A test of the significance of intermolecular vibrational coupling in isotopic fractionation

DOE PAGES

Herman, Michael F.; Currier, Robert P.; Peery, Travis B.; ...

2017-07-15

Intermolecular coupling of dipole moments is studied for a model system consisting of two diatomic molecules (AB monomers) arranged co-linearly and which can form non-covalently bound dimers. The dipolar coupling is a function of the bond length in each molecule as well as of the distance between the centers-of-mass of the two molecules. The calculations show that intermolecular coupling of the vibrations results in an isotope-dependent modification of the AB-AB intermolecular potential. This in turn alters the energies of the low-lying bound states of the dimers, producing isotope-dependent changes in the AB-AB dimer partition function. Explicit inclusion of intermolecular vibrationalmore » coupling then changes the predicted gas-dimer isotopic fractionation. In addition, a mass dependence in the intermolecular potential can also result in changes in the number of bound dimer states in an equilibrium mixture. This in turn leads to a significant dimer population shift in the model monomer-dimer equilibrium system considered here. Finally, the results suggest that intermolecular coupling terms should be considered when probing the origins of isotopic fractionation.« less

An ab initio study of intermolecular interactions of nitromethane dimer and nitromethane trimer.

PubMed

Li, Jinshan; Zhao, Feng; Jing, Fuqian

2003-02-01

Different geometries of nitromethane dimer and nitromethane trimer have been fully optimized employing the density functional theory B3LYP method and the 6-31++G** basis set. Three-body interaction energy has been obtained with the ab initio supermolecular approach at the levels of MP2/6-31++G**//B3LYP/6-31++G** and MP2/aug-cc-pVDZ//B3LYP/6-31++G**. The internal rotation of methyl group induced by intermolecular interaction has been observed theoretically. For the optimized structures of nitromethane dimer, the strength of C--H...O--N H-bond ranges from -9.0 to -12.4 kJ mol(-1) at the MP2/aug-cc-pVDZ//B3LYP/6-31++G** level, and the B3LYP method underestimates the interaction strength compared with the MP2 method, while MP2/6-31++G**//B3LYP/6-31++G** calculated DeltaE(C) is within 2.5 kJ mol(-1) of the corresponding value at the MP4(SDTQ)/6-31G**//B3LYP/6-31++G** level. The analytic atom-atom intermolecular potential has been successfully regressed by using the MP2/6-31++G**//B3LYP/6-31++G** calculated interaction energies of nitromethane dimer. For the optimized structures of nitromethane trimer the three-body interaction energies occupy small percentage of corresponding total binding energies, but become important for the compressed nitromethane explosive. In addition, it has been discovered that the three-body interaction energy in the cyclic nitromethane trimer is more and more negative as intermolecular distances decrease from 2.2 to 1.7 A. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 345-352, 2003

Determining the Intermolecular Potential Energy in a Gas: A Physical Chemistry Experiment

ERIC Educational Resources Information Center

Olbregts, J.; Walgraeve, J. P.

1976-01-01

Describes an experiment in which gas viscosity coefficients over a large temperature range are used to determine the parameters of the intermolecular potential energy and other properties such as virial coefficients. (MLH)

Real-time fluorescence quenching-based detection of nitro-containing explosive vapours: what are the key processes?

PubMed

Shaw, P E; Burn, P L

2017-11-15

The detection of explosives continues to be a pressing global challenge with many potential technologies being pursued by the scientific research community. Luminescence-based detection of explosive vapours with an organic semiconductor has attracted much interest because of its potential for detectors that have high sensitivity, compact form factor, simple operation and low-cost. Despite the abundance of literature on novel sensor materials systems there are relatively few mechanistic studies targeted towards vapour-based sensing. In this Perspective, we will review the progress that has been made in understanding the processes that control the real-time luminescence quenching of thin films by analyte vapours. These are the non-radiative quenching process by which the sensor exciton decays, the analyte-sensor intermolecular binding interaction, and the diffusion process for the analyte vapours in the film. We comment on the contributions of each of these processes towards the sensing response and, in particular, the relative roles of analyte diffusion and exciton diffusion. While the latter has been historically judged to be one of, if not the primary, causes for the high sensitivity of many conjugated polymers to nitrated vapours, recent evidence suggests that long exciton diffusion lengths are unnecessary. The implications of these results on the development of sensor materials for real-time detection are discussed.

On the influence of the intermolecular potential on the wetting properties of water on silica surfaces

NASA Astrophysics Data System (ADS)

Pafong, E.; Geske, J.; Drossel, B.

2016-09-01

We study the wetting properties of water on silica surfaces using molecular dynamics (MD) simulations. To describe the intermolecular interaction between water and silica atoms, two types of interaction potential models are used: the standard BródkA and Zerda (BZ) model and the Gulmen and Thompson (GT) model. We perform an in-depth analysis of the influence of the choice of the potential on the arrangement of the water molecules in partially filled pores and on top of silica slabs. We find that at moderate pore filling ratios, the GT silica surface is completely wetted by water molecules, which agrees well with experimental findings, while the commonly used BZ surface is less hydrophilic and is only partially wetted. We interpret our simulation results using an analytical calculation of the phase diagram of water in partially filled pores. Moreover, an evaluation of the contact angle of the water droplet on top of the silica slab reveals that the interaction becomes more hydrophilic with increasing slab thickness and saturates around 2.5-3 nm, in agreement with the experimentally found value. Our analysis also shows that the hydroaffinity of the surface is mainly determined by the electrostatic interaction, but the van der Waals interaction nevertheless is strong enough that it can turn a hydrophobic surface into a hydrophilic surface.

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

Herman, Michael F.; Currier, Robert P.; Peery, Travis B.

Intermolecular coupling of dipole moments is studied for a model system consisting of two diatomic molecules (AB monomers) arranged co-linearly and which can form non-covalently bound dimers. The dipolar coupling is a function of the bond length in each molecule as well as of the distance between the centers-of-mass of the two molecules. The calculations show that intermolecular coupling of the vibrations results in an isotope-dependent modification of the AB-AB intermolecular potential. This in turn alters the energies of the low-lying bound states of the dimers, producing isotope-dependent changes in the AB-AB dimer partition function. Explicit inclusion of intermolecular vibrationalmore » coupling then changes the predicted gas-dimer isotopic fractionation. In addition, a mass dependence in the intermolecular potential can also result in changes in the number of bound dimer states in an equilibrium mixture. This in turn leads to a significant dimer population shift in the model monomer-dimer equilibrium system considered here. Finally, the results suggest that intermolecular coupling terms should be considered when probing the origins of isotopic fractionation.« less

Plucking a hydrogen bond: A near infrared study of all four intermolecular modes in (DF)2

NASA Astrophysics Data System (ADS)

Davis, Scott; Anderson, David T.; Nesbitt, David J.

1996-10-01

The near ir combination band spectra of supersonically cooled (DF)2 in the 2900 to 3300 cm-1 region have been recorded with a high resolution slit jet spectrometer. Twelve vibration-rotation-tunneling (VRT) bands are observed, representing each of the four intermolecular modes (van der Waals stretch ν4, geared bend ν5, out-of-plane torsion ν6, and antigeared bend ν3) built as combination bands on either the ν1 (free) or ν2 (bound) DF stretches. Analysis of the rotationally resolved spectra provide spectroscopic constants, intermolecular frequencies, tunneling splittings, and predissociation rates as a function of both intra- and intermolecular excitation. The intermolecular frequencies demonstrate a small but systematic dependence on intramolecular mode, which is exploited to yield frequency predictions relevant to far-ir studies, as well as facilitate direct comparison with full 6-D quantum calculations on trial potential surfaces. The tunneling splittings demonstrate a much stronger dependence upon intermolecular mode, increasing by as much as an order of magnitude for geared bend excitation. Conversely, high resolution line shape analysis reveals that vibrational predissociation broadening is only modestly affected by intermolecular excitation, and instead exhibits mode specific behavior controlled predominantly by intramolecular excitation. Detailed H/D isotopic vibrational shifts are obtained by comparison with previous combination band studies of all four intermolecular modes in (HF)2. In contrast to the strong state mixing previously observed for (HF)2, the van der Waals stretch and geared bend degrees of freedom are largely decoupled in (DF)2, due to isotopically ``detuning'' of resonances between bend-stretch intermolecular vibrations. Four-dimensional quantum calculations of the (HF)2 and (DF)2 eigenfunctions indicate that the isotopic dependence of this bend-stretch resonance behavior is incorrectly predicted by current hydrogen bond potential surfaces.

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

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

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

2014-10-07

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

Analytic Morse/long-range potential energy surfaces and "adiabatic-hindered-rotor" treatment for a symmetric top-linear molecule dimer: A case study of CH3F-H2

NASA Astrophysics Data System (ADS)

Zhang, Xiao-Long; Ma, Yong-Tao; Zhai, Yu; Li, Hui

2018-03-01

A first effective six-dimensional ab initio potential energy surface (PES) for CH3F-H2 which explicitly includes the intramolecular Q3 stretching normal mode of the CH3F monomer is presented. The electronic structure computations have been carried out at the explicitly correlated coupled cluster level of theory [CCSD(T)-F12a] with an augmented correlation-consistent triple zeta basis set. Five-dimensional analytical intermolecular PESs for ν3(CH3F) = 0 and 1 are then obtained by fitting the vibrationally averaged potentials to the Morse/Long-Range (MLR) potential function form. The MLR function form is applied to the nonlinear molecule-linear molecule case for the first time. These fits to 25 015 points have root-mean-square deviations of 0.74 cm-1 and 0.082 cm-1 for interaction energies less than 0.0 cm-1. Using the adiabatic hindered-rotor approximation, three-dimensional PESs for CH3F-paraH2 are generated from the 5D PESs over all possible orientations of the hydrogen monomer. The infrared and microwave spectra for CH3F-paraH2 dimer are predicted for the first time. These analytic PESs can be used for modeling the dynamical behavior in CH3F-(H2)N clusters, including the possible appearance of microscopic superfluidity.

Multidimensional intermolecular dynamics from tunable far-infrared laser spectroscopy: Angular-radial coupling in the intermolecular potential of argon--H sub 2 O

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

Cohen, R.C.; Saykally, R.J.

1991-12-01

Five new vibration--rotation tunneling states of Ar--H{sub 2}O (the {Sigma} and {Pi}(1{sub 11}) and the {Sigma} and {Pi}(2{sub 12}) internal rotor states and the {ital n}=1, {Pi}(1{sub 01}) stretching-internal rotor combination level) have been accessed by tunable far-infrared laser spectroscopy. The measured vibrational band origins of transitions to these states are within 2% of predictions made from an anisotropic three-dimensional intermolecular potential surface (denoted AW1) derived from a nonlinear least-squares fit to previous far-infrared spectral data (J. Phys. Chem. {bold 94}, 7991(1990)). This provides strong evidence that the AW1 intermolecular potential surface incorporates much of the essential physics of themore » intermolecular forces which bind the cluster. However, larger deviations from the predictions are found in the observed rotational term values. A detailed analysis of these deviations clearly demonstrates the need for even stronger angular-radial coupling in the Ar--H{sub 2}O intermolecular potential than the already substantial coupling present in the AW1 surface. Specifically, the presently observed {Sigma}(1{sub 11}) state and the {ital n}=1, {Sigma}(0{sub 00}) state are found to be approximately 65:35 mixtures of the basis states which represent pure stretching and internal rotation. The {Sigma}(2{sub 12}) level is found to be mixed just as strongly with {ital n}=2, {Sigma}(1{sub 01}). The formalism for accurately deperturbing vibration--rotation--tunneling states coupled by Coriolis interactions used in the above analysis is presented.« less

Estimation of Some Parameters from Morse-Morse-Spline-Van Der Waals Intermolecular Potential

NASA Astrophysics Data System (ADS)

Coroiu, I.

2007-04-01

Some parameters such as transport cross-sections and isotopic thermal diffusion factor have been calculated from an improved intermolecular potential, Morse-Morse-Spline-van der Waals (MMSV) potential proposed by R.A. Aziz et al. The treatment was completely classical and no corrections for quantum effects were made. The results would be employed for isotope separations of different spherical and quasi-spherical molecules.

Project SQUID: The Viscosity of the Isotopes of Hydrogen and Their Intermolecular Force Potentials

DTIC Science & Technology

1963-12-01

values of the pseudo- Lennard - Jones potential for either hydrogen o- deuteriua. On the present evidence, and cn the present evidence alone, it would...W4drogesror deuterium forces the conclusion that neither gas obeys a lenrArd- Jones six- twelve potential , it is, nevertheless, useful to discuss the values...VISCOSITY OF THE ISOTOPES OF HYDROGEN AND THEIR INTERMOLECULAR FORCE POTENTIALS * by S. Kestir and A Nagashima Broow University December 1963 PROJECT SQUID

Scanning probe microscopy of biomedical interfaces

NASA Astrophysics Data System (ADS)

Vansteenkiste, S. O.; Davies, M. C.; Roberts, C. J.; Tendler, S. J. B.; Williams, P. M.

1998-02-01

The development of the scanning probe microscopes over the past decade has provided a number of exciting new surface analytical techniques making a significant progress in the characterisation of biomedical interfaces. In this review, several examples are presented to illustrate that SPM is a powerful and promising tool for surface investigations including biomolecules, cell membranes, polymers and even living cells. The ability of the SPM instrument to monitor adhesion phenomena and provide quantitative information about intermolecular interactions is also described. Moreover, the huge potential of the scanning probe microscopes to study dynamic processes at interfaces under nearly physiological conditions is highlighted. Novel applications in the field of biochemistry, microbiology, biomaterial engineering, drug delivery and even medicine are discussed.

Terahertz laser spectroscopy of the water dimer intermolecular vibrations. I. (D2O)2

NASA Astrophysics Data System (ADS)

Braly, L. B.; Cruzan, J. D.; Liu, K.; Fellers, R. S.; Saykally, R. J.

2000-06-01

Terahertz laser VRT spectra of the water dimer consisting of 731 transitions measured with an average precision of 2 MHz and involving four (D2O)2 intermolecular vibrations (one previously published) have been measured between 65 and 104 cm-1. The precisely determined energy level patterns differ both qualitatively and quantitatively from the predictions of several dimer potentials tested, and reveal an ordering of the intermolecular vibrations which differs dramatically from that predicted by standard normal mode analysis. Strong coupling is indicated between the low barrier tunneling motions and the intermolecular vibrations as well as among different vibrations. Particularly, the 83 cm-1 (acceptor wag) and 90 cm-1 (D2O)2 (acceptor twist) vibrations interact through a Coriolis perturbation. These spectra provide the basis for our recent determination of the water pair potential. The corresponding data set for (H2O)2 is presented in an accompanying paper.

Equation of state and critical point behavior of hard-core double-Yukawa fluids.

PubMed

Montes, J; Robles, M; López de Haro, M

2016-02-28

A theoretical study on the equation of state and the critical point behavior of hard-core double-Yukawa fluids is presented. Thermodynamic perturbation theory, restricted to first order in the inverse temperature and having the hard-sphere fluid as the reference system, is used to derive a relatively simple analytical equation of state of hard-core multi-Yukawa fluids. Using such an equation of state, the compressibility factor and phase behavior of six representative hard-core double-Yukawa fluids are examined and compared with available simulation results. The effect of varying the parameters of the hard-core double-Yukawa intermolecular potential on the location of the critical point is also analyzed using different perspectives. The relevance of this analysis for fluids whose molecules interact with realistic potentials is also pointed out.

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

PubMed

Makarewicz, Jan; Shirkov, Leonid

2016-05-28

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

Machine Learning Intermolecular Potentials for 1,3,5-Triamino-2,4,6-trinitrobenzene (TATB) Using Symmetry-Adapted Perturbation Theory

DTIC Science & Technology

2018-04-25

unlimited. NOTICES Disclaimers The findings in this report are not to be construed as an official Department of the Army position unless so...this report, intermolecular potentials for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) are developed using machine learning techniques. Three...potentials based on support vector regression, kernel ridge regression, and a neural network are fit using symmetry-adapted perturbation theory. The

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

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

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

Exploring the intermolecular interactions acting in solvent-modified MEKC by Molecular Dynamics and NMR: The effect of n-butanol on the separation of diclofenac and its impurities.

PubMed

Caprini, Claudia; Pasquini, Benedetta; Melani, Fabrizio; Del Bubba, Massimo; Giuffrida, Alessandro; Calleri, Enrica; Orlandini, Serena; Furlanetto, Sandra

2018-02-05

An integrated approach involving CE experiments, Molecular Dynamics (MD) simulations and two-dimensional NOE spectroscopy (2D-NOESY) experiments was employed to elucidate the intermolecular interactions and the separation mechanisms involved in a solvent-modified MEKC method for the simultaneous determination of diclofenac sodium and its impurities. The CE findings indicated that the addition of n-butanol (nBuOH) to the SDS micellar solution played a primary role for controlling the partitioning into the mixed micelles and the migration of the analytes and that the presence of nBuOH as cosurfactant was compulsory for achieving the complete separation of the compounds. The different capacity factors of the analytes were calculated and a change in solute association with the mixed micelle when changing the SDS/nBuOH molar ratio was highlighted. The optimal SDS/nBuOH molar ratio for the electrophoretic separation was 1:8. On the other hand, both MD simulations and NMR experiments indicated that the most favorable molar ratio for the formation of mixed SDS/nBuOH micelles was 1:2. These results suggested that probably there is an excess of nBuOH in the background electrolyte, both as free molecules and in form of aggregates, which is able to interact with the analytes, and thus may compete with mixed micelles for the considered compounds. The calculated values of gain in potential energy of the analytes when included in mixed micelles were in agreement with the observed migration order of the compounds. The role of methyl-β-cyclodextrin (MβCyD) in the background electrolyte was also investigated, since the addition of this CyD to the solvent-modified MEKC system was found to be useful to reduce the analysis time. MD simulations and 2D-NOESY spectra highlighted the formation of inclusion complexes with MβCyD not only with the analytes, but also with SDS. MβCyD may lower the availability of both SDS and nBuOH for forming micelles and mostly may compete with the mixed micelle as a second pseudostationary phase. Copyright © 2017 Elsevier B.V. All rights reserved.

Point charge representation of multicenter multipole moments in calculation of electrostatic properties

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Shibata, M.; Ornstein, R. L.; Rein, R.

1993-01-01

Distributed Point Charge Models (PCM) for CO, (H2O)2, and HS-SH molecules have been computed from analytical expressions using multi-center multipole moments. The point charges (set of charges including both atomic and non-atomic positions) exactly reproduce both molecular and segmental multipole moments, thus constituting an accurate representation of the local anisotropy of electrostatic properties. In contrast to other known point charge models, PCM can be used to calculate not only intermolecular, but also intramolecular interactions. Comparison of these results with more accurate calculations demonstrated that PCM can correctly represent both weak and strong (intramolecular) interactions, thus indicating the merit of extending PCM to obtain improved potentials for molecular mechanics and molecular dynamics computational methods.

Complete equation of state for shocked liquid nitrogen: Analytical developments

DOE PAGES

Winey, J. M.; Gupta, Y. M.

2016-08-02

The thermodynamic response of liquid nitrogen has been studied extensively, in part, due to the long-standing interest in the high pressure and high temperature dissociation of shocked molecular nitrogen. Previous equation of state (EOS) developments regarding shocked liquid nitrogen have focused mainly on the use of intermolecular pair potentials in atomistic calculations. Here, we present EOS developments for liquid nitrogen, incorporating analytical models, for use in continuum calculations of the shock compression response. The analytical models, together with available Hugoniot data, were used to extrapolate a low pressure reference EOS for molecular nitrogen [Span, et al., J. Phys. Chem. Ref.more » Data 29, 1361 (2000)] to high pressures and high temperatures. Using the EOS presented here, the calculated pressures and temperatures for single shock, double shock, and multiple shock compression of liquid nitrogen provide a good match to the measured results over a broad range of P-T space. Our calculations provide the first comparison of EOS developments with recently-measured P-T states under multiple shock compression. The present EOS developments are general and are expected to be useful for other liquids that have low pressure reference EOS information available.« less

Comparison of Cluster, Slab, and Analytic Potential Models for the Dimethyl Methylphosphonate (DMMP)/TiO2 (110) Intermolecular Interaction

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

Yang, Li; Tunega, Daniel; Xu, Lai

2013-08-29

In a previous study (J. Phys. Chem. C 2011, 115, 12403) cluster models for the TiO2 rutile (110) surface and MP2 calculations were used to develop an analytic potential energy function for dimethyl methylphosphonate (DMMP) interacting with this surface. In the work presented here, this analytic potential and MP2 cluster models are compared with DFT "slab" calculations for DMMP interacting with the TiO2 (110) surface and with DFT cluster models for the TiO2 (110) surface. The DFT slab calculations were performed with the PW91 and PBE functionals. The analytic potential gives DMMP/ TiO2 (110) potential energy curves in excellent agreementmore » with those obtained from the slab calculations. The cluster models for the TiO2 (110) surface, used for the MP2 calculations, were extended to DFT calculations with the B3LYP, PW91, and PBE functional. These DFT calculations do not give DMMP/TiO2 (110) interaction energies which agree with those from the DFT slab calculations. Analyses of the wave functions for these cluster models show that they do not accurately represent the HOMO and LUMO for the surface, which should be 2p and 3d orbitals, respectively, and the models also do not give an accurate band gap. The MP2 cluster models do not accurately represent the LUMO and that they give accurate DMMP/TiO2 (110) interaction energies is apparently fortuitous, arising from their highly inaccurate band gaps. Accurate cluster models, consisting of 7, 10, and 15 Ti-atoms and which have the correct HOMO and LUMO properties, are proposed. The work presented here illustrates the care that must be taken in "constructing" cluster models which accurately model surfaces.« less

Probing hydrogen bond potentials via combination band spectroscopy: A near infrared study of the geared bend/van der Waals stretch intermolecular modes in (HF)2

NASA Astrophysics Data System (ADS)

Anderson, David T.; Davis, Scott; Nesbitt, David J.

1996-04-01

High resolution near infrared spectra of the two lowest frequency intermolecular modes in HF-stretch excited states of (HF)2 have been characterized using a slit-jet infrared spectrometer. In the spectral region surveyed, ten vibration-rotation-tunneling (VRT) bands are observed and assigned to the low frequency ``van der Waals stretch'' (ν4) and ``geared bend'' (ν5) intermolecular modes, in combination with either the hydrogen bond acceptor (ν1) or donor (ν2) high-frequency intramolecular HF stretches. Analysis of the rotationally resolved spectra provide intermolecular frequencies, rotational constants, tunneling splittings, and predissociation rates for the ν4/ν5 intermolecular excited states. The intermolecular vibrational frequencies in the combination states display a systematic dependence on intramolecular redshift that allows far-IR intermolecular frequencies to be reliably extrapolated from the near-IR data. Approximately tenfold increases in the hydrogen bond interconversion tunneling splittings with either ν4 or ν5 excitation indicate that both intermolecular modes correlate strongly to the tunneling coordinate. The high resolution VRT line shapes reveal mode specific predissociation broadening sensitive predominantly to intramolecular excitation, with weaker but significant additional effects due to low frequency intermolecular excitation. Analysis of the high resolution spectroscopic data for these ν4 and ν5 combination bands suggests strong state mixing between what has previously been considered van der Waals stretch and geared bend degrees of freedom.

The effect of the intermolecular potential formulation on the state-selected energy exchange rate coefficients in N2-N2 collisions.

PubMed

Kurnosov, Alexander; Cacciatore, Mario; Laganà, Antonio; Pirani, Fernando; Bartolomei, Massimiliano; Garcia, Ernesto

2014-04-05

The rate coefficients for N2-N2 collision-induced vibrational energy exchange (important for the enhancement of several modern innovative technologies) have been computed over a wide range of temperature. Potential energy surfaces based on different formulations of the intramolecular and intermolecular components of the interaction have been used to compute quasiclassically and semiclassically some vibrational to vibrational energy transfer rate coefficients. Related outcomes have been rationalized in terms of state-to-state probabilities and cross sections for quasi-resonant transitions and deexcitations from the first excited vibrational level (for which experimental information are available). On this ground, it has been possible to spot critical differences on the vibrational energy exchange mechanisms supported by the different surfaces (mainly by their intermolecular components) in the low collision energy regime, though still effective for temperatures as high as 10,000 K. It was found, in particular, that the most recently proposed intermolecular potential becomes the most effective in promoting vibrational energy exchange near threshold temperatures and has a behavior opposite to the previously proposed one when varying the coupling of vibration with the other degrees of freedom. Copyright © 2014 Wiley Periodicals, Inc.

p-halo N4-phenyl substituted thiosemicarbazones: Crystal structure, supramolecular architecture, characterization and bio-assay of their Co(III) and Ni(II) complexes

NASA Astrophysics Data System (ADS)

Kotian, Avinash; Kumara, Karthik; Kamat, Vinayak; Naik, Krishna; Kokare, Dhoolesh G.; Nevrekar, Anupama; Lokanath, Neratur Krishnappagowda; Revankar, Vidyanand K.

2018-03-01

In the present work, three potential metal ion chelating ligands, p-halo N4-phenyl substituted thiosemicarbazones are synthesized and characterized. The molecular structure of all (E)-4-(4-halophenyl)-1-(3-hydroxyiminobutan-2-ylidene) thiosemicarbazones (halo = F/Cl/Br) are determined by single crystal X-ray diffraction method. All the molecules have crystallized in monoclinic crystal system with P21/n space group. The ligands show Csbnd H⋯S and Nsbnd H⋯S intermolecular interactions, which are responsible to form the supramolecular self-assemblies through R22(8), R22(12) and R22(14) ring motifs. Hirshfeld surface analysis is carried out to explore the intermolecular interactions. A series of Co(III) and Ni(II) mononuclear transition metal complexes derived from these ligands have been synthesized and characterized by various spectro-analytical methods. The metal to ligand stoichiometry has been found to be 1:2 in all the complexes. The synthesized compounds have been investigated for their in vitro antimicrobial potencies. The compounds are found to be more active than the standard used, in the case of E. coli and A. niger. Additionally, they are also screened for their in vitro antitubercular activity.

Molecular simulation of the thermodynamic, structural, and vapor-liquid equilibrium properties of neon

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Frascoli, Federico; Sadus, Richard J.

2016-09-01

The thermodynamic, structural, and vapor-liquid equilibrium properties of neon are comprehensively studied using ab initio, empirical, and semi-classical intermolecular potentials and classical Monte Carlo simulations. Path integral Monte Carlo simulations for isochoric heat capacity and structural properties are also reported for two empirical potentials and one ab initio potential. The isobaric and isochoric heat capacities, thermal expansion coefficient, thermal pressure coefficient, isothermal and adiabatic compressibilities, Joule-Thomson coefficient, and the speed of sound are reported and compared with experimental data for the entire range of liquid densities from the triple point to the critical point. Lustig's thermodynamic approach is formally extended for temperature-dependent intermolecular potentials. Quantum effects are incorporated using the Feynman-Hibbs quantum correction, which results in significant improvement in the accuracy of predicted thermodynamic properties. The new Feynman-Hibbs version of the Hellmann-Bich-Vogel potential predicts the isochoric heat capacity to an accuracy of 1.4% over the entire range of liquid densities. It also predicts other thermodynamic properties more accurately than alternative intermolecular potentials.

Constructing high-accuracy intermolecular potential energy surface with multi-dimension Morse/Long-Range model

NASA Astrophysics Data System (ADS)

Zhai, Yu; Li, Hui; Le Roy, Robert J.

2018-04-01

Spectroscopically accurate Potential Energy Surfaces (PESs) are fundamental for explaining and making predictions of the infrared and microwave spectra of van der Waals (vdW) complexes, and the model used for the potential energy function is critically important for providing accurate, robust and portable analytical PESs. The Morse/Long-Range (MLR) model has proved to be one of the most general, flexible and accurate one-dimensional (1D) model potentials, as it has physically meaningful parameters, is flexible, smooth and differentiable everywhere, to all orders and extrapolates sensibly at both long and short ranges. The Multi-Dimensional Morse/Long-Range (mdMLR) potential energy model described herein is based on that 1D MLR model, and has proved to be effective and accurate in the potentiology of various types of vdW complexes. In this paper, we review the current status of development of the mdMLR model and its application to vdW complexes. The future of the mdMLR model is also discussed. This review can serve as a tutorial for the construction of an mdMLR PES.

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

NASA Astrophysics Data System (ADS)

Moghadasi, Jalil; Yousefi, Fakhri; Papari, Mohammad Mehdi; Faghihi, Mohammad Ali; Mohsenipour, Ali Asghar

2009-09-01

It is the purpose of this paper to extract unlike intermolecular potential energies of five carbon dioxide-based binary gas mixtures including CO2-He, CO2-Ne, CO2-Ar, CO2-Kr, and CO2-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 K < T < 3273.15 K is reproduced from the present unlike intermolecular 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.

Terahertz laser spectroscopy of the water dimer intermolecular vibrations. I. (D{sub 2}O){sub 2}

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

Braly, L. B.; Cruzan, J. D.; Liu, K.

Terahertz laser VRT spectra of the water dimer consisting of 731 transitions measured with an average precision of 2 MHz and involving four (D{sub 2}O){sub 2} intermolecular vibrations (one previously published) have been measured between 65 and 104 cm{sup -1}. The precisely determined energy level patterns differ both qualitatively and quantitatively from the predictions of several dimer potentials tested, and reveal an ordering of the intermolecular vibrations which differs dramatically from that predicted by standard normal mode analysis. Strong coupling is indicated between the low barrier tunneling motions and the intermolecular vibrations as well as among different vibrations. Particularly, themore » 83 cm{sup -1} (acceptor wag) and 90 cm{sup -1} (D{sub 2}O){sub 2} (acceptor twist) vibrations interact through a Coriolis perturbation. These spectra provide the basis for our recent determination of the water pair potential. The corresponding data set for (H{sub 2}O){sub 2} is presented in an accompanying paper. (c) 2000 American Institute of Physics.« less

The molecular structure and absorption spectrum of hydroxy substituted dibenzoylmethanatoboron difluoride in solution: A theoretical and experimental study

NASA Astrophysics Data System (ADS)

Gelfand, Natalia; Freidzon, Alexandra; Fedorenko, Elena

2018-01-01

Electronic spectroscopy and quantum chemistry are used to study the structure and absorption spectra of the hydroxy substituted dibenzoylmethanatoboron difluoride (OHDBMBF2) in solutions. Introducing a hydroxy group in the diketonate moiety allows the dye to form intermolecular complexes with proton acceptors, such as solvents or analytes, thus making it a promising chemical sensor. Our calculations show that donor oxygen-containing solvents break the intramolecular hydrogen bond Osbnd H···Odik and form an intermolecular Osbnd H···Osolv bond thus disrupting the coplanarity of the dye and affecting the position and shape of its absorption bands. The spectra calculated with explicit solvent combined with polarizable continuum model (PCM) better agree with the experiment than those calculated only within PCM.

The intermolecular Pauson-Khand reaction.

PubMed

Gibson, Susan E; Mainolfi, Nello

2005-05-13

Five membered carbocycles are important building blocks for many biologically active molecules. Moreover, substituted cyclopentenones (e.g. cyclopentenone prostaglandins) exhibit characteristic biological activity. The efficiency and atom economy of the Pauson-Khand reaction render this process potentially one of the most attractive methods for the synthesis of such compounds. Although it was discovered in its intermolecular form, the scope of the intermolecular Pauson-Khand reaction has always been limited by the poor reactivity and selectivity of the alkene component. The past decade, especially the last three years, has seen concerted efforts to broaden the scope of this reaction. In this overview, we provide a comprehensive and critical coverage of the intermolecular Pauson-Khand reaction based on the reactivity characteristics of different classes of alkenes and a rationalization of successes and misfortunes in this area.

The intermolecular vibrations of the water dimer

NASA Astrophysics Data System (ADS)

Braly, Linda Beth

Terahertz laser spectra of water dimer intermolecular vibrations have yielded four (D2O)2 VRT bands (one previously published) and five (H2O)2 VRT bands measured with ca. 1 MHz precision and assigned between 65 and 142 cm-1. The results differ both qualitatively and quantitatively from the predictions of popular, effective pair potentials tested. The spectra also reveal an ordering of the intermolecular vibrations which differs dramatically from that predicted by a normal mode analysis. Strong coupling is indicated between the low barrier tunneling motions and the intermolecular vibrations as well as between different vibrations. In particular the 102.1 cm-1 (H2O) 2 band assigned as the acceptor wag has two types of perturbations. The first perturbation involves coupling of two of the tunneling components between the Ka = 0 and 1 levels similar to that occurring in ground state between Ka = 0 and 1 levels. This is treated with an effective Coriolis coupling constant. These seconded perturbation involves one tunneling component with Ka = 1 coupling with a tunneling component with Ka = 0 of the 108 cm-1 acceptor twist vibration. A more detailed Coriolis coupling scheme is required to deperturb these states. Also it is indicated that the 103.1 cm-1 (H2O) 2 band assigned as the donor in-plane bend is coupled to the acceptor wag resulting in a lowering of the in-plane bend frequency and raising the acceptor wag frequency. In addition the 141 cm-1 (H2O)2 band shows perturbations which could not be. resolved at this time. And the 83 cm-1 (acceptor wag) and 90 cm-1 (D2O)2 (acceptor twist) band are perturbing one another through a Coriolis interaction. A subset of the (D2O)2 data have been used in an ongoing effort to determine an accurate IPS via least-squares fitting to an analytical form. The results from the most recent fit which produced VRT(ASP- W)II are presented and compared with the experimental data. The IPS was used to calculate the eigenstates of the water dimer using the Split Wigner Psuedo Spectral (SWPS) method. The transitions could then be calculated from the eigenstates. This improved IPS reproduces the dominant features of the VRT spectra quite well. The ultimate goal of this water dimer research project is to determine the ``perfect'' water pair potential from the spectroscopic data.

The breakup mechanism of biomolecular and colloidal aggregates in a shear flow

NASA Astrophysics Data System (ADS)

Ó Conchúir, Breanndán; Zaccone, Alessio

2014-03-01

The theory of self-assembly of colloidal particles in shear flow is incomplete. Previous analytical approaches have failed to capture the microscopic interplay between diffusion, shear and intermolecular interactions which controls the aggregates fate in shear. In this work we analytically solved the drift-diffusion equation for the breakup rate of a dimer in flow. Then applying rigidity percolation theory, we found that the lifetime of a generic cluster formed under shear is controlled by the typical lifetime of a single bond in its interior, which in turn depends on the efficiency of the stress transmitted from other bonds in the cluster. We showed that aggregate breakup is a thermally-activated process where the activation energy is controlled by the interplay between intermolecular forces and the shear drift, and where structural parameters determine whether cluster fragmentation or surface erosion prevails. In our latest work, we analyzed floppy modes and nonaffine deformations to derive a lower bound on the fractal dimension df below which aggregates are mechanically unstable, ie. for large aggregates df ~= 2.4. This theoretical framework is in quantitative agreement with experiments and can be used for population balance modeling of colloidal and protein aggregation.

Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions.

PubMed Central

Keskin, O.; Bahar, I.; Badretdinov, A. Y.; Ptitsyn, O. B.; Jernigan, R. L.

1998-01-01

Whether knowledge-based intra-molecular inter-residue potentials are valid to represent inter-molecular interactions taking place at protein-protein interfaces has been questioned in several studies. Differences in the chain connectivity effect and in residue packing geometry between interfaces and single chain monomers have been pointed out as possible sources of distinct energetics for the two cases. In the present study, the interfacial regions of protein-protein complexes are examined to extract inter-molecular inter-residue potentials, using the same statistical methods as those previously adopted for intra-molecular residue pairs. Two sets of energy parameters are derived, corresponding to solvent-mediation and "average residue" mediation. The former set is shown to be highly correlated (correlation coefficient 0.89) with that previously obtained for inter-residue interactions within single chain monomers, while the latter exhibits a weaker correlation (0.69) with its intra-molecular counterpart. In addition to the close similarity of intra- and inter-molecular solvent-mediated potentials, they are shown to be significantly more residue-specific and thereby discriminative compared to the residue-mediated ones, indicating that solvent-mediation plays a major role in controlling the effective inter-residue interactions, either at interfaces, or within single monomers. Based on this observation, a reduced set of energy parameters comprising 20 one-body and 3 two-body terms is proposed (as opposed to the 20 x 20 tables of inter-residue potentials), which reproduces the conventional 20 x 20 tables with a correlation coefficient of 0.99. PMID:9865952

Oriented covalent immobilization of antibodies for measurement of intermolecular binding forces between zipper-like contact surfaces of split inteins.

PubMed

Sorci, Mirco; Dassa, Bareket; Liu, Hongwei; Anand, Gaurav; Dutta, Amit K; Pietrokovski, Shmuel; Belfort, Marlene; Belfort, Georges

2013-06-18

In order to measure the intermolecular binding forces between two halves (or partners) of naturally split protein splicing elements called inteins, a novel thiol-hydrazide linker was designed and used to orient immobilized antibodies specific for each partner. Activation of the surfaces was achieved in one step, allowing direct intermolecular force measurement of the binding of the two partners of the split intein (called protein trans-splicing). Through this binding process, a whole functional intein is formed resulting in subsequent splicing. Atomic force microscopy (AFM) was used to directly measure the split intein partner binding at 1 μm/s between native (wild-type) and mixed pairs of C- and N-terminal partners of naturally occurring split inteins from three cyanobacteria. Native and mixed pairs exhibit similar binding forces within the error of the measurement technique (~52 pN). Bioinformatic sequence analysis and computational structural analysis discovered a zipper-like contact between the two partners with electrostatic and nonpolar attraction between multiple aligned ion pairs and hydrophobic residues. Also, we tested the Jarzynski's equality and demonstrated, as expected, that nonequilibrium dissipative measurements obtained here gave larger energies of interaction as compared with those for equilibrium. Hence, AFM coupled with our immobilization strategy and computational studies provides a useful analytical tool for the direct measurement of intermolecular association of split inteins and could be extended to any interacting protein pair.

Long-stem shaped multifunctional molecular beacon for highly sensitive nucleic acids determination via intramolecular and intermolecular interactions based strand displacement amplification.

PubMed

Xu, Jianguo; Zheng, Tingting; Le, Jingqing; Jia, Lee

2017-11-20

Occurrence and application of oligonucleotide probes have promoted great progress in the biochemical analysis field due to their unique biological and chemical properties. In this work, a long-stem shaped multifunctional molecular beacon (LS-MMB) that is responsive to a cancer-related gene, p53, is well-prepared. By designing the probe with long-paired bases at its two ends and short-paired bases between the middle region and the 3' end, the LS-MMB is intelligently endowed with the ability to recognize the target analyte, serve as the polymerization primer/template, and signal the hybridization event synchronously, which is distinctly advantageous over the traditional molecular beacons (MBs). Moreover, it is excitingly found that the LS-MMB can be employed to exert intramolecular and intermolecular interactions for strand displacement amplification (SDA) without the involvement of any assistant probes; this therapy results in a really easy and rapid sensing system that provides an extremely low background noise and high target output signal. In this case, an excellent sensitivity and specificity to detect target gene down to picomolar level and resolution to even one nucleotide variation are achieved, respectively. In addition, the application potential for real genomic DNA analysis is realized. We envision that the probe of LS-MMB can act as a universal platform for biosensing and biomedical research.

Effect of surface tension on the behavior of adhesive contact based on Lennard-Jones potential law

NASA Astrophysics Data System (ADS)

Zhu, Xinyao; Xu, Wei

2018-02-01

The present study explores the effect of surface tension on adhesive contact behavior where the adhesion is interpreted by long-range intermolecular forces. The adhesive contact is analyzed using the equivalent system of a rigid sphere and an elastic half space covered by a membrane with surface tension. The long-range intermolecular forces are modeled with the Lennard‒Jones (L‒J) potential law. The current adhesive contact issue can be represented by a nonlinear integral equation, which can be solved by Newton‒Raphson method. In contrast to previous studies which consider intermolecular forces as short-range, the present study reveals more details of the features of adhesive contact with surface tension, in terms of jump instabilities, pull-off forces, pressure distribution within the contact area, etc. The transition of the pull-off force is not only consistent with previous studies, but also presents some new interesting characteristics in the current situation.

Ab initio intermolecular potential energy surface for the CO2—N2 system and related thermophysical properties

NASA Astrophysics Data System (ADS)

Crusius, Johann-Philipp; Hellmann, Robert; Castro-Palacio, Juan Carlos; Vesovic, Velisa

2018-06-01

A four-dimensional potential energy surface (PES) for the interaction between a rigid carbon dioxide molecule and a rigid nitrogen molecule was constructed based on quantum-chemical ab initio calculations up to the coupled-cluster level with single, double, and perturbative triple excitations. Interaction energies for a total of 1893 points on the PES were calculated using the counterpoise-corrected supermolecular approach and basis sets of up to quintuple-zeta quality with bond functions. The interaction energies were extrapolated to the complete basis set limit, and an analytical site-site potential function with seven sites for carbon dioxide and five sites for nitrogen was fitted to the interaction energies. The CO2—N2 cross second virial coefficient as well as the dilute gas shear viscosity, thermal conductivity, and binary diffusion coefficient of CO2—N2 mixtures were calculated for temperatures up to 2000 K to validate the PES and to provide reliable reference values for these important properties. The calculated values are in very good agreement with the best experimental data.

Hydrogen bond spectroscopy in the near infrared: Out-of-plane torsion and antigeared bend combination bands in (HF)2

NASA Astrophysics Data System (ADS)

Anderson, David T.; Davis, Scott; Nesbitt, David J.

1996-09-01

High-resolution near infrared spectra of the two ``high'' frequency intermolecular modes of (HF)2 have been characterized in HF-stretch excited states using a slit jet spectrometer. In the spectral region between 4280 and 4480 cm-1, four vibration-rotation-tunneling (VRT) bands are observed and assigned to tunneling pairs of the out-of-plane torsion (ν6) and antigeared bend (ν3) intermolecular modes, in combination with the hydrogen bond donor (ν2) and acceptor (ν1) high-frequency intramolecular HF stretches, respectively. Analysis of the jet-cooled, rotationally resolved spectra provide intermolecular frequencies, rotational constants, tunneling splittings, and predissociation rates for the ν3/ν6 intermolecular excited states. The relatively small changes in the hydrogen bond interconversion tunneling splitting with either ν3 or ν6 excitation indicate that neither intermolecular mode is strongly coupled to the tunneling coordinate. The high-resolution VRT linewidths reveal mode specific predissociation broadening sensitive predominantly to intramolecular excitation, but with significant additional effects due to low-frequency intermolecular excitation as well. The intermolecular vibrational frequencies in the combination states display a systematic dependence on intramolecular redshift that allows all four intermolecular fundamental frequencies to be extrapolated from the near-ir data. Agreement between full 6-D quantum calculations and experiment for the out-of-plane torsion (ν6) vibration is remarkably good (0.5%). However, significant discrepancies (≳10%) between theory and experiment are obtained for the antigeared bend (ν3), indicating the need for further refinement of the HF dimer potential surface. Finally, the observation of all four intermolecular modes allows zero-point contributions to the binding energy to be reliably estimated. The revised value for the binding energy, De=1580(35) cm-1, is slightly higher than semiempirical estimates but now in excellent agreement with recent high level ab initio calculations.

Chiral self-discrimination of the enantiomers of alpha-phenylethylamine derivatives in proton NMR.

