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Sample records for intermolecular interaction energies

  1. The same number of optimized parameters scheme for determining intermolecular interaction energies

    Kristensen, Kasper; Ettenhuber, Patrick; Eriksen, Janus Juul; Jensen, Frank; Jørgensen, Poul

    2015-01-01

    We propose the Same Number Of Optimized Parameters (SNOOP) scheme as an alternative to the counterpoise method for treating basis set superposition errors in calculations of intermolecular interaction energies. The key point of the SNOOP scheme is to enforce that the number of optimized wave...... numerically. Numerical results for second-order Møller-Plesset perturbation theory (MP2) and coupled-cluster with single, double, and approximate triple excitations (CCSD(T)) show that the SNOOP scheme in general outperforms the uncorrected and counterpoise approaches. Furthermore, we show that SNOOP...

  2. Energy Decomposition Analysis with a Stable Charge-Transfer Term for Interpreting Intermolecular Interactions.

    Lao, Ka Un; Herbert, John M

    2016-06-14

    Many schemes for decomposing quantum-chemical calculations of intermolecular interaction energies into physically meaningful components can be found in the literature, but the definition of the charge-transfer (CT) contribution has proven particularly vexing to define in a satisfactory way and typically depends strongly on the choice of basis set. This is problematic, especially in cases of dative bonding and for open-shell complexes involving cation radicals, for which one might expect significant CT. Here, we analyze CT interactions predicted by several popular energy decomposition analyses and ultimately recommend the definition afforded by constrained density functional theory (cDFT), as it is scarcely dependent on basis set and provides results that are in accord with chemical intuition in simple cases, and in quantitative agreement with experimental estimates of the CT energy, where available. For open-shell complexes, the cDFT approach affords CT energies that are in line with trends expected based on ionization potentials and electron affinities whereas some other definitions afford unreasonably large CT energies in large-gap systems, which are sometimes artificially offset by underestimation of van der Waals interactions by density functional theory. Our recommended energy decomposition analysis is a composite approach, in which cDFT is used to define the CT component of the interaction energy and symmetry-adapted perturbation theory (SAPT) defines the electrostatic, polarization, Pauli repulsion, and van der Waals contributions. SAPT/cDFT provides a stable and physically motivated energy decomposition that, when combined with a new implementation of open-shell SAPT, can be applied to supramolecular complexes involving molecules, ions, and/or radicals. PMID:27049750

  3. Local intermolecular interactions for selective CO2 capture by zeolitic imidazole frameworks: energy decomposition analysis

    Intermolecular energy decomposition analysis (EDA) is reported for the binding of CO2 with zeolitic imidazole frameworks (ZIF) to provide a molecular level interpretation of the recent capacity and selectivity measurements of several ZIFs and to suggest a theoretical guideline to improve their performance further, using 1 nm size of organic linker fragment of the ZIFs as a target molecule. The EDA suggests that the local electronic interaction of CO2 and the substituent groups, mainly frozen density and polarization interactions with little charge transfer, is the primary binding interaction, but the electron correlation effects can be equally or more important depending on the binding geometry and functional groups. The present correlated calculations identify the preferred ZIF binding sites for various gases including CO2 to be mostly near the benzene substituent groups rather than the plane of imidazole rings. We predict that the NH2-substituted ZIF would have an enhanced capacity of CO2 as compared to the NO2-substituted ZIF that was recently synthesized and reported to be one of the materials with the best capacity results along with high gas selectivity. The present calculations may imply that the local functionality of the linking organics, rather than detailed framework structures, may be of primary importance in designing certain high capacity MOF or ZIF materials.

  4. An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method

    Asada, Naoya; Dmitri G Fedorov; Kitaura, Kazuo; Nakanishi, Isao; Merz, Kenneth M.

    2012-01-01

    We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4′-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to th...

  5. He-, Ne-, and Ar-phosgene intermolecular potential energy surfaces

    Munteanu, Cristian R.; Henriksen, Christian; Felker, Peter M.; Fernández, Berta

    2013-01-01

    Using the CCSD(T) model, we evaluated the intermolecular potential energy surfaces of the He-, Ne-, and Ar-phosgene complexes. We considered a representative number of intermolecular geometries for which we calculated the corresponding interaction energies with the augmented (He complex) and doub...

  6. Probing intermolecular protein-protein interactions in the calcium-sensing receptor homodimer using bioluminescence resonance energy transfer (BRET)

    Jensen, Anders A.; Hansen, Jakob L; Sheikh, Søren P;

    2002-01-01

    -induced intermolecular movements in the CaR homodimer using the new bioluminescence resonance energy transfer technique, BRET2, which is based on the transference of energy from Renilla luciferase (Rluc) to the green fluorescent protein mutant GFP2. We tagged CaR with Rluc and GFP2 at different intracellular locations...

  7. Phosphate Stabilization of Intermolecular Interactions

    Jackson, Shelley N.; Wang, Hay-Yan J.; Yergey, Alfred; Woods, Amina S.

    2006-01-01

    Receptor heteromerization is an important phenomenon that results from the interaction of epitopes on two receptors. Previous studies have suggested the possibility of Dopamine D2- NMDA receptors’ interaction. We believe that the interaction is through an acidic epitope of the NMDA NR1 subunit (KVNSEEEEEDA) and a basic epitope of the D2 third intracellular loop (VLRRRRRKRVN), which was shown to also interact with the Adenosine A2A receptor. In previous work we highlighted the role of certain ...

  8. Bowl inversion state controlled by intermolecular interactions

    Full text: Bowl-shaped pi-conjugated compounds are important not only as model compounds of fullerenes but also as possible hosts for different guest molecules. Recent studies regarding the storage of possible energy carriers such as hydrogen and methane in nano-structured carbon materials have further increased the interest in well defined model compounds that allow for a detailed investigation of host-guest interactions in order to optimize the storage capacity of technologically relevant carbon-based materials. Within this context we investigated the structural properties of monolayer films of sumanene (C21H12) deposited on Ag(111). Based on STM experiments we find that the fraction of molecules having a bowl-down adsorption geometry is coverage-dependent, indicating that the bowl-inversion state is determined by intermolecular interactions. The experimental findings are rationalized by density functional theory (DFT) calculations, which reveal a subtle interplay between molecule-substrate and molecule- molecule interactions that is responsible for the abrupt structural change involving inversion of a fraction of the molecules and reorientation of the molecules with respect to the surface normal. (author)

  9. An energy decomposition analysis for intermolecular interactions from an absolutely localized molecular orbital reference at the coupled-cluster singles and doubles level

    We propose a wave function-based method for the decomposition of intermolecular interaction energies into chemically-intuitive components, isolating both mean-field- and explicit correlation-level contributions. We begin by solving the locally-projected self-consistent field for molecular interactions equations for a molecular complex, obtaining an intramolecularly polarized reference of self-consistently optimized, absolutely-localized molecular orbitals (ALMOs), determined with the constraint that each fragment MO be composed only of atomic basis functions belonging to its own fragment. As explicit inter-electronic correlation is integral to an accurate description of weak forces underlying intermolecular interaction potentials, namely, coordinated fluctuations in weakly interacting electronic densities, we add dynamical correlation to the ALMO polarized reference at the coupled-cluster singles and doubles level, accounting for explicit dispersion and charge-transfer effects, which map naturally onto the cluster operator. We demonstrate the stability of energy components with basis set extension, follow the hydrogen bond-breaking coordinate in the Cs-symmetry water dimer, decompose the interaction energies of dispersion-bound rare gas dimers and other van der Waals complexes, and examine charge transfer-dominated donor-acceptor interactions in borane adducts. We compare our results with high-level calculations and experiment when possible.

  10. Energy-dispersive NEXAFS. A novel tool for the investigation of intermolecular interaction and structural phase dynamics

    Scholz, Markus

    2013-06-27

    In the context of this thesis, the novel method soft X-ray energy-dispersive NEXAFS spectroscopy was explored and utilized to investigate intermolecular coupling and post-growth processes with a temporal resolution of seconds. 1,4,5,8- naphthalene tetracarboxylic acid dianhydride (NTCDA)multilayer films were the chosen model system for these investigations. The core hole-electron correlation in coherently coupled molecules was studied by means of energy-dispersive near-edge X-ray absorption fine-structure spectroscopy. A transient phase was found which exists during the transition between a disordered condensed phase and the bulk structure. This phase is characterized by distinct changes in the spectral line shape and energetic position of the X-ray absorption signal at the C K-edge. The findings were explained with the help of theoretical models based on the coupling of transition dipole moments, which are well established for optically excited systems. In consequence, the experimental results provides evidence for a core hole-electron pair delocalized over several molecules. Furthermore, the structure formation of NTCDA multilayer films on Ag(111) surfaces was investigated. With time-resolved and energy-dispersive NEXAFS experiments the intensity evolution in s- and p-polarization showed a very characteristic behavior. By combining these findings with the results of time-dependent photoemission measurements, several sub-processes were identified in the post- growth behavior. Upon annealing, the amorphous but preferentially flat-lying molecules flip into an upright orientation. After that follows a phase characterized by strong intermolecular coupling. Finally, three-dimensional islands are established. Employing the Kolmogorov-Johnson-Mehl-Avrami model, the activation energies of the sub-processes were determined.

  11. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    Venkatesha R. Hathwar

    2015-09-01

    Full Text Available Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ...Cπ interactions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. The quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.

  12. Resonant intermolecular transfer of vibrational energy in liquid water

    Woutersen, Sander; Bakker, Huib J.

    1999-12-01

    Many biological, chemical and physical processes involve the transfer of energy. In the case of electronic excitations, transfer between molecules is rapid, whereas for vibrations in the condensed phase, resonant energy transfer is an unlikely process because the typical timescale of vibrational relaxation (a few picoseconds) is much shorter than that of resonant intermolecular vibrational energy transfer. For the OH-stretch vibration in liquid water, which is of particular importance due to its coupling to the hydrogen bond, extensive investigations have shown that vibrational relaxation takes place with a time constant of 740 +/- 25 femtoseconds (ref. 7). So for resonant intermolecular energy transfer to occur in liquid water, the interaction between the OH-stretch modes of different water molecules needs to be extremely strong. Here we report time-resolved pump-probe laser spectroscopy measurements that reveal the occurrence of fast resonant intermolecular transfer of OH-stretch excitations over many water molecules before the excitation energy is dissipated. We find that the transfer process is mediated by dipole-dipole interactions (the Förster transfer mechanism) and additional mechanisms that are possibly based on intermolecular anharmonic interactions involving hydrogen bonds. Our findings suggest that liquid water may play an important role in transporting vibrational energy between OH groups located on either different biomolecules or along extended biological structures. OH groups in a hydrophobic environment should accordingly be able to remain in a vibrationally excited state longer than OH groups in a hydrophilic environment.

  13. The diversity of physical forces and mechanisms in intermolecular interactions

    Intermolecular interactions became an inherent part of the structure–function paradigm. Therefore, the generalized concept of protein stability and interactions should consider the balance of stabilizing forces working in different types of intermolecular interactions. We consider here two 'extremes' of protein interactions, viral protein with high intrinsic disorder and hyperthermostable protein complexes. Intermolecular interactions provide folding upon binding as a part of function in the viral case, while they secure and stabilize specific native interfaces as a prerequisite for function in hyperthermostable complexes. We propose a generalized concept of protein stability and interactions, which includes intermolecular interactions comprising distinct combinations of stabilizing forces depending on the types of interacting partners

  14. Interatomic and intermolecular interactions studied by imaging techniques

    Full text: Non-covalent interatomic and intermolecular interactions govern behaviour in a wide variety of environments. For example, they determine the aggregation of atoms and molecules, govern the structure of polymers and biological molecules, determine solvation properties, and modify chemical reactions in solution. The fundamental understanding of these interactions can be approached particularly well via spectroscopic probing of van der Waals molecules, with small model systems providing insights into the essential interaction mechanisms. Van der Waals molecules are dimers, or larger aggregates, of two or more species held together by non-covalent interactions. A crucial experimental value is the binding energy of the van der Waals molecules, which measures the strength of the intermolecular bond. This is difficult to measure. For example, the benzene-Ar complex has been studied for over 20 years because it is one of the simplest examples of dispersion interactions involving an aromatic, and such interactions are important in a biological context, yet its binding energy has remained elusive. Our group has used the technique of velocity map imaging to investigate the translational energy released in the dissociation of van der Waals molecules. The cut-off in the translational energy release distribution allows the binding energy of the complex to be determined. This approach has been applied to a number of van der Waals species. The translational energy released, in combination with spectroscopic probes, allows the distribution of rotational energy in the fragments to be determined, which provides insights into the dissociation process. The presentation will review the method and give a number of examples from the systems studied to date. Recently, we have begun velocity map imaging studies of NO-Ar dissociation as a precursor to studies of the dissociation of NO-diatomic species. The aim of this work is to determine the correlated product distributions

  15. Ab initio ground state phenylacetylene-argon intermolecular potential energy surface and rovibrational spectrum

    Cybulski, Hubert; Fernandez, Berta; Henriksen, Christian; Felker, Peter M.

    2012-01-01

    We evaluate the phenylacetylene-argon intermolecular potential energy surface by fitting a representative number of ab initio interaction energies to an analytic function. These energies are calculated at a grid of intermolecular geometries, using the CCSD(T) method and the aug-cc-pVDZ basis set...

  16. Defining the contributions of permanent electrostatics, Pauli repulsion, and dispersion in density functional theory calculations of intermolecular interaction energies.

    Horn, Paul R; Mao, Yuezhi; Head-Gordon, Martin

    2016-03-21

    In energy decomposition analysis of Kohn-Sham density functional theory calculations, the so-called frozen (or pre-polarization) interaction energy contains contributions from permanent electrostatics, dispersion, and Pauli repulsion. The standard classical approach to separate them suffers from several well-known limitations. We introduce an alternative scheme that employs valid antisymmetric electronic wavefunctions throughout and is based on the identification of individual fragment contributions to the initial supersystem wavefunction as determined by an energetic optimality criterion. The density deformations identified with individual fragments upon formation of the initial supersystem wavefunction are analyzed along with the distance dependence of the new and classical terms for test cases that include the neon dimer, ammonia borane, water-Na(+), water-Cl(-), and the naphthalene dimer. PMID:27004862

  17. Basis sets for the evaluation of van der Waals complex interaction energies: Ne-N2 intermolecular potential and microwave spectrum.

    Baranowska-Łączkowska, Angelika; Fernández, Berta

    2014-01-30

    In order to obtain efficient basis sets for the evaluation of van der Waals complex intermolecular potentials, we carry out systematic basis set studies. For this, interaction energies at representative geometries on the potential energy surfaces are evaluated using the CCSD(T) correlation method and large polarized LPol-n and augmented polarization-consistent aug-pc-2 basis sets extended with different sets of midbond functions. On the basis of the root mean square errors calculated with respect to the values for the most accurate potentials available, basis sets are selected for fitting the corresponding interaction energies and getting analytical potentials. In this work, we study the Ne-N2 van der Waals complex and after the above procedure, the aug-pc-2-3321 and the LPol-ds-33221 basis set results are fitted. The obtained potentials are characterized by T-shaped global minima at distances between the Ne atom and the N2 center of mass of 3.39 Å, with interaction energies of -49.36 cm(-1) for the aug-pc-2-3321 surface and -50.28 cm(-1) for the LPol-ds-33221 surface. Both sets of results are in excellent agreement with the reference surface. To check the potentials further microwave transition frequencies are calculated that agree well with the experimental and the aV5Z-33221 values. The success of this study suggests that it is feasible to carry out similar accurate calculations of interaction energies and ro-vibrational spectra at reduced cost for larger complexes than has been possible hitherto. PMID:24375320

  18. Covalent intermolecular interaction of the nitric oxide dimer (NO)2

    Zhang, Hui; Zheng, Gui-Li; Lv, Gang; Geng, Yi-Zhao; Ji, Qing

    2015-09-01

    Covalent bonds arise from the overlap of the electronic clouds in the internucleus region, which is a pure quantum effect and cannot be obtained in any classical way. If the intermolecular interaction is of covalent character, the result from direct applications of classical simulation methods to the molecular system would be questionable. Here, we analyze the special intermolecular interaction between two NO molecules based on quantum chemical calculation. This weak intermolecular interaction, which is of covalent character, is responsible for the formation of the NO dimer, (NO)2, in its most stable conformation, a cis conformation. The natural bond orbital (NBO) analysis gives an intuitive illustration of the formation of the dimer bonding and antibonding orbitals concomitant with the breaking of the π bonds with bond order 0.5 of the monomers. The dimer bonding is counteracted by partially filling the antibonding dimer orbital and the repulsion between those fully or nearly fully occupied nonbonding dimer orbitals that make the dimer binding rather weak. The direct molecular mechanics (MM) calculation with the UFF force fields predicts a trans conformation as the most stable state, which contradicts the result of quantum mechanics (QM). The lesson from the investigation of this special system is that for the case where intermolecular interaction is of covalent character, a specific modification of the force fields of the molecular simulation method is necessary. Project supported by the National Natural Science Foundation of China (Grant Nos. 90403007 and 10975044), the Key Subject Construction Project of Hebei Provincial Universities, China, the Research Project of Hebei Education Department, China (Grant Nos. Z2012067 and Z2011133), the National Natural Science Foundation of China (Grant No. 11147103), and the Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China (Grant No. Y5

  19. Abstracts of 6. International Conference on Intermolecular Interactions in Matter

    6. International Conference on Intermolecular Interactions in Matter is cyclically organised international forum for discussion of most important problems connected with solid state physics, material engineering and crystallography. Especially investigations of low dimensional systems as multilayers, thin films, nanocrystalline systems have been extensively presented and discussed. The methods of crystal growth as well as modern methods for crystal manufacturing process control and material properties investigations have been also performed in the course of the conference

  20. Cation-π interactions: accurate intermolecular potential from symmetry-adapted perturbation theory.

    Ansorg, Kay; Tafipolsky, Maxim; Engels, Bernd

    2013-09-01

    Symmetry-adapted perturbation theory (SAPT) is used to decompose the total intermolecular interaction energy between the ammonium cation and a benzene molecule into four physically motivated individual contributions: electrostatics, exchange, dispersion, and induction. Based on this rigorous decomposition, it is shown unambiguously that both the electrostatic and the induction energy components contribute almost equally to the attractive forces stabilizing the dimer with a nonnegligible contribution coming from the dispersion term. A polarizable potential model for the interaction of ammonium cation with benzene is parametrized by fitting these four energy components separately using the functional forms of the AMOEBA force field augmented with the missing charge penetration energy term calculated as a sum over pairwise electrostatic energies between spherical atoms. It is shown that the proposed model is able to produce accurate intermolecular interaction energies as compared to ab initio results, thus avoiding error compensation to a large extent. PMID:23924321

  1. Intermolecular Sulfur···Oxygen Interactions: Theoretical and Statistical Investigations.

    Zhang, Xuejin; Gong, Zhen; Li, Jian; Lu, Tao

    2015-10-26

    Intermolecular S···O interactions are very common and are important in biological systems, but until recently, the presence of these contacts in protein-ligand systems largely depended on serendipitous discovery instead of rational design. Here we provide insight into the phenomenon of intermolecular S···O contacts by focusing on three sulfur-containing aromatic rings. Quantum mechanics is employed to characterize the strength and directionality of the S···O interactions and to determine their energy dependence on their geometric parameters. Protein Data Bank mining is performed to systematically determine the occurrence and geometry of intermolecular S···O interactions, and several representative examples are discussed. Three typical cases are investigated using a combined quantum mechanics/molecular mechanics approach to demonstrate the potential of these interactions in improving binding affinities and physiochemical properties. Overall, our work elucidates the structures and energy features of intermolecular S···O interactions and addresses their use in molecular design. PMID:26393532

  2. Towards the biaxial nematic phase via specific intermolecular interactions

    Omnes, L

    2001-01-01

    The work described in this thesis has been focussed on the search of an elusive liquid crystal phase, known as the biaxial nematic phase. Indeed, despite nearly thirty years of intense research, no-one has been able to characterise unambiguously a biaxial nematic phase in a low-molar-mass thermotropic system. Our research is based on the concept of molecular biaxiality as distinct from shape biaxiality. Thus, we are seeking to design palladium complexes where specific intermolecular interactions could exist. Therefore, a few original synthetic strategies were developed to tackle the challenge of discovering the biaxial nematic phase

  3. A quantitative analysis of weak intermolecular interactions & quantum chemical calculations (DFT) of novel chalcone derivatives

    Chavda, Bhavin R.; Gandhi, Sahaj A.; Dubey, Rahul P.; Patel, Urmila H.; Barot, Vijay M.

    2016-05-01

    The novel chalcone derivatives have widespread applications in material science and medicinal industries. The density functional theory (DFT) is used to optimized the molecular structure of the three chalcone derivatives (M-I, II, III). The observed discrepancies between the theoretical and experimental (X-ray data) results attributed to different environments of the molecules, the experimental values are of the molecule in solid state there by subjected to the intermolecular forces, like non-bonded hydrogen bond interactions, where as isolated state in gas phase for theoretical studies. The lattice energy of all the molecules have been calculated using PIXELC module in Coulomb -London -Pauli (CLP) package and is partitioned into corresponding coulombic, polarization, dispersion and repulsion contributions. Lattice energy data confirm and strengthen the finding of the X-ray results that the weak but significant intermolecular interactions like C-H…O, Π- Π and C-H… Π plays an important role in the stabilization of crystal packing.

  4. Nanophotonic boost of intermolecular energy transfer

    de Roque, P M; Sapienza, R

    2015-01-01

    We propose a scheme for efficient long-range energy transfer between two distant light emitters separated by more than one wavelength of light, i.e. much beyond the classical Forster radius. A hybrid nanoantenna-waveguide system mediates the transmission of energy, showing enhancements up to 10^8 as compared to vacuum. Our model shows how energy transfer in nanostructured media can be boosted, beyond the simple donor Purcell enhancement, and in particular for large donor-acceptor separations. The scheme we propose connects realistic emitters and could lead to practical on-chip implementations.

  5. New bases for the evaluation of interaction energies: An ab initio study of the CO-Ne van der Waals complex intermolecular potential and ro-vibrational spectrum

    Graphical abstract: CO-Ne IPES. Highlights: → From the LPol, MLPol, and aug-pc-2 bases we obtained new bases for the evaluation of CO-Ne interaction energies. → We checked the bases on the evaluation of the rovibrational spectrum. → The results were satisfactory, being the new bases more efficient than those previously available. - Abstract: Recently we have derived new efficient basis sets for the evaluation of interaction energies in the X-Y (X, Y = He, Ne, Ar) van der Waals complexes. Here we extend the study to the CO-Ne complex. For this, we start with a systematic basis set study, where the LPol, MLPol and Jensen's aug-pc-2 basis sets are considered as starting point (for the Ne atom LPol bases are developed). As reference we take interaction energy results obtained with Dunning's augmented correlation consistent polarized valence basis sets. In all cases we test extensions with different sets of midbond functions. With the selected bases we evaluate CCSD(T) interaction potentials, and to check the potentials further, we obtain the ro-vibrational spectrum of the complex. The results are compared to the available experimental data.

  6. Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization

    Christensen, Anders S; Cui, Qiang

    2015-01-01

    Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculated at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O and S are presented. The RMSD interaction energy is improved from 6.07 kcal/mol to 1...

  7. Intermolecular interactions in rifabutin—2-hydroxypropyl-β-cyclodextrin—water solutions

    Anshakova, A. V.; Yermolenko, Yu. V.; Konyukhov, V. Yu.; Polshakov, V. I.; Maksimenko, O. O.; Gelperina, S. E.

    2015-05-01

    The possibility of a intermolecular complex rifabutin (RB)-2-hydroxypropyl-β-cyclodextrin (HP-β-CD) formed as a result of the interaction of the piperidine fragment of the RB molecule and the hydrophobic cavity of the HP-β-CD molecule was found. The stability constant of the intermolecular complex was determined.

  8. Correlated intermolecular interaction components from asymptotically corrected Kohn-Sham orbitals

    SONG; Huajie; XIAO; Heming; DONG; Haishan

    2004-01-01

    The symmetry-adapted perturbation theory (SAPT) that has the ability in decomposition of the total interaction energy into physically meaningful components is used to provide a more fundamental understanding of intermolecular forces. This work was motivated by the difficulty of standard SAPT in computing the intermolecular interactions for large energetic dimer systems. SAPT based on Kohn-Sham orbitals (SAPT(DFT)) proves computationally efficient for these large systems, but has been shown to perform poorly for interaction energy components. The deficiencies of SAPT(DFT) result from wrong asymptotical behaviors of commonly used exchange-correlation potentials. To remove the deficiencies, two asymptotic corrections by means of van Leeuwen and Baerends (LB) model potential and Fermi-Amaldi (FA) type potential were applied into three small test systems comprising He2, HF2 and (N2)2 and a set of larger nitramide dimers at several separations. The results showed that when utilizing newly developed frequency-dependent density susceptibilities (FDDS) technique for computing dispersion energy, the FA asymptotic correction is very effective to circumvent these deficiencies in SAPT(DFT) and yields a good accuracy over the LB correction. The FA corrected SAPT(DFT) approach is capable of correctly predicting all the quantitative trends in binding energies for all test cases and substantially reduces computational cost as compared with the standard SAPT calculations. The successful application of the approach to nitramide dimer demonstrates that it potentially provides a good means to calculate accurately intermolecular forces in larger system such as energetic systems.

  9. Squeezing water clusters between graphene sheets: energetics, structure, and intermolecular interactions.

    McKenzie, S; Kang, H C

    2014-12-21

    The behavior of water confined at the nanoscale between graphene sheets has attracted much theoretical and experimental attention recently. However, the interactions, structure, and energy of water at the molecular scale underpinning the behavior of confined water have not been characterized by first-principles calculations. In this work we consider small water clusters up to the hexamer adsorbed between graphene sheets using density functional theory calculations with van der Waals corrections. We investigate the effects on structure, energy, and intermolecular interactions due to confinement between graphene sheets. For interlayer distances of about one nanometer or more, the cluster adsorption energy increases approximately linearly with the cluster size by 0.1 eV per molecule in the cluster. As the interlayer distance decreases, the cluster adsorption energy reaches a maximum at 6 to 7 Å with approximately 0.16 eV stabilization energy relative to large interlayer distances. This suggests the possibility of controlling the amount of adsorption in graphene nanomaterials by varying the interlayer distance. We also quantify the intermolecular hydrogen bonding in the clusters by calculating the dissociation energy required to remove one molecule from each cluster. For each cluster size, this is constant for interlayer distances larger than approximately 6 to 8 Å. For smaller distances the intermolecular interaction decreases rapidly thus leading to weaker cohesion between molecules in a squeezed cluster. We expect a mechanism of concerted motion for hydrogen-bonded water molecules confined between graphene sheets, as has been observed for water confined within the carbon nanotubes. Thus, the decrease in the dissociation energy we observed here is consistent with experimental results for water transport through graphene and related membranes that are of interest in nanofiltration. We also calculate the corrugation in the interaction potential between graphene

  10. Theoretical Studies on the Intermolecular Interactions of Aza-calix[2]arene[2]-triazines with RDX

    LIU Yong-Mei; SHI Wen-Jing; ZHAO Shu-Sen; REN Fu-De; CAO Duan-Lin

    2011-01-01

    Six fully optimized structures of the aza-calix[2]arene[2]-triazines/RDX supramolecular complexes have been obtained at the DFT-B3LYP/6-311++G** level, and the corresponding intermolecular interactions have been investigated using the B3LYP, mPWPW91 and MP2 methods at the 6-311++G** level, respectively. The natural bond orbital (NBO) and atoms in molecules (AIM) analyses have been performed to reveal the origin of interactions. To our interest, the result indicates that the strongest interaction is up to -22.34 kJ/mol after basis set superposition error (BSSE) and zero point energy (ZPE) correction at the MP2/6-311++G** level. Furthermore, the intermolecular interactions between aza-calix[2]arene[2]-triazines with the substituted amidos and RDX are stronger than those of other complexes. Thus, the complexes with amidos can be used as the candidates to increase the stability of explosive and eliminate the explosive wastewater.

  11. Probing Intermolecular Interactions in Polycyclic Aromatic Hydrocarbons with 2D IR Spectroscopy

    Krummel, Amber

    2014-03-01

    Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the environment and impact geochemical processes that are critical to sustainable energy resources. For example, asphaltenes exist naturally in geologic formations and their aggregates heavily impact the petroleum economy. Unfortunately, the chemical dynamics that drive asphaltene nanoaggregation processes are still poorly understood. Solvent dynamics and intermolecular interactions such as π-stacking interactions play integral roles in asphaltene nanoaggregation. Linear and nonlinear vibrational spectroscopy including two-dimensional infrared spectroscopy (2DIR), are well suited to explore these fundamental interactions. Teasing apart the vibrational characteristics in PAHs that model asphaltenic compounds represents an important step towards utilizing 2D IR spectroscopy to understand the intermolecular interactions that are prevalent in asphaltene nanoaggregation. A solar dye, N,N'-Dioctyl-3,4,9,10-perylenedicarboximide, is used in this work to model aphaltenes. Carbonyl and ring vibrations are used to probe the nanoaggregates of the model compounds. However, the characteristics of these normal modes change as a function of the size of the conjugated ring system. Thus, in order to fully understand the nature of these normal modes, we include a systematic study of a series of quinones. Our investigation employs a combination of 2DIR spectroscopy and electronic structure calculations to explore vibrational coupling in quinones and PAHs. We compare the calculated vibrational characteristics to those extracted from 2DIR spectra. ATK acknowledges the Donors of the American Chemical Society Petroleum Research Fund for support of this research.

  12. Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization

    Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculated at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O, and S are presented. The Root Mean Square Deviation (RMSD) interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged species, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than Neglect of Diatomic Differential Overlap type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets

  13. Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization

    Christensen, Anders S., E-mail: andersx@chem.wisc.edu, E-mail: cui@chem.wisc.edu; Cui, Qiang, E-mail: andersx@chem.wisc.edu, E-mail: cui@chem.wisc.edu [Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706 (United States); Elstner, Marcus [Theoretische Chemische Biologie, Universität Karlsruhe, Kaiserstr. 12, 76131 Karlsruhe (Germany)

    2015-08-28

    Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculated at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O, and S are presented. The Root Mean Square Deviation (RMSD) interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged species, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than Neglect of Diatomic Differential Overlap type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets.

  14. Identification and measurement of intermolecular interaction in polyester/polystyrene blends by FTIR-photoacoustic spectrometry

    Fourier transform infrared photoacoustic spectrometry was used to reveal and identify n-p type intermolecular interaction formed in plastic comprising binary blends of polystyrene and a biodegradable polymer, either polylactic acid, polycaprolactone or poly(tetramethyleneadipate-co-terephthalate)....

  15. Intermolecular Interaction Potential Energy and Force%分子间的相互作用势能与分子力

    罗兴垅

    2012-01-01

    引入相对距离R、相对势能U与相对力F,导出了米势的相对势能U(R)及其相应的相对力F(R)与参数n、m的关系,并精确地绘制了伦纳德-琼斯势的相对势能U(R)曲线及其相应的相对力F(R)曲线和平衡位置附近的近似相对势能U(X)曲线、近似相对力F(X)曲线.%The paper introduces the relative distance,relative potential energy and relative power,derives the relative potential energy of Mie potential and its corresponding relative force and the relationships of parameter n and m,and accurately draws the relative potential energy curve of Leonard-Jones potential and its corresponding relative force curve and near the equilibrium position the approximate relative potential energy curve and the approximate relative force curve.

