/LANL2DZ/6-31G(d) level were made on anti-eclipsed, anti-staggered, syn-eclipsed, syn-staggered conformers of hypothetical Fischer type Mo(CO)5[C(OEt)Me] and Mo(CO)5[C(OMe)Et] carbene complexes in the gas phase. The most stable conformer of the complexes was found to be anti-staggered according to the total energy values calculated at given level. Structural parameters, vibration spectra, charge distributions, molecular orbital energy diagrams, contour diagrams of frontier orbitals, molecular electrostatic potential maps and some electronic structure descriptors were obtained for the most stable conformers. NMR spectra of the most stable conformers were calculated at GIAO/B3LYP/LANL2DZ level. The most stable conformer geometry was found to be distorted octahedral. IR and NMR spectra of the complexes are consistent with their geometry. HOMOs of the complexes were found to be center-atomic character and LUMOs were carbene-carbon character. From the calculated charge analysis and molecular electrostatic potential maps, it is found that carbene-carbon acts as electrofil and metal center nucleophile. It is suggested that the catalytic properties of the carbene complexes may be due to the fact that the carbene-carbon behave as electrophile and metal center nucleophile. Some electronic structure descriptors of the complexes were calculated and the molecular properties were estimated.

Tetramer model of leukoemeraldine-emeraldine electrochemistry in the presence of trihalogenoacetic acids. DFT approach.

PubMed

Barbosa, Nuno Almeida; Grzeszczuk, Maria; Wieczorek, Robert

2015-01-15

First results of the application of the DFT computational approach to the reversible electrochemistry of polyaniline are presented. A tetrameric chain was used as the simplest model of the polyaniline polymer species. The system under theoretical investigation involved six tetramer species, two electrons, and two protons, taking part in 14 elementary reactions. Moreover, the tetramer species were interacting with two trihalogenoacetic acid molecules. Trifluoroacetic, trichloroacetic, and tribromoacetic acids were found to impact the redox transformation of polyaniline as shown by cyclic voltammetry. The theoretical approach was considered as a powerful tool for investigating the main factors of importance for the experimental behavior. The DFT method provided molecular structures, interaction energies, and equilibrium energies of all of the tetramer-acid complexes. Differences between the energies of the isolated tetramer species and their complexes with acids are discussed in terms of the elementary reactions, that is, ionization potentials and electron affinities, equilibrium constants, electrode potentials, and reorganization energies. The DFT results indicate a high impact of the acid on the reorganization energy of a particular elementary electron-transfer reaction. The ECEC oxidation path was predicted by the calculations. The model of the reacting system must be extended to octamer species and/or dimeric oligomer species to better approximate the real polymer situation.

Computational study of small molecule binding for both tethered and free conditions

PubMed Central

2010-01-01

Using a calix[4]arene-benzene complex as a test system we compare the potential of mean force for when the calix[4]arene is tethered versus free. When the complex is in vacuum our results show that the difference between tethered and free is primarily due to the entropic contribution to the potential of mean force resulting in a significant binding free energy difference of 6.6 kJ/mol. By contrast, when the complex is in water our results suggest that there is no appreciable difference between tethered and free. This study elucidates the roles of entropy and enthalpy for this small molecule system and emphasizes the point that tethering the receptor has the potential to dramatically impact the binding properties. These findings should be taken into consideration when using calixarene molecules in nanosensor design. PMID:20369865

A combining rule calculation of the ground-state van der Waals potentials of the magnesium rare-gas complexes

NASA Astrophysics Data System (ADS)

Saidi, Samah; Alharzali, Nissrin; Berriche, Hamid

2017-04-01

The potential energy curves and spectroscopic constants of the ground-state of the Mg-Rg (Rg = He, Ne, Ar, Kr, and Xe) van der Waals complexes are generated by the Tang-Toennies potential model and a set of derived combining rules. The parameters of the model are calculated from the potentials of the homonuclear magnesium and rare-gas dimers. The predicted spectroscopic constants are comparable to other available theoretical and experimental results, except in the case of Mg-He, we note that there are large differences between various determinations. Moreover, in order to reveal relative differences between species more obviously we calculated the reduced potential of these five systems. The curves are clumped closely together, but at intermediate range the Mg-He reduced potential is clearly very different from the others.

Simple method for determining binding energies of fullerene and complex atomic negative ions

NASA Astrophysics Data System (ADS)

Felfli, Zineb; Msezane, Alfred

2017-04-01

A robust potential which embeds fully the vital core polarization interaction has been used in the Regge pole method to explore low-energy electron scattering from C60, Eu and Nb through the total cross sections (TCSs) calculations. From the characteristic dramatically sharp resonances in the TCSs manifesting negative ion formation in these systems, we extracted the binding energies for the C60, Euand Nbanions they are found to be in outstanding agreement with the measured electron affinities of C60, Eu and Nb. Common among these considered systems, including the standard atomic Au is the formation of their ground state negative ions at the second Ramsauer-Townsend (R-T) minima of their TCSs. Indeed, this is a signature of all the fullerenes and complex atoms considered thus far. Shape resonances, R-T minima and binding energies of the resultant anions are presented. This work was supported by U.S. DOE, Basic Energy Sciences, Office of Energy Research.

Sampling the energy landscape of Pt13 with metadynamics

NASA Astrophysics Data System (ADS)

Pavan, Luca; Di Paola, Cono; Baletto, Francesca

2013-02-01

The potential energy surface of a metallic nanoparticle formed by 13 atoms of platinum is efficiently explored using metadynamics in combination with empirical potential molecular dynamics. The scenario obtained is wider and more complex of what was previously reported: more than thirty independent energy basins are found, corresponding to different local minima of Pt. It is demonstrated that in almost all the cases these motifs are local minima even at ab-initio level, hence proving the effectiveness of the method to sample the energy landscape. A classification of the minima in structural families is proposed, and a discussion regarding the shape and the connections between energy basins is reported. ISSPIC 16 - 16th International Symposium on Small Particles and Inorganic Clusters, edited by Kristiaan Temst, Margriet J. Van Bael, Ewald Janssens, H.-G. Boyen and Françoise Remacle.

Carbene-aerogen bonds: an ab initio study

NASA Astrophysics Data System (ADS)

Esrafili, Mehdi D.; Sabouri, Ayda

2017-04-01

Through the use of ab initio calculations, the possibility of formation of σ-hole interaction between ZO3 (Z = Ar, Kr and Xe) and carbene species is investigated. Since singlet carbenes show a negative electrostatic potential on their divalent carbon atom, they can favourably interact with the positive electrostatic potential generated by the σ-hole of Z atom of ZO3. The characteristic of this interaction, termed as 'carbene-aerogen' bond, is analysed in terms of geometric, interaction energies and electronic features. The energy decomposition analysis indicates that for all complexes analysed here, the electrostatic energy is more negative than the polarisation or dispersion energy term. According to the electron density analysis, some partial covalent character can be ascribed to XeṡṡṡC interactions. In addition, the carbene-aerogen bond exhibits cooperative effects with the HṡṡṡO hydrogen-bonding interaction in ternary complexes where both interactions coexist. For a given carbene, the amount of these cooperative effects increases with the size of the Z atom. The results obtained in this work may be helpful for the extension and future application of σ-hole intermolecular interactions as well as coordination chemistry.

A new ab initio potential energy surface for the NH-He complex

NASA Astrophysics Data System (ADS)

Ramachandran, R.; Kłos, J.; Lique, F.

2018-02-01

We present a new three-dimensional potential energy surface (PES) for the NH(X3Σ-)-He van der Waals system, which explicitly takes into account the NH vibrational motion. The NH-He PES was obtained using the open-shell single- and double-excitation coupled cluster approach with non-iterative perturbational treatment of triple excitations. The augmented correlation-consistent aug-cc-pVXZ (X = Q, 5, 6) basis sets were employed, and the energies obtained were then extrapolated to the complete basis set limit. Using this new PES, we have studied the spectroscopy of the NH-He complex and we have determined a new rotational constant that agrees well with the available experimental data. Collisional excitation of NH(X3Σ-) by He was also studied at the close-coupling level. Calculations of the collisional excitation cross sections of the fine-structure levels of NH by He were performed for energies up to 3500 cm-1, which yield, after thermal average, rate coefficients up to 350 K. The calculated rate coefficients are compared with available experimental measurements at room temperature, and a reasonably good agreement is found between experimental and theoretical data.

Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia

PubMed Central

Urrios, Arturo; de Nadal, Eulàlia; Solé, Ricard; Posas, Francesc

2016-01-01

Engineered synthetic biological devices have been designed to perform a variety of functions from sensing molecules and bioremediation to energy production and biomedicine. Notwithstanding, a major limitation of in vivo circuit implementation is the constraint associated to the use of standard methodologies for circuit design. Thus, future success of these devices depends on obtaining circuits with scalable complexity and reusable parts. Here we show how to build complex computational devices using multicellular consortia and space as key computational elements. This spatial modular design grants scalability since its general architecture is independent of the circuit’s complexity, minimizes wiring requirements and allows component reusability with minimal genetic engineering. The potential use of this approach is demonstrated by implementation of complex logical functions with up to six inputs, thus demonstrating the scalability and flexibility of this method. The potential implications of our results are outlined. PMID:26829588

Insight into π-hole interactions containing the inorganic heterocyclic compounds S2N2/SN2P2.

PubMed

Lu, Bo; Zhang, Xueying; Meng, Lingpeng; Zeng, Yanli

2017-08-01

Similar to σ-hole interactions, the π-hole interaction has attracted much attention in recent years. According to the positive electrostatic potentials above and below the surface of inorganic heterocyclic compounds S 2 N 2 and three SN 2 P 2 isomers (heterocyclic compounds 1-4), and the negative electrostatic potential outside the X atom of XH 3 (X = N, P, As), S 2 N 2 /SN 2 P 2 ⋯XH 3 (X = N, P, As) complexes were constructed and optimized at the MP2/aug-cc-pVTZ level. The X atom of XH 3 (X = N, P, As) is almost perpendicular to the ring of the heterocyclic compounds. The π-hole interaction energy becomes greater as the trend goes from 1⋯XH 3 to 4⋯XH 3 . These π-hole interactions are weak and belong to "closed-shell" noncovalent interactions. According to the energy decomposition analysis, of the three attractive terms, the dispersion energy contributes more than the electrostatic energy. The polarization effect also plays an important role in the formation of π-hole complexes, with the contrasting phenomena of decreasing electronic density in the π-hole region and increasing electric density outside the X atom of XH 3 (X = N, P, As). Graphical abstract Computed density difference plots for the complexes 3⋯NH 3 (a 1 ), 3⋯PH 3 (b 1 ), 3⋯AsH 3 (c 1 ) and electron density shifts for the complexes 3⋯NH 3 (a 2 ), 3⋯PH 3 (b 2 ),3⋯AsH 3 (c 2 ) on the 0.001 a.u. contour.

Multistate metadynamics for automatic exploration of conical intersections

NASA Astrophysics Data System (ADS)

Lindner, Joachim O.; Röhr, Merle I. S.; Mitrić, Roland

2018-05-01

We introduce multistate metadynamics for automatic exploration of conical intersection seams between adiabatic Born-Oppenheimer potential energy surfaces in molecular systems. By choosing the energy gap between the electronic states as a collective variable the metadynamics drives the system from an arbitrary ground-state configuration toward the intersection seam. Upon reaching the seam, the multistate electronic Hamiltonian is extended by introducing biasing potentials into the off-diagonal elements, and the molecular dynamics is continued on a modified potential energy surface obtained by diagonalization of the latter. The off-diagonal bias serves to locally open the energy gap and push the system to the next intersection point. In this way, the conical intersection energy landscape can be explored, identifying minimum energy crossing points and the barriers separating them. We illustrate the method on the example of furan, a prototype organic molecule exhibiting rich photophysics. The multistate metadynamics reveals plateaus on the conical intersection energy landscape from which the minimum energy crossing points with characteristic geometries can be extracted. The method can be combined with the broad spectrum of electronic structure methods and represents a generally applicable tool for the exploration of photophysics and photochemistry in complex molecules and materials.

DFT/TDDFT investigation on the photophysical properties of a series of phosphorescent cyclometalated complexes based on the benchmark complex FIrpic

NASA Astrophysics Data System (ADS)

Han, Deming; Gong, Ping; Lv, Shuhui; Zhao, Lihui; Zhao, Henan

2018-05-01

The photophysical properties of four Ir(III) complexes have been investigated by means of the density functional theory/time-dependent density functional theory (DFT/TDDFT). The effect of the electron-withdrawing and electron-donating substituents on charge injection, transport, absorption and phosphorescent properties has been studied. The theoretical calculation shows that the lowest-lying singlet absorptions for complexes 1-4 are located at 387, 385, 418 and 386 nm, respectively. For 1-4, the phosphorescence at 465, 485, 494 and 478 nm is mainly attributed to the LUMO → HOMO and LUMO → HOMO-1 transition configurations characteristics. In addition, ionisation potential (IP), electron affinities (EAs) and reorganisation energy have been investigated to evaluate the charge transfer and balance properties between hole and electron. The balance of the reorganisation energies for complex 3 is better than others. The difference between hole transport and electron transport for complex 3 is the smallest among these complexes, which is beneficial to achieve the hole and electron transfer balance in emitting layer.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bazillian, Morgan; Pedersen, Ascha Lychett; Pless, Jacuelyn

Shale gas resource potential in China is assessed to be large, and its development could have wide-ranging economic, environmental, and energy security implications. Although commercial scale shale gas development has not yet begun in China, it holds the potential to change the global energy landscape. Chinese decision-makers are wrestling with the challenges associated with bringing the potential to reality: geologic complexity; infrastructure and logistical difficulties; technological, institutional, social and market development issues; and environmental impacts, including greenhouse gas emissions, impacts on water availability and quality, and air pollution. This paper briefly examines the current situation and outlook for shale gasmore » in China, and explores existing and potential avenues for international cooperation. We find that despite some barriers to large-scale development, Chinese shale gas production has the potential to grow rapidly over the medium-term.« less

Short-term stream water temperature observations permit rapid assessment of potential climate change impacts

Treesearch

Peter Caldwell; Catalina Segura; Shelby Gull Laird; Ge Sun; Steven G. McNulty; Maria Sandercock; Johnny Boggs; James M. Vose

2015-01-01

Assessment of potential climate change impacts on stream water temperature (Ts) across large scales remains challenging for resource managers because energy exchange processes between the atmosphere and the stream environment are complex and uncertain, and few long-term datasets are available to evaluate changes over time. In this study, we...

S-Wave Dispersion Relations: Exact Left Hand E-Plane Discontinuity from the Born Series

NASA Technical Reports Server (NTRS)

Bessis, D.; Temkin, A.

1999-01-01

We show, for a superposition of Yukawa potentials, that the left hand cut discontinuity in the complex E plane of the (S-wave) scattering amplitude is given exactly, in an interval depending on n, by the discontinuity of the Born series stopped at order n. This also establishes an inverse and unexpected correspondence of the Born series at positive high energies and negative low energies. We can thus construct a viable dispersion relation (DR) for the partial (S-) wave amplitude. The high numerical precision achievable by the DR is demonstrated for the exponential potential at zero scattering energy. We also briefly discuss the extension of our results to Field Theory.

Synthesis, crystallographic, spectral, and spectrophotometric studies of proton transfer complex of 1,2-dimethylimidazole with 3,5-dinitrobenzoic acid in different polar solvents

NASA Astrophysics Data System (ADS)

Miyan, Lal; Zulkarnain; Ahmad, Afaq

2017-04-01

The molecular interaction between 1, 2-dimethylimidazole (DMI) and 3,5-dinitrobenzoic acid (DNBA) has been investigated in methanol at room temperature. The stoichiometry of the synthesized CT complex was found to be 1:1 using the straight line method of Benesi-Hildebrand equation. The structure of the resulting CT complex was isolating and characterized using X-ray crystallography, FTIR and 1H NMR spectroscopic techniques. The thermal composition and stability of the CT complex were analyzed using thermogravimetric and differential thermal analysis (TGA and DTA). UV-visible spectrophotometric technique was used to the determine the various important physical parameters such as formation constant (KCT), molar extinction coefficient (εCT), energy of interaction (ECT), ionization potential (ID), resonance energy (RN), free energy (ΔG°), oscillator strength (ƒ) and transition dipole moment (μN). The effect of polarity of the solvent and concentration of acceptor on these parameters have been investigated. The results indicate that charge transfer complex (CTC) is more stable in less polar solvent due to the high value of the formation constant. A polymeric network through hydrogen bonding interaction between neighboring moieties was observed. This has also been attributed to the formation of 1:1 type CT complex.

Uranium extraction by complexation with siderophores

NASA Astrophysics Data System (ADS)

Bahamonde Castro, Cristina

One of the major concerns of energy production is the environmental impact associated with the extraction of natural resources. Nuclear energy fuel is obtained from uranium, an abundant and naturally occurring element in the environment, but the currently used techniques for uranium extraction leave either a significant fingerprint (open pit mines) or a chemical residue that alters the pH of the environment (acid or alkali leaching). It is therefore clear that a new and greener approach to uranium extraction is needed. Bioleaching is one potential alternative. In bioleaching, complexants naturally produced from fungi or bacteria may be used to extract the uranium. In the following research, the siderophore enterobactin, which is naturally produced by bacteria to extract and solubilize iron from the environment, is evaluated to determine its potential for complexing with uranium. To determine whether enterobactin could be used for uranium extraction, its acid dissociation and its binding strength with the metal of interest must be determined. Due to the complexity of working with radioactive materials, lanthanides were used as analogs for uranium. In addition, polyprotic acids were used as structural and chemical analogs for the siderophore during method development. To evaluate the acid dissociation of enterobactin and the subsequent binding constants with lanthanides, three different analytical techniques were studied including: potentiometric titration, UltraViolet Visible (UV-Vis) spectrophotometry and Isothermal Titration Calorimetry (ITC). After evaluation of three techniques, a combination of ITC and potentiometric titrations was deemed to be the most viable way for studying the siderophore of interest. The results obtained from these studies corroborate the ideal pH range for enterobactin complexation to the lanthanide of interest and pave the way for determining the strength of complexation relative to other naturally occurring metals. Ultimately, this fundamental research enhances our current understanding of heavy metal complexation to naturally occurring complexants, which may enhance the metals mobility in the environment or potentially be used as a greener alternative in uranium extraction or remediation.

Ferrocenyl-functionalised terpyridines and their transition-metal complexes: syntheses, structures and spectroscopic and electrochemical properties.

PubMed

Siemeling, Ulrich; Vor der Brüggen, Jens; Vorfeld, Udo; Neumann, Beate; Stammler, Anja; Stammler, Hans-George; Brockhinke, Andreas; Plessow, Regina; Zanello, Piero; Laschi, Franco; Fabrizi de Biani, Fabrizia; Fontani, Marco; Steenken, Steen; Stapper, Marion; Gurzadyan, Gagik

2003-06-16

Terpyridine ligands of the type Fc'-X-tpy (Fc'=ferrocenyl or octamethylferrocenyl, X=rigid spacer, tpy'=4'-substituted 2,2':6',2''-terpyridine) were prepared, crystallographically characterised and used for the synthesis of di- and trinuclear bis(terpyridine) complexes of RuII, FeII and ZnII. Donor-sensitiser dyads and triads based on RuII were thoroughly investigated by (spectro)electrochemistry, UV/Vis, transient absorption and luminescence spectroscopy, and an energy level scheme was derived on the basis of the data collected. Intramolecular quenching of the photoexcited RuII complexes by the redox-active Fc' groups can occur reductively and by energy transfer. Both the redox potential of the donor Fc' and the nature of the spacer X have a decisive influence on excited-state lifetimes and emission properties of the complexes. Some of the compounds show room-temperature luminescence, which is unprecedented for ferrocenyl-functionalised compounds of this kind.

Spectrophotometric and spectroscopic studies of charge transfer complexes of p-toluidine as an electron donor with picric acid as an electron acceptor in different solvents

NASA Astrophysics Data System (ADS)

Singh, Neeti; Khan, Ishaat M.; Ahmad, Afaq

2010-04-01

The charge transfer complexes of the donor p-toluidine with π-acceptor picric acid have been studied spectrophotometrically in various solvents such as carbon tetrachloride, chloroform, dichloromethane acetone, ethanol, and methanol at room temperature using absorption spectrophotometer. The results indicate that formation of CTC in non-polar solvent is high. The stoichiometry of the complex was found to be 1:1 ratio by straight-line method between donor and acceptor with maximum absorption bands. The data are discussed in terms of formation constant ( KCT), molar extinction coefficient ( ɛCT), standard free energy (Δ Go), oscillator strength ( f), transition dipole moment ( μEN), resonance energy ( RN) and ionization potential ( ID). The results indicate that the formation constant ( KCT) for the complex was shown to be dependent upon the nature of electron acceptor, donor and polarity of solvents that were used.

Spectroscopic studies of multiple charge transfer complexes of p-toluidine with π-acceptor picric acid in different polar solvents

NASA Astrophysics Data System (ADS)

Singh, Neeti; Ahmad, Afaq

2010-04-01

The charge transfer complexes of the donor p-toluidine with π-acceptor picric acid have been studied spectrophotometrically in various solvents such as acetone, ethanol, and methanol at room temperature using absorption spectrophotometer. The results indicate that formation of CTC in less polar solvent is high. The stoichiometry of the complex was found to be 1: 1 ratio by straight line method between donor and acceptor with maximum absorption bands. The data are discussed in terms of formation constant ( K CT), molar extinction coefficient (ɛCT), standard free energy (Δ G°), oscillator strength ( f), transition dipole moment (μEN), resonance energy ( R N) and ionization potential ( I D). The results indicate that the formation constant ( K CT) for the complex were shown to be dependent upon the nature of electron acceptor, donor and polarity of solvents which were used.

Excited state electron and energy relays in supramolecular dinuclear complexes revealed by ultrafast optical and X-ray transient absorption spectroscopy

DOE PAGES

Hayes, Dugan; Kohler, Lars; Hadt, Ryan G.; ...

2017-11-28

Here, the kinetics of photoinduced electron and energy transfer in a family of tetrapyridophenazine-bridged heteroleptic homo- and heterodinuclear copper(I) bis(phenanthroline)/ruthenium(II) polypyridyl complexes were studied using ultrafast optical and multi-edge X-ray transient absorption spectroscopies. This work combines the synthesis of heterodinuclear Cu(I)–Ru(II) analogs of the homodinuclear Cu(I)–Cu(I) targets with spectroscopic analysis and electronic structure calculations to first disentangle the dynamics at individual metal sites by taking advantage of the element and site specificity of X-ray absorption and theoretical methods. The excited state dynamical models developed for the heterodinuclear complexes are then applied to model the more challenging homodinuclear complexes. These resultsmore » suggest that both intermetallic charge and energy transfer can be observed in an asymmetric dinuclear copper complex in which the ground state redox potentials of the copper sites are offset by only 310 meV. We also demonstrate the ability of several of these complexes to effectively and unidirectionally shuttle energy between different metal centers, a property that could be of great use in the design of broadly absorbing and multifunctional multimetallic photocatalysts. This work provides an important step toward developing both a fundamental conceptual picture and a practical experimental handle with which synthetic chemists, spectroscopists, and theoreticians may collaborate to engineer cheap and efficient photocatalytic materials capable of performing coulombically demanding chemical transformations.« less

Excited state electron and energy relays in supramolecular dinuclear complexes revealed by ultrafast optical and X-ray transient absorption spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hayes, Dugan; Kohler, Lars; Hadt, Ryan G.

Here, the kinetics of photoinduced electron and energy transfer in a family of tetrapyridophenazine-bridged heteroleptic homo- and heterodinuclear copper(I) bis(phenanthroline)/ruthenium(II) polypyridyl complexes were studied using ultrafast optical and multi-edge X-ray transient absorption spectroscopies. This work combines the synthesis of heterodinuclear Cu(I)–Ru(II) analogs of the homodinuclear Cu(I)–Cu(I) targets with spectroscopic analysis and electronic structure calculations to first disentangle the dynamics at individual metal sites by taking advantage of the element and site specificity of X-ray absorption and theoretical methods. The excited state dynamical models developed for the heterodinuclear complexes are then applied to model the more challenging homodinuclear complexes. These resultsmore » suggest that both intermetallic charge and energy transfer can be observed in an asymmetric dinuclear copper complex in which the ground state redox potentials of the copper sites are offset by only 310 meV. We also demonstrate the ability of several of these complexes to effectively and unidirectionally shuttle energy between different metal centers, a property that could be of great use in the design of broadly absorbing and multifunctional multimetallic photocatalysts. This work provides an important step toward developing both a fundamental conceptual picture and a practical experimental handle with which synthetic chemists, spectroscopists, and theoreticians may collaborate to engineer cheap and efficient photocatalytic materials capable of performing coulombically demanding chemical transformations.« less

Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling

PubMed Central

Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

2014-01-01

Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES) simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape. PMID:25340714

Potential energy and dipole moment surfaces of the triplet states of the O2(X3Σg-) - O2(X3Σg-,a1Δg,b1Σg+) complex

NASA Astrophysics Data System (ADS)

Karman, Tijs; van der Avoird, Ad; Groenenboom, Gerrit C.

2017-08-01

We compute four-dimensional diabatic potential energy surfaces and transition dipole moment surfaces of O2-O2, relevant for the theoretical description of collision-induced absorption in the forbidden X3Σg- → a1Δg and X3Σg- → b1Σg+ bands at 7883 cm-1 and 13 122 cm-1, respectively. We compute potentials at the multi-reference configuration interaction (MRCI) level and dipole surfaces at the MRCI and complete active space self-consistent field (CASSCF) levels of theory. Potentials and dipole surfaces are transformed to a diabatic basis using a recent multiple-property-based diabatization algorithm. We discuss the angular expansion of these surfaces, derive the symmetry constraints on the expansion coefficients, and present working equations for determining the expansion coefficients by numerical integration over the angles. We also present an interpolation scheme with exponential extrapolation to both short and large separations, which is used for representing the O2-O2 distance dependence of the angular expansion coefficients. For the triplet ground state of the complex, the potential energy surface is in reasonable agreement with previous calculations, whereas global excited state potentials are reported here for the first time. The transition dipole moment surfaces are strongly dependent on the level of theory at which they are calculated, as is also shown here by benchmark calculations at high symmetry geometries. Therefore, ab initio calculations of the collision-induced absorption spectra cannot become quantitatively predictive unless more accurate transition dipole surfaces can be computed. This is left as an open question for method development in electronic structure theory. The calculated potential energy and transition dipole moment surfaces are employed in quantum dynamical calculations of collision-induced absorption spectra reported in Paper II [T. Karman et al., J. Chem. Phys. 147, 084307 (2017)].

Potential energy and dipole moment surfaces of the triplet states of the O2(X3Σg-) - O2(X3Σg-,a1Δg,b1Σg+) complex.

PubMed

Karman, Tijs; van der Avoird, Ad; Groenenboom, Gerrit C

2017-08-28

We compute four-dimensional diabatic potential energy surfaces and transition dipole moment surfaces of O 2 -O 2 , relevant for the theoretical description of collision-induced absorption in the forbidden X 3 Σ g -  → a 1 Δ g and X 3 Σ g -  → b 1 Σ g + bands at 7883 cm -1 and 13 122 cm -1 , respectively. We compute potentials at the multi-reference configuration interaction (MRCI) level and dipole surfaces at the MRCI and complete active space self-consistent field (CASSCF) levels of theory. Potentials and dipole surfaces are transformed to a diabatic basis using a recent multiple-property-based diabatization algorithm. We discuss the angular expansion of these surfaces, derive the symmetry constraints on the expansion coefficients, and present working equations for determining the expansion coefficients by numerical integration over the angles. We also present an interpolation scheme with exponential extrapolation to both short and large separations, which is used for representing the O 2 -O 2 distance dependence of the angular expansion coefficients. For the triplet ground state of the complex, the potential energy surface is in reasonable agreement with previous calculations, whereas global excited state potentials are reported here for the first time. The transition dipole moment surfaces are strongly dependent on the level of theory at which they are calculated, as is also shown here by benchmark calculations at high symmetry geometries. Therefore, ab initio calculations of the collision-induced absorption spectra cannot become quantitatively predictive unless more accurate transition dipole surfaces can be computed. This is left as an open question for method development in electronic structure theory. The calculated potential energy and transition dipole moment surfaces are employed in quantum dynamical calculations of collision-induced absorption spectra reported in Paper II [T. Karman et al., J. Chem. Phys. 147, 084307 (2017)].

Benefits Estimation Model for Automated Vehicle Operations: Phase 2 Final Report

DOT National Transportation Integrated Search

2018-01-01

Automated vehicles have the potential to bring about transformative safety, mobility, energy, and environmental benefits to the surface transportation system. They are also being introduced into a complex transportation system, where second-order imp...

Electron-induced scattering dynamics of Boron, Aluminium and Gallium trihalides in the intermediate energy domain

NASA Astrophysics Data System (ADS)

Verma, Pankaj; Alam, Mohammad Jane; Ahmad, Shabbir; Antony, Bobby

2018-05-01

This article is focused on the calculation of electron-induced ionisation and total scattering cross sections by Boron, Aluminium and Gallium trihalide molecules in the intermediate energy domain. The computational formalism, spherical complex optical potential has been employed for the study of these two scattering cross sections. The ionisation cross section has been derived from the inelastic cross section using a semi-empirical method called complex scattering potential-ionisation contribution (CSP-ic) method. We have also calculated the ionisation cross section using the BEB theory with Hartree-Fock and density functional theory (DFT- ωB97XD) orbitals so that a comparison can be made with the cross sections predicted by CSP-ic method. For this theoretical study, we have also calculated polarisability and bond length of some targets which were not found in literature using DFT/B3LYP in Gaussian 09 software.

A complex study of 5-amino-3-methyl-4-[2-(5-amino-1,3,4-oxadiazolo)]-isoxazole monohydrate: A new low-molecular-weight immune response modifier

NASA Astrophysics Data System (ADS)

Ryng, Stanisław; Zimecki, Michał; Jezierska-Mazzarello, Aneta; Panek, Jarosław J.; Mączyński, Marcin; Głowiak, Tadeusz; Sawka-Dobrowolska, Wanda; Koll, Aleksander

2011-07-01

A new potential lead structure with immunological activity, 5-amino-3-methyl-4-[2-(5-amino-1,3,4-oxadiazolo)]-isoxazole monohydrate, was synthesized. A detailed description of synthesis is presented together with X-ray structural analysis. In vitro assays showed that the compound had a potent immunosuppressive activity. Next, Density Functional Theory (DFT) was employed to shed a light on molecular properties of the investigated isoxazole derivative. The molecular modeling part included geometric as well as electronic structure descriptions: (i) the conformational analysis was performed to localize the most appropriate conformation; (ii) the coordination energy and Basis Set Superposition Error (BSSE) were estimated for the complex of the isoxazole derivative interacting with water molecule; (iii) the potential energy distribution was used to assign molecular vibrations, and NBO population analysis served to describe the electronic structure; (iv) the electrostatic potential map was generated to provide the graphical presentation of regions exposed for intermolecular interactions. The contacts between the water molecule and the nitrogen atom of the isoxazole ring edge were present in the solid phase. On the other hand, the theoretical DFT prediction was that the oxygen atom of the edge should form a more stable complex with the water molecule.

Selective CO2 reduction conjugated with H2O oxidation utilizing semiconductor/metal-complex hybrid photocatalysts

NASA Astrophysics Data System (ADS)

Morikawa, T.; Sato, S.; Arai, T.; Uemura, K.; Yamanaka, K. I.; Suzuki, T. M.; Kajino, T.; Motohiro, T.

2013-12-01

We developed a new hybrid photocatalyst for CO2 reduction, which is composed of a semiconductor and a metal complex. In the hybrid photocatalyst, ΔG between the position of conduction band minimum (ECBM) of the semiconductor and the CO2 reduction potential of the complex is an essential factor for realizing fast electron transfer from the conduction band of semiconductor to metal complex leading to high photocatalytic activity. On the basis of this concept, the hybrid photocatalyst InP/Ru-complex, which functions in aqueous media, was developed. The photoreduction of CO2 to formate using water as an electron donor and a proton source was successfully achieved as a Z-scheme system by functionally conjugating the InP/Ru-complex photocatalyst for CO2 reduction with a TiO2 photocatalyst for water oxidation. The conversion efficiency from solar energy to chemical energy was ca. 0.04%, which approaches that for photosynthesis in a plant. Because this system can be applied to many other inorganic semiconductors and metal-complex catalysts, the efficiency and reaction selectivity can be enhanced by optimization of the electron transfer process including the energy-band configurations, conjugation conformations, and catalyst structures. This electrical-bias-free reaction is a huge leap forward for future practical applications of artificial photosynthesis under solar irradiation to produce organic species.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Curchod, Basile F. E.; Agostini, Federica, E-mail: agostini@mpi-halle.mpg.de; Gross, E. K. U.

Nonadiabatic quantum interferences emerge whenever nuclear wavefunctions in different electronic states meet and interact in a nonadiabatic region. In this work, we analyze how nonadiabatic quantum interferences translate in the context of the exact factorization of the molecular wavefunction. In particular, we focus our attention on the shape of the time-dependent potential energy surface—the exact surface on which the nuclear dynamics takes place. We use a one-dimensional exactly solvable model to reproduce different conditions for quantum interferences, whose characteristic features already appear in one-dimension. The time-dependent potential energy surface develops complex features when strong interferences are present, in clear contrastmore » to the observed behavior in simple nonadiabatic crossing cases. Nevertheless, independent classical trajectories propagated on the exact time-dependent potential energy surface reasonably conserve a distribution in configuration space that mimics one of the exact nuclear probability densities.« less

Quantum mechanical design and structures of hexanuclear sandwich complex and its multidecker sandwich clusters (Li6)n([18]annulene)n+1 (n = 1-3).

PubMed

Wang, Shu-Jian; Li, Ying; Wu, Di; Wang, Yin-Feng; Li, Zhi-Ru

2012-09-13

By means of density functional theory, a hexanuclear sandwich complex [18]annulene-Li6-[18]annulene which consists of a central Li6 hexagon ring and large face-capping ligands, [18]annulene, is designed and investigated. The large interaction energy and HOMO-LUMO gap suggest that this novel charge-separated complex is highly stable and may be experimentally synthesized. In addition, the stability found in the [18]annulene-Li6-[18]annulene complex extends to multidecker sandwich clusters (Li6)n([18]annulene)n+1 (n = 2-3). The energy gain upon addition of a [18]annulene-Li6 unit to (Li6)n-1([18]annulene)n is pretty large (96.97-98.22 kcal/mol), indicating that even larger multideckers will also be very stable. Similar to ferrocene, such a hexanuclear sandwich complex could be considered as a versatile building block to find potential applications in different areas of chemistry, such as nanoscience and material science.

Spectroscopic and physical measurements on charge-transfer complexes: Interactions between norfloxacin and ciprofloxacin drugs with picric acid and 3,5-dinitrobenzoic acid acceptors

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; Elfalaky, A.; Elesh, Eman

2011-03-01

Charge-transfer complexes formed between norfloxacin (nor) or ciprofloxacin (cip) drugs as donors with picric acid (PA) and/or 3,5-dinitrobenzoic acid (DNB) as π-acceptors have been studied spectrophotometrically in methanol solvent at room temperature. The results indicated the formation of CT-complexes with molar ratio1:1 between donor and acceptor at maximum CT-bands. In the terms of formation constant ( KCT), molar extinction coefficient ( ɛCT), standard free energy (Δ Go), oscillator strength ( f), transition dipole moment (μ), resonance energy ( RN) and ionization potential ( ID) were estimated. IR, H NMR, UV-Vis techniques, elemental analyses (CHN) and TG-DTG investigations were used to characterize the structural of charge-transfer complexes. It indicates that the CT interaction was associated with a proton migration from each acceptor to nor or cip donors which followed by appearing intermolecular hydrogen bond. In addition, X-ray investigation was carried out to scrutinize the crystal structure of the resulted CT-complexes.

Low energy electron-impact ionization of hydrogen atom for coplanar equal-energy-sharing kinematics in Debye plasmas

NASA Astrophysics Data System (ADS)

Li, Jun; Zhang, Song Bin; Ye, Bang Jiao; Wang, Jian Guo; Janev, R. K.

2016-12-01

Low energy electron-impact ionization of hydrogen atom in Debye plasmas has been investigated by employing the exterior complex scaling method. The interactions between the charged particles in the plasma have been represented by Debye-Hückel potentials. Triple differential cross sections (TDCS) in the coplanar equal-energy-sharing geometry at an incident energy of 15.6 eV for different screening lengths are reported. As the screening strength increases, TDCS change significantly. The evolutions of dominant typical peak structures of the TDCS are studied in detail for different screening lengths and for different coplanar equal-energy-sharing geometries.

Analysis of a fuel cell on-site integrated energy system for a residential complex

NASA Technical Reports Server (NTRS)

Simons, S. N.; Maag, W. L.

1979-01-01

Declining supplies of domestic oil and gas and the increased cost of energy resulted in a renewed emphasis in utilizing available resources in the most efficient manner possible. This, in turn, brought about a reassessment of a number of methods for converting fossil fuels to end uses at the highest practical efficiency. One of these is the on-site integrated energy system (OS/IES). This system provides electric power from an on-site power plant and recovers heat from the power plant that would normally be rejected to the environment. An OS/IES is potentially useful in any application that requires both electricity and heat. Several OS/IES are analyzed for a residential complex. The paper is divided into two sections; the first compares three energy supply systems, the second compares various designs for fuel cell OS/IES.

Three-Particle Complexes in Two-Dimensional Semiconductors

NASA Astrophysics Data System (ADS)

Ganchev, Bogdan; Drummond, Neil; Aleiner, Igor; Fal'ko, Vladimir

2015-03-01

We evaluate binding energies of trions X±, excitons bound by a donor or acceptor charge XD (A ) , and overcharged acceptors or donors in two-dimensional atomic crystals by mapping the three-body problem in two dimensions onto one particle in a three-dimensional potential treatable by a purposely developed boundary-matching-matrix method. We find that in monolayers of transition metal dichalcogenides the dissociation energy of X± is typically much larger than that of localized exciton complexes, so that trions are more resilient to heating, despite the fact that their recombination line in optics is less redshifted from the exciton line than the line of XD (A ) .

Binding energies and spatial structures of small carrier complexes in monolayer transition-metal dichalcogenides via diffusion Monte Carlo

DOE PAGES

Mayers, Matthew Z.; Berkelbach, Timothy C.; Hybertsen, Mark S.; ...

2015-10-09

Ground-state diffusion Monte Carlo is used to investigate the binding energies and intercarrier radial probability distributions of excitons, trions, and biexcitons in a variety of two-dimensional transition-metal dichalcogenide materials. We compare these results to approximate variational calculations, as well as to analogous Monte Carlo calculations performed with simplified carrier interaction potentials. Our results highlight the successes and failures of approximate approaches as well as the physical features that determine the stability of small carrier complexes in monolayer transition-metal dichalcogenide materials. In conclusion, we discuss points of agreement and disagreement with recent experiments.

Theoretical insights of proton transfer and hydrogen bonded charge transfer complex of 1,2-dimethylimidazolium-3,5-dinitrobenzoate crystal

NASA Astrophysics Data System (ADS)

Afroz, Ziya; Faizan, Mohd.; Alam, Mohammad Jane; Ahmad, Shabbir; Ahmad, Afaq

2018-04-01

Proton transfer (PT) and hydrogen bonded charge transfer (HBCT) 1:1 complex of 1,2-dimethylimidazole (DMI) and 3,5-dinitrobenzoic acid (DNBA) have been theoretically analyzed and compared with reported experimental results. Both the structures in the isolated gaseous state have been optimized at DFT/B3LYP/6-311G(d,p) level of theory and further, the PT energy barrier has been calculated from potential energy surface scan. Along with structural investigations, theoretical vibrational spectra have been inspected and compared with the FTIR spectrum. Moreover, frontier molecular analysis has also been carried out.

Nuclear quantum effects on adsorption of H2 and isotopologues on metal ions

NASA Astrophysics Data System (ADS)

Savchenko, Ievgeniia; Gu, Bing; Heine, Thomas; Jakowski, Jacek; Garashchuk, Sophya

2017-02-01

The nuclear quantum effects on the zero-point energy (ZPE), influencing adsorption of H2 and isotopologues on metal ions, are examined using normal mode analysis of ab initio electronic structure results for complexes with 17 metal cations. The lightest metallic nuclei, Li and Be, are found to be the most 'quantum'. The largest selectivity in adsorption is predicted for Cu, Ni and Co ions. Analysis of the nuclear wavepacket dynamics on the ground state electronic potential energy surfaces (PES) performed for complexes of Li+ and Cu+2 with H2/D2/HD shows that the PES anharmonicity changes the ZPE by up to 9%.

Theoretical study of optical activity of 1:1 hydrogen bond complexes of water with S-warfarin

NASA Astrophysics Data System (ADS)

Dadsetani, Mehrdad; Abdolmaleki, Ahmad; Zabardasti, Abedin

2016-11-01

The molecular interaction between S-warfarin (SW) and a single water molecule was investigated using the B3LYP method at 6-311 ++G(d,p) basis set. The vibrational spectra of the optimized complexes have been investigated for stabilization checking. Quantum theories of atoms in molecules, natural bond orbitals, molecular electrostatic potentials and energy decomposition analysis methods have been applied to analyze the intermolecular interactions. The intermolecular charge transfer in the most stable complex is in the opposite direction from those in the other complexes. The optical spectra and the hyperpolarizabilities of SW-water hydrogen bond complexes have been computed.

Communication: THz absorption spectrum of the CO2-H2O complex: observation and assignment of intermolecular van der Waals vibrations.

PubMed

Andersen, J; Heimdal, J; Mahler, D W; Nelander, B; Larsen, R Wugt

2014-03-07

Terahertz absorption spectra have been recorded for the weakly bound CO2-H2O complex embedded in cryogenic neon matrices at 2.8 K. The three high-frequency van der Waals vibrational transitions associated with out-of-plane wagging, in-plane rocking, and torsional motion of the isotopic H2O subunit have been assigned and provide crucial observables for benchmark theoretical descriptions of this systems' flat intermolecular potential energy surface. A (semi)-empirical value for the zero-point energy of 273 ± 15 cm(-1) from the class of intermolecular van der Waals vibrations is proposed and the combination with high-level quantum chemical calculations provides a value of 726 ± 15 cm(-1) for the dissociation energy D0.

Proton transfer reactions and dynamics in CH(3)OH-H(3)O(+)-H(2)O complexes.

PubMed

Sagarik, Kritsana; Chaiwongwattana, Sermsiri; Vchirawongkwin, Viwat; Prueksaaroon, Supakit

2010-01-28

Proton transfer reactions and dynamics in hydrated complexes formed from CH(3)OH, H(3)O(+) and H(2)O were studied using theoretical methods. The investigations began with searching for equilibrium structures at low hydration levels using the DFT method, from which active H-bonds in the gas phase and continuum aqueous solution were characterized and analyzed. Based on the asymmetric stretching coordinates (Deltad(DA)), four H-bond complexes were identified as potential transition states, in which the most active unit is represented by an excess proton nearly equally shared between CH(3)OH and H(2)O. These cannot be definitive due to the lack of asymmetric O-H stretching frequencies (nu(OH)) which are spectral signatures of transferring protons. Born-Oppenheimer molecular dynamics (BOMD) simulations revealed that, when the thermal energy fluctuations and dynamics were included in the model calculations, the spectral signatures at nu(OH) approximately 1000 cm(-1) appeared. In continuum aqueous solution, the H-bond complex with incomplete water coordination at charged species turned out to be the only active transition state. Based on the assumption that the thermal energy fluctuations and dynamics could temporarily break the H-bonds linking the transition state complex and water molecules in the second hydration shell, elementary reactions of proton transfer were proposed. The present study showed that, due to the coupling among various vibrational modes, the discussions on proton transfer reactions cannot be made based solely on static proton transfer potentials. Inclusion of thermal energy fluctuations and dynamics in the model calculations, as in the case of BOMD simulations, together with systematic IR spectral analyses, have been proved to be the most appropriate theoretical approaches.

Options to improve energy efficiency for educational building

NASA Astrophysics Data System (ADS)

Jahan, Mafruha

The cost of energy is a major factor that must be considered for educational facility budget planning purpose. The analysis of energy related issues and options can be complex and requires significant time and detailed effort. One way to facilitate the inclusion of energy option planning in facility planning efforts is to utilize a tool that allows for quick appraisal of the facility energy profile. Once such an appraisal is accomplished, it is then possible to rank energy improvement options consistently with other facility needs and requirements. After an energy efficiency option has been determined to have meaningful value in comparison with other facility planning options, it is then possible to utilize the initial appraisal as the basis for an expanded consideration of additional facility and energy use detail using the same analytic system used for the initial appraisal. This thesis has developed a methodology and an associated analytic model to assist in these tasks and thereby improve the energy efficiency of educational facilities. A detailed energy efficiency and analysis tool is described that utilizes specific university building characteristics such as size, architecture, envelop, lighting, occupancy, thermal design which allows reducing the annual energy consumption. Improving the energy efficiency of various aspects of an educational building's energy performance can be complex and can require significant time and experience to make decisions. The approach developed in this thesis initially assesses the energy design for a university building. This initial appraisal is intended to assist administrators in assessing the potential value of energy efficiency options for their particular facility. Subsequently this scoping design can then be extended as another stage of the model by local facility or planning personnel to add more details and engineering aspects to the initial screening model. This approach can assist university planning efforts to identify the most cost effective combinations of energy efficiency strategies. The model analyzes and compares the payback periods of all proposed Energy Performance Measures (EPMs) to determine which has the greatest potential value.

Recent advances in QM/MM free energy calculations using reference potentials.

PubMed

Duarte, Fernanda; Amrein, Beat A; Blaha-Nelson, David; Kamerlin, Shina C L

2015-05-01

Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meaningful become more and more difficult to fulfill. The use of simplified models to describe complex biological systems has long been shown to be an effective way to overcome some of the limitations associated with this computational cost in a rational way. Hybrid QM/MM approaches have rapidly become one of the most popular computational tools for studying chemical reactivity in biomolecular systems. However, the high cost involved in performing high-level QM calculations has limited the applicability of these approaches when calculating free energies of chemical processes. In this review, we present some of the advances in using reference potentials and mean field approximations to accelerate high-level QM/MM calculations. We present illustrative applications of these approaches and discuss challenges and future perspectives for the field. The use of physically-based simplifications has shown to effectively reduce the cost of high-level QM/MM calculations. In particular, lower-level reference potentials enable one to reduce the cost of expensive free energy calculations, thus expanding the scope of problems that can be addressed. As was already demonstrated 40 years ago, the usage of simplified models still allows one to obtain cutting edge results with substantially reduced computational cost. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

Are Anion/π Interactions Actually a Case of Simple Charge–Dipole Interactions?†

PubMed Central

Wheeler, Steven E.; Houk, K. N.

2011-01-01

Substituent effects in Cl− ••• C6H6−nXn complexes, models for anion/π interactions, have been examined using density functional theory and robust ab initio methods paired with large basis sets. Predicted interaction energies for 83 model Cl− ••• C6H6−nXn complexes span almost 40 kcal mol−1 and show an excellent correlation (r = 0.99) with computed electrostatic potentials. In contrast to prevailing models of anion/π interactions, which rely on substituent-induced changes in the aryl π-system, it is shown that substituent effects in these systems are due mostly to direct interactions between the anion and the substituents. Specifically, interaction energies for Cl− ••• C6H6−nXn complexes are recovered using a model system in which the substituents are isolated from the aromatic ring and π-resonance effects are impossible. Additionally, accurate potential energy curves for Cl− interacting with prototypical anion-binding arenes can be qualitatively reproduced by adding a classical charge–dipole interaction to the Cl− ••• C6H6 interaction potential. In substituted benzenes, binding of anions arises primarily from interactions of the anion with the local dipoles induced by the substituents, not changes in the interaction with the aromatic ring itself. When designing anion-binding motifs, phenyl rings should be viewed as a scaffold upon which appropriate substituents can be placed, because there are no attractive interactions between anions and the aryl π-system of substituted benzenes. PMID:20433187

Structural Mechanism behind Distinct Efficiency of Oct4/Sox2 Proteins in Differentially Spaced DNA Complexes

PubMed Central

Yesudhas, Dhanusha; Anwar, Muhammad Ayaz; Panneerselvam, Suresh; Durai, Prasannavenkatesh; Shah, Masaud; Choi, Sangdun

2016-01-01

The octamer-binding transcription factor 4 (Oct4) and sex-determining region Y (SRY)-box 2 (Sox2) proteins induce various transcriptional regulators to maintain cellular pluripotency. Most Oct4/Sox2 complexes have either 0 base pairs (Oct4/Sox20bp) or 3 base pairs (Oct4/Sox23bp) separation between their DNA-binding sites. Results from previous biochemical studies have shown that the complexes separated by 0 base pairs are associated with a higher pluripotency rate than those separated by 3 base pairs. Here, we performed molecular dynamics (MD) simulations and calculations to determine the binding free energy and per-residue free energy for the Oct4/Sox20bp and Oct4/Sox23bp complexes to identify structural differences that contribute to differences in induction rate. Our MD simulation results showed substantial differences in Oct4/Sox2 domain movements, as well as secondary-structure changes in the Oct4 linker region, suggesting a potential reason underlying the distinct efficiencies of these complexes during reprogramming. Moreover, we identified key residues and hydrogen bonds that potentially facilitate protein-protein and protein-DNA interactions, in agreement with previous experimental findings. Consequently, our results confess that differential spacing of the Oct4/Sox2 DNA binding sites can determine the magnitude of transcription of the targeted genes during reprogramming. PMID:26790000

Experimental and theoretical study of the electronic spectrum of the BAr2 complex: Transition to the excited valence B(2s2p2 2D) state

NASA Astrophysics Data System (ADS)

Krumrine, Jennifer R.; Alexander, Millard H.; Yang, Xin; Dagdigian, Paul J.

2000-03-01

The 2s2p22D←2s22p 2P valence transition in the BAr2 cluster is investigated in a collaborative experimental and theoretical study. Laser fluorescence excitation spectra of a supersonic expansion of B atoms entrained in Ar at high source backing pressures display several features not assignable to the BAr complex. Resonance fluorescence is not observed, but instead emission from the lower 3s state. Size-selected fluorescence depletion spectra show that these features in the excitation spectrum are primarily due to the BAr2 complex. This electronic transition within BAr2 is modeled theoretically, similarly to our earlier study of the 3s←2p transition [M. H. Alexander et al., J. Chem. Phys. 106, 6320 (1997)]. The excited potential energy surfaces of the fivefold degenerate B(2s2p22D) state within the ternary complex are computed in a pairwise-additive model employing diatomic BAr potential energy curves which reproduce our previous experimental observations on the electronic states emanating from the B(2D)+Ar asymptote. The simulated absorption spectrum reproduces reasonably well the observed fluorescence depletion spectrum. The theoretical model lends insight into the energetics of the approach of B to multiple Ar atoms, and how the orientation of B p-orbitals governs the stability of the complex.

Theoretical study of mixed MLaX(4) (M = Na, K, Cs; X = F, Cl, Br, I) rare earth/alkali metal halide complexes.

PubMed

Groen, Cornelis Petrus; Oskam, Ad; Kovács, Attila

2003-02-10

The structure, bonding, and vibrational properties of the mixed MLaX(4) (M = Na, K, Cs; X = F, Cl, Br, I) rare earth/alkali metal halide complexes have been studied using the MP2 method in conjunction with polarized triple-zeta valence basis sets and quasi-relativistic effective core potentials for the heavy atoms. From the three characteristic structures, possessing 1- (C(3)(v)), 2- (C(2)(v)), or 3-fold coordination (C(3)(v)) between the alkali metal and the bridging halide atoms, the bi- and tridentate forms are stable isomers with close dissociation energies. In general, for the complexes existing of lighter alkali metals and halogens, the bidentate structure corresponds to the global minimum of the potential energy surface, while the heavier analogues favor the tridentate structure. At experimentally relevant temperatures (T > 800 K), however, the isomerization entropy leads to a domination of the bidentate structures over the tridentate forms for all complexes. An important effect of the size of the alkali metal is manifested in the larger stabilities of the K and Cs complexes. The natural atomic charges are in agreement with strong electrostatic interactions in the title complexes. The marginal covalent contributions show a slight increasing trend in the heavier analogues. The calculated vibrational data indicate that infrared spectroscopy may be an effective tool for experimental investigation and characterization of MLaX(4) molecules.

Luminescent molecular rods - transition-metal alkynyl complexes.