PubMed

Huang, Shao-Hua; Bai, Zheng-Wu; Feng, Ji-Wen

2009-05-01

Two types of chiral analytes, the urea and amide derivatives of alpha-phenylethylamine, were prepared. The effect of inter-molecular hydrogen-bonding interaction on self-discrimination of the enantiomers of analytes has been investigated using high-resolution (1)H NMR. It was found that the urea derivatives with double-hydrogen-bonding interaction exhibit not only the stronger hydrogen-bonding interaction but also better self-recognition abilities than the amide derivatives (except for one bearing two NO(2) groups). The present results suggest that double-hydrogen-bonding interaction promotes the self-discrimination ability of the chiral compounds. Copyright (c) 2009 John Wiley & Sons, Ltd.

An Analytical Approach for Relating Boiling Points of Monofunctional Organic Compounds to Intermolecular Forces

ERIC Educational Resources Information Center

Struyf, Jef

2011-01-01

The boiling point of a monofunctional organic compound is expressed as the sum of two parts: a contribution to the boiling point due to the R group and a contribution due to the functional group. The boiling point in absolute temperature of the corresponding RH hydrocarbon is chosen for the contribution to the boiling point of the R group and is a…

Multi-property isotropic intermolecular potentials and predicted spectral lineshapes of collision-induced absorption (CIA), collision-induced light scattering (CILS) and collision-induced hyper-Rayleigh scattering (CIHR) for H2sbnd Ne, -Kr and -Xe

NASA Astrophysics Data System (ADS)

El-Kader, M. S. A.; Godet, J.-L.; Gustafsson, M.; Maroulis, G.

2018-04-01

Quantum mechanical lineshapes of collision-induced absorption (CIA), collision-induced light scattering (CILS) and collision-induced hyper-Rayleigh scattering (CIHR) at room temperature (295 K) are computed for gaseous mixtures of molecular hydrogen with neon, krypton and xenon. The induced spectra are detected using theoretical values for induced dipole moment, pair-polarizability trace and anisotropy, hyper-polarizability and updated intermolecular potentials. Good agreement is observed for all spectra when the literature and the present potentials which are constructed from the transport and thermo-physical properties are used.

Weak competing interactions control assembly of strongly bonded TCNQ ionic acceptor molecules on silver surfaces

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

Park, Changwon; Rojas, Geoffrey A.; Jeon, Seokmin

2014-09-19

The energy scales of interactions that control molecular adsorption and assembly on surfaces can vary by several orders of magnitude, yet the importance of each contributing interaction is not apparent a priori. Tetracyanoquinodimethane (TCNQ) is an archetypal electron acceptor molecule and it is a key component of organic metals. On metal surfaces, this molecule also acts as an electron acceptor, producing negatively charged adsorbates. It is therefore rather intriguing to observe attractive molecular interactions in this system that were reported previously for copper and silver surfaces. In this paper, our experiments compared TCNQ adsorption on noble metal surfaces of Ag(100)more » and Ag(111). In both cases we found net attractive interactions down to the lowest coverage. However, the morphology of the assemblies was strikingly different, with two-dimensional islands on Ag(100) and one-dimensional chains on Ag(111) surfaces. This observation suggests that the registry effect governed by the molecular interaction with the underlying lattice potential is critical in determining the dimensionality of the molecular assembly. Using first-principles density functional calculations with a van der Waals correction scheme, we revealed that the strengths of major interactions (i.e., lattice potential corrugation, intermolecular attraction, and charge-transfer-induced repulsion) are all similar in energy. The van der Waals interactions, in particular, almost double the strength of attractive interactions, making the intermolecular potential comparable in strength to the diffusion potential and promoting self-assembly. However, it is the anisotropy of local intermolecular interactions that is primarily responsible for the difference in the topology of the molecular islands on Ag(100) and Ag(111) surfaces. Finally, we anticipate that the intermolecular potential will become more attractive and dominant over the diffusion potential with increasing molecular size, providing new design strategies for the structure and charge transfer within molecular layers.« less

Perturbation analyses of intermolecular interactions

NASA Astrophysics Data System (ADS)

Koyama, Yohei M.; Kobayashi, Tetsuya J.; Ueda, Hiroki R.

2011-08-01

Conformational fluctuations of a protein molecule are important to its function, and it is known that environmental molecules, such as water molecules, ions, and ligand molecules, significantly affect the function by changing the conformational fluctuations. However, it is difficult to systematically understand the role of environmental molecules because intermolecular interactions related to the conformational fluctuations are complicated. To identify important intermolecular interactions with regard to the conformational fluctuations, we develop herein (i) distance-independent and (ii) distance-dependent perturbation analyses of the intermolecular interactions. We show that these perturbation analyses can be realized by performing (i) a principal component analysis using conditional expectations of truncated and shifted intermolecular potential energy terms and (ii) a functional principal component analysis using products of intermolecular forces and conditional cumulative densities. We refer to these analyses as intermolecular perturbation analysis (IPA) and distance-dependent intermolecular perturbation analysis (DIPA), respectively. For comparison of the IPA and the DIPA, we apply them to the alanine dipeptide isomerization in explicit water. Although the first IPA principal components discriminate two states (the α state and PPII (polyproline II) + β states) for larger cutoff length, the separation between the PPII state and the β state is unclear in the second IPA principal components. On the other hand, in the large cutoff value, DIPA eigenvalues converge faster than that for IPA and the top two DIPA principal components clearly identify the three states. By using the DIPA biplot, the contributions of the dipeptide-water interactions to each state are analyzed systematically. Since the DIPA improves the state identification and the convergence rate with retaining distance information, we conclude that the DIPA is a more practical method compared with the IPA. To test the feasibility of the DIPA for larger molecules, we apply the DIPA to the ten-residue chignolin folding in explicit water. The top three principal components identify the four states (native state, two misfolded states, and unfolded state) and their corresponding eigenfunctions identify important chignolin-water interactions to each state. Thus, the DIPA provides the practical method to identify conformational states and their corresponding important intermolecular interactions with distance information.

Perturbation analyses of intermolecular interactions.

PubMed

Koyama, Yohei M; Kobayashi, Tetsuya J; Ueda, Hiroki R

2011-08-01

Conformational fluctuations of a protein molecule are important to its function, and it is known that environmental molecules, such as water molecules, ions, and ligand molecules, significantly affect the function by changing the conformational fluctuations. However, it is difficult to systematically understand the role of environmental molecules because intermolecular interactions related to the conformational fluctuations are complicated. To identify important intermolecular interactions with regard to the conformational fluctuations, we develop herein (i) distance-independent and (ii) distance-dependent perturbation analyses of the intermolecular interactions. We show that these perturbation analyses can be realized by performing (i) a principal component analysis using conditional expectations of truncated and shifted intermolecular potential energy terms and (ii) a functional principal component analysis using products of intermolecular forces and conditional cumulative densities. We refer to these analyses as intermolecular perturbation analysis (IPA) and distance-dependent intermolecular perturbation analysis (DIPA), respectively. For comparison of the IPA and the DIPA, we apply them to the alanine dipeptide isomerization in explicit water. Although the first IPA principal components discriminate two states (the α state and PPII (polyproline II) + β states) for larger cutoff length, the separation between the PPII state and the β state is unclear in the second IPA principal components. On the other hand, in the large cutoff value, DIPA eigenvalues converge faster than that for IPA and the top two DIPA principal components clearly identify the three states. By using the DIPA biplot, the contributions of the dipeptide-water interactions to each state are analyzed systematically. Since the DIPA improves the state identification and the convergence rate with retaining distance information, we conclude that the DIPA is a more practical method compared with the IPA. To test the feasibility of the DIPA for larger molecules, we apply the DIPA to the ten-residue chignolin folding in explicit water. The top three principal components identify the four states (native state, two misfolded states, and unfolded state) and their corresponding eigenfunctions identify important chignolin-water interactions to each state. Thus, the DIPA provides the practical method to identify conformational states and their corresponding important intermolecular interactions with distance information.

A general transformation to canonical form for potentials in pairwise interatomic interactions.

PubMed

Walton, Jay R; Rivera-Rivera, Luis A; Lucchese, Robert R; Bevan, John W

2015-06-14

A generalized formulation of explicit force-based transformations is introduced to investigate the concept of a canonical potential in both fundamental chemical and intermolecular bonding. Different classes of representative ground electronic state pairwise interatomic interactions are referenced to a chosen canonical potential illustrating application of such transformations. Specifically, accurately determined potentials of the diatomic molecules H2, H2(+), HF, LiH, argon dimer, and one-dimensional dissociative coordinates in Ar-HBr, OC-HF, and OC-Cl2 are investigated throughout their bound potentials. Advantages of the current formulation for accurately evaluating equilibrium dissociation energies and a fundamentally different unified perspective on nature of intermolecular interactions will be emphasized. In particular, this canonical approach has significance to previous assertions that there is no very fundamental distinction between van der Waals bonding and covalent bonding or for that matter hydrogen and halogen bonds.

Development of a "First Principles" Water Potential with Flexible Monomers: Dimer Potential Energy Surface, VRT Spectrum, and Second Virial Coefficient.

PubMed

Babin, Volodymyr; Leforestier, Claude; Paesani, Francesco

2013-12-10

The development of a "first principles" water potential with flexible monomers (MB-pol) for molecular simulations of water systems from gas to condensed phases is described. MB-pol is built upon the many-body expansion of the intermolecular interactions, and the specific focus of this study is on the two-body term (V2B) representing the full-dimensional intermolecular part of the water dimer potential energy surface. V2B is constructed by fitting 40,000 dimer energies calculated at the CCSD(T)/CBS level of theory and imposing the correct asymptotic behavior at long-range as predicted from "first principles". The comparison of the calculated vibration-rotation tunneling (VRT) spectrum and second virial coefficient with the corresponding experimental results demonstrates the accuracy of the MB-pol dimer potential energy surface.

Lattice dynamics of solid N2 with an ab initio intermolecular potential

NASA Astrophysics Data System (ADS)

Luty, T.; van der Avoird, A.; Berns, R. M.

1980-11-01

We have performed harmonic and self-consistent phonon lattice dynamics calculations for α and γ N2 crystals using an intermolecular potential from ab initio calculations. This potential contains electrostatic (multipole) interactions, up to all R-9 terms inclusive, anisotropic dispersion interactions up to all R-10 terms inclusive, and anisotropic overlap interactions caused by charge penetration and exchange between the molecules. The lattice constants, cohesion energy, the frequencies of the translational phonon modes and the Grüneisen parameters for the librational modes are in good agreement with experimental values, confirming the quality of the potential. The frequencies of the librational modes and those of the mixed modes are less well reproduced, especially at temperatures near the α-β phase transition. Probably, the self-consistent phonon method used does not fully account for the anharmonicity in the librations.

Controlled Self-Assembly of Low-Dimensional Alq3 Nanostructures from 1D Nanowires to 2D Plates via Intermolecular Interactions

NASA Astrophysics Data System (ADS)

Gu, Jianmin; Yin, Baipeng; Fu, Shaoyan; Jin, Cuihong; Liu, Xin; Bian, Zhenpan; Li, Jianjun; Wang, Lu; Li, Xiaoyu

2018-03-01

Due to the intense influence of the shape and size of the photon building blocks on the limitation and guidance of optical waves, an important strategy is the fabrication of different structures. Herein, organic semiconductor tris-(8-hydroxyquinoline)aluminium (Alq3) nanostructures with controllable morphology, ranging from one-dimensional nanowires to two-dimensional plates, have been prepared through altering intermolecular interactions with employing the anti-solvent diffusion cooperate with solvent-volatilization induced self-assembly method. The morphologies of the formed nanostructures, which are closely related to the stacking modes of the molecules, can be exactly controlled by altering the polarity of anti-solvents that can influence various intermolecular interactions. The synthesis strategy reported here can potentially be extended to other functional organic nanomaterials.

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

PubMed

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

2014-03-07

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

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

Shirkov, Leonid; Makarewicz, Jan, E-mail: jama@amu.edu.pl

An ab initio intermolecular potential energy surface (PES) has been constructed for the benzene-krypton (BKr) van der Waals (vdW) complex. The interaction energy has been calculated at the coupled cluster level of theory with single, double, and perturbatively included triple excitations using different basis sets. As a result, a few analytical PESs of the complex have been determined. They allowed a prediction of the complex structure and its vibrational vdW states. The vibrational energy level pattern exhibits a distinct polyad structure. Comparison of the equilibrium structure, the dipole moment, and vibrational levels of BKr with their experimental counterparts has allowedmore » us to design an optimal basis set composed of a small Dunning’s basis set for the benzene monomer, a larger effective core potential adapted basis set for Kr and additional midbond functions. Such a basis set yields vibrational energy levels that agree very well with the experimental ones as well as with those calculated from the available empirical PES derived from the microwave spectra of the BKr complex. The basis proposed can be applied to larger complexes including Kr because of a reasonable computational cost and accurate results.« less

A critical evaluation of perturbation theories by Monte Carlo simulation of the first four perturbation terms in a Helmholtz energy expansion for the Lennard-Jones fluid

NASA Astrophysics Data System (ADS)

van Westen, Thijs; Gross, Joachim

2017-07-01

The Helmholtz energy of a fluid interacting by a Lennard-Jones pair potential is expanded in a perturbation series. Both the methods of Barker-Henderson (BH) and of Weeks-Chandler-Andersen (WCA) are evaluated for the division of the intermolecular potential into reference and perturbation parts. The first four perturbation terms are evaluated for various densities and temperatures (in the ranges ρ*=0 -1.5 and T*=0.5 -12 ) using Monte Carlo simulations in the canonical ensemble. The simulation results are used to test several approximate theoretical methods for describing perturbation terms or for developing an approximate infinite order perturbation series. Additionally, the simulations serve as a basis for developing fully analytical third order BH and WCA perturbation theories. The development of analytical theories allows (1) a careful comparison between the BH and WCA formalisms, and (2) a systematic examination of the effect of higher-order perturbation terms on calculated thermodynamic properties of fluids. Properties included in the comparison are supercritical thermodynamic properties (pressure, internal energy, and chemical potential), vapor-liquid phase equilibria, second virial coefficients, and heat capacities. For all properties studied, we find a systematically improved description upon using a higher-order perturbation theory. A result of particular relevance is that a third order perturbation theory is capable of providing a quantitative description of second virial coefficients to temperatures as low as the triple-point of the Lennard-Jones fluid. We find no reason to prefer the WCA formalism over the BH formalism.

Study of interaction in silica glass via model potential approach

NASA Astrophysics Data System (ADS)

Mann, Sarita; Rani, Pooja

2016-05-01

Silica is one of the most commonly encountered substances in daily life and in electronics industry. Crystalline SiO2 (in several forms: quartz, cristobalite, tridymite) is an important constituent of many minerals and gemstones, both in pure form and mixed with related oxides. Cohesive energy of amorphous SiO2 has been investigated via intermolecular potentials i.e weak Van der Waals interaction and Morse type short-range interaction. We suggest a simple atom-atom based Van der Waals as well as Morse potential to find cohesive energy of glass. It has been found that the study of silica structure using two different model potentials is significantly different. Van der Waals potential is too weak (P.E =0.142eV/molecule) to describe the interaction between silica molecules. Morse potential is a strong potential, earlier given for intramolecular bonding, but if applied for intermolecular bonding, it gives a value of P.E (=-21.92eV/molecule) to appropriately describe the structure of silica.

Terahertz spectroscopy and solid-state density functional theory calculation of anthracene: Effect of dispersion force on the vibrational modes

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

Zhang, Feng; Tominaga, Keisuke, E-mail: atmyh@ntu.edu.tw, E-mail: tominaga@kobe-u.ca.jp, E-mail: junichi.nishizawa@hanken.jp; Hayashi, Michitoshi, E-mail: atmyh@ntu.edu.tw, E-mail: tominaga@kobe-u.ca.jp, E-mail: junichi.nishizawa@hanken.jp

2014-05-07

The phonon modes of molecular crystals in the terahertz frequency region often feature delicately coupled inter- and intra-molecular vibrations. Recent advances in density functional theory such as DFT-D{sup *} have enabled accurate frequency calculation. However, the nature of normal modes has not been quantitatively discussed against experimental criteria such as isotope shift (IS) and correlation field splitting (CFS). Here, we report an analytical mode-decoupling method that allows for the decomposition of a normal mode of interest into intermolecular translation, libration, and intramolecular vibrational motions. We show an application of this method using the crystalline anthracene system as an example. Themore » relationship between the experimentally obtained IS and the IS obtained by PBE-D{sup *} simulation indicates that two distinctive regions exist. Region I is associated with a pure intermolecular translation, whereas region II features coupled intramolecular vibrations that are further coupled by a weak intermolecular translation. We find that the PBE-D{sup *} data show excellent agreement with the experimental data in terms of IS and CFS in region II; however, PBE-D{sup *} produces significant deviations in IS in region I where strong coupling between inter- and intra-molecular vibrations contributes to normal modes. The result of this analysis is expected to facilitate future improvement of DFT-D{sup *}.« less

Quantum mechanical force field for water with explicit electronic polarization.

PubMed

Han, Jaebeom; Mazack, Michael J M; Zhang, Peng; Truhlar, Donald G; Gao, Jiali

2013-08-07

A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across biological ion channels through membranes.

Simulation studies for surfaces and materials strength

NASA Technical Reports Server (NTRS)

Halicioglu, T.

1985-01-01

From intermolecular force studies, it is now known that the overall non-additive contribution to the lattice enegy is positive so that analysis based on only pairwise additivity suggests a shallower intermolecular potential than the true value. Two body contributions alone are also known to be categorically unable to even qualitatively describe some configurations of molecular clusters in the gas phase or the general relaxation and reconstruction of fcc crystal surfaces. In addition, the many-body contribution was shown to play a key role in the stability of certain crystal structures. In these recent analyses, a relatively simple potential energy function (PEF), comprising only a two-body Mie-type potential plus a three-body Axilrod-Teller-type potential, was found to be extremely effective. This same parametric PEF is applied to describe the bulk stability and surface energy for the diamond cubic structure. To test the stability condition, the FCC, BCC, diamond cubic, graphite and beta-tin structures were considered.

AIE-doped poly(ionic liquid) photonic spheres: a single sphere-based customizable sensing platform for the discrimination of multi-analytes† †Electronic supplementary information (ESI) available: Synthesis and characterization of the AIE luminogen, experimental details, response profiles and results of the multivariate analysis. See DOI: 10.1039/c7sc02409f Click here for additional data file.

PubMed Central

Zhang, Wanlin; Gao, Ning; Cui, Jiecheng; Wang, Chen; Wang, Shiqiang; Zhang, Guanxin; Dong, Xiaobiao

2017-01-01

By simultaneously exploiting the unique properties of ionic liquids and aggregation-induced emission (AIE) luminogens, as well as photonic structures, a novel customizable sensing system for multi-analytes was developed based on a single AIE-doped poly(ionic liquid) photonic sphere. It was found that due to the extraordinary multiple intermolecular interactions involved in the ionic liquid units, one single sphere could differentially interact with broader classes of analytes, thus generating response patterns with remarkable diversity. Moreover, the optical properties of both the AIE luminogen and photonic structure integrated in the poly(ionic liquid) sphere provide multidimensional signal channels for transducing the involved recognition process in a complementary manner and the acquisition of abundant and sufficient sensing information could be easily achieved on only one sphere sensor element. More importantly, the sensing performance of our poly(ionic liquid) photonic sphere is designable and customizable through a simple ion-exchange reaction and target-oriented multi-analyte sensing can be conveniently realized using a selective receptor species, such as counterions, showing great flexibility and extendibility. The power of our single sphere-based customizable sensing system was exemplified by the successful on-demand detection and discrimination of four multi-analyte challenge systems: all 20 natural amino acids, nine important phosphate derivatives, ten metal ions and three pairs of enantiomers. To further demonstrate the potential of our spheres for real-life application, 20 amino acids in human urine and their 26 unprecedented complex mixtures were also discriminated between by the single sphere-based array. PMID:28989662

Gold(I)-Catalysed Hydroarylation of 1,3-Disubstituted Allenes with Efficient Axial-to-Point Chirality Transfer.

PubMed

Sutherland, Daniel R; Kinsman, Luke; Angiolini, Stuart M; Rosair, Georgina M; Lee, Ai-Lan

2018-05-11

Hydroarylation of enantioenriched 1,3-disubstituted allenes has the potential to proceed with axial-to-point chirality transfer to yield enantioenriched allylated (hetero)aryl compounds. However, the gold-catalysed intermolecular reaction was previously reported to occur with no chirality transfer owing to competing allene racemisation. Herein, we describe the development of the first intermolecular hydroarylations of allenes to proceed with efficient chirality transfer and summarise some of the key criteria for achieving high regio- and stereoselectivity. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A catalytic tethering strategy: simple aldehydes catalyze intermolecular alkene hydroaminations.

PubMed

MacDonald, Melissa J; Schipper, Derek J; Ng, Peter J; Moran, Joseph; Beauchemin, André M

2011-12-21

Herein we describe a catalytic tethering strategy in which simple aldehyde precatalysts enable, through temporary intramolecularity, room-temperature intermolecular hydroamination reactivity and the synthesis of vicinal diamines. The catalyst allows the formation of a mixed aminal from an allylic amine and a hydroxylamine, resulting in a facile intramolecular hydroamination event. The promising enantioselectivities obtained with a chiral aldehyde also highlight the potential of this catalytic tethering approach in asymmetric catalysis and demonstrate that efficient enantioinduction relying only on temporary intramolecularity is possible. © 2011 American Chemical Society

Influence of pressure on the crystallization of systems characterized by different intermolecular attraction

NASA Astrophysics Data System (ADS)

Koperwas, K.; Affouard, F.; Gerges, J.; Valdes, L.-C.; Adrjanowicz, K.; Paluch, M.

2017-12-01

In this paper, we examine, in terms of the classical nucleation theory, how the strengthening of the attractive intermolecular interactions influences the crystallization process for systems like Lennard-Jones at different isobaric conditions. For this purpose, we modify the standard Lennard-Jones potential, and as a result, we obtain three different systems characterized by various strengths of attractive potentials occurring between molecules, which are in direct relationship to the physical quantities describing molecules, e.g., its polarizability or dipole moment. Based on performed analysis, we demonstrate that the molecular attraction primarily impacts the thermodynamics of the interface between liquid and crystal. This is reflected in the behavior of nucleation and overall crystallization rates during compression of the system.

Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

PubMed Central

Nagy, Peter I.

2014-01-01

A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed. PMID:25353178

Intermolecular vibrational modes and H-bond interactions in crystalline urea investigated by terahertz spectroscopy and theoretical calculation

NASA Astrophysics Data System (ADS)

Zhao, Yonghong; Li, Zhi; Liu, Jianjun; Hu, Cong; Zhang, Huo; Qin, Binyi; Wu, Yifang

2018-01-01

The characteristic absorption spectra of crystalline urea in 0.6-1.8 THz region have been measured by terahertz time-domain spectroscopy at room temperature experimentally. Five broad absorption peaks were observed at 0.69, 1.08, 1.27, 1.47 and 1.64 THz respectively. Moreover, density functional theory (DFT) calculation has been performed for the isolated urea molecule, and there is no infrared intensity in the region below 1.8 THz. This means that single molecule calculations are failure to predict the experimental spectra of urea crystals. To simulate these spectra, calculations on a cluster of seven urea molecules using M06-2X and B3LYP-D3 are performed, and we found that M06-2X perform better. The observed THz vibrational modes are assigned to bending and torsional modes related to the intermolecular H-bond interactions with the help of potential energy distribution (PED) method. Using the reduced-density-gradient (RDG) analysis, the positions and types of intermolecular H-bond interactions in urea crystals are visualized. Therefore, we can confirm that terahertz spectroscopy can be used as an effective means to detect intermolecular H-bond interactions in molecular crystals.

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

PubMed Central

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

Thz Spectroscopy and DFT Modeling of Intermolecular Vibrations in Hydrophobic Amino Acids

NASA Astrophysics Data System (ADS)

Williams, michael R. C.; Aschaffenburg, Daniel J.; Schmuttenmaer, Charles A.

2013-06-01

Vibrations that involve intermolecular displacements occur in molecular crystals at frequencies in the 0.5-5 THz range (˜15-165 cm^{-1}), and these motions are direct indicators of the interaction potential between the molecules. The intermolecular potential energy surface of crystalline hydrophobic amino acids is inherently interesting simply because of the wide variety of forces (electrostatic, dipole-dipole, hydrogen-bonding, van der Waals) that are present. Furthermore, an understanding of these particular interactions is immediately relevant to important topics like protein conformation and pharmaceutical polymorphism. We measured the low-frequency absorption spectra of several polycrystalline hydrophobic amino acids using THz time-domain spectroscopy, and in addition we carried out DFT calculations using periodic boundary conditions and an exchange-correlation functional that accounts for van der Waals dispersion forces. We chose to investigate a series of similar amino acids with closely analogous unit cells (leucine, isoleucine, and allo-isoleucine, in racemic or pseudo-racemic mixtures). This allows us to consider trends in the vibrational spectra as a function of small changes in molecular arrangement and/or crystal geometry. In this way, we gain confidence that peak assignments are not based on serendipitous similarities between calculated and observed features.

A general intermolecular force field based on tight-binding quantum chemical calculations

NASA Astrophysics Data System (ADS)

Grimme, Stefan; Bannwarth, Christoph; Caldeweyher, Eike; Pisarek, Jana; Hansen, Andreas

2017-10-01

A black-box type procedure is presented for the generation of a molecule-specific, intermolecular potential energy function. The method uses quantum chemical (QC) information from our recently published extended tight-binding semi-empirical scheme (GFN-xTB) and can treat non-covalently bound complexes and aggregates with almost arbitrary chemical structure. The necessary QC information consists of the equilibrium structure, Mulliken atomic charges, charge centers of localized molecular orbitals, and also of frontier orbitals and orbital energies. The molecular pair potential includes model density dependent Pauli repulsion, penetration, as well as point charge electrostatics, the newly developed D4 dispersion energy model, Drude oscillators for polarization, and a charge-transfer term. Only one element-specific and about 20 global empirical parameters are needed to cover systems with nuclear charges up to radon (Z = 86). The method is tested for standard small molecule interaction energy benchmark sets where it provides accurate intermolecular energies and equilibrium distances. Examples for structures with a few hundred atoms including charged systems demonstrate the versatility of the approach. The method is implemented in a stand-alone computer code which enables rigid-body, global minimum energy searches for molecular aggregation or alignment.

NMR Detection Using Laser-Polarized Xenon as a DipolarSensor

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

Granwehr, Josef; Urban, Jeffry T.; Trabesinger, Andreas H.

2005-02-28

Hyperpolarized Xe-129 can be used as a sensor to indirectly detect NMR spectra of heteronuclei that are neither covalently bound nor necessarily in direct contact with the Xe atoms, but coupled through long-range intermolecular dipolar couplings. In order to reintroduce long-range dipolar couplings the sample symmetry has to be broken. This can be done either by an asymmetric sample arrangement, or by breaking the symmetry of the spin magnetization with field gradient pulses. Experiments are performed where only a small fraction of the available Xe-129 magnetization is used for each point, so that a single batch of xenon suffices formore » the point-by-point acquisition of a heteronuclear NMR spectrum. Examples with H-1 as analyte nucleus show that these methods have the potential to obtain spectra with a resolution that is high enough to determine homonuclear J couplings. The applicability of this technique with remote detection is discussed.« less

Long-Range Repulsion Between Spatially Confined van der Waals Dimers

NASA Astrophysics Data System (ADS)

Sadhukhan, Mainak; Tkatchenko, Alexandre

2017-05-01

It is an undisputed textbook fact that nonretarded van der Waals (vdW) interactions between isotropic dimers are attractive, regardless of the polarizability of the interacting systems or spatial dimensionality. The universality of vdW attraction is attributed to the dipolar coupling between fluctuating electron charge densities. Here, we demonstrate that the long-range interaction between spatially confined vdW dimers becomes repulsive when accounting for the full Coulomb interaction between charge fluctuations. Our analytic results are obtained by using the Coulomb potential as a perturbation over dipole-correlated states for two quantum harmonic oscillators embedded in spaces with reduced dimensionality; however, the long-range repulsion is expected to be a general phenomenon for spatially confined quantum systems. We suggest optical experiments to test our predictions, analyze their relevance in the context of intermolecular interactions in nanoscale environments, and rationalize the recent observation of anomalously strong screening of the lateral vdW interactions between aromatic hydrocarbons adsorbed on metal surfaces.

Melting Behavior of a Model Molecular Crystalline GeI4

NASA Astrophysics Data System (ADS)

Fuchizaki, Kazuhiro; Asano, Yuta

2015-06-01

A model molecular crystalline GeI4 was examined using molecular dynamics simulation. The model was constructed in such a way that rigid tetrahedral molecules interact with each other via Lennard-Jones potentials whose centers are located at the vertices of a tetrahedron. Because no other interaction that can "soften" the intermolecular interaction was introduced, the melting curve of the model crystalline material does not exhibit the anomaly that was found for the real substance. However, the current investigation is useful in that it could settle the upper bound of pressure below which the model can predict properties of the molecular liquid. Moreover, singularity-free nature of the melting curve allowed us to analytically treat the melting curve in the light of the Kumari-Dass-Kechin equation. As a result, we could definitely conclude that the well-known Simon equation for the melting curve is merely an approximate expression. The condition for the validity of Simon's equation was identified.

Modeling Adsorption-Desorption Processes at the Intermolecular Interactions Level

NASA Astrophysics Data System (ADS)

Varfolomeeva, Vera V.; Terentev, Alexey V.

2018-01-01

Modeling of the surface adsorption and desorption processes, as well as the diffusion, are of considerable interest for the physical phenomenon under study in ground tests conditions. When imitating physical processes and phenomena, it is important to choose the correct parameters to describe the adsorption of gases and the formation of films on the structural materials surface. In the present research the adsorption-desorption processes on the gas-solid interface are modeled with allowance for diffusion. Approaches are proposed to describe the adsorbate distribution on the solid body surface at the intermolecular interactions level. The potentials of the intermolecular interaction of water-water, water-methane and methane-methane were used to adequately modeling the real physical and chemical processes. The energies calculated by the B3LYP/aug-cc-pVDZ method. Computational algorithms for determining the average molecule area in a dense monolayer, are considered here. Differences in modeling approaches are also given: that of the proposed in this work and the previously approved probabilistic cellular automaton (PCA) method. It has been shown that the main difference is due to certain limitations of the PCA method. The importance of accounting the intermolecular interactions via hydrogen bonding has been indicated. Further development of the adsorption-desorption processes modeling will allow to find the conditions for of surface processes regulation by means of quantity adsorbed molecules control. The proposed approach to representing the molecular system significantly shortens the calculation time in comparison with the use of atom-atom potentials. In the future, this will allow to modeling the multilayer adsorption at a reasonable computational cost.

Complete characterization of the water dimer vibrational ground state and testing the VRT(ASP-W)III, SAPT-5st, and VRT(MCY-5f) surfaces

NASA Astrophysics Data System (ADS)

Keutsch, Frank N.; Goldman, Nir; Harker, Heather A.; Leforestier, Claude; Saykally, Richard J.

We report the observation of extensive a- and c-type rotation-tunnelling (RT) spectra of (H2O)2 for Ka =0-3, and (D2O)2 for Ka =0-4. These data allow a detailed characterization of the vibrational ground state to energies comparable to those of the low-lying (70-80 cm-1) intermolecular vibrations. We present a comparison of the experimentally determined molecular constants and tunnelling splittings with those calculated on the VRT(ASP-W)III, SAPT-5st, and VRT(MCY-5f) intermolecular potential energy surfaces. The SAPT-5st potential reproduces the vibrational ground state properties of the water dimer very well. The VRT(MCY-5f) and especially the VRT(ASP-W)III potentials show larger disagreements, in particular for the bifurcation tunnelling splitting.

Optimization of intermolecular potential parameters for the CO2/H2O mixture.

PubMed

Orozco, Gustavo A; Economou, Ioannis G; Panagiotopoulos, Athanassios Z

2014-10-02

Monte Carlo simulations in the Gibbs ensemble were used to obtain optimized intermolecular potential parameters to describe the phase behavior of the mixture CO2/H2O, over a range of temperatures and pressures relevant for carbon capture and sequestration processes. Commonly used fixed-point-charge force fields that include Lennard-Jones 12-6 (LJ) or exponential-6 (Exp-6) terms were used to describe CO2 and H2O intermolecular interactions. For force fields based on the LJ functional form, changes of the unlike interactions produced higher variations in the H2O-rich phase than in the CO2-rich phase. A major finding of the present study is that for these potentials, no combination of unlike interaction parameters is able to adequately represent properties of both phases. Changes to the partial charges of H2O were found to produce significant variations in both phases and are able to fit experimental data in both phases, at the cost of inaccuracies for the pure H2O properties. By contrast, for the Exp-6 case, optimization of a single parameter, the oxygen-oxygen unlike-pair interaction, was found sufficient to give accurate predictions of the solubilities in both phases while preserving accuracy in the pure component properties. These models are thus recommended for future molecular simulation studies of CO2/H2O mixtures.

Vibrational coherence in polar solutions of Zn(II) tetrakis(N-methylpyridyl)porphyrin with Soret-band excitation: rapidly damped intermolecular modes with clustered solvent molecules and slowly damped intramolecular modes from the porphyrin macrocycle.

PubMed

Dillman, Kevin L; Shelly, Katherine R; Beck, Warren F

2009-04-30

Ground-state coherent wavepacket motions arising from intermolecular modes with clustered, first-shell solvent molecules were observed using the femtosecond dynamic absorption technique in polar solutions of Zn(II) meso-tetrakis(N-methylpyridyl)porphyrin (ZnTMPyP) with excitation in the Soret absorption band. As was observed previously in bacteriochlorophyll a solution, the pump-probe transients in ZnTMPyP solutions are weakly modulated by slowly damped (effective damping time gamma > 1 ps) features that are assigned to intramolecular modes, the skeletal normal modes of vibration of the porphyrin. The 40 cm(-1) and 215 cm(-1) modes from the metal-doming and metal-solvent-ligand modes, respectively, are members of this set of modulation components. A slowly damped 2-4 cm(-1) component is assigned to the internal rotation of the N-methylpyridyl rings with respect to the porphyrin macrocycle; this mode obtains strong resonance Raman intensity enhancement from an extensive delocalization of pi-electron density from the porphyrin in the ground state onto the rings in the pi* excited states. The dominant features observed in the pump-probe transients are a pair of rapidly damped (gamma < 250 fs) modulation components arising from intermolecular modes with solvent molecules. This structural assignment is supported by an isotope-dependent shift of the average mode frequencies in methanol and perdeuterated methanol. The solvent dependence of the mean intermolecular mode frequency is consistent with a van der Waals intermolecular potential that has significant contributions only from the London dispersion and induction interactions; ion-dipole or ion-induced-dipole terms do not make large contributions because the pi-electron density is not extensively delocalized onto the N-methylpyridyl rings. The modulation depth associated with the intermolecular modes exhibits a marked dependence on the electronic structure of the solvent that is probably related to the degree of covalency; the strongest modulations are observed in acetonitrile and dimethylsulfoxide. The results strongly support a structural assignment of the low-frequency modes that are coupled to the primary and secondary electron-transfer reactions in photosynthetic reaction centers to intermolecular modes between the redox-active chromophores and first-solvation shell groups from the surrounding protein, and an important additional function of the intermolecular modes in the stabilization of charged intermediates is suggested.

Intermolecular potentials and the accurate prediction of the thermodynamic properties of water

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

Shvab, I.; Sadus, Richard J., E-mail: rsadus@swin.edu.au

2013-11-21

The ability of intermolecular potentials to correctly predict the thermodynamic properties of liquid water at a density of 0.998 g/cm{sup 3} for a wide range of temperatures (298–650 K) and pressures (0.1–700 MPa) is investigated. Molecular dynamics simulations are reported for the pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, and Joule-Thomson coefficient of liquid water using the non-polarizable SPC/E and TIP4P/2005 potentials. The results are compared with both experiment data and results obtained from the ab initio-based Matsuoka-Clementi-Yoshimine non-additive (MCYna) [J. Li, Z. Zhou, and R. J. Sadus, J. Chem. Phys.more » 127, 154509 (2007)] potential, which includes polarization contributions. The data clearly indicate that both the SPC/E and TIP4P/2005 potentials are only in qualitative agreement with experiment, whereas the polarizable MCYna potential predicts some properties within experimental uncertainty. This highlights the importance of polarizability for the accurate prediction of the thermodynamic properties of water, particularly at temperatures beyond 298 K.« less

Broken symmetry phase transition in solid p-H 2, o-D 2 and HD: crystal field effects

NASA Astrophysics Data System (ADS)

Freiman, Yu. A.; Hemley, R. J.; Jezowski, A.; Tretyak, S. M.

1999-04-01

We report the effect of the crystal field (CF) on the broken symmetry phase transition (BSP) in solid parahydrogen, orthodeuterium, and hydrogen deuteride. The CF was calculated taking into account a distortion from the ideal HCP structure. We find that, in addition to the molecular field generated by the coupling terms in the intermolecular potential, the Hamiltonian of the system contains a crystal-field term, originating from single-molecular terms in the intermolecular potential. Ignoring the CF is the main cause of the systematic underestimation of the transition pressure, characteristic of published theories of the BSP transition. The distortion of the lattice that gives rise to the negative CF in response to the applied pressure is in accord with the general Le Chatelier-Braun principle.

Frenkel-Charge-Transfer exciton intermixing theory for molecular crystals with two isolated Frenkel exciton states.

NASA Astrophysics Data System (ADS)

Bondarev, Igor; Popescu, Adrian

We develop an analytical theory for the intra-intermolecular exciton intermixing in periodic 1D chains of planar organic molecules with two isolated low-lying Frenkel exciton states, typical of copper phthalocyanine (CuPc) and other transition metal phthalocyanine molecules. We formulate the Hamiltonian and use the exact Bogoliubov diagonalization procedure to derive the eigen energy spectrum for the two lowest intramolecular Frenkel excitons coupled to the intermolecular charge transfer (CT) exciton state. By comparing our theoretical spectrum with available experimental CuPc absorption data, we obtain the parameters of the Frenkel-CT exciton intermixing in CuPc thin films. The two Frenkel exciton states here are spaced apart by 0.26 eV, and the charge transfer exciton state is 50 meV above the lowest Frenkel exciton. Both Frenkel excitons are strongly mixed with the CT exciton, showing the coupling constant 0.17 eV in agreement with earlier electron transport experiments. Our results can be used for the proper interpretation of the physical properties of crystalline phthalocyanines. DOE-DE-SC0007117 (I.B.), UNC-GA ROI Grant (A.P.).

DEVELOPMENT OF A MODEL THAT CONTAINS BOTH MULTIPOLE MOMENTS AND GAUSSIANS FOR THE CALCULATION OF MOLECULAR ELECTROSTATIC POTENTIALS

EPA Science Inventory

The electrostatic interaction is a critical component of intermolecular interactions in biological processes. Rapid methods for the computation and characterization of the molecular electrostatic potential (MEP) that segment the molecular charge distribution and replace this cont...

Terahertz laser spectroscopy of the water dimer intermolecular vibrations. II. (H2O)2

NASA Astrophysics Data System (ADS)

Braly, L. B.; Liu, K.; Brown, M. G.; Keutsch, F. N.; Fellers, R. S.; Saykally, R. J.

2000-06-01

Terahertz VRT laser spectra of four (H2O)2 intermolecular vibrations consisting of 362 transitions have been measured between 87 and 108 cm-1 with ca. 2 MHz precision. The results differ both qualitatively and quantitatively from the predictions of dimer potentials tested. The spectra also reveal an ordering of the intermolecular vibrations which differs dramatically from that predicted by normal mode analysis. Strong coupling is indicated between the low barrier tunneling motions and the intermolecular vibrations as well as among different vibrations. In particular the 102.1 cm-1 (H2O)2 vibration assigned as the acceptor wag (ν8) exhibits two types of perturbations. In one of these a component of Ka=1 coupling with a tunneling component of Ka=0 in the 108 cm-1 acceptor twist (ν11) vibration. There is also an indication that the 103.1 cm-1 (H2O)2 band assigned as the donor in-plane bend (ν6) is coupled to the acceptor wag resulting in a lower of the in-plane bend frequency and a higher acceptor wag frequency. Detailed analysis of the VRT levels confirms the extreme nonrigidity of this complex, indicating that the use of approximate models with reduced dimensionality to calculate its properties are likely to fail.

Decomposition of Intermolecular Interactions in the Crystal Structure of Some Diacetyl Platinum(II) Complexes: Combined Hirshfeld, AIM, and NBO Analyses.

PubMed

Soliman, Saied M; Barakat, Assem

2016-12-06

Intermolecular interactions play a vital role in crystal structures. Therefore, we conducted a topological study, using Hirshfeld surfaces and atom in molecules (AIM) analysis, to decompose and analyze, respectively, the different intermolecular interactions in six hydrazone-diacetyl platinum(II) complexes. Using AIM and natural bond orbital (NBO) analyses, we determined the type, nature, and strength of the interactions. All the studied complexes contain C-H⋯O interactions, and the presence of bond critical points along the intermolecular paths underlines their significance. The electron densities (ρ(r)) at the bond critical points (0.0031-0.0156 e/a₀³) fall within the typical range for H-bonding interactions. Also, the positive values of the Laplacian of the electron density (∇²ρ(r)) revealed the depletion of electronic charge on the interatomic path, another characteristic feature of closed-shell interactions. The ratios of the absolute potential energy density to the kinetic energy density (| V (r)|/ G (r)) and ρ(r) are highest for the O2⋯H15-N3 interaction in [Pt(COMe)₂(2-pyCMe=NNH₂)] (1); hence, this interaction has the highest covalent character of all the O⋯H intermolecular interactions. Interestingly, in [Pt(COMe)₂(H₂NN=CMe-CMe=NNH₂)] (3), there are significant N-H⋯Pt interactions. Using the NBO method, the second-order interaction energies, E (2) , of these interactions range from 3.894 to 4.061 kJ/mol. Furthermore, the hybrid Pt orbitals involved in these interactions are comprised of d xy , d xz , and s atomic orbitals.

Intermolecular interactions between σ- and π-holes of bromopentafluorobenzene and pyridine: computational and experimental investigations.

PubMed

Yang, Fang-Ling; Yang, Xing; Wu, Rui-Zhi; Yan, Chao-Xian; Yang, Fan; Ye, Weichun; Zhang, Liang-Wei; Zhou, Pan-Pan

2018-04-25

The characters of σ- and π-holes of bromopentafluorobenzene (C6F5Br) enable it to interact with an electron-rich atom or group like pyridine which possesses an electron lone-pair N atom and a π ring. Theoretical studies of intermolecular interactions between C6F5Br and C5H5N have been carried out at the M06-2X/aug-cc-pVDZ level without and with the counterpoise method, together with single point calculations at M06-2X/TZVP, wB97-XD/aug-cc-pVDZ and CCSD(T)/aug-cc-pVDZ levels. The σ- and π-holes of C6F5Br exhibiting positive electrostatic potentials make these sites favorably interact with the N atom and the π ring of C5H5N with negative electrostatic potentials, leading to five different dimers connected by a σ-holen bond, a σ-holeπ bond or a π-holeπ bond. Their geometrical structures, characteristics, nature and spectroscopy behaviors were systematically investigated. EDA analyses reveal that the driving forces in these dimers are different. NCI, QTAIM and NBO analyses confirm the existence of intermolecular interactions formed via σ- and π-holes of C6F5Br and the N atom and the π ring of C5H5N. The experimental IR and Raman spectra gave us important information about the formation of molecular complexes between C6F5Br and C5H5N. We expect that the results could provide valuable insights into the investigation of intermolecular interactions involving σ- and π-holes.