  16. Self-Assembly and Intermolecular Forces When Cellulose and Water Interact Using Molecular Modeling

    Ali Chami Khazraji

    2013-01-01

    Full Text Available Cellulose chains are linear and aggregation occurs via both intra- and intermolecular hydrogen bonds. Cellulose has a strong affinity to itself and toward materials containing hydroxyls groups. Based on the preponderance of hydroxyl functional groups, cellulose is very reactive with water. At room temperature, cellulose chains will have at least a monomolecular layer of water associated to it. The formation of hydrogen bonds at the cellulose/water interface is shown to depend essentially on the adsorption site, for example, the equatorial hydroxyls or OH moieties pointing outward from the cellulose chains. The vdW forces also contribute significantly to the adsorption energy. They are a considerable cohesive energy into the cellulose network. At the surface of the cellulose chains, many intermolecular hydrogen bonds of the cellulose chains are lost. However, they are compensated by hydrogen bonds with water molecules. Electronic clouds can be distorted and create electrostatic dipoles. The large antibonding electron cloud that exists around the glucosidic bonds produces an induced polarization at the approach of water molecules. The electron cloud can be distorted and create an electrostatic dipole. It applies to the total displacement of the atoms within the material. Orbitals play a special role in reaction mechanism. Hydrophilic/hydrophobic nature of cellulose is based on its structural anisotropy. Cellulose-water interactions are exothermic reactions. These interactions may occur spontaneously and result in higher randomness of the system. They are denoted by a negative heat flow (heat is lost to the surroundings. Energy does not need to be inputted in order for cellulose-water interactions to occur.

  17. Modulation of the intermolecular interaction of myoglobin by removal of the heme

    Imamura, Hiroshi; Morita, Takeshi [Chiba University, 1-33 Yayoi, Inage, Chiba 263-8522 (Japan); Sumi, Tomonari [Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530 (Japan); Isogai, Yasuhiro [Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398 (Japan); Kato, Minoru [Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577 (Japan); Nishikawa, Keiko, E-mail: k.nishikawa@faculty.chiba-u.jp [Chiba University, 1-33 Yayoi, Inage, Chiba 263-8522 (Japan)

    2013-11-01

    The present study analysed small-angle X-ray scattering profiles of myoglobin to examine how removal of the heme changes the intermolecular interaction. Toward understanding intermolecular interactions governing self-association of proteins, the present study investigated a model protein, myoglobin, using a small-angle X-ray scattering technique. It has been known that removal of the heme makes myoglobin aggregation-prone. The interparticle interferences of the holomyoglobin and the apomyoglobin were compared in terms of the structure factor. Analysis of the structure factor using a model potential of Derjaguin–Laudau–Verwey–Overbeek (DLVO) suggests that the intermolecular interaction potential of apomyoglobin is more attractive than that of holomyoglobin at short range from the protein molecule.

  18. Influence of Electrostatic and Intermolecular Interactions on the Solution Behavior and Electrospinning of Functional Nanofibers

    Hunley, Matthew T

    2010-01-01

    The solution rheological and electrospinning behavior of a series of charge-containing polymers, surface-active agents, and carbon nanotube composites was studied to investigate the effect of intermolecular interactions, including electrostatic interactions, hydrogen bonding, surface activity, and surface functionalization of carbon nanotubes. The synthesis of novel polyelectrolytes with varied topologies, charge content, and counterions tailored the charged macromolecules to elucidate struc...

  19. Characterization of intermolecular interaction between Cl2 and HX (X=F, Cl and Br: An ab initio, DFT, NBO and AIM study

    Morteza Vatanparast

    2014-10-01

    Full Text Available The character of the intermolecular interactions in Cl2-HX (X =F, Cl and Br complexes has been investigated by means of the second-order Möller–Plesset perturbation theory (MP2 and the density functional theory (DFT calculations. The results show that there are two types of lowest interaction potential equilibrium structures in the interactions between Cl2 and HX: X∙∙∙Cl type geometry and hydrogen-bonded geometry. The calculated interaction energies show that the X∙∙∙Cl type structures are more stable than the corresponding hydrogen-bonded structures. The nature of the intermolecular interactions has been also investigated by natural bond orbital (NBO and atoms in molecules (AIM. The AIM analysis reveals that both types of intermolecular interactions are “closed-shell” noncovalent interactions.

  20. Biaxial Dielectrophoresis Force Spectroscopy: A Stoichiometric Approach for Examining Intermolecular Weak Binding Interactions.

    Park, In Soo; Kwak, Tae Joon; Lee, Gyudo; Son, Myeonggu; Choi, Jeong Woo; Choi, Seungyeop; Nam, Kihwan; Lee, Sei-Young; Chang, Woo-Jin; Eom, Kilho; Yoon, Dae Sung; Lee, Sangyoup; Bashir, Rashid; Lee, Sang Woo

    2016-04-26

    The direct quantification of weak intermolecular binding interactions is very important for many applications in biology and medicine. Techniques that can be used to investigate such interactions under a controlled environment, while varying different parameters such as loading rate, pulling direction, rupture event measurements, and the use of different functionalized probes, are still lacking. Herein, we demonstrate a biaxial dielectrophoresis force spectroscopy (BDFS) method that can be used to investigate weak unbinding events in a high-throughput manner under controlled environments and by varying the pulling direction (i.e., transverse and/or vertical axes) as well as the loading rate. With the BDFS system, we can quantitatively analyze binding interactions related to hydrogen bonding or ionic attractions between functionalized microbeads and a surface within a microfluidic device. Our BDFS system allowed for the characterization of the number of bonds involved in an interaction, bond affinity, kinetic rates, and energy barrier heights and widths from different regimes of the energy landscape. PMID:27007455

  1. Similarity-transformed perturbation theory on top of truncated local coupled cluster solutions: Theory and applications to intermolecular interactions.

    Azar, Richard Julian; Head-Gordon, Martin

    2015-05-28

    Your correspondents develop and apply fully nonorthogonal, local-reference perturbation theories describing non-covalent interactions. Our formulations are based on a Löwdin partitioning of the similarity-transformed Hamiltonian into a zeroth-order intramonomer piece (taking local CCSD solutions as its zeroth-order eigenfunction) plus a first-order piece coupling the fragments. If considerations are limited to a single molecule, the proposed intermolecular similarity-transformed perturbation theory represents a frozen-orbital variant of the "(2)"-type theories shown to be competitive with CCSD(T) and of similar cost if all terms are retained. Different restrictions on the zeroth- and first-order amplitudes are explored in the context of large-computation tractability and elucidation of non-local effects in the space of singles and doubles. To accurately approximate CCSD intermolecular interaction energies, a quadratically growing number of variables must be included at zeroth-order. PMID:26026428

  2. Similarity-transformed perturbation theory on top of truncated local coupled cluster solutions: Theory and applications to intermolecular interactions

    Your correspondents develop and apply fully nonorthogonal, local-reference perturbation theories describing non-covalent interactions. Our formulations are based on a Löwdin partitioning of the similarity-transformed Hamiltonian into a zeroth-order intramonomer piece (taking local CCSD solutions as its zeroth-order eigenfunction) plus a first-order piece coupling the fragments. If considerations are limited to a single molecule, the proposed intermolecular similarity-transformed perturbation theory represents a frozen-orbital variant of the “(2)”-type theories shown to be competitive with CCSD(T) and of similar cost if all terms are retained. Different restrictions on the zeroth- and first-order amplitudes are explored in the context of large-computation tractability and elucidation of non-local effects in the space of singles and doubles. To accurately approximate CCSD intermolecular interaction energies, a quadratically growing number of variables must be included at zeroth-order

  3. Liquid chloroform structure from computer simulation with a full ab initio intermolecular interaction potential

    We have calculated the intermolecular interaction energies of the chloroform dimer in 12 orientations using the second-order Møller-Plesset perturbation theory. Single point energies of important geometries were calibrated by the coupled cluster with single and double and perturbative triple excitation method. Dunning's correlation consistent basis sets up to aug-cc-pVQZ have been employed in extrapolating the interaction energies to the complete basis set limit values. With the ab initio potential data we constructed a 5-site force field model for molecular dynamics simulations. We compared the simulation results with recent experiments and obtained quantitative agreements for the detailed atomwise radial distribution functions. Our results were also consistent with previous results using empirical force fields with polarization effects. Moreover, the calculated diffusion coefficients reproduced the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with existing empirical force fields for liquid chloroform

  4. Ab initio intermolecular potential energy surface and thermophysical properties of nitrous oxide

    Crusius, Johann-Philipp, E-mail: johann-philipp.crusius@uni-rostock.de; Hassel, Egon [Lehrstuhl für Technische Thermodynamik, Universität Rostock, 18059 Rostock (Germany); Hellmann, Robert, E-mail: robert.hellmann@uni-rostock.de; Bich, Eckard [Institut für Chemie, Universität Rostock, 18059 Rostock (Germany)

    2015-06-28

    We present an analytical intermolecular potential energy surface (PES) for two rigid nitrous oxide (N{sub 2}O) molecules derived from high-level quantum-chemical ab initio calculations. Interaction energies for 2018 N{sub 2}O–N{sub 2}O configurations were computed utilizing the counterpoise-corrected supermolecular approach at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. A site-site potential function with seven sites per N{sub 2}O molecule was fitted to the pair interaction energies. We validated our PES by computing the second virial coefficient as well as shear viscosity and thermal conductivity in the dilute-gas limit. The values of these properties are substantiated by the best experimental data.

  5. Ab initio intermolecular potential energy surface and thermophysical properties of nitrous oxide.

    Crusius, Johann-Philipp; Hellmann, Robert; Hassel, Egon; Bich, Eckard

    2015-06-28

    We present an analytical intermolecular potential energy surface (PES) for two rigid nitrous oxide (N2O) molecules derived from high-level quantum-chemical ab initio calculations. Interaction energies for 2018 N2O-N2O configurations were computed utilizing the counterpoise-corrected supermolecular approach at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. A site-site potential function with seven sites per N2O molecule was fitted to the pair interaction energies. We validated our PES by computing the second virial coefficient as well as shear viscosity and thermal conductivity in the dilute-gas limit. The values of these properties are substantiated by the best experimental data. PMID:26133428

  6. Ab initio intermolecular potential energy surface and thermophysical properties of nitrous oxide

    We present an analytical intermolecular potential energy surface (PES) for two rigid nitrous oxide (N2O) molecules derived from high-level quantum-chemical ab initio calculations. Interaction energies for 2018 N2O–N2O configurations were computed utilizing the counterpoise-corrected supermolecular approach at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. A site-site potential function with seven sites per N2O molecule was fitted to the pair interaction energies. We validated our PES by computing the second virial coefficient as well as shear viscosity and thermal conductivity in the dilute-gas limit. The values of these properties are substantiated by the best experimental data

  7. Intermolecular interactions governing the partition between particulate and gas phases for typical organic pollutants

    YU HaiYing; QIAO XianLiang; YANG Ping; DING GuangHui; CHEN JingWen

    2007-01-01

    The partition coefficients between particulate and gas phases (Kp) for organic pollutants are of great importance to characterize the behavior of organic pollutants in atmosphere, and are basic data needed by ecological risk assessment. Partial least squares (PLS) regression with 16 theoretical molecular structural descriptors was used to develop polyparameter linear free energy relationship (LFER) model for Kp of 18 aliphatic hydrocarbons, 21 polycyclic aromatic hydrocarbons (PAHs), 16 polychlorinated biphenyls (PCBs) and 13 polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs). The obtained model has a good predictive ability and robustness, which can be used for estimating Kp of chemicals with similar structures. Intermolecular dispersive interactions play a leading role in governing Kp, followed by charge-transfer interactions and hindrance effects of molecular size. The respective models developed for different group compounds imply that the action mechanism is similar, and dipole-dipole and dipole-induced dipole interactions play a minor role in governing Kp of n-alkanes, PCBs and PCDD/Fs.

  8. Evidence for a noncovalent intermolecular interaction of opiates with thiamine.

    Misra, A L; Vadlamani, N L; Pontani, R B

    1977-11-01

    Opiate agonists and antagonists formed reversible molecular complexes with thiamine. The absorption maxima of these complexes were at wavelengths longer than those of the individual components and their intensities depended on the concentration and nature of the opiate component. The possible implications of such an interaction are discussed. PMID:928957

  9. Polarization contributions to intermolecular interactions revisited with fragment electric-field response functions

    Horn, Paul R., E-mail: prhorn@berkeley.edu, E-mail: mhg@cchem.berkeley.edu; Head-Gordon, Martin, E-mail: prhorn@berkeley.edu, E-mail: mhg@cchem.berkeley.edu [Department of Chemistry, Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, USA and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    2015-09-21

    The polarization energy in intermolecular interactions treated by self-consistent field electronic structure theory is often evaluated using a constraint that the atomic orbital (AO) to molecular orbital transformation is blocked by fragments. This approach is tied to AO basis sets, overestimates polarization energies in the overlapping regime, particularly in large AO basis sets, and lacks a useful complete basis set limit. These problems are addressed by the construction of polarization subspaces based on the responses of isolated fragments to weak electric fields. These subspaces are spanned by fragment electric-field response functions, which can capture effects up to the dipole (D), or quadrupole (DQ) level, or beyond. Schemes are presented for the creation of both non-orthogonal and orthogonal fragment subspaces, and the basis set convergence of the polarization energies computed using these spaces is assessed. Numerical calculations for the water dimer, water–Na{sup +}, water–Mg{sup 2+}, water–F{sup −}, and water–Cl{sup −} show that the non-orthogonal DQ model is very satisfactory, with small differences relative to the orthogonalized model. Additionally, we prove a fundamental difference between the polarization degrees of freedom in the fragment-blocked approaches and in constrained density schemes. Only the former are capable of properly prohibiting charge delocalization during polarization.

  10. Polarization contributions to intermolecular interactions revisited with fragment electric-field response functions.

    Horn, Paul R; Head-Gordon, Martin

    2015-09-21

    The polarization energy in intermolecular interactions treated by self-consistent field electronic structure theory is often evaluated using a constraint that the atomic orbital (AO) to molecular orbital transformation is blocked by fragments. This approach is tied to AO basis sets, overestimates polarization energies in the overlapping regime, particularly in large AO basis sets, and lacks a useful complete basis set limit. These problems are addressed by the construction of polarization subspaces based on the responses of isolated fragments to weak electric fields. These subspaces are spanned by fragment electric-field response functions, which can capture effects up to the dipole (D), or quadrupole (DQ) level, or beyond. Schemes are presented for the creation of both non-orthogonal and orthogonal fragment subspaces, and the basis set convergence of the polarization energies computed using these spaces is assessed. Numerical calculations for the water dimer, water-Na(+), water-Mg(2+), water-F(-), and water-Cl(-) show that the non-orthogonal DQ model is very satisfactory, with small differences relative to the orthogonalized model. Additionally, we prove a fundamental difference between the polarization degrees of freedom in the fragment-blocked approaches and in constrained density schemes. Only the former are capable of properly prohibiting charge delocalization during polarization. PMID:26395691

  11. Polarization contributions to intermolecular interactions revisited with fragment electric-field response functions

    The polarization energy in intermolecular interactions treated by self-consistent field electronic structure theory is often evaluated using a constraint that the atomic orbital (AO) to molecular orbital transformation is blocked by fragments. This approach is tied to AO basis sets, overestimates polarization energies in the overlapping regime, particularly in large AO basis sets, and lacks a useful complete basis set limit. These problems are addressed by the construction of polarization subspaces based on the responses of isolated fragments to weak electric fields. These subspaces are spanned by fragment electric-field response functions, which can capture effects up to the dipole (D), or quadrupole (DQ) level, or beyond. Schemes are presented for the creation of both non-orthogonal and orthogonal fragment subspaces, and the basis set convergence of the polarization energies computed using these spaces is assessed. Numerical calculations for the water dimer, water–Na+, water–Mg2+, water–F−, and water–Cl− show that the non-orthogonal DQ model is very satisfactory, with small differences relative to the orthogonalized model. Additionally, we prove a fundamental difference between the polarization degrees of freedom in the fragment-blocked approaches and in constrained density schemes. Only the former are capable of properly prohibiting charge delocalization during polarization

  12. Ab initio investigation of intermolecular interactions in solid benzene

    Bludský, Ota; Rubeš, Miroslav

    2008-01-01

    Roč. 77, - (2008), 092103/1-092103/4. ISSN 1098-0121 R&D Projects: GA MŠk LC512; GA AV ČR IAA400550613 Institutional research plan: CEZ:AV0Z40550506 Keywords : augmented-wawe method * rare-gas solids * energies Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.322, year: 2008

  13. Intermolecular interactions in the bilirubin-cholate-silica system

    Vlasova, N. N.; Golovkova, L. P.; Severinovskaya, O. V.

    2007-06-01

    Bilirubin-cholate interactions in aqueous solutions were studied. The constants of binding of bilirubin with taurocholate dimers and taurodeoxycholate trimers were calculated. The adsorption of bilirubin and cholates on the surface of highly dispersed silica was studied. It was shown that taurine-conjugated cholates are poorly adsorbed from micellar solutions on the silica surface, the specific amount of bilirubin adsorbed decreases with increasing concentration of cholates in the solution, the affinity of free bilirubin for the silica surface is independent of the nature of the cholic acid, and that the affinity of cholate-bilirubin complexes for the silica surface is lower than the affinity of free bilirubin.

  14. Atom depth analysis delineates mechanisms of protein intermolecular interactions

    Alocci, Davide, E-mail: alodavide@gmail.com [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy); Bernini, Andrea, E-mail: andrea.bernini@unisi.it [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy); Niccolai, Neri, E-mail: neri.niccolai@unisi.it [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy); SienaBioGrafix Srl, via A. Fiorentina 1, 53100 Siena (Italy)

    2013-07-12

    Highlights: •3D atom depth analysis is proposed to identify different layers in protein structures. •Amino acid contents for each layers have been analyzed for a large protein dataset. •Charged amino acids in the most external layer are present at very different extents. •Atom depth indexes of K residues reflect their side chains flexibility. •Mobile surface charges can be responsible for long range protein–protein recognition. -- Abstract: The systematic analysis of amino acid distribution, performed inside a large set of resolved protein structures, sheds light on possible mechanisms driving non random protein–protein approaches. Protein Data Bank entries have been selected using as filters a series of restrictions ensuring that the shape of protein surface is not modified by interactions with large or small ligands. 3D atom depth has been evaluated for all the atoms of the 2,410 selected structures. The amino acid relative population in each of the structural layers formed by grouping atoms on the basis of their calculated depths, has been evaluated. We have identified seven structural layers, the inner ones reproducing the core of proteins and the outer one incorporating their most protruding moieties. Quantitative analysis of amino acid contents of structural layers identified, as expected, different behaviors. Atoms of Q, R, K, N, D residues are increasingly more abundant in going from core to surfaces. An opposite trend is observed for V, I, L, A, C, and G. An intermediate behavior is exhibited by P, S, T, M, W, H, F and Y. The outer structural layer hosts predominantly E and K residues whose charged moieties, protruding from outer regions of the protein surface, reorient free from steric hindrances, determining specific electrodynamics maps. This feature may represent a protein signature for long distance effects, driving the formation of encounter complexes and the eventual short distance approaches that are required for protein

  15. Benchmark Calculations of Three-Body Intermolecular Interactions and the Performance of Low-Cost Electronic Structure Methods.

    Řezáč, Jan; Huang, Yuanhang; Hobza, Pavel; Beran, Gregory J O

    2015-07-14

    Many-body noncovalent interactions are increasingly important in large and/or condensed-phase systems, but the current understanding of how well various models predict these interactions is limited. Here, benchmark complete-basis set coupled cluster singles, doubles, and perturbative triples (CCSD(T)) calculations have been performed to generate a new test set for three-body intermolecular interactions. This "3B-69" benchmark set includes three-body interaction energies for 69 total trimer structures, consisting of three structures from each of 23 different molecular crystals. By including structures that exhibit a variety of intermolecular interactions and packing arrangements, this set provides a stringent test for the ability of electronic structure methods to describe the correct physics involved in the interactions. Both MP2.5 (the average of second- and third-order Møller-Plesset perturbation theory) and spin-component-scaled CCSD for noncovalent interactions (SCS-MI-CCSD) perform well. MP2 handles the polarization aspects reasonably well, but it omits three-body dispersion. In contrast, many widely used density functionals corrected with three-body D3 dispersion correction perform comparatively poorly. The primary difficulty stems from the treatment of exchange and polarization in the functionals rather than from the dispersion correction, though the three-body dispersion may also be moderately underestimated by the D3 correction. PMID:26575743

  16. Redetermined structure, intermolecular interactions and absolute configuration of royleanone

    Hoong-Kun Fun

    2011-05-01

    Full Text Available The structure of the title diterpenoid, C20H28O3, {systematic name: (4bS,8aS-3-hydroxy-2-isopropyl-4b,8,8-trimethyl-4b,5,6,7,8,8a,9,10-octahydrophenanthrene-1,4-dione} is confirmed [Eugster et al. (1993. Private communication (refcode HACGUN. CCDC, Union Road, Cambridge] and its packing is now described. Its absolute structure was established by refinement against data collected with Cu radiation: the two stereogenic centres both have S configurations. One cyclohexane ring adopts a chair conformation whereas the other cyclohexane ring is in a half-chair conformation and the benzoquinone ring is slightly twisted. An intramolecular O—H...O hydrogen bond generates an S(5 ring motif. In the crystal, molecules are linked into chains along [010] by O—H...O hydrogen bonds and weak C—H...O interactions. The packing also features C...O [3.131 (3 Å] short contacts.

  17. Study of intermolecular interactions in binary mixtures of ethanol in methanol

    Maharolkar, Aruna P.; Khirade, P. W.; Murugkar, A. G.

    2016-05-01

    Present paper deals with study of physicochemical properties like viscosity, density and refractive index for the binary mixtures of ethanol and methanol over the entire concentration range were measured at 298.15 K. The experimental data further used to determine the excess properties viz. excess molar volume, excess viscosity, excess molar refraction. The values of excess properties further fitted with Redlich-Kister (R-K Fit) equation to calculate the binary coefficients and standard deviation. The resulting excess parameters are used to indicate the presence of intermolecular interactions and strength of intermolecular interactions between the molecules in the binary mixtures. Excess parameters indicate structure making factor in the mixture predominates in the system.

  18. Intermolecular interactions between imidazole derivatives intercalated in layered solids. Substituent group effect

    González, M.; Lemus-Santana, A.A. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico); Rodríguez-Hernández, J. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico); Instituto de Ciencia y Tecnología de Materiales, Universidad de La Habana, Havana (Cuba); Aguirre-Velez, C.I. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico); Knobel, M. [Institute of Physics “Gleb Wataghin”, UNICAMP, 13083-970 Campinas, SP (Brazil); Reguera, E., E-mail: edilso.reguera@gmail.com [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico)

    2013-08-15

    This study sheds light on the intermolecular interactions between imidazole derive molecules (2-methyl-imidazole, 2-ethyl-imidazole and benzimidazole) intercalated in T[Ni(CN){sub 4}] layers to form a solid of formula unit T(ImD){sub 2}[Ni(CN){sub 4}]. These hybrid inorganic–organic solids were prepared by soft chemical routes and their crystal structures solved and refined from X-ray powder diffraction data. The involved imidazole derivative molecules were found coordinated through the pyridinic N atom to the axial positions for the metal T in the T[Ni(CN){sub 4}] layer. In the interlayers region ligand molecules from neighboring layers remain stacked in a face-to-face configuration through dipole–dipole and quadrupole–quadrupole interactions. These intermolecular interactions show a pronounced dependence on the substituent group and are responsible for an ImD-pillaring concatenation of adjacent layers. This is supported by the structural information and the recorded magnetic data in the 2–300 K temperature range. The samples containing Co and Ni are characterized by presence of spin–orbit coupling and pronounced temperature dependence for the effective magnetic moment except for 2-ethyl-imidazole related to the local distortion for the metal coordination environment. For this last one ligand a weak ferromagnetic ordering ascribed to a super-exchange interaction between T metals from neighboring layers through the ligands π–π interaction was detected. - Graphical abstract: In the interlayers region imidazole derivative molecules are oriented according to their dipolar and quadrupolar interactions and minimizing the steric impediment. Highlights: • Imidazole derivatives intercalation compounds. • Intermolecular interaction between intercalated imidazole derivatives. • Hybrid inorganic–organic solids. • Pi–pi interactions and ferromagnetic coupling. • Dipolar and quadrupolar interactions between intercalated imidazole derivatives.

  19. Intermolecular interactions between imidazole derivatives intercalated in layered solids. Substituent group effect

    This study sheds light on the intermolecular interactions between imidazole derive molecules (2-methyl-imidazole, 2-ethyl-imidazole and benzimidazole) intercalated in T[Ni(CN)4] layers to form a solid of formula unit T(ImD)2[Ni(CN)4]. These hybrid inorganic–organic solids were prepared by soft chemical routes and their crystal structures solved and refined from X-ray powder diffraction data. The involved imidazole derivative molecules were found coordinated through the pyridinic N atom to the axial positions for the metal T in the T[Ni(CN)4] layer. In the interlayers region ligand molecules from neighboring layers remain stacked in a face-to-face configuration through dipole–dipole and quadrupole–quadrupole interactions. These intermolecular interactions show a pronounced dependence on the substituent group and are responsible for an ImD-pillaring concatenation of adjacent layers. This is supported by the structural information and the recorded magnetic data in the 2–300 K temperature range. The samples containing Co and Ni are characterized by presence of spin–orbit coupling and pronounced temperature dependence for the effective magnetic moment except for 2-ethyl-imidazole related to the local distortion for the metal coordination environment. For this last one ligand a weak ferromagnetic ordering ascribed to a super-exchange interaction between T metals from neighboring layers through the ligands π–π interaction was detected. - Graphical abstract: In the interlayers region imidazole derivative molecules are oriented according to their dipolar and quadrupolar interactions and minimizing the steric impediment. Highlights: • Imidazole derivatives intercalation compounds. • Intermolecular interaction between intercalated imidazole derivatives. • Hybrid inorganic–organic solids. • Pi–pi interactions and ferromagnetic coupling. • Dipolar and quadrupolar interactions between intercalated imidazole derivatives

  20. Intermolecular interactions in mixtures of ethyl formate with methanol, ethanol, and 1-propanol on density, viscosity, and ultrasonic data

    Elangovan, S.; Mullainathan, S.

    2014-12-01

    Density (ρ), viscosity (η), and ultrasonic velocity ( U) have been measured for binary mixtures of ethyl formate with methanol, ethanol, and 1-propanol at 303 K. From the experimental data, adiabatic compressibility (β), acoustic impedance ( Z), viscous relaxation time (τ), free length ( L f), free volume ( V f), internal pressure (πi), and Gibbs free energy (Δ G) have been deduced. It is shown that strength of intermolecular interactions between ethyl formate with selected 1-alcohols were in the order of methanol < ethanol < 1-propanol.

  1. Intermolecular potential energy surface and thermophysical properties of ethylene oxide.

    Crusius, Johann-Philipp; Hellmann, Robert; Hassel, Egon; Bich, Eckard

    2014-10-28

    A six-dimensional potential energy hypersurface (PES) for two interacting rigid ethylene oxide (C2H4O) molecules was determined from high-level quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the MP2 and CCSD(T) levels of theory was utilized to determine interaction energies for 10178 configurations of two molecules. An analytical site-site potential function with 19 sites per ethylene oxide molecule was fitted to the interaction energies and fine tuned to agree with data for the second acoustic virial coefficient from accurate speed of sound measurements. The PES was validated by computing the second virial coefficient, shear viscosity, and thermal conductivity. The values of these properties are substantiated by the best experimental data as they tend to fall within the uncertainty intervals and also obey the experimental temperature functions, except for viscosity, where experimental data are insufficient. Due to the lack of reliable data, especially for the transport properties, our calculated values are currently the most accurate estimates for these properties of ethylene oxide. PMID:25362314

  2. Intermolecular potential energy surface and thermophysical properties of ethylene oxide

    Crusius, Johann-Philipp, E-mail: johann-philipp.crusius@uni-rostock.de; Hassel, Egon [Lehrstuhl für Technische Thermodynamik, Universität Rostock, 18059 Rostock (Germany); Hellmann, Robert; Bich, Eckard [Institut für Chemie, Universität Rostock, 18059 Rostock (Germany)

    2014-10-28

    A six-dimensional potential energy hypersurface (PES) for two interacting rigid ethylene oxide (C{sub 2}H{sub 4}O) molecules was determined from high-level quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the MP2 and CCSD(T) levels of theory was utilized to determine interaction energies for 10178 configurations of two molecules. An analytical site-site potential function with 19 sites per ethylene oxide molecule was fitted to the interaction energies and fine tuned to agree with data for the second acoustic virial coefficient from accurate speed of sound measurements. The PES was validated by computing the second virial coefficient, shear viscosity, and thermal conductivity. The values of these properties are substantiated by the best experimental data as they tend to fall within the uncertainty intervals and also obey the experimental temperature functions, except for viscosity, where experimental data are insufficient. Due to the lack of reliable data, especially for the transport properties, our calculated values are currently the most accurate estimates for these properties of ethylene oxide.

  3. Physical nature of intermolecular interactions inside Sir2 homolog active site: molecular dynamics and ab initio study.

    Czeleń, Przemysław; Czyżnikowska, Żaneta

    2016-06-01

    In the present study, we analyze the interactions of NAD+-dependent deacetylase (Sir2 homolog yeast Hst2) with carba-nicotinamide-adenine-dinucleotide (ADP-HPD). For the Sir2 homolog, a yeast Hst2 docking procedure was applied. The structure of the protein-ADP-HPD complex obtained during the docking procedure was used as a starting point for molecular dynamics simulation. The intermolecular interaction energy partitioning was performed for protein-ADP-HPD complex resulting from molecular dynamics simulation. The analysis was performed for ADP-HPD and 15 amino acids forming a deacetylase binding pocket. Although the results indicate that the first-order electrostatic interaction energy is substantial, the presence of multiple hydrogen bonds in investigated complexes can lead to significant value of induction component. PMID:27154340

  4. An isotopic mass effect on the intermolecular potential

    Herman, Michael F.; Currier, Robert P.; Clegg, Samuel M.

    2015-10-01

    The impact of isotopic variation on the electronic energy and intermolecular potentials is often suppressed when calculating isotopologue thermodynamics. Intramolecular potential energy surfaces for distinct isotopologues are in fact equivalent under the Born-Oppenheimer approximation, which is sometimes used to imply that the intermolecular interactions are independent of isotopic mass. In this communication, the intermolecular dipole-dipole interaction between hetero-nuclear diatomic molecules is considered. It is shown that the intermolecular potential contains mass-dependent terms even though each nucleus moves on a Born-Oppenheimer surface. The analysis suggests that mass dependent variations in intermolecular potentials should be included in comprehensive descriptions of isotopologue thermodynamics.

  5. Intermolecular interactions in solid-state metalloporphyrins and their impacts on crystal and molecular structures.

    Hunter, Seth C; Smith, Brenda A; Hoffmann, Christina M; Wang, Xiaoping; Chen, Yu-Sheng; McIntyre, Garry J; Xue, Zi-Ling

    2014-11-01

    A variable-temperature (VT) crystal structure study of [Fe(TPP)Cl] (TPP(2-) = meso-tetraphenylporphyrinate) and Hirshfeld surface analyses of its structures and previously reported structures of [M(TPP)(NO)] (M = Fe, Co) reveal that intermolecular interactions are a significant factor in structure disorder in the three metalloporphyrins and phase changes in the nitrosyl complexes. These interactions cause, for example, an 8-fold disorder in the crystal structures of [M(TPP)(NO)] at room temperature that obscures the M-NO binding. Hirshfeld analyses of the structure of [Co(TPP)(NO)] indicate that the phase change from I4/m to P1 leads to an increase in void-volume percentage, permitting additional structural compression through tilting of the phenyl rings to offset the close-packing interactions at the interlayer positions in the crystal structures with temperature decrease. X-ray and neutron structure studies of [Fe(TPP)Cl] at 293, 143, and 20 K reveal a tilting of the phenyl groups away from being perpendicular to the porphyrin ring as a result of intermolecular interactions. Structural similarities and differences among the three complexes are identified and described by Hirshfeld surface and void-volume calculations. PMID:25338536

  6. Vibrational Circular Dichroism (VCD) Reveals Subtle Conformational Aspects and Intermolecular Interactions in the Carnitine Family.

    Mazzeo, Giuseppe; Abbate, Sergio; Longhi, Giovanna; Castiglioni, Ettore; Villani, Claudio

    2015-12-01

    Vibrational circular dichroism spectra (VCD) in the mid-IR region and electronic circular dichroism (ECD) spectra for three carnitine derivatives in the form of hydrochloride salts were recorded in deuterated methanol solutions. Density Functional Theory calculations help one to understand the significance of the observed VCD bands. VCD and ECD spectra are informative about the absolute configuration of the molecule, but VCD data reveal also some conformational aspects in the N,N,N-trimethyl moiety and inform us about intermolecular interactions gained from the carbonyl stretching region for the acyl substituted carnitines. PMID:26447810

  7. Intermolecular interactions in methyl formate-ethanol mixtures at 303-313 K according to ultrasonic data

    Elangovan, S.; Mullainathan, S.

