Wang, Feng; Stuart, Steven J.; Latour, Robert A.
2009-01-01
The adsorption behavior of a biomolecule, such as a peptide or protein, to a functionalized surface is of fundamental importance for a broad range of applications in biotechnology. The adsorption free energy for these types of interactions can be determined from a molecular dynamics simulation using the partitioning between adsorbed and nonadsorbed states, provided that sufficient sampling of both states is obtained. However, if interactions between the solute and the surface are strong, the solute will tend to be trapped near the surface during the simulation, thus preventing the adsorption free energy from being calculated by this method. This situation occurs even when using an advanced sampling algorithm such as replica-exchange molecular dynamics (REMD). In this paper, the authors demonstrate the fundamental basis of this problem using a model system consisting of one sodium ion (Na+) as the solute positioned over a surface functionalized with one negatively charged group (COO−) in explicit water. With this simple system, the authors show that sufficient sampling in the coordinate normal to the surface cannot be obtained by conventional REMD alone. The authors then present a method to overcome this problem through the use of an adaptive windowed-umbrella sampling technique to develop a biased-energy function that is combined with REMD. This approach provides an effective method for the calculation of adsorption free energy for solute-surface interactions. PMID:19768127
NASA Astrophysics Data System (ADS)
Battle, Keith; Alan Salter, E.; Wesley Edmunds, R.; Wierzbicki, Andrzej
2010-04-01
Antifreeze proteins (AFPs) are a unique class of proteins that inhibit ice growth without changing the melting point of ice. In this work, we study the detailed molecular mechanism of interactions between the hydrophobic side of the winter flounder (WF) AFP and two mutants, AAAA and SSSS, in which threonine residues are substituted by serines and alanines, respectively. Umbrella sampling molecular dynamics simulations of the separation of the proteins from the (2 0 1) surface in an explicit water box is carried out to calculate the potential of mean force free energies of adsorption using AMBER10i. We estimate wild-type WF's free energy of adsorption to ice to be about -12.0 kcal/mol. Gas-phase pseudopotential plane-wave calculations of methane adsorption onto select surfaces of ice are also carried out under periodic boundary conditions to address the possible enthalpic role of WF's methyl groups in binding. The contributions of hydrophobic residues to the free energy of adsorption are discussed.
NASA Astrophysics Data System (ADS)
Yano, Masato; Hirose, Kenji; Yoshikawa, Minoru; Thermal management technology Team
Facile property calculation model for adsorption chillers was developed based on equilibrium adsorption cycles. Adsorption chillers are one of promising systems that can use heat energy efficiently because adsorption chillers can generate cooling energy using relatively low temperature heat energy. Properties of adsorption chillers are determined by heat source temperatures, adsorption/desorption properties of adsorbent, and kinetics such as heat transfer rate and adsorption/desorption rate etc. In our model, dependence of adsorption chiller properties on heat source temperatures was represented using approximated equilibrium adsorption cycles instead of solving conventional time-dependent differential equations for temperature changes. In addition to equilibrium cycle calculations, we calculated time constants for temperature changes as functions of heat source temperatures, which represent differences between equilibrium cycles and real cycles that stemmed from kinetic adsorption processes. We found that the present approximated equilibrium model could calculate properties of adsorption chillers (driving energies, cooling energies, and COP etc.) under various driving conditions quickly and accurately within average errors of 6% compared to experimental data.
Staemmler, Volker
2011-06-30
The method of local increments is used in connection with an embedded cluster approach and wave function based quantum chemical ab initio methods to describe the adsorption of a single CO molecule on the MgO(001) surface. The first step in this approach is a conventional Hartree-Fock calculation. The occupied orbitals are then localized by means of the Foster-Boys localization procedure, and the full system is decomposed into several "subunits" that consist of the orbitals localized at the CO molecule and at the Mg and O atoms of the MgO cluster. The correlation energy is expanded into a series of local n-body increments that are evaluated separately and independently. In this way, big savings in computer time can be achieved because (a) the treatment of a large system is replaced with a series of much faster calculations for small subsystems and (b) the big basis sets necessary for describing dispersion effects are only needed for the atoms in the respective subsystem while all other atoms can be treated by medium size Hartree-Fock type basis sets. The coupled electron pair approach, CEPA, an approximate coupled cluster method, is used to calculate the correlation energies of the various subsystems. For the vertical adsorption of CO on top a Mg atom of the MgO(001) surface with the C atom toward Mg, the individual one- and two-body increments are calculated as functions of the CO-MgO separation and a full potential energy curve is constructed from them. A very shallow minimum with an adsorption energy of 0.016 eV at a Mg-C distance of 3.04 Å is found at the Hartree-Fock level, while inclusion of correlation (dispersion) effects shortens the Mg-C distance to 2.59 Å and yields a much larger adsorption energy of 0.124 eV. This is in very good agreement with the best experimental value of 0.14 eV. The basis set superposition error, BSSE, was fully corrected for by the counterpoise method and the bonding mechanism was analyzed at the Hartree-Fock level by means of
Kaiser, Alexander; Zöttl, Samuel; Bartl, Peter; Leidlmair, Christian; Mauracher, Andreas; Probst, Michael; Denifl, Stephan; Echt, Olof; Scheier, Paul
2013-01-01
Methane adsorption on positively charged aggregates of C60 is investigated by both mass spectrometry and computer simulations. Calculated adsorption energies of 118–281 meV are in the optimal range for high-density storage of natural gas. Groove sites, dimple sites, and the first complete adsorption shells are identified experimentally and confirmed by molecular dynamics simulations, using a newly developed force field for methane–methane and fullerene–methane interaction. The effects of corrugation and curvature are discussed and compared with data for adsorption on graphite, graphene, and carbon nanotubes. PMID:23744834
Adsorption of O on Mo(110) surface from first-principles calculation
Zhou, Yungang; Zu, Xiaotao T.; Ni, Jiening; Gao, Fei
2009-01-01
First-principles calculations based on density functional theory (DFT) have been performed to study O adsorption in on-surface and subsurface sites. For different coverages, hollow site is found to be the most stable on-surface adsorption site. The subsurface adsorption at the bare Mo surface is found unfavored. The most stable subsurface site, the tetrahedral site, has a higher adsorption energy than on-surface sites. The pre-adsorbed O overlayer reduces the adsorption energy of subsurface O atoms, particularly for the octahedral site at p(2×2) phase. Also, vibrational frequencies, work-function and density of states are presented for O adsorption in on-surface sites.
Dissociative versus molecular adsorption of phenol on Si(100)2×1 : A first-principles calculation
NASA Astrophysics Data System (ADS)
Carbone, Marilena; Meloni, Simone; Caminiti, Ruggero
2007-08-01
We investigated the competitive adsorption of a bifunctional molecule, phenol, on Si(100)2×1 by ab initio calculations. We performed geometry optimizations of phenol adsorbed either molecularly or dissociatively, on five possible sites (top, bridge, valley bridge, cave, and pedestal), in the low coverage regime. We found that the dissociative adsorption of phenol on top of a silicon dimer is the most favorable adsorption configuration. In the group of dissociative adsorption the phenol initially placed on the bridge or the valley-bridge sites ends up as a toplike local minima. The pedestal and cave sites remain as low-adsorption energy “open” sites. In the group of molecular adsorption, a higher adsorption energy is associated to the adsorption through an addition reaction and loss of the aromatic character (bridge, valley-bridge, and pedestal sites). Standard butterfly or diagonal butterfly are the corresponding optimized geometries. Retention of aromatic character and lower adsorption energy are associated to the adsorption on the top and cave sites. The ordering of adsorption sites according to the adsorption energy shows a mixture of the dissociative and the molecular sites. In the case of adsorption on the top site, the adsorption energies after a rotation of the phenoxy fragment along the bonding axis and hydrogen migration on the surface are very similar. The bend of the phenoxy fragment on the surface, instead, is not favored (the adsorption energy is 1.004eV lower compared to the vertical position). Different electron density maps were calculated for different adsorption sites and modes. Finally, we investigated the possibility that molecularly adsorbed phenol behaves as a precursor for the dissociative one by nudged elastic band calculations. We found a barrier of the same order of magnitude of the thermodynamic energy at room temperature for the conversion of the valley-bridge molecular into the top dissociative site.
Preferential orientation of CO adsorption on Ni as determined by extended Hueckel calculations.
NASA Technical Reports Server (NTRS)
Robertson, J. C.; Wilmsen, C. W.
1972-01-01
The adsorption of CO on the nickel surface has been calculated using a modified extended Hueckel technique for a number of different orientations of the CO with respect to the nickel surface. The calculations show that double site adsorption with the CO molecule normal to the surface and the carbon atom closest to the metal gives the most stable configuration (2.57 eV). The single site absorbs with an energy of 2.39 eV. However, other configurations also give fairly large bonding energies. The CO normal to the surface with oxygen closest to the metal gives a heat of adsorption of 0.37 eV. Two-center adsorption with the CO axis parallel to the surface and the molecule symmetrically placed between the nearest neighbors gives a chemisorption energy of 1.34 eV. These values compare with an experimental value of 1.98 eV.
Computation of Adsorption Energies of Some Interstellar Species
NASA Astrophysics Data System (ADS)
Sil, Milan; Chakrabarti, Sandip Kumar; Das, Ankan; Majumdar, Liton; Gorai, Prasanta; Etim, Emmanuel; Arunan, Elangannan
2016-07-01
Adsorption energies of surface species are most crucial for chemical complexity of interstellar grain mantle. Aim of this work is to study the variation of the adsorption energies depending upon the nature of adsorbent. We use silicate and carbonaceous grains for the absorbents. For silicate grains, we use very simple crystalline ones, namely, Enstatite (MgSiO_3)_n, Ferrosilite (FeSiO_3)_n, Forsterite (Mg_2SiO_4)_n and Fayalite (Fe_2SiO_4)_n. We use n=1, 2, 4, 8 to study the variation of adsorption energies with the increase in cluster size. For carbonaceous grain, we use Coronene (polyaromatic hydrocarbon surface). Adsorption energy of all these species are calculated by means of quantum chemical calculation using self consistent density functional theory (DFT). MPWB1K hybrid meta-functional is employed since it has been proven useful to study the systems with weak interactions such as van der Waals interactions. Optimization are also carried out with MPWB1K/6-311g(d) and MPWB1K/6311g(d,p) and a comparison of adsorption energies are discussed for these two different basis sets. We use crystalline structure of the adsorbent. The adsorbate is placed in the different site of the grain with a suitable distance. The energy of adsorption for a species on the grain surface is defined as follows: E_a_d_s = E_s_s - (E_s_u_r_f_a_c_e + E_s_p_e_c_i_e_s), where E_a_d_s is the adsorption energy, E_s_s is the optimized energy for species placed in a suitable distance from the grain surface, E_s_u_r_f_a_c_e and E_s_p_e_c_i_e_s respectively are the optimized energies of the surface and species separately.
Dissociative adsorption of water on Au/MgO/Ag(001) from first principles calculations
NASA Astrophysics Data System (ADS)
Nevalaita, J.; Häkkinen, H.; Honkala, K.
2015-10-01
The molecular and dissociative adsorption of water on a Ag-supported 1 ML, 2 ML and 3 ML-a six atomic layer-thick MgO films with a single Au adatom is investigated using density functional theory calculations. The obtained results are compared to a bulk MgO(001) surface with an Au atom. On thin films the negatively charged Au strengthens the binding of the polar water molecule due to the attractive Au-H interaction. The adsorption energy trends of OH and H with respect to the film thickness depend on an adsorption site. In the case OH or H binds atop Au on MgO/Ag(001), the adsorption becomes more exothermic with the increasing film thickness, while the reverse trend is seen when the adsorption takes place on bare MgO/Ag(001). This behavior can be explained by different bonding mechanisms identified with the Bader analysis. Interestingly, we find that the rumpling of the MgO film and the MgO-Ag interface distance correlate with the charge transfer over the thin film and the interface charge, respectively. Moreover, we employ a modified Born-Haber-cycle to analyze the effect of film thickness to the adsorption energy of isolated Au and OH species on MgO/Ag(001). The analysis shows that the attractive Coulomb interaction between the negatively charged adsorbate and the positive MgO-Ag-interface does not completely account for the weaker binding with increasing film thickness. The redox energy associated with the charge transfer from the interface to the adsorbate is more exothermic with the increasing film thickness and partly compensates the decrease in the attractive Coulomb interaction.
First principles calculations of the Sc adsorption on Si(001)-c(2 × 4)
NASA Astrophysics Data System (ADS)
Romero, M. T.; Cocoletzi, Gregorio H.; Takeuchi, Noboru
2012-09-01
We have investigated the energetics and the atomic structure of the adsorption of Sc on the Si(001)-c(2 × 4) surface using first principles total energy calculations, within the periodic density functional. The Sc adsorption has been studied at high symmetry sites considering different concentrations. We have first explored the one atom case and then increased the coverage up to a 0.25 of a monolayer of Sc. For the adsorption of one Sc atom we have obtained that the most stable configuration corresponds to the adsorption in the trench between two Si dimers, at the C1 (cave) site. The interaction of the adsorbed Sc with the Si dimers induces a decrease of the dimers buckling amplitude. On the other hand Si dimers without interaction with the adsorbate have buckling amplitudes similar to those of the clean Si surface. When the Sc coverage is increased to two Sc atoms, the most stable structure corresponds to the adsorption at two consecutive V (valley-bridge) sites along the trench between Si dimers, resulting in the weakening of some of the Si dimers bonds. This result indicates that the formation of one dimensional Sc chains on the silicon surface is energetically and kinetically favorable.
The Calculation of Adsorption Isotherms from Chromatographic Peak Shapes
ERIC Educational Resources Information Center
Neumann, M. G.
1976-01-01
Discusses the relationship between adsorption isotherms and elution peak shapes in gas chromatography, and describes a laboratory experiment which involves the adsorption of hexane, cyclohexane, and benzene on alumina at different temperatures. (MLH)
Ab-initio calculation of C and CO adsorption on the Co (110) surface
NASA Astrophysics Data System (ADS)
Chin, Shin-Liang; Ionescu, Adrian; Reeve, Robert M.; Cheng, Jun; Barnes, Crispin H. W.
2013-02-01
The adsorption energies, structural, electrical and magnetic properties of adsorption of C and CO on the fcc Co (110) surface have been investigated using density functional theory. The preferential adsorption site for the fcc Co (110) has been calculated. For the case of C adsorption, the preferential adsorption site is the long-bridge for both the 0.5 and 1.0 monolayers (ML) coverages. Whilst for the CO case, the preferential adsorption sites are at the atop and short-bridge site for 0.5 and 1.0 ML coverages respectively. Structurally, the first two layers of the bare Co (110) surface expand whereas the second and third layers contract. Upon adsorption of either C or CO, however, the degree of expansion and compression reduces. Magnetically, the adsorbates were found to couple ferrimagnetically to the surface and suppress the magnetic moment of the Co layers beneath them. The C adsorbate has a much stronger suppression effect as compared to the CO adsorbate. At 0.5 ML coverage, the C adatom suppresses up to 47% of the magnetic moment in the surface layer compared to a clean Co (110), whereas the CO adsorbate only suppresses up to 16%. For the 1.0 ML coverage case, both the C and CO adsorbates suppress almost equivalently well at 68% and 63% respectively. We also report on a correlation between the amount of charge transfer and the degree of suppression of the surface magnetic moment. Finally, we observe that the electronic charge is shared in the [001] direction for the C adsorbate and in the [11¯0] direction for the CO adsorbate. This anisotropy of surface bonding, in conjunction with the ligand field theory, explains the mechanism behind the spin reorientation transition that occurs uniquely on the CO/Co(110) system.
NASA Astrophysics Data System (ADS)
Liu, Xiaojie; Wang, C. Z.; Hupalo, M.; Yao, Y. X.; Tringides, M. C.; Lu, W. C.; Ho, K. M.
2010-12-01
Adsorption of rare-earth (RE) adatoms (Nd, Gd, Eu, and Yb) on graphene was studied by first-principles calculations based on the density-functional theory. The calculations show that the hollow site of graphene is the energetically favorable adsorption site for all the RE adatoms studied. The adsorption energies and diffusion barriers of Nd and Gd on graphene are found to be larger than those of Eu and Yb. Comparison with scanning tunneling microscopy experiments for Gd and Eu epitaxially grown on graphene confirms these calculated adsorption and barrier differences, since fractal-like islands are observed for Gd and flat-topped crystalline islands for Eu. The formation of flat Eu islands on graphene can be attributed to its low diffusion barrier and relatively larger ratio of adsorption energy to its bulk cohesive energy. The interactions between the Nd and Gd adatoms and graphene cause noticeable in-plane lattice distortions in the graphene layer. Adsorption of the RE adatoms on graphene also induces significant electric dipole and magnetic moments.
First-principles calculations of the indigo encapsulation and adsorption by MgO nanotubes
Sánchez-Ochoa, F. Cocoletzi, Gregorio H.; Canto, Gabriel I.; Takeuchi, Noboru
2014-06-07
We have performed ab-initio calculations to investigate the structural and electronic properties of (m,m) chiral magnesium oxide nanotubes, (m,m)MgONTs, to explore the encapsulation, inclusion, and adsorption of dyes (organic molecules) such as Indigo (IND). Studies start by determining the structural parameters of the MgO nanotubes with different diameters and the IND. The indigo encapsulation into the MgONT is studied considering four (m,m) chiralities which yield 4 different NT diameters. In the endohedral functionalization, the indigo is within the NT at a tilt angle as in previous theoretical studies of organic molecules inside carbon and boron-nitride nanotubes. Results show that the encapsulation is a strong exothermic process with the m = 6 case exhibiting the largest encapsulation energy. It is also explored the indigo adsorption on the NT surface in the parallel and perpendicular configurations. The perpendicular configuration of the IND adsorption on the (8,8)MgONT exhibits the largest energy. The indigo inclusion within the NTs meets a potential barrier when m < 6, however this barrier diminishes as the index increases. Additionally, we have determined the total density of states (DOS), partial DOS, electron charge redistributions, and the highest occupied molecular orbital–lowest unoccupied molecular orbital levels for the NTs with m = 6. Very strong binding energies and electron charge transfer from the IND to NTs is present in the atomic structures.
First-principles calculations of the indigo encapsulation and adsorption by MgO nanotubes
NASA Astrophysics Data System (ADS)
Sánchez-Ochoa, F.; Cocoletzi, Gregorio H.; Canto, Gabriel I.; Takeuchi, Noboru
2014-06-01
We have performed ab-initio calculations to investigate the structural and electronic properties of (m,m) chiral magnesium oxide nanotubes, (m,m)MgONTs, to explore the encapsulation, inclusion, and adsorption of dyes (organic molecules) such as Indigo (IND). Studies start by determining the structural parameters of the MgO nanotubes with different diameters and the IND. The indigo encapsulation into the MgONT is studied considering four (m,m) chiralities which yield 4 different NT diameters. In the endohedral functionalization, the indigo is within the NT at a tilt angle as in previous theoretical studies of organic molecules inside carbon and boron-nitride nanotubes. Results show that the encapsulation is a strong exothermic process with the m = 6 case exhibiting the largest encapsulation energy. It is also explored the indigo adsorption on the NT surface in the parallel and perpendicular configurations. The perpendicular configuration of the IND adsorption on the (8,8)MgONT exhibits the largest energy. The indigo inclusion within the NTs meets a potential barrier when m < 6, however this barrier diminishes as the index increases. Additionally, we have determined the total density of states (DOS), partial DOS, electron charge redistributions, and the highest occupied molecular orbital-lowest unoccupied molecular orbital levels for the NTs with m = 6. Very strong binding energies and electron charge transfer from the IND to NTs is present in the atomic structures.
Theoretical investigation of lead vapor adsorption on kaolinite surfaces with DFT calculations.
Wang, Xinye; Huang, Yaji; Pan, Zhigang; Wang, Yongxing; Liu, Changqi
2015-09-15
Kaolinite can be used as the in-furnace sorbent/additive to adsorb lead (Pb) vapor at high temperature. In this paper, the adsorptions of Pb atom, PbO molecule and PbCl2 molecule on kaolinie surfaces were investigated by density functional theory (DFT) calculation. Si surface is inert to Pb vapor adsorption while Al surfaces with dehydroxylation are active for the unsaturated Al atoms and the O atoms losing H atoms. The adsorption energy of PbO is much higher than that of Pb atom and PbCl2. Considering the energy barriers, it is easy for PbO and PbCl2 to adsorb on Al surfaces but difficult to escape. The high energy barriers of de-HCl process cause the difficulties of PbCl2 to form PbO·Al2O3·2SiO2 with kaolinite. Considering the inertia of Si atoms and the activity of Al atoms after dehydroxylation, calcination, acid/alkali treatment and some other treatment aiming at amorphous silica producing and Al activity enhancement can be used as the modification measures to improve the performance of kaolinite as the in-furnace metal capture sorbent. PMID:25880048
Biogas - the calculable energy
NASA Astrophysics Data System (ADS)
Kith, Károly; Nagy, Orsolya; Balla, Zoltán; Tamás, András
2015-04-01
EU actions against climate change are rising energy prices, both have emphasized the use of renewable energy,increase investments and energy efficiency. A number of objectives formulated in the EC decree no. 29/2009 by 2020. This document is based on the share of renewable energies in energy consumption should be increased to 20% (EC, 2009). The EU average is 20% but the share of renewables vary from one member state to another. In Hungary in 2020, 14.65% renewable energy share is planned to be achieved. According to the latest Eurostat data, the share of renewable energy in energy consumption of the EU average was 14.1%, while in Hungary, this share was 9.6% in 2012. (EUROSTAT, 2014). The use of renewable energy plant level is influenced by several factors. The most important of these is the cost savings and efficiency gains. Hungarian investments in renewable energy production usually have high associated costs and the payback period is substantially more than five years, depending on the support rate. For example, the payback period is also influenced by the green electricity generated feed prices, which is one of the lowest in Hungary compared the Member States of the European Union. Consequently, it is important to increase the production of green energy. Nowadays, predictable biogas energy is an outstanding type of decentralized energy production. It follows directly that agricultural by-products can be used to produce energy and they also create jobs by the construction of a biogas plant. It is important to dispose of and destroy hazardous and noxious substances in energy production. It follows from this that the construction of biogas plants have a positive impact, in addition to green energy which is prepared to reduce the load on the environment. The production of biogas and green electricity is one of the most environment friendly forms of energy production. Biogas production also has other important ecological effects, such as the substitution of
NASA Astrophysics Data System (ADS)
Abild-Pedersen, F.; Greeley, J.; Studt, F.; Rossmeisl, J.; Munter, T. R.; Moses, P. G.; Skúlason, E.; Bligaard, T.; Nørskov, J. K.
2007-07-01
Density functional theory calculations are presented for CHx, x=0,1,2,3, NHx, x=0,1,2, OHx, x=0,1, and SHx, x=0,1 adsorption on a range of close-packed and stepped transition-metal surfaces. We find that the adsorption energy of any of the molecules considered scales approximately with the adsorption energy of the central, C, N, O, or S atom, the scaling constant depending only on x. A model is proposed to understand this behavior. The scaling model is developed into a general framework for estimating the reaction energies for hydrogenation and dehydrogenation reactions.
Lithium adsorption on graphite from density functional theory calculations.
Valencia, Felipe; Romero, Aldo H; Ancilotto, Francesco; Silvestrelli, Pier Luigi
2006-08-01
The structural, energetic, and electronic properties of the Li/graphite system are studied through density functional theory (DFT) calculations using both the local spin density approximation (LSDA), and the gradient-corrected Perdew-Burke-Ernzerhof (PBE) approximation to the exchange-correlation energy. The calculations were performed using plane waves basis, and the electron-core interactions are described using pseudopotentials. We consider a disperse phase of the adsorbate comprising one Li atom for each 16 graphite surface cells, in a slab geometry. The close contact between the Li nucleus and the graphene plane results in a relatively large binding energy (larger than 1.1 eV). A detailed analysis of the electronic charge distribution, density difference distribution, and band structures indicates that one valence electron is entirely transferred from the atom to the surface, which gives rise to a strong interaction between the resulting lithium ion and the cloud of pi electrons in the substrate. We show that it is possible to explain the differences in the binding of Li, Na, and K adatoms on graphite considering the properties of the corresponding cation/aromatic complexes. PMID:16869593
Water adsorption on O(2x2)/Ru(0001) from STM experiments andfirst-principles calculations
Cabrera-Sanfelix, P.; Sanchez-Portal, D.; Mugarza, A.; Shimizu,T.K.; Salmeron, M.; Arnau, A.
2007-10-15
We present a combined theoretical and experimental study of water adsorption on Ru(0001) pre-covered with 0.25 monolayers (ML) of oxygen forming a (2 x 2) structure. Several structures were analyzed by means of Density Functional Theory calculations for which STM simulations were performed and compared with experimental data. Up to 0.25 monolayers the molecules bind to the exposed Ru atoms of the 2 x 2 unit cell via the lone pair orbitals. The molecular plane is almost parallel to the surface with its H atoms pointing towards the chemisorbed O atoms of the 2 x 2 unit cell forming hydrogen bonds. The existence of these additional hydrogen bonds increases the adsorption energy of the water molecule to approximately 616 meV, which is {approx}220 meV more stable than on the clean Ru(0001) surface with a similar configuration. The binding energy shows only a weak dependence on water coverage, with a shallow minimum for a row structure at 0.125 ML. This is consistent with the STM experiments that show a tendency of the molecules to form linear rows at intermediate coverage. Our calculations also suggest the possible formation of water dimers near 0.25 ML.
All-electron scalar relativistic calculation of water molecule adsorption onto small gold clusters.
Kuang, Xiang-Jun; Wang, Xin-Qiang; Liu, Gao-Bin
2011-08-01
An all-electron scalar relativistic calculation was performed on Au( n )H(2)O (n = 1-13) clusters using density functional theory (DFT) with the generalized gradient approximation at PW91 level. The calculation results reveal that, after adsorption, the small gold cluster would like to bond with oxygen and the H(2)O molecule prefers to occupy the single fold coordination site. Reflecting the strong scalar relativistic effect, Au( n ) geometries are distorted slightly but still maintain a planar structure. The Au-Au bond is strengthened and the H-O bond is weakened, as manifested by the shortening of the Au-Au bond-length and the lengthening of the H-O bond-length. The H-O-H bond angle becomes slightly larger. The enhancement of reactivity of the H(2)O molecule is obvious. The Au-O bond-lengths, adsorption energies, VIPs, HLGs, HOMO (LUMO) energy levels, charge transfers and the highest vibrational frequencies of the Au-O mode for Au( n )H(2)O clusters exhibit an obvious odd-even oscillation. The most favorable adsorption between small gold clusters and the H(2)O molecule takes place when the H(2)O molecule is adsorbed onto an even-numbered Au( n ) cluster and becomes an Au( n )H(2)O cluster with an even number of valence electrons. The odd-even alteration of magnetic moments is observed in Au( n )H(2)O clusters and may serve as material with a tunable code capacity of "0" and "1" by adsorbing a H(2)O molecule onto an odd or even-numbered small gold cluster. PMID:21140279
NASA Astrophysics Data System (ADS)
Hong, Sampyo; Rahman, Talat S.
2007-04-01
We have carried out first-principles calculations of H adsorption on Pd(211) using density-functional theory with the generalized gradient approximation in the plane-wave basis to find out that the most preferred is the threefold hollow site on the terrace of Pd(211) with an adsorption energy of 0.52eV : the hcp and fcc sites being almost energetically equally favorable. For subsurface H adsorption on Pd(211), the octahedral site with an adsorption energy of 0.19eV is slightly more favorable than the tetrahedral site (0.18eV) . Our calculated activation energy barrier for H to diffuse from the preferred surface site to the subsurface one on Pd(211) is 0.33eV , as compared with 0.41eV on Pd(111). Thus, there is an enhancement of the probability of finding subsurface hydrogen in Pd(211). Additionally, we find the diffusion barriers for H on the terraces of Pd(211) to be 0.11eV , while that along the step edge to be only 0.05eV and that within the second layer (subsurface) to be 0.15eV .
Nature of adsorption on TiC(111) investigated with density-functional calculations
NASA Astrophysics Data System (ADS)
Ruberto, Carlo; Lundqvist, Bengt I.
2007-06-01
Extensive density-functional calculations are performed for chemisorption of atoms in the three first periods (H, B, C, N, O, F, Al, Si, P, S, and Cl) on the polar TiC(111) surface. Calculations are also performed for O on TiC(001), for full O(1×1) monolayer on TiC(111), as well as for bulk TiC and for the clean TiC(111) and (001) surfaces. Detailed results concerning atomic structures, energetics, and electronic structures are presented. For the bulk and the clean surfaces, previous results are confirmed. In addition, detailed results are given on the presence of C-C bonds in the bulk and at the surface, as well as on the presence of a Ti-based surface resonance (TiSR) at the Fermi level and of C-based surface resonances (CSR’s) in the lower part of the surface upper valence band. For the adsorption, adsorption energies Eads and relaxed geometries are presented, showing great variations characterized by pyramid-shaped Eads trends within each period. An extraordinarily strong chemisorption is found for the O atom, 8.8eV /adatom. On the basis of the calculated electronic structures, a concerted-coupling model for the chemisorption is proposed, in which two different types of adatom-substrate interactions work together to provide the obtained strong chemisorption: (i) adatom-TiSR and (ii) adatom-CSR’s. This model is used to successfully describe the essential features of the calculated Eads trends. The fundamental nature of this model, based on the Newns-Anderson model, should make it apt for general application to transition-metal carbides and nitrides and for predictive purposes in technological applications, such as cutting-tool multilayer coatings and MAX phases.
NASA Astrophysics Data System (ADS)
McCoy, Rhonda Patrice
from the center ring was shortened because of metal-ligand coordination. These observations are correlated to the shifts in Raman frequencies; a decrease in bond length resulted in a shift to a higher vibrational energy. The surface-enhanced Raman spectrum of DAFO was obtained on silver colloids and gold nanorods. The resulting SER spectra were compared to their corresponding normal Raman spectra, there were changes in relative band intensities and there were bands shifted because of adsorption; these observations were used to probe orientation. Orientation is determined by applying surface selections rules developed by both Creighton and Moskovits. The rules indicate, when the vibrational modes assigned to out-of-plane modes are observed as enhanced in the SER spectrum, the ligand is considered parallel relative to the metal surface, and when the vibrational modes assigned to in-plane modes are observed as enhanced, the ligand is not parallel relative to the metal surface. The relative surface enhancement factors were calculated by normalizing the spectra and then by taking the ratio of ISERS/INR. Based on the enhancement factors, the bands assigned to in-plane modes exhibited the highest enhancement factors on the Au and Ag SER spectra. This observation suggests that DAFO is not parallel to the metal nano-surfaces. In the Ag SERS spectrum the bands with the highest enhancement factors were assigned to quadrant ring stretching and cyclopentone bending. Analysis of the carbonyl stretching frequency on the Ag spectrum revealed the frequency shifted to a lower vibrational energy. This shift has been ascribed to the carbonyl bond losing double bond character, which permits the interaction between the metal and the carbonyl oxygen. It was proposed the DAFO ligand is sandwiched between the silver hydrosol. The TER spectrum of DAFO was obtained; analysis of the spectrum revealed similarities to the Ag SERS spectrum. The carbonyl stretching frequency was lowered, the bands
Gas Adsorption and Selectivity in Zeolitic Imidazolate Frameworks from First Principles Calculations
NASA Astrophysics Data System (ADS)
Ray, Keith; Olmsted, David; He, Ning; Houndonougbo, Yao; Laird, Brian; Asta, Mark
2012-02-01
Zeolitic Imidazolate Framework (ZIFs) are excellent candidate materials for carbon capture and gas separation. Here we employ the van der Waals density functional (vdW-DF) [1] in an analysis of the binding energetics for CO2, CH4 and N2 molecules in a set of ZIFs featuring different chemical functionalizations. We investigate multiple low-energy binding sites, which differ in their positions relative to functional groups on the imidazole linkers. In all cases an accurate treatment of van der Waals forces appears essential to provide reasonable binding energy magnitudes. We report results obtained from different parameterizations of the vdW-DF, providing comparisons between calculations and experimental values of the heat of adsorption [2]. This research is supported by the Energy Frontier Research Center ``Molecularly Engineered Energy Materials,'' funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001342. [1] M. Dion, H. Rydberg, E. Schroder, D. C. Langreth, B. I. Lundqvist, Phys. Rev. Let. 92, 246401 (2004) [2] W. Morris, B. Leung, H. Furukawa, O. K. Yaghi, N. He, H. Hayashi, Y. Houndonougbo, M. Asta, B. B. Laird, O. M. Yaghi, J. AM. CHEM. SOC. 2010, 132, 11006-11008
Scaling Relationships for Adsorption Energies of C2 Hydrocarbons on Transition Metal Surfaces
Jones, G
2011-08-18
Using density functional theory calculations we show that the adsorption energies for C{sub 2}H{sub x}-type adsorbates on transition metal surfaces scale with each other according to a simple bond order conservation model. This observation generalizes some recently recognized adsorption energy scaling laws for AH{sub x}-type adsorbates to unsaturated hydrocarbons and establishes a coherent simplified description of saturated as well as unsaturated hydrocarbons adsorbed on transition metal surfaces. A number of potential applications are discussed. We apply the model to the dehydrogenation of ethane over pure transition metal catalysts. Comparison with the corresponding full density functional theory calculations shows excellent agreement.
Screened Hybrid Exact Exchange Schemes to Adsorption Energies on Perovskite Oxides
NASA Astrophysics Data System (ADS)
Santos, Elton; Vojvodic, Aleksandra; Norskov, Jens K.
The bond formation between an oxide surface and oxygen, which is one of the important intermediates for oxygen evolution reaction, is investigated using hybrid functionals. We show that there exists a linear correlation between the adsorption energies of oxygen on LaMO3 (M =Sc-Cu) oxides at hybrid calculations to those computed using semilocal density functionals through the magnetic properties of the bulk phase. The energetics of the spin-polarized surfaces follow the same trend as corresponding bulk systems, which can be treated at a much lower computational cost. The difference in adsorption energy due to magnetism is linearly correlated to the magnetization energy of bulk, i.e., the energy difference between the spin-polarized and the non spin-polarized solutions. This suggests that one could estimate the correction to the semilocal density functional adsorption energies directly from the hybrid bulk magnetization energy.
Han, Yong; Evans, James W.
2015-10-27
Large-scale first-principles density functional theory calculations are performed to investigate the adsorption and diffusion of Ru adatoms on monolayer graphene (G) supported on Ru(0001). The G sheet exhibits a periodic moiré-cell superstructure due to lattice mismatch. Within a moiré cell, there are three distinct regions: fcc, hcp, and mound, in which the C6-ring center is above a fcc site, a hcp site, and a surface Ru atom of Ru(0001), respectively. The adsorption energy of a Ru adatom is evaluated at specific sites in these distinct regions. We find the strongest binding at an adsorption site above a C atom inmore » the fcc region, next strongest in the hcp region, then the fcc-hcp boundary (ridge) between these regions, and the weakest binding in the mound region. Behavior is similar to that observed from small-unit-cell calculations of Habenicht et al. [Top. Catal. 57, 69 (2014)], which differ from previous large-scale calculations. We determine the minimum-energy path for local diffusion near the center of the fcc region and obtain a local diffusion barrier of ~0.48 eV. We also estimate a significantly lower local diffusion barrier in the ridge region. These barriers and information on the adsorption energy variation facilitate development of a realistic model for the global potential energy surface for Ru adatoms. Furthermore, this in turn enables simulation studies elucidating diffusion-mediated directed-assembly of Ru nanoclusters during deposition of Ru on G/Ru(0001).« less
Han, Yong; Evans, James W.
2015-10-27
Large-scale first-principles density functional theory calculations are performed to investigate the adsorption and diffusion of Ru adatoms on monolayer graphene (G) supported on Ru(0001). The G sheet exhibits a periodic moiré-cell superstructure due to lattice mismatch. Within a moiré cell, there are three distinct regions: fcc, hcp, and mound, in which the C6-ring center is above a fcc site, a hcp site, and a surface Ru atom of Ru(0001), respectively. The adsorption energy of a Ru adatom is evaluated at specific sites in these distinct regions. We find the strongest binding at an adsorption site above a C atom in the fcc region, next strongest in the hcp region, then the fcc-hcp boundary (ridge) between these regions, and the weakest binding in the mound region. Behavior is similar to that observed from small-unit-cell calculations of Habenicht et al. [Top. Catal. 57, 69 (2014)], which differ from previous large-scale calculations. We determine the minimum-energy path for local diffusion near the center of the fcc region and obtain a local diffusion barrier of ~0.48 eV. We also estimate a significantly lower local diffusion barrier in the ridge region. These barriers and information on the adsorption energy variation facilitate development of a realistic model for the global potential energy surface for Ru adatoms. Furthermore, this in turn enables simulation studies elucidating diffusion-mediated directed-assembly of Ru nanoclusters during deposition of Ru on G/Ru(0001).
Fischer, Michael
2015-10-14
The chabazite-type silicoaluminophosphate SAPO-34 is a promising adsorbent for applications in thermal energy storage using water adsorption-desorption cycles. In order to develop a microscopic understanding of the impact of local heterogeneities and defects on the water adsorption properties, the interaction of different models of SAPO-34 with water was studied using dispersion-corrected density-functional theory (DFT-D) calculations. In addition to SAPO-34 with isolated silicon atoms, the calculations considered models incorporating two types of heterogeneities (silicon islands, aluminosilicate domains), and two defect-containing (partially and fully desilicated) systems. DFT-D optimisations were performed for systems with small amounts of adsorbed water, in which all H2O molecules can interact with framework protons, and systems with large amounts of adsorbed water (30 H2O molecules per unit cell). At low loadings, the host-guest interaction energy calculated for SAPO-34 with isolated Si atoms amounts to approximately -90 kJ mol(-1). While the presence of local heterogeneities leads to the creation of some adsorption sites that are energetically slightly more favourable, the interaction strength is drastically reduced in systems with defects. At high water loadings, energies in the range of -70 kJ mol(-1) are obtained for all models. The DFT-D interaction energies are in good agreement with experimentally measured heats of water adsorption. A detailed analysis of the equilibrium structures was used to gain insights into the binding modes at low coverages, and to assess the extent of framework deprotonation and changes in the coordination environment of aluminium atoms at high water loadings. PMID:26352329
Han, Yong; Evans, James W.
2015-10-28
Large-scale first-principles density functional theory calculations are performed to investigate the adsorption and diffusion of Ru adatoms on monolayer graphene (G) supported on Ru(0001). The G sheet exhibits a periodic moiré-cell superstructure due to lattice mismatch. Within a moiré cell, there are three distinct regions: fcc, hcp, and mound, in which the C{sub 6}-ring center is above a fcc site, a hcp site, and a surface Ru atom of Ru(0001), respectively. The adsorption energy of a Ru adatom is evaluated at specific sites in these distinct regions. We find the strongest binding at an adsorption site above a C atom in the fcc region, next strongest in the hcp region, then the fcc-hcp boundary (ridge) between these regions, and the weakest binding in the mound region. Behavior is similar to that observed from small-unit-cell calculations of Habenicht et al. [Top. Catal. 57, 69 (2014)], which differ from previous large-scale calculations. We determine the minimum-energy path for local diffusion near the center of the fcc region and obtain a local diffusion barrier of ∼0.48 eV. We also estimate a significantly lower local diffusion barrier in the ridge region. These barriers and information on the adsorption energy variation facilitate development of a realistic model for the global potential energy surface for Ru adatoms. This in turn enables simulation studies elucidating diffusion-mediated directed-assembly of Ru nanoclusters during deposition of Ru on G/Ru(0001)
Liu, Kexi; Lei, Yinkai; Wang, Guofeng
2013-11-28
Oxygen adsorption energy is directly relevant to the catalytic activity of electrocatalysts for oxygen reduction reaction (ORR). In this study, we established the correlation between the O{sub 2} adsorption energy and the electronic structure of transition metal macrocyclic complexes which exhibit activity for ORR. To this end, we have predicted the molecular and electronic structures of a series of transition metal macrocyclic complexes with planar N{sub 4} chelation, as well as the molecular and electronic structures for the O{sub 2} adsorption on these macrocyclic molecules, using the density functional theory calculation method. We found that the calculated adsorption energy of O{sub 2} on the transition metal macrocyclic complexes was linearly related to the average position (relative to the lowest unoccupied molecular orbital of the macrocyclic complexes) of the non-bonding d orbitals (d{sub z{sup 2}}, d{sub xy}, d{sub xz}, and d{sub yz}) which belong to the central transition metal atom. Importantly, our results suggest that varying the energy level of the non-bonding d orbitals through changing the central transition metal atom and/or peripheral ligand groups could be an effective way to tuning their O{sub 2} adsorption energy for enhancing the ORR activity of transition metal macrocyclic complex catalysts.
Surface complexation modeling calculation of Pb(II) adsorption onto the calcined diatomite
NASA Astrophysics Data System (ADS)
Ma, Shu-Cui; Zhang, Ji-Lin; Sun, De-Hui; Liu, Gui-Xia
2015-12-01
Removal of noxious heavy metal ions (e.g. Pb(II)) by surface adsorption of minerals (e.g. diatomite) is an important means in the environmental aqueous pollution control. Thus, it is very essential to understand the surface adsorptive behavior and mechanism. In this work, the Pb(II) apparent surface complexation reaction equilibrium constants on the calcined diatomite and distributions of Pb(II) surface species were investigated through modeling calculations of Pb(II) based on diffuse double layer model (DLM) with three amphoteric sites. Batch experiments were used to study the adsorption of Pb(II) onto the calcined diatomite as a function of pH (3.0-7.0) and different ionic strengths (0.05 and 0.1 mol L-1 NaCl) under ambient atmosphere. Adsorption of Pb(II) can be well described by Freundlich isotherm models. The apparent surface complexation equilibrium constants (log K) were obtained by fitting the batch experimental data using the PEST 13.0 together with PHREEQC 3.1.2 codes and there is good agreement between measured and predicted data. Distribution of Pb(II) surface species on the diatomite calculated by PHREEQC 3.1.2 program indicates that the impurity cations (e.g. Al3+, Fe3+, etc.) in the diatomite play a leading role in the Pb(II) adsorption and dominant formation of complexes and additional electrostatic interaction are the main adsorption mechanism of Pb(II) on the diatomite under weak acidic conditions.
NASA Astrophysics Data System (ADS)
Tasinato, Nicola; Moro, Daniele; Stoppa, Paolo; Pietropolli Charmet, Andrea; Toninello, Piero; Giorgianni, Santi
2015-10-01
Photodegradation over titanium dioxide (TiO2) is a very appealing technology for removing environmental pollutants from the air, the adsorption interaction being the first step of the whole reaction pathway. In the present work the adsorption of F2Cdbnd CFCl (chlorotrifluoroethene, halon 1113), a compound used by industry and detected in the atmosphere, on a commercial TiO2 nano-powder is investigated experimentally by in situ DRIFT spectroscopy and theoretically through periodic ab initio calculations rooted in DFT. The spectra of the adsorbed molecule suggest that the anchoring to the surface mainly takes place through F atoms. Theoretically, five adsorption configurations for the molecule interacting with the anatase (1 0 1) surface are simulated at B3LYP level and for each of them, structures, binding energies and vibrational frequencies are derived. The interplay between theory and experiments shows the coexistence of different adsorption configurations, the foremost ones featuring the interaction of one F atom with a fivefold coordinated Ti4+ of the surface. These two adsorption models, which mostly differ for the orientation of the adsorbate with respect to the surface, feature a binding energy of -45.6 and -41.0 kJ mol-1 according to dispersion corrected DFT calculations. The favorable adsorption interaction appears as an important requirement toward the application of titanium dioxide technologies for the photocatalytic degradation of halon 1113.
Peptide adsorption on the hydrophobic surface: A free energy perspective
NASA Astrophysics Data System (ADS)
Sheng, Yuebiao; Wang, Wei; Chen, P.
2011-05-01
Protein adsorption is a very attractive topic which relates to many novel applications in biomaterials, biotechnology and nanotechnology. Ionic complementary peptides are a group of novel nano-biomaterials with many biomedical applications. In this work, molecular dynamics simulations of the ionic-complementary peptide EAK16-II on a hydrophobic graphite surface were performed under neutral, acidic and basic solution conditions. Adsorption free energy contour maps were obtained by analyzing the dynamical trajectories. Hydrophobic interactions were found to govern the adsorption of the first peptide molecule, and both hydrophobic and electrostatic interactions contributed to the adsorption of the second peptide molecule. Especially under acidic and basic solution conditions, interplay existed among chain-chain hydrophobic, chain-surface hydrophobic and chain-chain electrostatic interactions during the adsorption of the second peptide molecule. Non-charged residues were found to lie on the graphite surface, while charged residue side-chains oriented towards the solution after the peptide deposited on the surface. These results provide a basis for understanding peptide adsorption on the hydrophobic surface under different solution conditions, which is useful for novel applications such as bioactive implant devices and drug delivery material design.
Light Pipe Energy Savings Calculator
NASA Astrophysics Data System (ADS)
Owens, Erin; Behringer, Ernest R.
2009-04-01
Dependence on fossil fuels is unsustainable and therefore a shift to renewable energy sources such as sunlight is required. Light pipes provide a way to utilize sunlight for interior lighting, and can reduce the need for fossil fuel-generated electrical energy. Because consumers considering light pipe installation may be more strongly motivated by cost considerations than by sustainability arguments, an easy means to examine the corresponding costs and benefits is needed to facilitate informed decision-making. The purpose of this American Physical Society Physics and Society Fellowship project is to create a Web-based calculator to allow users to quantify the possible cost savings for their specific light pipe application. Initial calculations show that the illumination provided by light pipes can replace electric light use during the day, and in many cases can supply greater illumination levels than those typically given by electric lighting. While the installation cost of a light pipe is significantly greater than the avoided cost of electricity over the lifetime of the light pipe at current prices, savings may be realized if electricity prices increase.
Rokhina, Ekaterina V; Lahtinen, Manu; Makarova, Katerina; Jegatheesan, Veeriah; Virkutyte, Jurate
2012-06-01
The nitric acid-functionalized commercial carbon nanofibers (CNFs) were comprehensively studied by instrumental (XRD, BET, SEM, TGA) and theoretical (DFT calculations) methods. The detailed surface study revealed the variation in the characteristics of functionalized CNFs, such as a decreased (up to 34%) surface area and impacted structural, electronic and chemical properties. The effects of functional groups were studied by comparison with pristine nanofibers. The results showed that the C-C bond lengths of the modified CNFs varied significantly. Chemical functionalization altered the frontier orbitals of the pristine material, and therefore altered the nature of their interactions with other substances. Moreover, the pristine and modified CNFs were tested for the removal of phenol from aqueous solutions. It was observed that surface modification tuned the adsorption capacity of carbon nanofibers (up to 0.35 mmol g(-1)), whereas original fibers did not demonstrate any adsorption capacity of phenol. PMID:22209137
First-principles calculations of NO and NO2 adsorption on a spinel ZnGaAlO4(100) surface
NASA Astrophysics Data System (ADS)
Xiang, Chao; Tan, Honglin; Lu, Jiansheng; Yu, Lan; Song, Peng; Zeng, Chunhua; Zhang, Defeng; Tao, Shigang
2014-07-01
Density functional theory (DFT) has been used to investigate the properties of NO and NO2 adsorption on a ZnGaAlO4(100) surface. The calculation results show that the minimum surface energy is 2.3073 J m-2. The configuration of NO adsorbed on the surface is more stable through an N-down orientation due to the strong hybridization between d states and the NO-π orbital. In particular, NO approaches Zn via its N side with an adsorption energy of -23.50 kcal mol-1, while the comparable value is -44.19 kcal mol-1 for NO2 adsorbed at Zn, suggesting a higher degree of adsorption stability. In addition, substitution of Al with Ga is responsible for the most stable mode of NO2 adsorption with a binding energy of -53.40 kcal mol-1. This demonstrates that the process of desorption of NO2 is thermodynamically feasible. NO2 adsorbed on the surface is activated, showing that the adsorption can directly lead to a dissociation of NO2. Moreover, the process of dissociation of NO2 adsorbed at Ga is favored due to a lower energy barrier of activation.
NASA Astrophysics Data System (ADS)
Liu, Jiexiang; Zhang, Xiaoguang
2013-01-01
NO, N2O and NO2 adsorption in [M‧]-MAPO-5 (M = Si, Ti; M‧ = Ag, Cu) models of the modified aluminophosphate molecular sieves was investigated by density functional theory (DFT) method. The equilibrium structural parameters and adsorption energies were obtained and compared. The structural parameters of NO and NO2 in the adsorbed state had a distinct change than that of N2O compared to their free gas state. [M‧]-MAPO-5 was more effective for the activation of NOx molecule compared to [M‧]-AlMOR (M‧ = Ag, Cu) models of the modified mordenite in our previous studies. The adsorption energies data indicated that adsorption strength of NOx followed the decreasing order of NO2 > NO > N2O. And adsorption complexes in η1-N mode were much stabler than that in η1-O mode, which was similar to that in [M‧]-AlMOR. [Cu]-MAPO-5 had a much stronger adsorption for NOx than [Ag]-MAPO-5. And [M‧]-SiMOR had a little stronger adsorption for NOx than [M‧]-TiMOR. Furthermore, the resistance capabilities of [M‧]-MAPO-5 to SO2, H2O and O2 were studied and analyzed. The interaction mechanism of NOx adsorption in [M‧]-MAPO-5 was also discussed by natural bond orbital (NBO) analysis, which was in reasonable agreement with the adsorption interaction strengths.
Ghose, Sanjit K.; Li, Yan; Yakovenko, Andrey; Dooryhee, Eric; Ehm, Lars; Ecker, Lynne E.; Dippel, Ann-Christin; Halder, Gregory J.; Strachan, Denis M.; Thallapally, Praveen K.
2015-04-16
Enhancement of adsorption capacity and separation of radioactive Xe/Kr at room temperature and above is a challenging problem. Here, we report a detailed structural refinement and analysis of the synchrotron X-ray powder diffraction data of Ni-DODBC metal organic framework with in situ Xe and Kr adsorption at room temperature and above. Our results reveal that Xe and Kr adsorb at the open metal sites, with adsorption geometries well reproduced by DFT calculations. The measured temperature-dependent adsorption capacity of Xe is substantially larger than that for Kr, indicating the selectivity of Xe over Kr and is consistent with the more negative adsorption energy (dominated by van der Waals dispersion interactions) predicted from DFT. Our results reveal critical structural and energetic information about host–guest interactions that dictate the selective adsorption mechanism of these two inert gases, providing guidance for the design and synthesis of new MOF materials for the separation of environmentally hazardous gases from nuclear reprocessing applications.
Surface free energy analysis of adsorbents used for radioiodine adsorption
NASA Astrophysics Data System (ADS)
González-García, C. M.; Román, S.; González, J. F.; Sabio, E.; Ledesma, B.
2013-10-01
In this work, the surface free energy of biomass-based activated carbons, both fresh and impregnated with triethylenediamine, has been evaluated. The contribution of Lifshitz van der Waals components was determined by the model proposed by van Oss et al. The results obtained allowed predicting the most probable configurations of the impregnant onto the carbon surface and its influence on the subsequent adsorption of radioactive methyl iodide.
Kuang, Xiang-Jun; Wang, Xin-Qiang; Liu, Gao-Bin
2015-02-01
Under the framework of DFT, an all-electron scalar relativistic calculation on the adsorption of Aun (n = 1-13) clusters toward methanol molecule has been performed with the generalized gradient approximation at PW91 level. Our calculation results reveal that the small gold cluster would like to bond with oxygen of methanol molecule at the edge of gold cluster plane. After adsorption, the chemical activities of hydroxyl group and methyl group are enhanced to some extent. The even-numbered AunCH3OH cluster with closed-shell electronic configuration is relatively more stable than the neighboring odd-numbered AunCH3OH cluster with open-shell electronic configuration. All the AunCH3OH clusters prefer low spin multiplicity (M = 1 for even-numbered AuNCH3OH clusters, M = 2 for odd-numbered AunCH3OH clusters) and the magnetic moments are mainly contributed by gold atoms. The odd-even alterations of magnetic moments and electronic configurations can be observed clearly and may be simply understood in terms of the electron pairing effect. PMID:26353643
First principles total energy studies of the adsorption of disilane on Ge(001)-c(2x4)
NASA Astrophysics Data System (ADS)
Cocoletzi, Gregorio H.; Sanchez-Castillo, A.; Takeuchi, N.
2004-03-01
We perform first principles total energy calculations to investigate the energetics and the atomic structure of the adsorption of silane (SiH_4) and disilane (Si_2H_6) on the Ge(001)-c(2× 4) surface. The adsorption of Si_2H6 is a dissociative process which first yields SiH3 and then SiH2 fragments. We first study the adsorption of SiH2 considering two different models; the intra-row and the on-dimer geometries. Our results show that the on-dimer site is more stable than the intra-row geometry. This is not a surprise since in the absence of H atoms adsorption in the on-dimer site leaves no dangling bonds. In contrast, when the SiH2 fragment is considered together with two H atoms, the intra-row geometry is favored energetically as compared with the on-dimer site. Similar results have been previously obtained for the adsorption of SiH2 on Si(001). Disilane adsorption is explored according to two different geometries. In the first one, we have considered the adsorption as two SiH3 fragments, while in the second, we have considered the adsorption as two SiH2 fragments plus 2 H fragments. It is found that the later geometry is energetically more favorable.
Water films on transition metal surfaces: A physical disclosure of adsorption energy
NASA Astrophysics Data System (ADS)
Revilla-López, Guillem; López, Nuria; Theoretical Heterogeneous Catalysis Group Team
2014-03-01
Our work reports novel physical models derived from DFT calculations including van der Waals forces for the adsorption of different water motifs: ice bilayer, √37 x √37-R 25.3° and rosette on transition metal surfaces. This energy decomposition scheme is obtained by analyzing the two driving energies of adsorption: water-water and water-metal interactions. The former explained by single water adsorption and the latter by ice resonance stabilization. These two magnitudes drive, to different extent, the adsorption of ice bilayer and √37 whereas rosette motif lacks the resonance contribution. The equations successfully reproduce and predict the experimental results for the wettability and the dissociation of water films on the fcc(111) and hcp(0001) facets of Pd, Pt, Ru Ir, Rh, Au, and Ag. So happens for the temperature of the hydrophobic/hydrophilic water film transition and for the effect of the surface roughness on it. Furthermore, the metastability and the wettability of other water films like √39 x √39-R 16.1° can be anticipated by the rationalization of their geometry and their dissociation state. The authors thank the ERC-2010-StG-258406 Bio2chem-d project, MINECO (CTQ2012-33826) and BSC-RES for supporting this work.
NASA Astrophysics Data System (ADS)
Grenev, I. V.; Gavrilov, V. Yu.
2014-01-01
Adsorption isotherms of molecular hydrogen are measured at 77 K in a series of AlPO alumophosphate zeolites with different microchannel sizes. The potential of the intermolecular interaction of H2 is calculated within the model of a cylindrical channel of variable size. Henry constants are calculated for this model for arbitrary orientations of the adsorbate molecules in microchannels. The experimental and calculated values of the Henry adsorption constant of H2 are compared at 77 K on AlPO zeolites. The constants of intermolecular interaction are determined for the H2-AlPO system.
Nie, JL; Xiao, Haiyan J.; Gao, Fei; Zu, Xiaotao T.
2009-05-12
First-principles calculations based on density functional theory with the generalized gradient approximation have been performed to study the aluminum (Al) adsorption on the (001) surface of α-uranium (α-U). The geometric, electronic and magnetic properties have been investigated at coverages of 0.25 and 0.5 monolayer. The results show that the quasi-trigonal sites are preferred at both coverages. The bonding of Al with U is found to be metallic, which mainly arises from the mixing of Al 3sp and U 5f states. A ferromagnetic phase is determined for the bare α-U(001) surface, while the adsorption of Al on the surface significantly perturbs the spin arrangement pattern and reduces the local magnetic moment, leading to a ferrimagnetic phase on the α-U(001) surface at the coverage of 0.5 monolayer. However, the Al overlayer is paramagnetic. Generally, the spin polarization has negligible effects on the geometric and electronic properties of Al atoms on the α-U(001) surface.
Jia, Juanjuan; Kara, Abdelkader; Pasquali, Luca; Bendounan, Azzedine; Sirotti, Fausto; Esaulov, Vladimir A
2015-09-14
Characteristic core level binding energies (CLBEs) are regularly used to infer the modes of molecular adsorption: orientation, organization, and dissociation processes. Here, we focus on a largely debated situation regarding CLBEs in the case of chalcogen atom bearing molecules. For a thiol, this concerns the case when the CLBE of a thiolate sulfur at an adsorption site can be interpreted alternatively as due to atomic adsorption of a S atom, resulting from dissociation. Results of an investigation of the characteristics of thiol self-assembled monolayers (SAMs) obtained by vacuum evaporative adsorption are presented along with core level binding energy calculations. Thiol ended SAMs of 1,4-benzenedimethanethiol (BDMT) obtained by evaporation on Au display an unconventional CLBE structure at about 161.25 eV, which is close to a known CLBE of a S atom on Au. Adsorption and CLBE calculations for sulfur atoms and BDMT molecules are reported and allow delineating trends as a function of chemisorption on hollow, bridge, and atop sites and including the presence of adatoms. These calculations suggest that the 161.25 eV peak is due to an alternative adsorption site, which could be associated to an atop configuration. Therefore, this may be an alternative interpretation, different from the one involving the adsorption of atomic sulfur resulting from the dissociation process of the S-C bond. Calculated differences in S(2p) CLBEs for free BDMT molecules, SH group sulfur on top of the SAM, and disulfide are also reported to clarify possible errors in assignments. PMID:26374051
Jia, Juanjuan; Kara, Abdelkader E-mail: vladimir.esaulov@u-psud.fr; Pasquali, Luca; Bendounan, Azzedine; Sirotti, Fausto; Esaulov, Vladimir A. E-mail: vladimir.esaulov@u-psud.fr
2015-09-14
Characteristic core level binding energies (CLBEs) are regularly used to infer the modes of molecular adsorption: orientation, organization, and dissociation processes. Here, we focus on a largely debated situation regarding CLBEs in the case of chalcogen atom bearing molecules. For a thiol, this concerns the case when the CLBE of a thiolate sulfur at an adsorption site can be interpreted alternatively as due to atomic adsorption of a S atom, resulting from dissociation. Results of an investigation of the characteristics of thiol self-assembled monolayers (SAMs) obtained by vacuum evaporative adsorption are presented along with core level binding energy calculations. Thiol ended SAMs of 1,4-benzenedimethanethiol (BDMT) obtained by evaporation on Au display an unconventional CLBE structure at about 161.25 eV, which is close to a known CLBE of a S atom on Au. Adsorption and CLBE calculations for sulfur atoms and BDMT molecules are reported and allow delineating trends as a function of chemisorption on hollow, bridge, and atop sites and including the presence of adatoms. These calculations suggest that the 161.25 eV peak is due to an alternative adsorption site, which could be associated to an atop configuration. Therefore, this may be an alternative interpretation, different from the one involving the adsorption of atomic sulfur resulting from the dissociation process of the S–C bond. Calculated differences in S(2p) CLBEs for free BDMT molecules, SH group sulfur on top of the SAM, and disulfide are also reported to clarify possible errors in assignments.
NASA Astrophysics Data System (ADS)
Jia, Juanjuan; Kara, Abdelkader; Pasquali, Luca; Bendounan, Azzedine; Sirotti, Fausto; Esaulov, Vladimir A.
2015-09-01
Characteristic core level binding energies (CLBEs) are regularly used to infer the modes of molecular adsorption: orientation, organization, and dissociation processes. Here, we focus on a largely debated situation regarding CLBEs in the case of chalcogen atom bearing molecules. For a thiol, this concerns the case when the CLBE of a thiolate sulfur at an adsorption site can be interpreted alternatively as due to atomic adsorption of a S atom, resulting from dissociation. Results of an investigation of the characteristics of thiol self-assembled monolayers (SAMs) obtained by vacuum evaporative adsorption are presented along with core level binding energy calculations. Thiol ended SAMs of 1,4-benzenedimethanethiol (BDMT) obtained by evaporation on Au display an unconventional CLBE structure at about 161.25 eV, which is close to a known CLBE of a S atom on Au. Adsorption and CLBE calculations for sulfur atoms and BDMT molecules are reported and allow delineating trends as a function of chemisorption on hollow, bridge, and atop sites and including the presence of adatoms. These calculations suggest that the 161.25 eV peak is due to an alternative adsorption site, which could be associated to an atop configuration. Therefore, this may be an alternative interpretation, different from the one involving the adsorption of atomic sulfur resulting from the dissociation process of the S-C bond. Calculated differences in S(2p) CLBEs for free BDMT molecules, SH group sulfur on top of the SAM, and disulfide are also reported to clarify possible errors in assignments.
Liu, Wei; Schuler, Bruno; Xu, Yong; Moll, Nikolaj; Meyer, Gerhard; Gross, Leo; Tkatchenko, Alexandre
2016-03-17
Reliability is one of the major concerns and challenges in designing organic/inorganic interfaces for (opto)electronic applications. Even small structural differences for molecules on substrates can result in a significant variation in the interface functionality, due to the strong correlation between geometry, stability, and electronic structure. Here, we employed state-of-the-art first-principles calculations with van der Waals interactions, in combination with atomic force microscopy experiments, to explore the interaction mechanism for three structurally related olympicene molecules adsorbed on the Cu(111) surface. The substitution of a single atom in the olympicene molecule switches the nature of adsorption from predominantly physisorptive character [olympicene on Cu(111)], to an intermediate state [olympicene-derived ketone on Cu(111)], then to chemisorptive character [olympicene radical on Cu(111)]. Despite the remarkable difference in adsorption structures (by up to 0.9 Å in adsorption height) and different nature of bonding, the olympicene, its ketone, and its radical derivatives have essentially identical binding energies and work functions upon interaction with the metal substrate. Our findings suggest that the stability and work functions of molecular adsorbates could be rendered insensitive to their adsorption structures, which could be a useful property for (opto)electronic applications. PMID:26928143
Synthesis of Ordered Mesoporous Silica for Energy-efficient Adsorption Systems
NASA Astrophysics Data System (ADS)
Endo, Akira; Komori, Kou; Inagi, Yuki; Fujisaki, Satoko; Yamamoto, Takuji
Energy-efficient adsorption systems, such as adsorption heat pump, desiccant cooling, humidity control system, and so on, are expected as a energy exchange process because they are able to utilize low temperature exhaust heat. As an adsorbent for such systems, materials with large adsorption capacity in the pressure range of practical operation are preferable. To enable the design and synthesis of materials with large heat storage capacity, the pore structure of adsorbents should be optimized for each systems. In this paper, we synthesized ordered mesoporous silica (MPS) with an arrow pore size distribution of around 2nm by a solvent evaporation method and evaluated their water adsorption properties. The adsorption isotherms for MPSs showed steep increase at a relative humidity corresponding to their pore size. Since MPSs have a large adsorption capacity than conventional materials in the relative humidity region of practical operation, they are expected for new adsorbents for energy-efficient adsorption systems.
NASA Astrophysics Data System (ADS)
Ovramenko, T.; Spillebout, F.; Bocquet, F. C.; Mayne, A. J.; Dujardin, G.; Sonnet, Ph.; Stauffer, L.; Ksari, Y.; Themlin, J.-M.
2013-04-01
Scanning tunneling microscopy (STM) studies of the fullerene C60 molecule adsorbed on the silicon carbide SiC(0001)-3×3 surface, combined with density functional theory (DFT) calculations, show that chemisorption of individual C60 molecules occurs through the formation of one bond to one silicon adatom only in contrast to multiple bond formation on other semiconducting surfaces. We observe three stable adsorption sites with respect to the Si adatoms of the surface unit cell. Comprehensive DFT calculations give different adsorption energies for the three most abundant sites showing that van der Waals forces between the C60 molecule and the neighboring surface atoms need to be considered. The C60 molecules are observed to form small clusters even at low coverage indicating the presence of a mobile molecular precursor state and nonnegligible intermolecular interactions.
Kustov, L.M.; Kazansky, V.B.; Beran, S.; Kubelkova, L.; Jiru, P.