Structure of Poly(dialkylsiloxane) Melts:  Comparisons of Wide-Angle X-ray Scattering, Molecular Dynamics Simulations, and Integral Equation Theory

DOE PAGES

Habenschuss, Anton; Tsige, Mesfin; Curro, John G.; ...

2007-08-21

Here, wide-angle X-ray scattering, molecular dynamics (MD) simulations, and integral equation theory are used to study the structure of poly(diethylsiloxane) (PDES), poly(ethylmethylsiloxane) (PEMS), and poly(dimethylsiloxane) (PDMS) melts. The structure functions of PDES, PEMS, and PDMS are similar, but systematic trends in the intermolecular packing are observed. The local intramolecular structure is extracted from the experimental structure functions. The bond distances and bond angles obtained, including the large Si-O-Si angle, are in good agreement with the explicit atom (EA) and united atom (UA) potentials used in the simulations and theory and from other sources. Very good agreement is found between themore » MD simulations using the EA potentials and the experimental scattering results. Good agreement is also found between the polymer reference interaction site model (PRISM theory) and the UA MD simulations. The intermolecular structure is examined experimentally using an appropriately weighted radial distribution function and with theory and simulation using intermolecular site/site pair correlation functions. Finally, experiment, simulation, and theory show systematic increases in the chain/chain packing distances in the siloxanes as the number of sites in the pendant side chains is increased.« less

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

NASA Astrophysics Data System (ADS)

Dadsetani, Mehrdad; Abdolmaleki, Ahmad; Zabardasti, Abedin

2016-11-01

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

Long range intermolecular interactions between the alkali diatomics Na2, K2, and NaK

NASA Astrophysics Data System (ADS)

Zemke, Warren T.; Byrd, Jason N.; Michels, H. Harvey; Montgomery, John A.; Stwalley, William C.

2010-06-01

Long range interactions between the ground state alkali diatomics Na2-Na2, K2-K2, Na2-K2, and NaK-NaK are examined. Interaction energies are first determined from ab initio calculations at the coupled-cluster with singles, doubles, and perturbative triples [CCSD(T)] level of theory, including counterpoise corrections. Long range energies calculated from diatomic molecular properties (polarizabilities and dipole and quadrupole moments) are then compared with the ab initio energies. A simple asymptotic model potential ELR=Eelec+Edisp+Eind is shown to accurately represent the intermolecular interactions for these systems at long range.

Long range intermolecular interactions between the alkali diatomics Na(2), K(2), and NaK.

PubMed

Zemke, Warren T; Byrd, Jason N; Michels, H Harvey; Montgomery, John A; Stwalley, William C

2010-06-28

Long range interactions between the ground state alkali diatomics Na(2)-Na(2), K(2)-K(2), Na(2)-K(2), and NaK-NaK are examined. Interaction energies are first determined from ab initio calculations at the coupled-cluster with singles, doubles, and perturbative triples [CCSD(T)] level of theory, including counterpoise corrections. Long range energies calculated from diatomic molecular properties (polarizabilities and dipole and quadrupole moments) are then compared with the ab initio energies. A simple asymptotic model potential E(LR)=E(elec)+E(disp)+E(ind) is shown to accurately represent the intermolecular interactions for these systems at long range.

Hydrogen bonding pattern in N-benzoyl(- DL-)- L-phenylalanines as revealed by solid-state NMR spectroscopy

NASA Astrophysics Data System (ADS)

Potrzebowski, M. J.; Schneider, C.; Tekely, P.

1999-11-01

The nature of the hydrogen bonding pattern has been investigated in N-benzoyl- DL-phenylalanine ( 1) and N-benzoyl- L-phenylalanine ( 2) polymorphes by solid-state NMR spectroscopy. It has been shown that the multiple resonances of carboxyl carbon in 2 are directly connected to different types of hydrogen bonding. The differences in intermolecular distances of carboxyl groups involved in different types of hydrogen bonding have been visualized by the 2D exchange and 1D ODESSA experiments. Potential applications of such a new approach include the exploration of intermolecular distances in hydrogen bonded compounds with singly labeled biomolecules.

Survey of High-Pressure Effects in Solids.

DTIC Science & Technology

1979-11-01

phenomenological Lennard - Jones and Morse potentials . The resulting study of the GrUneisen parameter is most illuminating. A more am- bitious program would to...the Gordon-Kim-Boyer scheme with our suggested modifications; use of the exchange-correlation potential in the local-density approximation i such an...Xenon Hugoniot Calculations and Experiments .......... 41 3.8. Xenon Intermolecular Potentials ...................... 42 3.9. Xenon Hugoniot Calculations

Exponential 6 parameterization for the JCZ3-EOS

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

McGee, B.C.; Hobbs, M.L.; Baer, M.R.

1998-07-01

A database has been created for use with the Jacobs-Cowperthwaite-Zwisler-3 equation-of-state (JCZ3-EOS) to determine thermochemical equilibrium for detonation and expansion states of energetic materials. The JCZ3-EOS uses the exponential 6 intermolecular potential function to describe interactions between molecules. All product species are characterized by r*, the radius of the minimum pair potential energy, and {var_epsilon}/k, the well depth energy normalized by Boltzmann`s constant. These parameters constitute the JCZS (S for Sandia) EOS database describing 750 gases (including all the gases in the JANNAF tables), and have been obtained by using Lennard-Jones potential parameters, a corresponding states theory, pure liquid shockmore » Hugoniot data, and fit values using an empirical EOS. This database can be used with the CHEETAH 1.40 or CHEETAH 2.0 interface to the TIGER computer program that predicts the equilibrium state of gas- and condensed-phase product species. The large JCZS-EOS database permits intermolecular potential based equilibrium calculations of energetic materials with complex elemental composition.« less

Theoretical studies of potential energy surface and rotational spectra of Xe -H2O van der Waals complex

NASA Astrophysics Data System (ADS)

Wang, Lin; Yang, Minghui

2008-11-01

In this work we report an ab initio intermolecular potential energy surface and theoretical spectroscopic studies for Xe -H2O complex. The ab initio energies are calculated with CCSD(T) method and large basis sets (aug-cc-pVQZ for H and O and aug-cc-pVQZ-PP for Xe) augmented by a {3s3p2d2f1g} set of bond functions. This potential energy surface has a global minimum corresponding to a planar and nearly linear hydrogen bonded configuration with a well depth of 192.5cm-1 at intermolecular distance of 4.0Å, which is consistent with the previous determined potential by Wen and Jäger [J. Phys. Chem. A 110, 7560 (2006)]. The bound state calculations have been performed for the complex by approximating the water molecule as a rigid rotor. The theoretical rotational transition frequencies, isotopic shifts, nuclear quadrupole coupling constants, and structure parameters are in good agreement with the experimental observed values. The wavefunctions are analyzed to understand the dynamics of the ground and the first excited states.

Programmable display of DNA-protein chimeras for controlling cell-hydrogel interactions via reversible intermolecular hybridization.

PubMed

Zhang, Zhaoyang; Li, Shihui; Chen, Niancao; Yang, Cheng; Wang, Yong

2013-04-08

Extensive studies have been recently carried out to achieve dynamic control of cell-material interactions primarily through physicochemical stimulation. The purpose of this study was to apply reversible intermolecular hybridization to program cell-hydrogel interactions in physiological conditions based on DNA-antibody chimeras and complementary oligonucleotides. The results showed that DNA oligonucleotides could be captured to and released from the immobilizing DNA-functionalized hydrogels with high specificity via DNA hybridization. Accordingly, DNA-antibody chimeras were captured to the hydrogels, successfully inducing specific cell attachment. The cell attachment to the hydrogels reached the plateau at approximately half an hour after the functionalized hydrogels and the cells were incubated together. The attached cells were rapidly released from the bound hydrogels when triggering complementary oligonucleotides were introduced to the system. However, the capability of the triggering complementary oligonucleotides in releasing cells was affected by the length of intermolecular hybridization. The length needed to be at least more than 20 base pairs in the current experimental setting. Notably, because the procedure of intermolecular hybridization did not involve any harsh condition, the released cells maintained the same viability as that of the cultured cells. The functionalized hydrogels also exhibited the potential to catch and release cells repeatedly. Therefore, this study demonstrates that it is promising to regulate cell-material interactions dynamically through the DNA-programmed display of DNA-protein chimeras.

Substitution effect on a hydroxylated chalcone: Conformational, topological and theoretical studies

NASA Astrophysics Data System (ADS)

Custodio, Jean M. F.; Vaz, Wesley F.; de Andrade, Fabiano M.; Camargo, Ademir J.; Oliveira, Guilherme R.; Napolitano, Hamilton B.

2017-05-01

The effect of substituents on two hydroxylated chalcones was studied in this work. The first chalcone, with a dimethylamine group (HY-DAC) and the second, with three methoxy groups (HY-TRI) were synthesized and crystallized from ethanol on centrosymmetric space group P21/c. The geometric parameters and supramolecular arrangement for both structures obtained from single crystal X-ray diffraction data were analyzed. The intermolecular interactions were investigated by Hirshfeld surfaces with their respective 2D plot for quantification of each type of contact. Additionally, the observed interactions were characterized by QTAIM analysis, and DFT calculations were applied for theoretical vibrational spectra, localization and quantification of frontier orbitals and potential electrostatic map. The flatness of both structures was affected by the substituents, which led to different monoclinic crystalline packing. The calculated harmonic vibrational frequencies and homo-lumo gap confirmed the stability of the structures, while intermolecular interactions were confirmed by potential electrostatic map and QTAIM analysis.

Exploring Molecular Speciation and Crystallization Mechanism of Amorphous 2-Phenylamino Nicotinic Acid.

PubMed

Kalra, Arjun; Lubach, Joseph W; Munson, Eric J; Li, Tonglei

2018-02-07

Molecular understanding of phase stability and transition of the amorphous state helps in formulation and manufacturing of poorly-soluble drugs. Crystallization of a model compound, 2-phenylamino nicotinic acid (2PNA), from the amorphous state was studied using solid-state analytical methods. Our previous report suggests that 2PNA molecules mainly develop intermolecular -COOH∙∙∙pyridine N (acid-pyridine) interactions in the amorphous state. In the current study, the molecular speciation is explored with regard to the phase transition from the amorphous to the crystalline state. Using spectroscopic techniques, the molecular interactions and structural evolvement during the recrystallization from the glassy state were investigated. The results unveiled that the structurally heterogeneous amorphous state contains acid-pyridine aggregates - either as hydrogen-bonded neutral molecules or as zwitterions - as well as a population of carboxylic acid dimers. Phase transition from the amorphous state results in crystal structures composed of carboxylic acid dimer (acid-acid) synthon or acid-pyridine chains depending on the crystallization conditions employed. The study underlines the structural evolvement, as well as its impact on the metastability, of amorphous samples from local, supramolecular assemblies to long-range intermolecular ordering through crystallization.

A quantitative study of the clustering of polycyclic aromatic hydrocarbons at high temperatures.

PubMed

Totton, Tim S; Misquitta, Alston J; Kraft, Markus

2012-03-28

The clustering of polycyclic aromatic hydrocarbon (PAH) molecules is investigated in the context of soot particle inception and growth using an isotropic potential developed from the benchmark PAHAP potential. This potential is used to estimate equilibrium constants of dimerisation for five representative PAH molecules based on a statistical mechanics model. Molecular dynamics simulations are also performed to study the clustering of homomolecular systems at a range of temperatures. The results from both sets of calculations demonstrate that at flame temperatures pyrene (C(16)H(10)) dimerisation cannot be a key step in soot particle formation and that much larger molecules (e.g. circumcoronene, C(54)H(18)) are required to form small clusters at flame temperatures. The importance of using accurate descriptions of the intermolecular interactions is demonstrated by comparing results to those calculated with a popular literature potential with an order of magnitude variation in the level of clustering observed. By using an accurate intermolecular potential we are able to show that physical binding of PAH molecules based on van der Waals interactions alone can only be a viable soot inception mechanism if concentrations of large PAH molecules are significantly higher than currently thought.

Dynamic Covalent Chemistry-based Sensing: Pyrenyl Derivatives of Phenylboronic Acid for Saccharide and Formaldehyde

NASA Astrophysics Data System (ADS)

Chang, Xingmao; Fan, Jiayun; Wang, Min; Wang, Zhaolong; Peng, Haonan; He, Gang; Fang, Yu

2016-08-01

We synthesized two specially designed pyrenyl (Py) derivatives of phenylboronic acid, PSNB1 and PSNB2, of which PSNB2 self-assemble to form dynamic aggregate in methanol-water mixture (1:99, v/v) via intermolecular H-bonding and pi-pi stacking. Interestingly, the dynamic aggregate shows smart response to presence of fructose (F) as evidenced by fluorescence color change from green to blue. More interestingly, the fluorescence emission of the resulted PSNB2-F changes from blue to green with the addition of formaldehyde (FA). The reason behind is formation of a PSNB2-F dimer via FA cross-linking. Based upon the reactions as found, sensitive and fast sensing of F and FA in water was realized, of which the experimental DLs could be significantly lower than 10 μM for both analytes, and the response times are less than 1 min. It is believed that not only the materials as created may have the potential to find real-life applications but also the strategy as developed can be adopted to develop other dynamic materials.

Intermolecular correlations are necessary to explain diffuse scattering from protein crystals

DOE PAGES

Peck, Ariana; Poitevin, Frederic; Lane, Thomas Joseph

2018-02-21

Conformational changes drive protein function, including catalysis, allostery, and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to advance our understanding of biological dynamics. However, recent work challenged this prevailing view, suggesting instead that diffuse scattering primarily originates from rigid body motions and could therefore be applied to improve structure determination. To investigate the nature of the disorder giving rise to diffuse scattering, and thus the potential applications of this signal, a diverse repertoire of disorder models was assessed for its ability to reproduce the diffuse signalmore » reconstructed from three protein crystals. This comparison revealed that multiple models of intramolecular conformational dynamics, including ensemble models inferred from the Bragg data, could not explain the signal. Models of rigid body or short-range liquid-like motions, in which dynamics are confined to the biological unit, showed modest agreement with the diffuse maps, but were unable to reproduce experimental features indicative of long-range correlations. Extending a model of liquid-like motions to include disorder across neighboring proteins in the crystal significantly improved agreement with all three systems and highlighted the contribution of intermolecular correlations to the observed signal. These findings anticipate a need to account for intermolecular disorder in order to advance the interpretation of diffuse scattering to either extract biological motions or aid structural inference.« less

Factors affecting the viscosity in high concentration solutions of different monoclonal antibodies.

PubMed

Yadav, Sandeep; Shire, Steven J; Kalonia, Devendra S

2010-12-01

The viscosity profiles of four different IgG(1) molecules were studied as a function of concentration at pH 6.0. At high concentrations, MAb-H and -A showed significantly higher viscosities as compared to MAb-G and -E. Zeta Potential (ξ) measurements showed that all the IgG(1) molecules carried a net positive charge at this pH. MAb-G showed the highest positive zeta potential followed by MAb-E, -H, and -A. A consistent interpretation of the impact of net charge on viscosity for these MAbs is not possible, suggesting that electroviscous effects cannot explain the differences in viscosity. Values of k(D) (dynamic light scattering) indicated that the intermolecular interactions were repulsive for MAb-E and -G; and attractive for MAb-H and -A. Solution storage modulus (G') in high concentration solutions was consistent with attractive intermolecular interactions for MAb-H and -A, and repulsive interactions for MAb-G and -E. Effect of salt addition on solution G' and k(D) indicated that the interactions were primarily electrostatic in nature. The concentration dependent viscosity data were analyzed using a modified Ross and Minton equation. The analysis explicitly differentiates between the effect of molecular shape, size, self-crowding, and electrostatic intermolecular interactions in governing high concentration viscosity behavior. © 2010 Wiley-Liss, Inc. and the American Pharmacists Association

Insights into intermolecular interactions, electrostatic properties and the stability of C646 in the binding pocket of p300 histone acetyltransferase enzyme: a combined molecular dynamics and charge density study.

PubMed

Sivanandam, Magudeeswaran; Saravanan, Kandasamy; Kumaradhas, Poomani

2017-10-30

Histone acetyltransferases (HATs) and histone deacetylases (HDACs) are enzymes that exhibit an important transcription activity. Dysfunction of these enzymes may lead to different diseases including cancer, cardiovascular, and other diseases. Therefore, these enzymes are the potential target for the generation of new therapeutics. C646 is a synthetic p300 HAT inhibitor; its structural and the electrostatic properties are the paradigm to understand its activity in the active site of p300 HAT enzyme. The docked C646 molecule in the active site forms expected key intermolecular interactions with the amino acid residues Trp1436, Tyr1467, and one water molecule (W1861); and these interactions are important for acetylation reaction. When compare the active site structure of C646 with the gas-phase structure, it is confirmed that the electron density distribution of polar bonds are highly altered, when the molecule present in the active site. In the gas-phase structure of C646, a large negative regions of electrostatic potential is found at the vicinity of O(4), O(5), and O(6) atoms; whereas, the negative region of these atoms are reduced in the active site. The molecular dynamics (MD) simulation also performed, it reveals the conformational stability and the intermolecular interactions of C646 molecule in the active site of p300.

Intermolecular correlations are necessary to explain diffuse scattering from protein crystals

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

Peck, Ariana; Poitevin, Frederic; Lane, Thomas Joseph

Conformational changes drive protein function, including catalysis, allostery, and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to advance our understanding of biological dynamics. However, recent work challenged this prevailing view, suggesting instead that diffuse scattering primarily originates from rigid body motions and could therefore be applied to improve structure determination. To investigate the nature of the disorder giving rise to diffuse scattering, and thus the potential applications of this signal, a diverse repertoire of disorder models was assessed for its ability to reproduce the diffuse signalmore » reconstructed from three protein crystals. This comparison revealed that multiple models of intramolecular conformational dynamics, including ensemble models inferred from the Bragg data, could not explain the signal. Models of rigid body or short-range liquid-like motions, in which dynamics are confined to the biological unit, showed modest agreement with the diffuse maps, but were unable to reproduce experimental features indicative of long-range correlations. Extending a model of liquid-like motions to include disorder across neighboring proteins in the crystal significantly improved agreement with all three systems and highlighted the contribution of intermolecular correlations to the observed signal. These findings anticipate a need to account for intermolecular disorder in order to advance the interpretation of diffuse scattering to either extract biological motions or aid structural inference.« less

Spectroscopic determination of the intermolecular potential energy surface for Ar-NH3

NASA Astrophysics Data System (ADS)

Schmuttenmaer, C. A.; Cohen, R. C.; Saykally, R. J.

1994-07-01

The three-dimensional intermolecular potential energy surface (IPS) for Ar-NH3 has been determined from a least-squares fit to 61 far infrared and microwave vibration-rotation-tunneling (VRT) measurements and to temperature-dependent second virial coefficients. The three intermolecular coordinates (R,θ,φ) are treated without invoking any approximations regarding their separability, and the NH3 inversion-tunneling motion is included adiabatically. A surface with 13 variable parameters has been optimized to accurately reproduce the spectroscopic observables, using the collocation method to treat the coupled multidimensional dynamics within a scattering formalism. Anisotropy in the IPS is found to significantly mix the free rotor basis functions. The 149.6 cm-1 global minimum on this surface occurs with the NH3 symmetry axis nearly perpendicular to the van der Waals bond axis (θ=96.6°), at a center-of-mass separation of 3.57 Å, and with the Ar atom midway between two of the NH3 hydrogen atoms (φ=60°). The position of the global minimum is very different from the center-of-mass distance extracted from microwave spectroscopic studies. Long-range (R≳3.8 Å) attractive interactions are greatest when either a N-H bond or the NH3 lone pair is directed toward the argon. Comparisons with ab initio surfaces for this molecule as well as the experimentally determined IPS for Ar-H2O are presented.

A Theoretical Study of the Hydration of Methane, from the Aqueous Solution to the sI Hydrate-Liquid Water-Gas Coexistence

PubMed Central

Luis, Daniel Porfirio; García-González, Alcione; Saint-Martin, Humberto

2016-01-01

Monte Carlo and molecular dynamics simulations were done with three recent water models TIP4P/2005 (Transferable Intermolecular Potential with 4 Points/2005), TIP4P/Ice (Transferable Intermolecular Potential with 4 Points/ Ice) and TIP4Q (Transferable Intermolecular Potential with 4 charges) combined with two models for methane: an all-atom one OPLS-AA (Optimal Parametrization for the Liquid State) and a united-atom one (UA); a correction for the C–O interaction was applied to the latter and used in a third set of simulations. The models were validated by comparison to experimental values of the free energy of hydration at 280, 300, 330 and 370 K, all under a pressure of 1 bar, and to the experimental radial distribution functions at 277, 283 and 291 K, under a pressure of 145 bar. Regardless of the combination rules used for σC,O, good agreement was found, except when the correction to the UA model was applied. Thus, further simulations of the sI hydrate were performed with the united-atom model to compare the thermal expansivity to the experiment. A final set of simulations was done with the UA methane model and the three water models, to study the sI hydrate-liquid water-gas coexistence at 80, 230 and 400 bar. The melting temperatures were compared to the experimental values. The results show the need to perform simulations with various different models to attain a reliable and robust molecular image of the systems of interest. PMID:27240339

Direct atomic force microscopic evidence of hydrogen bonding interaction in phosphatidic acid Langmuir-Blodgett bilayer

NASA Astrophysics Data System (ADS)

Chunbo, Yuan; Ying, Wu; Yueming, Sun; Zuhong, Lu; Juzheng, Liu

1997-12-01

Molecularly resolved atomic force microscopic images of phosphatidic acid Langmuir-Blodgett bilayers show that phosphate groups in polar region of the films are packing in a distorted hexagonal organization with long-range orientational and positional order. Intermolecular hydrogen bonding interactions, which should be responsible for the ordering and stability of bilayers, are visualized directly between adjacent phosphate groups in the polar region of the bilayer. Some adjacent phosphatidic acid molecules link each other through the formation of intermolecular hydrogen bonds between phosphate groups in polar region to form local supramolecules, which provide the bilayer's potential as a functionized film in the investigation on the lateral conductions of protons in the biological bilayers.

Thermodynamic curvature for attractive and repulsive intermolecular forces

NASA Astrophysics Data System (ADS)

May, Helge-Otmar; Mausbach, Peter; Ruppeiner, George

2013-09-01

The thermodynamic curvature scalar R for the Lennard-Jones system is evaluated in phase space, including vapor, liquid, and solid state. We paid special attention to the investigation of R along vapor-liquid, liquid-solid, and vapor-solid equilibria. Because R is a measure of interaction strength, we traced out the line R=0 dividing the phase space into regions with effectively attractive (R<0) or repulsive (R>0) interactions. Furthermore, we analyzed the dependence of R on the strength of attraction applying a perturbation ansatz proposed by Weeks-Chandler-Anderson. Our results show clearly a transition from R>0 (for poorly repulsive interaction) to R<0 when loading attraction in the intermolecular potential.

Advances in chemoselective intermolecular cross-benzoin-type condensation reactions.

PubMed

Gaggero, Nicoletta; Pandini, Stefano

2017-08-23

The intermolecular cross-benzoin and acyloin condensation reactions are powerful approaches to α-hydroxy carbonyls in a single step. However, their potentiality suffers from the occurrence of side reactions including self-condensation and the formation of the undesired cross-acyloin. The broad range of azolium salt precatalysts available confers high tunability to NHC mediated benzoin condensation, assuring a good level of selectivity to the direct coupling between two non-equivalent aldehydes. Many efforts have also been devoted to the design of strategies that expand the range of suitable reaction partners beyond the traditional aldehydes and to the discovery of novel umpolung catalytic systems. The synthesis of both racemic and enantiomerically enriched acyloins is reviewed.

Rhodium(III)-Catalyzed Activation of C(sp3)-H Bonds and Subsequent Intermolecular Amidation at Room Temperature.

PubMed

Huang, Xiaolei; Wang, Yan; Lan, Jingbo; You, Jingsong

2015-08-03

Disclosed herein is a Rh(III)-catalyzed chelation-assisted activation of unreactive C(sp3)-H bonds, thus enabling an intermolecular amidation to provide a practical and step-economic route to 2-(pyridin-2-yl)ethanamine derivatives. Substrates with other N-donor groups are also compatible with the amidation. This protocol proceeds at room temperature, has a relatively broad functional-group tolerance and high selectivity, and demonstrates the potential of rhodium(III) in the promotive functionalization of unreactive C(sp3)-H bonds. A rhodacycle having a SbF6(-) counterion was identified as a plausible intermediate. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure and bonding in beta-HMX-characterization of a trans-annular N...N interaction.

PubMed

Zhurova, Elizabeth A; Zhurov, Vladimir V; Pinkerton, A Alan

2007-11-14

Chemical bonding in the beta-phase of the 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX) crystal based on the experimental electron density obtained from X-ray diffraction data at 20 K, and solid state theoretical calculations, has been analyzed in terms of the quantum theory of atoms in molecules. Features of the intra- and intermolecular bond critical points and the oxygen atom lone-pair locations are discussed. An unusual N...N bonding interaction across the 8-membered ring has been discovered and characterized. Hydrogen bonding, O...O and O...C intermolecular interactions are reported. Atomic charges and features of the electrostatic potential are discussed.

Catching the role of anisotropic electronic distribution and charge transfer in halogen bonded complexes of noble gases

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

Bartocci, Alessio; Cappelletti, David; Pirani, Fernando

2015-05-14

The systems studied in this work are gas-phase weakly bound adducts of the noble-gas (Ng) atoms with CCl{sub 4} and CF{sub 4}. Their investigation was motivated by the widespread current interest for the intermolecular halogen bonding (XB), a structural motif recognized to play a role in fields ranging from elementary processes to biochemistry. The simulation of the static and dynamic behaviors of complex systems featuring XB requires the formulation of reliable and accurate model potentials, whose development relies on the detailed characterization of strength and nature of the interactions occurring in simple exemplary halogenated systems. We thus selected the prototypicalmore » Ng-CCl{sub 4} and Ng-CF{sub 4} and performed high-resolution molecular beam scattering experiments to measure the absolute scale of their intermolecular potentials, with high sensitivity. In general, we expected to probe typical van der Waals interactions, consisting of a combination of size (exchange) repulsion with dispersion/induction attraction. For the He/Ne-CF{sub 4}, the analysis of the glory quantum interference pattern, observable in the velocity dependence of the integral cross section, confirmed indeed this expectation. On the other hand, for the He/Ne/Ar-CCl{sub 4}, the scattering data unravelled much deeper potential wells, particularly for certain configurations of the interacting partners. The experimental data can be properly reproduced only including a shifting of the repulsive wall at shorter distances, accompanied by an increased role of the dispersion attraction, and an additional short-range stabilization component. To put these findings on a firmer ground, we performed, for selected geometries of the interacting complexes, accurate theoretical calculations aimed to evaluate the intermolecular interaction and the effects of the complex formation on the electron charge density of the constituting moieties. It was thus ascertained that the adjustments of the potential suggested by the analysis of the experiments actually reflect two chemically meaningful contributions, namely, a stabilizing interaction arising from the anisotropy of the charge distribution around the Cl atom in CCl{sub 4} and a stereospecific electron transfer that occurs at the intermolecular distances mainly probed by the experiments. Our model calculations suggest that the largest effect is for the vertex geometry of CCl{sub 4} while other geometries appear to play a minor to negligible role.« less

Summary Report for the CONSET Program at AEDC

DTIC Science & Technology

1980-09-01

the Lennard - Jones 12-6 intermolecular potential function, reduced onset pressures (P;) and temperatures (T;) have been determined using (lo) 16 AEDC...different, and this illustrates the inadequacy of the two-parameter Lennard - Jones potential for describing the interaction of polar molecules. As is well...molecules well described by the 12-6 Lennard - Jones potential will have common onset loci depending upon the specific heat ratio. However, polar molecules

MOLECULAR INTERACTION POTENTIALS FOR THE DEVELOPMENT OF STRUCTURE-ACTIVITY RELATIONSHIPS

EPA Science Inventory

Abstract
One reasonable approach to the analysis of the relationships between molecular structure and toxic activity is through the investigation of the forces and intermolecular interactions responsible for chemical toxicity. The interaction between the xenobiotic and the bio...

Learning that Prepares for More Learning: Symbolic Mathematics in Physical Chemistry

ERIC Educational Resources Information Center

Zielinski, Theresa Julia

2004-01-01

The well-crafted templates are useful to learn the new concepts of chemistry. The templates focus on pressure-volume work, the Boltzmann distribution, the Gibbs free energy function, intermolecular potentials, the second virial coefficient and quantum mechanical tunneling.

Characterization of the glass transition of water predicted by molecular dynamics simulations using nonpolarizable intermolecular potentials.

PubMed

Kreck, Cara A; Mancera, Ricardo L

2014-02-20

Molecular dynamics simulations allow detailed study of the experimentally inaccessible liquid state of supercooled water below its homogeneous nucleation temperature and the characterization of the glass transition. Simple, nonpolarizable intermolecular potentials are commonly used in classical molecular dynamics simulations of water and aqueous systems due to their lower computational cost and their ability to reproduce a wide range of properties. Because the quality of these predictions varies between the potentials, the predicted glass transition of water is likely to be influenced by the choice of potential. We have thus conducted an extensive comparative investigation of various three-, four-, five-, and six-point water potentials in both the NPT and NVT ensembles. The T(g) predicted from NPT simulations is strongly correlated with the temperature of minimum density, whereas the maximum in the heat capacity plot corresponds to the minimum in the thermal expansion coefficient. In the NVT ensemble, these points are instead related to the maximum in the internal pressure and the minimum of its derivative, respectively. A detailed analysis of the hydrogen-bonding properties at the glass transition reveals that the extent of hydrogen-bonds lost upon the melting of the glassy state is related to the height of the heat capacity peak and varies between water potentials.

Terahertz laser spectroscopy of the water dimer intermolecular vibrations. II. (H{sub 2}O){sub 2}

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

Braly, L. B.; Liu, K.; Brown, M. G.

Terahertz VRT laser spectra of four (H{sub 2}O){sub 2} intermolecular vibrations consisting of 362 transitions have been measured between 87 and 108 cm{sup -1} with ca. 2 MHz precision. The results differ both qualitatively and quantitatively from the predictions of dimer potentials tested. The spectra also reveal an ordering of the intermolecular vibrations which differs dramatically from that predicted by normal mode analysis. Strong coupling is indicated between the low barrier tunneling motions and the intermolecular vibrations as well as among different vibrations. In particular the 102.1 cm{sup -1} (H{sub 2}O){sub 2} vibration assigned as the acceptor wag ({nu}{sub 8})more » exhibits two types of perturbations. In one of these a component of K{sub a}=1 coupling with a tunneling component of K{sub a}=0 in the 108 cm{sup -1} acceptor twist ({nu}{sub 11}) vibration. There is also an indication that the 103.1 cm{sup -1} (H{sub 2}O){sub 2} band assigned as the donor in-plane bend ({nu}{sub 6}) is coupled to the acceptor wag resulting in a lower of the in-plane bend frequency and a higher acceptor wag frequency. Detailed analysis of the VRT levels confirms the extreme nonrigidity of this complex, indicating that the use of approximate models with reduced dimensionality to calculate its properties are likely to fail. (c) 2000 American Institute of Physics.« less

Do surfaces of positive electrostatic potential on different halogen derivatives in molecules attract? like attracting like!

PubMed

Varadwaj, Arpita; Varadwaj, Pradeep R; Yamashita, Koichi

2018-03-15

Coulomb's law states that like charges repel, and unlike charges attract. However, it has recently been theoretically revealed that two similarly charged conducting spheres will almost always attract each other when both are in close proximity. Using multiscale first principles calculations, we illustrate practical examples of several intermolecular complexes that are formed by the consequences of attraction between positive atomic sites of similar or dissimilar electrostatic surface potential on interacting molecules. The results of the quantum theory of atoms in molecules and symmetry adapted perturbation theory support the attraction between the positive sites, characterizing the F•••X (X = F, Cl, Br) intermolecular interactions in a series of 20 binary complexes as closed-shell type, although the molecular electrostatic surface potential approach does not (a failure!). Dispersion that has an r -6 dependence, where r is the equilibrium distance of separation, is found to be the sole driving force pushing the two positive sites to attract. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Breakdown of the single-exchange approximation in third-order symmetry-adapted perturbation theory.

PubMed

Lao, Ka Un; Herbert, John M

2012-03-22

We report third-order symmetry-adapted perturbation theory (SAPT) calculations for several dimers whose intermolecular interactions are dominated by induction. We demonstrate that the single-exchange approximation (SEA) employed to derive the third-order exchange-induction correction (E(exch-ind)((30))) fails to quench the attractive nature of the third-order induction (E(ind)((30))), leading to one-dimensional potential curves that become attractive rather than repulsive at short intermolecular separations. A scaling equation for (E(exch-ind)((30))), based on an exact formula for the first-order exchange correction, is introduced to approximate exchange effects beyond the SEA, and qualitatively correct potential energy curves that include third-order induction are thereby obtained. For induction-dominated systems, our results indicate that a "hybrid" SAPT approach, in which a dimer Hartree-Fock calculation is performed in order to obtain a correction for higher-order induction, is necessary not only to obtain quantitative binding energies but also to obtain qualitatively correct potential energy surfaces. These results underscore the need to develop higher-order exchange-induction formulas that go beyond the SEA. © 2012 American Chemical Society

CO{sub 2} isolated line shapes by classical molecular dynamics simulations: Influence of the intermolecular potential and comparison with new measurements

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

Larcher, G.; Tran, H., E-mail: ha.tran@lisa.u-pec.fr; Schwell, M.

2014-02-28

Room temperature absorption spectra of various transitions of pure CO{sub 2} have been measured in a broad pressure range using a tunable diode-laser and a cavity ring-down spectrometer, respectively, in the 1.6 μm and 0.8 μm regions. Their spectral shapes have been calculated by requantized classical molecular dynamics simulations. From the time-dependent auto-correlation function of the molecular dipole, including Doppler and collisional effects, spectral shapes are directly computed without the use of any adjusted parameter. Analysis of the spectra calculated using three different anisotropic intermolecular potentials shows that the shapes of pure CO{sub 2} lines, in terms of both themore » Lorentz widths and non-Voigt effects, slightly depend on the used potential. Comparisons between these ab initio calculations and the measured spectra show satisfactory agreement for all considered transitions (from J = 6 to J = 46). They also show that non-Voigt effects on the shape of CO{sub 2} transitions are almost independent of the rotational quantum number of the considered lines.« less

X-ray Intermolecular Structure Factor (XISF): separation of intra- and intermolecular interactions from total X-ray scattering data

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

Mou, Q.; Benmore, C. J.; Yarger, J. L.

2015-06-01

XISF is a MATLAB program developed to separate intermolecular structure factors from total X-ray scattering structure factors for molecular liquids and amorphous solids. The program is built on a trust-region-reflective optimization routine with the r.m.s. deviations of atoms physically constrained. XISF has been optimized for performance and can separate intermolecular structure factors of complex molecules.

X-ray Intermolecular Structure Factor ( XISF ): separation of intra- and intermolecular interactions from total X-ray scattering data

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

Mou, Q.; Benmore, C. J.; Yarger, J. L.

2015-05-09

XISFis a MATLAB program developed to separate intermolecular structure factors from total X-ray scattering structure factors for molecular liquids and amorphous solids. The program is built on a trust-region-reflective optimization routine with the r.m.s. deviations of atoms physically constrained.XISFhas been optimized for performance and can separate intermolecular structure factors of complex molecules.

Room temperature ionic liquids: A simple model. Effect of chain length and size of intermolecular potential on critical temperature.

PubMed

Chapela, Gustavo A; Guzmán, Orlando; Díaz-Herrera, Enrique; del Río, Fernando

2015-04-21

A model of a room temperature ionic liquid can be represented as an ion attached to an aliphatic chain mixed with a counter ion. The simple model used in this work is based on a short rigid tangent square well chain with an ion, represented by a hard sphere interacting with a Yukawa potential at the head of the chain, mixed with a counter ion represented as well by a hard sphere interacting with a Yukawa potential of the opposite sign. The length of the chain and the depth of the intermolecular forces are investigated in order to understand which of these factors are responsible for the lowering of the critical temperature. It is the large difference between the ionic and the dispersion potentials which explains this lowering of the critical temperature. Calculation of liquid-vapor equilibrium orthobaric curves is used to estimate the critical points of the model. Vapor pressures are used to obtain an estimate of the triple point of the different models in order to calculate the span of temperatures where they remain a liquid. Surface tensions and interfacial thicknesses are also reported.

Collisional excitation of molecules in dense interstellar clouds

NASA Technical Reports Server (NTRS)

Green, S.

1985-01-01

State transitions which permit the identification of the molecular species in dense interstellar clouds are reviewed, along with the techniques used to calculate the transition energies, the database on known molecular transitions and the accuracy of the values. The transition energies cannot be measured directly and therefore must be modeled analytically. Scattering theory is used to determine the intermolecular forces on the basis of quantum mechanics. The nuclear motions can also be modeled with classical mechanics. Sample rate constants are provided for molecular systems known to inhabit dense interstellar clouds. The values serve as a database for interpreting microwave and RF astrophysical data on the transitions undergone by interstellar molecules.

An approach to the origin of self-replicating system. I - Intermolecular interactions

NASA Technical Reports Server (NTRS)

Macelroy, R. D.; Coeckelenbergh, Y.; Rein, R.

1978-01-01

The present paper deals with the characteristics and potentialities of a recently developed computer-based molecular modeling system. Some characteristics of current coding systems are examined and are extrapolated to the apparent requirements of primitive prebiological coding systems.

TDDFT study of twisted intramolecular charge transfer and intermolecular double proton transfer in the excited state of 4‧-dimethylaminoflavonol in ethanol solvent

NASA Astrophysics Data System (ADS)

Wang, Ye; Shi, Ying; Cong, Lin; Li, Hui

2015-02-01

Time-dependent density functional theory method at the def-TZVP/B3LYP level was employed to investigate the intramolecular and intermolecular hydrogen bonding dynamics in the first excited (S1) state of 4‧-dimethylaminoflavonol (DMAF) monomer and in ethanol solution. In the DMAF monomer, we demonstrated that the intramolecular charge transfer (ICT) takes place in the S1 state. This excited state ICT process was followed by intramolecular proton transfer. Our calculated results are in good agreement with the mechanism proposed in experimental work. For the hydrogen-bonded DMAF-EtOH complex, it was demonstrated that the intermolecular hydrogen bonds can induce the formation of the twisted intramolecular charge transfer (TICT) state and the conformational twisting is along the C3-C4 bond. Moreover, the intermolecular hydrogen bonds can also facilitate the intermolecular double proton transfer in the TICT state. A stepwise intermolecular double proton transfer process was revealed. Therefore, the intermolecular hydrogen bonds can alter the mechanism of intramolecular charge transfer and proton transfer in the excited state for the DMAF molecule.

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

Mackeprang, Kasper; Kjaergaard, Henrik G., E-mail: hgk@chem.ku.dk; Salmi, Teemu

We describe the vibrational transitions of the donor unit in water dimer with an approach that is based on a three-dimensional local mode model. We perform a perturbative treatment of the intermolecular vibrational modes to improve the transition wavenumber of the hydrogen bonded OH-stretching transition. The model accurately predicts the transition wavenumbers of the vibrations in water dimer compared to experimental values and provides a physical picture that explains the redshift of the hydrogen bonded OH-oscillator. We find that it is unnecessary to include all six intermolecular modes in the vibrational model and that their effect can, to a goodmore » approximation, be computed using a potential energy surface calculated at a lower level electronic structure method than that used for the unperturbed model.« less

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

PubMed

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. © 2016 Wiley Periodicals, Inc.

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

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

Monte Carlo simulations of liquid tetrahydrofuran including pseudorotationa)

NASA Astrophysics Data System (ADS)

Chandrasekhar, Jayaraman; Jorgensen, William L.

1982-11-01

Monte Carlo statistical mechanics simulations have been carried out for liquid tetrahydrofuran (THF) with and without pseudorotation at 1 atm and 25 °C. The intermolecular potential functions consisted of Lennard-Jones and Coulomb terms in the TIPS format reported previously for ethers. Pseudorotation of the ring was described using the generalized coordinates defined by Cremer and Pople, viz., the puckering amplitude and the phase angle of the ring. The corresponding intramolecular potential function was derived from molecular mechanics (MM2) calculations. Compared to the gas phase, the rings tend to be more flat and the population of the C2 twist geometry is slightly higher in liquid THF. However, pseudorotation has negligible effect on the calculated intermolecular structure and thermodynamic properties. The computed density, heat of vaporization, and heat capacity are in good agreement with experiment. The results are also compared with those from previous simulations of acyclic ethers. The present study provides the foundation for investigations of the solvating ability of THF.

Nature and potency interactions of the hydrogen bond through the NBO analysis for charge transfer complex between 2-amino-4-hydroxy-6-methylpyrimidine and 2,3-pyrazinedicarboxylic acid

NASA Astrophysics Data System (ADS)

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

2018-05-01

The intermolecular interactions in complex formation between 2-amino-4-hydroxy-6-methylpyrimidine (AHMP) and 2,3-pyrazinedicarboxylicacid (PDCA) have been explored using density functional theory calculations. The isolated 1:1 molecular geometry of proton transfer (PT) complex between AHMP and PDCA has been optimized on a counterpoise corrected potential energy surface (PES) at DFT-B3LYP/6-31G(d,p) level of theory in the gaseous phase. Further, the formation of hydrogen bonded charge transfer (HBCT) complex between PDCA and AHMP has been also discussed. PT energy barrier between two extremes is calculated using potential energy surface (PES) scan by varying bond length. The intermolecular interactions have been analyzed from theoretical perspective of natural bond orbital (NBO) analysis. In addition, the interaction energy between molecular fragments involved in the complex formation has been also computed by counterpoise procedure at same level of theory.

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

Makarewicz, Jan, E-mail: jama@amu.edu.pl; Shirkov, Leonid

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

Observation of aggregation triggered by Resonance Energy Transfer (RET) induced intermolecular pairing force.

PubMed

Pan, Xiaoyong; Wang, Weizhi; Ke, Lin; Zhang, Nan

2017-07-20

In this report, we showed the existence of RET induced intermolecular pairing force by comparing their fluorescence behaviors under room illumination vs standing in dark area for either PFluAnt solution or PFluAnt&PFOBT mixture. Their prominent emission attenuation under room illumination brought out the critical role of photo, i.e. RET induced intermolecular pairing force in induction of polymer aggregation. Constant UV-Vis absorption and fluorescence spectra in terms of both peak shapes and maximum wavelengths implied no chemical decomposition was involved. Recoverable fluorescence intensity, fluorescence lifetime as well as NMR spectra further exclude photo induced decomposition. The controllable on/off state of RET induced intermolecular pairing force was verified by the masking effect of outside PFluAnt solution which function as filter to block the excitation of inside PFluAnt and thus off the RET induced intermolecular pairing force. Theoretical calculation suggest that magnitude of RET induced intermolecular pairing force is on the same scale as that of van der Waals interaction. Although the absolute magnitude of RET induced intermolecular pairing force was not tunable, its effect can be magnified by intentionally turn it "on", which was achieved by irradiance with 5 W desk lamp in this report.