    2014-04-01

    Density (ρ), viscosity (η), and ultrasonic velocity ( U) have been measured for a binary mixture composed of methyl formate and ethanol at 303, 308, and 313 K. The adiabatic compressibility (β), acoustic impedance (Z), free length ( L f ), free volume ( V f ), internal pressure (π i ), viscous relaxation time (τ), and Gibbs free energy (Δ G) were calculated from the experimental data. The excess values of these parameters (β E , Z E , L {/f E }, V {/f E }, π {/i E }, τ E , and Δ G E ) have also been calculated using the determined parameters and interpreted in terms of molecular interactions. The deviations in the sign and values of these excess parameters from the ideal mixing reveal the nature of intermolecular interactions between components of the mixture.

  8. Interfacial and intermolecular interactions determining the rotational orientation of C60 adsorbed on Au(111)

    Paßens, Michael; Karthäuser, Silvia

    2015-12-01

    Close-packed monolayers of fullerenes on metallic substrates are very rich systems with respect to their rotational degrees of freedom and possible interactions with different adsorption sites or next neighbours. In this connection, we report in detail on the (2√3 × 2√3)R30°-superstructure of C60 with respect to the Au(111)-surface. We use molecular orbital imaging in systematic UHV-STM studies to reveal the delicate balance of interfacial and intermolecular interactions in this system. Thus, bright C60-molecules in 5:6-top and 6:6-top geometries are observed depending on the respective next neighbours. Moreover, tiny changes in the appearance of the unoccupied molecular orbitals of dim C60-molecules in hex-vac positions are identified which are caused by the respective interaction with the facets surrounding the Au-vacancy.

  9. Intermolecular interactions during complex coacervation of pea protein isolate and gum arabic.

    Liu, Shuanghui; Cao, Yuan-Long; Ghosh, Supratim; Rousseau, Dérick; Low, Nicholas H; Nickerson, Michael T

    2010-01-13

    The nature of intermolecular interactions during complexation between pea protein isolate (PPI) and gum arabic (GA) was investigated as a function of pH (4.30-2.40) by turbidimetric analysis and confocal scanning microscopy in the presence of destabilizing agents (100 mM NaCl or 100 mM urea) and at different temperatures (6-60 degrees C). Complex formation followed two pH-dependent structure-forming events associated with the formation of soluble and insoluble complexes and involved interactions between GA and PPI aggregates. Complex formation was driven by electrostatic attractive forces between complementary charged biopolymers, with secondary stabilization by hydrogen bonding. Hydrophobic interactions were found to enhance complex stability at lower pH (pH 3.10), but not with its formation. PMID:19938857

  10. Permutationally invariant fitting of intermolecular potential energy surfaces: A case study of the Ne-C2H2 system

    Li, Jun; Guo, Hua

    2015-12-01

    The permutation invariant polynomial-neural network (PIP-NN) approach is extended to fit intermolecular potential energy surfaces (PESs). Specifically, three PESs were constructed for the Ne-C2H2 system. PES1 is a full nine-dimensional PIP-NN PES directly fitted to ˜42 000 ab initio points calculated at the level of CCSD(T)-F12a/cc-pCVTZ-F12, while the other two consist of the six-dimensional PES for C2H2 [H. Han, A. Li, and H. Guo, J. Chem. Phys. 141, 244312 (2014)] and an intermolecular PES represented in either the PIP (PES2) or PIP-NN (PES3) form. The comparison of fitting errors and their distributions, one-dimensional cuts and two-dimensional contour plots of the PESs, as well as classical trajectory collisional energy transfer dynamics calculations shows that the three PESs are very similar. We conclude that full-dimensional PESs for non-covalent interacting molecular systems can be constructed efficiently and accurately by the PIP-NN approach for both the constituent molecules and intermolecular parts.

  11. Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: An ab initio study

    Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D., E-mail: sdchao@spring.iam.ntu.edu.tw [Institute of Applied Mechanics, National Taiwan University, Taipei 106, Taiwan (China)

    2014-10-07

    We perform an ab initio computational study of molecular complexes with the general formula CF{sub 3}X—B that involve one trifluorohalomethane CF{sub 3}X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH{sub 3} and PH{sub 3}), two n-pairs (H{sub 2}O and H{sub 2}S), two n-pairs with an unsaturated bond (H{sub 2}CO and H{sub 2}CS), and a single π-pair (C{sub 2}H{sub 4}) and two π-pairs (C{sub 2}H{sub 2}). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C–X bond lengths shorten, while the C–X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.

  12. Gold behaves as hydrogen in the intermolecular self-interaction of metal aurides MAu4 (M = Ti, Zr, and Hf).

    Jung, Jaehoon; Kim, Hyemi; Kim, Jong Chan; Park, Min Hee; Han, Young-Kyu

    2011-03-01

    We performed density functional calculations to examine the intermolecular self-interaction of metal tetraauride MAu(4) (M = Ti, Zr, and Hf) clusters. We found that the metal auride clusters have strong dimeric interactions (2.8-3.1 eV) and are similar to the metal hydride analogues with respect to structure and bonding nature. Similarly to (MH(4))(2), the (μ-Au)(3) C(s) structures with three three-center two-electron (3c-2e) bonds were found to be the most stable. Natural orbital analysis showed that greater than 96 % of the Au 6s orbital contributes to the 3c-2e bonds, and this predominant s orbital is responsible for the similarity between metal aurides and metal hydrides (>99 % H 1s). The favorable orbital interaction between occupied Au 6s and unoccupied metal d orbitals leads to a stronger dimeric interaction for MAu(4)-MAu(4) than the interaction for MH(4)-MH(4). There is a strong relationship between the dimeric interaction energy and the chemical hardness of its monomer for (MAu(4))(2) and (MH(4))(2). PMID:21225974

  13. Crystal structures and intermolecular interactions of two novel antioxidant triazolyl-benzimidazole compounds

    Karayel, A.; Özbey, S.; Ayhan-Kılcıgil, G.; Kuş, C.

    2015-12-01

    The crystal structures of 5-(2-( p-chlorophenylbenzimidazol-1-yl-methyl)-4-(3-fluorophenyl)-2,4-dihydro-[1,2,4]-triazole-3-thione (G6C) and 5-(2-( p-chlorophenylbenzimidazol-1-yl-methyl)-4-(2-methylphenyl)-2,4-dihydro-[1,2,4]-triazole-3-thione (G4C) have been determined by single-crystal X-ray diffraction. Benzimidazole ring systems in both molecules are planar. The triazole part is almost perpendicular to the phenyl and the benzimidazole parts of the molecules in order to avoid steric interactions between the rings. The crystal structures are stabilized by intermolecular hydrogen bonds between the amino group of the triazole and the nitrogen atom of benzimidazole of a neighboring molecule.

  14. Crystal structures and intermolecular interactions of two novel antioxidant triazolyl-benzimidazole compounds

    Karayel, A., E-mail: matchlessjimmy@163.com, E-mail: yccaoh@hotmail.com; Özbey, S. [Hacettepe University, Physics Engineering Department (Turkey); Ayhan-Kılcıgil, G.; Kuş, C. [Ankara University, Department of Pharmaceutical Chemistry, Faculty of Pharmacy (Turkey)

    2015-12-15

    The crystal structures of 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(3-fluorophenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G6C) and 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(2-methylphenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G4C) have been determined by single-crystal X-ray diffraction. Benzimidazole ring systems in both molecules are planar. The triazole part is almost perpendicular to the phenyl and the benzimidazole parts of the molecules in order to avoid steric interactions between the rings. The crystal structures are stabilized by intermolecular hydrogen bonds between the amino group of the triazole and the nitrogen atom of benzimidazole of a neighboring molecule.

  15. Manifestation of structure and intermolecular interactions of biologically active brassinosteroids in infrared spectra

    Borisevich, N. A.; Skornyakov, I. V.; Khripach, V. A.; Tolstorozhev, G. B.; Zhabinskii, V. N.

    2007-09-01

    We have analyzed the IR spectra obtained for steroidal phytohormones 24-epibrassinolide, 24-epicastasterone, 28-homobrassinolide, and 28-homocastasterone. The characteristic frequencies of the stretching vibrations of the hydrocarbon groups CH3, CH2, and CH and also the C=O groups in the spectra of brassinolides are higher than in the spectra of castasterones, which makes it possible to identify them from the IR spectra. Study of the spectra of these brassinosteroids in different media (pressed samples in KBr, films, solutions in CHCl3 and CDCl3) allowed us to establish the presence of intermolecular interactions in which C=O and OH groups, OH-OH groups participate, and also the possible formation of intramolecular hydrogen bonds between the OH groups of the molecules.

  16. Description of cross peaks induced by intermolecular vibrational energy transfer in two-dimensional infrared spectroscopy

    Villaeys, Albert A

    2013-01-01

    In the present work, the analytical description of an intermolecular vibrational energy transfer, analyzed by two dimensional infrared spectroscopy, is established. The energy transfer process takes place between the dark combination states of low frequency modes pertaining to different molecules. The appearance of the cross peaks results from coherent transfer between these combination states and an optically active state of the acceptor molecule. Such a process has recently been observed experimentally between the nitrile groups of acetonitrile-d3 and benzonitrile molecules. This molecular system will be used as a model for the simulations of their two-dimensional infrared spectra. The dependence of the cross-peak growth, which is a signature of the intermolecular energy transfer, will be discussed in detail as a function of the molecular dynamical constants.

  17. Intermolecular nonradiative energy transfer in clusters with plasmonic nanoparticles

    Kucherenko, M. G.; Stepanov, V. N.; Kruchinin, N. Yu.

    2015-01-01

    The influence of carbon (fullerenes, nanotubes) and metal (Ni, Co, Cu, Ag) nanoparticles on the nonradiative electronic excitation energy transfer between the molecules of organic dyes (acrylic orange as a donor and Nile blue as an acceptor) in alcohol solutions of polyvinylbutyral is studied. It is found that, at particular concentrations of the mixture components, plasmonic nanoparticles affect the nonradiative electronic excitation energy transfer, which is manifested in an increase in the intensity of sensitized fluorescence of acceptors with simultaneous quenching of the fluorescence of donors. A very simple model is proposed to illustrate the observed redistribution of luminescence intensity between the spectral bands of the general spectrum. Molecular-dynamic calculations of the structure of nanocomposites performed for the same purpose confirmed the formation of associated molecular plasmonic complexes fixed by macrochain links.

  18. Intermolecular interactions and 3D structure in cellulose-NaOH-urea aqueous system.

    Jiang, Zhiwei; Fang, Yan; Xiang, Junfeng; Ma, Yanping; Lu, Ang; Kang, Hongliang; Huang, Yong; Guo, Hongxia; Liu, Ruigang; Zhang, Lina

    2014-08-28

    The dissolution of cellulose in NaOH/urea aqueous solution at low temperature is a key finding in cellulose science and technology. In this paper, (15)N and (23)Na NMR experiments were carried out to clarify the intermolecular interactions in cellulose/NaOH/urea aqueous solution. It was found that there are direct interactions between OH(-) anions and amino groups of urea through hydrogen bonds and no direct interaction between urea and cellulose. Moreover, Na(+) ions can interact with both cellulose and urea in an aqueous system. These interactions lead to the formation of cellulose-NaOH-urea-H2O inclusion complexes (ICs). (23)Na relaxation results confirmed that the formation of urea-OH(-) clusters can effectively enhance the stability of Na(+) ions that attracted to cellulose chains. Low temperature can enhance the hydrogen bonding interaction between OH(-) ions and urea and improve the binding ability of the NaOH/urea/H2O clusters that attached to cellulose chains. Cryo-TEM observation confirmed the formation of cellulose-NaOH-urea-H2O ICs, which is in extended conformation with mean diameter of about 3.6 nm and mean length of about 300 nm. Possible 3D structure of the ICs was proposed by the M06-2X/6-31+G(d) theoretical calculation, revealing the O3H···O5 intramolecular hydrogen bonds could remain in the ICs. This work clarified the interactions in cellulose/NaOH/urea aqueous solution and the 3D structure of the cellulose chain in dilute cellulose/NaOH/urea aqueous solution. PMID:25111839

  19. Effects of Weak Intermolecular Interactions on the Molecular Isomerism of Tricobalt Metal Chains

    Poulsen, R.; Overgaard, J; Schulman, A; Østergaard, C; Murillo, C; Spackman, M; Iversen, B

    2009-01-01

    Depending on the number of interstitial solvent molecules, n, crystals of the linear chain compound Co3(dipyridylamide)4Cl2{center_dot}nCH2Cl2 adopt either symmetrical or unsymmetrical metal chain structures. We explore here the possible reasons for such behavior using Hirshfeld surface analysis of intermolecular interactions as well as the charge density determined from 100(1) K X-ray diffraction data on the unsymmetrical complex Co3(dipyridylamide)4Cl2{center_dot}2.11CH2Cl2, u-1, and crystal structures of u-1 determined from single crystal synchrotron X-ray diffraction data at 20, 150, and 300 K. The new crystal structures are compared with previous structural results on a crystal with slightly different solvent content. This change in solvent content only affects the bond distances to atom Co(3), which are also strongly affected by temperature changes due to a spin crossover transition. Large differences in intermolecular interactions are revealed by the Hirshfeld surface analysis between symmetrical (s-1) and unsymmetrical (u-1) crystal solvates, suggesting that the molecular isomerism is strongly influenced by crystal packing effects. Topological analysis of the static electron density of u-1 suggests that there is direct metal-metal bonding for both the shorter Co(1)-Co(2) and the longer Co(2)-Co(3) contact. The approximate description of the system as a (Co2)2+-dimer and an isolated Co2+-ion is reflected in the character of the metal-ligand interactions, which are more ionic for the isolated Co(3) atom, and the topological charges Co(1)+0.50, Co(2)+0.77, and Co(3)+1.36. The two termini of u-1 are found to be very different, both in terms of structural surroundings as well as topology. The central Co(2) atom is similar to a cobalt atom in a tetragonally distorted octahedral environment resulting in preferred occupancy in the t2g orbitals. The Co(1) atom has significant deformation in the xz and yz planes (z along the chain axis, x and y toward ligands

  20. Intercalation of organic molecules in 2D copper (II) nitroprusside: Intermolecular interactions and magnetic properties

    Osiry, H.; Cano, A.; Lemus-Santana, A. A.; Rodríguez, A.; Carbonio, R. E.; Reguera, E.

    2015-10-01

    This contribution discusses the intercalation of imidazole and its 2-ethyl derivative, and pyridine in 2D copper nitroprusside. In the interlayer region, neighboring molecules remain interacting throu gh their dipole and quadrupole moments, which supports the solid 3D crystal structure. The crystal structure of this series of intercalation compounds was solved and refined from powder X-ray diffraction patterns complemented with spectroscopic information. The intermolecular interactions were studied from the refined crystal structures and low temperature magnetic measurements. Due to strong attractive forces between neighboring molecules, the resulting π-π cloud overlapping enables the ferromagnetic coupling between metal centers on neighboring layers, which was actually observed for the solids containing imidazole and pyridine as intercalated molecules. For these two solids, the magnetic data were properly described with a model of six neighbors. For the solid containing 2-ethylimidazole and for 2D copper nitroprusside, a model of four neighbors in a plane is sufficient to obtain a reliable data fitting.

  1. Intercalation of organic molecules in 2D copper (II) nitroprusside: Intermolecular interactions and magnetic properties

    This contribution discusses the intercalation of imidazole and its 2-ethyl derivative, and pyridine in 2D copper nitroprusside. In the interlayer region, neighboring molecules remain interacting throu gh their dipole and quadrupole moments, which supports the solid 3D crystal structure. The crystal structure of this series of intercalation compounds was solved and refined from powder X-ray diffraction patterns complemented with spectroscopic information. The intermolecular interactions were studied from the refined crystal structures and low temperature magnetic measurements. Due to strong attractive forces between neighboring molecules, the resulting π–π cloud overlapping enables the ferromagnetic coupling between metal centers on neighboring layers, which was actually observed for the solids containing imidazole and pyridine as intercalated molecules. For these two solids, the magnetic data were properly described with a model of six neighbors. For the solid containing 2-ethylimidazole and for 2D copper nitroprusside, a model of four neighbors in a plane is sufficient to obtain a reliable data fitting. - Highlights: • Intercalation of organic molecules in 2D copper (II) nitroprusside. • Molecular properties of intercalation compounds of 2D copper (II) nitroprusside. • Magnetic properties of hybrid inorganic–organic solids. • Hybrid inorganic–organic 3D framework

  2. Intercalation of organic molecules in 2D copper (II) nitroprusside: Intermolecular interactions and magnetic properties

    Osiry, H.; Cano, A.; Lemus-Santana, A.A.; Rodríguez, A. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional (Mexico); Carbonio, R.E. [INFIQC-CONICET, Departamento de Físico Química, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba (Argentina); Reguera, E., E-mail: edilso.reguera@gmail.com [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional (Mexico)

    2015-10-15

    This contribution discusses the intercalation of imidazole and its 2-ethyl derivative, and pyridine in 2D copper nitroprusside. In the interlayer region, neighboring molecules remain interacting throu gh their dipole and quadrupole moments, which supports the solid 3D crystal structure. The crystal structure of this series of intercalation compounds was solved and refined from powder X-ray diffraction patterns complemented with spectroscopic information. The intermolecular interactions were studied from the refined crystal structures and low temperature magnetic measurements. Due to strong attractive forces between neighboring molecules, the resulting π–π cloud overlapping enables the ferromagnetic coupling between metal centers on neighboring layers, which was actually observed for the solids containing imidazole and pyridine as intercalated molecules. For these two solids, the magnetic data were properly described with a model of six neighbors. For the solid containing 2-ethylimidazole and for 2D copper nitroprusside, a model of four neighbors in a plane is sufficient to obtain a reliable data fitting. - Highlights: • Intercalation of organic molecules in 2D copper (II) nitroprusside. • Molecular properties of intercalation compounds of 2D copper (II) nitroprusside. • Magnetic properties of hybrid inorganic–organic solids. • Hybrid inorganic–organic 3D framework.

  3. Intermolecular interactions in ternary solutions of some 1,2,4-triazolium ylids studied by spectral means

    Closca, Valentina; Melniciuc-Puica, Nicoleta; Dorohoi, Dana Ortansa; Benchea, A. C.

    2014-08-01

    Triazolium ylids are dipolar molecules with separated charges in their ground electronic state; the positive charge is located on one Nitrogen atom belonging to the heterocycle and the negative charge is located near the ylid carbanion. The intramolecular charge transfer from the carbanion to heterocycle gives a visible electronic absorption band, very sensitive to the solvent nature. Its position in the wavenumber scale offers information about the intermolecular interactions in which the ylid molecules are engaged. The spectral study revealed the presence of both universal and specific interactions in solutions of 1,2,4-triazolium ylids with protic solvents. By choosing adequate binary solvents, the contribution of the specific interaction of the weak hydrogen bond between the -OH atomic group of the protic solvents and the ylid carbanion can be estimated. Ternary solutions of the studied ylids achieved with Methanol +Benzene, Water + Ethanol and 1,3 Propanediol + Dimethyl formamide binary solvents are analyzed from spectral point of view and the difference between the potential energies in molecular pairs of the types: 1,2,4-triazolium ylid-protic solvent and 1,2,4-triazolium ylid-non protic were estimated on the basis of the statistic cell model of ternary solutions.

  4. A combined experimental and quantum chemical studies on molecular structure, spectral properties, intra and intermolecular interactions and first hyperpolarizability of 4-(benzyloxy)benzaldehyde thiosemicarbazone and its dimer

    Kumar, Amit; Rawat, Poonam; Baboo, Vikas; Verma, Divya; Singh, R. N.; Saxena, Deepti; Gauniyal, H. M.; Pandey, Anoop Kumar; Pal, Harish

    2013-02-01

    In the present work, a detailed spectroscopic analysis of 4-(benzyloxy)benzaldehyde thiosemicarbazone (3) has been carried out using 1H NMR, 13C NMR, UV-Visible and FT-IR spectroscopic techniques. The quantum chemical calculations have been carried out using DFT level of theory, B3LYP functional and 6-31G(d,p) basis set. The calculated thermodynamic parameters show that the formation of 3 is an exothermic and spontaneous reaction at 25 °C. The vibrational analysis indicates the formation of dimer in the solid state by intermolecular hydrogen bonding (Nsbnd H⋯Sdbnd C) and the binding energy of dimer is calculated to be 11.2 kcal/mol, using DFT calculation. NBO analysis is carried out to investigate the charge transfer in various intra and intermolecular interactions involved in dimer. Topological parameters at bond critical points (BCPs) are calculated to analyze the strength and nature of various intra and intermolecular interactions in dimer by Bader's 'Atoms in molecules' AIM theory in detail. The local reactivity descriptors such as Fukui functions (fk+, fk-), local softnesses (sk+, sk-) and electrophilicity indices (ωk+, ωk-) analysis are performed to determine the reactive sites within molecule. Non linear optical (NLO) behavior of title compound is investigated by the computed value of first hyperpolarizability (β0).

  5. Kirromycin-induced modifications facilitate the separation of EF-Tu species and reveal intermolecular interactions.

    Anborgh, P H; Swart, G W; Parmeggiani, A

    1991-11-01

    A simplified method for the separation of a kirromycin-sensitive tufB-encoded elongation factor Tu (EF-TuBs) from a kirromycin-resistant tufA product (EF-TuAr) was obtained by exploiting the specific increase of negative [corrected] charges induced by the antibiotic, resulting in a retarded elution of kirromycin-bound EF-TuBs on ionic chromatography. The kirromycin-free EF-TuBs is active in poly(Phe) synthesis and shows similar properties to EF-TuAsBs. As expected for these two distinct species, the dissociation of the EF-TuArBs.GTP complex in the presence of kirromycin shows a biphasic curve; in contrast, a monophasic GTP dissociation rate was found for a combination of two mutated EF-Tu species, EF-TuArBo, revealing the existence of intermolecular interactions. These observations prove for the first time the existence of cooperative phenomena between EF-Tu species in vitro, as suggested earlier by in vivo experiments. PMID:1959611

  6. Intermolecular vs molecule–substrate interactions: A combined STM and theoretical study of supramolecular phases on graphene/Ru(0001

    Michael Roos

    2011-07-01

    Full Text Available The competition between intermolecular interactions and long-range lateral variations in the substrate–adsorbate interaction was studied by scanning tunnelling microscopy (STM and force field based calculations, by comparing the phase formation of (sub- monolayers of the organic molecules (i 2-phenyl-4,6-bis(6-(pyridin-3-yl-4-(pyridin-3-ylpyridin-2-ylpyrimidine (3,3'-BTP and (ii 3,4,9,10-perylene tetracarboxylic-dianhydride (PTCDA on graphene/Ru(0001. For PTCDA adsorption, a 2D adlayer phase was formed, which extended over large areas, while for 3,3'-BTP adsorption linear or ring like structures were formed, which exclusively populated the areas between the maxima of the moiré structure of the buckled graphene layer. The consequences for the competing intermolecular interactions and corrugation in the adsorption potential are discussed and compared with the theoretical results.

  7. Dynamics of intermolecular interactions in CCl4via the isotope effect by femtosecond time-resolved spectroscopy.

    Konarska, Jadwiga; Gadomski, Wojciech; Ratajska-Gadomska, Bożena; Polok, Kamil; Pudłowski, Grzegorz; Kardaś, Tomasz M

    2016-06-21

    We report our study on the ultrafast dynamics of intermolecular interactions in liquid CCl4. A transient transmission time domain signal, obtained in the 40 ps delay range, exhibits beating at the difference frequency of the totally symmetric stretching vibrations of the tetrachloride isotopologues. We show that the spectra obtained as the windowed Fourier transform of different parts of the time domain signal in the range of this totally symmetric vibration, split due to the isotope effect, carry the information about the dynamics of the coherently excited, coupled molecules. We use a simple theoretical model in order to prove that the intermolecular interaction influences the relative amplitudes of the isotopologue peaks in the spectrum. Moreover, we demonstrate that the pump induced coherence in the system leads to additional strengthening of the interaction, which can be observed in the spectra obtained from the experimental time domain signal. PMID:27244535

  8. MECHANICAL RELAXATION AND INTERMOLECULAR INTERACTION IN EPOXY RESINS/POLY (ETHYLENE OXIDE)BLENDS CURED WITH PHTHALIC ANHYDRIDE

    LUO Xiaolie; ZHENG Sixun; MA Dezhu; HU Keliang

    1995-01-01

    The miscibility of the blend,composed of a bisphenol A epoxy resins (Diglycidyl etherof bisphenol A) (DGEBA) and poly(ethylene oxide) (PEO) and crosslinked by phthalicanhydride (PA) was studied using dynamic mechanical method. Single glass transitiontemperatures intermediate between the two pure components were observed for all blendlevels. The secondary relaxation mechanism should relate to not only diester linkage, butalso hydroxyether structural unit in the system. Fourier transform infrared spectroscopy(FTIR) is applied to study the curing reaction and intermolecular specific interaction of thesystem. The results indicate the PEO participates the crosslinking reaction, accelerates thecuring reaction and make the reaction more perfect. The shifts of the hydroxyl band andcarbonyl band demonstrate the presence of the intermolecular interaction in the curedblend. Moreover, the molecular interaction between the side hydroxyl in the hydroxyetherunits and the ether bond in PEO macromolecules is stronger.

  9. Intermolecular vs molecule-substrate interactions: A combined STM and theoretical study of supramolecular phases on graphene/Ru(0001).

    Roos, Michael; Uhl, Benedikt; Künzel, Daniela; Hoster, Harry E; Groß, Axel; Behm, R Jürgen

    2011-01-01

    The competition between intermolecular interactions and long-range lateral variations in the substrate-adsorbate interaction was studied by scanning tunnelling microscopy (STM) and force field based calculations, by comparing the phase formation of (sub-) monolayers of the organic molecules (i) 2-phenyl-4,6-bis(6-(pyridin-3-yl)-4-(pyridin-3-yl)pyridin-2-yl)pyrimidine (3,3'-BTP) and (ii) 3,4,9,10-perylene tetracarboxylic-dianhydride (PTCDA) on graphene/Ru(0001). For PTCDA adsorption, a 2D adlayer phase was formed, which extended over large areas, while for 3,3'-BTP adsorption linear or ring like structures were formed, which exclusively populated the areas between the maxima of the moiré structure of the buckled graphene layer. The consequences for the competing intermolecular interactions and corrugation in the adsorption potential are discussed and compared with the theoretical results. PMID:22003444

  10. Intermolecular vs molecule–substrate interactions: A combined STM and theoretical study of supramolecular phases on graphene/Ru(0001)

    Roos, Michael; Uhl, Benedikt; Künzel, Daniela; Hoster, Harry E; Groß, Axel

    2011-01-01

    Summary The competition between intermolecular interactions and long-range lateral variations in the substrate–adsorbate interaction was studied by scanning tunnelling microscopy (STM) and force field based calculations, by comparing the phase formation of (sub-) monolayers of the organic molecules (i) 2-phenyl-4,6-bis(6-(pyridin-3-yl)-4-(pyridin-3-yl)pyridin-2-yl)pyrimidine (3,3'-BTP) and (ii) 3,4,9,10-perylene tetracarboxylic-dianhydride (PTCDA) on graphene/Ru(0001). For PTCDA adsorption, a 2D adlayer phase was formed, which extended over large areas, while for 3,3'-BTP adsorption linear or ring like structures were formed, which exclusively populated the areas between the maxima of the moiré structure of the buckled graphene layer. The consequences for the competing intermolecular interactions and corrugation in the adsorption potential are discussed and compared with the theoretical results. PMID:22003444

  11. Conformational analysis, inter-molecular interactions, electronic properties and vibrational spectroscopic studies on cis-4-hydroxy-d-proline

    Ambrish Kumar Srivastava

    2016-12-01

    Full Text Available The present study deals with a non-native amino acid, cis-4-hydroxy-d-proline (CHDP using density functional theory at B3LYP/6-31+G(d,p level. The potential energy surface scan reveals the global minimum structure of CHDP along with two potential conformers. Highest occupied molecular orbital, lowest unoccupied molecular orbital, and molecular electrostatic potential surfaces are used to explain the chemical reactivity of title molecule. The atomic charge analysis has been carried out using Mulliken and natural population schemes. The equilibrium geometry of CHDP dimer has been obtained and inter-molecular interactions are explored using QTAIM and Natural bonding orbital analyses. Vibrational spectroscopic analysis has been performed on CHDP monomer and dimer at the same level of theory. Assignments to all vibrational modes up to 400 cm−1 have been offered along with their potential energy distribution to the maximum possible accuracy. The calculated frequencies are scaled by an equation, rather than by a constant factor and then compared with experimental FT-IR frequencies obtained by KBr disc and Nujol mull techniques. A number of electronic and thermodynamic parameters have also been evaluated for CHDP monomer and dimer.

  12. DFT study of the conductance of molecular wire: The effect of coupling geometry and intermolecular interaction on the transport properties

    QI; Yuanhua; GUAN; Daren; LIU; Chengbu

    2006-01-01

    The density functional theory (DFT) combining with the non-equilibrium Green functions (NEGF) method is applied to the study of the electronic transport properties for a Di-thiol-benzene (DTB) molecule coupled to two Au(111) surfaces. The dependence of the transport properties on the bias, the coupling geometry of the molecule-electrode interface, and the intermolecular interaction are examined in detail. The results show that the existence of the hydrogen atom at the end of the DTB molecule would significantly decrease the transmission coefficients, and then the differential conductance (dI/dV). By changing the position of the DTB molecule located between two electrodes a maximum value of calculated current is observed. It is also found that the intermolecular interaction will strongly influence the transport properties of the system studied.

  13. Analysis of intermolecular interactions in 3-(4-fluoro-3-phenoxyphenyl)-1-((4-methylpiperazin-1-yl)methyl)-1H-1,2,4-triazole-5-thiol

    Piyush Panini; Rahul Shukla; T P Mohan; B Vishalakshi; Deepak Chopra

    2014-09-01

    In the present study, we have prepared and structurally characterized a derivative of 1,2,4 triazoles, namely 3-(4-fluoro-3-phenoxyphenyl)-1-((4-methylpiperazin-1-yl)methyl)-1H-1,2,4-triazole-5-thiol (T-1) via single crystal X-ray diffraction. The crystal structure was observed to be stabilized by the presence of various intermolecular interactions in the crystalline solid such as O-H…S, C-H…F, C-H…S, C-H…N, C-H…O, C-H$\\ldots$ , $\\ldots$ and $\\ldots$ intermolecular interactions. The interaction energy of these interactions was evaluated through PIXEL method with decomposition of the total energy into the coulombic, polarization, dispersion and repulsion contribution. The study of the nature of H-bonds with sulfur reveals that stabilization due to contribution from polarization plays a significant role. It is noteworthy that the presence of the solvent molecules in the crystal structure were observed to provide stabilization to an otherwise destabilized molecular pair (comprising of two molecules of 1,2,4 triazoles in the asymmetric unit).

  14. Theory of intermolecular forces

    Margenau, H; Ter Haar, D

    1971-01-01

    Theory of Intermolecular Forces deals with the exposition of the principles and techniques of the theory of intermolecular forces. The text focuses on the basic theory and surveys other aspects, with particular attention to relevant experiments. The initial chapters introduce the reader to the history of intermolecular forces. Succeeding chapters present topics on short, intermediate, and long range atomic interactions; properties of Coulomb interactions; shape-dependent forces between molecules; and physical adsorption. The book will be of good use to experts and students of quantum mechanics

  15. Rubrene: The interplay between intramolecular and intermolecular interactions determines the planarization of its tetracene core in the solid state

    Sutton, Christopher

    2015-06-15

    Rubrene is one of the most studied molecular semiconductors; its chemical structure consists of a tetracene backbone with four phenyl rings appended to the two central fused rings. Derivatization of these phenyl rings can lead to two very different solid-state molecular conformations and packings: One in which the tetracene core is planar and there exists substantive overlap among neighboring π-conjugated backbones; and another where the tetracene core is twisted and the overlap of neighboring π-conjugated backbones is completely disrupted. State-of-the-art electronic-structure calculations show for all isolated rubrene derivatives that the twisted conformation is more favorable (by -1.7 to -4.1 kcal mol-1), which is a consequence of energetically unfavorable exchange-repulsion interactions among the phenyl side groups. Calculations based on available crystallographic structures reveal that planar conformations of the tetracene core in the solid state result from intermolecular interactions that can be tuned through well-chosen functionalization of the phenyl side groups, and lead to improved intermolecular electronic couplings. Understanding the interplay of these intramolecular and intermolecular interactions provides insight into how to chemically modify rubrene and similar molecular semiconductors to improve the intrinsic materials electronic properties.