1987-09-24
Low temperature adsorption of CO was studied on H-ZSM-5 zeolites modified by dehydroxylation, ionic exchange with Al/sup 3 +/, and impregnation with Al/sub 2/O/sub 3/ and on Na-ZSM-5 and CaH-ZSM-5 zeolites. It was found that interaction of CO with framework OH groups results in the formation of a hydrogen-bonded CO complex whose OH bond frequency is decreased by 310-320 cm/sup -1/ compared with that of free hydroxyls. For the less acidic framework hydroxyls in large cavities of H/sub 70/Na/sub 30/-Y zeolite the observed shift is 275 cm/sup -1/. With ZSM-5 zeolites, at least six types of electron-accepting sites are observed originating from nonframework Al species (band of CO in the interaction complex: 2132, 2222, 2202, 2195, and 2198 cm/sup -1/) and the Al/sub 2/O/sub 3/ microcrystalline phase (CO band at 2153 cm/sup -1/). The CO bond orders calculated by the CNDO/2 method for the CO interaction complexes with models of surface sites increase in the following order: > O-CO < > OH-CO approx. ..-->.. Al-CO approx. = Na-CO < alumina-CO approx. = Ca-CO < ..-->.. Si-CO < Al(cationic)-CO. A correlation between the calculated bond orders of CO and the observed vibrational frequencies of CO-forming interaction complexes is drawn.
NASA Astrophysics Data System (ADS)
Bo, Xu; Huan-Sheng, Lu; Bo, Liu; Gang, Liu; Mu-Sheng, Wu; Chuying, Ouyang
2016-06-01
The adsorption and diffusion behaviors of alkali and alkaline-earth metal atoms on silicane and silicene are both investigated by using a first-principles method within the frame of density functional theory. Silicane is staler against the metal adatoms than silicene. Hydrogenation makes the adsorption energies of various metal atoms considered in our calculations on silicane significantly lower than those on silicene. Similar diffusion energy barriers of alkali metal atoms on silicane and silicene could be observed. However, the diffusion energy barriers of alkali-earth metal atoms on silicane are essentially lower than those on silicene due to the small structural distortion and weak interaction between metal atoms and silicane substrate. Combining the adsorption energy with the diffusion energy barriers, it is found that the clustering would occur when depositing metal atoms on perfect hydrogenated silicene with relative high coverage. In order to avoid forming a metal cluster, we need to remove the hydrogen atoms from the silicane substrate to achieve the defective silicane. Our results are helpful for understanding the interaction between metal atoms and silicene-based two-dimensional materials. Project supported by the Natural Science Foundation of Jiangxi Province, China (Grant Nos. 20152ACB21014, 20151BAB202006, and 20142BAB212002) and the Fund from the Jiangxi Provincial Educational Committee, China (Grant No. GJJ14254). Bo Xu is also supported by the Oversea Returned Project from the Ministry of Education, China.
Folman, M.; Fastow, M.; Kozirovski, Y.
1997-03-05
In our recent investigation of the IR spectrum of CO physically adsorbed on C{sub 60} films, two well-resolved absorption bands at 2135 and 2128 cm{sup -1} were found, suggesting that the molecule is adsorbed on two different sites. To determine the nature of these adsorption sites, calculations of adsorption potentials and spectral shifts for the CO/C{sub 60} system were performed. The calculations were done for the fcc (100), fcc (111) hcp (001), and hcp (111) surface planes. In the calculations the 6-exponential and the Lennard-Jones potentials were used. A number of adsorption sites were chosen. These included the void space between four, three, and two neighboring C{sub 60} molecules and the center of the hexagon and the pentagon on the C{sub 60} surface. The calculated potentials and spectral shifts clearly indicate that adsorption sites in the voids between the C{sub 60} molecules are energetically preferred over sites on top of single C{sub 60} molecules. Comparison is made between results obtained with the two potentials and with results obtained previously with the two other carbon allotropes: graphite and diamond. 11 refs., 4 figs., 3 tabs.
Good Practices in Free-energy Calculations
NASA Technical Reports Server (NTRS)
Pohorille, Andrew; Jarzynski, Christopher; Chipot, Christopher
2013-01-01
As access to computational resources continues to increase, free-energy calculations have emerged as a powerful tool that can play a predictive role in drug design. Yet, in a number of instances, the reliability of these calculations can be improved significantly if a number of precepts, or good practices are followed. For the most part, the theory upon which these good practices rely has been known for many years, but often overlooked, or simply ignored. In other cases, the theoretical developments are too recent for their potential to be fully grasped and merged into popular platforms for the computation of free-energy differences. The current best practices for carrying out free-energy calculations will be reviewed demonstrating that, at little to no additional cost, free-energy estimates could be markedly improved and bounded by meaningful error estimates. In energy perturbation and nonequilibrium work methods, monitoring the probability distributions that underlie the transformation between the states of interest, performing the calculation bidirectionally, stratifying the reaction pathway and choosing the most appropriate paradigms and algorithms for transforming between states offer significant gains in both accuracy and precision. In thermodynamic integration and probability distribution (histogramming) methods, properly designed adaptive techniques yield nearly uniform sampling of the relevant degrees of freedom and, by doing so, could markedly improve efficiency and accuracy of free energy calculations without incurring any additional computational expense.
NASA Astrophysics Data System (ADS)
Fischer-Wolfarth, Jan-Henrik; Hartmann, Jens; Farmer, Jason A.; Flores-Camacho, J. Manuel; Campbell, Charles T.; Schauermann, Swetlana; Freund, Hans-Joachim
2011-02-01
A new ultrahigh vacuum microcalorimeter for measuring heats of adsorption and adsorption-induced surface reactions on complex single crystal-based model surfaces is described. It has been specifically designed to study the interaction of gaseous molecules with well-defined model catalysts consisting of metal nanoparticles supported on single crystal surfaces or epitaxial thin oxide films grown on single crystals. The detection principle is based on the previously described measurement of the temperature rise upon adsorption of gaseous molecules by use of a pyroelectric polymer ribbon, which is brought into mechanical/thermal contact with the back side of the thin single crystal. The instrument includes (i) a preparation chamber providing the required equipment to prepare supported model catalysts involving well-defined nanoparticles on clean single crystal surfaces and to characterize them using surface analysis techniques and in situ reflectivity measurements and (ii) the adsorption/reaction chamber containing a molecular beam, a pyroelectric heat detector, and calibration tools for determining the absolute reactant fluxes and adsorption heats. The molecular beam is produced by a differentially pumped source based on a multichannel array capable of providing variable fluxes of both high and low vapor pressure gaseous molecules in the range of 0.005-1.5 × 1015 molecules cm-2 s-1 and is modulated by means of the computer-controlled chopper with the shortest pulse length of 150 ms. The calorimetric measurements of adsorption and reaction heats can be performed in a broad temperature range from 100 to 300 K. A novel vibrational isolation method for the pyroelectric detector is introduced for the reduction of acoustic noise. The detector shows a pulse-to-pulse standard deviation ≤15 nJ when heat pulses in the range of 190-3600 nJ are applied to the sample surface with a chopped laser. Particularly for CO adsorption on Pt(111), the energy input of 15 nJ (or 120 nJ cm
Optimal smoothing of site-energy distributions from adsorption isotherms
Brown, L.F.; Travis, B.J.
1983-01-01
The equation for the adsorption isotherm on a heterogeneous surface is a Fredholm integral equation. In solving it for the site-energy distribution (SED), some sort of smoothing must be carried out. The optimal amount of smoothing will give the most information that is possible without introducing nonexistent structure into the SED. Recently, Butler, Reeds, and Dawson proposed a criterion (the BRD criterion) for choosing the optimal smoothing parameter when using regularization to solve Fredholm equations. The BRD criterion is tested for its suitability in obtaining optimal SED's. This criterion is found to be too conservative. While using it never introduces nonexistent structure into the SED, significant information is often lost. At present, no simple criterion for choosing the optimal smoothing parameter exists, and a modeling approach is recommended.
NASA Technical Reports Server (NTRS)
Oh, B. K.; Kim, S. K.
1974-01-01
A model of helium adsorption on an argon crystal is built up from the premise that local adsorption predominates in the first layer and nonlocal adsorption in the second. Application of the virial expansion theorem to the second layer gives a series in which the first term represents the motion of a single molecule in the external potential field and the second a two-body interaction under this field. The thermodynamic functions of the adsorbed phase are calculated ab initio, the gas-solid interaction potential being derived from lattice summation and the partition function from an appropriate choice of a site-spacing polynomial to describe the periodic potential. The mutual interaction of adsorbed molecules is calculated with a two-dimensional Lennard-Jones potential. The second virial coefficient is calculated and its dependence on temperature and choice of potential is studied. It is found that the second virial coefficient is very well approximated by a two-dimensional gas in free space. The adsorption isotherm, isosteric heat, and specific heat are obtained and compared with the results of Ross and Steele, giving excellent agreement.
Arnadottir, Liney; Stuve, Eric M.; Jonsson, Hannes
2010-10-01
Adsorption and rotation of water monomer, dimer, and trimer on the (111) terrace, (221) and (322) stepped, and (763) and (854) kinked surfaces of platinum were studied by density functional theory calculations using the PW91 approximation to the energy functional. On the (111) terrace, water monomer and the donor molecule of the dimer and trimer adsorb at atop sites. The permolecule adsorption energies of the monomer, dimer, and trimer are 0.30, 0.45, and 0.48 eV, respectively. Rotation of monomers, dimers, and trimers on the terrace is facile with energy barriers of 0.02 eV or less. Adsorption on steps and kinks is stronger than on the terrace, as evidenced by monomer adsorption energies of 0.46 to 0.55 eV. On the (221) stepped surface the zigzag extended configuration is most stable with a per-molecule adsorption energy of 0.57 eV. On the (322) stepped surface the dimer, two configurations of the trimer, and the zigzag configuration have similar adsorption energies of 0.55 ± 0.02 eV. Hydrogen bonding is strongest in the dimer and trimer adsorbed on the terrace, with respective energies of 0.30 and 0.27 eV, and accounts for their increased adsorption energies relative to the monomer. Hydrogen bonding is weak to moderate for adsorption at steps, with energies of 0.04 to 0.15 eV, as the much stronger water-metal interactions inhibit adsorption geometries favorable to hydrogen bonding. Correlations of hydrogen bond angles and energies with hydrogen bond lengths are presented. On the basis of these DFT/PW91 results, a model for water cluster formation on the Pt(111) surface can be formulated where kink sites nucleate chains along the top of step edges, consistent with the experimental findings of Morgenstern et al., Phys. Rev. Lett., 77 (1996) 703.
Bellucci, Francesco; Lee, Sang Soo; Kubicki, James D.; Bandura, Andrei V.; Zhang, Zhan; Wesolowski, David J.; Fenter, Paul
2015-01-29
We study adsorption of Rb+ to the quartz(101)–aqueous interface at room temperature with specular X-ray reflectivity, resonant anomalous X-ray reflectivity, and density functional theory. The interfacial water structures observed in deionized water and 10 mM RbCl solution at pH 9.8 were similar, having a first water layer at height of 1.7 ± 0.1 Å above the quartz surface and a second layer at 4.8 ± 0.1 Å and 3.9 ± 0.8 Å for the water and RbCl solutions, respectively. The adsorbed Rb+ distribution is broad and consists of presumed inner-sphere (IS) and outer-sphere (OS) complexes at heights of 1.8 ±more » 0.1 and 6.4 ± 1.0 Å, respectively. Projector-augmented planewave density functional theory (DFT) calculations of potential configurations for neutral and negatively charged quartz(101) surfaces at pH 7 and 12, respectively, reveal a water structure in agreement with experimental results. These DFT calculations also show differences in adsorbed speciation of Rb+ between these two conditions. At pH 7, the lowest energy structure shows that Rb+ adsorbs dominantly as an IS complex, whereas at pH 12 IS and OS complexes have equivalent energies. The DFT results at pH 12 are generally consistent with the two site Rb distribution observed from the X-ray data at pH 9.8, albeit with some differences that are discussed. In conclusion, surface charge estimated on the basis of the measured total Rb+ coverage was -0.11 C/m2, in good agreement with the range of the surface charge magnitudes reported in the literature.« less
Adsorption Energy Trends on UO2 and ThO2 Surfaces
NASA Astrophysics Data System (ADS)
Skomurski, F. N.; Shuller, L. C.; Ewing, R. C.; Becker, U.
2006-05-01
Uranium dioxide (UO2) comprises approximately 96 percent of spent nuclear fuel (SNF). Therefore, the interaction of UO2 surfaces with adsorbates such as water and oxygen affects the stability of SNF as a wasteform in a geologic repository. While spectroscopic studies are used to observe surface-adsorbate interactions, questions remain regarding the mechanisms driving the initial reactions between UO2 surfaces and adsorbates. Through the use of quantum mechanical techniques, adsorption and dissociation interactions between different UO2 surfaces and oxygen and water are explored as a function of surface structure. Comparisons are also made with thorium dioxide (ThO2), a nuclear material that is isostructural with UO2, in order to test surface-adsorbate interactions as a function of insulating versus semi-conducting material properties, respectively. In this study, the density functional theory-based quantum mechanical code, CASTEP (CAmbridge Serial Total Energy Package), is used to calculate adsorption energies and changes in electronic structure between clean and adsorbate-covered UO2 and ThO2 surfaces. Four different adsorption cases are tested on the UO2 (111) and (110) surfaces: (i) one-half mono-layer (ML) of molecular water, (ii) one-half ML of dissociated water, (iii) one-half ML of dissociated oxygen, and (iv) a combined molecular water and dissociated oxygen case. The same cases are also tested on the ThO2 (111) surface. Calculations involving the oxidation of bulk UO2 are also performed for comparison with surface processes.
Fischer-Wolfarth, Jan-Henrik; Hartmann, Jens; Farmer, Jason A; Flores-Camacho, J Manuel; Campbell, Charles T; Schauermann, Swetlana; Freund, Hans-Joachim
2011-02-01
A new ultrahigh vacuum microcalorimeter for measuring heats of adsorption and adsorption-induced surface reactions on complex single crystal-based model surfaces is described. It has been specifically designed to study the interaction of gaseous molecules with well-defined model catalysts consisting of metal nanoparticles supported on single crystal surfaces or epitaxial thin oxide films grown on single crystals. The detection principle is based on the previously described measurement of the temperature rise upon adsorption of gaseous molecules by use of a pyroelectric polymer ribbon, which is brought into mechanical∕thermal contact with the back side of the thin single crystal. The instrument includes (i) a preparation chamber providing the required equipment to prepare supported model catalysts involving well-defined nanoparticles on clean single crystal surfaces and to characterize them using surface analysis techniques and in situ reflectivity measurements and (ii) the adsorption∕reaction chamber containing a molecular beam, a pyroelectric heat detector, and calibration tools for determining the absolute reactant fluxes and adsorption heats. The molecular beam is produced by a differentially pumped source based on a multichannel array capable of providing variable fluxes of both high and low vapor pressure gaseous molecules in the range of 0.005-1.5 × 10(15) molecules cm(-2) s(-1) and is modulated by means of the computer-controlled chopper with the shortest pulse length of 150 ms. The calorimetric measurements of adsorption and reaction heats can be performed in a broad temperature range from 100 to 300 K. A novel vibrational isolation method for the pyroelectric detector is introduced for the reduction of acoustic noise. The detector shows a pulse-to-pulse standard deviation ≤15 nJ when heat pulses in the range of 190-3600 nJ are applied to the sample surface with a chopped laser. Particularly for CO adsorption on Pt(111), the energy input of 15 n
Predicting enzyme adsorption to lignin films by calculating enzyme surface hydrophobicity.
Sammond, Deanne W; Yarbrough, John M; Mansfield, Elisabeth; Bomble, Yannick J; Hobdey, Sarah E; Decker, Stephen R; Taylor, Larry E; Resch, Michael G; Bozell, Joseph J; Himmel, Michael E; Vinzant, Todd B; Crowley, Michael F
2014-07-25
The inhibitory action of lignin on cellulase cocktails is a major challenge to the biological saccharification of plant cell wall polysaccharides. Although the mechanism remains unclear, hydrophobic interactions between enzymes and lignin are hypothesized to drive adsorption. Here we evaluate the role of hydrophobic interactions in enzyme-lignin binding. The hydrophobicity of the enzyme surface was quantified using an estimation of the clustering of nonpolar atoms, identifying potential interaction sites. The adsorption of enzymes to lignin surfaces, measured using the quartz crystal microbalance, correlates to the hydrophobic cluster scores. Further, these results suggest a minimum hydrophobic cluster size for a protein to preferentially adsorb to lignin. The impact of electrostatic contribution was ruled out by comparing the isoelectric point (pI) values to the adsorption of proteins to lignin surfaces. These results demonstrate the ability to predict enzyme-lignin adsorption and could potentially be used to design improved cellulase cocktails, thus lowering the overall cost of biofuel production. PMID:24876380
Predicting Enzyme Adsorption to Lignin Films by Calculating Enzyme Surface Hydrophobicity*
Sammond, Deanne W.; Yarbrough, John M.; Mansfield, Elisabeth; Bomble, Yannick J.; Hobdey, Sarah E.; Decker, Stephen R.; Taylor, Larry E.; Resch, Michael G.; Bozell, Joseph J.; Himmel, Michael E.; Vinzant, Todd B.; Crowley, Michael F.
2014-01-01
The inhibitory action of lignin on cellulase cocktails is a major challenge to the biological saccharification of plant cell wall polysaccharides. Although the mechanism remains unclear, hydrophobic interactions between enzymes and lignin are hypothesized to drive adsorption. Here we evaluate the role of hydrophobic interactions in enzyme-lignin binding. The hydrophobicity of the enzyme surface was quantified using an estimation of the clustering of nonpolar atoms, identifying potential interaction sites. The adsorption of enzymes to lignin surfaces, measured using the quartz crystal microbalance, correlates to the hydrophobic cluster scores. Further, these results suggest a minimum hydrophobic cluster size for a protein to preferentially adsorb to lignin. The impact of electrostatic contribution was ruled out by comparing the isoelectric point (pI) values to the adsorption of proteins to lignin surfaces. These results demonstrate the ability to predict enzyme-lignin adsorption and could potentially be used to design improved cellulase cocktails, thus lowering the overall cost of biofuel production. PMID:24876380
Calculating Free Energies Using Average Force
NASA Technical Reports Server (NTRS)
Darve, Eric; Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)
2001-01-01
A new, general formula that connects the derivatives of the free energy along the selected, generalized coordinates of the system with the instantaneous force acting on these coordinates is derived. The instantaneous force is defined as the force acting on the coordinate of interest so that when it is subtracted from the equations of motion the acceleration along this coordinate is zero. The formula applies to simulations in which the selected coordinates are either unconstrained or constrained to fixed values. It is shown that in the latter case the formula reduces to the expression previously derived by den Otter and Briels. If simulations are carried out without constraining the coordinates of interest, the formula leads to a new method for calculating the free energy changes along these coordinates. This method is tested in two examples - rotation around the C-C bond of 1,2-dichloroethane immersed in water and transfer of fluoromethane across the water-hexane interface. The calculated free energies are compared with those obtained by two commonly used methods. One of them relies on determining the probability density function of finding the system at different values of the selected coordinate and the other requires calculating the average force at discrete locations along this coordinate in a series of constrained simulations. The free energies calculated by these three methods are in excellent agreement. The relative advantages of each method are discussed.
Normal Mode Analysis in Zeolites: Toward an Efficient Calculation of Adsorption Entropies.
De Moor, Bart A; Ghysels, An; Reyniers, Marie-Françoise; Van Speybroeck, Veronique; Waroquier, Michel; Marin, Guy B
2011-04-12
An efficient procedure for normal-mode analysis of extended systems, such as zeolites, is developed and illustrated for the physisorption and chemisorption of n-octane and isobutene in H-ZSM-22 and H-FAU using periodic DFT calculations employing the Vienna Ab Initio Simulation Package. Physisorption and chemisorption entropies resulting from partial Hessian vibrational analysis (PHVA) differ at most 10 J mol(-1) K(-1) from those resulting from full Hessian vibrational analysis, even for PHVA schemes in which only a very limited number of atoms are considered free. To acquire a well-conditioned Hessian, much tighter optimization criteria than commonly used for electronic energy calculations in zeolites are required, i.e., at least an energy cutoff of 400 eV, maximum force of 0.02 eV/Å, and self-consistent field loop convergence criteria of 10(-8) eV. For loosely bonded complexes the mobile adsorbate method is applied, in which frequency contributions originating from translational or rotational motions of the adsorbate are removed from the total partition function and replaced by free translational and/or rotational contributions. The frequencies corresponding with these translational and rotational modes can be selected unambiguously based on a mobile block Hessian-PHVA calculation, allowing the prediction of physisorption entropies within an accuracy of 10-15 J mol(-1) K(-1) as compared to experimental values. The approach presented in this study is useful for studies on other extended catalytic systems. PMID:26606357
Predicting proteinase specificities from free energy calculations.
Mekonnen, Seble Merid; Olufsen, Magne; Smalås, Arne O; Brandsdal, Bjørn O
2006-10-01
The role of the primary binding residue (P1) in complexes between three different subtilases (subtilisin Carlsberg, thermitase and proteinase K) and their canonical protein inhibitor eglin c have been studied by free energy calculations. Based on the crystal structures of eglin c in complex with subtilisin Carlsberg and thermitase, and a homology model of the eglin c-proteinase K complex, a total of 57 mutants have been constructed and docked into their host proteins. The binding free energy was then calculated using molecular dynamics (MD) simulations combined with the linear interaction energy (LIE) method for all complexes differing only in the nature of the amino acid at the P1 position. LIE calculations for 19 different complexes for each subtilase were thus carried out excluding proline. The effects of substitutions at the P1 position on the binding free energies are found to be very large, and positively charged residues (Arg, Lys and His) are particularly deleterious for all three enzymes. The charged variants of the acidic side chains are found to bind more favorably as compared to their protonated states in all three subtilases. Furthermore, hydrophobic amino acids are accommodated most favorably at the S1-site in all three enzymes. Comparison of the three series of binding free energies shows only minor differences in the 19 computed relative binding free energies among these subtilases. This is further reflected in the correlation coefficient between the 23 relative binding free energies obtained, including the possible protonation states of ionizable side chains, but excluding the P1 Pro, for subtilisin Carlsberg versus thermitase (0.95), subtilisin versus proteinase K (0.94) and thermitase versus proteinase K (0.96). PMID:16386933
Optimization of adsorption processes for climate control and thermal energy storage
Narayanan, S; Yang, S; Kim, H; Wang, EN
2014-10-01
Adsorption based heat-pumps have received significant interest owing to their promise of higher efficiencies and energy savings when coupled with waste heat and solar energy compared to conventional heating and cooling systems. While adsorption systems have been widely studied through computational analysis and experiments, general design guidelines to enhance their overall performance have not been proposed. In this work, we identified conditions suitable for the maximum utilization of the adsorbent to enhance the performance of both intermittent as well as continuously operating adsorption systems. A detailed computational model was developed based on a general framework governing adsorption dynamics in a single adsorption layer and pellet. We then validated the computational analysis using experiments with a model system of zeolite 13X-water for different operating conditions. A dimensional analysis was subsequently carried out to optimize adsorption performance for any desired operating condition, which is determined by the choice of adsorbent-vapor pair, adsorption duration, operational pressure, intercrystalline porosity, adsorbent crystal size, and intracrystalline vapor diffusivity. The scaling analysis identifies the critical dimensionless parameters and provides a simple guideline to determine the most suitable geometry for the adsorbent particles. Based on this selection criterion, the computational model was used to demonstrate maximum utilization of the adsorbent for any given operational condition. By considering a wide range of parametric variations for performance optimization, these results offer important insights for designing adsorption beds for heating and cooling systems. (C) 2014 Elsevier Ltd. All rights reserved.
Kocman, Mikuláš; Jurečka, Petr; Dubecký, Matúš; Otyepka, Michal; Cho, Yeonchoo; Kim, Kwang S
2015-03-01
Hydrogen storage in carbonaceous materials and their derivatives is currently a widely investigated topic. The rational design of novel adsorptive materials is often attempted with the help of computational chemistry tools, in particular density functional theory (DFT). However, different exchange-correlation functionals provide a very wide range of hydrogen binding energies. The aim of this article is to offer high level QM reference data based on coupled-cluster singles and doubles calculations with perturbative triple excitations, CCSD(T), and a complete basis set limit estimate that can be used to assess the accuracy of various DFT-based predictions. For one complex, the CCSD(T) result is verified against diffusion quantum Monte Carlo calculations. Reference binding curves are calculated for two model compounds representing weak and strong hydrogen adsorption: coronene (-4.7 kJ mol(-1) per H2), and coronene modified with boron and lithium (-14.3 kJ mol(-1)). The reference data are compared to results obtained with widely used density functionals including pure DFT, M06, DFT-D3, PBE-TS, PBE + MBD, optB88-vdW, vdW-DF, vdW-DF2 and VV10. We find that whereas DFT-D3 shows excellent results for weak hydrogen adsorption on coronene, most of the less empirical density based dispersion functionals except VV10 overestimate this interaction. On the other hand, some of the less empirical density based dispersion functionals better describe stronger binding in the more polar coroB2Li22H2 complex which is one of realistic models for high-capacity hydrogen storage materials. Our results may serve as a guide for choosing suitable DFT methods for quickly evaluating hydrogen binding potential and as a reference for assessing the accuracy of the previously published DFT results. PMID:25655486
Bond-Energy and Surface-Energy Calculations in Metals
ERIC Educational Resources Information Center
Eberhart, James G.; Horner, Steve
2010-01-01
A simple technique appropriate for introductory materials science courses is outlined for the calculation of bond energies in metals from lattice energies. The approach is applied to body-centered cubic (bcc), face-centered cubic (fcc), and hexagonal-closest-packed (hcp) metals. The strength of these bonds is tabulated for a variety metals and is…
Zero energy scattering calculation in Euclidean space
NASA Astrophysics Data System (ADS)
Carbonell, J.; Karmanov, V. A.
2016-03-01
We show that the Bethe-Salpeter equation for the scattering amplitude in the limit of zero incident energy can be transformed into a purely Euclidean form, as it is the case for the bound states. The decoupling between Euclidean and Minkowski amplitudes is only possible for zero energy scattering observables and allows determining the scattering length from the Euclidean Bethe-Salpeter amplitude. Such a possibility strongly simplifies the numerical solution of the Bethe-Salpeter equation and suggests an alternative way to compute the scattering length in Lattice Euclidean calculations without using the Luscher formalism. The derivations contained in this work were performed for scalar particles and one-boson exchange kernel. They can be generalized to the fermion case and more involved interactions.
Alexandrov, Vitali Y.; Rosso, Kevin M.
2013-10-02
Interfacial reactivity of redox-active iron-bearing mineral surfaces plays a crucial role in many environmental processes including biogeochemical cycling of various elements and contaminants. Herein, we apply density-functional-theory (DFT) calculations to provide atomistic insights into the heterogeneous reaction between aqueous Fe(II) and the Fe-bearing clay mineral nontronite Fe2Si4O10(OH)2 by studying its adsorption mechanism and interfacial Fe(II)-Fe(III) electron transfer (ET) at edge and basal surfaces. We find that edge-bound Fe(II) adsorption complexes at different surface sites (ferrinol, silanol and mixed) may coexist on both (010) and (110) edge facets, with complexes at ferrinol FeO(H) sites being the most energetically favorable and coupled to proton transfer. Calculation of the ET activation energy suggests that interfacial ET into dioctahedral Fe(III) sheets is probable at the clay edges and occurs predominantly but not exclusively through the complexes adsorbed at ferrinol sites and might also involve mixed sites. No clear evidence is found for complexes on basal surface that are compatible with ET through the basal sheet despite this experimentally hypothesized ET interface. This study suggests a strong pH-dependence of Fe(II) surface complexation at basal versus edge facets and highlights the importance of the protonation state of bridging ligands and proton coupled electron transfer to facilitate ET into Fe-rich clay minerals.
Free-Energy Calculations. A Mathematical Perspective
NASA Technical Reports Server (NTRS)
Pohorille, Andrzej
2015-01-01
conductance, defined as the ratio of ionic current through the channel to applied voltage, can be calculated in MD simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. If the current is small, a voltage significantly higher than the experimental one needs to be applied to collect sufficient statistics of ion crossing events. Then, the calculated conductance has to be extrapolated to the experimental voltage using procedures of unknown accuracy. Instead, we propose an alternative approach that applies if ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. Then, it is possible to test the assumptions of the equation, recover the full voltage/current dependence, determine the reliability of the calculated conductance and reconstruct the underlying (equilibrium) free energy profile, all from MD simulations at a single voltage. We will present the underlying theory, model calculations that test this theory and simulations on ion conductance through a channel that has been extensively studied experimentally. To our knowledge this is the first case in which the complete, experimentally measured dependence of the current on applied voltage has been reconstructed from MD simulations.
NASA Astrophysics Data System (ADS)
Meehan, Timothy Erickson
1992-01-01
Unrestricted Hartree-Fock calculations were performed on Fe_{x}CO clusters to model the CO(alpha_1), CO(alpha_2), and CO( alpha_3) adsorptions on the Fe(100) surface. Clusters of FeCO(C_{4v}) and a multiplicity of 5, Fe_2 CO(C_{2v}) and a multiplicity of 7, and Fe_2CO(C _{s}) and a multiplicity of 7, were constructed to model, respectively, the adsorption for the on top site, bridging site, and tilted CO structure at the 4-fold site. The CO position was optimized with respect to the Fe bulk distances using gradient techniques and the partial geometry optimization. CO stretching frequencies were calculated for each optimized geometry, and we find no evidence supporting CO adsorption in the bridging site. Using a full basis set the calculated CO stretching frequencies for the FeCO(C_{4v}), Fe_2CO(C_ {2v}), and the Fe_2 CO(C_{s}) clusters are 1992, 1767, and 771 cm^{ -1}, respectively. The CSOV analysis was executed to analyze the major orbital interactions between the CO and Fe_{x} clusters. For both Fe_2CO clusters, the CO pi^* perpendicular to the Fe _2 axis had a more significant contribution involving the pi backdonation from the Fe_2 clusters. Furthermore, the spin minority d electrons are mainly responsible for the pi backdonation. Due to problems with SCF convergence incurred during the Fe_{x}CO studies, we were forced to investigate a number of different techniques to achieve SCF convergence. Therefore, techniques that generate starting guesses of the eigenvectors for the SCF procedure and techniques used to accelerate SCF convergence are reviewed. The standard guesses of H _{core} and charge build -up are examined, and we introduce a new incremental cluster method for generating starting guesses for large clusters. The standard techniques of extrapolation, DIIS, damping, level shifting, restrict, and symmetry blocking are examined, and we also developed the hacker method and partial geometry optimization as new techniques to achieve SCF convergence. Results
NASA Astrophysics Data System (ADS)
Nakamura, Hiroki; Okumura, Masahiko; Machida, Masahiko
2013-02-01
Zeolites have attracted attention in the reprocessing of radioactive nuclear waste because of their high selective affinity for radioisotopes of Cs. Very recently, their useful properties have been widely utilized in decontamination after the accident at the Fukushima Daiichi Nuclear Power Plants. In this study, we study the high selectivity in the Cs adsorption of zeolites using first-principles calculations and clarify the mechanism of the cation selectivity of zeolites. We obtain energy surfaces on all capture locations for Cs/Na ions inside the micropores of a zeolite, ``mordenite'', and find three crucial conditions for the highly ion-selective exchange of Na for Cs: i) micropores with a radius of ˜3 Å, ii) a moderate Al/Si ratio, and iii) a uniform distribution of Al atoms around each micropore. These insights suggest a guideline for developing zeolites with high Cs selectivity and for enhancing the cation selectivity in more general situations.
Jin, Qiang; Yang, Yan; Dong, Xianbin; Fang, Jimin
2016-01-01
Many models (e.g., Langmuir model, Freundlich model and surface complexation model) have been successfully used to explain the mechanism of metal ion adsorption on the pure mineral materials. These materials usually have a homogeneous surface where all sites have the same adsorption energies. However, it's hardly appropriate for such models to describe the adsorption on heterogeneous surfaces (e.g., sediment surface), site energy distribution analysis can be to. In the present study, the site energy distribution analysis was used to describe the surface properties and adsorption behavior of the non-residual and residual components extracted from the natural aquatic sediment samples. The residues were prepared "in-situ" by using the sequential extraction procedure. The present study is intended to investigate the roles of different components and the change of site energy distribution at different temperatures of the sediment samples in controlling Cu (Ⅱ) adsorption. The results of the site energy distribution analysis indicated firstly, that the sorption sites of iron/manganese hydrous oxides (IMHO) and organic matter (OM) have higher energy. Secondly, light fraction (LF) and carbonates have little influence on site energy distribution. Finally, there was increase in site energies with the increase of temperature. Specially, low temperature (5 °C) significantly influenced the site energies of IMHO and OM, and also had obvious effect on the energy distribution of the sediments after removing target components. The site energy distribution analysis proved to be a useful method for us to further understand the energetic characteristics of sediment in comparison with those previously obtained. PMID:26552542
Abramyan, Tigran M.; Snyder, James A.; Yancey, Jeremy A.; Thyparambil, Aby A.; Wei, Yang; Stuart, Steven J.; Latour, Robert A.
2015-01-01
Interfacial force field (IFF) parameters for use with the CHARMM force field have been developed for interactions between peptides and high-density polyethylene (HDPE). Parameterization of the IFF was performed to achieve agreement between experimental and calculated adsorption free energies of small TGTG–X–GTGT host–guest peptides (T = threonine, G = glycine, and X = variable amino-acid residue) on HDPE, with ±0.5 kcal/mol agreement. This IFF parameter set consists of tuned nonbonded parameters (i.e., partial charges and Lennard–Jones parameters) for use with an in-house-modified CHARMM molecular dynamic program that enables the use of an independent set of force field parameters to control molecular behavior at a solid–liquid interface. The R correlation coefficient between the simulated and experimental peptide adsorption free energies increased from 0.00 for the standard CHARMM force field parameters to 0.88 for the tuned IFF parameters. Subsequent studies are planned to apply the tuned IFF parameter set for the simulation of protein adsorption behavior on an HDPE surface for comparison with experimental values of adsorbed protein orientation and conformation. PMID:25818122
Pore size distribution calculation from 1H NMR signal and N2 adsorption-desorption techniques
NASA Astrophysics Data System (ADS)
Hassan, Jamal
2012-09-01
The pore size distribution (PSD) of nano-material MCM-41 is determined using two different approaches: N2 adsorption-desorption and 1H NMR signal of water confined in silica nano-pores of MCM-41. The first approach is based on the recently modified Kelvin equation [J.V. Rocha, D. Barrera, K. Sapag, Top. Catal. 54(2011) 121-134] which deals with the known underestimation in pore size distribution for the mesoporous materials such as MCM-41 by introducing a correction factor to the classical Kelvin equation. The second method employs the Gibbs-Thompson equation, using NMR, for melting point depression of liquid in confined geometries. The result shows that both approaches give similar pore size distribution to some extent, and also the NMR technique can be considered as an alternative direct method to obtain quantitative results especially for mesoporous materials. The pore diameter estimated for the nano-material used in this study was about 35 and 38 Å for the modified Kelvin and NMR methods respectively. A comparison between these methods and the classical Kelvin equation is also presented.
18 CFR 11.13 - Energy gains calculations.
Code of Federal Regulations, 2010 CFR
2010-04-01
... calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY... FEDERAL POWER ACT Charges for Headwater Benefits § 11.13 Energy gains calculations. (a) Energy gains at a... not complex or in which headwater benefits are expected to be small, calculations will be made...
Phenolic resin-based porous carbons for adsorption and energy storage applications
NASA Astrophysics Data System (ADS)
Wickramaratne, Nilantha P.
The main objective of this dissertation research is to develop phenolic resin based carbon materials for range of applications by soft-templating and Stober-like synthesis strategies. Applications Studied in this dissertation are adsorption of CO2, bio-molecular and heavy metal ions, and energy storage devices. Based on that, our goal is to design carbon materials with desired pore structure, high surface area, graphitic domains, incorporated metal nanoparticles, and specific organic groups and heteroatoms. In this dissertation the organic-organic self-assembly of phenolic resins and triblock copolymers under acidic conditions will be used to obtain mesoporous carbons/carbon composites and Stober-like synthesis involving phenolic resins under basic condition will be used to prepare polymer/carbon particles and their composites. The structure of this dissertation consists of an introductory chapter (Chapter 1) discussing the general synthesis of carbon materials, particularly the soft-templating strategy and Stober-like carbon synthesis. Also, Chapter 1 includes a brief outline of applications namely adsorption of CO2, biomolecule and heavy metal ions, and supercapacitors. Chapter 2 discusses the techniques used for characterization of the carbon materials studied. This chapter starts with nitrogen adsorption analysis, which is used to measure the specific surface area, pore volume, distribution of pore sizes, and pore width. In addition to nitrogen adsorption, powder X-ray diffraction (XRD), transmission electron microscopy (TEM), high resolution thermogravimetric analysis (HR-TGA), cyclic voltammetry (CV) and CHNS elemental analysis (EA) are mentioned too. Chapter 3 is focused on carbon materials for CO2 adsorption. There are different types of porous solid materials such as silicate, MOFs, carbons, and zeolites studied for CO2 adsorption. However, the carbon based materials are considered to be the best candidates for CO 2 adsorption to the industrial point of
Zuo, Linzi; Guo, Yong; Li, Xiao; Fu, Heyun; Qu, Xiaolei; Zheng, Shourong; Gu, Cheng; Zhu, Dongqiang; Alvarez, Pedro J J
2016-01-19
A large effort is being made to develop nanosorbents with tunable surface chemistry for enhanced adsorption affinity and selectivity toward target organic contaminants. Heteroatom N-doped multiwall carbon nanotubes (N-MCNT) were synthesized by chemical vapor deposition of pyridine and were further investigated for the adsorptive removal of several aromatic chemicals varying in electronic donor and acceptor ability from aqueous solutions using a batch technique. Compared with commercial nondoped multiwall carbon nanotubes (MCNT), N-MCNT had similar specific surface area, morphology, and pore-size distribution but more hydrophilic surfaces and more surface defects due to the doping of graphitic and pyridinic N atoms. N-MCNT exhibited enhanced adsorption (2-10 folds) for the π-donor chemicals (2-naphthol and 1-naphthalmine) at pH ∼6 but similar adsorption for the weak π-donor chemical (naphthalene) and even lower adsorption (up to a 2-fold change) for the π-acceptor chemical (1,3-dinitrobenzene). The enhanced adsorption of 2-naphthol and 1-naphthalmine to N-MCNT was mainly attributed to the favored π-π electron-donor-acceptor (EDA) interaction between the π-donor adsorbate molecule and the polarized N-heterocyclic aromatic ring (π-acceptor) on N-MCNT. The proposed adsorption enhancement mechanisms were further tested through the pH effects on adsorption and the density function theory (DFT) calculation. The results show for the first time that the adsorptive interaction of π-donor aromatic compounds with carbon nanomaterials can be facilitated by N-doping. PMID:26669961
First Principles Calculations of Oxygen Adsorption on the UN(001) Surface
Zhukovskii, Yuri F.; Bocharov, Dmitry; Kotomin, Eugene Alexej; Evarestov, Robert; Bandura, A. V.
2009-01-01
Fabrication, handling and disposal of nuclear fuel materials require comprehensive knowledge of their surface morphology and reactivity. Due to unavoidable contact with air components (even at low partial pressures), UN samples contain considerable amount of oxygen impurities affecting fuel properties. In this study we focus on reactivity of the energetically most stable (001) substrate of uranium nitride towards the atomic oxygen as one of initial stages for further UN oxidation. The basic properties of O atoms adsorbed on the UN(001) surface are simulated here combining the two first principles calculation methods based on the plane wave basis set and that of the localized orbitals.
NASA Astrophysics Data System (ADS)
Shang, Jin; Li, Gang; Singh, Ranjeet; Xiao, Penny; Danaci, David; Liu, Jefferson Z.; Webley, Paul A.
2014-02-01
The crucial role of dispersion force in correctly describing the adsorption of some typical small-size gas molecules (e.g., CO2, N2, and CH4) in ion-exchanged chabazites has been investigated at different levels of theory, including the standard density functional theory calculation using the Perdew, Burke, and Ernzerhof (PBE) exchange-correlation functional and van der Waals density functional theory (vdWDFT) calculations using different exchange-correlation models - vdW_DF2, optB86b, optB88, and optPBE. Our results show that the usage of different vdWDFT functionals does not significantly change the adsorption configuration or the profile of static charge rearrangement of the gas-chabazite complexes, in comparison with the results obtained using the PBE. The calculated values of adsorption enthalpy using different functionals are compared with our experimental results. We conclude that the incorporation of dispersion interaction is imperative to correctly predict the trend of adsorption enthalpy values, in terms of different gas molecules and Cs+ cation densities in the adsorbents, even though the absolute values of adsorption enthalpy are overestimated by approximate 10 kJ/mol compared with experiments.
Ab initio calculations for dissociative hydrogen adsorption on lithium oxide surfaces
Sutjianto, A. |; Tam, S.W.; Curtiss, L.A.; Johnson, C.E.; Pandey, R.
1994-12-01
Lithium ceramics are one class of materials being considered as tritium breeders for fusion technology,and hydrogen is known to enhance the release of tritium from lithium ceramic materials. Dissociative hydrogen chemisorption on the Li{sub 2}O surfaces of the (100), (110), and (111) planes has been investigated with ab initio Hartree-Fock calculations. Calculations for unrelaxed crystal Li{sub 2}O structures indicated that except for the (100) surface, the (110) and (111) surfaces are stable. Results on the heterolytic sites of n-layer (110) (where n {ge} 2) slabs and three-layer (111) slabs suggest that dissociative hydrogen chemisorption is endothermic. For a one-layer (110) slab at 100% surface coverage, the dissociative hydrogen chemisorption is exothermic, forming OH{sup {minus}} and Li{sup +}H{sup {minus}}Li{sup +}. The results also indicate that the low coordination environment in surface step structures, such as kinks and ledges, may plan an important role in the hydrogen chemisorption process. On the homolytic sites of the (110) and (111) surfaces, there is no hydrogen chemisorption.
NASA Astrophysics Data System (ADS)
Veiga, R. G. A.; Miwa, R. H.; McLean, A. B.
2016-03-01
We report first-principles calculations of the energetic stability and electronic properties of metal-phthalocyanine (MPc) molecules (M = Cr, Mn, Fe, Co, Ni, Cu, and Zn) adsorbed on the δ -doped Si(111)-B (√{3 }×√{3 }) reconstructed surface. (i) It can be seen that CrPc, MnPc, FePc, and CoPc are chemically anchored to the topmost Si atom. (ii) Contrastingly, the binding of the NiPc, CuPc, and ZnPc molecules to the Si (111 ) -B (√{3 }×√{3 }) surface is exclusively ruled by van der Waals interactions, the main implication being that these molecules may diffuse and rearrange to form clusters and/or self-organized structures on this surface. The electronic structure calculations reveal that in point (i), owing to the formation of the metal-Si covalent bond, the net magnetic moment of the molecule is quenched by 1 μB , remaining unchanged in point (ii). In particular, the magnetic moment of CuPc (1 μB ) is preserved after adsorption. Finally, we verify that the formation of ZnPc, CuPc, and NiPc molecular (self-assembled) arrangements on the Si(111)-B (√{3 }×√{3 } ) surface is energetically favorable, in good agreement with recent experimental findings.
Xu, Pengcheng; Yu, Haitao; Li, Xinxin
2016-05-01
Activation-energy (Ea) value for trace-amount adsorption of gas molecules on material is rapidly and inexpensively obtained, for the first time, from a microgravimetric analysis experiment. With the material loaded, a resonant microcantilever is used to record in real time the adsorption process at two temperatures. The kinetic parameter Ea is thereby extracted by solving the Arrhenius equation. As an example, two CO2 capture nanomaterials are examined by the Ea extracting method for evaluation/optimization and, thereby, demonstrating the applicability of the microgravimetric analysis method. The achievement helps to solve the absence in rapid quantitative characterization of sorption kinetics and opens a new route to investigate molecule adsorption processes and materials. PMID:27100734
Wei, Yang; Latour, Robert A.
2009-01-01
With the increasing interest in protein adsorption in fields ranging from bionanotechnology to biomedical engineering, there is a growing need to understand protein-surface interactions at a fundamental level, such as the interaction between individual amino acid residues of a protein and functional groups presented by a surface. However, relatively little data are available that experimentally provide a quantitative, comparative measure of these types of interactions. To address this deficiency, the objective of this study was to generate a database of experimentally measured standard state adsorption free energy (ΔGoads) values for a wide variety of amino acid residue-surface interactions using a host-guest peptide and alkanethiol self-assembled monolayers (SAMs) with polymer-like functionality as the model system. The host-guest amino acid sequence was synthesized in the form of TGTG-X-GTGT where G & T are glycine and threonine amino acid residues and X represents a variable residue. In this paper, we report ΔGoads values for the adsorption of twelve different types of the host-guest peptides on a set of nine different SAM surfaces, for a total of 108 peptide-surface systems. The ΔGoads values for these 108 peptide-surface combinations show clear trends in adsorption behavior that are dependent on both peptide composition and surface chemistry. These data provide a benchmark experimental data set from which fundamental interactions that govern peptide and protein adsorption behavior can be better understood and compared. PMID:19432493
NASA Astrophysics Data System (ADS)
Vivcharuk, Victor; Tomberli, Bruno; Tolokh, Igor S.; Gray, C. G.
2008-03-01
Molecular dynamics (MD) simulations are used to study the interaction of a zwitterionic palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayer with the cationic antimicrobial peptide bovine lactoferricin (LFCinB) in a 100 mM NaCl solution at 310 K. The interaction of LFCinB with POPC is used as a model system for studying the details of membrane-peptide interactions, with the peptide selected because of its antimicrobial nature. Seventy-two 3 ns MD simulations, with six orientations of LFCinB at 12 different distances from a POPC membrane, are carried out to determine the potential of mean force (PMF) or free energy profile for the peptide as a function of the distance between LFCinB and the membrane surface. To calculate the PMF for this relatively large system a new variant of constrained MD and thermodynamic integration is developed. A simplified method for relating the PMF to the LFCinB-membrane binding free energy is described and used to predict a free energy of adsorption (or binding) of -1.05±0.39kcal/mol , and corresponding maximum binding force of about 20 pN, for LFCinB-POPC. The contributions of the ions-LFCinB and the water-LFCinB interactions to the PMF are discussed. The method developed will be a useful starting point for future work simulating peptides interacting with charged membranes and interactions involved in the penetration of membranes, features necessary to understand in order to rationally design peptides as potential alternatives to traditional antibiotics.
Rangan, Sylvie; Ruggieri, Charles; Bartynski, Robert; Martínez, José Ignacio; Flores, Fernando; Ortega, José
2016-01-01
The adsorption of a densely packed Zinc(II) tetraphenylporphyrin monolayer on a rutile TiO2(110)-(1×1) surface has been studied using a combination of experimental and theoretical methods, aimed at analyzing the relation between adsorption behavior and barrier height formation. The adsorption configuration of ZnTPP was determined from scanning tunnel microscopy (STM) imaging, density functional theory (DFT) calculations and STM image simulation. The corresponding energy alignment was experimentally determined from X-ray and UV-photoemission spectroscopies and inverse photoemission spectroscopy. These results were found in good agreement with an appropriately corrected DFT model, pointing to the importance of local bonding and intermolecular interactions in the establishment of barrier heights. PMID:26998188
Energy Band Calculations for Maximally Even Superlattices
NASA Astrophysics Data System (ADS)
Krantz, Richard; Byrd, Jason
2007-03-01
Superlattices are multiple-well, semiconductor heterostructures that can be described by one-dimensional potential wells separated by potential barriers. We refer to a distribution of wells and barriers based on the theory of maximally even sets as a maximally even superlattice. The prototypical example of a maximally even set is the distribution of white and black keys on a piano keyboard. Black keys may represent wells and the white keys represent barriers. As the number of wells and barriers increase, efficient and stable methods of calculation are necessary to study these structures. We have implemented a finite-element method using the discrete variable representation (FE-DVR) to calculate E versus k for these superlattices. Use of the FE-DVR method greatly reduces the amount of calculation necessary for the eigenvalue problem.
Strong and weak adsorption of CO2 on PuO2 (1 1 0) surfaces from first principles calculations
NASA Astrophysics Data System (ADS)
Yu, H. L.; Deng, X. D.; Li, G.; Lai, X. C.; Meng, D. Q.
2014-10-01
The CO2 adsorption on plutonium dioxide (PuO2) (1 1 0) surface was studied using projector-augmented wave (PAW) method based on density-functional theory corrected for onsite Coulombic interactions (GGA + U). It is found that CO2 has several different adsorption features on PuO2 (1 1 0) surface. Both weak and strong adsorptions exist between CO2 and the PuO2 (1 1 0) surface. Further investigation of partial density of states (PDOS) and charge density difference on two typical absorption sites reveal that electrostatic interactions were involved in the weak interactions, while covalent bonding was developed in the strong adsorptions.
Sorescu, D.C.
2006-04-01
A previous set of investigations related to adsorption, diffusion, and dissociation properties of CO [D. C. Sorescu, D. L. Thompson, M. M. Hurley, and C. F. Chabalowski, Phys. Rev. B 66, 035416 (2002)] and H2 [D. C. Sorescu, Catal. Today 105, 44 (2005)] on Fe(100) surface have been extended to the case of chemisorption properties of CHx (x=0,4) species on the same surface. Similar to our previous studies, the current work is based on first-principles plane-wave calculations using spin-polarized density functional theory (DFT) and the generalized gradient approximation (GGA). The calculations employ slab geometry and periodic boundary conditions. It was determined that CHx (x=0,2) species preferentially adsorb at the four-folded sites while the CH3 species prefer the binding at the bridge site. In contradistinction, the CH4 molecule is only weakly physisorbed on the surface, independent of surface site or molecular orientation. In the case of the C atom, the adsorption investigations have been extended to include both the coverage effects as well as the possibility for absorption at subsurface sites. The presence of the C atom at either hollow or subsurface sites was found to increase the stability of the other atomic (C, H, O) and molecular or radical species [CO, CHx (x=1,4)] adsorbed on the surface. Beside chemisorption properties, the activation energies for surface diffusion have been determined for all individual CHx (x=0,3)species while in the case of C atom diffusion to subsurface sites have also been considered. Finally, we have determined the minimum energy path for the elementary hydrogenation reactions of CHx (x=0,3) species. We found that for the ensemble of surface processes involving dissociation of CO and H2 on Fe(100) surface followed by hydrogenation of CHx (x=0,3) species with formation of CH4, the CO dissociation is the rate determining step with an activation energy of 24.5 kcal/mol.
NASA Astrophysics Data System (ADS)
Thirumalai, Hari; Kitchin, John R.
2016-08-01
Adsorption, a fundamental process in heterogeneous catalysis is known to be dependent on the adsorbate-adsorbate and surface-adsorbate bonds. van der Waals (vdW) interactions are one of the types of interactions that have not been examined thoroughly as a function of adsorbate coverage. In this work we quantify the vdW interactions for atomic adsorbates on late transition metal surfaces, and determine how these long range forces affect the coverage dependent adsorption energies. We calculate the adsorption energies of carbon, nitrogen, oxygen, sulfur, fluorine, bromine and chlorine species on Pt(111) and Pd(111) at coverages ranging from 1/4 to 1 ML using the BEEF-vdW functional. We observe that adsorption energies remain coverage dependent, and this coverage dependence is shown to be statistically significant. vdW interactions are found to be coverage dependent, but more significantly, they are found to be dependent on molecular properties such as adsorbate size, and consequently, correlate with the adsorbate effective nuclear charge. We observe that these interactions account for a reduction in the binding energy of the system, due to the destabilizing attractive interactions between the adsorbates which weaken its bond with the surface.
Low-energy calculations for nuclear photodisintegration
NASA Astrophysics Data System (ADS)
Deflorian, S.; Efros, V. D.; Leidemann, W.
2016-03-01
In the Standard Solar Model a central role in the nucleosynthesis is played by reactions of the kind {}{Z_1}{A_1}{X_1} + {}{Z_2}{A_2}{X_2} to {}{Z_1 + {Z_2}}{A_1 + {A_2}}Y + γ , which enter the proton-proton chains. These reactions can also be studied through the inverse photodisintegration reaction. One option is to use the Lorentz Integral Transform approach, which transforms the continuum problem into a bound state-like one. A way to check the reliability of such methods is a direct calculation, for example using the Kohn Variational Principle to obtain the scattering wave function and then directly calculate the response function of the reaction.
Calculation of molecular free energies in classical potentials
NASA Astrophysics Data System (ADS)
Farhi, Asaf; Singh, Bipin
2016-02-01
Free energies of molecules can be calculated by quantum chemistry computations or by normal mode classical calculations. However, the first can be computationally impractical for large molecules and the second is based on the assumption of harmonic dynamics. We present a novel, accurate and complete calculation of molecular free energies in standard classical potentials. In this method we transform the molecule by relaxing potential terms which depend on the coordinates of a group of atoms in that molecule and calculate the free energy difference associated with the transformation. Then, since the transformed molecule can be treated as non-interacting systems, the free energy associated with these atoms is analytically or numerically calculated. This two-step calculation can be applied to calculate free energies of molecules or free energy difference between (possibly large) molecules in a general environment. We demonstrate the method in free energy calculations for methanethiol and butane molecules in vacuum and solvent. We suggest the potential application of free energy calculation of chemical reactions in classical molecular simulations.
Evaluation of the isosteric heat of adsorption at zero coverage for hydrogen on activated carbons
NASA Astrophysics Data System (ADS)
Dohnke, E.; Beckner, M.; Romanos, J.; Olsen, R.; Wexler, C.; Pfeifer, P.
2011-03-01
Activated carbons made from corn cob show promise as materials for high-capacity hydrogen storage. As part of our characterization of these materials, we are interested in learning how different production methods affect the adsorption energies. In this talk, we will show how hydrogen adsorption isotherms may be used to calculate these adsorption energies at zero coverage using Henry's law. We will additionally discuss differences between the binding energy and the isosteric heat of adsorption by applying this analysis at different temperatures.
NASA Astrophysics Data System (ADS)
Watson, G. W.; Wells, R. P. K.; Willock, D. J.; Hutchings, G. J.
2000-07-01
The adsorption of ethene on the {111} surface of copper has been studied by using density functional theory calculations with gradient corrections. The surface is described by a periodic (3×3) slab, three layers thick, with ethene adsorbed on one side. The energy of the adsorption shows great sensitivity to the k-point sampling employed, with single k-point calculations overestimating the binding by over 800% when compared with a calculation converged with respect to the k-point sampling. In addition, the structure of the adsorbed molecule is considerably distorted, which is in contradiction with conclusions drawn from the experimental vibrational frequencies. Calculations that are converged with respect to the k-point sampling indicate a much weaker interaction between the molecule and the surface, with adsorption energies of 11.1 and 10.9 kJ mol -1 for atop-h and atop-b, respectively. This weaker interaction leads to a geometry for the adsorbed molecule that is close to the gas-phase ethene structure, in agreement with the vibrational frequencies. We have proposed a model of molecular adsorption that is a balance between attraction, resulting from localised bond formation, and repulsion, due to interaction between the extended electronic states and the molecule's electron density. If the extended electronic states are underestimated, as in cluster or low k-point calculations, the repulsion is underestimated. This results in stronger bonding to the surface and overestimation of the adsorption energy.
NASA Astrophysics Data System (ADS)
Biswas, Nandita; Thomas, Susy; Kapoor, Sudhir; Mishra, Amaresh; Wategaonkar, Sanjay; Mukherjee, Tulsi
2008-11-01
Structural and vibrational properties of mono- and multichromophoric hemicyanine (HC) dyes in solution and adsorbed on silver-coated films have been investigated using optical absorption and resonance Raman scattering techniques, with interpretations aided by theoretical calculations. This is the first report on the Raman spectroscopic studies of multichromophoric HC derivatives. The structure of the monomer, N-propyl-4-(p-N,N-dimethylamino styryl)pyridinium bromide (HC3), and its charged and neutral silver complexes (HC3-Ag) in the ground electronic (S0) state were optimized using density functional calculations with the B3LYP method using the 6-31G* and LANL2DZ basis sets. The ground state structure of N-hexyl-4-(p-N,N-dimethylamino styryl)pyridinium bromide (HC6) and multichromophoric HC dyes were computed using the HF /6-31G* method. The negligible shift or broadening observed in the electronic absorption and resonance Raman spectra in solution with increasing size of the HC chromophore suggests that the excitations are localized within individual monomer units in bis and tetra chromophores. However, in the tris chromophore, considerable redshift and broadening were observed, indicating a significant electronic interaction between the nonbonded electrons of the N atom and the aromatic π-system that is supported by the calculated excitation energies using the time-dependent density functional theory method. The effect of HC dye concentration on the electronic absorption spectra of the silver-coated film showed significant broadening, which was attributed to the formation of H- and J-aggregates in addition to the formation of a metal-molecule complex. A considerable redshift along various vibrations observed in the surface-enhanced resonance Raman scattering (SERRS) spectra of the HC derivatives indicates that adsorption on the silver surface leads to a considerable interaction of the electron rich moiety of HC derivatives with the silver surface. The
Carbon monoxide adsorption on beryllium surfaces
NASA Astrophysics Data System (ADS)
Allouche, A.
2013-02-01
Density functional calculations are here carried out to study the carbon monoxide molecule adsorption on pristine, hydrogenated and hydroxylated beryllium Be (0001) surfaces. The adsorption energies and structures, the activation barriers to molecular adsorption and dissociation are calculated. These reactions are described in terms of potential energy surfaces and electronic density of states. The quantum results are discussed along two directions: the beryllium surface reactivity in the domain of nuclear fusion devices and the possible usage of beryllium as a catalyst of Fischer-Tropsch-type synthesis.
Calculation of energy deposition distributions for simple geometries
NASA Technical Reports Server (NTRS)
Watts, J. W., Jr.
1973-01-01
When high-energy charged particles pass through a thin detector, the ionization energy loss in that detector is subject to fluctuations or straggling which must be considered in interpreting the data. Under many conditions, which depend upon the charge and energy of the incident particle and the detector geometry, the ionization energy lost by the particle is significantly different from the energy deposited in the detector. This problem divides naturally into a calculation of the energy loss that results in excitation and low-energy secondary electrons which do not travel far from their production points, and a calculation of energy loss that results in high-energy secondary electrons which can escape from the detector. The first calculation is performed using a modification of the Vavilov energy loss distribution. A cutoff energy is introduced above which all electrons are ignored and energy transferred to low energy particles is assumed to be equivalent to the energy deposited by them. For the second calculation, the trajectory of the primary particle is considered as a source of secondary high-energy electrons. The electrons from this source are transported using Monte Carlo techniques and multiple scattering theory, and the energy deposited by them in the detector is calculated. The results of the two calculations are then combined to predict the energy deposition distribution. The results of these calculations are used to predict the charge resolution of parallel-plate pulse ionization chambers that are being designed to measure the charge spectrum of heavy nuclei in the galactic cosmic-ray flux.
Liu, Kai; Zhang, Siyu; Hu, Xiyue; Zhang, Kunyang; Roy, Ajay; Yu, Gang
2015-07-21
To examine the effects of different functionalization methods on adsorption behavior, anionic-exchange MIL-101(Cr) metal-organic frameworks (MOFs) were synthesized using preassembled modification (PAM) and postsynthetic modification (PSM) methods. Perfluorooctanoic acid (PFOA) adsorption results indicated that the maximum PFOA adsorption capacity was 1.19 and 1.89 mmol g(-1) for anionic-exchange MIL-101(Cr) prepared by PAM and PSM, respectively. The sorption equilibrium was rapidly reached within 60 min. Our results indicated that PSM is a better modification technique for introducing functional groups onto MOFs for adsorptive removal because PAM places functional groups onto the aperture of the nanopore, which hinders the entrance of organic contaminants. Our experimental results and the results of complementary density functional theory calculations revealed that in addition to the anion-exchange mechanism, the major PFOA adsorption mechanism is a combination of Lewis acid/base complexation between PFOA and Cr(III) and electrostatic interaction between PFOA and the protonated carboxyl groups of the bdc (terephthalic acid) linker. PMID:26066631
NASA Astrophysics Data System (ADS)
Migliorini, Davide; Nattino, Francesco; Kroes, Geert-Jan
2016-02-01
The fundamental understanding of molecule-surface reactions is of great importance to heterogeneous catalysis, motivating many theoretical and experimental studies. Even though much attention has been dedicated to the dissociative chemisorption of N2 on tungsten surfaces, none of the existing theoretical models has been able to quantitatively reproduce experimental reaction probabilities for the sticking of N2 to W(110). In this work, the dissociative chemisorption of N2 on W(110) has been studied with both static electronic structure and ab initio molecular dynamics (AIMD) calculations including the surface temperature effects through surface atom motion. Calculations have been performed using density functional theory, testing functionals that account for the long range van der Waals (vdW) interactions, which were previously only considered in dynamical calculations within the static surface approximation. The vdW-DF2 functional improves the description of the potential energy surface for N2 on W(110), returning less deep molecular adsorption wells and a better ratio between the barriers for the indirect dissociation and the desorption, as suggested by previous theoretical work and experimental evidence. Using the vdW-DF2 functional less trapping-mediated dissociation is obtained compared to results obtained with standard semi-local functionals such as PBE and RPBE, improving agreement with experimental data at Ei = 0.9 eV. However, at Ei = 2.287 and off-normal incidence, the vdW-DF2 AIMD underestimates the experimental reaction probabilities, showing that also with the vdW-DF2 functional the N2 on W(110) interaction is not yet described with quantitative accuracy.
Migliorini, Davide; Nattino, Francesco; Kroes, Geert-Jan
2016-02-28
The fundamental understanding of molecule-surface reactions is of great importance to heterogeneous catalysis, motivating many theoretical and experimental studies. Even though much attention has been dedicated to the dissociative chemisorption of N2 on tungsten surfaces, none of the existing theoretical models has been able to quantitatively reproduce experimental reaction probabilities for the sticking of N2 to W(110). In this work, the dissociative chemisorption of N2 on W(110) has been studied with both static electronic structure and ab initio molecular dynamics (AIMD) calculations including the surface temperature effects through surface atom motion. Calculations have been performed using density functional theory, testing functionals that account for the long range van der Waals (vdW) interactions, which were previously only considered in dynamical calculations within the static surface approximation. The vdW-DF2 functional improves the description of the potential energy surface for N2 on W(110), returning less deep molecular adsorption wells and a better ratio between the barriers for the indirect dissociation and the desorption, as suggested by previous theoretical work and experimental evidence. Using the vdW-DF2 functional less trapping-mediated dissociation is obtained compared to results obtained with standard semi-local functionals such as PBE and RPBE, improving agreement with experimental data at E(i) = 0.9 eV. However, at E(i) = 2.287 and off-normal incidence, the vdW-DF2 AIMD underestimates the experimental reaction probabilities, showing that also with the vdW-DF2 functional the N2 on W(110) interaction is not yet described with quantitative accuracy. PMID:26931713
Shalabi, Ahmad S; Assem, Mervat M; Soliman, Kamal A
2011-12-01
We have analyzed, by means of density functional theory calculations and the embedded cluster model, the adsorption and spin-state properties of Cr, Ni, Mo, and Pt deposited on a MgO crystal. We considered deposition at the Mg(2+) site of a defect-free surface and at Li(+) and Na(+) sites of impurity-containing surfaces. To avoid artificial polarization effects, clusters of moderate sizes with no border anions were embedded in simulated Coulomb fields that closely approximate the Madelung fields of the host surfaces. The interaction between a transition metal atom and a surface results from a competition between Hund's rule for the adsorbed atom and the formation of a chemical bond at the interface. We found that the adsorption energies of the metal atoms are significantly enhanced by the cation impurities, and the adsorption energies of the low-spin states of spin-quenched complexes are always more favorable than those of the high-spin states. Spin polarization effects tend to preserve the spin states of the adsorbed atoms relative to those of the isolated atoms. The metal-support interactions stabilize the low-spin states of the adsorbed metals with respect to the isolated metals, but the effect is not always enough to quench the spin. Spin quenching occurs for Cr and Mo complexes at the Mg(2+) site of the pure surface and at Li(+) and Na(+) sites of the impurity-containing surfaces. Variations of the spin-state properties of free metals and of the adsorption and spin-state properties of metal complexes are correlated with the energies of the frontier orbitals. The electrostatic potential energy curves provide further understanding of the nature of the examined properties. PMID:21369929
NASA Astrophysics Data System (ADS)
Haubrich, J.; Becker, C.; Wandelt, K.