PubMed

Yam, Vivian Wing-Wah; Wong, Keith Man-Chung

2005-01-01

A number of transition-metal complexes have been reported to exhibit rich luminescence, usually originating from phosphorescence. Such luminescence properties of the triplet excited state with a large Stoke's shift, long lifetime, high luminescence quantum yield as well as lower excitation energy, are envisaged to serve as an ideal candidate in the area of potential applications for chemosensors, dye-sensitized solar cells, flat panel displays, optics, new materials and biological sciences. Organic alkynes (poly-ynes), with extended or conjugatedπ-systems and rigid structure with linear geometry, have become a significant research area due to their novel electronic and physical properties and their potential applications in nanotechnology. Owing to the presence of unsaturated sp-hybridized carbon atoms, the alkynyl unit can serve as a versatile building block in the construction of alkynyl transition-metal complexes, not only throughσ-bonding but also viaπ-bonding interactions. By incorporation of linear alkynyl groups into luminescent transition-metal complexes, the alkynyl moiety with goodσ-donor,π-donor andπ-acceptor abilities is envisaged to tune or perturb the emission behaviors, including emission energy (color), intensity and lifetime by its role as an auxiliary ligand as well as to govern the emission origin from its direct involvement. This review summarizes recent efforts on the synthesis of luminescent rod-like alkynyl complexes with different classes of transition metals and details the effects of the introduction of alkynyl groups on the luminescence properties of the complexes.

A new ab initio potential energy surface for the Ne-H 2 interaction

NASA Astrophysics Data System (ADS)

Lique, François

2009-03-01

A new accurate three-dimensional potential energy surface for the Ne-H 2 system, which explicitly takes into account the r-dependence of the H 2 vibration, was determined from ab initio calculations. It was obtained with the single and double excitation coupled-cluster method with noniterative perturbational treatment of triple excitation [CCSD(T)]. Calculations was been performed using the augmented correlation-consistent polarized quintuple zeta basis set (aug-cc-pV5Z) for the three atoms. We checked the accuracy of the present ab initio calculations. We have determined, using the new Ne-H 2 potential energy surface, differential cross-sections for the rotational excitation of the H 2 and D 2 molecules in collision with Ne and we have compared them with experimental results of Faubel et al. [M. Faubel, F.A. Gianturco, F. Ragnetti, L.Y. Rusin, F. Sondermann, U. Tappe, J.P. Toennies, J. Chem. Phys. 101 (1994) 8800]. The overall agreement confirms that the new potential energy surface can be used for the simulation of molecular collisions and/or molecular spectroscopy of the van der Waals complex Ne-H 2.

Novel Zn(II) complexes of 1,3-diphenyl-4-(arylazo)pyrazol-5-one derivatives: Synthesis, spectroscopic properties, DFT calculations and first order nonlinear optical properties

NASA Astrophysics Data System (ADS)

Abdel-Latif, Samir A.; Mohamed, Adel A.

2018-03-01

Eight novel Zn(II) complexes with substituted 1,3-diphenyl-4-(arylazo)pyrazol-5-one (L1-L4) derivatives have been synthesized and elucidated using various physicochemical techniques. Quantum mechanical calculations of energies, geometries were done by DFT using B3LYP/GEN functional combined with 6.311G (d,p) and LAN2DZ basis sets. The analyses of HOMO and LUMO have been used to explain the charge transfer within the ligands and complexes. The calculated small energy gap between HOMO and LUMO energies shows that the charge transfer occurs within Zn(II) complexes. Geometrical parameters, molecular electrostatic potential maps (MEP) and total electron densities analyses of the ligands and their Zn complexes have been carried out. Molecular stability, hyperconjugative interactions, intramolecular charge transfer (ICT) and bond strength has been investigated by the applying of natural bond orbital (NBO) analysis. Total static dipole moment (μ), the mean polarizability (<α>), the anisotropy of the polarizability (Δα), the mean first-order hyperpolarizability (<β>) have been also performed. The obtained values show that Zn(II) complexes is brilliant candidate to NLO materials. The analyses of the 1:1 complexes indicate that the Zn(II) ion is five-coordinated with water molecules at axial position in case of L1, L2 and L4 whereas, six-coordinated with L3 and non-electrolytic behaviour of complexes indicates the absence of counter ion.

An Energy-Efficient Compressive Image Coding for Green Internet of Things (IoT).

PubMed

Li, Ran; Duan, Xiaomeng; Li, Xu; He, Wei; Li, Yanling

2018-04-17

Aimed at a low-energy consumption of Green Internet of Things (IoT), this paper presents an energy-efficient compressive image coding scheme, which provides compressive encoder and real-time decoder according to Compressive Sensing (CS) theory. The compressive encoder adaptively measures each image block based on the block-based gradient field, which models the distribution of block sparse degree, and the real-time decoder linearly reconstructs each image block through a projection matrix, which is learned by Minimum Mean Square Error (MMSE) criterion. Both the encoder and decoder have a low computational complexity, so that they only consume a small amount of energy. Experimental results show that the proposed scheme not only has a low encoding and decoding complexity when compared with traditional methods, but it also provides good objective and subjective reconstruction qualities. In particular, it presents better time-distortion performance than JPEG. Therefore, the proposed compressive image coding is a potential energy-efficient scheme for Green IoT.

Structural and mechanistic aspects of Mn-oxo and co-based compounds in water oxidation catalysis and potential applications in solar fuel production.

PubMed

Hou, Harvey J M

2010-08-01

To address the issues of energy crisis and global warming, novel renewable carbon-free or carbon-neutral energy sources must be identified and developed. A deeper understanding of photosynthesis is the key to provide a solid foundation to facilitate this transformation. To mimic the water oxidation of photosystem II oxygen evolving complex, Mn-oxo complexes and Co-phosphate catalytic material were discovered in solar energy storage. Building on these discoveries, recent advances in solar energy conversion showed a compelling working principle by combing the active Mn-oxo and Co-based catalysts in water splitting with semiconductor hetero-nanostructures for effective solar energy harnessing. In this review the appealing systems including Mn-oxo tetramer/Nafion, Mn-oxo dimer/TiO(2), Mn-oxo oligomer/WO(3), Co-Pi/Fe(2)O(3), and Co-Pi/ZnO are summarized and discussed. These accomplishments offer a promising framework and have a profound impact in the field of solar fuel production.

Introducing sampling entropy in repository based adaptive umbrella sampling

NASA Astrophysics Data System (ADS)

Zheng, Han; Zhang, Yingkai

2009-12-01

Determining free energy surfaces along chosen reaction coordinates is a common and important task in simulating complex systems. Due to the complexity of energy landscapes and the existence of high barriers, one widely pursued objective to develop efficient simulation methods is to achieve uniform sampling among thermodynamic states of interest. In this work, we have demonstrated sampling entropy (SE) as an excellent indicator for uniform sampling as well as for the convergence of free energy simulations. By introducing SE and the concentration theorem into the biasing-potential-updating scheme, we have further improved the adaptivity, robustness, and applicability of our recently developed repository based adaptive umbrella sampling (RBAUS) approach [H. Zheng and Y. Zhang, J. Chem. Phys. 128, 204106 (2008)]. Besides simulations of one dimensional free energy profiles for various systems, the generality and efficiency of this new RBAUS-SE approach have been further demonstrated by determining two dimensional free energy surfaces for the alanine dipeptide in gas phase as well as in water.

Absorption dynamics and delay time in complex potentials

NASA Astrophysics Data System (ADS)

Villavicencio, Jorge; Romo, Roberto; Hernández-Maldonado, Alberto

2018-05-01

The dynamics of absorption is analyzed by using an exactly solvable model that deals with an analytical solution to Schrödinger’s equation for cutoff initial plane waves incident on a complex absorbing potential. A dynamical absorption coefficient which allows us to explore the dynamical loss of particles from the transient to the stationary regime is derived. We find that the absorption process is characterized by the emission of a series of damped periodic pulses in time domain, associated with damped Rabi-type oscillations with a characteristic frequency, ω = (E + ε)/ℏ, where E is the energy of the incident waves and ‑ε is energy of the quasidiscrete state of the system induced by the absorptive part of the Hamiltonian; the width γ of this resonance governs the amplitude of the pulses. The resemblance of the time-dependent absorption coefficient with a real decay process is discussed, in particular the transition from exponential to nonexponential regimes, a well-known feature of quantum decay. We have also analyzed the effect of the absorptive part of the potential on the dynamical delay time, which behaves differently from the one observed in attractive real delta potentials, exhibiting two regimes: time advance and time delay.

Determination of Ground Heat Exchangers Temperature Field in Geothermal Heat Pumps

NASA Astrophysics Data System (ADS)

Zhurmilova, I.; Shtym, A.

2017-11-01

For the heating and cooling supply of buildings and constructions geothermal heat pumps using low-potential ground energy are applied by means of ground exchangers. The process of heat transfer in a system of ground exchangers is a phenomenon of complex heat transfer. The paper presents a mathematical modeling of heat exchange processes, the temperature fields are built which are necessary for the determination of the ground array that ensures an adequate supply of low potential energy excluding the freezing of soil around the pipes in the ground heat exchangers and guaranteeing a reliable operation of geothermal heat pumps.

Demand Response Resource Quantification with Detailed Building Energy Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hale, Elaine; Horsey, Henry; Merket, Noel

Demand response is a broad suite of technologies that enables changes in electrical load operations in support of power system reliability and efficiency. Although demand response is not a new concept, there is new appetite for comprehensively evaluating its technical potential in the context of renewable energy integration. The complexity of demand response makes this task difficult -- we present new methods for capturing the heterogeneity of potential responses from buildings, their time-varying nature, and metrics such as thermal comfort that help quantify likely acceptability of specific demand response actions. Computed with an automated software framework, the methods are scalable.

Communication: A new ab initio potential energy surface for HCl-H2O, diffusion Monte Carlo calculations of D0 and a delocalized zero-point wavefunction.

PubMed

Mancini, John S; Bowman, Joel M

2013-03-28

We report a global, full-dimensional, ab initio potential energy surface describing the HCl-H2O dimer. The potential is constructed from a permutationally invariant fit, using Morse-like variables, to over 44,000 CCSD(T)-F12b∕aug-cc-pVTZ energies. The surface describes the complex and dissociated monomers with a total RMS fitting error of 24 cm(-1). The normal modes of the minima, low-energy saddle point and separated monomers, the double minimum isomerization pathway and electronic dissociation energy are accurately described by the surface. Rigorous quantum mechanical diffusion Monte Carlo (DMC) calculations are performed to determine the zero-point energy and wavefunction of the complex and the separated fragments. The calculated zero-point energies together with a De value calculated from CCSD(T) with a complete basis set extrapolation gives a D0 value of 1348 ± 3 cm(-1), in good agreement with the recent experimentally reported value of 1334 ± 10 cm(-1) [B. E. Casterline, A. K. Mollner, L. C. Ch'ng, and H. Reisler, J. Phys. Chem. A 114, 9774 (2010)]. Examination of the DMC wavefunction allows for confident characterization of the zero-point geometry to be dominant at the C(2v) double-well saddle point and not the C(s) global minimum. Additional support for the delocalized zero-point geometry is given by numerical solutions to the 1D Schrödinger equation along the imaginary-frequency out-of-plane bending mode, where the zero-point energy is calculated to be 52 cm(-1) above the isomerization barrier. The D0 of the fully deuterated isotopologue is calculated to be 1476 ± 3 cm(-1), which we hope will stand as a benchmark for future experimental work.

Charge-transfer complexes of sulfamethoxazole drug with different classes of acceptors

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; El-Korashy, Sabry A.; El-Deen, Ibrahim M.; El-Sayed, Shaima M.

2010-09-01

The charge-transfer complexes of the donor sulfamethoxazole (SZ) with iodine (I 2), 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ), p-chloranil (CHL) and picric acid (PA) have been studied spectrophotometrically in chloroform or methanol at room temperature using absorption spectrophotometer. The results indicate that formation of CT-complexes in case of four acceptors. The stoichiometry of the complexes was found to be 1:1 ratio by molar ratio method between donor and acceptor with maximum absorption bands (CT band). The data are discussed in terms of formation constant ( KCT), molar extinction coefficient ( ɛCT), standard free energy (Δ G°), oscillator strength (ƒ), transition dipole moment ( μ), resonance energy ( RN) and ionization potential ( ID). The results indicate that the formation constant ( KCT) for the complexes were shown to be dependent upon the nature of electron acceptor, donor and polarity of solvents which were used. IR, 1H NMR, mass spectra, UV-Vis techniques, elemental analyses (CHN) and TG-DTG investigation were used to characterize the four sulfamethoxazole charge-transfer complexes.

Performance of the Effective Core Potentials of Ca, Hg and Pb in Complexes with Ligands Containing N and O Donor Atoms.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramirez, Jose Z.; Vargas, Rubicelia; Garza, Jorge

This paper presents a systematic study of the performance of the relativistic effective core potentials (RECPs) proposed by Stoll-Preuss, Christiansen-Ermler and Hay-Wadt for Ca2+, Hg2+ and Pb2+. The RECPs performance is studied when these cations are combined with ethylene glycol, 2-aminoethanol and ethylenediamine to form bidentate complexes. First, the description of the bidentate ligands is analyzed with the Kohn-Sham method by using SVWN, BLYP and B3LYP exchange-correlation functionals and they are compared with the Moeller-Plesset perturbation theory (MP2), for all these methods the TZVP basis set was used. We found that the BLYP exchange-correlation functional gives similar results that thosemore » obtained by the B3LYP and MP2 methods. Thus, the bidentate metal complexes were studied with the BLYP method combined with the RECPs. In order to compare RECPs performance, all the systems considered in this work were studied with the relativistic all-electron Douglas-Kroll (DK3) method. We observed that the Christiansen-Ermler RECPs give the best energetic and geometrical description for Ca and Hg complexes when compared with the all-electron method. For Pb complexes the spin-orbit interaction and Basis Set Superposition error must be taken into account in the RECP. In general, the trend showed in the complexation energies with the all-electron method is followed by the complexation energies computed with all the pseudopotential tested in this work. Battelle operates PNNL for the USDOE.« less

Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria.

PubMed

Inaoka, Daniel Ken; Shiba, Tomoo; Sato, Dan; Balogun, Emmanuel Oluwadare; Sasaki, Tsuyoshi; Nagahama, Madoka; Oda, Masatsugu; Matsuoka, Shigeru; Ohmori, Junko; Honma, Teruki; Inoue, Masayuki; Kita, Kiyoshi; Harada, Shigeharu

2015-07-07

Recent studies on the respiratory chain of Ascaris suum showed that the mitochondrial NADH-fumarate reductase system composed of complex I, rhodoquinone and complex II plays an important role in the anaerobic energy metabolism of adult A. suum. The system is the major pathway of energy metabolism for adaptation to a hypoxic environment not only in parasitic organisms, but also in some types of human cancer cells. Thus, enzymes of the pathway are potential targets for chemotherapy. We found that flutolanil is an excellent inhibitor for A. suum complex II (IC50 = 0.058 μM) but less effectively inhibits homologous porcine complex II (IC50 = 45.9 μM). In order to account for the specificity of flutolanil to A. suum complex II from the standpoint of structural biology, we determined the crystal structures of A. suum and porcine complex IIs binding flutolanil and its derivative compounds. The structures clearly demonstrated key interactions responsible for its high specificity to A. suum complex II and enabled us to find analogue compounds, which surpass flutolanil in both potency and specificity to A. suum complex II. Structures of complex IIs binding these compounds will be helpful to accelerate structure-based drug design targeted for complex IIs.

Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria

PubMed Central

Inaoka, Daniel Ken; Shiba, Tomoo; Sato, Dan; Balogun, Emmanuel Oluwadare; Sasaki, Tsuyoshi; Nagahama, Madoka; Oda, Masatsugu; Matsuoka, Shigeru; Ohmori, Junko; Honma, Teruki; Inoue, Masayuki; Kita, Kiyoshi; Harada, Shigeharu

2015-01-01

Recent studies on the respiratory chain of Ascaris suum showed that the mitochondrial NADH-fumarate reductase system composed of complex I, rhodoquinone and complex II plays an important role in the anaerobic energy metabolism of adult A. suum. The system is the major pathway of energy metabolism for adaptation to a hypoxic environment not only in parasitic organisms, but also in some types of human cancer cells. Thus, enzymes of the pathway are potential targets for chemotherapy. We found that flutolanil is an excellent inhibitor for A. suum complex II (IC50 = 0.058 μM) but less effectively inhibits homologous porcine complex II (IC50 = 45.9 μM). In order to account for the specificity of flutolanil to A. suum complex II from the standpoint of structural biology, we determined the crystal structures of A. suum and porcine complex IIs binding flutolanil and its derivative compounds. The structures clearly demonstrated key interactions responsible for its high specificity to A. suum complex II and enabled us to find analogue compounds, which surpass flutolanil in both potency and specificity to A. suum complex II. Structures of complex IIs binding these compounds will be helpful to accelerate structure-based drug design targeted for complex IIs. PMID:26198225

Nanotechnology for sustainability: what does nanotechnology offer to address complex sustainability problems?

NASA Astrophysics Data System (ADS)

Wiek, Arnim; Foley, Rider W.; Guston, David H.

2012-09-01

Nanotechnology is widely associated with the promise of positively contributing to sustainability. However, this view often focuses on end-of-pipe applications, for instance, for water purification or energy efficiency, and relies on a narrow concept of sustainability. Approaching sustainability problems and solution options from a comprehensive and systemic perspective instead may yield quite different conclusions about the contribution of nanotechnology to sustainability. This study conceptualizes sustainability problems as complex constellations with several potential intervention points and amenable to different solution options. The study presents results from interdisciplinary workshops and literature reviews that appraise the contribution of the selected nanotechnologies to mitigate such problems. The study focuses exemplarily on the urban context to make the appraisals tangible and relevant. The solution potential of nanotechnology is explored not only for well-known urban sustainability problems such as water contamination and energy use but also for less obvious ones such as childhood obesity. Results indicate not only potentials but also limitations of nanotechnology's contribution to sustainability and can inform anticipatory governance of nanotechnology in general, and in the urban context in particular.

Tight-binding calculation studies of vacancy and adatom defects in graphene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Wei; Lu, Wen-Cai; Zhang, Hong-Xing

2016-02-19

Computational studies of complex defects in graphene usually need to deal with a larger number of atoms than the current first-principles methods can handle. We show a recently developed three-center tight-binding potential for carbon is very efficient for large scale atomistic simulations and can accurately describe the structures and energies of various defects in graphene. Using the three-center tight-binding potential, we have systematically studied the stable structures and formation energies of vacancy and embedded-atom defects of various sizes up to 4 vacancies and 4 embedded atoms in graphene. In conclusion, our calculations reveal low-energy defect structures and provide a moremore » comprehensive understanding of the structures and stability of defects in graphene.« less

Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

PubMed Central

Tofoleanu, Florentina; Pickard, Frank C.; König, Gerhard; Huang, Jing; Damjanović, Ana; Baek, Minkyung; Seok, Chaok; Brooks, Bernard R.

2016-01-01

Herein, we report the absolute binding free energy calculations of CBClip complexes in the SAMPL5 blind challenge. Initial conformations of CBClip complexes were obtained using docking and molecular dynamics simulations. Free energy calculations were performed using thermodynamic integration (TI) with soft-core potentials and Bennett’s acceptance ratio (BAR) method based on a serial insertion scheme. We compared the results obtained with TI simulations with soft-core potentials and Hamiltonian replica exchange simulations with the serial insertion method combined with the BAR method. The results show that the difference between the two methods can be mainly attributed to the van der Waals free energies, suggesting that either the simulations used for TI or the simulations used for BAR, or both are not fully converged and the two sets of simulations may have sampled difference phase space regions. The penalty scores of force field parameters of the 10 guest molecules provided by CHARMM Generalized Force Field can be an indicator of the accuracy of binding free energy calculations. Among our submissions, the combination of docking and TI performed best, which yielded the root mean square deviation of 2.94 kcal/mol and an average unsigned error of 3.41 kcal/mol for the ten guest molecules. These values were best overall among all participants. However, our submissions had little correlation with experiments. PMID:27677749

Simulation of Reversible Protein–Protein Binding and Calculation of Binding Free Energies Using Perturbed Distance Restraints

PubMed Central

2017-01-01

Virtually all biological processes depend on the interaction between proteins at some point. The correct prediction of biomolecular binding free-energies has many interesting applications in both basic and applied pharmaceutical research. While recent advances in the field of molecular dynamics (MD) simulations have proven the feasibility of the calculation of protein–protein binding free energies, the large conformational freedom of proteins and complex free energy landscapes of binding processes make such calculations a difficult task. Moreover, convergence and reversibility of resulting free-energy values remain poorly described. In this work, an easy-to-use, yet robust approach for the calculation of standard-state protein–protein binding free energies using perturbed distance restraints is described. In the binding process the conformations of the proteins were restrained, as suggested earlier. Two approaches to avoid end-state problems upon release of the conformational restraints were compared. The method was evaluated by practical application to a small model complex of ubiquitin and the very flexible ubiquitin-binding domain of human DNA polymerase ι (UBM2). All computed free energy differences were closely monitored for convergence, and the calculated binding free energies had a mean unsigned deviation of only 1.4 or 2.5 kJ·mol–1 from experimental values. Statistical error estimates were in the order of thermal noise. We conclude that the presented method has promising potential for broad applicability to quantitatively describe protein–protein and various other kinds of complex formation. PMID:28898077

Predicting the potentials, solubilities and stabilities of metal-acetylacetonates for non-aqueous redox flow batteries using density functional theory calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kucharyson, J. F.; Cheng, L.; Tung, S. O.

New active materials are needed to improve the performance and reduce the cost of non-aqueous redox flow batteries (RFBs) for grid-scale energy storage applications. Efforts to develop better performing materials, which have largely been empirical, would benefit from a better understanding of relationships between structural, electronic and RFB-relevant functional properties. This paper focuses on metal-acetylacetonates, a class of metal coordination complexes that has shown promise for use in RFBs, and describes correlations between their experimentally measured standard potentials, solubilities, and stabilities (cycle lifes), and selected chemical, structural and electronic properties determined from Density Functional Theory (DFT) calculations. The training setmore » consisted of 16 complexes including 5 different metals and 11 different substituents on the acetylacetonate ligand. Standard potentials for those compounds were calculated and are in good agreement with experimentally measured results. A predictive equation based on the solvation energies and dipole moments, two easily computed properties, reasonably modeled the experimentally determined solubilities. Importantly, we were able to identify a descriptor for the stability of acetylacetonates. The experimentally determined stability, quantified as the cycle life to a given degree of degradation, correlated with the percentage of the highest occupied (HOMO) or lowest unoccupied molecular orbital (LUMO) on the metal of the complex. This percentage is influenced by the degree of ligand innocence (irreducibility), and complexes with the most innocent ligands yielded the most stable redox reactions. To this end, VO(acetylacetonate)(2) and Fe(acetylacetonate)(3), with nearly 80% of the HOMO and LUMO on the metal, possessed the most stable oxidation and reduction half-reactions, respectively. The structure-function relationships and correlations presented in this paper could be used to predict new, highly soluble and stable complexes for RFB applications.« less

Long-term Energy and Emissions Savings Potential in New York City Buildings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhatt, Vatsal; Lee, John; Klein, Yehuda

2012-09-30

The New York State Energy Research and Development Authority (NYSERDA) partnered with the Brookhaven National Laboratory (BNL) and the City University of New York (CUNY) to develop an integrated methodology that is capable of quantifying the impact of energy efficiency and load management options in buildings, including CUNY’s campus buildings, housing projects, hospitals, and hotels, while capturing the synergies and offsets in a complex and integrated energy-environmental system. The results of this work serve as a guideline in implementing urban energy efficiency and other forms of urban environmental improvement through cost-effective planning at the institutional and local level.

Reaction Mechanisms on Multiwell Potential Energy Surfaces in Combustion (and Atmospheric) Chemistry

DOE PAGES

Osborn, David L.

2017-03-15

Chemical reactions occurring on a potential energy surface with multiple wells are ubiquitous in low temperature combustion and the oxidation of volatile organic compounds in earth’s atmosphere. The rich variety of structural isomerizations that compete with collisional stabilization make characterizing such complex-forming reactions challenging. This review describes recent experimental and theoretical advances that deliver increasingly complete views of their reaction mechanisms. New methods for creating reactive intermediates coupled with multiplexed measurements provide many experimental observables simultaneously. Automated methods to explore potential energy surfaces can uncover hidden reactive pathways, while master equation methods enable a holistic treatment of both sequential andmore » well-skipping pathways. Our ability to probe and understand nonequilibrium effects and reaction sequences is increasing. These advances provide the fundamental science base for predictive models of combustion and the atmosphere that are crucial to address global challenges.« less

Reaction Mechanisms on Multiwell Potential Energy Surfaces in Combustion (and Atmospheric) Chemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Osborn, David L.

Chemical reactions occurring on a potential energy surface with multiple wells are ubiquitous in low temperature combustion and the oxidation of volatile organic compounds in earth’s atmosphere. The rich variety of structural isomerizations that compete with collisional stabilization make characterizing such complex-forming reactions challenging. This review describes recent experimental and theoretical advances that deliver increasingly complete views of their reaction mechanisms. New methods for creating reactive intermediates coupled with multiplexed measurements provide many experimental observables simultaneously. Automated methods to explore potential energy surfaces can uncover hidden reactive pathways, while master equation methods enable a holistic treatment of both sequential andmore » well-skipping pathways. Our ability to probe and understand nonequilibrium effects and reaction sequences is increasing. These advances provide the fundamental science base for predictive models of combustion and the atmosphere that are crucial to address global challenges.« less

Dynamics of harpooning studied by transition state spectroscopy. II. LiṡṡFH

NASA Astrophysics Data System (ADS)

Hudson, A. J.; Oh, H. B.; Polanyi, J. C.; Piecuch, P.

2000-12-01

The van der Waals complex LiṡṡFH was formed in crossed beams and the transition state of the excited-state reaction, Li*(2p 2P)+HF→LiF+H, was accessed by photoexcitation of this complex. The dynamics of the excited-state reaction were probed by varying the excitation wavelength over the range 570-970 nm while recording the photodepletion of the complex. The findings were interpreted using high-level ab initio calculations of the ground and lowest excited-state potential-energy surfaces.

Angular selective window systems: Assessment of technical potential for energy savings

DOE PAGES

Fernandes, Luis L.; Lee, Eleanor S.; McNeil, Andrew; ...

2014-10-16

Static angular selective shading systems block direct sunlight and admit daylight within a specific range of incident solar angles. The objective of this study is to quantify their potential to reduce energy use and peak demand in commercial buildings using state-of-the art whole-building computer simulation software that allows accurate modeling of the behavior of optically-complex fenestration systems such as angular selective systems. Three commercial systems were evaluated: a micro-perforated screen, a tubular shading structure, and an expanded metal mesh. This evaluation was performed through computer simulation for multiple climates (Chicago, Illinois and Houston, Texas), window-to-wall ratios (0.15-0.60), building codes (ASHRAEmore » 90.1-2004 and 2010) and lighting control configurations (with and without). The modeling of the optical complexity of the systems took advantage of the development of state-of-the-art versions of the EnergyPlus, Radiance and Window simulation tools. Results show significant reductions in perimeter zone energy use; the best system reached 28% and 47% savings, respectively without and with daylighting controls (ASHRAE 90.1-2004, south facade, Chicago,WWR=0.45). As a result, angular selectivity and thermal conductance of the angle-selective layer, as well as spectral selectivity of low-emissivity coatings, were identified as factors with significant impact on performance.« less

Linear energy relationships for the octahedral preference of Mg, Ca and transition metal ions.

PubMed

Pontikis, George; Borden, James; Martínek, Václav; Florián, Jan

2009-04-16

The geometry, atomic charges, force constants, and relative energies of the symmetric and distorted M(2+)(H(2)O)(4)(F(-))(2), M(3+)(H(2)O)(4)(F(-))(2), M(2+)(H(2)O)(3)(F(-))(2), and M(3+)(H(2)O)(3)(F(-))(2) metal complexes, M = Mg, Ca, Co, Cu, Fe, Mn, Ni, Zn, Cr, V, were calculated by using the B3LYP/TZVP density functional method in both gas phase and aqueous solution, modeled using the polarized continuum model. The deformation energy associated with moving one water ligand 12 degrees from the initial "octahedral" arrangement, in which all O-M-O, O-M-F, and F-M-F angles are either 90 degrees or 180 degrees, was calculated to examine the angular ligand flexibility. For all M(2+)(H(2)O)(4)(F(-))(2) complexes, this distortion increased the energy of the complex in proportion to the electrostatic potential-derived (ESP) charge of the metal, and in proportion to D(-10), where D is the distance from the distorted ligand to its closest neighbor. The octahedral stability was further examined by calculating the energies for the removal of a water ligand from the octahedral complex to form a square-pyramidal or trigonal-bipyramidal complex. The octahedral preference, defined as the negative of the corresponding binding energy of the ligand, was found to linearly correlate with the ESP charge of the metal in both the gas phase and aqueous solution. The obtained results indicate that quantum-mechanical covalent effects are of secondary importance for both the flexibility and the octahedral preference of M(2+)(H(2)O)(4)(F(-))(2) and M(3+)(H(2)O)(4)(F(-))(2) complexes. This conclusion and supporting data are important for the development of consistent molecular mechanical force fields of the studied metal ions.

Mechanosensing Potentials Gate Fuel Consumption in a Bipedal DNA Nanowalker

NASA Astrophysics Data System (ADS)

Tee, Shern Ren; Hu, Xinpeng; Loh, Iong Ying; Wang, Zhisong

2018-03-01

A bipedal DNA nanowalker was recently reported to convert chemical energy into directional motion autonomously and efficiently. To elucidate its chemomechanical coupling mechanisms, three-dimensional molecular modeling is used to obtain coarse-grained foot-track binding potentials of the DNA nanowalker via unbiased and biased sampling techniques (for the potentials' basin and high-energy edges, respectively). The binding state that is protected against fuel-induced dissociation responds asymmetrically to forward versus backward forces, unlike the unprotected state, demonstrating a mechanosensing capability to gate fuel binding. Despite complex DNA mechanics, the foot-track potential exhibits a surprisingly neat three-part profile, offering some general guidelines to rationally design efficient nanowalkers. Subsequent modeling of the bipedal walker attached to the track gives estimates of the free energy for each bipedal state, showing how the mechanosensing foot-track binding breaks the symmetry between the rear and front feet, enabling the rear foot to be selectively dissociated by fuel and generating efficient chemomechanical coupling.

Theoretical insights into the π-hole interactions in the complexes containing triphosphorus hydride (P3H3) and its derivatives.

PubMed

Wang, Yuehong; Li, Xiaoyan; Zeng, Yanli; Meng, Lingpeng; Zhang, Xueying

2017-04-01

The π-hole of triphosphorus hydride (P 3 H 3 ) and its derivatives Z 3 X 3 (Z = P, As; X = H, F, Cl, Br) was discovered and analyzed. MP2/aug-cc-pVDZ calculations were performed on the π-hole interactions in the HCN...Z 3 X 3 complexes and the mutual influence between π-hole interactions and the hydrogen bond in the HCN...HCN...Z 3 X 3 and HCN...Z 3 X 3 ...HCN complexes studied. The π-hole interaction belongs to the typical closed-shell noncovalent interaction. The linear relationship was found between the most positive electrostatic potential of the π-hole (V S,max ) and the interaction energy. Moreover, the V S,max of the π-hole was also found to be linearly correlated to the electrostatic energy term, indicating the important contribution of the electrostatic energy term to the π-hole interaction. There is positive cooperativity between the π-hole interaction and the hydrogen bond in the termolecular complexes. The π-hole interaction has a greater influence on the hydrogen bond than vice versa. The mutual enhancing effect between the π-hole interaction and the hydrogen bond in the HCN...HCN...Z 3 X 3 complexes is greater than that in the HCN...Z 3 X 3 ...HCN complexes.

Space and energy. [space systems for energy generation, distribution and control

NASA Technical Reports Server (NTRS)

Bekey, I.

1976-01-01

Potential contributions of space to energy-related activities are discussed. Advanced concepts presented include worldwide energy distribution to substation-sized users using low-altitude space reflectors; powering large numbers of large aircraft worldwide using laser beams reflected from space mirror complexes; providing night illumination via sunlight-reflecting space mirrors; fine-scale power programming and monitoring in transmission networks by monitoring millions of network points from space; prevention of undetected hijacking of nuclear reactor fuels by space tracking of signals from tagging transmitters on all such materials; and disposal of nuclear power plant radioactive wastes in space.

Joint experimental-theoretical investigation of the lower bound states of the NO(X2Pi)-Kr complex.

PubMed

Wen, Bo; Meyer, Henning; Kłos, Jacek; Alexander, Millard H

2009-07-02

We describe the first measurement of the near IR spectrum of the NO-Kr van der Waals complex. A variant of IR-REMPI double-resonance spectroscopy is employed in which the IR and UV lasers are scanned simultaneously in such a way that throughout the scan the sum of the two photon energies is kept constant, matching a UV resonance of the system. In the region of the first overtone vibration of the NO monomer, we observe several rotationally resolved bands for the NO-Kr complex. In addition to the origin band located at 3723.046 cm(-1), we observe excited as well as hot bands involving the excitation of one or two quanta of z-axis rotation. Another band is assigned to the excitation of one quantum of bending vibration. The experimental spectra are compared with results of bound-state calculations for a new set of potential energy surfaces calculated at the spin-restricted coupled cluster level. For the average vibration-rotation energies, there is excellent agreement between the theoretical results based on the coupled states (CS) approximation and the full close-coupling (CC) treatment. Finer details like the electrostatic splitting and the P-type doubling of the rotational levels are accounted for only within the CC formalism. The comparison of the CC results with the measured spectra confirms the high quality of the PESs. However, the high resolution of the experiments is sufficient to identify some inaccuracies in the difference between the potential energy surfaces of A' and A'' reflection symmetry.

Stalking Higher Energy Conformers on the Potential Energy Surface of Charged Species.

PubMed

Brites, Vincent; Cimas, Alvaro; Spezia, Riccardo; Sieffert, Nicolas; Lisy, James M; Gaigeot, Marie-Pierre

2015-03-10

Combined theoretical DFT-MD and RRKM methodologies and experimental spectroscopic infrared predissociation (IRPD) strategies to map potential energy surfaces (PES) of complex ionic clusters are presented, providing lowest and high energy conformers, thresholds to isomerization, and cluster formation pathways. We believe this association not only represents a significant advance in the field of mapping minima and transition states on the PES but also directly measures dynamical pathways for the formation of structural conformers and isomers. Pathways are unraveled over picosecond (DFT-MD) and microsecond (RRKM) time scales while changing the amount of internal energy is experimentally achieved by changing the loss channel for the IRPD measurements, thus directly probing different kinetic and isomerization pathways. Demonstration is provided for Li(+)(H2O)3,4 ionic clusters. Nonstatistical formation of these ionic clusters by both direct and cascade processes, involving isomerization processes that can lead to trapping of high energy conformers along the paths due to evaporative cooling, has been unraveled.

Computational Analysis of a Zn-Bound Tris(imidazolyl) Calix[6]arene Aqua Complex: Toward Incorporating Second-Coordination Sphere Effects into Carbonic Anhydrase Biomimetics.

PubMed

Koziol, Lucas; Essiz, Sebnem G; Wong, Sergio E; Lau, Edmond Y; Valdez, Carlos A; Satcher, Joe H; Aines, Roger D; Lightstone, Felice C

2013-03-12

Molecular dynamics simulations and quantum-mechanical calculations were performed to characterize a supramolecular tris(imidazolyl) calix[6]arene Zn(2+) aqua complex, as a biomimetic model for the catalyzed hydration of carbon dioxide to bicarbonate, H2O + CO2 → H(+) + HCO3(-). On the basis of potential-of-mean-force (PMF) calculations, stable conformations had distorted 3-fold symmetry and supported either one or zero encapsulated water molecules. The conformation with an encapsulated water molecule is calculated to be lower in free energy than the conformation with an empty cavity (ΔG = 1.2 kcal/mol) and is the calculated free-energy minimum in solution. CO2 molecule partitioning into the cavity is shown to be very facile, proceeding with a barrier of 1.6 kcal/mol from a weak encounter complex which stabilizes the species by about 1.0 kcal/mol. The stabilization energy of CO2 is calculated to be larger than that of H2O (ΔΔG = 1.4 kcal/mol), suggesting that the complex will preferentially encapsulate CO2 in solution. In contrast, the PMF for a bicarbonate anion entering the cavity is calculated to be repulsive in all nonbonding regions of the cavity, due to the diameter of the calix[6]arene walls. Geometry optimization of the Zn-bound hydroxide complex with an encapsulated CO2 molecule showed that multiple noncovalent interactions direct the reactants into optimal position for nucleophilic addition to occur. The calixarene complex is a structural mimic of the hydrophilic/hydrophobic divide in the enzyme, providing a functional effect for CO2 addition in the catalytic cycle. The results show that Zn-binding calix[6]arene scaffolds can be potential synthetic biomimetics for CO2 hydration catalysis, both in terms of preferentially encapsulating CO2 from solution and by spatially fixing the reactive species inside the cavity.

Group 4 transition metal CH2=MF2, CHF=MF2, and HC/MF3 complexes formed by C-F activation and alpha-fluorine transfer.

PubMed

Lyon, Jonathan T; Andrews, Lester

2007-06-11

Group 4 transition metal methylidene difluoride complexes (CH2=MF2) are formed by the reaction of methylene fluoride with laser-ablated metal atoms and are isolated in an argon matrix. Isotopic substitution of the CH2F2 precursor and theoretical computations (B3LYP and CCSD) confirm product identifications and assignments. Our calculations indicate that the CH2=MF2 complexes have near C2v symmetry and are considerably more stable than other possible products (CH2(mu-F)MF and CHF=MHF). The primary reaction exothermicity provides more than enough energy to activate the initial bridge-bonded CH2(mu-F)MF products on the triplet potential energy surface to complete an alpha-F transfer to form the very stable CH2=MF2 products. Analogous experiments with CHF3 produce CHF=TiF2, which is not distorted at the C-H bond, whereas the heavier group 4 metals form lower-energy triplet HC/MF3 complexes, which contain weak degenerate C(p)-M(d) pi-bonding interactions. Comparisons are made with the CH2=MHF methylidene species, which showed considerable agostic distortions.

Dual Role of Protein Phosphorylation in DNA Activator/Coactivator Binding

PubMed Central

Dadarlat, Voichita M.; Skeel, Robert D.

2011-01-01

Binding free energies are calculated for the phosphorylated and unphosphorylated complexes between the kinase inducible domain (KID) of the DNA transcriptional activator cAMP response element binding (CREB) protein and the KIX domain of its coactivator, CREB-binding protein (CBP). To our knowledge, this is the first application of a method based on a potential of mean force (PMF) with restraining potentials to compute the binding free energy of protein-protein complexes. The KID:KIX complexes are chosen here because of their biological relevance to the DNA transcription process and their relatively small size (81 residues for the KIX domain of CBP, and 28 residues for KID). The results for pKID:KIX and KID:KIX are −9.55 and −4.96 kcal/mol, respectively, in good agreement with experimental estimates (−8.8 and −5.8 kcal/mol, respectively). A comparison between specific contributions to protein-protein binding for the phosphorylated and unphosphorylated complexes reveals a dual role for the phosphorylation of KID at Ser-133 in effecting a more favorable free energy of the bound system: 1), stabilization of the unbound conformation of phosphorylated KID due to favorable intramolecular interactions of the phosphate group of Ser-133 with the charged groups of an arginine-rich region spanning both α-helices, which lowers the configurational entropy; and 2), more favorable intermolecular electrostatic interactions between pSer-133 and Arg-131 of KID, and Lys-662, Tyr-658, and Glu-666 of KIX. Charge reduction through ligand phosphorylation emerges as a possible mechanism for controlling the unbound state conformation of KID and, ultimately, gene expression. This work also demonstrates that the PMF-based method with restraining potentials provides an added benefit in that important elements of the binding pathway are evidenced. Furthermore, the practicality of the PMF-based method for larger systems is validated by agreement with experiment. In addition, we provide a somewhat differently structured exposition of the PMF-based method with restraining potentials and outline its generalization to systems in which both protein and ligand may adopt unbound conformations that are different from those of the bound state. PMID:21244843

Sulfur K-edge XAS of WV=O vs. MoV=O Bis(dithiolene) Complexes: Contributions of Relativistic Effects to Electronic Structure and Reactivity of Tungsten Enzymes†

PubMed Central

Tenderholt, Adam L.; Szilagyi, Robert K.; Holm, Richard H.; Hodgson, Keith O.; Hedman, Britt; Solomon, Edward I.

2009-01-01

Molybdenum- or tungsten-containing enzymes catalyze oxygen atom transfer reactions involved in carbon, sulfur, or nitrogen metabolism. It has been observed that reduction potentials and oxygen atom transfer rates are different for W relative to Mo enzymes and the isostructural Mo/W complexes. Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations on [MoVO(bdt)2]− and [WVO(bdt)2]−, where bdt = benzene-1,2-dithiolate(2−), have been used to determine that the energies of the half-filled redox-active orbital, and thus the reduction potentials and M=O bond strengths, are different for these complexes due to relativistic effects in the W sites. PMID:17720249

Equilibrium location for spherical DNA and toroidal cyclodextrin

NASA Astrophysics Data System (ADS)

Sarapat, Pakhapoom; Baowan, Duangkamon; Hill, James M.

2018-05-01

Cyclodextrin comprises a ring structure composed of glucose molecules with an ability to form complexes of certain substances within its central cavity. The compound can be utilised for various applications including food, textiles, cosmetics, pharmaceutics, and gene delivery. In gene transfer, the possibility of forming complexes depends upon the interaction energy between cyclodextrin and DNA molecules which here are modelled as a torus and a sphere, respectively. Our proposed model is derived using the continuum approximation together with the Lennard-Jones potential, and the total interaction energy is obtained by integrating over both the spherical and toroidal surfaces. The results suggest that the DNA prefers to be symmetrically situated about 1.2 Å above the centre of the cyclodextrin to minimise its energy. Furthermore, an optimal configuration can be determined for any given size of torus and sphere.

Advances in Household Appliances- A Review

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bansal, Pradeep; Vineyard, Edward Allan; Abdelaziz, Omar

2011-01-01

An overview of options and potential barriers and risks for reducing the energy consumption, peak demand, and emissions for seven key energy consuming residential products (refrigerator-freezers, dishwashers, clothes washers, clothes dryers, electric ovens, gas ovens and microwave ovens) is presented. The paper primarily concentrates on the potential energy savings from the use of advanced technologies in appliances for the U.S. market. The significance and usefulness of each technology was evaluated in order to prioritize the R&D needs to improve energy efficiency of appliances in view of energy savings, cost, and complexity. The paper provides a snapshot of the future R&Dmore » needs for each of the technologies along with the associated barriers. Although significant energy savings may be achieved, one of the major barriers in most cases is high first cost. One way of addressing this issue and promoting the introduction of new technologies is to level the playing field for all manufacturers by establishing Minimum Energy Performance Standards (MEPS) which are not cost prohibitive and promoting energy efficient products through incentives to both manufacturers and consumers.« less

The Zinc-Schiff Base-Novicidin Complex as a Potential Prostate Cancer Therapy

PubMed Central

Milosavljevic, Vedran; Haddad, Yazan; Merlos Rodrigo, Miguel Angel; Moulick, Amitava; Polanska, Hana; Hynek, David; Heger, Zbynek; Kopel, Pavel; Adam, Vojtech

2016-01-01

Prostate cancer cells control energy metabolism by chelating intracellular zinc. Thus, zinc delivery has been a popular therapeutic approach for prostate cancer. Here, we propose the use of the membrane-penetrating peptide Novicidin connected to zinc-Schiff base as a carrier vehicle for the delivery of zinc to prostate cells. Mass spectrometry, electrochemistry and spectrophotometry confirmed the formation/stability of this complex and provided insight regarding the availability of zinc for complex interactions. This delivery system showed minor toxicity in normal PNT1A cells and high potency towards PC3 tumor cells. The complex preferentially penetrated PC3 tumor cells in contrast to confinement to the membranes of PNT1A. Furthermore, zinc uptake was confirmed in both cell lines. Molecular analysis was used to confirm the activation of zinc stress (e.g., ZnT-1) and apoptosis (e.g., CASP-1). Our results strongly suggest that the zinc-Schiff base-Novicidin complex has great potential as a novel anticancer drug. PMID:27727290

Selective CO{sub 2} reduction conjugated with H{sub 2}O oxidation utilizing semiconductor/metal-complex hybrid photocatalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morikawa, T., E-mail: morikawa@mosk.tytlabs.co.jp; Sato, S., E-mail: morikawa@mosk.tytlabs.co.jp; Arai, T., E-mail: morikawa@mosk.tytlabs.co.jp

2013-12-10

We developed a new hybrid photocatalyst for CO{sub 2} reduction, which is composed of a semiconductor and a metal complex. In the hybrid photocatalyst, ΔG between the position of conduction band minimum (E{sub CBM}) of the semiconductor and the CO{sub 2} reduction potential of the complex is an essential factor for realizing fast electron transfer from the conduction band of semiconductor to metal complex leading to high photocatalytic activity. On the basis of this concept, the hybrid photocatalyst InP/Ru-complex, which functions in aqueous media, was developed. The photoreduction of CO{sub 2} to formate using water as an electron donor andmore » a proton source was successfully achieved as a Z-scheme system by functionally conjugating the InP/Ru-complex photocatalyst for CO{sub 2} reduction with a TiO{sub 2} photocatalyst for water oxidation. The conversion efficiency from solar energy to chemical energy was ca. 0.04%, which approaches that for photosynthesis in a plant. Because this system can be applied to many other inorganic semiconductors and metal-complex catalysts, the efficiency and reaction selectivity can be enhanced by optimization of the electron transfer process including the energy-band configurations, conjugation conformations, and catalyst structures. This electrical-bias-free reaction is a huge leap forward for future practical applications of artificial photosynthesis under solar irradiation to produce organic species.« less

EPR & Klein Paradoxes in Complex Hamiltonian Dynamics and Krein Space Quantization

NASA Astrophysics Data System (ADS)

Payandeh, Farrin

2015-07-01

Negative energy states are applied in Krein space quantization approach to achieve a naturally renormalized theory. For example, this theory by taking the full set of Dirac solutions, could be able to remove the propagator Green function's divergences and automatically without any normal ordering, to vanish the expected value for vacuum state energy. However, since it is a purely mathematical theory, the results are under debate and some efforts are devoted to include more physics in the concept. Whereas Krein quantization is a pure mathematical approach, complex quantum Hamiltonian dynamics is based on strong foundations of Hamilton-Jacobi (H-J) equations and therefore on classical dynamics. Based on complex quantum Hamilton-Jacobi theory, complex spacetime is a natural consequence of including quantum effects in the relativistic mechanics, and is a bridge connecting the causality in special relativity and the non-locality in quantum mechanics, i.e. extending special relativity to the complex domain leads to relativistic quantum mechanics. So that, considering both relativistic and quantum effects, the Klein-Gordon equation could be derived as a special form of the Hamilton-Jacobi equation. Characterizing the complex time involved in an entangled energy state and writing the general form of energy considering quantum potential, two sets of positive and negative energies will be realized. The new states enable us to study the spacetime in a relativistic entangled “space-time” state leading to 12 extra wave functions than the four solutions of Dirac equation for a free particle. Arguing the entanglement of particle and antiparticle leads to a contradiction with experiments. So, in order to correct the results, along with a previous investigation [1], we realize particles and antiparticles as physical entities with positive energy instead of considering antiparticles with negative energy. As an application of modified descriptions for entangled (space-time) states, the original version of EPR paradox can be discussed and the correct answer can be verified based on the strong rooted complex quantum Hamilton-Jacobi theory [2-27] and as another example we can use the negative energy states, to remove the Klein's paradox without the need of any further explanations or justifications like backwardly moving electrons. Finally, comparing the two approaches, we can point out to the existence of a connection between quantum Hamiltonian dynamics, standard quantum field theory, and Krein space quantization [28-43].

Energy design for protein-protein interactions

PubMed Central

Ravikant, D. V. S.; Elber, Ron

2011-01-01

Proteins bind to other proteins efficiently and specifically to carry on many cell functions such as signaling, activation, transport, enzymatic reactions, and more. To determine the geometry and strength of binding of a protein pair, an energy function is required. An algorithm to design an optimal energy function, based on empirical data of protein complexes, is proposed and applied. Emphasis is made on negative design in which incorrect geometries are presented to the algorithm that learns to avoid them. For the docking problem the search for plausible geometries can be performed exhaustively. The possible geometries of the complex are generated on a grid with the help of a fast Fourier transform algorithm. A novel formulation of negative design makes it possible to investigate iteratively hundreds of millions of negative examples while monotonically improving the quality of the potential. Experimental structures for 640 protein complexes are used to generate positive and negative examples for learning parameters. The algorithm designed in this work finds the correct binding structure as the lowest energy minimum in 318 cases of the 640 examples. Further benchmarks on independent sets confirm the significant capacity of the scoring function to recognize correct modes of interactions. PMID:21842951

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Suvam; Naghma, Rahla; Kaur, Jaspreet

The total and ionization cross sections for electron scattering by benzene, halobenzenes, toluene, aniline, and phenol are reported over a wide energy domain. The multi-scattering centre spherical complex optical potential method has been employed to find the total elastic and inelastic cross sections. The total ionization cross section is estimated from total inelastic cross section using the complex scattering potential-ionization contribution method. In the present article, the first theoretical calculations for electron impact total and ionization cross section have been performed for most of the targets having numerous practical applications. A reasonable agreement is obtained compared to existing experimental observationsmore » for all the targets reported here, especially for the total cross section.« less

Taser and Conducted Energy Weapons.

PubMed

LeClair, Thomas G; Meriano, Tony

2015-01-01

It is clear that CEWs are an increasingly prevalent law enforcement tool, adopted to address a complex and challenging problem. The potential for serious injury from a single deployment of a CEW is extremely low. The debate regarding the link between these electrical weapons and sudden in-custody death is likely to continue because their use is often in complex and volatile situations. Any consideration of injuries has to be put into that context. One must also consider what injuries to a subject would result if an alternative force method was used. Furthermore, the potential benefits of CEWs, including reduction in injuries to the public and law-enforcement officers, need to be considered.

On improving the performance of nonphotochemical quenching in CP29 light-harvesting antenna complex

NASA Astrophysics Data System (ADS)

Berman, Gennady P.; Nesterov, Alexander I.; Sayre, Richard T.; Still, Susanne

2016-03-01

We model and simulate the performance of charge-transfer in nonphotochemical quenching (NPQ) in the CP29 light-harvesting antenna-complex associated with photosystem II (PSII). The model consists of five discrete excitonic energy states and two sinks, responsible for the potentially damaging processes and charge-transfer channels, respectively. We demonstrate that by varying (i) the parameters of the chlorophyll-based dimer, (ii) the resonant properties of the protein-solvent environment interaction, and (iii) the energy transfer rates to the sinks, one can significantly improve the performance of the NPQ. Our analysis suggests strategies for improving the performance of the NPQ in response to environmental changes, and may stimulate experimental verification.

Photophysical studies of chromium sensitizers designed for excited state hole transfer to semiconductors and sequential hole/electron transfers from photoexcited cadmium sulfide nanorods to mononuclear ruthenium water-oxidation catalysts

NASA Astrophysics Data System (ADS)

Tseng, Huan-Wei

This dissertation describes three research projects related to solar cells and solar water splitting with a goal of utilizing solar energy, a renewable energy source. The first project is focused on photophysical studies of four newly-synthesized Cr(III) tris-bipyridyl complexes featuring the 4-dmcbpy (dimethyl 2,2'-bipyridine-4,4'-dicarboxylate) ligand. Static and time-resolved emission results suggest that the complexes store ˜1.7 eV of energy for multiple microseconds. Using cyclic voltammetry, it is found that the inclusion of 4-dmcbpy shifts the E1/2 of CrIII/II by +0.2 V from the homoleptic parent complexes without 4-dmcbpy. All four complexes have excited state potentials of CrIII*/II between +1.8 and +2.0 V vs. NHE, placing them among the most powerful photooxidants reported and making them candidates for hole-injection sensitizers. The second project continues with Cr(III) complexes, but using iminopyridine Schiff base ligands. Two complexes feature hexadentate ligands and the other two are their tris-bidentate analogues. One of each pair contains methyl ester groups for attachment to semiconductors. Cyclic voltammograms show that the hexadentate and tris-bidentate analogues have almost identical reduction potentials, but the addition of ester substituents shifts the reduction potentials by +0.2 V. The absorption spectra of the hexadentate complexes show improved absorption of visible light compared to the tris-bidentate analogues. For freshly prepared sample solutions in CH3CN, time-resolved emission and transient absorption measurements for the Cr(III) tris-bidentate ester complex show a doublet excited state with a 17-19 microsecond lifetime at room temperature, while no emission or transient absorption signals from the doublet states are observed for the hexadentate analogue under the same conditions. The dramatic difference is due to the presence of a nonligated bridgehead nitrogen atom. The third project features charge transfer interactions between a photoexcited cadmium sulfide nanorod and [Ru(diethyl 2,2'-bipyridine-4,4'-dicarboxylate)(2,2':6',2"-terpyridine)Cl] +, a mononuclear water-oxidation catalyst. Upon photoexcitation, hole transfer from the cadmium sulfide nanorod oxidizes the catalyst (Ru 2+ → Ru3+) on a 100 ps to 1 ns timescale. This is followed by electron transfer (10-100 ns) from the nanorod to reduce the Ru3+ center. The relatively slow electron transfer dynamics may provide opportunities for the accumulation of multiple holes at the catalyst, which is required for water oxidation.