  16. Noncovalent intermolecular interactions between dehydroepiandrosterone and the active site of human dehydroepiandrosterone sulphotransferase: A density functional theory based treatment

    Astani, Elahe; Heshmati, Emran; Chen, Chun-Jung; Hadipour, Nasser L.; Shekarsaraei, Setareh

    2016-04-01

    A theoretical study was performed to characterize noncovalent intermolecular interactions, especially hydrogen bond (HB), in the active site of enzyme human dehydroepiandrosterone sulphotransferase (SULT2A1/DHEA) using the local (M06-L) and hybrid (M06, M06-2X) meta-GGA functionals of density functional theory (DFT). Results revealed that DHEA is able to form HBs with residues His99, Tyr231, Met137 and Met16 in the active site of the SULT2A1/DHEA. It was found that DHEA interacts with the other residues through electrostatic and Van der Waals interactions.

  17. Ab initio Calculation of Intermolecular Dispersion Energy and Induction Energy of Nitramide Dimer

    SONG, Hua-Jie(宋华杰); XIAO, He-Ming(肖鹤鸣); DONG, Hai-Shan(董海山); HUANG, Yi-Gang(黄奕刚); LONG, Xin-Ping(龙新平); TANG, Yei-Peng(汤业鹏)

    2004-01-01

    The dispersion energies, induction energies and their exchange counterparts (exchange-dispersion and exchange-induction energies) between two interacting nitramide molecules at several separations are derived based upon symmetry-adapted perturbation theory (SAPT). The results show that (1) the effect of intramonomer electron correlation on dispersion energies and induction energies for nitramide dimer system is remarkable especially in the region near the van der Waals minimum distance (0.42 nm). (2) At smaller separations the dispersion energies and the induction energies are largely quenched by their exchange counterparts, and this case in induction interaction is much more remarkable than in dispersion interaction. (3) Since at shorter distances there exists the strong short-range interaction due to electron transfer which quickly decays and even disappears at larger separations, the two different R-dependency formulae of induction energies were found: one is ca. R-12.7 at short distances, and the other ca. R-7.0 at large separations. The latter R-dependency is similar to that (ca. R-7.2) of dispersion. (4) In the case of strong polar interaction existing in nitramide dimer, the "true" induction correlation terms of higher order than tE(22)ind may be important.

  18. A quantum chemical insight to intermolecular hydrogen bonding interaction between cytosine and nitrosamine: Structural and energetic investigations

    Khalili, Behzad

    2016-03-01

    Hydrogen bond interactions which are formed during complex formation between cytosine and nitrosamine have been fully investigated using B3LYP, B3PW91 and MP2 methods in conjunction with various basis sets including 6-311++G (d,p), 6-311++G (2d,2p), 6-311++G (df,pd) and AUG-cc-pVDZ. Three regions around the most stable conformer of cytosine in the gas phase with six possible double H-bonded interactions were considered. Two intermolecular hydrogen bonds of type NC-N-HNA and O-H(N-H)C-ONA were found on the potential energy surface in a cyclic system with 8-member in CN1, CN3, CN5 and 7-member in CN2, CN4, CN6 systems. Results of binding energy calculation at all applied methods reveal that the CN1 structure is the most stable one which is formed by interaction of nitrosamine with cytosine in S1 region. The BSSE-corrected binding energy for six complex system is ranging from -23.8 to -43.6 kJ/mol at MP2/6-311++G (df,pd) level and the stability order is as CN1 > CN2 > CN3 > CN4 > CN5 > CN6 in all studied levels of theories. The NBO results reveal that the charge transfer occurred from cytosine to nitrosamine in CN1, CN3, CN5 and CN6 whereas this matter in the case of CN2 and CN4 was reversed. The relationship between BEs with red shift of H-bond involved bonds vibrational frequencies, charge transfer energies during complex formation and electron densities at H-bond BCPs were discussed. In addition activation energetic properties related to the proton transfer process between cytosine and nitrosamine have been calculated at MP2/6-311++G (df,pd) level. AIM results imply that H-bond interactions are electrostatic with partially covalent characteristic in nature.

  19. Intermolecular vs molecule–substrate interactions: A combined STM and theoretical study of supramolecular phases on graphene/Ru(0001)

    Roos, Michael; Uhl, Benedikt; Künzel, Daniela; Harry E. Hoster; Groß, Axel; Behm, R Jürgen

    2011-01-01

    The competition between intermolecular interactions and long-range lateral variations in the substrate–adsorbate interaction was studied by scanning tunnelling microscopy (STM) and force field based calculations, by comparing the phase formation of (sub-) monolayers of the organic molecules (i) 2-phenyl-4,6-bis(6-(pyridin-3-yl)-4-(pyridin-3-yl)pyridin-2-yl)pyrimidine (3,3'-BTP) and (ii) 3,4,9,10-perylene tetracarboxylic-dianhydride (PTCDA) on graphene/Ru(0001). For PTCDA adsorption, a 2D adla...

  20. Intermolecular vs molecule–substrate interactions: A combined STM and theoretical study of supramolecular phases on graphene/Ru(0001)

    Michael Roos; Benedikt Uhl; Daniela Künzel; Harry E. Hoster; Axel Groß; R. Jürgen Behm

    2011-01-01

    The competition between intermolecular interactions and long-range lateral variations in the substrate–adsorbate interaction was studied by scanning tunnelling microscopy (STM) and force field based calculations, by comparing the phase formation of (sub-) monolayers of the organic molecules (i) 2-phenyl-4,6-bis(6-(pyridin-3-yl)-4-(pyridin-3-yl)pyridin-2-yl)pyrimidine (3,3'-BTP) and (ii) 3,4,9,10-perylene tetracarboxylic-dianhydride (PTCDA) on graphene/Ru(0001). For PTCDA adsorption, a 2...

  1. Intermolecular interaction of thiosemicarbazone derivatives to solvents and a potential Aedes aegypti target

    da Silva, João Bosco P.; Hallwass, Fernando; da Silva, Aluizio G.; Moreira, Diogo Rodrigo; Ramos, Mozart N.; Espíndola, José Wanderlan P.; de Oliveira, Ana Daura T.; Brondani, Dalci José; Leite, Ana Cristina L.; Merz, Kenneth M.

    2015-08-01

    DFT calculations were used to access information about structure, energy and electronic properties of series of phenyl- and phenoxymethyl-(thio)semicarbazone derivatives with demonstrated activity against the larvae of Aedes aegypti in stage L4. The way as the thiosemicarbazone derivatives can interact with solvents like DMSO and water were analyzed from the comparison between calculated and experimental 1H NMR chemical shifts. The evidences of thiosemicarbazone derivatives making H-bond interaction to solvent have provide us insights on how they can interact with a potential A. aegypti's biological target, the Sterol Carrier Protein-2.

  2. On the representation of the electric charge distribution in ethane for calculations of the molecular quadrupole moment and intermolecular electrostatic energy

    Hansen, Flemming Yssing; Alldredge, G. P.; Bruch, L. W.;

    1985-01-01

    and gives a repulsive rather than an attractive electrostatic interaction at typical intermolecular distances. In the local multipole model, the atom-site dipoles give the largest contribution to both the molecular quadrupole moment and the intermolecular interaction. The Journal of Chemical Physics...

  3. Ab initio intermolecular potential energy surfaces of He-CS2, Ne-CS2 and Ar-CS2 complexes

    Farrokhpour, H.; Tozihi, M.

    2013-03-01

    The potential energy surfaces of the He-CS2, Ne-CS2 and Ar-CS2 van der Waals complexes were calculated for the first time at the CCSD(T) level of theory using the aug-cc-pVDZ basis set augmented with a set of midbond functions (3s3p2d1f1g). It was found that the calculated interaction potential, using the applied basis set, readily converges to the complete basis set limit. For a broad range of intermolecular separations and configurations, the interaction energies were obtained by the supermolecular approach with the full counterpoise correction for the basis set superposition error (BSSE). In addition, symmetry-adapted perturbation theory (SAPT) calculations were performed with the same basis set in order to determine the character of the interaction energy of the most stable configuration of each complex at different intermolecular separations in order to make a comparison with the CCSD(T) results. The CCSD(T) calculated potential energy surface of each complex was fitted to an analytic expression to obtain the values of the isotropic dipole-dipole ( ? ) and dipole-quadruple ( ? ) dispersion coefficients of each complex. Finally, the interaction second virial coefficients (B12) were obtained using the calculated potential energy surface and used together with the experimental second virial coefficients of pure gases (CS2, Ar, Ne and He) to obtain the second virial coefficient of mixtures of CS2 with rare gas at different temperatures and mole fractions.

  4. Coordination compounds of tetravalent silicon, germanium and tin: the structure, chemical bonding and intermolecular interactions in them

    Korlyukov, A. A.

    2015-04-01

    The review is devoted to analysis and generalization of the results of (i) quantum chemical studies on the structure, chemical bonding and intermolecular interactions in coordination compounds of tetravalent silicon, germanium and tin in crystals, in solutions and in the gas phase and (ii) experimental investigations of the electron density distribution in these systems. The bibliography includes 147 references. In memoriam of Corresponding Member of the Russian Academy of Sciences M Yu Antipin (1951 - 2013), Academician of the Russian Academy of Sciences M G Voronkov (1921 - 2014) and Dr. S P Knyazev, Lomonosov Moscow University of Fine Chemical Technology (1949 - 2012).

  5. Intermolecular Tl···H-C anagostic interactions in luminescent pyridyl functionalized thallium(I) dithiocarbamates.

    Kumar, Vinod; Singh, Vikram; Gupta, Ajit N; Drew, Michael G B; Singh, Nanhai

    2015-01-28

    Crystal structures of novel pyridyl functionalised [Tl(L)]∞ (L = (N-benzyl-N-methylpyridyl) dithiocarbamate(L1) 1, bis(N-methylpyridyl) dithiocarbamate(L2) 2, (N-methyl(1,4-benzodioxane-6-yl)-N-methylpyridyl)dithiocarbamate(L3) 3, (N-ferrocenyl-N-methylpyridyl) dithiocarbamate(L4) 4) complexes revealed rare intermolecular C-H···Tl anagostic and C-S···Tl interactions forming a six-membered chelate ring about the metal center, which have been assessed by DFT calculations. The strong thallophilic bonding is responsible for the strong luminescent characteristics of the complexes in the solid phase. PMID:25461980

  6. Lack of evidence for intermolecular epistatic interactions between adiponectin and resistin gene polymorphisms in Malaysian male subjects

    Cia-Hin Lau

    2012-01-01

    Full Text Available Epistasis (gene-gene interaction is a ubiquitous component of the genetic architecture of complex traits such as susceptibility to common human diseases. Given the strong negative correlation between circulating adiponectin and resistin levels, the potential intermolecular epistatic interactions between ADIPOQ (SNP+45T > G, SNP+276G > T, SNP+639T > C and SNP+1212A > G and RETN (SNP-420C > G and SNP+299G > A gene polymorphisms in the genetic risk underlying type 2 diabetes (T2DM and metabolic syndrome (MS were assessed. The potential mutual influence of the ADIPOQ and RETN genes on their adipokine levels was also examined. The rare homozygous genotype (risk alleles of SNP-420C > G at the RETN locus tended to be co-inherited together with the common homozygous genotypes (protective alleles of SNP+639T > C and SNP+1212A > G at the ADIPOQ locus. Despite the close structural relationship between the ADIPOQ and RETN genes, there was no evidence of an intermolecular epistatic interaction between these genes. There was also no reciprocal effect of the ADIPOQ and RETN genes on their adipokine levels, i.e., ADIPOQ did not affect resistin levels nor did RETN affect adiponectin levels. The possible influence of the ADIPOQ gene on RETN expression warrants further investigation.

  7. The role of intermolecular interactions in the prediction of the phase equilibria of carbon dioxide hydrates.

    Costandy, Joseph; Michalis, Vasileios K; Tsimpanogiannis, Ioannis N; Stubos, Athanassios K; Economou, Ioannis G

    2015-09-01

    The direct phase coexistence methodology was used to predict the three-phase equilibrium conditions of carbon dioxide hydrates. Molecular dynamics simulations were performed in the isobaric-isothermal ensemble for the determination of the three-phase coexistence temperature (T3) of the carbon dioxide-water system, at pressures in the range of 200-5000 bar. The relative importance of the water-water and water-guest interactions in the prediction of T3 is investigated. The water-water interactions were modeled through the use of TIP4P/Ice and TIP4P/2005 force fields. The TraPPE force field was used for carbon dioxide, and the water-guest interactions were probed through the modification of the cross-interaction Lennard-Jones energy parameter between the oxygens of the unlike molecules. It was found that when using the classic Lorentz-Berthelot combining rules, both models fail to predict T3 accurately. In order to rectify this problem, the water-guest interaction parameters were optimized, based on the solubility of carbon dioxide in water. In this case, it is shown that the prediction of T3 is limited only by the accuracy of the water model in predicting the melting temperature of ice. PMID:26342376

  8. The origins of intra- and inter-molecular vibrational couplings: A case study of H2O-Ar on full and reduced-dimensional potential energy surface

    The origin and strength of intra- and inter-molecular vibrational coupling is difficult to probe by direct experimental observations. However, explicitly including or not including some specific intramolecular vibrational modes to study intermolecular interaction provides a precise theoretical way to examine the effects of anharmonic coupling between modes. In this work, a full-dimension intra- and inter-molecular ab initio potential energy surface (PES) for H2O–Ar, which explicitly incorporates interdependence on the intramolecular (Q1,  Q2,  Q3) normal-mode coordinates of the H2O monomer, has been calculated. In addition, four analytic vibrational-quantum-state-specific PESs are obtained by least-squares fitting vibrationally averaged interaction energies for the (v1,  v2,  v3) =  (0,  0,  0), (0,  0,  1), (1,  0,  0), (0,  1,  0) states of H2O to the three-dimensional Morse/long-range potential function. Each vibrationally averaged PES fitted to 442 points has root-mean-square (rms) deviation smaller than 0.15 cm−1, and required only 58 parameters. With the 3D PESs of H2O–Ar dimer system, we employed the combined radial discrete variable representation/angular finite basis representation method and Lanczos algorithm to calculate rovibrational energy levels. This showed that the resulting vibrationally averaged PESs provide good representations of the experimental infrared data, with rms discrepancies smaller than 0.02 cm−1 for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H2O in H2O–Ar complex are predicted for the first time and are found to be in good agreement with the (extrapolated) experimental values. Upon introduction of additional intramolecular degrees of freedom into the intermolecular potential energy surface, there is clear spectroscopic evidence of intra- and intermolecular vibrational couplings

  9. Intermolecular interactions and proton transfer in the hydrogen halide-superoxide anion complexes.

    Lee, Sebastian J R; Mullinax, J Wayne; Schaefer, Henry F

    2016-02-17

    The superoxide radical anion O2(-) is involved in many important chemical processes spanning different scientific disciplines (e.g., environmental and biological sciences). Characterizing its interaction with various substrates to help elucidate its rich chemistry may have far reaching implications. Herein, we investigate the interaction between O2(-) (X[combining tilde] (2)Πg) and the hydrogen halides (X[combining tilde] (1)Σ) with coupled-cluster theory. In contrast to the short (1.324 Å) hydrogen bond formed between the HF and O2(-) monomers, a barrierless proton transfer occurs for the heavier hydrogen halides with the resulting complexes characterized as long (>1.89 Å) hydrogen bonds between halide anions and the HO2 radical. The dissociation energy with harmonic zero-point vibrational energy (ZPVE) for FHO2(-) (X[combining tilde] (2)A'') → HF (X[combining tilde] (1)Σ) + O2(-) (X[combining tilde] (2)Πg) is 31.2 kcal mol(-1). The other dissociation energies with ZPVE for X(-)HO2 (X[combining tilde] (2)A'') → X(-) (X[combining tilde] (1)Σ) + HO2 (X[combining tilde] (2)A'') are 25.7 kcal mol(-1) for X = Cl, 21.9 kcal mol(-1) for X = Br, and 17.9 kcal mol(-1) for X = I. Additionally, the heavier hydrogen halides can form weak halogen bonds H-XO2(-) (X[combining tilde] (2)A'') with interaction energies including ZPVE of -2.3 kcal mol(-1) for HCl, -8.3 kcal mol(-1) for HBr, and -16.7 kcal mol(-1) for HI. PMID:26852733

  10. Method for Slater-Type Density Fitting for Intermolecular Electrostatic Interactions with Charge Overlap. I. The Model.

    Öhrn, Anders; Hermida-Ramon, Jose M; Karlström, Gunnar

    2016-05-10

    The effects of charge overlap, or charge penetration, are neglected in most force fields and interaction terms in QM/MM methods. The effects are however significant at intermolecular distances near the van der Waals minimum. In the present study, we propose a method to evaluate the intermolecular Coloumb interaction using Slater-type functions, thus explicitly modeling the charge overlap. The computational cost of the method is low, which allows it to be used in large systems with most force fields as well as in QM/MM schemes. The charge distribution is modeled as a distributed multipole expansion up to quadrupole and Slater-type functions of angular momentum up to L = 1. The exponents of the Slater-type functions are obtained using a divide-and-conquer method to avoid the curse of dimensionality that otherwise is present for large nonlinear optimizations. A Levenberg-Marquardt algorithm is applied in the fitting process. A set of parameters is obtained for each molecule, and the process is fully automated. Calculations have been performed in the carbon monoxide and the water dimers to illustrate the model. Results show a very good accuracy of the model with relative errors in the electrostatic potential lower than 3% over all reasonable separations. At very short distances where the charge overlaps is the most significant, errors are lower than 8% and lower than 3.5% at distances near the van der Waals minimum. PMID:27015000

  11. Intermolecular interaction between rare earth and manganese precursors in metalorganic chemical vapor deposition of perovskite manganite films

    Nakamura, Toshihiro [Department of Engineering Science, Osaka Electro-Communication University, 18-8 Hatsu-cho, Neyagawa, Osaka 572-8530 (Japan)

    2015-07-15

    The gas-phase reaction mechanism was investigated in liquid delivery metalorganic chemical vapor deposition (MOCVD) of praseodymium and lanthanum manganite films. We studied the gas-phase behavior of praseodymium, lanthanum, and manganese precursors under actual CVD conditions by in situ infrared absorption spectroscopy. The rate of the decrease of the infrared absorbance due to Pr(DPM){sub 3} was almost constant even if Mn(DPM){sub 3} was added, indicating that the intermolecular interaction between Pr and Mn precursors in the gas phase is relatively weak in MOCVD of praseodymium manganite films. On the other hand, the temperature dependence of the infrared absorption indicates that the thermal decomposition of La(DPM){sub 3} was promoted in the presence of Mn(DPM){sub 3}. The significant intermolecular interaction occurs between La and Mn precursors in the gas phase in MOCVD of lanthanum manganite films. (copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  12. Investigation on Intermolecular Interaction in Supersaturation State of Cadmium Sulphate Mixed Zinc tris-THIOUREA Sulphate Solutions

    Muley, G. G.; Naik, A. B.; Gambhire, A. B.

    2014-06-01

    Zinc tris-thiourea sulphate (ZTS) is a well known nonlinear optical (NLO) crystal widely used for various NLO applications. The NLO, physical and chemical properties can be modified by adding impurities and/or modifying crystal growth conditions. The impurities present in the growth solution and growth conditions can affect the crystal growth parameters at great extent. Thus, the study on the nature of intermolecular interaction with the dopant in the solution during crystal growth process becomes important. In the present investigation, the ultrasonic velocity was measured in the aqueous solutions of pure and cadmium sulphate mixed ZTS in the supersaturation state at 313.15 K. The thermodynamic parameters such as adiabatic compressibility, inter molecular free length, acoustic impedance and relative associations have been calculated from the ultrasonic data and densities of water and solutions at 313.15 K, and the nature of intermolecular interaction has been discussed. FT-IR spectra of all mixtures in the solid form at room temperature were recorded and the shifts in the absorption peaks corresponding to the functional groups of ZTS have been reported.

  13. Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism.

    Chris A Kieslich

    Full Text Available HIV-1 entry into host cells is mediated by interactions between the V3-loop of viral glycoprotein gp120 and chemokine receptor CCR5 or CXCR4, collectively known as HIV-1 coreceptors. Accurate genotypic prediction of coreceptor usage is of significant clinical interest and determination of the factors driving tropism has been the focus of extensive study. We have developed a method based on nonlinear support vector machines to elucidate the interacting residue pairs driving coreceptor usage and provide highly accurate coreceptor usage predictions. Our models utilize centroid-centroid interaction energies from computationally derived structures of the V3-loop:coreceptor complexes as primary features, while additional features based on established rules regarding V3-loop sequences are also investigated. We tested our method on 2455 V3-loop sequences of various lengths and subtypes, and produce a median area under the receiver operator curve of 0.977 based on 500 runs of 10-fold cross validation. Our study is the first to elucidate a small set of specific interacting residue pairs between the V3-loop and coreceptors capable of predicting coreceptor usage with high accuracy across major HIV-1 subtypes. The developed method has been implemented as a web tool named CRUSH, CoReceptor USage prediction for HIV-1, which is available at http://ares.tamu.edu/CRUSH/.

  14. Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism

    Kieslich, Chris A.; Tamamis, Phanourios; Guzman, Yannis A.; Onel, Melis; Floudas, Christodoulos A.

    2016-01-01

    HIV-1 entry into host cells is mediated by interactions between the V3-loop of viral glycoprotein gp120 and chemokine receptor CCR5 or CXCR4, collectively known as HIV-1 coreceptors. Accurate genotypic prediction of coreceptor usage is of significant clinical interest and determination of the factors driving tropism has been the focus of extensive study. We have developed a method based on nonlinear support vector machines to elucidate the interacting residue pairs driving coreceptor usage and provide highly accurate coreceptor usage predictions. Our models utilize centroid-centroid interaction energies from computationally derived structures of the V3-loop:coreceptor complexes as primary features, while additional features based on established rules regarding V3-loop sequences are also investigated. We tested our method on 2455 V3-loop sequences of various lengths and subtypes, and produce a median area under the receiver operator curve of 0.977 based on 500 runs of 10-fold cross validation. Our study is the first to elucidate a small set of specific interacting residue pairs between the V3-loop and coreceptors capable of predicting coreceptor usage with high accuracy across major HIV-1 subtypes. The developed method has been implemented as a web tool named CRUSH, CoReceptor USage prediction for HIV-1, which is available at http://ares.tamu.edu/CRUSH/. PMID:26859389

  15. Relativistic effects in the intermolecular interaction-induced nuclear magnetic resonance parameters of xenon dimer

    Hanni, Matti; Lantto, Perttu; Ilias, Miroslav;

    2007-01-01

    Relativistic effects on the 129Xe nuclear magnetic resonance shielding and 131Xe nuclear quadrupole coupling (NQC) tensors are examined in the weakly bound Xe2 system at different levels of theory including the relativistic four-component Dirac-Hartree-Fock (DHF) method. The intermolecular...... leading-order one-electron Breit-Pauli perturbation theory (BPPT) is applied using a common gauge origin. Electron correlation effects are studied at the nonrelativistic (NR) coupled-cluster singles and doubles with perturbational triples [CCSD(T)] level of theory. The fully relativistic second...... obtained for d and ?s in Xe2. For these properties, the currently most complete theoretical description is obtained by a piecewise approximation where the uncorrelated relativistic DHF results obtained close to the basis-set limit are corrected, on the one hand, for NR correlation effects and, on the other...

  16. Transport properties in mixtures involving carbon dioxide at low and moderate density: test of several intermolecular potential energies and comparison with experiment

    Moghadasi, Jalil; Yousefi, Fakhri [Shiraz University, Department of Chemistry, Shiraz (Iran); Papari, Mohammad Mehdi; Faghihi, Mohammad Ali [Shiraz University of Technology, Department of Chemistry, Shiraz (Iran); Mohsenipour, Ali Asghar [University of Waterloo, Department of Chemical Engineering, Waterloo (Canada)

    2009-09-15

    It is the purpose of this paper to extract unlike intermolecular potential energies of five carbon dioxide-based binary gas mixtures including CO{sub 2}-He, CO{sub 2}-Ne, CO{sub 2}-Ar, CO{sub 2}-Kr, and CO{sub 2}-Xe from viscosity data and compare the calculated potentials with other models potential energy reported in literature. Then, dilute transport properties consisting of viscosity, diffusion coefficient, thermal diffusion factor, and thermal conductivity of aforementioned mixtures are calculated from the calculated potential energies and compared with literature data. Rather accurate correlations for the viscosity coefficient of afore-cited mixtures embracing the temperature range 200 Kintermolecular potentials energy. Our estimated accuracies for the viscosity are to within {+-}2%. In addition, the calculated potential energies are used to present smooth correlations for other transport properties. The accuracies of the binary diffusion coefficients are of the order of {+-}3%. Finally, the unlike interaction energy and the calculated low density viscosity have been employed to calculate high density viscosities using Vesovic-Wakeham method. (orig.)

  17. Tuning intermolecular interactions in dioctyl-substituted polyfluorene via hydrostatic pressure.

    Paudel, K; Knoll, H; Chandrasekhar, M; Guha, S

    2010-04-01

    Polyfluorenes (PFs) represent a unique class of poly-para-phenylene-based blue-emitting polymers with intriguing structure-property relationships. Slight variations in the choice of functionalizing side chains result in dramatic differences in the inter- and intrachain structures in PFs. Dioctyl-substituted PF (PF8) is characterized by different backbone conformations that depend upon the torsion angle between the monomers. We present photoluminescence (PL) and Raman scattering studies of bulk samples and thin films of dioctyl-substituted PF (PF8) under hydrostatic pressure. The bulk sample was further thermally annealed and studied as a function of pressure. The PL energies of the as-is and thermally annealed samples both red shift but at very different rates, and the difference between their pressure coefficients elucidates the role of the backbone torsional angle. This is further corroborated by density functional theoretical calculations of a fluorene oligomer, where the energy gap is calculated as a function of both the torsion angle as well as compression. The Raman peaks harden with increasing pressures; the intraring C-C stretch frequency at 1600 cm(-1) has a pressure coefficient of 7.2 cm(-1)/GPa and exhibits asymmetric line shapes at higher pressures, characteristic of a strong electron-phonon interaction. PMID:20235499

  18. Formation of intermolecular crosslinks by the actinocin derivatives with DNA in interaction under conditions of semidilute solution

    Interaction of native calf thymus DNA (ctDNA) with the actinocin derivatives containing protonated diethylamino groups, dimethylamino groups and unsubstituted amino groups and having different length of the alkyl chain have been studied by the method of viscometry. An anomalous hydrodynamic behavior of solutions of DNA with very low amount of ligands prepared under conditions of semidilute solution was revealed. We assumed that such an anomalous behavior of solutions of DNA complexes with actinocin derivatives associated with the formation of intermolecular crosslinks while the preparation of the complex was in terms of overlapping of macromolecular coils in solution. Comparative study of the hydrodynamic behavior of the DNA complexes with various actinocin structures lead us to the conclusion of the formation of crosslinks by the compounds containing protonated diethylamino groups

  19. Quaternion contact ribbons: a new tool for visualizing intra- and intermolecular interactions in proteins.

    Albrecht, K; Hart, J; Shaw, A; Dunker, A K

    1996-01-01

    Protein side chain interactions between residues separated by at least one loop or turn or break in the amino acid sequence are called 'nonlocal contacts' in this manuscript, and contiguous sets of such interactions located between segments of secondary structure are called 'contact zones.' A new interactive program, the quaternion contact ribbon tool, has been developed to help protein chemists identify, straighten if twisted, and display contact zones between two neighboring segments of helix. PMID:9390222

  20. Study of intermolecular interactions in binary mixtures of 2-(dimethylamino)ethanol with methanol and ethanol at various temperatures

    Graphical abstract: The densities and ultrasonic speeds of the binary mixtures over the entire composition range were measured at various temperatures at atmospheric pressure. The excess molar volumes, isentropic compressibilities, and molar isentropic compressions have been calculated. The variations of these parameters with composition and temperature are discussed. The IR spectra were recorded they further supported the conclusion drawn from excess parameters, which indicates the presence of intermolecular hydrogen bonding between the oxygen atom of DMAE molecules and hydrogen atom of methanol and ethanol molecules in these mixtures.. - Highlights: • The study reports density and ultrasonic velocity data of 2-(dimethylamino)ethanol + methanol/ethanol mixtures. • To elucidate the interactions in 2-(dimethylamino)ethanol + methanol/ethanol binary mixtures. • Provides information on nature and relative strength of interactions in these mixtures. • Correlates physicochemical properties with interactions in these mixtures. - Abstract: The densities, ρ and ultrasonic speeds, u of the binary mixtures of 2-(dimethylamino)ethanol (DMAE) with methanol/ethanol, including those of pure liquids, over the entire composition range were measured at 298.15, 308.15 and 318.15 K. From the experimental data, the excess molar volumes, VmE and excess isentropic compressibilities, κsE have been calculated. The excess partial molar volumes, V¯m,1E and V¯m,2E and excess partial molar isentropic compressions, K¯s,m,1E and K¯s,m,2E over the whole composition range; and partial molar volumes, V¯m,1° and V¯m,2°, partial molar isentropic compressions, K¯s,m,1° and K¯s,m,2°, excess partial molar volumes, V¯m,1°E and V¯m,2°E, and excess partial molar isentropic compressions, K¯s,m,1°E and K¯s,m,2°E at infinite dilution have also been calculated. The variations of these parameters with composition and temperature are discussed in terms of intermolecular

  1. Investigation of intermolecular interactions between single walled nanotubes and conjugated oligomers using the dispersion-corrected DFT methods

    Lagowski, Jolanta B.; Aljohani, Suad; Khan, M. Zahidul H.; Zhao, Yuming

    The area of carbon nanotubes (CNT)-polymer composites has been progressing rapidly in recent years. Pure CNT and CNT-polymer composites have many useful (industry related) properties: ranging from electronic electrical conductivity to superior strength. However the full potential of using CNTs as reinforcements (in say a polymer matrix) has been severely limited because of complications associated with the dispersion of CNTs. CNTs tend to entangle with each other forming materials that have properties that fall short of the expectations. The goal of this work is to identify the type of conjugated oligomers that are best suited for the dispersion of single walled CNT (SWCNT). For this purpose, various methods of dispersion corrected density functional theory (DFT-D/B97D, /WB97XD, /CAM-B3LYP) have been used to investigate the interaction between the SWCNT and the organic conjugated oligomers with different end groups (aldehyde (ALD) and dithiafulvenyl (DTF)). We investigate the effect of intermolecular interactions on the structure, polarity and energetics of the oligomers and SWCNT combinations. The comparison of results obtained using different DFT approximations is made. Our results show that DFT-endcapped oligomer interact more strongly with CNT than ALD-endcapped oligomer. The financial support from NSERC, SACBC and Memorial University and the computational resources from Compute Canada were received.