A molecular dynamics study on the role of attractive and repulsive forces in internal energy, internal pressure and structure of dense fluids

NASA Astrophysics Data System (ADS)

Goharshadi, Elaheh K.; Morsali, Ali; Mansoori, G. Ali

2007-01-01

Isotherms of experimental data of internal pressure of dense fluids versus molar volume, Vm are shown to have each a maximum point at a Vmax below the critical molar volume. In this study, we investigated the role of attractive and repulsive intermolecular energies on this behavior using a molecular dynamics simulation technique. In the simulation, we choose the Lennard-Jones (LJ) intermolecular potential energy function. The LJ potential is known to be an effective potential representing a statistical average of the true pair and many-body interactions in simple molecular systems. The LJ potential function is divided into attractive and repulsive parts. MD calculations have produced internal energy, potential energy, transitional kinetic energy, and radial distribution function (RDF) for argon at 180 K and 450 K using LJ potential, LJ repulsive, and LJ attractive parts. It is shown that the LJ potential function is well capable of predicting the inflection point in the internal energy-molar volume curve as well as maximum point in the internal pressure-molar volume curve. It is also shown that at molar volumes higher than Vmax, the attractive forces have strong influence on determination of internal energy and internal pressure. At volumes lower than Vmax, neither repulsive nor attractive forces are dominating. Also, the coincidence between RDFs resulting from LJ potential and repulsive parts of LJ potential improves as molar volume approaches Vmax from high molar volumes. The coincidence becomes complete at Vmax ⩾ V.

On the possibility of singlet fission in crystalline quaterrylene

NASA Astrophysics Data System (ADS)

Wang, Xiaopeng; Liu, Xingyu; Cook, Cameron; Schatschneider, Bohdan; Marom, Noa

2018-05-01

Singlet fission (SF), the spontaneous down-conversion of a singlet exciton into two triplet excitons residing on neighboring molecules, is a promising route to improve organic photovoltaic (OPV) device efficiencies by harvesting two charge carriers from one photon. However, only a few materials have been discovered that exhibit intermolecular SF in the solid state, most of which are acene derivatives. Recently, there has been a growing interest in rylenes as potential SF materials. We use many-body perturbation theory in the GW approximation and the Bethe-Salpeter equation to investigate the possibility of intermolecular SF in crystalline perylene and quaterrylene. A new method is presented for determining the percent charge transfer (%CT) character of an exciton wave-function from double-Bader analysis. This enables relating exciton probability distributions to crystal packing. Based on comparison to known and predicted SF materials with respect to the energy conservation criterion (ES-2ET) and %CT, crystalline quaterrylene is a promising candidate for intermolecular SF. Furthermore, quaterrylene is attractive for OPV applications, thanks to its high stability and narrow optical gap. Perylene is not expected to exhibit SF; however, it is a promising candidate for harvesting sub-gap photons by triplet-triplet annihilation.

Intermolecular Modes between LH2 Bacteriochlorophylls and Protein Residues: The Effect on the Excitation Energies.

PubMed

Anda, André; De Vico, Luca; Hansen, Thorsten

2017-06-08

Light-harvesting system 2 (LH2) executes the primary processes of photosynthesis in purple bacteria; photon absorption, and energy transportation to the reaction center. A detailed mechanistic insight into these operations is obscured by the complexity of the light-harvesting systems, particularly by the chromophore-environment interaction. In this work, we focus on the effects of the protein residues that are ligated to the bacteriochlorophylls (BChls) and construct potential energy surfaces of the ground and first optically excited state for the various BChl-residue systems where we in each case consider two degrees of freedom in the intermolecular region. We find that the excitation energies are only slightly affected by the considered modes. In addition, we see that axial ligands and hydrogen-bonded residues have opposite effects on both excitation energies and oscillator strengths by comparing to the isolated BChls. Our results indicate that only a small part of the chromophore-environment interaction can be associated with the intermolecular region between a BChl and an adjacent residue, but that it may be possible to selectively raise or lower the excitation energy at the axial and planar residue positions, respectively.

On the possibility of singlet fission in crystalline quaterrylene.

PubMed

Wang, Xiaopeng; Liu, Xingyu; Cook, Cameron; Schatschneider, Bohdan; Marom, Noa

2018-05-14

Singlet fission (SF), the spontaneous down-conversion of a singlet exciton into two triplet excitons residing on neighboring molecules, is a promising route to improve organic photovoltaic (OPV) device efficiencies by harvesting two charge carriers from one photon. However, only a few materials have been discovered that exhibit intermolecular SF in the solid state, most of which are acene derivatives. Recently, there has been a growing interest in rylenes as potential SF materials. We use many-body perturbation theory in the GW approximation and the Bethe-Salpeter equation to investigate the possibility of intermolecular SF in crystalline perylene and quaterrylene. A new method is presented for determining the percent charge transfer (%CT) character of an exciton wave-function from double-Bader analysis. This enables relating exciton probability distributions to crystal packing. Based on comparison to known and predicted SF materials with respect to the energy conservation criterion (E S -2E T ) and %CT, crystalline quaterrylene is a promising candidate for intermolecular SF. Furthermore, quaterrylene is attractive for OPV applications, thanks to its high stability and narrow optical gap. Perylene is not expected to exhibit SF; however, it is a promising candidate for harvesting sub-gap photons by triplet-triplet annihilation.

Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of a biomolecule: 5-Hydroxymethyluracil

NASA Astrophysics Data System (ADS)

Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

2014-06-01

In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were investigated. The FT-IR (4000-400 cm-1) spectrum of the molecule in the solid phase was recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared intensities of the title molecule in the ground state were calculated using density functional B3LYP and M06-2X methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data, and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 5-hydroxymethyluracil molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on its vibrational frequencies. It was observed that the Nsbnd H stretching modes shifted to lower frequencies, while its in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular Nsbnd H⋯O hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

Intermolecular cope-type hydroamination of alkenes and alkynes using hydroxylamines.

PubMed

Moran, Joseph; Gorelsky, Serge I; Dimitrijevic, Elena; Lebrun, Marie-Eve; Bédard, Anne-Catherine; Séguin, Catherine; Beauchemin, André M

2008-12-31

The development of the Cope-type hydroamination as a method for the metal- and acid-free intermolecular hydroamination of hydroxylamines with alkenes and alkynes is described. Aqueous hydroxylamine reacts efficiently with alkynes in a Markovnikov fashion to give oximes and with strained alkenes to give N-alkylhydroxylamines, while unstrained alkenes are more challenging. N-Alkylhydroxylamines also display similar reactivity with strained alkenes and give modest to good yields with vinylarenes. Electron-rich vinylarenes lead to branched products while electron-deficient vinylarenes give linear products. A beneficial additive effect is observed with sodium cyanoborohydride, the extent of which is dependent on the structure of the hydroxylamine. The reaction conditions are found to be compatible with common protecting groups, free OH and NH bonds, as well as bromoarenes. Both experimental and theoretical results suggest the proton transfer step of the N-oxide intermediate is of vital importance in the intermolecular reactions of alkenes. Details are disclosed concerning optimization, reaction scope, limitations, and theoretical analysis by DFT, which includes a detailed molecular orbital description for the concerted hydroamination process and an exhaustive set of calculated potential energy surfaces for the reactions of various alkenes, alkynes, and hydroxylamines.

Catalytic conversion in nanoporous materials: Concentration oscillations and spatial correlations due to inhibited transport and intermolecular interactions

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

Garcia, Andres; Evans, James W.

2016-11-03

We show that steady-state catalytic conversion in nanoporous materials can occur in a quasi-counter-diffusion mode with the reactant (product) concentration strongly decaying (growing) into the pore, but also with oscillations in the total concentration. These oscillations reflect the response of the fluid to the transition from an extended to a confined environment near the pore opening. We focus on the regime of strongly inhibited transport in narrow pores corresponding to single-file diffusion. Here, limited penetration of the reactant into the pores and the associated low reaction yield is impacted by strong spatial correlations induced by both reaction (non-equilibrium correlations) andmore » also by intermolecular interactions (thermodynamic correlations). We develop a generalized hydrodynamic formulation to effectively describe inhibited transport accounting for the effect of these correlations, and incorporate this description of transport into appropriate reaction-diffusion equations. These equations accurately describe both shorter-range concentration oscillations near the pore opening and the longer-range mesoscale variation of concentration profiles in the pore (and thus also describe reaction yield). Success of the analytic theory is validated by comparison with a precise kinetic Monte Carlo simulation of an appropriate molecular-level stochastic reaction-diffusion model. As a result, this work elucidates unconventional chemical kinetics in interacting confined systems.« less

A Molecular Dynamics Study on Selective Cation Depletion from an Ionic Liquid Droplet under an Electric Field

NASA Astrophysics Data System (ADS)

Yang, Yudong; Ahn, Myungmo; Im, Dojin; Oh, Jungmin; Kang, Inseok

2017-11-01

General electrohydrodynamic behavior of ionic liquid droplets under an electric field is investigated using MD simulations. Especially, a unique behavior of ion depletion of an ionic liquid droplet under a uniform electric field is studied. Shape deformation due to electric stress and ion distributions inside the droplet are calculated to understand the ionic motion of imidazolium-based ionic liquid droplets with 200 ion pairs of 2 kinds of ionic liquids: EMIM-NTf2 and EMIM-ES. The intermolecular force between cations and anions can be significantly different due to the nature of the structure and charge distribution of the ions. Together with an analytical interpretation of the conducting droplet in an electric field, the MD simulation successfully explains the mechanism of selective ion depletion of an ionic liquid droplet in an electric field. The selective ion depletion phenomenon has been adopted to explain the experimentally observed retreating motion of a droplet in a uniform electric field. The effect of anions on the cation depletion phenomenon can be accounted for from a direct approach to the intermolecular interaction. This research was supproted by the National Research Foundation of Korea (NRF) Grant funded by the Korea government (MSIP) (No. 2017R1D1A1B05035211).

Production of low kinetic energy electrons and energetic ion pairs by Intermolecular Coulombic Decay.

PubMed

Hergenhahn, Uwe

2012-12-01

The paper gives an introduction into Interatomic and Intermolecular Coulombic Decay (ICD). ICD is an autoionization process, which contrary to Auger decay involves neighbouring sites of the initial vacancy as an integral part of the decay transition. As a result of ICD, slow electrons are produced which generally are known to be active in radiation damage. The author summarizes the properties of ICD and reviews a number of important experiments performed in recent years. Intermolecular Coulombic Decay can generally take place in weakly bonded aggregates in the presence of ionizing particles or ionizing radiation. Examples collected here mostly use soft X-rays produced by synchrotron radiation to ionize, and use rare-gas clusters, water clusters or solutes in a liquid jet to observe ICD after irradiation. Intermolecular Coulombic Decay is initiated by single ionization into an excited state. The subsequent relaxation proceeds via an ultra-fast energy transfer to a neighbouring site, where a second ionization occurs. Secondary electrons from ICD have clearly been identified in numerous systems. ICD can take place after primary ionization, as the second step of a decay cascade which also involves Auger decay, or after resonant excitation with an energy which exceeds the ionization potential of the system. ICD is expected to play a role whenever particles or radiation with photon energies above the ionization energies for inner valence electrons are present in weakly bonded matter, e.g., biological tissue. The process produces at the same time a slow electron and two charged atomic or molecular fragments, which will lead to structural changes around the ionized site.

Signatures of Solvation Thermodynamics in Spectra of Intermolecular Vibrations

PubMed Central

2017-01-01

This study explores the thermodynamic and vibrational properties of water in the three-dimensional environment of solvated ions and small molecules using molecular simulations. The spectrum of intermolecular vibrations in liquid solvents provides detailed information on the shape of the local potential energy surface, which in turn determines local thermodynamic properties such as the entropy. Here, we extract this information using a spatially resolved extension of the two-phase thermodynamics method to estimate hydration water entropies based on the local vibrational density of states (3D-2PT). Combined with an analysis of solute–water and water–water interaction energies, this allows us to resolve local contributions to the solvation enthalpy, entropy, and free energy. We use this approach to study effects of ions on their surrounding water hydrogen bond network, its spectrum of intermolecular vibrations, and resulting thermodynamic properties. In the three-dimensional environment of polar and nonpolar functional groups of molecular solutes, we identify distinct hydration water species and classify them by their characteristic vibrational density of states and molecular entropies. In each case, we are able to assign variations in local hydration water entropies to specific changes in the spectrum of intermolecular vibrations. This provides an important link for the thermodynamic interpretation of vibrational spectra that are accessible to far-infrared absorption and Raman spectroscopy experiments. Our analysis provides unique microscopic details regarding the hydration of hydrophobic and hydrophilic functional groups, which enable us to identify interactions and molecular degrees of freedom that determine relevant contributions to the solvation entropy and consequently the free energy. PMID:28783431

THz spectroscopy: An emerging technology for pharmaceutical development and pharmaceutical Process Analytical Technology (PAT) applications

NASA Astrophysics Data System (ADS)

Wu, Huiquan; Khan, Mansoor

2012-08-01

As an emerging technology, THz spectroscopy has gained increasing attention in the pharmaceutical area during the last decade. This attention is due to the fact that (1) it provides a promising alternative approach for in-depth understanding of both intermolecular interaction among pharmaceutical molecules and pharmaceutical product quality attributes; (2) it provides a promising alternative approach for enhanced process understanding of certain pharmaceutical manufacturing processes; and (3) the FDA pharmaceutical quality initiatives, most noticeably, the Process Analytical Technology (PAT) initiative. In this work, the current status and progress made so far on using THz spectroscopy for pharmaceutical development and pharmaceutical PAT applications are reviewed. In the spirit of demonstrating the utility of first principles modeling approach for addressing model validation challenge and reducing unnecessary model validation "burden" for facilitating THz pharmaceutical PAT applications, two scientific case studies based on published THz spectroscopy measurement results are created and discussed. Furthermore, other technical challenges and opportunities associated with adapting THz spectroscopy as a pharmaceutical PAT tool are highlighted.

Crystal growth, structure and morphology of hydrocortisone methanol solvate

NASA Astrophysics Data System (ADS)

Chen, Jianxin; Wang, Jiangkang; Zhang, Ying; Wu, Hong; Chen, Wei; Guo, Zhichao

2004-04-01

Hydrocortisone (HC), an important grucocorticoid, was crystallized from methanol solvent in the form of its methanol solvate. Its crystal structure belongs to orthorhombic, space group P2 12 12 1, with the unit cell parameters a=7.712(3) Å, b=14.392(5) Å, c=18.408(6) Å, Z=4. The methanol takes part in intermolecular hydrogen bonding, so if we change the solvent, the crystal habit of HC maybe different. The long parallelepiped morphology was also predicted by Cerius 2TM simulation program. The influence of intermolecular interaction was taken into account in the attachment energy model. The morphology calculation performed on the potential energy minimized model using a generic DREIDING 2.21 force field and developed minimization protocol with derived partial charges fits the experimental crystal shape well.

Structural Design and Photochemical Preparation of Ultrathin Molecular Film Materials

DTIC Science & Technology

2006-12-01

tetracene and pentacene that have great potential as organic semiconducting materials, have been determined. Overall, we have gained to great extend a...layer of linear acenes, molecules such as tetracene and pentacene that have great potential as organic semiconducting materials, have been determined...intermolecular interaction of mono- and multi-layer linear acenes on metal A systematic study of adsorption of linear acenes, from benzene to pentacene , on metal

Perspectives on NMR in drug discovery: a technique comes of age

PubMed Central

Pellecchia, Maurizio; Bertini, Ivano; Cowburn, David; Dalvit, Claudio; Giralt, Ernest; Jahnke, Wolfgang; James, Thomas L.; Homans, Steve W.; Kessler, Horst; Luchinat, Claudio; Meyer, Bernd; Oschkinat, Hartmut; Peng, Jeff; Schwalbe, Harald; Siegal, Gregg

2009-01-01

In the past decade, the potential of harnessing the ability of nuclear magnetic resonance (NMR) spectroscopy to monitor intermolecular interactions as a tool for drug discovery has been increasingly appreciated in academia and industry. In this Perspective, we highlight some of the major applications of NMR in drug discovery, focusing on hit and lead generation, and provide a critical analysis of its current and potential utility. PMID:19172689

Development of Phase-Stable Photon Upconverters for Efficient Solar Energy Utilization

NASA Astrophysics Data System (ADS)

Murakami, Yoichi

Photon upconversion based on triplet-triplet annihilation (TTA) of excited triplet molecules is drawing attention due to its applicability for weak incident light, possessing a potential for improving efficiencies of solar energy conversion devices. Since energy transfer between triplet levels of different molecules and TTA are based on the Dexter mechanism, inter-molecular collision is necessary and hence the majority of previous studies have been done with organic solvents, which are volatile and flammable. This paper presents the development and characterization of phase-stable photon upconverters fabricated with ionic liquids, which are room temperature molten salts with negligible vapor pressure and high thermal stability. The employed aromatic molecules, which are carrier of photo-created energies and are non-polar (or weakly polar) molecules, are found to be stable in the polar environment of ionic liquids, contrary to expectation. The mechanism of the stable solvation is proposed. The upconversion quantum yields are found to rapidly saturate as the excitation light power increases. An analytical model was developed and compared with the experimental data. It is shown that ionic liquids are not viscous media for the purpose of TTA-based upconversion.

Novelty of Dynamic Process in the Synthesis of Biocompatible Silica Nanotubes by Biomimetic Glycyldodecylamide as a Soft Template.

PubMed

Choi, Hyejung; Kim, Joong-Jo; Mo, Yong-Hwan; Reddy, Benjaram M; Park, Sang-Eon

2017-10-10

A dynamic process in the synthesis of silica nanotubes (SNTs) by utilizing glycyldodecylamide (GDA) as a soft template was thoroughly investigated. The morphological evolution from GDA to SNTs was deeply explored to elucidate the formation mechanism for optimizing the synthesis procedure. Various analytical tools, namely, XRD, FTIR, SEM, TEM, Z-potential, and N 2 adsorption/desorption isotherms, were employed during the synthesis procedure. The interactive structure of GDA was also investigated using TEM-EDX as a function of aging time. These studies revealed the stepwise morphology of nanograin, nanofiber, curved plate, and nanotube in the ethanol/water solution when aged at room temperature. The supramolecular GDA molded the vesicle type nanostructure which was surrounded by silica and facilitated the formation of uniform SNTs. The stimulus for GDA to be curved into a vesicle was the intermolecular hydrogen bonding between adjacent amide groups of the template molecules. This was illustrated by FTIR spectra of GDA-silica intermediate by detecting the transition of amide I peak from 1678 to 1635 cm -1 . The effect of hydrogen bonding became stronger when the sample was aged.

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

PubMed

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

2017-03-05

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

The development of novel simulation methodologies and intermolecular potential models for real fluids

NASA Astrophysics Data System (ADS)

Errington, Jeffrey Richard

This work focuses on the development of intermolecular potential models for real fluids. United-atom models have been developed for both non-polar and polar fluids. The models have been optimized to the vapor-liquid coexistence properties. Histogram reweighting techniques were used to calculate phase behavior. The Hamiltonian scaling grand canonical Monte Carlo method was developed to enable the determination of thermodynamic properties of several related Hamiltonians from a single simulation. With this method, the phase behavior of variations of the Buckingham exponential-6 potential was determined. Reservoir grand canonical Monte Carlo simulations were developed to simulate molecules with complex architectures and/or stiff intramolecular constraints. The scheme is based on the creation of a reservoir of ideal chains from which structures are selected for insertion during a simulation. New intermolecular potential models have been developed for water, the n-alkane homologous series, benzene, cyclohexane, carbon dioxide, ammonia and methanol. The models utilize the Buckingham exponential-6 potential to model non-polar interactions and point charges to describe polar interactions. With the exception of water, the new models reproduce experimental saturated densities, vapor pressures and critical parameters to within a few percent. In the case of water, we found a set of parameters that describes the phase behavior better than other available point charge models while giving a reasonable description of the liquid structure. The mixture behavior of water-hydrocarbon mixtures has also been examined. The Henry's law constants of methane, ethane, benzene and cyclohexane in water were determined using Widom insertion and expanded ensemble techniques. In addition the high-pressure phase behavior of water-methane and water-ethane systems was studied using the Gibbs ensemble method. The results from this study indicate that it is possible to obtain a good description of the phase behavior of pure components using united-atom models. The mixture behavior of non-polar systems, including highly asymmetric components, was in good agreement with experiment. The calculations for the highly non-ideal water-hydrocarbon mixtures reproduced experimental behavior with varying degrees of success. The results indicate that multibody effects, such as polarizability, must be taken into account when modeling mixtures of polar and non-polar components.

Desensitization of metastable intermolecular composites

DOEpatents

Busse, James R [South Fork, CO; Dye, Robert C [Los Alamos, NM; Foley, Timothy J [Los Alamos, NM; Higa, Kelvin T [Ridgecrest, CA; Jorgensen, Betty S [Jemez Springs, NM; Sanders, Victor E [White Rock, NM; Son, Steven F [Los Alamos, NM

2011-04-26

A method to substantially desensitize a metastable intermolecular composite material to electrostatic discharge and friction comprising mixing the composite material with an organic diluent and removing enough organic diluent from the mixture to form a mixture with a substantially putty-like consistency, as well as a concomitant method of recovering the metastable intermolecular composite material.

Desensitization and recovery of metastable intermolecular composites

DOEpatents

Busse, James R [South Fork, CO; Dye, Robert C [Los Alamos, NM; Foley, Timothy J [Los Alamos, NM; Higa, Kelvin T [Ridgecrest, CA; Jorgensen, Betty S [Jemez Springs, NM; Sanders, Victor E [White Rock, NM; Son, Steven F [Los Alamos, NM

2010-09-07

A method to substantially desensitize a metastable intermolecular composite material to electrostatic discharge and friction comprising mixing the composite material with an organic diluent and removing enough organic diluent from the mixture to form a mixture with a substantially putty-like consistency, as well as a concomitant method of recovering the metastable intermolecular composite material.

Universal scaling of potential energy functions describing intermolecular interactions. II. The halide-water and alkali metal-water interactions

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

Werhahn, Jasper C.; Akase, Dai; Xantheas, Sotiris S.

2014-08-14

The scaled versions of the newly introduced [S. S. Xantheas and J. C. Werhahn, J. Chem. Phys.141, 064117 (2014)] generalized forms of some popular potential energy functions (PEFs) describing intermolecular interactions – Mie, Lennard-Jones, Morse, and Buckingham exponential-6 – have been used to fit the ab initio relaxed approach paths and fixed approach paths for the halide-water, X -(H 2O), X = F, Cl, Br, I, and alkali metal-water, M +(H 2O), M = Li, Na, K, Rb, Cs, interactions. The generalized forms of those PEFs have an additional parameter with respect to the original forms and produce fits tomore » the ab initio data that are between one and two orders of magnitude better in the χ 2 than the original PEFs. They were found to describe both the long-range, minimum and repulsive wall of the respective potential energy surfaces quite accurately. Overall the 4-parameter extended Morse (eM) and generalized Buckingham exponential-6 (gBe-6) potentials were found to best fit the ab initio data for these two classes of ion-water interactions. Finally, the fitted values of the parameter of the (eM) and (gBe-6) PEFs that control the repulsive wall of the potential correlate remarkably well with the ionic radii of the halide and alkali metal ions.« less

Cycloaddition Reactions of Cobalt-Complexed Macrocyclic Alkynes: The Transannular Pauson-Khand Reaction.

PubMed

Karabiyikoglu, Sedef; Boon, Byron A; Merlic, Craig A

2017-08-04

The Pauson-Khand reaction is a powerful tool for the synthesis of cyclopentenones through the efficient [2 + 2 + 1] cycloaddition of dicobalt alkyne complexes with alkenes. While intermolecular and intramolecular variants are widely known, transannular versions of this reaction are unknown and the basis of this study. Macrocyclic enyne and dienyne complexes were readily synthesized by palladium(II)-catalyzed oxidative macrocyclizations of bis(vinyl boronate esters) or ring-closing metathesis reactions followed by complexation with dicobalt octacarbonyl. Several reaction modalities of these macrocyclic complexes were uncovered. In addition to the first successful transannular Pauson-Khand reactions, other intermolecular and transannular cycloaddition reactions included intermolecular Pauson-Khand reactions, transannular [4 + 2] cycloaddition reactions, intermolecular [2 + 2 + 2] cycloaddition reactions, and intermolecular [2 + 2 + 1 + 1] cycloaddition reactions. The structural and reaction requirements for each process are presented.

Mononuclear late first row transition metal complexes of ONO donor hydrazone ligand: Synthesis, characterization, crystallographic insight, in vivo and in vitro anti-inflammatory activity

NASA Astrophysics Data System (ADS)

Kendur, Umashri; Chimmalagi, Geeta H.; Patil, Sunil M.; Gudasi, Kalagouda B.; Frampton, Christopher S.; Mangannavar, Chandrashekhar V.; Muchchandi, Iranna S.

2018-02-01

Air and moisture stable coordination compounds of late first row transition metal ions, viz., Co(II), Ni(II), Cu(II) and Zn(II) with a newly designed ligand, (E)-2-amino-N'-(1-(2-hydroxy-6-methyl-4-oxo-4H-pyran-3-yl)ethylidene)benzohydrazide (H2L) were prepared and extensively characterized using various spectro-analytical techniques. The ligand acts both in mono as well as doubly deprotonated manner. The ligand to metal stoichiometry was found to be 1:2 in case of complexes using chloride salts, whereas 1:1 in case of copper (II) complex using its acetate salt. The molecular structures of H2L, nickel and copper complexes were unambiguously determined by single-crystal X-ray diffraction studies reveal that H2L exists in a zwitterionic form while copper complex has copper centre in a distorted square planar environment. On the other hand, cobalt, nickel and zinc complexes display distorted octahedral coordination around the metal ion. In case of [Ni(HL)2].H2O, intramolecular Csbnd H⋯π stacking interaction were observed between the centroid of five membered chelate ring and phenyl proton C5sbnd H5 and intermolecular Csbnd H⋯π stacking interaction between the centroid of phenyl ring, dehydroacetic acid (DHA) ring and phenyl protons. The [Cu(L)DMF] complex is stabilized by intramolecular hydrogen bonding N1H⋯N2 and by intermolecular hydrogen bonding N1H⋯O4. Intermolecular interactions were investigated by Hirshfeld surfaces. Further, H2L and its metal complexes were screened for their in vivo and in vitro anti-inflammatory activities. The activity of the ligand has enhanced on coordination with transition metals. The tested compounds have shown excellent activity, which is almost equipotent to the standard used in the study.

Intermolecular dynamics of substitued benzene and cyclohexane liquids, studied by femtosecond nonlinear-optical polarization spectroscopy

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

Chang, Y.J.; Castner, E.W. Jr.

Femtosecond time-resolved optical-heterodyne detected Raman-induced Kerr effect spectroscopy (OHD-RIKES) is shown to be a powerful and comprehensive tool for studying the intermolecular dynamics occurring in liquids. The observed dynamics include both the underdamped or coherent inertial motions, and the longer time scale diffusive relaxation. The inertial dynamics include phonon-like intermolecular vibrations, intermolecular collisions, and librational caging motions. Data are presented and analyzed for a series of five liquids: cyclohexane, methylcyclohexane, toluene, benzyl alcohol, and benzonitrile, listed in order of increasing polarity. We explore the effects of aromaticity (e.g., methylcyclohexane vs toluene), symmetry reduction (cyclohexane vs methylcyclohexane), and substitution effects (e.g.,more » substituted benzene series) on the ultrafast intermolecular dynamics, for a group of molecular liquids of similar size and volume. We analyze the intermolecular dynamics in both the time and frequency domains by means of Fourier transformations. When Fourier-transformed into the frequency domain, the OHD-RIKES ultrafast transients of the intermolecular dynamics can be directly compared with the frequency domain spectra obtained from the far-infrared absorption and depolarized Raman techniques. This is done using the Gaussian librational caging model of Lynden-Bell and Steele, which results in a power-law scaling relation between dipole and polarizability time correlation functions. 122 refs., 7 figs., 7 tabs.« less

The intermolecular interaction in D2 - CX4 and O2 - CX4 (X = F, Cl) systems: Molecular beam scattering experiments as a sensitive probe of the selectivity of charge transfer component.

PubMed

Cappelletti, David; Falcinelli, Stefano; Pirani, Fernando

2016-10-07

Gas phase collisions of a D 2 projectile by CF 4 and by CCl 4 targets have been investigated with the molecular beam technique. The integral cross section, Q, has been measured for both collisional systems in the thermal energy range and oscillations due to the quantum "glory" interference have been resolved in the velocity dependence of Q. The analysis of the measured Q(v) data provided novel information on the anisotropic potential energy surfaces of the studied systems at intermediate and large separation distances. The relative role of the most relevant types of contributions to the global interaction has been characterized. Extending the phenomenology of a weak intermolecular halogen bond, the present work demonstrates that while D 2 - CF 4 is basically bound through the balance between size (Pauli) repulsion and dispersion attraction, an appreciable intermolecular bond stabilization by charge transfer is operative in D 2 - CCl 4 . We also demonstrated that the present analysis is consistent with that carried out for the F( 2 P)-D 2 and Cl( 2 P)-D 2 systems, previously characterized by scattering experiments performed with state-selected halogen atom beams. A detailed comparison of the present and previous results on O 2 -CF 4 and O 2 -CCl 4 systems pinpointed striking differences in the behavior of hydrogen and oxygen molecules when they interact with the same partner, mainly due to the selectivity of the charge transfer component. The present work contributes to cast light on the nature and role of the intermolecular interaction in prototype systems, involving homo-nuclear diatoms and symmetric halogenated molecules.

A high-throughput assay for DNA topoisomerases and other enzymes, based on DNA triplex formation.

PubMed

Burrell, Matthew R; Burton, Nicolas P; Maxwell, Anthony

2010-01-01

We have developed a rapid, high-throughput assay for measuring the catalytic activity (DNA supercoiling or relaxation) of topoisomerase enzymes that is also capable of monitoring the activity of other enzymes that alter the topology of DNA. The assay utilises intermolecular triplex formation to resolve supercoiled and relaxed forms of DNA, the principle being the greater efficiency of a negatively supercoiled plasmid to form an intermolecular triplex with an immobilised oligonucleotide than the relaxed form. The assay provides a number of advantages over the standard gel-based methods, including greater speed of analysis, reduced sample handling, better quantitation and improved reliability and accuracy of output data. The assay is performed in microtitre plates and can be adapted to high-throughput screening of libraries of potential inhibitors of topoisomerases including bacterial DNA gyrase.

Quantitative determination of the lateral density and intermolecular correlation between proteins anchored on the membrane surfaces using grazing incidence small-angle X-ray scattering and grazing incidence X-ray fluorescence.

PubMed

Abuillan, Wasim; Vorobiev, Alexei; Hartel, Andreas; Jones, Nicola G; Engstler, Markus; Tanaka, Motomu

2012-11-28

As a physical model of the surface of cells coated with densely packed, non-crystalline proteins coupled to lipid anchors, we functionalized the surface of phospholipid membranes by coupling of neutravidin to biotinylated lipid anchors. After the characterization of fine structures perpendicular to the plane of membrane using specular X-ray reflectivity, the same membrane was characterized by grazing incidence small angle X-ray scattering (GISAXS). Within the framework of distorted wave Born approximation and two-dimensional Percus-Yevick function, we can analyze the form and structure factors of the non-crystalline, membrane-anchored proteins for the first time. As a new experimental technique to quantify the surface density of proteins on the membrane surface, we utilized grazing incidence X-ray fluorescence (GIXF). Here, the mean intermolecular distance between proteins from the sulfur peak intensities can be calculated by applying Abelé's matrix formalism. The characteristic correlation distance between non-crystalline neutravidin obtained by the GISAXS analysis agrees well with the intermolecular distance calculated by GIXF, suggesting a large potential of the combination of GISAXS and GIXF in probing the lateral density and correlation of non-crystalline proteins displayed on the membrane surface.

Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect

NASA Astrophysics Data System (ADS)

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

2018-03-01

We present a simple coarse-grained model with the molecular crowding effect in solvent to investigate the structure and dynamics of protein complexes including association and/or dissociation processes and investigate some physical properties such as the structure and the reaction rate from the viewpoint of the hydrophobic intermolecular interactions of protein complex. In the present coarse-grained model, a function depending upon the density of hydrophobic amino acid residues in a binding area of the complex is introduced, and the function involves the molecular crowding effect for the intermolecular interactions of hydrophobic amino acid residues between proteins. We propose a hydrophobic intermolecular potential energy between proteins by using the density-dependent function. The present coarse-grained model is applied to the complex of cytochrome f and plastocyanin by using the Langevin dynamics simulation to investigate some physical properties such as the complex structure, the electron transfer reaction rate constant from plastocyanin to cytochrome f and so on. We find that for proceeding the electron transfer reaction, the distance between metals in their active sites is necessary within about 18 Å. We discuss some typical complex structures formed in the present simulation in relation to the molecular crowding effect on hydrophobic interactions.

Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of a biomolecule: 5-Hydroxymethyluracil.

PubMed

Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

2014-06-05

In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were investigated. The FT-IR (4000-400cm(-1)) spectrum of the molecule in the solid phase was recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared intensities of the title molecule in the ground state were calculated using density functional B3LYP and M06-2X methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data, and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 5-hydroxymethyluracil molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on its vibrational frequencies. It was observed that the NH stretching modes shifted to lower frequencies, while its in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular NH⋯O hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented. Copyright © 2014 Elsevier B.V. All rights reserved.

Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of 4-chlorobenzothioamide

NASA Astrophysics Data System (ADS)

Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

2013-09-01

In the present work, the experimental and theoretical vibrational spectra of 4-chlorobenzothioamide were investigated. The FT-IR (400-4000 cm-1) and μ-Raman spectra (100-4000 cm-1) of 4-chlorobenzothioamide in the solid phase were recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared and Raman intensities of the title molecule in the ground state were calculated using ab initio Hartree-Fock and density functional theory (B3LYP) methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and the theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 4-chlorobenzothioamide was also simulated to evaluate the effect of intermolecular hydrogen bonding on the vibrational frequencies. It was observed that the Nsbnd H stretching modes shifted to lower frequencies, while the in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular Nsbnd H⋯S hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

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

Bereau, Tristan, E-mail: bereau@mpip-mainz.mpg.de; Lilienfeld, O. Anatole von

We estimate polarizabilities of atoms in molecules without electron density, using a Voronoi tesselation approach instead of conventional density partitioning schemes. The resulting atomic dispersion coefficients are calculated, as well as many-body dispersion effects on intermolecular potential energies. We also estimate contributions from multipole electrostatics and compare them to dispersion. We assess the performance of the resulting intermolecular interaction model from dispersion and electrostatics for more than 1300 neutral and charged, small organic molecular dimers. Applications to water clusters, the benzene crystal, the anti-cancer drug ellipticine—intercalated between two Watson-Crick DNA base pairs, as well as six macro-molecular host-guest complexes highlightmore » the potential of this method and help to identify points of future improvement. The mean absolute error made by the combination of static electrostatics with many-body dispersion reduces at larger distances, while it plateaus for two-body dispersion, in conflict with the common assumption that the simple 1/R{sup 6} correction will yield proper dissociative tails. Overall, the method achieves an accuracy well within conventional molecular force fields while exhibiting a simple parametrization protocol.« less

Ultrafast structural molecular dynamics investigated with 2D infrared spectroscopy methods.

PubMed

Kraack, Jan Philip

2017-10-25

Ultrafast, multi-dimensional infrared (IR) spectroscopy has been advanced in recent years to a versatile analytical tool with a broad range of applications to elucidate molecular structure on ultrafast timescales, and it can be used for samples in a many different environments. Following a short and general introduction on the benefits of 2D IR spectroscopy, the first part of this chapter contains a brief discussion on basic descriptions and conceptual considerations of 2D IR spectroscopy. Outstanding classical applications of 2D IR are used afterwards to highlight the strengths and basic applicability of the method. This includes the identification of vibrational coupling in molecules, characterization of spectral diffusion dynamics, chemical exchange of chemical bond formation and breaking, as well as dynamics of intra- and intermolecular energy transfer for molecules in bulk solution and thin films. In the second part, several important, recently developed variants and new applications of 2D IR spectroscopy are introduced. These methods focus on (i) applications to molecules under two- and three-dimensional confinement, (ii) the combination of 2D IR with electrochemistry, (iii) ultrafast 2D IR in conjunction with diffraction-limited microscopy, (iv) several variants of non-equilibrium 2D IR spectroscopy such as transient 2D IR and 3D IR, and (v) extensions of the pump and probe spectral regions for multi-dimensional vibrational spectroscopy towards mixed vibrational-electronic spectroscopies. In light of these examples, the important open scientific and conceptual questions with regard to intra- and intermolecular dynamics are highlighted. Such questions can be tackled with the existing arsenal of experimental variants of 2D IR spectroscopy to promote the understanding of fundamentally new aspects in chemistry, biology and materials science. The final part of the chapter introduces several concepts of currently performed technical developments, which aim at exploiting 2D IR spectroscopy as an analytical tool. Such developments embrace the combination of 2D IR spectroscopy and plasmonic spectroscopy for ultrasensitive analytics, merging 2D IR spectroscopy with ultra-high-resolution microscopy (nanoscopy), future variants of transient 2D IR methods, or 2D IR in conjunction with microfluidics. It is expected that these techniques will allow for groundbreaking research in many new areas of natural sciences.

The Effect of Attractive Interactions and Macromolecular Crowding on Crystallins Association

PubMed Central

Wei, Jiachen; Dobnikar, Jure; Curk, Tine; Song, Fan

2016-01-01

In living systems proteins are typically found in crowded environments where their effective interactions strongly depend on the surrounding medium. Yet, their association and dissociation needs to be robustly controlled in order to enable biological function. Uncontrolled protein aggregation often causes disease. For instance, cataract is caused by the clustering of lens proteins, i.e., crystallins, resulting in enhanced light scattering and impaired vision or blindness. To investigate the molecular origins of cataract formation and to design efficient treatments, a better understanding of crystallin association in macromolecular crowded environment is needed. Here we present a theoretical study of simple coarse grained colloidal models to characterize the general features of how the association equilibrium of proteins depends on the magnitude of intermolecular attraction. By comparing the analytic results to the available experimental data on the osmotic pressure in crystallin solutions, we identify the effective parameters regimes applicable to crystallins. Moreover, the combination of two models allows us to predict that the number of binding sites on crystallin is small, i.e. one to three per protein, which is different from previous estimates. We further observe that the crowding factor is sensitive to the size asymmetry between the reactants and crowding agents, the shape of the protein clusters, and to small variations of intermolecular attraction. Our work may provide general guidelines on how to steer the protein interactions in order to control their association. PMID:26954357

Intermolecular Potentials of Methane Assessed by Second Virial Coefficients, ab Initio Dimer Interaction Energies, and Aggregate Cohesive Energies.

PubMed

Ribeiro, Douglas S

2017-06-01

This study presents computations of three energy related properties for 26 previously published multisite intermolecular potentials of methane: MM2, MM3, MM2en, MM3en, MM2mc, MM3mc, MM3envir, RMK, OPLS all-atom, MUB-2, AMBER, BOYD, Williams, Sheikh, MG, Tsuzuki, E2-Gay, E4-Gay, MP4exp-6(iii), MP4exp-6(iv), Rowley-A, Rowley-B, TraPPE-EH, Ouyang, CLC, and Chao and three united atom potentials: Saager-Fischer (SF), OPLS united atom, and HFD. The three properties analyzed are the second virial coefficients for 14 temperature points in the range of 110 to 623.15 K, the interaction energies for 12 orientations of the methane dimer as a function of distance followed by a comparison to three ab initio data sets and the cohesive energy of the aggregate of 512 methane molecules. The latter computed energies are correlated to latent heat of evaporation of 11 potentials and are proposed as surrogate approximate parameters for ΔH vap for the studied potentials. The 10 best performing potentials are selected by rms order in each one of the properties and three of them are found to be present simultaneously in the three sets: Tsuzuki, MM3mc, and MM2mc. On the basis of the cohesive energy of the aggregate, a quantitative measure of the anisotropy of the potentials is proposed. The results are discussed on the basis of anisotropy, nonadditivity and ability of the potentials to reproduce ab initio data. It is concluded that the nonadditivity of the pair potentials holds and the available ab initio data did not lead to pair potentials that are cohesive enough to reproduce accurately the second virial coefficients.

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

PubMed Central

Christensen, Anders S.; Elstner, Marcus; 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 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. PMID:26328834

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

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

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; Elstner, Marcus

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 calculatedmore » 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.« less

Characterization of Intermolecular Interactions at Play in the 2,2,2-TRIFLUOROETHANOL Trimers Using Cavity and Chirped-Pulse Microwave Spectroscopy

NASA Astrophysics Data System (ADS)

Seifert, Nathan A.; Thomas, Javix; Jäger, Wolfgang; Xu, Yunjie

2017-06-01

2,2,2-trifluoroethanol (TFE) is a common aqueous co-solvent in biological chemistry which may induce or destabilize secondary structures of proteins and polypeptides, thanks to its diverse intermolecular linkages originating from the hydrogen bonding potential of both the hydroxyl and perfluoro groups. Theoretically, the TFE monomer is predicted to have two stable gauche (gauche^{+}/gauche^{-}) conformations whereas the trans form is unstable or is supported only by a very shallow potential. Only the gauche conformers have been identified in the gas phase, whereas liquid phase studies suggest a trans:gauche ratio of 2:3. The question at which sample (cluster) size the trans form of TFE would appear was one major motivation for our study. Here, we report the detection of three trimers of TFE using Balle-Flygare cavity and chirped-pulse Fourier transform microwave spectroscopy (CP-FTMW) techniques. The most stable observed trimer features one trans- and two gauche-TFE subunits. The other two trimers, observed using a newly constructed 2-6 GHz CP-FTMW spectrometer, consist of only the two gauche conformers of TFE. Quantum Theory of Atoms in Molecules (QTAIM) and non-covalent interactions (NCI) analyses give detailed insights into which intermolecular interactions are at play to stabilize the trans form of TFE in the most stable trimer. M. Buck, Q. Rev. Biophys. 1998, 31, 297-335. I. Bakó, T. Radnai, M. Claire, B. Funel, J. Chem. Phys. 2004, 121, 12472-12480. R. F. W. Bader, Chem. Rev. 1991, 91, 893-928. E. R. Johnson, S. Keinan, P. Mori-Sánchez, J. Contreras-Garcia, A. J. Cohen, W. Yang, J. Am. Chem. Soc., 2010, 132, 6498-6506.

Using quantum chemistry muscle to flex massive systems: How to respond to something perturbing

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

Bertoni, Colleen

Computational chemistry uses the theoretical advances of quantum mechanics and the algorithmic and hardware advances of computer science to give insight into chemical problems. It is currently possible to do highly accurate quantum chemistry calculations, but the most accurate methods are very computationally expensive. Thus it is only feasible to do highly accurate calculations on small molecules, since typically more computationally efficient methods are also less accurate. The overall goal of my dissertation work has been to try to decrease the computational expense of calculations without decreasing the accuracy. In particular, my dissertation work focuses on fragmentation methods, intermolecular interactionsmore » methods, analytic gradients, and taking advantage of new hardware.« less

Corresponding-states laws for protein solutions.

PubMed

Katsonis, Panagiotis; Brandon, Simon; Vekilov, Peter G

2006-09-07

The solvent around protein molecules in solutions is structured and this structuring introduces a repulsion in the intermolecular interaction potential at intermediate separations. We use Monte Carlo simulations with isotropic, pair-additive systems interacting with such potentials. We test if the liquid-liquid and liquid-solid phase lines in model protein solutions can be predicted from universal curves and a pair of experimentally determined parameters, as done for atomic and colloid materials using several laws of corresponding states. As predictors, we test three properties at the critical point for liquid-liquid separation: temperature, as in the original van der Waals law, the second virial coefficient, and a modified second virial coefficient, all paired with the critical volume fraction. We find that the van der Waals law is best obeyed and appears more general than its original formulation: A single universal curve describes all tested nonconformal isotropic pair-additive systems. Published experimental data for the liquid-liquid equilibrium for several proteins at various conditions follow a single van der Waals curve. For the solid-liquid equilibrium, we find that no single system property serves as its predictor. We go beyond corresponding-states correlations and put forth semiempirical laws, which allow prediction of the critical temperature and volume fraction solely based on the range of attraction of the intermolecular interaction potential.