AN ASSESSMENT OF CENTRAL-STATION CONGENERATION SYSTEMS FOR INDUSTRIAL COMPLEXES

EPA Science Inventory

This report assesses the potential for cogeneration system development based on an analysis of the economic, environmental, energy efficiency and social aspects of such systems. The cogeneration system is an application of the principle of cogeneration in which utility-sized powe...

Molecular modeling, dynamics studies and density functional theory approaches to identify potential inhibitors of SIRT4 protein from Homo sapiens : a novel target for the treatment of type 2 diabetes.

PubMed

Choubey, Sanjay K; Prabhu, Dhamodharan; Nachiappan, Mutharasappan; Biswal, Jayshree; Jeyakanthan, Jeyaraman

2017-11-01

Type 2 diabetes is one of the biggest health challenges in the world and WHO projects it to be the 7th leading cause of death in 2030. It is a chronic condition affecting the way our body metabolizes sugar. Insulin resistance is high risk factor marked by expression of Lipoprotein Lipases and Peroxisome Proliferator-Activated Receptor that predisposes to type 2 diabetes. AMP-dependent protein kinase in AMPK signaling pathway is a central sensor of energy status. Deregulation of AMPK signaling leads to inflammation, oxidative stress, and deactivation of autophagy which are implicated in pathogenesis of insulin resistance. SIRT4 protein deactivates AMPK as well as directly inhibits insulin secretion. SIRT4 overexpression leads to dyslipidimeia, decreased fatty acid oxidation, and lipogenesis which are the characteristic features of insulin resistance promoting type 2 diabetes. This makes SIRT4 a novel therapeutic target to control type 2 diabetes. Virtual screening and molecular docking studies were performed to obtain potential ligands. To further optimize the geometry of protein-ligand complexes Quantum Polarized Ligand Docking was performed. Binding Free Energy was calculated for the top three ligand molecules. In view of exploring the stereoelectronic features of the ligand, density functional theory approach was implemented at B3LYP/6-31G* level. 30 ns MD simulation studies of the protein-ligand complexes were done. The present research work proposes ZINC12421989 as potential inhibitor of SIRT4 with docking score (-7.54 kcal/mol), docking energy (-51.34 kcal/mol), binding free energy (-70.21 kcal/mol), and comparatively low energy gap (-0.1786 eV) for HOMO and LUMO indicating reactivity of the lead molecule.

N-Heterocyclic carbene metal complexes: photoluminescence and applications.

PubMed

Visbal, Renso; Gimeno, M Concepción

2014-05-21

This review covers the advances made in the synthesis of luminescent transition metal complexes containing N-heterocyclic carbene (NHC) ligands. The presence of a high field strength ligand such as an NHC in the complexes gives rise to high energy emissions, and consequently, to the desired blue colour needed for OLED applications. Furthermore, the great versatility of NHC ligands for structural modifications, together with the use of other ancillary ligands in the complex, provides numerous possibilities for the synthesis of phosphorescent materials, with emission colours over the entire visible spectra and potential future applications in fields such as photochemical water-splitting, chemosensors, dye-sensitised solar cells, oxygen sensors, and medicine.

Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

PubMed Central

Lapelosa, Mauro; Gallicchio, Emilio; Levy, Ronald M.

2011-01-01

The Binding Energy Distribution Analysis Method (BEDAM) is employed to compute the standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) with implicit solvation. Binding free energy estimates are in reasonably good agreement with experimental affinities. The conformations of the complexes identified by the simulations are in good agreement with crystallographic data, which was not used to restrain ligand orientations. The BEDAM method is based on λ -hopping Hamiltonian parallel Replica Exchange (HREM) molecular dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential, and multi-state free energy estimators (MBAR). Achieving converged and accurate results depends on all of these elements of the calculation. Convergence of the binding free energy is tied to the level of convergence of binding energy distributions at critical intermediate states where bound and unbound states are at equilibrium, and where the rate of binding/unbinding conformational transitions is maximal. This finding mirrors similar observations in the context of order/disorder transitions as for example in protein folding. Insights concerning the physical mechanism of ligand binding and unbinding are obtained. Convergence for the largest FK506 ligand is achieved only after imposing strict conformational restraints, which however require accurate prior structural knowledge of the structure of the complex. The analytical AGBNP2 model is found to underestimate the magnitude of the hydrophobic driving force towards binding in these systems characterized by loosely packed protein-ligand binding interfaces. Rescoring of the binding energies using a numerical surface area model corrects this deficiency. This study illustrates the complex interplay between energy models, exploration of conformational space, and free energy estimators needed to obtain robust estimates from binding free energy calculations. PMID:22368530

Geobacter Project

DOE Office of Scientific and Technical Information (OSTI.GOV)

Derek Lovley; Maddalena Coppi; Stacy Ciufo

Analysis of the Genetic Potential and Gene Expression of Microbial Communities Involved in the In Situ Bioremediation of Uranium and Harvesting Electrical Energy from Organic Matter The primary goal of this research is to develop conceptual and computational models that can describe the functioning of complex microbial communities involved in microbial processes of interest to the Department of Energy. Microbial Communities to be Investigated: (1) Microbial community associated with the in situ bioremediation of uranium-contaminated groundwater; and (2) Microbial community that is capable of harvesting energy from waste organic matter in the form of electricity.

Millisecond infrared laser pulses depolarize and elicit action potentials on in-vitro dorsal root ganglion neurons

PubMed Central

Paris, Lambert; Marc, Isabelle; Charlot, Benoit; Dumas, Michel; Valmier, Jean; Bardin, Fabrice

2017-01-01

This work focuses on the optical stimulation of dorsal root ganglion (DRG) neurons through infrared laser light stimulation. We show that a few millisecond laser pulse at 1875 nm induces a membrane depolarization, which was observed by the patch-clamp technique. This stimulation led to action potentials firing on a minority of neurons beyond an energy threshold. A depolarization without action potential was observed for the majority of DRG neurons, even beyond the action potential energy threshold. The use of ruthenium red, a thermal channel blocker, stops the action potential generation, but has no effects on membrane depolarization. Local temperature measurements reveal that the depolarization amplitude is sensitive to the amplitude of the temperature rise as well as to the time rate of change of temperature, but in a way which may not fully follow a photothermal capacitive mechanism, suggesting that more complex mechanisms are involved. PMID:29082085

Dioxygen activation by non-adiabatic oxidative addition to a single metal center [O 2 activation by non-adiabatic oxidative addition to a single metal center

DOE Office of Scientific and Technical Information (OSTI.GOV)

Akturk, Eser S.; Yap, Glenn P. A.; Theopold, Klaus H.

2015-10-16

A chromium(I) dinitrogen complex reacts rapidly with O 2 to form the mononuclear dioxo complex [Tp tBu,MeCr V(O) 2] (Tp tBu,Me=hydrotris(3- tert-butyl-5-methylpyrazolyl)borate), whereas the analogous reaction with sulfur stops at the persulfido complex [Tp tBu,MeCr III(S 2)]. The transformation of the putative peroxo intermediate [Tp tBu,MeCr III(O 2)] (S= 3/ 2) into [Tp tBu,MeCr V(O) 2] (S= 1/ 2) is spin-forbidden. The minimum-energy crossing point for the two potential energy surfaces has been identified. Finally, although the dinuclear complex [(Tp tBu,MeCr) 2(μ-O) 2] exists, mechanistic experiments suggest that O 2 activation occurs on a single metal center, by an oxidativemore » addition on the quartet surface followed by crossover to the doublet surface.« less

Spectroscopic and thermal investigations of charge-transfer complexes formed between sulfadoxine drug and different types of acceptors

NASA Astrophysics Data System (ADS)

Refat, Moamen S.

2011-01-01

Charge-transfer reactions between sulfadoxine (SDOX) as a donor with iodine (I 2), 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ), p-chloranil (CHL) and picric acid (PA) have been studied in solid and solution forms. The stoichiometry of all complexes was found to be 1:1 by molar ratio method between donor and acceptor at a CT-band absorption bands. The data are discussed in terms of formation constant ( KCT), molar extinction coefficient ( ɛCT), standard free energy (Δ Go), oscillator strength (ƒ), transition dipole moment ( μ), resonance energy ( RN) and ionization potential ( ID). The results indicate that the formation constant ( KCT) for the complexes were shown to be dependent upon the nature of electron acceptor, donor and polarity of solvents which were used. IR, 1H NMR and UV-Vis spectroscopic techniques, Elemental analyses (CHN) and TG-DTG investigation were used to characterize the four sulfadoxine charge-transfer complexes.

Spectrophotometric and spectroscopic studies of charge transfer complexes of p-toluidine as an electron donor with picric acid as an electron acceptor in different solvents.

PubMed

Singh, Neeti; Khan, Ishaat M; Ahmad, Afaq

2010-04-01

The charge transfer complexes of the donor p-toluidine with pi-acceptor picric acid have been studied spectrophotometrically in various solvents such as carbon tetrachloride, chloroform, dichloromethane acetone, ethanol, and methanol at room temperature using absorption spectrophotometer. The results indicate that formation of CTC in non-polar solvent is high. The stoichiometry of the complex was found to be 1:1 ratio by straight-line method between donor and acceptor with maximum absorption bands. The data are discussed in terms of formation constant (K(CT)), molar extinction coefficient (epsilon(CT)), standard free energy (DeltaG(o)), oscillator strength (f), transition dipole moment (mu(EN)), resonance energy (R(N)) and ionization potential (I(D)). The results indicate that the formation constant (K(CT)) for the complex was shown to be dependent upon the nature of electron acceptor, donor and polarity of solvents that were used. Copyright 2010 Elsevier B.V. All rights reserved.

IR, 1H NMR, mass, XRD and TGA/DTA investigations on the ciprofloxacin/iodine charge-transfer complex.

PubMed

Refat, Moamen S; El-Hawary, W F; Moussa, Mohamed A A

2011-05-01

The charge-transfer complex (CTC) of ciprofloxacin drug (CIP) as a donor with iodine (I(2)) as a sigma acceptor has been studied spectrophotometrically in CHCl(3). At maximum absorption bands, the stoichiometry of CIP:iodine system was found to be 1:1 ratio according to molar ratio method. The essential spectroscopic data like formation constant (K(CT)), molar extinction coefficient (ɛ(CT)), standard free energy (ΔG°), oscillator strength (f), transition dipole moment (μ), resonance energy (R(N)) and ionization potential (I(D)) were estimated. The spectroscopic techniques such as IR, (1)H NMR, mass and UV-vis spectra and elemental analyses (CHN) as well as TG-DTG and DTA investigations were used to characterize the chelating behavior of CIP/iodine charge-transfer complex. The iodine CT interaction was associated with a presence of intermolecular hydrogen bond. The X-ray investigation was carried out to investigate the iodine doping in the synthetic CT complex. Copyright © 2011 Elsevier B.V. All rights reserved.

Kinetic Isotope Effects as a Probe for the Protonolysis Mechanism of Alkylmetal Complexes: VTST/MT Calculations Based on DFT Potential Energy Surfaces.

PubMed

Mai, Binh Khanh; Kim, Yongho

2016-10-03

Protonolysis by platinum or palladium complexes has been extensively studied because it is the microscopic reverse of the C-H bond activation reaction. The protonolysis of (COD)Pt II Me 2 , which exhibits abnormally large kinetic isotope effects (KIEs), is proposed to occur via a concerted pathway (S E 2 mechanism) with large tunneling. However, further investigation of KIEs for the protonolysis of ZnMe 2 and others led to a conclusion that there is no noticeable correlation between the mechanism and magnitude of KIE. In this study, we demonstrated that variational transition state theory including multidimensional tunneling (VTST/MT) could accurately predict KIEs and Arrhenius parameters of the protonolysis of alkylmetal complexes based on the potential energy surfaces generated by density functional theory. The predicted KIEs, E a D - E a H values, and A H /A D ratios for the protonolysis of (COD)Pt II Me 2 and Zn II Me 2 by TFA agreed very well with experimental values. The protonolysis of ZnMe 2 with the concerted pathway has a very flat potential energy surface, which produces a very small tunneling effect and therefore a small KIE. The predicted KIE for the stepwise protonolysis (S E (ox) mechanism) of (COD)Pt II Me 2 was much smaller than that of the concerted pathway, but greater than the KIE of the concerted protonolysis of ZnMe 2 . A large KIE, which entails a significant tunneling effect, could be used as an experimental probe of the concerted pathway. However, a normal or small KIE should not be used as an indicator of the stepwise mechanism, and the interplay between experiments and reliable theory including tunneling would be essential to uncover the mechanism correctly.

The energy cost of action potential propagation in dopamine neurons: clues to susceptibility in Parkinson's disease.

PubMed

Pissadaki, Eleftheria K; Bolam, J Paul

2013-01-01

Dopamine neurons of the substantia nigra pars compacta (SNc) are uniquely sensitive to degeneration in Parkinson's disease (PD) and its models. Although a variety of molecular characteristics have been proposed to underlie this sensitivity, one possible contributory factor is their massive, unmyelinated axonal arbor that is orders of magnitude larger than other neuronal types. We suggest that this puts them under such a high energy demand that any stressor that perturbs energy production leads to energy demand exceeding supply and subsequent cell death. One prediction of this hypothesis is that those dopamine neurons that are selectively vulnerable in PD will have a higher energy cost than those that are less vulnerable. We show here, through the use of a biology-based computational model of the axons of individual dopamine neurons, that the energy cost of axon potential propagation and recovery of the membrane potential increases with the size and complexity of the axonal arbor according to a power law. Thus SNc dopamine neurons, particularly in humans, whose axons we estimate to give rise to more than 1 million synapses and have a total length exceeding 4 m, are at a distinct disadvantage with respect to energy balance which may be a factor in their selective vulnerability in PD.

The energy cost of action potential propagation in dopamine neurons: clues to susceptibility in Parkinson's disease

PubMed Central

Pissadaki, Eleftheria K.; Bolam, J. Paul

2013-01-01

Dopamine neurons of the substantia nigra pars compacta (SNc) are uniquely sensitive to degeneration in Parkinson's disease (PD) and its models. Although a variety of molecular characteristics have been proposed to underlie this sensitivity, one possible contributory factor is their massive, unmyelinated axonal arbor that is orders of magnitude larger than other neuronal types. We suggest that this puts them under such a high energy demand that any stressor that perturbs energy production leads to energy demand exceeding supply and subsequent cell death. One prediction of this hypothesis is that those dopamine neurons that are selectively vulnerable in PD will have a higher energy cost than those that are less vulnerable. We show here, through the use of a biology-based computational model of the axons of individual dopamine neurons, that the energy cost of axon potential propagation and recovery of the membrane potential increases with the size and complexity of the axonal arbor according to a power law. Thus SNc dopamine neurons, particularly in humans, whose axons we estimate to give rise to more than 1 million synapses and have a total length exceeding 4 m, are at a distinct disadvantage with respect to energy balance which may be a factor in their selective vulnerability in PD. PMID:23515615

Design of specially adapted reactive coordinates to economically compute potential and kinetic energy operators including geometry relaxation

NASA Astrophysics Data System (ADS)

Thallmair, Sebastian; Roos, Matthias K.; de Vivie-Riedle, Regina

2016-06-01

Quantum dynamics simulations require prior knowledge of the potential energy surface as well as the kinetic energy operator. Typically, they are evaluated in a low-dimensional subspace of the full configuration space of the molecule as its dimensionality increases proportional to the number of atoms. This entails the challenge to find the most suitable subspace. We present an approach to design specially adapted reactive coordinates spanning this subspace. In addition to the essential geometric changes, these coordinates take into account the relaxation of the non-reactive coordinates without the necessity of performing geometry optimizations at each grid point. The method is demonstrated for an ultrafast photoinduced bond cleavage in a commonly used organic precursor for the generation of electrophiles. The potential energy surfaces for the reaction as well as the Wilson G-matrix as part of the kinetic energy operator are shown for a complex chemical reaction, both including the relaxation of the non-reactive coordinates on equal footing. A microscopic interpretation of the shape of the G-matrix elements allows to analyze the impact of the non-reactive coordinates on the kinetic energy operator. Additionally, we compare quantum dynamics simulations with and without the relaxation of the non-reactive coordinates included in the kinetic energy operator to demonstrate its influence.

Design of specially adapted reactive coordinates to economically compute potential and kinetic energy operators including geometry relaxation.

PubMed

Thallmair, Sebastian; Roos, Matthias K; de Vivie-Riedle, Regina

2016-06-21

Quantum dynamics simulations require prior knowledge of the potential energy surface as well as the kinetic energy operator. Typically, they are evaluated in a low-dimensional subspace of the full configuration space of the molecule as its dimensionality increases proportional to the number of atoms. This entails the challenge to find the most suitable subspace. We present an approach to design specially adapted reactive coordinates spanning this subspace. In addition to the essential geometric changes, these coordinates take into account the relaxation of the non-reactive coordinates without the necessity of performing geometry optimizations at each grid point. The method is demonstrated for an ultrafast photoinduced bond cleavage in a commonly used organic precursor for the generation of electrophiles. The potential energy surfaces for the reaction as well as the Wilson G-matrix as part of the kinetic energy operator are shown for a complex chemical reaction, both including the relaxation of the non-reactive coordinates on equal footing. A microscopic interpretation of the shape of the G-matrix elements allows to analyze the impact of the non-reactive coordinates on the kinetic energy operator. Additionally, we compare quantum dynamics simulations with and without the relaxation of the non-reactive coordinates included in the kinetic energy operator to demonstrate its influence.

Theoretical Investigation of the Electronic Structure of Fe(II) Complexes at Spin-State Transitions

PubMed Central

2013-01-01

The electronic structure relevant to low spin (LS)↔high spin (HS) transitions in Fe(II) coordination compounds with a FeN6 core are studied. The selected [Fe(tz)6]2+ (1) (tz = 1H-tetrazole), [Fe(bipy)3]2+ (2) (bipy = 2,2′-bipyridine), and [Fe(terpy)2]2+ (3) (terpy = 2,2′:6′,2″-terpyridine) complexes have been actively studied experimentally, and with their respective mono-, bi-, and tridentate ligands, they constitute a comprehensive set for theoretical case studies. The methods in this work include density functional theory (DFT), time-dependent DFT (TD-DFT), and multiconfigurational second order perturbation theory (CASPT2). We determine the structural parameters as well as the energy splitting of the LS–HS states (ΔEHL) applying the above methods and comparing their performance. We also determine the potential energy curves representing the ground and low-energy excited singlet, triplet, and quintet d6 states along the mode(s) that connect the LS and HS states. The results indicate that while DFT is well suited for the prediction of structural parameters, an accurate multiconfigurational approach is essential for the quantitative determination of ΔEHL. In addition, a good qualitative agreement is found between the TD-DFT and CASPT2 potential energy curves. Although the TD-DFT results might differ in some respect (in our case, we found a discrepancy at the triplet states), our results suggest that this approach, with due care, is very promising as an alternative for the very expensive CASPT2 method. Finally, the two-dimensional (2D) potential energy surfaces above the plane spanned by the two relevant configuration coordinates in [Fe(terpy)2]2+ were computed at both the DFT and CASPT2 levels. These 2D surfaces indicate that the singlet–triplet and triplet–quintet states are separated along different coordinates, i.e., different vibration modes. Our results confirm that in contrast to the case of complexes with mono- and bidentate ligands, the singlet–quintet transitions in [Fe(terpy)2]2+ cannot be described using a single configuration coordinate. PMID:25821416

Effective control of complex turbulent dynamical systems through statistical functionals.

PubMed

Majda, Andrew J; Qi, Di

2017-05-30

Turbulent dynamical systems characterized by both a high-dimensional phase space and a large number of instabilities are ubiquitous among complex systems in science and engineering, including climate, material, and neural science. Control of these complex systems is a grand challenge, for example, in mitigating the effects of climate change or safe design of technology with fully developed shear turbulence. Control of flows in the transition to turbulence, where there is a small dimension of instabilities about a basic mean state, is an important and successful discipline. In complex turbulent dynamical systems, it is impossible to track and control the large dimension of instabilities, which strongly interact and exchange energy, and new control strategies are needed. The goal of this paper is to propose an effective statistical control strategy for complex turbulent dynamical systems based on a recent statistical energy principle and statistical linear response theory. We illustrate the potential practical efficiency and verify this effective statistical control strategy on the 40D Lorenz 1996 model in forcing regimes with various types of fully turbulent dynamics with nearly one-half of the phase space unstable.

Building a foundation for structure-based cellulosome design for cellulosic ethanol: Insight into cohesin-dockerin complexation from computer simulation

PubMed Central

Xu, Jiancong; Crowley, Michael F; Smith, Jeremy C

2009-01-01

The organization and assembly of the cellulosome, an extracellular multienzyme complex produced by anaerobic bacteria, is mediated by the high-affinity interaction of cohesin domains from scaffolding proteins with dockerins of cellulosomal enzymes. We have performed molecular dynamics simulations and free energy calculations on both the wild type (WT) and D39N mutant of the C. thermocellum Type I cohesin-dockerin complex in aqueous solution. The D39N mutation has been experimentally demonstrated to disrupt cohesin-dockerin binding. The present MD simulations indicate that the substitution triggers significant protein flexibility and causes a major change of the hydrogen-bonding network in the recognition strips—the conserved loop regions previously proposed to be involved in binding—through electrostatic and salt-bridge interactions between β-strands 3 and 5 of the cohesin and α-helix 3 of the dockerin. The mutation-induced subtle disturbance in the local hydrogen-bond network is accompanied by conformational rearrangements of the protein side chains and bound water molecules. Additional free energy perturbation calculations of the D39N mutation provide differences in the cohesin-dockerin binding energy, thus offering a direct, quantitative comparison with experiments. The underlying molecular mechanism of cohesin-dockerin complexation is further investigated through the free energy profile, that is, potential of mean force (PMF) calculations of WT cohesin-dockerin complex. The PMF shows a high-free energy barrier against the dissociation and reveals a stepwise pattern involving both the central β-sheet interface and its adjacent solvent-exposed loop/turn regions clustered at both ends of the β-barrel structure. PMID:19384997

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghatak, Ananya, E-mail: gananya04@gmail.com; Mandal, Raka Dona Ray, E-mail: rakad.ray@gmail.com; Mandal, Bhabani Prasad, E-mail: bhabani.mandal@gmail.com

We complexify a 1-d potential V(x)=V{sub 0}cosh{sup 2}μ(tanh[(x−μd)/d]+tanh(μ)){sup 2} which exhibits bound, reflecting and free states to study various properties of a non-Hermitian system. This potential turns out a PT-symmetric non-Hermitian potential when one of the parameters (μ,d) becomes imaginary. For the case of μ→iμ, we have an entire real bound state spectrum. Explicit scattering states are constructed to show reciprocity at certain discrete values of energy even though the potential is not parity symmetric. Coexistence of deep energy minima of transmissivity with the multiple spectral singularities (MSS) is observed. We further show that this potential becomes invisible from themore » left (or right) at certain discrete energies. The penetrating states in the other case (d→id) are always reciprocal even though it is PT-invariant and no spectral singularity (SS) is present in this case. The presence of MSS and reflectionlessness is also discussed for the free states in the later case. -- Highlights: •Existence of multiple spectral singularities (MSS) in PT-symmetric non-Hermitian system is shown. •Reciprocity is restored at discrete positive energies even for parity non-invariant complex system. •Co-existence of MSS with deep energy minima of transitivity is obtained. •Possibilities of both unidirectional and bidirectional invisibility are explored for a non-Hermitian system. •Penetrating states are shown to be reciprocal for all energies for PT-symmetric system.« less

Variational Approach to Enhanced Sampling and Free Energy Calculations

NASA Astrophysics Data System (ADS)

Valsson, Omar; Parrinello, Michele

2014-08-01

The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo simulations, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to alleviate this problem. Many are based on the introduction of a bias potential which is a function of a small number of collective variables. However constructing such a bias is not simple. Here we introduce a functional of the bias potential and an associated variational principle. The bias that minimizes the functional relates in a simple way to the free energy surface. This variational principle can be turned into a practical, efficient, and flexible sampling method. A number of numerical examples are presented which include the determination of a three-dimensional free energy surface. We argue that, beside being numerically advantageous, our variational approach provides a convenient and novel standpoint for looking at the sampling problem.

Path Integral Metadynamics.

PubMed

Quhe, Ruge; Nava, Marco; Tiwary, Pratyush; Parrinello, Michele

2015-04-14

We develop a new efficient approach for the simulation of static properties of quantum systems using path integral molecular dynamics in combination with metadynamics. We use the isomorphism between a quantum system and a classical one in which a quantum particle is mapped into a ring polymer. A history dependent biasing potential is built as a function of the elastic energy of the isomorphic polymer. This enhances fluctuations in the shape and size of the necklace in a controllable manner and allows escaping deep energy minima in a limited computer time. In this way, we are able to sample high free energy regions and cross barriers, which would otherwise be insurmountable with unbiased methods. This substantially improves the ability of finding the global free energy minimum as well as exploring other metastable states. The performance of the new technique is demonstrated by illustrative applications on model potentials of varying complexity.

Combining a reactive potential with a harmonic approximation for molecular dynamics simulation of failure: construction of a reduced potential

NASA Astrophysics Data System (ADS)

Tejada, I. G.; Brochard, L.; Stoltz, G.; Legoll, F.; Lelièvre, T.; Cancès, E.

2015-01-01

Molecular dynamics is a simulation technique that can be used to study failure in solids, provided the inter-atomic potential energy is able to account for the complex mechanisms at failure. Reactive potentials fitted on ab initio results or on experimental values have the ability to adapt to any complex atomic arrangement and, therefore, are suited to simulate failure. But the complexity of these potentials, together with the size of the systems considered, make simulations computationally expensive. In order to improve the efficiency of numerical simulations, simpler harmonic potentials can be used instead of complex reactive potentials in the regions where the system is close to its ground state and a harmonic approximation reasonably fits the actual reactive potential. However the validity and precision of such an approach has not been investigated in detail yet. We present here a methodology for constructing a reduced potential and combining it with the reactive one. We also report some important features of crack propagation that may be affected by the coupling of reactive and reduced potentials. As an illustrative case, we model a crystalline two-dimensional material (graphene) with a reactive empirical bond-order potential (REBO) or with harmonic potentials made of bond and angle springs that are designed to reproduce the second order approximation of REBO in the ground state. We analyze the consistency of this approximation by comparing the mechanical behavior and the phonon spectra of systems modeled with these potentials. These tests reveal when the anharmonicity effects appear. As anharmonic effects originate from strain, stress or temperature, the latter quantities are the basis for establishing coupling criteria for on the fly substitution in large simulations.

The boomerang effect in electron-hydrogen molecule scattering as determined by time-dependent calculations

NASA Astrophysics Data System (ADS)

Ben-Asher, Anael; Moiseyev, Nimrod

2017-05-01

The appearance of oscillations in the energy-dependent cross sections of the vibrational excitation ν =0 →ν ≥3 of the hydrogen molecule in its electronic ground state as predicted by Mündel, Berman, and Domcke [Phys. Rev. A 32, 181 (1985)] was confirmed in the electron scattering experiments by Allan [J. Phys. B: At. Mol. Phys. 18, L451 (1985)]. These unusual structures were obtained in spite of the extremely short lifetime of H2- in its ro-vibrational states. Based on the standard (Hermitian) time-independent scattering calculations, Horáček et al. [Phys. Rev. A 73, 022701 (2006)] associated these oscillations with the boomerang effect. Here, we show the boomerang effect as developed in time, based on our time-dependent nuclear wavepacket (WP) calculations. The nuclear WP dynamics of H2- is determined using the non-Hermitian quantum mechanics (NH-QM) which enables the use of the Born-Oppenheimer approximation with complex potential energy surfaces. This NH-QM approach, which enables us the association of the nuclear WP dynamics as obtained from the complex potential energy curve of H2- with the evolution of cross section in time, can enlighten the dynamics in other scattering experiments.

The boomerang effect in electron-hydrogen molecule scattering as determined by time-dependent calculations.

PubMed

Ben-Asher, Anael; Moiseyev, Nimrod

2017-05-28

The appearance of oscillations in the energy-dependent cross sections of the vibrational excitation ν=0→ν≥3 of the hydrogen molecule in its electronic ground state as predicted by Mündel, Berman, and Domcke [Phys. Rev. A 32, 181 (1985)] was confirmed in the electron scattering experiments by Allan [J. Phys. B: At. Mol. Phys. 18, L451 (1985)]. These unusual structures were obtained in spite of the extremely short lifetime of H 2 - in its ro-vibrational states. Based on the standard (Hermitian) time-independent scattering calculations, Horáček et al. [Phys. Rev. A 73, 022701 (2006)] associated these oscillations with the boomerang effect. Here, we show the boomerang effect as developed in time, based on our time-dependent nuclear wavepacket (WP) calculations. The nuclear WP dynamics of H 2 - is determined using the non-Hermitian quantum mechanics (NH-QM) which enables the use of the Born-Oppenheimer approximation with complex potential energy surfaces. This NH-QM approach, which enables us the association of the nuclear WP dynamics as obtained from the complex potential energy curve of H 2 - with the evolution of cross section in time, can enlighten the dynamics in other scattering experiments.

Zero-point corrections and temperature dependence of HD spin-spin coupling constants of heavy metal hydride and dihydrogen complexes calculated by vibrational averaging.

PubMed

Mort, Brendan C; Autschbach, Jochen

2006-08-09

Vibrational corrections (zero-point and temperature dependent) of the H-D spin-spin coupling constant J(HD) for six transition metal hydride and dihydrogen complexes have been computed from a vibrational average of J(HD) as a function of temperature. Effective (vibrationally averaged) H-D distances have also been determined. The very strong temperature dependence of J(HD) for one of the complexes, [Ir(dmpm)Cp*H2]2 + (dmpm = bis(dimethylphosphino)methane) can be modeled simply by the Boltzmann average of the zero-point vibrationally averaged JHD of two isomers. For this complex and four others, the vibrational corrections to JHD are shown to be highly significant and lead to improved agreement between theory and experiment in most cases. The zero-point vibrational correction is important for all complexes. Depending on the shape of the potential energy and J-coupling surfaces, for some of the complexes higher vibrationally excited states can also contribute to the vibrational corrections at temperatures above 0 K and lead to a temperature dependence. We identify different classes of complexes where a significant temperature dependence of J(HD) may or may not occur for different reasons. A method is outlined by which the temperature dependence of the HD spin-spin coupling constant can be determined with standard quantum chemistry software. Comparisons are made with experimental data and previously calculated values where applicable. We also discuss an example where a low-order expansion around the minimum of a complicated potential energy surface appears not to be sufficient for reproducing the experimentally observed temperature dependence.

Short-range stabilizing potential for computing energies and lifetimes of temporary anions with extrapolation methods.

PubMed

Sommerfeld, Thomas; Ehara, Masahiro

2015-01-21

The energy of a temporary anion can be computed by adding a stabilizing potential to the molecular Hamiltonian, increasing the stabilization until the temporary state is turned into a bound state, and then further increasing the stabilization until enough bound state energies have been collected so that these can be extrapolated back to vanishing stabilization. The lifetime can be obtained from the same data, but only if the extrapolation is done through analytic continuation of the momentum as a function of the square root of a shifted stabilizing parameter. This method is known as analytic continuation of the coupling constant, and it requires--at least in principle--that the bound-state input data are computed with a short-range stabilizing potential. In the context of molecules and ab initio packages, long-range Coulomb stabilizing potentials are, however, far more convenient and have been used in the past with some success, although the error introduced by the long-rang nature of the stabilizing potential remains unknown. Here, we introduce a soft-Voronoi box potential that can serve as a short-range stabilizing potential. The difference between a Coulomb and the new stabilization is analyzed in detail for a one-dimensional model system as well as for the (2)Πu resonance of CO2(-), and in both cases, the extrapolation results are compared to independently computed resonance parameters, from complex scaling for the model, and from complex absorbing potential calculations for CO2(-). It is important to emphasize that for both the model and for CO2(-), all three sets of results have, respectively, been obtained with the same electronic structure method and basis set so that the theoretical description of the continuum can be directly compared. The new soft-Voronoi-box-based extrapolation is then used to study the influence of the size of diffuse and the valence basis sets on the computed resonance parameters.

COMPARATIVE POTENCY OF COMPLEX MIXTURES: USE OF SHORT-TERM GENETIC BIOASSAYS IN CANCER RISK ASSESSMENT

EPA Science Inventory

The primary problem regarding the introduction of new energy sources is whether they will alter the mutagenicity, carcinogenicity and potential human cancer risk from combustion emissions. New risk assessment methodologies utilizing data from short-term bioassays, therefore, are ...

Potential ecological roles of Artemisinin produced by Artemisis annua L

USDA-ARS?s Scientific Manuscript database

Artemisia annua L. (annual wormwood, Asteraceae) and its secondary metabolite artemisinin, a unique sesquiterpene lactone with an endoperoxide bridge, has gained much attention due to its antimalarial properties. Artemisinin is a complex structure that is requires a significant amount of energy for ...

A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer

NASA Astrophysics Data System (ADS)

Kawaguchi, Kazutomo; Nakagawa, Satoshi; Kurniawan, Isman; Kodama, Koichi; Arwansyah, Muhammad Saleh; Nagao, Hidemi

2018-03-01

We present a simple coarse-grained model of the effective interaction for charged amino acid residues, such as Glu and Lys, in a water solvent. The free-energy profile as a function of the distance between two charged amino acid side-chain analogues in an explicit water solvent is calculated with all-atom molecular dynamics simulation and thermodynamic integration method. The calculated free-energy profile is applied to the coarse-grained potential of the effective interaction between two amino acid residues. The Langevin dynamics simulations with our coarse-grained potential are performed for association of a small protein complex, GCN4-pLI tetramer. The tetramer conformation reproduced by our coarse-grained model is similar to the X-ray crystallographic structure. We show that the effective interaction between charged amino acid residues stabilises association and orientation of protein complex. We also investigate the association pathways of GCN4-pLI tetramer.

Calculation of Cyclodextrin Binding Affinities: Energy, Entropy, and Implications for Drug Design

PubMed Central

Chen, Wei; Chang, Chia-En; Gilson, Michael K.

2004-01-01

The second generation Mining Minima method yields binding affinities accurate to within 0.8 kcal/mol for the associations of α-, β-, and γ-cyclodextrin with benzene, resorcinol, flurbiprofen, naproxen, and nabumetone. These calculations require hours to a day on a commodity computer. The calculations also indicate that the changes in configurational entropy upon binding oppose association by as much as 24 kcal/mol and result primarily from a narrowing of energy wells in the bound versus the free state, rather than from a drop in the number of distinct low-energy conformations on binding. Also, the configurational entropy is found to vary substantially among the bound conformations of a given cyclodextrin-guest complex. This result suggests that the configurational entropy must be accounted for to reliably rank docked conformations in both host-guest and ligand-protein complexes. In close analogy with the common experimental observation of entropy-enthalpy compensation, the computed entropy changes show a near-linear relationship with the changes in mean potential plus solvation energy. PMID:15339804

Ab initio anharmonic vibrational frequency predictions for linear proton-bound complexes OC-H(+)-CO and N(2)-H(+)-N(2).

PubMed

Terrill, Kasia; Nesbitt, David J

2010-08-01

Ab initio anharmonic transition frequencies are calculated for strongly coupled (i) asymmetric and (ii) symmetric proton stretching modes in the X-H(+)-X linear ionic hydrogen bonded complexes for OCHCO(+) and N(2)HN(2)(+). The optimized potential surface is calculated in these two coordinates for each molecular ion at CCSD(T)/aug-cc-pVnZ (n = 2-4) levels and extrapolated to the complete-basis-set limit (CBS). Slices through both 2D surfaces reveal a relatively soft potential in the asymmetric proton stretching coordinate at near equilibrium geometries, which rapidly becomes a double minimum potential with increasing symmetric proton acceptor center of mass separation. Eigenvalues are obtained by solution of the 2D Schrödinger equation with potential/kinetic energy coupling explicity taken into account, converged in a distributed Gaussian basis set as a function of grid density. The asymmetric proton stretch fundamental frequency for N(2)HN(2)(+) is predicted at 848 cm(-1), with strong negative anharmonicity in the progression characteristic of a shallow "particle in a box" potential. The corresponding proton stretch fundamental for OCHCO(+) is anomalously low at 386 cm(-1), but with a strong alternation in the vibrational spacing due to the presence of a shallow D(infinityh) transition state barrier (Delta = 398 cm(-1)) between the two equivalent minimum geometries. Calculation of a 2D dipole moment surface and transition matrix elements reveals surprisingly strong combination and difference bands with appreciable intensity throughout the 300-1500 cm(-1) region. Corrected for zero point (DeltaZPE) and thermal vibrational excitation (DeltaE(vib)) at 300 K, the single and double dissociation energies in these complexes are in excellent agreement with thermochemical gas phase ion data.

Electrocatalytic Oxidation of Formate with Nickel Diphosphane Dipeptide Complexes. Effect of Ligands Modified with Amino Acids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galan, Brandon R.; Reback, Matthew L.; Jain, Avijita

2013-09-03

A series of nickel bis-diphosphine complexes with dipeptides appended to the ligands were investigated for the catalytic oxidation of formate. Typical rates of ~7 s -1 were found, similar to the parent complex (~8 s -1), with amino acid size and positioning contributing very little to rate or operating potential. Hydroxyl functionalities did result in lower rates, which were recovered by protecting the hydroxyl group. The results suggest that the overall dielectric introduced by the dipeptides does not play an important role in catalysis, but free hydroxyl groups do influence activity suggesting contributions from intra- or intermolecular interactions. These observationsmore » are important in developing a fundamental understanding of the affect that an enzyme-like outer coordination sphere can have upon molecular catalysts. This work was funded by the US DOE Basic Energy Sciences, Chemical Sciences, Geoscience and Biosciences Division (BRG, AJ, AMA, WJS), the US DOE Basic Energy Sciences, Physical Bioscience program (MLR). Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.« less

Source Recertification, Refurbishment, and Transfer Logistics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gastelum, Zoe N.; Duckworth, Leesa L.; Greenfield, Bryce A.

2013-09-01

The 2012 Gap Analysis of Department of Energy Radiological Sealed Sources, Standards, and Materials for Safeguards Technology Development [1] report, and the subsequent Reconciliation of Source Needs and Surpluses across the U.S. Department of Energy National Laboratory Complex [2] report, resulted in the identification of 33 requests for nuclear or radiological sealed sources for which there was potentially available, suitable material from within the U.S. Department of Energy (DOE) complex to fill the source need. Available, suitable material was defined by DOE laboratories as material slated for excess, or that required recertification or refurbishment before being used for safeguards technologymore » development. This report begins by outlining the logistical considerations required for the shipment of nuclear and radiological materials between DOE laboratories. Then, because of the limited need for transfer of matching sources, the report also offers considerations for an alternative approach – the shipment of safeguards equipment between DOE laboratories or technology testing centers. Finally, this report addresses repackaging needs for the two source requests for which there was available, suitable material within the DOE complex.« less

Lanthanide and transition metal complexes of bioactive coumarins: molecular modeling and spectroscopic studies.

PubMed

Georgieva, I; Mihaylov, Tz; Trendafilova, N

2014-06-01

The present paper summarizes theoretical and spectroscopic investigations on a series of active coumarins and their lanthanide and transition metal complexes with application in medicine and pharmacy. Molecular modeling as well as IR, Raman, NMR and electronic spectral simulations at different levels of theory were performed to obtain important molecular descriptors: total energy, formation energy, binding energy, stability, conformations, structural parameters, electron density distribution, molecular electrostatic potential, Fukui functions, atomic charges, and reactive indexes. The computations are performed both in gas phase and in solution with consideration of the solvent effect on the molecular structural and energetic parameters. The investigations have shown that the advanced computational methods are reliable for prediction of the metal-coumarin binding mode, electron density distribution, thermodynamic properties as well as the strength and nature of the metal-coumarin interaction (not experimentally accessible) and correctly interpret the experimental spectroscopic data. Known results from biological tests for cytotoxic, antimicrobial, anti-fungal, spasmolytic and anti-HIV activities on the studied metal complexes are reported and discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

Electronic structure of monodentate-coordinated diphosphine complexes. Photoelectron spectra of Mo(CO)[sub 5](P(CH[sub 3])[sub 2]CH[sub 2]P(CH[sub 3])[sub 2]) and Mo(CO)[sub 5](P(CH[sub 3])[sub 2]CH[sub 2]CH[sub 2]P(CH[sub 3])[sub 2])

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lichtenberger, D.L.; Jatcko, M.E.

1992-02-05

Photoelectron spectroscopy is used to study the electronic structure of molybdenum carbonyl complexes that contain diphosphine ligands bound to the metal through only one of the two phosphorus atoms. Photoelectron spectra are reported for Mo(CO)[sub 5]DMPE and Mo(CO)[sub 5]DMPM and compared to the spectra of Mo(CO)[sub 5]PMe[sub 3] and the corresponding free phosphine and diphosphine ligands (PMe[sub 3] is trimethylphosphine, DMPE is 1,2-bis(dimethylphosphino)ethane, and DMPM is bis(dimethylphosphino)methane). The energy splittings between the d[sup 6] metal-based ionizations of these complexes indicate that the [pi]-back-bonding ability is the same for each of these phosphine ligands and is relatively small, about 25% thatmore » of carbon monoxide. The metal-based ionizations shift only slightly to lower binding energy from the PMe[sub 3] to the DMPE to the DMPM complex due to a slightly increasing negative charge potential at the metal along this series. This would normally be interpreted as slightly increasing [sigma]-donor strength in the order PMe[sub 3] < DMPE < DMPM. However, the difference between the ionization energy of the coordinated lone pair (CLP) of the phosphine and the ionization energy of the lone pair of the free ligand indicates an opposite trend in [sigma]-donor strength with PMe[sub 3] (1.28 eV) > DMPE (1.27 eV) > DMPM (1.23 eV). The shift of the uncoordinated phosphine lone-pair ionization (ULP) of the monocoordinated diphosphine complexes, which is affected primarily by charge potential effects, reveals that the important factor is a transfer of negative charge from the uncoordinated end of the phosphine through the alkyl linkage to the coordinated phosphine. Aside from these subtle details of charge distribution, the primary conclusion is that the diphosphine ligands, DMPE and DMPM, have [sigma]-donor and [pi]-acceptor strengths extremely similar to those of PMe[sub 3].« less

Cobalt(II) complexes with azole-pyridine type ligands for non-aqueous redox-flow batteries: Tunable electrochemistry via structural modification

NASA Astrophysics Data System (ADS)

Armstrong, Craig G.; Toghill, Kathryn E.

2017-05-01

A single species redox flow battery employing a new class of cobalt(II) complexes with 'tunable' tridentate azole-pyridine type ligands is reported. Four structures were synthesised and their electrochemical, physical and battery characteristics were investigated as a function of successive substitution of the ligand terminal pyridyl donors. The Co(II/I) and Co(III/II) couples are stable and quasi-reversible on gold and glassy carbon electrodes, however redox potentials are tunable allowing the cobalt potential difference to be preferentially increased from 1.07 to 1.91 V via pyridine substitution with weaker σ-donating/π-accepting 3,5-dimethylpyrazole groups. The charge-discharge properties of the system were evaluated using an H-type glass cell and graphite rod electrodes. The complexes delivered high Coulombic efficiencies of 89.7-99.8% and very good voltaic efficiencies of 70.3-81.0%. Consequently, energy efficiencies are high at 63.1-80.8%, marking an improvement on other similar non-aqueous systems. Modification of the ligands also improved solubility from 0.18 M to 0.50 M via pyridyl substitution with 3,5-dimethylpyrazole, though the low solubility of the complexes limits the overall energy capacity to between 2.58 and 12.80 W h L-1. Preliminary flow cell studies in a prototype flow cell are also demonstrated.

The natural science underlying big history.

PubMed

Chaisson, Eric J

2014-01-01

Nature's many varied complex systems-including galaxies, stars, planets, life, and society-are islands of order within the increasingly disordered Universe. All organized systems are subject to physical, biological, or cultural evolution, which together comprise the grander interdisciplinary subject of cosmic evolution. A wealth of observational data supports the hypothesis that increasingly complex systems evolve unceasingly, uncaringly, and unpredictably from big bang to humankind. These are global history greatly extended, big history with a scientific basis, and natural history broadly portrayed across ∼14 billion years of time. Human beings and our cultural inventions are not special, unique, or apart from Nature; rather, we are an integral part of a universal evolutionary process connecting all such complex systems throughout space and time. Such evolution writ large has significant potential to unify the natural sciences into a holistic understanding of who we are and whence we came. No new science (beyond frontier, nonequilibrium thermodynamics) is needed to describe cosmic evolution's major milestones at a deep and empirical level. Quantitative models and experimental tests imply that a remarkable simplicity underlies the emergence and growth of complexity for a wide spectrum of known and diverse systems. Energy is a principal facilitator of the rising complexity of ordered systems within the expanding Universe; energy flows are as central to life and society as they are to stars and galaxies. In particular, energy rate density-contrasting with information content or entropy production-is an objective metric suitable to gauge relative degrees of complexity among a hierarchy of widely assorted systems observed throughout the material Universe. Operationally, those systems capable of utilizing optimum amounts of energy tend to survive, and those that cannot are nonrandomly eliminated.

Excited state electron and energy relays in supramolecular dinuclear complexes revealed by ultrafast optical and X-ray transient absorption spectroscopy† †Electronic supplementary information (ESI) available: Synthesis schemes, experimental methods, NMR spectra, X-ray crystallographic information, emission spectra, cyclic voltammetry, electronic structure calculations, data analysis and numerical methods, and other additional figures. CCDC 1561879. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc04055e

PubMed Central

Kohler, Lars; Hadt, Ryan G.; Zhang, Xiaoyi; Liu, Cunming

2017-01-01

The kinetics of photoinduced electron and energy transfer in a family of tetrapyridophenazine-bridged heteroleptic homo- and heterodinuclear copper(i) bis(phenanthroline)/ruthenium(ii) polypyridyl complexes were studied using ultrafast optical and multi-edge X-ray transient absorption spectroscopies. This work combines the synthesis of heterodinuclear Cu(i)–Ru(ii) analogs of the homodinuclear Cu(i)–Cu(i) targets with spectroscopic analysis and electronic structure calculations to first disentangle the dynamics at individual metal sites by taking advantage of the element and site specificity of X-ray absorption and theoretical methods. The excited state dynamical models developed for the heterodinuclear complexes are then applied to model the more challenging homodinuclear complexes. These results suggest that both intermetallic charge and energy transfer can be observed in an asymmetric dinuclear copper complex in which the ground state redox potentials of the copper sites are offset by only 310 meV. We also demonstrate the ability of several of these complexes to effectively and unidirectionally shuttle energy between different metal centers, a property that could be of great use in the design of broadly absorbing and multifunctional multimetallic photocatalysts. This work provides an important step toward developing both a fundamental conceptual picture and a practical experimental handle with which synthetic chemists, spectroscopists, and theoreticians may collaborate to engineer cheap and efficient photocatalytic materials capable of performing coulombically demanding chemical transformations. PMID:29629153

The Natural Science Underlying Big History

PubMed Central

Chaisson, Eric J.

2014-01-01

Nature's many varied complex systems—including galaxies, stars, planets, life, and society—are islands of order within the increasingly disordered Universe. All organized systems are subject to physical, biological, or cultural evolution, which together comprise the grander interdisciplinary subject of cosmic evolution. A wealth of observational data supports the hypothesis that increasingly complex systems evolve unceasingly, uncaringly, and unpredictably from big bang to humankind. These are global history greatly extended, big history with a scientific basis, and natural history broadly portrayed across ∼14 billion years of time. Human beings and our cultural inventions are not special, unique, or apart from Nature; rather, we are an integral part of a universal evolutionary process connecting all such complex systems throughout space and time. Such evolution writ large has significant potential to unify the natural sciences into a holistic understanding of who we are and whence we came. No new science (beyond frontier, nonequilibrium thermodynamics) is needed to describe cosmic evolution's major milestones at a deep and empirical level. Quantitative models and experimental tests imply that a remarkable simplicity underlies the emergence and growth of complexity for a wide spectrum of known and diverse systems. Energy is a principal facilitator of the rising complexity of ordered systems within the expanding Universe; energy flows are as central to life and society as they are to stars and galaxies. In particular, energy rate density—contrasting with information content or entropy production—is an objective metric suitable to gauge relative degrees of complexity among a hierarchy of widely assorted systems observed throughout the material Universe. Operationally, those systems capable of utilizing optimum amounts of energy tend to survive, and those that cannot are nonrandomly eliminated. PMID:25032228

A full-dimensional potential energy surface and quantum dynamics of inelastic collision process for H2-HF

NASA Astrophysics Data System (ADS)

Yang, Dongzheng; Huang, Jing; Zuo, Junxiang; Hu, Xixi; Xie, Daiqian

2018-05-01

A full-dimensional ab initio potential energy surface for the H2-HF van der Waals complex was constructed by employing the coupled-cluster singles and doubles with noniterative inclusion of connected triples with augmented correlation-consistent polarised valence quadruple-zeta basis set plus bond functions. Using the improved coupled-states approximation including the nearest neighbor Coriolis couplings, we calculated the state-to-state scattering dynamics for pure rotational and ro-vibrational energy transfer processes. For pure rotational energy transfer, our results showed a different dynamical behavior for para-H2 and ortho-H2 in collision with hydrogen fluoride (HF), which is consistent with the previous study. Interestingly, some strong resonant peaks were presented in the cross sections for ro-vibrational energy transfer. In addition, the calculated vibrational-resolved rate constant is in agreement with the experimental results reported by Bott et al. These dynamics data can be further applied to the numerical simulation of HF chemical lasers.

Extrapolating bound state data of anions into the metastable domain

NASA Astrophysics Data System (ADS)

Feuerbacher, Sven; Sommerfeld, Thomas; Cederbaum, Lorenz S.

2004-10-01

Computing energies of electronically metastable resonance states is still a great challenge. Both scattering techniques and quantum chemistry based L2 methods are very time consuming. Here we investigate two more economical extrapolation methods. Extrapolating bound states energies into the metastable region using increased nuclear charges has been suggested almost 20 years ago. We critically evaluate this attractive technique employing our complex absorbing potential/Green's function method that allows us to follow a bound state into the continuum. Using the 2Πg resonance of N2- and the 2Πu resonance of CO2- as examples, we found that the extrapolation works suprisingly well. The second extrapolation method involves increasing of bond lengths until the sought resonance becomes stable. The keystone is to extrapolate the attachment energy and not the total energy of the system. This method has the great advantage that the whole potential energy curve is obtained with quite good accuracy by the extrapolation. Limitations of the two techniques are discussed.

Regulation of energy balance by a gut-brain axis and involvement of the gut microbiota.

PubMed

Bauer, Paige V; Hamr, Sophie C; Duca, Frank A

2016-02-01

Despite significant progress in understanding the homeostatic regulation of energy balance, successful therapeutic options for curbing obesity remain elusive. One potential target for the treatment of obesity is via manipulation of the gut-brain axis, a complex bidirectional communication system that is crucial in maintaining energy homeostasis. Indeed, ingested nutrients induce secretion of gut peptides that act either via paracrine signaling through vagal and non-vagal neuronal relays, or in an endocrine fashion via entry into circulation, to ultimately signal to the central nervous system where appropriate responses are generated. We review here the current hypotheses of nutrient sensing mechanisms of enteroendocrine cells, including the release of gut peptides, mainly cholecystokinin, glucagon-like peptide-1, and peptide YY, and subsequent gut-to-brain signaling pathways promoting a reduction of food intake and an increase in energy expenditure. Furthermore, this review highlights recent research suggesting this energy regulating gut-brain axis can be influenced by gut microbiota, potentially contributing to the development of obesity.

How computational methods and relativistic effects influence the study of chemical reactions involving Ru-NO complexes?

PubMed

Orenha, Renato Pereira; Santiago, Régis Tadeu; Haiduke, Roberto Luiz Andrade; Galembeck, Sérgio Emanuel

2017-05-05

Two treatments of relativistic effects, namely effective core potentials (ECP) and all-electron scalar relativistic effects (DKH2), are used to obtain geometries and chemical reaction energies for a series of ruthenium complexes in B3LYP/def2-TZVP calculations. Specifically, the reaction energies of reduction (A-F), isomerization (G-I), and Cl - negative trans influence in relation to NH 3 (J-L) are considered. The ECP and DKH2 approaches provided geometric parameters close to experimental data and the same ordering for energy changes of reactions A-L. From geometries optimized with ECP, the electronic energies are also determined by means of the same ECP and basis set combined with the computational methods: MP2, M06, BP86, and its derivatives, so as B2PLYP, LC-wPBE, and CCSD(T) (reference method). For reactions A-I, B2PLYP provides the best agreement with CCSD(T) results. Additionally, B3LYP gave the smallest error for the energies of reactions J-L. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

All-in-One Shape-Adaptive Self-Charging Power Package for Wearable Electronics.