  2. Reliable prediction of three-body intermolecular interactions using dispersion-corrected second-order Møller-Plesset perturbation theory

    Three-body and higher intermolecular interactions can play an important role in molecular condensed phases. Recent benchmark calculations found problematic behavior for many widely used density functional approximations in treating 3-body intermolecular interactions. Here, we demonstrate that the combination of second-order Møller-Plesset (MP2) perturbation theory plus short-range damped Axilrod-Teller-Muto (ATM) dispersion accurately describes 3-body interactions with reasonable computational cost. The empirical damping function used in the ATM dispersion term compensates both for the absence of higher-order dispersion contributions beyond the triple-dipole ATM term and non-additive short-range exchange terms which arise in third-order perturbation theory and beyond. Empirical damping enables this simple model to out-perform a non-expanded coupled Kohn-Sham dispersion correction for 3-body intermolecular dispersion. The MP2 plus ATM dispersion model approaches the accuracy of O(N6) methods like MP2.5 or even spin-component-scaled coupled cluster models for 3-body intermolecular interactions with only O(N5) computational cost

  3. Intermolecular spectroscopy of gases

    Spectroscopic techniques have been very successfully applied to the study of individual molecules. The same techniques can also be used to investigate intermolecular interactions. Collision-induced absorption (CIA) and collision-induced light scattering (CILS) are important examples of intermolecular interactions. These effects can be described by the dynamical information contained in the general intermolecular correlation functions. One of the aims of this review is to stress the central role of these correlation functions in the field of intermolecular spectroscopy. Because they have a well-defined physical meaning, they are very suitable for the purpose of introducing new physical approximations, particularly in the case of liquids. Some aspects of the theory of CIA will be discussed, mainly as applied to gases. References to similar situations in CILS will occasionally be made, but no comprehensive review will be attempted. One of the basic quantities in CIA is the absorption coefficient. The question is investigated wether it can be expanded in powers of the density. Finally, the moments of the spectrum, interference effects and line shapes are discussed. (KBE)

  4. Intermolecular interactions of the p85alpha regulatory subunit of phosphatidylinositol 3-kinase

    Harpur, A G; Layton, M. J.; Das, P; Bottomley, M J; Panayotou, G.; Driscoll, P. C.; Waterfield, M D

    1999-01-01

    The regulatory subunit of phosphatidylinositol 3-kinase, p85, contains a number of well defined domains involved in protein-protein interactions, including an SH3 domain and two SH2 domains. In order to investigate in detail the nature of the interactions of these domains with each other and with other binding partners, a series of deletion and point mutants was constructed, and their binding characteristics and apparent molecular masses under native conditions were analyzed. The SH3 domain a...

  5. 12C/13C and H/D vapor pressure isotope effects of fluoroform: intermolecular interactions in liquid fluoroform

    A precision cryostat of the Bigeleisen-Brooks-Ribnikar-Ishida (BBIR) type with associated vacuum systems has been constructed and the appropriate temperature/pressure measurement and control systems designed and implemented. Various improvements in the cryostat design were incorporated in order to facilitate the assembly and repair processes. A major design change involved the incorporation of a digital stand alone computer to control cryostat operations. This apparatus was used to measure the 12C/13C and H/D Vapor Pressure Isotope Effects of Fluoroform. Analysis of the measured VPIE results, in light of existing experimental data and theories, has demonstrated the need of a temperature dependent liquid force field, specifically a temperature-dependent interaction force constant between the C-H stretching motion and translational motion in the direction of the figure axis of CHF3. This result is consistent with the observed spectroscopic data and vibrational and configurational models of fluoroform dimers. The intermolecular interaction is believed to be a weak hydrogen-bond in nature

  6. [Intermolecular Interactions between Cytisine and Bovine Serum Albumin A Synchronous Fluorescence Spectroscopic Analysis and Molecular Docking Research].

    Wu, Yu-hang; Han, Zhong-bao; Ma, Jia-ze; He, Yan; Liu, Li-yan; Xin, Shi-gang; Yu, Zhan

    2016-03-01

    Cytisine (Cy) is one of the alkaloids that exist naturally in the plant genera Laburnum of the family Fabaceae. With strong bioactivities, Cy is commercialized for smoking cessation for years. In this work, the study of intermolecular interactions between Cy and bovine serum albumin (BSA) was performed by applying fluorescence spectroscopic methods under simulated physiological conditions. The mechanism of fluorescence quenching of BSA by Cy was also studied. Parameters such as bathing temperature, time and solution pH were investigated to optimize the fluorescence quenching. The binding type, binding ratio and binding constant between BSA and Cy were calculated by using the Stem-Volmer equation. Experimental results indicated that Cy can quench the fluorescent emission of BSA statically by forming a 1 : 1 type non-covalent complex and the binding constant is 5.6 x 10(3) L x mol(-1). Synchronous fluorescence spectral research shows Cy may affect the fluorescence emission of Trp residues of BSA. Furthermore, molecular docking is utilized to model the complex and probe the plausible quenching mechanism. It can be noted that the hydrogen bindings and hydrophobic interactions between Cy and BSA change the micro-environment of Trp213, which leads to the fluorescence quenching of BSA. PMID:27400521

  7. Oligophenylenevinylenes in spatially confined nanochannels: Monitoring intermolecular interactions by UV/Vis and Raman spectroscopy

    Aloshyna, Mariya; Medina, Begona Milian; Poulsen, Lars; Moreau, Juliette; Beljonne, David; Cornil, Jerome; Silvestro, Giuseppe Di; Cerminara, Michele; Meinardi, Francesco; Tubino, Riccardo; Detert, Heiner; Schrader, Sigurd; Egelhaaf, Hans-Joachim; Botta, Chiara; Gierschner, Johannes

    2008-01-01

    -guest interactions are elucidated by UV/Vis and Raman spectroscopy. The impact of the local environment of the chromophore on the optical and photophysical properties is discussed in light of quantum-chemical calculations. In stark contrast to thin films where preferential side-by-side orientation leads to quenching...

  8. Intermolecular forces, spontaneous emission, and superradiance in a dielectric medium : Polariton-mediated interactions

    Knoester, Jasper; Mukamel, Shaul

    1989-01-01

    A reduced equation of motion that describes the excited-state dynamics of interacting two-level impurity molecules in a dielectric host crystal is derived starting from a microscopic model for the total system. Our theory generalizes the derivation of the conventional superradiance master equation f

  9. De novo design of protein-protein interactions through modification of inter-molecular helix-helix interface residues.

    Yagi, Sota; Akanuma, Satoshi; Yamagishi, Manami; Uchida, Tatsuya; Yamagishi, Akihiko

    2016-05-01

    For de novo design of protein-protein interactions (PPIs), information on the shape and chemical complementarity of their interfaces is generally required. Recent advances in computational PPI design have allowed for de novo design of protein complexes, and several successful examples have been reported. In addition, a simple and easy-to-use approach has also been reported that arranges leucines on a solvent-accessible region of an α-helix and places charged residues around the leucine patch to induce interactions between the two helical peptides. For this study, we adopted this approach to de novo design a new PPI between the helical bundle proteins sulerythrin and LARFH. A non-polar patch was created on an α-helix of LARFH around which arginine residues were introduced to retain its solubility. The strongest interaction found was for the LARFH variant cysLARFH-IV-3L3R and the sulerythrin mutant 6L6D (KD=0.16 μM). This artificial protein complex is maintained by hydrophobic and ionic interactions formed by the inter-molecular helical bundle structure. Therefore, by the simple and easy-to-use approach to create de novo interfaces on the α-helices, we successfully generated an artificial PPI. We also created a second LARFH variant with the non-polar patch surrounded by positively charged residues at each end. Upon mixing this LARFH variant with 6L6D, mesh-like fibrous nanostructures were observed by atomic force microscopy. Our method may, therefore, also be applicable to the de novo design of protein nanostructures. PMID:26867971

  10. Tuning of intermolecular interactions results in packing diversity in imidazolin-5-ones

    Ashish Singh; Basanta Kumar Rajbongshi; Gurunath Ramanathan

    2014-09-01

    Crystal structures of four green fluorescent protein (GFP) chromophore analogues with different packing interactions could be tuned by appropriate substitutions around the imidazolin-5-one ring are reported here. Compound 1 was crystallized from tetrahydrofuran at room temperature while compounds 2-4 have been crystallized from a mixture of methanol and dichloromethane in 3:1 ratio. Molecule 1, 2 and 3 crystallized in monoclinic lattice while molecule 4 preferred to crystallize in a triclinic crystal system. The crystal packing of these molecules was stabilized by C-H$\\ldots$ stacking and C-H $\\ldots$ O type of supramolecular interactions. The results reveal that packing diversity can be easily accomplished in these molecules by tuning the substituents around the imidazolin-5-one ring. Photophysical studies also reveal that all have good quantum yield and fluoresce typically in red region due to presence of electron donating groups around the imidazolin-5-one ring.

  11. Structural investigations on N'-substituted N-acylguanidines - Intermolecular interactions with solvents, anions and receptors

    Kleinmaier, Roland

    2011-01-01

    Acylguanidines are an abundant class of compounds with various applications in organic and pharmaceutical chemistry. Within the subgroup of N’-substituted and especially monoalkylated N-acylguanidines, highly potent and selective ligands for G protein coupled receptors have been identified in recent years. In the field of molecular recognition, acylguanidines are valued for their ability to form strong fork-like hydrogen bond (H-bond) interactions with carboxylate anions. Although their basic...

  12. Intermolecular interactions in cyclic complexes with hydrogen bond of bifunctional N-containing compounds in solution

    The structure of molecular and ionic hydrogen-bonded complexes formed by bifunctional N-containing molecules, which can act as proton donor and proton acceptor simultaneously, and the nature of molecular interactions in these complexes were studied in solution. The spectroscopic, steric and thermodynamic characteristics of self-associates of 3,5-dimethylpyrazole, diphenylformamidine, diphenylguanidine and diphenyltriazene and complexes of these compounds with carboxylic acids were obtained. The quantum chemical calculations of the structure of complexes and the vibrational frequencies in IR spectra were carried out in the harmonic approximation and with the anharmonic effects taken into account. It was shown that under the interaction with weak carboxylic acids (HCOOH, CH3COOH, CH2ClCOOH) the complexes have molecular structure with two H-bonds NH...O=C and OH...N, and the interaction with strong acids (CHCl2COOH, CCl3COOH, CF3COOH) results in formation of cyclic hydrogen-bonded ionic pairs with proton transfer from hydroxyl group to the N atom of the azo-compound. (authors)

  13. Studies on intermolecular interaction on binary mixtures of methyl orange-water system: excess molar functions of ultrasonic parameters at different concentrations and at different temperatures.

    Thanuja, B; Kanagam, Charles; Sreedevi, S

    2011-11-01

    Density (ρ), viscosity (η) and ultrasonic velocity (u) of binary mixtures of methyl orange and water were measured at different concentrations and at different temperatures; several useful parameters such as excess volume, excess velocity, and excess adiabatic compressibility have been calculated. These parameters are used to explain the nature of intermolecular interactions taking place in the binary mixture. The above study is helpful in understanding the dye/solvent interaction at different concentration and temperatures. PMID:21596612

  14. Quantifying intermolecular interactions in solid state indapamide and other popular diuretic drugs: Insights from Hirshfeld surface study

    Bojarska, Joanna; Fruziński, Andrzej; Maniukiewicz, Waldemar

    2016-07-01

    Hirshfeld surfaces (HS) and two-dimensional fingerprint plots are used to analyze the intermolecular interactions in indapamide and other popular thiazide diuretic derivatives. The crystal structure of indapamide (INDP) at 100 K determined by single-crystal X-ray analysis, is also reported. The title compound crystallizes in the centrosymmetric I2/a space group with one indapamide and half water molecule (lying on the glide plane) in the asymmetric unit. An interplay of N-H⋯O hydrogen bonds connects the indapamide molecules generating chains with the graph-set motifs: C (8) and C23 (16), and together with C-H⋯O and π⋯π stacking interactions create a 3D net. The Hirshfeld surface study facilitates comparison of diverse and numerous intercontacts, such as H⋯H, O⋯H, Cl⋯H, C⋯C (π⋯π), C⋯O (π⋯lone pair), O⋯O (lone pair⋯lone pair), Cl⋯O, Cl⋯Cl, N⋯N, C⋯H (C-H⋯π) with regard to building self-assembled framework of indapamide and related thiazide derivatives retrieved from the Cambridge Structural Database. The HS analysis highlights that H⋯H, O⋯H/H⋯O and C⋯H/H⋯C contacts play an influential role contributing to about 80% of the HS areas in this class of compounds. Nevertheless, in the case of INDP the H⋯H interactions, while in hydrochlorothiazide (HCTZ) O⋯H/H⋯O are dominant amongst all intercontacts towards the HS. Notably, indapamide has the highest proportion of C⋯C contacts.

  15. Competing intermolecular interactions of artemisinin-type agents and aspirin with membrane phospholipids: Combined model mass spectrometry and quantum-chemical study

    Highlights: • Competitive binding of artemisinin agents and aspirin with phospholipids is shown. • Complexation between the antimalarial drugs and aspirin molecules is also found. • Energetically favorable structures of the model complexes are identified by DFT. • Membranotropic activity of the studied drugs can be modified under joint usage. - Abstract: Study of intermolecular interactions of antimalarial artemisinin-type drugs and aspirin with membrane phospholipids is important in term of elucidation of the drugs activity modification under their joint usage. Combined experimental and computational study of the interaction of dihydroartemisinin, α-artemether, and artesunate with aspirin (ASP) and dipalmitoylphosphatidylcholine (DPPC) is performed by electrospray ionization (ESI) mass spectrometry and by DFT B3LYP/aug-cc-pVDZ methods. The results of the ESI investigation of systems containing artemisinin-type agent, ASP and DPPC, reveal a competition between the antimalarial agents and ASP for binding with DPPC molecules. The complexation between the antimalarial drugs and ASP is also found. Observed phenomena suggest that membranotropic activity of artemisin-type agents and aspirin is modified under their combined usage. To elucidate structure-energy characteristics of the non-covalent complexes studied the model DFT calculations are performed for dihydroartemisinin · ASP complex and complexes of the each drug with phosphatidylcholine head of DPPC in neutral and cationized forms

  16. Competing intermolecular interactions of artemisinin-type agents and aspirin with membrane phospholipids: Combined model mass spectrometry and quantum-chemical study

    Pashynska, Vlada, E-mail: vlada@vl.kharkov.ua [B.Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine, Lenin Ave., 47, 61103 Kharkov (Ukraine); Stepanian, Stepan [B.Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine, Lenin Ave., 47, 61103 Kharkov (Ukraine); Gömöry, Agnes; Vekey, Karoly [Institute of Organic Chemistry of Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Magyar tudosok korutja, 2, Budapest H-1117 (Hungary); Adamowicz, Ludwik [University of Arizona, Department of Chemistry and Biochemistry, Tucson, AZ 85721 (United States)

    2015-07-09

    Highlights: • Competitive binding of artemisinin agents and aspirin with phospholipids is shown. • Complexation between the antimalarial drugs and aspirin molecules is also found. • Energetically favorable structures of the model complexes are identified by DFT. • Membranotropic activity of the studied drugs can be modified under joint usage. - Abstract: Study of intermolecular interactions of antimalarial artemisinin-type drugs and aspirin with membrane phospholipids is important in term of elucidation of the drugs activity modification under their joint usage. Combined experimental and computational study of the interaction of dihydroartemisinin, α-artemether, and artesunate with aspirin (ASP) and dipalmitoylphosphatidylcholine (DPPC) is performed by electrospray ionization (ESI) mass spectrometry and by DFT B3LYP/aug-cc-pVDZ methods. The results of the ESI investigation of systems containing artemisinin-type agent, ASP and DPPC, reveal a competition between the antimalarial agents and ASP for binding with DPPC molecules. The complexation between the antimalarial drugs and ASP is also found. Observed phenomena suggest that membranotropic activity of artemisin-type agents and aspirin is modified under their combined usage. To elucidate structure-energy characteristics of the non-covalent complexes studied the model DFT calculations are performed for dihydroartemisinin · ASP complex and complexes of the each drug with phosphatidylcholine head of DPPC in neutral and cationized forms.

  17. Weak interactions in barbituric acid derivatives. Unusually steady intermolecular organic “sandwich” complexes. π π Stacking versus hydrogen bonding interactions

    Khrustalev, Victor N.; Krasnov, Konstantin A.; Timofeeva, Tatiana V.

    2008-04-01

    The 4-methoxy-6,6-dimethyl-5,6,7,8-tetrahydro[1,3]dioxolo[4,5- g]isoquinolin-6-ium ( 1) and 2-(1 H-indol-3-yl)-1-ethanaminium (tryptaminium) ( 2) salts of 1,3-dimethyl-2,4,6-trioxoperhydro-pyrimidine-5-spiro-6'-{4'-methoxy-7'-(1,3-dimethyl-2,4,6-trioxoper-hydropyrimidin-5-yl)-5',6',7',8'-tetrahydro[1,3]dioxolo[4,5- g]naphthalene} ( 3) have been prepared and their structures have been investigated by single-crystal X-ray diffraction analysis. It has been found on the basis of the crystal packing arrangement as well as physical and chemical properties that derivatives 1 and 2 form unusually steady intermolecular sandwich-like complexes both in the crystal and in solution, which are stabilized by weak C sbnd H… n(O dbnd C) hydrogen bonds and π-π stacking. The interplay between the intermolecular π-π stacking and strong N sbnd H…O hydrogen bond interactions and its influence on the "sandwich" structures of 1 and 2 are discussed.

  18. Redetermined structure, inter-molecular inter-actions and absolute configuration of royleanone.

    Fun, Hoong-Kun; Chantrapromma, Suchada; Salae, Abdul Wahab; Razak, Ibrahim Abdul; Karalai, Chatchanok

    2011-05-01

    The structure of the title diterpenoid, C(20)H(28)O(3), {systematic name: (4bS,8aS)-3-hy-droxy-2-isopropyl-4b,8,8-trimethyl-4b,5,6,7,8,8a,9,10-octa-hydro-phenanthrene-1,4-dione} is confirmed [Eugster et al. (1993 ▶). Private communication (refcode HACGUN). CCDC, Union Road, Cambridge] and its packing is now described. Its absolute structure was established by refinement against data collected with Cu radiation: the two stereogenic centres both have S configurations. One cyclo-hexane ring adopts a chair conformation whereas the other cyclo-hexane ring is in a half-chair conformation and the benzoquinone ring is slightly twisted. An intra-molecular O-H⋯O hydrogen bond generates an S(5) ring motif. In the crystal, mol-ecules are linked into chains along [010] by O-H⋯O hydrogen bonds and weak C-H⋯O inter-actions. The packing also features C⋯O [3.131 (3) Å] short contacts. PMID:21754362

  19. Spectroscopic Characterization of Intermolecular Interaction of Amyloid β Promoted on GM1 Micelles

    Maho Yagi-Utsumi

    2011-01-01

    Full Text Available Clusters of GM1 gangliosides act as platforms for conformational transition of monomeric, unstructured amyloid β (Aβ to its toxic β-structured aggregates. We have previously shown that Aβ(1–40 accommodated on the hydrophobic/hydrophilic interface of lyso-GM1 or GM1 micelles assumes α-helical structures under ganglioside-excess conditions. For better understanding of the mechanisms underlying the α-to-β conformational transition of Aβ on GM1 clusters, we performed spectroscopic characterization of Aβ(1–40 titrated with GM1. It was revealed that the thioflavin T- (ThT- reactive β-structure is more populated in Aβ(1–40 under conditions where the Aβ(1–40 density on GM1 micelles is high. Under this circumstance, the C-terminal hydrophobic anchor Val39-Val40 shows two distinct conformational states that are reactive with ThT, while such Aβ species were not generated by smaller lyso-GM1 micelles. These findings suggest that GM1 clusters promote specific Aβ-Aβ interactions through their C-termini coupled with formation of the ThT-reactive β-structure depending on sizes and curvatures of the clusters.

  20. Fabrication and Intermolecular Interactions of Silk Fibroin/Hydroxybutyl Chitosan Blended Nanofibers

    Xiu-Mei Mo

    2011-03-01

    Full Text Available The native extracellular matrix (ECM is composed of a cross-linked porous network of multifibril collagens and glycosaminoglycans. Nanofibrous scaffolds of silk fibroin (SF and hydroxybutyl chitosan (HBC blends were fabricated using 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP and trifluoroacetic acid (TFA as solvents to biomimic the native ECM via electrospinning. Scanning electronic microscope (SEM showed that relatively uniform nanofibers could be obtained when 12% SF was blended with 6% HBC at the weight ratio of 50:50. Meanwhile, the average nanofibrous diameter increased when the content of HBC in SF/HBC blends was raised from 20% to 100%. Fourier transform infrared spectra (FTIR and 13C nuclear magnetic resonance (NMR showed SF and HBC molecules existed in hydrogen bonding interactions but HBC did not induce conformation of SF transforming from random coil form to β-sheet structure. X-ray diffraction (XRD confirmed the different structure of SF/HBC blended nanofibers from both SF and HBC. Thermogravimetry-Differential thermogravimetry (TG-DTG results demonstrated that the thermal stability of SF/HBC blend nanofibrous scaffolds was improved. The results indicated that the rearrangement of HBC and SF molecular chain formed a new structure due to stronger hydrogen bonding between SF and HBC. These electrospun SF/HBC blended nanofibers may provide an ideal tissue engineering scaffold and wound dressing.

  1. Intermolecular potential energy surface and thermophysical properties of the CH4-N2 system

    Hellmann, Robert; Bich, Eckard; Vogel, Eckhard; Vesovic, Velisa

    2014-12-01

    A five-dimensional potential energy surface (PES) for the interaction of a rigid methane molecule with a rigid nitrogen molecule was determined from quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the CCSD(T) level of theory was utilized to compute a total of 743 points on the PES. The interaction energies were calculated using basis sets of up to quadruple-zeta quality with bond functions and were extrapolated to the complete basis set limit. An analytical site-site potential function with nine sites for methane and five sites for nitrogen was fitted to the interaction energies. The PES was validated by calculating the cross second virial coefficient as well as the shear viscosity and binary diffusion coefficient in the dilute-gas limit for CH4-N2 mixtures. An improved PES was obtained by adjusting a single parameter of the analytical potential function in such a way that quantitative agreement with the most accurate experimental values of the cross second virial coefficient was achieved. The transport property values obtained with the adjusted PES are in good agreement with the best experimental data.

  2. Fine structures in vibrational circular dichroism spectra of chiral molecules with rotatable hydroxyl groups and their application in the analysis of local intermolecular interactions

    Konno, Kohzo; Shiina, Isamu; Yui, Hiroharu

    2013-03-01

    The effect of hydroxyl group on vibrational circular dichroism is addressed. (-)-Menthol is investigated as a representative chiral molecule which has been widely used as a chiral starting material. Free rotation of the hydroxyl group in (-)-menthol allows it to exist in various conformations in solution. The variety of conformations inevitably affects local intermolecular interactions and the resultant efficiency of asymmetric syntheses. However, the precise relationship between the conformations and intermolecular interactions arising from rotation of the hydroxyl group has remained an unsolved issue despite the molecule's importance. Here, the conformations and interactions are investigated using vibrational circular dichroism (VCD). VCD is quite sensitive to slight differences in the conformation of chiral molecules and their local environment. We examined various conformers in (-)-menthol and compared the VCD spectrum with that of (-)-menthone. It revealed the rotation of the polar hydroxyl group sensitively affects the VCD activity, resulting in the emergence of various patterns in the corresponding VCD spectra, especially in the wavenumber regions at around 1064 cm-1 and 1254 cm-1. Among these regions, the latter one is further investigated to examine the feasibility of applying the sensitive response to the analysis on the local intermolecular environment. It includes solute-solvent interactions via hydroxyl groups, which is important for biomacromolecule structural stability and efficient stereoselective syntheses. As a consequence, distinctive fine structures in the VCD spectra, including an unpredicted band, are observed when varying temperature and concentration. Their possible assignment is also discussed.

  3. Push it to the limit: Characterizing the convergence of common sequences of basis sets for intermolecular interactions as described by density functional theory.

    Witte, Jonathon; Neaton, Jeffrey B; Head-Gordon, Martin

    2016-05-21

    With the aim of systematically characterizing the convergence of common families of basis sets such that general recommendations for basis sets can be made, we have tested a wide variety of basis sets against complete-basis binding energies across the S22 set of intermolecular interactions-noncovalent interactions of small and medium-sized molecules consisting of first- and second-row atoms-with three distinct density functional approximations: SPW92, a form of local-density approximation; B3LYP, a global hybrid generalized gradient approximation; and B97M-V, a meta-generalized gradient approximation with nonlocal correlation. We have found that it is remarkably difficult to reach the basis set limit; for the methods and systems examined, the most complete basis is Jensen's pc-4. The Dunning correlation-consistent sequence of basis sets converges slowly relative to the Jensen sequence. The Karlsruhe basis sets are quite cost effective, particularly when a correction for basis set superposition error is applied: counterpoise-corrected def2-SVPD binding energies are better than corresponding energies computed in comparably sized Dunning and Jensen bases, and on par with uncorrected results in basis sets 3-4 times larger. These trends are exhibited regardless of the level of density functional approximation employed. A sense of the magnitude of the intrinsic incompleteness error of each basis set not only provides a foundation for guiding basis set choice in future studies but also facilitates quantitative comparison of existing studies on similar types of systems. PMID:27208948

  4. Role of intermolecular interactions on the electronic and geometric structure of a large Pi-conjugated molecule adsorbed on a metal surface

    Kilian, L.; Hauschild, A.; Temirov, R.; Soubatch, S.; Schoell, A.; Bendounan, A.; Reinert, F.; Lee, T. L.; Tautz, F. S.; Sokolowski, M.; Umbach, E

    2008-01-01

    The organic semiconductor molecule 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) exhibits two adsorption states on the Ag(111) surface: one in a metastable disordered phase, prepared at low temperatures, the other in the long-range ordered monolayer phase obtained at room temperature. Notably, the two states differ substantial in their vertical bonding distances, intramolecular distortions, and electronic structures. The difference is explained by intermolecular interactions, which ar...

  5. Collecting high-order interactions in an effective pairwise intermolecular potential using the hydrated ion concept: The hydration of Cf{sup 3+}

    Galbis, Elsa; Pappalardo, Rafael R.; Marcos, Enrique Sánchez, E-mail: sanchez@us.es [Departmento de Química Física, Universidad de Sevilla, 41012 Seville (Spain); Hernández-Cobos, Jorge [Instituto de Ciencias Físicas, UNAM, Apartado Postal 48-3, 62251 Cuernavaca (Mexico)

    2014-06-07

    This work proposes a new methodology to build interaction potentials between a highly charged metal cation and water molecules. These potentials, which can be used in classical computer simulations, have been fitted to reproduce quantum mechanical interaction energies (MP2 and BP86) for a wide range of [M(H{sub 2}O){sub n}]{sup m+}(H{sub 2}O){sub ℓ} clusters (n going from 6 to 10 and ℓ from 0 to 18). A flexible and polarizable water shell model (Mobile Charge Density of Harmonic Oscillator) has been coupled to the cation-water potential. The simultaneous consideration of poly-hydrated clusters and the polarizability of the interacting particles allows the inclusion of the most important many-body effects in the new polarizable potential. Applications have been centered on the californium, Cf(III) the heaviest actinoid experimentally studied in solution. Two different strategies to select a set of about 2000 structures which are used for the potential building were checked. Monte Carlo simulations of Cf(III)+500 H{sub 2}O for three of the intermolecular potentials predict an aquaion structure with coordination number close to 8 and average R{sub Cf−−O} in the range 2.43–2.48 Å, whereas the fourth one is closer to 9 with R{sub Cf−−O} = 2.54 Å. Simulated EXAFS spectra derived from the structural Monte Carlo distribution compares fairly well with the available experimental spectrum for the simulations bearing 8 water molecules. An angular distribution similar to that of a square antiprism is found for the octa-coordination.

  6. Comparison of the Effective Fragment Potential Method with Symmetry-Adapted Perturbation Theory in the Calculation of Intermolecular Energies for Ionic Liquids.

    Tan, Samuel Y S; Izgorodina, Ekaterina I

    2016-06-14

    The effective fragment potential (EFP) method that decomposes the interaction energy as a sum of the five fundamental forces-electrostatic, exchange-repulsion, polarization, dispersion, and charge transfer-was applied to a large test set of ionic liquid ion pairs and compared against the state-of-the-art method, Symmetry-Adapted Perturbation Theory (SAPT). The ion pairs include imidazolium and pyrrolidinium cations combined with anions that are routinely used in the field of ionic liquids. The aug-cc-pVDZ, aug-cc-pVTZ, and 6-311++G(d,p) basis sets were used for EFP, while SAPT2+3/aug-cc-pVDZ provided the benchmark energies. Differences between the two methods were found to be large, and strongly dependent on the anion type. For the aug-cc-pVTZ basis set, which produced the least errors, average relative errors were between 2.3% and 18.4% for pyrrolidinium ion pairs and between 2.1% and 27.7% for imidazolium ion pairs for each individual energetic component (excluding charge transfer), as well as the total interaction energy. Charge transfer gave the largest relative errors: 56% and 63% on average for pyrrolidinium- and imidazolium-based ion pairs, respectively. Scaling of the EFP components against SAPT2+3 showed improvement for polarization (induction) and dispersion terms, thus indicating potential for the development of cost-effective alternatives for intermolecular induction and dispersion potentials for ionic liquids. PMID:27116302

  7. Intramolecular photo-switching and intermolecular energy transfer as primary photoevents in photoreceptive processes: The case of Euglena gracilis

    In this paper we report the results of measurements performed by FLIM on the photoreceptor of Euglenagracilis. This organelle consists of optically bistable proteins, characterized by two thermally stable isomeric forms: A498, non fluorescent and B462, fluorescent. Our data indicate that the primary photoevent of Euglena photoreception upon photon absorption consists of two contemporaneous different phenomena: an intramolecular photo-switch (i.e., A498 becomes B462), and a intermolecular and unidirectional Forster-type energy transfer. During the FRET process, the fluorescent B462 form acts as donor for the non-fluorescent A498 form of the protein nearby, which acts as acceptor. We hypothesize that in nature these phenomena follow each other with a domino progression along the orderly organized and closely packed proteins in the photoreceptor layer(s), modulating the isomeric composition of the photoreceptive protein pool. This mechanism guarantees that few photons are sufficient to produce a signal detectable by the cell.

  8. Benchmark Calculations of Three-Body Intermolecular Interactions and the Performance of Low-Cost Electronic Structure Methods

    Řezáč, Jan; Huang, Y.; Hobza, Pavel; Beran, G. J. O.

    2015-01-01

    Roč. 11, č. 7 (2015), s. 3065-3079. ISSN 1549-9618 R&D Projects: GA ČR GP13-01214P; GA ČR GBP208/12/G016 Institutional support: RVO:61388963 Keywords : density functional theory * Plesset perturbation theory * noncovalent interactions * interaction energies Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.498, year: 2014

  9. Study on Application of Model Core Potential to Intermolecular Interaction%模型势MCP应用于分子间相互作用的研究

    赵秀英; 孙涛; 王一波

    2011-01-01

    使用模型势MCP计算了含重元素的氢键和vail der Waals相互作用体系的几何结构与结合能。结果表明,在MP2水平,应用MCP基组研究分子间相互作用时,可以使用Boys和Bernardi提出的均衡校正法进行基函数重叠误差(BSSE)校正;与同一水平的全电子基组相比,经BSSE校正后的结合能AEcP平均相对误差为5.2%,结果准确,但是BSSE普遍较大;使用MCP基组的计算时间远小于全电子基组,MCP方法的效率随原子的电子层数增加而提高。%We use Model Core Potential to calculate the geometry and binding energy of systems with heavy elements that consist hydrogen bond and van der Walls. The results show that we can use the counterpoise method proposed by Boys and Bernardi when studying intermolecular interactions within MCP basis sets at MP2 level. Compared to all-electron basis sets at the same level, the average relative error of binding energy was 5.2 %. This result was accurate, but BSSE was generally large for MCP basis sets. The calculation time was much shorter for MCP basis sets than that of all-electron basis sets. Also, the efficiency of MCP method is improved with the increase of the core electron shell of heavy elements.