2009-06-01
We present a detailed analysis of the electronic and geometric bonding properties of the model alkene ethene on different mono- and bimetallic surfaces to establish the difference between adsorption energy and interaction energy and to elucidate the chemical character of a single platinum atom in different chemical environments. The adsorption of ethene on Pt(1 1 1) at 100 K leads to two adsorption states, which are commonly described as being of di- σ-type (bidentate, μ 2η 2) and π-type (monodentate, μ 1η 2). While the later is the minority species on Pt(1 1 1) it is of larger abundance on the platinum alloys. We have chosen π-bonded ethene for our study since it can be found on Pt(1 1 1), the Pt 3Sn and Pt 2Sn surface alloys, and Cu 3Pt(1 1 1). Density functional theory calculations of the adsorption structures, site and decomposed densities of states, as well as partial charge densities in conjunction with vibrational spectroscopy show that the bonding, i.e. the interaction energy, of the π ethene is only weakly influenced by alloying. Even in a copper matrix - as in the case of Cu 3Pt(1 1 1) - the bonding platinum atom essentially keeps its chemical identity and the interaction energy is reduced by only 14% compared to Pt(1 1 1). This observation suggests that bonding on surfaces is a strongly localized phenomenon. However, the adsorption energy decreases significantly due to alloying, which is attributed to the varying local relaxation of the different metal surfaces.
Bellucci, Francesco; Lee, Sang Soo; Kubicki, James D.; Bandura, Andrei V.; Zhang, Zhan; Wesolowski, David J.; Fenter, Paul
2015-01-29
We study adsorption of Rb^{+} to the quartz(101)–aqueous interface at room temperature with specular X-ray reflectivity, resonant anomalous X-ray reflectivity, and density functional theory. The interfacial water structures observed in deionized water and 10 mM RbCl solution at pH 9.8 were similar, having a first water layer at height of 1.7 ± 0.1 Å above the quartz surface and a second layer at 4.8 ± 0.1 Å and 3.9 ± 0.8 Å for the water and RbCl solutions, respectively. The adsorbed Rb^{+} distribution is broad and consists of presumed inner-sphere (IS) and outer-sphere (OS) complexes at heights of 1.8 ± 0.1 and 6.4 ± 1.0 Å, respectively. Projector-augmented planewave density functional theory (DFT) calculations of potential configurations for neutral and negatively charged quartz(101) surfaces at pH 7 and 12, respectively, reveal a water structure in agreement with experimental results. These DFT calculations also show differences in adsorbed speciation of Rb^{+} between these two conditions. At pH 7, the lowest energy structure shows that Rb^{+} adsorbs dominantly as an IS complex, whereas at pH 12 IS and OS complexes have equivalent energies. The DFT results at pH 12 are generally consistent with the two site Rb distribution observed from the X-ray data at pH 9.8, albeit with some differences that are discussed. In conclusion, surface charge estimated on the basis of the measured total Rb^{+} coverage was -0.11 C/m^{2}, in good agreement with the range of the surface charge magnitudes reported in the literature.
NASA Astrophysics Data System (ADS)
Becker, C. A.; Olmsted, D. L.; Asta, M.; Hoyt, J. J.; Foiles, S. M.
2009-02-01
Monte Carlo and molecular-dynamics simulations are employed in a study of the equilibrium structural and thermodynamic properties of crystal-melt interfaces in a model binary alloy system described by Lennard-Jones interatomic interactions with zero size mismatch, a ratio of interaction strengths equal to 0.75, and interspecies interactions given by Lorentz-Berthelot mixing rules. This alloy system features a simple lens-type solid-liquid phase diagram at zero pressure, with nearly ideal solution thermodynamics in the solid and liquid solution phases. Equilibrium density profiles are computed for (100)-oriented crystal-melt interfaces and are used to derive the magnitudes of the relative adsorption coefficients (Γi(j)) at six temperatures along the solidus/liquidus boundary. The values for Γ1(2) , the relative adsorption of the lower melting-point species (1) with respect to the higher melting point species (2), are found to vary monotonically with temperature, with values that are positive and in the range of a few atomic percent per interface site. By contrast, values of Γ2(1) display a much more complex temperature dependence with a large peak in the magnitude of the relative adsorption more than ten times larger than those found for Γ1(2) . The capillary fluctuation method is used to compute the temperature dependence of the magnitudes and anisotropies of the crystal-melt interfacial free energy (γ) . At all temperatures we obtain the ordering γ100>γ110>γ111 for the high-symmetry (100), (110), and (111) interface orientations. The values of γ monotonically decrease with decreasing temperature (i.e., increasing concentration of the lower melting-point species). Using the calculated temperature-dependent values of γ and Γ1(2) in the Gibbs adsorption theorem, we estimate that roughly 25% of the temperature dependence of γ for the alloys can be attributed to interface adsorption, while the remaining contribution arises from the relative excess entropy
Lorenz, Marco; Civalleri, Bartolomeo; Maschio, Lorenzo; Sgroi, Mauro; Pullini, Daniele
2014-09-15
The physisorption of water on graphene is investigated with the hybrid density functional theory (DFT)-functional B3LYP combined with empirical corrections, using moderate-sized basis sets such as 6-31G(d). This setup allows to model the interaction of water with graphene going beyond the quality of classical or semiclassical simulations, while still keeping the computational costs under control. Good agreement with respect to Coupled Cluster with singles and doubles excitations and perturbative triples (CCSD(T)) results is achieved for the adsorption of a single water molecule in a benchmark with two DFT-functionals (Perdew/Burke/Ernzerhof (PBE), B3LYP) and Grimme's empirical dispersion and counterpoise corrections. We apply the same setting to graphene supported by epitaxial hexagonal boron nitride (h-BN), leading to an increased interaction energy. To further demonstrate the achievement of the empirical corrections, we model, entirely from first principles, the electronic properties of graphene and graphene supported by h-BN covered with different amounts of water (one, 10 water molecules per cell and full coverage). The effect of h-BN on these properties turns out to be negligibly small, making it a good candidate for a substrate to grow graphene on. PMID:25056422
Global versus local adsorption selectivity
NASA Astrophysics Data System (ADS)
Pauzat, Françoise; Marloie, Gael; Markovits, Alexis; Ellinger, Yves
2015-10-01
The origin of the enantiomeric excess found in the amino acids present in the organic matter of carbonaceous meteorites is still unclear. Selective adsorption of one of the two enantiomers existing after a racemic formation could be part of the answer. Hereafter we report a comparative study of the adsorption of the R and S enantiomers of α-alanine and lactic acid on the hydroxylated { } chiral surface of α-quartz using numerical simulation techniques. Structurally different adsorption sites were found with opposite R versus S selectivity for the same molecule-surface couple, raising the problem of whether to consider adsorption as a local property or as a global response characteristic of the whole surface. To deal with the second term of this alternative, a statistical approach was designed, based on the occurrence of each adsorption site whose energy was calculated using first principle periodic density functional theory. It was found that R-alanine and S-lactic acid are the enantiomers preferentially adsorbed, even if the adsorption process on the quartz { } surface stays with a disappointingly poor enantio-selectivity. Nevertheless, it highlighted the important point that considering adsorption as a global property changes perspectives in the search for more efficient enantio-selective supports and more generally changes the way to apprehend adsorption processes in astro-chemistry/biology.
Phosphate adsorption on lanthanum loaded biochar.
Wang, Zhanghong; Shen, Dekui; Shen, Fei; Li, Tianyu
2016-05-01
To attain a low-cost and high-efficient phosphate adsorbent, lanthanum (La) loaded biochar (La-BC) prepared by a chemical precipitation method was developed. La-BC and its pristine biochar (CK-BC) were comparatively characterized using zeta potential, BET surface area, scanning electron microscopy/energy dispersive spectrometer (SEM-EDS), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FT-IR). The adsorption ability and the mechanisms during adsorption process for the La-BC samples were also investigated. La loaded on the surface of biochar can be termed as La-composites (such as LaOOH, LaONO3 and La(OH)3), leading to the decrease of negative charge and surface area of biochar. La-BC exhibited the high adsorption capacity to phosphate compared to CK-BC. Adsorption isotherm and adsorption kinetic studies showed that the Langmuir isotherm and second order model could well describe the adsorption process of La-BC, indicating that the adsorption was dominated by a homogeneous and chemical process. The calculated maximum adsorption capacity was as high as 46.37 mg g(-1) (computed in P). Thermodynamic analysis revealed that the adsorption was spontaneous and endothermic. SEM, XRD, XPS and FT-IR analysis suggested that the multi-adsorption mechanisms including precipitation, ligand exchange and complexation interactions can be evidenced during the phosphate adsorption process by La-composites in La-BC. PMID:26871732
Adsorption energy and spin state of first-row transition metals adsorbed on MgO(100)
NASA Astrophysics Data System (ADS)
Markovits, A.; Paniagua, J. C.; López, N.; Minot, C.; Illas, F.
2003-03-01
Slab and cluster model spin-polarized calculations have been carried out to study various properties of isolated first-row transition metal atoms adsorbed on the anionic sites of the regular MgO(100) surface. The calculated adsorption energies follow the trend of the metal cohesive energies, indicating that the changes in the metal-support and metal-metal interactions along the series are dominated by atomic properties. In all cases, except for Ni at the generalized gradient approximation level, the number of unpaired electron is maintained as in the isolated metal atom. The energy required to change the atomic state from high to low spin has been computed using the PW91 and B3LYP density-functional-theory-based methods. PW91 fails to predict the proper ground state of V and Ni, but the results for the isolated and adsorbed atom are consistent within the method. B3LYP properly predicts the ground state of all first-row transition atom the high- to low-spin transition considered is comparable to experiment. In all cases, the interaction with the surface results in a reduced high- to low-spin transition energy.
Ersan, Gamze; Apul, Onur G; Karanfil, Tanju
2016-07-01
The objective of this paper was to create a comprehensive database for the adsorption of organic compounds by carbon nanotubes (CNTs) and to use the Linear Solvation Energy Relationship (LSER) technique for developing predictive adsorption models of organic compounds (OCs) by multi-walled carbon nanotubes (MWCNTs) and single-walled carbon nanotubes (SWCNTs). Adsorption data for 123 OCs by MWCNTs and 48 OCs by SWCNTs were compiled from the literature, including some experimental results obtained in our laboratory. The roles of selected OCs properties and CNT types were examined with LSER models. The results showed that the r(2) values of the LSER models displayed small variability for aromatic compounds smaller than 220 g/mol, after which a decreasing trend was observed. The data available for aliphatics was mainly for molecular weights smaller than 250 g/mol, which showed a similar trend to that of aromatics. The r(2) values for the LSER model on the adsorption of aromatic and aliphatic OCs by SWCNTs and MWCNTs were relatively similar indicating the linearity of LSER models did not depend on the CNT types. Among all LSER model descriptors, V term (molecular volume) for aromatic OCs and B term (basicity) for aliphatic OCs were the most predominant descriptors on both type of CNTs. The presence of R term (excess molar refractivity) in LSER model equations resulted in decreases for both V and P (polarizability) parameters without affecting the r(2) values. Overall, the results demonstrate that successful predictive models can be developed for the adsorption of OCs by MWCNTs and SWCNTs with LSER techniques. PMID:27064209
Guidelines for the analysis of free energy calculations.
Klimovich, Pavel V; Shirts, Michael R; Mobley, David L
2015-05-01
Free energy calculations based on molecular dynamics simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. But these calculations are still difficult and tedious to analyze, and best practices for analysis are not well defined or propagated. Essentially, each group analyzing these calculations needs to decide how to conduct the analysis and, usually, develop its own analysis tools. Here, we review and recommend best practices for analysis yielding reliable free energies from molecular simulations. Additionally, we provide a Python tool, alchemical-analysis.py, freely available on GitHub as part of the pymbar package (located at http://github.com/choderalab/pymbar), that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages. Both this review and the tool covers analysis of alchemical calculations generally, including free energy estimates via both thermodynamic integration and free energy perturbation-based estimators. Our Python tool also handles output from multiple types of free energy calculations, including expanded ensemble and Hamiltonian replica exchange, as well as standard fixed ensemble calculations. We also survey a range of statistical and graphical ways of assessing the quality of the data and free energy estimates, and provide prototypes of these in our tool. We hope this tool and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations. PMID:25808134
Guidelines for the analysis of free energy calculations
Klimovich, Pavel V.; Shirts, Michael R.; Mobley, David L.
2015-01-01
Free energy calculations based on molecular dynamics (MD) simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. But these calculations are still difficult and tedious to analyze, and best practices for analysis are not well defined or propagated. Essentially, each group analyzing these calculations needs to decide how to conduct the analysis and, usually, develop its own analysis tools. Here, we review and recommend best practices for analysis yielding reliable free energies from molecular simulations. Additionally, we provide a Python tool, alchemical–analysis.py, freely available on GitHub at https://github.com/choderalab/pymbar–examples, that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages. Both this review and the tool covers analysis of alchemical calculations generally, including free energy estimates via both thermodynamic integration and free energy perturbation-based estimators. Our Python tool also handles output from multiple types of free energy calculations, including expanded ensemble and Hamiltonian replica exchange, as well as standard fixed ensemble calculations. We also survey a range of statistical and graphical ways of assessing the quality of the data and free energy estimates, and provide prototypes of these in our tool. We hope these tools and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations. PMID:25808134
Spectroscopically Accurate Calculations of the Rovibrational Energies of Diatomic Hydrogen
NASA Astrophysics Data System (ADS)
Perry, Jason
2005-05-01
The Born-Oppenheimer approximation has been used to calculate the rotational and vibrational states of diatomic hydrogen. Because it is an approximation, our group now wants to use a Born-Oppenheimer potential to calculate the electronic energy that has been corrected to match closely with spectroscopic results. We are using a code that has corrections for adiabatic, relativistic, radiative, and non-adiabatic effects. The rovibrational energies have now been calculated for both bound and quasi-bound states. We also want to compute quadrupole transition probabilities for diatomic hydrogen. These calculations aspire to investigate diatomic hydrogen in astrophysical environments.
18 CFR 11.13 - Energy gains calculations.
Code of Federal Regulations, 2011 CFR
2011-04-01
... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT ANNUAL CHARGES UNDER PART I OF...
18 CFR 11.13 - Energy gains calculations.
Code of Federal Regulations, 2014 CFR
2014-04-01
... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT ANNUAL CHARGES UNDER PART I OF...
18 CFR 11.13 - Energy gains calculations.
Code of Federal Regulations, 2013 CFR
2013-04-01
... 18 Conservation of Power and Water Resources 1 2013-04-01 2013-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT ANNUAL CHARGES UNDER PART I OF...
18 CFR 11.13 - Energy gains calculations.
Code of Federal Regulations, 2012 CFR
2012-04-01
... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT ANNUAL CHARGES UNDER PART I OF...
de Graaf, Joost; Dijkstra, Marjolein; van Roij, René
2009-11-01
We present a numerical technique, namely, triangular tessellation, to calculate the free energy associated with the adsorption of a colloidal particle at a flat interface. The theory and numerical scheme presented here are sufficiently general to handle nonconvex patchy colloids with arbitrary surface patterns characterized by a wetting angle, e.g., amphiphilicity. We ignore interfacial deformation due to capillary, electrostatic, or gravitational forces, but the method can be extended to take such effects into account. It is verified that the numerical method presented is accurate and sufficiently stable to be applied to more general situations than presented in this paper. The merits of the tessellation method prove to outweigh those of traditionally used semianalytic approaches, especially when it comes to generality and applicability. PMID:20364983
Gor, Gennady Y; Bernstein, Noam
2016-04-14
When fluids are adsorbed on a solid surface they induce noticeable stresses, which cause the deformation of the solid. D. H. Bangham and co-authors performed a series of experimental measurements of adsorption-induced strains, and concluded that physisorption causes expansion, which is proportional to the lowering of the surface energy Δγ. This statement is referred to as the Bangham effect or Bangham's law. However, it is known that the quantity that controls the deformation is actually the change in surface stress Δf rather than surface energy Δγ, but this difference has not been considered in the context of adsorption-induced deformation of mesoporous materials. We use the Brunauer-Emmett-Teller (BET) theory to derive both values and show the difference between them. We find the condition when the difference between the two vanishes, and Bangham's law is applicable; it is likely that this condition is satisfied in most cases, and prediction of strain based on Δγ is a good approximation. We show that this is the case for adsorption of argon and water on Vycor glass. Finally, we show that the difference between Δγ and Δf can explain some of the experimental data that contradicts Bangham's law. PMID:27001041
New approach to calculating the potential energy of colliding nuclei
Kurmanov, R. S.; Kosenko, G. I.
2014-12-15
The differential method proposed by the present authors earlier for the reduction of volume integrals in calculating the potential energy of a compound nucleus is generalized to the case of two interacting nuclei. The Coulomb interaction energy is obtained for the cases of a sharp and a diffuse boundary of nuclei, while the nuclear interaction energy is found only for nuclei with a sharp boundary, the finiteness of the nuclear-force range being taken into account. The present method of calculations permits reducing the time it takes to compute the potential energy at least by two orders of magnitude.
Calculation of Rydberg energy levels for the francium atom
NASA Astrophysics Data System (ADS)
Huang, Shi-Zhong; Chu, Jin-Min
2010-06-01
Based on the weakest bound electron potential model theory, the Rydberg energy levels and quantum defects of the np2Po1/2 (n = 7-50) and np2Po3/2 (n = 7-50) spectrum series for the francium atom are calculated. The calculated results are in excellent agreement with the 48 measured levels, and 40 energy levels for highly excited states are predicted.
Protein thermostability calculations using alchemical free energy simulations.
Seeliger, Daniel; de Groot, Bert L
2010-05-19
Thermal stability of proteins is crucial for both biotechnological and therapeutic applications. Rational protein engineering therefore frequently aims at increasing thermal stability by introducing stabilizing mutations. The accurate prediction of the thermodynamic consequences caused by mutations, however, is highly challenging as thermal stability changes are caused by alterations in the free energy of folding. Growing computational power, however, increasingly allows us to use alchemical free energy simulations, such as free energy perturbation or thermodynamic integration, to calculate free energy differences with relatively high accuracy. In this article, we present an automated protocol for setting up alchemical free energy calculations for mutations of naturally occurring amino acids (except for proline) that allows an unprecedented, automated screening of large mutant libraries. To validate the developed protocol, we calculated thermodynamic stability differences for 109 mutations in the microbial Ribonuclease Barnase. The obtained quantitative agreement with experimental data illustrates the potential of the approach in protein engineering and design. PMID:20483340
NASA Astrophysics Data System (ADS)
Gololobova, E. G.; Gorichev, I. G.; Lainer, Yu. A.; Skvortsova, I. V.
2011-05-01
A procedure was proposed for the calculation of the acid-base equilibrium constants at an alumina/electrolyte interface from experimental data on the adsorption of singly charged ions (Na+, Cl-) at various pH values. The calculated constants (p K {1/0}= 4.1, p K {2/0}= 11.9, p K {3/0}= 8.3, and p K {4/0}= 7.7) are shown to agree with the values obtained from an experimental pH dependence of the electrokinetic potential and the results of potentiometric titration of Al2O3 suspensions.
Is ring breaking feasible in relative binding free energy calculations?
Liu, Shuai; Wang, Lingle; Mobley, David L
2015-04-27
Our interest is relative binding free energy (RBFE) calculations based on molecular simulations. These are promising tools for lead optimization in drug discovery, computing changes in binding free energy due to modifications of a lead compound. However, in the "alchemical" framework for RBFE calculations, some types of mutations have the potential to introduce error into the computed binding free energies. Here we explore the magnitude of this error in several different model binding calculations. We find that some of the calculations involving ring breaking have significant errors, and these errors are especially large in bridged ring systems. Since the error is a function of ligand strain, which is unpredictable in advance, we believe that ring breaking should be avoided when possible. PMID:25835054
Free energy calculations for molecular solids using GROMACS
NASA Astrophysics Data System (ADS)
Aragones, J. L.; Noya, E. G.; Valeriani, C.; Vega, C.
2013-07-01
In this work, we describe a procedure to evaluate the free energy of molecular solids with the GROMACS molecular dynamics package. The free energy is calculated using the Einstein molecule method that can be regarded as a small modification of the Einstein crystal method. Here, the position and orientation of the molecules is fixed by using an Einstein field that binds with harmonic springs at least three non-collinear atoms (or points of the molecule) to their reference positions. The validity of the Einstein field is tested by performing free-energy calculations of methanol, water (ice), and patchy colloids molecular solids. The free energies calculated with GROMACS show a very good agreement with those obtained using Monte Carlo and with previously published results.
Calle-Vallejo, F; Martínez, J I; García-Lastra, J M; Rossmeisl, J; Koper, M T M
2012-03-16
Despite their importance in physics and chemistry, the origin and extent of the scaling relations between the energetics of adsorbed species on surfaces remain elusive. We demonstrate here that scalability is not exclusive to adsorbed atoms and their hydrogenated species but rather a general phenomenon between any set of adsorbates bound similarly to the surface. On the example of the near-surface alloys of Pt, we show that scalability is a result of identical variations of adsorption energies with respect to the valence configuration of both the surface components and the adsorbates. PMID:22540492
Complementing the adsorption energies of CO2, H2S and NO2 to h-BN sheets by doping with carbon
NASA Astrophysics Data System (ADS)
Sagynbaeva, Myskal; Hussain, Tanveer; Panigrahi, Puspamitra; Johansson, Borje; Ahuja, Rajeev
2015-03-01
We predict the adsorption proficiency of hexagonal boron nitride (h-BN) sheets to toxic gas molecules like CO2, H2S and NO2 on the basis of first-principles density functional theory calculations. The computed energies predict the pristine h-BN sheet to have very little affinity towards the mentioned gas molecules. However, while doping C at the N site of the h-BN sheet brings a significant enhancement to the estimated adsorption energies, doping C at B site of the sheet is found to be energetically not so favorable. To have a higher coverage effect, the concentration of C doping on the h-BN sheet is further increased which resulted in upsurging the adsorption energies for the mentioned gas molecules. Among the three, CO2, H2S are found to be physisorbed to the C-doped h-BN sheets, where as the C-doped sheets are found to have strong affinity towards NO2 gas molecules.
S-matrix calculations of energy levels of alkalilike ions
NASA Astrophysics Data System (ADS)
Sapirstein, Jonathan; Cheng, K. T.
2013-05-01
A recent S-matrix based QED calculation of energy levels of the lithium isoelectronic sequence is extended to the general case of a valence electron outside an arbitrary filled core. Formulas are presented that allow calculation of the energy levels of valence ns , np1 / 2 , np3 / 2 , nd3 / 2 , and nd5 / 2 states. Emphasis is placed on modifications of the lithiumlike formulas required because more than one core state is present, and a discussion of an unusual feature of the two-photon exchange contribution involving autoiononizing states is given. The method is illustrated with a calculation of energy levels of the sodium isoelectronic sequence, with results for 3s1 / 2 , 3p1 / 2 , and 3p3 / 2 energies tabulated for the range Z = 20 - 100 . A detailed breakdown of the calculation is given for Z = 74 . Comparison with experiment and other calculations is given, and prospects for extension of the method to ions with more complex electronic structure discussed. The work of JS was supported in part by NSF Grant No. PHY-1068065. The work of KTC was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
Theoretical study on the adsorption of carbon dioxide on individual and alkali-metal doped MOF-5s
NASA Astrophysics Data System (ADS)
Ha, Nguyen Thi Thu; Lefedova, O. V.; Ha, Nguyen Ngoc
2016-01-01
Density functional theory (DFT) calculations were performed to investigate the adsorption of carbon dioxide (CO2) on metal-organic framework (MOF-5) and alkali-metal (Li, K, Na) doped MOF-5s. The adsorption energy calculation showed that metal atom adsorption is exothermic in MOF-5 system. Moreover, alkali-metal doping can significantly improve the adsorption ability of carbon dioxide on MOF-5. The best influence is observed for Li-doping.
Performance calculation and simulation system of high energy laser weapon
NASA Astrophysics Data System (ADS)
Wang, Pei; Liu, Min; Su, Yu; Zhang, Ke
2014-12-01
High energy laser weapons are ready for some of today's most challenging military applications. Based on the analysis of the main tactical/technical index and combating process of high energy laser weapon, a performance calculation and simulation system of high energy laser weapon was established. Firstly, the index decomposition and workflow of high energy laser weapon was proposed. The entire system was composed of six parts, including classical target, platform of laser weapon, detect sensor, tracking and pointing control, laser atmosphere propagation and damage assessment module. Then, the index calculation modules were designed. Finally, anti-missile interception simulation was performed. The system can provide reference and basis for the analysis and evaluation of high energy laser weapon efficiency.
Calculating fusion neutron energy spectra from arbitrary reactant distributions
NASA Astrophysics Data System (ADS)
Eriksson, J.; Conroy, S.; Andersson Sundén, E.; Hellesen, C.
2016-02-01
The Directional Relativistic Spectrum Simulator (DRESS) code can perform Monte-Carlo calculations of reaction product spectra from arbitrary reactant distributions, using fully relativistic kinematics. The code is set up to calculate energy spectra from neutrons and alpha particles produced in the D(d, n)3He and T(d, n)4He fusion reactions, but any two-body reaction can be simulated by including the corresponding cross section. The code has been thoroughly tested. The kinematics calculations have been benchmarked against the kinematics module of the ROOT Data Analysis Framework. Calculated neutron energy spectra have been validated against tabulated fusion reactivities and against an exact analytical expression for the thermonuclear fusion neutron spectrum, with good agreement. The DRESS code will be used as the core of a detailed synthetic diagnostic framework for neutron measurements at the JET and MAST tokamaks.
Lead Optimization Mapper: Automating free energy calculations for lead optimization
Liu, Shuai; Wu, Yujie; Lin, Teng; Abel, Robert; Redmann, Jonathan P.; Summa, Christopher M.; Jaber, Vivian R.; Lim, Nathan M.; Mobley, David L.
2013-01-01
Alchemical free energy calculations hold increasing promise as an aid to drug discovery efforts. However, applications of these techniques in discovery projects have been relatively few, partly because of the difficulty of planning and setting up calculations. Here, we introduce Lead Optimization Mapper, LOMAP, an automated algorithm to plan efficient relative free energy calculations between potential ligands within a substantial library of perhaps hundreds of compounds. In this approach, ligands are first grouped by structural similarity primarily based on the size of a (loosely defined) maximal common substructure, and then calculations are planned within and between sets of structurally related compounds. An emphasis is placed on ensuring that relative free energies can be obtained between any pair of compounds without combining the results of too many different relative free energy calculations (to avoid accumulation of error) and by providing some redundancy to allow for the possibility of error and consistency checking and provide some insight into when results can be expected to be unreliable. The algorithm is discussed in detail and a Python implementation, based on both Schrödinger's and OpenEye's APIs, has been made available freely under the BSD license. PMID:24072356
Metal-phthalocyanine ordered layers on Au(110): Metal-dependent adsorption energy
Massimi, Lorenzo Angelucci, Marco; Gargiani, Pierluigi; Betti, Maria Grazia; Montoro, Silvia; Mariani, Carlo
2014-06-28
Iron-phthalocyanine and cobalt-phthalocyanine chains, assembled along the Au(110)-(1×2) reconstructed channels, present a strong interaction with the Au metallic states, via the central metal ion. X-ray photoemission spectroscopy from the metal-2p core-levels and valence band high-resolution ultraviolet photoelectron spectroscopy bring to light signatures of the interaction of the metal-phthalocyanine single-layer with gold. The charge transfer from Au to the molecule causes the emerging of a metal-2p core level component at lower binding energy with respect to that measured in the molecular thin films, while the core-levels associated to the organic macrocycle (C and N 1s) are less influenced by the adsorption, and the macrocycles stabilize the interaction, inducing a strong interface dipole. Temperature Programmed Desorption experiments and photoemission as a function of temperature allow to estimate the adsorption energy for the thin-films, mainly due to the molecule-molecule van der Waals interaction, while the FePc and CoPc single-layers remain adsorbed on the Au surface up to at least 820 K.
Total-energy and pressure calculations for random substitutional alloys
Johnson, D.D. ); Nicholson, D.M. ); Pinski, F.J. ); Gyoerffy, B.L. ); Stocks, G.M. )
1990-05-15
We present the details and the derivation of density-functional-based expressions for the total energy and pressure for random substitutional alloys (RSA) using the Korringa-Kohn-Rostoker Green's-function approach in combination with the coherent-potential approximation (CPA) to treat the configurational averaging. This includes algebraic cancellation of various electronic core contributions to the total energy and pressure, as in ordered-solid muffin-tin-potential calculations. Thus, within the CPA, total-energy and pressure calculations for RSA have the same foundation and have been found to have the same accuracy as those obtained in similar calculations for ordered solids. Results of our calculations for the impurity formation energy, and for the bulk moduli, the lattice parameters, and the energy of mixing as a function of concentration in fcc Cu{sub {ital c}}Zn{sub 1{minus}{ital c}} alloys show that this generalized density-functional theory will be useful in studying alloy phase stability.
Ion beam energy spectrum calculation via dosimetry data deconvolution.
Harper-Slaboszewicz, Victor Jozef; Sharp, Andrew Clinton
2010-10-01
The energy spectrum of a H{sup +} beam generated within the HERMES III accelerator is calculated from dosimetry data to refine future experiments. Multiple layers of radiochromic film are exposed to the beam. A graphic user interface was written in MATLAB to align the film images and calculate the beam's dose depth profile. Singular value regularization is used to stabilize the unfolding and provide the H{sup +} beam's energy spectrum. The beam was found to have major contributions from 1 MeV and 8.5 MeV protons. The HERMES III accelerator is typically used as a pulsed photon source to experimentally obtain photon impulse response of systems due to high energy photons. A series of experiments were performed to explore the use of Hermes III to generate an intense pulsed proton beam. Knowing the beam energy spectrum allows for greater precision in experiment predictions and beam model verification.
Calculation of exchange energies using algebraic perturbation theory
Burrows, B. L.; Dalgarno, A.; Cohen, M.
2010-04-15
An algebraic perturbation theory is presented for efficient calculations of localized states and hence of exchange energies, which are the differences between low-lying states of the valence electron of a molecule, formed by the collision of an ion Y{sup +} with an atom X. For the case of a homonuclear molecule these are the gerade and ungerade states and the exchange energy is an exponentially decreasing function of the internuclear distance. For such homonuclear systems the theory is used in conjunction with the Herring-Holstein technique to give accurate exchange energies for a range of intermolecular separations R. Since the perturbation parameter is essentially 1/R, this method is suitable for large R. In particular, exchange energies are calculated for X{sub 2}{sup +} systems, where X is H, Li, Na, K, Rb, or Cs.
NASA Astrophysics Data System (ADS)
Khaled, K. F.
2010-09-01
The effects of thiourea derivatives, namely N-methyl thiourea (MTU), N-propyl thiourea (PTU) and N-allyl thiourea (ATU) on the corrosion behaviour of iron in 1.0 M solution of HNO 3 have been investigated in relation to the concentration of thiourea derivatives. The experimental data obtained using the techniques of weight loss, Tafel polarization and electrochemical impedance spectroscopy, EIS. The results showed that these compounds revealed a good corrosion inhibition, (ATU) being the most efficient and (MTU) the least. Computational studies have been used to find the most stable adsorption sites for thiourea derivatives. This information help to gain further insight about corrosion system, such as the most likely point of attack for corrosion on iron (1 1 0), the most stable site for thiourea derivatives adsorption and the binding energy of the adsorbed layer. The efficiency order of the inhibitors obtained by experimental results was verified by theoretical analysis.
NASA Astrophysics Data System (ADS)
Chen, Lanli; Wang, Xiaofang; Shi, Siqi; Cui, Yuanyuan; Luo, Hongjie; Gao, Yanfeng
2016-03-01
VO2 is an attractive material for application to thermochromic optoelectronic devices such as smart windows, and Ag/VO2 double-layered structure can effectively decrease the phase transition temperature (Tc) of VO2 thin film, which is very important for practical application of VO2. Previous works has shown that the decrease in phase transition temperature (Tc) seems to be relevant with the work function of VO2 in Ag/VO2 double-layered thin film, although the underlying mechanism of tuning its Tc by Ag incorporation and adsorption on the VO2(1 0 0) surface has been rarely investigated. Our first-principles calculations reveal that the adsorption of Ag atoms on the VO2(1 0 0) surface rather than incorporation of Ag exhibits a lower work function, which is ascribed to an integrated effect of charge transfer from Ag to VO2(1 0 0) surface and enhanced surface dipole moment. The results suggest that the decrease in work function of VO2 with Ag adsorption favors the reduction in Tc. The current findings are helpful to understand the fundamental mechanism for yielding high-efficiency VO2-based optoelectronic devices.
Sun, Xiongfei; Peng, Xing; Xu, Xianglan; Jin, Hua; Wang, Hongming; Wang, Xiang
2016-09-01
To explore metal oxide-support interactions and their effect, H2 adsorption and dissociation on PdO(101)/TiO2(110) films with different film thicknesses, in comparison with that on pure PdO(101) surface without TiO2(110) support, were studied by density functional theory calculation. A monolayer PdO(101) film supported on TiO2 facet shows different properties to a pure PdO(101) surface. On the monolayer PdO(101)/TiO2(110) film, TiO2 support leads to stronger molecular adsorption of H2 on coordinatively unsaturated Pd top sites than that on a pure PdO surface. H2 dissociation with the formation of OH was preferred thermodynamically but slightly unfavorable kinetically on the monolayer PdO film due to the TiO2 support effect. Graphical abstract On the monolayer PdO(101)/TiO2(110) film, the TiO2 support effect leads to stronger H2 molecular adsorption on coordinatively unsaturated Pd top sites than on pure PdO surface. H2 dissociation with the formation of OH is preferred thermodynamically but slightly unfavorable kinetically on the film due to the TiO2 support effect. PMID:27491853
Lu, Zhijiang; MacFarlane, John K; Gschwend, Philip M
2016-01-01
Black carbons (BCs) dominate the sorption of many hydrophobic organic compounds (HOCs) in soils and sediments, thereby reducing the HOCs' mobilities and bioavailabilities. However, we do not have data for diverse HOCs' sorption to BC because it is time-consuming and labor-intensive to obtain isotherms on soot and other BCs. In this study, we developed a frontal analysis chromatographic method to investigate the adsorption of 21 organic compounds with diverse functional groups to NIST diesel soot. This method was precise and time-efficient, typically taking only a few hours to obtain an isotherm. Based on 102 soot-carbon normalized sorption coefficients (KsootC) acquired at different sorbate concentrations, a sorbate-activity-dependent polyparameter linear free-energy relationship was established: logKsootC = (3.74 ± 0.11)V + ((-0.35 ± 0.02)log ai)E + (-0.62 ± 0.10)A + (-3.35 ± 0.11)B + (-1.45 ± 0.09); (N = 102, R(2) = 0.96, SE = 0.18), where V, E, A, and B are the sorbate's McGowan's characteristic volume, excess molar refraction, and hydrogen acidity and basicity, respectively; and ai is the sorbate's aqueous activity reflecting the system's approach to saturation. The difference in dispersive interactions with the soot versus with the water was the dominant factor encouraging adsorption, and H-bonding interactions discouraged this process. Using this relationship, soot-water and sediment-water or soil-water adsorption coefficients of HOCs of interest (PAHs and PCBs) were estimated and compared with the results reported in the literature. PMID:26587648
On the calculation of classical vibrational energy exchange
NASA Astrophysics Data System (ADS)
Gibbons, John P.; Stettler, John D.
1982-07-01
A three-dimensional, Monte Carlo classical model for the calculation of vibrational energy relaxation and transfer rates for both diatomic—monatomic and diatomic—diatomic systems was developed, analyzed and implemented. Mediation by internal angular momentum changes was demonstrated to be important in these energy transfer processes. This mechanism was incorporated into the model in order to achieve statistically significant results within reasonable computer running times. This made possible the extension of the model calculations to much lower temperatures than had been previously investigated. This calculational procedure was applied to Ar—O 2, to He—O 2 and to the near resonant CO—N 2 process at several temperatures between room temperature and 4000 K with the use of exponential repulsive intermolecular potential. Three different sets of potential parameters obtained from three independent sources were used. The results were compared to experiment.
The Calculation of Accurate Metal-Ligand Bond Energies
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W.; Partridge, Harry, III; Ricca, Alessandra; Arnold, James O. (Technical Monitor)
1997-01-01
The optimization of the geometry and calculation of zero-point energies are carried out at the B3LYP level of theory. The bond energies are determined at this level, as well as at the CCSD(T) level using very large basis sets. The successive OH bond energies to the first row transition metal cations are reported. For most systems there has been an experimental determination of the first OH. In general, the CCSD(T) values are in good agreement with experiment. The bonding changes from mostly covalent for the early metals to mostly electrostatic for the late transition metal systems.
Accurate calculation of diffraction-limited encircled and ensquared energy.
Andersen, Torben B
2015-09-01
Mathematical properties of the encircled and ensquared energy functions for the diffraction-limited point-spread function (PSF) are presented. These include power series and a set of linear differential equations that facilitate the accurate calculation of these functions. Asymptotic expressions are derived that provide very accurate estimates for the relative amount of energy in the diffraction PSF that fall outside a square or rectangular large detector. Tables with accurate values of the encircled and ensquared energy functions are also presented. PMID:26368873
Calculation of Mg(+)-ligand relative binding energies
NASA Technical Reports Server (NTRS)
Partridge, Harry; Bauschlicher, Charles W., Jr.
1992-01-01
The calculated relative binding energies of 16 organic molecules to Mg(+) are compared with experimental results where available. The geometries of the ligands and the Mg(+)-ligand complexes arc optimized at the self-consistent field level using a 6-31G* basis set. The Mg(+) binding energies are evaluated using second-order perturbation theory and basis sets of triple-sigma quality augmented with two sets of polarization functions. This level of theory is calibrated against higher levels of theory for selected systems. The computed binding energies are accurate to about 2 kcal/mol.
Three dimensional calculation of flux of low energy atmospheric neutrinos
NASA Technical Reports Server (NTRS)
Lee, H.; Bludman, S. A.
1985-01-01
Results of three-dimensional Monte Carlo calculation of low energy flux of atmospheric neutrinos are presented and compared with earlier one-dimensional calculations 1,2 valid at higher neutrino energies. These low energy neutrinos are the atmospheric background in searching for neutrinos from astrophysical sources. Primary cosmic rays produce the neutrino flux peaking at near E sub=40 MeV and neutrino intensity peaking near E sub v=100 MeV. Because such neutrinos typically deviate by 20 approximately 30 from the primary cosmic ray direction, three-dimensional effects are important for the search of atmospheric neutrinos. Nevertheless, the background of these atmospheric neutrinos is negligible for the detection of solar and supernova neutrinos.
NASA Astrophysics Data System (ADS)
Furmaniak, Sylwester; Terzyk, Artur P.; Gauden, Piotr A.; Harris, Peter J. F.; Kowalczyk, Piotr
2009-08-01
Using the virtual porous carbon model proposed by Harris et al, we study the effect of carbon surface oxidation on the pore size distribution (PSD) curve determined from simulated Ar, N2 and CO2 isotherms. It is assumed that surface oxidation is not destructive for the carbon skeleton, and that all pores are accessible for studied molecules (i.e., only the effect of the change of surface chemical composition is studied). The results obtained show two important things, i.e., oxidation of the carbon surface very slightly changes the absolute porosity (calculated from the geometric method of Bhattacharya and Gubbins (BG)); however, PSD curves calculated from simulated isotherms are to a greater or lesser extent affected by the presence of surface oxides. The most reliable results are obtained from Ar adsorption data. Not only is adsorption of this adsorbate practically independent from the presence of surface oxides, but, more importantly, for this molecule one can apply the slit-like model of pores as the first approach to recover the average pore diameter of a real carbon structure. For nitrogen, the effect of carbon surface chemical composition is observed due to the quadrupole moment of this molecule, and this effect shifts the PSD curves compared to Ar. The largest differences are seen for CO2, and it is clearly demonstrated that the PSD curves obtained from adsorption isotherms of this molecule contain artificial peaks and the average pore diameter is strongly influenced by the presence of electrostatic adsorbate-adsorbate as well as adsorbate-adsorbent interactions.
Furmaniak, Sylwester; Terzyk, Artur P; Gauden, Piotr A; Harris, Peter J F; Kowalczyk, Piotr
2009-08-01
Using the virtual porous carbon model proposed by Harris et al, we study the effect of carbon surface oxidation on the pore size distribution (PSD) curve determined from simulated Ar, N(2) and CO(2) isotherms. It is assumed that surface oxidation is not destructive for the carbon skeleton, and that all pores are accessible for studied molecules (i.e., only the effect of the change of surface chemical composition is studied). The results obtained show two important things, i.e., oxidation of the carbon surface very slightly changes the absolute porosity (calculated from the geometric method of Bhattacharya and Gubbins (BG)); however, PSD curves calculated from simulated isotherms are to a greater or lesser extent affected by the presence of surface oxides. The most reliable results are obtained from Ar adsorption data. Not only is adsorption of this adsorbate practically independent from the presence of surface oxides, but, more importantly, for this molecule one can apply the slit-like model of pores as the first approach to recover the average pore diameter of a real carbon structure. For nitrogen, the effect of carbon surface chemical composition is observed due to the quadrupole moment of this molecule, and this effect shifts the PSD curves compared to Ar. The largest differences are seen for CO(2), and it is clearly demonstrated that the PSD curves obtained from adsorption isotherms of this molecule contain artificial peaks and the average pore diameter is strongly influenced by the presence of electrostatic adsorbate-adsorbate as well as adsorbate-adsorbent interactions. PMID:21828590
Composite electron propagator methods for calculating ionization energies
NASA Astrophysics Data System (ADS)
Díaz-Tinoco, Manuel; Dolgounitcheva, O.; Zakrzewski, V. G.; Ortiz, J. V.
2016-06-01
Accurate ionization energies of molecules may be determined efficiently with composite electron-propagator (CEP) techniques. These methods estimate the results of a calculation with an advanced correlation method and a large basis set by performing a series of more tractable calculations in which large basis sets are used with simpler approximations and small basis sets are paired with more demanding correlation techniques. The performance of several CEP methods, in which diagonal, second-order electron propagator results with large basis sets are combined with higher-order results obtained with smaller basis sets, has been tested for the ionization energies of closed-shell molecules from the G2 set. Useful compromises of accuracy and computational efficiency employ complete-basis-set extrapolation for second-order results and small basis sets in third-order, partial third-order, renormalized partial-third order, or outer valence Green's function calculations. Analysis of results for vertical as well as adiabatic ionization energies leads to specific recommendations on the best use of regular and composite methods. Results for 22 organic molecules of interest in the design of photovoltaic devices, benzo[a]pyrene, Mg-octaethylporphyrin, and C60 illustrate the capabilities of CEP methods for calculations on large molecules.
Calculating Free Energy Changes in Continuum Solvation Models.
Ho, Junming; Ertem, Mehmed Z
2016-02-25
We recently showed for a large data set of pKas and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents [ Phys. Chem. Chem. Phys. 2015 , 17 , 2859 ]. In this paper, we significantly expand the scope of our study to examine the suitability of this approach for calculating general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMD-M062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems. This includes cluster-continuum schemes for pKa calculations as well as various neutral, radical, and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar-the mean errors for Gibbs free energy changes of neutral and ionic reactions are approximately 5 and 25 kJ mol(-1), respectively. In systems where there are significant structural changes due to solvation, as is the case for certain ionic transition states and amino acids, the direct approach generally afford free energy changes that are in better agreement with experiment. PMID:26878566
Composite electron propagator methods for calculating ionization energies.
Díaz-Tinoco, Manuel; Dolgounitcheva, O; Zakrzewski, V G; Ortiz, J V
2016-06-14
Accurate ionization energies of molecules may be determined efficiently with composite electron-propagator (CEP) techniques. These methods estimate the results of a calculation with an advanced correlation method and a large basis set by performing a series of more tractable calculations in which large basis sets are used with simpler approximations and small basis sets are paired with more demanding correlation techniques. The performance of several CEP methods, in which diagonal, second-order electron propagator results with large basis sets are combined with higher-order results obtained with smaller basis sets, has been tested for the ionization energies of closed-shell molecules from the G2 set. Useful compromises of accuracy and computational efficiency employ complete-basis-set extrapolation for second-order results and small basis sets in third-order, partial third-order, renormalized partial-third order, or outer valence Green's function calculations. Analysis of results for vertical as well as adiabatic ionization energies leads to specific recommendations on the best use of regular and composite methods. Results for 22 organic molecules of interest in the design of photovoltaic devices, benzo[a]pyrene, Mg-octaethylporphyrin, and C60 illustrate the capabilities of CEP methods for calculations on large molecules. PMID:27305999
Binding Energy Calculations for Novel Ternary Ionic Lattices
NASA Astrophysics Data System (ADS)
Rodríguez-Mijangos, Ricardo; Vazquez-Polo, Gustavo
2002-03-01
Theoretical calculations for the binding energy between metalic ions and negative ions on a novel ternary ionic lattice is carried out for several solid solutions prepared with different concentrations and characterized recently (1). The ternary lattices that reach a good miscibility are: KCl(x)KBr(y)RbCl(z) in three different concentrations: (x=y=z=0.33), (x=0.5, y=0.25, z=0.25) and (x=0.33, y=0.07, z=0.60). The binding energy for these novel structures is calculated from the lattice constants obtained by X ray diffractometry analysis performed on the samples and the Vegard law (2). For the repulsive force exponent m, an average of the m values was considered. The energy values obtained by the Born´expression are compared with corresponding energy values from the lattice with more complex expressions, such as the Born Mayer, Born-Van der Walls. There is a good aggreement between all these calculations. (1)R. R. Mijangos, A. Cordero-Borboa, E. Alvarez, M. Cervantes, Physics Letters A 282 (2001) 195-200. (2) G. Vazquez-Polo, R. R. Mijangos et al. Revista Mexicana de Fisica, 47, Diciembre 2001. In Press.
Ultrasonic energy in liposome production: process modelling and size calculation.
Barba, A A; Bochicchio, S; Lamberti, G; Dalmoro, A
2014-04-21
The use of liposomes in several fields of biotechnology, as well as in pharmaceutical and food sciences is continuously increasing. Liposomes can be used as carriers for drugs and other active molecules. Among other characteristics, one of the main features relevant to their target applications is the liposome size. The size of liposomes, which is determined during the production process, decreases due to the addition of energy. The energy is used to break the lipid bilayer into smaller pieces, then these pieces close themselves in spherical structures. In this work, the mechanisms of rupture of the lipid bilayer and the formation of spheres were modelled, accounting for how the energy, supplied by ultrasonic radiation, is stored within the layers, as the elastic energy due to the curvature and as the tension energy due to the edge, and to account for the kinetics of the bending phenomenon. An algorithm to solve the model equations was designed and the relative calculation code was written. A dedicated preparation protocol, which involves active periods during which the energy is supplied and passive periods during which the energy supply is set to zero, was defined and applied. The model predictions compare well with the experimental results, by using the energy supply rate and the time constant as fitting parameters. Working with liposomes of different sizes as the starting point of the experiments, the key parameter is the ratio between the energy supply rate and the initial surface area. PMID:24647821
NASA Astrophysics Data System (ADS)
Xu, Fei; Tang, Zhiwei; Huang, Siqi; Chen, Luyi; Liang, Yeru; Mai, Weicong; Zhong, Hui; Fu, Ruowen; Wu, Dingcai
2015-06-01
Exceptionally large surface area and well-defined nanostructure are both critical in the field of nanoporous carbons for challenging energy and environmental issues. The pursuit of ultrahigh surface area while maintaining definite nanostructure remains a formidable challenge because extensive creation of pores will undoubtedly give rise to the damage of nanostructures, especially below 100 nm. Here we report that high surface area of up to 3,022 m2 g-1 can be achieved for hollow carbon nanospheres with an outer diameter of 69 nm by a simple carbonization procedure with carefully selected carbon precursors and carbonization conditions. The tailor-made pore structure of hollow carbon nanospheres enables target-oriented applications, as exemplified by their enhanced adsorption capability towards organic vapours, and electrochemical performances as electrodes for supercapacitors and sulphur host materials for lithium-sulphur batteries. The facile approach may open the doors for preparation of highly porous carbons with desired nanostructure for numerous applications.
Adsorption of hydrogen on boron-doped graphene: A first-principles prediction
Zhou, Yungang; Zu, Xiaotao T.; Gao, Fei; Nie, JL; Xiao, H. Y.
2009-01-01
The doping effects of boron on the atomic adsorption of hydrogen on graphene have been investigated using density functional theory calculations. The hydrogen adsorption energies and electronic structures have been considered for pristine and B-doped graphene with the adsorption of hydrogen on top of carbon or boron atom. It is found that the B-doping forms an electron-deficient structure, and decreases the hydrogen adsorption energy dramatically. For the adsorption of hydrogen on top of other sites, similar results also have been found. These results indicate that the hydrogen storage capacity is improved by the doping of B atom.
Parhi, Purnendu; Golas, Avantika; Barnthip, Naris; Noh, Hyeran; Vogler, Erwin A.
2009-01-01
Silanized-glass-particle adsorbent capacities are extracted from adsorption isotherms of human serum albumin (HSA, 66 kDa), immunoglobulin G (IgG, 160 kDa), fibrinogen (Fib, 341 kDa), and immunoglobulin M (IgM, 1000 kDa) for adsorbent surface energies sampling the observable range of water wettability. Adsorbent capacity expressed as either mass-or-moles per-unit-adsorbent-area increases with protein molecular weight (MW) in a manner that is quantitatively inconsistent with the idea that proteins adsorb as a monolayer at the solution-material interface in any physically-realizable configuration or state of denaturation. Capacity decreases monotonically with increasing adsorbent hydrophilicity to the limit-of-detection (LOD) near τo = 30 dyne/cm (θ~65o) for all protein/surface combinations studied (where τo≡γlvocosθ is the water adhesion tension, γlvo is the interfacial tension of pure-buffer solution, and θ is the buffer advancing contact angle). Experimental evidence thus shows that adsorbent capacity depends on both adsorbent surface energy and adsorbate size. Comparison of theory to experiment implies that proteins do not adsorb onto a two-dimensional (2D) interfacial plane as frequently depicted in the literature but rather partition from solution into a three-dimensional (3D) interphase region that separates the physical surface from bulk solution. This interphase has a finite volume related to the dimensions of hydrated protein in the adsorbed state (defining “layer” thickness). The interphase can be comprised of a number of adsorbed-protein layers depending on the solution concentration in which adsorbent is immersed, molecular volume of the adsorbing protein (proportional to MW), and adsorbent hydrophilicity. Multilayer adsorption accounts for adsorbent capacity over-and-above monolayer and is inconsistent with the idea that protein adsorbs to surfaces primarily through protein/surface interactions because proteins within second (or higher
Density functional study of the cysteine adsorption on Au nanoclusters
NASA Astrophysics Data System (ADS)
Pérez, L. A.; López-Lozano, X.; Garzón, I. L.
2009-04-01
The adsorption of the cysteine amino acid (H-SCβH2-CαH-NH2-COOH) on the Au55 cluster is investigated through density functional theory calculations. Two isomers, with icosahedral (Ih) and chiral (C1) geometries, of the Au55 cluster are used to calculate the adsorption energy of the cysteine on different facets of these isomers. Results, only involving the S(thiolate)-Au bonding show that the higher adsorption energies are obtained when the sulfur atom is bonded to an asymmetrical bridge site at the facet containing Au atoms with the lowest coordination of the C1 cluster isomer.
Self-consistent calculations of alpha-decay energies
Tolokonnikov, S. V.; Lutostansky, Yu. S.; Saperstein, E. E.
2013-06-15
On the basis of the self-consistent theory of finite Fermi systems, the energies of alphadecay chains were calculated for several new superheavy nuclei discovered recently in experiments of the Dubna-Livermore Collaboration headed by Yu.Ts. Oganessian. The approach in question is implemented on the basis of the generalized method of the density functional proposed by Fayans and his coauthors. The version used here relies on the functional DF3-a proposed recently for describing a wide array of nuclear data, including data on superheavy nuclei. A detailed comparison of the results obtained on this basis with the predictions of different approaches, including the self-consistent Skyrme-Hartree-Fock method, the micro-macro method in the version developed by Sobiczewski and his coauthors, and the phenomenological method of Liran and his coauthors, is performed. The resulting alpha-decay energies are used to calculate respective lifetimes with the aid of the phenomenological Parkhomenko-Sobiczewski formula.
Improved initial guess for minimum energy path calculations.
Smidstrup, Søren; Pedersen, Andreas; Stokbro, Kurt; Jónsson, Hannes
2014-06-01
A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of pairwise distances at each discretization point along the path and the nudged elastic band method then used to find an optimal path on this image dependent pair potential (IDPP) surface. This provides an initial path for the more computationally intensive calculations of a minimum energy path on an energy surface obtained, for example, by ab initio or density functional theory. The optimal path on the IDPP surface is significantly closer to a minimum energy path than a linear interpolation of the Cartesian coordinates and, therefore, reduces the number of iterations needed to reach convergence and averts divergence in the electronic structure calculations when atoms are brought too close to each other in the initial path. The method is illustrated with three examples: (1) rotation of a methyl group in an ethane molecule, (2) an exchange of atoms in an island on a crystal surface, and (3) an exchange of two Si-atoms in amorphous silicon. In all three cases, the computational effort in finding the minimum energy path with DFT was reduced by a factor ranging from 50% to an order of magnitude by using an IDPP path as the initial path. The time required for parallel computations was reduced even more because of load imbalance when linear interpolation of Cartesian coordinates was used. PMID:24907989
Improved initial guess for minimum energy path calculations
Smidstrup, Søren; Pedersen, Andreas; Stokbro, Kurt
2014-06-07
A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of pairwise distances at each discretization point along the path and the nudged elastic band method then used to find an optimal path on this image dependent pair potential (IDPP) surface. This provides an initial path for the more computationally intensive calculations of a minimum energy path on an energy surface obtained, for example, by ab initio or density functional theory. The optimal path on the IDPP surface is significantly closer to a minimum energy path than a linear interpolation of the Cartesian coordinates and, therefore, reduces the number of iterations needed to reach convergence and averts divergence in the electronic structure calculations when atoms are brought too close to each other in the initial path. The method is illustrated with three examples: (1) rotation of a methyl group in an ethane molecule, (2) an exchange of atoms in an island on a crystal surface, and (3) an exchange of two Si-atoms in amorphous silicon. In all three cases, the computational effort in finding the minimum energy path with DFT was reduced by a factor ranging from 50% to an order of magnitude by using an IDPP path as the initial path. The time required for parallel computations was reduced even more because of load imbalance when linear interpolation of Cartesian coordinates was used.
Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm
NASA Technical Reports Server (NTRS)
Darve, Eric; Wilson, Micahel A.; Pohorille, Andrew
2000-01-01
One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous
Non-Equilibrium Properties from Equilibrium Free Energy Calculations
NASA Technical Reports Server (NTRS)
Pohorille, Andrew; Wilson, Michael A.
2012-01-01
Calculating free energy in computer simulations is of central importance in statistical mechanics of condensed media and its applications to chemistry and biology not only because it is the most comprehensive and informative quantity that characterizes the eqUilibrium state, but also because it often provides an efficient route to access dynamic and kinetic properties of a system. Most of applications of equilibrium free energy calculations to non-equilibrium processes rely on a description in which a molecule or an ion diffuses in the potential of mean force. In general case this description is a simplification, but it might be satisfactorily accurate in many instances of practical interest. This hypothesis has been tested in the example of the electrodiffusion equation . Conductance of model ion channels has been calculated directly through counting the number of ion crossing events observed during long molecular dynamics simulations and has been compared with the conductance obtained from solving the generalized Nernst-Plank equation. It has been shown that under relatively modest conditions the agreement between these two approaches is excellent, thus demonstrating the assumptions underlying the diffusion equation are fulfilled. Under these conditions the electrodiffusion equation provides an efficient approach to calculating the full voltage-current dependence routinely measured in electrophysiological experiments.
Free energy calculations for a flexible water model.
Habershon, Scott; Manolopoulos, David E
2011-11-28
In this work, we consider the problem of calculating the classical free energies of liquids and solids for molecular models with intramolecular flexibility. We show that thermodynamic integration from the fully-interacting solid of interest to a Debye crystal reference state, with anisotropic harmonic interactions derived from the Hessian of the original crystal, provides a straightforward route to calculating the Gibbs free energy of the solid. To calculate the molecular liquid free energy, it is essential to correctly account for contributions from both intermolecular and intramolecular motion; we employ thermodynamic integration to a Lennard-Jones reference fluid, coupled with direct evaluation of the molecular ro-vibrational partition function. These approaches are used to study the low-pressure classical phase diagram of the flexible q-TIP4P/F water model. We find that, while the experimental ice-I/liquid and ice-III/liquid coexistence lines are described reasonably well by this model, the ice-II phase is predicted to be metastable. In light of this finding, we go on to examine how the coupling between intramolecular flexibility and intermolecular interactions influences the computed phase diagram by comparing our results with those of the underlying rigid-body water model. PMID:21887423
Free energy calculation of permeation through aquaporin-5
NASA Astrophysics Data System (ADS)
Bastien, David
The work of this paper continues upon the large area of research being done on aquaporins (AQPs). AQPs are proteins that take on the role of facilitating the transfer of substances, mainly water, across cell membranes. There are many different types of AQPs, with each of these highly selective proteins conducting only certain solutes, along with unique permeability rates. The permeation characteristics of aquaporins rely mostly on the residue hydrophobicity and steric restraints of the aromatic arginine (ar/R) region of the protein channel. The purpose of this paper is to analyze the structures of aquaporin-5 (AQP5) and aquaglycerolporin (Glpf), including a radius profile of the respective protein channels, and to compare them to permeation events using steered molecular dynamics (SMD) pulling simulations. Two in silico experiments are performed in order to achieve the free Energy landscape of a single water molecule permeating through the four channels of both Aqp5 and GlpF. The equilibrium free energy curves are calculated from the non-equilibrium, irreversible work measurements using the fluctuation-dissipation theorem (FDT) of Brownian dynamicis (BD). The free energy profiles are then compared and related to the structural profiles of AQP5 and GlpF. The change in free energy across the ar/R region in AQP5 is found to be reasonably larger than that of GlpF. The free energy profiles of AQP5 and GlpF agree with the diameter profile of the channels respectively. Furthermore, free energy calculations are computed for the permeation of Na+ and Cl- ions through the central pore of Aqp5, which provide some insight into the structural mechanisms of AQP5. The free energy barrier for ion transport through the central pore is found to be very large, peaking at around 11 Kcal/mol for chloride and 20 Kcal/mol for sodium.
Zhen, Wenlong; Gao, Haibo; Tian, Bin; Ma, Jiantai; Lu, Gongxuan
2016-05-01
An effective cocatalyst is crucial for enhancing the visible photocatalytic performance of the hydrogen generation reaction. By using density-functional theory (DFT) and frontier molecular orbital (FMO) theory calculation analysis, the hydrogen adsorption free energy (ΔGH) of Ni-Mo alloy (458 kJ·mol(-1)) is found to be lower than that of Ni itself (537 kJ·mol(-1)). Inspired by these results, the novel, highly efficient cocatalyst NiMo@MIL-101 for photocatalysis of the hydrogen evolution reaction (HER) was fabricated using the double solvents method (DSM). In contrast with Ni@MIL-101 and Mo@MIL-101, NiMo@MIL-101 exhibited an excellent photocatalytic performance (740.2 μmol·h(-1) for HER), stability, and high apparent quantum efficiency (75.7%) under 520 nm illumination at pH 7. The NiMo@MIL-101 catalyst also showed a higher transient photocurrent, lower overpotential (-0.51 V), and longer fluorescence lifetime (1.57 ns). The results uncover the dependence of the photocatalytic activity of HER on the ΔGH of Ni-Mo (MoNi4) alloy nanoclusters, i.e., lower ΔGH corresponding to higher HER activity for the first time. The NiMo@MIL-101 catalyst could be a promising candidate to replace precious-metal catalysts of the HER. PMID:27070204
Methanol adsorption on the clean CeO₂(111) surface: A density functional theory study
Mei, Donghai; Deskins, N. Aaron; Dupuis, Michel; Ge, Qingfeng
2007-07-19
Molecular and dissociative adsorption of methanol at various sites on the stoichiometric CeO₂(111) surface have been studied using density functional theory periodic calculations. At 0.25 monolayer (ML) coverage, the dissociative adsorption with an adsorption energy of 0.55 eV is slightly favored. The most stable state is the dissociative adsorption of methanol via C-H bond breaking, forming a coadsorbed hydroxymethyl group and hydrogen adatom on two separate O₃C surface sites. The strongest molecular adsorption occurs through an O-Ce₇subC connection with an adsorption energy of 0.48 eV. At methanol coverage of 0.5 ML, the dissociative adsorption and the molecular adsorption became competitive. The adsorption energy per methanol molecule for both adsorption modes falls into a narrow range of 0.46-0.55 eV. As methanol coverage increases beyond 0.5 ML, the molecular adsorption becomes more energetically favorable than the dissociative adsorption because of the attractive hydrogen bonding between coadsorbed methanol molecules. At full monolayer, the adsorption energy of molecular adsorption is 0.40 eV per molecule while the adsorption energy for total dissociative adsorption of methanol is only 0.17 eV. The results at different methanol coverages indicate that methanol can adsorb on a defect-free CeO₂(111) surface, which are also consistent with experimental observations. This research was performed using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory, which is a U.S. Department of Energy national scientific user facility located at Pacific Northwest National Laboratory (PNNL) in Richland, Washington. Computing time was made available under a Computational Grand Challenge “Computational Catalysis”. This work also financially supported by the Laboratory Directed Research and Development project of PNNL.
Variational calculations of the HT{sup +} rovibrational energies
Bekbaev, A. K.; Korobov, V. I.; Dineykhan, M.
2011-04-15
In this Brief Report, we use the exponential explicitly correlated variational basis set of the type exp(-{alpha}{sub n}R-{beta}{sub n}r{sub 1}-{gamma}{sub n}r{sub 2}) to calculate systematically the nonrelativistic bound-state energies for the hydrogen molecular ion HT{sup +}. We perform calculations for the states of the total orbital angular momentum L=0 and 1 with the complete set of vibrational quantum numbers v= 0-23, as well as for the states of L= 2-5 and v= 0-5. The E1 dipole transition moments, which are of importance for the planning of spectroscopic laser experiments, have been obtained as well.
Prediction of Protein Solubility from Calculation of Transfer Free Energy
Tjong, Harianto; Zhou, Huan-Xiang
2008-01-01
Solubility plays a major role in protein purification, and has serious implications in many diseases. We studied the effects of pH and mutations on protein solubility by calculating the transfer free energy from the condensed phase to the solution phase. The condensed phase was modeled as an implicit solvent, with a dielectric constant lower than that of water. To account for the effects of pH, the protonation states of titratable side chains were sampled by running constant-pH molecular dynamics simulations. Conformations were then selected for calculations of the electrostatic solvation energy: once for the condensed phase, and once for the solution phase. The average transfer free energy from the condensed phase to the solution phase was found to predict reasonably well the variations in solubility of ribonuclease Sa and insulin with pH. This treatment of electrostatic contributions combined with a similar approach for nonelectrostatic contributions led to a quantitative rationalization of the effects of point mutations on the solubility of ribonuclease Sa. This study provides valuable insights into the physical basis of protein solubility. PMID:18515380
SCALE Continuous-Energy Eigenvalue Sensitivity Coefficient Calculations
Perfetti, Christopher M.; Rearden, Bradley T.; Martin, William R.