PubMed

Guo, Hengyu; Yeh, Min-Hsin; Lai, Ying-Chih; Zi, Yunlong; Wu, Changsheng; Wen, Zhen; Hu, Chenguo; Wang, Zhong Lin

2016-11-22

Recently, a self-charging power unit consisting of an energy harvesting device and an energy storage device set the foundation for building a self-powered wearable system. However, the flexibility of the power unit working under extremely complex deformations (e.g., stretching, twisting, and bending) becomes a key issue. Here, we present a prototype of an all-in-one shape-adaptive self-charging power unit that can be used for scavenging random body motion energy under complex mechanical deformations and then directly storing it in a supercapacitor unit to build up a self-powered system for wearable electronics. A kirigami paper based supercapacitor (KP-SC) was designed to work as the flexible energy storage device (stretchability up to 215%). An ultrastretchable and shape-adaptive silicone rubber triboelectric nanogenerator (SR-TENG) was utilized as the flexible energy harvesting device. By combining them with a rectifier, a stretchable, twistable, and bendable, self-charging power package was achieved for sustainably driving wearable electronics. This work provides a potential platform for the flexible self-powered systems.

Energy savings opportunity survey at Walter Reed Army Medical Center, Washington, DC. Final Submittal report

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1987-10-22

This Energy Savings Opportunity Survey (ESOS) was performed for sixteen (16) buildings at Walter Reed Army Medical Center (WPAMC) in Washington, D.C. This survey was intended to reevaluate and update projects from a previous Energy Engineering Analysis Program (EEAP) survey performed at WRAMC. However, the previous EEAP survey was determined by the contracting officer to be incomplete and not worthy of further consideration. Therefore, this survey involved the complete reevaluation of the buildings to determine their potential energy cost savings. Six (6) projects and nine (9) low cost/no cost energy conservation opportunities (ECO`s) are recommended for implementation in the buildings.more » These projects and ECO`s are projected to annually save $448,263 at an implementation cost of $891,659. The simple payback (i.e., implementation cost divided by cost savings) for the recommendations in the survey is 1.99 years. The two (2) projects with the greatest cost savings are a stack heat recovery system (Project Number 5) and HVAC modifications (Project Number 1). These two (2) projects will provide 67% of the projected total savings for the survey. The sixteen (16) buildings in this survey represent only 22% of the total floor area of the Walter Reed Army Medical Center complex. It is believed that significant potential energy cost savings amounting to two (2) million dollars may be achieved in the remaining buildings in the complex not included in this survey. Specifically it is believed the main hospital building contains many opportunities for substantial cost savings.« less

Quantum mechanical calculation of aqueuous uranium complexes: carbonate, phosphate, organic and biomolecular species

PubMed Central

Kubicki, James D; Halada, Gary P; Jha, Prashant; Phillips, Brian L

2009-01-01

Background Quantum mechanical calculations were performed on a variety of uranium species representing U(VI), U(V), U(IV), U-carbonates, U-phosphates, U-oxalates, U-catecholates, U-phosphodiesters, U-phosphorylated N-acetyl-glucosamine (NAG), and U-2-Keto-3-doxyoctanoate (KDO) with explicit solvation by H2O molecules. These models represent major U species in natural waters and complexes on bacterial surfaces. The model results are compared to observed EXAFS, IR, Raman and NMR spectra. Results Agreement between experiment and theory is acceptable in most cases, and the reasons for discrepancies are discussed. Calculated Gibbs free energies are used to constrain which configurations are most likely to be stable under circumneutral pH conditions. Reduction of U(VI) to U(IV) is examined for the U-carbonate and U-catechol complexes. Conclusion Results on the potential energy differences between U(V)- and U(IV)-carbonate complexes suggest that the cause of slower disproportionation in this system is electrostatic repulsion between UO2 [CO3]35- ions that must approach one another to form U(VI) and U(IV) rather than a change in thermodynamic stability. Calculations on U-catechol species are consistent with the observation that UO22+ can oxidize catechol and form quinone-like species. In addition, outer-sphere complexation is predicted to be the most stable for U-catechol interactions based on calculated energies and comparison to 13C NMR spectra. Outer-sphere complexes (i.e., ion pairs bridged by water molecules) are predicted to be comparable in Gibbs free energy to inner-sphere complexes for a model carboxylic acid. Complexation of uranyl to phosphorus-containing groups in extracellular polymeric substances is predicted to favor phosphonate groups, such as that found in phosphorylated NAG, rather than phosphodiesters, such as those in nucleic acids. PMID:19689800

Computing resonance energies, widths, and wave functions using a Lanczos method in real arithmetic.

PubMed

Tremblay, Jean Christophe; Carrington, Tucker

2005-06-22

We introduce new ideas for calculating resonance energies and widths. It is shown that a non-Hermitian-Lanczos approach can be used to compute eigenvalues of H+W, where H is the Hamiltonian and W is a complex absorbing potential (CAP), without evaluating complex matrix-vector products. This is done by exploiting the link between a CAP-modified Hamiltonian matrix and a real but nonsymmetric matrix U suggested by Mandelshtam and Neumaier [J. Theor. Comput. Chem. 1, 1 (2002)] and using a coupled-two-term Lanczos procedure. We use approximate resonance eigenvectors obtained from the non-Hermitian-Lanczos algorithm and a very good CAP to obtain very accurate energies and widths without solving eigenvalue problems for many values of the CAP strength parameter and searching for cusps. The method is applied to the resonances of HCO. We compare properties of the method with those of established approaches.

Sodium-based hydrides for thermal energy applications

NASA Astrophysics Data System (ADS)

Sheppard, D. A.; Humphries, T. D.; Buckley, C. E.

2016-04-01

Concentrating solar-thermal power (CSP) with thermal energy storage (TES) represents an attractive alternative to conventional fossil fuels for base-load power generation. Sodium alanate (NaAlH4) is a well-known sodium-based complex metal hydride but, more recently, high-temperature sodium-based complex metal hydrides have been considered for TES. This review considers the current state of the art for NaH, NaMgH3- x F x , Na-based transition metal hydrides, NaBH4 and Na3AlH6 for TES and heat pumping applications. These metal hydrides have a number of advantages over other classes of heat storage materials such as high thermal energy storage capacity, low volume, relatively low cost and a wide range of operating temperatures (100 °C to more than 650 °C). Potential safety issues associated with the use of high-temperature sodium-based hydrides are also addressed.

The reactivity of sodium alanates with O[2], H[2]O, and CO[2] : an investigation of complex metal hydride contamination in the context of automotive systems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dedrick, Daniel E.; Bradshaw, Robert W.; Behrens, Richard, Jr.

2007-08-01

Safe and efficient hydrogen storage is a significant challenge inhibiting the use of hydrogen as a primary energy carrier. Although energy storage performance properties are critical to the success of solid-state hydrogen storage systems, operator and user safety is of highest importance when designing and implementing consumer products. As researchers are now integrating high energy density solid materials into hydrogen storage systems, quantification of the hazards associated with the operation and handling of these materials becomes imperative. The experimental effort presented in this paper focuses on identifying the hazards associated with producing, storing, and handling sodium alanates, and thus allowingmore » for the development and implementation of hazard mitigation procedures. The chemical changes of sodium alanates associated with exposure to oxygen and water vapor have been characterized by thermal decomposition analysis using simultaneous thermogravimetric modulated beam mass spectrometry (STMBMS) and X-ray diffraction methods. Partial oxidation of sodium alanates, an alkali metal complex hydride, results in destabilization of the remaining hydrogen-containing material. At temperatures below 70 C, reaction of sodium alanate with water generates potentially combustible mixtures of H{sub 2} and O{sub 2}. In addition to identifying the reaction hazards associated with the oxidation of alkali-metal containing complex hydrides, potential treatment methods are identified that chemically stabilize the oxidized material and reduce the hazard associated with handling the contaminated metal hydrides.« less

Quantum chemical characterization of zwitterionic structures: Supramolecular complexes for modifying the wettability of oil-water-limestone system.

PubMed

Lopez-Chavez, Ernesto; Garcia-Quiroz, Alberto; Gonzalez-Garcia, Gerardo; Orozco-Duran, Gabriela E; Zamudio-Rivera, Luis S; Martinez-Magadan, José M; Buenrostro-Gonzalez, Eduardo; Hernandez-Altamirano, Raul

2014-06-01

In this work, we present a quantum chemical study pertaining to some supramolecular complexes acting as wettability modifiers of oil-water-limestone system. The complexes studied are derived from zwitterionic liquids of the types N'-alkyl-bis, N-alquenil, N-cycloalkyl, N-amyl-bis-beta amino acid or salts acting as sparkling agents. We studied two molecules of zwitterionic liquids (ZL10 and ZL13), HOMO and LUMO levels, and the energy gap between them, were calculated, as well as the electron affinity (EA) and ionization potential (IP), chemical potential, chemical hardness, chemical electrophilicity index and selectivity descriptors such Fukui indices. In this work, electrochemical comparison was realized with cocamidopropyl betaine (CPB), which is a structure zwitterionic liquid type, nowadays widely applied in enhanced recovery processes. Copyright © 2014 Elsevier Inc. All rights reserved.

A quantum-rovibrational-state-selected study of the reaction in the collision energy range of 0.05-10.00 eV: translational, rotational, and vibrational energy effects.

PubMed

Xu, Yuntao; Xiong, Bo; Chang, Yih-Chung; Pan, Yi; Lo, Po Kam; Lau, Kai Chung; Ng, C Y

2017-04-12

We report detailed absolute integral cross sections (σ's) for the quantum-rovibrational-state-selected ion-molecule reaction in the center-of-mass collision energy (E cm ) range of 0.05-10.00 eV, where (vvv) = (000), (100), and (020), and . Three product channels, HCO + + OH, HOCO + + H, and CO + + H 2 O, are identified. The measured σ(HCO + ) curve [σ(HCO + ) versus E cm plot] supports the hypothesis that the formation of the HCO + + OH channel follows an exothermic pathway with no potential energy barriers. Although the HOCO + + H channel is the most exothermic, the σ(HOCO + ) is found to be significantly lower than the σ(HCO + ). The σ(HOCO + ) curve is bimodal, indicating two distinct mechanisms for the formation of HOCO + . The σ(HOCO + ) is strongly inhibited at E cm < 0.4 eV, but is enhanced at E cm > 0.4 eV by (100) vibrational excitation. The E cm onsets of σ(CO + ) determined for the (000) and (100) vibrational states are in excellent agreement with the known thermochemical thresholds. This observation, along with the comparison of the σ(CO + ) curves for the (100) and (000) states, shows that kinetic and vibrational energies are equally effective in promoting the CO + channel. We have also performed high-level ab initio quantum calculations on the potential energy surface, intermediates, and transition state structures for the titled reaction. The calculations reveal potential barriers of ≈0.5-0.6 eV for the formation of HOCO + , and thus account for the low σ(HOCO + ) and its bimodal profile observed. The E cm enhancement for σ(HOCO + ) at E cm ≈ 0.5-5.0 eV can be attributed to the direct collision mechanism, whereas the formation of HOCO + at low E cm < 0.4 eV may involve a complex mechanism, which is mediated by the formation of a loosely sticking complex between HCO + and OH. The direct collision and complex mechanisms proposed also allow the rationalization of the vibrational inhibition at low E cm and the vibrational enhancement at high E cm observed for the σ(HOCO + ).

Enhancement of photoisomerization of polymethine dyes in complexes with biomacromolecules

NASA Astrophysics Data System (ADS)

Tatikolov, Alexander S.; Akimkin, Timofei M.; Pronkin, Pavel G.; Yarmoluk, Sergiy M.

2013-01-01

Photochemical processes (photoisomerization and generation of the triplet state) of the thiacarbocyanine dyes 3,3',9-trimethylthiacarbocyanine iodide (Cyan 2), 3,3'-diethyl-9-methylthiacarbocyanine iodide (DMTC), and 3,3',9-triethylthiacarbocyanine iodide (TETC) in complexes with biomacromolecules—DNA and chondroitin-4-sulfate—were studied by flash photolysis. It has been shown that, along with generation of the triplet state, enhancement of the photoisomer formation is observed for Cyan 2 and DMTC complexed with the biomolecules. This effect can be explained by the influence of the biopolymer matrix on the potential energy curves of the photoisomerization process.

Infrared and Microwave Spectra of Ne-WATER Complex

NASA Astrophysics Data System (ADS)

Liu, Xunchen; Thomas, Javix; Xu, Yunjie; Hou, Dan; Li, Hui

2016-06-01

The binary complex of rare gas atom and water is an ideal model to study the anisotropic potential energy surface of van der Waals interaction and the large amplitude motion. Although Xe-H_2O, Kr-H_2O, Ar-H_2O, Ar-D_2O and even Ne-D_2O complexes were studied by microwave or high resolution infrared spectroscopy, the lighter Ne-H_2O complex has remained unidentified. In this talk, we will present the theoretical and experimental investigation of the Ne-H_2O complex. A four-dimension PES for H_2O-Ne which only depended on the intramolecular (Q2) normal-mode coordinate of H2O monomer was calculated in this work to determine the rovibrational energy levels and mid-infrared transitions. Aided with the calculated transitions, we were able to assigned the high resolution mid-infrared spectra of both 20Ne-H_2O and 22Ne-H_2O complexes that are generated with a pulsed supersonic molecular beam in a multipass direct absorption spectrometer equiped with an external cavity quantum cascade laser at 6 μm. Several bands of both para and ortho Ne-H2O were assigned and fitted using the Hamiltonian with strong Coriolis and angular-radical coupling terms. The predicted groud state energy levels are then confirmed by the J=1-0 and J=2-1 transitions measurement using a cavity based Fourier transform microwave spectrometer.

Development of a fountain detector for spectroscopy of secondary electrons in scanning electron microscopy

NASA Astrophysics Data System (ADS)

Agemura, Toshihide; Kimura, Takashi; Sekiguchi, Takashi

2018-04-01

The low-pass secondary electron (SE) detector, the so-called “fountain detector (FD)”, for scanning electron microscopy has high potential for application to the imaging of low-energy SEs. Low-energy SE imaging may be used for detecting the surface potential variations of a specimen. However, the detected SEs include a certain fraction of tertiary electrons (SE3s) because some of the high-energy backscattered electrons hit the grid to yield SE3s. We have overcome this difficulty by increasing the aperture ratio of the bias and ground grids and using the lock-in technique, in which the AC field with the DC offset was applied on the bias grid. The energy-filtered SE images of a 4H-SiC p-n junction show complex behavior according to the grid bias. These observations are clearly explained by the variations of Auger spectra across the p-n junction. The filtered SE images taken with the FD can be applied to observing the surface potential variation of specimens.

Extending the Diffuse Layer Model of Surface Acidity Behavior: III. Estimating Bound Site Activity Coefficients

EPA Science Inventory

Although detailed thermodynamic analyses of the 2-pK diffuse layer surface complexation model generally specify bound site activity coefficients for the purpose of accounting for those non-ideal excess free energies contributing to bound site electrochemical potentials, in applic...

Synthesis, characterization and in vitro antimicrobial studies of Co(II), Ni(II) and Cu(II) complexes derived from macrocyclic compartmental ligand

NASA Astrophysics Data System (ADS)

El-Gammal, O. A.; Bekheit, M. M.; El-Brashy, S. A.

2015-02-01

New Co(II), Ni(II) and Cu(II) complexes derived from tetradentate macrocyclic nitrogen ligand, (1E,4E,8E,12E)-5,8,13,16-tetramethyl-1,4,9,12-tetrazacyclohexadeca-4,8,12,16-tetraene (EDHDH) have been synthesized. The complexes have been characterized by elemental analysis, spectral (IR, UV-Vis, 1H NMR and ESR (for Cu(II) complex)) mass, and magnetic as well as thermal analysis measurements. The complexes afforded the formulae: [Cu(EDHDH)Cl2]·2EtOH and [M(EDHDH)X2]·nH2O where M = Co(II) and Ni(II), X = Cl- or OH-, n = 1,0, respectively. The data revealed an octahedral arrangement with N4 tetradentate donor sites in addition to two Cl atoms occupying the other two sites. ESR spectrum of Cu2+ complex confirmed the suggested geometry with values of a α2and β2 indicating that the in-plane σ-bonding and in-plane π-bonding are appreciably covalent, and are consistent with very strong σ-in-plane bonding in the complexes. The molecular modeling is drawn and showed the bond length, bond angle, chemical reactivity, energy components (kcal/mol) and binding energy (kcal/mol) for all the title compounds using DFT method. Also, the thermal behavior and the kinetic parameters of degradation were determined using Coats-Redfern and Horowitz-Metzger methods. Moreover, the in vitro antibacterial studies of all compounds screened against pathogenic bacteria (two Gram +ve and two Gram -ve) to assess their inhibiting potential. The assay indicated that the inhibition potential is metal ion dependent. The ligand, EDHDH, Co(II) and Cu(II) complexes exhibited a remarkable antibacterial activity against Streptococcus Pyogenes as Gram +ve and Proteus vulgaris as Gram -ve bacterial strains. On the other hand, Ni(II) complex revealed a moderate antibacterial activity against both Gram +ve organisms and no activity against Gram -ve bacterial strain.

PT-symmetry breaking with divergent potentials: Lattice and continuum cases

NASA Astrophysics Data System (ADS)

Joglekar, Yogesh N.; Scott, Derek D.; Saxena, Avadh

2014-09-01

We investigate the parity- and time-reversal (PT-) symmetry breaking in lattice models in the presence of long-ranged, non-Hermitian, PT-symmetric potentials that remain finite or become divergent in the continuum limit. By scaling analysis of the fragile PT threshold for an open finite lattice, we show that continuum loss-gain potentials Vα(x)∝i|x|αsgn(x) have a positive PT-breaking threshold for α >-2, and a zero threshold for α ≤-2. When α <0 localized states with complex (conjugate) energies in the continuum energy band occur at higher loss-gain strengths. We investigate the signatures of PT-symmetry breaking in coupled waveguides, and show that the emergence of localized states dramatically shortens the relevant time scale in the PT-symmetry broken region.

Wavelet analysis can sensitively describe dynamics of ethanol evoked local field potentials of the slug (Limax marginatus) brain.

PubMed

Schütt, Atsuko; Ito, Iori; Rosso, Osvaldo A; Figliola, Alejandra

2003-10-30

Odorants evoke characteristic, but complex, local field potentials (LFPs) in the molluscan brain. Wavelet tools in combination with Fourier analysis can detect and characterize hitherto unknown discrete, slow potentials underlying the conspicuous oscillations. Ethanol was one of the odorants that we have extensively studied (J. Neurosci. Methods, 119 (2002) 89). To detect new features and to elucidate their functions, we tested the wavelet tools on the ethanol-evoked LFP responses of the slug (Limax) procerebrum. Recordings were made in vitro from the neuropile and the cell layer. The present study led to the following findings: (i) Mutual exclusion. Energy concentrated mainly in two ranges, (a) 0.1-0.4 Hz and (b) 1.56-12.5 Hz, and the sum of energy remained constant throughout experiments regardless of the condition. A redistribution of relative energy within this sum seemed to occur in the course of main, possible interactions between the two components excluding each other ('mutual exclusion'). (ii) Transient signal ordering and disordering. Ethanol stimulation alternatingly evoked periods of strongly time evolving oscillation dominated by the energy of 1.56-12.5 Hz (increase of entropy=disordered or complexly ordered state) and those of near-silence were predominated by the energy of 0.1-0.4 Hz (decrease of entropy=ordered state). (iii) About 0.1 Hz slow wave oscillation. It was robust. The dominant energy oscillation and the resulting large entropy fluctuation were negatively correlated to each other, and revealed strong frequency-tuning or synchronization at this frequency. Our findings suggest that discrete slow waves play functionally important roles in the invertebrate brain, as widely known in vertebrate EEG. Wavelet tools allow an easy interpretation of several minutes of frequency variations in a single display and give precise information on stimulus-evoked complex change of the neural system describing the new state 'more ordered' or 'non-ordered or more complexly ordered'.

Tuning of the ionization potential of paddlewheel diruthenium(II, II) complexes with fluorine atoms on the benzoate ligands.

PubMed

Miyasaka, Hitoshi; Motokawa, Natsuko; Atsuumi, Ryo; Kamo, Hiromichi; Asai, Yuichiro; Yamashita, Masahiro

2011-01-21

A series of paddlewheel diruthenium(ii, ii) complexes with various fluorine-substituted benzoate ligands were isolated as THF adducts and structurally characterized: [Ru(2)(F(x)PhCO(2))(4)(THF)(2)] (F(x)PhCO(2)(-) = o-fluorobenzoate, o-F; m-fluorobenzoate, m-F; p-fluorobenzoate, p-F; 2,6-difluorobenzoate, 2,6-F(2); 3,4-difluorobenzoate, 3,4-F(2); 3,5-difluorobenzoate, 3,5-F(2); 2,3,4-trifluorobenzoate, 2,3,4-F(3); 2,3,6-trifluorobenzoate, 2,3,6-F(3); 2,4,5-trifluorobenzoate, 2,4,5-F(3); 2,4,6-trifluorobenzoate, 2,4,6-F(3); 3,4,5-trifluorobenzoate, 3,4,5-F(3); 2,3,4,5-tetrafluorobenzoate, 2,3,4,5-F(4); 2,3,5,6-tetrafluorobenzoate, 2,3,5,6-F(4); pentafluorobenzoate, F(5)). By adding fluorine atoms on the benzoate ligands, it was possible to tune the redox potential (E(1/2)) for [Ru(2)(II,II)]/[Ru(2)(II,III)](+) over a wide range of potentials from -40 mV to 350 mV (vs. Ag/Ag(+) in THF). 2,3,6-F(3), 2,3,4,5-F(4), 2,3,5,6-F(4) and F(5) were relatively air-stable compounds even though they are [Ru(2)(II,II)] species. The redox potential in THF was dependent on an electronic effect rather than on a structural (steric) effect of the o-F atoms, although more than one substituent in the m- and p-positions shifted E(1/2) to higher potentials in relation to the general Hammett equation. A quasi-Hammett parameter for an o-F atom (σ(o)) was estimated to be ∼0.2, and a plot of E(1/2)vs. a sum of Hammett parameters including σ(o) was linear. In addition, the HOMO energy levels, which was calculated based on atomic coordinates of solid-state structures, as well as the redox potential were affected by adding F atoms. Nevertheless, a steric contribution stabilizing their static structures in the solid state was present in addition to the electronic effect. On the basis of the electronic effect, the redox potential of these complexes is correlated to the HOMO energy level, and the electronic effect of F atoms is the main factor controlling the ionization potential of the complexes with ligands free from the rotational constraint, i.e. complexes in solution.

Effect of a magnetic field on the track structure of low-energy electrons: a Monte Carlo study

NASA Astrophysics Data System (ADS)

Bug, M. U.; Gargioni, E.; Guatelli, S.; Incerti, S.; Rabus, H.; Schulte, R.; Rosenfeld, A. B.

2010-10-01

The increasing use of MRI-guided radiation therapy evokes the necessity to investigate the potential impact of a magnetic field on the biological effectiveness of therapeutic radiation beams. While it is known that a magnetic field, applied during irradiation, can improve the macroscopic absorbed dose distribution of electrons in the tumor region, effects on the microscopic distribution of energy depositions and ionizations have not yet been investigated. An effect on the number of ionizations in a DNA segment, which is related to initial DNA damage in form of complex strand breaks, could be beneficial in radiation therapy. In this work we studied the effects of a magnetic field on the pattern of ionizations at nanometric level by means of Monte Carlo simulations using the Geant4-DNA toolkit. The track structure of low-energy electrons in the presence of a uniform static magnetic field of strength up to 14 T was calculated for a simplified DNA segment model in form of a water cylinder. In the case that no magnetic field is applied, nanodosimetric results obtained with Geant4-DNA were compared with those from the PTB track structure code. The obtained results suggest that any potential enhancement of complexity of DNA strand breaks induced by irradiation in a magnetic field is not related to modifications of the low-energy secondary electrons track structure.

Scattering study of the Ne + NeH+(v0 = 0, j0 = 0) → NeH+ + Ne reaction on an ab initio based analytical potential energy surface

NASA Astrophysics Data System (ADS)

Koner, Debasish; Barrios, Lizandra; González-Lezana, Tomás; Panda, Aditya N.

2016-01-01

Initial state selected dynamics of the Ne + NeH+(v0 = 0, j0 = 0) → NeH+ + Ne reaction is investigated by quantum and statistical quantum mechanical (SQM) methods on the ground electronic state. The three-body ab initio energies on a set of suitably chosen grid points have been computed at CCSD(T)/aug-cc-PVQZ level and analytically fitted. The fitting of the diatomic potentials, computed at the same level of theory, is performed by spline interpolation. A collinear [NeHNe]+ structure lying 0.72 eV below the Ne + NeH+ asymptote is found to be the most stable geometry for this system. Energies of low lying vibrational states have been computed for this stable complex. Reaction probabilities obtained from quantum calculations exhibit dense oscillatory structures, particularly in the low energy region and these get partially washed out in the integral cross section results. SQM predictions are devoid of oscillatory structures and remain close to 0.5 after the rise at the threshold thus giving a crude average description of the quantum probabilities. Statistical cross sections and rate constants are nevertheless in sufficiently good agreement with the quantum results to suggest an important role of a complex-forming dynamics for the title reaction.

On improving the performance of nonphotochemical quenching in CP29 light-harvesting antenna complex

DOE PAGES

Berman, Gennady Petrovich; Nesterov, Alexander I.; Sayre, Richard Thomas; ...

2016-02-02

In this study, we model and simulate the performance of charge-transfer in nonphotochemical quenching (NPQ) in the CP29 light-harvesting antenna-complex associated with photosystem II (PSII). The model consists of five discrete excitonic energy states and two sinks, responsible for the potentially damaging processes and charge-transfer channels, respectively. We demonstrate that by varying (i) the parameters of the chlorophyll-based dimer, (ii) the resonant properties of the protein-solvent environment interaction, and (iii) the energy transfer rates to the sinks, one can significantly improve the performance of the NPQ. In conclusion, our analysis suggests strategies for improving the performance of the NPQ inmore » response to environmental changes, and may stimulate experimental verification.« less

Electron impact scattering study of hypohalous acids HOX (X = F, Cl, Br, I)

NASA Astrophysics Data System (ADS)

Yadav, Hitesh; Bhutadia, Harshad; Prajapati, Dinesh; Desai, Hardik; Vinodkumar, Minaxi; Vinodkumar, P. C.

2018-05-01

In this article we aim to report total cross sections (TCS) QT, total elastic cross sections (Qel), total inelastic cross sections (Qinel) i.e. (total ionizations cross sections (Qion)+total electronic excitation cross sections (Qexc)) from threshold of the target to 5000 eV energy range. We have used a well-defined theoretical methodology Spherical Complex Optical Potential (SCOP) to compute QT, Qel and Qinel and Complex Scattering Potential - ionization contribution (CSP - ic) method to report the (Qion). The cross-sectional data reported here for the Hypohalous Acids is for the first time and the present data can become a guideline for the experimentalist to study these targets.

Lifetimes and wave functions of ozone metastable vibrational states near the dissociation limit in a full-symmetry approach

NASA Astrophysics Data System (ADS)

Lapierre, David; Alijah, Alexander; Kochanov, Roman; Kokoouline, Viatcheslav; Tyuterev, Vladimir

2016-10-01

Energies and lifetimes (widths) of vibrational states above the lowest dissociation limit of O163 were determined using a previously developed efficient approach, which combines hyperspherical coordinates and a complex absorbing potential. The calculations are based on a recently computed potential energy surface of ozone determined with a spectroscopic accuracy [Tyuterev et al., J. Chem. Phys. 139, 134307 (2013), 10.1063/1.4821638]. The effect of permutational symmetry on rovibrational dynamics and the density of resonance states in O3 is discussed in detail. Correspondence between quantum numbers appropriate for short- and long-range parts of wave functions of the rovibrational continuum is established. It is shown, by symmetry arguments, that the allowed purely vibrational (J =0 ) levels of O163 and O183, both made of bosons with zero nuclear spin, cannot dissociate on the ground-state potential energy surface. Energies and wave functions of bound states of the ozone isotopologue O163 with rotational angular momentum J =0 and 1 up to the dissociation threshold were also computed. For bound levels, good agreement with experimental energies is found: The rms deviation between observed and calculated vibrational energies is 1 cm-1. Rotational constants were determined and used for a simple identification of vibrational modes of calculated levels.

BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations.

PubMed

Fu, Haohao; Gumbart, James C; Chen, Haochuan; Shao, Xueguang; Cai, Wensheng; Chipot, Christophe

2018-03-26

Quantifying protein-ligand binding has attracted the attention of both theorists and experimentalists for decades. Many methods for estimating binding free energies in silico have been reported in recent years. Proper use of the proposed strategies requires, however, adequate knowledge of the protein-ligand complex, the mathematical background for deriving the underlying theory, and time for setting up the simulations, bookkeeping, and postprocessing. Here, to minimize human intervention, we propose a toolkit aimed at facilitating the accurate estimation of standard binding free energies using a geometrical route, coined the binding free-energy estimator (BFEE), and introduced it as a plug-in of the popular visualization program VMD. Benefitting from recent developments in new collective variables, BFEE can be used to generate the simulation input files, based solely on the structure of the complex. Once the simulations are completed, BFEE can also be utilized to perform the post-treatment of the free-energy calculations, allowing the absolute binding free energy to be estimated directly from the one-dimensional potentials of mean force in simulation outputs. The minimal amount of human intervention required during the whole process combined with the ergonomic graphical interface makes BFEE a very effective and practical tool for the end-user.

Potential energy surfaces related to the ion-molecule reaction C/sup +/ + H/sub 2/

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liskow, D.H.; Bender, C.F.; Schaefer, H.F. III

1974-10-01

The C/sup +/ + H/sub 2/ ion-molecule reaction has been studied by several experimental groups and appears likely to become the focal point of much experimental and theoretical activity. Ab initio self-consistent-field and configuration interaction calculations have accordingly been carried out for this system. A double zeta basis set of contracted Gaussian functions was employed and as many as 648 configurations included. For isosceles triangle configurations (C/sub 2V/ point group) the /sup 2/A/sub 1/, /sup 2/B/sub 1/, and /sup 2/B/sub 2/ potential surfaces were considered, while for linear geometries (C/sub infinity V) the /sup 2/..sigma../sup +/ and /sup 2/PI surfacesmore » were studied. For general (C/sub S/) geometry, the lowest /sup 2/A' potential surface was considered. Properties reported include minimum energy paths and energy profiles for the various processes considered. The intuitive correlation diagram of Mahan and Sloane is given qualitative reliability. Pathways to CH/sub 2//sup +/ complex formation are shown to depend crucially on the C/sub S/ potential surface.« less

N(2)O in small para-hydrogen clusters: Structures and energetics.

PubMed

Zhu, Hua; Xie, Daiqian

2009-04-30

We present the minimum-energy structures and energetics of clusters of the linear N(2)O molecule with small numbers of para-hydrogen molecules with pairwise additive potentials. Interaction energies of (p-H(2))-N(2)O and (p-H(2))-(p-H(2)) complexes were calculated by averaging the corresponding full-dimensional potentials over the H(2) angular coordinates. The averaged (p-H(2))-N(2)O potential has three minima corresponding to the T-shaped and the linear (p-H(2))-ONN and (p-H(2))-NNO structures. Optimization of the minimum-energy structures was performed using a Genetic Algorithm. It was found that p-H(2) molecules fill three solvation rings around the N(2)O axis, each of them containing up to five p-H(2) molecules, followed by accumulation of two p-H(2) molecules at the oxygen and nitrogen ends. The first solvation shell is completed at N = 17. The calculated chemical potential oscillates with cluster size up to the completed first solvation shell. These results are consistent with the available experimental measurements. (c) 2009 Wiley Periodicals, Inc.

Energy capture and storage in asymmetrically multistable modular structures inspired by skeletal muscle

NASA Astrophysics Data System (ADS)

Kidambi, Narayanan; Harne, Ryan L.; Wang, K. W.

2017-08-01

The remarkable versatility and adaptability of skeletal muscle that arises from the assembly of its nanoscale cross-bridges into micro-scale assemblies known as sarcomeres provides great inspiration for the development of advanced adaptive structures and material systems. Motivated by the capability of cross-bridges to capture elastic strain energy to improve the energetic efficiency of sudden movements and repeated motions, and by models of cross-bridge power stroke motions and sarcomere contractile behaviors that incorporate asymmetric, bistable potential energy landscapes, this research develops and studies modular mechanical structures that trap and store energy in higher-energy configurations. Modules exhibiting tailorable asymmetric bistability are first designed and fabricated, revealing how geometric parameters influence the asymmetry of the resulting double-well energy landscapes. These experimentally-observed characteristics are then investigated with numerical and analytical methods to characterize the dynamics of asymmetrically bistable modules. The assembly of such modules into greater structures generates complex, multi-well energy landscapes with stable system configurations exhibiting different quantities of stored elastic potential energy. Dynamic analyses illustrate the ability of these structures to capture a portion of the initial kinetic energy due to impulsive excitations as recoverable strain potential energy, and reveal how stiffness parameters, damping, and the presence of thermal noise in micro- and nano-scale applications influence energy capture behaviors. The insights gained could foster the development of advanced structural/material systems inspired by skeletal muscle, including actuators that effectively capture, store, and release energy, as well as adaptive, robust, and reusable armors and protective devices.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Langner, Rois; Hendron, Bob; Pless, Shanti

Small buildings have been left behind in the energy efficiency marketplace because financial and technical resources have flowed to larger commercial buildings. DOE's Building Technologies Office works with the commercial building industry to accelerate the uptake of energy efficiency technologies and techniques in existing and new commercial buildings (DOE 2013). BTO recognizes the SBSP sector'spotential for significant energy savings and the need for investments in resources that are tailored to this sector's unique needs. The industry research and recommendations described in this report identify potential approaches and strategic priorities that BTO could explore over the next 3-5 years that willmore » support the implementation of high-potential energy efficiency opportunities for thisimportant sector. DOE is uniquely positioned to provide national leadership, objective information, and innovative tools, technologies, and services to support cost-effective energy savings in the fragmented and complex SBSP sector. Properly deployed, the DOE effort could enhance and complement current energy efficiency approaches. Small portfolios are loosely and qualitatively defined asportfolios of buildings that include only a small number of small buildings. This distinction is important because the report targets portfolio owners and managers who generally do not have staff and other resources to track energy use and pursue energy efficiency solutions.« less

Light energy conservation processes in Halobacterium halobium cells

NASA Technical Reports Server (NTRS)

Bogomolni, R. A.

1977-01-01

Proton pumping driven by light or by respiration generates an electrochemical potential difference across the membrane in Halobacterium halobium. The pH changes induced by light or by respiration in cell suspensions are complicated by proton flows associated with the functioning of the cellular energy transducers. A proton-per-ATP ratio of about 3 is calculated from simultaneous measurements of phosphorylation and the proton inflow. This value is compatible with the chemiosmotic coupling hypothesis. The time course of the light-induced changes in membrane potential indicates that light-driven pumping increases a dark pre-existing potential of about 130 mV only by a small amount (20 to 30 mV). The complex kinetic features of the membrane potential changes do not closely follow those of the pH changes, which suggests that flows of ions other than protons are involved. A qualitative model consistent with the available data is presented.

Potential hepatic toxicity of buprofezin at sublethal concentrations: ROS-mediated conversion of energy metabolism.

PubMed

Ji, Xiaotong; Ku, Tingting; Zhu, Na; Ning, Xia; Wei, Wei; Li, Guangke; Sang, Nan

2016-12-15

Buprofezin is known for its broad-spectrum action and environmental safety. The popularity of buprofezin has raised concerns about its potentially adverse effects on human health and risk to the environment. In this study, we first identified the liver as one of the major organs in which buprofezin accumulated, and we detected a severe oxidative stress response. Next, we demonstrated that sublethal concentrations of buprofezin promoted the conversion of energy metabolism from the aerobic tricarboxylic acid (TCA) cycle and oxidative phosphorylation to anaerobic glycolysis. Importantly, reactive oxygen species (ROS) generation partially accounted for the shunting of the energy metabolism through the buprofezin-mediated inhibition of cytochrome c oxidase activity. ROS directly perturbed the activities of several key TCA cycle enzymes, stimulated glycolysis, and indirectly disturbed the activity of the respiratory chain complex by altering mitochondrial DNA (mtDNA). These findings clarify the potential mechanisms of buprofezin toxicity and provide biomarkers for buprofezin-mediated hepatotoxicity at sublethal concentrations. Copyright © 2016 Elsevier B.V. All rights reserved.

Variationally Optimized Free-Energy Flooding for Rate Calculation.

PubMed

McCarty, James; Valsson, Omar; Tiwary, Pratyush; Parrinello, Michele

2015-08-14

We propose a new method to obtain kinetic properties of infrequent events from molecular dynamics simulation. The procedure employs a recently introduced variational approach [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] to construct a bias potential as a function of several collective variables that is designed to flood the associated free energy surface up to a predefined level. The resulting bias potential effectively accelerates transitions between metastable free energy minima while ensuring bias-free transition states, thus allowing accurate kinetic rates to be obtained. We test the method on a few illustrative systems for which we obtain an order of magnitude improvement in efficiency relative to previous approaches and several orders of magnitude relative to unbiased molecular dynamics. We expect an even larger improvement in more complex systems. This and the ability of the variational approach to deal efficiently with a large number of collective variables will greatly enhance the scope of these calculations. This work is a vindication of the potential that the variational principle has if applied in innovative ways.

Quantum Transport and Non-Hermiticity on Flat-Band Lattices

NASA Astrophysics Data System (ADS)

Park, Hee Chul; Ryu, Jung-Wan; Myoung, Nojoon

2018-04-01

We investigate quantum transport in a flat-band lattice induced in a twisted cross-stitch lattice with Hermitian or non-Hermitian potentials, with a combination of parity and time-reversal symmetry invariant. In the given system, the transmission probability demonstrates a resonant behavior on the real part of the energy bands. Both of the potentials break the parity symmetry, which lifts the degeneracy of the flat and dispersive bands. In addition, non-Hermiticity conserving PT-symmetry induces a transition between the unbroken and broken PT-symmetric phases through exceptional points in momentum space. Characteristics of non-Hermitian and Hermitian bandgaps are distinguishable: The non-Hermitian bandgap is induced by separation toward complex energy, while the Hermitian bandgap is caused by the expelling of available states into real energy. Deviation of the two bandgaps follows as a function of the quartic power of the induced potential. It is notable that non-Hermiticity plays an important role in the mechanism of generating a bandgap distinguishable from a Hermitian bandgap.

On the Free Energy That Drove Primordial Anabolism

PubMed Central

Kaufmann, Michael

2009-01-01

A key problem in understanding the origin of life is to explain the mechanism(s) that led to the spontaneous assembly of molecular building blocks that ultimately resulted in the appearance of macromolecular structures as they are known in modern biochemistry today. An indispensable thermodynamic prerequisite for such a primordial anabolism is the mechanistic coupling to processes that supplied the free energy required. Here I review different sources of free energy and discuss the potential of each form having been involved in the very first anabolic reactions that were fundamental to increase molecular complexity and thus were essential for life. PMID:19468343

Theoretical investigation of rotationally inelastic collisions of CH(X2Π) with hydrogen atoms

NASA Astrophysics Data System (ADS)

Dagdigian, Paul J.

2017-06-01

We report calculations of state-to-state cross sections for collision-induced rotational transitions of CH(X2Π) with atomic hydrogen. These calculations employed the four adiabatic potential energy surfaces correlating CH(X2Π) + H(2S), computed in this work through the multi-reference configuration interaction method [MRCISD + Q(Davidson)]. Because of the presence of deep wells on three of the potential energy surfaces, the scattering calculations were carried out using the quantum statistical method of Manolopoulos and co-workers [Chem. Phys. Lett. 343, 356 (2001)]. The computed cross sections included contributions from only direct scattering since the CH2 collision complex is expected to decay predominantly to C + H2. Rotationally energy transfer rate constants were computed for this system since these are required for astrophysical modeling.

Bright Photon Upconversion on Composite Organic Lanthanide Molecules through Localized Thermal Radiation.

PubMed

Ye, Huanqing; Bogdanov, Viktor; Liu, Sheng; Vajandar, Saumitra; Osipowicz, Thomas; Hernández, Ignacio; Xiong, Qihua

2017-12-07

Converting low-energy photons via thermal radiation can be a potential approach for utilizing infrared (IR) photons to improve photovoltaic efficiency. Lanthanide-containing materials have achieved great progress in IR-to-visible photon upconversion (UC). Herein, we first report bright photon, tunable wavelength UC through localized thermal radiation at the molecular scale with low excitation power density (<10 W/cm 2 ) realized on lanthanide complexes of perfluorinated organic ligands. This is enabled by engineering the pathways of nonradiative de-excitation and energy transfer in a composite of ytterbium and terbium perfluoroimidodiphosphinates. The IR-excited thermal UC and wavelength control is realized through the terbium activators sensitized by the ytterbium sensitizers having high luminescence efficiency. The metallic molecular composite thus can be a potential energy material in the use of the IR solar spectrum for thermal photovoltaic applications.

Spectroscopic and thermal investigations on the charge transfer interaction between risperidone as a schizophrenia drug with some traditional π-acceptors: Part 2

NASA Astrophysics Data System (ADS)

El-Habeeb, Abeer A.; Al-Saif, Foziah A.; Refat, Moamen S.

2013-03-01

The focus of present investigation was to assess the utility of non-expensive techniques in the evaluation of risperidone (Ris) in solid and solution states with different traditional π-acceptors and subsequent incorporation of the analytical determination into pharmaceutical formulation for a faster release of risperidone. Charge-transfer complexes (CTC) of risperidone with picric acid (PA), 2,3-dichloro-5,6-dicyano-p-benzoquinon (DDQ), tetracyanoquinodimethane (TCNQ), tetracyano ethylene (TCNE), tetrabromo-p-quinon (BL) and tetrachloro-p-quinon (CL) have been studied spectrophotometrically in absolute methanol at room temperature. The stoichiometries of the complexes were found to be 1:1 ratio by the photometric molar ratio between risperidone and the π-acceptors. The equilibrium constants, molar extinction coefficient (ɛCT) and spectroscopic-physical parameters (standard free energy (ΔGo), oscillator strength (f), transition dipole moment (μ), resonance energy (RN) and ionization potential (ID)) of the complexes were determined upon the modified Benesi-Hildebrand equation. Risperidone in pure form was applied in this study. The results indicate that the formation constants for the complexes depend on the nature of electron acceptors and donor, and also the spectral studies of the complexes were determined by (infrared, Raman, and 1H NMR) spectra and X-ray powder diffraction (XRD). The most stable mono-protonated form of Ris is characterized by the formation of +Nsbnd H (pyrimidine ring) intramolecular hydrogen bonded. In the high-wavenumber spectral region ˜3400 cm-1, the bands of the +Nsbnd H stretching vibrations and of the pyrimidine nitrogen atom could be potentially useful to discriminate the investigated forms of Ris. The infrared spectra of both Ris complexes are confirming the participation of +Nsbnd H pyrimidine ring in the donor-acceptor interaction.

DFT-based molecular modeling and vibrational study of the La(III) complex of 3,3'-(benzylidene)bis(4-hydroxycoumarin).

PubMed

Mihaylov, Tzvetan; Trendafilova, Natasha; Georgieva, Ivelina

2008-05-01

Molecular modeling of the La(III) complex of 3,3'-(benzylidene)bis(4-hydroxycoumarin) (PhDC) was performed using density functional theory (DFT) methods at B3LYP/6-31G(d) and BP86/TZP levels. Both Stuttgart-Dresden effective core potential and ZORA approximation were applied to the La(III) center. The electron density distribution and the nucleophilic centers of the deprotonated ligand PhDC(2-) in a solvent environment were estimated on the basis of Hirshfeld atomic charges, electrostatic potential values at the nuclei, and Nalewajski-Mrozek bond orders. In accordance with the empirical formula La(PhDC)(OH)(H(2)O), a chain structure of the complex was simulated by means of two types of molecular fragment: (1) two La(III) cations bound to one PhDC(2-) ligand, and (2) two PhDC(2-) ligands bound to one La(III) cation. Different orientations of PhDC(2-), OH(-) and H(2)O ligands in the La(III) complexes were investigated using 20 possible [La(PhDC(2-))(2)(OH)(H(2)O)](2-) fragments. Energy calculations predicted that the prism-like structure based on "tail-head" cis-LML2 type binding and stabilized via HO...HOH intramolecular hydrogen bonds is the most probable structure for the La(III) complex. The calculated vibrational spectrum of the lowest energy La(III) model fragment is in very good agreement with the experimental IR spectrum of the complex, supporting the suggested ligand binding mode to La(III) in a chain structure, namely, every PhDC(2-) interacts with two La(III) cations through both carbonylic and both hydroxylic oxygens, and every La(III) cation binds four oxygen atoms of two different PhDC(2-).

Weak polyelectrolyte complexation driven by associative charging.

PubMed

Rathee, Vikramjit S; Zervoudakis, Aristotle J; Sidky, Hythem; Sikora, Benjamin J; Whitmer, Jonathan K

2018-03-21

Weak polyelectrolytes are relevant for a wide range of fields; in particular, they have been investigated as "smart" materials for chemical separations and drug delivery. The charges on weak polyelectrolytes are dynamic, causing polymer chains to adopt different equilibrium conformations even with relatively small changes to the surrounding environment. Currently, there exists no comprehensive picture of this behavior, particularly where polymer-polymer interactions have the potential to affect charging properties significantly. In this study, we elucidate the novel interplay between weak polyelectrolyte charging and complexation behavior through coupled molecular dynamics and Monte Carlo simulations. Specifically, we investigate a model of two equal-length and oppositely charging polymer chains in an implicit salt solution represented through Debye-Hückel interactions. The charging tendency of each chain, along with the salt concentration, is varied to determine the existence and extent of cooperativity in charging and complexation. Strong cooperation in the charging of these chains is observed at large Debye lengths, corresponding to low salt concentrations, while at lower Debye lengths (higher salt concentrations), the chains behave in apparent isolation. When the electrostatic coupling is long-ranged, we find that a highly charged chain strongly promotes the charging of its partner chain, even if the environment is unfavorable for an isolated version of that partner chain. Evidence of this phenomenon is supported by a drop in the potential energy of the system, which does not occur at the lower Debye lengths where both potential energies and charge fractions converge for all partner chain charging tendencies. The discovery of this cooperation will be helpful in developing "smart" drug delivery mechanisms by allowing for better predictions for the dissociation point of delivery complexes.

Weak polyelectrolyte complexation driven by associative charging

NASA Astrophysics Data System (ADS)

Rathee, Vikramjit S.; Zervoudakis, Aristotle J.; Sidky, Hythem; Sikora, Benjamin J.; Whitmer, Jonathan K.

2018-03-01

Weak polyelectrolytes are relevant for a wide range of fields; in particular, they have been investigated as "smart" materials for chemical separations and drug delivery. The charges on weak polyelectrolytes are dynamic, causing polymer chains to adopt different equilibrium conformations even with relatively small changes to the surrounding environment. Currently, there exists no comprehensive picture of this behavior, particularly where polymer-polymer interactions have the potential to affect charging properties significantly. In this study, we elucidate the novel interplay between weak polyelectrolyte charging and complexation behavior through coupled molecular dynamics and Monte Carlo simulations. Specifically, we investigate a model of two equal-length and oppositely charging polymer chains in an implicit salt solution represented through Debye-Hückel interactions. The charging tendency of each chain, along with the salt concentration, is varied to determine the existence and extent of cooperativity in charging and complexation. Strong cooperation in the charging of these chains is observed at large Debye lengths, corresponding to low salt concentrations, while at lower Debye lengths (higher salt concentrations), the chains behave in apparent isolation. When the electrostatic coupling is long-ranged, we find that a highly charged chain strongly promotes the charging of its partner chain, even if the environment is unfavorable for an isolated version of that partner chain. Evidence of this phenomenon is supported by a drop in the potential energy of the system, which does not occur at the lower Debye lengths where both potential energies and charge fractions converge for all partner chain charging tendencies. The discovery of this cooperation will be helpful in developing "smart" drug delivery mechanisms by allowing for better predictions for the dissociation point of delivery complexes.

Early-Late Heterobimetallic Complexes Linked by Phosphinoamide Ligands. Tuning Redox Potentials and Small Molecule Activation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thomas, Christine M.

2015-08-01

Recent attention in the chemical community has been focused on the energy efficient and environmentally benign conversion of abundant small molecules (CO2, H2O, etc.) to useful liquid fuels. This project addresses these goals by examining fundamental aspects of catalyst design to ultimately access small molecule activation processes under mild conditions. Specifically, Thomas and coworkers have targetted heterobimetallic complexes that feature metal centers with vastly different electronic properties, dictated both by their respective positions on the periodic table and their coordination environment. Unlike homobimetallic complexes featuring identical or similar metals, the bonds between metals in early/late heterobimetallics are more polarized, withmore » the more electron-rich late metal center donating electron density to the more electron-deficient early metal center. While metal-metal bonds pose an interesting strategy for storing redox equivalents and stabilizing reactive metal fragments, the polar character of metal-metal bonds in heterobimetallic complexes renders these molecules ideally poised to react with small molecule substrates via cleavage of energy-rich single and double bonds. In addition, metal-metal interactions have been shown to dramatically affect redox potentials and promote multielectron redox activity, suggesting that metal-metal interactions may provide a mechanism to tune redox potentials and access substrate reduction/activation at mild overpotentials. This research project has provided a better fundamental understanding of how interactions between transition metals can be used as a strategy to promote and/or control chemical transformations related to the clean production of fuels. While this project focused on the study of homogeneous systems, it is anticipated that the broad conclusions drawn from these investigations will be applicable to heterogeneous catalysis as well, particularly on heterogeneous processes that occur at interfaces in multicomponent systems.« less

Identification of chikungunya virus nsP2 protease inhibitors using structure-base approaches.

PubMed

Nguyen, Phuong T V; Yu, Haibo; Keller, Paul A

2015-04-01

The nsP2 protease of chikungunya virus (CHIKV) is one of the essential components of viral replication and it plays a crucial role in the cleavage of polyprotein precursors for the viral replication process. Therefore, it is gaining attention as a potential drug design target against CHIKV. Based on the recently determined crystal structure of the nsP2 protease of CHIKV, this study identified potential inhibitors of the virus using structure-based approaches with a combination of molecular docking, virtual screening and molecular dynamics (MD) simulations. The top hit compounds from database searching, using the NCI Diversity Set II, with targeting at five potential binding sites of the nsP2 protease, were identified by blind dockings and focused dockings. These complexes were then subjected to MD simulations to investigate the stability and flexibility of the complexes and to gain a more detailed insight into the interactions between the compounds and the enzyme. The hydrogen bonds and hydrophobic contacts were characterized for the complexes. Through structural alignment, the catalytic residues Cys1013 and His1083 were identified in the N-terminal region of the nsP2 protease. The absolute binding free energies were estimated by the linear interaction energy approach and compared with the binding affinities predicted with docking. The results provide valuable information for the development of inhibitors for CHIKV. Crown Copyright © 2015. Published by Elsevier Inc. All rights reserved.

Expert Elicitation Methods in Quantifying the Consequences of Acoustic Disturbance from Offshore Renewable Energy Developments.

PubMed

Donovan, Carl; Harwood, John; King, Stephanie; Booth, Cormac; Caneco, Bruno; Walker, Cameron

2016-01-01

There are many developments for offshore renewable energy around the United Kingdom whose installation typically produces large amounts of far-reaching noise, potentially disturbing many marine mammals. The potential to affect the favorable conservation status of many species means extensive environmental impact assessment requirements for the licensing of such installation activities. Quantification of such complex risk problems is difficult and much of the key information is not readily available. Expert elicitation methods can be employed in such pressing cases. We describe the methodology used in an expert elicitation study conducted in the United Kingdom for combining expert opinions based on statistical distributions and copula-like methods.

Condensate oscillations in a Penrose tiling lattice

NASA Astrophysics Data System (ADS)

Akdeniz, Z.; Vignolo, P.

2017-07-01

We study the dynamics of a Bose-Einstein condensate subject to a particular Penrose tiling lattice. In such a lattice, the potential energy at each site depends on the neighbour sites, accordingly to the model introduced by Sutherland [16]. The Bose-Einstein wavepacket, initially at rest at the lattice symmetry center, is released. We observe a very complex time-evolution that strongly depends on the symmetry center (two choices are possible), on the potential energy landscape dispersion, and on the interaction strength. The condensate-width oscillates at different frequencies and we can identify large-frequency reshaping oscillations and low-frequency rescaling oscillations. We discuss in which conditions these oscillations are spatially bounded, denoting a self-trapping dynamics.

Internal gravity, self-energy, and disruption of comets and asteroids

NASA Astrophysics Data System (ADS)

Dobrovolskis, Anthony R.; Korycansky, D. G.