  10. The origins of intra- and inter-molecular vibrational couplings: A case study of H{sub 2}O-Ar on full and reduced-dimensional potential energy surface

    Hou, Dan; Ma, Yong-Tao; Zhang, Xiao-Long; Li, Hui, E-mail: Prof-huili@jlu.edu.cn [Institute of Theoretical Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023 (China)

    2016-01-07

    The origin and strength of intra- and inter-molecular vibrational coupling is difficult to probe by direct experimental observations. However, explicitly including or not including some specific intramolecular vibrational modes to study intermolecular interaction provides a precise theoretical way to examine the effects of anharmonic coupling between modes. In this work, a full-dimension intra- and inter-molecular ab initio potential energy surface (PES) for H{sub 2}O–Ar, which explicitly incorporates interdependence on the intramolecular (Q{sub 1},  Q{sub 2},  Q{sub 3}) normal-mode coordinates of the H{sub 2}O monomer, has been calculated. In addition, four analytic vibrational-quantum-state-specific PESs are obtained by least-squares fitting vibrationally averaged interaction energies for the (v{sub 1},  v{sub 2},  v{sub 3}) =  (0,  0,  0), (0,  0,  1), (1,  0,  0), (0,  1,  0) states of H{sub 2}O to the three-dimensional Morse/long-range potential function. Each vibrationally averaged PES fitted to 442 points has root-mean-square (rms) deviation smaller than 0.15 cm{sup −1}, and required only 58 parameters. With the 3D PESs of H{sub 2}O–Ar dimer system, we employed the combined radial discrete variable representation/angular finite basis representation method and Lanczos algorithm to calculate rovibrational energy levels. This showed that the resulting vibrationally averaged PESs provide good representations of the experimental infrared data, with rms discrepancies smaller than 0.02 cm{sup −1} for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H{sub 2}O in H{sub 2}O–Ar complex are predicted for the first time and are found to be in good agreement with the (extrapolated) experimental values. Upon introduction of additional intramolecular degrees of freedom into the intermolecular potential energy surface, there is clear

  11. The role of weak intermolecular C-H…F interactions in supramolecular assembly: Structural investigations on 3,5- dibenzylidene-piperidin-4-one and database analysis

    R S Rathore; N S Karthikeyan; Y Alekhya; K Sathiyanarayanan; P G Aravindan

    2011-07-01

    The fluorinated and non-fluorinated dibenzylidene-4-piperidones were synthesized and their structures examined using X-ray crystallography. Interestingly, the para-fluorosubstituted dibenzylidene compound, in contrast to other analogs, is characterized by C-H…F bonded one-dimensional packing motif. To evaluate the ability of hydrogen bond donors and acceptors for forming interactions, in general and competitive situation, we have defined statistical descriptors. Analysis of Cambridge Structural Database using these newly defined parameters reveals high propensity of C-H…F interactions in organic crystals. The present structural study suggests much larger role of fluorine driven intermolecular interactions that are even though weak, but possess significant ability to direct and alter the packing.

  12. Structure of an acidic phospholipase A2 from Indian saw-scaled viper (Echis carinatus) at 2.6 A resolution reveals a novel intermolecular interaction.

    Jasti, Jayasankar; Paramasivam, M; Srinivasan, A; Singh, T P

    2004-01-01

    The crystal structure of an acidic phospholipase A(2) from the venom of Echis carinatus (saw-scaled viper; scPLA(2)) has been determined at 2.6 A resolution and refined to a crystallographic R factor of 0.192. Although the overall structure of scPLA(2) is essentially similar to those of other group II acidic PLA(2)s from different species, it shows unique features in several parts. Particularly noteworthy is the C-terminal part, which folds differently to those of other group II PLA(2)s. This part is considered to be responsible for inhibition of the platelet-aggregation activity. The calcium-binding loop is tightly organized with sevenfold coordination. Another striking feature of scPLA(2) is the involvement of Asn79 O(delta1) of a symmetry-related molecule in a coordination linkage with Ca(2+) of the calcium-binding loop. This is the first observation of an internal metal ion participating in an intermolecular interaction. The beta-wing of a molecule is deeply inserted into the hydrophobic channel of another molecule and forms several intermolecular interactions. This results in the formation of an infinite chain of molecules. These chains are stacked in an antiparallel arrangement in the crystals. PMID:14684894

  13. Interacting Agegraphic Dark Energy

    Wei, Hao; Cai, Rong-Gen

    2007-01-01

    A new dark energy model, named "agegraphic dark energy", has been proposed recently, based on the so-called K\\'{a}rolyh\\'{a}zy uncertainty relation, which arises from quantum mechanics together with general relativity. In this note, we extend the original agegraphic dark energy model by including the interaction between agegraphic dark energy and pressureless (dark) matter. In the interacting agegraphic dark energy model, there are many interesting features different from the original agegrap...

  14. DFT study of isocyanate chemisorption on Cu(100): Correlation between substrate-adsorbate charge transfer and intermolecular interactions

    Belelli, Patricia G.; Garda, Graciela R.; Ferullo, Ricardo M.

    2011-07-01

    The adsorption of isocyanate (- NCO) species on Cu(100) was studied using the density functional theory (DFT) and the periodic slab model. The calculations indicate that at low and intermediate coverages NCO adsorbs preferentially on bridge and hollow sites. Work function and dipole moment changes show a significant negative charge transfer from Cu to NCO. The resulting charged NCO species interact repulsively among themselves being these dipole-dipole interactions particularly intensive when they are adsorbed in adjacent sites. Consequently, isocyanates tend to be separated from each other generating the vacant sites required for the dissociation to N and CO. This condition for NCO dissociation has been suggested in the past from experimental observations. A comparison was also performed with the NCO adsorption on Pd(100). In particular, the calculated minimal energy barrier for NCO dissociation was found to be higher on Cu(100) than on Pd(100) in accord with the well known higher NCO stability on Cu(100).

  15. Intramolecular photo-switching and intermolecular energy transfer as primary photoevents in photoreceptive processes: The case of Euglena gracilis

    Mercatelli, Raffaella; Quercioli, Franco [Istituto Sistemi Complessi, CNR, Via Madonna del Piano 10, 50019 Sesto Fiorentino (Italy); Barsanti, Laura; Evangelista, Valter [Istituto di Biofisica, CNR, Via Moruzzi 1, 56124 Pisa (Italy); Coltelli, Primo [ISTI, CNR, Via Moruzzi 1, 56124 Pisa (Italy); Passarelli, Vincenzo; Frassanito, Anna Maria [Istituto di Biofisica, CNR, Via Moruzzi 1, 56124 Pisa (Italy); Gualtieri, Paolo, E-mail: paolo.gualtieri@pi.ibf.cnr.it [Istituto di Biofisica, CNR, Via Moruzzi 1, 56124 Pisa (Italy)

    2009-07-24

    In this paper we report the results of measurements performed by FLIM on the photoreceptor of Euglenagracilis. This organelle consists of optically bistable proteins, characterized by two thermally stable isomeric forms: A{sub 498,} non fluorescent and B{sub 462}, fluorescent. Our data indicate that the primary photoevent of Euglena photoreception upon photon absorption consists of two contemporaneous different phenomena: an intramolecular photo-switch (i.e., A{sub 498} becomes B{sub 462}), and a intermolecular and unidirectional Forster-type energy transfer. During the FRET process, the fluorescent B{sub 462} form acts as donor for the non-fluorescent A{sub 498} form of the protein nearby, which acts as acceptor. We hypothesize that in nature these phenomena follow each other with a domino progression along the orderly organized and closely packed proteins in the photoreceptor layer(s), modulating the isomeric composition of the photoreceptive protein pool. This mechanism guarantees that few photons are sufficient to produce a signal detectable by the cell.

  16. Data in support of intermolecular interactions at early stage of protein/detergent particle association induced by salt/polyethylene glycol mixtures

    Odahara, Takayuki; Odahara, Koji

    2016-01-01

    The data provide information in support of the research article, “Intermolecular interactions at early stage of protein/detergent particle association induced by salt/polyethylene glycol mixtures” [1]. The data regarding variation of absorption spectra is used as an indicator of the duration of Rp. viridis PRU and RC, Rb. sphaeroides RC and LH2, and Rb. capsulatus LH2 in the native state in the presence of NaCl/polyethylene glycol (PEG) mixture. The data about minimum concentrations of salt and PEG whose aqueous phases are mutually separated presents information on additional influence of Tris buffer and N-octyl-β-d-glucoside on the salt–PEG phase separation. PMID:27135050

  17. Data in support of intermolecular interactions at early stage of protein/detergent particle association induced by salt/polyethylene glycol mixtures.

    Odahara, Takayuki; Odahara, Koji

    2016-06-01

    The data provide information in support of the research article, "Intermolecular interactions at early stage of protein/detergent particle association induced by salt/polyethylene glycol mixtures" [1]. The data regarding variation of absorption spectra is used as an indicator of the duration of Rp. viridis PRU and RC, Rb. sphaeroides RC and LH2, and Rb. capsulatus LH2 in the native state in the presence of NaCl/polyethylene glycol (PEG) mixture. The data about minimum concentrations of salt and PEG whose aqueous phases are mutually separated presents information on additional influence of Tris buffer and N-octyl-β-d-glucoside on the salt-PEG phase separation. PMID:27135050

  18. Ligand field and intermolecular interactions tuning the magnetic properties of spin-crossover Fe(II) polymer with 4,4′-bipyridine

    A new spin crossover coordination polymer (SCO-CPs) of Fe(II)-4,4′-bipyridine (4,4′-bipy) family: (Fe(4,4′-bipy)2(H2O)2)·(4,4′-bipy)· 8(H2O)·2(ClO4) (3), which displays half spin transitions between 100 and 300 K, has been synthesized and structurally characterized. Compound 3 featured with two-dimensional (2-D) grids connected by hydrogen bonds and π…π packing between one-dimensional (1-D) chains, the 2-D grids expand to three-dimensional (3-D) architecture supported by a “S-shaped holder” involving lattice 4-4′-bipy, water molecules and perchlorate anion. We compared 3 with the other two analogous complexes: ((Fe(4,4′-bipy) (H2O)2 (NCS)2)·4,4′-bipy, 1 and (Fe(4,4′-bipy)2(NCS)2)·mSolv, 2) through Hirshfeld surfaces analysis, which revealed that the low ligand field strength (NCS−) and lone-pair…H contacts contribute to the stabilization of HS (high-spin) state of the Fe(II) ion, while the high ligand field strength (4,4′-bipy) and strong intermolecular contacts (hydrogen bonds and π…π packing interactions) make for the LS (low-spin) state. - Highlights: ●A new member of Fe(||)-4,4′-bipy family has been prepared. ●It displays half spin transitions tuned by ligand field and intermolecular interactions. ●We have made a detailed comparison of this new member with two other analogous complexes

  19. Extended intermolecular interactions in a serine protease-canonical inhibitor complex account for strong and highly specific inhibition.

    Fodor, Krisztián; Harmat, Veronika; Hetényi, Csaba; Kardos, József; Antal, József; Perczel, András; Patthy, András; Katona, Gergely; Gráf, László

    2005-07-01

    We have previously shown that a trypsin inhibitor from desert locust Schistocerca gregaria (SGTI) is a taxon-specific inhibitor that inhibits arthropod trypsins, such as crayfish trypsin, five orders of magnitude more effectively than mammalian trypsins. Thermal denaturation experiments, presented here, confirm the inhibition kinetics studies; upon addition of SGTI the melting temperatures of crayfish and bovine trypsins increased 27 degrees C and 4.5 degrees C, respectively. To explore the structural features responsible for this taxon specificity we crystallized natural crayfish trypsin in complex with chemically synthesized SGTI. This is the first X-ray structure of an arthropod trypsin and also the highest resolution (1.2A) structure of a trypsin-protein inhibitor complex reported so far. Structural data show that in addition to the primary binding loop, residues P3-P3' of SGTI, the interactions between SGTI and the crayfish enzyme are also extended over the P12-P4 and P4'-P5' regions. This is partly due to a structural change of region P10-P4 in the SGTI structure induced by binding of the inhibitor to crayfish trypsin. The comparison of SGTI-crayfish trypsin and SGTI-bovine trypsin complexes by structure-based calculations revealed a significant interaction energy surplus for the SGTI-crayfish trypsin complex distributed over the entire binding region. The new regions that account for stronger and more specific binding of SGTI to crayfish than to bovine trypsin offer new inhibitor sites to engineer in order to develop efficient and specific protease inhibitors for practical use. PMID:15922357

  20. DFT study of NH 3 dissociation on Si(1 1 1)-7 × 7. The role of intermolecular interactions

    Ferullo, Ricardo M.; Fuente, Silvia A.; Belelli, Patricia G.; Castellani, Norberto J.

    2007-04-01

    The adsorption of NH 3 molecule on the Si(1 1 1)-7 × 7 surface modelled with a cluster has been studied using density functional theory (DFT). The results indicate the existence of a precursor state for the non-dissociative chemisorption. The active site for the molecular chemisorption is the adatom; while the NH 3 molecule adsorbs on the Si restatom via this preadsorbed state, the adsorption on the Si adatom is produced practically without an energy barrier. The ammonia adsorption on the adatom induces an electron transfer from the dangling bond of this atom to the dangling bond of the adjacent Si restatom, hindering this site for the adsorption of a second NH 3 incoming molecule. However, this second molecule links strongly by means of two H-bonds. The dissociative chemisorption process was studied considering one and two ammonia molecules. For the dissociation of a lonely NH 3 molecule an energy barrier of ˜0.3 eV was calculated, yielding NH 2 on the adatom and H on the restatom. When two molecules are adsorbed, the NH 3-NH 3 interaction yields the weakening of a N-H bond of the ammonia molecule adsorbed closer the Si surface. As a consequence, the dissociation barrier practically disappears. Thus, the presence of a second NH 3 molecule at the adatom-restatom pair of the Si(1 1 1)-7 × 7 surface makes the dissociative reaction self-assisted, the total adsorption process elapsing with a negligible activation barrier (less than 0.01 eV).

  1. Theoretical studies for the N2–N2O van der Waals complex: The potential energy surface, intermolecular vibrations, and rotational transition frequencies

    Theoretical studies of the potential energy surface (PES) and bound states are performed for the N2–N2O van der Waals (vdW) complex. A four-dimensional intermolecular PES is constructed at the level of single and double excitation coupled-cluster method with a non-iterative perturbation treatment of triple excitations [CCSD(T)] with aug-cc-pVTZ basis set supplemented with bond functions. Two equivalent T-shaped global minima are located, in which the O atom of N2O monomer is near the N2 monomer. The intermolecular fundamental vibrational states are assigned by inspecting the orientation of the nodal surface of the wavefunctions. The calculated frequency for intermolecular disrotation mode is 23.086 cm−1, which is in good agreement with the available experimental data of 22.334 cm−1. A negligible tunneling splitting with the value of 4.2 MHz is determined for the ground vibrational state and the tunneling splitting increases as the increment of the vibrational frequencies. Rotational levels and transition frequencies are calculated for both isotopomers 14N2–N2O and 15N2–N2O. The accuracy of the PES is validated by the good agreement between theoretical and experimental results for the transition frequencies and spectroscopic parameters

  2. Theoretical studies for the N{sub 2}–N{sub 2}O van der Waals complex: The potential energy surface, intermolecular vibrations, and rotational transition frequencies

    Zheng, Rui [Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071 (China); School of Mathematics and Information Science, North China University of Water Resources and Electric Power, Zhengzhou 450011 (China); Zheng, Limin; Yang, Minghui, E-mail: yplu@ntu.edu.sg, E-mail: yangmh@wipm.ac.cn [Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071 (China); Lu, Yunpeng, E-mail: yplu@ntu.edu.sg, E-mail: yangmh@wipm.ac.cn [Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore)

    2015-10-21

    Theoretical studies of the potential energy surface (PES) and bound states are performed for the N{sub 2}–N{sub 2}O van der Waals (vdW) complex. A four-dimensional intermolecular PES is constructed at the level of single and double excitation coupled-cluster method with a non-iterative perturbation treatment of triple excitations [CCSD(T)] with aug-cc-pVTZ basis set supplemented with bond functions. Two equivalent T-shaped global minima are located, in which the O atom of N{sub 2}O monomer is near the N{sub 2} monomer. The intermolecular fundamental vibrational states are assigned by inspecting the orientation of the nodal surface of the wavefunctions. The calculated frequency for intermolecular disrotation mode is 23.086 cm{sup −1}, which is in good agreement with the available experimental data of 22.334 cm{sup −1}. A negligible tunneling splitting with the value of 4.2 MHz is determined for the ground vibrational state and the tunneling splitting increases as the increment of the vibrational frequencies. Rotational levels and transition frequencies are calculated for both isotopomers {sup 14}N{sub 2}–N{sub 2}O and {sup 15}N{sub 2}–N{sub 2}O. The accuracy of the PES is validated by the good agreement between theoretical and experimental results for the transition frequencies and spectroscopic parameters.

  3. Analysis of Cl…Cl and C-H…Cl intermolecular interactions involving chlorine in substituted 2-chloroquinoline derivatives

    Venkatesha R Hathwar; S Mohana Roopan; R Subashini; F Nawaz Khan; T N Guru Row

    2010-09-01

    Six crystal structures of substituted 2-chloroquinoline derivatives have been analysed to evaluate the role of Cl atom as a self recognizing unit resulting in the formation of Cl…Cl and C-H…Cl interactions to generate supramolecular assembly in the solid state. The features of Type I and Type II geometries associated with Cl…Cl interactions have been analysed to show directional preferences leading to differences in the packing motifs in these crystal structures. C-H…Cl interactions are generated exclusively in structures depicting Type II Cl…Cl interaction have been observed in these structures.

  4. Intermolecular, ion-molecular and interionic interactions in solutions of lithium and tetrabutylammonium salts in mixtures of methanol with propylene carbonate

    Interparticle interactions are investigated in solutions of LiI, LiBr, LiCl, LiNCS, (C4H9)4NI, (C4H9)4NBr, (C4H9)4NCl in mixtures of methanol with propylene carbonate in absence of self-association of molecules of methanol and in different salt concentrations by the methods of IR spectroscopy. Intermolecular and ion-molecular interactions are studied on IR absorption lines of valent vibrations of OH-groups of methanol (3300-3500 cm-1), interionic interaction - on lines of valent CN (2000-2100 cm-1) and deformation O-Cl-O (625 cm-1) vibrations of NVS- and ClO4- correspondingly. Concentrations of lithium complexes forming in solutions are calculated on intensities of valent absorption lines of OH-groups of methanol. In the case of salt concentration increase the content of complexes decreases. Ousting of solvent molecule by anions in complex happens so faster as electron-donor ability of it is higher

  5. Interacting Dark Energy

    Zhang, Xinmin

    2004-01-01

    In this paper I discuss some of the phenomenologies of models of the dark energy interacting with the ordinary matter. After a very brief review about the current constraint on the equation of the state of the dark energy from the SN and a new scenario of dark energy {\\it the Quintom}, I present models of Quintessential Baryo(Lepto)genesis, Quintessino dark matter and mass varying neutrinos in details.

  6. Kinetic theory for flows of nonhomogeneous rodlike liquid crystalline polymers with a nonlocal intermolecular potential.

    Wang, Qi; E, Weinan; Liu, Chun; Zhang, Pingwen

    2002-05-01

    The Doi kinetic theory for flows of homogeneous, rodlike liquid crystalline polymers (LCPs) is extended to model flows of nonhomogeneous, rodlike LCPs through a nonlocal (long-range) intermolecular potential. The theory features (i) a nonlocal, anisotropic, effective intermolecular potential in an integral form that is consistent with the chemical potential, (ii) short-range elasticity as well as long-range isotropic and anisotropic elasticity, (iii) a closed-form stress expression accounting for the nonlocal molecular interaction, and (iv) an extra elastic body force exclusively associated with the integral form of the intermolecular potential. With the effective intermolecular potential, the theory is proven to be well posed in that it warrants a positive entropy production and thereby the second law of thermodynamics. Approximate theories are obtained by gradient expansions of the number density function in the free energy density. PMID:12059561

  7. Intramolecular versus intermolecular hydrogen bonding in solution

    Vliegenthart, J. F. G.; Kroon, Jan; Kroon-Batenburg, L.M.J.; Leeflang, B.R.

    1994-01-01

    The balance between intra- and intermolecular hydrogen bonding is studied for a solution of methyl beta-cellobioside in water and dimethylsulfoxide by 1H NMR and molecular dynamics simulations. In water O(3) predominantly interacts with water molecules, whereas in dimethylsulfoxide it is intramolecularly hydrogen bonded to O(5Œ). The temperature coefficient of the chemical shift of the hydroxy groups appears to be a reliable indicator of intermolecular hydrogen-bond formation, whereas the ex...

  8. Relationship between molecular weight of poly(ethylene)glycol and intermolecular interaction of Taka-amylase A monomers

    Onuma, Kazuo; Furubayashi, Naoki; Shibata, Fujiko; Kobayashi, Yoshiko; Kaito, Sachiko; Ohnishi, Yuki; Inaka, Koji

    2010-04-01

    Dynamic and static light scattering investigations of Taka-amylase A (TAA) protein monomers were done using solutions containing poly(ethylene)glycol (PEG) with molecular weights of 1500, 4000, 8000, and 20 000. The anomalies observed in a previous study using a weight of 8000, in which the hydrodynamic TAA monomer radius at a zero protein concentration and the molecular weight of the monomers decreased when the PEG concentration was increased, were observed for all four weights. These anomalies became more pronounced as the PEG molecular weight was increased. The overall interaction parameter did not move further in the direction of the attractive force despite an increase in the PEG concentration from 6% to 12.5% for the PEG 8000 and 20 000 solutions. This was due to the change in the relative contributions of the static structure factor (direct interaction) and the hydrodynamic interaction factor (indirect interaction) against the overall interaction parameter. For the PEG 1500 and 4000 solutions, the change in the overall interaction parameter with an increase in the PEG concentration was controlled by changing the static structure factor. For the PEG 8000 and 20 000 solutions, a change in the hydrodynamic interaction factor with an increase in the PEG concentration offset the change in the static structure factor, unexpectedly resulting in the overall interaction parameter being independent of the PEG concentration. This suggests that the scale and density of a PEG network structure, which are thought to be the origin of the observed anomalies, change nonlinearly with the PEG molecular weight.

  9. Electronic transitions and intermolecular forces

    This thesis describes two different subjects - electronic transitions and intermolecular forces - that are related mainly by the following observation: The wavenumber at which an electronic transition in an atom or molecule occurs, depends on the environment of that atom or molecule. This implies, for instance, that when a molecule becomes solvated its absorption spectrum may be shifted either to the blue or to the red side of the original gasphase spectrum. In part I attention is paid to the experimental aspects of VUV spectroscopy, both in the gasphase and in the condensed phase. In part II a series of papers are presented, dealing with the calculation of intermolecular forces (and some related topics) both for the ground state and for the excited state interactions, using different non-empirical methods. The calculations provide, among other results, a semiquantitative interpretation of the spectral blue shifts encountered in our experiments. (Auth.)

  10. A quantum-chemical validation about the formation of hydrogen bonds and secondary interactions in intermolecular heterocyclic systems

    Boaz Galdino Oliveira

    2009-08-01

    Full Text Available We have performed a detailed theoretical study in order to understand the charge density topology of the C2H4O···C2H2 and C2H4S···C2H2 heterocyclic hydrogen-bonded complexes. Through the calculations derived from Quantum Theory of Atoms in Molecules (QTAIM, it was observed the formation of hydrogen bonds and secondary interactions. Such analysis was performed through the determination of optimized geometries at B3LYP/6-31G(d,p level of theory, by which is that QTAIM topological operators were computed, such as the electronic density ρ(r, Laplacian Ñ2ρ(r, and ellipticity ε. The examination of the hydrogen bonds has been performed through the measurement of ρ(r, Ñ2ρ(r and ε between (O···H—C and (S···H—C, whereas the secondary interaction between axial hydrogen atoms Hα and carbon of acetylene. In this insight, it was verified the existence of secondary interaction only in C2H4S···C2H2 complex because its structure is propitious to form multiple interactions.

  11. Structural analysis of intermolecular interactions in the kinesin adaptor complex fasciculation and elongation protein zeta 1/ short coiled-coil protein (FEZ1/SCOCO.

    Marcos Rodrigo Alborghetti

    Full Text Available Cytoskeleton and protein trafficking processes, including vesicle transport to synapses, are key processes in neuronal differentiation and axon outgrowth. The human protein FEZ1 (fasciculation and elongation protein zeta 1 / UNC-76, in C. elegans, SCOCO (short coiled-coil protein / UNC-69 and kinesins (e.g. kinesin heavy chain / UNC116 are involved in these processes. Exploiting the feature of FEZ1 protein as a bivalent adapter of transport mediated by kinesins and FEZ1 protein interaction with SCOCO (proteins involved in the same path of axonal growth, we investigated the structural aspects of intermolecular interactions involved in this complex formation by NMR (Nuclear Magnetic Resonance, cross-linking coupled with mass spectrometry (MS, SAXS (Small Angle X-ray Scattering and molecular modelling. The topology of homodimerization was accessed through NMR (Nuclear Magnetic Resonance studies of the region involved in this process, corresponding to FEZ1 (92-194. Through studies involving the protein in its monomeric configuration (reduced and dimeric state, we propose that homodimerization occurs with FEZ1 chains oriented in an anti-parallel topology. We demonstrate that the interaction interface of FEZ1 and SCOCO defined by MS and computational modelling is in accordance with that previously demonstrated for UNC-76 and UNC-69. SAXS and literature data support a heterotetrameric complex model. These data provide details about the interaction interfaces probably involved in the transport machinery assembly and open perspectives to understand and interfere in this assembly and its involvement in neuronal differentiation and axon outgrowth.

  12. All-atom Molecular Dynamic Simulations and NMR Spectra Study on Intermolecular Interactions of N,N-dimethylacetamide-Water System

    Rong Zhang; Zai-you Tan; San-lai Luo

    2008-01-01

    N,N-dimethylacetamide (DMA) has been investigated extensively in studying models of peptide bonds. An all-atom MD simulation and the NMR spectra were performed to investigate the interactions in the DMA- water system. The radial distribution functions (RDFs) and the hydrogen-bonding network were used in MD simulations. There are strong hydrogen bonds and weak C-H…O contacts in the mixtures, as shown by the analysis of the RDFs. The insight structures in the DMA-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Chemical shifts of the hydrogen atom of water molecule with concentration and temperatures are adopted to study the interactions in the mixtures. The results of NMR spectra show good agreement with the statistical results of hydrogen bonds in MD simulations.

  13. Weak intermolecular interactions of chromium, molybdenum and vanadium bis-arene complexes with CH- and OH-acids

    Using the method of IR spectroscopy coordination interactions of molybdenum and vanadium organometallic compounds (OMC) (bis-ethyl benzene molybdenum, bisethyl benzene vanadium) with hydroperoxides of ternary butyl and cumyl, as well as with ternary butanol and phenol are investigated. Possible types of OMC coordination with CH- and OH-acids are considered. The role of coordination complexes in the oxidation mechanism of bis-arene derivatives of transition metals by hydroperoxides is discussed

  14. Self-assembly polymorphism of 2,7-bis-nonyloxy-9-fluorenone: solvent induced the diversity of intermolecular dipole-dipole interactions.

    Cui, Lihua; Miao, Xinrui; Xu, Li; Hu, Yi; Deng, Wenli

    2015-02-01

    In this present work, a scanning tunneling microscope (STM) operated under ambient conditions was utilized to probe the self-assembly behavior of 2,7-bis-nonyloxy-9-fluorenone (F-OC9) at the liquid-solid (l/s) interface. On the highly oriented pyrolytic graphite (HOPG) surface, two-dimensional (2D) polymorphism with diversity of intermolecular dipole interactions induced by solvent was found. Solvents ranged from hydrophilic solvating properties with high polarity, such as viscous alkylated acids, to nonpolar alkylated aromatics and alkanes. 1-Octanol and dichloromethane were used to detect the assembly of F-OC9 at the gas-solid (g/s) interface. The opto-electronic properties of F-OC9 were determined by UV-vis and fluorescence spectroscopy in solution. Our results showed that there were tremendous solvent-dependent self-assemblies in 2D ordering for the surface-confined target molecules. When a homologous series of alkanoic acids ranging from heptanoic to nonanoic acid were employed as solvents, the self-assembled monolayer evolved from low-density coadsorbed linear lamellae to a semi-circle-like pattern at relatively high concentrations, which was proven to be the thermodynamic state as it was the sole phase observed at the g/s interface after the evaporation of solvent. Moreover, by increasing the chain length of the alkylated acids, the weight of the carboxylic group, also being the group responsible for the dielectric properties, diminished from heptanoic to nonanoic acid, which could make the easier/earlier appearance of a linear coadsorption effect. However, this was not the case for nonpolar 1-phenyloctane and n-tetradecane: no concentration effect was detected. It showed a strong tendency to aggregate to generate coexistence of separate domains of different phases due to the fast nucleation sites. Furthermore, thermodynamic calculations indicated that the stable structural coexistence of the fluorenone derivative was attributed to synergistic intermolecular

  15. Solid-State [2+2] Photodimerization and Photopolymerization of a,w-Diarylpolyene Monomers: Effective Utilization of Noncovalent Intermolecular Interactions in Crystals

    Yoriko Sonoda

    2010-12-01

    Full Text Available [2+2] Photocycloaddition of olefins is a very useful reaction in synthetic organic chemistry to obtain cyclobutane-containing molecules, which are almost inaccessible by other methods. The reaction, when performed in the crystalline state, occurs more efficiently and selectively than in homogeneous solution due to tight and regular molecular arrangement in the crystal state. Despite numerous examples for the solid-state [2+2] photodimerization of monoenes, however, it is still a challenge to prepare not only dimers but also higher oligomers and polymers from conjugated polyenes, which have multiple reactive double bonds in a molecule. In our recent studies of the solid-state photoreactions of a,w-diarylpolyenes, noncovalent intermolecular interactions in crystals were effectively utilized to prealign molecules in stacking arrangements, suitable for the [2+2] reaction. With appropriate ring-substituents, [2+2] photodimerization and photopolymerization of the polyenes took place, although the degree of polymerization was relatively low. This review will describe the details of these reactions.

  16. Intra and inter-molecular interactions dictate the aggregation state of irinotecan co-encapsulated with floxuridine inside liposomes

    Dicko, A.; Frazier, A.A.; Liboiron, B.D.;

    2008-01-01

    PURPOSE: The inter/intramolecular interactions between drugs (floxuridine, irinotecan) and excipients (copper gluconate, triethanolamine) in the dual-drug liposomal formulation CPX-1 were elucidated in order to identify the physicochemical properties that allow coordinated release of irinotecan and...... aggregation state of the drugs within the liposomes. RESULTS: Coordinated release of the drugs from liposomes was disrupted by removing copper gluconate. Approximately 45% of the total irinotecan was detectable in the copper-containing CPX-1 formulation by NMR, which decreased to 19% without copper present in...... the liposomal interior. Formation of higher order, NMR-silent aggregates was associated with slower and uncoordinated irinotecan release relative to floxuridine and loss of the synergistic drug/drug ratio. Solution spectroscopy and calorimetry revealed that while all formulation components were...

  17. Interactive Energy Planning

    Blarke, Morten Boje

    2006-01-01

    anchoring along the shores of the land of communications and collaboration. Whether or not a particular typology is applicable, theory and praxis are establishing standpoints, which strengthens our understanding of the planning complex, and which should inspire improved energy planning methodologies and......Though it is being questioned whether planning theory should be fitted into neat typologies, some have described evolving planning theory as a journey away from ethnocentrism, through the lands of rationalism, pragmatism, socio-ecological idealism, political-economic mobilization, currently...... tools. This paper presents an “Interactive Energy Planning” framework, which is intended to support interactivity in planning, building on important theoretical and experimental advances in planning. In particular, the paper explores the potential significance of allowing a critical perspective on...

  18. Intermolecular Interaction between Anchoring Subunits Specify Subcellular Targeting and Function of RGS Proteins in Retina ON-Bipolar Neurons.