2016-02-25
Sensitivity coefficients describe the fractional change in a system response that is induced by changes to system parameters and nuclear data. The Tools for Sensitivity and UNcertainty Analysis Methodology Implementation (TSUNAMI) code within the SCALE code system makes use of eigenvalue sensitivity coefficients for an extensive number of criticality safety applications, including quantifying the data-induced uncertainty in the eigenvalue of critical systems, assessing the neutronic similarity between different critical systems, and guiding nuclear data adjustment studies. The need to model geometrically complex systems with improved fidelity and the desire to extend TSUNAMI analysis to advanced applications has motivated the developmentmore » of a methodology for calculating sensitivity coefficients in continuous-energy (CE) Monte Carlo applications. The Contributon-Linked eigenvalue sensitivity/Uncertainty estimation via Tracklength importance CHaracterization (CLUTCH) and Iterated Fission Probability (IFP) eigenvalue sensitivity methods were recently implemented in the CE-KENO framework of the SCALE code system to enable TSUNAMI-3D to perform eigenvalue sensitivity calculations using continuous-energy Monte Carlo methods. This work provides a detailed description of the theory behind the CLUTCH method and describes in detail its implementation. This work explores the improvements in eigenvalue sensitivity coefficient accuracy that can be gained through the use of continuous-energy sensitivity methods and also compares several sensitivity methods in terms of computational efficiency and memory requirements.« less
Exploiting the Properties of Aquaporin to Calculate Free Energy
NASA Astrophysics Data System (ADS)
Espejel, Hugo; Chen, Liao
2010-03-01
Aquaporins' (AQPs) main purpose is to facilitate the transfer of water molecules through a molecular membrane. We can calculate the free energy of the AQP system when water permeates through it. This is performed using the Visual Molecular Dynamics (VMD) and the Nanoscale Molecular Dynamics (NAMD) programs. In our first set of experiments, AQP is submerged in a body of water, in which case a water molecule near AQP is pulled through the protein. The data is then used to calculate the free energy using two different equations: the Jarzynski equality and the fluctuation-dissipation theorem. The values from both equations are then compared to examine their accuracy. The second set of experiments has the same set up, but now AQP is embedded in a lipid bilayer. We found that both equations give values that are much smaller than kT. This verifies that AQP is a channel for water molecules because the pulling of water gives constant values of free energy. We also found that the water molecules' negative poles were all pointing towards the center of the AQP channel. This means that the process of proton transport in AQP is overwhelmingly difficult.
Zell, Zachary A; Isa, Lucio; Ilg, Patrick; Leal, L Gary; Squires, Todd M
2014-01-14
The self-assembly of polymer-based surfactants and nanoparticles on fluid-fluid interfaces is central to many applications, including dispersion stabilization, creation of novel 2D materials, and surface patterning. Very often these processes involve compressing interfacial monolayers of particles or polymers to obtain a desired material microstructure. At high surface pressures, however, even highly interfacially active objects can desorb from the interface. Methods of directly measuring the energy which keeps the polymer or particles bound to the interface (adsorption/desorption energies) are therefore of high interest for these processes. Moreover, though a geometric description linking adsorption energy and wetting properties through the definition of a contact angle can be established for rigid nano- or microparticles, such a description breaks down for deformable or aggregating objects. Here, we demonstrate a technique to quantify desorption energies directly, by comparing surface pressure-density compression measurements using a Wilhelmy plate and a custom-microfabricated deflection tensiometer. We focus on poly(ethylene oxide)-based polymers and nanoparticles. For PEO-based homo- and copolymers, the adsorption energy of PEO chains scales linearly with molecular weight and can be tuned by changing the subphase composition. Moreover, the desorption surface pressure of PEO-stabilized nanoparticles corresponds to the saturation surface pressure for spontaneously adsorbed monolayers, yielding trapping energies of ∼10(3) k(B)T. PMID:24328531
Effect of nitrogen doping of graphene oxide on hydrogen and hydroxyl adsorption
NASA Astrophysics Data System (ADS)
Min, Byeong June; Jeong, Hae Kyung
2014-05-01
We investigate how nitrogen-doping affects the hydrogen (H) and the hydroxyl (OH) adsorption on graphene oxide (GO) and on nitrogen-doped GO (NGO) via pseudopotential plane wave density functional calculations within the local spin density approximation. We find that the nitrogendoping brings about drastic changes in the hydrogen and the hydroxyl adsorption energetics, but its effects depend sensitively on the nitrogen configuration in NGO. The H and the OH adsorption energies are comparable only for pyrrolic NGO. In GO and quarternary NGO, the H adsorption energy is greater than the OH adsorption energy while the trend is reversed in pyridinic NGO. Also, the OH adsorption process is less affected by nitrogen-doping than the H adsorption is.
Parquet decomposition calculations of the electronic self-energy
NASA Astrophysics Data System (ADS)
Gunnarsson, O.; Schäfer, T.; LeBlanc, J. P. F.; Merino, J.; Sangiovanni, G.; Rohringer, G.; Toschi, A.
2016-06-01
The parquet decomposition of the self-energy into classes of diagrams, those associated with specific scattering processes, can be exploited for different scopes. In this work, the parquet decomposition is used to unravel the underlying physics of nonperturbative numerical calculations. We show the specific example of dynamical mean field theory and its cluster extensions [dynamical cluster approximation (DCA)] applied to the Hubbard model at half-filling and with hole doping: These techniques allow for a simultaneous determination of two-particle vertex functions and self-energies and, hence, for an essentially "exact" parquet decomposition at the single-site or at the cluster level. Our calculations show that the self-energies in the underdoped regime are dominated by spin-scattering processes, consistent with the conclusions obtained by means of the fluctuation diagnostics approach [O. Gunnarsson et al., Phys. Rev. Lett. 114, 236402 (2015), 10.1103/PhysRevLett.114.236402]. However, differently from the latter approach, the parquet procedure displays important changes with increasing interaction: Even for relatively moderate couplings, well before the Mott transition, singularities appear in different terms, with the notable exception of the predominant spin channel. We explain precisely how these singularities, which partly limit the utility of the parquet decomposition and, more generally, of parquet-based algorithms, are never found in the fluctuation diagnostics procedure. Finally, by a more refined analysis, we link the occurrence of the parquet singularities in our calculations to a progressive suppression of charge fluctuations and the formation of a resonance valence bond state, which are typical hallmarks of a pseudogap state in DCA.
Investigation of Multipole Electrostatics in Hydration Free Energy Calculations
Shi, Yue; Wu, Chuanjie; Ponder, Jay W.; Ren, Pengyu
2010-01-01
Hydration free energy (HFE) is generally used for evaluating molecular solubility, which is an important property for pharmaceutical and chemical engineering processes. Accurately predicting HFE is also recognized as one fundamental capability of molecular mechanics force field. Here we present a systematic investigation on HFE calculations with AMOEBA polarizable force field at various parameterization and simulation conditions. The HFEs of seven small organic molecules have been obtained alchemically using the Bennett Acceptance Ratio (BAR) method. We have compared two approaches to derive the atomic multipoles from quantum mechanical (QM) calculations: one directly from the new distributed multipole analysis (DMA) and the other involving fitting to the electrostatic potential around the molecules. Wave functions solved at the MP2 level with four basis sets (6-311G*, 6-311++G(2d,2p), cc-pVTZ, and aug-cc-pVTZ) are used to derive the atomic multipoles. HFEs from all four basis sets show a reasonable agreement with experimental data (root mean square error 0.63 kcal/mol for aug-ccpVTZ). We conclude that aug-cc-pVTZ gives the best performance when used with AMOEBA, and 6-311++G(2d,2p) is comparable but more efficient for larger systems. The results suggest that the inclusion of diffuse basis functions is important for capturing intermolecular interactions. The effect of long-range correction to van der Waals interaction on the hydration free energies is about 0.1 kcal/mol when the cutoff is 12Å, and increases linearly with the number of atoms in the solute/ligand. In addition, we also discussed the results from a hybrid approach that combines polarizable solute with fixed-charge water in the hydration free energy calculation. PMID:20925089
Empirically corrected HEAT method for calculating atomization energies
Brand, Holmann V
2008-01-01
We describe how to increase the accuracy ofthe most recent variants ofthe HEAT method for calculating atomization energies of molecules by means ofextremely simple empirical corrections that depend on stoichiometry and the number ofunpaired electrons in the molecule. Our corrections reduce the deviation from experiment for all the HEAT variants. In particular, our corrections reduce the average absolute deviation and the root-mean-square deviation ofthe 456-QP variant to 0.18 and 0.23 kJoule/mol (i.e., 0.04 and 0.05 kcallmol), respectively.
Multiple scattering calculations of relativistic electron energy loss spectra
NASA Astrophysics Data System (ADS)
Jorissen, K.; Rehr, J. J.; Verbeeck, J.
2010-04-01
A generalization of the real-space Green’s-function approach is presented for ab initio calculations of relativistic electron energy loss spectra (EELS) which are particularly important in anisotropic materials. The approach incorporates relativistic effects in terms of the transition tensor within the dipole-selection rule. In particular, the method accounts for relativistic corrections to the magic angle in orientation resolved EELS experiments. The approach is validated by a study of the graphite CK edge, for which we present an accurate magic angle measurement consistent with the predicted value.
Model for analytical calculation of nuclear photoabsorption at intermediate energies
NASA Astrophysics Data System (ADS)
Hütt, M.-Th.; Milstein, A. I.; Schumacher, M.
1997-02-01
The universal curve {σ}/{A} of nuclear photoabsorption is investigated within a Fermi gas model of nuclear matter. An energy range from pion threshold up to 400 MeV is considered. The interactions between nucleon, pion, Δ-isobar and photon are considered in the non-relativistic approximation with corrections of the order {1}/{M} taken into account with respect to proton mass. Analytical expressions are obtained, in which the influence of nuclear correlations and two-nucleon contributions is studied explicitly. The contributions of real and virtual pions are found to be sufficient to obtain agreement with experimental data in this energy range. An extension of the model calculation to nucleon knock-out reactions is discussed.
Calculated photoelectron pitch angle and energy spectra. [in upper atmosphere
NASA Technical Reports Server (NTRS)
Mantas, G. P.; Bowhill, S. A.
1974-01-01
Calculations of the steady-state photoelectron energy and angular distribution in the altitude region between 120 and 1000 km are presented. The distribution is found to be isotropic at all altitudes below 250 km, while above this altitude anisotropies in both pitch angle and energy are found. The isotropy found in the angular distribution below 250 km implies that photoelectron transport below 250 km is insignificant, while the angular anisotropy found above this altitude implies a net photoelectron current in the upward direction. The energy anisotropy above 500 km arises from the selective backscattering of the low energy photoelectron population of the upward flux component by Coulomb collisions with the ambient ions. The total photoelectron flux attains its maximum value between about 40 and 70 km above the altitude at which the photoelectron production rate is maximum. The displacement of the maximum of the equilibrium flux is attributed to an increasing (with altitude) photoelectron lifetime. Photoelectrons at altitudes above that where the flux is maximum are on the average more energetic than those below that altitude.
Xu, Fei; Tang, Zhiwei; Huang, Siqi; Chen, Luyi; Liang, Yeru; Mai, Weicong; Zhong, Hui; Fu, Ruowen; Wu, Dingcai
2015-01-01
Exceptionally large surface area and well-defined nanostructure are both critical in the field of nanoporous carbons for challenging energy and environmental issues. The pursuit of ultrahigh surface area while maintaining definite nanostructure remains a formidable challenge because extensive creation of pores will undoubtedly give rise to the damage of nanostructures, especially below 100 nm. Here we report that high surface area of up to 3,022 m2 g−1 can be achieved for hollow carbon nanospheres with an outer diameter of 69 nm by a simple carbonization procedure with carefully selected carbon precursors and carbonization conditions. The tailor-made pore structure of hollow carbon nanospheres enables target-oriented applications, as exemplified by their enhanced adsorption capability towards organic vapours, and electrochemical performances as electrodes for supercapacitors and sulphur host materials for lithium–sulphur batteries. The facile approach may open the doors for preparation of highly porous carbons with desired nanostructure for numerous applications. PMID:26072734
Adsorption Refrigeration System
Wang, Kai; Vineyard, Edward Allan
2011-01-01
Adsorption refrigeration is an environmentally friendly cooling technology which could be driven by recovered waste heat or low-grade heat such as solar energy. In comparison with absorption system, an adsorption system has no problems such as corrosion at high temperature and salt crystallization. In comparison with vapor compression refrigeration system, it has the advantages of simple control, no moving parts and less noise. This paper introduces the basic theory of adsorption cycle as well as the advanced adsorption cycles such as heat and mass recovery cycle, thermal wave cycle and convection thermal wave cycle. The types, characteristics, advantages and drawbacks of different adsorbents used in adsorption refrigeration systems are also summarized. This article will increase the awareness of this emerging cooling technology among the HVAC engineers and help them select appropriate adsorption systems in energy-efficient building design.
Scattering Theory Calculations of Casimir Energies at High Curvature
NASA Astrophysics Data System (ADS)
Graham, Noah; Emig, Thorsten; Forrow, Aden; Jaffe, Robert; Kardar, Mehran; Maghrebi, Mohammad; Rahi, Jamal; Shpunt, Alex
2013-03-01
Scattering theory provides a powerful tool for capturing the response of an object to electromagnetic charge and field fluctuations. Techniques based on scattering theory have made possible a wide range of new calculations of Casimir energies. In this approach, the Casimir interaction energy for a collection of objects can be expressed in terms of the scattering T-matrices for each object individually, combined with universal translation matrices describing the objects' relative positions and orientations. These translation matrices are derived from an expansion of the free Green's function in an appropriate coordinate system, independent of the details of the objects themselves. This method proves particularly valuable for geometries involving high curvature, such as edges and tips. I will describe this approach in general terms and then give results from several problems to which it has been applied successfully. I will also discuss new developments in scattering theory that have been motivated by these problems. I would like to request that this abstract be part of a session on Casimir physics. Supported by the National Science Foundation, the US Department of Energy, the Defense Advanced Research Projects Agency, and the Deutsche Forschungsgemeinschaft
3DRISM Multigrid Algorithm for Fast Solvation Free Energy Calculations.
Sergiievskyi, Volodymyr P; Fedorov, Maxim V
2012-06-12
In this paper we present a fast and accurate method for modeling solvation properties of organic molecules in water with a main focus on predicting solvation (hydration) free energies of small organic compounds. The method is based on a combination of (i) a molecular theory, three-dimensional reference interaction sites model (3DRISM); (ii) a fast multigrid algorithm for solving the high-dimensional 3DRISM integral equations; and (iii) a recently introduced universal correction (UC) for the 3DRISM solvation free energies by properly scaled molecular partial volume (3DRISM-UC, Palmer et al., J. Phys.: Condens. Matter2010, 22, 492101). A fast multigrid algorithm is the core of the method because it helps to reduce the high computational costs associated with solving the 3DRISM equations. To facilitate future applications of the method, we performed benchmarking of the algorithm on a set of several model solutes in order to find optimal grid parameters and to test the performance and accuracy of the algorithm. We have shown that the proposed new multigrid algorithm is on average 24 times faster than the simple Picard method and at least 3.5 times faster than the MDIIS method which is currently actively used by the 3DRISM community (e.g., the MDIIS method has been recently implemented in a new 3DRISM implicit solvent routine in the recent release of the AmberTools 1.4 molecular modeling package (Luchko et al. J. Chem. Theory Comput. 2010, 6, 607-624). Then we have benchmarked the multigrid algorithm with chosen optimal parameters on a set of 99 organic compounds. We show that average computational time required for one 3DRISM calculation is 3.5 min per a small organic molecule (10-20 atoms) on a standard personal computer. We also benchmarked predicted solvation free energy values for all of the compounds in the set against the corresponding experimental data. We show that by using the proposed multigrid algorithm and the 3DRISM-UC model, it is possible to obtain good
Valence calculations of lanthanide anion binding energies: a comprehensive study
NASA Astrophysics Data System (ADS)
O'Malley, Steven M.; Beck, Donald R.
2009-05-01
We have applied a methodology of universal jls restrictions on the 4f^n subgroup of relativistic configuration-interaction calculations of progressively more complex lanthanide anionsootnotetextS. M. O'Malley and D. R. Beck, Phys. Rev. A 77, 012505 (2008).^,ootnotetextS. M. O'Malley and D. R. Beck, Phys. Rev. A 78, 012510 (2008).^,ootnotetextS. M. O'Malley and D. R. Beck, Phys. Rev. A, in press.. Our completed study of the row predicts bound 6p attachments to all lanthanide ground state configurations except Yb, additional 6p attachments to excited opposite parity configurations in Tb and Lu, and 6s attachments to excited open-6s thresholds in La, Ce, Pr, and Gd. In total we predict more than 100 bound states for the lanthanide anions, and we hope this comprehensive study encourages further experimentalootnotetexte.g. V. T. Davis et al., Nucl. Instrum. Methods Phys. Res. B 241, 118 (2005).^,ootnotetexte.g. C. W. Walter et al., Phys. Rev. A 76, 052702 (2007). interest in these anions. Such measurements will be useful in ``fine tuning'' these ab initio binding energies to account for missing core-valence correlation and the approximations that were necessary in these complex calculations.
Srinivasan, Sriram Goverapet; Shivaramaiah, Radha; Kent, Paul R. C.; Stack, Andrew G.; Navrotsky, Alexandra; Riman, Richard; Anderko, Andre; Bryantsev, Vyacheslav S.
2016-07-11
Bastnasite is a fluoro-carbonate mineral that is the largest source of rare earth elements such as Y, La and Ce. With increasing demand for REE in many emerging technologies, there is an urgent need for improving the efficiency of ore beneficiation by froth flotation. In order to design improved flotation agents that can selectively bind to the mineral surface, a fundamental understanding of the bulk and surface properties of bastnasite is essential. Density functional theory calculations using the PBEsol exchange correlation functional and the DFT-D3 dispersion correction reveal that the most stable form of La bastnsite is isomorphic to themore » structure of Ce bastnasite belonging to the P2c space group, while the Inorganic Crystal Structure Database structure in the P2m space group is ca. 11.3 kJ/mol higher in energy per LaFCO3 formula unit. We report powder X-ray diffraction measurements on synthetic of La bastnasite to support these theoretical findings. Six different surfaces are studied by DFT, namely [100], [0001], [101], [102], [104] and [112]. Among these, the [100] surface is the most stable with a surface energy of 0.73 J/m2 in vacuum and 0.45 J/m2 in aqueous solution. We predicted the shape of a La bastnasite nanoparticle via thermodynamic Wulff construction to be a hexagonal prism with [100] and [0001] facets, chiseled at its ends by the [101] and [102] facets. The average surface energy of the nanoparticle in the gas phase is estimated to be 0.86 J/m2, in good agreement with a value of 1.11 J/m2 measured by calorimetry. The calculated adsorption energy of a water molecule varies widely with the surface plane and specific adsorption sites on a given surface. Moreover, the first layer of water molecules is predicted to adsorb strongly on the La-bastnasite surface, in agreement with water adsorption calorimetry experiments. Our work provides an important step towards a detailed atomistic understanding of the bastnasite water interface and designing
Free-energy calculation via mean-force dynamics using a logarithmic energy landscape.
Morishita, Tetsuya; Itoh, Satoru G; Okumura, Hisashi; Mikami, Masuhiro
2012-06-01
A method for free-energy calculation based on mean-force dynamics (fictitious dynamics on a potential of mean force) is presented. The method utilizes a logarithmic form of free energy to enhance crossing barriers on a free-energy landscape, which results in efficient sampling of "rare" events. Invoking a conserved quantity in mean-force dynamics, free energy can be estimated on-the-fly without postprocessing. This means that an estimate of the free-energy profile can be locally made in contrast to the other methods based on mean-force dynamics such as metadynamics. The method is benchmarked against conventional methods and its high efficiency is demonstrated in the free-energy calculation for a glycine dipeptide molecule. PMID:23005238
Jia, Xiangyu; Wang, Meiting; Shao, Yihan; König, Gerhard; Brooks, Bernard R; Zhang, John Z H; Mei, Ye
2016-02-01
In this work, the solvation free energies of 20 organic molecules from the 4th Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL4) have been calculated. The sampling of phase space is carried out at a molecular mechanical level, and the associated free energy changes are estimated using the Bennett Acceptance Ratio (BAR). Then the quantum mechanical (QM) corrections are computed through the indirect Non-Boltzmann Bennett's acceptance ratio (NBB) or the thermodynamics perturbation (TP) method. We show that BAR+TP gives a minimum analytic variance for the calculated solvation free energy at the Gaussian limit and performs slightly better than NBB in practice. Furthermore, the expense of the QM calculations in TP is only half of that in NBB. We also show that defining the biasing potential as the difference of the solute-solvent interaction energy, instead of the total energy, can converge the calculated solvation free energies much faster but possibly to different values. Based on the experimental solvation free energies which have been published before, it is discovered in this study that BLYP yields better results than MP2 and some other later functionals such as B3LYP, M06-2X, and ωB97X-D. PMID:26731197
INDIVIDUALISED CALCULATION OF TISSUE IMPARTED ENERGY IN BREAST TOMOSYNTHESIS.
Geeraert, N; Klausz, R; Muller, S; Bloch, I; Bosmans, H
2016-06-01
The imparted energy to the glandular tissue in the breast (glandular imparted energy, GIE) is proposed for an improved assessment of the individual radiation-induced risk resulting from X-ray breast imaging. GIE is computed from an estimation of the quantity and localisation of glandular tissue in the breast. After a digital breast tomosynthesis (DBT) acquisition, the volumetric glandular content (volumetric breast density, VBD) is computed from the central X-ray projection. The glandular tissue distribution is determined by labelling the DBT voxels to ensure the conservation of the VBD. Finally, the GIE is calculated by Monte Carlo computation on the resulting tissue-labelled DBT volume. For verification, the method was applied to 10 breast-shaped digital phantoms made of different glandular spheres in an adipose background, and to a digital anthropomorphic phantom. Results were compared to direct GIE computations on the phantoms considered as 'ground-truth'. The major limitations in accuracy are those of DBT, in particular the limited z-resolution. However, for most phantoms, the results can be considered as acceptable. PMID:27127209
The DLVO-Lifshitz theory of colloid stability is applied to adsorption of poliovirus on oxide surfaces common in soil and aquatic environments. Excellent agreement was found between colloid stability theory and adsorption free energies calculated from mass-action principles. Coll...
Hydrogen adsorption on sulphur-doped SiC nanotubes
NASA Astrophysics Data System (ADS)
Sevak Singh, Ram
2016-07-01
Hydrogen (H2) is an energy carrier and clean fuel that can be used for a broad range of applications that include fuel cell vehicles. Therefore, development of materials for hydrogen storage is demanded. Nanotubes, in this context, are appropriate materials. Recently, silicon carbide nanotube (SiCNTs) have been predicted as potential nanomaterials for hydrogen storage, and atomic doping into the nanotubes improves the H2 adsorption. Here, we report H2 adsorption properties of sulphur-doped (S-doped) SiCNTs using first-principles calculations based on density functional theory. The H2 adsorption properties are investigated by calculations of energy band structures, density of states (DOS), adsorption energy and Mulliken charge population analysis. Our findings show that, compared to the intrinsic SiCNT, S-doped SiCNT is more sensitive to H2 adsorption. H2 gas adsorption on S-doped C-sites of SiCNT brings about significant modulation of the electronic structure of the nanotube, which results in charge transfer from the nanotube to the gas, and dipole–dipole interactions cause chemisorptions of hydrogen. However, in the case of H2 gas adsorption on S-doped Si-sites of the nanotube, lesser charge transfer from the nanotube to the gas results in physisorptions of the gas. The efficient hydrogen sensing properties of S-doped SiCNTs, studied here, may have potential for its practical realization for hydrogen storage application.
Identification of HIV Inhibitors Guided by Free Energy Perturbation Calculations
Acevedo, Orlando; Ambrose, Zandrea; Flaherty, Patrick T.; Aamer, Hadega; Jain, Prashi; Sambasivarao, Somisetti V.
2013-01-01
Free energy perturbation (FEP) theory coupled to molecular dynamics (MD) or Monte Carlo (MC) statistical mechanics offers a theoretically precise method for determining the free energy differences of related biological inhibitors. Traditionally requiring extensive computational resources and expertise, it is only recently that its impact is being felt in drug discovery. A review of computer-aided anti-HIV efforts employing FEP calculations is provided here that describes early and recent successes in the design of human immunodeficiency virus type 1 (HIV-1) protease and non-nucleoside reverse transcriptase inhibitors. In addition, our ongoing work developing and optimizing leads for small molecule inhibitors of cyclophilin A (CypA) is highlighted as an update on the current capabilities of the field. CypA has been shown to aid HIV-1 replication by catalyzing the cis/trans isomerization of a conserved Gly-Pro motif in the N-terminal domain of HIV-1 capsid (CA) protein. In the absence of a functional CypA, e.g., by the addition of an inhibitor such as cyclosporine A (CsA), HIV-1 has reduced infectivity. Our simulations of acylurea-based and 1-indanylketone-based CypA inhibitors have determined that their nanomolar and micromolar binding affinities, respectively, are tied to their ability to stabilize Arg55 and Asn102. A structurally novel 1-(2,6-dichlorobenzamido) indole core was proposed to maximize these interactions. FEP-guided optimization, experimental synthesis, and biological testing of lead compounds for toxicity and inhibition of wild-type HIV-1 and CA mutants have demonstrated a dose-dependent inhibition of HIV-1 infection in two cell lines. While the inhibition is modest compared to CsA, the results are encouraging. PMID:22316150
5 CFR 591.220 - How does OPM calculate energy utility cost indexes?
Code of Federal Regulations, 2011 CFR
2011-01-01
... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...
5 CFR 591.220 - How does OPM calculate energy utility cost indexes?
Code of Federal Regulations, 2014 CFR
2014-01-01
... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...
5 CFR 591.220 - How does OPM calculate energy utility cost indexes?
Code of Federal Regulations, 2013 CFR
2013-01-01
... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...
5 CFR 591.220 - How does OPM calculate energy utility cost indexes?
Code of Federal Regulations, 2012 CFR
2012-01-01
... 5 Administrative Personnel 1 2012-01-01 2012-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...
5 CFR 591.220 - How does OPM calculate energy utility cost indexes?
Code of Federal Regulations, 2010 CFR
2010-01-01
... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...
Calculating activation energies for temperature compensation in circadian rhythms
NASA Astrophysics Data System (ADS)
Bodenstein, C.; Heiland, I.; Schuster, S.
2011-10-01
Many biological species possess a circadian clock, which helps them anticipate daily variations in the environment. In the absence of external stimuli, the rhythm persists autonomously with a period of approximately 24 h. However, single pulses of light, nutrients, chemicals or temperature can shift the clock phase. In the case of light- and temperature-cycles, this allows entrainment of the clock to cycles of exactly 24 h. Circadian clocks have the remarkable property of temperature compensation, that is, the period of the circadian rhythm remains relatively constant within a physiological range of temperatures. For several organisms, temperature-regulated processes within the circadian clock have been identified in recent years. However, how these processes contribute to temperature compensation is not fully understood. Here, we theoretically investigate temperature compensation in general oscillatory systems. It is known that every oscillator can be locally temperature compensated around a reference temperature, if reactions are appropriately balanced. A balancing is always possible if the control coefficient with respect to the oscillation period of at least one reaction in the oscillator network is positive. However, for global temperature compensation, the whole physiological temperature range is relevant. Here, we use an approach which leads to an optimization problem subject to the local balancing principle. We use this approach to analyse different circadian clock models proposed in the literature and calculate activation energies that lead to temperature compensation.
Path-breaking schemes for nonequilibrium free energy calculations
NASA Astrophysics Data System (ADS)
Chelli, Riccardo; Gellini, Cristina; Pietraperzia, Giangaetano; Giovannelli, Edoardo; Cardini, Gianni
2013-06-01
We propose a path-breaking route to the enhancement of unidirectional nonequilibrium simulations for the calculation of free energy differences via Jarzynski's equality [C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)], 10.1103/PhysRevLett.78.2690. One of the most important limitations of unidirectional nonequilibrium simulations is the amount of realizations necessary to reach suitable convergence of the work exponential average featuring the Jarzynski's relationship. In this respect, a significant improvement of the performances could be obtained by finding a way of stopping trajectories with negligible contribution to the work exponential average, before their normal end. This is achieved using path-breaking schemes which are essentially based on periodic checks of the work dissipated during the pulling trajectories. Such schemes can be based either on breaking trajectories whose dissipated work exceeds a given threshold or on breaking trajectories with a probability increasing with the dissipated work. In both cases, the computer time needed to carry out a series of nonequilibrium trajectories is reduced up to a factor ranging from 2 to more than 10, at least for the processes under consideration in the present study. The efficiency depends on several aspects, such as the type of process, the number of check-points along the pathway and the pulling rate as well. The method is illustrated through radically different processes, i.e., the helix-coil transition of deca-alanine and the pulling of the distance between two methane molecules in water solution.
Manzhos, Sergei; Segawa, Hiroshi; Yamashita, Koichi
2012-02-01
We perform a comparative theoretical analysis of adsorption of dyes NK1 (2E,4E-2-cyano-5-(4-dimethylaminophenyl)penta-2,4-dienoic acid) and NK7 (2E,4E-2-cyano-5-(4-diphenylaminophenyl)penta-2,4-dienoic acid) on clean and water-covered anatase (101) surfaces of TiO(2). Ligand substitution away from the anchoring group changes the energy level matching between the dye's LUMO and the oxide's conduction band. Monodentate binding and bidentate binding configurations of the dyes to TiO(2) are found to have similar adsorption energies even though the injection from the bidentate mode is found to dominate. Water has a strong effect on adsorption, inducing deprotonation and affecting strongly and differently between the dyes the energy level matching, leading to a shut-off of the injection from NK7 of bidentate adsorption configuration. Ab initio molecular dynamics simulations show a strong effect of nuclear motion on energy levels, specifically, increasing the driving force for injection in the monodentate regime. PMID:22194034
Adsorption of CO Molecules on Si(001) at Room Temperature
NASA Astrophysics Data System (ADS)
Seo, Eonmi; Eom, Daejin; Kim, Hanchul; Koo, Ja-Yong
2015-03-01
Initial adsorption of CO molecules on Si(001) is investigated by using room-temperature (RT) scanning tunneling microscopy (STM) and density functional theory calculations. Theoretical calculations show that only one adsorption configuration of terminal-bond CO (T-CO) is stable and that the bridge-bond CO is unstable. All the abundantly observed STM features due to CO adsorption can be identified as differently configured T-COs. The initial sticking probability of CO molecules on Si(001) at RT is estimated to be as small as ~ 1 x 10-4 monolayer/Langmuir, which is significantly increased at high-temperature adsorption experiments implying a finite activation barrier for adsorption. Thermal annealing at 900 K for 5 min results in the dissociation of the adsorbed CO molecules with the probability of 60-70% instead of desorption, indicating both a strong chemisorption state and an activated dissociation process. The unique adsorption state with a large binding energy, a tiny sticking probability, and a finite adsorption barrier is in stark contrast with the previous low-temperature (below 100 K) observations of a weak binding, a high sticking probability, and a barrierless adsorption. We speculate that the low-temperature results might be a signature of a physisorption state in the condensed phase.
Caveat Emptor: Calculating All the Costs of Energy.
ERIC Educational Resources Information Center
Zinberg, Dorothy S.
This paper examines the energy problem. Specific topics discussed include the recent history of oil and gas consumption in the United States, conservation, coal, solar energy, and nuclear energy. While solutions to the energy problem differ, there is an urgent need for broad, public debate. Ultimately, the decisions made regarding energy will be…
Adsorption energy of small molecules on core-shell Fe@Au nanoparticles: tuning by shell thickness.
Benoit, Magali; Tarrat, Nathalie; Morillo, Joseph
2016-03-23
The adsorption of several small molecules on different gold surfaces, Au(001), strained Au(001) and Au(001) epitaxied on Fe(001), has been characterized using density functional theory. The surface strain leads to a less energetically favourable adsorption for all studied molecules. Moreover, the presence of the iron substrate induces an additional decrease of the binding energy, for 1 and 2 Au monolayers. For carbon monoxide (CO), the structural and energetic variations with the number of Au monolayers deposited on Fe have been analyzed and correlated with the distance between the carbon atom and the gold surface. The effect of the subsurface layer has been evidenced for 1 and 2 monolayers. The other molecules show different quantitative behavior depending on the type of their interaction with the gold surface. However, the iron substrate weakens the interaction, either for the chemisorbed species or for the physisorbed species. 2 Au monolayers seem to be the best compromise to decrease the reactivity of the gold surface towards adsorption while preventing the Fe oxidation. PMID:26971708
Michalkova, A; Gorb, L; Hill, F; Leszczynski, J
2011-03-24
This study presents new insight into the prediction of partitioning of organic compounds between a carbon surface (soot) and water, and it also sheds light on the sluggish desorption of interacting molecules from activated and nonactivated carbon surfaces. This paper provides details about the structure and interactions of benzene, polycyclic aromatic hydrocarbons, and aromatic nitrocompounds with a carbon surface modeled by coronene using a density functional theory approach along with the M05-2X functional. The adsorption was studied in vacuum and from water solution. The molecules studied are physisorbed on the carbon surface. While the intermolecular interactions of benzene and hydrocarbons are governed by dispersion forces, nitrocompounds are adsorbed also due to quite strong electrostatic interactions with all types of carbon surfaces. On the basis of these results, we conclude that the method of prediction presented in this study allows one to approach the experimental level of accuracy in predicting thermodynamic parameters of adsorption on a carbon surface from the gas phase. The empirical modification of the polarized continuum model leads also to a quantitative agreement with the experimental data for the Gibbs free energy values of the adsorption from water solution. PMID:21361266
Ding, H; Chen, C; Zhang, X
2016-01-01
The linear solvation energy relationship (LSER) was applied to predict the adsorption coefficient (K) of synthetic organic compounds (SOCs) on single-walled carbon nanotubes (SWCNTs). A total of 40 log K values were used to develop and validate the LSER model. The adsorption data for 34 SOCs were collected from 13 published articles and the other six were obtained in our experiment. The optimal model composed of four descriptors was developed by a stepwise multiple linear regression (MLR) method. The adjusted r(2) (r(2)adj) and root mean square error (RMSE) were 0.84 and 0.49, respectively, indicating good fitness. The leave-one-out cross-validation Q(2) ([Formula: see text]) was 0.79, suggesting the robustness of the model was satisfactory. The external Q(2) ([Formula: see text]) and RMSE (RMSEext) were 0.72 and 0.50, respectively, showing the model's strong predictive ability. Hydrogen bond donating interaction (bB) and cavity formation and dispersion interactions (vV) stood out as the two most influential factors controlling the adsorption of SOCs onto SWCNTs. The equilibrium concentration would affect the fitness and predictive ability of the model, while the coefficients varied slightly. PMID:26854726
Initial heats of H{sub 2}S adsorption on activated carbons: Effect of surface features
Bagreev, A.; Adib, F.; Bandosz, T.J.
1999-11-15
The sorption of hydrogen sulfide was studied on activated carbons of various origins by means of inverse gas chromatography at infinite dilution. The conditions of the experiment were dry and anaerobic. Prior to the experiments the surface of some carbon samples was oxidized using either nitric acid or ammonium persulfate. Then the structural parameters of carbons were evaluated from the sorption of nitrogen. From the IGC experiments at various temperatures, heats of adsorption were calculated. The results showed that the heat of H{sub 2}S adsorption under dry anaerobic conditions does not depend on surface chemistry. The dependence of the heat of adsorption on the characteristic energy of nitrogen adsorption calculated from the Dubinin-Raduskevich equation was found. This correlation can be used to predict the heat of H{sub 2}S adsorption based on the results obtained from nitrogen adsorption.
Adsorption-driven translocation of polymer chain into nanopores
NASA Astrophysics Data System (ADS)
Yang, Shuang; Neimark, Alexander V.
2012-06-01
The polymer translocation into nanopores is generally facilitated by external driving forces, such as electric or hydrodynamic fields, to compensate for entropic restrictions imposed by the confinement. We investigate the dynamics of translocation driven by polymer adsorption to the confining walls that is relevant to chromatographic separation of macromolecules. By using the self-consistent field theory, we study the passage of a chain trough a small opening from cis to trans compartments of spherical shape with adsorption potential applied in the trans compartment. The chain transfer is modeled as the Fokker-Plank diffusion along the free energy landscape of the translocation pass represented as a sum of the free energies of cis and trans parts of the chain tethered to the pore opening. We investigate how the chain length, the size of trans compartment, the magnitude of adsorption potential, and the extent of excluded volume interactions affect the translocation time and its distribution. Interplay of these factors brings about a variety of different translocation regimes. We show that excluded volume interactions within a certain range of adsorption potentials can cause a local minimum on the free energy landscape, which is absent for ideal chains. The adsorption potential always leads to the decrease of the free energy barrier, increasing the probability of successful translocation. However, the translocation time depends non-monotonically of the magnitude of adsorption potential. Our calculations predict the existence of the critical magnitude of adsorption potential, which separates favorable and unfavorable regimes of translocation.
Adsorption-driven translocation of polymer chain into nanopores.
Yang, Shuang; Neimark, Alexander V
2012-06-01
The polymer translocation into nanopores is generally facilitated by external driving forces, such as electric or hydrodynamic fields, to compensate for entropic restrictions imposed by the confinement. We investigate the dynamics of translocation driven by polymer adsorption to the confining walls that is relevant to chromatographic separation of macromolecules. By using the self-consistent field theory, we study the passage of a chain trough a small opening from cis to trans compartments of spherical shape with adsorption potential applied in the trans compartment. The chain transfer is modeled as the Fokker-Plank diffusion along the free energy landscape of the translocation pass represented as a sum of the free energies of cis and trans parts of the chain tethered to the pore opening. We investigate how the chain length, the size of trans compartment, the magnitude of adsorption potential, and the extent of excluded volume interactions affect the translocation time and its distribution. Interplay of these factors brings about a variety of different translocation regimes. We show that excluded volume interactions within a certain range of adsorption potentials can cause a local minimum on the free energy landscape, which is absent for ideal chains. The adsorption potential always leads to the decrease of the free energy barrier, increasing the probability of successful translocation. However, the translocation time depends non-monotonically of the magnitude of adsorption potential. Our calculations predict the existence of the critical magnitude of adsorption potential, which separates favorable and unfavorable regimes of translocation. PMID:22697566
Effects of CO/CO2/NO on elemental lead adsorption on carbonaceous surfaces.
Gao, Zhengyang; Yang, Weijie
2016-07-01
The adsorption processes of elemental lead on carbonaceous surfaces which adsorbed CO/CO2/NO flue gases were investigated to understand the effects of CO/CO2/NO on elemental lead adsorption on carbonaceous surfaces with density functional theory. All calculations including optimizations, energies, and frequencies were conducted at B3PW91 density functional theory level, utilizing SDD basis set for lead and 6-31G(d) Pople basis set for other atoms. The results indicate that CO, CO2, and NO can promote the adsorption of elemental lead on the carbonaceous surface, but probably compete for adsorption sites with elemental lead. The promotion effects on adsorption can be attributed to active sites on the carbonaceous surface rather than flue gas adsorption on the carbonaceous surface. In addition, the adsorption order of three kinds of flue gas on the carbonaceous surface is CO2 > NO > CO > Pb on average. Furthermore, the enhancement order of three kinds of flue gas on the elemental lead adsorption on carbonaceous surfaces is CO-CS > CO2-CS > NO-CS > CS in general. In particular, atomic charge and adsorption energy have good linear relationship in the process of elemental lead adsorption. Graphical Abstract Competitive adsorption between flue gas and elemental lead on carbonaceous surfaces. PMID:27342251
Asnin, Leonid; Kaczmarski, Krzysztof; Guiochon, Georges A
2008-01-01
The retention mechanism of the enantiomers of naproxen on a Pirkle-type chiral stationary phase (CSP) was studied. This CSP is made of a porous silica grafted with quinidine carbamate. It can interact with the weak organic electrolyte naproxen either by adsorbing it or by ion-exchange. Using frontal chromatography, we explored the adsorption equilibrium under such experimental conditions that naproxen dissociates or cannot dissociate. Under conditions preventing ionic dissociation, the adsorption isotherms were measured, the adsorption energy distributions determined, and the chromatographic profiles calculated. Three different types of the adsorption sites were found for both enantiomers. The density and the binding energy of these sites depend on the nature of the organic modifier. Different solute species, anions, neutral molecules, solvent-ion associates, and solute dimers can coexist in solution, giving rise to different forms of adsorption. This study showed the unexpected occurrence of secondary steps in the breakthrough profiles of S-naproxen in the adsorption mode at high concentrations. Being enantioselective, this phenomenon was assumed to result from the association of solute molecules involving a chiral selector moiety. A multisite Langmuir adsorption model was used to calculate band profiles. Although this model accounts excellently for the experimental adsorption isotherms, it does not explain all the features of the breakthrough profiles. A comparison between the calculated and experimental profiles allowed useful conclusions concerning the effects of the adsorbate-adsorbate and adsorbate-solvent interactions on the adsorption mechanism.
Functionalized mesoporous silica materials for molsidomine adsorption: Thermodynamic study
Alyoshina, Nonna A.; Parfenyuk, Elena V.
2013-09-15
A series of unmodified and organically modified mesoporous silica materials was prepared. The unmodified mesoporous silica was synthesized via sol–gel synthesis in the presence of D-glucose as pore-forming agent. The functionalized by phenyl, aminopropyl and mercaptopropyl groups silica materials were prepared via grafting. The fabricated adsorbent materials were characterized by Fourier transform infrared spectroscopy (FTIR) analysis, N{sub 2} adsorption/desorption and elemental analysis methods. Then their adsorption properties for mesoionic dug molsidomine were investigated at 290–313 K and physiological pH value. Thermodynamic parameters of molsidomine adsorption on the synthesized materials have been calculated. The obtained results showed that the adsorption process of molsidomine on the phenyl modified silica is the most quantitatively and energetically favorable. The unmodified and mercaptopropyl modified silica materials exhibit significantly higher adsorption capacities and energies for molsidomine than the aminopropyl modified sample. The effects are discussed from the viewpoint of nature of specific interactions responsible for the adsorption. - Graphical abstract: Comparative analysis of the thermodynamic characteristics of molsidomine adsorption showed that the adsorption process on mesoporous silica materials is controlled by chemical nature of surface functional groups. Molsidomine adsorption on the phenyl modified silica is the most quantitatively and energetically favorable. Taking into account ambiguous nature of mesoionic compounds, it was found that molsidomine is rather aromatic than dipolar. Display Omitted - Highlights: • Unmodified and organically modified mesoporous silica materials were prepared. • Molsidomine adsorption on the silica materials was studied. • Phenyl modified silica shows the highest adsorption capacity and favorable energy. • Molsidomine exhibits the lowest affinity to aminopropyl modified silica.
NASA Astrophysics Data System (ADS)
Geweke, Jan; Shirhatti, Pranav R.; Rahinov, Igor; Bartels, Christof; Wodtke, Alec M.
2016-08-01
In this work we seek to examine the nature of collisional energy transfer between HCl and Au(111) for nonreactive scattering events that sample geometries near the transition state for dissociative adsorption by varying both the vibrational and translational energy of the incident HCl molecules in the range near the dissociation barrier. Specifically, we report absolute vibrational excitation probabilities for HCl(v = 0 → 1) and HCl(v = 1 → 2) scattering from clean Au(111) as a function of surface temperature and incidence translational energy. The HCl(v = 2 → 3) channel could not be observed—presumably due to the onset of dissociation. The excitation probabilities can be decomposed into adiabatic and nonadiabatic contributions. We find that both contributions strongly increase with incidence vibrational state by a factor of 24 and 9, respectively. This suggests that V-T as well as V-EHP coupling can be enhanced near the transition state for dissociative adsorption at a metal surface. We also show that previously reported HCl(v = 0 → 1) excitation probabilities [Q. Ran et al., Phys. Rev. Lett. 98, 237601 (2007)]—50 times smaller than those reported here—were influenced by erroneous assignment of spectroscopic lines used in the data analysis.
Geweke, Jan; Shirhatti, Pranav R; Rahinov, Igor; Bartels, Christof; Wodtke, Alec M
2016-08-01
In this work we seek to examine the nature of collisional energy transfer between HCl and Au(111) for nonreactive scattering events that sample geometries near the transition state for dissociative adsorption by varying both the vibrational and translational energy of the incident HCl molecules in the range near the dissociation barrier. Specifically, we report absolute vibrational excitation probabilities for HCl(v = 0 → 1) and HCl(v = 1 → 2) scattering from clean Au(111) as a function of surface temperature and incidence translational energy. The HCl(v = 2 → 3) channel could not be observed-presumably due to the onset of dissociation. The excitation probabilities can be decomposed into adiabatic and nonadiabatic contributions. We find that both contributions strongly increase with incidence vibrational state by a factor of 24 and 9, respectively. This suggests that V-T as well as V-EHP coupling can be enhanced near the transition state for dissociative adsorption at a metal surface. We also show that previously reported HCl(v = 0 → 1) excitation probabilities [Q. Ran et al., Phys. Rev. Lett. 98, 237601 (2007)]-50 times smaller than those reported here-were influenced by erroneous assignment of spectroscopic lines used in the data analysis. PMID:27497574
NASA Astrophysics Data System (ADS)
Gao, Yang; Zhang, Li Mei; Kong, Chun Cai; Yang, Zhi Mao; Chen, Yong Mei
2016-08-01
The NO adsorption and dissociation on neutral, charged and Ni-doped Pd13 clusters were studied by using density functional calculations. Our results revealed that NO always prefers to adsorb on the hollow site rather than the top or bridge sites. However, the charge state and Ni doping remarkably influence NO adsorption energy, dissociation barrier and reaction energy. The reaction on Pd13- has the lowest energy barrier and largest reaction energy. The Hirshfeld charge analysis discloses that the origin of the catalytic activity difference is the charge transfer from clusters to NO in the metastable NO adsorption state.
Trypsin-Ligand Binding Free Energy Calculation with AMOEBA
Shi, Yue; Jiao, Dian; Schnieders, Michael J.; Ren, Pengyu
2010-01-01
The binding free energies of several benzamidine-like inhibitors to trypsin were examined using a polarizable potential. All the computed binding free energies are in good agreement with the experimental data. From free energy decomposition, electrostatic interaction was found to be the driving force for the binding. Structural analysis shows that the ligands form hydrogen bonds with residues and water molecules nearby in a competitive fashion. The dependence of binding free energy on molecular dipole moment and polarizability was also studied. While the binding free energy is independent on the dipole moment, it shows a negative correlation with the polarizability. PMID:19965178
Adsorption of CO2 on Cu2O (1 1 1) oxygen-vacancy surface: First-principles study
NASA Astrophysics Data System (ADS)
Wu, Huanwen; Zhang, Ning; Wang, Hongming; Hong, Sanguo
2013-05-01
The adsorption of CO2 on Cu2O (1 1 1) oxygen-vacancy surface has been investigated by using the first-principles calculations based on the density functional theory (DFT). The geometry, adsorption energy, charge population and projected density of states (PDOS) were calculated. The results show dissociative adsorption of CO2 on the surface is thermodynamically unfeasible. The oxygen vacancy has the negative effects on the adsorption of CO2 at the coordinately unsaturated surface copper and oxygen (CuCUS and OCUS) sites. Oxygen vacancies are the active sites. CO2 can be directly adsorbed and converted into CO2δ- radical anion species at these sites.
A Density Functional Theory Study of Formaldehyde Adsorption on Ceria
Mei, Donghai; Deskins, N. Aaron; Dupuis, Michel
2007-11-01
Molecular adsorption of formaldehyde on the stoichiometric CeO2(111) and CeO2(110) surfaces was studied using periodic density functional theory. Two adsorption modes (strong chemisorbed and weak physisorbed) were identified on both surfaces. This is consistent with recent experimental observations. On the (111) surface, formaldehyde strongly chemisorbs with an adsorption energy of 0.86 eV to form a dioxymethylene-like structure, in which a surface O lifts from the surface to bind with the C of formaldehyde. A weak physisorbed state with adsorption energy of 0.28 eV was found with the O of formaldehyde interacting with a surface Ce. On the (110) surface, dioxymethyelene formation was also observed, with an adsorption energy of 1.31 eV. The weakly adsorbed state of formaldehyde on the (110) surface was energetically comparable to the weak adsorption state on the (111) surface, but adsorption occurred through a formaldehyde C and surface O interaction. Analysis of the local density of states and charge density differences after adsorption shows that strong covalent bonding occurs between the C of formaldehyde and surface O when dioxymethylene forms. Calculated vibrational frequencies also confirm dioxymethylene formation. Our results also show that as the coverage increases, the adsorption of formaldehyde on the (111) surface becomes weak, but is nearly unaffected on the (110) surface. This work was supported by a Laboratory Directed Research and Development (LDRD) project of the Pacific Northwest National Laboratory (PNNL). The computations were performed using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory, which is a U.S. Department of Energy national scientific user facility located at PNNL in Richland, Washington. Computing time was made under a Computational Grand Challenge “Computational Catalysis”. Part of the computing time was also granted by the National Energy Research Scientific Computing
High coverage hydrogen adsorption on the Fe3O4(1 1 0) surface
NASA Astrophysics Data System (ADS)
Yu, Xiaohu; Zhang, Xuemei; Wang, Shengguang
2015-10-01
Hydrogen adsorption on the A and B termination layers of the Fe3O4(1 1 0) surface at different coverage has been systematically studied by density functional theory calculations including an on-site Hubbard term (GGA + U). The adsorption of hydrogen prefers surface oxygen atoms on both layers. The more stable A layer has stronger adsorption energy than the less stable B layer. The saturation coverage has two dissociatively adsorbed H2 on the A layer, and one dissociatively adsorbed H2 on the B layer. The adsorption mechanism has been analyzed on the basis of projected density of states (PDOS).
Adsorption of alkali metals on Ge(001)(2×1) surface
Xiao, H Y.; Zu, Xiaotao; Zhang, Yanfeng; Gao, Fei
2006-01-09
Ab initio total energy calculations have been performed for Na, K and Rb adsorption on Ge(001)(2?1) surface. It was found that the adsorption site of AM is AM size dependent. Structural analysis showed that the Ge-Ge dimer bond becomes stronger with increasing AM size. As the coverage increases from 0.5 to 1 ML it turns out that no depolarization effect occurs upon Na adsorption, while this effect become more important with increasing AM size. We also found that for all adsorption systems investigated the germanium surface is metallic and semiconducting for the coverage of 0.5 and 1 ML, respectively.
The different adsorption mechanism of methane molecule onto a boron nitride and a graphene flakes
Seyed-Talebi, Seyedeh Mozhgan; Neek-Amal, M.
2014-10-21
Graphene and single layer hexagonal boron-nitride are two newly discovered 2D materials with wonderful physical properties. Using density functional theory, we study the adsorption mechanism of a methane molecule over a hexagonal flake of single layer hexagonal boron-nitride (h-BN) and compare the results with those of graphene. We found that independent of the used functional in our ab-initio calculations, the adsorption energy in the h-BN flake is larger than that for graphene. Despite of the adsorption energy profile of methane over a graphene flake, we show that there is a long range behavior beyond minimum energy in the adsorption energy of methane over h-BN flake. This result reveals the higher sensitivity of h-BN sheet to the adsorption of a typical closed shell molecule with respect to graphene. The latter gives insight in the recent experiments of graphene over hexagonal boron nitride.
The different adsorption mechanism of methane molecule onto a boron nitride and a graphene flakes
NASA Astrophysics Data System (ADS)
Seyed-Talebi, Seyedeh Mozhgan; Neek-Amal, M.
2014-10-01
Graphene and single layer hexagonal boron-nitride are two newly discovered 2D materials with wonderful physical properties. Using density functional theory, we study the adsorption mechanism of a methane molecule over a hexagonal flake of single layer hexagonal boron-nitride (h-BN) and compare the results with those of graphene. We found that independent of the used functional in our ab-initio calculations, the adsorption energy in the h-BN flake is larger than that for graphene. Despite of the adsorption energy profile of methane over a graphene flake, we show that there is a long range behavior beyond minimum energy in the adsorption energy of methane over h-BN flake. This result reveals the higher sensitivity of h-BN sheet to the adsorption of a typical closed shell molecule with respect to graphene. The latter gives insight in the recent experiments of graphene over hexagonal boron nitride.
Quantum Monte Carlo calculation of the binding energy of the beryllium dimer
NASA Astrophysics Data System (ADS)
Deible, Michael J.; Kessler, Melody; Gasperich, Kevin E.; Jordan, Kenneth D.
2015-08-01
The accurate calculation of the binding energy of the beryllium dimer is a challenging theoretical problem. In this study, the binding energy of Be2 is calculated using the diffusion Monte Carlo (DMC) method, using single Slater determinant and multiconfigurational trial functions. DMC calculations using single-determinant trial wave functions of orbitals obtained from density functional theory calculations overestimate the binding energy, while DMC calculations using Hartree-Fock or CAS(4,8), complete active space trial functions significantly underestimate the binding energy. In order to obtain an accurate value of the binding energy of Be2 from DMC calculations, it is necessary to employ trial functions that include excitations outside the valence space. Our best estimate DMC result for the binding energy of Be2, obtained by using configuration interaction trial functions and extrapolating in the threshold for the configurations retained in the trial function, is 908 cm-1, only slightly below the 935 cm-1 value derived from experiment.
[Adsorption of Congo red from aqueous solution on hydroxyapatite].
Zhan, Yan-Hui; Lin, Jian-Wei
2013-08-01
The adsorption of Congo red (CR) from aqueous solution on hydroxyapatite was investigated using batch experiments. The hydroxyapatite was effective for CR removal from aqueous solution. The adsorption kinetics of CR on hydroxyapatite well followed a pseudo-second-order model. The equilibrium adsorption data of CR on hydroxyapatite could be described by the Langmuir, Freundlich and Dubinin-Radushkevich (D-R) isotherm models. Thermodynamic parameters such as Gibbs free energy change, enthalpy change and entropy change were calculated and showed that the adsorption of CR on hydroxyapatite was spontaneous and exothermic in nature. The CR adsorption capacity for hydroxyapatite decreased significantly with increasing pH from 8 to 10. Thermal regeneration showed that hydroxyapatite could be used for six desorption-adsorption cycles with high removal efficiency for CR in each cycle. The mechanisms for CR adsorption on hydroxyapatite with pH value below the pH at point of zero charge (pH(PZC)) include electrostatic attraction, hydrogen bonding and Lewis acid-base interaction. The mechanisms for CR adsorption on hydroxyapatite with pH value above its pH(PZC) include hydrogen bonding and Lewis acid-base interaction. Results of this work indicate that hydroxyapatite is a promising adsorbent for CR removal from aqueous solution. PMID:24191561
Ovchinnikov, Victor; Cecchini, Marco; Karplus, Martin
2013-01-24
A simple and robust formulation of the path-independent confinement method for the calculation of free energies is presented. The simplified confinement method (SCM) does not require matrix diagonalization or switching off the molecular force field, and has a simple convergence criterion. The method can be readily implemented in molecular dynamics programs with minimal or no code modifications. Because the confinement method is a special case of thermodynamic integration, it is trivially parallel over the integration variable. The accuracy of the method is demonstrated using a model diatomic molecule, for which exact results can be computed analytically. The method is then applied to the alanine dipeptide in vacuum, and to the α-helix ↔ β-sheet transition in a 16-residue peptide modeled in implicit solvent. The SCM requires less effort for the calculation of free energy differences than previous formulations because it does not require computing normal modes. The SCM has a diminished advantage for determining absolute free energy values, because it requires decreasing the MD integration step to obtain accurate results. An approximate confinement procedure is introduced, which can be used to estimate directly the configurational entropy difference between two macrostates, without the need for additional computation of the difference in the free energy or enthalpy. The approximation has convergence properties similar to those of the standard confinement method for the calculation of free energies. The use of the approximation requires about 5 times less wall-clock simulation time than that needed to compute enthalpy differences to similar precision from an MD trajectory. For the biomolecular systems considered in this study, the errors in the entropy approximation are under 10%. Practical applications of the methods to proteins are currently limited to implicit solvent simulations. PMID:23268557
Subtleties in Energy Calculations in the Image Method
ERIC Educational Resources Information Center
Taddei, M. M.; Mendes, T. N. C.; Farina, C.
2009-01-01
In this pedagogical work, we point out a subtle mistake that can be made by undergraduate or graduate students in the computation of the electrostatic energy of a system containing charges and perfect conductors if they naively use the image method. Specifically, we show that naive expressions for the electrostatic energy for these systems…
NASA Astrophysics Data System (ADS)
Zheng, Yuanliao; Huang, Yan; Shu, Haibo; Zhou, Xiaohao; Ding, Jiayi; Chen, Xiaoshuang; Lu, Wei
2016-04-01
The effect of lithium adsorption on the phase transition from 1H-MoS2 to 1T-MoS2 is studied by first-principles computations. The results indicate the possibilities of the phase transition for the lithium adsorption. Based on the results of charge density difference and charge-transfer of molybdenum disulfide with lithium adsorption, we elucidated that the mechanism of the changes of electronic property accompanying the phase transition is attributed to the electron transfer of different atoms. According to the result of transition state, it can be found that the phase-transition barrier is related to the coverage of lithium atoms on MoS2 surface. It may be helpful to obtaining experimentally the stable 1T-MoS2 structure.
Adsorption of sulfur dioxide on ammonia-treated activated carbon fibers
Mangun, C.L.; DeBarr, J.A.; Economy, J.
2001-01-01
A series of activated carbon fibers (ACFs) and ammonia-treated ACFs prepared from phenolic fiber precursors have been studied to elucidate the role of pore size, pore volume, and pore surface chemistry on adsorption of sulfur dioxide and its catalytic conversion to sulfuric acid. As expected, the incorporation of basic functional groups into the ACFs was shown as an effective method for increasing adsorption of sulfur dioxide. The adsorption capacity for dry SO2 did not follow specific trends; however the adsorption energies calculated from the DR equation were found to increase linearly with nitrogen content for each series of ACFs. Much higher adsorption capacities were achieved for SO2 in the presence of oxygen and water due to its catalytic conversion to H2SO4. The dominant factor for increasing adsorption of SO2 from simulated flue gas for each series of fibers studied was the weight percent of basic nitrogen groups present. In addition, the adsorption energies calculated for dry SO2 were shown to be linearly related to the adsorption capacity of H2SO4 from this flue gas for all fibers. It was shown that optimization of this parameter along with the pore volume results in higher adsorption capacities for removal of SO2 from flue gases. ?? 2001 Elsevier Science Ltd. All rights reserved.
Van der Waals corrected DFT study of adsorption of groups VA and VIA hydrides on graphene monoxide
NASA Astrophysics Data System (ADS)
Notash, M. Yaghoobi; Ebrahimzadeh, A. Rastkar
2016-06-01
Adsorption properties of H2O, H2S, NH3 and PH3 on graphene monoxide (GMO) nano flack are investigated using density functional theory (DFT). Calculations were carried out by van der Waals correction and general gradient approximation. The adsorption energies and charge transfer between species are obtained and discussed for the considered positions of adsorbate molecules. Charge transfer analysis show that the gas molecules act as an electron acceptor in all cases. The analysis of the adsorption energies suggest GMO can be a good candidate for the adsorption of these molecules.
Periodic Density Functional Theory Study of Water Adsorption on the a-Quartz (101) Surface.
Bandura, Andrei V.; Kubicki, James D.; Sofo, Jorge O.
2011-01-01
Plane wave density functional theory (DFT) calculations have been performed to study the atomic structure, preferred H2O adsorption sites, adsorption energies, and vibrational frequencies for water adsorption on the R-quartz (101) surface. Surface energies and atomic displacements on the vacuum-reconstructed, hydrolyzed, and solvated surfaces have been calculated and compared with available experimental and theoretical data. By considering different initial positions of H2O molecules, the most stable structures of water adsorption at different coverages have been determined. Calculated H2O adsorption energies are in the range -55 to -65 kJ/mol, consistent with experimental data. The lowest and the highest O-H stretching vibrational bands may be attributed to different states of silanol groups on the watercovered surface. The dissociation energy of the silanol group on the surface covered by the adsorption monolayer is estimated to be 80 kJ/mol. The metastable states for the protonated surface bridging O atoms (Obr), which may lead to hydrolysis of siloxane bonds, have been investigated. The calculated formation energy of a Q2 center from a Q3 center on the (101) surface with 2/3 dense monolayer coverage is equal to 70 kJ/mol which is in the range of experimental activation energies for quartz dissolution.
Oxyfluoroborate host glass for upconversion application: phonon energy calculation
NASA Astrophysics Data System (ADS)
Abdel-Baki, Manal; El-Diasty, Fouad
2016-04-01
Reducing the glass phonon energy is an essential procedure to achieve high efficient radiative upconversion process. The degree of covalence of chemical bonds is responsible for the high oscillator strength of intracenter transitions in rare-earth ions. So, conversion covalent to ionic glass character is proposed as a structure-sensitive criterion that controls the phonon energy of the glasses. A series of oxyfluoro aluminum-borate host glasses used for upconversion application is prepared by the conventional melt-quenching technique. Through lithium oxide substitution by lithium fluoride, the ionic-covalent property of Li+ ion successes to regulate the band gap energies of the studied glasses. Furthermore, a new method to determine the glass phonon energy is offered.
Tung, Wei-Cheng; Adamowicz, Ludwik
2014-03-28
Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH(+) ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations. PMID:24697449
NASA Astrophysics Data System (ADS)
Tung, Wei-Cheng; Adamowicz, Ludwik
2014-03-01
Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH+ ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations.
Horn, Paul R; Head-Gordon, Martin
2016-02-28
In energy decomposition analysis (EDA) of intermolecular interactions calculated via density functional theory, the initial supersystem wavefunction defines the so-called "frozen energy" including contributions such as permanent electrostatics, steric repulsions, and dispersion. This work explores the consequences of the choices that must be made to define the frozen energy. The critical choice is whether the energy should be minimized subject to the constraint of fixed density. Numerical results for Ne2, (H2O)2, BH3-NH3, and ethane dissociation show that there can be a large energy lowering associated with constant density orbital relaxation. By far the most important contribution is constant density inter-fragment relaxation, corresponding to charge transfer (CT). This is unwanted in an EDA that attempts to separate CT effects, but it may be useful in other contexts such as force field development. An algorithm is presented for minimizing single determinant energies at constant density both with and without CT by employing a penalty function that approximately enforces the density constraint. PMID:26931692
NASA Astrophysics Data System (ADS)
Horn, Paul R.; Head-Gordon, Martin
2016-02-01
In energy decomposition analysis (EDA) of intermolecular interactions calculated via density functional theory, the initial supersystem wavefunction defines the so-called "frozen energy" including contributions such as permanent electrostatics, steric repulsions, and dispersion. This work explores the consequences of the choices that must be made to define the frozen energy. The critical choice is whether the energy should be minimized subject to the constraint of fixed density. Numerical results for Ne2, (H2O)2, BH3-NH3, and ethane dissociation show that there can be a large energy lowering associated with constant density orbital relaxation. By far the most important contribution is constant density inter-fragment relaxation, corresponding to charge transfer (CT). This is unwanted in an EDA that attempts to separate CT effects, but it may be useful in other contexts such as force field development. An algorithm is presented for minimizing single determinant energies at constant density both with and without CT by employing a penalty function that approximately enforces the density constraint.
Energy levels of isoelectronic impurities by large scale LDA calculations
Li, Jingbo; Wang, Lin-Wang
2002-11-22
Isoelectronic impurity states are localized states induced by stoichiometric single atom substitution in bulk semiconductor. Photoluminescence spectra indicate deep impurity levels of 0.5 to 0.9eV above the top of valence band for systems like: GaN:As, GaN:P, CdS:Te, ZnS:Te. Previous calculations based on small supercells seemingly confirmed these experimental results. However, the current ab initio calculations based on thousand atom supercells indicate that the impurity levels of the above systems are actually much shallower(0.04 to 0.23 eV), and these impurity levels should be compared with photoluminescence excitation spectra, not photoluminescence spectra.
NASA Astrophysics Data System (ADS)
Cahyanto, Wahyu Tri; Widanarto, Wahyu; Shukri, Ganes; Kasai, Hideaki
2016-02-01
We present density functional calculations for the adsorption of hydroxymethylidyne (COH) on Pt, PtRu, and PtRuMo (111) surfaces. Here we clarify the adsorption mechanism by using a charge transfer analysis related to the adsorption energy. We observe that the preferred binding sites for COH are the hcp hollow Pt-Pt-Pt, hcp hollow Pt-Ru-Pt, and hcp hollow Pt-Ru-Pt adsorption sites for Pt, PtRu, and PtRuMo, respectively. Addition of Ru to form a PtRu surface increases the adsorption energy, while addition of Mo to form a PtRuMo surface decreases it. Our analyses show that the adsorption energy is determined by electron transfer between the molecular COH and the metal surfaces associated with bonding.