2018-03-01

The internal gravity and self-gravitational energy of a comet, asteroid, or small moon have applications to their geophysics, including their formation, evolution, cratering, and disruption, the stresses and strains inside such objects, sample return, eventual asteroid mining, and planetary defense strategies for potentially hazardous objects. This paper describes the relation of an object's self-energy to its collisional disruption energy, and shows how to determine an object's self-energy from its internal gravitational potential. Any solid object can be approximated to any desired accuracy by a polyhedron of sufficient complexity. An analytic formula is known for the gravitational potential of any homogeneous polyhedron, but it is widely believed that this formula applies only on the surface or outside of the object. Here we show instead that this formula applies equally well inside the object. We have used these formulae to develop a numerical code which evaluates the self-energy of any homogeneous polyhedron, along with the gravitational potential and attraction both inside and outside of the object, as well as the slope of its surface. Then we use our code to find the internal, external, and surface gravitational fields of the Platonic solids, asteroid (216) Kleopatra, and comet 67P/Churyumov-Gerasimenko, as well as their surface slopes and their self-gravitational energies. We also present simple spherical, ellipsoidal, cuboidal, and duplex models of Kleopatra and comet 67P, and show how to generalize our methods to inhomogeneous objects and magnetic fields. At present, only the self-energies of spheres, ellipsoids, and cuboids (boxes) are known analytically (or semi-analytically). The Supplementary Material contours the central potential and self-energy of homogeneous ellipsoids and cuboids of all aspect ratios, and also analytically the self-gravitational energy of a "duplex" consisting of two coupled spheres. The duplex is a good model for "contact binary" comets and asteroids; in fact, most comets seem to be bilobate, and might be described better as "dirty snowmen" than as "dirty snowballs".

Design of specially adapted reactive coordinates to economically compute potential and kinetic energy operators including geometry relaxation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thallmair, Sebastian; Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians-Universität München, D-80538 München; Roos, Matthias K.

Quantum dynamics simulations require prior knowledge of the potential energy surface as well as the kinetic energy operator. Typically, they are evaluated in a low-dimensional subspace of the full configuration space of the molecule as its dimensionality increases proportional to the number of atoms. This entails the challenge to find the most suitable subspace. We present an approach to design specially adapted reactive coordinates spanning this subspace. In addition to the essential geometric changes, these coordinates take into account the relaxation of the non-reactive coordinates without the necessity of performing geometry optimizations at each grid point. The method is demonstratedmore » for an ultrafast photoinduced bond cleavage in a commonly used organic precursor for the generation of electrophiles. The potential energy surfaces for the reaction as well as the Wilson G-matrix as part of the kinetic energy operator are shown for a complex chemical reaction, both including the relaxation of the non-reactive coordinates on equal footing. A microscopic interpretation of the shape of the G-matrix elements allows to analyze the impact of the non-reactive coordinates on the kinetic energy operator. Additionally, we compare quantum dynamics simulations with and without the relaxation of the non-reactive coordinates included in the kinetic energy operator to demonstrate its influence.« less

Double proton transfer behavior and one-electron oxidation effect in double H-bonded glycinamide-formic acid complex.

PubMed

Li, Ping; Bu, Yuxiang

2004-11-22

The behavior of double proton transfer occurring in a representative glycinamide-formic acid complex has been investigated at the B3LYP/6-311 + + G( * *) level of theory. Thermodynamic and, especially, kinetic parameters, such as tautomeric energy, equilibrium constant, and barrier heights have been discussed, respectively. The relevant quantities involved in the double proton transfer process, such as geometrical changes, interaction energies, and intrinsic reaction coordinate calculations have also been studied. Computational results show that the participation of a formic acid molecule favors the proceeding of the proton transfer for glycinamide compared with that without mediate-assisted case. The double proton transfer process proceeds with a concerted mechanism rather than a stepwise one since no ion-pair complexes have been located during the proton transfer process. The calculated barrier heights are 11.48 and 0.85 kcal/mol for the forward and reverse directions, respectively. However, both of them have been reduced by 2.95 and 2.61 kcal/mol to 8.53 and -1.76 kcal/mol if further inclusion of zero-point vibrational energy corrections, where the negative barrier height implies that the reverse reaction should proceed with barrierless spontaneously, analogous to that occurring between glycinamide and formamide. Furthermore, solvent effects on the thermodynamic and kinetic processes have also been predicted qualitatively employing the isodensity surface polarized continuum model within the framework of the self-consistent reaction field theory. Additionally, the oxidation process for the double H-bonded glycinamide-formic acid complex has also been investigated. Contrary to that neutral form possessing a pair of two parallel intermolecular H bonds, only a single H bond with a comparable strength has been found in its ionized form. The vertical and adiabatic ionization potentials for the neutral complex have been determined to be about 9.40 and 8.69 eV, respectively, where ionization is mainly localized on the glycinamide fragment. Like that ionized glycinamide-formamide complex, the proton transfer in the ionized complex is characterized by a single-well potential, implying that the proton initially attached to amide N4 in the glycinamide fragment cannot be transferred to carbonyl O13 in the formic acid fragment at the geometry of the optimized complex. Copyright 2004 American Institute of Physics.

Energy Efficiency in Public Buildings through Context-Aware Social Computing.

PubMed

García, Óscar; Alonso, Ricardo S; Prieto, Javier; Corchado, Juan M

2017-04-11

The challenge of promoting behavioral changes in users that leads to energy savings in public buildings has become a complex task requiring the involvement of multiple technologies. Wireless sensor networks have a great potential for the development of tools, such as serious games, that encourage acquiring good energy and healthy habits among users in the workplace. This paper presents the development of a serious game using CAFCLA, a framework that allows for integrating multiple technologies, which provide both context-awareness and social computing. Game development has shown that the data provided by sensor networks encourage users to reduce energy consumption in their workplace and that social interactions and competitiveness allow for accelerating the achievement of good results and behavioral changes that favor energy savings.

High-dimensional fitting of sparse datasets of CCSD(T) electronic energies and MP2 dipole moments, illustrated for the formic acid dimer and its complex IR spectrum

NASA Astrophysics Data System (ADS)

Qu, Chen; Bowman, Joel M.

2018-06-01

We present high-level, coupled-mode calculations of the infrared spectrum of the cyclic formic acid dimer. The calculations make use of full-dimensional, ab initio potential energy and dipole moment surfaces. The potential is a linear least-squares fit to 13 475 CCSD(T)-F12a/haTZ (haTZ means aug-cc-pVTZ basis set for O and C, and cc-pVTZ for H) energies, and the dipole moment surface is a fit to the dipole components, calculated at the MP2/haTZ level of theory. The variables of both fits are all (45) internuclear distances (actually Morse variables). The potential, which is fully permutationally invariant, is the one published recently and the dipole moment surface is newly reported here. Details of the fits, especially the dipole moment, and the database of configurations are given. The infrared spectrum of the dimer is calculated by solving the nuclear Schrödinger equation using a vibrational self-consistent field and virtual-state configuration interaction method, with subsets of the 24 normal modes, up to 15 modes. The calculations indicate strong mode-coupling in the C—H and O—H stretching region of the spectrum. Comparisons are made with experiments and the complexity of the experimental spectrum in the C—H and O—H stretching region is successfully reproduced.

Dark spectroscopy at lepton colliders

NASA Astrophysics Data System (ADS)

Hochberg, Yonit; Kuflik, Eric; Murayama, Hitoshi

2018-03-01

Rich and complex dark sectors are abundant in particle physics theories. Here, we propose performing spectroscopy of the mass structure of dark sectors via mono-photon searches at lepton colliders. The energy of the mono-photon tracks the invariant mass of the invisible system it recoils against, which enables studying the resonance structure of the dark sector. We demonstrate this idea with several well-motivated models of dark sectors. Such spectroscopy measurements could potentially be performed at Belle II, BES-III and future low-energy lepton colliders.

Infrared Stark and Zeeman spectroscopy of OH–CO: The entrance channel complex along the OH + CO → trans-HOCO reaction pathway

DOE PAGES

Brice, Joseph T.; Liang, Tao; Raston, Paul L.; ...

2016-09-27

Here, sequential capture of OH and CO by superfluid helium droplets leads exclusively to the formation of the linear, entrance-channel complex, OH-CO. This species is characterized by infrared laser Stark and Zeeman spectroscopy via measurements of the fundamental OH stretching vibration. Experimental dipole moments are in disagreement with ab initio calculations at the equilibrium geometry, indicating large-amplitude motion on the ground state potential energy surface. Vibrational averaging along the hydroxyl bending coordinate recovers 80% of the observed deviation from the equilibrium dipole moment. Inhomogeneous line broadening in the zero-field spectrum is modeled with an effective Hamiltonian approach that aims tomore » account for the anisotropic molecule-helium interaction potential that arises as the OH-CO complex is displaced from the center of the droplet.« less

Metaphors to Drive By: Exploring New Ways to Guide Human-Robot Interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

David J. Bruemmer; David I. Gertman; Curtis W. Nielsen

2007-08-01

Autonomous behaviors created by the research and development community are not being extensively utilized within energy, defense, security, or industrial contexts. This paper provides evidence that the interaction methods used alongside these behaviors may not provide a mental model that can be easily adopted or used by operators. Although autonomy has the potential to reduce overall workload, the use of robot behaviors often increased the complexity of the underlying interaction metaphor. This paper reports our development of new metaphors that support increased robot complexity without passing the complexity of the interaction onto the operator. Furthermore, we illustrate how recognition ofmore » problems in human-robot interactions can drive the creation of new metaphors for design and how human factors lessons in usability, human performance, and our social contract with technology have the potential for enormous payoff in terms of establishing effective, user-friendly robot systems when appropriate metaphors are used.« less

Theory of slightly fluctuating ratchets

NASA Astrophysics Data System (ADS)

Rozenbaum, V. M.; Shapochkina, I. V.; Lin, S. H.; Trakhtenberg, L. I.

2017-04-01

We consider a Brownian particle moving in a slightly fluctuating potential. Using the perturbation theory on small potential fluctuations, we derive a general analytical expression for the average particle velocity valid for both flashing and rocking ratchets with arbitrary, stochastic or deterministic, time dependence of potential energy fluctuations. The result is determined by the Green's function for diffusion in the time-independent part of the potential and by the features of correlations in the fluctuating part of the potential. The generality of the result allows describing complex ratchet systems with competing characteristic times; these systems are exemplified by the model of a Brownian photomotor with relaxation processes of finite duration.

Understanding self-assembly of charged-neutral block copolymer (BCP) and surfactant complexes using molecular dynamics (MD) simulation

NASA Astrophysics Data System (ADS)

Goswami, Monojoy; Sumpter, Bobby; Kilbey, Michael

Here we report the formation of phase separated BCP-surfactant complexes resulting from the electrostatic self-assembly of charge-neutral block copolymers with oppositely charged surfactants. Complexation behaviors of oppositely charged polyelectrolytes has gained considerable attention in the field of soft condensed matter physics due to their potential application as functional nanomaterials for batteries, wastewater treatment and drug delivery systems. Numerous experiments have examined the self-assembled structures resulting from complexation of charge-neutral BCP and surfactants, however, there is a lack of comprehensive understanding at the fundamental level. To help bridge this gap, we use, MD simulations to study self-assembly and dynamics of the BCP-surfactant complex at the molecular level. Our results show an overcharging effect in BCPs with hydrophobic neutral blocks and a formation of core-shell colloidal structure. Hydrophilic neutral blocks, on the other hand, show stable, hairy colloidal structures with neutral blocks forming a loosely-bound, fuzzy outer layer. Our results qualitatively agree with previous SANS and SAXS experiments. This work was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Materials Science and Engineering Division.

Absorption spectrometric and thermodynamic study of charge transfer complexes of menadione (Vitamin K 3) with a series of phenols

NASA Astrophysics Data System (ADS)

Pal, Purnendu; Bhattacharya, Sumanta; Mukherjee, Asok K.; Mukherjee, Dulal C.

2005-03-01

The electron donor-acceptor (EDA) interactions between menadione (i.e., 2-methyl-1,4-naphthoquinone, which is also called 'Vitamin K 3') and a series of phenols (viz., phenol, resorcinol and p-quinol) have been studied in CCl 4 medium. In all the cases, charge transfer (CT) bands have been located. The CT transition energies ( hνCT) of the complexes are found to change systematically with change in the number and position of the -OH groups in the aromatic ring of the phenol moiety. From the trends in the hνCT values, the Hückel parameters ( hÖ and kC-Ö) for the -OH group have been obtained. The CT transition energies are well correlated with the ionisation potentials of the phenols. From an analysis of this variation the electron affinity of Vitamin K 3 has been found to be 2.28 eV. The stoichiometry of the complexes in each case has been found to be 1(menadione):2 (phenol). Formation constants of the complexes have been determined at four different temperatures from which the enthalpies and entropies of formation of the complexes have been estimated.

Absorption spectrometric and thermodynamic study of charge transfer complexes of menadione (Vitamin K3) with a series of phenols.

PubMed

Pal, Purnendu; Bhattacharya, Sumanta; Mukherjee, Asok K; Mukherjee, Dulal C

2005-03-01

The electron donor-acceptor (EDA) interactions between menadione (i.e., 2-methyl-1,4-naphthoquinone, which is also called 'Vitamin K3') and a series of phenols (viz., phenol, resorcinol and p-quinol) have been studied in CCl4 medium. In all the cases, charge transfer (CT) bands have been located. The CT transition energies (h nu(CT)) of the complexes are found to change systematically with change in the number and position of the -OH groups in the aromatic ring of the phenol moiety. From the trends in the h nu(CT) values, the Hückel parameters (h(O) and k(C-O)) for the -OH group have been obtained. The CT transition energies are well correlated with the ionisation potentials of the phenols. From an analysis of this variation the electron affinity of Vitamin K3 has been found to be 2.28 eV. The stoichiometry of the complexes in each case has been found to be 1(menadione):2 (phenol). Formation constants of the complexes have been determined at four different temperatures from which the enthalpies and entropies of formation of the complexes have been estimated.

Theoretical study of mixed LiLnX4 (Ln = La, Dy; X = F, Cl, Br, I) rare earth/alkali halide complexes.

PubMed

Groen, C P; Oskam, A; Kovács, A

2000-12-25

The structure, bonding and vibrational properties of the mixed LiLnX4 (Ln = La, Dy; X = F, Cl, Br, I) rare earth/alkali halide complexes were studied using various quantum chemical methods (HF, MP2 and the Becke3-Lee-Yang-Parr exchange-correlation density functional) in conjunction with polarized triple-zeta valence basis sets and quasi-relativistic effective core potentials for the heavy atoms. Our comparative study indicated the superiority of MP2 theory while the HF and B3-LYP methods as well as less sophisticated basis sets failed for the correct energetic relations. In particular, f polarization functions on Li and X proved to be important for the Li...X interaction in the complexes. From the three characteristic structures of such complexes, possessing 1-(C3v), 2-(C2v), or 3-fold coordination (C3v) between the alkali metal and the bridging halide atoms, the bi- and tridentate forms are located considerably lower on the potential energy surface then the monodentate isomer. Therefore only the bi- and tridentate isomers have chemical relevance. The monodentate isomer is only a high-lying local minimum in the case of X = F. For X = Cl, Br, and I this structure is found to be a second-order saddle point. The bidentate structure was found to be the global minimum for the systems with X = F, Cl, and Br. However, the relative stability with respect to the tridentate structure is very small (1-5 kJ/mol) for the heavier halide derivatives and the relative order is reversed in the case of the iodides. The energy difference between the three structures and the dissociation energy decrease in the row F to I. The ionic bonding in the complexes was characterized by natural charges and a topological analysis of the electron density distribution according to Bader's theorem. Variation of the geometrical and bonding characteristics between the lanthanum and dysprosium complexes reflects the effect of "lanthanide contraction". The calculated vibrational data indicate that infrared spectroscopy may be an effective tool for experimental investigation and characterization of LiLnX4 molecules.

The solution of the optimization problem of small energy complexes using linear programming methods

NASA Astrophysics Data System (ADS)

Ivanin, O. A.; Director, L. B.

2016-11-01

Linear programming methods were used for solving the optimization problem of schemes and operation modes of distributed generation energy complexes. Applicability conditions of simplex method, applied to energy complexes, including installations of renewable energy (solar, wind), diesel-generators and energy storage, considered. The analysis of decomposition algorithms for various schemes of energy complexes was made. The results of optimization calculations for energy complexes, operated autonomously and as a part of distribution grid, are presented.

Anti-tumor activity and mechanism of apoptosis of A549 induced by ruthenium complex.

PubMed

Sun, Dongdong; Mou, Zhipeng; Li, Nuan; Zhang, Weiwei; Wang, Yazhe; Yang, Endong; Wang, Weiyun

2016-12-01

Two new ruthenium (II) polypyridyl complexes [Ru(MeIm) 4 (pip)] 2+ (1) and [Ru(MeIm) 4 (4-npip)] 2+ (2) were synthesized under the guidance of computational studies (DFT). Their binding property to human telomeric G-quadruplex studied by UV-Vis absorption spectroscopy, the fluorescent resonance energy transfer (FRET) melting assay and circular dichroism (CD) spectroscopy for validating the theoretical prediction. Both of them were evaluated for their potential anti-proliferative activity against four human tumor cell lines. Complex 2 shows growth inhibition against all the cell lines tested, especially the human lung tumor cell (A549). The RTCA analysis not only validated the inhibition activity but also showed the ability of reducing A549 cells' migration. DNA-flow cytometric analysis, mitochondrial membrane potential (ΔΨm) and the scavenger measurements of reactive oxygen species (ROS) analysis carried out to investigate the mechanism of cell growth inhibition and apoptosis-inducing effect of complex 2. The results demonstrated that complex 2 induces tumor cells apoptosis by acting on both mitochondrial homeostasis destruction and death receptor signaling pathways. And those suggested that complex 2 could be a candidate for further evaluation as a chemotherapeutic agent against human tumor.

A Study of Energy Partitioning Using A Set of Related Explosive Formulations

NASA Astrophysics Data System (ADS)

Lieber, Mark; Foster, Joseph C., Jr.; Stewart, D. Scott

2011-06-01

Condensed phase high explosives convert potential energy stored in the electro-magnetic field structure of complex molecules to kinetic energy during the detonation process. This energy is manifest in the internal thermodynamic energy and the translational flow of the products. Historically, the explosive design problem has focused on intramolecular stoichiometry providing prompt reactions based on transport physics at the molecular scale. Modern material design has evolved to approaches that employee intermolecular ingredients to alter the spatial and temporal distribution of energy release. CHEETA has been used to produce data for a set of fictitious explosive formulations based on C-4 to study the partitioning of the available energy between internal and flow energy in the detonation. The equation of state information from CHEETA has been used in ALE3D to develop an understanding of the relationship between variations in the formulation parameters and the internal energy cycle in the products.

Complexation of C60 fullerene with aromatic drugs.

PubMed

Evstigneev, Maxim P; Buchelnikov, Anatoly S; Voronin, Dmitry P; Rubin, Yuriy V; Belous, Leonid F; Prylutskyy, Yuriy I; Ritter, Uwe

2013-02-25

The contributions of various physical factors to the energetics of complexation of aromatic drug molecules with C(60) fullerene are investigated in terms of the calculated magnitudes of equilibrium complexation constants and the components of the net Gibbs free energy. Models of complexation are developed taking into account the polydisperse nature of fullerene solutions in terms of the continuous or discrete (fractal) aggregation of C(60) molecules. Analysis of the energetics has shown that stabilization of the ligand-fullerene complexes in aqueous solution is mainly determined by intermolecular van der Waals interactions and, to lesser extent, by hydrophobic interactions. The results provide a physicochemical basis for a potentially new biotechnological application of fullerenes as modulators of biological activity of aromatic drugs. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interpreting Vibrational Sum-frequency Spectra of Sulfur Dioxide at the Air/Water Interface: A Comprehensive Molecular Dynamics Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baer, Marcel; Mundy, Christopher J.; Chang, Tsun-Mei

We investigated the solvation and spectroscopic properties of SO2 at the air/water interface using molecular simulation techniques. Molecular interactions from both Kohn-Sham (KS) density functional theory (DFT) and classical polarizable models were utilized to understand the properties of SO2:(H2O)x complexes in the vicinity of the air/water interface. The KS-DFT was included to allow comparisons with sum-frequency generation spectroscopy through the identification of surface SO2:(H2O)x complexes. Using our simulation results, we were able to develop a much more detailed picture for the surface structure of SO2 that is consistent with the spectroscopic data obtained Richmond and coworkers (J. Am. Chem. Soc.more » 127, 16806 (2005)). We also found many similarities and differences between to the two interaction potentials, including a noticeable weakness of the classical potential model in reproducing the asymmetric hydrogen bonding of water with SO2 due to its inability to account for SO2 resonance structures. This work was supported by the US Department of Energy Basic Energy Sciences' Chemical Sciences, Geosciences & Biosciences Division. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.« less

SiO2 nanoparticle-induced impairment of mitochondrial energy metabolism in hepatocytes directly and through a Kupffer cell-mediated pathway in vitro

PubMed Central

Xue, Yang; Chen, Qingqing; Ding, Tingting; Sun, Jiao

2014-01-01

The liver has been shown to be a primary target organ for SiO2 nanoparticles in vivo, and may be highly susceptible to damage by these nanoparticles. However, until now, research focusing on the potential toxic effects of SiO2 nanoparticles on mitochondria-associated energy metabolism in hepatocytes has been lacking. In this work, SiO2 nanoparticles 20 nm in diameter were evaluated for their ability to induce dysfunction of mitochondrial energy metabolism. First, a buffalo rat liver (BRL) cell line was directly exposed to SiO2 nanoparticles, which induced cytotoxicity and mitochondrial damage accompanied by decreases in mitochondrial dehydrogenase activity, mitochondrial membrane potential, enzymatic expression in the Krebs cycle, and activity of the mitochondrial respiratory chain complexes I, III and IV. Second, the role of rat-derived Kupffer cells was evaluated. The supernatants from Kupffer cells treated with SiO2 nanoparticles were transferred to stimulate BRL cells. We observed that SiO2 nanoparticles had the ability to activate Kupffer cells, leading to release of tumor necrosis factor-α, nitric oxide, and reactive oxygen species from these cells and subsequently to inhibition of mitochondrial respiratory chain complex I activity in BRL cells. PMID:24959077

Graphane versus graphene: a computational investigation of the interaction of nucleobases, aminoacids, heterocycles, small molecules (CO2, H2O, NH3, CH4, H2), metal ions and onium ions.

PubMed

Umadevi, Deivasigamani; Narahari Sastry, G

2015-11-11

Graphane has emerged as a two-dimensional hydrocarbon with interesting physical properties and potential applications. Understanding the interaction of graphane with various molecules and ions is crucial to appreciate its potential applications. We investigated the interaction of nucleobases, aminoacids, saturated and unsaturated heterocycles, small molecules, metal ions and onium ions with graphane by using density functional theory calculations. The preferred orientations of these molecules and ions on the graphane surface have been analysed. The binding energies of graphane with these molecules have been compared with the corresponding binding energies of graphene. Our results reveal that graphane forms stable complexes with all the molecules and ions yet showing lesser binding affinity when compared to graphene. As an exemption, the preferential strong binding of H2O with graphane than graphene reveals the fact that graphane is more hydrophilic than graphene. Charge transfer between graphane and the molecules and ions have been found to be an important factor in determining the binding strength of the complexes. The effect of the interaction of these molecules and ions on the HOMO-LUMO energy gap of graphane has also been investigated.

Medium Effects are as Important as Catalyst Design for Selectivity in Electrocatalytic Oxygen Reduction by Iron-porphyrin Complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rigsby, Matthew L.; Wasylenko, Derek J.; Pegis, Michael L.

2015-04-08

Several substituted iron porphyrin com-plexes were evaluated for oxygen reduction reaction (ORR) electrocatalysis in different homogeneous and heterogeneous media. The selectivity for 4-electron re-duction to H2O vs. 2-electron reduction to H2O2 varies substantially from one medium to another for a given catalyst. In many cases, the influence of the medium in which the catalyst is evaluated has a larger effect on the observed selectivity than the factors attributable to chemical modification of the catalyst. For instance, introduction of potential proton relays has variable effects depending on the catalyst medium. Thus, comparisons of ORR selectivity results need to be interpreted withmore » caution, as the catalysis is a property not just of the catalyst, but also of the larger mesoscale environment be-yond the catalyst. Still, in all the direct pairwise comparisons in the same medium, the catalysts with potential proton relays have similar or better selectivity for the preferred 4e– path. This work was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences.« less

Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials.

PubMed

Boereboom, Jelle M; Potestio, Raffaello; Donadio, Davide; Bulo, Rosa E

2016-08-09

Adaptive quantum mechanical (QM)/molecular mechanical (MM) methods enable efficient molecular simulations of chemistry in solution. Reactive subregions are modeled with an accurate QM potential energy expression while the rest of the system is described in a more approximate manner (MM). As solvent molecules diffuse in and out of the reactive region, they are gradually included into (and excluded from) the QM expression. It would be desirable to model such a system with a single adaptive Hamiltonian, but thus far this has resulted in distorted structures at the boundary between the two regions. Solving this long outstanding problem will allow microcanonical adaptive QM/MM simulations that can be used to obtain vibrational spectra and dynamical properties. The difficulty lies in the complex QM potential energy expression, with a many-body expansion that contains higher order terms. Here, we outline a Hamiltonian adaptive multiscale scheme within the framework of many-body potentials. The adaptive expressions are entirely general, and complementary to all standard (nonadaptive) QM/MM embedding schemes available. We demonstrate the merit of our approach on a molecular system defined by two different MM potentials (MM/MM'). For the long-range interactions a numerical scheme is used (particle mesh Ewald), which yields energy expressions that are many-body in nature. Our Hamiltonian approach is the first to provide both energy conservation and the correct solvent structure everywhere in this system.

Design of State-of-the-art Flow Cells for Energy Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Ping

The worldwide energy demand is increasing every day and it necessitates rational and efficient usage of renewable energy. Undoubtedly, utilization of renewable energy can address various environmental challenges. However, all current renewable energy resources (wind, solar, and hydroelectric power) are intermittent and fluctuating in their nature that raises an important question of introducing effective energy storage solutions. Utilization of redox flow cells (RFCs) has recently been recognized as a viable technology for large-scale energy storage and, hence, is well suited for integrating renewable energy and balancing electricity grids. In brief, RFC is an electrochemical storage device where energy is storedmore » in chemical bonds, similar to a battery, but with reactants external to the cell. The state-of-the-art in flow cell technology uses an aqueous acidic electrolyte and simple metal redox couples. Thus, there is an urgent call to develop efficient (high-energy density) and low-cost RFCs to meet the efflorescent energy storage demands. To address the first challenge of achieving high-energy density, we plan to design and further modify complexes composed of bifunctional multidentate ligands and specific metal centers, capable of storing as many electrons as possible. In order to address the second challenge of reducing cost of the RFCs, we plan to use iron (Fe) metal as it regularly occupies multiple oxidation states and is the second most abundant metal in the earth’s crust that makes it an ideal metal for improved energy densities, higher potentials, and numbers of electrons per molecule while maintaining potential cost competitiveness. Density functional theory calculations considering solvation effects will be performed to yield accurate predictions of redox potentials.« less

Colonisation of fish and crabs of wave energy foundations and the effects of manufactured holes - a field experiment.

PubMed

Langhamer, Olivia; Wilhelmsson, Dan

2009-10-01

Several Western European countries are planning for a significant development of offshore renewable energy along the European Atlantic Ocean coast, including many thousands of wave energy devices and wind turbines. There is an increasing interest in articulating the added values of the creation of artificial hard bottom habitats through the construction of offshore renewable energy devices, for the benefit of fisheries management and conservation. The Lysekil Project is a test park for wave power located about 100 km north of Gothenburg at the Swedish west coast. A wave energy device consists of a linear wave power generator attached to a foundation on the seabed, and connected by a wire to a buoy at the surface. Our field experiment examined the function of wave energy foundations as artificial reefs. In addition, potentials for enhancing the abundance of associated fish and crustaceans through manufactured holes of the foundations were also investigated. Assemblages of mobile organisms were examined by visual censuses in July and August 2007, 3 months after deployment of the foundations. Results generally show low densities of mobile organisms, but a significantly higher abundance of fish and crabs on the foundations compared to surrounding soft bottoms. Further, while fish numbers were not influenced by increased habitat complexity (holes), it had a significantly positive effect on quantities of edible crab (Cancer pagurus), on average leading to an almost five-fold increase in densities of this species. Densities of spiny starfish (Marthasterias glacialis) were negatively affected by the presence of holes, potentially due to increased predator abundance (e.g. C. pagurus). These results suggest a species-specific response to enhanced habitat complexity.

Precise determination of lattice phase shifts and mixing angles

DOE PAGES

Lu, Bing -Nan; Lähde, Timo A.; Lee, Dean; ...

2016-07-09

Here, we introduce a general and accurate method for determining lattice phase shifts and mixing angles, which is applicable to arbitrary, non-cubic lattices. Our method combines angular momentum projection, spherical wall boundaries and an adjustable auxiliary potential. This allows us to construct radial lattice wave functions and to determine phase shifts at arbitrary energies. For coupled partial waves, we use a complex-valued auxiliary potential that breaks time-reversal invariance. We benchmark our method using a system of two spin-1/2 particles interacting through a finite-range potential with a strong tensor component. We are able to extract phase shifts and mixing angles formore » all angular momenta and energies, with precision greater than that of extant methods. We discuss a wide range of applications from nuclear lattice simulations to optical lattice experiments.« less

Nickel-based anodic electrocatalysts for fuel cells and water splitting

NASA Astrophysics Data System (ADS)

Chen, Dayi

Our world is facing an energy crisis, so people are trying to harvest and utilize energy more efficiently. One of the promising ways to harvest energy is via solar water splitting to convert solar energy to chemical energy stored in hydrogen. Another of the options to utilize energy more efficiently is to use fuel cells as power sources instead of combustion engines. Catalysts are needed to reduce the energy barriers of the reactions happening at the electrode surfaces of the water-splitting cells and fuel cells. Nickel-based catalysts happen to be important nonprecious electrocatalysts for both of the anodic reactions in alkaline media. In alcohol fuel cells, nickel-based catalysts catalyze alcohol oxidation. In water splitting cells, they catalyze water oxidation, i.e., oxygen evolution. The two reactions occur in a similar potential range when catalyzed by nickel-based catalysts. Higher output current density, lower oxidation potential, and complete substrate oxidation are preferred for the anode in the applications. In this dissertation, the catalytic properties of nickel-based electrocatalysts in alkaline medium for fuel oxidation and oxygen evolution are explored. By changing the nickel precursor solubility, nickel complex nanoparticles with tunable sizes on electrode surfaces were synthesized. Higher methanol oxidation current density is achieved with smaller nickel complex nanoparticles. DNA aggregates were used as a polymer scaffold to load nickel ion centers and thus can oxidize methanol completely at a potential about 0.1 V lower than simple nickel electrodes, and the methanol oxidation pathway is changed. Nickel-based catalysts also have electrocatalytic activity towards a wide range of substrates. Experiments show that methanol, ethanol, glycerol and glucose can be deeply oxidized and carbon-carbon bonds can be broken during the oxidation. However, when comparing methanol oxidation reaction to oxygen evolution reaction catalyzed by current nickel-based catalysts, methanol oxidation suffers from high overpotential and catalyst poisoning by high concentration of substrates, so current nickel-based catalysts are more suitable to be used as oxygen evolution catalysts. A photoanode design that applies nickel oxides to a semiconductor that is incorporated with surface-plasmonic metal electrodes to do solar water oxidation with visible light is proposed.

Dependence of hydropower energy generation on forests in the Amazon Basin at local and regional scales.

PubMed

Stickler, Claudia M; Coe, Michael T; Costa, Marcos H; Nepstad, Daniel C; McGrath, David G; Dias, Livia C P; Rodrigues, Hermann O; Soares-Filho, Britaldo S

2013-06-04

Tropical rainforest regions have large hydropower generation potential that figures prominently in many nations' energy growth strategies. Feasibility studies of hydropower plants typically ignore the effect of future deforestation or assume that deforestation will have a positive effect on river discharge and energy generation resulting from declines in evapotranspiration (ET) associated with forest conversion. Forest loss can also reduce river discharge, however, by inhibiting rainfall. We used land use, hydrological, and climate models to examine the local "direct" effects (through changes in ET within the watershed) and the potential regional "indirect" effects (through changes in rainfall) of deforestation on river discharge and energy generation potential for the Belo Monte energy complex, one of the world's largest hydropower plants that is currently under construction on the Xingu River in the eastern Amazon. In the absence of indirect effects of deforestation, simulated deforestation of 20% and 40% within the Xingu River basin increased discharge by 4-8% and 10-12%, with similar increases in energy generation. When indirect effects were considered, deforestation of the Amazon region inhibited rainfall within the Xingu Basin, counterbalancing declines in ET and decreasing discharge by 6-36%. Under business-as-usual projections of forest loss for 2050 (40%), simulated power generation declined to only 25% of maximum plant output and 60% of the industry's own projections. Like other energy sources, hydropower plants present large social and environmental costs. Their reliability as energy sources, however, must take into account their dependence on forests.

Role of halogen and hydrogen bonds for stabilization of antithyroid drugs with hypohalous acids (HOX, X = I, Br, and Cl) adducts

NASA Astrophysics Data System (ADS)

El-Sheshtawy, Hamdy S.; El-Mehasseb, Ibrahim

2017-11-01

The mechanism for the inhibition of thyroid hormones by the thioamide-like antithyroid drug is a key process in the thyroid gland function. Therefore, in this study theoretical investigation of the molecular interaction between two antithyroid drugs, namely methimazol (MMI) and thiazoline-2-thione (T2T), with the hypohalous acids (HOX, X = I, Br, and Cl), which act as heme-linked halogenated species to tyrosine residue was discussed. The calculations were performed by M06-2X and MP2 using aug-cc-pVDZ level of theory. In addition, wB97xd/6-31G* level of theory was used in order to account for the dispersion forces. The results show the possible formation of three adducts, which is stabilized by halogen bond (I), both halogen and hydrogen bonds (II), two hydrogen bonds (III). The binding energies of the complexes reveals stabilization in the order III > II > I. The binding energies of the complexes was increased with increasing the electron affinity and polarizability of halogen atom, the dipole moment of the complexes (I and II), the electrostatic potential on halogen atom (Vmax:i.e σ-hole), and the charge-transfer process through the halogen bond in I. On the other hand, the binding energies of the complexes decreased with increasing the halogen atom electronegativity and the dipole moment of complex III. Natural bond orbital (NBO) analysis was used to investigate the molecular orbital interactions and the charge transfer process upon complexation.

Highly accurate potential energy surface for the He-H2 dimer

NASA Astrophysics Data System (ADS)

Bakr, Brandon W.; Smith, Daniel G. A.; Patkowski, Konrad

2013-10-01

A new highly accurate interaction potential is constructed for the He-H2 van der Waals complex. This potential is fitted to 1900 ab initio energies computed at the very large-basis coupled-cluster level and augmented by corrections for higher-order excitations (up to full configuration interaction level) and the diagonal Born-Oppenheimer correction. At the vibrationally averaged H-H bond length of 1.448736 bohrs, the well depth of our potential, 15.870 ± 0.065 K, is nearly 1 K larger than the most accurate previous studies have indicated. In addition to constructing our own three-dimensional potential in the van der Waals region, we present a reparameterization of the Boothroyd-Martin-Peterson potential surface [A. I. Boothroyd, P. G. Martin, and M. R. Peterson, J. Chem. Phys. 119, 3187 (2003)] that is suitable for all configurations of the triatomic system. Finally, we use the newly developed potentials to compute the properties of the lone bound states of 4He-H2 and 3He-H2 and the interaction second virial coefficient of the hydrogen-helium mixture.

Need for Systematic Retrofit Analysis in Multifamily Buildings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Malhotra, Mini; Im, Piljae

2014-01-01

Multifamily housing offers high potential for energy savings through retrofits. A comprehensive energy audit with systematic evaluation of alternative energy measures is one of the key steps to realizing the full energy savings potential. However, this potential often remains unrealized when the selection of measures is (1) based on a one-size-fits-all approach originating from accustomed practices, (2) intended merely to meet code-compliance requirements, and/or (3) influenced by owner renter split incentive. In such cases, the benefits of comprehensive energy auditing are disregarded in view of the apparent difficulty in diagnosing multifamily buildings, evaluating alternative measures, and installing customized sets ofmore » measures. This paper highlights some of the barriers encountered in a multifamily housing retrofit project in Georgia and demonstrates the merits of systematic retrofit analysis by identifying opportunities for higher energy savings and improved comfort and indoor air quality that were missed in this project. The study uses a whole-building energy analysis conducted for a 10-unit, low-rise, multifamily building of a 110-unit apartment complex. The analysis projected a 24% energy savings from the measures installed in the building with a payback period of 10 years. Further analysis with a systematic evaluation of alternative measures showed that without compromising on the objectives of durability, livability, and appearance of the building, energy savings of up to 34% were achievable with a payback period of 7 years. The paper concludes by outlining recommendations that may benefit future retrofit projects by improving the audit process, streamlining tasks, and achieving higher energy savings.« less

Power, Profits, and Politics: Energy Security and Cooperation in Eurasia

NASA Astrophysics Data System (ADS)

Svyatets, Ekaterina

This study explores varying outcomes of energy cooperation, defined as diplomatic relations, bilateral trade, and investment in oil and natural gas. Tests of theories pertinent to energy security - broadly speaking, realism, liberalism, and domestic politics---reveal that they alone can offer only a narrow and one-sided explanation, not embracing the complexity of energy issues. Nevertheless, using them as a starting point, this study outlined a structured framework that incorporates three variables---economic potential, geopolitical rivalry, and domestic interest groups---that are applied to the cases of U.S.-Russia, U.S.-Azerbaijan, and Russia-Germany energy ties. This study concludes that if the economic potential (defined by geographic proximity and resource availability) is very high, such as in the case of Russia-Germany, states can overcome geopolitical rivalries and historical enmities in favor of energy cooperation. However, if the economic potential is relatively low (because of geographic obstacles or easily available alternative suppliers, as in the cases of U.S.-Russia and U.S.-Azerbaijan), then geopolitics prevails---for example, to bypass Russia or to limit American access to contracts in Russia when U.S.-Russian relations are strained. In all the cases explored here, domestic interest groups have mixed influence: if they are united along energy issues, they usually successfully achieve their energy policy goals, although the impact of these groups often becomes intertwined with state interests. In other situations, when powerful interest groups are divided or focused on non-energy-related issues (such as ethnic priorities), their influence over energy deals is much lower.

Energy profile of nanobody-GFP complex under force.

PubMed

Klamecka, Kamila; Severin, Philip M; Milles, Lukas F; Gaub, Hermann E; Leonhardt, Heinrich

2015-09-10

Nanobodies (Nbs)-the smallest known fully functional and naturally occuring antigen-binding fragments-have attracted a lot of attention throughout the last two decades. Exploring their potential beyond the current use requires more detailed characterization of their binding forces as those cannot be directly derived from the binding affinities. Here we used atomic force microscope to measure rupture force of the Nb-green fluorescent protein (GFP) complex in various pulling geometries and derived the energy profile characterizing the interaction along the direction of the pulling force. We found that-despite identical epitopes-the Nb binds stronger (41-56 pN) to enhanced GFP than to wild-type GFP (28-45 pN). Measured forces make the Nb-GFP pair a potent reference for investigating molecular forces in living systems both in and ex vivo.

Nuclear quantum effects on adsorption of H 2 and isotopologues on metal ions

DOE PAGES

Savchenko, Ievgeniia; Gu, Bing; Heine, Thomas; ...

2017-01-03

The nuclear quantum effects on the zero-point energy (ZPE), influencing adsorption of Hmore » $$_2$$ and isotopologues on metal ions, are examined in this study using normal mode analysis of ab initio electronic structure results for complexes with 17 metal cations. To estimate for the anharmonicity, a nuclear wavepacket dynamics on the ground state electronic potential energy surfaces (PES) have been employed for complexes of Li$^+$ and Cu$$^{+2}$$ with H$$_2$$, D$$_2$$, HD. The dynamics analysis shows that incorporation of the PES anharmonicity changes the ZPE by up to 9%. Finally, the lightest metallic nuclei, Li and Be, are found to be the most 'quantum'. The largest selectivity in adsorption is predicted for Cu, Ni and Co ions.« less

Hunger and Satiety Mechanisms and Their Potential Exploitation in the Regulation of Food Intake.

PubMed

Amin, Tehmina; Mercer, Julian G

2016-03-01

Effective strategies to combat recent rises in obesity levels are limited. The accumulation of excess body fat results when energy intake exceeds that expended. Energy balance is controlled by hypothalamic responses, but these can be overridden by hedonic/reward brain systems. This override, combined with unprecedented availability of cheap, energy-dense, palatable foods, may partly explain the increase in overweight and obesity. The complexity of the processes that regulate feeding behaviour has driven the need for further fundamental research. Full4Health is an EU-funded project conceived to advance our understanding of hunger and satiety mechanisms. Food intake has an impact on and is also affected by the gut-brain signalling which controls hunger and appetite. This review describes selected recent research from Full4Health and how new mechanistic findings could be exploited to adapt and control our physiological responses to food, potentially providing an alternative solution to addressing the global problems related to positive energy balance.

Diets of giants: the nutritional value of herbivorous dinosaur diet during the Mesozoic

NASA Astrophysics Data System (ADS)

Gill, Fiona; Hummel, Juergen; Sharifi, Reza; Lee, Alexandra; Lomax, Barry

2017-04-01

A major uncertainty in estimating energy budgets and population densities of extinct animals is the carrying capacity of their ecosystems, constrained by net primary productivity (NPP) and digestible energy content of that NPP. The hypothesis that increases in NPP of land plants due to elevated atmospheric CO2 contributed to the unparalleled size of the sauropods, the largest ever land animals, has recently been rejected, based on modern studies on herbivorous insects. However, the nutritional value of plants grown under elevated CO2 levels might be very different for vertebrate megaherbivores with more complex digestive systems and different protein:energy requirements than insects. Here we show that the metabolisable energy (ME) value of five species of potential dinosaur food plants does not decline consistently with increasing CO2 growth concentrations, with maxima observed at 1200 ppm CO2. Our data potentially rebut the hypothesis of constraints on herbivore diet quality in the Mesozoic due to CO2 levels.

Low-energy electron elastic scattering and impact ionization with hydrogenlike helium in Debye plasmas

NASA Astrophysics Data System (ADS)

Li, Jun; Zhang, Song Bin; Ye, Bang Jiao; Wang, Jian Guo; Janev, R. K.

2017-09-01

Low-energy electron elastic scattering and impact ionization with hydrogenlike helium in Debye plasmas have been investigated by employing the exterior complex scaling method. The interactions between charged particles in the plasmas have been represented by Debye-Hückel potentials. The 1 s -1 s elastic collision strengths below the n =2 excitation threshold of He+ dominated by resonance structures are calculated for different screening lengths. As the screening strength increases, the resonance peaks studied [2(1,0) 2 +1Se,3Po,1De , and 2(0,1) 2 +1Po] exhibit blueshifts and then redshifts with a further increase of the screening strength, which results in dramatic changes of the collision strengths. It is found that these dynamic variation features of the resonances are related to the changes of energy levels of He+ in the screened potential and geometric configurations of resonances. Triple-differential-ionization cross sections in coplanar geometries at 6-Ry incident electron energy are also reported, significant changes are observed with varying screening length.

RACER a Coarse-Grained RNA Model for Capturing Folding Free Energy in Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Cheng, Sara; Bell, David; Ren, Pengyu

RACER is a coarse-grained RNA model that can be used in molecular dynamics simulations to predict native structures and sequence-specific variation of free energy of various RNA structures. RACER is capable of accurate prediction of native structures of duplexes and hairpins (average RMSD of 4.15 angstroms), and RACER can capture sequence-specific variation of free energy in excellent agreement with experimentally measured stabilities (r-squared =0.98). The RACER model implements a new effective non-bonded potential and re-parameterization of hydrogen bond and Debye-Huckel potentials. Insights from the RACER model include the importance of treating pairing and stacking interactions separately in order to distinguish folded an unfolded states and identification of hydrogen-bonding, base stacking, and electrostatic interactions as essential driving forces for RNA folding. Future applications of the RACER model include predicting free energy landscapes of more complex RNA structures and use of RACER for multiscale simulations.

Seeking potential anticonvulsant agents that target GABAA receptors using experimental and theoretical procedures

NASA Astrophysics Data System (ADS)

Saavedra-Vélez, Margarita Virginia; Correa-Basurto, José; Matus, Myrna H.; Gasca-Pérez, Eloy; Bello, Martiniano; Cuevas-Hernández, Roberto; García-Rodríguez, Rosa Virginia; Trujillo-Ferrara, José; Ramos-Morales, Fernando Rafael

2014-12-01

The aim of this study was to identify compounds that possess anticonvulsant activity by using a pentylenetetrazol (PTZ)-induced seizure model. Theoretical studies of a set of ligands, explored the binding affinities of the ligands for the GABAA receptor (GABAAR), including some benzodiazepines. The ligands satisfy the Lipinski rules and contain a pharmacophore core that has been previously reported to be a GABAAR activator. To select the ligands with the best physicochemical properties, all of the compounds were analyzed by quantum mechanics and the energies of the highest occupied molecular orbital and lowest unoccupied molecular orbital were determined. Docking calculations between the ligands and the GABAAR were used to identify the complexes with the highest Gibbs binding energies. The identified compound D1 (dibenzo( b,f)(1,4)diazocine-6,11(5H,12H)-dione) was synthesized, experimentally tested, and the GABAAR-D1 complex was submitted to 12-ns-long molecular dynamics (MD) simulations to corroborate the binding conformation obtained by docking techniques. MD simulations were also used to analyze the decomposition of the Gibbs binding energy of the residues involved in the stabilization of the complex. To validate our theoretical results, molecular docking and MD simulations were also performed for three reference compounds that are currently in commercial use: clonazepam (CLZ), zolpidem and eszopiclone. The theoretical results show that the GABAAR-D1, and GABAAR-CLZ complexes bind to the benzodiazepine binding site, share a similar map of binding residues, and have similar Gibbs binding energies and entropic components. Experimental studies using a PTZ-induced seizure model showed that D1 possesses similar activity to CLZ, which corroborates the predicted binding free energy identified by theoretical calculations.

Body shape helps legged robots climb and turn in complex 3-D terrains

NASA Astrophysics Data System (ADS)

Han, Yuanfeng; Wang, Zheliang; Li, Chen

Analogous to streamlined shapes that reduce drag in fluids, insects' ellipsoid-like rounded body shapes were recently discovered to be ``terradynamically streamlined'' and enhance locomotion in cluttered terrain by facilitating body rolling. Here, we hypothesize that there exist more terradynamic shapes that facilitate other modes of locomotion like climbing and turning in complex 3-D terrains by facilitating body pitching and yawing. To test our hypothesis, we modified the body shape of a legged robot by adding an elliptical and a rectangular shell and tested how it negotiated with circular and square vertical pillars. With a rectangular shell the robot always pitched against square pillars in an attempt to climb, whereas with an elliptical shell it always yawed and turned away from circular pillars given a small initial lateral displacement. Square / circular pillars facilitated pitching / yawing, respectively. To begin to reveal the contact physics, we developed a locomotion energy landscape model. Our model revealed that potential energy barriers to transition from pitching to yawing are high for angular locomotor and obstacle shapes (rectangular / square) but vanish for rounded shapes (elliptical / circular). Our study supports the plausibility of locomotion energy landscapes for understanding the rich locomotor transitions in complex 3-D terrains.

Detection of ochratoxin A (OTA) in coffee using chemiluminescence resonance energy transfer (CRET) aptasensor.

PubMed

Jo, Eun-Jung; Mun, Hyoyoung; Kim, Su-Ji; Shim, Won-Bo; Kim, Min-Gon

2016-03-01

We report a chemiluminescence resonance energy transfer (CRET) aptasensor for the detection of ochratoxin A (OTA) in roasted coffee beans. The aptamer sequences used in this study are 5'-DNAzyme-Linker-OTA aptamer-3'-dabcyl. Dabcyl at the end of the OTA aptamer region plays as a quencher in CRET aptasensor. When hemin and OTA are added, the dabcyl-labeled OTA aptamer approaches to the G-quadruplex-hemin complex by formation of the G-quadruplex-OTA complex. The G-quadruplex-hemin complexes possess horseradish peroxidase (HRP)-like activity, and therefore, the HRP-mimicking DNAzyme (HRPzyme) catalyzes peroxidation in the presence of luminol and H2O2. Resonance energy transfer between luminol (donor) and dabcyl (acceptor) enables quenching of chemiluminescence signals. The signal decreases with increasing the concentration of OTA within the range of 0.1-100ngmL(-1) (limit of detection 0.22ngmL(-1)), and the level of recovery of the respective 1ngmL(-1) and 10ngmL(-1) spiked coffee samples was 71.5% and 93.3%. These results demonstrated the potential of the proposed method for OTA analysis in diverse foods. Copyright © 2015 Elsevier Ltd. All rights reserved.

High sensitization efficiency and energy transfer routes for population inversion at low pump intensity in Er organic complexes for IR amplification.

PubMed

Hu, J X; Karamshuk, S; Gorbaciova, J; Ye, H Q; Lu, H; Zhang, Y P; Zheng, Y X; Liang, X; Hernández, I; Wyatt, P B; Gillin, W P

2018-02-19

Organic erbium complexes have long been of interest due to their potential for using the strong absorption into the organic to sensitise the erbium emission. Despite this interest there is remarkably little quantitative information on how effective the approach is and the discussion of the energy transfer mechanism is generally vague. Here we accurately quantify the sensitisation as a function of excitation pump density and model it using a rate equation approach. As a result, we can calculate the degree of population inversion for the erbium ions as a function of the pump intensity. We demonstrate that even when we increase the erbium concentration in the films from ~10 to ~80% we find a relatively small decrease in the sensitisation which we attribute to the large (>20 Å) Förster radius for the sensitisation process. We show that we can obtain population inversion in our films at very low pump powers ~600 mW/cm 2 . The calculated Förster radius for the organic erbium complexes suggests design rules for energy transfer between antennas and erbium ions in molecular systems and hybrid organic-inorganic nanoparticles.

Enhanced photocurrent production by bio-dyes of photosynthetic macromolecules on designed TiO2 film

PubMed Central

Yu, Daoyong; Wang, Mengfei; Zhu, Guoliang; Ge, Baosheng; Liu, Shuang; Huang, Fang

2015-01-01

The macromolecular pigment-protein complex has the merit of high efficiency for light-energy capture and transfer after long-term photosynthetic evolution. Here bio-dyes of A. platensis photosystem I (PSI) and spinach light-harvesting complex II (LHCII) are spontaneously sensitized on three types of designed TiO2 films, to assess the effects of pigment-protein complex on the performance of bio-dye sensitized solar cells (SSC). Adsorption models of bio-dyes are proposed based on the 3D structures of PSI and LHCII, and the size of particles and inner pores in the TiO2 film. PSI shows its merit of high efficiency for captured energy transfer, charge separation and transfer in the electron transfer chain (ETC), and electron injection from FB to the TiO2 conducting band. After optimization, the best short current (JSC) and photoelectric conversion efficiency (η) of PSI-SSC and LHCII-SSC are 1.31 mA cm-2 and 0.47%, and 1.51 mA cm-2 and 0.52%, respectively. The potential for further improvement of this PSI based SSC is significant and could lead to better utilization of solar energy. PMID:25790735

Stacking and T-shape competition in aromatic-aromatic amino acid interactions.

PubMed

Chelli, Riccardo; Gervasio, Francesco Luigi; Procacci, Piero; Schettino, Vincenzo

2002-05-29

The potential of mean force of interacting aromatic amino acids is calculated using molecular dynamics simulations. The free energy surface is determined in order to study stacking and T-shape competition for phenylalanine-phenylalanine (Phe-Phe), phenylalanine-tyrosine (Phe-Tyr), and tyrosine-tyrosine (Tyr-Tyr) complexes in vacuo, water, carbon tetrachloride, and methanol. Stacked structures are favored in all solvents with the exception of the Tyr-Tyr complex in carbon tetrachloride, where T-shaped structures are also important. The effect of anchoring the two alpha-carbons (C(alpha)) at selected distances is investigated. We find that short and large C(alpha)-C(alpha) distances favor stacked and T-shaped structures, respectively. We analyze a set of 2396 protein structures resolved experimentally. Comparison of theoretical free energies for the complexes to the experimental analogue shows that Tyr-Tyr interaction occurs mainly at the protein surface, while Phe-Tyr and Phe-Phe interactions are more frequent in the hydrophobic protein core. This is confirmed by the Voronoi polyhedron analysis on the database protein structures. As found from the free energy calculation, analysis of the protein database has shown that proximal and distal interacting aromatic residues are predominantly stacked and T-shaped, respectively.

Theoretical study of hydrated copper(II) interactions with guanine: a computational density functional theory study.