    Sarria, Ignacio; Orlandi, Cesare; McCall, Maureen A; Gregg, Ronald G; Martemyanov, Kirill A

    2016-03-01

    In vertebrate retina, light responses generated by the rod photoreceptors are transmitted to the second-order neurons, the ON-bipolar cells (ON-BC), and this communication is indispensible for vision in dim light. In ON-BCs, synaptic transmission is initiated by the metabotropic glutamate receptor, mGluR6, that signals via the G-protein Go to control opening of the effector ion channel, TRPM1. A key role in this process belongs to the GTPase Activating Protein (GAP) complex that catalyzes Go inactivation upon light-induced suppression of glutamate release in rod photoreceptors, thereby driving ON-BC depolarization to changes in synaptic input. The GAP complex has a striking molecular complexity. It contains two Regulator of G-protein Signaling (RGS) proteins RGS7 and RGS11 that directly act on Go and two adaptor subunits: RGS Anchor Protein (R9AP) and the orphan receptor, GPR179. Here we examined the organizational principles of the GAP complex in ON-BCs. Biochemical experiments revealed that RGS7 binds to a conserved site in GPR179 and that RGS11 in vivo forms a complex only with R9AP. R9AP and GPR179 are further integrated via direct protein-protein interactions involving their cytoplasmic domains. Elimination of GPR179 prevents postsynaptic accumulation of R9AP. Furthermore, concurrent knock-out of both R9AP and RGS7 does not reconfigure the GAP complex and completely abolishes synaptic transmission, resulting in a novel mouse model of night blindness. Based on these results, we propose a model of hierarchical assembly and function of the GAP complex that supports ON-BCs visual signaling. PMID:26961947

  19. Intermolecular and surface forces

    Israelachvili, Jacob N

    2011-01-01

    This reference describes the role of various intermolecular and interparticle forces in determining the properties of simple systems such as gases, liquids and solids, with a special focus on more complex colloidal, polymeric and biological systems. The book provides a thorough foundation in theories and concepts of intermolecular forces, allowing researchers and students to recognize which forces are important in any particular system, as well as how to control these forces. This third edition is expanded into three sections and contains five new chapters over the previous edition.· starts fr

  20. Energy of the quasi-free electron in H2, D2, and O2: Probing intermolecular potentials within the local Wigner-Seitz model

    We present for the first time the quasi-free electron energy V0(ρ) for H2, D2, and O2 from gas to liquid densities, on noncritical isotherms and on a near critical isotherm in each fluid. These data illustrate the ability of field enhanced photoemission (FEP) to determine V0(ρ) accurately in strongly absorbing fluids (e.g., O2) and fluids with extremely low critical temperatures (e.g., H2 and D2). We also show that the isotropic local Wigner-Seitz model for V0(ρ) — when coupled with thermodynamic data for the fluid — can yield optimized parameters for intermolecular potentials, as well as zero kinetic energy electron scattering lengths

  1. Interactions in Dark Energy Models

    Zhang, Yi; Hui LI; Gong, Yungui; Zhu, Zong-Hong

    2011-01-01

    We perform a full dynamical analysis by considering the interactions between dark energy and radiation, and dark energy and dark matter. We find that the interaction helps alleviate the coincidence problem for the quintessence model.

  2. Intramolecular and intermolecular hydrogen bonds in aminophenols

    IR-Fourier spectroscopy methods are adopted to study intramolecular and intermolecular hydrogen bonds that form in CCl4 solutions of aminophenol derivatives and in a solid phase of these compounds pressed in KBr. If a hydroxyl group is present in the molecule in the ortho-position to an amino group, then intramolecular interactions between OH and NH groups will take place in aminophenol solutions. Intramolecular O-HO=S=O and N-H...O=S=O hydrogen bonds are found in solutions of compounds containing a sulfonamide fragment. Additional acylation of the amino group causes an intramolecular O-H...O=C hydrogen bond to form in solutions. Functional groups OH, NH, SO2, and C=O interact with one another in various ways in the solid phase to form intermolecular hydrogen bonds in aminophenols. (authors) Keywords aminophenol - IR spectrum - intramolecular hydrogen bond - intermolecular hydrogen bond

  3. Broadband visible light-harvesting naphthalenediimide (NDI) triad: study of the intra-/intermolecular energy/electron transfer and the triplet excited state.

    Wu, Shuang; Zhong, Fangfang; Zhao, Jianzhang; Guo, Song; Yang, Wenbo; Fyles, Tom

    2015-05-21

    A triad based on naphthalenediimides (NDI) was prepared to study the intersystem crossing (ISC), the fluorescence-resonance-energy-transfer (FRET), as well as the photoinduced electron transfer (PET) processes. In the triad, the 2-bromo-6-alkylaminoNDI moiety was used as singlet energy donor and the spin converter, whereas 2,6-dialkylaminoNDI was used as the singlet/triplet energy acceptor. This unique structural protocol and thus alignment of the energy levels ensures the competing ISC and FRET in the triad. The photophysical properties of the triad and the reference compounds were studied with steady-state UV-vis absorption spectra, fluorescence spectra, nanosecond transient absorption spectra, cyclic voltammetry, and DFT/TDDFT calculations. FRET was confirmed with steady-state UV-vis absorption and fluorescence spectroscopy. Intramolecular electron transfer was observed in polar solvents, demonstrated by the quenching of both the fluorescence and triplet state of the energy acceptor. Nanosecond transient absorption spectroscopy shows that the T1 state of the triad is exclusively localized on the 2,6-dialkylaminoNDI moiety in the triad upon selective photoexcitation into the energy donor, which indicates the intramolecular triplet state energy transfer. The intermolecular triplet state energy transfer between the two reference compounds was investigated with nanosecond transient absorption spectroscopy. The photophysical properties were rationalized by TDDFT calculations. PMID:25919420

  4. Accurate non-covalent interaction energies via an efficient MP2 scaling procedure

    Fabiano, E; Grabowski, I

    2015-01-01

    Using the observed proportionality of CCSD(T) and MP2 correlation interaction energies [I. Grabowski, E. Fabiano, F. Della Sala, Phys. Chem. Chem. Phys. 15, 15485 (2013)] we propose a simple scaling procedure to compute accurate interaction energies of non-covalent complexes. Our method makes use of MP2 and CCSD(T) correlation energies, computed in relatively small basis sets, and fitted scaling coefficients to yield interaction energies of almost complete basis set limit CCSD(T) quality. Thanks to the good transferability of the scaling coefficients involved in the calculations, good results can be easily obtained for different intermolecular distances.

  5. Separation of intra- and intermolecular contributions to the PELDOR signal

    Schöps, Philipp; Plackmeyer, Jörn; Marko, Andriy

    2016-08-01

    Pulsed Electron-electron Double Resonance (PELDOR) is commonly used to measure distances between native paramagnetic centers or spin labels attached to complex biological macromolecules. In PELDOR the energies of electron magnetic dipolar interactions are measured by analyzing the oscillation frequencies of the recorded time resolved signal. Since PELDOR is an ensemble method, the detected signal contains contributions from intramolecular, as well as intermolecular electron spin interactions. The intramolecular part of the signal contains the information about the structure of the studied molecules, thus it is very important to accurately separate intra- and intermolecular contributions to the total signal. This separation can become ambiguous, when the length of the PELDOR signal is not much longer than twice the oscillation period of the signal. In this work we suggest a modulation depth scaling method, which can use short PELDOR signals in order to extract the intermolecular contribution. Using synthetic data we demonstrate the advantages of the new approach and analyze its stability with regard to signal noise. The method was also successfully tested on experimental data of three systems measured at Q-Band frequencies, two model compounds in deuterated and protonated solvents and one biological sample, namely BetP. The application of the new method with an assigned value of the signal modulation depth enables us to determine the interspin distances in all cases. This is especially interesting for the model compound with an interspin distance of 5.2 nm in the protonated solvent and the biological sample, since an accurate separation of the intra- and intermolecular PELDOR signal contributions would be difficult with the standard approach in those cases.

  6. Energy component analysis of π interactions.

    Sherrill, C David

    2013-04-16

    Fundamental features of biomolecules, such as their structure, solvation, and crystal packing and even the docking of drugs, rely on noncovalent interactions. Theory can help elucidate the nature of these interactions, and energy component analysis reveals the contributions from the various intermolecular forces: electrostatics, London dispersion terms, induction (polarization), and short-range exchange-repulsion. Symmetry-adapted perturbation theory (SAPT) provides one method for this type of analysis. In this Account, we show several examples of how SAPT provides insight into the nature of noncovalent π-interactions. In cation-π interactions, the cation strongly polarizes electrons in π-orbitals, leading to substantially attractive induction terms. This polarization is so important that a cation and a benzene attract each other when placed in the same plane, even though a consideration of the electrostatic interactions alone would suggest otherwise. SAPT analysis can also support an understanding of substituent effects in π-π interactions. Trends in face-to-face sandwich benzene dimers cannot be understood solely in terms of electrostatic effects, especially for multiply substituted dimers, but SAPT analysis demonstrates the importance of London dispersion forces. Moreover, detailed SAPT studies also reveal the critical importance of charge penetration effects in π-stacking interactions. These effects arise in cases with substantial orbital overlap, such as in π-stacking in DNA or in crystal structures of π-conjugated materials. These charge penetration effects lead to attractive electrostatic terms where a simpler analysis based on atom-centered charges, electrostatic potential plots, or even distributed multipole analysis would incorrectly predict repulsive electrostatics. SAPT analysis of sandwich benzene, benzene-pyridine, and pyridine dimers indicates that dipole/induced-dipole terms present in benzene-pyridine but not in benzene dimer are relatively

  7. Study of intermolecular interactions in the system of equilibrium catalytic transesterification of esters. 4. Fourier IR studies of the interaction of alcohols with esters

    Interaction of alcohols ROH with esters PhCOOR (R = Me, n-Bu, n-C7H15) in binary mixtures and in solutions in non-polar solvents was studies over a wide temperature range by means of Fourier IR spectroscopy. Even with alcohol taken in a great excess, two bands are observed in the region of ΝCO vibrations. The low-frequency band, correspond to the ester molecules bonded by hydrogen bonds of the C=O...HO type. The high-frequence band is shifted by 3-5 cm-1 with respect to the ester ΝCO band. The discreteness of the shift, indicates that an H-complex of one more type is formed between the alcohol and the ester. The analysis of data available allows one to conclude that the complex formation involves the alkoxyl oxygen atom of the ester. The formation enthalpies were determined for H-bond of n-BuOH with the esters and with transesterification catalysts B(OBu)3

  8. Intermolecular interactions in nuclear magnetic resonance: medium shifts of the 1H and 13C nuclei in methane in the gas phase and in solution and of gaseous 3He

    An analysis has been carried out of the continuum and the binary collision models used in the description of NMR solvent shifts caused by Van der Waals intermolecular interactions. The basic assumption underlying the models, i.e. σ sub(w)= -BE2 (I) is examined. The possible effects on I of such phenomena as B anisotropy and field gradients are discussed, as well as the inadequacy of I in representing the true intermolecular shielding. A new expression for E2 is proposed, which in connection with I forms the bais of a modified binary collision model. The new E2 expression takes into account the dynamic character of the interaction. The major obstacle to the binary collision model, the requirement for accurate parameters for the intermolecular potential employed in the statistical-mechanical averaging, is alleviated by the establishment of priority rules to be used in the selection of these paramters. The proposed binary collision model and a collision model are used to interpret the 1H and 13C medium shifts of methane in the gas phase and in solution. The proton shift data conform equally well to either model; the 13C data indicate that a large solvent-dependent term contributes to the observed medium shifts in addition to I. Proton and 13C B parameters of methane in the gas phase and in solution are discussed. Preliminary results of 3He medium shifts as a function of gas density are presented. An extracted B parameter based on the proposed binary collision model appears to agree well with the result of a quantum-mechanical calculation of B for a 3He atom in a uniform static electric field. (LL)

  9. Inhomogeneous and interacting vacuum energy

    De-Santiago, Josue; Wang, Yuting

    2012-01-01

    Vacuum energy is a simple model for dark energy driving an accelerated expansion of the universe. If the vacuum energy is inhomogeneous in spacetime then it must be interacting. We present the general equations for a spacetime-dependent vacuum energy in cosmology, including inhomogeneous perturbations. We show how any dark energy cosmology can be described by an interacting vacuum+matter. Different models for the interaction can lead to different behaviour (e.g., sound speed for dark energy perturbations) and hence could be distinguished by cosmological observations. As an example we present the cosmic microwave microwave background anisotropies and the matter power spectrum for two different versions of a generalised Chaplygin gas cosmology.

  10. Strong orbital interaction in a weak CH-π hydrogen bonding system.

    Li, Jianfu; Zhang, Rui-Qin

    2016-01-01

    For the first time, the intermolecular orbital interaction between benzene and methane in the benzene-methane complex, a representative of weak interaction system, has been studied by us using ab initio calculations based on different methods and basis sets. Our results demonstrate obvious intermolecular orbital interaction between benzene and methane involving orbital overlaps including both occupied and unoccupied orbitals. Similar to interatomic orbital interaction, the intermolecular interaction of orbitals forms "bonding" and "antibonding" orbitals. In the interaction between occupied orbitals, the total energy of the complex increases because of the occupation of the antibonding orbital. The existence of the CH-π hydrogen bond between benzene and methane causes a decrease in rest energy level, leading to at least -1.51 kcal/mol intermolecular interaction energy. Our finding extends the concept of orbital interaction from the intramolecular to the intermolecular regime and gives a reliable explanation of the deep orbital reformation in the benzene-methane complex. PMID:26927609

  11. Intermolecular vibrations and spin--orbit predissociation dynamics of NeOH (X 2Π)

    Stimulated emission pumping of NeOH is used to access the bound intermolecular vibrational levels supported by the OH X 2Π3/2+Ne potential energy surface as well as predissociative levels correlating with the spin--orbit excited state of OH X 2Π1/2+Ne which lie more than 100 cm-1 above the dissociation limit. Intermolecular stretching intervals and rotor constants yield the radial dependence of the average interaction between Ne and OH X 2Π3/2,1/2, while the spacings between angular levels provide information on the anisotropy of the potentials. The lifetime of spin--orbit predissociative levels is found to increase by a factor of 3 upon intermolecular stretching excitation, from 8.5 ps to more than 27 ps. This increase in lifetime is attributed to the fall-off in the coupling between the two spin--orbit states with increasing intermolecular separation distance. The dominant coupling for spin--orbit predissociation is provided by the difference potential, the change in the intermolecular potential when the unpaired electron of OH lies in or out of the NeOH plane. The energies, rotor constants, and lifetimes of the bound and predissociative NeOH levels observed experimentally are compared with theoretical calculations of these quantities based on ab initio potentials for Ne+OH X 2Π by Yang and Alexander (accompanying paper). Remarkably good agreement is found between experiment and theory, given the weakness of the Ne+OH X 2Π interaction. copyright 1995 American Institute of Physics

  12. Multiplicities in high energy interactions

    This paper reviews the data on multiplicities in high energy interactions. Results from e+e- annihilation, from neutrino interactions, and from hadronic collisions, both diffractive and nondiffractive, are compared and contrasted. The energy dependence of the mean charged multiplicity, , as well as the rapidity density at Y = 0 are presented. For hadronic collisions, the data on neutral pion production shows a strong correlation with . The heavy particle fractions increase with √s up to the highest energies. The charged particle multiplicity distributions for each type of reaction show a scaling behavior when expressed in terms of the mean. Attempts to understand this behavior, which was first predicted by Koba, Nielsen, and Olesen, are discussed. The multiplicity correlations and the energy variation of the shape of the KNO scaling distribution provide important constraints on models. Some extrapolations to the energies of the Superconducting Super Collider are made. 51 refs., 27 figs

  13. Identification of amino acid residues of a designed ankyrin repeat protein potentially involved in intermolecular interactions with CD4: analysis by molecular dynamics simulations.

    Nimmanpipug, Piyarat; Khampa, Chalermpon; Lee, Vannajan Sanghiran; Nangola, Sawitree; Tayapiwatana, Chatchai

    2011-11-01

    We applied molecular dynamics simulations to investigate the binding properties of a designed ankyrin repeat protein, the DARPin-CD4 complex. DARPin 23.2 has been reported to disturb the human immunodeficiency virus (HIV) viral entry process by Schweizer et al. The protein docking simulation was analysed by comparing the specific ankyrin binder (DARPin 23.2) to an irrelevant control (2JAB) in forming a composite with CD4. To determine the binding free energy of both ankyrins, the MM/PBSA and MM/GBSA protocols were used. The free energy decomposition of both complexes were analysed to explore the role of certain amino acid residues in complex configuration. Interestingly, the molecular docking analysis of DARPin 23.2 revealed a similar CD4 interaction regarding the gp120 theoretical anchoring motif. In contrast, the binding of control ankyrin to CD4 occurred at a different location. This observation suggests that there is an advantage to the molecular modification of DARPin 23.2, an enhanced affinity for CD4. PMID:21962990

  14. Models of Interacting Dark Energy

    Zimdahl, W

    2012-01-01

    Any non-gravitational coupling between dark matter and dark energy modifies the cosmological dynamics. Interactions in the dark sector are considered to be relevant to address the coincidence problem. Moreover, in various models the observed accelerated expansion of the Universe is a pure interaction phenomenon. Here we review recent approaches in which a coupling between both dark components is crucial for the evolution of the Universe.

  15. How resonance assists hydrogen bonding interactions: an energy decomposition analysis.

    Beck, John Frederick; Mo, Yirong

    2007-01-15

    Block-localized wave function (BLW) method, which is a variant of the ab initio valence bond (VB) theory, was employed to explore the nature of resonance-assisted hydrogen bonds (RAHBs) and to investigate the mechanism of synergistic interplay between pi delocalization and hydrogen-bonding interactions. We examined the dimers of formic acid, formamide, 4-pyrimidinone, 2-pyridinone, 2-hydroxpyridine, and 2-hydroxycyclopenta-2,4-dien-1-one. In addition, we studied the interactions in beta-diketone enols with a simplified model, namely the hydrogen bonds of 3-hydroxypropenal with both ethenol and formaldehyde. The intermolecular interaction energies, either with or without the involvement of pi resonance, were decomposed into the Hitler-London energy (DeltaEHL), polarization energy (DeltaEpol), charge transfer energy (DeltaECT), and electron correlation energy (DeltaEcor) terms. This allows for the examination of the character of hydrogen bonds and the impact of pi conjugation on hydrogen bonding interactions. Although it has been proposed that resonance-assisted hydrogen bonds are accompanied with an increasing of covalency character, our analyses showed that the enhanced interactions mostly originate from the classical dipole-dipole (i.e., electrostatic) attraction, as resonance redistributes the electron density and increases the dipole moments in monomers. The covalency of hydrogen bonds, however, changes very little. This disputes the belief that RAHB is primarily covalent in nature. Accordingly, we recommend the term "resonance-assisted binding (RAB)" instead of "resonance-assisted hydrogen bonding (RHAB)" to highlight the electrostatic, which is a long-range effect, rather than the electron transfer nature of the enhanced stabilization in RAHBs. PMID:17143867

  16. Intermolecular symmetry-adapted perturbation theory study of large organic complexes

    Binding energies for the complexes of the S12L database by Grimme [Chem. Eur. J. 18, 9955 (2012)] were calculated using intermolecular symmetry-adapted perturbation theory combined with a density-functional theory description of the interacting molecules. The individual interaction energy decompositions revealed no particular change in the stabilisation pattern as compared to smaller dimer systems at equilibrium structures. This demonstrates that, to some extent, the qualitative description of the interaction of small dimer systems may be extrapolated to larger systems, a method that is widely used in force-fields in which the total interaction energy is decomposed into atom-atom contributions. A comparison of the binding energies with accurate experimental reference values from Grimme, the latter including thermodynamic corrections from semiempirical calculations, has shown a fairly good agreement to within the error range of the reference binding energies

  17. Interfacial charge rearrangement and intermolecular interactions: Density-functional theory study of free-base porphine adsorbed on Ag(111) and Cu(111)

    Müller, Moritz; Maurer, Reinhard J; Reuter, Karsten

    2015-01-01

    We employ dispersion-corrected density-functional theory to study the adsorption of tetrapyrrole 2H-porphine (2H-P) at Cu(111) and Ag(111). Various contributions to adsorbate-substrate and adsorbate-adsorbate interactions are systematically extracted to analyze the self-assembly behavior of this basic building block to porphyrin-based metal-organic nanostructures. This analysis reveals a surprising importance of substrate-mediated van der Waals interactions between 2H-P molecules, in contrast to negligible direct dispersive interactions. The resulting net repulsive interactions rationalize the experimentally observed tendency for single molecule adsorption.

  18. Interacting Induced Dark Energy Model

    Bahrehbakhsh, Amir F

    2016-01-01

    Similar to the idea of the brane world scenarios, but based on the approach of the induced matter theory, for a non--vacuum five--dimensional version of general relativity, we propose a model in which the conventional matter sources considered as all kind of the matter (the baryonic and dark) and the induced terms emerging from the extra dimension supposed to be as dark energy. Then we investigate the FLRW type cosmological equations and illustrate that the model is capable to explain respectively the deceleration and then acceleration eras of the universe expansion with an interacting term between the matter and dark energy.

  19. Fixed points in interacting dark energy models

    Chen, Xi-ming; Gong, Yungui

    2008-01-01

    The dynamical behaviors of two interacting dark energy models are considered. In addition to the scaling attractors found in the non-interacting quintessence model with exponential potential, new accelerated scaling attractors are also found in the interacting dark energy models. The coincidence problem is reduced to the choice of parameters in the interacting dark energy models.

  20. Evidence for Intermolecular Interactions between the Intracellular Domains of the Arabidopsis Receptor-Like Kinase ACR4, Its Homologs and the Wox5 Transcription Factor

    Meyer, Matthew R.; Shah, Shweta; Zhang, J.; Rohrs, Henry; Rao, A. Gururaj

    2015-01-01

    Arabidopsis CRINKLY4 (ACR4) is a receptor-like kinase (RLK) involved in the global development of the plant. The Arabidopsis genome encodes four homologs of ACR4 that contain sequence similarity and analogous architectural elements to ACR4, termed Arabidopsis CRINKLY4 Related (AtCRRs) proteins. Additionally, a signaling module has been previously proposed including a postulated peptide ligand, CLE40, the ACR4 RLK, and the WOX5 transcription factor that engage in a possible feedback mechanism controlling stem cell differentiation. However, little biochemical evidence is available to ascertain the molecular aspects of receptor heterodimerization and the role of phosphorylation in these interactions. Therefore, we have undertaken an investigation of the in vitro interactions between the intracellular domains (ICD) of ACR4, the CRRs and WOX5. We demonstrate that interaction can occur between ACR4 and all four CRRs in the unphosphorylated state. However, phosphorylation dependency is observed for the interaction between ACR4 and CRR3. Furthermore, sequence analysis of the ACR4 gene family has revealed a conserved ‘KDSAF’ motif that may be involved in protein-protein interactions among the receptor family. We demonstrate that peptides harboring this conserved motif in CRR3 and CRK1are able to bind to the ACR4 kinase domain. Our investigations also indicate that the ACR4 ICD can interact with and phosphorylate the transcription factor WOX5. PMID:25756623

  1. Electroweak interactions at LEP energies

    What determined the energies of LEP and the SLC? Essentially they were determined by the desire to produce the Z0 in e+e- collisions. Since the mass of the Z0 is of order 90 MeV we need electron and positron energies of at least 45 MeV in the collider. We can already produce Z0 at the SPS and Tevatron, so why was so much effort and money spent to produce them also at the new accelerators? The answer is that the e+e- collisions the Z0 particles are produced in the s channel, and are thus produced resonantly, and therefore copiously. We shall see that the resonance peak in e+e- → f bar f is several hundred times the cross section off peak. In the terminology introduced by the nuclear physicists looking for funding of high intensity 1 GeV machines, LEP is a Z0 factory. Using LEP we can study the properties of the Z0, and of the electroweak interactions, with a detail and precision never before possible. It is already possible, after only short runs at LEP to see clearly the effects of the radiative corrections in the electroweak interactions. It has been the that the electroweak interaction is now entering a stage equivalent to the heady days of the Lamb shift in QED. In this paper, the author shows how to calculate some of the processes that have been, will be and may be observed at these energies in the production and decay of the Z0. This paper calculates the decay rate for Z0 → f bar f, to exhibit the Z0 peak , and also calculate the forward-backward asymmetry in this process which permits an alternative measurement of the parameters of the interaction

  2. A new method for quick predicting the strength of intermolecular hydrogen bonds

    2009-01-01

    A new method is proposed to quick predict the strength of intermolecular hydrogen bonds.The method is employed to produce the hydrogen-bonding potential energy curves of twenty-nine hydro-gen-bonded dimers.The calculation results show that the hydrogen-bonding potential energy curves obtained from this method are in good agreement with those obtained from MP2/6-31+G calculations by including the BSSE correction,which demonstrate that the method proposed in this work can be used to calculate the hydrogen-bonding interactions in peptides.

  3. Weak interactions at high energies

    Review lectures are presented on the phenomenological implications of the modern spontaneously broken gauge theories of the weak and electromagnetic interactions, and some observations are made about which high energy experiments probe what aspects of gauge theories. Basic quantum chromodynamics phenomenology is covered including momentum dependent effective quark distributions, the transverse momentum cutoff, search for gluons as sources of hadron jets, the status and prospects for the spectroscopy of fundamental fermions and how fermions may be used to probe aspects of the weak and electromagnetic gauge theory, studies of intermediate vector bosons, and miscellaneous possibilities suggested by gauge theories from the Higgs bosons to speculations about proton decay. 187 references

  4. High-Energy Neutrino Interactions

    2002-01-01

    This experiment studies neutrino interactions in iron at the highest available energies using the narrow-band neutrino beam N3 and the wide-band neutrino beam N1. The basis of the detector is a massive target-calorimeter in which the energy deposited by a neutrino (or antineutrino) is measured by electronic techniques and the momentum of outgoing muons is determined by magnetic deflection. The detector is constructed in the form of a 20 m long iron-cored toroidal magnet, composed of modules of length 70~cm and 90~cm, and of 3.75~m diameter. Drift chambers placed in between each module measure the trajectory of muons from the neutrino interactions. The modules are of three types. The first ten modules are constructed of 2.5~cm iron plates with 20~scintillator planes inserted between the plates. The next five modules are constructed of 5~cm plates with 15~planes of scintillator and the last six modules are constructed of 15~cm plates with 5~planes of scintillators. The total mass of the detector is @=~1400 tons...

  5. Structural modeling and intermolecular correlation of liquid chlorine dioxide

    Chlorine dioxide (ClO2) is water-soluble yellow gas at room temperature. It has long been used as a disinfectant of tap water and various commodities owing to its strong oxidizing activity against various microbial proteins. The oxidizing activity is believed to be due to the presence of unpaired electron in its molecular orbital. Despite wealth of physicochemical studies of gaseous ClO2, little is known about liquid ClO2, especially about fine molecular structure and intermolecular interactions of liquid ClO2. The purpose of this study is to elucidate the fine structure and intermolecular orientations of ClO2 molecules in its liquid state using a high-energy X-ray diffraction technique. The measurements of liquid ClO2 were carried out at -50 to 0 degree Celsius using a two-axis diffractometer installed at the BL04B2 beamline in the third-generation synchrotron radiation facility SPring-8 (Hyogo, Japan). The incident X-ray beamline was 113.4 keV in energy and 0.1093 Armstrong in wavelength from a Si(111) monochromator with the third harmonic reflection. Liquid ClO2 held in a quartz capillary tube was placed in a temperature-controlled vacuum chamber. We obtained a structure factor S(Q) to a range of Q = 0.3-30 Amstrong-1 and a pair distribution function g(r) upon Fourier transform of the S(Q). The total g(r) showed peaks at 1.46, 2.08, 2.48, 3.16 and 4.24 Armstrong. From intramolecular bond lengths of 1.46 Armstrong for Cl-O and 2.48 Armstrong for O-O, O-Cl-O bond angle was estimated to be 116.1 degrees. Peaks at 3.16 and 4.24 Armstrong in the total g(r) strongly indicate presence of specific intermolecular orientations of ClO2 molecules that are distinct from those observed as a dimer in the solid phase ClO2. This view was further supported by molecular simulation using a reverse Monte Carlo method (RMC). (author)

  6. Molecular near-field antenna effect in resonance hyper-Raman scattering: Intermolecular vibronic intensity borrowing of solvent from solute through dipole-dipole and dipole-quadrupole interactions

    We quantitatively interpret the recently discovered intriguing phenomenon related to resonance Hyper-Raman (HR) scattering. In resonance HR spectra of all-trans-β-carotene (β-carotene) in solution, vibrations of proximate solvent molecules are observed concomitantly with the solute β-carotene HR bands. It has been shown that these solvent bands are subject to marked intensity enhancements by more than 5 orders of magnitude under the presence of β-carotene. We have called this phenomenon the molecular-near field effect. Resonance HR spectra of β-carotene in benzene, deuterated benzene, cyclohexane, and deuterated cyclohexane have been measured precisely for a quantitative analysis of this effect. The assignments of the observed peaks are made by referring to the infrared, Raman, and HR spectra of neat solvents. It has been revealed that infrared active and some Raman active vibrations are active in the HR molecular near-field effect. The observed spectra in the form of difference spectra (between benzene/deuterated benzene and cyclohexane/deuterated cyclohexane) are quantitatively analyzed on the basis of the extended vibronic theory of resonance HR scattering. The theory incorporates the coupling of excited electronic states of β-carotene with the vibrations of a proximate solvent molecule through solute–solvent dipole–dipole and dipole–quadrupole interactions. It is shown that the infrared active modes arise from the dipole–dipole interaction, whereas Raman active modes from the dipole–quadrupole interaction. It is also shown that vibrations that give strongly polarized Raman bands are weak in the HR molecular near-field effect. The observed solvent HR spectra are simulated with the help of quantum chemical calculations for various orientations and distances of a solvent molecule with respect to the solute. The observed spectra are best simulated with random orientations of the solvent molecule at an intermolecular distance of 10 Å

  7. Molecular near-field antenna effect in resonance hyper-Raman scattering: Intermolecular vibronic intensity borrowing of solvent from solute through dipole-dipole and dipole-quadrupole interactions

    Shimada, Rintaro; Hamaguchi, Hiro-o, E-mail: hhama@nctu.edu.tw [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan (China)

    2014-05-28

    We quantitatively interpret the recently discovered intriguing phenomenon related to resonance Hyper-Raman (HR) scattering. In resonance HR spectra of all-trans-β-carotene (β-carotene) in solution, vibrations of proximate solvent molecules are observed concomitantly with the solute β-carotene HR bands. It has been shown that these solvent bands are subject to marked intensity enhancements by more than 5 orders of magnitude under the presence of β-carotene. We have called this phenomenon the molecular-near field effect. Resonance HR spectra of β-carotene in benzene, deuterated benzene, cyclohexane, and deuterated cyclohexane have been measured precisely for a quantitative analysis of this effect. The assignments of the observed peaks are made by referring to the infrared, Raman, and HR spectra of neat solvents. It has been revealed that infrared active and some Raman active vibrations are active in the HR molecular near-field effect. The observed spectra in the form of difference spectra (between benzene/deuterated benzene and cyclohexane/deuterated cyclohexane) are quantitatively analyzed on the basis of the extended vibronic theory of resonance HR scattering. The theory incorporates the coupling of excited electronic states of β-carotene with the vibrations of a proximate solvent molecule through solute–solvent dipole–dipole and dipole–quadrupole interactions. It is shown that the infrared active modes arise from the dipole–dipole interaction, whereas Raman active modes from the dipole–quadrupole interaction. It is also shown that vibrations that give strongly polarized Raman bands are weak in the HR molecular near-field effect. The observed solvent HR spectra are simulated with the help of quantum chemical calculations for various orientations and distances of a solvent molecule with respect to the solute. The observed spectra are best simulated with random orientations of the solvent molecule at an intermolecular distance of 10 Å.

  8. Theoretical study of intermolecular energy transfer involving electronically excited molecules: He(1S) + H2(B 1Σ/sub u/+)

    To further understanding of gas phase collision dynamics involving electronically-excited molecules, a fully quantum mechanical study of He + H2(B 1Σ/sub u/+) was undertaken. Iterative natural orbital configuration interaction (CI) calculations were performed to obtain the interaction potential between He and H2(B 1Σ/sub u/+). The potential energy surface (PES) is highly anisotropic and has a van der Waals well of about 0.03 eV for C/sub 2v/ approach. Avoided PES crossings occur with He + H2(E,F 1Σ/sub g/+) and with He + H2(X 1Σ/sub g/+) and cause a local maximum and a deep minimum in the He + H2(B 1Σ/sub u/+) PES, respectively. The crossing with He + H2(X 1Σ/sub g/+) provides a mechanism for fluorescence quenching. The computed CI energies were combined with previous multi-reference double excitation CI calculations and fit with analytic functions for convenience in scattering calculations. Accurate dipole polarizabilities and quadrupole moment of H2(B 1Σ/sub u/+) were computed for use in the multipole expansion, which is the analytic form of the long-range PES. 129 refs., 28 figs., 35 tabs

  9. Intermolecular Interactions of Xe Atoms Confined in One-dimensional Nanochannels of Tris(o-phenylenedioxy)cyclotriphosphazene as Studied by High-pressure 129Xe NMR

    Kobayashi, Hirokazu; Ueda, Takahiro; Miyakubo, Keisuke; Eguchi, Taro

    2003-12-01

    The pressure dependence of the 129Xe chemical shift tensor confined in the Tris(o-phenylenedioxy) cyclotriphosphazene (TPP) nanochannel was investigated by high-pressure 129Xe NMR spectroscopy. The observed 129Xe spectrum in the one-dimensional TPP nanochannel (0.45 nm in diameter) exhibits a powder pattern broadened by an axially symmetric chemical shift tensor. As the pressure increases from 0.02 to 7.0 MPa, a deshielding of 90 ppm is observed for the perpendicular component of the chemical shift tensor δ⊥, whereas a deshielding of about 30 ppm is observed for the parallel one, δ‖. This suggests that the components of the chemical shift tensor, δ‖ and δ⊥, are mainly dominated by the Xe-wall and Xe-Xe interaction, respectively. Furthermore, the effect of helium, which is present along with xenon gas, on the 129Xe chemical shift is examined in detail. The average distance between the Xe atoms in the nanochannel is estimated to be 0.54 nm. This was found by using δ⊥ at the saturated pressure of xenon, and comparing the increment of the chemical shift value in δ⊥ to that of a β -phenol/Xe compound.