A Variational Approach to Enhanced Sampling and Free Energy Calculations
NASA Astrophysics Data System (ADS)
Parrinello, Michele
2015-03-01
The presence of kinetic bottlenecks severely hampers the ability of widely used sampling methods like molecular dynamics or Monte Carlo to explore complex free energy landscapes. One of the most popular methods for addressing this problem is umbrella sampling which is based on the addition of an external bias which helps overcoming the kinetic barriers. The bias potential is usually taken to be a function of a restricted number of collective variables. However constructing the bias is not simple, especially when the number of collective variables increases. Here we introduce a functional of the bias which, when minimized, allows us to recover the free energy. We demonstrate the usefulness and the flexibility of this approach on a number of examples which include the determination of a six dimensional free energy surface. Besides the practical advantages, the existence of such a variational principle allows us to look at the enhanced sampling problem from a rather convenient vantage point.
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.
Oxygen adsorption on the Al₉Co₂(001) surface: first-principles and STM study.
Villaseca, S Alarcón; Loli, L N Serkovic; Ledieu, J; Fournée, V; Gille, P; Dubois, J-M; Gaudry, E
2013-09-01
Atomic oxygen adsorption on a pure aluminum terminated Al9Co2(001) surface is studied by first-principle calculations coupled with STM measurements. Relative adsorption energies of oxygen atoms have been calculated on different surface sites along with the associated STM images. The local electronic structure of the most favourable adsorption site is described. The preferential adsorption site is identified as a 'bridge' type site between the cluster entities exposed at the (001) surface termination. The Al-O bonding between the adsorbate and the substrate presents a covalent character, with s-p hybridization occurring between the states of the adsorbed oxygen atom and the aluminum atoms of the surface. The simulated STM image of the preferential adsorption site is in agreement with experimental observations. This work shows that oxygen adsorption generates important atomic relaxations of the topmost surface layer and that sub-surface cobalt atoms strongly influence the values of the adsorption energies. The calculated Al-O distances are in agreement with those reported in Al2O and Al2O3 oxides and for oxygen adsorption on Al(111). PMID:23883551
Site-Specific Scaling Relations for Hydrocarbon Adsorption on Hexagonal Transition Metal Surfaces
Montemore, Matthew M.; Medlin, James W.
2013-10-03
Screening a large number of surfaces for their catalytic performance remains a challenge, leading to the need for simple models to predict adsorption properties. To facilitate rapid prediction of hydrocarbon adsorption energies, scaling relations that allow for calculation of the adsorption energy of any intermediate attached to any symmetric site on any hexagonal metal surface through a carbon atom were developed. For input, these relations require only simple electronic properties of the surface and of the gas-phase reactant molecules. Determining adsorption energies consists of up to four steps: (i) calculating the adsorption energy of methyl in the top site using density functional theory or by simple relations based on the electronic structure of the surface; (ii) using modified versions of classical scaling relations to scale between methyl in the top site and C₁ species with more metal-surface bonds (i.e., C, CH, CH₂) in sites that complete adsorbate tetravalency; (iii) using gas-phase bond energies to predict adsorption energies of longer hydrocarbons (i.e., CR, CR₂, CR₃); and (iv) expressing energetic changes upon translation of hydrocarbons to various sites in terms of the number of agostic interactions and the change in the number of carbon-metal bonds. Combining all of these relations allows accurate scaling over a wide range of adsorbates and surfaces, resulting in efficient screening of catalytic surfaces and a clear elucidation of adsorption trends. The relations are used to explain trends in methane reforming, hydrocarbon chain growth, and propane dehydrogenation.
Advancing QCD-based calculations of energy loss
NASA Astrophysics Data System (ADS)
Tywoniuk, Konrad
2013-08-01
We give a brief overview of the basics and current developments of QCD-based calculations of radiative processes in medium. We put an emphasis on the underlying physics concepts and discuss the theoretical uncertainties inherently associated with the fundamental parameters to be extracted from data. An important area of development is the study of the single-gluon emission in medium. Moreover, establishing the correct physical picture of multi-gluon emissions is imperative for comparison with data. We will report on progress made in both directions and discuss perspectives for the future.
Turbulent energy exchange: Calculation and relevance for profile prediction
Candy, J.
2013-08-15
The anomalous heat production due to turbulence is neither routinely calculated in nonlinear gyrokinetic simulations nor routinely retained in profile prediction studies. In this work, we develop a symmetrized method to compute the exchange which dramatically reduces the intermittency in the time-dependent moment, thereby improving the accuracy of the time-average. We also examine the practical impact on transport-timescale simulations, and show that the exchange has only a minor impact on profile evolution for a well-studied DIII-D discharge.
NASA Astrophysics Data System (ADS)
Deshpande, Rahul Shrikant
The gas adsorption properties and porosity of cyanide-bridged transition metal-based gels are investigated in the first part of this dissertation. The cyanide bridges, connecting two transition metal centers, are characteristic of these gels; hence, these gels are termed cyanogels. Aerogel versus xerogel structures have a profound effect, both, on the thermodynamics and kinetics of gas adsorption on these cyanogels. Carbon dioxide is selectively adsorbed on palladium-cobalt-based cyanogels; the adsorption is fully reversible on both types of gels discussed. The thermodynamics and kinetics of the gas adsorption processes on these gels are analyzed here. From the ease and reproducibility of the CO2 desorption and the associated enthalpy values, it is concluded that CO2 is physisorbed on these gels. Both the adsorption and desorption processes are first-order in the gels. Adsorption of carbon monoxide on the palladium-cobalt cyanogels is also investigated. Unlike CO 2 physisorption, carbon monoxide is chemisorbed on these gels. An uptake of CO brings about a profound change in the xerogel morphology. The palladium-cobalt-based aerogels possess both micro- and mesoporosity; the xerogels are predominantly microporous with a narrow microporosity. The aerogel surfaces are found to be fractal as analyzed by gas adsorption. Unlike the aerogels, the xerogels do not possess surface fractality. The mechanism of adsorption of different gases on these gels is analyzed based on the gel morphologies. These transition metal-based gels are promising for a variety of applications such as heterogeneous catalysts, gas filters and magnetic materials. The porosity of these gels can be exploited to make gel-embedded filters to separate mixtures of gases based on the their differential adsorption propensities. The reversible adsorption of CO2 can be harnessed practically by using these gels as CO2 storage reservoirs. In the second part of this dissertation, the first, balanced, white
Nanoscale elastic properties of montmorillonite upon water adsorption.
Ebrahimi, Davoud; Pellenq, Roland J-M; Whittle, Andrew J
2012-12-11
Smectites are an important group of clay minerals that experience swelling upon water adsorption. This paper uses molecular dynamics with the CLAYFF force field to simulate isothermal isobaric water adsorption of interlayer Wyoming Na-montmorillonite, a member of the smectite group. Nanoscale elastic properties of the clay-interlayer water system are calculated from the potential energy of the model system. The transverse isotropic symmetry of the elastic constant matrix was assessed by calculating Euclidean and Riemannian distance metrics. Simulated elastic constants of the clay mineral are compared with available results from acoustic and nanoindentation measurements. PMID:23181550
The Suppression of Energy Discretization Errors in Multigroup Transport Calculations
Larsen, Edward
2013-06-17
The Objective of this project is to develop, implement, and test new deterministric methods to solve, as efficiently as possible, multigroup neutron transport problems having an extremely large number of groups. Our approach was to (i) use the standard CMFD method to "coarsen" the space-angle grid, yielding a multigroup diffusion equation, and (ii) use a new multigrid-in-space-and-energy technique to efficiently solve the multigroup diffusion problem. The overall strategy of (i) how to coarsen the spatial an energy grids, and (ii) how to navigate through the various grids, has the goal of minimizing the overall computational effort. This approach yields not only the fine-grid solution, but also coarse-group flux-weighted cross sections that can be used for other related problems.
An artificial energy method for calculating flows with shocks
NASA Technical Reports Server (NTRS)
Rose, M. E.
1980-01-01
The artificial-viscosity method, first proposed by von Neumann and Richtmyer, introduces an artificial viscous pressure term in regions of compression such that an increase in entropy occurs in shock transition zones. The paper describes how dissipative flows can be induced by reducing the total energy available for adiabatic processes in shock zones. A class of inviscid fluid flows, called semiflows, is described in which the flows exhibit thermodynamic differences. Induced dissipative flows modify the pressure in regions of compression in a manner analogous to the artificial-viscosity method and for a gas, the effect is equivalent to suitably modifying the gas constant in the equation of state. By employing MacCormack's method and the usual non-adiabatic equations, numerical solutions of a Riemann problem are compared with the modified artificial energy method, showing that the dissipation effect predicted by the analytical formulation is reflected in the numerical method as well.
Ab initio molecular dynamics calculations of ion hydration free energies
Leung, Kevin; Rempe, Susan B.; Lilienfeld, O. Anatole von
2009-05-28
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or '{lambda}-path' technique to compute the intrinsic hydration free energies of Li{sup +}, Cl{sup -}, and Ag{sup +} ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential ({phi}) contributions, we obtain absolute AIMD hydration free energies ({Delta}G{sub hyd}) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model {phi} predictions. The sums of Li{sup +}/Cl{sup -} and Ag{sup +}/Cl{sup -} AIMD {Delta}G{sub hyd}, which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag{sup +}+Ni{sup +}{yields}Ag+Ni{sup 2+} in water. The predictions for this reaction suggest that existing estimates of {Delta}G{sub hyd} for unstable radiolysis intermediates such as Ni{sup +} may need to be extensively revised.
Calculations of energy levels and lifetimes of low-lying states of barium and radium
Dzuba, V. A.; Ginges, J. S. M.
2006-03-15
We use the configuration-interaction method and many-body perturbation theory to perform accurate calculations of energy levels, transition amplitudes, and lifetimes of low-lying states of barium and radium. Calculations for radium are needed for the planning of measurements of parity- and time-invariance-violating effects which are strongly enhanced in this atom. Calculations for barium are used to control the accuracy of the calculations.
Self-consistent van der Waals density functional study of benzene adsorption on Si(100)
NASA Astrophysics Data System (ADS)
Hamamoto, Yuji; Hamada, Ikutaro; Inagaki, Kouji; Morikawa, Yoshitada
2016-06-01
The adsorption of benzene on the Si(100) surface is studied theoretically using the self-consistent van der Waals density functional (vdW-DF) method. The adsorption energies of two competing adsorption structures, butterfly (BF) and tight-bridge (TB) structures, are calculated with several vdW-DFs at saturation coverage. Our results show that recently proposed vdW-DFs with high accuracy all prefer TB to BF, in accord with more accurate calculations based on exact exchange and correlation within the random-phase approximation. Detailed analyses reveal the important roles played by the molecule-surface interaction and molecular deformation upon adsorption, and we suggest that their precise description is a prerequisite for accurate prediction of the most stable adsorption structure of organic molecules on semiconductor surfaces.
Free-energy calculation methods for collective phenomena in membranes
NASA Astrophysics Data System (ADS)
Smirnova, Yuliya G.; Fuhrmans, Marc; Barragan Vidal, Israel A.; Müller, Marcus
2015-09-01
Collective phenomena in membranes are those which involve the co-operative reorganization of many molecules. Examples of these are membrane fusion, pore formation, bending, adhesion or fission. The time and length scales, on which these processes occur, pose a challenge for atomistic simulations. Therefore, in order to solve the length scale problem it is popular to introduce a coarse-grained representation. To facilitate sampling of the relevant states additional computational techniques, which encourage the system to explore the free-energy landscape far from equilibrium and visit transition states, are needed. These computational techniques provide insights about the free-energy changes involved in collective transformations of membranes, yielding information about the rate limiting states, the transformation mechanism and the influence of architectural, compositional and interaction parameters. A common approach is to identify an order parameter (or reaction coordinate), which characterizes the pathway of membrane reorganization. However, no general strategy exists to define such an order parameter that can properly describe cooperative reorganizations in membranes. Recently developed methods can overcome this problem of the order-parameter choice and allow us to study collective phenomena in membranes. We will discuss such methods as thermodynamic integration, umbrella sampling, and the string method and results provided by their applications to particle-based simulations, particularly focusing on membrane fusion and pore formation.
Parallel implementation of electronic structure energy, gradient, and Hessian calculations.
Lotrich, V; Flocke, N; Ponton, M; Yau, A D; Perera, A; Deumens, E; Bartlett, R J
2008-05-21
ACES III is a newly written program in which the computationally demanding components of the computational chemistry code ACES II [J. F. Stanton et al., Int. J. Quantum Chem. 526, 879 (1992); [ACES II program system, University of Florida, 1994] have been redesigned and implemented in parallel. The high-level algorithms include Hartree-Fock (HF) self-consistent field (SCF), second-order many-body perturbation theory [MBPT(2)] energy, gradient, and Hessian, and coupled cluster singles, doubles, and perturbative triples [CCSD(T)] energy and gradient. For SCF, MBPT(2), and CCSD(T), both restricted HF and unrestricted HF reference wave functions are available. For MBPT(2) gradients and Hessians, a restricted open-shell HF reference is also supported. The methods are programed in a special language designed for the parallelization project. The language is called super instruction assembly language (SIAL). The design uses an extreme form of object-oriented programing. All compute intensive operations, such as tensor contractions and diagonalizations, all communication operations, and all input-output operations are handled by a parallel program written in C and FORTRAN 77. This parallel program, called the super instruction processor (SIP), interprets and executes the SIAL program. By separating the algorithmic complexity (in SIAL) from the complexities of execution on computer hardware (in SIP), a software system is created that allows for very effective optimization and tuning on different hardware architectures with quite manageable effort. PMID:18500853
Parallel implementation of electronic structure energy, gradient, and Hessian calculations
NASA Astrophysics Data System (ADS)
Lotrich, V.; Flocke, N.; Ponton, M.; Yau, A. D.; Perera, A.; Deumens, E.; Bartlett, R. J.
2008-05-01
ACES III is a newly written program in which the computationally demanding components of the computational chemistry code ACES II [J. F. Stanton et al., Int. J. Quantum Chem. 526, 879 (1992); [ACES II program system, University of Florida, 1994] have been redesigned and implemented in parallel. The high-level algorithms include Hartree-Fock (HF) self-consistent field (SCF), second-order many-body perturbation theory [MBPT(2)] energy, gradient, and Hessian, and coupled cluster singles, doubles, and perturbative triples [CCSD(T)] energy and gradient. For SCF, MBPT(2), and CCSD(T), both restricted HF and unrestricted HF reference wave functions are available. For MBPT(2) gradients and Hessians, a restricted open-shell HF reference is also supported. The methods are programed in a special language designed for the parallelization project. The language is called super instruction assembly language (SIAL). The design uses an extreme form of object-oriented programing. All compute intensive operations, such as tensor contractions and diagonalizations, all communication operations, and all input-output operations are handled by a parallel program written in C and FORTRAN 77. This parallel program, called the super instruction processor (SIP), interprets and executes the SIAL program. By separating the algorithmic complexity (in SIAL) from the complexities of execution on computer hardware (in SIP), a software system is created that allows for very effective optimization and tuning on different hardware architectures with quite manageable effort.
NASA Astrophysics Data System (ADS)
Parsons, Drew F.; Salis, Andrea
2015-04-01
The relationship between surface charge and surface potential at the solid-liquid interface is often determined by a charge regulation process, the chemisorption of a potential determining ion such as H+. A subtle ion-specific effect can be observed when other ions compete with the primary potential determining ion to bind to a surface site. Site competition may involve alternative ions competing for a first binding site, e.g., metals ions competing with H+ to bind to a negatively charged oxide or carboxyl site. Second-binding sites with site competition may also be found, including amphoteric OH2+ sites, or anion binding to amine groups. In this work, a general theoretical model is developed to describe the competitive adsorption of ions at surface sites. Applied to the calculation of forces, the theory predicts a 20% increase in repulsion between titania surfaces in 1 mM NaCl, and a 25% reduction in repulsion between silica surfaces in 0.1M NaCl compared to calculations neglecting ion site competition.
Parsons, Drew F; Salis, Andrea
2015-04-01
The relationship between surface charge and surface potential at the solid-liquid interface is often determined by a charge regulation process, the chemisorption of a potential determining ion such as H(+). A subtle ion-specific effect can be observed when other ions compete with the primary potential determining ion to bind to a surface site. Site competition may involve alternative ions competing for a first binding site, e.g., metals ions competing with H(+) to bind to a negatively charged oxide or carboxyl site. Second-binding sites with site competition may also be found, including amphoteric OH2 (+) sites, or anion binding to amine groups. In this work, a general theoretical model is developed to describe the competitive adsorption of ions at surface sites. Applied to the calculation of forces, the theory predicts a 20% increase in repulsion between titania surfaces in 1 mM NaCl, and a 25% reduction in repulsion between silica surfaces in 0.1M NaCl compared to calculations neglecting ion site competition. PMID:25854258
Adsorption of pyridine onto the metal organic framework MIL-101.
Kim, Mi Jin; Park, Se Min; Song, Sun-Jung; Won, Jiyeon; Lee, Jin Yong; Yoon, Minyoung; Kim, Kimoon; Seo, Gon
2011-09-15
The adsorption of pyridine onto the metal organic framework MIL-101 was investigated by experimental and theoretical methods. The amount of pyridine adsorbed on MIL-101 was extraordinarily large at 20 °C, corresponding to about 950 mg/g of dried MIL-101 and approximately half of the voids being filled. Most of the pyridine that had filled the voids was rapidly removed by evacuation at room temperature, but some of the pyridine was so strongly adsorbed that it was retained even under evacuation at 150 °C. Although IR spectra of the adsorbed pyridine indicated the adsorption of pyridine as pyridinium ions and coordinated pyridine at low temperatures, increasing the adsorption temperature induced partial cleavage of the pyridine rings. The high stabilization energy of pyridine on the coordinative unsaturated sites (CUS) of MIL-101, obtained by theoretical calculation, -103 kJ/mol, supported the strong adsorption of pyridine on the CUS. PMID:21700293
Sparta, Manuel; Hansen, Mikkel B; Matito, Eduard; Toffoli, Daniele; Christiansen, Ove
2010-10-12
The availability of an accurate representation of the potential energy surface (PES) is an essential prerequisite in an anharmonic vibrational calculation. At the same time, the high dimensionality of the fully coupled PES and the adverse scaling properties with respect to the molecular size make the construction of an accurate PES a computationally demanding task. In the past few years, our group tested and developed a series of tools and techniques aimed at defining computationally efficient, black-box protocols for the construction of PESs for use in vibrational calculations. This includes the definition of an adaptive density-guided approach (ADGA) for the construction of PESs from an automatically generated set of evaluation points. Another separate aspect has been the exploration of the use of derivative information through modified Shepard (MS) interpolation/extrapolation procedures. With this article, we present an assembled machinery where these methods are embedded in an efficient way to provide both a general machinery as well as concrete computational protocols. In this framework we introduce and discuss the accuracy and computational efficiency of two methods, called ADGA[2gx3M] and ADGA[2hx3M], where the ADGA recipe is used (with MS interpolation) to automatically define modest sized grids for up to two-mode couplings, while MS extrapolation based on, respectively, gradients only and gradients and Hessians from the ADGA determined points provides access to sufficiently accurate three-mode couplings. The performance of the resulting potentials is investigated in vibrational coupled cluster (VCC) calculations. Three molecular systems serve as benchmarks: a trisubstituted methane (CHFClBr), methanimine (CH2NH), and oxazole (C3H3NO). Furthermore, methanimine and oxazole are addressed in accurate calculations aiming to reproduce experimental results. PMID:26616778
Study on the adsorption properties of O3, SO2, and SO3 on B-doped graphene using DFT calculations
NASA Astrophysics Data System (ADS)
Rad, Ali Shokuhi; Shabestari, Sahand Sadeghi; Mohseni, Soheil; Aghouzi, Samaneh Alijantabar
2016-05-01
We investigated the structure, adsorption, electronic states, and charge transfer of O3, SO2 and SO3 molecules on the surface of a B-doped graphene using density functional theory (DFT). We found weak physisorption of SO2 (-10.9 kJ/mole, using B3LYP-D) and SO3 (-15.7 kJ/mole, using B3LYP-D) on the surface of B-doped graphene while there is strong chemisorption for O3 (-96.3 kJ/mole, using B3LYP-D) on this surface. Our results suggest the potential of B-doped graphene as a selective sensor/adsorbent for O3 molecule. We noticed some change in hybridizing of boron from sp2 to sp3 upon adsorption of O3 which cases transformation of the adsorbent from 2D to 3D.
NASA Astrophysics Data System (ADS)
Szatanik-Kloc, Alicja
2016-07-01
The plant reactions on Al-stress include i.a. change of the surface area of the roots, which in the physicochemistry of plants characterizes the transport of water and ions through the root. The object of this study is the specific surface area of the roots of plants which are tolerant to aluminium, such as rye. Plants of rye were grown in a nutrient solution for 14 days at pH 4.5 in the presence of Al3+ ions of concentration 10, 20, and 40 mg dm-3. The control plants were grown continuously at pH 7 or pH 4.5 without Al3+. The apparent surface area and adsorption energy of the plants roots were determined from water vapour adsorption - desorption data. The apparent surface area of roots growing in the aluminium was (with respect to control) statistically significantly lower. There were no statistically significant differences in the apparent surface area of the roots which grew in pH 7, pH 4.5 without Al3+. The average water vapour adsorption energy of the root surface, under stress conditions decreased. In the roots grown in the presence of Al+3, there was a slight decrease in high energy adsorption centres and an increase in the amount of low-energy centres.
Adsorption of silver dimer on graphene - A DFT study
Kaur, Gagandeep; Gupta, Shuchi; Rani, Pooja; Dharamvir, Keya
2014-04-24
We performed a systematic density functional theory (DFT) study of the adsorption of silver dimer (Ag{sub 2}) on graphene using SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) package, in the generalized gradient approximation (GGA). The adsorption energy, geometry, and charge transfer of Ag2-graphene system are calculated. The minimum energy configuration for a silver dimer is parallel to the graphene sheet with its two atoms directly above the centre of carbon-carbon bond. The negligible charge transfer between the dimer and the surface is also indicative of a weak bond. The methodology demonstrated in this paper may be applied to larger silver clusters on graphene sheet.
Chiral effect of the dissociative adsorption of molecular oxygen on the carbon nanotube surface
NASA Astrophysics Data System (ADS)
Shamina, E. N.; Lebedev, N. G.
2015-05-01
The electronic-energy characteristics of the adsorption of the oxygen molecule in the ground triplet and excited singlet states on the surface of chiral and achiral single-walled carbon nanotubes were studied by semiempirical MNDO and PM3 quantum-chemical methods using the molecular cluster model with boundary pseudoatoms. The energies of dissociative adsorption of molecular oxygen on the surface of nanotubes were calculated. The chiral effect of the dissociative adsorption of the O2 molecule was predicted and studied. The diameters of the carbon nanotubes that adsorb molecular oxygen most effectively were predicted. A physical rationale of the obtained dependences was presented.
Xu, Xianglan; Sun, Xiongfei; Sun, Baozhen; Peng, Honggen; Liu, Wenming; Wang, Xiang
2016-07-01
To explore metal oxide-support interaction and its effect on O2 adsorption, periodic DFT calculations were used to explore the most preferred O2 molecular and dissociative adsorption on stoichiometric (MO2) and defective (MO2-x) (M=Ru, Ir, Sn) films supported on rutile TiO2(110), and compared with that on pure surfaces without TiO2(110) support. For defective RuO2-x films, it is revealed that the TiO2(110) support and the film thickness have an evident impact on the O2 adsorbed species. On the contrary, the two factors show little influence for defective IrO2-x and SnO2-x films. The analyses for Bader charge and density of states indicate that the reducibility change of the unsaturated surface Ru atoms, which are adjacent to the bridge oxygen vacancies, is responsible for this O2 adsorption alteration. These results provide insights into the oxide-oxide interaction, and its effect on the properties of supported oxide catalysts. PMID:27060230
Perfetti, Christopher M; Rearden, Bradley T
2014-01-01
This work introduces a new approach for calculating sensitivity coefficients for generalized neutronic responses to nuclear data uncertainties using continuous-energy Monte Carlo methods. The approach presented in this paper, known as the GEAR-MC method, allows for the calculation of generalized sensitivity coefficients for multiple responses in a single Monte Carlo calculation with no nuclear data perturbations or knowledge of nuclear covariance data. The theory behind the GEAR-MC method is presented here, and proof of principle is demonstrated by using the GEAR-MC method to calculate sensitivity coefficients for responses in several 3D, continuous-energy Monte Carlo applications.
NASA Astrophysics Data System (ADS)
Derfel, Grzegorz; Buczkowska, Mariola
2011-07-01
The influence of ion adsorption on the behavior of the nematic liquid crystal layers is studied numerically. The homeotropic flexoelectric layer subjected to the dc electric field is considered. Selective adsorption of positive ions is assumed. The analysis is based on the free energy formalism for ion adsorption. The distributions of director orientation angle, electric potential, and ion concentrations are calculated by numerical resolving of suitable torques equations and Poisson equation. The threshold voltages for the deformations are also determined. It was shown that adsorption affects the distributions of both cations and anions. Sufficiently large number of adsorbed ions leads to spontaneous deformation arising without any threshold if the total number of ions creates sufficiently strong electric field with significant field gradients in the neighborhood of electrodes. The spontaneous deformations are favored by strong flexoelectricity, large thickness, large ion concentrations, weak anchoring, and large adsorption energy.
Quantum Monte Carlo investigations of adsorption energetics on graphene.
Hsing, C R; Wei, C M; Chou, M Y
2012-10-01
We have performed calculations of adsorption energetics on the graphene surface using the state-of-the-art diffusion quantum Monte Carlo method. Two types of configurations are considered in this work: the adsorption of a single O, F, or H atom on the graphene surface and the H-saturated graphene system (graphane). The adsorption energies are compared with those obtained from density functional theory with various exchange-correlation functionals. The results indicate that the approximate exchange-correlation functionals significantly overestimate the binding of O and F atoms on graphene, although the preferred adsorption sites are consistent. The energy errors are much less for atomic hydrogen adsorbed on the surface. We also find that a single O or H atom on graphene has a higher energy than in the molecular state, while the adsorption of a single F atom is preferred over the gas phase. In addition, the energetics of graphane is reported. The calculated equilibrium lattice constant turns out to be larger than that of graphene, at variance with a recent experimental suggestion. PMID:22909778
Adsorption of CO on Ni/Cu(110) bimetallic surfaces
NASA Astrophysics Data System (ADS)
Demirci, E.; Carbogno, C.; Groß, A.; Winkler, A.
2009-08-01
The adsorption behavior of CO on bimetallic Ni/Cu(110) surfaces has been studied experimentally by thermal-desorption spectroscopy and theoretically by density-functional theory (DFT) calculations. The bimetallic surfaces were produced either by evaporation of nickel or by decomposition of Ni(CO)4 on Cu(110). Adsorption of CO at 180 K on such a bimetallic surface yields three new adsorption states with adsorption energies between that of CO on clean Cu(110) and clean Ni(110). The new desorption peaks from the bimetallic surface, designated as β1-β3 , can be observed at 250, 300, and 360 K, respectively. These new states are most pronounced when (1)/(2) monolayer of nickel is present on the copper surface. DFT calculations, using the Vienna ab initio simulation package code, were performed to identify the most probable Ni/Cu atomic arrangements at the bimetallic surface to reconcile with the experimental results. It turned out that CO adsorption on nickel dimers consisting of in-surface and adjacent subsurface atoms can best explain the observed experimental data. The result shows that CO adsorption is determined by local (geometric) effects rather than by long-range (electronic) effects. These findings should contribute to a better understanding of tailoring catalytic processes with the help of bimetallic catalysts.
Calculating kinetics parameters and reactivity changes with continuous-energy Monte Carlo
Kiedrowski, Brian C; Brown, Forrest B; Wilson, Paul
2009-01-01
The iterated fission probability interpretation of the adjoint flux forms the basis for a method to perform adjoint weighting of tally scores in continuous-energy Monte Carlo k-eigenvalue calculations. Applying this approach, adjoint-weighted tallies are developed for two applications: calculating point reactor kinetics parameters and estimating changes in reactivity from perturbations. Calculations are performed in the widely-used production code, MCNP, and the results of both applications are compared with discrete ordinates calculations, experimental measurements, and other Monte Carlo calculations.
A Python tool to set up relative free energy calculations in GROMACS.
Klimovich, Pavel V; Mobley, David L
2015-11-01
Free energy calculations based on molecular dynamics (MD) simulations have seen a tremendous growth in the last decade. However, it is still difficult and tedious to set them up in an automated manner, as the majority of the present-day MD simulation packages lack that functionality. Relative free energy calculations are a particular challenge for several reasons, including the problem of finding a common substructure and mapping the transformation to be applied. Here we present a tool, alchemical-setup.py, that automatically generates all the input files needed to perform relative solvation and binding free energy calculations with the MD package GROMACS. When combined with Lead Optimization Mapper (LOMAP; Liu et al. in J Comput Aided Mol Des 27(9):755-770, 2013), recently developed in our group, alchemical-setup.py allows fully automated setup of relative free energy calculations in GROMACS. Taking a graph of the planned calculations and a mapping, both computed by LOMAP, our tool generates the topology and coordinate files needed to perform relative free energy calculations for a given set of molecules, and provides a set of simulation input parameters. The tool was validated by performing relative hydration free energy calculations for a handful of molecules from the SAMPL4 challenge (Mobley et al. in J Comput Aided Mol Des 28(4):135-150, 2014). Good agreement with previously published results and the straightforward way in which free energy calculations can be conducted make alchemical-setup.py a promising tool for automated setup of relative solvation and binding free energy calculations. PMID:26487189
Effect of composition on antiphase boundary energy in Ni3Al based alloys: Ab initio calculations
NASA Astrophysics Data System (ADS)
Gorbatov, O. I.; Lomaev, I. L.; Gornostyrev, Yu. N.; Ruban, A. V.; Furrer, D.; Venkatesh, V.; Novikov, D. L.; Burlatsky, S. F.
2016-06-01
The effect of composition on the antiphase boundary (APB) energy of Ni-based L 12-ordered alloys is investigated by ab initio calculations employing the coherent potential approximation. The calculated APB energies for the {111} and {001} planes reproduce experimental values of the APB energy. The APB energies for the nonstoichiometric γ' phase increase with Al concentration and are in line with the experiment. The magnitude of the alloying effect on the APB energy correlates with the variation of the ordering energy of the alloy according to the alloying element's position in the 3 d row. The elements from the left side of the 3 d row increase the APB energy of the Ni-based L 12-ordered alloys, while the elements from the right side slightly affect it except Ni. The way to predict the effect of an addition on the {111} APB energy in a multicomponent alloy is discussed.
A Simple Approach for the Calculation of Energy Levels of Light Atoms
ERIC Educational Resources Information Center
Woodyard, Jack R., Sr.
1972-01-01
Describes a method for direct calculation of energy levels by using elementary techniques. Describes the limitations of the approach but also claims that with a minimum amount of labor a student can get greater understanding of atomic physics problems. (PS)
Ghosh, Soumya; Hammes-Schiffer, Sharon
2015-01-01
Electrochemical electron transfer reactions play an important role in energy conversion processes with many technological applications. Electrodes modified by self-assembled monolayers (SAMs) exhibit reduced double layer effects and are used in molecular electronics. An important quantity for calculating the electron transfer rate constant is the reorganization energy, which is associated with changes in the solute geometry and the environment. In this Letter, an approach for calculating the electrochemical reorganization energy for a redox molecule attached to or near a SAM modified electrode is presented. This integral equations formalism polarizable continuum model (IEF-PCM) approach accounts for the detailed electronic structure of the molecule, as well as the contributions from the electrode, SAM, and electronic and inertial solvent responses. The calculated total reorganization energies are in good agreement with experimental data for a series of metal complexes in aqueous solution. This approach will be useful for calculating electron transfer rate constants for molecular electrocatalysts. PMID:26263083
NASA Astrophysics Data System (ADS)
Wu, Zhe-Ying; Qi, Chong; Wyss, Ramon; Liu, Hong-Liang
2015-08-01
Background: The deviation between different model calculations that may occur when one goes toward regions where the masses are unknown is getting increased attention. This is related to the uncertainties of the different models which may have not been fully understood. Purpose: To explore in detail the effect of the isospin dependence of the spin-orbital force in the Woods-Saxon potential on global binding energy and deformation calculations. Method: The microscopic energies and nuclear deformations of about 1850 even-even nuclei are calculated systematically within the macroscopic-microscopic framework using three Woods-Saxon parametrizations, with different isospin dependencies, which were constructed mainly for nuclear spectroscopy calculations. Calculations are performed in the deformation space (β2,γ ,β4) . Both the monopole and doubly stretched quadrupole interactions are considered for the pairing channel. Results: The ground-state deformations obtained by the three calculations are quite similar to each other. Large differences are seen mainly in neutron-rich nuclei and in superheavy nuclei. Systematic calculations on the shape-coexisting second minima are also presented. As for the microscopic energies of the ground states, the results are also very close to each other. Only in a few cases the difference is larger than 2 MeV. The total binding energy is estimated by adding the macroscopic energy provided by the usual liquid drop model with its parameters fitted through the least square root and minimax criteria. Calculations are also compared with the results of other macroscopic-microscopic mass models. Conclusions: All the three calculations give similar values for the deformations, microscopic energies, and binding energies of most nuclei. One may expect to have a better understanding of the isospin dependence of the spin-orbital force with more data on proton- and neutron-rich nuclei.
Wind Energy Finance (WEF): An Online Calculator for Economic Analysis of Wind Projects
Not Available
2004-02-01
This brochure provides an overview of Wind Energy Finance (WEF), a free online cost of energy calculator developed by the National Renewable Energy Laboratory that provides quick, detailed economic evaluation of potential utility-scale wind energy projects. The brochure lists the features of the tool, the inputs and outputs that a user can expect, visuals of the screens and a Cash Flow Results table, and contact information.
NASA Astrophysics Data System (ADS)
Ratsch, Christian; Kaminski, Jakub
In this talk we will present a new approach for the calculation of surface energies of periodic crystal. For non-polar materials slabs (which are terminated by two identical surfaces) the task of calculating the surface energy is trivial. But it is more problematic for polar systems where both terminating surfaces are different, as there is no single established method allowing for equal treatment of a wide range of surface morphologies and orientations. Our proposed new approach addresses this problem. It relies on carefully chosen capping atoms and the assumptions that their bond energy contributions can be used to approximate the total energy of the surface. The choice of the capping atoms is governed by a set of simple guidelines that are applicable for surfaces with different terminations. We present the results for different semiconductor materials and show that our approach leads to surfaces energies with errors as low as 2%. We show that hydrogen is not always the best choice for a capping atom if accurate surface energies are the target of the calculations. Our approach is suitable for high-throughput screening of new material interfaces, as accurate calculations of surface energies can be performed in an unsupervised algorithm. A New Approach for Surface Energy Calculations Applicable to High-throughput Design of New Interfaces.
Variational calculation of highly excited rovibrational energy levels of H2O2.
Polyansky, Oleg L; Kozin, Igor N; Ovsyannikov, Roman I; Małyszek, Paweł; Koput, Jacek; Tennyson, Jonathan; Yurchenko, Sergei N
2013-08-15
Results are presented for highly accurate ab initio variational calculation of the rotation-vibration energy levels of H2O2 in its electronic ground state. These results use a recently computed potential energy surface and the variational nuclear-motion programs WARV4, which uses an exact kinetic energy operator, and TROVE, which uses a numerical expansion for the kinetic energy. The TROVE calculations are performed for levels with high values of rotational excitation, J up to 35. The purely ab initio calculations of the rovibrational energy levels reproduce the observed levels with a standard deviation of about 1 cm(-1), similar to that of the J = 0 calculation, because the discrepancy between theory and experiment for rotational energies within a given vibrational state is substantially determined by the error in the vibrational band origin. Minor adjustments are made to the ab initio equilibrium geometry and to the height of the torsional barrier. Using these and correcting the band origins using the error in J = 0 states lowers the standard deviation of the observed-calculated energies to only 0.002 cm(-1) for levels up to J = 10 and 0.02 cm(-1) for all experimentally known energy levels, which extend up to J = 35. PMID:23611762
T. Downar
2009-03-31
The overall objective of the work here has been to eliminate the approximations used in current resonance treatments by developing continuous energy multi-dimensional transport calculations for problem dependent self-shielding calculations. The work here builds on the existing resonance treatment capabilities in the ORNL SCALE code system.
METHODOLOGICAL NOTES: Energy density calculations for ball-lightning-like luminous silicon balls
NASA Astrophysics Data System (ADS)
Paiva, Gerson S.; Ferreira, Joacy V.; Bastos, Cristiano C.; dos Santos, Marcus V.; Pavão, Antonio C.
2010-05-01
The energy density of a luminous silicon ball [Phys. Rev. Lett. 98 048501 (2007)] is calculated for a model with a metal core surrounded by an atmosphere of silicon oxides. Experimental data combined with the molecular orbital calculations of the oxidation enthalpy lead to a mean energy density of 3.9 MJ m-3, which is within the range of estimates from other ball lightning models. This result provides good evidence to support the silicon-based model.
Cimino, Richard T; Rasmussen, Christopher J; Brun, Yefim; Neimark, Alexander V
2016-11-01
Polymer adsorption is a ubiquitous phenomenon with numerous technological and healthcare applications. The mechanisms of polymer adsorption on surfaces and in pores are complex owing to a competition between various entropic and enthalpic factors. Due to adsorption of monomers to the surface, the chain gains in enthalpy yet loses in entropy because of confining effects. This competition leads to the existence of critical conditions of adsorption when enthalpy gain and entropy loss are in balance. The critical conditions are controlled by the confining geometry and effective adsorption energy, which depends on the solvent composition and temperature. This phenomenon has important implications in polymer chromatography, since the retention at the critical point of adsorption (CPA) is chain length independent. However, the mechanisms of polymer adsorption in pores are poorly understood and there is an ongoing discussion in the theoretical literature about the very existence of CPA for polymer adsorption on porous substrates. In this work, we examine the mechanisms of chain adsorption on a model porous substrate using Monte Carlo (MC) simulations. We distinguish three adsorption mechanisms depending on the chain location: on external surface, completely confined in pores, and also partially confined in pores in so-called "flower" conformations. The free energies of different conformations of adsorbed chains are calculated by the incremental gauge cell MC method that allows one to determine the partition coefficient as a function of the adsorption potential, pore size, and chain length. We confirm the existence of the CPA for chain length independent separation on porous substrates, which is explained by the dominant contributions of the chain adsorption at the external surface, in particular in flower conformations. Moreover, we show that the critical conditions for porous and nonporous substrates are identical and depend only on the surface chemistry. The theoretical
George, K.; Schweizer, T.
2008-01-01
This report details the methodology used by DOE to calculate levelized cost of wind energy and demonstrates the variation in COE estimates due to different financing assumptions independent of wind generation technology.
Quantum Monte Carlo calculation of the binding energy of the beryllium dimer
Deible, Michael J.; Kessler, Melody; Gasperich, Kevin E.; Jordan, Kenneth D.
2015-08-28
The accurate calculation of the binding energy of the beryllium dimer is a challenging theoretical problem. In this study, the binding energy of Be{sub 2} is calculated using the diffusion Monte Carlo (DMC) method, using single Slater determinant and multiconfigurational trial functions. DMC calculations using single-determinant trial wave functions of orbitals obtained from density functional theory calculations overestimate the binding energy, while DMC calculations using Hartree-Fock or CAS(4,8), complete active space trial functions significantly underestimate the binding energy. In order to obtain an accurate value of the binding energy of Be{sub 2} from DMC calculations, it is necessary to employ trial functions that include excitations outside the valence space. Our best estimate DMC result for the binding energy of Be{sub 2}, obtained by using configuration interaction trial functions and extrapolating in the threshold for the configurations retained in the trial function, is 908 cm{sup −1}, only slightly below the 935 cm{sup −1} value derived from experiment.
Quantum Monte Carlo calculation of the binding energy of the beryllium dimer.
Deible, Michael J; Kessler, Melody; Gasperich, Kevin E; Jordan, Kenneth D
2015-08-28
The accurate calculation of the binding energy of the beryllium dimer is a challenging theoretical problem. In this study, the binding energy of Be2 is calculated using the diffusion Monte Carlo (DMC) method, using single Slater determinant and multiconfigurational trial functions. DMC calculations using single-determinant trial wave functions of orbitals obtained from density functional theory calculations overestimate the binding energy, while DMC calculations using Hartree-Fock or CAS(4,8), complete active space trial functions significantly underestimate the binding energy. In order to obtain an accurate value of the binding energy of Be2 from DMC calculations, it is necessary to employ trial functions that include excitations outside the valence space. Our best estimate DMC result for the binding energy of Be2, obtained by using configuration interaction trial functions and extrapolating in the threshold for the configurations retained in the trial function, is 908 cm(-1), only slightly below the 935 cm(-1) value derived from experiment. PMID:26328827
Metals on graphene: correlation between adatom adsorption behavior and growth morphology
Liu, Xiaojie; Wang, Cai-Zhuang; Hupalo, Myron; Lu, Wencai; Tringides, Michael C.; Yao, Yongxin; Ho, Kai-Ming
2012-05-19
We present a systematic study of metal adatom adsorption on graphene by ab initio calculations. The calculations cover alkali metals, sp-simple metals, 3d and group 10 transition metals, noble metals, as well as rare earth metals. The correlation between the adatom adsorption properties and the growth morphology of the metals on graphene is also investigated. We show that the growth morphology is related to the ratio of the metal adsorption energy to its bulk cohesive energy (E(a)/E(c)) and the diffusion barrier (ΔE) of the metal adatom on graphene. Charge transfer, electric dipole and magnetic moments, and graphene lattice distortion induced by metal adsorption would also affect the growth morphologies of the metal islands. We also show that most of the metal nanostructures on graphene would be thermally stable against coarsening.
Nuclear data processing for energy release and deposition calculations in the MC21 Monte Carlo code
Trumbull, T. H.
2013-07-01
With the recent emphasis in performing multiphysics calculations using Monte Carlo transport codes such as MC21, the need for accurate estimates of the energy deposition-and the subsequent heating - has increased. However, the availability and quality of data necessary to enable accurate neutron and photon energy deposition calculations can be an issue. A comprehensive method for handling the nuclear data required for energy deposition calculations in MC21 has been developed using the NDEX nuclear data processing system and leveraging the capabilities of NJOY. The method provides a collection of data to the MC21 Monte Carlo code supporting the computation of a wide variety of energy release and deposition tallies while also allowing calculations with different levels of fidelity to be performed. Detailed discussions on the usage of the various components of the energy release data are provided to demonstrate novel methods in borrowing photon production data, correcting for negative energy release quantities, and adjusting Q values when necessary to preserve energy balance. Since energy deposition within a reactor is a result of both neutron and photon interactions with materials, a discussion on the photon energy deposition data processing is also provided. (authors)
Phenomenological calculation of nuclear binding energy and density with Yukawa-potentials
NASA Astrophysics Data System (ADS)
Scheid, W.
2016-01-01
In this paper, we study a phenomenological collective model for the calculation of the nuclear density and ground state binding energy of nuclei. The proton density is assumed proportional to the nuclear density. The total binding energy of the nuclear matter consists of the binding energy of infinite nuclear matter, of two Yukawa-potentials, of the Coulomb-energy and of the symmetry-energy. The parameters of the Yukawa-potential are fitted with the Bethe-Weizsäcker (BW) mass formula. The resulting binding energies and nuclear densities agree quite satisfying with known nuclear values.
Douillard, Jean-Marc; Salles, Fabrice; Henry, Marc; Malandrini, Harold; Clauss, Frédéric
2007-01-15
The surface energies of talc and chlorite is computed using a simple model, which uses the calculation of the electrostatic energy of the crystal. It is necessary to calculate the atomic charges. We have chosen to follow Henry's model of determination of partial charges using scales of electronegativity and hardness. The results are in correct agreement with a determination of the surface energy obtained from an analysis of the heat of immersion data. Both results indicate that the surface energy of talc is lower than the surface energy of chlorite, in agreement with observed behavior of wettability. The influence of Al and Fe on this phenomenon is discussed. Surface energy of this type of solids seems to depend more strongly on the geometry of the crystal than on the type of atoms pointing out of the surface; i.e., the surface energy depends more on the physics of the system than on its chemistry. PMID:17081554
Adsorption and Desorption of Nitrogen and Water Vapor by clay
NASA Astrophysics Data System (ADS)
Cui, Deshan; Chen, Qiong; Xiang, Wei; Huang, Wei
2015-04-01
Adsorption and desorption of nitrogen and water vapor by clay has a significant impact on unsaturated soil physical and mechanical properties. In order to study the adsorption and desorption characteristics of nitrogen and water vapor by montmorillonite, kaolin and sliding zone soils, the Autosorb-iQ specific surface area and pore size analyzer instrument of United State was taken to carry out the analysis test. The adsorption and desorption of nitrogen at 77K and water vapor at 293K on clay sample were conducted. The theories of BET, FHH and hydration energy were taken to calculate the specific surface, surface fractal dimension and adsorption energy. The results show that the calculated specific surface of water vapor by clay is bigger than nitrogen adsorption test because clay can adsorb more water vapor molecule than nitrogen. Smaller and polar water vapor molecule can access the micropore and then adsorb on the mineral surface and mineral intralayer, which make the mineral surface cations hydrate and the mineral surface smoother. Bigger and nonpolar nitrogen molecule can not enter into the micropore as water vapor molecule and has weak interaction with clay surface.
Water and Carbon Dioxide Adsorption at Olivine Surfaces
Kerisit, Sebastien N.; Bylaska, Eric J.; Felmy, Andrew R.
2013-11-14
Plane-wave density functional theory (DFT) calculations were performed to simulate water and carbon dioxide adsorption at the (010) surface of five olivine minerals, namely, forsterite (Mg2SiO4), calcio-olivine (Ca2SiO4), tephroite (Mn2SiO4), fayalite (Fe2SiO4), and Co-olivine (Co2SiO4). Adsorption energies per water molecule obtained from energy minimizations varied from -78 kJ mol-1 for fayalite to -128 kJ mol-1 for calcio-olivine at sub-monolayer coverage and became less exothermic as coverage increased. In contrast, carbon dioxide adsorption energies at sub-monolayer coverage ranged from -20 kJ mol-1 for fayalite to -59 kJ mol-1 for calcio-olivine. Therefore, the DFT calculations show a strong driving force for carbon dioxide displacement by water at the surface of all olivine minerals in a competitive adsorption scenario. Additionally, adsorption energies for both water and carbon dioxide were found to be more exothermic for the alkaline-earth (AE) olivines than for the transition-metal (TM) olivines and to not correlate with the solvation enthalpies of the corresponding divalent cations. However, a correlation was obtained with the charge of the surface divalent cation indicating that the more ionic character of the AE cations in the olivine structure relative to the TM cations leads to greater interactions with adsorbed water and carbon dioxide molecules at the surface and thus more exothermic adsorption energies for the AE olivines. For calcio-olivine, which exhibits the highest divalent cation charge of the five olivines, ab initio molecular dynamics simulations showed that this effect leads both water and carbon dioxide to react with the surface and form hydroxyl groups and a carbonate-like species, respectively.
PERTURB: A program for calculating vibrational energies by generalized algebraic quantization
NASA Astrophysics Data System (ADS)
Fried, Laurence E.; Ezra, Gregory S.
1988-09-01
We describe PERTURB, a special purpose algebraic manipulation program which calculates vibrational eigenvalues in coupled oscillator systems. PERTURB implements the method of generalized algebraic quantization (AQ), in which Van Vleck perturbation theory is formulated in a mock phase space. The phase space formulation enables quantum and classical perturbation theory to be treated on the same footing, and allows the systematic calculation of corrections to classical perturbation results in powers of h̷. Generalized AQ is a powerful and efficient technique for calculating semiclassical vibrational energy levels. In many cases, including just the first correction to classical perturbation theory yields highly accurate energies.
Continuous-energy eigenvalue sensitivity coefficient calculations in TSUNAMI-3D
Perfetti, C. M.; Rearden, B. T.
2013-07-01
Two methods for calculating eigenvalue sensitivity coefficients in continuous-energy Monte Carlo applications were implemented in the KENO code within the SCALE code package. The methods were used to calculate sensitivity coefficients for several test problems and produced sensitivity coefficients that agreed well with both reference sensitivities and multigroup TSUNAMI-3D sensitivity coefficients. The newly developed CLUTCH method was observed to produce sensitivity coefficients with high figures of merit and a low memory footprint, and both continuous-energy sensitivity methods met or exceeded the accuracy of the multigroup TSUNAMI-3D calculations. (authors)
Development of a SCALE Tool for Continuous-Energy Eigenvalue Sensitivity Coefficient Calculations
Perfetti, Christopher M; Rearden, Bradley T
2013-01-01
Two methods for calculating eigenvalue sensitivity coefficients in continuous-energy Monte Carlo applications were implemented in the KENO code within the SCALE code package. The methods were used to calculate sensitivity coefficients for several criticality safety problems and produced sensitivity coefficients that agreed well with both reference sensitivities and multigroup TSUNAMI-3D sensitivity coefficients. The newly developed CLUTCH method was observed to produce sensitivity coefficients with high figures of merit and low memory requirements, and both continuous-energy sensitivity methods met or exceeded the accuracy of the multigroup TSUNAMI-3D calculations.
Development of a SCALE Tool for Continuous-Energy Eigenvalue Sensitivity Coefficient Calculations
NASA Astrophysics Data System (ADS)
Perfetti, Christopher M.; Rearden, Bradley T.
2014-06-01
Two methods for calculating eigenvalue sensitivity coefficients in continuous-energy Monte Carlo applications were implemented in the KENO code within the SCALE code package. The methods were used to calculate sensitivity coefficients for several criticality safety problems and produced sensitivity coefficients that agreed well with both reference sensitivities and multigroup TSUNAMI-3D sensitivity coefficients. The newly developed CLUTCH method was observed to produce sensitivity coefficients with high figures of merit and low memory requirements, and both continuous-energy sensitivity methods met or exceeded the accuracy of the multigroup TSUNAMI-3D calculations.
Atomic and molecular adsorption on Au(111)
Santiago-Rodríguez, Yohaselly; Herron, Jeffrey A.; Curet-Arana, María C.; Mavrikakis, Manos
2014-09-01
Periodic self-consistent density functional theory (DFT-GGA) calculations were used to study the adsorption of several atomic species, molecular species and molecular fragments on the Au(111) surface with a coverage of 1/4 monolayer (ML). Binding geometries, binding energies, and diffusion barriers were calculated for 27 species. Furthermore, we calculated the surface deformation energy associated with the binding events. The binding strength for all the analyzed species can be ordered as follows: NH_{3} < NO < CO < CH_{3} < HCO < NH_{2} < COOH < OH < HCOO < CNH_{2} < H < N < NH < NOH < COH < Cl,< HCO_{3} < CH_{2} < CN b HNO < O < F < S < C < CH. Although the atomic species preferred to bind at the three-fold fcc site, no tendency was observed in site preference for the molecular species and fragments. The intramolecular and adsorbate-surface vibrational frequencies were calculated for all the adsorbates on their most energetically stable adsorption site. Most of the theoretical binding energies and frequencies agreed with experimental values reported in the literature. In general, the values obtained with the PW91 functional are more accurate than RPBE in reproducing these experimental binding energies. The energies of the adsorbed species were used to calculate the thermochemical potential energy surfaces for decomposition of CO, NO, N_{2}, NH_{3} and CH_{4}, oxidation of CO, and hydrogenation of CO, CO_{2} and NO, giving insight into the thermochemistry of these reactions on gold nanoparticles. These potential energy surfaces demonstrated that: the decomposition of species is not energetically favorable on Au(111); the desorption of NH_{3}, NO and CO are more favorable than their decomposition; the oxidation of CO and hydrogenation of CO and NO on Au(111) to form HCO and HNO, respectively, are also thermodynamically favorable.
Simple energy-calculation method for solar industrial-process-heat steam systems
NASA Astrophysics Data System (ADS)
Gee, R. C.
1983-01-01
Designing a solar industrial process heat (IPH) system, sizing its components and predicting its annual energy delivery requires a method for calculating solar system performance. A calculation method that is accurate, easy to use, accounts for the impact of all important system parameters, and does not require use of a computer is described. Only simple graphs and a hand calculator are required to predict annual collector field performance and annual system losses. The energy calculation method is applicable to a variety of solar system configurations. The calculation method applied only to parabolic trough steam generation systems that do not employ thermal storage is described. Both flash tank and unfired boiler steam systems are covered.
Simple energy-calculation method for solar industrial-process-heat steam systems
Gee, R.
1983-01-01
Designing a solar industrial-process heat (IPH) system, sizing its components and predicting its annual energy delivery requires a method for calculating solar system performance. A calculation method that is accurate, easy to use, accounts for the impact of all important system parameters, and does not require use of a computer is described. Only simple graphs and a hand calculator are required to predict annual collector field performance and annual system losses. The energy-calculation method is applicable to a variety of solar-system configurations. The calculation method applied only to parabolic-trough steam-generation systems that do not employ thermal storage is described. Both flash tank and unfired-boiler steam systems are covered.
NASA Astrophysics Data System (ADS)
Montgomery, Jason
2007-12-01
Scattering resonances play a key role in many chemical processes, including unimolecular and bimolecular reactions and photodissociation. A significant theoretical emphasis over the past several decades has been placed on accurate resonance calculations for polyatomic systems. In spite of such efforts, a quantum treatment of molecular systems which exhibit a high density of states and strong coordinate coupling near dissociation remains a formidable task. The research described herein employs improved quantum mechanical methods to calculate a representation of nuclear motion, both bound and unbound, which is used subsequently to calculate accurate resonance energies and lifetimes for two triatomic systems: the neon trimer and ozone. Specifically, theory and results are given regarding the construction of an optimal, L2 eigenbasis using techniques such as the discrete variable representation, the energy selected basis (ESB) method, and iterative diagonalization methods. A new energy selection method is also developed and implemented for the neon trimer. Subsequent resonance calculations are described which make use of the artificial boundary inhomogeneity (ABI) method, adapted to work with the above mentioned ESB and hyperspherical coordinates. The ABI method is used to calculate a set of linearly independent wavefunctions (LIWs) at a given energy for the representation of the scattering wavefunction. Resonance parameters are obtained by imposing scattering boundary conditions on a linear combination of LIWs and solving for the S-matrix, S, its energy derivative, dS/dE, and the Smith lifetime matrix, Q. When available, comparisons are made with previously reported calculations.
Kinetics and Thermodynamics of Reserpine Adsorption onto Strong Acidic Cationic Exchange Fiber
Guo, Zhanjing; Liu, Xiongmin; Huang, Hongmiao
2015-01-01
The kinetics and thermodynamics of the adsorption process of reserpine adsorbed onto the strong acidic cationic exchange fiber (SACEF) were studied by batch adsorption experiments. The adsorption capacity strongly depended on pH values, and the optimum reserpine adsorption onto the SACEF occurred at pH = 5 of reserpine solution. With the increase of temperature and initial concentration, the adsorption capacity increased. The equilibrium was attained within 20 mins. The adsorption process could be better described by the pseudo-second-order model and the Freundlich isotherm model. The calculated activation energy Ea was 4.35 kJ/mol. And the thermodynamic parameters were: 4.97<ΔH<7.44 kJ/mol, -15.29<ΔG<-11.87 kJ/mol and 41.97<ΔS<47.35 J/mol·K. The thermodynamic parameters demonstrated that the adsorption was an endothermic, spontaneous and feasible process of physisorption within the temperature range between 283 K and 323 K and the initial concentration range between 100 mg/L and 300 mg/L. All the results showed that the SACEF had a good adsorption performance for the adsorption of reserpine from alcoholic solution. PMID:26422265
Meson self-energies calculated by the relativistic particle-hole-antiparticle representation
Nakano, M.; Noda, N.; Mitsumori, T.; Koide, K.; Kouno, H.; Hasegawa, A.; Liu, L.
1997-12-01
A new formulation of meson self-energies is introduced for {sigma},{omega},{pi},{rho},{delta}, and {eta} mesons on the basis of the particle-hole-antiparticle representation. We have studied the difference between the meson self-energy (MSE) of this representation and the MSE of the traditional density-Feynman (DF) representation. It is shown that the new formulation describes exactly the physical processes such as particle-hole excitations or particle-antiparticle excitations, and that, on the other hand, the meson self-energy based on the DF representation includes unphysical components. By numerical calculations, the meson self-energies describing the particle-hole excitations are shown to be close to each other for most of the meson self-energy in low momentum (R{lt}500 MeV) and low energy (R{sub 0}{lt}200 MeV). This fact implies that former calculations using the low momentum and low-energy part do not change greatly. The density part of the density-Feynman representation has been shown to have a resonant structure around the energy of particle-antiparticle excitation, which causes a large difference between the two representations in the meson spectrum calculations. Our investigation concludes that the former calculations based on the density-Feynman representation are not invalidated in many cases, but the particle-hole-antiparticle representation is more appropriate to treat exactly the physical processes. {copyright} {ital 1997} {ital The American Physical Society}
Augustine, R.L.; Lahanas, K.M.; Cole, F.
1992-11-01
An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.
Augustine, R.L.; Lahanas, K.M.; Cole, F.
1992-01-01
An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.
ERIC Educational Resources Information Center
Barbiric, Dora; Tribe, Lorena; Soriano, Rosario
2015-01-01
In this laboratory, students calculated the nutritional value of common foods to assess the energy content needed to answer an everyday life application; for example, how many kilometers can an average person run with the energy provided by 100 g (3.5 oz) of beef? The optimized geometries and the formation enthalpies of the nutritional components…
Electron affinities (EAs) and free energies for electron attachment have been calculated for 42 polynuclear aromatic hydrocarbons and related molecules by a variety of theoretical models, including Koopmans' theorem methods and the L1E method from differences in energy between th...
Yang, W.; Wu, H.; Cao, L.
2012-07-01
More and more MOX fuels are used in all over the world in the past several decades. Compared with UO{sub 2} fuel, it contains some new features. For example, the neutron spectrum is harder and more resonance interference effects within the resonance energy range are introduced because of more resonant nuclides contained in the MOX fuel. In this paper, the wavelets scaling function expansion method is applied to study the resonance behavior of plutonium isotopes within MOX fuel. Wavelets scaling function expansion continuous-energy self-shielding method is developed recently. It has been validated and verified by comparison to Monte Carlo calculations. In this method, the continuous-energy cross-sections are utilized within resonance energy, which means that it's capable to solve problems with serious resonance interference effects without iteration calculations. Therefore, this method adapts to treat the MOX fuel resonance calculation problem natively. Furthermore, plutonium isotopes have fierce oscillations of total cross-section within thermal energy range, especially for {sup 240}Pu and {sup 242}Pu. To take thermal resonance effect of plutonium isotopes into consideration the wavelet scaling function expansion continuous-energy resonance calculation code WAVERESON is enhanced by applying the free gas scattering kernel to obtain the continuous-energy scattering source within thermal energy range (2.1 eV to 4.0 eV) contrasting against the resonance energy range in which the elastic scattering kernel is utilized. Finally, all of the calculation results of WAVERESON are compared with MCNP calculation. (authors)
Investigation of the adsorption of amino acids on Pd(1 1 1): A density functional theory study
NASA Astrophysics Data System (ADS)
James, Joanna N.; Han, Jeong Woo; Sholl, David S.
2014-05-01
Density functional theory calculations have been used to study the adsorption of glycine, alanine, norvaline, valine, proline, cysteine, and serine on Pd(1 1 1). Most amino acids except cysteine adsorb onto the surface in a tridentate fashion through a nitrogen atom and both oxygen atoms. For cysteine, an additional bond is formed with the surface due to the strong affinity of the sulfur atom, resulting in a significantly larger adsorption energy. The adsorption patterns of amino acids we examined are supported by the shifts in vibrational frequencies associated with NHH and COO. The adsorption strength of amino acids depends on how much the molecules deform during the adsorption process. Understanding the adsorption of amino acids on Pd(1 1 1) provides fundamental information for future consideration of the interactions between their derivatives or more complicated biomolecules and metal surfaces.
CCSD(T)/CBS fragment-based calculations of lattice energy of molecular crystals.
Červinka, Ctirad; Fulem, Michal; Růžička, Květoslav
2016-02-14
A comparative study of the lattice energy calculations for a data set of 25 molecular crystals is performed using an additive scheme based on the individual energies of up to four-body interactions calculated using the coupled clusters with iterative treatment of single and double excitations and perturbative triples correction (CCSD(T)) with an estimated complete basis set (CBS) description. The CCSD(T)/CBS values on lattice energies are used to estimate sublimation enthalpies which are compared with critically assessed and thermodynamically consistent experimental values. The average absolute percentage deviation of calculated sublimation enthalpies from experimental values amounts to 13% (corresponding to 4.8 kJ mol(-1) on absolute scale) with unbiased distribution of positive to negative deviations. As pair interaction energies present a dominant contribution to the lattice energy and CCSD(T)/CBS calculations still remain computationally costly, benchmark calculations of pair interaction energies defined by crystal parameters involving 17 levels of theory, including recently developed methods with local and explicit treatment of electronic correlation, such as LCC and LCC-F12, are also presented. Locally and explicitly correlated methods are found to be computationally effective and reliable methods enabling the application of fragment-based methods for larger systems. PMID:26874495
CCSD(T)/CBS fragment-based calculations of lattice energy of molecular crystals
NASA Astrophysics Data System (ADS)
Červinka, Ctirad; Fulem, Michal; Růžička, Květoslav
2016-02-01
A comparative study of the lattice energy calculations for a data set of 25 molecular crystals is performed using an additive scheme based on the individual energies of up to four-body interactions calculated using the coupled clusters with iterative treatment of single and double excitations and perturbative triples correction (CCSD(T)) with an estimated complete basis set (CBS) description. The CCSD(T)/CBS values on lattice energies are used to estimate sublimation enthalpies which are compared with critically assessed and thermodynamically consistent experimental values. The average absolute percentage deviation of calculated sublimation enthalpies from experimental values amounts to 13% (corresponding to 4.8 kJ mol-1 on absolute scale) with unbiased distribution of positive to negative deviations. As pair interaction energies present a dominant contribution to the lattice energy and CCSD(T)/CBS calculations still remain computationally costly, benchmark calculations of pair interaction energies defined by crystal parameters involving 17 levels of theory, including recently developed methods with local and explicit treatment of electronic correlation, such as LCC and LCC-F12, are also presented. Locally and explicitly correlated methods are found to be computationally effective and reliable methods enabling the application of fragment-based methods for larger systems.
Complete calculation of electroweak corrections for polarized Møller scattering at high energies
NASA Astrophysics Data System (ADS)
Zykunov, V. A.
2009-09-01
A complete calculation of electroweak radiative corrections to observables of polarized Møller scattering at high energies was performed. This calculation took explicitly into account contributions caused by hard bremsstrahlung. A FORTRAN code that permitted including radiative corrections to high-energy Møller scattering under arbitrary electron-detection conditions was written. It was shown that the electroweak corrections caused by hard bremsstrahlung were rather strongly dependent on the choice of experimental cuts and changed substantially the polarization asymmetry in the region of high energies and over a broad interval of scattering angles.
Kerisit, Sebastien N.; Zarzycki, Piotr P.; Rosso, Kevin M.
2015-04-30
The interaction of Fe(II) with ferric oxide/oxyhydroxide phases is central to the biogeochemical redox chemistry of iron. Molecular simulation techniques were employed to determine the mechanisms and quantify the rates of Fe(II) oxidative adsorption at the hematite (001)-water interface. Molecular dynamics potential of mean force calculations of Fe(II) adsorbing on the hematite surface revealed the presence of three free energy minima corresponding to Fe(II) adsorbed in an outersphere complex, a monodentate innersphere complex, and a tridentate innersphere complex. The free energy barrier for adsorption from the outersphere position to the monodentate innersphere site was calculated to be similar to the activation enthalpy for water exchange around aqueous Fe(II). Adsorption at both innersphere sites was predicted to be unfavorable unless accompanied by release of protons. Molecular dynamics umbrella sampling simulations and ab initio cluster calculations were performed to determine the rates of electron transfer from Fe(II) adsorbed as an innersphere and outersphere complex. The electron transfer rates were calculated to range from 10^-4 to 10^2 s-1, depending on the adsorption site and the potential parameter set, and were generally slower than those obtained in the bulk hematite lattice. The most reliable estimate of the rate of electron transfer from Fe(II) adsorbed as an outersphere complex to lattice Fe(III) was commensurate with the rate of adsorption as an innersphere complex suggesting that adsorption does not necessarily need to precede oxidation.