MOLSIM: A modular molecular simulation software

PubMed Central

Jurij, Reščič

2015-01-01

The modular software MOLSIM for all‐atom molecular and coarse‐grained simulations is presented with focus on the underlying concepts used. The software possesses four unique features: (1) it is an integrated software for molecular dynamic, Monte Carlo, and Brownian dynamics simulations; (2) simulated objects are constructed in a hierarchical fashion representing atoms, rigid molecules and colloids, flexible chains, hierarchical polymers, and cross‐linked networks; (3) long‐range interactions involving charges, dipoles and/or anisotropic dipole polarizabilities are handled either with the standard Ewald sum, the smooth particle mesh Ewald sum, or the reaction‐field technique; (4) statistical uncertainties are provided for all calculated observables. In addition, MOLSIM supports various statistical ensembles, and several types of simulation cells and boundary conditions are available. Intermolecular interactions comprise tabulated pairwise potentials for speed and uniformity and many‐body interactions involve anisotropic polarizabilities. Intramolecular interactions include bond, angle, and crosslink potentials. A very large set of analyses of static and dynamic properties is provided. The capability of MOLSIM can be extended by user‐providing routines controlling, for example, start conditions, intermolecular potentials, and analyses. An extensive set of case studies in the field of soft matter is presented covering colloids, polymers, and crosslinked networks. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:25994597

Optical Measurements in Non-Equilibrium Plasmas and Flows

DTIC Science & Technology

2009-09-01

collision model, the exponent x is equal to 0.5, from simple kinetic theory. For most realistic inter-molecular potentials, the exponent x is in the range...Chemical Physics, Vol. 89, p. 5568 (1988). 9. Rosasco, G.J., Lempert, W., Hurst , W.S., and Fein, A., in “Spectral Line Shapes, Vol 2, Walter de Gruyter

Altering intra- to inter-molecular hydrogen bonding by dimethylsulfoxide: A TDDFT study of charge transfer for coumarin 343

NASA Astrophysics Data System (ADS)

Liu, Xiaochun; Yin, Hang; Li, Hui; Shi, Ying

2017-04-01

DFT and TDDFT methods were carried out to investigate the influences of intramolecular and intermolecular hydrogen bonding on excited state charge transfer for coumarin 343 (C343). Intramolecular hydrogen bonding is formed between carboxylic acid group and carbonyl group in C343 monomer. However, in dimethylsulfoxide (DMSO) solution, DMSO 'opens up' the intramolecular hydrogen bonding and forms solute-solvent intermolecular hydrogen bonded C343-DMSO complex. Analysis of frontier molecular orbitals reveals that intramolecular charge transfer (ICT) occurs in the first excited state both for C343 monomer and complex. The results of optimized geometric structures indicate that the intramolecular hydrogen bonding interaction is strengthened while the intermolecular hydrogen bonding is weakened in excited state, which is confirmed again by monitoring the shifts of characteristic peaks of infrared spectra. We demonstrated that DMSO solvent can not only break the intramolecular hydrogen bonding to form intermolecular hydrogen bonding with C343 but also alter the mechanism of excited state hydrogen bonding strengthening.

Morphology and the Strength of Intermolecular Contact in Protein Crystals

NASA Technical Reports Server (NTRS)

Matsuura, Yoshiki; Chernov, Alexander A.

2002-01-01

The strengths of intermolecular contacts (macrobonds) in four lysozyme crystals were estimated based on the strengths of individual intermolecular interatomic interaction pairs. The periodic bond chain of these macrobonds accounts for the morphology of protein crystals as shown previously. Further in this paper, the surface area of contact, polar coordinate representation of contact site, Coulombic contribution on the macrobond strength, and the surface energy of the crystal have been evaluated. Comparing location of intermolecular contacts in different polymorphic crystal modifications, we show that these contacts can form a wide variety of patches on the molecular surface. The patches are located practically everywhere on this surface except for the concave active site. The contacts frequently include water molecules, with specific intermolecular hydrogen-bonds on the background of non-specific attractive interactions. The strengths of macrobonds are also compared to those of other protein complex systems. Making use of the contact strengths and taking into account bond hydration we also estimated crystal-water interfacial energies for different crystal faces.

Femtogram detection of explosive nitroaromatics: fluoranthene-based fluorescent chemosensors.

PubMed

Venkatramaiah, N; Kumar, Shiv; Patil, Satish

2012-11-12

Herein we report a novel fluoranthene-based fluorescent fluorophore 7,10-bis(4-bromophenyl)-8,9-bis[4-(hexyloxy)phenyl]fluoranthene (S(3)) and its remarkable properties in applications of explosive detection. The sensitivity towards the detection of nitroaromatics (NACs) was evaluated through fluorescence quenching in solution, vapor, and contact mode approaches. The contact mode approach using thin-layer silica chromatographic plates exhibited a femtogram (1.15 fg cm(-2)) detection limit for trinitrotoluene (TNT) and picric acid (PA), whereas the solution-phase quenching showed PA detection at the 2-20 ppb level. Fluorescence lifetime measurements revealed that the quenching is static in nature and the quenching process is fully reversible. Binding energies between model binding sites of the S(3) and analyte compounds reveal that analyte molecules enter into the cavity created by substituted phenyl rings of fluoranthene and are stabilized by strong intermolecular interactions with alkyl chains. It is anticipated that the sensor S(3) could be a promising material for the construction of portable optical devices for the detection of onsite explosive nitroaromatics. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Van Vleet, Mary J.; Misquitta, Alston J.; Stone, Anthony J.

Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones or Born-Mayer forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, andmore » robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Lastly, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.« less

Infrared and Ultraviolet Spectroscopy of Gas-Phase Imidazolium and Pyridinium Ionic Liquids.

NASA Astrophysics Data System (ADS)

Young, Justin W.; Booth, Ryan S.; Annesley, Christopher; Stearns, Jaime A.

2015-06-01

Ionic liquids (ILs) are a highly variable and potentially game-changing class of molecules for a number of Air Force applications such as satellite propulsion, but the complex nature of IL structure and intermolecular interactions makes it difficult to adequately predict structure-property relationships in order to make new IL-based technology a reality. For example, methylation of imidazolium ionic liquids leads to a substantial increase in viscosity but the underlying physical mechanism is not understood. In addition, the role of hydrogen bonding in ILs, and especially its relationship to macroscopic properties, is a matter of ongoing research. Here we describe the gas-phase spectroscopy of a series of imidazolium- and pyridinium-based ILs, using a combination of infrared spectroscopy and density functional theory to establish the intermolecular interactions present in various ILs, to assess how well they are described by theory, and to relate microscopic structure to macroscopic properties.

Coarse-Grained Simulation of Solvated Cellulose Ib Microfibril

NASA Astrophysics Data System (ADS)

Fan, Bingxin; Maranas, Janna; Zhong, Linghao; Zhen Zhao Collaboration

2013-03-01

We construct a coarse-grained (CG) model of cellulose microfibrils in water. The force field is derived from atomistic simulation of a 40 glucose-unit-long microfibril by requiring consistency between the chain configuration, intermolecular packing and hydrogen bonding of the two levels of modeling. Intermolecular interactions such as hydrogen bonding are added sequentially until the force field holds the microfibril crystal structure. This stepwise process enables us to evaluate the importance of each potential and provides insight to ordered and disordered regions. We simulate cellulose microfibrils with 100 to 400 residues, comparable to the smallest observed microfibrils. Microfibrils longer than 100nm would form a bending region along their longitudinal direction. Multiple bends are observed in the microfibril containing 400 residues. Although the cause is not clear, the bending regions may provide us insights about the periodicity and the behavior of the disordered regions in the microfibril.

Effect of dynamic disorder on charge transport along a pentacene chain

NASA Astrophysics Data System (ADS)

Böhlin, J.; Linares, M.; Stafström, S.

2011-02-01

The lattice equation of motion and a numerical solution of the time-dependent Schrödinger equation provide us with a microscopic picture of charge transport in highly ordered molecular crystals. We have chosen the pentacene single crystal as a model system, and we study charge transport as a function of phonon-mode time-dependent fluctuations in the intermolecular electron transfer integral. For comparison, we include similar fluctuations also in the intramolecular potentials. The variance in these energy quantities is closely related to the temperature of the system. The pentacene system is shown to be very sensitive to fluctuation in the intermolecular transfer integral, revealing a transition from adiabatic to nonadiabatic polaron transport for increasing temperatures. The extension of the polaron at temperatures above 200 K is limited by the electron localization length rather than the interplay between the electron transfer integral and the electron-phonon coupling strength.

Measurement of the. nu. sub 8 intermolecular vibration of (D sub 2 O) sub 2 by tunable far infrared laser spectroscopy

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

Pugliano, N.; Saykally, R.J.

The first accurate measurement of an intermolecular vibration of the water dimer is reported. Five vibration--rotation-tunneling (VRT) bands of the perdeuterated isotope, located near 84 cm{sup {minus}1}, have been assigned to the {ital A}{sub 1}/{ital E}/{ital B}{sub 1} tunneling components of the {ital K}{sub {ital a}}=0{l arrow}0 and {ital K}{sub {ital a}}=1{l arrow}0 subbands. The vibration involves large amplitude motion of the hydrogen bond acceptor and is assigned as the {nu}{sub 8} acceptor wag. The spectra indicate strong coupling of both the donor--acceptor interconversion and donor tunneling motions to the excited vibrational coordinate. This measurement provides a benchmark for futuremore » efforts toward the determination of an accurate potential energy surface for the water dimer.« less

Quantifying intermolecular interactions of ionic liquids using cohesive energy densities.

PubMed

Lovelock, Kevin R J

2017-12-01

For ionic liquids (ILs), both the large number of possible cation + anion combinations and their ionic nature provide a unique challenge for understanding intermolecular interactions. Cohesive energy density, ced , is used to quantify the strength of intermolecular interactions for molecular liquids, and is determined using the enthalpy of vaporization. A critical analysis of the experimental challenges and data to obtain ced for ILs is provided. For ILs there are two methods to judge the strength of intermolecular interactions, due to the presence of multiple constituents in the vapour phase of ILs. Firstly, ced IP , where the ionic vapour constituent is neutral ion pairs, the major constituent of the IL vapour. Secondly, ced C+A , where the ionic vapour constituents are isolated ions. A ced IP dataset is presented for 64 ILs. For the first time an experimental ced C+A , a measure of the strength of the total intermolecular interaction for an IL, is presented. ced C+A is significantly larger for ILs than ced for most molecular liquids, reflecting the need to break all of the relatively strong electrostatic interactions present in ILs. However, the van der Waals interactions contribute significantly to IL volatility due to the very strong electrostatic interaction in the neutral ion pair ionic vapour. An excellent linear correlation is found between ced IP and the inverse of the molecular volume. A good linear correlation is found between IL ced IP and IL Gordon parameter (which are dependent primarily on surface tension). ced values obtained through indirect methods gave similar magnitude values to ced IP . These findings show that ced IP is very important for understanding IL intermolecular interactions, in spite of ced IP not being a measure of the total intermolecular interactions of an IL. In the outlook section, remaining challenges for understanding IL intermolecular interactions are outlined.

Quantifying intermolecular interactions of ionic liquids using cohesive energy densities

PubMed Central

2017-01-01

For ionic liquids (ILs), both the large number of possible cation + anion combinations and their ionic nature provide a unique challenge for understanding intermolecular interactions. Cohesive energy density, ced, is used to quantify the strength of intermolecular interactions for molecular liquids, and is determined using the enthalpy of vaporization. A critical analysis of the experimental challenges and data to obtain ced for ILs is provided. For ILs there are two methods to judge the strength of intermolecular interactions, due to the presence of multiple constituents in the vapour phase of ILs. Firstly, cedIP, where the ionic vapour constituent is neutral ion pairs, the major constituent of the IL vapour. Secondly, cedC+A, where the ionic vapour constituents are isolated ions. A cedIP dataset is presented for 64 ILs. For the first time an experimental cedC+A, a measure of the strength of the total intermolecular interaction for an IL, is presented. cedC+A is significantly larger for ILs than ced for most molecular liquids, reflecting the need to break all of the relatively strong electrostatic interactions present in ILs. However, the van der Waals interactions contribute significantly to IL volatility due to the very strong electrostatic interaction in the neutral ion pair ionic vapour. An excellent linear correlation is found between cedIP and the inverse of the molecular volume. A good linear correlation is found between IL cedIP and IL Gordon parameter (which are dependent primarily on surface tension). ced values obtained through indirect methods gave similar magnitude values to cedIP. These findings show that cedIP is very important for understanding IL intermolecular interactions, in spite of cedIP not being a measure of the total intermolecular interactions of an IL. In the outlook section, remaining challenges for understanding IL intermolecular interactions are outlined. PMID:29308254

The Odd Power of Dispersion

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

Xu, Peng

2014-12-01

In ancient China, water has been regarded as one of the five vital components of life. It has been observed that water has many fascinating properties: water is ‘soft’ yet it can penetrate a hard rock; water is ‘pure’ yet it can tolerate other beings. Because of its unique properties, water is often associated with good quality and has been given the highest praise by Laozi in his book Tao Te Ching saying: the highest/best quality that one can have is being like water. However, little did people understand why and how water possesses such fascinating properties. Modern scientific developmentsmore » made people realize that the macroscopic liquid water is made of a large number of water molecules held together via a network of hydrogen bonds. And those wonderful properties of water are merely the macroscopic manifestations of the interactions between water molecules and other molecules. For example, the dissolving ability of water is due to the fact that the interaction between a water molecule and the other molecular species is stronger than the interactions among their own molecular species. In fact the interactions between any two molecules are governed by the same physics and are termed intermolecular interaction (or intermolecular forces in some literature, although technically ‘force’ is incorrect usage here). Although the very existence of the intermolecular interactions is easily proved, e.g. the mere presence of the solid phase of matter, and scientists today have recognized that the seemingly weak intermolecular interactions essentially hold the world together through a delicate and cooperative process, the theoretical understanding of various intermolecular interactions is still far from satisfactory. On the practical side, theoreticians need to balance computational cost and accuracy. Because of the relatively small magnitudes of the intermolecular interactions, errors that appear tiny compared to the usual chemical (covalent) bonding may change conclusions qualitatively. High-level ab initio methods including explicit description of electron correlation can achieve the desired accuracy at very high computational cost. (Chapter 5 and 6) However the cooperative network of hundreds of thousands of molecules that reflects the true power of intermolecular interactions cannot be modeled easily by ab initio methods. Deeper understanding of intermolecular interactions yields better theoretical models; better theoretical models facilitate and even deepen the understanding of intermolecular interactions. With the aforementioned motivation in mind, a significant portion of this dissertation is dedicated to developing a method to describe the intermolecular interactions accurately with affordable computational resources.« less

X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water.

PubMed

Xie, Wangshen; Orozco, Modesto; Truhlar, Donald G; Gao, Jiali

2009-02-17

A recently proposed electronic structure-based force field called the explicit polarization (X-Pol) potential is used to study many-body electronic polarization effects in a protein, in particular by carrying out a molecular dynamics (MD) simulation of bovine pancreatic trypsin inhibitor (BPTI) in water with periodic boundary conditions. The primary unit cell is cubic with dimensions ~54 × 54 × 54 Å(3), and the total number of atoms in this cell is 14281. An approximate electronic wave function, consisting of 29026 basis functions for the entire system, is variationally optimized to give the minimum Born-Oppenheimer energy at every MD step; this allows the efficient evaluation of the required analytic forces for the dynamics. Intramolecular and intermolecular polarization and intramolecular charge transfer effects are examined and are found to be significant; for example, 17 out of 58 backbone carbonyls differ from neutrality on average by more than 0.1 electron, and the average charge on the six alanines varies from -0.05 to +0.09. The instantaneous excess charges vary even more widely; the backbone carbonyls have standard deviations in their fluctuating net charges from 0.03 to 0.05, and more than half of the residues have excess charges whose standard deviation exceeds 0.05. We conclude that the new-generation X-Pol force field permits the inclusion of time-dependent quantum mechanical polarization and charge transfer effects in much larger systems than was previously possible.

Density functional description of size-dependent effects at nucleation on neutral and charged nanoparticles

NASA Astrophysics Data System (ADS)

Shchekin, Alexander K.; Lebedeva, Tatiana S.

2017-03-01

A numerical study of size-dependent effects in the thermodynamics of a small droplet formed around a solid nanoparticle has been performed within the square-gradient density functional theory. The Lennard-Jones fluid with the Carnahan-Starling model for the hard-sphere contribution to intermolecular interaction in liquid and vapor phases and interfaces has been used for description of the condensate. The intermolecular forces between the solid core and condensate molecules have been taken into account with the help of the Lennard-Jones part of the total molecular potential of the core. The influence of the electric charge of the particle has been considered under assumption of the central Coulomb potential in the medium with dielectric permittivity depending on local condensate density. The condensate density profiles and equimolecular radii for equilibrium droplets at different values of the condensate chemical potential have been computed in the cases of an uncharged solid core with the molecular potential, a charged core without molecular potential, and a core with joint action of the Coulomb and molecular potentials. The appearance of stable equilibrium droplets even in the absence of the electric charge has been commented. As a next step, the capillary, disjoining pressure, and electrostatic contributions to the condensate chemical potential have been considered and compared with the predictions of classical thermodynamics in a wide range of values of the droplet and the particle equimolecular radii. With the help of the found dependence of the condensate chemical potential in droplet on the droplet size, the activation barrier for nucleation on uncharged and charged particles has been computed as a function of the vapor supersaturation. Finally, the work of droplet formation and the work of wetting the particle have been found as functions of the droplet size.

Asymmetric intermolecular cobalt-catalyzed Pauson-Khand reaction using a P-stereogenic bis-phosphane.

PubMed

Orgué, Sílvia; León, Thierry; Riera, Antoni; Verdaguer, Xavier

2015-01-16

The asymmetric intermolecular and catalytic Pauson-Khand reaction has remained an elusive goal since Khand and Pauson discovered this transformation. Using a novel family of P-stereogenic phosphanes, we developed the first catalytic system with useful levels of enantioselection for the reaction of norbornadiene and trimethylsilylacetylene. The results demonstrate that Co-bisphosphane systems are sufficiently reactive and that they lead to high selectivity in the intermolecular process.

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

Torii, Hajime, E-mail: torii.hajime@shizuoka.ac.jp

The intensity of the band at ∼200 cm{sup −1} (∼6 THz) in the Terahertz spectrum of liquid water mainly arises from the modulations of the extent of intermolecular charge transfer through hydrogen bonds, called intermolecular charge fluxes, occurring upon molecular translations along the O…H hydrogen bonds. To obtain reasonable spectral profiles from simulations, it is necessary to effectively incorporate the effects of those intermolecular charge fluxes, but apparently it is not possible by simple classical molecular dynamics simulations with fixed atomic partial charges even if they are amended by molecular induced dipoles due to intermolecular electrostatic interactions. The present paper showsmore » how we can do reasonably correct spectral simulations, without resorting to fully ab initio molecular dynamics.« less

Intermolecular artifacts in probe microscope images of C60 assemblies

NASA Astrophysics Data System (ADS)

Jarvis, Samuel Paul; Rashid, Mohammad Abdur; Sweetman, Adam; Leaf, Jeremy; Taylor, Simon; Moriarty, Philip; Dunn, Janette

2015-12-01

Claims that dynamic force microscopy has the capability to resolve intermolecular bonds in real space continue to be vigorously debated. To date, studies have been restricted to planar molecular assemblies with small separations between neighboring molecules. Here we report the observation of intermolecular artifacts over much larger distances in 2D assemblies of C60 molecules, with compelling evidence that in our case the tip apex is terminated by a C60 molecule (rather than the CO termination typically exploited in ultrahigh resolution force microscopy). The complete absence of directional interactions such as hydrogen or halogen bonding, the nonplanar structure of C60, and the fullerene termination of the tip apex in our case highlight that intermolecular artifacts are ubiquitous in dynamic force microscopy.

Intermolecular interactions and the thermodynamic properties of supercritical fluids.

PubMed

Yigzawe, Tesfaye M; Sadus, Richard J

2013-05-21

The role of different contributions to intermolecular interactions on the thermodynamic properties of supercritical fluids is investigated. Molecular dynamics simulation results are reported for the energy, pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, Joule-Thomson coefficient, and speed of sound of fluids interacting via both the Lennard-Jones and Weeks-Chandler-Andersen potentials. These properties were obtained for a wide range of temperatures, pressures, and densities. For each thermodynamic property, an excess value is determined to distinguish between attraction and repulsion. It is found that the contributions of intermolecular interactions have varying effects depending on the thermodynamic property. The maxima exhibited by the isochoric and isobaric heat capacities, isothermal compressibilities, and thermal expansion coefficient are attributed to interactions in the Lennard-Jones well. Repulsion is required to obtain physically realistic speeds of sound and both repulsion and attraction are necessary to observe a Joule-Thomson inversion curve. Significantly, both maxima and minima are observed for the isobaric and isochoric heat capacities of the supercritical Lennard-Jones fluid. It is postulated that the loci of these maxima and minima converge to a common point via the same power law relationship as the phase coexistence curve with an exponent of β = 0.32. This provides an explanation for the terminal isobaric heat capacity maximum in supercritical fluids.

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

Zheng, Rui; School of Mathematics and Information Science, North China University of Water Resources and Electric Power, Zhengzhou 450011; Zheng, Limin

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 formore » 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.« less

Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of 4-chlorobenzothioamide.

PubMed

Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

2013-09-01

In the present work, the experimental and theoretical vibrational spectra of 4-chlorobenzothioamide were investigated. The FT-IR (400-4000 cm(-1)) and μ-Raman spectra (100-4000 cm(-1)) of 4-chlorobenzothioamide in the solid phase were recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared and Raman intensities of the title molecule in the ground state were calculated using ab initio Hartree-Fock and density functional theory (B3LYP) methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and the theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 4-chlorobenzothioamide was also simulated to evaluate the effect of intermolecular hydrogen bonding on the vibrational frequencies. It was observed that the N-H stretching modes shifted to lower frequencies, while the in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular N-H···S hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented. Copyright © 2013 Elsevier B.V. All rights reserved.

Chromosomal Expression of the Haemophilus influenzae Hap Autotransporter Allows Fine-Tuned Regulation of Adhesive Potential via Inhibition of Intermolecular Autoproteolysis

PubMed Central

Fink, Doran L.; St. Geme III, Joseph W.

2003-01-01

The Haemophilus influenzae Hap autotransporter is a nonpilus adhesin that promotes adherence to respiratory epithelial cells and selected extracellular matrix proteins and facilitates bacterial aggregation and microcolony formation. Hap consists of a 45-kDa outer membrane translocator domain called Hapβ and a 110-kDa extracellular passenger domain called HapS. All adhesive activity resides within HapS, which also contains protease activity and directs its own secretion from the bacterial cell surface via intermolecular autoproteolysis. In the present study, we sought to determine the relationship between the magnitude of Hap expression, the efficiency of Hap autoproteolysis, and the level of Hap-mediated adherence and aggregation. We found that a minimum threshold of Hap precursor was required for autoproteolysis and that this threshold approximated expression of Hap from a chromosomal allele, as occurs in H. influenzae clinical isolates. Chromosomal expression of wild-type Hap was sufficient to promote significant adherence to epithelial cells and extracellular matrix proteins, and adherence was enhanced substantially by inhibition of autoproteolysis. In contrast, chromosomal expression of Hap was sufficient to promote bacterial aggregation only when autoproteolysis was inhibited, indicating that the threshold for Hap-mediated aggregation is above the threshold for autoproteolysis. These results highlight the critical role of autoproteolysis and an intermolecular mechanism of cleavage in controlling the diverse adhesive activities of Hap. PMID:12591878

A corresponding-states framework for the description of the Mie family of intermolecular potentials

NASA Astrophysics Data System (ADS)

Ramrattan, N. S.; Avendaño, C.; Müller, E. A.; Galindo, A.

2015-05-01

The Mie (λr, λa) intermolecular pair potential has been suggested as an alternative to the traditional Lennard-Jones (12-6) potential for modelling real systems both via simulation and theory as its implementation leads to an accuracy and flexibility in the determination of thermophysical properties that cannot be obtained when potentials of fixed range are considered. An additional advantage of using variable-range potentials is noted in the development of coarse-grained models where, as the superatoms become larger, the effective potentials are seen to become softer. However, the larger number of parameters that characterise the Mie potential (λr, λa, σ, ɛ) can hinder a rational study of the particular effects that each individual parameter have on the observed thermodynamic properties and phase equilibria, and higher degeneracy of models is observed. Here a three-parameter corresponding states model is presented in which a cohesive third parameter α is proposed following a perturbation expansion and assuming a mean-field limit. It is shown that in this approximation the free energy of any two Mie systems sharing the same value of α will be the same. The parameter α is an explicit function of the repulsive and attractive exponents and consequently dictates the form of the intermolecular pair potential. Molecular dynamics simulations of a variety of Mie systems over a range of values of α are carried out and the solid-liquid, liquid-vapour and vapour-solid phase boundaries for the systems considered are presented. Using the simulation data, we confirm that systems of the same α exhibit conformal phase behaviour for the fluid-phase properties as well as for the solid-fluid boundary, although larger differences are noted in the solid region; these can be related to the approximations in the definition of the parameter. Furthermore, it is found that the temperature range over which the vapour-liquid envelope of a given Mie system is stable follows a linear dependency with α when expressed as the ratio of the critical-point temperature to the triple-point temperature. The limit where potentials of the Mie family will not present a stable fluid envelope is predicted in terms of the parameter α and the result is found to be in excellent agreement with previous studies. This unique relation between the fluid range and the cohesive parameter α is shown to be useful to limit the pairs of Mie exponents that can be used in coarse-grained potentials to treat real systems in order to obtain temperature ranges of stability for the fluid envelope consistent with experiment.

Mononuclear zinc(II) complexes of 2-((2-(piperazin-1-yl)ethylimino)methyl)-4-substituted phenols: Synthesis, structural characterization, DNA binding and cheminuclease activities

NASA Astrophysics Data System (ADS)

Ravichandran, J.; Gurumoorthy, P.; Karthick, C.; Kalilur Rahiman, A.

2014-03-01

Four new zinc(II) complexes [Zn(HL1-4)Cl2] (1-4), where HL1-4 = 2-((2-(piperazin-1-yl)ethylimino)methyl)-4-substituted phenols, have been isolated and fully characterized using various spectro-analytical techniques. The X-ray crystal structure of complex 4 shows the distorted trigonal-bipyramidal coordination geometry around zinc(II) ion. The crystal packing is stabilized by intermolecular NH⋯O hydrogen bonding interaction. The complexes display no d-d electronic band in the visible region due to d10 electronic configuration of zinc(II) ion. The electrochemical properties of the synthesized ligands and their complexes exhibit similar voltammogram at reduction potential due to electrochemically innocent Zn(II) ion, which evidenced that the electron transfer is due to the nature of the ligand. Binding interaction of complexes with calf thymus DNA was studied by UV-Vis absorption titration, viscometric titration and cyclic voltammetry. All complexes bind with CT DNA by intercalation, giving the binding affinity in the order of 2 > 1 ≫ 3 > 4. The prominent cheminuclease activity of complexes on plasmid DNA (pBR322 DNA) was observed in the absence and presence of H2O2. Oxidative pathway reveals that the underlying mechanism involves hydroxyl radical.

Towards Development of a Super Ceramic Composite - Initial Investigation into Improvement of Strength and Toughness of Polycrystalline Ceramics

DTIC Science & Technology

2012-08-01

sintering of SiC. James Lill (2010) evaluated the Reactive Empirical Bond Order potentials of Brenner (Brenner 1990); the Adaptive Intermolecular Reactive...Protection mechanisms of the iron-plated armor of a deep-sea hydrothermal vent gastropod . PNAS 107(3):987-997. Yu, J., S. B. Sinnott, and S. R. Phillpot

H2O-CH4 and H2S-CH4 complexes: a direct comparison through molecular beam experiments and ab initio calculations.

PubMed

Cappelletti, David; Bartocci, Alessio; Frati, Federica; Roncaratti, Luiz F; Belpassi, Leonardo; Tarantelli, Francesco; Lakshmi, Prabha Aiswarya; Arunan, Elangannan; Pirani, Fernando

2015-11-11

New molecular beam scattering experiments have been performed to measure the total (elastic plus inelastic) cross sections as a function of the velocity in collisions between water and hydrogen sulfide projectile molecules and the methane target. Measured data have been exploited to characterize the range and strength of the intermolecular interaction in such systems, which are of relevance as they drive the gas phase molecular dynamics and the clathrate formation. Complementary information has been obtained by rotational spectra, recorded for the hydrogen sulfide-methane complex, with a pulsed nozzle Fourier transform microwave spectrometer. Extensive ab initio calculations have been performed to rationalize all the experimental findings. The combination of experimental and theoretical information has established the ground for the understanding of the nature of the interaction and allows for its basic components to be modelled, including charge transfer, in these weakly bound systems. The intermolecular potential for H2S-CH4 is significantly less anisotropic than for H2O-CH4, although both of them have potential minima that can be characterized as 'hydrogen bonded'.

Phytochemical, spectroscopic and density functional theory study of Diospyrin, and non-bonding interactions of Diospyrin with atmospheric gases

NASA Astrophysics Data System (ADS)

Fazl-i-Sattar; Ullah, Zakir; Ata-ur-Rahman; Rauf, Abdur; Tariq, Muhammad; Tahir, Asif Ali; Ayub, Khurshid; Ullah, Habib

2015-04-01

Density functional theory (DFT) and phytochemical study of a natural product, Diospyrin (DO) have been carried out. A suitable level of theory was developed, based on correlating the experimental and theoretical data. Hybrid DFT method at B3LYP/6-31G (d,p) level of theory is employed for obtaining the electronic, spectroscopic, inter-molecular interaction and thermodynamic properties of DO. The exact structure of DO is confirmed from the nice validation of the theory and experiment. Non-covalent interactions of DO with different atmospheric gases such as NH3, CO2, CO, and H2O were studied to find out its electroactive nature. The experimental and predicted geometrical parameters, IR and UV-vis spectra (B3LYP/6-31+G (d,p) level of theory) show excellent correlation. Inter-molecular non-bonding interaction of DO with atmospheric gases is investigated through geometrical parameters, electronic properties, charge analysis, and thermodynamic parameters. Electronic properties include, ionization potential (I.P.), electron affinities (E.A.), electrostatic potential (ESP), density of states (DOS), HOMO, LUMO, and band gap. All these characterizations have corroborated each other and confirmed the presence of non-covalent nature in DO with the mentioned gases.

Molecular structure, Hirshfeld surface analysis, theoretical investigations and nonlinear optical properties of a novel crystalline chalcone derivative: (E)-1-(5-bromothiophen-2-yl)-3-(p-tolyl)prop-2-en-1-one

NASA Astrophysics Data System (ADS)

Pramodh, B.; Lokanath, N. K.; Naveen, S.; Naresh, P.; Ganguly, S.; Panda, J.

2018-06-01

In the present work, the crystal structure of a novel chalcone derivative, (E)-1-(5-bromothiophen-2-yl)-3-(p-tolyl) prop-2-en-1-one has been confirmed by X-ray diffraction studies. Hirshfeld surface analysis was carried out to explore the intermolecular interactions. From the Hirshfeld surface analysis it was observed that H⋯H (26.7%) and C⋯H (26.3%) are the major contributors to the intermolecular interactions which stabilizes the crystal structure. The coordinates were optimized using the density functional theory (DFT) calculations using B3LYP hybrid functions with 6-31G(d) basis set. The structural parameters obtained from XRD studies compliment with those calculated using DFT calculations. The HOMO and LUMO energy gap was found to be 4.1778 eV. The molecular electrostatic potential (MEP) was plotted to identify the possible reactions sites of the molecule. Further, non-linear optical (NLO) properties were investigated by calculating hyperpolarizabilities which indicate that the title compound would be a potential candidate for the NLO applications.

Static and dynamic investigations of poly(aspartic acid) and Pluronic F127 complex prepared by self-assembling in aqueous solution

NASA Astrophysics Data System (ADS)

Nita, Loredana E.; Chiriac, Aurica P.; Bercea, Maria; Nistor, Manuela T.

2015-12-01

The present investigation is focused on evaluation of self-assembling ability in aqueous solutions of two water soluble polymers: poly(aspartic acid) (PAS) and Pluronic F127 (PL). The intermolecular complexes, realized between polyacid and neutral copolymer surfactant in different ratios, have been studied by combining various characterization techniques as rheology, DLS, spectroscopy, microscopy, chemical imaging, and zeta potential determination, measurements performed in static and/or dynamic conditions. In static conditions, when the equilibrium state between PAS/PL polymeric pair was reached, and depending on the polymers mixture composition, and of experimental rheological conditions, positive or negative deviations from the additive rule are registered. Conformational changes of the macromolecular chains and correspondingly physical interactions are generated between PL and PAS for self-assembly and the formation of interpolymer complex as suprastructure with micellar configuration. The phenomenon was better evidenced in case of 1/1 wt ratio between the two polymers. In dynamic conditions of determination, during ;in situ; evaluation of the hydrodynamic diameter, zeta potential and conductivity, when the equilibrium state is not reached and as result either the intermolecular bonds are not achieved, the self-assembling process is not so obvious evidenced.

Contrasting intermolecular and intramolecular exciplex formation of a 1,4-dicyano-2-methylnaphthalene-N,N-dimethyl-p-toluidine dyad.

PubMed

Imoto, Mitsutaka; Ikeda, Hiroshi; Fujii, Takayuki; Taniguchi, Hisaji; Tamaki, Akihiro; Takeda, Motonori; Mizuno, Kazuhiko

2010-05-07

An intramolecular exciplex is formed upon excitation of the cyclohexane solution of the 1,4-dicyano-2-methylnaphthalene-N,N-dimethyl-p-toluidine dyad, but little if any intramolecular CT complex exists in the ground state of this substance in solution. In contrast, in the crystalline state, the dyad forms an intermolecular mixed-stack CT complex in the ground state and an intermolecular exciplex when it is photoexcited.

Effects of sodium salt types on the intermolecular interaction of sodium alginate/antarctic krill protein composite fibers.

PubMed

Zhang, Rui; Guo, Jing; Liu, Yuanfa; Chen, Shuang; Zhang, Sen; Yu, Yue

2018-06-01

Sodium alginate (SA) and antarctic krill protein (AKP) were blended to fabricate the SA/AKP composite fibers by the conventional wet spinning method using 5% CaCl 2 as coagulation solution. The sodium salt was added to the SA/AKP solution to adjust the ionization degree and intermolecular interaction of composite system. The main purpose of this study is to investigate the influences of sodium salt types (NaCl, CH 3 COONa, Na 2 SO 4 ) on the intermolecular interaction of SA/AKP composite fibers. The intermolecular interaction, morphology, crystallinity, thermal stability and mechanical properties of SA/AKP composite fibers were analyzed by fourier transform infrared spectroscopy (FT-IR), scanning electron microscope (SEM), x-ray diffraction (XRD), thermogravimetric analysis (TGA). The results show that the types of sodium salt have obvious influences on the content of both β-sheet, intermolecular hydrogen bond, breaking strength and surface morphology in SA/AKP composite fibers, but have a negligible effect on the crystallinity and thermal stability. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

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

Huang, Yuanhang; Beran, Gregory J. O., E-mail: gregory.beran@ucr.edu

2015-07-28

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 simplemore » 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(N{sup 6}) methods like MP2.5 or even spin-component-scaled coupled cluster models for 3-body intermolecular interactions with only O(N{sup 5}) computational cost.« less

Chemical origin of blue- and redshifted hydrogen bonds: intramolecular hyperconjugation and its coupling with intermolecular hyperconjugation.

PubMed

Li, An Yong

2007-04-21

Upon formation of a H bond Y...H-XZ, intramolecular hyperconjugation n(Z)-->sigma*(X-H) of the proton donor plays a key role in red- and blueshift characters of H bonds and must be introduced in the concepts of hyperconjugation and rehybridization. Intermolecular hyperconjugation transfers electron density from Y to sigma*(X-H) and causes elongation and stretch frequency redshift of the X-H bond; intramolecular hyperconjugation couples with intermolecular hyperconjugation and can adjust electron density in sigma*(X-H); rehybridization causes contraction and stretch frequency blueshift of the X-H bond on complexation. The three factors--intra- and intermolecular hyperconjugations and rehybridization--determine commonly red- or blueshift of the formed H bond. A proton donor that has strong intramolecular hyperconjugation often forms blueshifted H bonds.

Dynamic Kerr effect in a strong uniform AC electric field for interacting polar and polarizable molecules in the mean field approximation

NASA Astrophysics Data System (ADS)

Deshmukh, Snehal D.; Déjardin, Pierre-Michel; Kalmykov, Yuri P.

2017-09-01

Analytical formulas for the electric birefringence response of interacting polar and anisotropically polarizable molecules due to a uniform alternating electric field are derived using Berne's forced rotational diffusion model [B. J. Berne, J. Chem. Phys. 62, 1154 (1975)] in the nonlinear version described by Warchol and Vaughan [J. Chem. Phys. 71, 502 (1979)]. It is found for noninteracting molecules that the signal consists of a frequency-dependent DC component superimposed on an oscillatory part with a frequency twice that of the AC driving field. However, unlike noninteracting molecules, the AC part strongly deviates from its dilute counterpart. This suggests a possible way of motivating new experimental studies of intermolecular interactions involving electro-optical methods and complementary nonlinear dielectric relaxation experiments.

Structural variability and the nature of intermolecular interactions in Watson-Crick B-DNA base pairs.

PubMed

Czyznikowska, Z; Góra, R W; Zaleśny, R; Lipkowski, P; Jarzembska, K N; Dominiak, P M; Leszczynski, J

2010-07-29

A set of nearly 100 crystallographic structures was analyzed using ab initio methods in order to verify the effect of the conformational variability of Watson-Crick guanine-cytosine and adenine-thymine base pairs on the intermolecular interaction energy and its components. Furthermore, for the representative structures, a potential energy scan of the structural parameters describing mutual orientation of the base pairs was carried out. The results were obtained using the hybrid variational-perturbational interaction energy decomposition scheme. The electron correlation effects were estimated by means of the second-order Møller-Plesset perturbation theory and coupled clusters with singles and doubles method adopting AUG-cc-pVDZ basis set. Moreover, the characteristics of hydrogen bonds in complexes, mimicking those appearing in B-DNA, were evaluated using topological analysis of the electron density. Although the first-order electrostatic energy is usually the largest stabilizing component, it is canceled out by the associated exchange repulsion in majority of the studied crystallographic structures. Therefore, the analyzed complexes of the nucleic acid bases appeared to be stabilized mainly by the delocalization component of the intermolecular interaction energy which, in terms of symmetry adapted perturbation theory, encompasses the second- and higher-order induction and exchange-induction terms. Furthermore, it was found that the dispersion contribution, albeit much smaller in terms of magnitude, is also a vital stabilizing factor. It was also revealed that the intermolecular interaction energy and its components are strongly influenced by four (out of six) structural parameters describing mutual orientation of bases in Watson-Crick pairs, namely shear, stagger, stretch, and opening. Finally, as a part of a model study, much of the effort was devoted to an extensive testing of the UBDB databank. It was shown that the databank quite successfully reproduces the electrostatic energy determined with the aid of ab initio methods.

Crystallization of amorphous solid dispersions of resveratrol during preparation and storage-Impact of different polymers.

PubMed

Wegiel, Lindsay A; Mauer, Lisa J; Edgar, Kevin J; Taylor, Lynne S

2013-01-01

The objective of this study was to investigate intermolecular interactions between resveratrol and polymers in amorphous blends and to study the potential correlations between compound-polymer interactions, manufacturability, and stability of the amorphous system to crystallization during storage. Polymers included two grades of poly (vinylpyrrolidone) (PVP), Eudragit E100 (E100), hydroxypropyl methylcellulose (HPMC), hydroxypropyl methylcellulose acetate succinate (HPMCAS), carboxymethyl cellulose acetate butyrate, and poly (acrylic acid) (PAA). Amorphous blends ("solid dispersions") were prepared by dissolving both resveratrol and polymer in a solvent followed by rotary evaporation. Crystallinity was evaluated using X-ray powder diffraction and was studied as a function of time. Mid-infrared (IR) spectroscopy was used to investigate resveratrol-polymer interactions. Polymer influence on the crystallization behavior of resveratrol varied and could be correlated to the polymer structure, whereby polymers with good hydrogen bond acceptor groups performed better as crystallization inhibitors. Resveratrol-polymer hydrogen bonding interactions could be inferred from the IR spectra. Somewhat surprisingly, E100 and resveratrol showed evidence of an acid-base reaction, in addition to intermolecular hydrogen bonding interactions. PVP K29/32 appeared to form stronger hydrogen bond interactions with resveratrol relative to HPMC, HPMCAS, and PAA, consistent with acceptor group chemistry. Long-term stability of the systems against crystallization suggested that stability is linked to the type and strength of intermolecular interactions present. whereby resveratrol blended with E100 and PVP K29/32 showed the greatest stability to crystallization. In conclusion, amorphous resveratrol is unstable and difficult to form, requiring the assistance of a polymeric crystallization inhibitor to facilitate the formation of an amorphous solid dispersion. Polymers effective at inhibiting crystallization were identified, and it is rationalized that their effectiveness is based on the type and strength of their intermolecular interactions with resveratrol. Copyright © 2012 Wiley Periodicals, Inc.

UPLC-ESI-MS study of the oxidation markers released from tannin depolymerization: toward a better characterization of the tannin evolution over food and beverage processing.

PubMed

Mouls, Laetitia; Fulcrand, Hélène

2012-11-01

Condensed tannins take an important part in the sensory quality of food and beverage. Sensory analyses are usually carried out with various tannin fractions isolated from food or beverage, and their interpretation are limited by the lack of knowledge in the fine and accurate molecular composition of the tannin fractions. Besides, the studies of the chemical reactivity conducted in model solutions with 'simple' flavanols allow a better understanding of their evolution pathways, but they cannot take into account their reactivity as polymers, specifically regarding oxidation. In particular, competition between intramolecular and intermolecular reactions may strongly impact on the tannin structures (size, branching and conformation) and consequently on their properties. An ultra-performance liquid chromatography-mass spectrometry electrospray ionization mass spectrometer analytical method was thus developed in order to identify oxidized tannins generated by autoxidation. Given the difficulties to separate and detect tannins with high DP, samples were depolymerized by chemical depolymerization prior to analysis. Since the linkages created by oxidation are not cleavable in the usual depolymerization conditions (contrarily to the original interflavanic linkages), specific oxidation residues are released from tannins structures after their autoxidation. Oxidation markers of both intermolecular and intramolecular mechanisms have been identified; these are mainly dimers and trimers, more or less oxidized, and some contain additional hydroxyl groups. Furthermore, the nature of the subunits (extension vs terminal) making up these dimers and trimers was clearly established. Copyright © 2012 John Wiley & Sons, Ltd.

Ultrasonic studies of intermolecular interactions in binary mixtures of 4-methoxy benzoin with various solvents: Excess molar functions of ultrasonic parameters at different concentrations and in different solvents.