PubMed

Pavelka, Matej; Shukla, Manoj K; Leszczynski, Jerzy; Burda, Jaroslav V

2008-01-17

Optimization of the hydrated Cu(II)(N7-guanine) structures revealed a number of minima on the potential energy surface. For selected structures, energy decompositions together with the determination of electronic properties (partial charges and electron spin densities) were performed. In the complexes of guanine with the bare copper cation and that with the monoaqua ligated cation, an electron transfer from guanine to Cu(II) was observed, resulting in a Cu(I)-guanine(+) type of complex. Conformers with two aqua ligands are borderline systems characterized by a Cu partial charge of +0.7e and a similar value of the spin density (0.6e) localized on guanine. When tetracoordination of copper was achieved, only then the prevailing electron spin density is unambiguously localized on copper. The energetic preference of diaqua-Cu-(N7,O6-guanine) over triaqua-Cu-(N7-guanine) was found for the four-coordinate structures. However, the energy difference between these two conformations decreases with the number of water molecules present in the systems, and in complexes with five water molecules this preference is preserved only at DeltaG level where thermal and entropy terms are included.

Structure, energetics and vibrational spectra of dimers, trimers, and tetramers of HX (X = Cl, Br, I)

NASA Astrophysics Data System (ADS)

Latajka, Zdzislaw; Scheiner, Steve

1997-03-01

The title complexes are studied by correlated ab initio methods using a pseudopotential double-ζ basis set, augmented by diffuse sp and two sets of polarization functions. The binding energies of the complexes decrease in the order HCl > HBr > HI. In the mixed HX…HX' dimers, the nature of the proton-donor molecule is more important than is the proton-acceptor with respect to the strength of the interaction. Only one minimum is found on the potential energy surface of the trimers and tetramers, which corresponds to the C nh cyclic structure. Enlargement of the complex leads to progressively greater individual H-bond energy and HX bond stretch, coupled with reduced intermolecular separation and smaller nonlinearity of each H-bond. Electron correlation makes a larger contribution as the atomic number of X increases. The highest degree of cooperativity is noted for oligomers of HCl and HBr, as compared to HI. The nonadditivity is dominated by terms present at the SCF level. The vibrational frequencies exhibit trends that generally parallel the energetics and geometry patterns, particularly the red shifts of the HX stretches and the intermolecular modes.

The X3LYP extended density functional accurately describes H-bonding but fails completely for stacking.

PubMed

Cerný, Jirí; Hobza, Pavel

2005-04-21

The performance of the recently introduced X3LYP density functional which was claimed to significantly improve the accuracy for H-bonded and van der Waals complexes was tested for extended H-bonded and stacked complexes (nucleic acid base pairs and amino acid pairs). In the case of planar H-bonded complexes (guanine...cytosine, adenine...thymine) the DFT results nicely agree with accurate correlated ab initio results. For the stacked pairs (uracil dimer, cytosine dimer, adenine...thymine and guanine...cytosine) the DFT fails completely and it was even not able to localize any minimum at the stacked subspace of the potential energy surface. The geometry optimization of all these stacked clusters leads systematically to the planar H-bonded pairs. The amino acid pairs were investigated in the crystal geometry. DFT again strongly underestimates the accurate correlated ab initio stabilization energies and usually it was not able to describe the stabilization of a pair. The X3LYP functional thus behaves similarly to other current functionals. Stacking of nucleic acid bases as well as interaction of amino acids was described satisfactorily by using the tight-binding DFT method, which explicitly covers the London dispersion energy.

Central and peripheral control of food intake.

PubMed

Abdalla, M M I

2017-01-01

The maintenance of the body weight at a stable level is a major determinant in keeping the higher animals and mammals survive. Th e body weight depends on the balance between the energy intake and energy expenditure. Increased food intake over the energy expenditure of prolonged time period results in an obesity. Th e obesity has become an important worldwide health problem, even at low levels. The obesity has an evil effect on the health and is associated with a shorter life expectancy. A complex of central and peripheral physiological signals is involved in the control of the food intake. Centrally, the food intake is controlled by the hypothalamus, the brainstem, and endocannabinoids and peripherally by the satiety and adiposity signals. Comprehension of the signals that control food intake and energy balance may open a new therapeutic approaches directed against the obesity and its associated complications, as is the insulin resistance and others. In conclusion, the present review summarizes the current knowledge about the complex system of the peripheral and central regulatory mechanisms of food intake and their potential therapeutic implications in the treatment of obesity.

Calculation of total and ionization cross sections for electron scattering by primary benzene compounds

NASA Astrophysics Data System (ADS)

Singh, Suvam; Naghma, Rahla; Kaur, Jaspreet; Antony, Bobby

2016-07-01

The total and ionization cross sections for electron scattering by benzene, halobenzenes, toluene, aniline, and phenol are reported over a wide energy domain. The multi-scattering centre spherical complex optical potential method has been employed to find the total elastic and inelastic cross sections. The total ionization cross section is estimated from total inelastic cross section using the complex scattering potential-ionization contribution method. In the present article, the first theoretical calculations for electron impact total and ionization cross section have been performed for most of the targets having numerous practical applications. A reasonable agreement is obtained compared to existing experimental observations for all the targets reported here, especially for the total cross section.

Quantifying Adoption Rates and Energy Savings Over Time for Advanced Manufacturing Technologies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hanes, Rebecca; Carpenter Petri, Alberta C; Riddle, Matt

Energy-efficient manufacturing technologies can reduce energy consumption and lower operating costs for an individual manufacturing facility, but increased process complexity and the resulting risk of disruption means that manufacturers may be reluctant to adopt such technologies. In order to quantify potential energy savings at scales larger than a single facility, it is necessary to account for how quickly and how widely the technology will be adopted by manufacturers. This work develops a methodology for estimating energy-efficient manufacturing technology adoption rates using quantitative, objectively measurable technology characteristics, including energetic, economic and technical criteria. Twelve technology characteristics are considered, and each characteristicmore » is assigned an importance weight that reflects its impact on the overall technology adoption rate. Technology characteristic data and importance weights are used to calculate the adoption score, a number between 0 and 1 that represents how quickly the technology is likely to be adopted. The adoption score is then used to estimate parameters for the Bass diffusion curve, which quantifies the change in the number of new technology adopters in a population over time. Finally, energy savings at the sector level are calculated over time by multiplying the number of new technology adopters at each time step with the technology's facility-level energy savings. The proposed methodology will be applied to five state-of-the-art energy-efficient technologies in the carbon fiber composites sector, with technology data obtained from the Department of Energy's 2016 bandwidth study. Because the importance weights used in estimating the Bass curve parameters are subjective, a sensitivity analysis will be performed on the weights to obtain a range of parameters for each technology. The potential energy savings for each technology and the rate at which each technology is adopted in the sector are quantified and used to identify the technologies which offer the greatest cumulative sector-level energy savings over a period of 20 years. Preliminary analysis indicates that relatively simple technologies, such as efficient furnaces, will be adopted more quickly and result in greater cumulative energy savings compared to more complex technologies that require process retrofitting, such as advanced control systems.« less

Perspectives on the metabolic management of epilepsy through dietary reduction of glucose and elevation of ketone bodies.

PubMed

Greene, Amanda E; Todorova, Mariana T; Seyfried, Thomas N

2003-08-01

Brain cells are metabolically flexible because they can derive energy from both glucose and ketone bodies (acetoacetate and beta-hydroxybutyrate). Metabolic control theory applies principles of bioenergetics and genome flexibility to the management of complex phenotypic traits. Epilepsy is a complex brain disorder involving excessive, synchronous, abnormal electrical firing patterns of neurons. We propose that many epilepsies with varied etiologies may ultimately involve disruptions of brain energy homeostasis and are potentially manageable through principles of metabolic control theory. This control involves moderate shifts in the availability of brain energy metabolites (glucose and ketone bodies) that alter energy metabolism through glycolysis and the tricarboxylic acid cycle, respectively. These shifts produce adjustments in gene-linked metabolic networks that manage or control the seizure disorder despite the continued presence of the inherited or acquired factors responsible for the epilepsy. This hypothesis is supported by information on the management of seizures with diets including fasting, the ketogenic diet and caloric restriction. A better understanding of the compensatory genetic and neurochemical networks of brain energy metabolism may produce novel antiepileptic therapies that are more effective and biologically friendly than those currently available.

Potential limitations of NRC in predicting energetic requirements of beef females within western U.S. grazing systems

USDA-ARS?s Scientific Manuscript database

Assessment of beef cow energy balance and efficiency in grazing-extensive rangelands has occurred on a nominal basis over short time intervals and has not accounted for the complexity of metabolic and digestive responses; behavioral adaptations to climatic, terrain, and vegetation variables; and doc...

Hot Water and Warm Homes from Sunlight. Teacher's Guide.

ERIC Educational Resources Information Center

Gould, Alan

A basic understanding of the potential of solar energy is increasingly relevant given the pollution caused by the burning of fossil fuel, health problems associated with that pollution, the possibility of global warming, and the complex issues raised by the dependence of industrialized nations on oil and natural gas. This teacher's guide presents…

Using soils and land potential as a basis for land use decisions and conservation planning: A resilience-based strategy

USDA-ARS?s Scientific Manuscript database

Land use decisions are becoming increasingly complex and contentious as demands for food, fiber, energy and infrastructure expand. Recent definitions of “planetary boundaries” and arbitrary land use limits circumscribing the “Safe Operating Space” for humans are helpful in drawing attention to globa...

Deprotonated Dicarboxylic Acid Homodimers: Hydrogen Bonds and Atmospheric Implications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hou, Gao-Lei; Valiev, Marat; Wang, Xue-Bin

Dicarboxylic acids represent an important class of water-soluble organic compounds found in the atmosphere. In this work we are studying properties of dicarboxylic acid homodimer complexes (HO 2(CH 2) nCO 2 -[HO 2(CH 2) nCO 2H], n = 0-12), as potentially important intermediates in aerosol formation processes. Our approach is based on experimental data from negative ion photoelectron spectra of the dimer complexes combined with updated measurements of the corresponding monomer species. These results are analyzed with quantum-mechanical calculations, which provide further information about equilibrium structures, thermochemical parameters associated with the complex formation, and evaporation rates. We find that uponmore » formation of the dimer complexes the electron binding energies increase by 1.3–1.7 eV (30.0–39.2 kcal/mol), indicating increased stability of the dimerized complexes. Calculations indicate that these dimer complexes are characterized by the presence of strong intermolecular hydrogen bonds with high binding energies and are thermodynamically favorable to form with low evaporation rates. Comparison with previously studied HSO 4 -[HO 2(CH 2) 2CO 2H] complex (J. Phys. Chem. Lett. 2013, 4, 779-785) shows that HO 2(CH 2) 2CO 2 -[HO 2(CH 2) 2CO 2H] has very similar thermochemical properties. These results imply that dicarboxylic acids not only can contribute to the heterogeneous complexes formation involving sulfuric acid and dicarboxylic acids, but also can promote the formation of homogenous complexes by involving dicarboxylic acids themselves.« less

On the structure and spin states of Fe(III)-EDDHA complexes.

PubMed

Gómez-Gallego, Mar; Fernández, Israel; Pellico, Daniel; Gutiérrez, Angel; Sierra, Miguel A; Lucena, Juan J

2006-07-10

DFT methods are suitable for predicting both the geometries and spin states of EDDHA-Fe(III) complexes. Thus, extensive DFT computational studies have shown that the racemic-Fe(III) EDDHA complex is more stable than the meso isomer, regardless of the spin state of the central iron atom. A comparison of the energy values obtained for the complexes under study has also shown that high-spin (S = 5/2) complexes are more stable than low-spin (S = 1/2) ones. These computational results matched the experimental results of the magnetic susceptibility values of both isomers. In both cases, their behavior has been fitted as being due to isolated high-spin Fe(III) in a distorted octahedral environment. The study of the correlation diagram also confirms the high-spin iron in complex 2b. The geometry optimization of these complexes performed with the standard 3-21G* basis set for hydrogen, carbon, oxygen, and nitrogen and the Hay-Wadt small-core effective core potential (ECP) including a double-xi valence basis set for iron, followed by single-point energy refinement with the 6-31G* basis set, is suitable for predicting both the geometries and the spin-states of EDDHA-Fe(III) complexes. The presence of a high-spin iron in Fe(III)-EDDHA complexes could be the key to understanding their lack of reactivity in electron-transfer processes, either chemically or electrochemically induced, and their resistance to photodegradation.

Development of a Suite of Analytical Tools for Energy and Water Infrastructure Knowledge Discovery

NASA Astrophysics Data System (ADS)

Morton, A.; Piburn, J.; Stewart, R.; Chandola, V.

2017-12-01

Energy and water generation and delivery systems are inherently interconnected. With demand for energy growing, the energy sector is experiencing increasing competition for water. With increasing population and changing environmental, socioeconomic, and demographic scenarios, new technology and investment decisions must be made for optimized and sustainable energy-water resource management. This also requires novel scientific insights into the complex interdependencies of energy-water infrastructures across multiple space and time scales. To address this need, we've developed a suite of analytical tools to support an integrated data driven modeling, analysis, and visualization capability for understanding, designing, and developing efficient local and regional practices related to the energy-water nexus. This work reviews the analytical capabilities available along with a series of case studies designed to demonstrate the potential of these tools for illuminating energy-water nexus solutions and supporting strategic (federal) policy decisions.

Synergies of solar energy across a land-food-energy-water nexus

NASA Astrophysics Data System (ADS)

Hoffacker, M. K.; Hernandez, R. R.; Allen, M. F.

2017-12-01

Land-cover change from energy development, including solar energy, presents trade-offs for the production of food and the conservation of natural ecosystems. Solar energy plays a critical role in contributing to the alternative energy mix to mitigate climate change and meet policy milestones; however, the extent that solar energy development can mitigate land scarcity, water shortages, and conservation is understudied. Here, we test whether projected electricity needs for the state of California (CA, United States [US]) can be met within land-cover types that can also generate environmental, social and fiscal co-benefits (techno-ecological synergies) including: the built environment, salt-affected land, contaminated land, and water reservoirs (as floatovoltaics). Additionally, we analyze general spatial trends and patterns related to clustering and proximity of techno-ecological opportunities and land-cover types (e.g. contamination sites and cities). In total, the Central Valley, a globally significant agricultural region, encompasses 15% of CA, 8,415 km2 of which was identified as potentially synergistic land for solar energy. These areas comprise a capacity-based energy potential of 17,348 TWh y-1 for photovoltaic (PV) and 1,655 TWh y-1 for concentrating solar power (CSP). Accounting for technology efficiencies, this exceeds California's 2025 projected electricity demands up to 13 and 2 times for PV and CSP, respectively. Further, 60% of contaminated lands are clustered within and up to 10 km of the 10 most populated cities in the Central Valley, where energy is consumed. Our study underscores the potential of strategic renewable energy siting to mitigate environmental trade-offs typically coupled with energy development sprawl in landscapes characterized by complex nexus issues.

Imaging a multidimensional multichannel potential energy surface: Photodetachment of H(-)(NH3) and NH4 (.).

PubMed

Hu, Qichi; Song, Hongwei; Johnson, Christopher J; Li, Jun; Guo, Hua; Continetti, Robert E

2016-06-28

Probes of the Born-Oppenheimer potential energy surfaces governing polyatomic molecules often rely on spectroscopy for the bound regions or collision experiments in the continuum. A combined spectroscopic and half-collision approach to image nuclear dynamics in a multidimensional and multichannel system is reported here. The Rydberg radical NH4 and the double Rydberg anion NH4 (-) represent a polyatomic system for benchmarking electronic structure and nine-dimensional quantum dynamics calculations. Photodetachment of the H(-)(NH3) ion-dipole complex and the NH4 (-) DRA probes different regions on the neutral NH4 PES. Photoelectron energy and angular distributions at photon energies of 1.17, 1.60, and 2.33 eV compare well with quantum dynamics. Photoelectron-photofragment coincidence experiments indicate dissociation of the nascent NH4 Rydberg radical occurs to H + NH3 with a peak kinetic energy of 0.13 eV, showing the ground state of NH4 to be unstable, decaying by tunneling-induced dissociation on a time scale beyond the present scope of multidimensional quantum dynamics.

Tuning the reactivity of mononuclear nonheme manganese(iv)-oxo complexes by triflic acid

DOE PAGES

Chen, Junying; Yoon, Heejung; Lee, Yong -Min; ...

2015-04-14

Triflic acid (HOTf)-bound nonheme Mn( IV)-oxo complexes, [(L)Mn IV(O)] 2+–(HOTf) 2 (L = N4Py and Bn-TPEN; N4Py = N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine and Bn-TPEN = N-benzyl-N,N',N'-tris(2-pyridylmethyl)ethane-1,2-diamine), were synthesized by adding HOTf to the solutions of the [(L)Mn IV(O)] 2+ complexes and were characterized by various spectroscopies. The one-electron reduction potentials of the Mn IV(O) complexes exhibited a significant positive shift upon binding of HOTf. The driving force dependences of electron transfer (ET) from electron donors to the Mn IV(O) and Mn IV(O)–(HOTf) 2 complexes were examined and evaluated in light of the Marcus theory of ET to determine the reorganization energies of ET.more » The smaller reorganization energies and much more positive reduction potentials of the [(L)Mn IV(O)] 2+–(HOTf) 2 complexes resulted in greatly enhanced oxidation capacity towards one-electron reductants and para-X-substituted-thioanisoles. The reactivities of the Mn(IV)-oxo complexes were markedly enhanced by binding of HOTf, such as a 6.4 × 10 5-fold increase in the oxygen atom transfer (OAT) reaction (i.e., sulfoxidation). Such a remarkable acceleration in the OAT reaction results from the enhancement of ET from para-X-substituted-thioanisoles to the MnIV(O) complexes as revealed by the unified ET driving force dependence of the rate constants of OAT and ET reactions of [(L)Mn IV(O)] 2+–(HOTf) 2. In contrast, deceleration was observed in the rate of H-atom transfer (HAT) reaction of [(L)Mn IV(O)] 2+–(HOTf) 2 complexes with 1,4-cyclohexadiene as compared with those of the [(L)Mn IV(O)] 2+ complexes. Thus, the binding of two HOTf molecules to the Mn IV(O) moiety resulted in remarkable acceleration of the ET rate when the ET is thermodynamically feasible. When the ET reaction is highly endergonic, the rate of the HAT reaction is decelerated due to the steric effect of the counter anion of HOTf.« less

Magnetohydrodynamics of atmospheric transients. IV - Nonplane two-dimensional analyses of energy conversion and magnetic field evolution. [during corona following solar flare

NASA Technical Reports Server (NTRS)

Wu, S. T.; Nakagawa, Y.; Han, S. M.; Dryer, M.

1982-01-01

The evolution of the magnetic field and the manner of conversion of thermal energy into different forms in the corona following a solar flare are investigated by means of a nonplane magnetohydrodynamic (MHD) analysis. All three components of magnetic field and velocity are treated in a physically self-consistent manner, with all physical variables as functions of time (t) and two spatial coordinates (r, theta). The difference arising from the initial magnetic field, either twisted (force-free) or non-twisted (potential), is demonstrated. Consideration is given to two initial field topologies (open vs. closed). The results demonstrate that the conversion of magnetic energy is faster for the case of the initially twisted (force-free) field than for the initially untwisted (potential) field. In addition, the twisted field is found to produce a complex structure of the density enhancements.

Theoretical survey of the reaction between osmium and acetaldehyde

NASA Astrophysics Data System (ADS)

Dai, Guo-Liang; Wang, Chuan-Feng

2012-05-01

The mechanism of the reaction of osmium atom with acetaldehyde has been investigated with a DFT approach. All the stationary points are determined at the UB3LYP/ sdd/6-311++G** level of the theory. Both ground and excited state potential energy surfaces are investigated in detail. The present results show that the title reaction start with the formation of a CH3CHO-metal complex followed by C-C, aldehyde C-H, C-O, and methyl C-H activation. These reactions can lead to four different products (HOsCH3 + CO, OsCO + CH4, OsCOCH3 + H, and OsO + C2H4). The minimum energy reaction path is found to involve the spin inversion in the initial reaction step. This potential energy curve-crossing dramatically affects reaction exothermic. The present results may be helpful in understanding the mechanism of the title reaction and further experimental investigation of the reaction.

Identification of structural motifs as tunneling two-level systems in amorphous alumina at low temperatures

NASA Astrophysics Data System (ADS)

Paz, Alejandro Pérez; Lebedeva, Irina V.; Tokatly, Ilya V.; Rubio, Angel

2014-12-01

One of the most accepted models that describe the anomalous thermal behavior of amorphous materials at temperatures below 1 K relies on the quantum mechanical tunneling of atoms between two nearly equivalent potential energy wells forming a two-level system (TLS). Indirect evidence for TLSs is widely available. However, the atomistic structure of these TLSs remains an unsolved topic in the physics of amorphous materials. Here, using classical molecular dynamics, we found several hitherto unknown bistable structural motifs that may be key to understanding the anomalous thermal properties of amorphous alumina at low temperatures. We show through free energy profiles that the complex potential energy surface can be reduced to canonical TLSs. The tunnel splitting predicted from instanton theory, the number density, dipole moment, and coupling to external strain of the discovered motifs are consistent with experiments.

Strong and weak adsorptions of polyelectrolyte chains onto oppositely charged spheres

NASA Astrophysics Data System (ADS)

Cherstvy, A. G.; Winkler, R. G.

2006-08-01

We investigate the complexation of long thin polyelectrolyte (PE) chains with oppositely charged spheres. In the limit of strong adsorption, when strongly charged PE chains adapt a definite wrapped conformation on the sphere surface, we analytically solve the linear Poisson-Boltzmann equation and calculate the electrostatic potential and the energy of the complex. We discuss some biological applications of the obtained results. For weak adsorption, when a flexible weakly charged PE chain is localized next to the sphere in solution, we solve the Edwards equation for PE conformations in the Hulthén potential, which is used as an approximation for the screened Debye-Hückel potential of the sphere. We predict the critical conditions for PE adsorption. We find that the critical sphere charge density exhibits a distinctively different dependence on the Debye screening length than for PE adsorption onto a flat surface. We compare our findings with experimental measurements on complexation of various PEs with oppositely charged colloidal particles. We also present some numerical results of the coupled Poisson-Boltzmann and self-consistent field equation for PE adsorption in an assembly of oppositely charged spheres.

Biophysical comparison of ATP synthesis mechanisms shows a kinetic advantage for the rotary process.

PubMed

Anandakrishnan, Ramu; Zhang, Zining; Donovan-Maiye, Rory; Zuckerman, Daniel M

2016-10-04

The ATP synthase (F-ATPase) is a highly complex rotary machine that synthesizes ATP, powered by a proton electrochemical gradient. Why did evolution select such an elaborate mechanism over arguably simpler alternating-access processes that can be reversed to perform ATP synthesis? We studied a systematic enumeration of alternative mechanisms, using numerical and theoretical means. When the alternative models are optimized subject to fundamental thermodynamic constraints, they fail to match the kinetic ability of the rotary mechanism over a wide range of conditions, particularly under low-energy conditions. We used a physically interpretable, closed-form solution for the steady-state rate for an arbitrary chemical cycle, which clarifies kinetic effects of complex free-energy landscapes. Our analysis also yields insights into the debated "kinetic equivalence" of ATP synthesis driven by transmembrane pH and potential difference. Overall, our study suggests that the complexity of the F-ATPase may have resulted from positive selection for its kinetic advantage.

Thermal Quantum Correlations in Photosynthetic Light-Harvesting Complexes

NASA Astrophysics Data System (ADS)

Mahdian, M.; Kouhestani, H.

2015-08-01

Photosynthesis is one of the ancient biological processes, playing crucial role converting solar energy to cellular usable currency. Environmental factors and external perturbations has forced nature to choose systems with the highest efficiency and performance. Recent theoretical and experimental studies have proved the presence of quantum properties in biological systems. Energy transfer systems like Fenna-Matthews-Olson (FMO) complex shows quantum entanglement between sites of Bacteriophylla molecules in protein environment and presence of decoherence. Complex biological systems implement more truthful mechanisms beside chemical-quantum correlations to assure system's efficiency. In this study we investigate thermal quantum correlations in FMO protein of the photosynthetic apparatus of green sulfur bacteria by quantum discord measure. The results confirmed existence of remarkable quantum correlations of of BChla pigments in room temperature. This results approve involvement of quantum correlation mechanisms for information storage and retention in living organisms that could be useful for further evolutionary studies. Inspired idea of this study is potentially interesting to practice by the same procedure in genetic data transfer mechanisms.

Scattering study of the Ne + NeH{sup +}(v{sub 0} = 0, j{sub 0} = 0) → NeH{sup +} + Ne reaction on an ab initio based analytical potential energy surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koner, Debasish; Panda, Aditya N., E-mail: adi07@iitg.ernet.in; Barrios, Lizandra

2016-01-21

Initial state selected dynamics of the Ne + NeH{sup +}(v{sub 0} = 0, j{sub 0} = 0) → NeH{sup +} + Ne reaction is investigated by quantum and statistical quantum mechanical (SQM) methods on the ground electronic state. The three-body ab initio energies on a set of suitably chosen grid points have been computed at CCSD(T)/aug-cc-PVQZ level and analytically fitted. The fitting of the diatomic potentials, computed at the same level of theory, is performed by spline interpolation. A collinear [NeHNe]{sup +} structure lying 0.72 eV below the Ne + NeH{sup +} asymptote is found to be the most stablemore » geometry for this system. Energies of low lying vibrational states have been computed for this stable complex. Reaction probabilities obtained from quantum calculations exhibit dense oscillatory structures, particularly in the low energy region and these get partially washed out in the integral cross section results. SQM predictions are devoid of oscillatory structures and remain close to 0.5 after the rise at the threshold thus giving a crude average description of the quantum probabilities. Statistical cross sections and rate constants are nevertheless in sufficiently good agreement with the quantum results to suggest an important role of a complex-forming dynamics for the title reaction.« less

A thermal storage capacity market for non dispatchable renewable energies

NASA Astrophysics Data System (ADS)

Bennouna, El Ghali; Mouaky, Ammar; Arrad, Mouad; Ghennioui, Abdellatif; Mimet, Abdelaziz

2017-06-01

Due to the increasingly high capacity of wind power and solar PV in Germany and some other European countries and the high share of variable renewable energy resources in comparison to fossil and nuclear capacity, a power reserve market structured by auction systems was created to facilitate the exchange of balance power capacities between systems and even grid operators. Morocco has a large potential for both wind and solar energy and is engaged in a program to deploy 2000MW of wind capacity by 2020 and 3000 MW of solar capacity by 2030. Although the competitiveness of wind energy is very strong, it appears clearly that the wind program could be even more ambitious than what it is, especially when compared to the large exploitable potential. On the other hand, heavy investments on concentrated solar power plants equipped with thermal energy storage have triggered a few years ago including the launching of the first part of the Nour Ouarzazate complex, the goal being to reach stable, dispatchable and affordable electricity especially during evening peak hours. This paper aims to demonstrate the potential of shared thermal storage capacity between dispatchable and non dispatchable renewable energies and particularly CSP and wind power. Thus highlighting the importance of a storage capacity market in parallel to the power reserve market and the and how it could enhance the development of both wind and CSP market penetration.

Spectral analysis and DFT computations of the hydrogen bonded complex between 2,6-diaminopyridine with 2,6-dichloro-4-nitrophenol in different solvents

NASA Astrophysics Data System (ADS)

Al-Ahmary, Khairia M.; Soliman, Saied M.; Habeeb, Moustafa M.; Al-Obidan, Areej H.

2017-09-01

New hydrogen bonded complex between 2,6-dichloro-4-nitrophenol (DCNP), proton donor with the proton acceptor 2,6-diaminopyridine (DAP) has been synthesized and characterized in solution and solid state by different spectroscopic techniques. Electronic spectra were used to identify the novel proton transfer complex through appearance of new absorption bands in acetonitrile (CH3CN), methanol (CH3OH) and mixture composed from 1:1 methanol and acetonitrile (AN-Me). The complex stoichiometry was determined to be 1:1 by job's method and photometric titrations. The formation constant was determined by applying minimum-maximum absorbances method where it reached high values confirming the complex high stability. A spectroscopic method for determining DAP was presented and validated statistically. The solid complex was characterized by elemental analysis, infrared and 1H NMR studies where the hydrogen bonded reaction occurs between the phenolic OH with the pyridine ring nitrogen as well as one amino group of DNP. The density functional theory DFT (B3LYP) method has been used to energy optimization of the reactants and complex in the ground state using two basis sets 6-31G(d) and 6-31 G+(d,p). The first one led to energy optimized structure through bifurcated hydrogen bond between OH of DCNP with the ring nitrogen and one amino group of DAP with optimization energy -1998.7 Hartree. The second one gave an optimized structure thought hydrogen bonding between OH and one amino group with lowered optimization energy -2018.1 Hartree. Hence, the experimental results will be simulated with the most stable one at DFT/B3LYB 6-31G+ (d,p). The most reactive electrophilic and nucleophilic sites of DCNP and DAP were predicted using the molecular electrostatic potential. The theoretical electronic spectra in the gas phase and the investigated solvents were calculated at TD-DFT/B3LYP 6-31G+ (d,p) and compared with measured electronic spectra where a satisfactory results have been obtained. An important aim of this work is analysis of the interaction energies between the filled natural bond orbitals (NBOs) and the empty ones in order to shed the light on the ease of electron delocalization among bonds in the novel hydrogen bonded complex.

Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins.

PubMed

May, Ali; Pool, René; van Dijk, Erik; Bijlard, Jochem; Abeln, Sanne; Heringa, Jaap; Feenstra, K Anton

2014-02-01

To assess whether two proteins will interact under physiological conditions, information on the interaction free energy is needed. Statistical learning techniques and docking methods for predicting protein-protein interactions cannot quantitatively estimate binding free energies. Full atomistic molecular simulation methods do have this potential, but are completely unfeasible for large-scale applications in terms of computational cost required. Here we investigate whether applying coarse-grained (CG) molecular dynamics simulations is a viable alternative for complexes of known structure. We calculate the free energy barrier with respect to the bound state based on molecular dynamics simulations using both a full atomistic and a CG force field for the TCR-pMHC complex and the MP1-p14 scaffolding complex. We find that the free energy barriers from the CG simulations are of similar accuracy as those from the full atomistic ones, while achieving a speedup of >500-fold. We also observe that extensive sampling is extremely important to obtain accurate free energy barriers, which is only within reach for the CG models. Finally, we show that the CG model preserves biological relevance of the interactions: (i) we observe a strong correlation between evolutionary likelihood of mutations and the impact on the free energy barrier with respect to the bound state; and (ii) we confirm the dominant role of the interface core in these interactions. Therefore, our results suggest that CG molecular simulations can realistically be used for the accurate prediction of protein-protein interaction strength. The python analysis framework and data files are available for download at http://www.ibi.vu.nl/downloads/bioinformatics-2013-btt675.tgz.

Ab-initio investigations for opto-electronic response of (Cd, Zn)Ga2Te4: Promising solar PV materials

NASA Astrophysics Data System (ADS)

Sahariya, Jagrati; Soni, Amit; Kumar, Pancham

2018-04-01

In this paper, the first principle calculations are performed to analyze the structural, electronic and optical behavior of promising solar materials (Cd,Zn)Ga2Te4. To perform these calculations we have used one of the most accurate Full Potential Linearized Augmented Plane Wave (FP-LAPW) method. The ground state properties of these compounds are confirmed over here after proper examination of energy and charge convergence using Perdew-Burke-Ernzerhof (PBE-sol) exchange correlation potential. The investigations performed such as energy band structure, Density of States (DOS), optical parameters like complex dielectric function and absorption co-efficient are discussed over here to understand the overall response of the chosen system.

Structure-based multiscale approach for identification of interaction partners of PDZ domains.

PubMed

Tiwari, Garima; Mohanty, Debasisa

2014-04-28

PDZ domains are peptide recognition modules which mediate specific protein-protein interactions and are known to have a complex specificity landscape. We have developed a novel structure-based multiscale approach which identifies crucial specificity determining residues (SDRs) of PDZ domains from explicit solvent molecular dynamics (MD) simulations on PDZ-peptide complexes and uses these SDRs in combination with knowledge-based scoring functions for proteomewide identification of their interaction partners. Multiple explicit solvent simulations ranging from 5 to 50 ns duration have been carried out on 28 PDZ-peptide complexes with known binding affinities. MM/PBSA binding energy values calculated from these simulations show a correlation coefficient of 0.755 with the experimental binding affinities. On the basis of the SDRs of PDZ domains identified by MD simulations, we have developed a simple scoring scheme for evaluating binding energies for PDZ-peptide complexes using residue based statistical pair potentials. This multiscale approach has been benchmarked on a mouse PDZ proteome array data set by calculating the binding energies for 217 different substrate peptides in binding pockets of 64 different mouse PDZ domains. Receiver operating characteristic (ROC) curve analysis indicates that, the area under curve (AUC) values for binder vs nonbinder classification by our structure based method is 0.780. Our structure based method does not require experimental PDZ-peptide binding data for training.

Structure-Function of the Cytochrome b 6f Complex of Oxygenic Photosynthesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cramer, W. A.; Yamashita, E.; Baniulis, D.

2014-03-20

Structure–function of the major integral membrane cytochrome b 6f complex that functions in cyanobacteria, algae, and green plants to transfer electrons between the two reaction center complexes in the electron transport chain of oxygenic photosynthesis is discussed in the context of recently obtained crystal structures of the complex and soluble domains of cytochrome f and the Rieske iron–sulfur protein. The energy-transducing function of the complex, generation of the proton trans-membrane electrochemical potential gradient, centers on the oxidation/reduction pathways of the plastoquinol/plastoquinone (QH 2/Q), the proton donor/acceptor within the complex. These redox reactions are carried out by five redox prosthetic groupsmore » embedded in each monomer, the high potential two iron–two sulfur cluster and the heme of cytochrome f on the electropositive side (p) of the complex, two noncovalently bound b-type hemes that cross the complex and the membrane, and a covalently bound c-type heme (c n) on the electronegative side (n). These five redox-active groups are organized in high- (cyt f/[2Fe–2S] and low-potential (hemes b p, b n, c n) electron transport pathways that oxidize and reduce the quinol and quinone on the p- and n-sides in a Q-cycle-type mechanism, while translocating as many as 2 H + to the p-side aqueous side for every electron transferred through the high potential chain to the photosystem I reaction center. The presence of heme c n and the connection of the n-side of the membrane and b 6f complex to the cyclic electron transport chain indicate that the Q cycle in the oxygenic photosynthetic electron transport chain differs from those connected to the bc 1 complex in the mitochondrial respiratory chain and the chain in photosynthetic bacteria. Inferences from the structure and C2 symmetry of the complex for the pathway of QH 2/Q transfer within the complex, problems posed by the presence of lipid in the inter-monomer cavity, and the narrow portal for QH2 passage through the p-side oxidation site proximal to the [2Fe–2S] cluster are discussed.« less

The guanidine and maleic acid (1:1) complex. The additional theoretical and experimental studies.

PubMed

Drozd, Marek; Dudzic, Damian

2012-04-01

On the basis of experimental literature data the theoretical studies for guanidinium and maleic acid complex with using DFT method are performed. In these studies the experimental X-ray data for two different forms of investigated crystal were used. During the geometry optimization process one equilibrium structure was found, only. According to this result the infrared spectrum for one theoretical molecule was calculated. On the basis of potential energy distribution (PED) analysis the clear-cut assignments of observed bands were performed. For the calculated molecule with energy minimum the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) were obtained and graphically illustrated. The energy difference (GAP) between HOMO and LUMO was analyzed. Additionally, the nonlinear properties of this molecule were calculated. The α and β (first and second order) hyperpolarizability values are obtained. On the basis of these results the title crystal was classified as new second order NLO generator. Copyright © 2011 Elsevier B.V. All rights reserved.

Mitochondrial protein hyperacetylation in the failing heart

PubMed Central

Horton, Julie L.; Martin, Ola J.; Lai, Ling; Richards, Alicia L.; Vega, Rick B.; Leone, Teresa C.; Pagliarini, David J.; Muoio, Deborah M.; Bedi, Kenneth C.; Coon, Joshua J.

2016-01-01

Myocardial fuel and energy metabolic derangements contribute to the pathogenesis of heart failure. Recent evidence implicates posttranslational mechanisms in the energy metabolic disturbances that contribute to the pathogenesis of heart failure. We hypothesized that accumulation of metabolite intermediates of fuel oxidation pathways drives posttranslational modifications of mitochondrial proteins during the development of heart failure. Myocardial acetylproteomics demonstrated extensive mitochondrial protein lysine hyperacetylation in the early stages of heart failure in well-defined mouse models and the in end-stage failing human heart. To determine the functional impact of increased mitochondrial protein acetylation, we focused on succinate dehydrogenase A (SDHA), a critical component of both the tricarboxylic acid (TCA) cycle and respiratory complex II. An acetyl-mimetic mutation targeting an SDHA lysine residue shown to be hyperacetylated in the failing human heart reduced catalytic function and reduced complex II–driven respiration. These results identify alterations in mitochondrial acetyl-CoA homeostasis as a potential driver of the development of energy metabolic derangements that contribute to heart failure. PMID:26998524

Mitochondrial protein hyperacetylation in the failing heart.

PubMed

Horton, Julie L; Martin, Ola J; Lai, Ling; Riley, Nicholas M; Richards, Alicia L; Vega, Rick B; Leone, Teresa C; Pagliarini, David J; Muoio, Deborah M; Bedi, Kenneth C; Margulies, Kenneth B; Coon, Joshua J; Kelly, Daniel P

2016-02-01

Myocardial fuel and energy metabolic derangements contribute to the pathogenesis of heart failure. Recent evidence implicates posttranslational mechanisms in the energy metabolic disturbances that contribute to the pathogenesis of heart failure. We hypothesized that accumulation of metabolite intermediates of fuel oxidation pathways drives posttranslational modifications of mitochondrial proteins during the development of heart failure. Myocardial acetylproteomics demonstrated extensive mitochondrial protein lysine hyperacetylation in the early stages of heart failure in well-defined mouse models and the in end-stage failing human heart. To determine the functional impact of increased mitochondrial protein acetylation, we focused on succinate dehydrogenase A (SDHA), a critical component of both the tricarboxylic acid (TCA) cycle and respiratory complex II. An acetyl-mimetic mutation targeting an SDHA lysine residue shown to be hyperacetylated in the failing human heart reduced catalytic function and reduced complex II-driven respiration. These results identify alterations in mitochondrial acetyl-CoA homeostasis as a potential driver of the development of energy metabolic derangements that contribute to heart failure.

Density functional perturbational orbital theory of spin polarization in electronic systems. II. Transition metal dimer complexes.

PubMed

Seo, Dong-Kyun

2007-11-14

We present a theoretical scheme for a semiquantitative analysis of electronic structures of magnetic transition metal dimer complexes within spin density functional theory (DFT). Based on the spin polarization perturbational orbital theory [D.-K. Seo, J. Chem. Phys. 125, 154105 (2006)], explicit spin-dependent expressions of the spin orbital energies and coefficients are derived, which allows to understand how spin orbitals form and change their energies and shapes when two magnetic sites are coupled either ferromagnetically or antiferromagnetically. Upon employment of the concept of magnetic orbitals in the active-electron approximation, a general mathematical formula is obtained for the magnetic coupling constant J from the analytical expression for the electronic energy difference between low-spin broken-symmetry and high-spin states. The origin of the potential exchange and kinetic exchange terms based on the one-electron picture is also elucidated. In addition, we provide a general account of the DFT analysis of the magnetic exchange interactions in compounds for which the active-electron approximation is not appropriate.

Energy Efficiency in Public Buildings through Context-Aware Social Computing

PubMed Central

García, Óscar; Alonso, Ricardo S.; Prieto, Javier; Corchado, Juan M.

2017-01-01

The challenge of promoting behavioral changes in users that leads to energy savings in public buildings has become a complex task requiring the involvement of multiple technologies. Wireless sensor networks have a great potential for the development of tools, such as serious games, that encourage acquiring good energy and healthy habits among users in the workplace. This paper presents the development of a serious game using CAFCLA, a framework that allows for integrating multiple technologies, which provide both context-awareness and social computing. Game development has shown that the data provided by sensor networks encourage users to reduce energy consumption in their workplace and that social interactions and competitiveness allow for accelerating the achievement of good results and behavioral changes that favor energy savings. PMID:28398237

Study of the Structural Stability in Intermetallics Using Displacive Transformation Paths

NASA Astrophysics Data System (ADS)

Sob, M.; Wang, L. G.; Vitek, V.

1997-03-01

Relative structural stability of TiAl, FeAl, NiAl and NiTi is studied by investigating displacive phase transformation paths. These include the well known tetragonal (Bain's) and trigonal deformation paths which correspond to large homogeneous straining, and also more complex paths that include the shuffling of atomic planes. The results of full-potential APW total energy calculations show that all higher-energy cubic structures studied are locally unstable with respect to some deformation modes. There may or may not be symmetry-dictated energy extrema corresponding to cubic lattices depending on the atomic ordering. However, other energy extrema that are not imposed by symmetry requirements occur along the transformation paths. Configurations corresponding to energy minima may represent metastable structures that can play an important role in interfaces and other extended defects.

Space-time dependence between energy sources and climate related energy production

NASA Astrophysics Data System (ADS)

Engeland, Kolbjorn; Borga, Marco; Creutin, Jean-Dominique; Ramos, Maria-Helena; Tøfte, Lena; Warland, Geir

2014-05-01

The European Renewable Energy Directive adopted in 2009 focuses on achieving a 20% share of renewable energy in the EU overall energy mix by 2020. A major part of renewable energy production is related to climate, called "climate related energy" (CRE) production. CRE production systems (wind, solar, and hydropower) are characterized by a large degree of intermittency and variability on both short and long time scales due to the natural variability of climate variables. The main strategies to handle the variability of CRE production include energy-storage, -transport, -diversity and -information (smart grids). The three first strategies aim to smooth out the intermittency and variability of CRE production in time and space whereas the last strategy aims to provide a more optimal interaction between energy production and demand, i.e. to smooth out the residual load (the difference between demand and production). In order to increase the CRE share in the electricity system, it is essential to understand the space-time co-variability between the weather variables and CRE production under both current and future climates. This study presents a review of the literature that searches to tackle these problems. It reveals that the majority of studies deals with either a single CRE source or with the combination of two CREs, mostly wind and solar. This may be due to the fact that the most advanced countries in terms of wind equipment have also very little hydropower potential (Denmark, Ireland or UK, for instance). Hydropower is characterized by both a large storage capacity and flexibility in electricity production, and has therefore a large potential for both balancing and storing energy from wind- and solar-power. Several studies look at how to better connect regions with large share of hydropower (e.g., Scandinavia and the Alps) to regions with high shares of wind- and solar-power (e.g., green battery North-Sea net). Considering time scales, various studies consider wind and solar power production and their co-fluctuation at small time scales. The multi-scale nature of the variability is less studied, i.e., the potential adverse or favorable co-fluctuation at intermediate time scales involving water scarcity or abundance, is less present in the literature.Our review points out that it could be especially interesting to promote research on how the pronounced large-scale fluctuations in inflow to hydropower (intra-annual run-off) and smaller scale fluctuations in wind- and solar-power interact in an energy system. There is a need to better represent the profound difference between wind-, solar- and hydro-energy sources. On the one hand, they are all directly linked to the 2-D horizontal dynamics of meteorology. On the other hand, the branching structure of hydrological systems transforms this variability and governs the complex combination of natural inflows and reservoir storage.Finally, we note that the CRE production is, in addition to weather, also influenced by the energy system and market, i.e., the energy transport and demand across scales as well as changes of market regulation. The CRE production system lies thus in this nexus between climate, energy systems and market regulations. The work presented is part of the FP7 project COMPLEX (Knowledge based climate mitigation systems for a low carbon economy; http://www.complex.ac.uk)

Visualization of complex DNA double-strand breaks in a tumor treated with carbon ion radiotherapy

PubMed Central

Oike, Takahiro; Niimi, Atsuko; Okonogi, Noriyuki; Murata, Kazutoshi; Matsumura, Akihiko; Noda, Shin-Ei; Kobayashi, Daijiro; Iwanaga, Mototaro; Tsuchida, Keisuke; Kanai, Tatsuaki; Ohno, Tatsuya; Shibata, Atsushi; Nakano, Takashi

2016-01-01

Carbon ion radiotherapy shows great potential as a cure for X-ray-resistant tumors. Basic research suggests that the strong cell-killing effect induced by carbon ions is based on their ability to cause complex DNA double-strand breaks (DSBs). However, evidence supporting the formation of complex DSBs in actual patients is lacking. Here, we used advanced high-resolution microscopy with deconvolution to show that complex DSBs are formed in a human tumor clinically treated with carbon ion radiotherapy, but not in a tumor treated with X-ray radiotherapy. Furthermore, analysis using a physics model suggested that the complexity of radiotherapy-induced DSBs is related to linear energy transfer, which is much higher for carbon ion beams than for X-rays. Visualization of complex DSBs in clinical specimens will help us to understand the anti-tumor effects of carbon ion radiotherapy. PMID:26925533

Perspective: Machine learning potentials for atomistic simulations

NASA Astrophysics Data System (ADS)

Behler, Jörg

2016-11-01

Nowadays, computer simulations have become a standard tool in essentially all fields of chemistry, condensed matter physics, and materials science. In order to keep up with state-of-the-art experiments and the ever growing complexity of the investigated problems, there is a constantly increasing need for simulations of more realistic, i.e., larger, model systems with improved accuracy. In many cases, the availability of sufficiently efficient interatomic potentials providing reliable energies and forces has become a serious bottleneck for performing these simulations. To address this problem, currently a paradigm change is taking place in the development of interatomic potentials. Since the early days of computer simulations simplified potentials have been derived using physical approximations whenever the direct application of electronic structure methods has been too demanding. Recent advances in machine learning (ML) now offer an alternative approach for the representation of potential-energy surfaces by fitting large data sets from electronic structure calculations. In this perspective, the central ideas underlying these ML potentials, solved problems and remaining challenges are reviewed along with a discussion of their current applicability and limitations.

Kinetics and thermodynamics of bovine serum albumin interactions with Congo red dye.

PubMed

de Paula, Hauster Maximiler Campos; Coelho, Yara Luiza; Agudelo, Alvaro Javier Patiño; Rezende, Jaqueline de Paula; Ferreira, Gabriel Max Dias; Ferreira, Guilherme Max Dias; Pires, Ana Clarissa Dos Santos; da Silva, Luis Henrique Mendes

2017-11-01

To optimize the therapeutic applications of Congo red (CR), a potential inhibitor of protein aggregation, the kinetics and thermodynamics of the interactions between CR and a model protein need to be understood. We used surface plasmon resonance (SPR) and fluorescence techniques to determine the dynamics and thermodynamic parameters for the formation of complexes between CR and bovine serum albumin (BSA). CR interacts with BSA through a transition complex; the activation energy for association (E act(a) ) was determined to be 35.88kJmol -1 , while the activation enthalpy (ΔH ‡ ), entropy (ΔS ‡ ), and Gibbs free energy (ΔG ‡ ) are 33.41kJmol -1 , 0.18Jmol -1 K -1 , and 33.35kJmol -1 , respectively. When this intermediate transforms into the final CR-BSA complex, the entropy of the system increases and part of the absorbed energy is released; this process is associated with a reverse activation energy (E act(d) ) of 20.17kJmol -1 , and values of ΔH ‡ , ΔS ‡ , and ΔG ‡ of 17.69kJmol -1 , -162.86Jmol -1 K -1 , and 66.25kJmol -1 , respectively. A comparison of the SPR and fluorescence results suggests that there is more than one site where BSA interacts with CR. Copyright © 2017 Elsevier B.V. All rights reserved.

Theoretical study on the antitumor properties of Ru(II) complexes containing 2-pyridyl, 2-pyridine-4-carboxylic acid ligands

NASA Astrophysics Data System (ADS)

Erkan kariper, Sultan; Sayin, Koray; Karakaş, Duran

2017-12-01

[Ru(bipy)2(CppH)]2+(1), [Ru(bipy)2(Cpp-NH-Hex-COOH)]2+(2), [Ru(dppz)2(CppH)]2+(3) and [Ru(dppz)2(Cpp-NH-Hex-COOH)]2+(4) were calculated by Hartree-Fock (HF), Density Functional Theory (DFT) hybrid B3LYP and Moller-Plesset Perturbation (MPn n = 2,3) theory method and CEP-4G, CEP-31G, CEP-121G, LANL2DZ, LANL2MB, SDD basic sets and a mixed basic set with the keyword GEN in gas phase and water. Structure parameters obtained from optimized structures were compared with experimental parameters. M062X/(6-31G(d))(CEP-4G) level was taken into account for the most appropriate calculation level. IR, UV-VIS and NMR spectrums were examined for structural characterization. The optimal structure was identified via structure parameters, IR, UV-VIS and NMR spectrums. For the most compatible structure, the highest molecular orbital energy (EHOMO) which one of the most effective chemical determiners on the antitumor activity of the complexes, the lowest molecular orbital energy (ELUMO), LUMO-HOMO energy gap, hardness (η), softness (σ), electronegativity (χ), chemical potential (μ), electrophilicity index (ω), molar volume (V), dipole moment (DM), total negative charge (TNC), enthalpy (H), entropy (S) and total energy (E) were calculated. The causes of anticancer activity of the complexes have been studied.

A computational study of anion-modulated cation-π interactions.

PubMed

Carrazana-García, Jorge A; Rodríguez-Otero, Jesús; Cabaleiro-Lago, Enrique M

2012-05-24

The interaction of anions with cation-π complexes formed by the guanidinium cation and benzene was thoroughly studied by means of computational methods. Potential energy surface scans were performed in order to evaluate the effect of the anion coming closer to the cation-π pair. Several structures of guanidinium-benzene complexes and anion approaching directions were examined. Supermolecule calculations were performed on ternary complexes formed by guanidinium, benzene, and one anion and the interaction energy was decomposed into its different two- and three-body contributions. The interaction energies were further dissected into their electrostatic, exchange, repulsion, polarization and dispersion contributions by means of local molecular orbital energy decomposition analysis. The results confirm that, besides the electrostatic cation-anion attraction, the effect of the anion over the cation-π interaction is mainly due to polarization and can be rationalized following the changes in the anion-π and the nonadditive (three-body) terms of the interaction. When the cation and the anion are on the same side of the π system, the three-body interaction is anticooperative, but when the anion and the cation are on opposite sides of the π system, the three-body interaction is cooperative. As far as we know, this is the first study where this kind of analysis is carried out with a structured cation as guanidinium with a significant biological interest.

Optimal energy growth in a stably stratified shear flow

NASA Astrophysics Data System (ADS)

Jose, Sharath; Roy, Anubhab; Bale, Rahul; Iyer, Krithika; Govindarajan, Rama

2018-02-01

Transient growth of perturbations by a linear non-modal evolution is studied here in a stably stratified bounded Couette flow. The density stratification is linear. Classical inviscid stability theory states that a parallel shear flow is stable to exponentially growing disturbances if the Richardson number (Ri) is greater than 1/4 everywhere in the flow. Experiments and numerical simulations at higher Ri show however that algebraically growing disturbances can lead to transient amplification. The complexity of a stably stratified shear flow stems from its ability to combine this transient amplification with propagating internal gravity waves (IGWs). The optimal perturbations associated with maximum energy amplification are numerically obtained at intermediate Reynolds numbers. It is shown that in this wall-bounded flow, the three-dimensional optimal perturbations are oblique, unlike in unstratified flow. A partitioning of energy into kinetic and potential helps in understanding the exchange of energies and how it modifies the transient growth. We show that the apportionment between potential and kinetic energy depends, in an interesting manner, on the Richardson number, and on time, as the transient growth proceeds from an optimal perturbation. The oft-quoted stabilizing role of stratification is also probed in the non-diffusive limit in the context of disturbance energy amplification.

MULTIMODE quantum calculations of vibrational energies and IR spectrum of the NO⁺(H₂O) cluster using accurate potential energy and dipole moment surfaces.

PubMed

Homayoon, Zahra

2014-09-28

A new, full (nine)-dimensional potential energy surface and dipole moment surface to describe the NO(+)(H2O) cluster is reported. The PES is based on fitting of roughly 32,000 CCSD(T)-F12/aug-cc-pVTZ electronic energies. The surface is a linear least-squares fit using a permutationally invariant basis with Morse-type variables. The PES is used in a Diffusion Monte Carlo study of the zero-point energy and wavefunction of the NO(+)(H2O) and NO(+)(D2O) complexes. Using the calculated ZPE the dissociation energies of the clusters are reported. Vibrational configuration interaction calculations of NO(+)(H2O) and NO(+)(D2O) using the MULTIMODE program are performed. The fundamental, a number of overtone, and combination states of the clusters are reported. The IR spectrum of the NO(+)(H2O) cluster is calculated using 4, 5, 7, and 8 modes VSCF/CI calculations. The anharmonic, coupled vibrational calculations, and IR spectrum show very good agreement with experiment. Mode coupling of the water "antisymmetric" stretching mode with the low-frequency intermolecular modes results in intensity borrowing.