ERIC Educational Resources Information Center
Wai, C. M.; Hutchinson, S. G.
1989-01-01
Discusses the calculation of free energy in reactions between silicon dioxide and carbon. Describes several computer programs for calculating the free energy minimization and their uses in chemistry classrooms. Lists 16 references. (YP)
McKechnie, Scott; Booth, George H.; Cohen, Aron J.; Cole, Jacqueline M.
2015-05-21
The best practice in computational methods for determining vertical ionization energies (VIEs) is assessed, via reference to experimentally determined VIEs that are corroborated by highly accurate coupled-cluster calculations. These reference values are used to benchmark the performance of density functional theory (DFT) and wave function methods: Hartree-Fock theory, second-order Møller-Plesset perturbation theory, and Electron Propagator Theory (EPT). The core test set consists of 147 small molecules. An extended set of six larger molecules, from benzene to hexacene, is also considered to investigate the dependence of the results on molecule size. The closest agreement with experiment is found for ionization energies obtained from total energy difference calculations. In particular, DFT calculations using exchange-correlation functionals with either a large amount of exact exchange or long-range correction perform best. The results from these functionals are also the least sensitive to an increase in molecule size. In general, ionization energies calculated directly from the orbital energies of the neutral species are less accurate and more sensitive to an increase in molecule size. For the single-calculation approach, the EPT calculations are in closest agreement for both sets of molecules. For the orbital energies from DFT functionals, only those with long-range correction give quantitative agreement with dramatic failing for all other functionals considered. The results offer a practical hierarchy of approximations for the calculation of vertical ionization energies. In addition, the experimental and computational reference values can be used as a standardized set of benchmarks, against which other approximate methods can be compared.
McKechnie, Scott; Booth, George H; Cohen, Aron J; Cole, Jacqueline M
2015-05-21
The best practice in computational methods for determining vertical ionization energies (VIEs) is assessed, via reference to experimentally determined VIEs that are corroborated by highly accurate coupled-cluster calculations. These reference values are used to benchmark the performance of density functional theory (DFT) and wave function methods: Hartree-Fock theory, second-order Møller-Plesset perturbation theory, and Electron Propagator Theory (EPT). The core test set consists of 147 small molecules. An extended set of six larger molecules, from benzene to hexacene, is also considered to investigate the dependence of the results on molecule size. The closest agreement with experiment is found for ionization energies obtained from total energy difference calculations. In particular, DFT calculations using exchange-correlation functionals with either a large amount of exact exchange or long-range correction perform best. The results from these functionals are also the least sensitive to an increase in molecule size. In general, ionization energies calculated directly from the orbital energies of the neutral species are less accurate and more sensitive to an increase in molecule size. For the single-calculation approach, the EPT calculations are in closest agreement for both sets of molecules. For the orbital energies from DFT functionals, only those with long-range correction give quantitative agreement with dramatic failing for all other functionals considered. The results offer a practical hierarchy of approximations for the calculation of vertical ionization energies. In addition, the experimental and computational reference values can be used as a standardized set of benchmarks, against which other approximate methods can be compared. PMID:26001454
Surface Segregation Energies of BCC Binaries from Ab Initio and Quantum Approximate Calculations
NASA Technical Reports Server (NTRS)
Good, Brian S.
2003-01-01
We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy method. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameterization. Quantum approximate segregation energies are computed with and without atomistic relaxation. The ab initio calculations are performed without relaxation for the most part, but predicted relaxations from quantum approximate calculations are used in selected cases to compute approximate relaxed ab initio segregation energies. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with other quantum approximate and ab initio theoretical work, and available experimental results.
Studies on the adsorption of sulfo-group-containing aromatics by chitosan-β-cyclodextrin.
Shi, Wenjian; Chen, Shuwei; Chang, Fei; Han, Yue; Zhang, Yuanzhang
2012-01-01
Chitosan-β-cyclodextrin (CTS-CD) prepared through a crosslinking reaction between chitosan and β-cyclodextrin was employed to adsorb the three following sulfo-group-containing aromatics: disodium 2-naphthol-3,6-disulfonate (R salt), 2-naphthalene sulfonic acid (NSA), and sodium dodecylbenzene sulfonate (SDBS). At 318 K, the saturated adsorption capacity of CTS-CD for R salt, NSA, and SDBS was 431, 416, and 376 mg/g, respectively. The experimental data fitted the second-order model well and the rate constant of the adsorption increased with the temperature increment. The values of apparent activation energy for R salt, NSA, and SDBS were calculated as 33.2, 34.2, and 16.8 kJ/mol respectively. The isothermal adsorption was found following the Langmuir adsorption equation. The negative values of ΔG and the positive values of ΔH indicated that the adsorption process was spontaneous and exothermic. PMID:22339013
Li, Z.; Pan, Y.K.; Tao, F.M.
1996-01-15
Bond function basis sets combined with the counterpoise procedure are used to calculate the molecular dissociation energies D{sub e} of 24 diatomic molecules and ions. The calculated values of D{sub e} are compared to those without bond functions and/or counterpoise corrections. The equilibrium bond lengths r{sub e}, and harmonic frequencies w{sub e} are also calculated for a few selected molecules. The calculations at the fourth-order-Moller-Plesset approximation (MP4) have consistently recovered about 95-99% of the experimental values for D{sub e}, compared to as low as 75% without use of bond functions. The calculated values of r{sub 3} are typically 0.01 {Angstrom} larger than the experimental values, and the calculated values of w{sub e} are over 95% of the experimental values. 37 refs., 2 tabs.
NASA Astrophysics Data System (ADS)
Zhao, Xiaojun; Zhang, Riguang; Ling, Lixia; Wang, Baojun
2014-11-01
The adsorption, dissociation and desorption of CO at different coverage over Rh(1 0 0) surface have been systematically investigated using density functional theory method together with the periodic slab model. Our results show that at the coverage less than or equal to 4/12 ML, CO favored the most stable bridge site adsorption, and the adsorption energies of CO have little difference; while at the coverage greater than or equal to 5/12 ML, the lateral repulsive interaction begins to affect the adsorption structures and the corresponding adsorption energies of adsorbed CO molecules, and the interaction will be stronger with the increasing of CO coverage, which leads to CO migration over Rh(1 0 0) surface when CO coverage is greater than or equal to 10/12 ML. The adsorption energies of these CO molecules will decrease successively until the saturated adsorption with the CO coverage of 12/12 ML. Further calculations on CO dissociation indicate that when CO coverage is greater than or equal to 3/12 ML, the dissociation of adsorbed CO molecules will be unfavorable both kinetically and thermodynamically, suggesting that only molecule CO adsorption are favored. Considering the catalytic activity of Rh(1 0 0) surface toward CO dissociation and the higher CO coverage under the continuous supply of CO in syngas conversion, it is to be expected that only molecule CO adsorption exist on Rh catalyst.
NASA Astrophysics Data System (ADS)
Li, Ming; Kapusta, Joseph I.
2016-08-01
We generalize calculations of the energy-momentum tensor for classical gluon fields in the boost-invariant McLerran-Venugopalan model using the small-τ power series expansion method. Results to all orders for the energy density and pressures are given in the leading Q2 approximation and with the inclusion of estimated running coupling effects. The energy density and transverse pressure decrease monotonically with time while the longitudinal pressure starts from a negative value and increases towards zero.
Gu, G.D.; Gann, R.D.; Cao, J.X.; Wu, R.Q.; Wen, J.; Xu, Z.; Gu, G.D.; Yarmoff, J.A.
2010-01-01
The adsorption of K and I on the surface of the high-T{sub c} cuprate BSCCO-2212 is investigated with low-energy (0.8 to 2 keV) Na{sup +} ion scattering and density functional theory (DFT). Samples were cleaved in ultrahigh vacuum and charge-resolved spectra of the scattered ions were collected with time-of-flight. The spectra contain a single peak representing Na scattered from Bi, as the clean surfaces are terminated by BiO. The neutralization of scattered Na depends on the local potential above the target site, and the angular dependence indicates that the clean surface has an inhomogeneous potential. Neutralization is dependent on the coverage of I, but independent of K adsorption. DFT suggests high-symmetry sites for the adsorption of both I and K, and that the potential above the Bi sites is altered by I by an amount consistent with the experimental findings, while the potential is not affected by K adsorption. DFT also enables an experimental determination of the 'freezing distance,' which is the effective point beyond which charge exchange does not occur, to be 1.6 {+-} 0.1 {angstrom} from the outermost Bi layer.
Monte Carlo calculation of the energy response characteristics of a RadFET radiation detector
NASA Astrophysics Data System (ADS)
Belicev, P.; Spasic Jokic, V.; Mayer, S.; Milosevic, M.; Ilic, R.; Pesic, M.
2010-07-01
The Metal -Oxide Semiconductor Field-Effect-Transistor (MOSFET, RadFET) is frequently used as a sensor of ionizing radiation in nuclear-medicine, diagnostic-radiology, radiotherapy quality-assurance and in the nuclear and space industries. We focused our investigations on calculating the energy response of a p-type RadFET to low-energy photons in range from 12 keV to 2 MeV and on understanding the influence of uncertainties in the composition and geometry of the device in calculating the energy response function. All results were normalized to unit air kerma incident on the RadFET for incident photon energy of 1.1 MeV. The calculations of the energy response characteristics of a RadFET radiation detector were performed via Monte Carlo simulations using the MCNPX code and for a limited number of incident photon energies the FOTELP code was also used for the sake of comparison. The geometry of the RadFET was modeled as a simple stack of appropriate materials. Our goal was to obtain results with statistical uncertainties better than 1% (fulfilled in MCNPX calculations for all incident energies which resulted in simulations with 1 - 2×109 histories.
Ghosh, Soumya; Hammes-Schiffer, Sharon
2015-01-02
Electrochemical electron transfer reactions play an important role in energy conversion processes with many technological applications. Electrodes modified by self-assembled monolayers (SAMs) are useful because the double layer effects are reduced. An important quantity for calculating the electron transfer rate constant is the reorganization energy, which is associated with changes in solute geometry and solvent configuration. In this Letter, an approach for calculating the electrochemical solvent reorganization energy for a redox molecule attached to or near a SAM modified electrode is presented. This integral equations formalism polarizable continuum model (IEF-PCM) approach accounts for the detailed electronic structure of the molecule, as well as the contributions from the electrode, SAM, and electronic and inertial solvent responses. The calculated total reorganization energies are in good agreement with experimental data for a series of metal complex in aqueous solution. This approach will be useful for calculating electron transfer rate constants for molecular electrocatalysts. 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.
Calculation of the characteristics of clinical high-energy photon beams with EGS5-MPI
NASA Astrophysics Data System (ADS)
Shimizu, M.; Morishita, Y.; Kato, M.; Kurosawa, T.; Tanaka, T.; Takata, N.; Saito, N.
2014-03-01
A graphite calorimeter has been developed as a Japanese primary standard of absorbed dose to water in the high-energy photon beams from a clinical linac. To obtain conversion factors for the graphite calorimeter, the beam characteristics of the high-energy photon beams from the clinical linac at National Metrology Institute of Japan were calculated with the EGS5 Monte Carlo simulation code. To run the EGS5 code on High Performance Computing machines that have more than 1000 CPU cores, we developed the EGS5 parallelisation package "EGS5-MPI" by implementing a message-passing interface. We calculated the photon energy spectra, which are in good agreement with those previously calculated by D. Sheikh-Bagheri and D. W. O. Rogers (Med. Phys. 29 3). We also estimated the percentage-depth-dose distributions of photon beams from the linac using the calculated photon energy spectra. These calculated percentage-depth-dose distributions were compared with our measured distributions and were found they are in good agreement as well. We will calculate conversion factors for the graphite calorimeter using our results.
NASA Astrophysics Data System (ADS)
Beragoui, Manel; Aguir, Chadlia; Khalfaoui, Mohamed; Enciso, Eduardo; Torralvo, Maria José; Duclaux, Laurent; Reinert, Laurence; Vayer, Marylène; Ben Lamine, Abdelmottaleb
2015-03-01
The present work involves the study of bovine serum albumin adsorption onto five functionalized polystyrene lattices. The adsorption measurements have been carried out using a quartz crystal microbalance. Poly(styrene-co-itaconic acid) was found to be an effective adsorbent for bovine serum albumin molecule adsorption. The experimental isotherm data were analyzed using theoretical models based on a statistical physics approach, namely monolayer, double layer with two successive energy levels, finite multilayer, and modified Brunauer-Emmet-Teller. The equilibrium data were then analyzed using five different non-linear error analysis methods and it was found that the finite multilayer model best describes the protein adsorption data. Surface characteristics, i.e., surface charge density and number density of surface carboxyl groups, were used to investigate their effect on the adsorption capacity. The combination of the results obtained from the number of adsorbed layers, the number of adsorbed molecules per site, and the thickness of the adsorbed bovine serum albumin layer allows us to predict that the adsorption of this protein molecule can also be distinguished by monolayer or multilayer adsorption with end-on, side-on, and overlap conformations. The magnitudes of the calculated adsorption energy indicate that bovine serum albumin molecules are physisorbed onto the adsorbent lattices.
Comparison between calculation and measurement of energy deposited by 800 MeV protons
Loewe, W.E.
1980-04-03
The High Energy Transport Code, HETC, was obtained from the Radiation Shielding Information Center (RSIC) at Oak Ridge National Laboratory and altered as necessary to run on a CDC 7600 using the LTSS software in use at LLNL. HETC was then used to obtain calculated estimates of energy deposited, for comparison with a series of benchmark experiments done by LLNL. These experiments used proton beams of various energies incident on well-defined composite targets in good geometry. In this report, two aspects of the comparison between calculated and experimental energy depositions from an 800 MeV proton beam are discussed. Both aspects involve the fact that workers at SAI had previously used their version of HETC to calculate this experiment and reported their comparison with the measured data. The first aspect addressed is that their calculated data and LLNL calculations do not agree, suggesting an error in the conversion process from the RSIC code. The second aspect is not independent of the first, but is of sufficient importance to merit separate emphasis. It is that the SAI calculations agree well with experiments at the detector plate located some distance from the shower plate, whereas the LLNL calculations show a clearcut discrepancy there in comparison with the experiment. A contract was let in January 1980 by LLNL with SAI in order to obtain full details on the two cited aspects of the comparison between calculated and experimental energy depositions from an 800 MeV proton beam. The ensuing discussion is based on the final report of that contracted work.
NASA Astrophysics Data System (ADS)
Takács, Erzsébet; Wojnárovits, László; Koczog Horváth, Éva; Fekete, Tamás; Borsa, Judit
2012-09-01
Cellulose as a renewable raw material was used for preparation of adsorbent of organic impurities in wastewater treatment. Hydrophobic surface of cellulose substrate was developed by grafting glycidyl methacrylate in simultaneous grafting using gamma irradiation initiation. Water uptake of cellulose significantly decreased while adsorption of phenol and a pesticide molecule (2,4-dichlorophenoxyacetic acid: 2,4-D) increased upon grafting. Adsorption equilibrium data fitted the Freundlich isotherm for both solutes.
Nitrogen Adsorption on Graphite: Defying Physisorption
NASA Astrophysics Data System (ADS)
Tkatchenko, Alexandre; Scheffler, Matthias
2010-03-01
The adsorption of a nitrogen molecule at the graphite surface can be considered a paradigm of molecular physisorption [1]. The binding of N2 can be phenomenologically described in terms of a competition between quadrupole--quadrupole and van der Waals dispersion energies. Of particular interest is the relative stability of the so-called ``in-plane'', ``out-of-plane'' and ``pin-wheel'' monolayer structures, in which the nitrogen molecules alternate between parallel and perpendicular configurations on the surface. By combining state-of-the-art electronic structure methods, such as dispersion-corrected density-functional theory and Møller-Plesset second-order perturbation theory along with high-level coupled cluster [CCSD(T)] calculations, we are able to gain quantitative insight into the adsorption mechanism of N2@graphite and achieve very good agreement with experimental desorption enthalpy. We challenge the commonly held view of a closed-shell adsorbed N2 molecule, finding a noticeable charge-density polarization for nitrogen in a perpendicular configuration on the surface. We map out the N2@graphite potential energy surface as a function of sliding and orientation and discuss the influence of quantum zero-point energy for different adsorption sites. [1] D. Marx and H. Wiechert, Adv. Chem. Phys. 95, 213 (1996).
Methane adsorption in nanoporous carbon: the numerical estimation of optimal storage conditions
NASA Astrophysics Data System (ADS)
Ortiz, L.; Kuchta, B.; Firlej, L.; Roth, M. W.; Wexler, C.
2016-05-01
The efficient storage and transportation of natural gas is one of the most important enabling technologies for use in energy applications. Adsorption in porous systems, which will allow the transportation of high-density fuel under low pressure, is one of the possible solutions. We present and discuss extensive grand canonical Monte Carlo (GCMC) simulation results of the adsorption of methane into slit-shaped graphitic pores of various widths (between 7 Å and 50 Å), and at pressures P between 0 bar and 360 bar. Our results shed light on the dependence of film structure on pore width and pressure. For large widths, we observe multi-layer adsorption at supercritical conditions, with excess amounts even at large distances from the pore walls originating from the attractive interaction exerted by a very high-density film in the first layer. We are also able to successfully model the experimental adsorption isotherms of heterogeneous activated carbon samples by means of an ensemble average of the pore widths, based exclusively on the pore-size distributions (PSD) calculated from subcritical nitrogen adsorption isotherms. Finally, we propose a new formula, based on the PSD ensemble averages, to calculate the isosteric heat of adsorption of heterogeneous systems from single-pore-width calculations. The methods proposed here will contribute to the rational design and optimization of future adsorption-based storage tanks.
AlaScan: A Graphical User Interface for Alanine Scanning Free-Energy Calculations.
Ramadoss, Vijayaraj; Dehez, François; Chipot, Christophe
2016-06-27
Computation of the free-energy changes that underlie molecular recognition and association has gained significant importance due to its considerable potential in drug discovery. The massive increase of computational power in recent years substantiates the application of more accurate theoretical methods for the calculation of binding free energies. The impact of such advances is the application of parent approaches, like computational alanine scanning, to investigate in silico the effect of amino-acid replacement in protein-ligand and protein-protein complexes, or probe the thermostability of individual proteins. Because human effort represents a significant cost that precludes the routine use of this form of free-energy calculations, minimizing manual intervention constitutes a stringent prerequisite for any such systematic computation. With this objective in mind, we propose a new plug-in, referred to as AlaScan, developed within the popular visualization program VMD to automate the major steps in alanine-scanning calculations, employing free-energy perturbation as implemented in the widely used molecular dynamics code NAMD. The AlaScan plug-in can be utilized upstream, to prepare input files for selected alanine mutations. It can also be utilized downstream to perform the analysis of different alanine-scanning calculations and to report the free-energy estimates in a user-friendly graphical user interface, allowing favorable mutations to be identified at a glance. The plug-in also assists the end-user in assessing the reliability of the calculation through rapid visual inspection. PMID:27214306
Dye adsorption behavior of Luffa cylindrica fibers.
Demir, H; Top, A; Balköse, D; Ulkü, S
2008-05-01
Using natural Luffa cylindrica fibers as adsorbent removal of methylene blue dye from aqueous solutions at different temperatures and dye concentrations was investigated in this study. Thermodynamics and kinetics of adsorption were also investigated. The adsorption isotherms could be well defined with Langmuir model instead of Freundlich model. The thermodynamic parameters of methylene blue (MB) adsorption indicated that the adsorption is exothermic and spontaneous. The average MB adsorption capacity was found out as 49 mg/g and average BET surface area of fibers was calculated as 123 m(2)/g. PMID:17919814
NASA Astrophysics Data System (ADS)
Li, Yongxiu; Zhang, Saiqun; Zhang, John Z. H.; He, Xiao
2016-05-01
Accurate description of the conformational energies of the amino acids is essential for molecular dynamics simulation of protein structures. In this study, we compute the relative energies at 51 conformations for a trialanine tetrapeptide at different levels of theory. The computed energies at various theoretical levels, including the semiempirical DFTB method, HF, DFT, MP2 and CCSD(T), are compared with each other. The calculated energies from density-fitting local CCSD(T)/CBS (complete basis set) calculations are taken as the benchmark. The accuracy of the theoretical methods is highly dependent on the electronic correlation and dispersion corrections as well as the size of the basis sets. The involvement of the empirical dispersion energies in HF and DFT methods consistently improves their performance. Considering both the accuracy and computational efficiency, the Minnesota density functional M06-L-D and M06-2X-D are efficient and accurate for modeling of trialanine structures.
Calculating Transition Energy Barriers and Characterizing Activation States for Steps of Fusion.
Ryham, Rolf J; Klotz, Thomas S; Yao, Lihan; Cohen, Fredric S
2016-03-01
We use continuum mechanics to calculate an entire least energy pathway of membrane fusion, from stalk formation, to pore creation, and through fusion pore enlargement. The model assumes that each structure in the pathway is axially symmetric. The static continuum stalk structure agrees quantitatively with experimental stalk architecture. Calculations show that in a stalk, the distal monolayer is stretched and the stored stretching energy is significantly less than the tilt energy of an unstretched distal monolayer. The string method is used to determine the energy of the transition barriers that separate intermediate states and the dynamics of two bilayers as they pass through them. Hemifusion requires a small amount of energy independently of lipid composition, while direct transition from a stalk to a fusion pore without a hemifusion intermediate is highly improbable. Hemifusion diaphragm expansion is spontaneous for distal monolayers containing at least two lipid components, given sufficiently negative diaphragm spontaneous curvature. Conversely, diaphragms formed from single-component distal monolayers do not expand without the continual injection of energy. We identify a diaphragm radius, below which central pore expansion is spontaneous. For larger diaphragms, prior studies have shown that pore expansion is not axisymmetric, and here our calculations supply an upper bound for the energy of the barrier against pore formation. The major energy-requiring deformations in the steps of fusion are: widening of a hydrophobic fissure in bilayers for stalk formation, splay within the expanding hemifusion diaphragm, and fissure widening initiating pore formation in a hemifusion diaphragm. PMID:26958888
NASA Astrophysics Data System (ADS)
Tan, Zhenyu; Dong, Lei; Tang, Fule
2012-08-01
The calculations of the characteristic quantities of low-energy electron (⩽20 keV) irradiation to the five typical spacecraft dielectrics, i.e. epoxy, kapton, mylar, polyethylene, and teflon, have been performed by means of Monte Carlo method. These characteristic quantities include the electron backscattering coefficient, the depth distributions of both energy deposition and deposited electrons, and the maximum penetration depth of deposited electrons in the dielectrics. A Monte Carlo model has been specifically constructed for simulating the transport of low-energy electrons in spacecraft dielectrics (organic materials). In this model, the description of the inelastic scattering of energetic electron is based on the dielectric approach developed previously and the Born-Ochkur's exchange correction is included. Especially, the optical energy loss functions of organic materials can be obtained using an empirical evaluation. In addition, the mean cross section based on the Mott model is proposed for calculating the elastic scattering of energetic electrons in organic materials for high simulation efficiency. The constructed Monte Carlo model has been examined by a series of calculations and comparisons with the reported experiments and other theoretical results. For the dielectrics under consideration and in the energy range of E0 ⩽ 20 keV, the calculated electron backscattering coefficients and the extrapolated range of deposited electrons are listed at selected energies in numerical form for convenient use, and an empirical expression of estimating the extrapolated range in the energy range of 1-20 keV is given. The distribution characteristics of both energy deposition and deposited electrons are presented, and it is found that kapton and mylar present the close characteristic quantities for each other, which is of significance for the choice of the dielectrics in design of spacecraft. The characteristic quantity calculations presented in this work are a
Calculation of intensity of high energy muon groups observed deep underground
NASA Technical Reports Server (NTRS)
Vavilov, Y. N.; Dedenko, L. G.
1985-01-01
The intensity of narrow muon groups observed in Kolar Gold Field (KGF) at the depth of 3375 m.w.e. was calculated in terms of quark-gluon strings model for high energy hadron - air nuclei interactions by the method of direct modeling of nuclear cascade in the air and muon propagation in the ground for normal primary cosmic ray composition. The calculated intensity has been found to be approx. 10 to the 4 times less than one observed experimentally.
Perfetti, Christopher M; Martin, William R; Rearden, Bradley T; Williams, Mark L
2012-01-01
Three methods for calculating continuous-energy eigenvalue sensitivity coefficients were developed and implemented into the SHIFT Monte Carlo code within the Scale code package. The methods were used for several simple test problems and were evaluated in terms of speed, accuracy, efficiency, and memory requirements. A promising new method for calculating eigenvalue sensitivity coefficients, known as the CLUTCH method, was developed and produced accurate sensitivity coefficients with figures of merit that were several orders of magnitude larger than those from existing methods.
Santoro, R.T.; Alsmiller, R.G. Jr.; Barnes, J.M.; Chapman, G.T.
1980-08-01
Integral experiments that measure the transport of approx. 14 MeV D-T neutrons through laminated slabs of proposed fusion reactor shield materials have been carried out. Measured and calculated neutron and gamma ray energy spectra are compared as a function of the thickness and composition of stainless steel type 304, borated polyethylene, and Hevimet (a tungsten alloy), and as a function of detector position behind these materials. The measured data were obtained using a NE-213 liquid scintillator using pulse-shape discrimination methods to resolve neutron and gamma ray pulse height data and spectral unfolding methods to convert these data to energy spectra. The calculated data were obtained using two-dimensional discrete ordinates radiation transport methods in a complex calculational network that takes into account the energy-angle dependence of the D-T neutrons and the nonphysical anomalies of the S/sub n/ method.
NASA Astrophysics Data System (ADS)
Vessally, Esmail; Aryana, Soma
2016-01-01
The purpose of this research is to study the solar energy storage in norbornadiene ( 1)/quadricyclane ( 2) system by four direct attachments of substituents at two carbon atoms on both sides of the double bonds C2=C3 and C5=C6 in 1 X and 2 X; calculating the relative energies at B3LYP/6-311++G** level of theory. The solar energy storage of four electron donating substituents, (push-push effect), X (X =-NH2,-OH) and four electron withdrawing substituents, (pull-pull effect) X (X =-CO2H,-CONH2,-NO2 and CN) were examined. The solar absorption bands were calculated for 1 X. The DFT calculations reveal that the bands were shifted to the visible spectrum region when the electron withdrawing substituents were used rather than the electron donating substituents.
NASA Technical Reports Server (NTRS)
Armstrong, T. W.; Alsmiller, R. G., Jr.; Chandler, K. C.
1972-01-01
Results obtained using a recently developed calculational method for determining the nucleon-meson cascade induced in thick materials by high-energy nucleons and charged pions are presented. The calculational method uses the intranuclear-cascade-evaporation model to treat nonelastic collisions by particles with energies approximately or smaller than GeV and an extrapolation model at higher energies. The following configurations are considered: (1) 19.2-GeV/c protons incident on iron; (2) 30.3-GeV/c protons incident on iron; (3) solar and galactic protons incident on the moon, and (4) galactic protons incident on tissue. For the first three configurations, experimental results are available and comparisons between the experimental and calculated results are given.
Infrared Spectra and Calculated Binding Energies of γ-BUTYROLACTONE Dimers and Trimers
NASA Astrophysics Data System (ADS)
Willis, Eric; Baumann, Chris
2014-06-01
Infrared spectra for matrix-isolated γ-butyrolactone and γ-butyrolactone-d_6 were obtained. The carbonyl stretching mode occurs at 1803 cm-1 for the monomer species, 1786 cm-1 for the dimer species, and 1774 cm-1 for the trimer species (1797, 1789 and 1770 cm-1 for the deuterated isotopomer.) Vibrational frequencies calculated using density functional theory are in agreement with the experimental values. Density functional theory was used to calculate the structures and binding energies of γ-butyrolactone dimers and trimers. Binding energies of 55-58 kJ mol-1 are predicted for the dimer structures. Optimized geometries for stacked and ring trimer structures have been calculated, with predicted binding energies of up to 68 kJ mol-1.
Ab initio calculations on collisions of low energy electrons with polyatomic molecules
Rescigno, T.N.
1991-08-01
The Kohn variational method is one of simplest, and oldest, techniques for performing scattering calculations. Nevertheless, a number of formal problems, as well as practical difficulties associated with the computation of certain required matrix elements, delayed its application to electron--molecule scattering problems for many years. This paper will describe the recent theoretical and computational developments that have made the complex'' Kohn variational method a practical tool for carrying out calculations of low energy electron--molecule scattering. Recent calculations on a number of target molecules will also be summarized. 41 refs., 7 figs.
Efficient calculation of potential energy surfaces for the generation of vibrational wave functions
NASA Astrophysics Data System (ADS)
Rauhut, Guntram
2004-11-01
An automatic procedure for the generation of potential energy surfaces based on high level ab initio calculations is described. It allows us to determine the vibrational wave functions for molecules of up to ten atoms. Speedups in computer time of about four orders of magnitude in comparison to standard implementations were achieved. Effects due to introduced approximations—within the computation of the potential—on fundamental modes obtained from vibrational self-consistent field and vibrational configuration interaction calculations are discussed. Benchmark calculations are provided for formaldehyde and 1,2,5-oxadiazole (furazan).
Efficient calculation of potential energy surfaces for the generation of vibrational wave functions.
Rauhut, Guntram
2004-11-15
An automatic procedure for the generation of potential energy surfaces based on high level ab initio calculations is described. It allows us to determine the vibrational wave functions for molecules of up to ten atoms. Speedups in computer time of about four orders of magnitude in comparison to standard implementations were achieved. Effects due to introduced approximations--within the computation of the potential--on fundamental modes obtained from vibrational self-consistent field and vibrational configuration interaction calculations are discussed. Benchmark calculations are provided for formaldehyde and 1,2,5-oxadiazole (furazan). PMID:15538851
NASA Technical Reports Server (NTRS)
Brown, R. L.; Laufer, A. H.
1981-01-01
Activation energies are calculated by the bond-energy-bond-order (BEBO) and the bond-strength-bond-length (BSBL) methods for the reactions of C2H radicals with H2, CH4, and C2H6 and for the reactions of CN radicals with H2 and CH4. The BSBL technique accurately predicts the activation energies for these reactions while the BEBO method yields energies averaging 9 kcal higher than those observed. A possible reason for the disagreement is considered.
Model potential calculation of the thermal donor energy spectrum in silicon
NASA Astrophysics Data System (ADS)
Chen, C. S.; Schroder, D. K.
1988-06-01
The two-parameter model potential originally proposed by Ning and Sah [Phys. Rev. B 4, 3468 (1971)] for calculating the ground-state energies of group V and group VI impurities in silicon is extended to the variational calculation of the thermal donor ionization energies. In the multivalley effective mass approximation, the theoretical results are in excellent agreement with the reported experimental data. This provides additional evidence for the assumption that thermal donors consist of five to thirteen oxygen atoms, as first proposed by Ourmazd, Schröter, and Bourret [J. Appl. Phys. 56, 1670 (1984)].
Model potential calculation of the thermal donor energy spectrum in silicon
Chen, C.S.; Schroder, D.K.
1988-06-15
The two-parameter model potential originally proposed by Ning and Sah (Phys. Rev. B 4, 3468 (1971)) for calculating the ground-state energies of group V and group VI impurities in silicon is extended to the variational calculation of the thermal donor ionization energies. In the multivalley effective mass approximation, the theoretical results are in excellent agreement with the reported experimental data. This provides additional evidence for the assumption that thermal donors consist of five to thirteen oxygen atoms, as first proposed by Ourmazd, Schroeter, and Bourret (J. Appl. Phys. 56, 1670 (1984)).
Calculation of the Relative Change in Binding Free Energy of a Protein-Inhibitor Complex
NASA Astrophysics Data System (ADS)
Bash, Paul A.; Singh, U. Chandra; Brown, Frank K.; Langridge, Robert; Kollman, Peter A.
1987-01-01
By means of a thermodynamic perturbation method implemented with molecular dynamics, the relative free energy of binding was calculated for the enzyme thermolysin complexed with a pair of phosphonamidate and phosphonate ester inhibitors. The calculated difference in free energy of binding was 4.21 ± 0.54 kilocalories per mole. This compares well with the experimental value of 4.1 kilocalories per mole. The method is general and can be used to determine a change or ``mutation'' in any system that can be suitably represented. It is likely to prove useful for protein and drug design.
Adsorption of molecular oxygen on VIIIB transition metal-doped graphene: A DFT study
NASA Astrophysics Data System (ADS)
Nasehnia, F.; Seifi, M.
2014-12-01
Adsorption of molecular oxygen with a triplet ground state on Fe-, Co-, Ni-, Ru-, Rh-, Pd-, OS-, Ir- and Pt-doped graphene is studied using density functional theory (DFT) calculations. The calculations show that O2 molecule is chemisorbed on the doped graphene sheets with large adsorption energies ranging from -0.653 eV to -1.851 eV and the adsorption process is irreversible. Mulliken atomic charge analysis of the structure shows that charge transfer from doped graphene sheets to O2 molecule. The amounts of transferred charge are between 0.375e- to 0.650e-, indicating a considerable change in the structures conductance. These results imply that the effect of O2 adsorption on transition metal-doped graphene structures can alter the possibility of using these materials as a toxic-gas (carbon monoxide, hydrogen fluoride, etc.) sensor.
Calculation of energy barriers for magnetic vortices in sub-100 nm dots
NASA Astrophysics Data System (ADS)
Lapa, Pavel; King, Andrew; Roshchin, Igor V.
2012-10-01
In a magnetic vortex, the magnetization is curling in plane everywhere except the ``core,'' where it is out of plane. Interest in switching of magnetic vortices in nanodots is stimulated by their potential application for magnetic memories and nano-oscillators. By combining analytical and micromagnetic techniques, we calculated energy barriers for vortex switching in 20 nm-thick iron dots as a function of applied in-plane field and dot diameter. Using analytical formula for magnetization distribution in the vortex,footnotetextN. A. Usov and S. E. Peschany, J. Magn. Magn. Mater. 118, 290 (1992). we performed micromagnetic calculations of the dot energy for different vortex core positions. In contrast to the ``rigid body approximation,'' the core size and core shape in our calculations were varied to achieve the energy minimum for every core displacement. The energy barriers required for vortex nucleation and annihilation were calculated as a function of magnetic field. By comparing these barriers to the thermal energy kBT we obtained the temperature dependences of the vortex nucleation and annihilation fields in good agreement with the experiment.footnotetextR. K. Dumas et al., Appl. Phys. Lett. 91, 202501 (2007).
NASA Astrophysics Data System (ADS)
Tian, Yu; Pan, Xiao-fan; Liu, Yue-jie; Zhao, Jing-xiang
2014-03-01
It is well known that pristine hexagonal boron nitride sheet (h-BN sheet) exhibits large insulating band gap, thus hindering its application to some extent. In this regard, surface chemisorption of certain groups on h-BN sheet is shown to be the most popular method to tune its band gap and thus modify its electronic properties. In the present work, we performed density functional theory (DFT) calculations to study the adsorption of CHO radicals with different coverages on h-BN sheet. Particular attention is paid to explore the effects of CHO adsorption on the geometrical structures and electronic properties of h-BN sheet. The results indicate that the adsorption of a single CHO radical on pristine h-BN sheet is very weak with a negligible adsorption energy (-0.09 eV). In contrast, upon adsorption of more CHO radicals on h-BN sheet, these adsorbates prefer to adsorb in pairs on the B and the nearest N atoms from both sides of h-BN sheet. An energy diagram of the average adsorption energy of CHO radicals on h-BN sheet as a function of its coverage indicates that up to 20 CHO radicals (40%) can be attached to h-BN sheet with the adsorption energy of -0.29 eV. More importantly, the adsorption of CHO radicals can induce certain impurity states within the band gap of h-BN sheet, thus reducing the band gap and enhancing its electrical conductivity.
Shape of the hydrogen adsorption regions of MOF-5 and its impact on the hydrogen storage capacity
NASA Astrophysics Data System (ADS)
Cabria, I.; López, M. J.; Alonso, J. A.
2008-11-01
The adsorption of molecular hydrogen on a metal-organic framework (MOF) material, MOF-5, has been studied using the density-functional formalism. The calculated potential-energy surface shows that there are two main adsorption regions: both near the OZn4 oxide cores at the vertices of the cubic skeleton of MOF-5. The adsorption energies in those regions are between 100 and 130 meV/molecule. Those adsorption regions have the shape of long, wide, and deep connected trenches and passage of the molecule between regions needs to surpass small barriers of 30-50 meV. The shape of these regions, and not only the presence of metal atoms, explains the large storage capacity measured for MOF-5. The elongated shape explains why some authors have previously identified only one type of adsorption site, associated to the Zn oxide core, and others identified two or three sites. One should consider adsorption regions rather than adsorption sites. A third region of adsorption is near the benzenic rings of the MOF-5. We have also analyzed the possibility of dissociative chemisorption. The chemisorption energy with respect to two separated H atoms is 1.33 eV/H atom; but, since dissociating the free molecule costs 4.75 eV, the physisorbed H2 molecule is more stable than the dissociated chemisorbed state by about 2 eV. Dissociation of the adsorbed molecule costs less energy, but the dissociation barrier is still high.
NASA Astrophysics Data System (ADS)
Gómez, Guillermina; Belelli, Patricia G.; Cabeza, Gabriela F.; Castellani, Norberto J.
2010-12-01
The adsorption of 1,3-butadiene (BD) on the Pd/Ni(1 1 1) multilayers has been studied using the VASP method in the framework of the density functional theory (DFT). The adsorption on two different configurations of the Pd n/Ni m(1 1 1) systems were considered. The most stable adsorption sites are dependent on the substrate composition and on the inclusion or not of spin polarization. On Pd 1Ni 3(1 1 1) surface, di-π-cis and 1,2,3,4-tetra-σ adsorption structures are the most stable for non-spin polarized (NSP) and spin polarized (SP) levels of calculation, respectively. Conversely, on Pd 3Ni 1(1 1 1) surface, the 1,2,3,4-tetra-σ adsorption structure is the most stable for both NSP and SP levels, respectively. The magnetization of the Pd atoms strongly modifies the adsorption energy of BD and its most stable adsorption mode. On the other hand, as a consequence of BD adsorption, the Pd magnetization decreases. The smaller adsorption energies of BD and 1-butene on the Pd 1Ni 3(1 1 1) surface than on Pd(1 1 1) can be associated to the strained Pd overlayer deposited on Ni(1 1 1).
Kinetic modeling of liquid-phase adsorption of Congo red dye using guava leaf-based activated carbon
NASA Astrophysics Data System (ADS)
Ojedokun, Adedamola Titi; Bello, Olugbenga Solomon
2016-02-01
Guava leaf, a waste material, was treated and activated to prepare adsorbent. The adsorbent was characterized using Scanning Electron Microscopy (SEM), Fourier Transform Infra Red (FTIR) and Energy-Dispersive X-ray (EDX) techniques. The carbonaceous adsorbent prepared from guava leaf had appreciable carbon content (86.84 %). The adsorption of Congo red dye onto guava leaf-based activated carbon (GLAC) was studied in this research. Experimental data were analyzed by four different model equations: Langmuir, Freundlich, Temkin and Dubinin-Radushkevich isotherms and it was found to fit Freundlich equation most. Adsorption rate constants were determined using pseudo-first-order, pseudo-second-order, Elovich and intraparticle diffusion model equations. The results clearly showed that the adsorption of CR dye onto GLAC followed pseudo-second-order kinetic model. Intraparticle diffusion was involved in the adsorption process. The mean energy of adsorption calculated from D-R isotherm confirmed the involvement of physical adsorption. Thermodynamic parameters were obtained and it was found that the adsorption of CR dye onto GLAC was an exothermic and spontaneous process at the temperatures under investigation. The maximum adsorption of CR dye by GLAC was found to be 47.62 mg/g. The study shows that GLAC is an effective adsorbent for the adsorption of CR dye from aqueous solution.
Adsorption of two sodium atoms on graphene -- A first principles study
Kaur, Gagandeep; Rani, Babita; Gupta, Shuchi; Dharamvir, Keya
2015-08-28
We perform a systematic density functional theory (DFT) study of the adsorption of two sodium atoms on graphene using the SIESTA package, in the generalized gradient approximation (GGA). The adsorption energy, geometry, magnetic moment and charge transfer of the Na{sub n}-graphene (n=1, 2) system are calculated. Three initial horizontal orientations of the pair of sodium atoms on graphene are studied. Our calculations reveal that sodium atoms bind weakly to the graphene surface which is in agreement with previous results. We also notice a charge transfer of 0.288e from a sodium adatom to the graphene sheet altering its magnetic moment (−0.318 µ{sub B}) that is reduced from the gas phase value of the isolated atom (1 µ{sub B}). The calculated adsorption energies suggest that clustering of Na atoms on graphene is energetically favorable.
Using Density Functional Theory (DFT) for the Calculation of Atomization Energies
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
The calculation of atomization energies using density functional theory (DFT), using the B3LYP hybrid functional, is reported. The sensitivity of the atomization energy to basis set is studied and compared with the coupled cluster singles and doubles approach with a perturbational estimate of the triples (CCSD(T)). Merging the B3LYP results with the G2(MP2) approach is also considered. It is found that replacing the geometry optimization and calculation of the zero-point energy by the analogous quantities computed using the B3LYP approach reduces the maximum error in the G2(MP2) approach. In addition to the 55 G2 atomization energies, some results for transition metal containing systems will also be presented.
Esque, Jeremy; Cecchini, Marco
2015-04-23
The calculation of the free energy of conformation is key to understanding the function of biomolecules and has attracted significant interest in recent years. Here, we present an improvement of the confinement method that was designed for use in the context of explicit solvent MD simulations. The development involves an additional step in which the solvation free energy of the harmonically restrained conformers is accurately determined by multistage free energy perturbation simulations. As a test-case application, the newly introduced confinement/solvation free energy (CSF) approach was used to compute differences in free energy between conformers of the alanine dipeptide in explicit water. The results are in excellent agreement with reference calculations based on both converged molecular dynamics and umbrella sampling. To illustrate the general applicability of the method, conformational equilibria of met-enkephalin (5 aa) and deca-alanine (10 aa) in solution were also analyzed. In both cases, smoothly converged free-energy results were obtained in agreement with equilibrium sampling or literature calculations. These results demonstrate that the CSF method may provide conformational free-energy differences of biomolecules with small statistical errors (below 0.5 kcal/mol) and at a moderate computational cost even with a full representation of the solvent. PMID:25807150
Pushpa, Raghani; Gironcoli, Stefano de; Narasimhan, Shobhana
2009-04-15
We have studied the adsorption of NO, and the coadsorption of N and O, on four physical and hypothetical systems: unstrained and strained Rh(100) surfaces and monolayers of Rh atoms on strained and unstrained MgO(100) surfaces. We find that as we go from Rh(100) to Rh/Mg0(100), via the other two hypothetical systems, the effective coordination progressively decreases, the d band narrows and its center shifts closer to the Fermi level, and the strength of adsorption and coadsorption increases. Both the strain and the presence of the oxide substrate contribute significantly to this. However, charge transfer is found to play a negligible role due to a canceling out between donation and back-donation processes. Our results suggest that lowering the effective coordination of Rh catalysts by strain, roughening, or the use of inert substrates might lower activation energies for the dissociation of NO.
Wang, Jiyao; Deng, Yuqing; Roux, Benoît
2006-01-01
The absolute (standard) binding free energy of eight FK506-related ligands to FKBP12 is calculated using free energy perturbation molecular dynamics (FEP/MD) simulations with explicit solvent. A number of features are implemented to improve the accuracy and enhance the convergence of the calculations. First, the absolute binding free energy is decomposed into sequential steps during which the ligand-surrounding interactions as well as various biasing potentials restraining the translation, orientation, and conformation of the ligand are turned “on” and “off.” Second, sampling of the ligand conformation is enforced by a restraining potential based on the root mean-square deviation relative to the bound state conformation. The effect of all the restraining potentials is rigorously unbiased, and it is shown explicitly that the final results are independent of all artificial restraints. Third, the repulsive and dispersive free energy contribution arising from the Lennard-Jones interactions of the ligand with its surrounding (protein and solvent) is calculated using the Weeks-Chandler-Andersen separation. This separation also improves convergence of the FEP/MD calculations. Fourth, to decrease the computational cost, only a small number of atoms in the vicinity of the binding site are simulated explicitly, while all the influence of the remaining atoms is incorporated implicitly using the generalized solvent boundary potential (GSBP) method. With GSBP, the size of the simulated FKBP12/ligand systems is significantly reduced, from ∼25,000 to 2500. The computations are very efficient and the statistical error is small (∼1 kcal/mol). The calculated binding free energies are generally in good agreement with available experimental data and previous calculations (within ∼2 kcal/mol). The present results indicate that a strategy based on FEP/MD simulations of a reduced GSBP atomic model sampled with conformational, translational, and orientational restraining
Phenomenological Rashba model for calculating the electron energy spectrum on a cylinder
NASA Astrophysics Data System (ADS)
Savinskiĭ, S. S.; Belosludtsev, A. V.
2007-05-01
The energy spectrum of an electron on the surface of a cylinder is calculated using the Pauli equation with an additional term that takes into account the spin-orbit interaction. This term is taken in the approximation of a phenomenological Rashba model, which provides exact expressions for the wave functions and the electron energy spectrum on the cylinder surface in a static magnetic field.
Variational calculation of energy levels for metastable states of antiprotonic helium
NASA Astrophysics Data System (ADS)
Hu, Mu-Hong; Yao, Si-Meng; Wang, Yi; Li, Wang; Gu, Ying-Ying; Zhong, Zhen-Xiang
2016-06-01
We apply the variational method in Hylleraas coordinates to solve the energy eigenvalue problem for antiprotonic helium molecular systems including p bar 3 He+ and p bar 4 He+. The numerical accuracy on the nonrelativistic energies is shown to reach 10-17, thus the precision of our results is only limited by the width of the metastable states. Expectation values of the Dirac delta operators for these states are also calculated.
Calculating the free energy of nearly jammed hard-particle packings using molecular dynamics
NASA Astrophysics Data System (ADS)
Donev, Aleksandar; Stillinger, Frank H.; Torquato, Salvatore
2007-07-01
We present a new event-driven molecular dynamics (MD) algorithm for measuring the free energy of nearly jammed packings of spherical and non-spherical hard particles. This Bounding Cell Molecular Dynamics (BCMD) algorithm exactly calculates the free-energy of a single-occupancy cell (SOC) model in which each particle is restricted to a neighborhood of its initial position using a hard-wall bounding cell. Our MD algorithm generalizes previous ones in the literature by enabling us to study non-spherical particles as well as to measure the free-energy change during continuous irreversible transformations. Moreover, we make connections to the well-studied problem of computing the volume of convex bodies in high dimensions using random walks. We test and verify the numerical accuracy of the method by comparing against rigorous asymptotic results for the free energy of jammed and isostatic disordered packings of both hard spheres and ellipsoids, for which the free energy can be calculated directly as the volume of a high-dimensional simplex. We also compare our results to previously published Monte Carlo results for hard-sphere crystals near melting and jamming and find excellent agreement. We have successfully used the BCMD algorithm to determine the configurational and free-volume contributions to the free energy of glassy states of binary hard disks [A. Donev, F.H. Stillinger, S. Torquato, Do binary hard disks exhibit an ideal glass transition? Phys. Rev. Lett. 96 (22) (2006) 225502]. The algorithm can also be used to determine phases with locally- or globally-minimal free energy, to calculate the free-energy cost of point and extended crystal defects, or to calculate the elastic moduli of glassy or crystalline solids, among other potential applications.
Hong, Tianzhen; Buhl, Fred; Haves, Philip
2008-03-28
California has been using DOE-2 as the main building energy analysis tool in the development of building energy efficiency standards (Title 24) and the code compliance calculations. However, DOE-2.1E is a mature program that is no longer supported by LBNL on contract to the USDOE, or by any other public or private entity. With no more significant updates in the modeling capabilities of DOE-2.1E during recent years, DOE-2.1E lacks the ability to model, with the necessary accuracy, a number of building technologies that have the potential to reduce significantly the energy consumption of buildings in California. DOE-2's legacy software code makes it difficult and time consuming to add new or enhance existing modeling features in DOE-2. Therefore the USDOE proposed to develop a new tool, EnergyPlus, which is intended to replace DOE-2 as the next generation building simulation tool. EnergyPlus inherited most of the useful features from DOE-2 and BLAST, and more significantly added new modeling capabilities far beyond DOE-2, BLAST, and other simulations tools currently available. With California's net zero energy goals for new residential buildings in 2020 and for new commercial buildings in 2030, California needs to evaluate and promote currently available best practice and emerging technologies to significantly reduce energy use of buildings for space cooling and heating, ventilating, refrigerating, lighting, and water heating. The California Energy Commission (CEC) needs to adopt a new building energy simulation program for developing and maintaining future versions of Title 24. Therefore, EnergyPlus became a good candidate to CEC for its use in developing and complying with future Title 24 upgrades. In 2004, the Pacific Gas and Electric Company contracted with ArchitecturalEnergy Corporation (AEC), Taylor Engineering, and GARD Analytics to evaluate EnergyPlus in its ability to model those energy efficiency measures specified in both the residential and
NASA Technical Reports Server (NTRS)
Marshall, C. J.; Marshall, P. W.; Howe, C. L.; Reed, R. A.; Weller, R. A.; Mendenhall, M.; Waczynski, A.; Ladbury, R.; Jordan, T. M.
2007-01-01
This paper presents a combined Monte Carlo and analytic approach to the calculation of the pixel-to-pixel distribution of proton-induced damage in a HgCdTe sensor array and compares the results to measured dark current distributions after damage by 63 MeV protons. The moments of the Coulombic, nuclear elastic and nuclear inelastic damage distributions were extracted from Monte Carlo simulations and combined to form a damage distribution using the analytic techniques first described in [1]. The calculations show that the high energy recoils from the nuclear inelastic reactions (calculated using the Monte Carlo code MCNPX [2]) produce a pronounced skewing of the damage energy distribution. While the nuclear elastic component (also calculated using the MCNPX) contributes only a small fraction of the total nonionizing damage energy, its inclusion in the shape of the damage across the array is significant. The Coulombic contribution was calculated using MRED [3-5], a Geant4 [4,6] application. The comparison with the dark current distribution strongly suggests that mechanisms which are not linearly correlated with nonionizing damage produced according to collision kinematics are responsible for the observed dark current increases. This has important implications for the process of predicting the on-orbit dark current response of the HgCdTe sensor array.
H2 adsorption in Li-decorated porous graphene
NASA Astrophysics Data System (ADS)
Seenithurai, S.; Pandyan, R. Kodi; Kumar, S. Vinodh; Munieswaran, P.; Saranya, C.; Mahendran, M.
2015-06-01
Porous graphene (PG) has been decorated with Li atoms and subsequently studied the hydrogen (H2) adsorption characteristics, by using Density Functional Theory (DFT)-based calculations. A 2×2 PG has been decorated with eight Li atoms. Upto four H2 molecules get adsorbed on each Li atom. The maximum H2 storage capacity that could be achieved in 2×2PG-8Li is 8.95 wt% which is higher than the U.S. DOE's revised target for the on-board vehicles. The average H2 adsorption binding energy is 0.535 eV/H2, which lies between 0.2-0.6 eV/H2 that is required for achieving adsorption and desorption at near ambient conditions. Thus, Li-decorated PG could be a viable option for on-board automobile applications.
NASA Astrophysics Data System (ADS)
Zhong, Zhaopeng
In the past twenty 20 years considerable progress has been made in developing new methods for solving the multi-dimensional transport problem. However the effort devoted to the resonance self-shielding calculation has lagged, and much less progress has been made in enhancing resonance-shielding techniques for generating problem-dependent multi-group cross sections (XS) for the multi-dimensional transport calculations. In several applications, the error introduced by self-shielding methods exceeds that due to uncertainties in the basic nuclear data, and often they can be the limiting factor on the accuracy of the final results. This work is to improve the accuracy of the resonance self-shielding calculation by developing continuous energy multi-dimensional transport calculations for problem dependent self-shielding calculations. A new method has been developed, it can calculate the continuous-energy neutron fluxes for the whole two-dimensional domain, which can be utilized as weighting function to process the self-shielded multi-group cross sections for reactor analysis and criticality calculations, and during this process, the two-dimensional heterogeneous effect in the resonance self-shielding calculation can be fully included. A new code, GEMINEWTRN (Group and Energy-Pointwise Methodology Implemented in NEWT for Resonance Neutronics) has been developed in the developing version of SCALE [1], it combines the energy pointwise (PW) capability of the CENTRM [2] with the two-dimensional discrete ordinates transport capability of lattice physics code NEWT [14]. Considering the large number of energy points in the resonance region (typically more than 30,000), the computational burden and memory requirement for GEMINEWTRN is tremendously large, some efforts have been performed to improve the computational efficiency, parallel computation has been implemented into GEMINEWTRN, which can save the computation and memory requirement a lot; some energy points reducing
A Method for Calculating Fermi Energy and Carrier Concentrations in Semiconducts
ERIC Educational Resources Information Center
Gaylord, T. K.; Linxwiler, J. N., Jr.
1976-01-01
An efficient numerical method for calculating the Fermi energy, the free electron and free hole concentrations, and the ionized impurity conductors in a semiconductor material is described. The method allows freedom with respect to type of material, temperature, and amount and type of donor and acceptor impurities. (Author/CP)
Microscopic calculations of nuclear and neutron matter, symmetry energy and neutron stars
Gandolfi, S.
2015-02-01
We present Quantum Monte Carlo calculations of the equation of state of neutron matter. The equation of state is directly related to the symmetry energy and determines the mass and radius of neutron stars, providing then a connection between terrestrial experiments and astronomical observations. As a result, we also show preliminary results of the equation of state of nuclear matter.
Calculation of the vacuum condensates of the trace of the energy-momentum tensor
Ksenzov, V. G.
2008-04-15
It is shown that a modification of the effective potential proposed by A.A. Migdal and Shifman makes it possible to calculate the vacuum condensates of the trace of the energy-momentum tensor in massless theories in various spacetime dimensions.
ERIC Educational Resources Information Center
Vargas, Francisco M.
2014-01-01
The temperature dependence of the Gibbs energy and important quantities such as Henry's law constants, activity coefficients, and chemical equilibrium constants is usually calculated by using the Gibbs-Helmholtz equation. Although, this is a well-known approach and traditionally covered as part of any physical chemistry course, the required…
Calculations of the heights, periods, profile parameters, and energy spectra of wind waves
NASA Technical Reports Server (NTRS)
Korneva, L. A.
1975-01-01
Sea wave behavior calculations require the precalculation of wave elements as well as consideration of the spectral functions of ocean wave formation. The spectrum of the random wave process is largely determined by the distribution of energy in the actual wind waves observed on the surface of the sea as expressed in statistical and spectral characteristics of the sea swell.
NASA Astrophysics Data System (ADS)
Endo, Kazunaka
2016-02-01
In the Auger electron spectra (AES) simulations, we define theoretical modified kinetic energies of AES in the density functional theory (DFT) calculations. The modified kinetic energies correspond to two final-state holes at the ground state and at the transition-state in DFT calculations, respectively. This method is applied to simulate Auger electron spectra (AES) of 2nd periodic atom (Li, Be, B, C, N, O, F)-involving substances (LiF, beryllium, boron, graphite, GaN, SiO2, PTFE) by deMon DFT calculations using the model molecules of the unit cell. Experimental KVV (valence band electrons can fill K-shell core holes or be emitted during KVV-type transitions) AES of the (Li, O) atoms in the substances agree considerably well with simulation of AES obtained with the maximum kinetic energies of the atoms, while, for AES of LiF, and PTFE substance, the experimental F KVV AES is almost in accordance with the spectra from the transitionstate kinetic energy calculations.
Thermodynamic and kinetic behaviors of trinitrotoluene adsorption on powdered activated carbons
Lee, J.W.; Hwang, K.J.; Shim, W.G.; Moon, I.S.
2006-07-01
Regulations on the removal of trinitrotoluene (TNT) from wastewater have become increasingly more stringent, demanding faster, less expensive, and more efficient treatment. This study focuses on the adsorption equilibrium and kinetics of TNT on powered activated carbons (PAC). Three types of PACs (i.e., wood based, coal based, and coconut-shell based) were studied as functions of temperature and pH. Thermodynamic properties including Gibbs free energy, enthalpy, and entropy, were evaluated by applying the Van't Hoff equation. In addition, the adsorption energy distribution functions which describe heterogeneous characteristics of porous solid sorbents were calculated by using the generalized nonlinear regularization method. Adsorption kinetic studies were carried out in batch adsorber under important conditions such as PAC types, temperature, pH, and concentration. We found that fast and efficient removal of TNT dissolved in water can be successfully achieved by PAC adsorption.
Hyperspherical hidden crossing calculation of Ps formation in low-energy e+-Na collisions
NASA Astrophysics Data System (ADS)
Ward, S. J.; Shertzer, J.
2011-05-01
The hyperspherical hidden crossing method (HHCM) can provide important insight into scattering processes. Previously, we have used the HHCM to calculate the Ps(1s)-formation cross section in low-energy e+-H and e+-Li collisions. Here we apply the HHCM to low-energy e+-Na collisions. We use the Peach model potential and treat e+e-Na+ as an effective three-body system. We calculate the Ps(1s)-formation cross sections for 0 <= L <= 3 and compare our results with a hyperspherical close-coupling calculation. The HHCM provides an explanation for the small S-wave Ps(1s)-formation cross section. The S-wave Stückelberg phase is close to π for the three collision systems due to destructive interference between the two amplitudes that correspond to different paths leading to Ps(1s) formation.
NASA Astrophysics Data System (ADS)
Zhang, Bo; Peng, Bo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai; Lu, Benzhuo
2015-05-01
We present PAFMPB, an updated and parallel version of the AFMPB software package for fast calculation of molecular solvation-free energy. The new version has the following new features: (1) The adaptive fast multipole method and the boundary element methods are parallelized; (2) A tool is embedded for automatic molecular VDW/SAS surface mesh generation, leaving the requirement for a mesh file at input optional; (3) The package provides fast calculation of the total solvation-free energy, including the PB electrostatic and nonpolar interaction contributions. PAFMPB is implemented in C and Fortran programming languages, with the Cilk Plus extension to harness the computing power of both multicore and vector processing. Computational experiments demonstrate the successful application of PAFMPB to the calculation of the PB potential on a dengue virus system with more than one million atoms and a mesh with approximately 20 million triangles.
Automated calculation of surface energy fluxes with high-frequency lake buoy data
Woolway, R Iestyn; Jones, Ian D; Hamilton, David P.; Maberly, Stephen C; Muroaka, Kohji; Read, Jordan S.; Smyth, Robyn L; Winslow, Luke A.
2015-01-01
Lake Heat Flux Analyzer is a program used for calculating the surface energy fluxes in lakes according to established literature methodologies. The program was developed in MATLAB for the rapid analysis of high-frequency data from instrumented lake buoys in support of the emerging field of aquatic sensor network science. To calculate the surface energy fluxes, the program requires a number of input variables, such as air and water temperature, relative humidity, wind speed, and short-wave radiation. Available outputs for Lake Heat Flux Analyzer include the surface fluxes of momentum, sensible heat and latent heat and their corresponding transfer coefficients, incoming and outgoing long-wave radiation. Lake Heat Flux Analyzer is open source and can be used to process data from multiple lakes rapidly. It provides a means of calculating the surface fluxes using a consistent method, thereby facilitating global comparisons of high-frequency data from lake buoys.
On calculating the energy characteristics of a metal film with a dielectric coating
NASA Astrophysics Data System (ADS)
Babich, A. V.
2014-02-01
A method for calculating the characteristics of a metal film in a dielectric surroundings is suggested. The most interesting case of asymmetric metal-dielectric sandwiches, in which the dielectrics on both sides of the film are different, is considered in the context of the Kohn-Sham modified method. The spectrum, the electron work function, and the surface energy of polycrystalline and single-crystal films placed into passive insulators are calculated for the first time. In general, the dielectric surroundings leads to a negative change in the electron work function and the surface energy. In addition to size-effect-related changes, the shift of the work function is determined by the arithmetic mean of the dielectric constants of the surrounding media. Calculations have been performed for Na, Al, and Pb.
Chakraborty, Arindam; Truhlar, Donald G; Bowman, Joel M; Carter, Stuart
2004-08-01
The rovibration partition function of CH4 was calculated in the temperature range of 100-1000 K using well-converged energy levels that were calculated by vibrational-rotational configuration interaction using the Watson Hamiltonian for total angular momenta J = 0-50 and the MULTIMODE computer program. The configuration state functions are products of ground-state occupied and virtual modals obtained using the vibrational self-consistent field method. The Gilbert and Jordan potential energy surface was used for the calculations. The resulting partition function was used to test the harmonic oscillator approximation and the separable-rotation approximation. The harmonic oscillator, rigid-rotator approximation is in error by a factor of 2.3 at 300 K, but we also propose a separable-rotation approximation that is accurate within 2% from 100 to 1000 K. PMID:15260761
Calculation of energy levels and transition amplitudes for barium and radium.
Dzuba, V. A.; Flambaum, V. V.; Physics; Univ. of New South Wales
2007-01-01
The radium atom is a promising system for studying parity and time invariance violating weak interactions. However, available experimental spectroscopic data for radium are insufficient for designing an optimal experimental setup. We calculate the energy levels and transition amplitudes for radium states of significant interest. Forty states corresponding to all possible configurations consisting of the 7s, 7p and 6d single-electron states as well as the states of the 7s8s, 7s8p and 7s7d configurations have been calculated. The energies of ten of these states corresponding to the 6d{sup 2}, 7s8s, 7p{sup 2} and 6d7p configurations are not known from experiment. Calculations for barium are used to control the accuracy.
Adsorption of di-2-pyridyl ketone salicyloylhydrazone on silica gel: characteristics and isotherms.
Antonio, P; Iha, K; Suárez-Iha, M E V
2004-10-01
The adsorption of DPKSH onto silica gel was investigated, at 25+/-1 degrees C and pH 1, 4.7 and 12. For the same DPKSH concentration interval, the minimum required time of contact for adsorption maximum at pH 4.7 was smaller than at pH 1 and the maximum amount of DPKSH adsorbed per gram of silica at pH 1 is smaller than at pH 4.7. At pH 12 the DPKSH adsorption onto silica gel was not significant. The adsorption data followed Langmuir, Freundlich and Dubinin-Radushkevich (D-R) isotherms. The maximum amount of solute adsorbed (m(ads)(max)) and the adsorption constant, K(L), were derived from Langmuir isotherm. The Freundlich constants 1/n and K(F) related, respectively, to the energetic heterogeneity of adsorption sites and an empirical constant were evaluated. The mean sorption free energy (E) of DPKSH adsorption onto silica gel was calculated from D-R isotherm indicating a physical adsorption mode. Finally, conductimetric titrations showed the silica particle basicity and acidity as 0.002 and 0.3mmolg(-1), respectively. PMID:18969629
Wang, Wendong; Ma, Cui; Zhang, Yinting; Yang, Shengjiong; Shao, Yue; Wang, Xiaochang
2016-07-01
Phosphate is one of the most predominant pollutants in natural waters. Laboratory experiments were conducted to investigate the phosphate adsorption performance of a (NFS) made from drinking water treatment residuals. The adsorption of phosphate on the NFS fitted well with the Freundlich isotherm and pseudo second-order kinetic models. At pH7.0, the maximum adsorption capacity of 1.03mg/g was achieved at 15°C corresponding to the wastewater temperature in cold months, and increased notably to 1.31mg/g at 35°C. Under both acidic conditions (part of the adsorption sites was consumed) and basic conditions (negative charges formed on the surface of NFS, which led to a static repulsion of PO4(3-) and HPO4(2-)), the adsorption of phosphate was slightly inhibited. Further study showed that part of the adsorption sites could be recovered by 0.25mol/L NaOH. The activation energy was calculated to be above 8.0kJ/mol, indicating that the adsorption of phosphate on NFS was probably a chemical process. Considering the strong phosphate adsorption capacity and recoverability, NFS showed great promise on enhancing phosphate removal from the secondary treated wastewater in the filtration process. PMID:27372133
The importance of geospatial data to calculate the optimal distribution of renewable energies
NASA Astrophysics Data System (ADS)
Díaz, Paula; Masó, Joan
2013-04-01
Specially during last three years, the renewable energies are revolutionizing the international trade while they are geographically diversifying markets. Renewables are experiencing a rapid growth in power generation. According to REN21 (2012), during last six years, the total renewables capacity installed grew at record rates. In 2011, the EU raised its share of global new renewables capacity till 44%. The BRICS nations (Brazil, Russia, India and China) accounted for about 26% of the total global. Moreover, almost twenty countries in the Middle East, North Africa, and sub-Saharan Africa have currently active markets in renewables. The energy return ratios are commonly used to calculate the efficiency of the traditional energy sources. The Energy Return On Investment (EROI) compares the energy returned for a certain source and the energy used to get it (explore, find, develop, produce, extract, transform, harvest, grow, process, etc.). These energy return ratios have demonstrated a general decrease of efficiency of the fossil fuels and gas. When considering the limitations of the quantity of energy produced by some sources, the energy invested to obtain them and the difficulties of finding optimal locations for the establishment of renewables farms (e.g. due to an ever increasing scarce of appropriate land) the EROI becomes relevant in renewables. A spatialized EROI, which uses variables with spatial distribution, enables the optimal position in terms of both energy production and associated costs. It is important to note that the spatialized EROI can be mathematically formalized and calculated the same way for different locations in a reproducible way. This means that having established a concrete EROI methodology it is possible to generate a continuous map that will highlight the best productive zones for renewable energies in terms of maximum energy return at minimum cost. Relevant variables to calculate the real energy invested are the grid connections between
Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.