PubMed

Thanuja, B; Nithya, G; Kanagam, Charles C

2012-11-01

Density (ρ), ultrasonic velocity (U), for the binary mixtures of 4-methoxy benzoin (4MB) with ethanol, chloroform, acetonitrile, benzene, and di-oxane were measured at 298K. The solute-solvent interactions and the effect of the polarity of the solvent on the type of intermolecular interactions are discussed here. From the above data, adiabatic compressibility (β), intermolecular free length (L(f)), acoustic impedance (Z), apparent molar volume (Ø), relative association (RA) have been calculated. Other useful parameters such as excess density, excess velocity and excess adiabatic compressibility have also been calculated. These parameters were used to study the nature and extent of intermolecular interactions between component molecules in the binary mixtures. Copyright © 2012 Elsevier B.V. All rights reserved.

Variational Approach in the Theory of Liquid-Crystal State

NASA Astrophysics Data System (ADS)

Gevorkyan, E. V.

2018-03-01

The variational calculus by Leonhard Euler is the basis for modern mathematics and theoretical physics. The efficiency of variational approach in statistical theory of liquid-crystal state and in general case in condensed state theory is shown. The developed approach in particular allows us to introduce correctly effective pair interactions and optimize the simple models of liquid crystals with help of realistic intermolecular potentials.

Methanol clusters (CH3OH)n: putative global minimum-energy structures from model potentials and dispersion-corrected density functional theory.

PubMed

Kazachenko, Sergey; Bulusu, Satya; Thakkar, Ajit J

2013-06-14

Putative global minima are reported for methanol clusters (CH3OH)n with n ≤ 15. The predictions are based on global optimization of three intermolecular potential energy models followed by local optimization and single-point energy calculations using two variants of dispersion-corrected density functional theory. Recurring structural motifs include folded and/or twisted rings, folded rings with a short branch, and stacked rings. Many of the larger structures are stabilized by weak C-H···O bonds.

Design and Conformational Analysis of Peptoids Containing N-Hydroxy Amides Reveals a Unique Sheet-Like Secondary Structure

PubMed Central

Crapster, J. Aaron; Stringer, Joseph R.; Guzei, Ilia A.; Blackwell, Helen E.

2011-01-01

N-hydroxy amides can be found in many naturally occurring and synthetic compounds and are known to act as both strong proton donors and chelators of metal cations. We have initiated studies of peptoids, or N-substituted glycines, that contain N-hydroxy amide side chains to investigate the potential effects of these functional groups on peptoid backbone amide rotamer equilibria and local conformations. We reasoned that the propensity of these functional groups to participate in hydrogen bonding could be exploited to enforce intramolecular or intermolecular interactions that yield new peptoid structures. Here, we report the design, synthesis, and detailed conformational analysis of a series of model N-hydroxy peptoids. These peptoids were readily synthesized, and their structures were analyzed in solution by 1D and 2D NMR and in the solid-state by X-ray crystallography. The N-hydroxy amides were found to strongly favor trans conformations with respect to the peptoid backbone in chloroform. More notably, unique sheet-like structures held together via intermolecular hydrogen bonds were observed in the X-ray crystal structures of an N-hydroxy amide peptoid dimer, which to our knowledge represent the first structure of this type reported for peptoids. These results suggest that the N-hydroxy amide can be utilized to control both local backbone geometries and longer-range intermolecular interactions in peptoids, and represents a new functional group in the peptoid design toolbox. PMID:22180908

Nuclear spin relaxation in ligands outside of the first coordination sphere in a gadolinium (III) complex: Effects of intermolecular forces

NASA Astrophysics Data System (ADS)

Kruk, Danuta; Kowalewski, Jozef

2002-07-01

This article describes paramagnetic relaxation enhancement (PRE) in systems with high electron spin, S, where there is molecular interaction between a paramagnetic ion and a ligand outside of the first coordination sphere. The new feature of our treatment is an improved handling of the electron-spin relaxation, making use of the Redfield theory. Following a common approach, a well-defined second coordination sphere is assumed, and the PRE contribution from these more distant and shorter-lived ligands is treated in a way similar to that used for the first coordination sphere. This model is called "ordered second sphere," OSS. In addition, we develop here a formalism similar to that of Hwang and Freed [J. Chem. Phys. 63, 4017 (1975)], but accounting for the electron-spin relaxation effects. We denote this formalism "diffuse second sphere," DSS. The description of the dynamics of the intermolecular dipole-dipole interaction is based on the Smoluchowski equation, with a potential of mean force related to the radial distribution function. We have used a finite-difference method to calculate numerically a correlation function for translational motion, taking into account the intermolecular forces leading to an arbitrary radial distribution of the ligand protons. The OSS and DSS models, including the Redfield description of the electron-spin relaxation, were used to interpret the PRE in an aqueous solution of a slowly rotating gadolinium (III) complex (S=7/2) bound to a protein.

Amino Acid Side Chain Interactions in the Presence of Salts

PubMed Central

Hassan, Sergio A.

2005-01-01

The effects of salt on the intermolecular interactions between polar/charged amino acids are investigated through molecular dynamics simulations. The mean forces and associated potentials are calculated for NaCl salt in the 0–2 M concentration range at 298 K. It is found that the addition of salt may stabilize or destabilize the interactions, depending on the nature of the interacting molecules. The degree of (de)stabilization is quantified, and the origin of the salt-dependent modulation is discussed based upon an analysis of solvent density profiles. To gain insight into the molecular origin of the salt modulation, spatial distribution functions (sdf’s) are calculated, revealing a high degree of solvent structuredness in all cases. The peaks in the sdf’s are consistent with long-range hydrogen-bonding networks connecting the solute hydrophilic groups, and that contribute to their intermolecular solvent-induced forces. The restructuring of water around the solutes as they dissociate from close contact is analyzed. This analysis offers clues on how the solvent structure modulates the effective intermolecular interactions in complex solutes. This modulation results from a critical balance between bulk electrostatic forces and those exerted by (i) the water molecules in the structured region between the monomers, which is disrupted by ions that transiently enter the hydration shells, and (ii) the ions in the hydration shells in direct interactions with the solutes. The implications of these findings in protein/ligand (noncovalent) association/dissociation mechanisms are briefly discussed. PMID:16479276

Quantitative analysis of intermolecular interactions in orthorhombic rubrene

DOE PAGES

Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; ...

2015-08-14

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,more » the presence of C π...C πinteractions 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. Finally, 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.« less

Asymmetric intermolecular Pauson-Khand reactions of unstrained olefins: the (o-dimethylamino)phenylsulfinyl group as an efficient chiral auxiliary.

PubMed

Rodríguez Rivero, Marta; De La Rosa, Juan Carlos; Carretero, Juan Carlos

2003-12-10

The first asymmetric version of intermolecular Pauson-Khand reactions of unstrained alkenes is described. Generally simple acyclic alkenes exhibit low reactivity and regioselectivity in intermolecular Pauson-Khand reactions; however, o-(dimethylamino)phenyl vinyl sulfoxide reacts under very mild conditions with a wide variety of terminal alkynes in a completely regioselective and highly stereoselective manner. The utility of the resulting 5-sulfinyl-2-cyclopentenones in asymmetric synthesis is illustrated by a very short enantioselective synthesis of the antibiotic (-)-pentenomycin I.

Theory of gas hydrates: effect of the approximation of rigid water lattice.

PubMed

Pimpalgaonkar, Hrushikesh; Veesam, Shivanand K; Punnathanam, Sudeep N

2011-08-25

One of the assumptions of the van der Waals and Platteeuw theory for gas hydrates is that the host water lattice is rigid and not distorted by the presence of guest molecules. In this work, we study the effect of this approximation on the triple-point lines of the gas hydrates. We calculate the triple-point lines of methane and ethane hydrates via Monte Carlo molecular simulations and compare the simulation results with the predictions of van der Waals and Platteeuw theory. Our study shows that even if the exact intermolecular potential between the guest molecules and water is known, the dissociation temperatures predicted by the theory are significantly higher. This has serious implications to the modeling of gas hydrate thermodynamics, and in spite of the several impressive efforts made toward obtaining an accurate description of intermolecular interactions in gas hydrates, the theory will suffer from the problem of robustness if the issue of movement of water molecules is not adequately addressed. © 2011 American Chemical Society

Programmable Assembly of Peptide Amphiphile via Noncovalent-to-Covalent Bond Conversion

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

Sato, Kohei; Ji, Wei; Palmer, Liam C.

Controlling the number of monomers in a supramolecular polymer has been a great challenge in programmable self-assembly of organic molecules. One approach has been to make use of frustrated growth of the supramolecular assembly by tuning the balance of attractive and repulsive intermolecular forces. We report here on the use of covalent bond formation among monomers, compensating for intermolecular electrostatic repulsion, as a mechanism to control the length of a supramolecular nanofiber formed by self-assembly of peptide amphiphiles. Circular dichroism spectroscopy in combination with dynamic light scattering, size-exclusion chromatography, and transmittance electron microscope analyses revealed that hydrogen bonds between peptidesmore » were reinforced by covalent bond formation, enabling the fiber elongation. To examine these materials for their potential biomedical applications, cytotoxicity of nanofibers against C2C12 premyoblast cells was tested. We demonstrated that cell viability increased with an increase in fiber length, presumably because of the suppressed disruption of cell membranes by the fiber end-caps.« less

Structure and stability of clusters of β-alanine in the gas phase: importance of the nature of intermolecular interactions.

PubMed

Piekarski, Dariusz Grzegorz; Díaz-Tendero, Sergio

2017-02-15

We present a theoretical study of neutral clusters of β-alanine molecules in the gas phase, (β-ala) n n ≤ 5. Classical molecular dynamics simulations carried out with different internal excitation energies provide information on the clusters formation and their thermal decomposition limits. We also present an assessment study performed with different families of density functionals using the dimer, (β-ala) 2 , as a benchmark system. The M06-2X functional provides the best agreement in geometries and relative energies in comparison with the reference values computed with the MP2 and CCSD(T) methods. The structure, stability, dissociation energies and vertical ionization potentials of the studied clusters have been investigated using this functional in combination with the 6-311++G(d,p) basis set. An exhaustive analysis of intermolecular interactions is also presented. These results provide new insights into the stability, interaction nature and formation mechanisms of clusters of amino acids in the gas phase.

A general approach to intermolecular carbonylation of arene C-H bonds to ketones through catalytic aroyl triflate formation

NASA Astrophysics Data System (ADS)

Garrison Kinney, R.; Tjutrins, Jevgenijs; Torres, Gerardo M.; Liu, Nina Jiabao; Kulkarni, Omkar; Arndtsen, Bruce A.

2018-02-01

The development of metal-catalysed methods to functionalize inert C-H bonds has become a dominant research theme in the past decade as an approach to efficient synthesis. However, the incorporation of carbon monoxide into such reactions to form valuable ketones has to date proved a challenge, despite its potential as a straightforward and green alternative to Friedel-Crafts reactions. Here we describe a new approach to palladium-catalysed C-H bond functionalization in which carbon monoxide is used to drive the generation of high-energy electrophiles. This offers a method to couple the useful features of metal-catalysed C-H functionalization (stable and available reagents) and electrophilic acylations (broad scope and selectivity), and synthesize ketones simply from aryl iodides, CO and arenes. Notably, the reaction proceeds in an intermolecular fashion, without directing groups and at very low palladium-catalyst loadings. Mechanistic studies show that the reaction proceeds through the catalytic build-up of potent aroyl triflate electrophiles.

Terahertz spectroscopy and computational investigation of the flufenamic acid/nicotinamide cocrystal.

PubMed

Delaney, Sean P; Korter, Timothy M

2015-04-02

Terahertz spectroscopy probes the low-frequency vibrations that are sensitive to both the intermolecular and intramolecular interactions of molecules in the solid state. Thus, terahertz spectroscopy can be a useful tool in the investigation of crystalline pharmaceutical compounds, where slight changes in the packing arrangement can modify the overall effectiveness of a drug formulation. This is especially true for cases of polymorphic systems, hydrates/solvates, and cocrystals. In this work, the cocrystal of flufenamic acid with nicotinamide was investigated using terahertz spectroscopy and solid-state density functional theory. The solid-state simulations enable understanding of the low-frequency vibrations seen in the terahertz spectra, while also providing insight into the energetics involved in the formation of the cocrystal. The comparison of the cocrystal to the pure forms of the molecular components reveals that the cocrystal has better overall binding energy, driven by increased intermolecular hydrogen bond strength and greater London dispersion forces and that the trifluoromethyl torsional potential is significantly different between the studied solids.

Beyond Born-Mayer: Improved models for short-range repulsion in ab initio force fields

DOE PAGES

Van Vleet, Mary J.; Misquitta, Alston J.; Stone, Anthony J.; ...

2016-06-23

Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones or Born-Mayer forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, andmore » robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Lastly, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.« less

Programmable Assembly of Peptide Amphiphile via Noncovalent-to-Covalent Bond Conversion

DOE PAGES

Sato, Kohei; Ji, Wei; Palmer, Liam C.; ...

2017-06-22

Controlling the number of monomers in a supramolecular polymer has been a great challenge in programmable self-assembly of organic molecules. One approach has been to make use of frustrated growth of the supramolecular assembly by tuning the balance of attractive and repulsive intermolecular forces. We report here on the use of covalent bond formation among monomers, compensating for intermolecular electrostatic repulsion, as a mechanism to control the length of a supramolecular nanofiber formed by self-assembly of peptide amphiphiles. Circular dichroism spectroscopy in combination with dynamic light scattering, size-exclusion chromatography, and transmittance electron microscope analyses revealed that hydrogen bonds between peptidesmore » were reinforced by covalent bond formation, enabling the fiber elongation. To examine these materials for their potential biomedical applications, cytotoxicity of nanofibers against C2C12 premyoblast cells was tested. We demonstrated that cell viability increased with an increase in fiber length, presumably because of the suppressed disruption of cell membranes by the fiber end-caps.« less

Temperature Dependence in the Terahertz Spectrum of Nicotinamide: Anharmonicity and Hydrogen-Bonded Network.

PubMed

Takahashi, Masae; Okamura, Nubuyuki; Fan, Xinyi; Shirakawa, Hitoshi; Minamide, Hiroaki

2017-04-06

We have investigated the terahertz-spectral property of nicotinamide focusing on the temperature dependence in the range of 14-300 K. We observed that almost all peaks in the terahertz spectrum of the nicotinamide crystal showed a remarkable shift with temperature, whereas the lowest-frequency peak at 34.8 cm -1 showed a negligible shift with temperature. By analyzing the terahertz spectrum with the dispersion-corrected density functional theory calculations, we found that the difference in the temperature dependence of the peak shift is well understood in terms of the presence/absence of stretching vibration of the intermolecular hydrogen bond in the mode and the change of cell parameters. The anharmonicity in the dissociation potential energy of very weak intermolecular hydrogen bonding causes the remarkable peak shift with temperature in the terahertz spectrum of nicotinamide. This finding suggests that the assignment and identification of peaks in the terahertz spectrum are systematically enabled by temperature-dependent measurements.

Electronic structure, dielectric response, and surface charge distribution of RGD (1FUV) peptide.

PubMed

Adhikari, Puja; Wen, Amy M; French, Roger H; Parsegian, V Adrian; Steinmetz, Nicole F; Podgornik, Rudolf; Ching, Wai-Yim

2014-07-08

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor.

Intermolecular Structural Change for Thermoswitchable Polymeric Photosensitizer

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

Park, Wooram; Park, Sin-Jung; Cho, Soojeong

2016-08-17

A switchable photosensitizer (PS), which can be activated at a spe-cific condition beside light, has tremendous advantages for photo-dynamic therapy (PDT). Herein, we developed a thermo-switchable polymeric photosensitizer (T-PPS) by conjugating PS (Pheophor-bide-a, PPb-a) to a temperature-responsive polymer backbone of biocompatible hydroxypropyl cellulose (HPC). Self-quenched PS molecules linked in close proximity by pi-pi stacking in T-PPS were easily transited to an active monomeric state by the tempera-ture induced phase transition of polymer backbones. The tempera-ture responsive inter-molecular interaction changes of PS molecules in T-PPS were demonstrated in synchrotron small-angle X-ray scattering (SAXS) and UV-Vis spectrophotometer analysis. The T-PPS allowed switchablemore » activation and synergistically enhanced cancer cell killing effect at the hyperthermia temperature (45 °C). Our developed T-PPS has the considerable potential not only as a new class of photomedicine in clinics but also as a biosensor based on temperature responsiveness.« less

Intermolecular G-quadruplex structure-based fluorescent DNA detection system.

PubMed

Zhou, Hui; Wu, Zai-Sheng; Shen, Guo-Li; Yu, Ru-Qin

2013-03-15

Adopting multi-donors to pair with one acceptor could improve the performance of fluorogenic detection probes. However, common dyes (e.g., fluorescein) in close proximity to each other would self-quench the fluorescence, and the fluorescence is difficult to restore. In this contribution, we constructed a novel "multi-donors-to-one acceptor" fluorescent DNA detection system by means of the intermolecular G-quadruplex (IGQ) structure-based fluorescence signal enhancement combined with the hairpin oligonucleotide. The novel IGQ-hairpin system was characterized using the p53 gene as the model target DNA. The proposed system showed an improved assay performance due to the introduction of IGQ-structure into fluorescent signaling probes, which could inhibit the background fluorescence and increase fluorescence restoration amplitude of fluoresceins upon target DNA hybridization. The proof-of-concept scheme is expected to provide new insight into the potential of G-quadruplex structure and promote the application of fluorescent oligonucleotide probes in fundamental research, diagnosis, and treatment of genetic diseases. Copyright © 2012 Elsevier B.V. All rights reserved.

Intermolecular orbital interaction in π systems

NASA Astrophysics Data System (ADS)

Zhao, Rundong; Zhang, Rui-Qin

2018-04-01

Intermolecular interactions, in regard to which people tend to emphasise the noncovalent van der Waals (vdW) forces when conducting investigations throughout chemistry, can influence the structure, stability and function of molecules and materials. Despite the ubiquitous nature of vdW interactions, a simplified electrostatic model has been popularly adopted to explain common intermolecular interactions, especially those existing in π-involved systems. However, this classical model has come under fire in revealing specific issues such as substituent effects, due to its roughness; and it has been followed in past decades by sundry explanations which sometimes bring in nebulous descriptions. In this account, we try to summarise and present a unified model for describing and analysing the binding mechanism of such systems from the viewpoint of energy decomposition. We also emphasise a commonly ignored factor - orbital interaction, pointing out that the noncovalent intermolecular orbital interactions actually exhibit similar bonding and antibonding phenomena as those in covalent bonds.

Study of intermolecular interactions in binary mixtures of 2'-chloro-4-methoxy-3-nitro benzil in various solvents and at different concentrations by the measurement of acoustic properties.

PubMed

Nithya, G; Thanuja, B; Kanagam, Charles C

2013-01-01

Density (ρ), ultrasonic velocity (u), adiabatic compressibility (β), apparent molar volume (Ø), acoustic impedance (Z), intermolecular free length (L(f)), relative association (RA) of binary mixtures of 2'-chloro-4-methoxy-3-nitro benzil (abbreviated as 2CBe) in ethanol, acetonitrile, chloroform, dioxane and benzene were measured at different concentrations at 298 K. Several useful parameters such as excess density, excess ultrasonic velocity, excess adiabatic compressibility, excess apparent molar volume, excess acoustic impedance and excess intermolecular free length have been calculated. These parameters are used to explain the nature of intermolecular interactions taking place in the binary mixture. The above study is useful in understanding the solute--solvent interactions occurring in different concentrations at room temperature. Copyright © 2012 Elsevier B.V. All rights reserved.

Grid-based Continual Analysis of Molecular Interior for Drug Discovery, QSAR and QSPR.

PubMed

Potemkin, Andrey V; Grishina, Maria A; Potemkin, Vladimir A

2017-01-01

In 1979, R.D.Cramer and M.Milne made a first realization of 3D comparison of molecules by aligning them in space and by mapping their molecular fields to a 3D grid. Further, this approach was developed as the DYLOMMS (Dynamic Lattice- Oriented Molecular Modelling System) approach. In 1984, H.Wold and S.Wold proposed the use of partial least squares (PLS) analysis, instead of principal component analysis, to correlate the field values with biological activities. Then, in 1988, the method which was called CoMFA (Comparative Molecular Field Analysis) was introduced and the appropriate software became commercially available. Since 1988, a lot of 3D QSAR methods, algorithms and their modifications are introduced for solving of virtual drug discovery problems (e.g., CoMSIA, CoMMA, HINT, HASL, GOLPE, GRID, PARM, Raptor, BiS, CiS, ConGO,). All the methods can be divided into two groups (classes):1. Methods studying the exterior of molecules; 2) Methods studying the interior of molecules. A series of grid-based computational technologies for Continual Molecular Interior analysis (CoMIn) are invented in the current paper. The grid-based analysis is fulfilled by means of a lattice construction analogously to many other grid-based methods. The further continual elucidation of molecular structure is performed in various ways. (i) In terms of intermolecular interactions potentials. This can be represented as a superposition of Coulomb, Van der Waals interactions and hydrogen bonds. All the potentials are well known continual functions and their values can be determined in all lattice points for a molecule. (ii) In the terms of quantum functions such as electron density distribution, Laplacian and Hamiltonian of electron density distribution, potential energy distribution, the highest occupied and the lowest unoccupied molecular orbitals distribution and their superposition. To reduce time of calculations using quantum methods based on the first principles, an original quantum free-orbital approach AlteQ is proposed. All the functions can be calculated using a quantum approach at a sufficient level of theory and their values can be determined in all lattice points for a molecule. Then, the molecules of a dataset can be superimposed in the lattice for the maximal coincidence (or minimal deviations) of the potentials (i) or the quantum functions (ii). The methods and criteria of the superimposition are discussed. After that a functional relationship between biological activity or property and characteristics of potentials (i) or functions (ii) is created. The methods of the quantitative relationship construction are discussed. New approaches for rational virtual drug design based on the intermolecular potentials and quantum functions are invented. All the invented methods are realized at www.chemosophia.com web page. Therefore, a set of 3D QSAR approaches for continual molecular interior study giving a lot of opportunities for virtual drug discovery, virtual screening and ligand-based drug design are invented. The continual elucidation of molecular structure is performed in the terms of intermolecular interactions potentials and in the terms of quantum functions such as electron density distribution, Laplacian and Hamiltonian of electron density distribution, potential energy distribution, the highest occupied and the lowest unoccupied molecular orbitals distribution and their superposition. To reduce time of calculations using quantum methods based on the first principles, an original quantum free-orbital approach AlteQ is proposed. The methods of the quantitative relationship construction are discussed. New approaches for rational virtual drug design based on the intermolecular potentials and quantum functions are invented. All the invented methods are realized at www.chemosophia.com web page. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Generation of crystal structures using known crystal structures as analogues

PubMed Central

Cole, Jason C.; Groom, Colin R.; Read, Murray G.; Giangreco, Ilenia; McCabe, Patrick; Reilly, Anthony M.; Shields, Gregory P.

2016-01-01

This analysis attempts to answer the question of whether similar molecules crystallize in a similar manner. An analysis of structures in the Cambridge Structural Database shows that the answer is yes – sometimes they do, particularly for single-component structures. However, one does need to define what we mean by similar in both cases. Building on this observation we then demonstrate how this correlation between shape similarity and packing similarity can be used to generate potential lattices for molecules with no known crystal structure. Simple intermolecular interaction potentials can be used to minimize these potential lattices. Finally we discuss the many limitations of this approach. PMID:27484374

Effective Fragment Potential Method for H-Bonding: How To Obtain Parameters for Nonrigid Fragments.

PubMed

Dubinets, Nikita; Slipchenko, Lyudmila V

2017-07-20

Accuracy of the effective fragment potential (EFP) method was explored for describing intermolecular interaction energies in three dimers with strong H-bonded interactions, formic acid, formamide, and formamidine dimers, which are a part of HBC6 database of noncovalent interactions. Monomer geometries in these dimers change significantly as a function of intermonomer separation. Several EFP schemes were considered, in which fragment parameters were prepared for a fragment in its gas-phase geometry or recomputed for each unique fragment geometry. Additionally, a scheme in which gas-phase fragment parameters are shifted according to relaxed fragment geometries is introduced and tested. EFP data are compared against the coupled cluster with single, double, and perturbative triple excitations (CCSD(T)) method in a complete basis set (CBS) and the symmetry adapted perturbation theory (SAPT). All considered EFP schemes provide a good agreement with CCSD(T)/CBS for binding energies at equilibrium separations, with discrepancies not exceeding 2 kcal/mol. However, only the schemes that utilize relaxed fragment geometries remain qualitatively correct at shorter than equilibrium intermolecular distances. The EFP scheme with shifted parameters behaves quantitatively similar to the scheme in which parameters are recomputed for each monomer geometry and thus is recommended as a computationally efficient approach for large-scale EFP simulations of flexible systems.

Density functional theory and phytochemical study of 8-hydroxyisodiospyrin

NASA Astrophysics Data System (ADS)

Ullah, Zakir; Ata-ur-Rahman; Fazl-i-Sattar; Rauf, Abdur; Yaseen, Muhammad; Hassan, Waseem; Tariq, Muhammad; Ayub, Khurshid; Tahir, Asif Ali; Ullah, Habib

2015-09-01

Comprehensive theoretical and experimental studies of a natural product, 8-hydroxyisodiospyrin (HDO) have been carried out. Based on the correlation of experimental and theoretical data, an appropriate computational model was developed for obtaining the electronic, spectroscopic, and thermodynamic parameters of HDO. First of all, the exact structure of HDO is confirmed from the nice correlation of theory and experiment, prior to determination of its electroactive nature. Hybrid density functional theory (DFT) is employed for all theoretical simulations. The experimental and predicted IR and UV-vis spectra [B3LYP/6-31+G(d,p) level of theory] have excellent correlation. Inter-molecular non-covalent interaction of HDO with different gases such as NH3, CO2, CO, H2O is investigated through geometrical counterpoise (gCP) i.e., B3LYP-gCP-D3/6-31G∗ method. Furthermore, the inter-molecular interaction is also supported by geometrical parameters, electronic properties, thermodynamic parameters and charge analysis. All these characterizations have corroborated each other and confirmed the electroactive nature (non-covalent interaction ability) of HDO for the studied gases. Electronic properties such as Ionization Potential (IP), Electron Affinities (EA), electrostatic potential (ESP), density of states (DOS), HOMO, LUMO, and band gap of HDO have been estimated for the first time theoretically.

Phytochemical, spectroscopic and density functional theory study of Diospyrin, and non-bonding interactions of Diospyrin with atmospheric gases.

PubMed

Fazl-i-Sattar; Ullah, Zakir; Ata-ur-Rahman; Rauf, Abdur; Tariq, Muhammad; Tahir, Asif Ali; Ayub, Khurshid; Ullah, Habib

2015-04-15

Density functional theory (DFT) and phytochemical study of a natural product, Diospyrin (DO) have been carried out. A suitable level of theory was developed, based on correlating the experimental and theoretical data. Hybrid DFT method at B3LYP/6-31G (d,p) level of theory is employed for obtaining the electronic, spectroscopic, inter-molecular interaction and thermodynamic properties of DO. The exact structure of DO is confirmed from the nice validation of the theory and experiment. Non-covalent interactions of DO with different atmospheric gases such as NH3, CO2, CO, and H2O were studied to find out its electroactive nature. The experimental and predicted geometrical parameters, IR and UV-vis spectra (B3LYP/6-31+G (d,p) level of theory) show excellent correlation. Inter-molecular non-bonding interaction of DO with atmospheric gases is investigated through geometrical parameters, electronic properties, charge analysis, and thermodynamic parameters. Electronic properties include, ionization potential (I.P.), electron affinities (E.A.), electrostatic potential (ESP), density of states (DOS), HOMO, LUMO, and band gap. All these characterizations have corroborated each other and confirmed the presence of non-covalent nature in DO with the mentioned gases. Copyright © 2015 Elsevier B.V. All rights reserved.

Chemical Dynamics Simulations of Intermolecular Energy Transfer: Azulene + N2 Collisions.

PubMed

Kim, Hyunsik; Paul, Amit K; Pratihar, Subha; Hase, William L

2016-07-14

Chemical dynamics simulations were performed to investigate collisional energy transfer from highly vibrationally excited azulene (Az*) in a N2 bath. The intermolecular potential between Az and N2, used for the simulations, was determined from MP2/6-31+G* ab initio calculations. Az* is prepared with an 87.5 kcal/mol excitation energy by using quantum microcanonical sampling, including its 95.7 kcal/mol zero-point energy. The average energy of Az* versus time, obtained from the simulations, shows different rates of Az* deactivation depending on the N2 bath density. Using the N2 bath density and Lennard-Jones collision number, the average energy transfer per collision ⟨ΔEc⟩ was obtained for Az* as it is collisionally relaxed. By comparing ⟨ΔEc⟩ versus the bath density, the single collision limiting density was found for energy transfer. The resulting ⟨ΔEc⟩, for an 87.5 kcal/mol excitation energy, is 0.30 ± 0.01 and 0.32 ± 0.01 kcal/mol for harmonic and anharmonic Az potentials, respectively. For comparison, the experimental value is 0.57 ± 0.11 kcal/mol. During Az* relaxation there is no appreciable energy transfer to Az translation and rotation, and the energy transfer is to the N2 bath.

Non-covalent interactions across organic and biological subsets of chemical space: Physics-based potentials parametrized from machine learning

NASA Astrophysics Data System (ADS)

Bereau, Tristan; DiStasio, Robert A.; Tkatchenko, Alexandre; von Lilienfeld, O. Anatole

2018-06-01

Classical intermolecular potentials typically require an extensive parametrization procedure for any new compound considered. To do away with prior parametrization, we propose a combination of physics-based potentials with machine learning (ML), coined IPML, which is transferable across small neutral organic and biologically relevant molecules. ML models provide on-the-fly predictions for environment-dependent local atomic properties: electrostatic multipole coefficients (significant error reduction compared to previously reported), the population and decay rate of valence atomic densities, and polarizabilities across conformations and chemical compositions of H, C, N, and O atoms. These parameters enable accurate calculations of intermolecular contributions—electrostatics, charge penetration, repulsion, induction/polarization, and many-body dispersion. Unlike other potentials, this model is transferable in its ability to handle new molecules and conformations without explicit prior parametrization: All local atomic properties are predicted from ML, leaving only eight global parameters—optimized once and for all across compounds. We validate IPML on various gas-phase dimers at and away from equilibrium separation, where we obtain mean absolute errors between 0.4 and 0.7 kcal/mol for several chemically and conformationally diverse datasets representative of non-covalent interactions in biologically relevant molecules. We further focus on hydrogen-bonded complexes—essential but challenging due to their directional nature—where datasets of DNA base pairs and amino acids yield an extremely encouraging 1.4 kcal/mol error. Finally, and as a first look, we consider IPML for denser systems: water clusters, supramolecular host-guest complexes, and the benzene crystal.

Tunable far infrared laser spectroscopy of van der Waals bonds: The intermolecular stretching vibration and effective radial potentials for Ar--H sub 2 O

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

Cohen, R.C.; Busarow, K.L.; Lee, Y.T.

1990-01-01

Measurements of the fundamental van der Waals stretching vibration {Sigma}(0{sub 00},{ital v}{sub {ital s}}=1) {l arrow}{Sigma}(0{sub 00},{ital v}{sub {ital s}}=0) of Ar--H{sub 2}O ({nu}{sub 0}=907 322.08(94) MHz) and a transition from the lowest excited internal rotor state {Sigma}(1{sub 01},{ital v}{sub {ital s}}=0) to the {Sigma}(1{sub 01},{ital v}{sub {ital s}}=1) level ({nu}{sub 0}=1019 239.4(1.0) MHz) are presented. A simultaneous rotational analysis of the new stretching data with the internal rotor bands observed by us previously (J. Chem. Phys. {bold 89}, 4494 (1988)), including the effects of Coriolis interactions, provides experimental evidence for the new assignment of the internal rotor transitions suggestedmore » by Hutson in the accompanying paper. Fits to the rotational term values for the {ital v}{sub {ital s}}=0 states are used to derive effective radial potential energy surfaces for each of the {Sigma} internal rotor states. The results show the well depth (153.4 cm{sup {minus}1}) of the effective radial potential for the {Sigma}(1{sub 01},{ital v}{sub {ital s}}=0) level to be approximately 25 cm{sup {minus}1} deeper than that for the {Sigma}(0{sub 00},{ital v}{sub {ital s}}=0) ground state of the complex, indicating that the former is stabilized considerably more by the anisotropic intermolecular potential energy surface than is the ground state.« less

Biopolymer-based nanocomposites: effect of lignin acetylation in cellulose triacetate films

PubMed Central

Nevárez, Laura Alicia Manjarrez; Casarrubias, Lourdes Ballinas; Celzard, Alain; Fierro, Vanessa; Muñoz, Vinicio Torres; Davila, Alejandro Camacho; Lubian, José Román Torres; Sánchez, Guillermo González

2011-01-01

We have prepared all-biopolymer nanocomposite films using lignin as a filler and cellulose triacetate (CTA) as a polymer matrix, and characterized them by several analytical methods. Three types of lignin were tested: organosolv, hydrolytic and kraft, with or without acetylation. They were used in the form of nanoparticles incorporated at 1 wt% in CTA. Self-supported films were prepared by vapor-induced phase separation at controlled temperature (35–55 °C) and relative humidity (10–70%). The efficiency of acetylation of each type of lignin was studied and discussed, as well as its effects on film structure, homogeneity and mechanical properties. The obtained results are explained in terms of intermolecular filler-matrix interaction at the nanometer scale, for which the highest mechanical resistance was reached using hydrolytic lignin in the nanocomposite. PMID:27877425

Multipole-Based Force Fields from ab Initio Interaction Energies and the Need for Jointly Refitting All Intermolecular Parameters.

PubMed

Kramer, Christian; Gedeck, Peter; Meuwly, Markus

2013-03-12

Distributed atomic multipole (MTP) moments promise significant improvements over point charges (PCs) in molecular force fields, as they (a) more realistically reproduce the ab initio electrostatic potential (ESP) and (b) allow to capture anisotropic atomic properties such as lone pairs, conjugated systems, and σ holes. The present work focuses on the question of whether multipolar electrostatics instead of PCs in standard force fields leads to quantitative improvements over point charges in reproducing intermolecular interactions. To this end, the interaction energies of two model systems, benzonitrile (BZN) and formamide (FAM) homodimers, are characterized over a wide range of dimer conformations. It is found that although with MTPs the monomer ab initio ESP can be captured better by about an order of magnitude compared to point charges (PCs), this does not directly translate into better describing ab initio interaction energies compared to PCs. Neither ESP-fitted MTPs nor refitted Lennard-Jones (LJ) parameters alone demonstrate a clear superiority of atomic MTPs. We show that only if both electrostatic and LJ parameters are jointly optimized in standard, nonpolarizable force fields, atomic are MTPs clearly beneficial for reproducing ab initio dimerization energies. After an exhaustive exponent scan, we find that for both BZN and FAM, atomic MTPs and a 9-6 LJ potential can reproduce ab initio interaction energies with ∼30% (RMSD 0.13 vs 0.18 kcal/mol) less error than point charges (PCs) and a 12-6 LJ potential. We also find that the improvement due to using MTPs with a 9-6 LJ potential is considerably more pronounced than with a 12-6 LJ potential (≈ 10%; RMSD 0.19 versus 0.21 kcal/mol).

The 129Xe nuclear shielding surfaces for Xe interacting with linear molecules CO2, N2, and CO

NASA Astrophysics Data System (ADS)

de Dios, Angel C.; Jameson, Cynthia J.

1997-09-01

We have calculated the intermolecular nuclear magnetic shielding surfaces for 129Xe in the systems Xe-CO2, Xe-N2, and Xe-CO using a gauge-invariant ab initio method at the coupled Hartree-Fock level with gauge-including atomic orbitals (GIAO). Implementation of a large basis set (240 basis functions) on the Xe gives very small counterpoise corrections which indicates that the basis set superposition errors in the calculated shielding values are negligible. These are the first intermolecular shielding surfaces for Xe-molecule systems. The surfaces are highly anisotropic and can be described adequately by a sum of inverse even powers of the distance with explicit angle dependence in the coefficients expressed by Legendre polynomials P2n(cos θ), n=0-3, for Xe-CO2 and Xe-N2. The Xe-CO shielding surface is well described by a similar functional form, except that Pn(cos θ), n=0-4 were used. When averaged over the anisotropic potential function these shielding surfaces provide the second virial coefficient of the nuclear magnetic resonance (NMR) chemical shift observed in gas mixtures. The energies from the self-consistent field (SCF) calculations were used to construct potential surfaces, using a damped dispersion form. These potential functions are compared with existing potentials in their predictions of the second virial coefficients of NMR shielding, the pressure virial coefficients, the density coefficient of the mean-square torque from infrared absorption, and the rotational constants and other average properties of the van der Waals complexes. Average properties of the van der Waals complexes were obtained by quantum diffusion Monte Carlo solutions of the vibrational motion using the various potentials and compared with experiment.

Homologous recombination occurs in a distinct retroviral subpopulation and exhibits high negative interference.

PubMed Central

Hu, W S; Bowman, E H; Delviks, K A; Pathak, V K

1997-01-01

Homologous recombination and deletions occur during retroviral replication when reverse transcriptase switches templates. While recombination occurs solely by intermolecular template switching (between copackaged RNAs), deletions can occur by an intermolecular or an intramolecular template switch (within the same RNA). To directly compare the rates of intramolecular and intermolecular template switching, two spleen necrosis virus-based vectors were constructed. Each vector contained a 110-bp direct repeat that was previously shown to delete at a high rate. The 110-bp direct repeat was flanked by two different sets of restriction site markers. These vectors were used to form heterozygotic virions containing RNAs of each parental vector, from which recombinant viruses were generated. By analyses of the markers flanking the direct repeats in recombinant and nonrecombinant proviruses, the rates of intramolecular and intermolecular template switching were determined. The results of these analyses indicate that intramolecular template switching is much more efficient than intermolecular template switching and that direct repeat deletions occur primarily through intramolecular template switching events. These studies also indicate that retroviral recombination occurs within a distinct viral subpopulation and exhibits high negative interference, whereby the selection of one recombination event increases the probability that a second recombination event will be observed. PMID:9223494

Free energies of binding from large-scale first-principles quantum mechanical calculations: application to ligand hydration energies.

PubMed

Fox, Stephen J; Pittock, Chris; Tautermann, Christofer S; Fox, Thomas; Christ, Clara; Malcolm, N O J; Essex, Jonathan W; Skylaris, Chris-Kriton

2013-08-15

Schemes of increasing sophistication for obtaining free energies of binding have been developed over the years, where configurational sampling is used to include the all-important entropic contributions to the free energies. However, the quality of the results will also depend on the accuracy with which the intermolecular interactions are computed at each molecular configuration. In this context, the energy change associated with the rearrangement of electrons (electronic polarization and charge transfer) upon binding is a very important effect. Classical molecular mechanics force fields do not take this effect into account explicitly, and polarizable force fields and semiempirical quantum or hybrid quantum-classical (QM/MM) calculations are increasingly employed (at higher computational cost) to compute intermolecular interactions in free-energy schemes. In this work, we investigate the use of large-scale quantum mechanical calculations from first-principles as a way of fully taking into account electronic effects in free-energy calculations. We employ a one-step free-energy perturbation (FEP) scheme from a molecular mechanical (MM) potential to a quantum mechanical (QM) potential as a correction to thermodynamic integration calculations within the MM potential. We use this approach to calculate relative free energies of hydration of small aromatic molecules. Our quantum calculations are performed on multiple configurations from classical molecular dynamics simulations. The quantum energy of each configuration is obtained from density functional theory calculations with a near-complete psinc basis set on over 600 atoms using the ONETEP program.

Computational study of the rovibrational spectrum of CO₂-CS₂.

PubMed

Brown, James; Wang, Xiao-Gang; Carrington, Tucker; Grubbs, G S; Dawes, Richard

2014-03-21

A new intermolecular potential energy surface, rovibrational transition frequencies, and line strengths are computed for CO2-CS2. The potential is made by fitting energies obtained from explicitly correlated coupled-cluster calculations using an interpolating moving least squares method. The rovibrational Schrödinger equation is solved with a symmetry-adapted Lanczos algorithm and an uncoupled product basis set. All four intermolecular coordinates are included in the calculation. In agreement with previous experiments, the global minimum of the potential energy surface (PES) is cross shaped. The PES also has slipped-parallel minima. Rovibrational wavefunctions are localized in the cross minima and the slipped-parallel minima. Vibrational parent analysis was used to assign vibrational labels to rovibrational states. Tunneling occurs between the two cross minima. Because more than one symmetry operation interconverts the two wells, the symmetry (-oo) of the upper component of the tunneling doublet is different from the symmetry (-ee) of the tunneling coordinate. This unusual situation is due to the multidimensional nature of the double well tunneling. For the cross ground vibrational state, calculated rotational constants differ from their experimental counterparts by less than 0.0001 cm(-1). Most rovibrational states were found to be incompatible with the standard effective rotational Hamiltonian often used to fit spectra. This appears to be due to coupling between internal and overall rotation of the dimer. A simple 2D model accounting for internal rotation was used for two cross-shaped fundamentals to obtain good fits.

Probing the global potential energy minimum of (CH2O)2: THz absorption spectrum of (CH2O)2 in solid neon and para-hydrogen.

PubMed

Andersen, J; Voute, A; Mihrin, D; Heimdal, J; Berg, R W; Torsson, M; Wugt Larsen, R

2017-06-28

The true global potential energy minimum configuration of the formaldehyde dimer (CH 2 O) 2 , including the presence of a single or a double weak intermolecular CH⋯O hydrogen bond motif, has been a long-standing subject among both experimentalists and theoreticians as two different energy minima conformations of C s and C 2h symmetry have almost identical energies. The present work demonstrates how the class of large-amplitude hydrogen bond vibrational motion probed in the THz region provides excellent direct spectroscopic observables for these weak intermolecular CH⋯O hydrogen bond motifs. The combination of concentration dependency measurements, observed isotopic spectral shifts associated with H/D substitutions and dedicated annealing procedures, enables the unambiguous assignment of three large-amplitude infrared active hydrogen bond vibrational modes for the non-planar C s configuration of (CH 2 O) 2 embedded in cryogenic neon and enriched para-hydrogen matrices. A (semi)-empirical value for the change of vibrational zero-point energy of 5.5 ± 0.3 kJ mol -1 is proposed for the dimerization process. These THz spectroscopic observations are complemented by CCSD(T)-F12/aug-cc-pV5Z (electronic energies) and MP2/aug-cc-pVQZ (force fields) electronic structure calculations yielding a (semi)-empirical value of 13.7 ± 0.3 kJ mol -1 for the dissociation energy D 0 of this global potential energy minimum.

Prediction of thermodynamic properties of coal derivatives. Progress report, September 1, 1981-August 31, 1982

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

Donohue, M.D.

It is the purpose of this research program to develop a model to predict the thermodynamic properties of coal derivatives. Unlike natural gas and petroleum, coal and its gasification and liquefaction products are predominantly aromatic and have substantial quadrupole moments. Because of these quadrupole forces, the numerous correlational techniques that have been developed for petroleum products cannot be used to predict the thermodynamic properties of coal derivatives. We are presently developing a correlation that will be useful in predicting the thermodynamic properties of coal derivatives. This theory is based on the Perturbed-Hard-Chain theory, but is different from PHCT in twomore » respects. First, PHCT uses a square-well to describe the intermolecular potential energy between two molecules. In our new theory, the Lennard-Jones potential energy function is used. The second difference is that we take into account the effect of quadrupole forces on the intermolecular potential energy. In PHCT these forces were ignored. In PHCT the contributions to the partition function (or equation of state) that arise from the attractive forces between molecules (regardless of whether these forces are treated as a square-well or by Lennard-Jones) are calculated by assuming that they are perturbations on a hard sphere. In calculating the contributions to the partition function that arise from the quadrupole-quadrupole interactions, we use a second order perturbation about the Lennard-Jones. For aromatic molecules, the effect of this additional perturbation is significant.« less

Probing the global potential energy minimum of (CH2O)2: THz absorption spectrum of (CH2O)2 in solid neon and para-hydrogen

NASA Astrophysics Data System (ADS)

Andersen, J.; Voute, A.; Mihrin, D.; Heimdal, J.; Berg, R. W.; Torsson, M.; Wugt Larsen, R.