  10. 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

  11. Energy of the quasi-free electron in H{sub 2}, D{sub 2}, and O{sub 2}: Probing intermolecular potentials within the local Wigner-Seitz model

    Evans, C. M., E-mail: cherice.evans@qc.cuny.edu; Krynski, Kamil [Department of Chemistry and Biochemistry, Queens College – CUNY, Flushing, New York 11367 (United States); Streeter, Zachary; Findley, G. L., E-mail: findley@ulm.edu [School of Sciences, University of Louisiana at Monroe, Monroe, Louisiana 71209 (United States)

    2015-12-14

    We present for the first time the quasi-free electron energy V{sub 0}(ρ) for H{sub 2}, D{sub 2}, and O{sub 2} from gas to liquid densities, on noncritical isotherms and on a near critical isotherm in each fluid. These data illustrate the ability of field enhanced photoemission (FEP) to determine V{sub 0}(ρ) accurately in strongly absorbing fluids (e.g., O{sub 2}) and fluids with extremely low critical temperatures (e.g., H{sub 2} and D{sub 2}). We also show that the isotropic local Wigner-Seitz model for V{sub 0}(ρ) — when coupled with thermodynamic data for the fluid — can yield optimized parameters for intermolecular potentials, as well as zero kinetic energy electron scattering lengths.

  12. 计算机模拟混合炸药分子间作用的研究进展%Progress of Computer Simulation for Intermolecular Interactions in Composite Explosive

    钱文; 舒远杰

    2013-01-01

    简介了量子化学、分子力学、分子动力学、耗散粒子动力学等常用计算机模拟方法,重点综述了采用这些方法研究单质炸药聚合体中、不同炸药分子间、炸药与其他组分间、添加改性组分间以及组分界面间等不同情形相互作用的进展,并展望了计算机模拟混合炸药分子间作用的发展方向,认为提高准确性和降低耗时、改进和发展分子力场以及实现多尺度模拟等将是今后研究的重点。%Computer simulation methods such as quantum chemistry calculation, molecular mechanics, molecular dynamics and dissipative particle dynamics were introduced.Its applications on different situations of interactions which exist in explosive dimer, trimer and crystal, between different explosive molecules, explosive molecule and the additives, different additives and on the in-terface were summarized.Future development of computer simulation for intermolecular interactions in composite explosive was prospected, the improvement of accuracy and speed, the modification and development of molecular forcefield, and the actualiza-tion of multi-scale simulation are considered as the hotspots of the research.

  13. A unified treatment of high energy interactions

    Drescher, H.J.; Werner, K. [Centre National de la Recherche Scientifique, 44 - Nantes (France). Lab. de Physique Subatomique et des Technologies Associees; Hladik, M. [Centre National de la Recherche Scientifique, 44 - Nantes (France). Lab. de Physique Subatomique et des Technologies Associees]|[SAP AG, Berlin (Germany); Ostapchenko, S. [Moscow State Univ. (Russian Federation). Inst. of Nuclear Physics]|[Centre National de la Recherche Scientifique, 44 - Nantes (France). Lab. de Physique Subatomique et des Technologies Associees

    1999-11-01

    It is well known that high energy interactions as different as electron-positron annihilation, deep inelastic lepton-nucleon scattering, proton-proton interactions, and nucleus-nucleus collisions have many features in common. Based upon this observation, a model for all these interactions is constructed which relies on the fundamental hypothesis that the behavior of high energy interactions is universal. (author) 19 refs.

  14. Spin radical enhanced magnetocapacitance effect in intermolecular excited states.

    Zang, Huidong; Wang, Jianguo; Li, Mingxing; He, Lei; Liu, Zitong; Zhang, Deqing; Hu, Bin

    2013-11-14

    This article reports the magnetocapacitance effect (MFC) based on both pristine polymer MEH-PPV and its composite system doped with spin radicals (6R-BDTSCSB). We observed that a photoexcitation leads to a significant positive MFC in the pristine MEH-PPV. Moreover, we found that a low doping of spin radicals in polymer MEH-PPV causes a significant change on the MFC signal: an amplitude increase and a line-shape narrowing under light illumination at room temperature. However, no MFC signal was observed under dark conditions in either the pristine MEH-PPV or the radical-doped MEH-PPV. Furthermore, the magnitude increase and line-shape narrowing caused by the doped spin radicals are very similar to the phenomena induced by increasing the photoexcitation intensity. Our studies suggest that the MFC is essentially originated from the intermolecular excited states, namely, intermolecular electron-hole pairs, generated by a photoexcitation in the MEH-PPV. More importantly, by comparing the effects of spin radicals and electrically polar molecules on the MFC magnitude and line shape, we concluded that the doped spin radicals can have the spin interaction with intermolecular excited states and consequently affect the internal spin-exchange interaction within intermolecular excited states in the development of MFC. Clearly, our experimental results indicate that dispersing spin radicals forms a convenient method to enhance the magnetocapacitance effect in organic semiconducting materials. PMID:24144347

  15. New type of dual solid-state thermochromism: modulation of intramolecular charge transfer by intermolecular pi-pi interactions, kinetic trapping of the aci-nitro group, and reversible molecular locking.

    Naumov, Pance; Lee, Sang Cheol; Ishizawa, Nobuo; Jeong, Young Gyu; Chung, Ihn Hee; Fukuzumi, Shunichi

    2009-10-22

    by intramolecular proton transfer of one amino proton to the nitro group, whereupon an aci-nitro form is thermally populated. Contrary to the numerous examples of solid thermochromic molecules based on either pericyclic reactions or keto-enol tautomerism, this system appears to be the first organic thermochromic family where the thermochromic change appears as an effect of intermolecular pi-pi interactions and thermal intramolecular proton transfer to aromatic nitro group. PMID:19780605

  16. New Type of Dual Solid-State Thermochromism: Modulation of Intramolecular Charge Transfer by Intermolecular π-π Interactions, Kinetic Trapping of the Aci-Nitro Group, and Reversible Molecular Locking

    Naumov, Panče; Lee, Sang Cheol; Ishizawa, Nobuo; Jeong, Young Gyu; Chung, Ihn Hee; Fukuzumi, Shunichi

    2009-09-01

    intramolecular proton transfer of one amino proton to the nitro group, whereupon an aci-nitro form is thermally populated. Contrary to the numerous examples of solid thermochromic molecules based on either pericyclic reactions or keto-enol tautomerism, this system appears to be the first organic thermochromic family where the thermochromic change appears as an effect of intermolecular π-π interactions and thermal intramolecular proton transfer to aromatic nitro group.

  17. Modeling Electronic-Nuclear Interactions for Excitation Energy Transfer Processes in Light-Harvesting Complexes.

    Lee, Mi Kyung; Coker, David F

    2016-08-18

    An accurate approach for computing intermolecular and intrachromophore contributions to spectral densities to describe the electronic-nuclear interactions relevant for modeling excitation energy transfer processes in light harvesting systems is presented. The approach is based on molecular dynamics (MD) calculations of classical correlation functions of long-range contributions to excitation energy fluctuations and a separate harmonic analysis and single-point gradient quantum calculations for electron-intrachromophore vibrational couplings. A simple model is also presented that enables detailed analysis of the shortcomings of standard MD-based excitation energy fluctuation correlation function approaches. The method introduced here avoids these problems, and its reliability is demonstrated in accurate predictions for bacteriochlorophyll molecules in the Fenna-Matthews-Olson pigment-protein complex, where excellent agreement with experimental spectral densities is found. This efficient approach can provide instantaneous spectral densities for treating the influence of fluctuations in environmental dissipation on fast electronic relaxation. PMID:27472379

  18. Simple non-empirical procedure for spin-component-scaled MP2 methods applied to the calculation of dissociation energy curve of noncovalently-interacting systems

    Grabowski, I; Della Sala, F

    2013-01-01

    We present a simple and non-empirical method to determine optimal scaling coefficients, within the (spin-component)-scaled MP2 approach, for calculating intermolecular potential energies of noncovalently-interacting systems. The method is based on an observed proportionality between (spin-component) MP2 and CCSD(T) energies for a wide range of intermolecular distances and allows to compute with high accuracy a large portion of the dissociation curve at the cost of a single CCSD(T) calculation. The accuracy of the present procedure is assessed for a series of noncovalently-interacting test systems: the obtained results reproduce CCSD(T) quality in all cases and definitely outperform conventional MP2, CCSD and SCS-MP2 results. The difficult case of the Beryllium dimer is also considered.

  19. Thermodynamics of interacting holographic dark energy

    Arevalo, Fabiola; Cifuentes, Paulo; Peña, Francisco

    2016-01-01

    The thermodynamics of a scheme of dark matter-dark energy interaction is studied considering a holographic model for the dark energy in a flat Friedmann-Lemaitre-Robertson-Walker background. We obtain a total entropy rate for a general horizon and we study the Generalized Second Law of Thermodynamics for a cosmological interaction as a free function. Additionally, we discuss two horizons related to the Ricci and Ricci-like model and its effect on an interacting system.

  20. The interaction region of high energy protons

    Dremin, I. M.; White, S. N.

    2016-01-01

    The spatial view of the interaction region of colliding high energy protons (in terms of impact parameter) is considered. It is shown that the region of inelastic collisions has a very peculiar shape. It saturates for central collisions at an energy of 7 TeV. We speculate on the further evolution with energy, which is contrasted to the "black disk" picture.

  1. Simulated imaging of intermolecular bonds using high throughput real-space density functional calculations

    Lee, Alex; Kim, Minjung; Chelikowsky, James

    2015-03-01

    Recent experimental noncontact atomic force microscopy (AFM) studies on 8-hydroxyquinoline (8-hq) assemblies have imaged distinct lines between molecules that are thought to represent intermolecular bonding. To aid the interpretation of these images, we calculate simulated AFM images of an 8-hq dimer with a CO functionalized tip using a real-space pseudopotential formalism. We examine the effects of Pauli repulsion and tip probe relaxation as explanations for the enhanced resolution that resolves these intermolecular force lines. Our study aims to compute ab initio real-space images of intermolecular interactions.

  2. Pion nucleon interaction at low energy

    A theory of the πN interaction at low energy is described. An analogy is made with an unusual approach to potential scattering theory. Phase shifts, cross sections, and scattering amplitudes and lengths are calculated. 28 references

  3. Molecular simulation of fluids with non-identical intermolecular potentials: Thermodynamic properties of 10-5 + 12-6 Mie potential binary mixtures

    Stiegler, Thomas [Technische Fakultät, Friedrich-Alexander-Universität Erlangen-Nürnberg, Martensstraße 5a, 91058 Erlangen (Germany); Sadus, Richard J., E-mail: rsadus@swin.edu.au [Centre for Molecular Simulation, Swinburne University of Technology, P.O. Box 218 Hawthorn, Victoria 3122 (Australia)

    2015-02-28

    General methods for combining interactions between particles characterised by non-identical intermolecular potentials are investigated. The combination methods are tested by performing molecular dynamics simulations to determine the pressure, energy, isochoric and isobaric heat capacities, thermal expansion coefficient, isothermal compressibility, Joule-Thomson coefficient, and speed of sound of 10-5 + 12-6 Mie potential binary mixtures. In addition to the two non-identical Mie potentials, mixtures are also studied with non-identical intermolecular parameters. The combination methods are compared with results obtained by simply averaging the Mie exponents. When either the energy or size parameters are non-identical, very significant differences emerge in the thermodynamic properties predicted by the alternative combination methods. The isobaric heat capacity is the thermodynamic property that is most affected by the relative magnitude of the intermolecular potential parameters and the method for combining non-identical potentials. Either the arithmetic or geometric combination of potentials provides a simple and effective way of performing simulations involving mixtures of components characterised by non-identical intermolecular potentials, which is independent of their functional form.

  4. A New Intermolecular Phosphoryl Transfer between Serine and Histidine Residues

    SU,Yu-Qian; NIU,Ming-Yu; CAO,Shu-Xia; ZHANG,Jian-Chen; QU,Ling-Bo; LIAO,Xin-Cheng; ZHAO,Yu-Fen

    2004-01-01

    @@ Phosphoryl transfer constitutes one of the most important reactions in functionalized molecules, bioorganic chemistry and biochemistry.[1] The transformations are involved in diverse processes, such as activated state change of phosphorus, DNA/RNA synthesis, energy metabolism and signal transduction. So, phosphoryl transfer reaction which can be performed by either intramolecular or intermolecular phosphorylation and dephosphorylation mechanism has been investigated by many scientists in wide fields.

  5. Dark energy interacting with two fluids

    Cruz, Norman [Departamento de Fisica, Facultad de Ciencia, Universidad de Santiago, Casilla 307, Santiago (Chile)], E-mail: ncruz@lauca.usach.cl; Lepe, Samuel [Instituto de Fisica, Facultad de Ciencias Basicas y Matematicas, Universidad Catolica de Valparaiso, Avenida Brasil 2950, Valparaiso (Chile)], E-mail: slepe@ucv.cl; Pena, Francisco [Departamento de Ciencias Fisicas, Facultad de Ingenieria, Ciencias y Administracion, Universidad de La Frontera, Avda. Francisco Salazar 01145, Casilla 54-D Temuco (Chile)], E-mail: fcampos@ufro.cl

    2008-05-29

    A cosmological model of dark energy interacting with dark matter and another general component of the universe is investigated. We found general constraints on these models imposing an accelerated expansion. The same is also studied in the case for holographic dark energy.

  6. Expectations for ultra-high energy interactions

    Strong interactions at ultra-high energies are discussed with emphasis on the hadrons produced in high energy collisions. Evidence is considered that quantum chromodynamics might be the right theory, and also some estimates are given of quantum chromodynamics asymptotic-freedom phenomena, the work under discussion being very preliminary. 6 references

  7. Dark energy interacting with two fluids

    Cruz, Norman; Lepe, Samuel; Pena, Francisco

    2008-01-01

    A cosmological model of dark energy interacting with dark matter and another general component of the universe is investigated. We found general constraints on these models imposing an accelerated expansion. The same is also studied in the case for holographic dark energy.

  8. Interacting Dark Energy Models -- Scalar Linear Perturbations

    Perico, E L D

    2016-01-01

    We extend the dark sector interacting models assuming the dark energy as the sum of independent contributions $\\rho_{\\Lambda} =\\sum_i\\rho_{\\Lambda i}$, associated with (and interacting with) each of the $i$ material species. We derive the linear scalar perturbations for two interacting dark energy scenarios, modeling its cosmic evolution and identifying their different imprints in the CMB and matter power spectrum. Our treatment was carried out for two phenomenological motivated expressions of the dark energy density, $\\rho_\\Lambda(H^2)$ and $\\rho_\\Lambda(R)$. The $\\rho_\\Lambda(H^2)$ description turned out to be a full interacting model, i.e., the dark energy interacts with everyone material species in the universe, whereas the $\\rho_\\Lambda(R)$ description only leads to interactions between dark energy and the non-relativistic matter components; which produces different imprints of the two models on the matter power spectrum. A comparison with the Planck 2015 data was made in order to constrain the free para...

  9. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

    Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

    2016-01-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370

  10. Second Law Considerations in Fourier Heat Conduction of a Lattice Chain in Relation to Intermolecular Potentials

    Jesudason, Christopher Gunaseelan

    2016-01-01

    Two aspects of conductive heat are focused here (i) the nature of conductive heat, defined as that form of energy that is transferred as a result of a temperature difference and (ii) the nature of the intermolecular potentials that induces both thermal energy flow and the temperature profile at the steady state for a 1-D lattice chain. It is found that the standard presuppositions of people like Benofy and Quay (BQ) following Joseph Fourier do not obtain for at least a certain specified regime of intermolecular potential parameters related to harmonic (quadratic) potentials for nearest neighbor interactions. For these harmonic potentials, it appears from the simulation results that steady state solutions exist utilizing non-synthetic thermostats that couple not just the two particles at the extreme ends of the lattice chain, but to a control volume of $N$ particles located at either ends of the chain that does not accord with the unique analytical solutions that obtains for single particle thermostatting at t...

  11. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics.

    Pyzer-Knapp, Edward O; Thompson, Hugh P G; Day, Graeme M

    2016-08-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370

  12. Interacting Induced Dark Energy Model

    Bahrehbakhsh, Amir F.

    2016-01-01

    Similar to the idea of the brane world scenarios, but based on the approach of the induced matter theory, for a non--vacuum five--dimensional version of general relativity, we propose a model in which the conventional matter sources considered as all kind of the matter (the baryonic and dark) and the induced terms emerging from the extra dimension supposed to be as dark energy. Then we investigate the FLRW type cosmological equations and illustrate that the model is capable to explain respect...

  13. Interacting holographic dark energy with logarithmic correction

    Jamil, Mubasher; Farooq, M. Umar

    2010-01-01

    The holographic dark energy (HDE) is considered to be the most promising candidate of dark energy. Its definition is originally motivated from the entropy-area relation which depends on the theory of gravity under consideration. Recently a new definition of HDE is proposed with the help of quantum corrections to the entropy-area relation in the setup of loop quantum cosmology. Using this new definition, we investigate the model of interacting dark energy and derive its effective equation of s...

  14. Interactive Joint Transfer of Energy and Information

    Popovski, Petar; Fouladgar, A. M.; Simeone, Osvaldo

    2013-01-01

    reception of a “1” signal, the recipient node “harvests”, with some probability, the energy contained in the signal and stores it for future communication tasks. Inner and outer bounds on the achievable rates are derived. Numerical results demonstrate the effectiveness of the proposed strategies and...... illustrate some key design insights. Index Terms— Two-way channel, interactive communication, energy transfer, energy harvesting....

  15. Low energy electron interactions with water

    Monckton, Rhiannon

    2014-01-01

    Understanding the radiation chemistry of water is important in many disciplines including the nuclear industry, astrochemistry, and medicine. In recent years, low-energy electrons have been paid much greater attention, due to their abundance and reactivity in irradiated materials. Electrons with energies < 20 eV may interact via the dissociative electron attachment (DEA) mechanism, which has been found to cause single-strand breaks in DNA.DEA in water involves the capture of a low energy elec...

  16. Energy balance invariance for interacting particle systems

    Yavari, Arash; Marsden, Jerrold E.

    2009-01-01

    This paper studies the principle of invariance of balance of energy and its consequences for a system of interacting particles under groups of transformations. Balance of energy and its invariance is first examined in Euclidean space. Unlike the case of continuous media, it is shown that conservation and balance laws do not follow from the assumption of invariance of balance of energy under time-dependent isometries of the ambient space. However, the postulate of invariance of balance of ener...

  17. Graph-theoretical identification of dissociation pathways on free energy landscapes of biomolecular interaction.

    Wang, Ling; Stumm, Boris; Helms, Volkhard

    2010-03-01

    Biomolecular association and dissociation reactions take place on complicated interaction free energy landscapes that are still very hard to characterize computationally. For large enough distances, though, it often suffices to consider the six relative translational and rotational degrees of freedom of the two particles treated as rigid bodies. Here, we computed the six-dimensional free energy surface of a dimer of water-soluble alpha-helices by scanning these six degrees of freedom in about one million grid points. In each point, the relative free energy difference was computed as the sum of the polar and nonpolar solvation free energies of the helix dimer and of the intermolecular coulombic interaction energy. The Dijkstra graph algorithm was then applied to search for the lowest cost dissociation pathways based on a weighted, directed graph, where the vertices represent the grid points, the edges connect the grid points and their neighbors, and the weights are the reaction costs between adjacent pairs of grid points. As an example, the configuration of the bound state was chosen as the source node, and the eight corners of the translational cube were chosen as the destination nodes. With the strong electrostatic interaction of the two helices giving rise to a clearly funnel-shaped energy landscape, the eight lowest-energy cost pathways coming from different orientations converge into a well-defined pathway for association. We believe that the methodology presented here will prove useful for identifying low-energy association and dissociation pathways in future studies of complicated free energy landscapes for biomolecular interaction. PMID:19603501

  18. Energy transfer dynamics and kinetics of elementary processes (promoted) by gas-phase CO2 -N2 collisions: Selectivity control by the anisotropy of the interaction.

    Lombardi, Andrea; Pirani, Fernando; Laganà, Antonio; Bartolomei, Massimiliano

    2016-06-15

    In this work, we exploit a new formulation of the potential energy and of the related computational procedures, which embodies the coupling between the intra and intermolecular components, to characterize possible propensities of the collision dynamics in energy transfer processes of interest for simulation and control of phenomena occurring in a variety of equilibrium and nonequilibrium environments. The investigation reported in the paper focuses on the prototype CO2 -N2 system, whose intramolecular component of the interaction is modeled in terms of a many body expansion while the intermolecular component is modeled in terms of a recently developed bonds-as-interacting-molecular-centers' approach. The main advantage of this formulation of the potential energy surface is that of being (a) truly full dimensional (i.e., all the variations of the coordinates associated with the molecular vibrations and rotations on the geometrical and electronic structure of the monomers, are explicitly taken into account without freezing any bonds or angles), (b) more flexible than other usual formulations of the interaction and (c) well suited for fitting procedures better adhering to accurate ab initio data and sensitive to experimental arrangement dependent information. Specific attention has been given to the fact that a variation of vibrational and rotational energy has a higher (both qualitative and quantitative) impact on the energy transfer when a more accurate formulation of the intermolecular interaction (with respect to that obtained when using rigid monomers) is adopted. This makes the potential energy surface better suited for the kinetic modeling of gaseous mixtures in plasma, combustion and atmospheric chemistry computational applications. © 2016 Wiley Periodicals, Inc. PMID:27031183

  19. Interacting holographic dark energy with logarithmic correction

    Jamil, Mubasher; Umar Farooq, M.

    2010-03-01

    The holographic dark energy (HDE) is considered to be the most promising candidate of dark energy. Its definition is motivated from the entropy-area relation which depends on the theory of gravity under consideration. Recently a new definition of HDE is proposed with the help of quantum corrections to the entropy-area relation in the setup of loop quantum cosmology. Employing this new definition, we investigate the model of interacting dark energy and derive its effective equation of state. Finally we establish a correspondence between generalized Chaplygin gas and entropy-corrected holographic dark energy.

  20. Interacting holographic dark energy with entropy corrections

    Jamil, Mubasher

    2010-01-01

    The holographic dark energy (HDE) is considered to be the most promising candidate of dark energy. Its definition is originally motivated from the entropy-area relation which depends on the theory of gravity under consideration. Recently a new definition of HDE is proposed with the help of quantum corrections to the entropy-area relation in the setup of loop quantum cosmology. Using this new definition, we investigate the model of interacting dark energy and derive its effective equation of state. Finally we establish a correspondence between generalized Chaplygin gas and entropy-corrected holographic dark energy.

  1. Interacting holographic dark energy with logarithmic correction

    The holographic dark energy (HDE) is considered to be the most promising candidate of dark energy. Its definition is motivated from the entropy-area relation which depends on the theory of gravity under consideration. Recently a new definition of HDE is proposed with the help of quantum corrections to the entropy-area relation in the setup of loop quantum cosmology. Employing this new definition, we investigate the model of interacting dark energy and derive its effective equation of state. Finally we establish a correspondence between generalized Chaplygin gas and entropy-corrected holographic dark energy

  2. Visualizing coherent intermolecular dipole-dipole coupling in real space.

    Zhang, Yang; Luo, Yang; Zhang, Yao; Yu, Yun-Jie; Kuang, Yan-Min; Zhang, Li; Meng, Qiu-Shi; Luo, Yi; Yang, Jin-Long; Dong, Zhen-Chao; Hou, J G

    2016-03-31

    Many important energy-transfer and optical processes, in both biological and artificial systems, depend crucially on excitonic coupling that spans several chromophores. Such coupling can in principle be described in a straightforward manner by considering the coherent intermolecular dipole-dipole interactions involved. However, in practice, it is challenging to directly observe in real space the coherent dipole coupling and the related exciton delocalizations, owing to the diffraction limit in conventional optics. Here we demonstrate that the highly localized excitations that are produced by electrons tunnelling from the tip of a scanning tunnelling microscope, in conjunction with imaging of the resultant luminescence, can be used to map the spatial distribution of the excitonic coupling in well-defined arrangements of a few zinc-phthalocyanine molecules. The luminescence patterns obtained for excitons in a dimer, which are recorded for different energy states and found to resemble σ and π molecular orbitals, reveal the local optical response of the system and the dependence of the local optical response on the relative orientation and phase of the transition dipoles of the individual molecules in the dimer. We generate an in-line arrangement up to four zinc-phthalocyanine molecules, with a larger total transition dipole, and show that this results in enhanced 'single-molecule' superradiance from the oligomer upon site-selective excitation. These findings demonstrate that our experimental approach provides detailed spatial information about coherent dipole-dipole coupling in molecular systems, which should enable a greater understanding and rational engineering of light-harvesting structures and quantum light sources. PMID:27029277

  3. Visualizing coherent intermolecular dipole–dipole coupling in real space

    Zhang, Yang; Luo, Yang; Zhang, Yao; Yu, Yun-Jie; Kuang, Yan-Min; Zhang, Li; Meng, Qiu-Shi; Luo, Yi; Yang, Jin-Long; Dong, Zhen-Chao; Hou, J. G.

    2016-03-01

    Many important energy-transfer and optical processes, in both biological and artificial systems, depend crucially on excitonic coupling that spans several chromophores. Such coupling can in principle be described in a straightforward manner by considering the coherent intermolecular dipole–dipole interactions involved. However, in practice, it is challenging to directly observe in real space the coherent dipole coupling and the related exciton delocalizations, owing to the diffraction limit in conventional optics. Here we demonstrate that the highly localized excitations that are produced by electrons tunnelling from the tip of a scanning tunnelling microscope, in conjunction with imaging of the resultant luminescence, can be used to map the spatial distribution of the excitonic coupling in well-defined arrangements of a few zinc-phthalocyanine molecules. The luminescence patterns obtained for excitons in a dimer, which are recorded for different energy states and found to resemble σ and π molecular orbitals, reveal the local optical response of the system and the dependence of the local optical response on the relative orientation and phase of the transition dipoles of the individual molecules in the dimer. We generate an in-line arrangement up to four zinc-phthalocyanine molecules, with a larger total transition dipole, and show that this results in enhanced ‘single-molecule’ superradiance from the oligomer upon site-selective excitation. These findings demonstrate that our experimental approach provides detailed spatial information about coherent dipole–dipole coupling in molecular systems, which should enable a greater understanding and rational engineering of light-harvesting structures and quantum light sources.

  4. Gravity and Cosmology with Interacting Dark Energy

    Silbergleit, A. S.

    2016-01-01

    Dark energy (DE) is not necessarily uniform when other sources of gravity are present: interaction with matter leads to its variation in space and time. We study cosmological implications of this fact by analyzing cosmological models in which DE density interacts with matter and thus changes with time. We model the DE--matter interaction by specifying the rate of change of the DE density as an arbitrary function of it and the density of matter, in a single--phase case. In the case of several ...

  5. Gravity and Cosmology with Interacting Dark Energy

    Silbergleit, A S

    2016-01-01

    Dark energy (DE) is not necessarily uniform when other sources of gravity are present: interaction with matter leads to its variation in space and time. We study cosmological implications of this fact by analyzing cosmological models in which DE density interacts with matter and thus changes with time. We model the DE--matter interaction by specifying the rate of change of the DE density as an arbitrary function of it and the density of matter, in a single--phase case. In the case of several matter components interacting with dark energy we assume the rate of every interacting phase density to be an arbitrary function of this density and the DE density. We describe some properties of cosmological solutions valid for a general law of DE--matter interaction, and discuss physical admissibility of the interaction laws. We study numerous families of exact solutions, both singular, non-singular, and mixed. Some of them exhibit interesting properties, such as, for instance, absence of the horizon problem due to the ...

  6. Interacting Ricci Dark Energy with Logarithmic Correction

    Pasqua, Antonio; Jamil, Mubasher; Myrzakulov, R

    2011-01-01

    Motivated by the holographic principle, it has been suggested that the dark energy density may be inversely proportional to the area $A$ of the event horizon of the universe. However, such a model would have a causality problem. In this work, we consider the entropy-corrected version of the holographic dark energy model in the non-flat FRW universe and we propose to replace the future event horizon area with the inverse of the Ricci scalar curvature. We obtain the equation of state (EoS) parameter $\\omega_{\\Lambda}$, the deceleration parameter $q$ and $\\Omega_D'$ in the presence of interaction between Dark Energy (DE) and Dark Matter (DM). Moreover, we reconstruct the potential and the dynamics of the tachyon, K-essence, dilaton and quintessence scalar field models according to the evolutionary behavior of the interacting entropy-corrected holographic dark energy model.

  7. Interacting Ricci dark energy with logarithmic correction

    Pasqua, Antonio; Khodam-Mohammadi, A.; Jamil, Mubasher; Myrzakulov, R.

    2012-07-01

    Motivated by the holographic principle, it has been suggested that the dark energy density may be inversely proportional to the area A of the event horizon of the universe. However, such a model would have a causality problem. In this work, we consider the entropy-corrected version of the holographic dark energy model in the non-flat FRW universe and we propose to replace the future event horizon area with the inverse of the Ricci scalar curvature. We obtain the equation of state (EoS) parameter ω Λ, the deceleration parameter q and ΩD' in the presence of interaction between Dark Energy (DE) and Dark Matter (DM). Moreover, we reconstruct the potential and the dynamics of the tachyon, K-essence, dilaton and quintessence scalar field models according to the evolutionary behavior of the interacting entropy-corrected holographic dark energy model.

  8. High energy interactions and extensive air showers

    We report on papers presented in the high energy sessions of the conference that do not deal with the theory and observations of muons and neutrinos. We concentrate on the development and testing of hadronic interaction models, their extension to ultrahigh energy and their importance for the analysis and interpretation of air shower data. We also summarize data on the cosmic ray spectrum and composition obtained with air showers

  9. Nonlinear interaction involving zero energy wave

    Three-wave interactions involving one or two modes with non-definite sign of wave energy, treated by second order differential equations in time, are studied. The third mode is assumed to suffer heavy linear damping, and is treated by means of Tang's adiabatic approximation. The possibility of negative pump energy and positive decay mode energy is shown to lead to an explosive situation. Self-similar explosive solutions are derived, and it is shown that almost any solution asymptotically approaches, in some sense, these self-similar solutions

  10. Interacting vacuum energy in the dark sector

    Chimento, L. P. [Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA, CONICET, Cuidad Universitaria, Buenos Aires 1428 (Argentina); Carneiro, S. [Instituto de Física, Uníversídade Federal da Bahia, 40210-340, Salvador, BA (Brazil)

    2015-03-26

    We analyse three cosmological scenarios with interaction in the dark sector, which are particular cases of a general expression for the energy flux from vacuum to matter. In the first case the interaction leads to a transition from an unstable de Sitter phase to a radiation dominated universe, avoiding in this way the initial singularity. In the second case the interaction gives rise to a slow-roll power-law inflation. Finally, the third scenario is a concordance model for the late-time universe, with the vacuum term decaying into cold dark matter. We identify the physics behind these forms of interaction and show that they can be described as particular types of the modified Chaplygin gas.