2015-03-07
A simultaneous use of the full molecular symmetry and of an exact kinetic energy operator (KEO) is of key importance for accurate predictions of vibrational levels at a high energy range from a potential energy surface (PES). An efficient method that permits a fast convergence of variational calculations would allow iterative optimization of the PES parameters using experimental data. In this work, we propose such a method applied to tetrahedral AB{sub 4} molecules for which a use of high symmetry is crucial for vibrational calculations. A symmetry-adapted contracted angular basis set for six redundant angles is introduced. Simple formulas using this basis set for explicit calculation of the angular matrix elements of KEO and PES are reported. The symmetric form (six redundant angles) of vibrational KEO without the sin(q){sup −2} type singularity is derived. The efficient recursive algorithm based on the tensorial formalism is used for the calculation of vibrational matrix elements. A good basis set convergence for the calculations of vibrational levels of the CH{sub 4} molecule is demonstrated.
NASA Astrophysics Data System (ADS)
Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.
2015-03-01
A simultaneous use of the full molecular symmetry and of an exact kinetic energy operator (KEO) is of key importance for accurate predictions of vibrational levels at a high energy range from a potential energy surface (PES). An efficient method that permits a fast convergence of variational calculations would allow iterative optimization of the PES parameters using experimental data. In this work, we propose such a method applied to tetrahedral AB4 molecules for which a use of high symmetry is crucial for vibrational calculations. A symmetry-adapted contracted angular basis set for six redundant angles is introduced. Simple formulas using this basis set for explicit calculation of the angular matrix elements of KEO and PES are reported. The symmetric form (six redundant angles) of vibrational KEO without the sin(q)-2 type singularity is derived. The efficient recursive algorithm based on the tensorial formalism is used for the calculation of vibrational matrix elements. A good basis set convergence for the calculations of vibrational levels of the CH4 molecule is demonstrated.
Calculated Energy Levels, Oscillator Strengths and Lifetimes in Al-like Argon
NASA Astrophysics Data System (ADS)
Gupta, G. P.; Msezane, A. Z.
Excitation energies, oscillator strengths and transition probabilities for electric-dipole-allowed and inter-combination transitions among the 25 LS levels belonging to the (1s22s22p6)3s23p, 3s3p2, 3s23d, 3p3, 3s3p3d, 3s24s, 3s24p, 3s24d, 3s24f and 3s3p4s configurations of Ar VI are calculated using extensive configuration-interaction (CI) wave functions. From our transition probabilities we have also calculated the radiative lifetimes of doublet and quartet states of Ar VI. Our results are compared with other available theoretical calculations and the experimental data. To assess the importance of relativistic effects on our calculated values, we have also carried out calculations in the intermediate-coupling scheme. These effects are incorporated through the Breit-Pauli approximation via spin-orbit, spin-other-orbit, spin-spin, Darwin and mass correction terms. Small adjustments to the diagonal elements of the Hamiltonian matrices have been made so that the energy splittings are as close as possible to the experimental values. The energy splitting of 54 fine-structure levels, the oscillator strengths and transition probabilities for some strong dipole-allowed and intercombination transitions and the lifetimes of some fine-structure levels are presented and compared with available experimental and other theoretical values. Our lifetime for the 3s3p(1Po)3d(2Po) level calculated in intermediate-coupling scheme, while differing significantly from our LS value, shows excellent agreement with the experimental result of Pinnington et al. In this calculation we also predict new data for several levels where no other theoretical and experimental results are available.
First-principles study of Mn adsorption on Al4C3(0 0 0 1) surface
NASA Astrophysics Data System (ADS)
Yao, L. F.; Li, K.; Zhou, N. G.
2016-02-01
First-principle calculation based on the density functional theory was adopted to investigate the adsorption energy, stability, electronic structure and bonding of Mn atom adsorption on Al-terminated and C-terminated Al4C3(0 0 0 1) surface under 0.25 ML and 0.5 ML. Results show that the structure of Mn adsorption on C-terminated Al4C3(0 0 0 1) surface is more stable than that on Al-terminated surface according to the formation energy calculation. For Mn adsorption on Al-terminated surface, Mn is more favorable to reside at the site H1 comparing with other sites. As well, for Mn adsorption on C-terminated surface, the structure of Mn adsorption at site H‧1 is the most stable one. By analyzing the electronic structure and bonding, it is found that the mixed metallic/covalent bonds are formed between Mn atoms and Al-terminated surface, while the covalent bonds are formed between Mn atoms and C-terminated surface. According to the interlayer spacing calculation, Al4C3(0 0 0 1) surfaces are reconstructed after Mn adsorption, which in turn affect the following stacking of Mg atoms on Al4C3(0 0 0 1) surface. The above analysis provided effective theoretical support to the experimental phenomenon that high Mn content has negative influence on the heterogeneous nucleation of Al4C3 particles for α-Mg grains.
A method for calculating strain energy release rate based on beam theory
NASA Technical Reports Server (NTRS)
Sun, C. T.; Pandey, R. K.
1993-01-01
The Timoshenko beam theory was used to model cracked beams and to calculate the total strain energy release rate. The root rotation of the beam segments at the crack tip were estimated based on an approximate 2D elasticity solution. By including the strain energy released due to the root rotations of the beams during crack extension, the strain energy release rate obtained using beam theory agrees very well with the 2D finite element solution. Numerical examples were given for various beam geometries and loading conditions. Comparisons with existing beam models were also given.
Similarity criteria in calculations of the energy characteristics of a cw oxygen - iodine laser
NASA Astrophysics Data System (ADS)
Mezhenin, A. V.; Azyazov, V. N.
2012-12-01
The calculated and experimental data on the energy efficiency of a cw oxygen - iodine laser (OIL) are analysed based on two similarity criteria, namely, on the ratio of the residence time of the gas mixture in the resonator to the characteristic time of extraction of the energy stored in singlet oxygen td and on the gain-to-loss ratio Π. It is shown that the simplified two-level laser model satisfactorily predicts the output characteristics of OILs with a stable resonator at τd <= 7. Efficient energy extraction from the OIL active medium is achieved in the case of τd = 5 - 7, Π = 4 - 8.
Similarity criteria in calculations of the energy characteristics of a cw oxygen - iodine laser
Mezhenin, A V; Azyazov, V N
2012-12-31
The calculated and experimental data on the energy efficiency of a cw oxygen - iodine laser (OIL) are analysed based on two similarity criteria, namely, on the ratio of the residence time of the gas mixture in the resonator to the characteristic time of extraction of the energy stored in singlet oxygen td and on the gain-to-loss ratio {Pi}. It is shown that the simplified two-level laser model satisfactorily predicts the output characteristics of OILs with a stable resonator at {tau}{sub d} {<=} 7. Efficient energy extraction from the OIL active medium is achieved in the case of {tau}{sub d} = 5 - 7, {Pi} = 4 - 8. (lasers)
Calculating splittings between energy levels of different symmetry using path-integral methods.
Mátyus, Edit; Althorpe, Stuart C
2016-03-21
It is well known that path-integral methods can be used to calculate the energy splitting between the ground and the first excited state. Here we show that this approach can be generalized to give the splitting patterns between all the lowest energy levels from different symmetry blocks that lie below the first-excited totally symmetric state. We demonstrate this property numerically for some two-dimensional models. The approach is likely to be useful for computing rovibrational energy levels and tunnelling splittings in floppy molecules and gas-phase clusters. PMID:27004864
Benhammou, Abdelaziz; Yaacoubi, Abdelrani; Nibou, Lahbib; Tanouti, Boumediane
2007-02-01
Batch adsorption of the chromium(VI) onto Moroccan stevensite pillared by Keggin aluminium hydroxypolycation (Al-stevensite) and cationic surfactant cetyltrimethylammoniumbromide (CTA-stevensite) was investigated. The results showed that the CTA-stevensite has a higher affinity than that of Al-stevensite for chromium(VI) adsorption. The adsorption capacities for natural stevensite, Al-stevensite and CTA-stevensite calculated according to the Dubinin-Kaganer-Radushkevich isotherm (DKR) are 13.7, 75.4 and 195.6mmolkg(-1), respectively. The study of the pH effect showed that the optimal range corresponding to the Cr(VI) maximum adsorption on Al-stevensite is pH 3.5-6 and that on CTA-stevensite is pH 2-6. The adsorption rates evaluated according to the pseudo-second-order model are 7.2, 207.2 and 178.5mmolkg(-1)min(-1) for the natural stevensite, Al-stevensite and CTA-stevensite, respectively. The low values of the adsorption energy calculated by (DKR) suggest that anion exchange is the main mechanism that governs the chromate adsorption. PMID:16876943
Theoretical study of the adsorption of DOPA-quinone and DOPA-quinone chlorides on Cu (1 0 0) surface
NASA Astrophysics Data System (ADS)
Chen, Shuang-Kou; Wang, Bo-Chu; Zhou, Tai-Gang; Huang, Wen-Zhang
2011-07-01
The marine mussel secreted adhesive proteins and could bind strongly to all kinds of surfaces. Studies indicated that there was an unusual amino acid 3,4-dihydroxy-L-phenylanine (DOPA). DOPA could be oxidized to DOPA-quinone easily, which had a superior ability to on surface directly. The technology of electrolyzing seawater was employed to generate HOCl solution to react with DOPA-quinone and form DOPA-quinone chlorides (DOPA-quinone-Cl) to hinder the adhesion. However, the detailed hinder-mechanism remained unknown to be fully explained. Herein, using quantum chemical density functional theory methods, we have systematically studied three kinds of adsorption for DOPA-quinone and DOPA-quinone-Cl on Cu (1 0 0) surface: hydroxyl oxygen-side vertical, carbonyl oxygen-side vertical, amino N-terminal vertical adsorptions and carried out geometry optimization and energy calculation. The results showed that two molecules could absorb on the Cu (1 0 0) through hydroxyl oxygen-side vertical adsorption, while the other two kinds of adsorption could not form an effective adsorption. Calculations of adsorption energy for hydroxyl oxygen-side vertical adsorption indicated that: after HOCl modification, adsorption energy decreased from -247.2310 kJ/mol to -177.0579 kJ/mol for DOPA-quinone and DOPA-quinone-Cl; and the Mulliken Charges Populations showed that the electrons transferred from surface to DOPA-quinone-Cl was less than that to DOPA-quinone, namely, the fewer the number of electrons transferred, the weaker interaction between molecular and surface. After the theoretical calculation, we found that the anti-foul goal had been achieved by electrolysis of seawater to generate HOCl to modify DOPA-quinone, which led to the reduction of adsorption energy and transferred electrons.
NASA Astrophysics Data System (ADS)
Whitney, K. G.; Chang, C. S.
2008-07-01
Analyses of the resonant multiphoton ionization of atoms require knowledge of ac Stark energy shifts and of multiphoton, bound-to-bound state, transition amplitudes. In this paper, we consider the three-photon photoionization of hydrogen atoms at frequencies that are at and surrounding the two-photon 1s to 2s resonance. AC energy shift sums of both the 1s and 2s states are calculated as a function of the laser frequency along with two-photon 1s → 2s resonant transition amplitude sums. These quantities are calculated using an extended version of a method, which has often been employed in a variety of ways, of calculating these sums by expressing them in terms of solutions to a variety of differential equations that are derived from the different sums being evaluated. We demonstrate how exact solutions are obtained to these differential equations, which lead to exact evaluations of the corresponding sums. A variety of different cases are analysed, some involving analytic continuation, some involving real number analysis and some involving complex number analysis. A dc Stark sum calculation of the 2s state is carried out to illustrate the case where analytic continuation, pole isolation and pole subtraction are required and where the calculation can be carried out analytically; the 2s state, ac Stark shift sum calculations involve a case where no analytic continuation is required, but where the solution to the differential equation produces complex numbers owing to the finite photoionization lifetime of the 2s state. Results from these calculations are then used to calculate three-photon ionization probabilities of relevance to an analysis of the multiphoton ionization data published by Kyrala and Nichols (1991 Phys. Rev. A 44, R1450).
From single molecules to water networks: Dynamics of water adsorption on Pt(111).
Naderian, Maryam; Groß, Axel
2016-09-01
The adsorption dynamics of water on Pt(111) was studied using ab initio molecular dynamics simulations based on density functional theory calculations including dispersion corrections. Sticking probabilities were derived as a function of initial kinetic energy and water coverage. In addition, the energy distribution upon adsorption was monitored in order to analyze the energy dissipation process. We find that on the water pre-covered surface the sticking probability is enhanced because of the attractive water-water interaction and the additional effective energy dissipation channels to the adsorbed water molecules. The water structures forming directly after the adsorption on the pre-covered surfaces do not necessarily correspond to energy minimum structures. PMID:27609006
A highly efficient hybrid method for calculating the hydration free energy of a protein.
Oshima, Hiraku; Kinoshita, Masahiro
2016-03-30
We develop a new method for calculating the hydration free energy (HFE) of a protein with any net charge. The polar part of the energetic component in the HFE is expressed as a linear combination of four geometric measures (GMs) of the protein structure and the generalized Born (GB) energy plus a constant. The other constituents in the HFE are expressed as linear combinations of the four GMs. The coefficients (including the constant) in the linear combinations are determined using the three-dimensional reference interaction site model (3D-RISM) theory applied to sufficiently many protein structures. Once the coefficients are determined, the HFE and its constituents of any other protein structure are obtained simply by calculating the four GMs and GB energy. Our method and the 3D-RISM theory give perfectly correlated results. Nevertheless, the computation time required in our method is over four orders of magnitude shorter. PMID:26576506
Efficient ab initio free energy calculations by classically assisted trajectory sampling
NASA Astrophysics Data System (ADS)
Wilson, Hugh F.
2015-12-01
A method for efficiently performing ab initio free energy calculations based on coupling constant thermodynamic integration is demonstrated. By the use of Boltzmann-weighted sums over states generated from a classical ensemble, the free energy difference between the classical and ab initio ensembles is readily available without the need for time-consuming integration over molecular dynamics trajectories. Convergence and errors in this scheme are discussed and characterised in terms of a quantity representing the degree of misfit between the classical and ab initio systems. Smaller but still substantial efficiency gains over molecular dynamics are also demonstrated for the calculation of average properties such as pressure and total energy for systems in equilibrium.
Learning Approach on the Ground State Energy Calculation of Helium Atom
Shah, Syed Naseem Hussain
2010-07-28
This research investigated the role of learning approach on the ground state energy calculation of Helium atom in improving the concepts of science teachers at university level. As the exact solution of several particles is not possible here we used approximation methods. Using this method one can understand easily the calculation of ground state energy of any given function. Variation Method is one of the most useful approximation methods in estimating the energy eigen values of the ground state and the first few excited states of a system, which we only have a qualitative idea about the wave function.The objective of this approach is to introduce and involve university teacher in new research, to improve their class room practices and to enable teachers to foster critical thinking in students.
Learning Approach on the Ground State Energy Calculation of Helium Atom
NASA Astrophysics Data System (ADS)
Shah, Syed Naseem Hussain
2010-07-01
This research investigated the role of learning approach on the ground state energy calculation of Helium atom in improving the concepts of science teachers at university level. As the exact solution of several particles is not possible here we used approximation methods. Using this method one can understand easily the calculation of ground state energy of any given function. Variation Method is one of the most useful approximation methods in estimating the energy eigen values of the ground state and the first few excited states of a system, which we only have a qualitative idea about the wave function. The objective of this approach is to introduce and involve university teacher in new research, to improve their class room practices and to enable teachers to foster critical thinking in students.
Long-range correlation energy calculated from coupled atomic response functions
Ambrosetti, Alberto; Reilly, Anthony M.; Tkatchenko, Alexandre; DiStasio, Robert A.
2014-05-14
An accurate determination of the electron correlation energy is an essential prerequisite for describing the structure, stability, and function in a wide variety of systems. Therefore, the development of efficient approaches for the calculation of the correlation energy (and hence the dispersion energy as well) is essential and such methods can be coupled with many density-functional approximations, local methods for the electron correlation energy, and even interatomic force fields. In this work, we build upon the previously developed many-body dispersion (MBD) framework, which is intimately linked to the random-phase approximation for the correlation energy. We separate the correlation energy into short-range contributions that are modeled by semi-local functionals and long-range contributions that are calculated by mapping the complex all-electron problem onto a set of atomic response functions coupled in the dipole approximation. We propose an effective range-separation of the coupling between the atomic response functions that extends the already broad applicability of the MBD method to non-metallic materials with highly anisotropic responses, such as layered nanostructures. Application to a variety of high-quality benchmark datasets illustrates the accuracy and applicability of the improved MBD approach, which offers the prospect of first-principles modeling of large structurally complex systems with an accurate description of the long-range correlation energy.
Hydrogen adsorption in ZIF-7: A DFT and ab-initio molecular dynamics study
NASA Astrophysics Data System (ADS)
Dixit, Mudit; Major, Dan Thomas; Pal, Sourav
2016-05-01
Primary H2 adsorption sites in a zeolitic imidazolate framework, ZIF-7, are identified using ab-initio density functional theory (DFT) based molecular dynamics annealing simulations. The simulations suggest several low energy adsorption sites. The effect of light transition metal decoration on hydrogen storage properties was studied. Our ab-intio DFT calculations illustrate that decorating the ZIF with Sc increases both the number of H2 molecules, as well as the H2 binding energy. The binding energy (∼25 kJ/mol per H2) at 8H2 loading in the pore, suggests that Sc-ZIFs can be potential candidates for hydrogen storage.
Ghatbandhe, A S; Yenkie, M K N
2008-04-01
Adsorption equilibrium, kinetics and thermodynamics of 2,4-dichlorophenol (2,4-DCP), one of the most commonly used chlorophenol, onto bituminous coal based Filtrasorb-400 grade granular activated carbon, were studied in aqueous solution in a batch system with respect to temperature. Uptake capacity of activated carbon found to increase with temperature. Langmuir isotherm models were applied to experimental equilibrium data of 2, 4-DCP adsorption and competitive studies with respect to XAD resin were carried out. Equilibrium data fitted very well to the Langmuir equilibrium model. Adsorbent monolayer capacity 'Q0, Langmuir constant 'b' and adsorption rate constant 'k(a)' were evaluated at different temperatures for activated carbon adsorption. This data was then used to calculate the energy of activation of adsorption and also the thermodynamic parameters, namely the free energy of adsorption, deltaG0, enthalpy of adsorption, deltaH0 and the entropy of adsorption deltaS0. The obtained results showed that the monolayer capacity increases with the increase in temperatures. The obtained values of thermodynamic parameters showed that adsorption of 2,4 DCP is an endothermic process. Synthetic resin was not found efficient to adsorb 2,4 DCP compared to activated carbon. The order of adsorption efficiencies of three resins used in the study found as XAD7HP > XAD4 > XAD1180. PMID:19295102
NASA Astrophysics Data System (ADS)
Öztürk, A.; Malkoc, E.
2014-04-01
In this work, natural untreated clay (NUC) was studied for the removal of Basic Yellow 2 (BY2) from aqueous solution in batch system. The effects of initial BY2 concentration, contact time, solution temperature and solution pH on BY2 adsorption were investigated. Nitrogen sorption measurements were employed to investigate the variation in surface and pore properties after dye adsorption. The adsorbent was characterized by means of FTIR, PSD, TEM, XRD and BET analysis. The equilibrium adsorption data were analyzed by Langmuir, Freundlich, Temkin and Scatchard isotherm models. The maximum monolayer adsorption capacity was found to be 833.33 mg/g at 25 °C (at room temperature). The pseudo-second-order kinetic model provided the best fit to the experimental datas compared with pseudo-first-order kinetic adsorption models. To explain mass transfer mechanism of BY2 adsorption, obtained experimental datas were applied Weber and Morris model, Body and Frusawa and Smith models. The results show that the adsorption process is controlled by film diffusion. The thermodynamic parameters such as, Gibbs free energy changes (ΔG°), standard enthalpy change (ΔH°) and standard entropy change (ΔS°) were determined. Adsorption of BY2 on NUC is exothermic and spontaneous in nature. The calculated activation energy of adsorption was found to be 5.24 kJ/mol for BY2. This value indicates that the adsorption process is a physisorption.
Lin, Bin; Wong, Ka-Yiu; Hu, Char; Kokubo, Hironori; Pettitt, B. Montgomery
2011-01-01
Although detailed atomic models may be applied for a full description of solvation, simpler phenomenological models are particularly useful to interpret the results for scanning many, large, complex systems where a full atomic model is too computationally expensive to use. Among the most costly are solvation free energy evaluations by simulation. Here we develop a fast way to calculate electrostatic solvation free energy while retaining much of the accuracy of explicit solvent free energy simulation. The basis of our method is to treat the solvent not as a structureless dielectric continuum, but as a structured medium by making use of universal proximal radial distribution functions. Using a deca-alanine peptide as a test case, we compare the use of our theory with free energy simulations and traditional continuum estimates of the electrostatic solvation free energy. PMID:21765968
Lin, Bin; Wong, Ka-Yiu; Hu, Char Y.; Kokubo, Hironori; Pettitt, Bernard M.
2011-07-07
Although detailed atomic models may be applied for a full description of solvation, simpler phenomenologicalmodels are particularly useful to interpret the results for scanning many large, complex systems, where a full atomic model is too computationally expensive to use. Among the most costly are solvation free-energy evaluations by simulation. Here we develop a fast way to calculate electrostatic solvation free energy while retaining much of the accuracy of explicit solvent free-energy simulation. The basis of our method is to treat the solvent not as a structureless dielectric continuum but as a structured medium by making use of universal proximal radial distribution functions. Using a deca-alanine peptide as a test case, we compare the use of our theory with free-energy simulations and traditional continuum estimates of the electrostatic solvation free energy.
The corrosive influence of chloride ions preference adsorption on α-Al2O3 (0 0 0 1) surface
NASA Astrophysics Data System (ADS)
Zhang, Chuan-Hui; Liu, Min; Jin, Ying; Sun, Dong-Bai
2015-08-01
Conductor-like screening model (COSMO), Periodic DFT calculations have been performed on a Al2O3 surface to model the influence of preference adsorption and interaction of chloride ions at increasing monolayer coverage on undefective passive film on Aluminum in solution environment. The results evidence that the critical monolayer of Cl- is 3/7, which is redefined. With increasing Cl- adsorption, both the first and second Cl- move from Al(1) atop and bridge10 sites to O(5) sites, suggesting that the weaker interaction between Cl- and Al2O3 surface but stronger interactions between three ions make the electrons uniformly occupy on the energy levels of them. More calculations shows that the preference adsorption sites of Cl- are independent of the surface area of oxide, and the adsorption energy decrease in three steps, each adsorption energy step only relate to the adsorption site and the morphology. On undefective oxide film, low coverage Cl- adsorption would restrain surface breakdown to happen which is consistent with the experiment results.
NASA Technical Reports Server (NTRS)
Marshall, C. J.; Ladbury, R.; Marshall, P. W.; Reed, R. A.; Howe, C.; Weller, B.; Mendenhall, M.; Waczynski, A.; Jordan, T. M.; Fodness, B.
2006-01-01
This paper presents a combined Monte Carlo and analytic approach to the calculation of the pixel-to-pixel distribution of proton-induced damage in a HgCdTe sensor array and compares the results to measured dark current distributions after damage by 63 MeV protons. The moments of the Coulombic, nuclear elastic and nuclear inelastic damage distribution were extracted from Monte Carlo simulations and combined to form a damage distribution using the analytic techniques first described in [I]. The calculations show that the high energy recoils from the nuclear inelastic reactions (calculated using the Monte Car10 code MCNPX [2]) produce a pronounced skewing of the damage energy distribution. The nuclear elastic component (also calculated using the MCNPX) has a negligible effect on the shape of the damage distribution. The Coulombic contribution was calculated using MRED [3,4], a Geant4 [4,5] application. The comparison with the dark current distribution strongly suggests that mechanisms which are not linearly correlated with nonionizing damage produced according to collision kinematics are responsible for the observed dark current increases. This has important implications for the process of predicting the on-orbit dark current response of the HgCdTe sensor array.
NASA Astrophysics Data System (ADS)
de Jong, Maarten; Qi, Liang; Olmsted, David L.; van de Walle, Axel; Asta, Mark
2016-03-01
A method is described for calculating the energetics of planar defects in alloys based on the special-quasirandom-structure (SQS) approach. We examine the accuracy of the approach employing atomistic calculations based on a classical embedded-atom-method (EAM) interatomic potential for hexagonal close packed (hcp) alloys, for which benchmark results can be obtained by direct configurational averaging. The results of these calculations demonstrate that the SQS-based approach can be employed to derive the concentration dependence of the energies of twin boundaries, unstable stacking faults, and surfaces to within an accuracy of approximately 10%. The SQS considered in this study contain up to 72 atoms and hence are small enough to be considered in first-principles density-functional-theory (DFT) based calculations. The application of the SQS-based approach in direct DFT-based calculations is demonstrated in a study of the concentration dependence of interfacial energies for {11 2 ¯1 } twins in hcp Ti-Al alloys.
Energy Loss Calculations for Target Thickness Determinations using SRIM and Excel
NASA Astrophysics Data System (ADS)
Pawlak, A. S.; Greene, J. P.
2011-10-01
The thickness of a thin target foil can be determined by measuring the energy loss of alpha particles that travel through it. In the Target Laboratory of the Physics Division at Argonne National Laboratory (ANL), this is accomplished by measuring the energy loss of the 5812 keV alpha particles emitted by a 2 49 Cf source using a silicon detector set-up. The energy loss is translated into the target foil thickness using the stopping power for 4He in the target material obtained from the stopping/range tables provided by SRIM. This calculation has until recently been carried out using a program developed for this purpose, ``ENELOSS.'' This program uses the stopping/range tables from the original work published by Ziegler. Additionally, due to its design, ENELOSS is unable to easily accommodate targets made from compounds. In order to perform theses measurements using the most recent SRIM data, and to better calculate the thickness of compound targets, we have developed a ``Thickness Calculation'' spreadsheet using Microsoft Excel. This spreadsheet approach is not limited to elemental targets and employs stopping/range tables from the most recent edition of SRIM available on the web. The calculations obtained allow for more accurate target thicknesses and automates the process conveniently for repetitive measurements. This work was supported by the U.S. DoE, Nuclear Physics Division, under Contract No. W-31-109-Eng-38.
The role of van der Waals interactions in the adsorption of noble gases on metal surfaces
Chen, De-Li; Al-Saidi, W A; Johnson, J Karl
2012-10-03
Adsorption of noble gases on metal surfaces is determined by weak interactions. We applied two versions of the nonlocal van der Waals density functional (vdW-DF) to compute adsorption energies of Ar, Kr, and Xe on Pt(111), Pd(111), Cu(111), and Cu(110) metal surfaces. We have compared our results with data obtained using other density functional approaches, including the semiempirical vdW corrected DFT-D2. The vdW-DF results show considerable improvements in the description of adsorption energies and equilibrium distances over other DFTbased methods, giving good agreement with experiments. We have also calculated perpendicular vibrational energies for noble gases on the metal surfaces using vdWDF data and found excellent agreement with available experimental results. Our vdW-DF calculations show that adsorption of noble gases on low-coordination sites is energetically favored over high-coordination sites, but only by a few meV. Analysis of the 2-dimensional potential energy surface shows that the high-coordination sites are local maxima on the 2-dimensional potential energy surface and therefore unlikely to be observed in experiments, which provides an explanation of the experimental observations. The DFT-D2 approach with the standard parameterization was found to overestimate the dispersion interactions, and to give the wrong adsorption site preference for four of the nine systems we studied.
NASA Astrophysics Data System (ADS)
Pavlyuchko, A. I.; Yurchenko, S. N.; Tennyson, Jonathan
2015-07-01
A procedure for calculation of rotational-vibrational states of medium-sized molecules is presented. It combines the advantages of variational calculations and perturbation theory. The vibrational problem is solved by diagonalising a Hamiltonian matrix, which is partitioned into two sub-blocks. The first, smaller sub-block includes matrix elements with the largest contribution to the energy levels targeted in the calculations. The second, larger sub-block comprises those basis states which have little effect on these energy levels. Numerical perturbation theory, implemented as a Jacobi rotation, is used to compute the contributions from the matrix elements of the second sub-block. Only the first sub-block needs to be stored in memory and diagonalised. Calculations of the vibrational-rotational energy levels also employ a partitioning of the Hamiltonian matrix into sub-blocks, each of which corresponds either to a single vibrational state or a set of resonating vibrational states, with all associated rotational levels. Physically, this partitioning is efficient when the Coriolis coupling between different vibrational states is small. Numerical perturbation theory is used to include the cross-contributions from different vibrational states. Separate individual sub-blocks are then diagonalised, replacing the diagonalisation of a large Hamiltonian matrix with a number of small matrix diagonalisations. Numerical examples show that the proposed hybrid variational-perturbation method greatly speeds up the variational procedure without significant loss of precision for both vibrational-rotational energy levels and transition intensities. The hybrid scheme can be used for accurate nuclear motion calculations on molecules with up to 15 atoms on currently available computers.
NASA Astrophysics Data System (ADS)
Komatsu, Y.; Umemura, M.; Shoji, M.; Shiraishi, K.; Kayanuma, M.; Yabana, K.
2014-03-01
Among several proposed biosignatures, red edge is a direct evidence of photosynthetic life if it is detected (Kiang et al 2007). Red edge is a sharp change in reflectance spectra of vegetation in NIR region (about 700-750 nm). The sign of red edge is observed by Earthshine or remote sensing (Wolstencroft & Raven 2002, Woolf et al 2002). But, why around 700-750 nm? The photosynthetic organisms on Earth have evolved to optimize the sunlight condition. However, if we consider about photosynthetic organism on extrasolar planets, they should have developed to utilize the spectra of its principal star. Thus, it is not strange even if it shows different vegetation spectra. In this study, we focused on the light absorption mechanism of photosynthetic organisms on Earth and investigated the fundamental properties of the light harvesting mechanisms, which is the first stage for the light absorption. Light harvesting complexes contain photosynthetic pigments like chlorophylls. Effective light absorption and the energy transfer are accomplished by the electronic excitations of collective photosynthetic pigments. In order to investigate this mechanism, we constructed an energy transfer model by using a dipole-dipole approximation for the interactions between electronic excitations. Transition moments and transition energies of each pigment are calculated at the time-dependent density functional theory (TDDFT) level (Marques & Gross 2004). Quantum dynamics simulation for the excitation energy transfer was calculated by the Liouvelle's equation. We adopted the model to purple bacteria, which has been studied experimentally and known to absorb lower energy. It is meaningful to focus on the mechanism of this bacteria, since in the future mission, M planets will become a important target. We calculated the oscillator strengths in one light harvesting complex and confirmed the validity by comparing to the experimental data. This complex is made of an inner and an outer ring. The
Adsorption of sugars on Al- and Ga-doped boron nitride surfaces: A computational study
NASA Astrophysics Data System (ADS)
Darwish, Ahmed A.; Fadlallah, Mohamed M.; Badawi, Ashraf; Maarouf, Ahmed A.
2016-07-01
Molecular adsorption on surfaces is a key element for many applications, including sensing and catalysis. Non-invasive sugar sensing has been an active area of research due to its importance to diabetes care. The adsorption of sugars on a template surface study is at the heart of matter. Here, we study doped hexagonal boron nitride sheets (h-BNNs) as adsorbing and sensing template for glucose and glucosamine. Using first principles calculations, we find that the adsorption of glucose and glucosamine on h-BNNs is significantly enhanced by the substitutional doping of the sheet with Al and Ga. Including long range van der Waals corrections gives adsorption energies of about 2 eV. In addition to the charge transfer occurring between glucose and the Al/Ga-doped BN sheets, the adsorption alters the size of the band gap, allowing for optical detection of adsorption. We also find that Al-doped boron nitride sheet is better than Ga-doped boron nitride sheet to enhance the adsorption energy of glucose and glucosamine. The results of our work can be potentially utilized when designing support templates for glucose and glucosamine.
Theoretical study of adsorption and dissociation of NH3 on pentanuclear Fe(111) surface
NASA Astrophysics Data System (ADS)
Purwiandono, G.; Triyono; Wijaya, K.
2016-02-01
Theoretical study regarding the adsorption and dissociation of NH3 molecule on Fe(111) surface has been carried out. The method used was DFT-B3LYP, and the basis sets used were ECP and 6-311G**. This research aimed at giving the theoretical understanding of adsorption and dissociation of NH3 molecule on Fe(111) surface. The adsorption and dissociation were studied based on the energetic parameter, bond length, electron population, vibration and orbital interaction. The result of theoretical calculation revealed that the on top position is the interaction position with the minimum energy for the adsorption of NH3 molecule on Fe(111) surface. The analysis of electron population of the two composing molecular orbitals indicated that the transfer of electron has an important role in the mechanism of adsorption. The visualization of molecular orbital showed that the transfer of electron occurred in the electron pairs of the interacting orbital. Relating to the adsorption mechanism and the overlapping of interaction orbitals, NH3 molecule provides the Highest Occupied Molecular Orbital (HOMO) as the interaction pair for the Lowest Unoccupied Molecular Orbital (LUMO) on Fe surface. The insignificant difference between the oxidation state of N and H atoms as well as the higher hemolytic N-H bond dissociation energy (compared to heterolytic dissociation) cause the adsorption mechanism of NH3 on Fe(111) model to occur through homolytic-dissociative chemisorption.
Perfetti, C.; Martin, W.; Rearden, B.; Williams, M.
2012-07-01
Three methods for calculating continuous-energy eigenvalue sensitivity coefficients were developed and implemented into the Shift Monte Carlo code within the SCALE code package. The methods were used for two small-scale test problems and were evaluated in terms of speed, accuracy, efficiency, and memory requirements. A promising new method for calculating eigenvalue sensitivity coefficients, known as the CLUTCH method, was developed and produced accurate sensitivity coefficients with figures of merit that were several orders of magnitude larger than those from existing methods. (authors)
An Exact Calculation of Electron-Ion Energy Splitting in a Hot Plasma
Singleton, Robert L
2012-09-10
In this brief report, I summarize the rather involved recent work of Brown, Preston, and Singleton (BPS). In Refs. [2] and [3], BPS calculate the energy partition into ions and electrons as a charged particle traverses a non-equilibrium two-temperature plasma. These results are exact to leading and next-to-leading order in the plasma coupling g, and are therefore extremely accurate in a weakly coupled plasma. The new BPS calculations are compared with the more standard work of Fraley et al. [12]. The results differ substantially at higher temperature when T{sub I} {ne} T{sub e}.
X-alpha calculation of transition energies in multiply ionized atoms
NASA Technical Reports Server (NTRS)
Ringers, D. A.; Chen, M. H.
1974-01-01
It is shown that the accuracy of calculations can be improved if appropriate (different) values of alpha are used for each configuration. Alternatively, the Slater Transition state can be used, wherein a total energy difference is related to a difference in single electron eigenvalues. By a series expansion, the value of alpha for an excited configuration can be related to its value for the ground state configuration. The terms Delta alpha (delta Epsilon/delta alpha) exhibit a similar dependence on atomic number as the ground state values of alpha. Results of sample calculations are reported and compared with experiment.
Calculation of quasiparticle energy spectrum of silicon using the correlated Hartree-Fock method
NASA Astrophysics Data System (ADS)
Ishihara, Takamitsu; Yamagami, Hiroshi; Matsuzawa, Kazuya; Yasuhara, Hiroshi
1999-06-01
We present quasiparticle energy spectrum calculations of silicon using the correlated Hartree-Fock method proposed by Yasuhara and Takada [Phys. Rev. B 43, 7200 (1991)], in which the information on the effective mass of an electron liquid is included in the form of a nonlocal spin-parallel potential in addition to a local potential. The calculated band gaps of silicon are much improved, compared with the local density approximation values. The minimum indirect band gap is evaluated to be 1.37 eV.
Rashev, Svetoslav; Moule, David C
2015-04-01
In this work we present a full 6D quartic potential energy surface (PES) for S0 thiophosgene in curvilinear symmetrized bond-angle coordinates. The PES was refined starting from an ab initio field derived from acc-pVTZ basis set with CCSD(T) corrections for electron correlation. In the present calculations we used our variational method that was recently tested on formaldehyde and some of its isotopomers, along with additional improvements. The lower experimentally known vibrational levels for 35Cl2CS were reproduced quite well in the calculations, which can be regarded as a test for the feasibility of the obtained quartic PES. PMID:25615683
Åsberg, Dennis; Samuelsson, Jörgen; Fornstedt, Torgny
2016-07-29
A fundamental investigation of the pressure effect on individual adsorption sites was undertaken based on adsorption energy distribution and adsorption isotherm measurements. For this purpose, we measured adsorption equilibrium data at pressures ranging from 100 to 1000bar at constant flow and over a wide concentration range for three low-molecular-weight solutes, antipyrine, sodium 2-naphthalenesulfonate, and benzyltriethylammonium chloride, on an Eternity C18 stationary phase. The adsorption energy distribution was bimodal for all solutes, remaining clearly so at all pressures. The bi-Langmuir model best described the adsorption in these systems and two types of adsorption sites were identified, one with a low and another with a high energy of interaction. Evidence exists that the low-energy interactions occur at the interface between the mobile and stationary phases and that the high-energy interactions occur nearer the silica surface, deeper in the C18 layer. The contribution of each type of adsorption site to the retention factor was calculated and the change in solute molar volume from the mobile to stationary phase during the adsorption process was estimated for each type of site. The change in solute molar volume was 2-4 times larger at the high-energy site, likely because of the greater loss of solute solvation layer when penetrating deeper into the C18 layer. The association equilibrium constant increased with increasing pressure while the saturation capacity of the low-energy site remained almost unchanged. The observed increase in saturation capacity for the high-energy site did not affect the column loading capacity, which was almost identical at 50- and 950-bar pressure drops over the column. PMID:27357740
Feasibility of a wavelet expansion method to treat energy in cell calculations
Van Rooijen, W. F. G.
2012-07-01
This paper discusses the application of the Discrete Wavelet Transform (DWT) for the functional expansion of the energy variable in a cell calculation. The motivation of the work is the desire to obtain a self-shielding methodology in which the treatment of the energy variable in a given material region can be automatically adapted to the complexity of the cross section in that region. Unfortunately, the work presented in this paper shows that it is generally not possible to obtain the desired adaptivity. The most fundamental reason is that in a multi-region system, the energy dependence of the flux in a given material region is a function of the energy dependent cross sections and sources in all material regions through which the neutrons have crossed before entering into the present material. The complexity of the energy dependence of the cross section in a material region is thus not necessarily linked to the energy dependence of the flux in that region. If one sacrifices the objective of adaptivity, then an accurate method can be obtained using the DWT as a functional expansion. However, the resulting system of equations is more complicated than the direct solution of a hyper-fine group calculation. The conclusion is thus that the DWT approach is not very practical. (authors)
Metadyn View: Fast web-based viewer of free energy surfaces calculated by metadynamics
NASA Astrophysics Data System (ADS)
Hošek, Petr; Spiwok, Vojtěch
2016-01-01
Metadynamics is a highly successful enhanced sampling technique for simulation of molecular processes and prediction of their free energy surfaces. An in-depth analysis of data obtained by this method is as important as the simulation itself. Although there are several tools to compute free energy surfaces from metadynamics data, they usually lack user friendliness and a build-in visualization part. Here we introduce Metadyn View as a fast and user friendly viewer of bias potential/free energy surfaces calculated by metadynamics in Plumed package. It is based on modern web technologies including HTML5, JavaScript and Cascade Style Sheets (CSS). It can be used by visiting the web site and uploading a HILLS file. It calculates the bias potential/free energy surface on the client-side, so it can run online or offline without necessity to install additional web engines. Moreover, it includes tools for measurement of free energies and free energy differences and data/image export.
Potential energy surface and second virial coefficient of methane-water from ab initio calculations
NASA Astrophysics Data System (ADS)
Akin-Ojo, Omololu; Szalewicz, Krzysztof
2005-10-01
Six-dimensional intermolecular potential energy surfaces (PESs) for the interaction of CH4 with H2O are presented, obtained from ab initio calculations using symmetry-adapted perturbation theory (SAPT) at two different levels of intramonomer correlation and the supermolecular approach at three different levels of electron correlation. Both CH4 and H2O are assumed to be rigid molecules with interatomic distances and angles fixed at the average values in the ground-state vibration. A physically motivated analytical expression for each PES has been developed as a sum of site-site functions. The PES of the CH4-H2O dimer has only two symmetry-distinct minima. From the SAPT calculations, the global minimum has an energy of -1.03kcal /mol at a geometry where H2O is the proton donor, HO -H⋯CH4, with the O-H-C angle of 165°, while the secondary minimum, with an energy of -0.72kcal/mol, has CH4 in the role of the proton donor (H3C -H⋯OH2). We estimated the complete basis set limit of the SAPT interaction energy at the global minimum to be -1.06kcal/mol. The classical cross second virial coefficient B12(T) has been calculated for the temperature range 298-653K. Our best results agree well with some experiments, allowing an evaluation of the quality of experimental results.
Chen, Z, J; Xiao, H. Y.; Zu, Xiaotao T.; Gao, Fei
2008-11-01
The electronic structures and defect formation energies for a series of stannate pyrochlores Ln2Sn2O7 *Ln=La, Pr, Nd, Sm, Gd, Tb, Ho, Er, Lu, and Y* have been investigated using the first-principles total energy calculations. The calculated results show that Ln-site cation ionic radius, x-O48f, lattice constant and the covalency of the *Sn–O48f* bond have a significant affect on the defect formation energies. The cation-antisite defect has the lowest formation energy, as compared with that of other defects, indicating that cation disorder causes local oxygen disordering. The present studies suggest that Lu2Sn2O7 is the most resistant to ion beam-induced amorphization. The electronic structure calculations reveal that Ln2Sn2O7 compounds have direct band gaps of 2.64– 2.95 eV at the * point in the Brillouin zone. © 2008 American Institute of Physics.
Theoretical calculations and vibrational potential energy surface of 4-silaspiro(3,3)heptane
Ocola, Esther J.; Medders, Cross; Laane, Jaan; Meinander, Niklas
2014-04-28
Theoretical computations have been carried out on 4-silaspiro(3,3)heptane (SSH) in order to calculate its molecular structure and conformational energies. The molecule has two puckered four-membered rings with dihedral angles of 34.2° and a tilt angle of 9.4° between the two rings. Energy calculations were carried out for different conformations of SSH. These results allowed the generation of a two-dimensional ring-puckering potential energy surface (PES) of the form V = a(x{sub 1}{sup 4} + x{sub 2}{sup 4}) – b(x{sub 1}{sup 2} + x{sub 2}{sup 2}) + cx{sub 1}{sup 2}x{sub 2}{sup 2}, where x{sub 1} and x{sub 2} are the ring-puckering coordinates for the two rings. The presence of sufficiently high potential energy barriers prevents the molecule from undergoing pseudorotation. The quantum states, wave functions, and predicted spectra resulting from the PESs were calculated.
Srinivasan, Kandadai; Saha, Bidyut Baran; Ng, Kim Choon; Dutta, Pradip; Prasad, Madhu
2011-07-21
We propose a new method for evaluating the adsorbed phase volume during physisorption of several gases on activated carbon specimens. We treat the adsorbed phase as another equilibrium phase which satisfies the Gibbs equation and hence assume that the law of rectilinear diameters is applicable. Since invariably the bulk gas phase densities are known along measured isotherms, the constants of the adsorbed phase volume can be regressed from the experimental data. We take the Dubinin-Astakhov isotherm as the model for verifying our hypothesis since it is one of the few equations that accounts for adsorbed phase volume changes. In addition, the pseudo-saturation pressure in the supercritical region is calculated by letting the index of the temperature term in Dubinin's equation to be temperature dependent. Based on over 50 combinations of activated carbons and adsorbates (nitrogen, oxygen, argon, carbon dioxide, hydrocarbons and halocarbon refrigerants) it is observed that the proposed changes fit experimental data quite well. PMID:21670804
Protein Adsorption in Three Dimensions
Vogler, Erwin A.
2011-01-01
Recent experimental and theoretical work clarifying the physical chemistry of blood-protein adsorption from aqueous-buffer solution to various kinds of surfaces is reviewed and interpreted within the context of biomaterial applications, especially toward development of cardiovascular biomaterials. The importance of this subject in biomaterials surface science is emphasized by reducing the “protein-adsorption problem” to three core questions that require quantitative answer. An overview of the protein-adsorption literature identifies some of the sources of inconsistency among many investigators participating in more than five decades of focused research. A tutorial on the fundamental biophysical chemistry of protein adsorption sets the stage for a detailed discussion of the kinetics and thermodynamics of protein adsorption, including adsorption competition between two proteins for the same adsorbent immersed in a binary-protein mixture. Both kinetics and steady-state adsorption can be rationalized using a single interpretive paradigm asserting that protein molecules partition from solution into a three-dimensional (3D) interphase separating bulk solution from the physical-adsorbent surface. Adsorbed protein collects in one-or-more adsorbed layers, depending on protein size, solution concentration, and adsorbent surface energy (water wettability). The adsorption process begins with the hydration of an adsorbent surface brought into contact with an aqueous-protein solution. Surface hydration reactions instantaneously form a thin, pseudo-2D interface between the adsorbent and protein solution. Protein molecules rapidly diffuse into this newly-formed interface, creating a truly 3D interphase that inflates with arriving proteins and fills to capacity within milliseconds at mg/mL bulk-solution concentrations CB. This inflated interphase subsequently undergoes time-dependent (minutes-to-hours) decrease in volume VI by expulsion of either-or-both interphase water and
NASA Astrophysics Data System (ADS)
Fu, Qingling; Deng, Yali; Li, Huishu; Liu, Jie; Hu, Hongqing; Chen, Shouwen; Sa, Tongmin
2009-02-01
The persistence of Bacillus thuringiensis ( Bt) toxins in soil is further enhanced through association with soil particles. Such persistence may improve the effectiveness of controlling target pests, but impose a hazard to non-target organisms in soil ecosystems. In this study, the equilibrium adsorption of the Bt toxin by four clay minerals (montmorillonite, kaolinite, goethite, and silicon dioxide) was investigated, and the kinetic and thermodynamic parameters were calculated. The results showed that Bt toxin could be adsorbed easily by minerals, and the adsorption was much easier at low temperature than at high temperature at the initial concentration varying from 0 to 1000 mg L -1. The adsorption fitted well to both Langmuir and Freundlich isotherm models, but the Freundlich equation was more suitable. The pseudo-second-order (PSO) was the best application model to describe the adsorption kinetic. The adsorption process appeared to be controlled by chemical process, and the intra-particle diffusion was not the only rate-controlling step. The negative standard free energy ( ΔGmθr) values of the adsorption indicated that the adsorption of the Bt toxin by the minerals was spontaneous, and the changes of the standard enthalpy ( ΔHmθr) showed that the adsorption of the Bt toxin by montmorillonite was endothermic while the adsorption by the other three minerals was exothermic.
Analyzing adsorption characteristics of CO2, N2 and H2O in MCM-41 silica by molecular simulation
NASA Astrophysics Data System (ADS)
Chang, Shing-Cheng; Chien, Shih-Yao; Chen, Chieh-Li; Chen, Cha'o.-Kuang
2015-03-01
The adsorption characteristics of carbon dioxide, nitrogen and water molecules in MCM-41 mesoporous molecular sieve have been investigated by the molecular simulation. We evaluate the pressure-adsorption isotherms and adsorption density profiles under variant gas pressure, operating temperature and mesopore radius of MCM-41 by the grand canonical Monte Carlo simulation. According to the calculated adsorption energy distributions, the adsorption mechanisms of gas in MCM-41 are mainly divided into three types, namely "surface adsorption" on the pore wall, "multilayer adsorption" on the adsorbed gas molecules and "molecular self-aggregation" near the pore center. In addition, the adsorption characteristics of water molecules in MCM-41 are found to be quite different from those of carbon dioxide and nitrogen due to the hydrogen bonds effect. The results indicate that the MCM-41 is practicable in engineering application for the capture, storage, and re-use of water molecules, since it is temperature-sensitive and can achieve significant adsorption loadings within a small range of pressure values via the capillary condensation phenomena.
Ihm, Yungok; Cooper, Valentino R; Gallego, Nidia C; Contescu, Cristian I; Morris, James R
2014-01-01
We demonstrate a successful, efficient framework for predicting gas adsorption properties in real materials based on first-principles calculations, with a specific comparison of experiment and theory for methane adsorption in activated carbons. These carbon materials have different pore size distributions, leading to a variety of uptake characteristics. Utilizing these distributions, we accurately predict experimental uptakes and heats of adsorption without empirical potentials or lengthy simulations. We demonstrate that materials with smaller pores have higher heats of adsorption, leading to a higher gas density in these pores. This pore-size dependence must be accounted for, in order to predict and understand the adsorption behavior. The theoretical approach combines: (1) ab initio calculations with a van der Waals density functional to determine adsorbent-adsorbate interactions, and (2) a thermodynamic method that predicts equilibrium adsorption densities by directly incorporating the calculated potential energy surface in a slit pore model. The predicted uptake at P=20 bar and T=298 K is in excellent agreement for all five activated carbon materials used. This approach uses only the pore-size distribution as an input, with no fitting parameters or empirical adsorbent-adsorbate interactions, and thus can be easily applied to other adsorbent-adsorbate combinations.
NASA Astrophysics Data System (ADS)
Rad, Ali Shokuhi
2016-09-01
The adsorption energies and orientation of single alcohol molecule (methanol and ethanol) on the surface of Pt-decorated graphene (PtG) were determined from first-principles density functional (DFT) calculations. We found the same adsorption energies as well as connecting distances upon adsorption of MeOH and EtOH on PtG surface, in which at their relaxed structures, the O atom of alcohol is closed to the Pt of PtG surface. We found high adsorption energies, low connecting distances, and high orbital hybridizing upon adsorption of EtOH and MeOH molecules on PtG surface. There are significant shifts in the location of both the HOMO and LUMO, in addition to variation in the charge transfer when the MeOH and EtOH are adsorbed on PtG surface.
NASA Astrophysics Data System (ADS)
Zeng, Xiancheng; Hu, Hao; Hu, Xiangqian; Yang, Weitao
2009-04-01
A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids "on-the-fly" QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.
Zeng Xiancheng; Hu Hao; Hu Xiangqian; Yang Weitao
2009-04-28
A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids 'on-the-fly' QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.
NASA Astrophysics Data System (ADS)
Guevara-Bertsch, M.; Ramírez-Hidalgo, G.; Chavarría-Sibaja, A.; Avendaño, E.; Araya-Pochet, J. A.; Herrera-Sancho, O. A.
2016-03-01
We investigate the variation of the oscillation frequency of the Mg2+ and O2- ions in the magnesium oxide lattice due to the interactions of the surface with water monolayers by means of Low Energy Electron Diffraction. Our key result is a new technique to determine the adsorbate vibrations produced by the water monolayers on the surface lattice as a consequence of their change in the surface Debye temperature and its chemical shift. The latter was systematically investigated for different annealing times and for a constant external thermal perturbation in the range of 110-300 K in order to accomplish adsorption or desorption of water monolayers in the surface lattice.
Ho, T.; Rabitz, H.
1996-02-01
A general interpolation method for constructing smooth molecular potential energy surfaces (PES{close_quote}s) from {ital ab} {ital initio} data are proposed within the framework of the reproducing kernel Hilbert space and the inverse problem theory. The general expression for an {ital a} {ital posteriori} error bound of the constructed PES is derived. It is shown that the method yields globally smooth potential energy surfaces that are continuous and possess derivatives up to second order or higher. Moreover, the method is amenable to correct symmetry properties and asymptotic behavior of the molecular system. Finally, the method is generic and can be easily extended from low dimensional problems involving two and three atoms to high dimensional problems involving four or more atoms. Basic properties of the method are illustrated by the construction of a one-dimensional potential energy curve of the He{endash}He van der Waals dimer using the exact quantum Monte Carlo calculations of Anderson {ital et} {ital al}. [J. Chem. Phys. {bold 99}, 345 (1993)], a two-dimensional potential energy surface of the HeCO van der Waals molecule using recent {ital ab} {ital initio} calculations by Tao {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 8680 (1994)], and a three-dimensional potential energy surface of the H{sup +}{sub 3} molecular ion using highly accurate {ital ab} {ital initio} calculations of R{umlt o}hse {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 2231 (1994)]. In the first two cases the constructed potentials clearly exhibit the correct asymptotic forms, while in the last case the constructed potential energy surface is in excellent agreement with that constructed by R{umlt o}hse {ital et} {ital al}. using a low order polynomial fitting procedure. {copyright} {ital 1996 American Institute of Physics.}
Buryak, Ilya; Vigasin, Andrey A.
2015-12-21
The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.
Bubin, Sergiy; Adamowicz, Ludwik
2014-01-14
Benchmark variational calculations are performed for the seven lowest 1s(2)2s np ((1)P), n = 2...8, states of the beryllium atom. The calculations explicitly include the effect of finite mass of (9)Be nucleus and account perturbatively for the mass-velocity, Darwin, and spin-spin relativistic corrections. The wave functions of the states are expanded in terms of all-electron explicitly correlated Gaussian functions. Basis sets of up to 12,500 optimized Gaussians are used. The maximum discrepancy between the calculated nonrelativistic and experimental energies of 1s(2)2s np ((1)P) →1s(2)2s(2) ((1)S) transition is about 12 cm(-1). The inclusion of the relativistic corrections reduces the discrepancy to bellow 0.8 cm(-1). PMID:24437871
NASA Astrophysics Data System (ADS)
Buryak, Ilya; Vigasin, Andrey A.
2015-12-01
The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.
GPU-based acceleration of free energy calculations in solid state physics
NASA Astrophysics Data System (ADS)
Januszewski, Michał; Ptok, Andrzej; Crivelli, Dawid; Gardas, Bartłomiej
2015-07-01
Obtaining a thermodynamically accurate phase diagram through numerical calculations is a computationally expensive problem that is crucially important to understanding the complex phenomena of solid state physics, such as superconductivity. In this work we show how this type of analysis can be significantly accelerated through the use of modern GPUs. We illustrate this with a concrete example of free energy calculation in multi-band iron-based superconductors, known to exhibit a superconducting state with oscillating order parameter (OP). Our approach can also be used for classical BCS-type superconductors. With a customized algorithm and compiler tuning we are able to achieve a 19×speedup compared to the CPU (119×compared to a single CPU core), reducing calculation time from minutes to mere seconds, enabling the analysis of larger systems and the elimination of finite size effects.
Dobos, A. P.
2012-05-01
This paper describes an improved algorithm for calculating the six parameters required by the California Energy Commission (CEC) photovoltaic (PV) Calculator module model. Rebate applications in California require results from the CEC PV model, and thus depend on an up-to-date database of module characteristics. Currently, adding new modules to the database requires calculating operational coefficients using a general purpose equation solver - a cumbersome process for the 300+ modules added on average every month. The combination of empirical regressions and heuristic methods presented herein achieve automated convergence for 99.87% of the 5487 modules in the CEC database and greatly enhance the accuracy and efficiency by which new modules can be characterized and approved for use. The added robustness also permits general purpose use of the CEC/6 parameter module model by modelers and system analysts when standard module specifications are known, even if the module does not exist in a preprocessed database.
Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach
Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A
2015-01-01
Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange. PMID:26418190
Ceriotti, Michele; Manolopoulos, David E
2012-09-01
Light nuclei at room temperature and below exhibit a kinetic energy which significantly deviates from the predictions of classical statistical mechanics. This quantum kinetic energy is responsible for a wide variety of isotope effects of interest in fields ranging from chemistry to climatology. It also furnishes the second moment of the nuclear momentum distribution, which contains subtle information about the chemical environment and has recently become accessible to deep inelastic neutron scattering experiments. Here, we show how, by combining imaginary time path integral dynamics with a carefully designed generalized Langevin equation, it is possible to dramatically reduce the expense of computing the quantum kinetic energy. We also introduce a transient anisotropic Gaussian approximation to the nuclear momentum distribution which can be calculated with negligible additional effort. As an example, we evaluate the structural properties, the quantum kinetic energy, and the nuclear momentum distribution for a first-principles simulation of liquid water. PMID:23005275
Efficient calculation of the polarizability: a simplified effective-energy technique
NASA Astrophysics Data System (ADS)
Berger, J. A.; Reining, L.; Sottile, F.
2012-09-01
In a recent publication [J.A. Berger, L. Reining, F. Sottile, Phys. Rev. B 82, 041103(R) (2010)] we introduced the effective-energy technique to calculate in an accurate and numerically efficient manner the GW self-energy as well as the polarizability, which is required to evaluate the screened Coulomb interaction W. In this work we show that the effective-energy technique can be used to further simplify the expression for the polarizability without a significant loss of accuracy. In contrast to standard sum-over-state methods where huge summations over empty states are required, our approach only requires summations over occupied states. The three simplest approximations we obtain for the polarizability are explicit functionals of an independent- or quasi-particle one-body reduced density matrix. We provide evidence of the numerical accuracy of this simplified effective-energy technique as well as an analysis of our method.
Adsorption of oxygen atom on MoSi2 (110) surface
NASA Astrophysics Data System (ADS)
Sun, S. P.; Li, X. P.; Wang, H. J.; Jiang, Y.; Yi, D. Q.
2016-09-01
The adsorption energy, structural relaxation and electronic properties of oxygen atom on MoSi2 (110) surface have been investigated by first-principles calculations. The energetic stability of MoSi2 low-index surfaces was analyzed, and the results suggested that MoSi2 (110) surface had energetically stability. The site of oxygen atom adsorbed on MoSi2 (110) surface were discussed, and the results indicated that the preference adsorption site of MoSi2 (110) surface for oxygen atom was H site (hollow position). Our calculated work should help to understand further the interaction between oxygen atoms and MoSi2 surfaces.
NASA Astrophysics Data System (ADS)
van de Bovenkamp, J.; van Mourik, T.; van Duijneveldt, F. B.
A multi-reference configuration interaction (MRCI) method is described, which is devised for the calculation of interaction energies of van der Waals complexes and applied to calculating the HeNe potential energy curve. The MRCI calculations make use of a generalized Poplecorrection in order to account for the lack of size consistency. The orbital space is partitioned into three subspaces: the first active space (AS1), which contains the strongly occupied orbitals; the second active space (AS2), which contains the main intra-correlating orbitals; and the external space (ES). It is shown that, to keep the error below 0.2K in the excitation scheme and the active orbital space it is sufficient to include only sigma-orbitals in AS2 and to use an excitation scheme (labelled Qq-MRCI) that encompasses only up to quadruply excited configurations. The final active orbital space (AS2) turned out to be 2s(He), 2psigma(He), 3s(Ne), 3psigma(Ne) and 3dsigma(Ne). Other MRCI variants, in which most or all quadruply excited configurations were deleted from the CI expansion (Qt- and Tt-MRCI), were found to be inadequate. Using the Qq-MRCI scheme together with a 197-orbital 'interaction optimized' basis set (IO197), the MRCI interaction energy at R = 5.7 a0 was calculated to be-21.12K. The corresponding values at the MP4 and CCSD(T) levels of theory are-20.06K and-20.99K, respectively, indicating that the MP4 method is inappropriate for highly accurate calculations on this system. Fitting the calculated data using a generalized Morse function, including an additional C6/R6 term to account for a correct long-range behaviour of the potential, the MRCI well depth was calculated to be-21.16K at Req = 5.73 a0. The MRCI and CCSD(T) potentials have the same quality and are found to be in good agreement with the HartreeFock dispersion (HFD-B) potential of Keil, M., Danielson, L. J., and Dunlop, P. J., 1991, J. Chem. Phys., 94, 296. It is concluded that, for basis IO197, the CCSD(T) method is
A Study of Adsorptive Characteristics of Australian Coals
NASA Astrophysics Data System (ADS)
Lan, Y. P.; Tsai, L. L.
2012-04-01
Ever since the Kyoto Protocol, controlling carbon dioxide emission and reducing its content in atmosphere are very important environmental issues up to today. One of the effective methods for permanent sequestration of anthropogenic CO2 is to inject CO2 into deep, unminable coal seams and recover coal bed methane at the same time. CO2-ECBM technology had been proved to be very promising to meet the needs of both environment and energy. Beside other external environment factors, capacity of CO2 adsorption and CH4 desorption are the most influencing factors in selection of sites for the geological storage of CO2. Therefore, the objective of this study is to understand the relationship between gas adsorption and CO2 sequestration, by various experiments for the characterization of Australian of coals. Generally speaking, coal seam gas comprises mostly of CH4, CO2, C2H6, and N2. However, some of the Australian coals were reported with significant amount of CO2 up to 90%, which might strongly affect their capacity of CO2 capture and storage (CCS). High to medium volatile bituminous coals from Sydney Basin and Bowen Basin, southeast Australia were selected in this study. Experiments include maceral composition and vitrinite reflectance measurements, petrographic analysis, Proximate analysis, Ultimate analysis, specific surface area analysis as well as CO2 and CH4 adsorption experiments were performed. Parameters for difference adsorption functions (Langmuir, BET, D-R and D-A) were then calculated to fit their adsorption isotherms the best fitting curve can then be found. Among these adsorption functions, Langmuir is the most basic and commonly used function theory. The results of all experiments were synthesized to discuss the relations among each other, so as to establish the relationship between gas adsorption and coal characteristics.
Calculation of positron binding energies using the generalized any particle propagator theory
Romero, Jonathan; Charry, Jorge A.; Flores-Moreno, Roberto; Varella, Márcio T. do N.; Reyes, Andrés
2014-09-21
We recently extended the electron propagator theory to any type of quantum species based in the framework of the Any-Particle Molecular Orbital (APMO) approach [J. Romero, E. Posada, R. Flores-Moreno, and A. Reyes, J. Chem. Phys. 137, 074105 (2012)]. The generalized any particle molecular orbital propagator theory (APMO/PT) was implemented in its quasiparticle second order version in the LOWDIN code and was applied to calculate nuclear quantum effects in electron binding energies and proton binding energies in molecular systems [M. Díaz-Tinoco, J. Romero, J. V. Ortiz, A. Reyes, and R. Flores-Moreno, J. Chem. Phys. 138, 194108 (2013)]. In this work, we present the derivation of third order quasiparticle APMO/PT methods and we apply them to calculate positron binding energies (PBEs) of atoms and molecules. We calculated the PBEs of anions and some diatomic molecules using the second order, third order, and renormalized third order quasiparticle APMO/PT approaches and compared our results with those previously calculated employing configuration interaction (CI), explicitly correlated and quantum Montecarlo methodologies. We found that renormalized APMO/PT methods can achieve accuracies of ∼0.35 eV for anionic systems, compared to Full-CI results, and provide a quantitative description of positron binding to anionic and highly polar species. Third order APMO/PT approaches display considerable potential to study positron binding to large molecules because of the fifth power scaling with respect to the number of basis sets. In this regard, we present additional PBE calculations of some small polar organic molecules, amino acids and DNA nucleobases. We complement our numerical assessment with formal and numerical analyses of the treatment of electron-positron correlation within the quasiparticle propagator approach.