2017-06-01

The true global potential energy minimum configuration of the formaldehyde dimer (CH2O)2, including the presence of a single or a double weak intermolecular CH⋯O hydrogen bond motif, has been a long-standing subject among both experimentalists and theoreticians as two different energy minima conformations of Cs and C2h symmetry have almost identical energies. The present work demonstrates how the class of large-amplitude hydrogen bond vibrational motion probed in the THz region provides excellent direct spectroscopic observables for these weak intermolecular CH⋯O hydrogen bond motifs. The combination of concentration dependency measurements, observed isotopic spectral shifts associated with H/D substitutions and dedicated annealing procedures, enables the unambiguous assignment of three large-amplitude infrared active hydrogen bond vibrational modes for the non-planar Cs configuration of (CH2O)2 embedded in cryogenic neon and enriched para-hydrogen matrices. A (semi)-empirical value for the change of vibrational zero-point energy of 5.5 ± 0.3 kJ mol-1 is proposed for the dimerization process. These THz spectroscopic observations are complemented by CCSD(T)-F12/aug-cc-pV5Z (electronic energies) and MP2/aug-cc-pVQZ (force fields) electronic structure calculations yielding a (semi)-empirical value of 13.7 ± 0.3 kJ mol-1 for the dissociation energy D0 of this global potential energy minimum.

Reversing the stereoselectivity of the intermolecular Pauson-Khand reaction: formation of endo-fused norbornadiene adducts.

PubMed

Rios, Ramon; Pericàs, Miquel A; Moyano, Albert; Maestro, Miguel A; Mahía, José

2002-04-04

[reaction: see text] An unprecedented endo-selective and regioselective intermolecular Pauson-Khand reaction takes place when heterobimetallic (Mo-Co) complexes derived from N-(2-alkynoyl)oxazolidinones or sultams are heated in the presence of norbornadiene.

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

USDA-ARS?s Scientific Manuscript database

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)....

Learning about Intermolecular Interactions from the Cambridge Structural Database

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.

2012-01-01

A clear understanding and appreciation of noncovalent interactions, especially hydrogen bonding, are vitally important to students of chemistry and the life sciences, including biochemistry, molecular biology, pharmacology, and medicine. The opportunities afforded by the IsoStar knowledge base of intermolecular interactions to enhance the…

Aqueous heterogeneity at the air/water interface revealed by 2D-HD-SFG spectroscopy.

PubMed

Hsieh, Cho-Shuen; Okuno, Masanari; Hunger, Johannes; Backus, Ellen H G; Nagata, Yuki; Bonn, Mischa

2014-07-28

Water molecules interact strongly with each other through hydrogen bonds. This efficient intermolecular coupling causes strong delocalization of molecular vibrations in bulk water. We study intermolecular coupling at the air/water interface and find intermolecular coupling 1) to be significantly reduced and 2) to vary strongly for different water molecules at the interface--whereas in bulk water the coupling is homogeneous. For strongly hydrogen-bonded OH groups, coupling is roughly half of that of bulk water, due to the lower density in the near-surface region. For weakly hydrogen-bonded OH groups that absorb around 3500 cm(-1), which are assigned to the outermost, yet hydrogen-bonded OH groups pointing towards the liquid, coupling is further reduced by an additional factor of 2. Remarkably, despite the reduced structural constraints imposed by the interfacial hydrogen-bond environment, the structural relaxation is slow and the intermolecular coupling of these water molecules is weak. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Boiling points of halogenated ethanes: an explanatory model implicating weak intermolecular hydrogen-halogen bonding.

PubMed

Beauchamp, Guy

2008-10-23

This study explores via structural clues the influence of weak intermolecular hydrogen-halogen bonds on the boiling point of halogenated ethanes. The plot of boiling points of 86 halogenated ethanes versus the molar refraction (linked to polarizability) reveals a series of straight lines, each corresponding to one of nine possible arrangements of hydrogen and halogen atoms on the two-carbon skeleton. A multiple linear regression model of the boiling points could be designed based on molar refraction and subgroup structure as independent variables (R(2) = 0.995, standard error of boiling point 4.2 degrees C). The model is discussed in view of the fact that molar refraction can account for approximately 83.0% of the observed variation in boiling point, while 16.5% could be ascribed to weak C-X...H-C intermolecular interactions. The difference in the observed boiling point of molecules having similar molar refraction values but differing in hydrogen-halogen intermolecular bonds can reach as much as 90 degrees C.

From intermolecular interactions to structures and properties of a novel cocrystal explosive: a first-principles study.

PubMed

Zhang, Lei; Wu, Ji-Zhou; Jiang, Sheng-Li; Yu, Yi; Chen, Jun

2016-09-29

By employing a first-principles method, we conducted a thorough study on a novel cocrystal explosive 1 : 1 NTO : TZTN and gained insight into the interaction-structure-property interrelationship. Mulliken bond orders, Hirshfeld surfaces, intermolecular binding energies, packing coefficients, and oxygen balance were calculated to analyze the intermolecular interactions and structures of the cocrystal explosive. The cocrystallization of NTO and TZTN molecules enhances the intermolecular binding force, which drives the synthesis of the cocrystal. However, the cocrystallization decreases the molecular packing density along the closest packed directions, which reduces the density by 10.5% and deteriorates the oxygen balance. All of these lead to a reduction in the detonation performance compared to NTO explosives. We have also proposed a new method to evaluate the impact sensitivity according to the lattice dynamics calculation. The cocrystal explosive has a lower impact sensitivity than TZTN but higher than NTO, which agrees well with experiments.

Ferrocenylaniline based amide analogs of methoxybenzoic acids: Synthesis, structural characterization and butyrylcholinesterase (BChE) inhibition studies

NASA Astrophysics Data System (ADS)

Altaf, Ataf Ali; Kausar, Samia; Hamayun, Muhammad; Lal, Bhajan; Tahir, Muhammad Nawaz; Badshah, Amin

2017-10-01

Three new ferrocene based amides were synthesized with slight structural difference. The general formula of the amides is C5H5FeC5H4C6H4NHCOC6H4(OCH3). The synthesized compounds were characterized by instrumental techniques like elemental analysis, FTIR and NMR spectroscopy. Structure of the two compounds was also studied by single crystal X-rays diffraction analysis. Structural studies provide the evidence that pMeO (one of the synthesized compounds) is an example of amides having no intermolecular hydrogen bonding in solid structure. In the BChE inhibition assay, compound (oMeO) having strong intermolecular force in the solid structure is less active than the compound (pMeO) with weak intermolecular forces in the solid structure. The docking studies proved that hydrogen bonding between inhibitor and BChE enzyme is of more importance for the activity, rather than intermolecular hydrogen bonding in the solid structure of inhibitor.

Empirical temperature-dependent intermolecular potentials determined by data mining from crystal data

NASA Astrophysics Data System (ADS)

Hofmann, D. W. M.; Kuleshova, L. N.

2018-05-01

Modern force fields are accurate enough to describe thermal effects in molecular crystals. Here, we have extended our earlier approach to discrete force fields for various temperatures to a force field with a continuous function. For the parametrisation of the force field, we used data mining on experimental structures with the temperature as an additional descriptor. The obtained force field can be used to minimise energy at a finite temperature and for molecular dynamics with zero-K potentials. The applicability of the method has been demonstrated for the prediction of crystal density, temperature density gradients and transition temperature.

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

NASA Astrophysics Data System (ADS)

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.

A first principles prediction of the crystal structure of C6Br2ClFH2

NASA Astrophysics Data System (ADS)

Misquitta, Alston J.; Welch, Gareth W. A.; Stone, Anthony J.; Price, Sarah L.

2008-04-01

We have constructed an intermolecular potential for the 1,3-dibromo-2-chloro-5-fluorobenzene molecule from first principles using SAPT(DFT) interaction energy calculations and the Williams-Stone-Misquitta method for obtaining molecular properties in distributed form. This molecule was included in the fourth Blind Test of crystal structure prediction organised by the Cambridge Crystallographic Data Centre. Using our potential, we have predicted the crystal structure of CBrClFH and found the lowest energy solution to be in excellent agreement with the experimentally observed crystal when it was subsequently revealed.

Investigation of intermolecular interaction of binary mixture of acrylonitrile with bromobenzene

NASA Astrophysics Data System (ADS)

Deshmukh, S. D.; Pattebahadur, K. L.; Mohod, A. G.; Patil, S. S.; Khirade, P. W.

2018-04-01

In this paper, study of binary mixture of Acrylonitrile (ACN)with Bromobenzene(BB) has been carried out at eleven concentrations at room temperature. The determined density(ρ) and refractive index (nD) values of binary mixture are used to calculate the excess properties of mixture over the entire composition range. The aforesaid parameters are used to calculate excess parameters and fitted to the Redlich-Kister equation to determine the bj coefficients. From the above parameters, intermolecular interaction and dynamics of molecules of binary mixture at molecular level are discussed. The Conformational analysis of the intermolecular interaction between Acrylonitrile and Bromobenzene is supported by the FTIR spectra.

The effect of varying linker length on ion-transport properties in polymeric ionic liquids

NASA Astrophysics Data System (ADS)

Keith, Jordan; Mogurampelly, Santosh; Wheatle, Bill; Ganesan, Venkat

We report results of atomistic molecular dynamics simulations on polymerized 1-butyl-3-(n-alkyl)imidazolium ionic liquids with PF6- counterions. Consistent with experimental observations, we observe that the mobility of the PF6- ions increases with increasing n-alkyl linker length. Analysis of our results suggests that the motion of PF6- ions is driven by intermolecular ion hopping between chains, which in turn is influenced by ion-pair coordination numbers and intermolecular ionic separation distances. With increasing linker length, we observe 1) the anions coordinating less closely with cations and 2) intermolecular hopping distances decreasing.

Rotational excitation of symmetric top molecules by collisions with atoms: Close coupling, coupled states, and effective potential calculations for NH3-He

NASA Technical Reports Server (NTRS)

Green, S.

1976-01-01

The formalism for describing rotational excitation in collisions between symmetric top rigid rotors and spherical atoms is presented both within the accurate quantum close coupling framework and also the coupled states approximation of McGuire and Kouri and the effective potential approximation of Rabitz. Calculations are reported for thermal energy NH3-He collisions, treating NH3 as a rigid rotor and employing a uniform electron gas (Gordon-Kim) approximation for the intermolecular potential. Coupled states are found to be in nearly quantitative agreement with close coupling results while the effective potential method is found to be at least qualitatively correct. Modifications necessary to treat the inversion motion in NH3 are discussed.

Sphericalization of the potential of interaction of anisotropic molecules with spherical particles

NASA Astrophysics Data System (ADS)

Fernández-Prini, R.; Japas, María L.

1986-09-01

The possibility of employing sphericalized intermolecular potentials to describe the interactions between nonpolar anisotropic molecules (CCl4 and benzene) with spherical nonpolar molecules (Ar, Xe, and CH4) has been tested for binary systems having liquid- and gas-like densities. Median and RAM sphericalization procedures have been used and their capacity to account for the experimental values of cross second virial coefficients and Henry's constants are compared. It is shown that the median sphericalized potentials, which are temperature and density independent, give a fairly good description of the data which is better than that provided by RAM potentials. The possibility of accounting correctly for the change of properties when the relative size of the interacting partners changes (e.g., conformal systems) is noteworthy.

Catalytic intermolecular carbon electrophile induced semipinacol rearrangement.

PubMed

Zhang, Qing-Wei; Zhang, Xiao-Bo; Li, Bao-Sheng; Xiang, Kai; Zhang, Fu-Min; Wang, Shao-Hua; Tu, Yong-Qiang

2013-02-25

A catalytic intermolecular carbon electrophile induced semipinacol rearrangement was realized and the asymmetric version was also preliminarily accomplished with 92% and 82% ee. The complex tricyclic system architecture with four continuous stereogenic centers could be achieved from simple starting materials in a single step under mild conditions.

Using Molecular Dynamics Simulation to Reinforce Student Understanding of Intermolecular Forces

ERIC Educational Resources Information Center

Burkholder, Phillip R.; Purser, Gordon H.; Cole, Renee S.

2008-01-01

Intermolecular forces play an important role in many aspects of chemistry ranging from inorganic to biological chemistry. These forces dictate molecular conformation, species aggregation (including self-assembly), trends in solubility and boiling points, adsorption characteristics, viscosity, phase changes, surface tension, capillary action, vapor…

Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: the role of intermolecular hydrodynamic interactions in barnase-barstar association.

PubMed

Frembgen-Kesner, Tamara; Elcock, Adrian H

2010-11-03

Theory and computation have long been used to rationalize the experimental association rate constants of protein-protein complexes, and Brownian dynamics (BD) simulations, in particular, have been successful in reproducing the relative rate constants of wild-type and mutant protein pairs. Missing from previous BD studies of association kinetics, however, has been the description of hydrodynamic interactions (HIs) between, and within, the diffusing proteins. Here we address this issue by rigorously including HIs in BD simulations of the barnase-barstar association reaction. We first show that even very simplified representations of the proteins--involving approximately one pseudoatom for every three residues in the protein--can provide excellent reproduction of the absolute association rate constants of wild-type and mutant protein pairs. We then show that simulations that include intermolecular HIs also produce excellent estimates of association rate constants, but, for a given reaction criterion, yield values that are decreased by ∼35-80% relative to those obtained in the absence of intermolecular HIs. The neglect of intermolecular HIs in previous BD simulation studies, therefore, is likely to have contributed to the somewhat overestimated absolute rate constants previously obtained. Consequently, intermolecular HIs could be an important component to include in accurate modeling of the kinetics of macromolecular association events. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Applications and Analogies: Phototherapy and the Treatment of Hyperbilirubinemia: A Demonstration of Intra- versus Intermolecular Hydrogen Bonding.

ERIC Educational Resources Information Center

Wilbraham, Antony C.

1984-01-01

Background information and procedures are provided for a demonstration of intramolecular versus intermolecular hydrogen bonding. The demonstration is based on structural changes in bilirubin molecules which lead to changes in physical properties. A list of further investigations to try is included. (JN)

Highly chemoselective intermolecular cross-benzoin reactions using an ad hoc designed novel N-heterocyclic carbene catalyst.

PubMed

Delany, Eoghan G; Connon, Stephen J

2018-01-31

The design of a novel N-heterocyclic carbene catalyst incorporating a bulky yet highly electron-deficient N-aryl substituent has allowed the development of an efficient protocol for the first highly chemoselective intermolecular benzoin condensations between two non-identical aromatic aldehydes.

Dancing Crystals: A Dramatic Illustration of Intermolecular Forces

ERIC Educational Resources Information Center

Mundell, Donald W.

2007-01-01

Crystals of naphthalene form on the surface of an acetone solution and dance about in an animated fashion illustrating surface tension, crystallization, and intermolecular forces. Additional experiments reveal the properties of the solution. Flows within the solutions can be visualized by various means. Previous demonstrations of surface motion…

Intermolecular rhodium-catalyzed [2 + 2 + 2] carbocyclization reactions of 1,6-enynes with symmetrical and unsymmetrical alkynes†

PubMed Central

Andrew Evans, P.; Sawyer, James R.; Lai, Kwong Wah; Huffman, John C.

2006-01-01

The crossed intermolecular rhodium-catalyzed [2 + 2 + 2] carbocyclization of carbon and heteroatom tethered 1,6-enynes can be accomplished with symmetrical and unsymmetrical alkynes, to afford the corresponding bicyclohexadienes in an efficient and highly selective manner. PMID:16075089

Aggregation and folding phase transitions of RNA molecules

NASA Astrophysics Data System (ADS)

Bundschuh, Ralf

2007-03-01

RNA is a biomolecule that is involved in nearly all aspects of cellular functions. In order to perform many of these functions, RNA molecules have to fold into specific secondary structures. This folding is driven by the tendency of the bases to form Watson-Crick base pairs. Beyond the biological importance of RNA, the relatively simple rules for structure formation of RNA make it a very interesting system from the statistical physics point of view. We will present examples of phase transitions in RNA secondary structure formation that are amenable to analytical descriptions. A special focus will be on aggregation between several RNA molecules which is important for some regulatory circuits based on RNA structure, triplet repeat diseases like Huntington's, and as a model for prion diseases. We show that depending on the relative strength of the intramolecular and the intermolecular base pairing, RNA molecules undergo a transition into an aggregated phase and quantitatively characterize this transition.

Recognition Tunneling

PubMed Central

Lindsay, Stuart; He, Jin; Sankey, Otto; Hapala, Prokop; Jelinek, Pavel; Zhang, Peiming; Chang, Shuai; Huang, Shuo

2010-01-01

Single molecules in a tunnel junction can now be interrogated reliably using chemically-functionalized electrodes. Monitoring stochastic bonding fluctuations between a ligand bound to one electrode and its target bound to a second electrode (“tethered molecule-pair” configuration) gives insight into the nature of the intermolecular bonding at a single molecule-pair level, and defines the requirements for reproducible tunneling data. Simulations show that there is an instability in the tunnel gap at large currents, and this results in a multiplicity of contacts with a corresponding spread in the measured currents. At small currents (i.e. large gaps) the gap is stable, and functionalizing a pair of electrodes with recognition reagents (the “free analyte” configuration) can generate a distinct tunneling signal when an analyte molecule is trapped in the gap. This opens up a new interface between chemistry and electronics with immediate implications for rapid sequencing of single DNA molecules. PMID:20522930

Spacecraft self-contamination due to back-scattering of outgas products

NASA Technical Reports Server (NTRS)

Robertson, S. J.

1976-01-01

The back-scattering of outgas contamination near an orbiting spacecraft due to intermolecular collisions was analyzed. Analytical tools were developed for making reasonably accurate quantitative estimates of the outgas contamination return flux, given a knowledge of the pertinent spacecraft and orbit conditions. Two basic collision mechanisms were considered: (1) collisions involving only outgas molecules (self-scattering) and (2) collisions between outgas molecules and molecules in the ambient atmosphere (ambient-scattering). For simplicity, the geometry was idealized to a uniformly outgassing sphere and to a disk oriented normal to the freestream. The method of solution involved an integration of an approximation of the Boltzmann kinetic equation known as the BGK (or Krook) model equation. Results were obtained in the form of simple equations relating outgas return flux to spacecraft and orbit parameters. Results were compared with previous analyses based on more simplistic models of the collision processes.

Holographic detection of hydrocarbon gases and other volatile organic compounds.

PubMed

Martínez-Hurtado, J L; Davidson, C A B; Blyth, J; Lowe, C R

2010-10-05

There is a need to develop sensors for real-time monitoring of volatile organic compounds (VOCs) and hydrocarbon gases in both external and indoor environments, since these compounds are of growing concern in human health and welfare. Current measurement technology for VOCs requires sophisticated equipment and lacks the prospect for rapid real-time monitoring. Holographic sensors can give a direct reading of the analyte concentration as a color change. We report a technique for recording holographic sensors by laser ablation of silver particles formed in situ by diffusion. This technique allows a readily available hydrophobic silicone elastomer to be transformed into an effective sensor for hydrocarbon gases and other volatile compounds. The intermolecular interactions present between the polymer and molecules are used to predict the sensor performance. The hydrophobicity of this material allows the sensor to operate without interference from water and other atmospheric gases and thus makes the sensor suitable for biomedical, industrial, or environmental analysis.

Molecular dynamics of the water liquid-vapor interface

NASA Technical Reports Server (NTRS)

Wilson, M. A.; Pohorille, A.; Pratt, L. R.; MacElroy, R. D. (Principal Investigator)

1987-01-01

The results of molecular dynamics calculations on the equilibrium interface between liquid water and its vapor at 325 K are presented. For the TIP4P model of water intermolecular pair potentials, the average surface dipole density points from the vapor to the liquid. The most common orientations of water molecules have the C2 nu molecular axis roughly parallel to the interface. The distributions are quite broad and therefore compatible with the intermolecular correlations characteristic of bulk liquid water. All near-neighbor pairs in the outermost interfacial layers are hydrogen bonded according to the common definition adopted here. The orientational preferences of water molecules near a free surface differ from those near rigidly planar walls which can be interpreted in terms of patterns found in hexagonal ice 1. The mean electric field in the interfacial region is parallel to the mean polarization which indicates that attention cannot be limited to dipolar charge distributions in macroscopic descriptions of the electrical properties of this interface. The value of the surface tension obtained is 132 +/- 46 dyn/cm, significantly different from the value for experimental water of 68 dyn/cm at 325 K.

Ionic liquid and nanoparticle hybrid systems: Emerging applications.

PubMed

He, Zhiqi; Alexandridis, Paschalis

2017-06-01

Having novel electronic and optical properties that emanate from their nano-scale dimensions, nanoparticles are central to numerous applications. Ionic liquids can confer to nanoparticle chemical protection and physicochemical property enhancement through intermolecular interactions and can consequently improve the stability and reusability of nanoparticle for various operations. With an aim to combine the novel properties of nanoparticles and ionic liquids, different structures have been generated, based on a balance of several intermolecular interactions. Such ionic liquid and nanoparticle hybrids are showing great potential in diverse applications. In this review, we first introduce various types of ionic liquid and nanoparticle hybrids, including nanoparticle colloidal dispersions in ionic liquids, ionic liquid-grafted nanoparticles, and nanoparticle-stabilized ionic liquid-based emulsions. Such hybrid materials exhibit interesting synergisms. We then highlight representative applications of ionic liquid and nanoparticle hybrids in the catalysis, electrochemistry and separations fields. Such hybrids can attain better stability and higher efficiency under a broad range of conditions. Novel and enhanced performance can be achieved in these applications by combining desired properties of ionic liquids and of nanoparticles within an appropriate hybrid nanostructure. Copyright © 2016 Elsevier B.V. All rights reserved.

Intermolecular Interactions in the TMEM16A Dimer Controlling Channel Activity.

PubMed

Scudieri, Paolo; Musante, Ilaria; Gianotti, Ambra; Moran, Oscar; Galietta, Luis J V

2016-12-08

TMEM16A and TMEM16B are plasma membrane proteins with Ca 2+ -dependent Cl - channel function. By replacing the carboxy-terminus of TMEM16A with the equivalent region of TMEM16B, we obtained channels with potentiation of channel activity. Progressive shortening of the chimeric region restricted the "activating domain" to a short sequence close to the last transmembrane domain and led to TMEM16A channels with high activity at very low intracellular Ca 2+ concentrations. To elucidate the molecular mechanism underlying this effect, we carried out experiments based on double chimeras, Forster resonance energy transfer, and intermolecular cross-linking. We also modeled TMEM16A structure using the Nectria haematococca TMEM16 protein as template. Our results indicate that the enhanced activity in chimeric channels is due to altered interaction between the carboxy-terminus and the first intracellular loop in the TMEM16A homo-dimer. Mimicking this perturbation with a small molecule could be the basis for a pharmacological stimulation of TMEM16A-dependent Cl - transport.

Intermolecular Interactions in the TMEM16A Dimer Controlling Channel Activity

PubMed Central

Scudieri, Paolo; Musante, Ilaria; Gianotti, Ambra; Moran, Oscar; Galietta, Luis J. V.

2016-01-01

TMEM16A and TMEM16B are plasma membrane proteins with Ca2+-dependent Cl− channel function. By replacing the carboxy-terminus of TMEM16A with the equivalent region of TMEM16B, we obtained channels with potentiation of channel activity. Progressive shortening of the chimeric region restricted the “activating domain” to a short sequence close to the last transmembrane domain and led to TMEM16A channels with high activity at very low intracellular Ca2+ concentrations. To elucidate the molecular mechanism underlying this effect, we carried out experiments based on double chimeras, Forster resonance energy transfer, and intermolecular cross-linking. We also modeled TMEM16A structure using the Nectria haematococca TMEM16 protein as template. Our results indicate that the enhanced activity in chimeric channels is due to altered interaction between the carboxy-terminus and the first intracellular loop in the TMEM16A homo-dimer. Mimicking this perturbation with a small molecule could be the basis for a pharmacological stimulation of TMEM16A-dependent Cl− transport. PMID:27929144

Mechanochemical Preparation of Stable Sub-100 nm γ-Cyclodextrin:Buckminsterfullerene (C60) Nanoparticles by Electrostatic or Steric Stabilization.

PubMed

Van Guyse, Joachim F R; de la Rosa, Victor R; Hoogenboom, Richard

2018-02-21

Buckminster fullerene (C 60 )'s main hurdle to enter the field of biomedicine is its low bioavailability, which results from its extremely low water solubility. A well-known approach to increase the water solubility of C 60 is by complexation with γ-cyclodextrins. However, the formed complexes are not stable in time as they rapidly aggregate and eventually precipitate due to attractive intermolecular forces, a common problem in inclusion complexes of cyclodextrins. In this study we attempt to overcome the attractive intermolecular forces between the complexes by designing custom γ-cyclodextrin (γCD)-based supramolecular hosts for C 60 that inhibit the aggregation found in native γCD-C 60 complexes. The approach entails the introduction of either repulsive electrostatic forces or increased steric hindrance to prevent aggregation, thus enhancing the biomedical application potential of C 60 . These modifications have led to new sub-100 nm nanostructures that show long-term stability in solution. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electrostatic properties of the pyrimethamine-2,4-dihydroxybenzoic acid cocrystal in methanol studied using transferred electron-density parameters.

PubMed

Faroque, Muhammad Umer; Noureen, Sajida; Ahmed, Maqsood; Tahir, Muhammad Nawaz

2018-01-01

The crystal structure of the cocrystal salt form of the antimalarial drug pyrimethamine with 2,4-dihydroxybenzoic acid in methanol [systematic name: 2,4-diamino-5-(4-chlorophenyl)-6-ethylpyrimidin-1-ium 2,4-dihydroxybenzoate methanol monosolvate, C 12 H 14 ClN 4 + ·C 7 H 5 O 4 - ·CH 3 OH] has been studied using X-ray diffraction data collected at room temperature. The crystal structure was refined using the classical Independent Atom Model (IAM) and the Multipolar Atom Model by transferring electron-density parameters from the ELMAM2 database. The Cl atom was refined anharmonically. The results of both refinement methods have been compared. The intermolecular interactions have been characterized on the basis of Hirshfeld surface analysis and topological analysis using Bader's theory of Atoms in Molecules. The results show that the molecular assembly is built primarily on the basis of charge transfer between 2,4-dihydroxybenzoic acid and pyrimethamine, which results in strong intermolecular hydrogen bonds. This fact is further validated by the calculation of the electrostatic potential based on transferred electron-density parameters.

The use of docking-based comparative intermolecular contacts analysis to identify optimal docking conditions within glucokinase and to discover of new GK activators

NASA Astrophysics Data System (ADS)

Taha, Mutasem O.; Habash, Maha; Khanfar, Mohammad A.

2014-05-01

Glucokinase (GK) is involved in normal glucose homeostasis and therefore it is a valid target for drug design and discovery efforts. GK activators (GKAs) have excellent potential as treatments of hyperglycemia and diabetes. The combined recent interest in GKAs, together with docking limitations and shortages of docking validation methods prompted us to use our new 3D-QSAR analysis, namely, docking-based comparative intermolecular contacts analysis (dbCICA), to validate docking configurations performed on a group of GKAs within GK binding site. dbCICA assesses the consistency of docking by assessing the correlation between ligands' affinities and their contacts with binding site spots. Optimal dbCICA models were validated by receiver operating characteristic curve analysis and comparative molecular field analysis. dbCICA models were also converted into valid pharmacophores that were used as search queries to mine 3D structural databases for new GKAs. The search yielded several potent bioactivators that experimentally increased GK bioactivity up to 7.5-folds at 10 μM.

Electronic Structure, Dielectric Response, and Surface Charge Distribution of RGD (1FUV) Peptide

PubMed Central

Adhikari, Puja; Wen, Amy M.; French, Roger H.; Parsegian, V. Adrian; Steinmetz, Nicole F.; Podgornik, Rudolf; Ching, Wai-Yim

2014-01-01

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor. PMID:25001596

Polyelectrolyte brushes in mixed ionic medium studied via intermolecular forces

NASA Astrophysics Data System (ADS)

Farina, Robert; Laugel, Nicolas; Pincus, Philip; Tirrell, Matthew

2011-03-01

The vast uses and applications of polyelectrolyte brushes make them an attractive field of research especially with the growing interest in responsive materials. Polymers which respond via changes in temperature, pH, and ionic strength are increasingly being used for applications in drug delivery, chemical gating, etc. When polyelectrolyte brushes are found in either nature (e.g., surfaces of cartilage and mammalian lung interiors) or commercially (e.g., skin care products, shampoo, and surfaces of medical devices) they are always surrounded by mixed ionic medium. This makes the study of these brushes in varying ionic environments extremely relevant for both current and future potential applications. The polyelectrolyte brushes in this work are diblock co-polymers of poly-styrene sulfonate (N=420) and poly-t-butyl styrene (N=20) which tethers to a hydrophobic surface allowing for a purely thermodynamic study of the polyelectrolyte chains. Intermolecular forces between two brushes are measured using the SFA. As multi-valent concentrations are increased, the brushes collapse internally and form strong adhesion between one another after contact (properties not seen in a purely mono-valent environment).

Manganese-catalysed benzylic C(sp3)-H amination for late-stage functionalization

NASA Astrophysics Data System (ADS)

Clark, Joseph R.; Feng, Kaibo; Sookezian, Anasheh; White, M. Christina

2018-06-01

Reactions that directly install nitrogen into C-H bonds of complex molecules are significant because of their potential to change the chemical and biological properties of a given compound. Although selective intramolecular C-H amination reactions are known, achieving high levels of reactivity while maintaining excellent site selectivity and functional-group tolerance remains a challenge for intermolecular C-H amination. Here, we report a manganese perchlorophthalocyanine catalyst [MnIII(ClPc)] for intermolecular benzylic C-H amination of bioactive molecules and natural products that proceeds with unprecedented levels of reactivity and site selectivity. In the presence of a Brønsted or Lewis acid, the [MnIII(ClPc)]-catalysed C-H amination demonstrates unique tolerance for tertiary amine, pyridine and benzimidazole functionalities. Mechanistic studies suggest that C-H amination likely proceeds through an electrophilic metallonitrene intermediate via a stepwise pathway where C-H cleavage is the rate-determining step of the reaction. Collectively, these mechanistic features contrast with previous base-metal-catalysed C-H aminations and provide new opportunities for tunable selectivities.

Manganese-catalysed benzylic C(sp3)-H amination for late-stage functionalization.

PubMed

Clark, Joseph R; Feng, Kaibo; Sookezian, Anasheh; White, M Christina

2018-06-01

Reactions that directly install nitrogen into C-H bonds of complex molecules are significant because of their potential to change the chemical and biological properties of a given compound. Although selective intramolecular C-H amination reactions are known, achieving high levels of reactivity while maintaining excellent site selectivity and functional-group tolerance remains a challenge for intermolecular C-H amination. Here, we report a manganese perchlorophthalocyanine catalyst [MnIII(ClPc)] for intermolecular benzylic C-H amination of bioactive molecules and natural products that proceeds with unprecedented levels of reactivity and site selectivity. In the presence of a Brønsted or Lewis acid, the [MnIII(ClPc)]-catalysed C-H amination demonstrates unique tolerance for tertiary amine, pyridine and benzimidazole functionalities. Mechanistic studies suggest that C-H amination likely proceeds through an electrophilic metallonitrene intermediate via a stepwise pathway where C-H cleavage is the rate-determining step of the reaction. Collectively, these mechanistic features contrast with previous base-metal-catalysed C-H aminations and provide new opportunities for tunable selectivities.

Intermolecular Interactions in the TMEM16A Dimer Controlling Channel Activity

NASA Astrophysics Data System (ADS)

Scudieri, Paolo; Musante, Ilaria; Gianotti, Ambra; Moran, Oscar; Galietta, Luis J. V.

2016-12-01

TMEM16A and TMEM16B are plasma membrane proteins with Ca2+-dependent Cl- channel function. By replacing the carboxy-terminus of TMEM16A with the equivalent region of TMEM16B, we obtained channels with potentiation of channel activity. Progressive shortening of the chimeric region restricted the “activating domain” to a short sequence close to the last transmembrane domain and led to TMEM16A channels with high activity at very low intracellular Ca2+ concentrations. To elucidate the molecular mechanism underlying this effect, we carried out experiments based on double chimeras, Forster resonance energy transfer, and intermolecular cross-linking. We also modeled TMEM16A structure using the Nectria haematococca TMEM16 protein as template. Our results indicate that the enhanced activity in chimeric channels is due to altered interaction between the carboxy-terminus and the first intracellular loop in the TMEM16A homo-dimer. Mimicking this perturbation with a small molecule could be the basis for a pharmacological stimulation of TMEM16A-dependent Cl- transport.

Resolution of differences between collision number definitions in particle and continuum simulations

NASA Technical Reports Server (NTRS)

Lumpkin, Forrest E., III; Haas, Brian L.; Boyd, Iain D.

1991-01-01

The use of the same symbol, Z, representing a 'collision number' for thermal relaxation, has led to confusion regarding its definition in the context of both continuum and particle simulations. Examination of the relaxation mechanics employed in particle simulations demonstrates that these definitions differ by a numerical factor that depends upon the intermolecular potential. Particle and continuum simulations employing appropriate definitions of Z lead to identical results during isothermal and adiabatic stationary relaxation.

Electron tunneling as a basis for semiconduction in proteins

NASA Technical Reports Server (NTRS)

Flax, L.; Flood, D.

1971-01-01

Electron tunneling is investigated as a possible mechanism for the conduction of electrical current in solids composed of protein molecules. An intermolecular potential barrier is assumed which takes into account the applied electric field and the possibility of image charge effects. The WKB approximation is used to calculate the net tunneling current density and resulting conductivity. The results suggest that electron tunneling per se is not a suitable mechanism for explaining the observed conductivities in such materials.

Study of intermolecular interactions in binary mixtures of ethanol in methanol

NASA Astrophysics Data System (ADS)

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.

Connecting Protein Structure to Intermolecular Interactions: A Computer Modeling Laboratory

ERIC Educational Resources Information Center

Abualia, Mohammed; Schroeder, Lianne; Garcia, Megan; Daubenmire, Patrick L.; Wink, Donald J.; Clark, Ginevra A.

2016-01-01

An understanding of protein folding relies on a solid foundation of a number of critical chemical concepts, such as molecular structure, intra-/intermolecular interactions, and relating structure to function. Recent reports show that students struggle on all levels to achieve these understandings and use them in meaningful ways. Further, several…

Student Understanding of Intermolecular Forces: A Multimodal Study

ERIC Educational Resources Information Center

Cooper, Melanie M.; Williams, Leah C.; Underwood, Sonia M.

2015-01-01

The ability to use representations of molecular structure to predict the macroscopic properties of a substance is central to the development of a robust understanding of chemistry. Intermolecular forces (IMFs) play an important role in this process because they provide a mechanism for how and why molecules interact. In this study, we investigate…

Studying Intermolecular Forces with a Dual Gas Chromatography and Boiling Point Investigation

ERIC Educational Resources Information Center

Cunningham, William Patrick; Xia, Ian; Wickline, Kaitlyn; Huitron, Eric Ivan Garcia; Heo, Jun

2018-01-01

A procedure for the study of structural differences and intermolecular attraction between ethanol and 1-butanol based in laboratory work is described. This study provides comparisons of data retrieved from both a determination of boiling point and gas chromatography traces for the mixture. The methodology reported here should provide instructors…

THE INTERACTION OF PARAMAGNETIC RELAXATION REAGENTS WITH INTRA- AND INTERMOLECULAR HYDROGEN BONDED PHENOLS

EPA Science Inventory

Intermolecular electron-nuclear 13-C relaxation times (T(1)sup e's) from solutions containing the paramagnetic relaxation reagent (PARR), Cr(acac)3, used in conjunction with 13-C T(1)'s in diamagnetic solutions (intramolecular 13-C - (1)H dipolar T(1)'s) provide a significant inc...

Catalytic Intermolecular Pauson - Khand Reactions in Supercritical Ethylene.

PubMed

Jeong; Hwang

2000-02-01

Ethylene is not only a substrate, but also a solvent: Catalytic intermolecular Pauson - Khand reactions of terminal alkynes were carried out in supercritical ethylene to provide 2-substituted cyclopentenones in moderate to high yields [Eq. (1)]. Under these conditions, even a low pressure of CO (5 atm) is sufficient for the reaction to take place.

Amyloid oligomer structure characterization from simulations: A general method

NASA Astrophysics Data System (ADS)

Nguyen, Phuong H.; Li, Mai Suan; Derreumaux, Philippe

2014-03-01

Amyloid oligomers and plaques are composed of multiple chemically identical proteins. Therefore, one of the first fundamental problems in the characterization of structures from simulations is the treatment of the degeneracy, i.e., the permutation of the molecules. Second, the intramolecular and intermolecular degrees of freedom of the various molecules must be taken into account. Currently, the well-known dihedral principal component analysis method only considers the intramolecular degrees of freedom, and other methods employing collective variables can only describe intermolecular degrees of freedom at the global level. With this in mind, we propose a general method that identifies all the structures accurately. The basis idea is that the intramolecular and intermolecular states are described in terms of combinations of single-molecule and double-molecule states, respectively, and the overall structures of oligomers are the product basis of the intramolecular and intermolecular states. This way, the degeneracy is automatically avoided. The method is illustrated on the conformational ensemble of the tetramer of the Alzheimer's peptide Aβ9-40, resulting from two atomistic molecular dynamics simulations in explicit solvent, each of 200 ns, starting from two distinct structures.

Exchange coupling and magnetic anisotropy of exchanged-biased quantum tunnelling single-molecule magnet Ni3Mn2 complexes using theoretical methods based on Density Functional Theory.

PubMed

Gómez-Coca, Silvia; Ruiz, Eliseo

2012-03-07

The magnetic properties of a new family of single-molecule magnet Ni(3)Mn(2) complexes were studied using theoretical methods based on Density Functional Theory (DFT). The first part of this study is devoted to analysing the exchange coupling constants, focusing on the intramolecular as well as the intermolecular interactions. The calculated intramolecular J values were in excellent agreement with the experimental data, which show that all the couplings are ferromagnetic, leading to an S = 7 ground state. The intermolecular interactions were investigated because the two complexes studied do not show tunnelling at zero magnetic field. Usually, this exchange-biased quantum tunnelling is attributed to the presence of intermolecular interactions calculated with the help of theoretical methods. The results indicate the presence of weak intermolecular antiferromagnetic couplings that cannot explain the ferromagnetic value found experimentally for one of the systems. In the second part, the goal is to analyse magnetic anisotropy through the calculation of the zero-field splitting parameters (D and E), using DFT methods including the spin-orbit effect.

Hydrogen bonds of sodium alginate/Antarctic krill protein composite material.

PubMed

Yang, Lijun; Guo, Jing; Yu, Yue; An, Qingda; Wang, Liyan; Li, Shenglin; Huang, Xuelin; Mu, Siyang; Qi, Shanwei

2016-05-20

Sodium alginate/Antarctic krill protein composite material (SA/AKP) was successfully obtained by blending method. The hydrogen bonds of SA/AKP composite material were analyzed by Fourier transform infrared spectroscopy (FT-IR) and Nuclear magnetic resonance hydrogen spectrum (HNMR). Experiment manifested the existence of intermolecular and intramolecular hydrogen bonds in SA/AKP system; strength of intermolecular hydrogen bond enhanced with the increase of AKP in the composite material and the interaction strength of hydrogen bonding followed the order: OH…Ether O>OH…π>OH…N. The percentage of intermolecular hydrogen bond decreased with increase of pH. At the same time, the effect of hydrogen bonds on properties of the composite material was discussed. The increase of intermolecular hydrogen bonding led to the decrease of crystallinity, increase of apparent viscosity and surface tension, as well as obvious decrease of heat resistance of SA/AKP composite material. SA/AKP fiber SEM images and energy spectrum showed that crystallized salt was separated from the fiber, which possibly led to the fibrillation of the composite fibers. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Novel Mechanism for Chemical Sensing Based on Solvent-Fluorophore-Substrate Interaction: Highly Selective Alcohol and Water Sensor with Large Fluorescence Signal Contrast.

PubMed

Chung, Kyeongwoon; Yang, Da Seul; Jung, Jaehun; Seo, Deokwon; Kwon, Min Sang; Kim, Jinsang

2016-10-06

Differentiation of solvents having similar physicochemical properties, such as ethanol and methanol, is an important issue of interest. However, without performing chemical analyses, discrimination between methanol and ethanol is highly challenging due to their similarity in chemical structure as well as properties. Here, we present a novel type of alcohol and water sensor based on the subtle differences in interaction among solvent analytes, fluorescent organic molecules, and a mesoporous silica gel substrate. A gradual change in the chemical structure of the fluorescent diketopyrrolopyrrole (DPP) derivatives alters their interaction with the substrate and solvent analyte, which creates a distinct intermolecular aggregation of the DPP derivatives on the silica gel substrate depending on the solvent environment and produces a change in the fluorescence color and intensity as a sensory signal. The devised sensor device, which is fabricated with simple drop-casting of the DPP derivative solutions onto a silica gel substrate, exhibited a completely reversible fluorescence signal change with large fluorescence signal contrast, which allows selective solvent detection by simple optical observation with the naked eye under UV light. Superior selectivity of the alcohol and water sensor system, which can clearly distinguish among ethanol, methanol, ethylene glycol, and water, is demonstrated.

Observation of steric hindrance effect controlling crystal packing structures and physical properties in three new isomeric nitronyl nitroxide radicals

NASA Astrophysics Data System (ADS)

Zhao, Hai-Rong; Sun, Jia-Sen; Sui, Yun-Xia; Ren, Xiao-Ming; Yao, Bin-Qian; Shen, Lin-Jiang; Meng, Qing-Jin

2009-07-01

Three isomeric nitronyl nitroxide radical compounds, 2-[ n-( N-benzyl)pyridinium]-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide bromide ( n = 2, 3 and 4 for 1, 2 and 3, respectively), have been synthesized and structurally characterized. The influence of steric hindrance on the molecular packing structures and physical properties has been observed. In the radical 1, such steric hindrance leads to a folding conformation of the imidazoline and benzene rings and the intramolecular C-H…π interaction between the methyl group and the benzene ring. There is no such effect in 2 and 3. In crystal of 2, there are the intermolecular C-H…π between methyl groups and benzene ring and intermolecular π…π stacking interaction between pyridine and benzene rings. Crystal of 2 with a chiral space group P2 12 12 1 shows the SHG response about 0.4 times as that of urea. In crystal of 3, there are three symmetry-independent radical molecules, which form an unusually six-membered supramolecular ring via intermolecular O…π interactions. For the solid sample of 3, the X-band EPR exhibits an axially symmetric signal and magnetic susceptibility data suggest intermolecular antiferromagnetic (AFM) coupling interactions and very weak intermolecular ferromagnetic (FM) coupling interactions which is more likely caused by magnetic anisotropy, while measurements of both 1 and 2 show isotropic X-band EPR signals and simple Currie-Weiss magnetic behavior.