MULTIMODE quantum calculations of vibrational energies and IR spectrum of the NO+(H2O) cluster using accurate potential energy and dipole moment surfaces

NASA Astrophysics Data System (ADS)

Homayoon, Zahra

2014-09-01

A new, full (nine)-dimensional potential energy surface and dipole moment surface to describe the NO+(H2O) cluster is reported. The PES is based on fitting of roughly 32 000 CCSD(T)-F12/aug-cc-pVTZ electronic energies. The surface is a linear least-squares fit using a permutationally invariant basis with Morse-type variables. The PES is used in a Diffusion Monte Carlo study of the zero-point energy and wavefunction of the NO+(H2O) and NO+(D2O) complexes. Using the calculated ZPE the dissociation energies of the clusters are reported. Vibrational configuration interaction calculations of NO+(H2O) and NO+(D2O) using the MULTIMODE program are performed. The fundamental, a number of overtone, and combination states of the clusters are reported. The IR spectrum of the NO+(H2O) cluster is calculated using 4, 5, 7, and 8 modes VSCF/CI calculations. The anharmonic, coupled vibrational calculations, and IR spectrum show very good agreement with experiment. Mode coupling of the water "antisymmetric" stretching mode with the low-frequency intermolecular modes results in intensity borrowing.

A general intermolecular force field based on tight-binding quantum chemical calculations

NASA Astrophysics Data System (ADS)

Grimme, Stefan; Bannwarth, Christoph; Caldeweyher, Eike; Pisarek, Jana; Hansen, Andreas

2017-10-01

A black-box type procedure is presented for the generation of a molecule-specific, intermolecular potential energy function. The method uses quantum chemical (QC) information from our recently published extended tight-binding semi-empirical scheme (GFN-xTB) and can treat non-covalently bound complexes and aggregates with almost arbitrary chemical structure. The necessary QC information consists of the equilibrium structure, Mulliken atomic charges, charge centers of localized molecular orbitals, and also of frontier orbitals and orbital energies. The molecular pair potential includes model density dependent Pauli repulsion, penetration, as well as point charge electrostatics, the newly developed D4 dispersion energy model, Drude oscillators for polarization, and a charge-transfer term. Only one element-specific and about 20 global empirical parameters are needed to cover systems with nuclear charges up to radon (Z = 86). The method is tested for standard small molecule interaction energy benchmark sets where it provides accurate intermolecular energies and equilibrium distances. Examples for structures with a few hundred atoms including charged systems demonstrate the versatility of the approach. The method is implemented in a stand-alone computer code which enables rigid-body, global minimum energy searches for molecular aggregation or alignment.

Chalcogen- and halogen-bonds involving SX2 (X = F, Cl, and Br) with formaldehyde.

PubMed

Mo, Lixin; Zeng, Yanli; Li, Xiaoyan; Zhang, Xueying; Meng, Lingpeng

2016-07-01

The capacity of SX2 (X = F, Cl, and Br) to engage in different kinds of noncovalent bonds was investigated by ab initio calculations. SCl2 (SBr2) has two σ-holes upon extension of Cl (Br)-S bonds, and two σ-holes upon extension of S-Cl (Br) bonds. SF2 contains only two σ-holes upon extension of the F-S bond. Consequently, SCl2 and SBr2 form chalcogen and halogen bonds with the electron donor H2CO while SF2 forms only a chalcogen bond, i.e., no F···O halogen bond was found in the SF2:H2CO complex. The S···O chalcogen bond between SF2 and H2CO is the strongest, while the strongest halogen bond is Br···O between SBr2 and H2CO. The nature of these two types of noncovalent interaction was probed by a variety of methods, including molecular electrostatic potentials, QTAIM, energy decomposition, and electron density shift maps. Termolecular complexes X2S···H2CO···SX'2 (X = F, Cl, Br, and X' = Cl, Br) were constructed to study the interplay between chalcogen bonds and halogen bonds. All these complexes contained S···O and Cl (Br)···O bonds, with longer intermolecular distances, smaller values of electron density, and more positive three-body interaction energies, indicating negative cooperativity between the chalcogen bond and the halogen bond. In addition, for all complexes studied, interactions involving chalcogen bonds were more favorable than those involving halogen bonds. Graphical Abstract Molecular electrostatic potential and contour map of the Laplacian of the electron density in Cl2S···H2CO···SCl2 complex.

A combined experimental and DFT study of active structures and self-cycle mechanisms of mononuclear tungsten peroxo complexes in oxidation reactions

NASA Astrophysics Data System (ADS)

Jin, Peng; Wei, Donghui; Wen, Yiqiang; Luo, Mengfei; Wang, Xiangyu; Tang, Mingsheng

2011-04-01

Tungsten peroxo complexes have been widely used in olefin epoxidation, alcohol oxidation, Baeyer-Villiger oxidation and other oxidation reactions, however, there is still not a unanimous viewpoint for the active structure of mononuclear tungsten peroxo complex by now. In this paper, the catalysis of mononuclear tungsten peroxo complexes 0- 5 with or without acidic ligands for the green oxidation of cyclohexene to adipic acid in the absence of organic solvent and phase-transfer catalyst has been researched in experiment. Then we have suggested two possible kinds of active structures of mononuclear tungsten peroxo complexes including peroxo ring ( nA, n = 0-1) and hydroperoxo ( nB, n = 0-1) structures, which have been investigated using density functional theory (DFT). Moreover, the calculations on self-cycle mechanisms involving the two types of active structures of tungsten peroxo complexes with and without oxalic acid ligand have also been carried out at the B3LYP/[LANL2DZ/6-31G(d, p)] level. The highest energy barrier are 26.17 kcal/mol ( 0A, peroxo ring structure without oxalic acid ligand), 23.91 kcal/mol ( 1A, peroxo ring structure with oxalic acid ligand), 18.19 kcal/mol ( 0B, hydroperoxo structure without oxalic acid ligand) and 13.10 kcal/mol ( 1B, hydroperoxo structure with oxalic acid ligand) in the four potential energy profiles, respectively. The results indicate that both the energy barriers of active structure self-cycle processes with oxalic acid ligands are lower than those without oxalic acid ligands, so the active structures with oxalic acid ligands should be easier to recycle, which is in good agreement with our experimental results. However, due to the higher energy of product than that of the reactant, the energy profile of the self-cycle process of 1B shows that the recycle of 1B could not occur at all in theory. Moreover, the crystal data of peroxo ring structure with oxalic acid ligand could be found in some experimental references. Thus, the viewpoint that the peroxo ring active structure should be the real active structure has been proved in this paper.

Flexible operation of batteries in power system scheduling with renewable energy

DOE PAGES

Li, Nan; Uckun, Canan; Constantinescu, Emil M.; ...

2015-12-17

The fast growing expansion of renewable energy increases the complexities in balancing generation and demand in the power system. The energy-shifting and fast-ramping capability of energy storage has led to increasing interests in batteries to facilitate the integration of renewable resources. In this paper, we present a two-step framework to evaluate the potential value of energy storage in power systems with renewable generation. First, we formulate a stochastic unit commitment approach with wind power forecast uncertainty and energy storage. Second, the solution from the stochastic unit commitment is used to derive a flexible schedule for energy storage in economic dispatchmore » where the look-ahead horizon is limited. Here, analysis is conducted on the IEEE 24-bus system to demonstrate the benefits of battery storage in systems with renewable resources and the effectiveness of the proposed battery operation strategy.« less

Prospects and applicability of wave energy for South Africa

NASA Astrophysics Data System (ADS)

Lavidas, George; Venugopal, Vengatesan

2018-03-01

Renewable energy offers significant opportunities for electricity diversification. South Africa belongs to the group of developing nations and encompasses a lot of potential for renewable energy developments. Currently, the majority of its electricity production originates from fossil fuels; however, incorporation of clean coal technologies will aid in reaching the assigned targets. This study offers a long-term wave power quantification analysis with a numerical wave model. The investigation includes long-term resource assessment in the region, variability, seasonal and monthly wave energy content. Locations with high-energy content but low variability pose an opportunity that can contribute in the alleviation of energy poverty. Application of wave converters depends on the combination of complex terms. The study presents resource levels and the joint distributions, which indicate suitability for converter selection. Depending on the region of interest, these characteristics change. Thus, this resource assessment adds knowledge on wave power and optimal consideration for wave energy applicability.

Probing Aspergillus niger glucose oxidase with pentacyanoferrate(III) aza- and thia-complexes.

PubMed

Kulys, J; Tetianec, L; Ziemys, A

2006-10-01

Complexes of pentacyanoferrate(III) and biologically relevant ligands, such as pyridine, pyrazole, imidazole, histidine, and other aza- and thia-heterocycles, were synthesized. Their spectral, electrochemical properties, electron exchange constants, electronic structure parameters, and reactivity with glucose oxidase from Aspergillus niger were determined. The formation of the complexes following ammonia replacement by the ligands was associated with the appearance of a new band of absorbance in the visible spectrum. The constants of the complexes formation calculated at a ligand-pentacyanoferrate(III) concentrations ratio of 10:1, were 7.5 x 10(-5), 7.7 x 10(-5), and 1.8 x 10(-3) s(-1) for benzotriazole, benzimidazole, and aminothiazole ligands, respectively. The complexes showed quasi-reversible redox conversion at a glassy carbon electrode. The redox potential of the complexes spanned the potential range from 70 to 240 mV vs. saturated calomel electrode (SCE) at pH7.2. For most of the complexes self-exchange constants (k(11)) were similar to or larger than that of hexacyanoferrate(III) (ferricyanide). The complexes containing pyridine derivatives and thia-heterocyclic ligands held a lower value of k(11) than that of ferricyanide. All complexes reacted with reduced glucose oxidase at pH7.2. The reactivity of the complex containing pyrazole was the largest in comparison to the rest of the complexes. Correlations between the complexes' reactivity and both the free energy of reaction and k(11) shows that the reactivity of pentacyanoferrates obeys the principles of Marcus's electron transfer theory. The obtained data suggest that large negative charges of the complexes decrease their reactivity.

Analysis of auroral particle fluxes

NASA Technical Reports Server (NTRS)

Chappell, C. R.

1972-01-01

The physical processes which describe the interaction of auroral electrons with the atmosphere appear to be more complex than just the Coulomb scattering of the incident primary electrons with a subsequent loss of energy. The comparison of the measured backscattered electron spectra with spectra predicted using a theoretical scattering calculation has led to a discrepancy for energies below about 1 to 2 keV. It was found that the very high ratio (100%) of backscattered to incident fluxes for these energies could be most reasonably explained by a parallel downward-directed electric field which prevents these lower energy electrons from entering the atmospheric scattering region. This parallel field with potential drop of about 1 keV is thought to have its origin in waveparticle interactions in the turbulent auroral ionosphere.

Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution.

PubMed

Comitani, Federico; Rossi, Kevin; Ceriotti, Michele; Sanz, M Eugenia; Molteni, Carla

2017-04-14

The conformational free energy landscape of aspartic acid, a proteogenic amino acid involved in a wide variety of biological functions, was investigated as an example of the complexity that multiple rotatable bonds produce even in relatively simple molecules. To efficiently explore such a landscape, this molecule was studied in the neutral and zwitterionic forms, in the gas phase and in water solution, by means of molecular dynamics and the enhanced sampling method metadynamics with classical force-fields. Multi-dimensional free energy landscapes were reduced to bi-dimensional maps through the non-linear dimensionality reduction algorithm sketch-map to identify the energetically stable conformers and their interconnection paths. Quantum chemical calculations were then performed on the minimum free energy structures. Our procedure returned the low energy conformations observed experimentally in the gas phase with rotational spectroscopy [M. E. Sanz et al., Phys. Chem. Chem. Phys. 12, 3573 (2010)]. Moreover, it provided information on higher energy conformers not accessible to experiments and on the conformers in water. The comparison between different force-fields and quantum chemical data highlighted the importance of the underlying potential energy surface to accurately capture energy rankings. The combination of force-field based metadynamics, sketch-map analysis, and quantum chemical calculations was able to produce an exhaustive conformational exploration in a range of significant free energies that complements the experimental data. Similar protocols can be applied to larger peptides with complex conformational landscapes and would greatly benefit from the next generation of accurate force-fields.

Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution

NASA Astrophysics Data System (ADS)

Comitani, Federico; Rossi, Kevin; Ceriotti, Michele; Sanz, M. Eugenia; Molteni, Carla

2017-04-01

The conformational free energy landscape of aspartic acid, a proteogenic amino acid involved in a wide variety of biological functions, was investigated as an example of the complexity that multiple rotatable bonds produce even in relatively simple molecules. To efficiently explore such a landscape, this molecule was studied in the neutral and zwitterionic forms, in the gas phase and in water solution, by means of molecular dynamics and the enhanced sampling method metadynamics with classical force-fields. Multi-dimensional free energy landscapes were reduced to bi-dimensional maps through the non-linear dimensionality reduction algorithm sketch-map to identify the energetically stable conformers and their interconnection paths. Quantum chemical calculations were then performed on the minimum free energy structures. Our procedure returned the low energy conformations observed experimentally in the gas phase with rotational spectroscopy [M. E. Sanz et al., Phys. Chem. Chem. Phys. 12, 3573 (2010)]. Moreover, it provided information on higher energy conformers not accessible to experiments and on the conformers in water. The comparison between different force-fields and quantum chemical data highlighted the importance of the underlying potential energy surface to accurately capture energy rankings. The combination of force-field based metadynamics, sketch-map analysis, and quantum chemical calculations was able to produce an exhaustive conformational exploration in a range of significant free energies that complements the experimental data. Similar protocols can be applied to larger peptides with complex conformational landscapes and would greatly benefit from the next generation of accurate force-fields.

Calculations of rate constants for the three-body recombination of H2 in the presence of H2

NASA Technical Reports Server (NTRS)

Schwenke, David W.

1988-01-01

A new global potential energy hypersurface for H2 + H2 is constructed and quasiclassical trajectory calculations performed using the resonance complex theory and energy transfer mechanism to estimate the rate of three body recombination over the temperature range 100 to 5000 K. The new potential is a faithful representation of ab initio electron structure calculations, is unchanged under the operation of exchanging H atoms, and reproduces the accurate H3 potential as one H atom is pulled away. Included in the fitting procedure are geometries expected to be important when one H2 is near or above the dissociation limit. The dynamics calculations explicitly include the motion of all four atoms and are performed efficiently using a vectorized variable-stepsize integrator. The predicted rate constants are approximately a factor of two smaller than experimental estimates over a broad temperature range.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Makarewicz, Jan, E-mail: jama@amu.edu.pl; Shirkov, Leonid

The pyridine-Ar (PAr) van der Waals (vdW) complex is studied using a high level ab initio method. Its structure, binding energy, and intermolecular vibrational states are determined from the analytical potential energy surface constructed from interaction energy (IE) values computed at the coupled cluster level of theory with single, double, and perturbatively included triple excitations with the augmented correlation consistent polarized valence double-ζ (aug-cc-pVDZ) basis set complemented by midbond functions. The structure of the complex at its global minimum with Ar at a distance of 3.509 Å from the pyridine plane and shifted by 0.218 Å from the center ofmore » mass towards nitrogen agrees well with the corresponding equilibrium structure derived previously from the rotational spectrum of PAr. The PAr binding energy D{sub e} of 392 cm{sup −1} is close to that of 387 cm{sup −1} calculated earlier at the same ab initio level for the prototypical benzene-Ar (BAr) complex. However, under an extension of the basis set, D{sub e} for PAr becomes slightly lower than D{sub e} for BAr. The ab initio vdW vibrational energy levels allow us to estimate the reliability of the methods for the determination of the vdW fundamentals from the rotational spectra. To disclose the character of the intermolecular interaction in PAr, the symmetry-adapted perturbation theory (SAPT) is employed for the analysis of different physical contributions to IE. It is found that SAPT components of IE can be approximately expressed in the binding region by only two of them: the exchange repulsion and dispersion energy. The total induction effect is negligible. The interrelations between various SAPT components found for PAr are fulfilled for a few other complexes involving aromatic molecules and Ar or Ne, which indicates that they are valid for all rare gas (Rg) atoms and aromatics.« less

Ab initio calculations of the effects of H+ and NH4+ on the initial decomposition of HMX.

PubMed

Wang, Luoxin; Tuo, Xinlin; Yi, Changhai; Wang, Xiaogong

2008-10-01

In this work, the effects of H(+) and NH(4)(+) on the initial decomposition of HMX were investigated on the basis of the B3P86/6-31G** and B3LYP/6-31G* calculations. Three initial decomposition pathways including the N-NO(2) bond fission, HONO elimination and C-N bond dissociation were considered for the complexes formed by HMX with H(+) (PHMX1 and PHMX2) or with NH(4)(+) (AHMX). We found that H(+) and NH(4)(+) did not evidently induce the HMX to trigger the N-NO(2) heterolysis because the energy barrier of N-NO(2) heterolysis was found to be higher than the bond dissociation energy of N-NO(2) homolytic cleavage. Meanwhile, the transition state barriers of the HONO elimination from the complexes were found to be similar to that from the isolated HMX, which means that the HONO elimination reaction of HMX was not affected by the H(+) and NH(4)(+). As for the ring-opening reaction of HMX due to the C-N bond dissociation, the calculated potential energy profile showed that the energy of the complex (AHMX) went uphill along the C-N bond length and no transition state existed on the curve. However, the transition state energy barriers of C-N bond dissociation were calculated to be only 5.0 kcal/mol and 5.5 kcal/mol for the PHMX1 and PHMX2 complexes, respectively, which were much lower than the C-N bond dissociation energy of isolated HMX. Moreover, among the three initial decomposition reactions, the C-N bond dissociation was also the most energetically favorable pathway for the PHMX1 and PHMX2. Our calculation results showed that the H(+) can significantly promote the initial thermal decomposition of C-N bond of HMX, which, however, is influenced by NH(4)(+) slightly.

Field Assessment of Energy Audit Tools for Retrofit Programs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edwards, J.; Bohac, D.; Nelson, C.

2013-07-01

This project focused on the use of home energy ratings as a tool to promote energy retrofits in existing homes. A home energy rating provides a quantitative appraisal of a home’s energy performance, usually compared to a benchmark such as the average energy use of similar homes in the same region. Rating systems based on energy performance models, the focus of this report, can establish a home’s achievable energy efficiency potential and provide a quantitative assessment of energy savings after retrofits are completed, although their accuracy needs to be verified by actual measurement or billing data. Ratings can also showmore » homeowners where they stand compared to their neighbors, thus creating social pressure to conform to or surpass others. This project field-tested three different building performance models of varying complexity, in order to assess their value as rating systems in the context of a residential retrofit program: Home Energy Score, SIMPLE, and REM/Rate.« less

Electronic structure and vibrational spectra of cis-diammine(orotato)platinum(II), a potential cisplatin analogue: DFT and experimental study

NASA Astrophysics Data System (ADS)

Wysokiński, Rafał; Hernik, Katarzyna; Szostak, Roman; Michalska, Danuta

2007-03-01

Orotic acid (vitamin B 13) is a key intermediate in biosynthesis of the pyrimidine nucleotides in living organisms, moreover, it may serve as the biological carrier for some metal ions. cis-Diammine(orotato)platinum(II), cis-[Pt(C 5H 2N 2O 4)(NH 3) 2] can be considered as a new potential cisplatin analogue. The FT-Raman and FT-IR spectra of the title complex are reported, for the first time. The molecular structure, vibrational frequencies, and the theoretical infrared and Raman intensities have been calculated by the density functional mPW1PW91 method. The detailed vibrational assignment has been made on the basis of the calculated potential energy distribution. The theoretically predicted IR and Raman spectra show very good agreement with experiment. Natural bond orbital (NBO) analyses were performed for cisplatin, carboplatin and the title complex. The results provided new data on the nature of platinum-ligand bonding in these compounds. Strong intramolecular hydrogen bond between the orotate ligand and the coordinated ammonia group stabilizes the structure of the platinum(II) complex. Thus, it is suggested that the orotate ligand in the title complex is more inert to the substitution reactions than the chloride ligands in cisplatin.

Gazprom Market for energy installations using fuel cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galitskiy, Yu.V.

1996-04-01

The Gazprom RAO [Russian joint-stock company] is a major industrial and financial complex whose job is to provide gas for the national economy of Russia, as well as to supply it under international and intergovernmental agreements. The existing capacity of its production structures and high level of scientific potential allow Gazprom to forecast the future with confidence.

Laser-driven localization of collective CO vibrations in metal-carbonyl complexes

NASA Astrophysics Data System (ADS)

Lisaj, Mateusz; Kühn, Oliver

2014-11-01

Using the example of a cobalt dicarbonyl complex it is shown that two perpendicular linearly polarized IR laser pulses can be used to trigger an excitation of the delocalized CO stretching modes, which corresponds to an alternating localization of the vibration within one CO bond. The switching time for localization in either of the two bonds is determined by the energy gap between the symmetric and asymmetric fundamental transition frequencies. The phase of the oscillation between the two local bond excitations can be tuned by the relative phase of the two pulses. The extend of control of bond localization is limited by the anharmonicity of the potential energy surfaces leading to wave packet dispersion. This prevents such a simple pulse scheme from being used for laser-driven bond breaking in the considered example.

Sound propagation from a ridge wind turbine across a valley.

PubMed

Van Renterghem, Timothy

2017-04-13

Sound propagation outdoors can be strongly affected by ground topography. The existence of hills and valleys between a source and receiver can lead to the shielding or focusing of sound waves. Such effects can result in significant variations in received sound levels. In addition, wind speed and air temperature gradients in the atmospheric boundary layer also play an important role. All of the foregoing factors can become especially important for the case of wind turbines located on a ridge overlooking a valley. Ridges are often selected for wind turbines in order to increase their energy capture potential through the wind speed-up effects often experienced in such locations. In this paper, a hybrid calculation method is presented to model such a case, relying on an analytical solution for sound diffraction around an impedance cylinder and the conformal mapping (CM) Green's function parabolic equation (GFPE) technique. The various aspects of the model have been successfully validated against alternative prediction methods. Example calculations with this hybrid analytical-CM-GFPE model show the complex sound pressure level distribution across the valley and the effect of valley ground type. The proposed method has the potential to include the effect of refraction through the inclusion of complex wind and temperature fields, although this aspect has been highly simplified in the current simulations.This article is part of the themed issue 'Wind energy in complex terrains'. © 2017 The Author(s).

Dependence of hydropower energy generation on forests in the Amazon Basin at local and regional scales

PubMed Central

Stickler, Claudia M.; Coe, Michael T.; Costa, Marcos H.; Nepstad, Daniel C.; McGrath, David G.; Dias, Livia C. P.; Rodrigues, Hermann O.; Soares-Filho, Britaldo S.

2013-01-01

Tropical rainforest regions have large hydropower generation potential that figures prominently in many nations’ energy growth strategies. Feasibility studies of hydropower plants typically ignore the effect of future deforestation or assume that deforestation will have a positive effect on river discharge and energy generation resulting from declines in evapotranspiration (ET) associated with forest conversion. Forest loss can also reduce river discharge, however, by inhibiting rainfall. We used land use, hydrological, and climate models to examine the local “direct” effects (through changes in ET within the watershed) and the potential regional “indirect” effects (through changes in rainfall) of deforestation on river discharge and energy generation potential for the Belo Monte energy complex, one of the world’s largest hydropower plants that is currently under construction on the Xingu River in the eastern Amazon. In the absence of indirect effects of deforestation, simulated deforestation of 20% and 40% within the Xingu River basin increased discharge by 4–8% and 10–12%, with similar increases in energy generation. When indirect effects were considered, deforestation of the Amazon region inhibited rainfall within the Xingu Basin, counterbalancing declines in ET and decreasing discharge by 6–36%. Under business-as-usual projections of forest loss for 2050 (40%), simulated power generation declined to only 25% of maximum plant output and 60% of the industry’s own projections. Like other energy sources, hydropower plants present large social and environmental costs. Their reliability as energy sources, however, must take into account their dependence on forests. PMID:23671098

Curcumin derivatives as metal-chelating agents with potential multifunctional activity for pharmaceutical applications.

PubMed

Ferrari, Erika; Benassi, Rois; Sacchi, Stefania; Pignedoli, Francesca; Asti, Mattia; Saladini, Monica

2014-10-01

Curcuminoids represent new perspectives for the development of novel therapeutics for Alzheimer's disease (AD), one probable mechanism of action is related to their metal complexing ability. In this work we examined the metal complexing ability of substituted curcuminoids to propose new chelating molecules with biological properties comparable with curcumin but with improved stability as new potential AD therapeutic agents. The K2T derivatives originate from the insertion of a -CH2COOC(CH3)3 group on the central atom of the diketonic moiety of curcumin. They retain the diketo-ketoenol tautomerism which is solvent dependent. In aqueous solution the prevalent form is the diketo one but the addition of metal ion (Ga(3+), Cu(2+)) causes the dissociation of the enolic proton creating chelate complexes and shifting the tautomeric equilibrium towards the keto-enol form. The formation of metal complexes is followed by both NMR and UV-vis spectroscopy. The density functional theory (DFT) calculations on K2T21 complexes with Ga(3+) and Cu(2+) are performed and compared with those on curcumin complexes. [Ga(K2T21)2(H2O)2](+) was found more stable than curcumin one. Good agreement is detected between calculated and experimental (1)H and (13)C NMR data. The calculated OH bond dissociation energy (BDE) and the OH proton dissociation enthalpy (PDE), allowed to predict the radical scavenging ability of the metal ion complexed with K2T21, while the calculated electronic affinity (EA) and ionization potential (IP) represent yardsticks of antioxidant properties. Eventually theoretical calculations suggest that the proton-transfer-associated superoxide-scavenging activity is enhanced after binding metal ions, and that Ga(3+) complexes display possible superoxide dismutase (SOD)-like activity. Copyright © 2014 Elsevier Inc. All rights reserved.

Zinc complexes as fluorescent chemosensors for nucleic acids: new perspectives for a "boring" element.

PubMed

Terenzi, Alessio; Lauria, Antonino; Almerico, Anna Maria; Barone, Giampaolo

2015-02-28

Zinc(II) complexes are effective and selective nucleic acid-binders and strongly fluorescent molecules in the low energy range, from the visible to the near infrared. These two properties have often been exploited to quantitatively detect nucleic acids in biological samples, in both in vitro and in vivo models. In particular, the fluorescent emission of several zinc(II) complexes is drastically enhanced or quenched by the binding to nucleic acids and/or upon visible light exposure, in a different fashion in bulk solution and when bound to DNA. The twofold objective of this perspective is (1) to review recent utilisations of zinc(II) complexes as selective fluorescent probes for nucleic acids and (2) to highlight their novel potential applications as diagnostic tools based on their photophysical properties.

Interactions of Marine Hydrokinetic Devices in Complex Bathymetries: Numerical Simulations in the Chacao Channel in Southern Chile.

NASA Astrophysics Data System (ADS)

Soto, K. A.; Escauriaza, C. R.; Richter, D. H.

2015-12-01

Many coastal areas in the South Pacific Ocean can provide significant marine energy resources in the near future. The installation of marine hydrokinetic (MHK) devices in these regions will require new approaches to understand physical and environmental processes that are relevant for the installation of turbine arrays, which are also specific of each site. The coastal morphology of the Chacao channel in southern Chile, which separates the Chiloé island from the main continent (41º47'S, 73º31'W) stands out as an important energy resource that can potentially contribute a significant power capacity. This coastal area not only sustains delicate ecosystems with limited anthropic intervention, but it is characterized by a complex bathymetry that can have important effects on the performance of MHK devices and their local impacts. To understand the interactions of the local bathymetry and ambient turbulence with turbine arrays, we carry out a series of numerical simulations with a coherent-structure resolving turbulence model using the actuator disk parameterization. The main objective of this study is to further our understanding on the physical processes associated with the installation of the turbine arrays. We perform simulations with different geometries and inlet boundary conditions, from simple cases in a rectangular channel, to more complex cases that include the high-resolution bathymetry of an extensive area of the Chacao channel. The results show how the interactions between the MHK devices, the local flow, and the bed can affect the energy flux and potential generation in specific sites. The results also provide new insights of local impacts of MHK devices and they can also help to optimize turbine arrays in natural environments. This work has been supported by Fondecyt project 1130940, and the Marine Energy Research & Innovation Center (MERIC) financed by Corfo and based in Santiago, Chile.

Bioinspired Design and Computational Prediction of Iron Complexes with Pendant Amines for the Production of Methanol from CO2 and H2.

PubMed

Chen, Xiangyang; Yang, Xinzheng

2016-03-17

Inspired by the active site structure of [FeFe]-hydrogenase, we built a series of iron dicarbonyl diphosphine complexes with pendant amines and predicted their potentials to catalyze the hydrogenation of CO2 to methanol using density functional theory. Among the proposed iron complexes, [(P(tBu)2N(tBu)2H)FeH(CO)2(COOH)](+) (5COOH) is the most active one with a total free energy barrier of 23.7 kcal/mol. Such a low barrier indicates that 5COOH is a very promising low-cost catalyst for high-efficiency conversion of CO2 and H2 to methanol under mild conditions. For comparison, we also examined Bullock's Cp iron diphosphine complex with pendant amines, [(P(tBu)2N(tBu)2H)FeHCp(C5F4N)](+) (5Cp-C5F4N), as a catalyst for hydrogenation of CO2 to methanol and obtained a total free energy barrier of 27.6 kcal/mol, which indicates that 5Cp-C5F4N could also catalyze the conversion of CO2 and H2 to methanol but has a much lower efficiency than our newly designed iron complexes.

Adaptive Monte Carlo methods

NASA Astrophysics Data System (ADS)

Fasnacht, Marc

We develop adaptive Monte Carlo methods for the calculation of the free energy as a function of a parameter of interest. The methods presented are particularly well-suited for systems with complex energy landscapes, where standard sampling techniques have difficulties. The Adaptive Histogram Method uses a biasing potential derived from histograms recorded during the simulation to achieve uniform sampling in the parameter of interest. The Adaptive Integration method directly calculates an estimate of the free energy from the average derivative of the Hamiltonian with respect to the parameter of interest and uses it as a biasing potential. We compare both methods to a state of the art method, and demonstrate that they compare favorably for the calculation of potentials of mean force of dense Lennard-Jones fluids. We use the Adaptive Integration Method to calculate accurate potentials of mean force for different types of simple particles in a Lennard-Jones fluid. Our approach allows us to separate the contributions of the solvent to the potential of mean force from the effect of the direct interaction between the particles. With contributions of the solvent determined, we can find the potential of mean force directly for any other direct interaction without additional simulations. We also test the accuracy of the Adaptive Integration Method on a thermodynamic cycle, which allows us to perform a consistency check between potentials of mean force and chemical potentials calculated using the Adaptive Integration Method. The results demonstrate a high degree of consistency of the method.

Probing Gas Adsorption in Zeolites by Variable-Temperature IR Spectroscopy: An Overview of Current Research.

PubMed

Garrone, Edoardo; Delgado, Montserrat R; Bonelli, Barbara; Arean, Carlos O

2017-09-15

The current state of the art in the application of variable-temperature IR (VTIR) spectroscopy to the study of (i) adsorption sites in zeolites, including dual cation sites; (ii) the structure of adsorption complexes and (iii) gas-solid interaction energy is reviewed. The main focus is placed on the potential use of zeolites for gas separation, purification and transport, but possible extension to the field of heterogeneous catalysis is also envisaged. A critical comparison with classical IR spectroscopy and adsorption calorimetry shows that the main merits of VTIR spectroscopy are (i) its ability to provide simultaneously the spectroscopic signature of the adsorption complex and the standard enthalpy change involved in the adsorption process; and (ii) the enhanced potential of VTIR to be site specific in favorable cases.

Chemical dynamics simulations of X- + CH3Y → XCH3 + Y- gas-phase S(N)2 nucleophilic substitution reactions. Nonstatistical dynamics and nontraditional reaction mechanisms.

PubMed

Manikandan, Paranjothy; Zhang, Jiaxu; Hase, William L

2012-03-29

Extensive classical chemical dynamics simulations of gas-phase X(-) + CH(3)Y → XCH(3) + Y(-) S(N)2 nucleophilic substitution reactions are reviewed and discussed and compared with experimental measurements and predictions of theoretical models. The primary emphasis is on reactions for which X and Y are halogen atoms. Both reactions with the traditional potential energy surface (PES), which include pre- and postreaction potential energy minima and a central barrier, and reactions with nontraditional PESs are considered. These S(N)2 reactions exhibit important nonstatistical atomic-level dynamics. The X(-) + CH(3)Y → X(-)---CH(3)Y association rate constant is less than the capture model as a result of inefficient energy transfer from X(-)+ CH(3)Y relative translation to CH(3)Y rotation and vibration. There is weak coupling between the low-frequency intermolecular modes of the X(-)---CH(3)Y complex and higher frequency CH(3)Y intramolecular modes, resulting in non-RRKM kinetics for X(-)---CH(3)Y unimolecular decomposition. Recrossings of the [X--CH(3)--Y](-) central barrier is important. As a result of the above dynamics, the relative translational energy and temperature dependencies of the S(N)2 rate constants are not accurately given by statistical theory. The nonstatistical dynamics results in nonstatistical partitioning of the available energy to XCH(3) +Y(-) reaction products. Besides the indirect, complex forming atomic-level mechanism for the S(N)2 reaction, direct mechanisms promoted by X(-) + CH(3)Y relative translational or CH(3)Y vibrational excitation are possible, e.g., the roundabout mechanism.

Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs.

PubMed

Harger, Matthew; Li, Daniel; Wang, Zhi; Dalby, Kevin; Lagardère, Louis; Piquemal, Jean-Philip; Ponder, Jay; Ren, Pengyu

2017-09-05

The capabilities of the polarizable force fields for alchemical free energy calculations have been limited by the high computational cost and complexity of the underlying potential energy functions. In this work, we present a GPU-based general alchemical free energy simulation platform for polarizable potential AMOEBA. Tinker-OpenMM, the OpenMM implementation of the AMOEBA simulation engine has been modified to enable both absolute and relative alchemical simulations on GPUs, which leads to a ∼200-fold improvement in simulation speed over a single CPU core. We show that free energy values calculated using this platform agree with the results of Tinker simulations for the hydration of organic compounds and binding of host-guest systems within the statistical errors. In addition to absolute binding, we designed a relative alchemical approach for computing relative binding affinities of ligands to the same host, where a special path was applied to avoid numerical instability due to polarization between the different ligands that bind to the same site. This scheme is general and does not require ligands to have similar scaffolds. We show that relative hydration and binding free energy calculated using this approach match those computed from the absolute free energy approach. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Bioelectrochemical system platform for sustainable environmental remediation and energy generation.

PubMed

Wang, Heming; Luo, Haiping; Fallgren, Paul H; Jin, Song; Ren, Zhiyong Jason

2015-01-01

The increasing awareness of the energy-environment nexus is compelling the development of technologies that reduce environmental impacts during energy production as well as energy consumption during environmental remediation. Countries spend billions in pollution cleanup projects, and new technologies with low energy and chemical consumption are needed for sustainable remediation practice. This perspective review provides a comprehensive summary on the mechanisms of the new bioelectrochemical system (BES) platform technology for efficient and low cost remediation, including petroleum hydrocarbons, chlorinated solvents, perchlorate, azo dyes, and metals, and it also discusses the potential new uses of BES approach for some emerging contaminants remediation, such as CO2 in air and nutrients and micropollutants in water. The unique feature of BES for environmental remediation is the use of electrodes as non-exhaustible electron acceptors, or even donors, for contaminant degradation, which requires minimum energy or chemicals but instead produces sustainable energy for monitoring and other onsite uses. BES provides both oxidation (anode) and reduction (cathode) reactions that integrate microbial-electro-chemical removal mechanisms, so complex contaminants with different characteristics can be removed. We believe the BES platform carries great potential for sustainable remediation and hope this perspective provides background and insights for future research and development. Copyright © 2015 Elsevier Inc. All rights reserved.

Rapid Convergence of Energy and Free Energy Profiles with Quantum Mechanical Size in Quantum Mechanical-Molecular Mechanical Simulations of Proton Transfer in DNA.

PubMed

Das, Susanta; Nam, Kwangho; Major, Dan Thomas

2018-03-13

In recent years, a number of quantum mechanical-molecular mechanical (QM/MM) enzyme studies have investigated the dependence of reaction energetics on the size of the QM region using energy and free energy calculations. In this study, we revisit the question of QM region size dependence in QM/MM simulations within the context of energy and free energy calculations using a proton transfer in a DNA base pair as a test case. In the simulations, the QM region was treated with a dispersion-corrected AM1/d-PhoT Hamiltonian, which was developed to accurately describe phosphoryl and proton transfer reactions, in conjunction with an electrostatic embedding scheme using the particle-mesh Ewald summation method. With this rigorous QM/MM potential, we performed rather extensive QM/MM sampling, and found that the free energy reaction profiles converge rapidly with respect to the QM region size within ca. ±1 kcal/mol. This finding suggests that the strategy of QM/MM simulations with reasonably sized and selected QM regions, which has been employed for over four decades, is a valid approach for modeling complex biomolecular systems. We point to possible causes for the sensitivity of the energy and free energy calculations to the size of the QM region, and potential implications.

A space-based, high-resolution view of notable changes in urban NO x pollution around the world (2005-2014)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duncan, Bryan N.; Lamsal, Lok N.; Thompson, Anne M.

Nitrogen oxides (NO x = NO + NO 2) are produced during combustion processes and, thus may serve as a proxy for fossil fuel-based energy usage and coemitted greenhouse gases and other pollutants. We use high-resolution nitrogen dioxide (NO 2) data from the Ozone Monitoring Instrument (OMI) to analyze changes in urban NO 2 levels around the world from 2005 to 2014, finding complex heterogeneity in the changes. We discuss several potential factors that seem to determine these NO x changes. First, environmental regulations resulted in large decreases. The only large increases in the United States may be associated withmore » three areas of intensive energy activity. Second, elevated NO 2 levels were observed over many Asian, tropical, and subtropical cities that experienced rapid economic growth. Two of the largest increases occurred over recently expanded petrochemical complexes in Jamnagar (India) and Daesan (Korea). Third, pollution transport from China possibly influenced the Republic of Korea and Japan, diminishing the impact of local pollution controls. However, in China, there were large decreases over Beijing, Shanghai, and the Pearl River Delta, which were likely associated with local emission control efforts. Fourth, civil unrest and its effect on energy usage may have resulted in lower NO 2 levels in Libya, Iraq, and Syria. Fifth, spatial heterogeneity within several megacities may reflect mixed efforts to cope with air quality degradation. We also show the potential of high-resolution data for identifying NO x emission sources in regions with a complex mix of sources. Finally, intensive monitoring of the world's tropical/subtropical megacities will remain a priority, as their populations and emissions of pollutants and greenhouse gases are expected to increase significantly.« less

A space-based, high-resolution view of notable changes in urban NOx pollution around the world (2005-2014)

NASA Astrophysics Data System (ADS)

Duncan, Bryan N.; Lamsal, Lok N.; Thompson, Anne M.; Yoshida, Yasuko; Lu, Zifeng; Streets, David G.; Hurwitz, Margaret M.; Pickering, Kenneth E.

2016-01-01

Nitrogen oxides (NOx = NO + NO2) are produced during combustion processes and, thus may serve as a proxy for fossil fuel-based energy usage and coemitted greenhouse gases and other pollutants. We use high-resolution nitrogen dioxide (NO2) data from the Ozone Monitoring Instrument (OMI) to analyze changes in urban NO2 levels around the world from 2005 to 2014, finding complex heterogeneity in the changes. We discuss several potential factors that seem to determine these NOx changes. First, environmental regulations resulted in large decreases. The only large increases in the United States may be associated with three areas of intensive energy activity. Second, elevated NO2 levels were observed over many Asian, tropical, and subtropical cities that experienced rapid economic growth. Two of the largest increases occurred over recently expanded petrochemical complexes in Jamnagar (India) and Daesan (Korea). Third, pollution transport from China possibly influenced the Republic of Korea and Japan, diminishing the impact of local pollution controls. However, in China, there were large decreases over Beijing, Shanghai, and the Pearl River Delta, which were likely associated with local emission control efforts. Fourth, civil unrest and its effect on energy usage may have resulted in lower NO2 levels in Libya, Iraq, and Syria. Fifth, spatial heterogeneity within several megacities may reflect mixed efforts to cope with air quality degradation. We also show the potential of high-resolution data for identifying NOx emission sources in regions with a complex mix of sources. Intensive monitoring of the world's tropical/subtropical megacities will remain a priority, as their populations and emissions of pollutants and greenhouse gases are expected to increase significantly.

Recent advances in QM/MM free energy calculations using reference potentials☆

PubMed Central

Duarte, Fernanda; Amrein, Beat A.; Blaha-Nelson, David; Kamerlin, Shina C.L.

2015-01-01

Background Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meaningful become more and more difficult to fulfill. The use of simplified models to describe complex biological systems has long been shown to be an effective way to overcome some of the limitations associated with this computational cost in a rational way. Scope of review Hybrid QM/MM approaches have rapidly become one of the most popular computational tools for studying chemical reactivity in biomolecular systems. However, the high cost involved in performing high-level QM calculations has limited the applicability of these approaches when calculating free energies of chemical processes. In this review, we present some of the advances in using reference potentials and mean field approximations to accelerate high-level QM/MM calculations. We present illustrative applications of these approaches and discuss challenges and future perspectives for the field. Major conclusions The use of physically-based simplifications has shown to effectively reduce the cost of high-level QM/MM calculations. In particular, lower-level reference potentials enable one to reduce the cost of expensive free energy calculations, thus expanding the scope of problems that can be addressed. General significance As was already demonstrated 40 years ago, the usage of simplified models still allows one to obtain cutting edge results with substantially reduced computational cost. This article is part of a Special Issue entitled Recent developments of molecular dynamics. PMID:25038480

A Space-based, High-resolution View of Notable Changes in Urban Nox Pollution Around the World (2005 - 2014)

NASA Technical Reports Server (NTRS)

Duncan, Bryan N.; Lamsal, Lok N.; Thompson, Anne M.; Yoshida, Yasuko; Lu, Zifeng; Streets, David G.; Hurwitz, Margaret M.; Pickering, Kenneth E.

2016-01-01

Nitrogen oxides (NOxNO+NO2) are produced during combustion processes and, thus may serve as a proxy for fossil fuel-based energy usage and committed greenhouse gases and other pollutants. We use high-resolution nitrogen dioxide (NO2) data from the Ozone Monitoring Instrument (OMI) to analyze changes in urban NO2 levels around the world from 2005 to 2014, finding complex heterogeneity in the changes. We discuss several potential factors that seem to determine these NOx changes. First, environmental regulations resulted in large decreases. The only large increases in the United States may be associated with three areas of intensive energy activity. Second, elevated NO2 levels were observed over many Asian, tropical, and subtropical cities that experienced rapid economic growth. Two of the largest increases occurred over recently expanded petrochemical complexes in Jamnagar (India) and Daesan (Korea). Third, pollution transport from China possibly influenced the Republic of Korea and Japan, diminishing the impact of local pollution controls. However, in China, there were large decreases over Beijing, Shanghai, and the Pearl River Delta, which were likely associated with local emission control efforts. Fourth, civil unrest and its effect on energy usage may have resulted in lower NO2 levels in Libya, Iraq, and Syria. Fifth, spatial heterogeneity within several megacities may reflect mixed efforts to cope with air quality degradation. We also show the potential of high-resolution data for identifying NOx emission sources in regions with a complex mix of sources. Intensive monitoring of the world's tropical subtropical megacities will remain a priority, as their populations and emissions of pollutants and greenhouse gases are expected to increase significantly.

Diatomics-in-molecules description of the Rg-Hal2 rare gas-halogen van der Waals complexes with applications to He-Cl2

NASA Astrophysics Data System (ADS)

Grigorenko, B. L.; Nemukhin, A. V.; Buchachenko, A. A.; Stepanov, N. F.; Umanskii, S. Ya.

1997-03-01

The diatomics-in-molecules (DIM) technique is applied for a description of the low-lying states of the Rg-Hal2 van der Waals complexes correlating with the lowest states of constituent atoms Rg(1S)+Hal(2Pj)+Hal(2Pj). The important feature of this approach is the construction of polyatomic basis functions as products of the Hal2 diatomic eigenstates classified within the Hund "c" scheme and the atomic rare gas wave function. Necessary transformations to the other basis set representations are described, and finally all the matrix elements are expressed in terms of nonrelativistic adiabatic energies of Hal2 and Rg Hal fragments and spin-orbit splitting constant of the halogen atom. Our main concern is to test the DIM-based approximations of different levels taking the He-Cl2 system as an example. Namely, we have compared the results obtained within a hierarchy of approaches: (1) the simplest pairwise potential scheme as a far extreme of the DIM model, (2) the same as (1) but with the different components (Σ and Π) for He-Cl interaction, (3) the accurate DIM technique without spin-orbit terms, and (4) the highest level which takes into account all these contributions. The results have been compared to the other DIM like models as well. The shapes of two-dimensional potential surfaces for the ground (X) and excited (B) states of HeCl2, binding energies De with respect to He+Cl2, stretching and bending vibrational frequencies of the complex, binding energies D0, and spectral shifts for the B←X transition are discussed.

Comparison of energy interaction parameters for the complexation of Pr(III) with glutathione reduced (GSH) in absence and presence of Zn(II) in aqueous and aquated organic solvents using 4f?4f transition spectra as PROBE

NASA Astrophysics Data System (ADS)

Singh, Th. David; Sumitra, Ch.; Yaiphaba, N.; Devi, H. Debecca; Devi, M. Indira; Singh, N. Rajmuhon

2005-04-01

The coordination chemistry of glutathione reduced (GSH) is of great importance as it acts as excellent model system for the binding of metal ions. The GSH complexation with metal ions is involved in the toxicology of different metal ions. Its coordination behaviour for soft metal ions and hard metal ions is found different because of the structure of GSH and its different potential binding sites. In our work we have studied two chemically dissimilar metal ions viz. Pr(III), which prefer hard donor site like carboxylic groups and Zn(II) the soft metal ion which prefer peptide-NH and sulphydryl groups. The absorption difference and comparative absorption spectroscopy involving 4f-4f transitions of the heterobimetallic Complexation of GSH with Pr(III) and Zn(II) has been explored in aqueous and aquated organic solvents. The variation in the energy parameters like Slater-Condon ( F K), Racah ( E K) and Lande ( ξ4f), Nephelauxetic parameter ( β) and bonding parameter ( b1/2) are computed to explain the nature of complexation.

Defect charge states in Si doped hexagonal boron-nitride monolayer

NASA Astrophysics Data System (ADS)

Mapasha, R. E.; Molepo, M. P.; Andrew, R. C.; Chetty, N.

2016-02-01

We perform ab initio density functional theory calculations to investigate the energetics, electronic and magnetic properties of isolated stoichiometric and non-stoichiometric substitutional Si complexes in a hexagonal boron-nitride monolayer. The Si impurity atoms substituting the boron atom sites SiB giving non-stoichiometric complexes are found to be the most energetically favourable, and are half-metallic and order ferromagnetically in the neutral charge state. We find that the magnetic moments and magnetization energies increase monotonically when Si defects form a cluster. Partial density of states and standard Mulliken population analysis indicate that the half-metallic character and magnetic moments mainly arise from the Si 3p impurity states. The stoichiometric Si complexes are energetically unfavorable and non-magnetic. When charging the energetically favourable non-stoichiometric Si complexes, we find that the formation energies strongly depend on the impurity charge states and Fermi level position. We also find that the magnetic moments and orderings are tunable by charge state modulation q  =  -2, -1, 0, +1, +2. The induced half-metallic character is lost (retained) when charging isolated (clustered) Si defect(s). This underlines the potential of a Si doped hexagonal boron-nitride monolayer for novel spin-based applications.

Photoionisation study of Xe.CF{sub 4} and Kr.CF{sub 4} van-der-Waals molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alekseev, V. A., E-mail: alekseev@va3474.spb.edu; Kevorkyants, R.; Garcia, G. A.

2016-05-14

We report on photoionization studies of Xe.CF{sub 4} and Kr.CF{sub 4} van-der-Waals complexes produced in a supersonic expansion and detected using synchrotron radiation and photoelectron-photoion coincidence techniques. The ionization potential of CF{sub 4} is larger than those of the Xe and Kr atoms and the ground state of the Rg.CF{sub 4}{sup +} ion correlates with Rg{sup +} ({sup 2}P{sub 3/2}) + CF{sub 4}. The onset of the Rg.CF{sub 4}{sup +} signals was found to be only ∼0.2 eV below the Rg ionization potential. In agreement with experiment, complementary ab initio calculations show that vertical transitions originating from the potential minimummore » of the ground state of Rg.CF{sub 4} terminate at a part of the potential energy surfaces of Rg.CF{sub 4}{sup +}, which are approximately 0.05 eV below the Rg{sup +} ({sup 2}P{sub 3/2}) + CF{sub 4} dissociation limit. In contrast to the neutral complexes, which are most stable in the face geometry, for the Rg.CF{sub 4}{sup +} ions, the calculations show that the minimum of the potential energy surface is in the vertex geometry. Experiments which have been performed only with Xe.CF{sub 4} revealed no Xe.CF{sub 4}{sup +} signal above the first ionization threshold of Xe, suggesting that the Rg.CF{sub 4}{sup +} ions are not stable above the first dissociation limit.« less

Acetonitrile-water hydrogen-bonded interaction: Matrix-isolation infrared and ab initio computation

NASA Astrophysics Data System (ADS)

Gopi, R.; Ramanathan, N.; Sundararajan, K.

2015-08-01

The 1:1 hydrogen-bonded complex of acetonitrile (CH3CN) and water (H2O) was trapped in Ar and N2 matrices and studied using infrared technique. Ab initio computations showed two types of complexes formed between CH3CN and H2O, a linear complex A with a Ctbnd N⋯H interaction between nitrogen of CH3CN and hydrogen of H2O and a cyclic complex B, in which the interactions are between the hydrogen of CH3CN with oxygen of H2O and hydrogen of H2O with π cloud of sbnd Ctbnd N of CH3CN. Vibrational wavenumber calculations revealed that both the complexes A and B were minima on the potential energy surface. Interaction energies computed at B3LYP/6-311++G(d,p) showed that linear complex A is more stable than cyclic complex B. Computations identified a blue shift of ∼11.5 cm-1 and a red shift of ∼6.5 cm-1 in the CN stretching mode for the complexes A and B, respectively. Experimentally, we observed a blue shift of ∼15.0 and ∼8.3 cm-1 in N2 and Ar matrices, respectively, in the CN stretching mode of CH3CN, which supports the formation of complex A. The Onsager Self Consistent Reaction Field (SCRF) model was used to explain the influence of matrices on the complexes A and B. To understand the nature of the interactions, Atoms in Molecules (AIM) and Natural Bond Orbital (NBO) analyses were carried out for the complexes A and B.

IR Spectra of (HCOOH)2 and (DCOOH)2: Experiment, VSCF/VCI, and Ab Initio Molecular Dynamics Calculations Using Full-Dimensional Potential and Dipole Moment Surfaces.

PubMed

Qu, Chen; Bowman, Joel M

2018-05-17

We report quantum VSCF/VCI and ab initio molecular dynamics (AIMD) calculations of the IR spectra of (HCOOH) 2 and (DCOOH) 2 , using full-dimensional, ab initio potential energy and dipole moment surfaces (PES and DMS). These surfaces are fits, using permutationally invariant polynomials, to 13 475 ab initio CCSD(T)-F12a electronic energies and MP2 dipole moments. Here "AIMD" means using these ab initio potential and dipole moment surfaces in the MD calculations. The VSCF/VCI calculations use all (24) normal modes for coupling, with a four-mode representation of the potential. The quantum spectra align well with jet-cooled and room-temperature experimental spectra over the spectral range 600-3600 cm -1 . Analyses of the complex O-H and C-H stretch bands are made based on the mixing of the VSCF/VCI basis functions. The comparisons of the AIMD IR spectra with both experimental and VSCF/VCI ones provide tests of the accuracy of the AIMD approach. These indicate good accuracy for simple bands but not for the complex O-H stretch band, which is upshifted from experimental and VSCF/VCI bands by roughly 300 cm -1 . In addition to testing the AIMD approach, the PES, DMS, and VSCF/VCI calculations for formic acid dimer provide opportunities for testing other methods to represent high-dimensional data and other methods that perform postharmonic vibrational calculations.

Evaluation of Several Two-Step Scoring Functions Based on Linear Interaction Energy, Effective Ligand Size, and Empirical Pair Potentials for Prediction of Protein-Ligand Binding Geometry and Free Energy

PubMed Central

Rahaman, Obaidur; Estrada, Trilce P.; Doren, Douglas J.; Taufer, Michela; Brooks, Charles L.; Armen, Roger S.

2011-01-01

The performance of several two-step scoring approaches for molecular docking were assessed for their ability to predict binding geometries and free energies. Two new scoring functions designed for “step 2 discrimination” were proposed and compared to our CHARMM implementation of the linear interaction energy (LIE) approach using the Generalized-Born with Molecular Volume (GBMV) implicit solvation model. A scoring function S1 was proposed by considering only “interacting” ligand atoms as the “effective size” of the ligand, and extended to an empirical regression-based pair potential S2. The S1 and S2 scoring schemes were trained and five-fold cross validated on a diverse set of 259 protein-ligand complexes from the Ligand Protein Database (LPDB). The regression-based parameters for S1 and S2 also demonstrated reasonable transferability in the CSARdock 2010 benchmark using a new dataset (NRC HiQ) of diverse protein-ligand complexes. The ability of the scoring functions to accurately predict ligand geometry was evaluated by calculating the discriminative power (DP) of the scoring functions to identify native poses. The parameters for the LIE scoring function with the optimal discriminative power (DP) for geometry (step 1 discrimination) were found to be very similar to the best-fit parameters for binding free energy over a large number of protein-ligand complexes (step 2 discrimination). Reasonable performance of the scoring functions in enrichment of active compounds in four different protein target classes established that the parameters for S1 and S2 provided reasonable accuracy and transferability. Additional analysis was performed to definitively separate scoring function performance from molecular weight effects. This analysis included the prediction of ligand binding efficiencies for a subset of the CSARdock NRC HiQ dataset where the number of ligand heavy atoms ranged from 17 to 35. This range of ligand heavy atoms is where improved accuracy of predicted ligand efficiencies is most relevant to real-world drug design efforts. PMID:21644546

Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy.