NASA Astrophysics Data System (ADS)
Widjaja, Hantarto; Jiang, Zhong-Tao; Altarawneh, Mohammednoor; Yin, Chun-Yang; Goh, Bee-Min; Mondinos, Nicholas; Amri, Amun; Dlugogorski, Bogdan Z.
2016-06-01
Elemental adsorption on graphene offers an effective procedure in fine-tuning electronic and mechanical properties of graphene. The effects of dopants depend on adsorption site, the degree of coverage as well as on the configuration of the deployed supercell. In this contribution, the density functional theory (DFT) calculations were performed to investigate the electronic structures of F and Cl adsorption (double-sided, top site) on graphene in terms of adsorption orientation, atomic ratios, i.e., from C:F/Cl = 18:2 to C:F/Cl = 2:2. Despite being members of the halogens group, F- and Cl-adsorbed on graphene show contrasting trends. F is adsorbed to graphene more strongly than Cl. F favours full and 25% adsorption coverage, while Cl favours 25% coverage. Both F and Cl cases open band gap (at Fermi energy) at certain atomic concentration coverage, but none creates magnetization.
Calculated dipole moment and energy in collision of a hydrogen molecule and a hydrogen atom
NASA Technical Reports Server (NTRS)
Patch, R. W.
1973-01-01
Calculations were carried out using three Slater-type 1s orbitals in the orthogonalized valencebond theory of McWeeny. Each orbital exponent was optimized, the H2 internuclear distance was varied from 7.416 x 10 to the -11th power to 7.673 x 10 to the -11th power m (1.401 to 1.450 bohrs). The intermolecular distance was varied from 1 to 4 bohrs (0.5292 to 2.117 x 10 to the 10th power). Linear, scalene, and isosceles configurations were used. A weighted average of the interaction energies was taken for each intermolecular distance. Although energies are tabulated, the principal purpose was to calculate the electric dipole moment and its derivative with respect to H2 internuclear distance.
Calculating alpha Eigenvalues in a Continuous-Energy Infinite Medium with Monte Carlo
Betzler, Benjamin R.; Kiedrowski, Brian C.; Brown, Forrest B.; Martin, William R.
2012-09-04
The {alpha} eigenvalue has implications for time-dependent problems where the system is sub- or supercritical. We present methods and results from calculating the {alpha}-eigenvalue spectrum for a continuous-energy infinite medium with a simplified Monte Carlo transport code. We formulate the {alpha}-eigenvalue problem, detail the Monte Carlo code physics, and provide verification and results. We have a method for calculating the {alpha}-eigenvalue spectrum in a continuous-energy infinite-medium. The continuous-time Markov process described by the transition rate matrix provides a way of obtaining the {alpha}-eigenvalue spectrum and kinetic modes. These are useful for the approximation of the time dependence of the system.
NASA Astrophysics Data System (ADS)
Teodoro, Tiago Quevedo; Haiduke, Roberto Luiz Andrade; Dammalapati, Umakanth; Knoop, Steven; Visscher, Lucas
2015-08-01
The potential energy curve for the ground-state of radium dimer (Ra2) is provided by means of atomic and molecular relativistic coupled cluster calculations. The short-range part of this curve is defined by an equilibrium bond length of 5.324 Å, a dissociation energy of 897 cm-1, and a harmonic vibrational frequency of 20.5 cm-1. The asymptotic behavior at large interatomic distances is characterized by the van der Waals coefficients C6 = 5.090 × 103, C8 = 6.978 × 105, and C10 = 8.786 × 107 atomic units. The two regions are matched in an analytical potential to provide a convenient representation for use in further calculations, for instance, to model cold collisions between radium atoms. This might become relevant in future experiments on ultracold, optically trapped, radioactive radium atoms that are used to search for a permanent electric dipole moment.
S-matrix Calculations of Energy Levels of the Lithium Isoelectronic Sequence
sapirstein, J; Cheng, K T
2010-11-02
A QED approach to the calculation of the spectra of the lithium isoelectronic sequence is implemented. A modified Furry representation based on the Kohn-Sham potential is used to evaluate all one- and two-photon diagrams with the exception of the two-loop Lamb shift. Three-photon diagrams are estimated with Hamiltonian methods. After incorporating recent calculations of the two-loop Lamb shift and recoil corrections a comprehensive tabulation of the 2s, 2p{sub 1/2} and 2p{sub 3/2} energy levels as well as the 2s - 2p{sub 1/2} and 2s - 2p{sub 3/2} transition energies for Z = 10 - 100 is presented.
Perdok, J F; Van Der Mei, H C; Busscher, H J; Genet, M J; Rouxhet, P G
1990-01-01
The adsorption of active agents from six commercially available mouthrinses to ground and polished enamel, with and without adsorbed salivary constituents, was monitored by contact angle measurements and X-ray Photoelectron Spectroscopy (XPS). Human enamel samples were treated with mouthrinses containing chlorhexidine (Peridex), stannous fluoride/amine fluoride (Meridol), thymol/benzoic acid (Listerine), sanguinarine (Veadent), sodium fluoride (Prodent), or cetylpyridinium chloride (Merocet). XPS indicated a sizeable adsorption of both active and non-active components for all products. After treatment, all enamel surface free energies increased except for the stannous fluoride/amine fluoride containing mouthrinse. It is suggested that non-active components in the products cause an increase in surface free energy. Despite this thermodynamically unfavorable increase in surface free energy, all rinses have plaque reducing effects, indicating that this unfavorable surface characteristic is overruled by the antibacterial properties of the components. Replacement of non-active components by less adsorbing surfactants could increase the efficiency of the products tested. PMID:2090159
Microscopic calculation of interacting boson model parameters by potential-energy surface mapping
Bentley, I.; Frauendorf, S.
2011-06-15
A coherent state technique is used to generate an interacting boson model (IBM) Hamiltonian energy surface which is adjusted to match a mean-field energy surface. This technique allows the calculation of IBM Hamiltonian parameters, prediction of properties of low-lying collective states, as well as the generation of probability distributions of various shapes in the ground state of transitional nuclei, the last two of which are of astrophysical interest. The results for krypton, molybdenum, palladium, cadmium, gadolinium, dysprosium, and erbium nuclei are compared with experiment.
Calculation of free energies in fluid membranes subject to heterogeneous curvature fields
NASA Astrophysics Data System (ADS)
Agrawal, Neeraj J.; Radhakrishnan, Ravi
2009-07-01
We present a computational methodology for incorporating thermal effects and calculating relative free energies for elastic fluid membranes subject to spatially dependent intrinsic curvature fields using the method of thermodynamic integration. Based on a simple model for the intrinsic curvature imposed only in a localized region of the membrane, we employ thermodynamic integration to calculate the free-energy change as a function of increasing strength of the intrinsic curvature field and a thermodynamic cycle to compute free-energy changes for different sizes of the localized region. By explicitly computing the free-energy changes and by quantifying the loss of entropy accompanied with increasing membrane deformation, we show that the membrane stiffness increases with increasing intrinsic field, thereby, renormalizing the membrane bending rigidity. The second main conclusion of this work is that the entropy of the membrane decreases with increasing size of the localized region subject to the curvature field. Our results help to quantify the free-energy change when a planar membrane deforms under the influence of curvature-inducing proteins at a finite temperature.
Predicting Fixation Tendencies of the H3N2 Influenza Virus by Free Energy Calculation
Pan, Keyao; Deem, Michael W.
2011-01-01
Influenza virus evolves to escape from immune system antibodies that bind to it. We used free energy calculations with Einstein crystals as reference states to calculate the difference of antibody binding free energy (ΔΔG) induced by amino acid substitution at each position in epitope B of the H3N2 influenza hemagglutinin, the key target for antibody. A substitution with positive ΔΔG value decreases the antibody binding constant. On average an uncharged to charged amino acid substitution generates the highest ΔΔG values. Also on average, substitutions between small amino acids generate ΔΔG values near to zero. The 21 sites in epitope B have varying expected free energy differences for a random substitution. Historical amino acid substitutions in epitope B for the A/Aichi/2/1968 strain of influenza A show that most fixed and temporarily circulating substitutions generate positive ΔΔG values. We propose that the observed pattern of H3N2 virus evolution is affected by the free energy landscape, the mapping from the free energy landscape to virus fitness landscape, and random genetic drift of the virus. Monte Carlo simulations of virus evolution are presented to support this view. PMID:21691431
Calculations of binding energies and masses of heavy quarkonia using renormalon cancellation
NASA Astrophysics Data System (ADS)
Contreras, Carlos; Cvetič, Gorazd; Gaete, Patricio
2004-08-01
We use various methods of Borel integration to calculate the binding ground energies and masses of bb¯ and tt¯ quarkonia. The methods take into account the leading infrared renormalon structure of the (hard+)soft part of the binding energies E(s), and of the corresponding quark pole masses mq, where the contributions of these singularities in M(s)=2mq+E(s) cancel. Beforehand, we carry out the separation of the binding energy into its (hard+)soft and ultrasoft parts. The resummation formalisms are applied to expansions of mq and E(s) in terms of quantities which do not involve renormalon ambiguity, such as MS¯ mass mq and αs(μ). The renormalization scales μ are different in calculations of mq, E(s) and E(us). The mass mb is extracted, and the binding energies Ett¯ and the peak (resonance) energies Eres. for tt¯ production are obtained.
Cecchini, M; Krivov, S V; Spichty, M; Karplus, M
2009-07-23
Conformational free-energy differences are key quantities for understanding important phenomena in molecular biology that involve large structural changes of macromolecules. In this paper, an improved version of the confinement approach, which is based on earlier developments, is used to determine the free energy of individual molecular states by progressively restraining the corresponding molecular structures to pure harmonic basins, whose absolute free energy can be computed by normal-mode analysis. The method is used to calculate the free-energy difference between two conformational states of the alanine dipeptide in vacuo, and of the beta-hairpin from protein G with an implicit solvation model. In all cases, the confinement results are in excellent agreement with the ones obtained from converged equilibrium molecular dynamics simulations, which have a much larger computational cost. The systematic and statistical errors of the results are evaluated and the origin of the errors is identified. The sensitivity of the calculated free-energy differences to structure-based definitions of the molecular states is discussed. A variant of the method, which closes the thermodynamic cycle by a quasi-harmonic rather than harmonic analysis, is introduced. The latter is proposed for possible use with explicit solvent simulations. PMID:19552392
Bhunia, Snehasis; Forster, Stefan; Vyas, Nidhi; Schmitt, Hans-Christian; Ojha, Animesh K
2015-12-01
Fourier transform Raman (FT-Raman) spectra of neat pyridine (Py) and surface enhanced Raman scattering (SERS) spectra of Py with silver nanoparticles (AgNPs) solution at different molar concentrations (X=1.5M, 1.0M, 0.50 M, 0.25 M, and 0.125 M) were recorded using 1064 nm excitation wavelength. The intensity of Raman bands at ∼1003 (ν11) and ∼1035 (ν21) cm(-1) of Py is enhanced in the SERS spectra. Two new Raman bands were observed at ∼1009 (ν12) and ∼1038 (ν22) cm(-1) in the SERS spectra. These bands correspond to the ring breathing vibrations of Py molecules adsorbed at the AgNPs surface. The value of intensity ratios (I12/I11) and (I21/I22) is increased with dilution and attains a maximum value at X=0.5M and upon further dilution (0.25 and 0.125 M) it drops gradually. The theoretically calculated Raman spectra were found to be in good agreement with experimentally observed Raman spectra. Both, experimental and theoretical investigations have confirmed that the Py interacts with AgNPs via the end-on geometry. PMID:26184474
NASA Astrophysics Data System (ADS)
He, Yan Bin; Jia, Jian Feng; Wu, Hai Shun
2015-02-01
In recent years, metal nanoparticles were found to be excellent catalysts for hydrogen generation from hydrazine for chemical hydrogen storage. In order to gain a better understanding of these catalytic systems, we have simulated the adsorption of hydrazine on rhodium nanoparticles surfaces by density functional theory (DFT) calculations with dispersion correction, DFT-D3 in the method of Grimme. The rhodium nanoparticles were modeled by the Rh(1 1 1) surface, in addition, the adsorptions at corners and edges sites of nanoparticles were considered by using rhodium adatoms on the surfaces. The calculations showed that hydrazine binds most strongly to the edge of nanoparticle with adsorption energy of -2.48 eV, where the hydrazine bridges adatoms of edge with the molecule twisted to avoid a cis structure; similar adsorption energy was found at the corner of nanoparticle, where the hydrazine bridges corner atom and surface atom with gauche configuration. However, we found that inclusion of the dispersion correction results in significant enhancement of molecule-substrate binding, thereby increasing the adsorption energy, especially the adsorption to the Rh(1 1 1) surface. The results demonstrate that the surface structure is a key factor to determine the thermodynamics of adsorption, with low coordinated atoms which providing sites of strong adsorption from the surface.
USING TIME VARIANT VOLTAGE TO CALCULATE ENERGY CONSUMPTION AND POWER USE OF BUILDING SYSTEMS
Makhmalbaf, Atefe; Augenbroe , Godfried
2015-12-09
Buildings are the main consumers of electricity across the world. However, in the research and studies related to building performance assessment, the focus has been on evaluating the energy efficiency of buildings whereas the instantaneous power efficiency has been overlooked as an important aspect of total energy consumption. As a result, we never developed adequate models that capture both thermal and electrical characteristics (e.g., voltage) of building systems to assess the impact of variations in the power system and emerging technologies of the smart grid on buildings energy and power performance and vice versa. This paper argues that the power performance of buildings as a function of electrical parameters should be evaluated in addition to systems’ mechanical and thermal behavior. The main advantage of capturing electrical behavior of building load is to better understand instantaneous power consumption and more importantly to control it. Voltage is one of the electrical parameters that can be used to describe load. Hence, voltage dependent power models are constructed in this work and they are coupled with existing thermal energy models. Lack of models that describe electrical behavior of systems also adds to the uncertainty of energy consumption calculations carried out in building energy simulation tools such as EnergyPlus, a common building energy modeling and simulation tool. To integrate voltage-dependent power models with thermal models, the thermal cycle (operation mode) of each system was fed into the voltage-based electrical model. Energy consumption of systems used in this study were simulated using EnergyPlus. Simulated results were then compared with estimated and measured power data. The mean square error (MSE) between simulated, estimated, and measured values were calculated. Results indicate that estimated power has lower MSE when compared with measured data than simulated results. Results discussed in this paper will illustrate the
NASA Astrophysics Data System (ADS)
Entringer, Anthony G.
The first high resolution electron energy loss spectroscopy (HREELS) studies of the oxidation and nitridation of germanium surfaces are reported. Both single crystal Ge(111) and disordered surfaces were studied. Surfaces were exposed to H, O_2, NO, N _2O, and N, after cleaning in ultra-high vacuum. The Ge surfaces were found to be non-reactive to molecular hydrogen (H_2) at room temperature. Exposure to atomic hydrogen (H) resulted hydrogen adsorption as demonstrated by the presence of Ge-H vibrational modes. The HREEL spectrum of the native oxide of Ge characteristic of nu -GeO_2 was obtained by heating the oxide to 200^circC. Three peaks were observed at 33, 62, and 106 meV for molecular oxygen (O_2) adsorbed on clean Ge(111) at room temperature. These peaks are indicative of dissociative bonding and a dominant Ge-O-Ge bridge structure. Subsequent hydrogen exposure resulted in a shift of the Ge-H stretch from its isolated value of 247 meV to 267 meV, indicative of a dominant +3 oxidation state. A high density of dangling bonds and defects and deeper oxygen penetration at the amorphous Ge surface result in a dilute bridge structure with a predominant +1 oxidation state for similar exposures. Molecules of N_2O decompose at the surfaces to desorbed N_2 molecules and chemisorbed oxygen atoms. In contrast, both oxygen and nitrogen are detected at the surfaces following exposure to NO molecules. Both NO and N_2O appear to dissociate and bond at the top surface layer. Molecular nitrogen (N_2) does not react with the Ge surfaces, however, a precursor Ge nitride is observed at room temperature following exposure to nitrogen atoms and ions. Removal of oxygen by heating of the NO-exposed surface to 550^circC enabled the identification of the Ge-N vibrational modes. These modes show a structure similar to that of germanium nitride. This spectrum is also identical to that of the N-exposed surface heated to 550^circC. Surface phonon modes of the narrow-gap semiconducting
Bimodality emerges from transport model calculations of heavy ion collisions at intermediate energy
NASA Astrophysics Data System (ADS)
Mallik, S.; Das Gupta, S.; Chaudhuri, G.
2016-04-01
This work is a continuation of our effort [S. Mallik, S. Das Gupta, and G. Chaudhuri, Phys. Rev. C 91, 034616 (2015)], 10.1103/PhysRevC.91.034616 to examine if signatures of a phase transition can be extracted from transport model calculations of heavy ion collisions at intermediate energy. A signature of first-order phase transition is the appearance of a bimodal distribution in Pm(k ) in finite systems. Here Pm(k ) is the probability that the maximum of the multiplicity distribution occurs at mass number k . Using a well-known model for event generation [Botzmann-Uehling-Uhlenbeck (BUU) plus fluctuation], we study two cases of central collision: mass 40 on mass 40 and mass 120 on mass 120. Bimodality is seen in both the cases. The results are quite similar to those obtained in statistical model calculations. An intriguing feature is seen. We observe that at the energy where bimodality occurs, other phase-transition-like signatures appear. There are breaks in certain first-order derivatives. We then examine if such breaks appear in standard BUU calculations without fluctuations. They do. The implication is interesting. If first-order phase transition occurs, it may be possible to recognize that from ordinary BUU calculations. Probably the reason this has not been seen already is because this aspect was not investigated before.
Sharp, K A
1998-01-01
A description is given of a method to calculate the electron transfer reorganization energy (lambda) in proteins using the linear or nonlinear Poisson-Boltzmann (PB) equation. Finite difference solutions to the linear PB equation are then used to calculate lambda for intramolecular electron transfer reactions in the photosynthetic reaction center from Rhodopseudomonas viridis and the ruthenated heme proteins cytochrome c, myoglobin, and cytochrome b and for intermolecular electron transfer between two cytochrome c molecules. The overall agreement with experiment is good considering both the experimental and computational difficulties in estimating lambda. The calculations show that acceptor/donor separation and position of the cofactors with respect to the protein/solvent boundary are equally important and, along with the overall polarizability of the protein, are the major determinants of lambda. In agreement with previous studies, the calculations show that the protein provides a low reorganization environment for electron transfer. Agreement with experiment is best if the protein polarizability is modeled with a low (<8) average effective dielectric constant. The effect of buried waters on the reorganization energy of the photosynthetic reaction center was examined and found to make a contribution ranging from 0.05 eV to 0.27 eV, depending on the donor/acceptor pair. PMID:9512022
NASA Technical Reports Server (NTRS)
Popinceanu, N. G.; Kremmer, I.
1974-01-01
A mechano-acoustic model is reported for calculating acoustic energy radiated by a working gear. According to this model, a gear is an acoustic coublet formed of the two wheels. The wheel teeth generate cylindrical acoustic waves while the front surfaces of the teeth behave like vibrating pistons. Theoretical results are checked experimentally and good agreement is obtained with open gears. The experiments show that the air noise effect is negligible as compared with the structural noise transmitted to the gear box.
New algorithms for the Vavilov distribution calculation and the corresponding energy loss sampling
Chibani, O. |
1998-10-01
Two new algorithms for the fast calculation of the Vavilov distribution within the interval 0.01 {le} {kappa} {le} 10, where neither the Gaussian approximation nor the Landau distribution may be used, are presented. These algorithms are particularly convenient for the sampling of the corresponding random energy loss. A comparison with the exact Vavilov distribution for the case of protons traversing Al slabs is given.
Tung, Wei-Cheng; Adamowicz, Ludwik
2014-03-28
Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH{sup +} ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations.
Dual-energy CT-based material extraction for tissue segmentation in Monte Carlo dose calculations
NASA Astrophysics Data System (ADS)
Bazalova, Magdalena; Carrier, Jean-François; Beaulieu, Luc; Verhaegen, Frank
2008-05-01
Monte Carlo (MC) dose calculations are performed on patient geometries derived from computed tomography (CT) images. For most available MC codes, the Hounsfield units (HU) in each voxel of a CT image have to be converted into mass density (ρ) and material type. This is typically done with a (HU; ρ) calibration curve which may lead to mis-assignment of media. In this work, an improved material segmentation using dual-energy CT-based material extraction is presented. For this purpose, the differences in extracted effective atomic numbers Z and the relative electron densities ρe of each voxel are used. Dual-energy CT material extraction based on parametrization of the linear attenuation coefficient for 17 tissue-equivalent inserts inside a solid water phantom was done. Scans of the phantom were acquired at 100 kVp and 140 kVp from which Z and ρe values of each insert were derived. The mean errors on Z and ρe extraction were 2.8% and 1.8%, respectively. Phantom dose calculations were performed for 250 kVp and 18 MV photon beams and an 18 MeV electron beam in the EGSnrc/DOSXYZnrc code. Two material assignments were used: the conventional (HU; ρ) and the novel (HU; ρ, Z) dual-energy CT tissue segmentation. The dose calculation errors using the conventional tissue segmentation were as high as 17% in a mis-assigned soft bone tissue-equivalent material for the 250 kVp photon beam. Similarly, the errors for the 18 MeV electron beam and the 18 MV photon beam were up to 6% and 3% in some mis-assigned media. The assignment of all tissue-equivalent inserts was accurate using the novel dual-energy CT material assignment. As a result, the dose calculation errors were below 1% in all beam arrangements. Comparable improvement in dose calculation accuracy is expected for human tissues. The dual-energy tissue segmentation offers a significantly higher accuracy compared to the conventional single-energy segmentation.
Weng, Meng-Hsiung; Ju, Shin-Pon; Chen, Hsin-Tsung; Chen, Hui-Lung; Lu, Jian-Ming; Lin, Ken-Huang; Lin, Jenn-Sen; Hsieh, Jin-Yuan; Yang, Hsi-Wen
2013-02-01
The adsorption and dissociation properties of carbon monoxide (CO) molecule on tungsten W(n) (n = 10-15) nanoparticles have been investigated by density-functional theory (DFT) calculations. The lowest-energy structures for W(n) (n = 10-15) nanoparticles are found by the basin-hopping method and big-bang method with the modified tight-binding many-body potential. We calculated the corresponding adsorption energies, C-O bond lengths and dissociation barriers for adsorption of CO on nanoparticles. The electronic properties of CO on nanoparticles are studied by the analysis of density of state and charge density. The characteristic of CO on W(n) nanoparticles are also compared with that of W bulk. PMID:23646573
Weather data for simplified energy calculation methods. Volume IV. United States: WYEC data
Olsen, A.R.; Moreno, S.; Deringer, J.; Watson, C.R.
1984-08-01
The objective of this report is to provide a source of weather data for direct use with a number of simplified energy calculation methods available today. Complete weather data for a number of cities in the United States are provided for use in the following methods: degree hour, modified degree hour, bin, modified bin, and variable degree day. This report contains sets of weather data for 23 cities using Weather Year for Energy Calculations (WYEC) source weather data. Considerable overlap is present in cities (21) covered by both the TRY and WYEC data. The weather data at each city has been summarized in a number of ways to provide differing levels of detail necessary for alternative simplified energy calculation methods. Weather variables summarized include dry bulb and wet bulb temperature, percent relative humidity, humidity ratio, wind speed, percent possible sunshine, percent diffuse solar radiation, total solar radiation on horizontal and vertical surfaces, and solar heat gain through standard DSA glass. Monthly and annual summaries, in some cases by time of day, are available. These summaries are produced in a series of nine computer generated tables.
Use of SCALE Continuous-Energy Monte Carlo Tools for Eigenvalue Sensitivity Coefficient Calculations
Perfetti, Christopher M; Rearden, Bradley T
2013-01-01
The TSUNAMI code within the SCALE code system makes use of eigenvalue sensitivity coefficients for an extensive number of criticality safety applications, such as quantifying the data-induced uncertainty in the eigenvalue of critical systems, assessing the neutronic similarity between different critical systems, and guiding nuclear data adjustment studies. The need to model geometrically complex systems with improved fidelity and the desire to extend TSUNAMI analysis to advanced applications has motivated the development of a methodology for calculating sensitivity coefficients in continuous-energy (CE) Monte Carlo applications. The CLUTCH and Iterated Fission Probability (IFP) eigenvalue sensitivity methods were recently implemented in the CE KENO framework to generate the capability for TSUNAMI-3D to perform eigenvalue sensitivity calculations in continuous-energy applications. This work explores the improvements in accuracy that can be gained in eigenvalue and eigenvalue sensitivity calculations through the use of the SCALE CE KENO and CE TSUNAMI continuous-energy Monte Carlo tools as compared to multigroup tools. The CE KENO and CE TSUNAMI tools were used to analyze two difficult models of critical benchmarks, and produced eigenvalue and eigenvalue sensitivity coefficient results that showed a marked improvement in accuracy. The CLUTCH sensitivity method in particular excelled in terms of efficiency and computational memory requirements.
NASA Astrophysics Data System (ADS)
Luna, D.; Alexander, P.; de la Torre, A.
2013-09-01
The application of the Global Positioning System (GPS) radio occultation (RO) method to the atmosphere enables the determination of height profiles of temperature, among other variables. From these measurements, gravity wave activity is usually quantified by calculating the potential energy through the integration of the ratio of perturbation and background temperatures between two given altitudes in each profile. The uncertainty in the estimation of wave activity depends on the systematic biases and random errors of the measured temperature, but also on additional factors like the selected vertical integration layer and the separation method between background and perturbation temperatures. In this study, the contributions of different parameters and variables to the uncertainty in the calculation of gravity wave potential energy in the lower stratosphere are investigated and quantified. In particular, a Monte Carlo method is used to evaluate the uncertainty that results from different GPS RO temperature error distributions. In addition, our analysis shows that RO data above 30 km height becomes dubious for gravity waves potential energy calculations.
NASA Technical Reports Server (NTRS)
Rosen, A.; Ellis, D. E.; Adachi, H.; Averill, F. W.
1976-01-01
A numerical-variational method for performing self-consistent molecular calculations in the Hartree-Fock-Slater (HFS) model is presented. Molecular wavefunctions are expanded in terms of basis sets constructed from numerical HFS solutions of selected one-center atomlike problems. Binding energies and wavefunctions for the molecules are generated using a discrete variational method for a given molecular potential. In the self-consistent-charge (SCC) approximation to the complete self-consistent-field (SCF) method, results of a Mulliken population analysis of the molecular eigenfunctions are used in each iteration to produce 'atomic' occupation numbers. The simplest SCC potential is then obtained from overlapping spherical atomlike charge distributions. Molecular ionization energies are calculated using the transition-state procedure; results are given for CO, H2O, H2S, AlCl, InCl, and the Ni5O surface complex. Agreement between experimental and theoretical ionization energies for the free-molecule valence levels is generally within 1 eV. The simple SCC procedure gives a reasonably good approximation to the molecular potential, as shown by comparison with experiment, and with complete SCF calculations for CO, H2O, and H2S.
Lundborg, Magnus; Lindahl, Erik
2015-01-22
Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized. PMID:25343332
Geszke-Moritz, Małgorzata; Moritz, Michał
2016-12-01
The present study deals with the adsorption of boldine onto pure and propyl-sulfonic acid-functionalized SBA-15, SBA-16 and mesocellular foam (MCF) materials. Siliceous adsorbents were characterized by nitrogen sorption analysis, transmission electron microscopy (TEM), scanning electron microscopy (SEM), Fourier-transform infrared (FT-IR) spectroscopy and thermogravimetric analysis. The equilibrium adsorption data were analyzed using the Langmuir, Freundlich, Redlich-Peterson, and Temkin isotherms. Moreover, the Dubinin-Radushkevich and Dubinin-Astakhov isotherm models based on the Polanyi adsorption potential were employed. The latter was calculated using two alternative formulas including solubility-normalized (S-model) and empirical C-model. In order to find the best-fit isotherm, both linear regression and nonlinear fitting analysis were carried out. The Dubinin-Astakhov (S-model) isotherm revealed the best fit to the experimental points for adsorption of boldine onto pure mesoporous materials using both linear and nonlinear fitting analysis. Meanwhile, the process of boldine sorption onto modified silicas was described the best by the Langmuir and Temkin isotherms using linear regression and nonlinear fitting analysis, respectively. The values of adsorption energy (below 8kJ/mol) indicate the physical nature of boldine adsorption onto unmodified silicas whereas the ionic interactions seem to be the main force of alkaloid adsorption onto functionalized sorbents (energy of adsorption above 8kJ/mol). PMID:27612776
Gritti, Fabrice; Pereira, Alberto dos Santos; Sandra, Pat; Guiochon, Georges
2009-11-27
The adsorption isotherms of pyridine were measured by frontal analysis (FA) on a column packed with shell particles of neat porous silica (Halo), using water-acetonitrile mixtures as the mobile phase at 295K. The isotherm data were measured for pyridine concentrations covering a dynamic range of four millions. The degree of heterogeneity of the surface was characterized by the adsorption energy distribution (AED) function calculated from the raw adsorption data, using the expectation-maximization (EM) procedure. The results showed that two different retention mechanisms dominate in Per aqueous liquid chromatography (PALC) at low acetonitrile concentrations and in hydrophilic interaction chromatography (HILIC) at high acetonitrile concentrations. In the PALC mode, the adsorption mechanism of pyridine on the silica surface is controlled by hydrophobic interactions that take place on very few and ultra-active adsorption sites, which might be pores on the irregular and rugose surface of the porous silica particles. The surface is seriously heterogeneous, with up to five distinct adsorption sites and five different energy peaks on the AED of the packing material. In contrast, in the HILIC mode, the adsorption behavior is quasi-homogeneous and pyridine retention is governed by its adsorption onto free silanol groups. For intermediate mobile phase compositions, the siloxane and the silanol groups are both significantly saturated with acetonitrile and water, respectively, causing a minimum of the retention factor of pyridine on the Halo column. PMID:19853257
Density functional study of the adsorption of aspirin on the hydroxylated (0 0 1) α-quartz surface
NASA Astrophysics Data System (ADS)
Abbasi, A.; Nadimi, E.; Plänitz, P.; Radehaus, C.
2009-08-01
In this study the adsorption geometry of aspirin molecule on a hydroxylated (0 0 1) α-quartz surface has been investigated using DFT calculations. The optimized adsorption geometry indicates that both, adsorbed molecule and substrate are strongly deformed. Strong hydrogen bonding between aspirin and surface hydroxyls, leads to the breaking of the original hydroxyl-hydroxyl hydrogen bonds (Hydrogenbridges) on the surface. In this case new hydrogen bonds on the hydroxylated (0 0 1) α-quartz surface appear which significantly differ from those at the clean surface. The 1.11 eV adsorption energy reveals that the interaction of aspirin with α-quartz is an exothermic chemical interaction.
Atomic and Molecular Adsorption on Re(0001)
Hahn, Konstanze; Mavrikakis, Manos
2014-02-01
Using periodic, self-consistent density functional theory calculations, the adsorption of several atomic (H, S, N, O and C) and molecular (CO2, N2, NH3, HCN, CO and NO) species and molecular fragments (NH2, NH, CN, CNH2, HNO, NOH, CH3, CH2, CH and OH) on the (0001) facet of rhenium at a coverage of 0.25 ML has been studied. Preferred binding sites with their corresponding binding energy and deformation energy of the surface, as well as an estimated diffusion barrier of each species have been determined. Atomic species and molecular fragments tend to bind to threefold sites, whereas molecular species tend to bind to top sites. The binding strength, with respect to the corresponding gas phase species and in increasing order for all species studied, is: CO2 < N2 < NH3 < CO < CH3 < HCN < NO < H < NH2 < OH < CH2 < CNH2 < CN < HNO < NH < NOH < S < N < O < CH < C. The vibrational frequencies of all species in their most energetically favorable adsorbed configuration have been calculated. Finally, the thermochemistry of adsorption and decomposition of NO, NO + H, NH3, N2, CO2, CO and CH4 on Re(0001) has been analyzed.
NASA Astrophysics Data System (ADS)
Yurchenko, Sergei N.; Thiel, Walter; Jensen, Per
2007-10-01
We present a new computational method with associated computer program TROVE (Theoretical ROVibrational Energies) to perform variational calculations of rovibrational energies for general polyatomic molecules of arbitrary structure in isolated electronic states. The (approximate) nuclear kinetic energy operator is represented as an expansion in terms of internal coordinates. The main feature of the computational scheme is a numerical construction of the kinetic energy operator, which is an integral part of the computation process. Thus the scheme is self-contained, i.e., it requires no analytical pre-derivation of the kinetic energy operator. It is also general, since it can be used in connection with any internal coordinates. The method represents an extension of our model for pyramidal XY 3 molecules reported previously [S.N. Yurchenko, M. Carvajal, P. Jensen, H. Lin, J.J. Zheng, W. Thiel, Mol. Phys. 103 (2005) 359]. Non-rigid molecules are treated in the Hougen-Bunker-Johns approach [J.T. Hougen, P.R. Bunker, J.W.C. Johns, J. Mol. Spectrosc. 34 (1970) 136]. In this case, the variational calculations employ a numerical finite basis representation for the large-amplitude motion using basis functions that are generated by Numerov-Cooley integration of the appropriate one-dimensional Schrödinger equation.
NASA Astrophysics Data System (ADS)
Sanchez-Parcerisa, D.; Cortés-Giraldo, M. A.; Dolney, D.; Kondrla, M.; Fager, M.; Carabe, A.
2016-02-01
In order to integrate radiobiological modelling with clinical treatment planning for proton radiotherapy, we extended our in-house treatment planning system FoCa with a 3D analytical algorithm to calculate linear energy transfer (LET) in voxelized patient geometries. Both active scanning and passive scattering delivery modalities are supported. The analytical calculation is much faster than the Monte-Carlo (MC) method and it can be implemented in the inverse treatment planning optimization suite, allowing us to create LET-based objectives in inverse planning. The LET was calculated by combining a 1D analytical approach including a novel correction for secondary protons with pencil-beam type LET-kernels. Then, these LET kernels were inserted into the proton-convolution-superposition algorithm in FoCa. The analytical LET distributions were benchmarked against MC simulations carried out in Geant4. A cohort of simple phantom and patient plans representing a wide variety of sites (prostate, lung, brain, head and neck) was selected. The calculation algorithm was able to reproduce the MC LET to within 6% (1 standard deviation) for low-LET areas (under 1.7 keV μm-1) and within 22% for the high-LET areas above that threshold. The dose and LET distributions can be further extended, using radiobiological models, to include radiobiological effectiveness (RBE) calculations in the treatment planning system. This implementation also allows for radiobiological optimization of treatments by including RBE-weighted dose constraints in the inverse treatment planning process.
Adsorption interactions of humic acids with biocides
NASA Astrophysics Data System (ADS)
Mal'Tseva, E. V.; Ivanov, A. A.; Yudina, N. V.
2009-11-01
The chemical composition of humic acids from brown coal (Aldrich) was determined by element analysis, 13C NMR spectroscopy, and potentiometric titration. The adsorption ability of humic acids with different biocides (cyproconasol, propiconasol, tebuconasol, irgarol 1051, and DCOIT) was studied. The adsorption ability of a mixture of biocides in aqueous solutions was higher than that of the individual components. The limiting concentration of humic acids at which adsorption of biocides was maximum was determined. Adsorption constants were calculated by the Freundlich equation for each biocide in aqueous solution.
Janke, Svenja M; Auerbach, Daniel J; Wodtke, Alec M; Kandratsenka, Alexander
2015-09-28
We have constructed a potential energy surface (PES) for H-atoms interacting with fcc Au(111) based on fitting the analytic form of the energy from Effective Medium Theory (EMT) to ab initio energy values calculated with density functional theory. The fit used input from configurations of the H-Au system with Au atoms at their lattice positions as well as configurations with the Au atoms displaced from their lattice positions. It reproduces the energy, in full dimension, not only for the configurations used as input but also for a large number of additional configurations derived from ab initio molecular dynamics (AIMD) trajectories at finite temperature. Adiabatic molecular dynamics simulations on this PES reproduce the energy loss behavior of AIMD. EMT also provides expressions for the embedding electron density, which enabled us to develop a self-consistent approach to simulate nonadiabatic electron-hole pair excitation and their effect on the motion of the incident H-atoms. For H atoms with an energy of 2.7 eV colliding with Au, electron-hole pair excitation is by far the most important energy loss pathway, giving an average energy loss ≈3 times that of the adiabatic case. This increased energy loss enhances the probability of the H-atom remaining on or in the Au slab by a factor of 2. The most likely outcome for H-atoms that are not scattered also depends prodigiously on the energy transfer mechanism; for the nonadiabatic case, more than 50% of the H-atoms which do not scatter are adsorbed on the surface, while for the adiabatic case more than 50% pass entirely through the 4 layer simulation slab. PMID:26429033
Janke, Svenja M.; Auerbach, Daniel J.; Kandratsenka, Alexander; Wodtke, Alec M.
2015-09-28
We have constructed a potential energy surface (PES) for H-atoms interacting with fcc Au(111) based on fitting the analytic form of the energy from Effective Medium Theory (EMT) to ab initio energy values calculated with density functional theory. The fit used input from configurations of the H–Au system with Au atoms at their lattice positions as well as configurations with the Au atoms displaced from their lattice positions. It reproduces the energy, in full dimension, not only for the configurations used as input but also for a large number of additional configurations derived from ab initio molecular dynamics (AIMD) trajectories at finite temperature. Adiabatic molecular dynamics simulations on this PES reproduce the energy loss behavior of AIMD. EMT also provides expressions for the embedding electron density, which enabled us to develop a self-consistent approach to simulate nonadiabatic electron-hole pair excitation and their effect on the motion of the incident H-atoms. For H atoms with an energy of 2.7 eV colliding with Au, electron-hole pair excitation is by far the most important energy loss pathway, giving an average energy loss ≈3 times that of the adiabatic case. This increased energy loss enhances the probability of the H-atom remaining on or in the Au slab by a factor of 2. The most likely outcome for H-atoms that are not scattered also depends prodigiously on the energy transfer mechanism; for the nonadiabatic case, more than 50% of the H-atoms which do not scatter are adsorbed on the surface, while for the adiabatic case more than 50% pass entirely through the 4 layer simulation slab.
NASA Astrophysics Data System (ADS)
Matos, Jeronimo; Yildirim, Handan; Kara, Abdelkader
2014-03-01
The characteristics of Benzene adsorption on metals and their alloy surfaces, and the interface features have been the subject of many experimental and theoretical studies. With the availability of the new vdW functionals, we revisit this organic molecule/metal system to assess the influence of vdW interactions on the adsorption as well as to examine the performance of these vdW functionals. We will present the adsorption geometries, adsorption energies and heights, the characteristics of interface electronic structure, and the charge transfer for Benzene adsorption on the (110) surfaces of seven transition metals; Au, Ag, Cu, Pd, Pt, Rh, and Ni. The calculations are carried out using PBE and vdW-DF family functionals implemented in the VASP package. We will provide comparisons with the available experimental and theoretical studies on the adsorption geometries and energies, and the effect introduced by varying surface chemistries. We will also provide comparisons with the recent study for Benzene adsorption on the (111) surfaces of the same metal substrates . This work is funded by the U.S. Department of Energy Basic Energy Science under Contract No DE-FG02-11ER16243.
Enhanced ligand sampling for relative protein-ligand binding free energy calculations.
Kaus, Joseph W; McCammon, J Andrew
2015-05-21
Free energy calculations are used to study how strongly potential drug molecules interact with their target receptors. The accuracy of these calculations depends on the accuracy of the molecular dynamics (MD) force field as well as proper sampling of the major conformations of each molecule. However, proper sampling of ligand conformations can be difficult when there are large barriers separating the major ligand conformations. An example of this is for ligands with an asymmetrically substituted phenyl ring, where the presence of protein loops hinders the proper sampling of the different ring conformations. These ring conformations become more difficult to sample when the size of the functional groups attached to the ring increases. The Adaptive Integration Method (AIM) has been developed, which adaptively changes the alchemical coupling parameter λ during the MD simulation so that conformations sampled at one λ can aid sampling at the other λ values. The Accelerated Adaptive Integration Method (AcclAIM) builds on AIM by lowering potential barriers for specific degrees of freedom at intermediate λ values. However, these methods may not work when there are very large barriers separating the major ligand conformations. In this work, we describe a modification to AIM that improves sampling of the different ring conformations, even when there is a very large barrier between them. This method combines AIM with conformational Monte Carlo sampling, giving improved convergence of ring populations and the resulting free energy. This method, called AIM/MC, is applied to study the relative binding free energy for a pair of ligands that bind to thrombin and a different pair of ligands that bind to aspartyl protease β-APP cleaving enzyme 1 (BACE1). These protein-ligand binding free energy calculations illustrate the improvements in conformational sampling and the convergence of the free energy compared to both AIM and AcclAIM. PMID:25906170
Enhanced Ligand Sampling for Relative Protein–Ligand Binding Free Energy Calculations
2016-01-01
Free energy calculations are used to study how strongly potential drug molecules interact with their target receptors. The accuracy of these calculations depends on the accuracy of the molecular dynamics (MD) force field as well as proper sampling of the major conformations of each molecule. However, proper sampling of ligand conformations can be difficult when there are large barriers separating the major ligand conformations. An example of this is for ligands with an asymmetrically substituted phenyl ring, where the presence of protein loops hinders the proper sampling of the different ring conformations. These ring conformations become more difficult to sample when the size of the functional groups attached to the ring increases. The Adaptive Integration Method (AIM) has been developed, which adaptively changes the alchemical coupling parameter λ during the MD simulation so that conformations sampled at one λ can aid sampling at the other λ values. The Accelerated Adaptive Integration Method (AcclAIM) builds on AIM by lowering potential barriers for specific degrees of freedom at intermediate λ values. However, these methods may not work when there are very large barriers separating the major ligand conformations. In this work, we describe a modification to AIM that improves sampling of the different ring conformations, even when there is a very large barrier between them. This method combines AIM with conformational Monte Carlo sampling, giving improved convergence of ring populations and the resulting free energy. This method, called AIM/MC, is applied to study the relative binding free energy for a pair of ligands that bind to thrombin and a different pair of ligands that bind to aspartyl protease β-APP cleaving enzyme 1 (BACE1). These protein–ligand binding free energy calculations illustrate the improvements in conformational sampling and the convergence of the free energy compared to both AIM and AcclAIM. PMID:25906170
The measurement and calculation of nanodosimetric energy distributions for electrons and photons
NASA Astrophysics Data System (ADS)
Evans, Thomas Michael
1997-09-01
Low dose and low dose rate fields constitute the majority of radiation exposure scenarios in radiation protection. Conversely, very little epidemiological or physical data are available at these levels. This situation exists because the parameters characterizing low dose and low dose rate environments are difficult to assess at cellular levels where the fundamental biological effects from radiation insults occur. The quantities required for a complete biological assessment are the distribution of energy deposition in biological targets and the cellular response to such insults. A new detector to measure physical energy depositions on nanometer scales was developed in this thesis. A computational tool was also developed to calculate clustered distributions of energy deposition from electrons and photons. A dosimeter has been developed which characterizes energy depositions from charged particles in nanometer dimensions. The dosimeter is a threshold-type detector based on the temperature response of the superheated liquid droplet detector (SLDD). SLDDs based on Freon-115 have been designed and tested. A data acquisition system that measures the acoustic signals from bubble nucleation events has been developed. An original electron track code, ESLOW3.1, has been developed. The code simulates electron tracks on an event-by-event basis down to an absolute minimum of 20 eV. The transport medium is water vapor. The cross sections have been compared with published data and theoretical models where available. Trial calculations of pertinent quantities are in good agreement with published results. A new operational quantity, the cluster spectrum, given the symbol c(/varepsilon), has been defined. This quantity is measured by the SLDD operated in nanodosimetry mode. The performance of the SLDD has been tested with a 60Co point source. The effective measurement range of the nanodosimeter is between 60 and 500 eV of energy deposition. Measured values of c(/varepsilon) are
Star sub-pixel centroid calculation based on multi-step minimum energy difference method
NASA Astrophysics Data System (ADS)
Wang, Duo; Han, YanLi; Sun, Tengfei
2013-09-01
The star's centroid plays a vital role in celestial navigation, star images which be gotten during daytime, due to the strong sky background, have a low SNR, and the star objectives are nearly submerged in the background, takes a great trouble to the centroid localization. Traditional methods, such as a moment method, weighted centroid calculation method is simple but has a big error, especially in the condition of a low SNR. Gaussian method has a high positioning accuracy, but the computational complexity. Analysis of the energy distribution in star image, a location method for star target centroids based on multi-step minimum energy difference is proposed. This method uses the linear superposition to narrow the centroid area, in the certain narrow area uses a certain number of interpolation to pixels for the pixels' segmentation, and then using the symmetry of the stellar energy distribution, tentatively to get the centroid position: assume that the current pixel is the star centroid position, and then calculates and gets the difference of the sum of the energy which in the symmetric direction(in this paper we take the two directions of transverse and longitudinal) and the equal step length(which can be decided through different conditions, the paper takes 9 as the step length) of the current pixel, and obtain the centroid position in this direction when the minimum difference appears, and so do the other directions, then the validation comparison of simulated star images, and compare with several traditional methods, experiments shows that the positioning accuracy of the method up to 0.001 pixel, has good effect to calculate the centroid of low SNR conditions; at the same time, uses this method on a star map which got at the fixed observation site during daytime in near-infrared band, compare the results of the paper's method with the position messages which were known of the star, it shows that :the multi-step minimum energy difference method achieves a better
Monte Carlo dose calculation improvements for low energy electron beams using eMC.
Fix, Michael K; Frei, Daniel; Volken, Werner; Neuenschwander, Hans; Born, Ernst J; Manser, Peter
2010-08-21
The electron Monte Carlo (eMC) dose calculation algorithm in Eclipse (Varian Medical Systems) is based on the macro MC method and is able to predict dose distributions for high energy electron beams with high accuracy. However, there are limitations for low energy electron beams. This work aims to improve the accuracy of the dose calculation using eMC for 4 and 6 MeV electron beams of Varian linear accelerators. Improvements implemented into the eMC include (1) improved determination of the initial electron energy spectrum by increased resolution of mono-energetic depth dose curves used during beam configuration; (2) inclusion of all the scrapers of the applicator in the beam model; (3) reduction of the maximum size of the sphere to be selected within the macro MC transport when the energy of the incident electron is below certain thresholds. The impact of these changes in eMC is investigated by comparing calculated dose distributions for 4 and 6 MeV electron beams at source to surface distance (SSD) of 100 and 110 cm with applicators ranging from 6 x 6 to 25 x 25 cm(2) of a Varian Clinac 2300C/D with the corresponding measurements. Dose differences between calculated and measured absolute depth dose curves are reduced from 6% to less than 1.5% for both energies and all applicators considered at SSD of 100 cm. Using the original eMC implementation, absolute dose profiles at depths of 1 cm, d(max) and R50 in water lead to dose differences of up to 8% for applicators larger than 15 x 15 cm(2) at SSD 100 cm. Those differences are now reduced to less than 2% for all dose profiles investigated when the improved version of eMC is used. At SSD of 110 cm the dose difference for the original eMC version is even more pronounced and can be larger than 10%. Those differences are reduced to within 2% or 2 mm with the improved version of eMC. In this work several enhancements were made in the eMC algorithm leading to significant improvements in the accuracy of the dose
Kumar, Rajesh; Jain, S K; Verma, S; Malodia, P
2015-10-15
In this article, 3-mercaptopropyl functionalized silica entrapped polyacrylamide hydrogel (MPFS-PAA) was prepared and characterized by FT-IR, scanning electron microscopy (SEM) and energy dispersion X-ray spectroscopy (EDS). Synthesized hydrogel was evaluated for removal of arsenic(III) from aqueous solution. Adsorption studies were carried out by batch method as function of contact time, initial concentration of arsenic and pH. As(III) adsorption data fitted well with Langmuir and Freundlich isotherm models. Adsorption capacity of arsenic 92.5 μg/g was obtained at initial concentration of 100 μg/L by Langmuir isotherm. Adsorption kinetics was tested for pseudo-second order reaction at different contact time. The rate constants of pseudo second order reaction were calculated and good correlation coefficient R(2) 99.67 obtained. The results indicates that MPFS-PAA is an effective adsorbent for removal of As(III) from aqueous solution. PMID:26151463
Adsorptive removal of methylene blue by agar: effects of NaCl and ethanol
2012-01-01
Adsorption of methylene blue (MB) on agar was investigated as a function of temperature (308-328 K), different concentrations of NaCl and HCl and various weight percentages of binary mixtures of ethanol with water. It was observed that the maximum experimental adsorption capacity, qm, exp, in water is up to 50 mg g-1 and decreases with increase in weight percentage of ethanol and NaCl and HCl concentration compared to that of water. Analysis of data using ARIAN model showed that MB adsorbs as monomer and dimer on the surface of agar. Binding constants of MB to agar were calculated using the Temkin isotherm. The process is exothermic in water and other solutions. The mean adsorption energy (E) value indicated binding of MB to agar is chemical adsorption. Kinetics of this interaction obeys from the pseudo-second-order model and diffusion of the MB molecules into the agar is the main rate-controlling step. PMID:22339759
Free energy calculations, enhanced by a Gaussian ansatz, for the "chemical work" distribution.
Boulougouris, Georgios C
2014-05-15
The evaluation of the free energy is essential in molecular simulation because it is intimately related with the existence of multiphase equilibrium. Recently, it was demonstrated that it is possible to evaluate the Helmholtz free energy using a single statistical ensemble along an entire isotherm by accounting for the "chemical work" of transforming each molecule, from an interacting one, to an ideal gas. In this work, we show that it is possible to perform such a free energy perturbation over a liquid vapor phase transition. Furthermore, we investigate the link between a general free energy perturbation scheme and the novel nonequilibrium theories of Crook's and Jarzinsky. We find that for finite systems away from the thermodynamic limit the second law of thermodynamics will always be an inequality for isothermal free energy perturbations, resulting always to a dissipated work that may tend to zero only in the thermodynamic limit. The work, the heat, and the entropy produced during a thermodynamic free energy perturbation can be viewed in the context of the Crooks and Jarzinsky formalism, revealing that for a given value of the ensemble average of the "irreversible" work, the minimum entropy production corresponded to a Gaussian distribution for the histogram of the work. We propose the evaluation of the free energy difference in any free energy perturbation based scheme on the average irreversible "chemical work" minus the dissipated work that can be calculated from the variance of the distribution of the logarithm of the work histogram, within the Gaussian approximation. As a consequence, using the Gaussian ansatz for the distribution of the "chemical work," accurate estimates for the chemical potential and the free energy of the system can be performed using much shorter simulations and avoiding the necessity of sampling the computational costly tails of the "chemical work." For a more general free energy perturbation scheme that the Gaussian ansatz may not be
Gomez, Guillermina; Belelli, Patricia G.; Cabeza, Gabriela F.; Castellani, Norberto J.
2010-12-15
The adsorption of 1,3-butadiene (BD) on the Pd/Ni(1 1 1) multilayers has been studied using the VASP method in the framework of the density functional theory (DFT). The adsorption on two different configurations of the Pd{sub n}/Ni{sub m}(1 1 1) systems were considered. The most stable adsorption sites are dependent on the substrate composition and on the inclusion or not of spin polarization. On Pd{sub 1}Ni{sub 3}(1 1 1) surface, di-{pi}-cis and 1,2,3,4-tetra-{sigma} adsorption structures are the most stable for non-spin polarized (NSP) and spin polarized (SP) levels of calculation, respectively. Conversely, on Pd{sub 3}Ni{sub 1}(1 1 1) surface, the 1,2,3,4-tetra-{sigma} adsorption structure is the most stable for both NSP and SP levels, respectively. The magnetization of the Pd atoms strongly modifies the adsorption energy of BD and its most stable adsorption mode. On the other hand, as a consequence of BD adsorption, the Pd magnetization decreases. The smaller adsorption energies of BD and 1-butene on the Pd{sub 1}Ni{sub 3}(1 1 1) surface than on Pd(1 1 1) can be associated to the strained Pd overlayer deposited on Ni(1 1 1). -- Graphical Abstract: The adsorption of 1,3-butadiene on Pd/Ni(1 1 1) multilayers was theoretically studied. The most stable adsorption site depends on the substrate composition and on the inclusion of spin polarization. Display Omitted
Free-energy calculations for semi-flexible macromolecules: applications to DNA knotting and looping.
Giovan, Stefan M; Scharein, Robert G; Hanke, Andreas; Levene, Stephen D
2014-11-01
We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases. PMID:25381542
Evaluation of Generalized Born Model Accuracy for Absolute Binding Free Energy Calculations.
Zeller, Fabian; Zacharias, Martin
2014-06-27
Generalized Born (GB) implicit solvent models are widely used in molecular dynamics simulations to evaluate the interactions of biomolecular complexes. The continuum treatment of the solvent results in significant computational savings in comparison to an explicit solvent representation. It is, however, not clear how accurately the GB approach reproduces the absolute free energies of biomolecular binding. On the basis of induced dissociation by means of umbrella sampling simulations, the absolute binding free energies of small proline-rich peptide ligands and a protein receptor were calculated. Comparative simulations according to the same protocol were performed by employing an explicit solvent model and various GB-type implicit solvent models in combination with a nonpolar surface tension term. The peptide ligands differed in a key residue at the peptide-protein interface, including either a nonpolar, a neutral polar, a positively charged, or a negatively charged group. For the peptides with a neutral polar or nonpolar interface residue, very good agreement between the explicit solvent and GB implicit solvent results was found. Deviations in the main separation free energy contributions are smaller than 1 kcal/mol. In contrast, for peptides with a charged interface residue, significant deviations of 2-4 kcal/mol were observed. The results indicate that recent GB models can compete with explicit solvent representations in total binding free energy calculations as long as no charged residues are present at the binding interface. PMID:24941018
Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping
NASA Astrophysics Data System (ADS)
Giovan, Stefan M.; Scharein, Robert G.; Hanke, Andreas; Levene, Stephen D.
2014-11-01
We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases.
Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping
Giovan, Stefan M.; Scharein, Robert G.; Hanke, Andreas; Levene, Stephen D.
2014-11-07
We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases.
Recent advances in QM/MM free energy calculations using reference potentials☆
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
Adsorption of CO molecules on doped graphene: A first-principles study
NASA Astrophysics Data System (ADS)
Wang, Weidong; Zhang, Yuxiang; Shen, Cuili; Chai, Yang
2016-02-01
As a typical kinds of toxic gases, CO plays an important role in environmental monitoring, control of chemical processes, space missions, agricultural and medical applications. Graphene is considered a potential candidate of gases sensor, so the adsorption of CO molecules on various graphene, including pristine graphene, Nitrogen-doped graphene (N-doped graphene) and Aluminum-doped graphene (Al-doped graphene), are studied by using first-principles calculations. The optimal configurations, adsorption energies, charge transfer, and electronic properties including band structures, density of states and differential charge density are obtained. The adsorption energies of CO molecules on pristine graphene and N-doped graphene are -0.01 eV, and -0.03 eV, respectively. In comparison, the adsorption energy of CO on Al-doped graphene is much larger, -2.69 eV. Our results also show that there occurs a large amount of charge transfer between CO molecules and graphene sheet after the adsorption, which suggests Al-doped graphene is more sensitive to the adsorption of CO than pristine graphene and N-doped graphene. Therefore, the sensitivity of gases on graphene can be drastically improved by introducing the suitable dopants.
Olsen, Richard; Leirvik, Kim N; Kvamme, Bjørn; Kuznetsova, Tatiana
2015-08-11
Molecular dynamics (MD) and Born-Oppenheimer MD (BOMD) simulations were employed to investigate adsorption of aqueous triethylene glycol (TEG) on a hydrated {101̅4} calcite surface at 298 K. We analyzed the orientation of TEG adsorbed on calcite, as well as the impact of TEG on the water density and adsorption free energy. The adsorption energies of TEG, free energy profiles for TEG, details of hydrogen bonding between water and adsorbed TEG, and dihedral angle distribution of adsorbed TEG were estimated. We found that while the first layer of water was mostly unaffected by the presence of adsorbed TEG, the density of the second water layer was decreased by 71% at 75% surface coverage of TEG. TEG primarily attached to the calcite surface via two adjacent adsorption sites. Hydrogen bonds between water and adsorbed TEG in the second layer almost exclusively involved the hydroxyl oxygen of TEG. The adsorption energy of TEG on calcite in a vacuum environment calculated by classical MD amounted to 217 kJ/mol, which agreed very well with estimates found by using BOMD. Adsorption on hydrated calcite yielded a drastically lower value of 33 kJ/mol, with the corresponding adsorption free energy of 55.3 kJ/mol, giving an entropy increase of 22.3 kJ/mol due to adsorption. We found that the presence of TEG resulted in a decreased magnitude of the adsorption free energy of water, thus decreasing the calcite wettability. This effect can have a profound effect on oil and gas reservoir properties and must be carefully considered when evaluating the risk of hydrate nucleation. PMID:26161580
HYDROGEN ADSORPTION ON β-TiAl (001) AND Ni/TiAl (001) SURFACES
NASA Astrophysics Data System (ADS)
Mubarak, A. A. Karim; Alelaimi, Mahmoud
2014-04-01
In this paper, we present first principles calculations of the energetic, electronic and magnetic properties of the variant termination of TiAl (001) and Ni/TiAl (001) surfaces with and without hydrogen atoms. The calculations have been performed within the density functional theory using full-potential linearized augmented plane wave method. The generalized gradient approximation (GGA) is utilized as the exchange-correlation energy. The octahedral site is the stable absorption site of H atom in the β-TiAl system. This absorption reduces the cohesive energy of β-TiAl system due to increase in the lattice constant. The surface energy for both TiAl (001) terminations is calculated. The stable adsorption site of H atoms on the variant termination of TiAl (001) surface is performed. The adsorption energy of hydrogen on Ti is more energetic than that on Al. The adsorption of H atom on both terminations of H/Ni/TiAl (001) is more preferable at the bridge site. The adsorption energies are enhanced on Ni atom due to the contraction between d-Ni bands and TiAl substrate band.
Mielke, Steven L. E-mail: truhlar@umn.edu; Truhlar, Donald G. E-mail: truhlar@umn.edu
2015-01-28
We present an improved version of our “path-by-path” enhanced same path extrapolation scheme for Feynman path integral (FPI) calculations that permits rapid convergence with discretization errors ranging from O(P{sup −6}) to O(P{sup −12}), where P is the number of path discretization points. We also present two extensions of our importance sampling and stratified sampling schemes for calculating vibrational–rotational partition functions by the FPI method. The first is the use of importance functions for dihedral angles between sets of generalized Jacobi coordinate vectors. The second is an extension of our stratification scheme to allow some strata to be defined based only on coordinate information while other strata are defined based on both the geometry and the energy of the centroid of the Feynman path. These enhanced methods are applied to calculate converged partition functions by FPI methods, and these results are compared to ones obtained earlier by vibrational configuration interaction (VCI) calculations, both calculations being for the Jordan–Gilbert potential energy surface. The earlier VCI calculations are found to agree well (within ∼1.5%) with the new benchmarks. The FPI partition functions presented here are estimated to be converged to within a 2σ statistical uncertainty of between 0.04% and 0.07% for the given potential energy surface for temperatures in the range 300–3000 K and are the most accurately converged partition functions for a given potential energy surface for any molecule with five or more atoms. We also tabulate free energies, enthalpies, entropies, and heat capacities.
NASA Astrophysics Data System (ADS)
Mielke, Steven L.; Truhlar, Donald G.
2015-01-01
We present an improved version of our "path-by-path" enhanced same path extrapolation scheme for Feynman path integral (FPI) calculations that permits rapid convergence with discretization errors ranging from O(P-6) to O(P-12), where P is the number of path discretization points. We also present two extensions of our importance sampling and stratified sampling schemes for calculating vibrational-rotational partition functions by the FPI method. The first is the use of importance functions for dihedral angles between sets of generalized Jacobi coordinate vectors. The second is an extension of our stratification scheme to allow some strata to be defined based only on coordinate information while other strata are defined based on both the geometry and the energy of the centroid of the Feynman path. These enhanced methods are applied to calculate converged partition functions by FPI methods, and these results are compared to ones obtained earlier by vibrational configuration interaction (VCI) calculations, both calculations being for the Jordan-Gilbert potential energy surface. The earlier VCI calculations are found to agree well (within ˜1.5%) with the new benchmarks. The FPI partition functions presented here are estimated to be converged to within a 2σ statistical uncertainty of between 0.04% and 0.07% for the given potential energy surface for temperatures in the range 300-3000 K and are the most accurately converged partition functions for a given potential energy surface for any molecule with five or more atoms. We also tabulate free energies, enthalpies, entropies, and heat capacities.
Fan, Jimin; Zhao, Zhihuan; Liu, Wenhui; Xue, Yongqiang; Yin, Shu
2016-05-15
The different crystal forms of nitrogen doped-titanium oxide (N-TiO2) with different particle sizes were produced by precipitation-solvothermal method and their adsorption mechanism were also investigated. The adsorption kinetics showed that rutile N-TiO2 displayed higher adsorption capacity than anatase for methyl orange (MO) and its adsorption behavior followed the pseudo-second-order kinetics. The equilibrium adsorption rate of N-TiO2 for MO was well fitted by the Langmuir isotherm model and the adsorption process was monolayer adsorption. The adsorption capacity decreased with increasing temperature. The average correlation coefficient was beyond 97%. The thermodynamic parameters (ΔaGm(ө), ΔaHm(ө), and ΔaSm(ө)) were calculated. It was found that anatase and rutile N-TiO2 had different adsorption enthalpy and entropy. The smaller the particle size, the greater the surface area and surface energy was, then ΔaGm(ө) decreased and the standard equilibrium constant increased at the same time. The adsorption process onto different crystalline phase N-TiO2 was exothermic and non-spontaneous. PMID:26945716
A program to calculate non-bonded interaction energy in biomolecular aggregates.
Sundaram, K; Prasad, C V
1982-02-01
This paper describes a program to calculate intermolecular as well as intramolecular electronic potential energy resulting from non-bonded interactions. The underlying theory is obtained by the application of Rayleigh-Schroedinger perturbation theory to non-overlap regions of a molecular system. The rigorous theoretical expressions for the energy terms are simplified by approximations consistent with those commonly employed in semi-empirical molecular orbital theories. The program is particularly suited for the study of biomolecular assemblies, and in situations where insight into contributions to total energy from various component interaction types is desired. The inclusion of the non-additive dispersion effects in this approach makes it especially interesting for the study of cooperative phenomena in the light of a recent finding [1]. PMID:7067416
S-model calculations for high-energy-electron-impact double ionization of helium
NASA Astrophysics Data System (ADS)
Gasaneo, G.; Mitnik, D. M.; Randazzo, J. M.; Ancarani, L. U.; Colavecchia, F. D.
2013-04-01
In this paper the double ionization of helium by high-energy electron impact is studied. The corresponding four-body Schrödinger equation is transformed into a set of driven equations containing successive orders in the projectile-target interaction. The transition amplitude obtained from the asymptotic limit of the first-order solution is shown to be equivalent to the familiar first Born approximation. The first-order driven equation is solved within a generalized Sturmian approach for an S-wave (e,3e) model process with high incident energy and small momentum transfer corresponding to published measurements. Two independent numerical implementations, one using spherical and the other hyperspherical coordinates, yield mutual agreement. From our ab initio solution, the transition amplitude is extracted, and single differential cross sections are calculated and could be taken as benchmark values to test other numerical methods in a previously unexplored energy domain.
Hansen, L.F.
1985-05-01
Neutron elastic and inelastic differential cross sections for targets between /sup 9/Be and /sup 239/Pu at energies, E > 14 MeV have been measured using the Livermore and Ohio University neutron time-of-flight facilities. We review here the data and the analyses based on two local microscopic optical potentials: that of Jeukenne, Lejeune and Mahaux, and that of Brieva and Rook. The results are also compared with calculations using global potentials. Coupled channel formalism has been used in the analysis of targets with strong deformations, such as Be, C, Ta, and actinides. The value of the microscopic optical potentials as a tool to predict elastic and inelastic neutron cross sections over a wide mass and energy range is discussed. The need for neutron measurements up to higher energies and their analysis in conjunction with (p,p) and charge exchange (p,n) data is addressed. 17 refs.