PubMed

Rahaman, Obaidur; Estrada, Trilce P; Doren, Douglas J; Taufer, Michela; Brooks, Charles L; Armen, Roger S

2011-09-26

The performances of several two-step scoring approaches for molecular docking were assessed for their ability to predict binding geometries and free energies. Two new scoring functions designed for "step 2 discrimination" were proposed and compared to our CHARMM implementation of the linear interaction energy (LIE) approach using the Generalized-Born with Molecular Volume (GBMV) implicit solvation model. A scoring function S1 was proposed by considering only "interacting" ligand atoms as the "effective size" of the ligand and extended to an empirical regression-based pair potential S2. The S1 and S2 scoring schemes were trained and 5-fold cross-validated on a diverse set of 259 protein-ligand complexes from the Ligand Protein Database (LPDB). The regression-based parameters for S1 and S2 also demonstrated reasonable transferability in the CSARdock 2010 benchmark using a new data set (NRC HiQ) of diverse protein-ligand complexes. The ability of the scoring functions to accurately predict ligand geometry was evaluated by calculating the discriminative power (DP) of the scoring functions to identify native poses. The parameters for the LIE scoring function with the optimal discriminative power (DP) for geometry (step 1 discrimination) were found to be very similar to the best-fit parameters for binding free energy over a large number of protein-ligand complexes (step 2 discrimination). Reasonable performance of the scoring functions in enrichment of active compounds in four different protein target classes established that the parameters for S1 and S2 provided reasonable accuracy and transferability. Additional analysis was performed to definitively separate scoring function performance from molecular weight effects. This analysis included the prediction of ligand binding efficiencies for a subset of the CSARdock NRC HiQ data set where the number of ligand heavy atoms ranged from 17 to 35. This range of ligand heavy atoms is where improved accuracy of predicted ligand efficiencies is most relevant to real-world drug design efforts.

The Rotational Spectrum of Complex Organic Molecules: 2(N)-METHYLAMINOETHANOL

NASA Astrophysics Data System (ADS)

Melandri, S.; Maris, A.; Calabrese, C.

2013-06-01

The detection of molecules in space, is based on their spectroscopic features and high resolution spectral data is needed to allow an unambiguous identification of them. Many of the molecules detected in space are complex organic molecules containing chains of carbon atoms and which therefore show a high degree of molecular flexibility. The high number of low energy conformations and the presence of large amplitude motions on shallow potential energy surfaces are peculiar to this kind of systems. The presence of a high number of stable conformers - often interconverting through small energy barriers - usually gives rise to very complex spectra, which represent a challenge for spectroscopic and computational methods. We report the rotational study of methylaminoethanol (MAE) performed by Free Jet Absorption Microwave Spectrocopy (FJAMW). For this species it has proved essential to compute the complete potential energy surfaces related to the low amplitude modes. This has been calculated at the B3LYP/6-311++G** level of theory while the stable geometries have been characterized MP2/6-311++G**. The interest in the conformational properties of MAE is twofold: in the first place, aminoethanol and thus also MAE can be considered precursors of aminoacids in the interstellar medium and secondly, the MAE side chain is present in important biological molecules such as adrenaline. The conformational preferences of MAE are dominated by the intramolecular hydrogen bond between the OH and NH2 groups and its flexibility and asymmetry generate a very high number of conformers. 24 stable conformations have been predicted and two conformers were observed by FJAMW spectroscopy with our 60-72 GHz spectrometer. With respect to a previous study we have extended the observed frequency range, partly reassigned the rotational spectrum of one of the conformers and determined the nuclear quadrupole constants. The search for higher energy conformers has also been undertaken. S. Charnley, in Proceedings of the workshop: The bridge between the Big Bang and Biology, CNR, Italy 1999. R. E. Penn and L. W. Buxton J. Mol. Spectrosc. {56} 229 1975.

Investigation of anticancer properties of caffeinated complexes via computational chemistry methods

NASA Astrophysics Data System (ADS)

Sayin, Koray; Üngördü, Ayhan

2018-03-01

Computational investigations were performed for 1,3,7-trimethylpurine-2,6-dione, 3,7-dimethylpurine-2,6-dione, their Ru(II) and Os(III) complexes. B3LYP/6-311 ++G(d,p)(LANL2DZ) level was used in numerical calculations. Geometric parameters, IR spectrum, 1H-, 13C and 15N NMR spectrum were examined in detail. Additionally, contour diagram of frontier molecular orbitals (FMOs), molecular electrostatic potential (MEP) maps, MEP contour and some quantum chemical descriptors were used in the determination of reactivity rankings and active sites. The electron density on the surface was similar to each other in studied complexes. Quantum chemical descriptors were investigated and the anticancer activity of complexes were more than cisplatin and their ligands. Additionally, molecular docking calculations were performed in water between related complexes and a protein (ID: 3WZE). The most interact complex was found as Os complex. The interaction energy was calculated as 342.9 kJ/mol.

General Retarded Contact Self-energies in and beyond the Non-equilibrium Green's Functions Method

NASA Astrophysics Data System (ADS)

Kubis, Tillmann; He, Yu; Andrawis, Robert; Klimeck, Gerhard

2016-03-01

Retarded contact self-energies in the framework of nonequilibrium Green's functions allow to model the impact of lead structures on the device without explicitly including the leads in the actual device calculation. Most of the contact self-energy algorithms are limited to homogeneous or periodic, semi-infinite lead structures. In this work, the complex absorbing potential method is extended to solve retarded contact self-energies for arbitrary lead structures, including irregular and randomly disordered leads. This method is verified for regular leads against common approaches and on physically equivalent, but numerically different irregular leads. Transmission results on randomly alloyed In0.5Ga0.5As structures show the importance of disorder in the leads. The concept of retarded contact self-energies is expanded to model passivation of atomically resolved surfaces without explicitly increasing the device's Hamiltonian.

Redox Species of Redox Flow Batteries: A Review.

PubMed

Pan, Feng; Wang, Qing

2015-11-18

Due to the capricious nature of renewable energy resources, such as wind and solar, large-scale energy storage devices are increasingly required to make the best use of the renewable power. The redox flow battery is considered suitable for large-scale applications due to its modular design, good scalability and flexible operation. The biggest challenge of the redox flow battery is the low energy density. The redox active species is the most important component in redox flow batteries, and the redox potential and solubility of redox species dictate the system energy density. This review is focused on the recent development of redox species. Different categories of redox species, including simple inorganic ions, metal complexes, metal-free organic compounds, polysulfide/sulfur and lithium storage active materials, are reviewed. The future development of redox species towards higher energy density is also suggested.

Investigations of photosynthetic light harvesting by two-dimensional electronic spectroscopy

NASA Astrophysics Data System (ADS)

Read, Elizabeth Louise

Photosynthesis begins with the harvesting of sunlight by antenna pigments, organized in a network of pigment-protein complexes that rapidly funnel energy to photochemical reaction centers. The intricate design of these systems---the widely varying structural motifs of pigment organization within proteins and protein organization within a larger, cooperative network---underlies the remarkable speed and efficiency of light harvesting. Advances in femtosecond laser spectroscopy have enabled researchers to follow light energy on its course through the energetic levels of photosynthetic systems. Now, newly-developed femtosecond two-dimensional electronic spectroscopy reveals deeper insight into the fundamental molecular interactions and dynamics that emerge in these structures. The following chapters present investigations of a number of natural light-harvesting complexes using two-dimensional electronic spectroscopy. These studies demonstrate the various types of information contained in experimental two-dimensional spectra, and they show that the technique makes it possible to probe pigment-protein complexes on the length- and time-scales relevant to their functioning. New methods are described that further extend the capabilities of two-dimensional electronic spectroscopy, for example, by independently controlling the excitation laser pulse polarizations. The experiments, coupled with theoretical simulation, elucidate spatial pathways of energy flow, unravel molecular and electronic structures, and point to potential new quantum mechanical mechanisms of light harvesting.

Excitons, trions, and biexcitons in transition-metal dichalcogenides: Magnetic-field dependence

NASA Astrophysics Data System (ADS)

Van der Donck, M.; Zarenia, M.; Peeters, F. M.

2018-05-01

The influence of a perpendicular magnetic field on the binding energy and structural properties of excitons, trions, and biexcitons in monolayers of semiconducting transition metal dichalcogenides (TMDs) is investigated. The stochastic variational method (SVM) with a correlated Gaussian basis is used to calculate the different properties of these few-particle systems. In addition, we present a simplified variational approach which supports the SVM results for excitons as a function of magnetic field. The exciton diamagnetic shift is compared with recent experimental results, and we extend this concept to trions and biexcitons. The effect of a local potential fluctuation, which we model by a circular potential well, on the binding energy of trions and biexcitons is investigated and found to significantly increase the binding of those excitonic complexes.

Excitation spectrum of a mixture of two Bose gases confined in a ring potential with interaction asymmetry

NASA Astrophysics Data System (ADS)

Roussou, A.; Smyrnakis, J.; Magiropoulos, M.; Efremidis, N. K.; Kavoulakis, G. M.; Sandin, P.; Ögren, M.; Gulliksson, M.

2018-04-01

We study the rotational properties of a two-component Bose–Einstein condensed gas of distinguishable atoms which are confined in a ring potential using both the mean-field approximation, as well as the method of diagonalization of the many-body Hamiltonian. We demonstrate that the angular momentum may be given to the system either via single-particle, or ‘collective’ excitation. Furthermore, despite the complexity of this problem, under rather typical conditions the dispersion relation takes a remarkably simple and regular form. Finally, we argue that under certain conditions the dispersion relation is determined via collective excitation. The corresponding many-body state, which, in addition to the interaction energy minimizes also the kinetic energy, is dictated by elementary number theory.

A high level Ab initio study of the anionic hydrogen-bonded complexes FH-CN-, FH-NC-, H2O-CN- and H2O-NC-

NASA Technical Reports Server (NTRS)

Lee, Timothy J.

1989-01-01

HF, H2O, CN- and their hydrogen-bonded complexes were studied using state-of-the-art ab initio quantum mechanical methods. A large Gaussian one particle basis set consisting of triple zeta plus double polarization plus diffuse s and p functions (TZ2P + diffuse) was used. The theoretical methods employed include self consistent field, second order Moller-Plesset perturbation theory, singles and doubles configuration interaction theory and the singles and doubles coupled cluster approach. The FH-CN- and FH-NC- and H2O-CN-, H2O-NC- pairs of complexes are found to be essentially isoenergetic. The first pair of complexes are predicted to be bound by approx. 24 kcal/mole and the latter pair bound by approximately 15 kcal/mole. The ab initio binding energies are in good agreement with the experimental values. The two being shorter than the analogous C-N hydrogen bond. The infrared (IR) spectra of the two pairs of complexes are also very similar, though a severe perturbation of the potential energy surface by proton exchange means that the accurate prediction of the band center of the most intense IR mode requires a high level of electronic structure theory as well as a complete treatment of anharmonic effects. The bonding of anionic hydrogen-bonded complexes is discussed and contrasted with that of neutral hydrogen-bonded complexes.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shevchenko, N. V.; Mares, J.; Gal, A.

Coupled-channels three-body calculations of an I=1/2,J{sup {pi}}=0{sup -} KNN quasibound state in the KNN-{pi}{sigma}N system were performed and the dependence of the resulting three-body energy on the two-body KN-{pi}{sigma} interaction was investigated. Earlier results of binding energy B{sub K{sup -}}{sub pp}{approx}50-70 MeV and width {gamma}{sub K{sup -}}{sub pp}{approx}100 MeV are confirmed [N. V. Shevchenko et al., Phys. Rev. Lett. 98, 082301 (2007)]. It is shown that a suitably constructed energy-independent complex KN potential gives a considerably shallower and narrower three-body quasibound state than the full coupled-channels calculation. Comparison with other calculations is made.

Ligand-protein docking using a quantum stochastic tunneling optimization method.

PubMed

Mancera, Ricardo L; Källblad, Per; Todorov, Nikolay P

2004-04-30

A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened. Copyright 2004 Wiley Periodicals, Inc. J Comput Chem 25: 858-864, 2004

A graph theory approach to identify resonant and non-resonant transmission paths in statistical modal energy distribution analysis

NASA Astrophysics Data System (ADS)

Aragonès, Àngels; Maxit, Laurent; Guasch, Oriol

2015-08-01

Statistical modal energy distribution analysis (SmEdA) extends classical statistical energy analysis (SEA) to the mid frequency range by establishing power balance equations between modes in different subsystems. This circumvents the SEA requirement of modal energy equipartition and enables applying SmEdA to the cases of low modal overlap, locally excited subsystems and to deal with complex heterogeneous subsystems as well. Yet, widening the range of application of SEA is done at a price with large models because the number of modes per subsystem can become considerable when the frequency increases. Therefore, it would be worthwhile to have at one's disposal tools for a quick identification and ranking of the resonant and non-resonant paths involved in modal energy transmission between subsystems. It will be shown that previously developed graph theory algorithms for transmission path analysis (TPA) in SEA can be adapted to SmEdA and prove useful for that purpose. The case of airborne transmission between two cavities separated apart by homogeneous and ribbed plates will be first addressed to illustrate the potential of the graph approach. A more complex case representing transmission between non-contiguous cavities in a shipbuilding structure will be also presented.

In silico search of energy metabolism inhibitors for alternative leishmaniasis treatments.

PubMed

Silva, Lourival A; Vinaud, Marina C; Castro, Ana Maria; Cravo, Pedro Vítor L; Bezerra, José Clecildo B

2015-01-01

Leishmaniasis is a complex disease that affects mammals and is caused by approximately 20 distinct protozoa from the genus Leishmania. Leishmaniasis is an endemic disease that exerts a large socioeconomic impact on poor and developing countries. The current treatment for leishmaniasis is complex, expensive, and poorly efficacious. Thus, there is an urgent need to develop more selective, less expensive new drugs. The energy metabolism pathways of Leishmania include several interesting targets for specific inhibitors. In the present study, we sought to establish which energy metabolism enzymes in Leishmania could be targets for inhibitors that have already been approved for the treatment of other diseases. We were able to identify 94 genes and 93 Leishmania energy metabolism targets. Using each gene's designation as a search criterion in the TriTrypDB database, we located the predicted peptide sequences, which in turn were used to interrogate the DrugBank, Therapeutic Target Database (TTD), and PubChem databases. We identified 44 putative targets of which 11 are predicted to be amenable to inhibition by drugs which have already been approved for use in humans for 11 of these targets. We propose that these drugs should be experimentally tested and potentially used in the treatment of leishmaniasis.

High level theoretical study of benzene-halide adducts: the importance of C-H-anion hydrogen bonding.

PubMed

Coletti, Cecilia; Re, Nazzareno

2009-02-26

High level ab initio calculations were performed on the interaction of halide anions (F(-), Cl(-), Br(-), and I(-)) to benzene. For these systems recent experimental and theoretical data are rather scarce, in spite of their growingly acknowledged importance for binding in complex biological systems. We have thus explored the complete basis set limit and the effect of counterpoise basis set superposition error corrections on the minimum geometries and energies of benzene-halide adducts in their possible interaction modes. The binding energy and enthalpy values (ranging from -15.3 kcal/mol for fluoride to -6.1 kcal/mol for iodide) show that the hydrogen bonding occurring in these complexes cannot be described as a weak interaction. We have furthermore investigated the topology of the minima and of other selected sections of the potential energy surface, so to gain further insight on the nature of the halide-benzene interaction. In particular, the geometry corresponding to the C(6v) symmetry, although being overall repulsive, has displayed the unprecedented presence of a small flex (a minimum in C(6v) symmetry) with interaction energy close to zero or slightly attractive.

Optimal waste-to-energy strategy assisted by GIS For sustainable solid waste management

NASA Astrophysics Data System (ADS)

Tan, S. T.; Hashim, H.

2014-02-01

Municipal solid waste (MSW) management has become more complex and costly with the rapid socio-economic development and increased volume of waste. Planning a sustainable regional waste management strategy is a critical step for the decision maker. There is a great potential for MSW to be used for the generation of renewable energy through waste incineration or landfilling with gas capture system. However, due to high processing cost and cost of resource transportation and distribution throughout the waste collection station and power plant, MSW is mostly disposed in the landfill. This paper presents an optimization model incorporated with GIS data inputs for MSW management. The model can design the multi-period waste-to-energy (WTE) strategy to illustrate the economic potential and tradeoffs for MSW management under different scenarios. The model is capable of predicting the optimal generation, capacity, type of WTE conversion technology and location for the operation and construction of new WTE power plants to satisfy the increased energy demand by 2025 in the most profitable way. Iskandar Malaysia region was chosen as the model city for this study.

Merits of flywheels for spacecraft energy storage

NASA Technical Reports Server (NTRS)

Gross, S.

1984-01-01

Flywheel energy storage systems which have a very good potential for use in spacecraft are discussed. This system can be superior to alkaline secondary batteries and regenerable fuel cells in most of the areas that are important in spacecraft applications. Of special importance, relative to batteries, are lighter weight, longer cycle and operating life, and high efficiency which minimizes solar array size and the amount of orbital makeup fuel required. Flywheel systems have a long shelf life, give a precise state of charge indication, have modest thermal control needs, are capable of multiple discharges per orbit, have simple ground handling needs, and have characteristics which would be useful for military applications. The major disadvantages of flywheel energy storage systems are that: power is not available during the launch phase without special provisions; and in flight failure of units may force shutdown of good counter rotating units, amplifying the effects of failure and limiting power distribution system options; no inherent emergency power capability unless specifically designed for, and a high level of complexity compared with batteries. The potential advantages of the flywheel energy storage system far outweigh the disadvantages.

Rectifying the output of vibrational piezoelectric energy harvester using quantum dots

NASA Astrophysics Data System (ADS)

Li, Lijie

2017-03-01

Piezoelectric energy harvester scavenges mechanical vibrations and generates electricity. Researchers have strived to optimize the electromechanical structures and to design necessary external power management circuits, aiming to deliver high power and rectified outputs ready for serving as batteries. Complex deformation of the mechanical structure results in charges with opposite polarities appearing on same surface, leading to current loss in the attached metal electrode. External power management circuits such as rectifiers comprise diodes that consume power and have undesirable forward bias. To address the above issues, we devise a novel integrated piezoelectric energy harvesting device that is structured by stacking a layer of quantum dots (QDs) and a layer of piezoelectric material. We find that the QD can rectify electrical charges generated from the piezoelectric material because of its adaptable conductance to the electrochemical potentials of both sides of the QDs layer, so that electrical current causing energy loss on the same surface of the piezoelectric material can be minimized. The QDs layer has the potential to replace external rectification circuits providing a much more compact and less power-consumption solution.

Multiscale Simulations of Protein Landscapes: Using Coarse Grained Models as Reference Potentials to Full Explicit Models

PubMed Central

Messer, Benjamin M.; Roca, Maite; Chu, Zhen T.; Vicatos, Spyridon; Kilshtain, Alexandra Vardi; Warshel, Arieh

2009-01-01

Evaluating the free energy landscape of proteins and the corresponding functional aspects presents a major challenge for computer simulation approaches. This challenge is due to the complexity of the landscape and the enormous computer time needed for converging simulations. The use of simplified coarse grained (CG) folding models offers an effective way of sampling the landscape but such a treatment, however, may not give the correct description of the effect of the actual protein residues. A general way around this problem that has been put forward in our early work (Fan et al, Theor Chem Acc (1999) 103:77-80) uses the CG model as a reference potential for free energy calculations of different properties of the explicit model. This method is refined and extended here, focusing on improving the electrostatic treatment and on demonstrating key applications. This application includes: evaluation of changes of folding energy upon mutations, calculations of transition states binding free energies (which are crucial for rational enzyme design), evaluation of catalytic landscape and simulation of the time dependent responses to pH changes. Furthermore, the general potential of our approach in overcoming major challenges in studies of structure function correlation in proteins is discussed. PMID:20052756

Estimation of Solar Energy on Vertical 3D Building Walls on City Quarter Scale

NASA Astrophysics Data System (ADS)

Jaugsch, F.; Löwner, M.-O.

2016-10-01

In urban areas, solar energy is one promising source of renewable energy to achieve the EU parliament's goal of reducing CO2 emissions by 20 % compared to 1990. Although annual radiation on vertical walls is lower than that on roof surfaces, they are larger in area and, therefore may contribute to energy production. On the other hand, the modelling of shadowing effects is cost intensive in an complex urban environment. Here we present a method for the calculation of solar potential on vertical walls for simple 2D maps with additional building height information. We introduced observer point columns that enable a fast decision whether a whole vertical set of observer points is illuminated or not. By the introduction of a maximum shade length, we reduce processing time in ArcGIS. 206,291 points of 130 buildings have been analysed in time steps of 15 minutes resulting in 15 769 pairs of solar angles. Results disprove the potential of vertical walls serving to fill the winter gap of roof mounted solar energy plants. Best wall orientation for the deployment of solar panels are west and east in summer, whereas it is southeast in winter.

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

NASA Astrophysics Data System (ADS)

Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

2012-12-01

We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation.

PubMed

Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

2012-12-07

We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

Integrated Solutions for a Complex Energy World - Continuum Magazine |

Science.gov Websites

NREL Integrated Solutions for a Complex Energy World Integrated Solutions for a Complex Energy World Energy systems integration optimizes electrical, thermal, fuel, and data technologies design and performance. An array of clean energy technologies, including wind, solar, and electric vehicle batteries, is

Quantum mechanical fragment methods based on partitioning atoms or partitioning coordinates.

PubMed

Wang, Bo; Yang, Ke R; Xu, Xuefei; Isegawa, Miho; Leverentz, Hannah R; Truhlar, Donald G

2014-09-16

Conspectus The development of more efficient and more accurate ways to represent reactive potential energy surfaces is a requirement for extending the simulation of large systems to more complex systems, longer-time dynamical processes, and more complete statistical mechanical sampling. One way to treat large systems is by direct dynamics fragment methods. Another way is by fitting system-specific analytic potential energy functions with methods adapted to large systems. Here we consider both approaches. First we consider three fragment methods that allow a given monomer to appear in more than one fragment. The first two approaches are the electrostatically embedded many-body (EE-MB) expansion and the electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE), which we have shown to yield quite accurate results even when one restricts the calculations to include only electrostatically embedded dimers. The third fragment method is the electrostatically embedded molecular tailoring approach (EE-MTA), which is more flexible than EE-MB and EE-MB-CE. We show that electrostatic embedding greatly improves the accuracy of these approaches compared with the original unembedded approaches. Quantum mechanical fragment methods share with combined quantum mechanical/molecular mechanical (QM/MM) methods the need to treat a quantum mechanical fragment in the presence of the rest of the system, which is especially challenging for those parts of the rest of the system that are close to the boundary of the quantum mechanical fragment. This is a delicate matter even for fragments that are not covalently bonded to the rest of the system, but it becomes even more difficult when the boundary of the quantum mechanical fragment cuts a bond. We have developed a suite of methods for more realistically treating interactions across such boundaries. These methods include redistributing and balancing the external partial atomic charges and the use of tuned fluorine atoms for capping dangling bonds, and we have shown that they can greatly improve the accuracy. Finally we present a new approach that goes beyond QM/MM by combining the convenience of molecular mechanics with the accuracy of fitting a potential function to electronic structure calculations on a specific system. To make the latter practical for systems with a large number of degrees of freedom, we developed a method to interpolate between local internal-coordinate fits to the potential energy. A key issue for the application to large systems is that rather than assigning the atoms or monomers to fragments, we assign the internal coordinates to reaction, secondary, and tertiary sets. Thus, we make a partition in coordinate space rather than atom space. Fits to the local dependence of the potential energy on tertiary coordinates are arrayed along a preselected reaction coordinate at a sequence of geometries called anchor points; the potential energy function is called an anchor points reactive potential. Electrostatically embedded fragment methods and the anchor points reactive potential, because they are based on treating an entire system by quantum mechanical electronic structure methods but are affordable for large and complex systems, have the potential to open new areas for accurate simulations where combined QM/MM methods are inadequate.

Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: correlated ab initio quantum-chemical, DFT and empirical calculations.

PubMed

Dobes, Petr; Otyepka, Michal; Strnad, Miroslav; Hobza, Pavel

2006-05-24

The interaction between roscovitine and cyclin-dependent kinase 2 (cdk2) was investigated by performing correlated ab initio quantum-chemical calculations. The whole protein was fragmented into smaller systems consisting of one or a few amino acids, and the interaction energies of these fragments with roscovitine were determined by using the MP2 method with the extended aug-cc-pVDZ basis set. For selected complexes, the complete basis set limit MP2 interaction energies, as well as the coupled-cluster corrections with inclusion of single, double and noninteractive triples contributions [CCSD(T)], were also evaluated. The energies of interaction between roscovitine and small fragments and between roscovitine and substantial sections of protein (722 atoms) were also computed by using density-functional tight-binding methods covering dispersion energy (DFTB-D) and the Cornell empirical potential. Total stabilisation energy originates predominantly from dispersion energy and methods that do not account for the dispersion energy cannot, therefore, be recommended for the study of protein-inhibitor interactions. The Cornell empirical potential describes reasonably well the interaction between roscovitine and protein; therefore, this method can be applied in future thermodynamic calculations. A limited number of amino acid residues contribute significantly to the binding of roscovitine and cdk2, whereas a rather large number of amino acids make a negligible contribution.

Evaluation of the potential for operating carbon neutral WWTPs in China.

PubMed

Hao, Xiaodi; Liu, Ranbin; Huang, Xin

2015-12-15

Carbon neutrality is starting to become a hot topic for wastewater treatment plants (WWTPs) all over the world, and carbon neutral operations have emerged in some WWTPs. Although China is still struggling to control its water pollution, carbon neutrality will definitely become a top priority for WWTPs in the near future. In this review, the potential for operating carbon neutral WWTPs in China is technically evaluated. Based on the A(2)/O process of a typical municipal WWTP, an evaluation model is first configured, which couples the COD/nutrient removals (mass balance) with the energy consumption/recovery (energy balance). This model is then applied to evaluate the potential of the organic (COD) energy with regards to carbon neutrality. The model's calculations reveal that anaerobic digestion of excess sludge can only provide some 50% of the total amount of energy consumption. Water source heat pumps (WSHP) can effectively convert the thermal energy contained in wastewater to heat WWTPs and neighbourhood buildings, which can supply a net electrical equivalency of 0.26 kWh when 1 m(3) of the effluent is cooled down by 1 °C. Photovoltaic (PV) technology can generate a limited amount of electricity, barely 10% of the total energy consumption. Moreover, the complexity of installing solar panels on top of tanks makes PV technology almost not worth the effort. Overall, therefore, organic and thermal energy sources can effectively supply enough electrical equivalency for China to approach to its target with regards to carbon neutral operations. Copyright © 2015 Elsevier Ltd. All rights reserved.

Assessing Potential Energy Savings in Household Travel: Methodological and Empirical Considerations of Vehicle Capability Constraints and Multi-day Activity Patterns

NASA Astrophysics Data System (ADS)

Bolon, Kevin M.

The lack of multi-day data for household travel and vehicle capability requirements is an impediment to evaluations of energy savings strategies, since (1) travel requirements vary from day-to-day, and (2) energy-saving transportation options often have reduced capability. This work demonstrates a survey methodology and modeling system for evaluating the energy-savings potential of household travel, considering multi-day travel requirements and capability constraints imposed by the available transportation resources. A stochastic scheduling model is introduced---the multi-day Household Activity Schedule Estimator (mPHASE)---which generates synthetic daily schedules based on "fuzzy" descriptions of activity characteristics using a finite-element representation of activity flexibility, coordination among household members, and scheduling conflict resolution. Results of a thirty-household pilot study are presented in which responses to an interactive computer assisted personal interview were used as inputs to the mPHASE model in order to illustrate the feasibility of generating complex, realistic multi-day household schedules. Study vehicles were equipped with digital cameras and GPS data acquisition equipment to validate the model results. The synthetically generated schedules captured an average of 60 percent of household travel distance, and exhibited many of the characteristics of complex household travel, including day-to-day travel variation, and schedule coordination among household members. Future advances in the methodology may improve the model results, such as encouraging more detailed and accurate responses by providing a selection of generated schedules during the interview. Finally, the Constraints-based Transportation Resource Assignment Model (CTRAM) is introduced. Using an enumerative optimization approach, CTRAM determines the energy-minimizing vehicle-to-trip assignment decisions, considering trip schedules, occupancy, and vehicle capability. Designed to accept either actual or synthetic schedules, results of an application of the optimization model to the 2001 and 2009 National Household Travel Survey data show that U.S. households can reduce energy use by 10 percent, on average, by modifying the assignment of existing vehicles to trips. Households in 2009 show a higher tendency to assign vehicles optimally than in 2001, and multi-vehicle households with diverse fleets have greater savings potential, indicating that fleet modification strategies may be effective, particularly under higher energy price conditions.

Electron transfer to nitrogenase in different genomic and metabolic backgrounds.

PubMed

Poudel, Saroj; Colman, Daniel R; Fixen, Kathryn R; Ledbetter, Rhesa N; Zheng, Yanning; Pence, Natasha; Seefeldt, Lance C; Peters, John W; Harwood, Caroline S; Boyd, Eric S

2018-02-26

Nitrogenase catalyzes the reduction of dinitrogen (N 2 ) using low potential electrons from ferredoxin (Fd) or flavodoxin (Fld) through an ATP dependent process. Since its emergence in an anaerobic chemoautotroph, this oxygen (O 2 ) sensitive enzyme complex has evolved to operate in a variety of genomic and metabolic backgrounds including those of aerobes, anaerobes, chemotrophs, and phototrophs. However, whether pathways of electron delivery to nitrogenase are influenced by these different metabolic backgrounds is not well understood. Here, we report the distribution of homologs of Fds, Flds, and Fd/Fld-reducing enzymes in 359 genomes of putative N 2 fixers (diazotrophs). Six distinct lineages of nitrogenase were identified and their distributions largely corresponded to differences in the host cells' ability to integrate O 2 or light into energy metabolism. Predicted pathways of electron transfer to nitrogenase in aerobes, facultative anaerobes, and phototrophs varied from those in anaerobes at the level of Fds/Flds used to reduce nitrogenase, the enzymes that generate reduced Fds/Flds, and the putative substrates of these enzymes. Proteins that putatively reduce Fd with hydrogen or pyruvate were enriched in anaerobes, while those that reduce Fd with NADH/NADPH were enriched in aerobes, facultative anaerobes, and anoxygenic phototrophs. The energy metabolism of aerobic, facultatively anaerobic, and anoxygenic phototrophic diazotrophs often yields reduced NADH/NADPH that is not sufficiently reduced to drive N 2 reduction. At least two mechanisms have been acquired by these taxa to overcome this limitation and to generate electrons with potentials capable of reducing Fd. These include the bifurcation of electrons or the coupling of Fd reduction to reverse ion translocation. IMPORTANCE Nitrogen fixation supplies fixed nitrogen to cells from a variety of genomic and metabolic backgrounds including those of aerobes, facultative anaerobes, chemotrophs, and phototrophs. Here, using informatics approaches applied to genomic data, we show that pathways of electron transfer to nitrogenase in metabolically diverse diazotrophic taxa have diversified primarily in response to host cells' acquired ability to integrate O 2 or light into their energy metabolism. Acquisition of two key enzyme complexes enabled aerobic and facultatively anaerobic phototrophic taxa to generate electrons of sufficiently low potential to reduce nitrogenase: the bifurcation of electrons via the Fix complex or the coupling of Fd reduction to reverse ion translocation via the Rhodobacter nitrogen fixation (Rnf) complex. Copyright © 2018 American Society for Microbiology.

Understanding pH Effects on Trichloroethylene and Perchloroethylene Adsorption to Iron in Permeable Reactive Barriers for Groundwater Remediation.

PubMed

Luo, Jing; Farrell, James

2013-01-01

Metallic iron filings are becoming increasing used in permeable reactive barriers for remediating groundwater contaminated by chlorinated solvents. Understanding solution pH effects on rates of reductive dechlorination in permeable reactive barriers is essential for designing remediation systems that can meet treatment objectives under conditions of varying groundwater properties. The objective of this research was to investigate how the solution pH value affects adsorption of trichloroethylene (TCE) and perchloroethylene (PCE) on metallic iron surfaces. Because adsorption is first required before reductive dechlorination can occur, pH effects on halocarbon adsorption energies may explain pH effects on dechlorination rates. Adsorption energies for TCE and PCE were calculated via molecular mechanics simulations using the Universal force field and a self-consistent reaction field charge equilibration scheme. A range in solution pH values was simulated by varying the amount of atomic hydrogen adsorbed on the iron. The potential energies associated TCE and PCE complexes were dominated by electrostatic interactions, and complex formation with the surface was found to result in significant electron transfer from the iron to the adsorbed halocarbons. Adsorbed atomic hydrogen was found to lower the energies of TCE complexes more than those for PCE. Attractions between atomic hydrogen and iron atoms were more favorable when TCE versus PCE was adsorbed to the iron surface. These two findings are consistent with the experimental observation that changes in solution pH affect TCE reaction rates more than those for PCE.

Predicting protein complex geometries with a neural network.

PubMed

Chae, Myong-Ho; Krull, Florian; Lorenzen, Stephan; Knapp, Ernst-Walter

2010-03-01

A major challenge of the protein docking problem is to define scoring functions that can distinguish near-native protein complex geometries from a large number of non-native geometries (decoys) generated with noncomplexed protein structures (unbound docking). In this study, we have constructed a neural network that employs the information from atom-pair distance distributions of a large number of decoys to predict protein complex geometries. We found that docking prediction can be significantly improved using two different types of polar hydrogen atoms. To train the neural network, 2000 near-native decoys of even distance distribution were used for each of the 185 considered protein complexes. The neural network normalizes the information from different protein complexes using an additional protein complex identity input neuron for each complex. The parameters of the neural network were determined such that they mimic a scoring funnel in the neighborhood of the native complex structure. The neural network approach avoids the reference state problem, which occurs in deriving knowledge-based energy functions for scoring. We show that a distance-dependent atom pair potential performs much better than a simple atom-pair contact potential. We have compared the performance of our scoring function with other empirical and knowledge-based scoring functions such as ZDOCK 3.0, ZRANK, ITScore-PP, EMPIRE, and RosettaDock. In spite of the simplicity of the method and its functional form, our neural network-based scoring function achieves a reasonable performance in rigid-body unbound docking of proteins. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

Noncovalent Interactions and Internal Dynamics in Pyridine-Ammonia: A Combined Quantum-Chemical and Microwave Spectroscopy Study.

PubMed

Spada, Lorenzo; Tasinato, Nicola; Vazart, Fanny; Barone, Vincenzo; Caminati, Walther; Puzzarini, Cristina

2017-04-06

The 1:1 complex of ammonia with pyridine is characterized by using state-of-the-art quantum-chemical computations combined with pulsed-jet Fourier-transform microwave spectroscopy. The computed potential energy landscape indicates the formation of a stable σ-type complex, which is confirmed experimentally: analysis of the rotational spectrum shows the presence of only one 1:1 pyridine-ammonia adduct. Each rotational transition is split into several components owing to the internal rotation of NH 3 around its C 3 axis and to the hyperfine structure of both 14 N quadrupolar nuclei, thus providing unequivocal proof that the two molecules form a σ-type complex involving both a N-H⋅⋅⋅N and a C-H⋅⋅⋅N hydrogen bond. The dissociation energy (BSSE- and ZPE-corrected) is estimated to be 11.5 kJ mol -1 . This work represents the first application of an accurate yet efficient computational scheme, designed for the investigation of small biomolecules, to a molecular cluster. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Non-Covalent Interactions and Internal Dynamics in Pyridine-Ammonia a Combined Quantum-Chemical and Microwave Spectroscopy Study

NASA Astrophysics Data System (ADS)

Spada, Lorenzo; Tasinato, Nicola; Vazart, Fanny; Barone, Vincenzo; Caminati, Walther; Puzzarini, Cristina

2017-06-01

The 1:1 complex of ammonia with pyridine has been characterized by using state-of-the-art quantum-chemical computations combined with pulsed-jet Fourier-Transform microwave spectroscopy. The computed potential energy landscape pointed out the formation of a stable σ-type complex, which has been confirmed experimentally: the analysis of the rotational spectrum showed the presence of only one 1:1 pyridine - ammonia adduct. Each rotational transition is split into several components due to the internal rotation of NH_3 around its C_3 axis and to the hyperfine structure of both ^{14}N quadrupolar nuclei, thus providing the unequivocal proof that the two molecules form a σ-type complex involving both a N-H\\cdotsN and a C-H\\cdotsN hydrogen bond. The dissociation energy (BSSE and ZPE corrected) has been estimated to be 11.5 kJ\\cdotmol^{-1}. This work represents the first application of an accurate, yet efficient computational scheme, designed for the investigation of small biomolecules, to a molecular cluster.

The Effect of Crystal Packing and ReIV Ions on the Magnetisation Relaxation of [Mn6]-Based Molecular Magnets

PubMed Central

Martínez-Lillo, José; Cano, Joan; Wernsdorfer, Wolfgang; Brechin, Euan K

2015-01-01

The energy barrier to magnetisation relaxation in single-molecule magnets (SMMs) proffers potential technological applications in high-density information storage and quantum computation. Leading candidates amongst complexes of 3d metals ions are the hexametallic family of complexes of formula [Mn6O2(R-sao)6(X)2(solvent)y] (saoH2=salicylaldoxime; X=mono-anion; y=4–6; R=H, Me, Et, and Ph). The recent synthesis of cationic [Mn6][ClO4]2 family members, in which the coordinating X ions were replaced with non-coordinating anions, opened the gateway to constructing families of novel [Mn6] salts in which the identity and nature of the charge balancing anions could be employed to alter the physical properties of the complex. Herein we demonstrate initial experiments to show that this is indeed possible. By replacing the diamagnetic ClO4− anions with the highly anisotropic ReIV ion in the form of [ReIVCl6]2−, the energy barrier to magnetisation relaxation is increased by up to 30 %. PMID:25951415

Exploring hydride-π interactions and their tuning by σ-hole bonds: an ab initio study

NASA Astrophysics Data System (ADS)

Esrafili, Mehdi D.; Asadollahi, Soheila; Mousavian, Parisasadat

2018-01-01

In the present work, ab initio calculations are performed to investigate the geometry, interaction energy and bonding properties of binary complexes formed between metal-hydrides HMX (M = Be, Mg, Zn and X = H, F, CH3) and a series of π-acidic heteroaromatic rings. In all the resulting complexes, the heteroaromatic ring acts as a Lewis acid (electron acceptor), while the H atom of the HMX molecule acts as a Lewis base (electron donor). The nature of this interaction, called 'hydride-π' interaction, is explored in terms of molecular electrostatic potential, non-covalent interaction, quantum theory of atoms in molecules and natural bond orbital analyses. The results show that the interaction energies of these hydride-π interactions are between -1.24 and -2.72 kcal/mol. Furthermore, mutual influence between the hydride-π and halogen- or pnicogen-bonding interactions is studied in complexes in which these interactions coexist. For a given π-acidic ring, the formation of the pnicogen-bonding induces a larger enhancing effect on the strength of hydride-π bond than the halogen-bonding.

Coordination chemistry in magnesium battery electrolytes: how ligands affect their performance.

PubMed

Shao, Yuyan; Liu, Tianbiao; Li, Guosheng; Gu, Meng; Nie, Zimin; Engelhard, Mark; Xiao, Jie; Lv, Dongping; Wang, Chongmin; Zhang, Ji-Guang; Liu, Jun

2013-11-04

Magnesium battery is potentially a safe, cost-effective, and high energy density technology for large scale energy storage. However, the development of magnesium battery has been hindered by the limited performance and the lack of fundamental understandings of electrolytes. Here, we present a study in understanding coordination chemistry of Mg(BH₄)₂ in ethereal solvents. The O donor denticity, i.e. ligand strength of the ethereal solvents which act as ligands to form solvated Mg complexes, plays a significant role in enhancing coulombic efficiency of the corresponding solvated Mg complex electrolytes. A new electrolyte is developed based on Mg(BH₄)₂, diglyme and LiBH₄. The preliminary electrochemical test results show that the new electrolyte demonstrates a close to 100% coulombic efficiency, no dendrite formation, and stable cycling performance for Mg plating/stripping and Mg insertion/de-insertion in a model cathode material Mo₆S₈ Chevrel phase.

Cyclopropanes and hypervalent iodine reagents: high energy compounds for applications in synthesis and catalysis.

PubMed

Fernández González, Davinia; De Simone, Filippo; Brand, Jonathan P; Nicolai, Stefano; Waser, Jérôme

2011-01-01

One of the major challenges faced by organic chemistry is the efficient synthesis of increasingly complex molecules. Since October 2007, the Laboratory of Catalysis and Organic Synthesis (LCSO) at EPFL has been working on the development of catalytic reactions based on the Umpolung of the innate reactivity of functional groups. Electrophilic acetylene synthons have been developed using the exceptional properties of ethynyl benziodoxolone (EBX) hypervalent iodine reagents for the alkynylation of heterocycles and olefins. The obtained acetylenes are important building blocks for organic chemistry, material sciences and chemical biology. The ring-strain energy of donor-acceptor cyclopropanes was then used in the first catalytic formal homo-Nazarov cyclization. In the case of aminocyclopropanes, the method could be applied in the synthesis of the alkaloids aspidospermidine and goniomitine. The developed methods are expected to have a broad potential for the synthesis and functionalization of complex organic molecules, including carbocycles and heterocycles.

Coordination Chemistry in magnesium battery electrolytes: how ligands affect their performance

DOE PAGES

Shao, Yuyan; Liu, Tianbiao L.; Li, Guosheng; ...

2013-11-04

Magnesium battery is potentially a safe, cost-effective, and high energy density technology for large scale energy storage. However, the development of magnesium battery has been hindered by the limited performance and the lack of fundamental understandings of electrolytes. Here, we present a coordination chemistry study of Mg(BH 4) 2 in ethereal solvents. The O donor denticity, i.e. ligand strength of the ethereal solvents which act as ligands to form solvated Mg complexes, plays a significant role in enhancing coulombic efficiency of the corresponding solvated Mg complex electrolytes. A new and safer electrolyte is developed based on Mg(BH4)2, diglyme and optimizedmore » LiBH4 additive. The new electrolyte demonstrates 100% coulombic efficiency, no dendrite formation, and stable cycling performance with the cathode capacity retention of ~90% for 300 cycles in a prototype magnesium battery.« less

Modeling, Analysis, and Interpretation of Photoelectron Energy Spectra at Enceladus Observed by Cassini

NASA Astrophysics Data System (ADS)

Taylor, S. A.; Coates, A. J.; Jones, G. H.; Wellbrock, A.; Fazakerley, A. N.; Desai, R. T.; Caro-Carretero, R.; Michiko, M. W.; Schippers, P.; Waite, J. H.

2018-01-01

The Electron Spectrometer (ELS) of the Cassini Plasma Spectrometer has observed photoelectrons produced in the plume of Enceladus. These photoelectrons are observed during Enceladus encounters in the energetic particle shadow where the spacecraft is largely shielded from penetrating radiation by the moon. We present a complex electron spectrum at Enceladus including evidence of two previously unidentified electron populations at 6-10 eV and 10-16 eV. We estimate that the proportion of "hot" (>15 eV) to "cold" (<15 eV) electrons during the Enceladus flybys is ≈ 0.1-0.5%. We have constructed a model of photoelectron production in the plume and compared it with ELS Enceladus flyby data by scaling and energy shifting according to spacecraft potential. We suggest that the complex structure of the electron spectrum observed can be explained entirely by photoelectron production in the plume ionosphere.

Role of optical computers in aeronautical control applications

NASA Technical Reports Server (NTRS)

Baumbick, R. J.

1981-01-01

The role that optical computers play in aircraft control is determined. The optical computer has the potential high speed capability required, especially for matrix/matrix operations. The optical computer also has the potential for handling nonlinear simulations in real time. They are also more compatible with fiber optic signal transmission. Optics also permit the use of passive sensors to measure process variables. No electrical energy need be supplied to the sensor. Complex interfacing between optical sensors and the optical computer is avoided if the optical sensor outputs can be directly processed by the optical computer.

Covalent bonding: the fundamental role of the kinetic energy.

PubMed

Bacskay, George B; Nordholm, Sture

2013-08-22

This work addresses the continuing disagreement between two prevalent schools of thought concerning the mechanism of covalent bonding. According to Hellmann, Ruedenberg, and Kutzelnigg, a lowering of the kinetic energy associated with electron delocalization is the key stabilization mechanism. The opposing view of Slater, Feynman, and Bader has maintained that the source of stabilization is electrostatic potential energy lowering due to electron density redistribution to binding regions between nuclei. Despite the large body of accurate quantum chemical work on a range of molecules, the debate concerning the origin of bonding continues unabated, even for H2(+), the simplest of covalently bound molecules. We therefore present here a detailed study of H2(+), including its formation, that uses a sequence of computational methods designed to reveal the relevant contributing mechanisms as well as the spatial density distributions of the kinetic and potential energy contributions. We find that the electrostatic mechanism fails to provide real insight or explanation of bonding, while the kinetic energy mechanism is sound and accurate but complex or even paradoxical to those preferring the apparent simplicity of the electrostatic model. We further argue that the underlying mechanism of bonding is in fact of dynamical character, and analyses that focus on energy do not reveal the origin of covalent bonding in full clarity.

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

DOE PAGES

Sornborger, Andrew Tyler; Stancil, Phillip; Geller, Michael R.

2018-03-22

Here, one of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputedmore » potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born–Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3–8 channels and circuit depths < 1000.« less

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sornborger, Andrew Tyler; Stancil, Phillip; Geller, Michael R.

Here, one of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputedmore » potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born–Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3–8 channels and circuit depths < 1000.« less

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

NASA Astrophysics Data System (ADS)

Sornborger, Andrew T.; Stancil, Phillip; Geller, Michael R.

2018-05-01

One of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputed potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born-Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈ 10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3-8 channels and circuit depths < 1000.

Integrative Approach for Computationally Inferring Interactions between the Alpha and Beta Subunits of the Calcium-Activated Potassium Channel (BK): a Docking Study

PubMed Central

González, Janneth; Gálvez, Angela; Morales, Ludis; Barreto, George E.; Capani, Francisco; Sierra, Omar; Torres, Yolima

2013-01-01

Three-dimensional models of the alpha- and beta-1 subunits of the calcium-activated potassium channel (BK) were predicted by threading modeling. A recursive approach comprising of sequence alignment and model building based on three templates was used to build these models, with the refinement of non-conserved regions carried out using threading techniques. The complex formed by the subunits was studied by means of docking techniques, using 3D models of the two subunits, and an approach based on rigid-body structures. Structural effects of the complex were analyzed with respect to hydrogen-bond interactions and binding-energy calculations. Potential interaction sites of the complex were determined by referencing a study of the difference accessible surface area (DASA) of the protein subunits in the complex. PMID:23492851

MM-ISMSA: An Ultrafast and Accurate Scoring Function for Protein-Protein Docking.

PubMed

Klett, Javier; Núñez-Salgado, Alfonso; Dos Santos, Helena G; Cortés-Cabrera, Álvaro; Perona, Almudena; Gil-Redondo, Rubén; Abia, David; Gago, Federico; Morreale, Antonio

2012-09-11

An ultrafast and accurate scoring function for protein-protein docking is presented. It includes (1) a molecular mechanics (MM) part based on a 12-6 Lennard-Jones potential; (2) an electrostatic component based on an implicit solvent model (ISM) with individual desolvation penalties for each partner in the protein-protein complex plus a hydrogen bonding term; and (3) a surface area (SA) contribution to account for the loss of water contacts upon protein-protein complex formation. The accuracy and performance of the scoring function, termed MM-ISMSA, have been assessed by (1) comparing the total binding energies, the electrostatic term, and its components (charge-charge and individual desolvation energies), as well as the per residue contributions, to results obtained with well-established methods such as APBSA or MM-PB(GB)SA for a set of 1242 decoy protein-protein complexes and (2) testing its ability to recognize the docking solution closest to the experimental structure as that providing the most favorable total binding energy. For this purpose, a test set consisting of 15 protein-protein complexes with known 3D structure mixed with 10 decoys for each complex was used. The correlation between the values afforded by MM-ISMSA and those from the other methods is quite remarkable (r(2) ∼ 0.9), and only 0.2-5.0 s (depending on the number of residues) are spent on a single calculation including an all vs all pairwise energy decomposition. On the other hand, MM-ISMSA correctly identifies the best docking solution as that closest to the experimental structure in 80% of the cases. Finally, MM-ISMSA can process molecular dynamics trajectories and reports the results as averaged values with their standard deviations. MM-ISMSA has been implemented as a plugin to the widely used molecular graphics program PyMOL, although it can also be executed in command-line mode. MM-ISMSA is distributed free of charge to nonprofit organizations.

Energy-Complexity Relations by Structural Complexity Methods

NASA Astrophysics Data System (ADS)

Ricca, Renzo L.

2011-09-01

In this paper we shall review some of the most recent developments and results on work on energy-complexity relations and, if time will allow it, we shall provide an analytical proof of eq. (3) below, a fundamental relation between energy and complexity established by numerical experiments.

Density-functional study on the dopant-segregation mechanism: Chemical potential dependence of dopant-defect complex at Si/SiO2 interface

NASA Astrophysics Data System (ADS)

Kawai, Hiroki; Nakasaki, Yasushi; Kanemura, Takahisa; Ishihara, Takamitsu

2018-04-01

Dopant segregation at Si/SiO2 interface has been a serious problem in silicon device technology. This paper reports a comprehensive density-functional study on the segregation mechanisms of boron, phosphorous, and arsenic at the Si/SiO2 interface. We found that three kinds of interfacial defects, namely, interstitial oxygen, oxygen vacancy, and silicon vacancy with two oxygen atoms, are stable in the possible chemical potential range. Thus, we consider these defects as trap sites for the dopants. For these defects, the dopant segregation energies, the electrical activities of the trapped dopants, and the kinetic energy barriers of the trapping/detrapping processes are calculated. As a result, trapping at the interstitial oxygen site is indicated to be the most plausible mechanism of the dopant segregation. The interstitial oxygen works as a major trap site since it has a high areal density at the Si/SiO2 interface due to the low formation energy.

FIRST PRINCIPLES STUDY ON ELECTRONIC AND OPTICAL PROPERTIES OF Al-DOPED γ-Ge3N4

NASA Astrophysics Data System (ADS)

Ding, Y. C.; Xiang, A. P.; Zhu, X. H.; Luo, J.; Hu, X. F.

2012-12-01

First principles study of the structural, electronic and optical properties of Al-doped γ-Ge3N4 with different concentration has been reported using the pseudo-potential plane wave method within the generalized gradient approximation (GGA). The binding energy and the formation energy suggest that Aluminum (Al) impurities prefer to substitute Ge at octahedral sites. Different doping concentrations are considered and the corresponding density of states (DOS) are analyzed. Calculated DOS indicates that there are holes in the top of the valance band after doping, meaning a p-type doping. We study the complex dielectric function, the absorption coefficient, and the electron energy loss spectra. It is demonstrated that for the low Al concentration, the material exhibits the dielectric behavior and for the high Al concentration, the material has possibilities to exhibit some metallic behavior. The γ-Ge3N4 doped with Al has a much higher static dielectric constant than undoped γ-Ge3N4, implying its potential applications in electronics and optics.

Exploring Chemical Space with the Alchemical Derivatives.

PubMed

Balawender, Robert; Welearegay, Meressa A; Lesiuk, Michał; De Proft, Frank; Geerlings, Paul

2013-12-10

In this paper, we verify the usefulness of the alchemical derivatives in the prediction of chemical properties. We concentrate on the stability of the transmutation products, where the term "transmutation" means the change of the nuclear charge at an atomic site at constant number of electrons. As illustrative transmutations showing the potential of the method in exploring chemical space, we present some examples of increasing complexity starting with the deprotonation, continuing with the transmutation of the nitrogen molecule, and ending with the substitution of isoelectronic B-N units for C-C units and N units for C-H units in carbocyclic systems. The basis set influence on the qualitative and quantitative accuracies of the alchemical predictions was investigated. The alchemical deprotonation energy (from the second order Taylor expansion) correlates well with the vertical deprotonation energy and can be used as a preliminary indicator for the experimental deprotonation energy. The results of calculations for the BN derivatives of benzene and pyrene show that this method has great potential for efficient and accurate scanning of chemical space.