Intermolecular cleavage by UmuD-like mutagenesis proteins

PubMed Central

McDonald, John P.; Frank, Ekaterina G.; Levine, Arthur S.; Woodgate, Roger

1998-01-01

The activity of a number of proteins is regulated by self-processing reactions. Elegant examples are the cleavage of the prokaryotic LexA and λCI transcriptional repressors and the UmuD-like mutagenesis proteins. Various studies support the hypothesis that LexA and λCI cleavage reactions are predominantly intramolecular in nature. The recently described crystal structure of the Escherichia coli UmuD′ protein (the posttranslational cleavage product of the UmuD protein) suggests, however, that the region of the protein corresponding to the cleavage site is at least 50 Å away from the catalytic active site. We considered the possibility, therefore, that the UmuD-like proteins might undergo self-processing that, in contrast to LexA and λCI, occurs via an intermolecular rather than intramolecular reaction. To test this hypothesis, we introduced into E. coli compatible plasmids with mutations at either the cleavage or the catalytic site of three UmuD-like proteins. Cleavage of these proteins only occurs in the presence of both plasmids, indicating that the reaction is indeed intermolecular in nature. Furthermore, this intermolecular reaction is completely dependent upon the multifunctional RecA protein and leads to the restoration of cellular mutagenesis in nonmutable E. coli strains. Intermolecular cleavage of a biotinylated UmuD active site mutant was also observed in vitro in the presence of the wild-type UmuD′ protein, indicating that in addition to the intact UmuD protein, the normal cleavage product (UmuD′) can also act as a classical enzyme. PMID:9465040

Rotational study of the NH{sub 3}–CO complex: Millimeter-wave measurements and ab initio calculations

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

Surin, L. A., E-mail: surin@ph1.uni-koeln.de; Institute of Spectroscopy, Russian Academy of Sciences, Fizicheskaya Str. 5, 142190 Troitsk, Moscow; Potapov, A.

2015-03-21

The rotational spectrum of the van der Waals complex NH{sub 3}–CO has been measured with the intracavity OROTRON jet spectrometer in the frequency range of 112–139 GHz. Newly observed and assigned transitions belong to the K = 0–0, K = 1–1, K = 1–0, and K = 2–1 subbands correlating with the rotationless (j{sub k}){sub NH3} = 0{sub 0} ground state of free ortho-NH{sub 3} and the K = 0–1 and K = 2–1 subbands correlating with the (j{sub k}){sub NH3} = 1{sub 1} ground state of free para-NH{sub 3}. The (approximate) quantum number K is the projection of themore » total angular momentum J on the intermolecular axis. Some of these transitions are continuations to higher J values of transition series observed previously [C. Xia et al., Mol. Phys. 99, 643 (2001)], the other transitions constitute newly detected subbands. The new data were analyzed together with the known millimeter-wave and microwave transitions in order to determine the molecular parameters of the ortho-NH{sub 3}–CO and para-NH{sub 3}–CO complexes. Accompanying ab initio calculations of the intermolecular potential energy surface (PES) of NH{sub 3}–CO has been carried out at the explicitly correlated coupled cluster level of theory with single, double, and perturbative triple excitations and an augmented correlation-consistent triple zeta basis set. The global minimum of the five-dimensional PES corresponds to an approximately T-shaped structure with the N atom closest to the CO subunit and binding energy D{sub e} = 359.21 cm{sup −1}. The bound rovibrational levels of the NH{sub 3}–CO complex were calculated for total angular momentum J = 0–6 on this intermolecular potential surface and compared with the experimental results. The calculated dissociation energies D{sub 0} are 210.43 and 218.66 cm{sup −1} for ortho-NH{sub 3}–CO and para-NH{sub 3}–CO, respectively.« less

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

Mamedov, Bahtiyar A.; Somuncu, Elif; Askerov, Iskender M.

In this work, a new theoretical approach is proposed for calculating fourth virial coefficient with Lennard-Jones potential. The established algorithm can be used to evaluate the thermodynamics properties and the intermolecular interaction potentials of liquids and gases with an improved accuracy. Note that the evaluation of the high-order virial coefficients is very valuable for accurate calculation of thermodynamic parameters. By using the suggested method, the fourth virial coefficient of CH{sub 4}, Ar, C{sub 2}H{sub 6} and SF{sub 6} molecules are evaluated. The calculation results are useful for accurate interpretation of the experimental data and of the determination of related physicalmore » properties.« less

Microscopic approaches to liquid nitromethane detonation properties.

PubMed

Hervouët, Anaïs; Desbiens, Nicolas; Bourasseau, Emeric; Maillet, Jean-Bernard

2008-04-24

In this paper, thermodynamic and chemical properties of nitromethane are investigated using microscopic simulations. The Hugoniot curve of the inert explosive is computed using Monte Carlo simulations with a modified version of the adaptative Erpenbeck equation of state and a recently developed intermolecular potential. Molecular dynamic simulations of nitromethane decomposition have been performed using a reactive potential, allowing the calculation of kinetic rate constants and activation energies. Finally, the Crussard curve of detonation products as well as thermodynamic properties at the Chapman-Jouguet (CJ) point are computed using reactive ensemble Monte Carlo simulations. Results are in good agreement with both thermochemical calculations and experimental measurements.

Temperature dependent fluorescence spectra arise from change in excited-state intramolecular proton transfer potential of 4‧-N,N-dimethylamino-3-hydroxyflavone-doped acetonitrile crystals

NASA Astrophysics Data System (ADS)

Furukawa, Kazuki; Yamamoto, Norifumi; Hino, Kazuyuki; Sekiya, Hiroshi

2016-01-01

The effect of intermolecular interaction on excited-state intramolecular proton transfer (ESIPT) in 4‧-N,N-dimethylamino-3-hydroxyflavone (DMHF) doped in acetonitrile crystals was investigated by measuring the temperature dependence of fluorescence excitation and fluorescence spectra. A solid/solid phase transition of DMHF-doped acetonitrile crystals occurred in the temperature between 210 and 218 K. Significant differences in the spectral profiles and shifts in the fluorescence spectra were observed in the low- and high-temperature regions of the phase transition. The temperature dependence of the ESIPT potential of DMHF is discussed.

Theoretical insights into the structures and mechanical properties of HMX/NQ cocrystal explosives and their complexes, and the influence of molecular ratios on their bonding energies.

PubMed

Li, Yong-Xiang; Chen, Shu-Sen; Ren, Fu-de

2015-09-01

Molecular dynamics (MD) methods were employed to study the binding energies and mechanical properties of selected crystal planes of 1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane (HMX)/nitroguanidine (NQ) cocrystals at different molecular molar ratios. The densities and detonation velocities of the cocrystals at different molar ratios were estimated. The intermolecular interaction and bond dissociation energy (BDE) of the N-NO2 bond in the HMX:NQ (1:1) complex were calculated using the B3LYP, MP2(full) and M06-2X methods with the 6-311++G(d,p) and 6-311++G(2df,2p) basis sets. The results indicated that the HMX/NQ cocrystal prefers cocrystalizing in a 1:1 molar ratio, and the cocrystallization is dominated by the (0 2 0) and (1 0 0) facets. The K, G, and E values of the ratio of 1:1 are smaller than those of the other ratios, and the 1:1 cocrystal has the best ductility. The N-NO2 bond becomes stronger upon the formation of the intermolecular H-bonding interaction and the sensitivity of HMX decreases in the cocrystal. This sensitivity change in the HMX/NQ cocrystal originates not only from the formation of the intermolecular interaction but also from the increment of the BDE of N-NO2 bond in comparison with isolated HMX. The HMX/NQ (1:1) cocrystal exhibits good detonation performance. Reduced density gradient (RDG) reveals the nature of cocrystallization. Analysis of the surface electrostatic potential further confirmed that the sensitivity decreases in complex (or cocrystal) in comparison with that in isolated HMX.

Boron nitride nanotubes for delivery of 5-fluorouracil as anticancer drug: a theoretical study

NASA Astrophysics Data System (ADS)

Shayan, Kolsoom; Nowroozi, Alireza

2018-01-01

The electronic structure and properties of the armchair boron nitride nanotubes (BNNTs) interacted with the 5-FU drug, as an anticancer drug, are studied at the B3LYP/6-31G(d,p) level of theory. D3-Corrections were carried out for the treatment of intermolecular interactions in the hybrid complexes and encapsulated nanotubes, exactly. Results have shown that the encapsulation and adsorption of 5-FU molecule on the studied BNNTs surface are favorable processes, with a few exceptions. Also, it is found that the encapsulated nanotubes are stable than the hybrid complexes. Furthermore, we estimated the strengths of the intermolecular bonds of the benchmark systems by energetic, geometric, topological and molecular orbital descriptors. Some analyses have been made to explore any changes in the binding characteristics of the drug molecule after its attachment to the nanotubes. According to the NBO results, the charge transfer phenomenon is observed from the bonding or nonbonding orbitals of drug to the antibonding orbitals of BNNTs. Moreover, HOMO-LUMO analysis indicated that, after the adsorption process, the HOMO value slightly increased, while the LUMO value in these systems significantly reduced in the both of Drug@BNNTs groups. So, the energy gaps between HOMO and LUMO (Eg) are reduced, which emphasis on the greater intermolecular bond strength. Finally, the stability and reactivity of the Drug@BNNTs complexes have been examined from the magnitudes of the chemical reactivity descriptors such as chemical potential, global hardness, and electrophilicity index. As a consequence, BNNTs can be considered as a drug delivery vehicle for the transportation of 5-FU as anticancer drug within the biological systems.

Proton storage site in bacteriorhodopsin: new insights from QM/MM simulations of microscopic pKa and infrared spectra

PubMed Central

Goyal, Puja; Ghosh, Nilanjan; Phatak, Prasad; Clemens, Maike; Gaus, Michael; Elstner, Marcus; Cui, Qiang

2011-01-01

Identifying the group that acts as the proton storage/loading site is a challenging but important problem for understanding the mechanism of proton pumping in biomolecular proton pumps, such as bacteriorhodopsin (bR) and cytochrome c oxidase. Recent experimental studies of bR propelled the idea that the proton storage/release group (PRG) in bR is not an amino acid but a water cluster embedded in the protein. We argue that this idea is at odds with our knowledge of protein electrostatics, since invoking the water cluster as PRG would require the protein to raise the pKa of a hydronium by almost 11 pKa units, which is difficult considering known cases of pKa shifts in proteins. Our recent QM/MM simulations suggested an alternative “intermolecular proton bond” model in which the stored proton is shared between two conserved Glu residues (194 and 204). Here we show that this model leads to microscopic pKa values consistent with available experimental data and the functional requirement of a PRG. Extensive QM/MM simulations also show that, independent of a number of technical issues, such as the influence of QM region size, starting x-ray structure and nuclear quantum effects, the “intermolecular proton bond” model is qualitatively consistent with available spectroscopic data. Potential of mean force calculations show explicitly that the stored proton strongly prefers the pair of Glu residues over the water cluster. The results and analyses help highlight the importance of considering protein electrostatics and provide arguments for why the “intermolecular proton bond” model is likely applicable to PRG in biomolecular proton pumps in general. PMID:21761868

Theoretical studies on the coupling interactions in H2SO4···HOO˙···(H2O)n (n = 0-2) clusters: toward understanding the role of water molecules in the uptake of HOO˙ radical by sulfuric acid aerosols.

PubMed

Li, Ping; Ma, Zhiying; Wang, Weihua; Zhai, Yazhou; Sun, Haitao; Bi, Siwei; Bu, Yuxiang

2011-01-21

A detailed knowledge of coupling interactions among sulfuric acid (H(2)SO(4)), the hydroperoxyl radical (HOO˙), and water molecules (H(2)O) is crucial for the better understanding of the uptake of HOO˙ radicals by sulfuric acid aerosols at different atmospheric humidities. In the present study, the equilibrium structures, binding energies, equilibrium distributions, and the nature of the coupling interactions in H(2)SO(4)···HOO˙···(H(2)O)(n) (n = 0-2) clusters have been systematically investigated at the B3LYP/6-311++G(3df,3pd) level of theory in combination with the atoms in molecules (AIM) theory, natural bond orbital (NBO) method, energy decomposition analyses, and ab initio molecular dynamics. Two binary, five ternary, and twelve tetramer clusters possessing multiple intermolecular H-bonds have been located on their potential energy surfaces. Two different modes for water molecules have been observed to influence the coupling interactions between H(2)SO(4) and HOO˙ through the formations of intermolecular H-bonds with or without breaking the original intermolecular H-bonds in the binary H(2)SO(4)···HOO˙ cluster. It was found that the introduction of one or two water molecules can efficiently enhance the interactions between H(2)SO(4) and HOO˙, implying the positive role of water molecules in the uptake of the HOO˙ radical by sulfuric acid aerosols. Additionally, the coupling interaction modes of the most stable clusters under study have been verified by the ab initio molecular dynamics.

Topology-based modeling of intrinsically disordered proteins: balancing intrinsic folding and intermolecular interactions.

PubMed

Ganguly, Debabani; Chen, Jianhan

2011-04-01

Coupled binding and folding is frequently involved in specific recognition of so-called intrinsically disordered proteins (IDPs), a newly recognized class of proteins that rely on a lack of stable tertiary fold for function. Here, we exploit topology-based Gō-like modeling as an effective tool for the mechanism of IDP recognition within the theoretical framework of minimally frustrated energy landscape. Importantly, substantial differences exist between IDPs and globular proteins in both amino acid sequence and binding interface characteristics. We demonstrate that established Gō-like models designed for folded proteins tend to over-estimate the level of residual structures in unbound IDPs, whereas under-estimating the strength of intermolecular interactions. Such systematic biases have important consequences in the predicted mechanism of interaction. A strategy is proposed to recalibrate topology-derived models to balance intrinsic folding propensities and intermolecular interactions, based on experimental knowledge of the overall residual structure level and binding affinity. Applied to pKID/KIX, the calibrated Gō-like model predicts a dominant multistep sequential pathway for binding-induced folding of pKID that is initiated by KIX binding via the C-terminus in disordered conformations, followed by binding and folding of the rest of C-terminal helix and finally the N-terminal helix. This novel mechanism is consistent with key observations derived from a recent NMR titration and relaxation dispersion study and provides a molecular-level interpretation of kinetic rates derived from dispersion curve analysis. These case studies provide important insight into the applicability and potential pitfalls of topology-based modeling for studying IDP folding and interaction in general. Copyright © 2011 Wiley-Liss, Inc.

Applications of nuclear magnetic resonance spectroscopy for the understanding of enantiomer separation mechanisms in capillary electrophoresis.

PubMed

Salgado, Antonio; Chankvetadze, Bezhan

2016-10-07

This review deals with the applications of nuclear magnetic resonance (NMR) spectroscopy to understand the mechanisms of chiral separation in capillary electrophoresis (CE). It is accepted that changes observed in the separation process, including the reversal of enantiomer migration order (EMO), can be caused by subtle modifications in the molecular recognition mechanisms between enantiomer and chiral selector. These modifications may imply minor structural differences in those selector-selectand complexes that arise from the above mentioned interactions. Therefore, it is mandatory to understand the fine intermolecular interactions between analytes and chiral selectors. In other words, it is necessary to know in detail the structures of the complexes formed by the enantiomer (selectand) and the selector. Any differences in the structures of these complexes arising from either enantiomer should be detected, so that enantiomeric bias in the separation process could be explained. As to the nature of these interactions, those have been extensively reviewed, and it is not intended to be discussed here. These interactions contemplate ionic, ion-dipole and dipole-dipole interactions, hydrogen bonding, van der Waals forces, π-π stacking, steric and hydrophobic interactions. The main subject of this review is to describe how NMR spectroscopy helps to gain insight into the non-covalent intermolecular interactions between selector and selectand that lead to enantiomer separation by CE. Examples in which diastereomeric species are created by covalent (irreversible) derivatization will not be considered here. This review is structured upon the different structural classes of chiral selectors employed in CE, in which NMR spectroscopy has made substantial contributions to rationalize the observed enantioseparations. Cases in which other techniques complement NMR spectroscopic data are also mentioned. Copyright © 2016 Elsevier B.V. All rights reserved.

Relating hydrogen-bonding interactions with the phase behavior of naproxen/PVP K 25 solid dispersions: evaluation of solution-cast and quench-cooled films.

PubMed

Paudel, Amrit; Nies, Erik; Van den Mooter, Guy

2012-11-05

In this work, we investigated the relationship between various intermolecular hydrogen-bonding (H-bonding) interactions and the miscibility of the model hydrophobic drug naproxen with the hydrophilic polymer polyvinylpyrrolidone (PVP) across an entire composition range of solid dispersions prepared by quasi-equilibrium film casting and nonequilibrium melt quench cooling. The binary phase behavior in solid dispersions exhibited substantial processing method dependence. The solid state solubility of crystalline naproxen in PVP to form amorphous solid dispersions was 35% and 70% w/w naproxen in solution-cast films and quench-cooled films, respectively. However, the presence of a single mixed phase glass transition indicated the amorphous miscibility to be 20% w/w naproxen for the films, beyond which amorphous-amorphous and/or crystalline phase separations were apparent. This was further supported by the solution state interactions data such as PVP globular size distribution and solution infrared spectral profiles. The borderline melt composition showed cooling rate dependence of amorphization. The glass transition and melting point depression profiles of the system were treated with the analytical expressions based on Flory-Huggins mixing theory to interpolate the equilibrium solid solubility. FTIR analysis and subsequent spectral deconvolution revealed composition and miscibility dependent variations in the strength of drug-polymer intermolecular H-bonding. Two types of H-bonded populations were evidenced from 25% w/w and 35% w/w naproxen in solution-cast films and quench-cooled films, respectively, with the higher fraction of strongly H-bonded population in the drug rich domains of phase separated amorphous film compositions and highly drug loaded amorphous quench-cooled dispersions.

Accurately predicting the structure, density, and hydrostatic compression of crystalline β-1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane based on its wave-function-based potential

NASA Astrophysics Data System (ADS)

Song, H.-J.; Huang, F.

2011-09-01

A wave-function-based intermolecular potential of the β phase 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX) molecule has been constructed from first principles using the Williams-Stone-Misquitta method and the symmetry-adapted perturbation theory. Using the potential and its derivatives, we have accurately predicted not only the structure and lattice energy of the crystalline β-HMX at 0 K, but also its densities at temperatures of 0-403 K within an accuracy of 1% of density. The calculated densities at pressures within 0-6 GPa excellently agree with the results from the experiments on hydrostatic compression.

On the accuracy of the 'decoupled l-dominant' approximation for atom-molecule scattering

NASA Technical Reports Server (NTRS)

Green, S.

1976-01-01

Cross sections for rotational excitation and spectral pressure broadening of HD, HCl, CO, and HCN due to collisions with low energy He atoms have been computed within the 'decoupled l-dominant' (DLD) approximation and are compared with accurate close coupling results and also with two similar approximations, the effective potential of Rabitz and the coupled states of McGuire and Kouri. DLD predictions of state-to-state cross sections are rather good, being only slightly less accurate than coupled states results. DLD is far superior to either the coupled states or effective potential methods for pressure broadening calculations, although it may not be uniformly of the quantitative accuracy desirable for obtaining intermolecular potentials from experimental data.

Synthesis of benzimidazoles by potassium tert-butoxide-promoted intermolecular cyclization reaction of 2-iodoanilines with nitriles.

PubMed

Xiang, Shi-Kai; Tan, Wen; Zhang, Dong-Xue; Tian, Xian-Li; Feng, Chun; Wang, Bi-Qin; Zhao, Ke-Qing; Hu, Ping; Yang, Hua

2013-11-14

The synthesis of benzimidazoles by intermolecular cyclization reaction of 2-iodoanilines with nitriles has been developed. These reactions proceeded without the aid of any transition metals or ligands and just using KOBu(t) as the base. A variety of substituted benzimidazole derivatives can be synthesized by the approach.

A Hands-On Activity to Build Mastery of Intermolecular Forces and Its Impacts on Student Learning

ERIC Educational Resources Information Center

Bruck, Laura B.

2016-01-01

The intermolecular forces activity presented in this article is designed to foster concept-building through students' use of concrete, manipulative objects, and it was developed to be pedagogically sound. Data analysis via pre- and posttesting and subsequent exam questions indicated that students who had the opportunity to participate in the…

Intermolecular Slip Mechanism in Tropocollagen Nanofibrils

DTIC Science & Technology

2009-01-01

Imperfecta or Ehlers - Danlos Syndrome . REPORT DOCUMENTATION PAGE (SF298) (Continuation Sheet) Continuation for Block 13 ARO Report Number Intermolecular slip...our studies could advance our knowledge of mechan- isms underlying important collagen-related diseases like Osteogenesis Imperfecta or Ehlers - Danlos ... Syndrome . Keywords: Collagen; Shear; Nanomechanics; Steered mo- lecular dynamics; Adhesion strength; Materiomics 1. Introduction Collagen is the

Methyl (4-bromo-benzene-sulfonamido)acetate.

PubMed

Arshad, Muhammad Nadeem; Tahir, M Nawaz; Khan, Islam Ullah; Ahmad, Ejaz; Shafiq, Muhammad

2008-11-20

The title compound, C(9)H(10)BrNO(4)S, is an inter-mediate for the formation of benzothia-zines. In the crystal structure, inter-molecular N-H⋯O hydrogen bonds link the mol-ecules, forming R(2) (2)(10) ring motifs, which are linked into a two-dimensional polymeric sheet through inter-molecular C-H⋯O hydrogen bonds.

Salting Effects as an Illustration of the Relative Strength of Intermolecular Forces

ERIC Educational Resources Information Center

Person, Eric C.; Golden, Donnie R.; Royce, Brenda R.

2010-01-01

This quick and inexpensive demonstration of the salting of an alcohol out of an aqueous solution illustrates the impact of intermolecular forces on solubility using materials familiar to many students. Ammonium sulfate (fertilizer) is added to an aqueous 35% solution of isopropyl alcohol (rubbing alcohol and water) containing food coloring as a…

Real-space identification of intermolecular bonding with atomic force microscopy.

PubMed

Zhang, Jun; Chen, Pengcheng; Yuan, Bingkai; Ji, Wei; Cheng, Zhihai; Qiu, Xiaohui

2013-11-01

We report a real-space visualization of the formation of hydrogen bonding in 8-hydroxyquinoline (8-hq) molecular assemblies on a Cu(111) substrate, using noncontact atomic force microscopy (NC-AFM). The atomically resolved molecular structures enable a precise determination of the characteristics of hydrogen bonding networks, including the bonding sites, orientations, and lengths. The observation of bond contrast was interpreted by ab initio density functional calculations, which indicated the electron density contribution from the hybridized electronic state of the hydrogen bond. Intermolecular coordination between the dehydrogenated 8-hq and Cu adatoms was also revealed by the submolecular resolution AFM characterization. The direct identification of local bonding configurations by NC-AFM would facilitate detailed investigations of intermolecular interactions in complex molecules with multiple active sites.

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

PubMed Central

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

2012-01-01

We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4′-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed method is shown to be efficient and accurate in the evaluation of the protein-ligand interaction energies. PMID:23050059

Communication: Density functional theory overcomes the failure of predicting intermolecular interaction energies

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

Podeszwa, Rafal; Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716; Szalewicz, Krzysztof

2012-04-28

Density-functional theory (DFT) revolutionized the ability of computational quantum mechanics to describe properties of matter and is by far the most often used method. However, all the standard variants of DFT fail to predict intermolecular interaction energies. In recent years, a number of ways to go around this problem has been proposed. We show that some of these approaches can reproduce interaction energies with median errors of only about 5% in the complete range of intermolecular configurations. Such errors are comparable to typical uncertainties of wave-function-based methods in practical applications. Thus, these DFT methods are expected to find broad applicationsmore » in modelling of condensed phases and of biomolecules.« less

Intra- and intermolecular fluorescence quenching of N-activated 4,5-dimethoxyphthalimides by sulfides, amines, and alkyl carboxylates.

PubMed

Griesbeck, Axel G; Schieffer, Stefan

2003-02-01

The fluorescent 4,5-dimethoxyphthalimides 1-10 were applied as sensors for intra- and intermolecular photoinduced electron transfer processes. Strong intramolecular fluorescence quenching was detected for the thioether 2 and the tertiary amine 3. The fluorescence of the carboxylic acids 4-7 is pH-dependent accounting for PET-quenching of the singlet excited phthalimide at pH > pKs. At low pH, chromophore protonation might contribute to moderate fluorescence quenching. The arylated phthalimides 9 and 10 show remarkable low fluorescence independent of pH and substituent pattern. Intermolecular fluorescence quenching was detected for the combinations of 1 with dimethyl sulfide, and 1 with triethylamine but not with metal carboxylates.

The study of intermolecular interactions in NLO crystal melaminium chloride hemihydrate using DFT simulation and Hirshfeld surface analysis

NASA Astrophysics Data System (ADS)

Sangeetha, K.; Kumar, V. R. Suresh; Marchewka, M. K.; Binoy, J.

2018-05-01

Since, the intermolecular interactions play a crucial role in the formation of crystalline network, its analysis throws light on structure dependent crystalline properties. In the present study, DFT based vibrational spectral investigation has been performed in the stretching region (3500 cm-1 - 2800 cm-1) of IR and Raman spectra of melaminium chloride hemihydrates. The intermolecular interaction has been investigated by analyzing the half width of the OH and NH stretching profile of the deconvoluted spectra. Correlation of vibrational spectra with Hirshfeld surface analysis and finger print plot has been contemplated and molecular docking studies has been performed on melaminium chloride hemihydrate to assess its role in the drug transport mechanism and toxicity to human body.

Solute-solvent contact by intermolecular cross relaxation. I. The nature of the water-hydrophobic interface.

PubMed

Nordstierna, Lars; Yushmanov, Pavel V; Furó, István

2006-08-21

Intermolecular cross-relaxation rates between solute and solvent were measured by {1H} 19F nuclear magnetic resonance experiments in aqueous molecular solutions of ammonium perfluoro-octanoate and sodium trifluoroacetate. The experiments performed at three different magnetic fields provide frequency-dependent cross-relaxation rates which demonstrate clearly the lack of extreme narrowing for nuclear spin relaxation by diffusionally modulated intermolecular interactions. Supplemented by suitable intramolecular cross-relaxation, longitudinal relaxation, and self-diffusion data, the obtained cross-relaxation rates are evaluated within the framework of recent relaxation models and provide information about the hydrophobic hydration. In particular, water dynamics around the trifluoromethyl group in ammonium perfluoro-octanoate are more retarded than that in the smaller trifluoroacetate.

The water dimer II: Theoretical investigations

NASA Astrophysics Data System (ADS)

Mukhopadhyay, Anamika; Xantheas, Sotiris S.; Saykally, Richard J.

2018-05-01

As the archetype of aqueous hydrogen bonding, the water dimer has been extensively studied by both theory and experiment for nearly seven decades. In this article, we present a detailed chronological review of the theoretical advances made using electronic structure methods to address the structure, hydrogen bonding and vibrational spectroscopy of the water dimer, as well as the role of its potential energy surface in the development of classical force fields to describe intermolecular interactions in clusters and the condensed phases of water.

Computer simulation study of the nematic-vapour interface in the Gay-Berne model

NASA Astrophysics Data System (ADS)

Rull, Luis F.; Romero-Enrique, José Manuel

2017-06-01

We present computer simulations of the vapour-nematic interface of the Gay-Berne model. We considered situations which correspond to either prolate or oblate molecules. We determine the anchoring of the nematic phase and correlate it with the intermolecular potential parameters. On the other hand, we evaluate the surface tension associated to this interface. We find a corresponding states law for the surface tension dependence on the temperature, valid for both prolate and oblate molecules.

Limiting assumptions in molecular modeling: electrostatics.

PubMed

Marshall, Garland R

2013-02-01

Molecular mechanics attempts to represent intermolecular interactions in terms of classical physics. Initial efforts assumed a point charge located at the atom center and coulombic interactions. It is been recognized over multiple decades that simply representing electrostatics with a charge on each atom failed to reproduce the electrostatic potential surrounding a molecule as estimated by quantum mechanics. Molecular orbitals are not spherically symmetrical, an implicit assumption of monopole electrostatics. This perspective reviews recent evidence that requires use of multipole electrostatics and polarizability in molecular modeling.

Meroterpenes from Marine Invertebrates: Structures, Occurrence, and Ecological Implications

PubMed Central

Menna, Marialuisa; Imperatore, Concetta; D’Aniello, Filomena; Aiello, Anna

2013-01-01

Meroterpenes are widely distributed among marine organisms; they are particularly abundant within brown algae, but other important sources include microorganisms and invertebrates. In the present review the structures and bioactivities of meroterpenes from marine invertebrates, mainly sponges and tunicates, are summarized. More than 300 molecules, often complex and with unique skeletons originating from intra- and inter-molecular cyclizations, and/or rearrangements, are illustrated. The reported syntheses are mentioned. The issue of a potential microbial link to their biosynthesis is also shortly outlined. PMID:23685889

An Intermolecular H-O Potential for Methyl Rotations in Solid Nitromethane

DTIC Science & Technology

1991-04-01

and Schiferl (1985). 3. DISCUSSION It is difficult to speculate on the origin of the various features (especially that at 3.5 A) of the final H-O...of nitromethane at room temperature and pressures up to 6 GPa has been investigated with single crystal X-ray diffraction (Cromer, Ryan, and Schiferl ...this purpose (Model Ill) is constructed from the coordinates in Table 3, 11 (Cromer, Ryan, and Schiferl 1985) at 3.5 GPa. The values of the internal

The Water Dimer II: Theoretical Investigations

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

Mukhopadhyay, Anamika; Xantheas, Sotiris S.; Saykally, Richard J.

As the archetype of aqueous hydrogen bonding, the water dimer has been extensively studied by both theory and experiment for nearly seven decades. Here in this article, we present a detailed chronological review of the theoretical advances made using electronic structure methods to address the structure, hydrogen bonding and vibrational spectroscopy of the water dimer, as well as the role of its potential energy surface in the development of classical force fields to describe intermolecular interaction in clusters and the condensed phases of water.

The Water Dimer II: Theoretical Investigations

DOE PAGES

Mukhopadhyay, Anamika; Xantheas, Sotiris S.; Saykally, Richard J.

2018-03-29

As the archetype of aqueous hydrogen bonding, the water dimer has been extensively studied by both theory and experiment for nearly seven decades. Here in this article, we present a detailed chronological review of the theoretical advances made using electronic structure methods to address the structure, hydrogen bonding and vibrational spectroscopy of the water dimer, as well as the role of its potential energy surface in the development of classical force fields to describe intermolecular interaction in clusters and the condensed phases of water.

A theoretical investigation into the strength of N-NO2 bonds, ring strain and electrostatic potential upon formation of intermolecular H-bonds between HF and the nitro group in nitrogen heterocyclic rings C n H2n N-NO2 (n = 2-5), RDX and HMX.

PubMed

Wang, Bao-Guo; Ren, Fu-de; Shi, Wen-Jing

2015-11-01

Changes in N-NO2 bond strength, ring strain energy and electrostatic potential upon formation of intermolecular H-bonds between HF and the nitro group in nitrogen heterocyclic rings C n H2n N-NO2 (n = 2-5), RDX and HMX were investigated using DFT-B3LYP and MP2(full) methods with the 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. Analysis of electron density shifts was also carried out. The results indicate that H-bonding energy correlates well with the increment of ring strain energy. Upon complex formation, the strength of the N-NO2 trigger-bond is enhanced, suggesting reduced sensitivity, while judged by the increased ring strain energy, sensitivity is increased. However, some features of the molecular surface electrostatic potential, such as a local maximum above the N-NO2 bond and ring, σ + (2) and electrostatic balance parameter ν, remain essentially unchanged upon complex formation, and only a small change in the impact sensitivity h 50 is suggested. It is not sufficient to determine sensitivity solely on the basis of trigger bond or ring strain; as a global feature of a molecule, the molecular surface electrostatic potential is available to help judge the change of sensitivity in H-bonded complexes. Graphical Abstract The strengthened N-NO2 bond suggests reduced sensitivity, while it is reverse by theincreased ring strain energy upon the complex formation. However, the molecular surfaceelectrostatic potential (V S) shows the little change of h 50. The V S should be taken into accountin the analysis of explosive sensitivity in the H-bonded complex.

Mechanism of intermolecular hydroacylation of vinylsilanes catalyzed by a rhodium(I) olefin complex: a DFT study.

PubMed

Meng, Qingxi; Shen, Wei; Li, Ming

2012-03-01

Density functional theory (DFT) was used to investigate the Rh(I)-catalyzed intermolecular hydroacylation of vinylsilane with benzaldehyde. All intermediates and transition states were optimized completely at the B3LYP/6-31G(d,p) level (LANL2DZ(f) for Rh). Calculations indicated that Rh(I)-catalyzed intermolecular hydroacylation is exergonic, and the total free energy released is -110 kJ mol(-1). Rh(I)-catalyzed intermolecular hydroacylation mainly involves the active catalyst CA2, rhodium-alkene-benzaldehyde complex M1, rhodium-alkene-hydrogen-acyl complex M2, rhodium-alkyl-acyl complex M3, rhodium-alkyl-carbonyl-phenyl complex M4, rhodium-acyl-phenyl complex M5, and rhodium-ketone complex M6. The reaction pathway CA2 + R2 → M1b → T1b → M2b → T2b1 → M3b1 → T4b → M4b → T5b → M5b → T6b → M6b → P2 is the most favorable among all reaction channels of Rh(I)-catalyzed intermolecular hydroacylation. The reductive elimination reaction is the rate-determining step for this pathway, and the dominant product predicted theoretically is the linear ketone, which is consistent with Brookhart's experiments. Solvation has a significant effect, and it greatly decreases the free energies of all species. The use of the ligand Cp' (Cp' = C(5)Me(4)CF(3)) decreased the free energies in general, and in this case the rate-determining step was again the reductive elimination reaction.

Development and Implementation of a Protein-Protein Binding Experiment to Teach Intermolecular Interactions in High School or Undergraduate Classrooms

ERIC Educational Resources Information Center

Johnson, Sadie M.; Javner, Cassidy; Hackel, Benjamin J.

2017-01-01

The goal of this study was to create an accessible, inexpensive, and engaging experiment to teach high school and undergraduate chemistry or biology students about intermolecular forces and how they contribute to the behavior of biomolecules. We developed an enzyme-linked immunosorbent assay (ELISA) to probe specific structure-function…

The effect of intermolecular hydrogen bonding on the fluorescence of a bimetallic platinum complex.

PubMed

Zhao, Guang-Jiu; Northrop, Brian H; Han, Ke-Li; Stang, Peter J

2010-09-02

The bimetallic platinum complexes are known as unique building blocks and arewidely utilized in the coordination-driven self-assembly of functionalized supramolecular metallacycles. Hence, photophysical study of the bimetallic platinum complexes will be very helpful for the understanding on the optical properties and further applications of coordination-driven self-assembled supramolecular metallacycles. Herein, we report steady-state and time-resolved spectroscopic experiments as well as quantum chemistry calculations to investigate the significant intermolecular hydrogen bonding effects on the intramolecular charge transfer (ICT) fluorescence of a bimetallic platinum compound 4,4'-bis(trans-Pt(PEt(3))(2)OTf)benzophenone 3 in solution. We demonstrated that the fluorescent state of compound 3 can be assigned as a metal-to-ligand charge transfer (MLCT) state. Moreover, it was observed that the formation of intermolecular hydrogen bonds can effectively lengthen the fluorescence lifetime of 3 in alcoholic solvents compared with that in hexane solvent. At the same time, the electronically excited states of 3 in solution are definitely changed by intermolecular hydrogen bonding interactions. As a consequence, we propose a new fluorescence modulation mechanism by hydrogen bonding to explain different fluorescence emissions of 3 in hydrogen-bonding solvents and nonhydrogen-bonding solvents.

Correlation of Intermolecular Acyl Transfer Reactivity with Noncovalent Lattice Interactions in Molecular Crystals: Toward Prediction of Reactivity of Organic Molecules in the Solid State.

PubMed

Krishnaswamy, Shobhana; Shashidhar, Mysore S

2018-04-06

Intermolecular acyl transfer reactivity in several molecular crystals was studied, and the outcome of the reactivity was analyzed in the light of structural information obtained from the crystals of the reactants. Minor changes in the molecular structure resulted in significant variations in the noncovalent interactions and packing of molecules in the crystal lattice, which drastically affected the facility of the intermolecular acyl transfer reactivity in these crystals. Analysis of the reactivity vs crystal structure data revealed dependence of the reactivity on electrophile···nucleophile interactions and C-H···π interactions between the reacting molecules. The presence of these noncovalent interactions augmented the acyl transfer reactivity, while their absence hindered the reactivity of the molecules in the crystal. The validity of these correlations allows the prediction of intermolecular acyl transfer reactivity in crystals and co-crystals of unknown reactivity. This crystal structure-reactivity correlation parallels the molecular structure-reactivity correlation in solution-state reactions, widely accepted as organic functional group transformations, and sets the stage for the development of a similar approach for reactions in the solid state.

Resonance energy transfer (RET)-Induced intermolecular pairing force: a tunable weak interaction and its application in SWNT separation.

PubMed

Pan, Xiaoyong; Chen, Hui; Wang, Wei Zhi; Ng, Siu Choon; Chan-Park, Mary B

2011-07-21

This paper explores evidence of an optically mediated interaction that is active in the separation mechanism of certain selective agents through consideration of the contrasting selective behaviors of two conjugated polymers with distinct optical properties. The involvement of a RET-induced intermolecular pairing force is implied by the different illumination response behaviors. The magnitude of this interaction scales with the external stimulus parameter, the illumination irradiance (I), and thus is tunable. This suggests a facile technique to modify the selectivity of polymers toward specific SWNT species by altering the polymer structure to adjust the corresponding intermolecular interaction. This is the first experimental verification and application of a RET-induced intermolecular pairing force to SWNT separation. With this kind of interaction taken into account, reasonable interpretation of some conflicting data, especially PLE maps, can be easily made. The above conclusion can be applied to other substances as long as they are electrically neutral and there is photon-induced RET between them. The significant magnitude of this interaction makes direct manipulation of molecules/particles possible and is expected to have applications in molecular engineering. © 2011 American Chemical Society

Elasticity and Strength of Biomacromolecular Crystals: Lysozyme

NASA Technical Reports Server (NTRS)

Holmes, A. M.; Witherow, W. K.; Chen, L. Q.; Chernov, A. A.

2003-01-01

The static Young modulus, E = 0.1 to 0.5 GPa, the crystal critical strength (sigma(sub c)) and its ratio to E,sigma(sub c)/E is approximately 10(exp 3), were measured for the first time for non cross-linked lysozyme crystals in solution. By using a triple point bending apparatus, we also demonstrated that the crystals were purely elastic. Softness of protein crystals built of hard macromolecules (26 GPa for lysozyme) is explained by the large size of the macromolecules as compared to the range of intermolecular forces and by the weakness of intermolecular bonds as compared to the peptide bond strength. The relatively large reported dynamic elastic moduli (approximately 8 GPa) from resonance light scattering should come from averaging over the moduli of intracrystalline water and intra- and intermolecular bonding.

Rhodium-catalyzed Intra- and Intermolecular [5+2] Cycloaddition of 3-Acyloxy-1,4-enyne and Alkyne with Concomitant 1,2-Acyloxy Migration

PubMed Central

Shu, Xing-Zhong; Li, Xiaoxun; Shu, Dongxu; Huang, Suyu; Schienebeck, Casi M.; Zhou, Xin; Robichaux, Patrick J.; Tang, Weiping

2012-01-01

A new type of rhodium-catalyzed [5+2] cycloaddition was developed for the synthesis of seven-membered rings with diverse functionalities. The ring formation was accompanied by a 1,2-acyloxy migration event. The 5- and 2-carbon components of the cycloaddition are 3-acyloxy-1,4-enynes (ACEs) and alkynes respectively. Cationic rhodium (I) catalysts worked most efficiently for the intramolecular cycloaddition, while only neutral rhodium (I) complexes could facilitate the intermolecular reaction. In both cases, electron-poor phosphite or phosphine ligands often improved the efficiency of the cycloadditions. The scope of ACEs and alkynes was investigated in both intra- and intermolecular reactions. The resulting seven-membered ring products have three double bonds that could be selectively functionalized. PMID:22364320

Diamond-like nanoparticles influence on flavonoids transport: molecular modelling

NASA Astrophysics Data System (ADS)

Plastun, Inna L.; Agandeeva, Ksenia E.; Bokarev, Andrey N.; Zenkin, Nikita S.

2017-03-01

Intermolecular interaction of diamond-like nanoparticles and flavonoids is investigated by numerical simulation. Using molecular modelling by the density functional theory method, we analyze hydrogen bonds formation and their influence on IR - spectra and structure of molecular complex which is formed due to interaction between flavonoids and nanodiamonds surrounded with carboxylic groups. Enriched adamantane (1,3,5,7 - adamantanetetracarboxylic acid) is used as an example of diamond-like nanoparticles. Intermolecular forces and structure of hydrogen bonds are investigated. IR - spectra and structure parameters of quercetin - adamantanetetracarboxylic acid molecular complex are obtained by numerical simulation using the Gaussian software complex. Received data coincide well with experimental results. Intermolecular interactions and hydrogen bonding structure in the obtained molecular complex are examined. Possibilities of flavonoids interaction with DNA at the molecular level are also considered.

Intermolecular hydrogen bonds in hetero-complexes of biologically active aromatic molecules probed by the methods of vibrational spectroscopy

NASA Astrophysics Data System (ADS)

Semenov, M. A.; Blyzniuk, Iu. N.; Bolbukh, T. V.; Shestopalova, A. V.; Evstigneev, M. P.; Maleev, V. Ya.

2012-09-01

By the methods of vibrational spectroscopy (Infrared and Raman) the investigation of the hetero-association of biologically active aromatic compounds: flavin-mononucleotide (FMN), ethidium bromide (EB) and proflavine (PRF) was performed in aqueous solutions. It was shown that between the functional groups (Cdbnd O and NH2) the intermolecular hydrogen bonds are formed in the hetero-complexes FMN-EB and FMN-PRF, additionally stabilizing these structures. An estimation of the enthalpy of Н-bonding obtained from experimental shifts of carbonyl vibrational frequencies has shown that the H-bonds do not dominate in the magnitude of experimentally measured total enthalpy of the hetero-association reactions. The main stabilization is likely due to intermolecular interactions of the molecules in these complexes and their interaction with water environment.

Subpiconewton intermolecular force microscopy.

PubMed

Tokunaga, M; Aoki, T; Hiroshima, M; Kitamura, K; Yanagida, T

1997-02-24

We refined scanning probe force microscopy to improve the sensitivity of force detection and control of probe position. Force sensitivity was increased by incorporating a cantilever with very low stiffness, 0.1 pN/ nm, which is over 1000-fold more flexible than is typically used in conventional atomic force microscopy. Thermal bending motions of the cantilever were reduced to less than 1 nm by exerting feed-back positioning with laser radiation pressure. The system was tested by measuring electrostatic repulsive forces or hydrophobic attractive forces in aqueous solutions. Subpiconewton intermolecular forces were resolved at controlled gaps in the nanometer range between the probe and a material surface. These levels of force and position sensitivity meet the requirements needed for future investigations of intermolecular forces between biological macromolecules such as proteins, lipids and DNA.

Study of molecular interactions in binary mixtures of 2-chloro-4'methoxy benzoin with various solvents through ultrasonic speed measurements

NASA Astrophysics Data System (ADS)

Thanuja, B.; Kanakam, C.; Nithya, G.

2013-12-01

Density ( ρ) and ultrasonic velocity ( U), for binary mixtures of 2-chloro-4'-methoxy benzoin with ethanol, chloroform, acetonitrile, benzene and 1,4-dioxane of different compositions have been measured at 298 K and explanation of solute solvent interactions and effect of polarity of the solvent on type of interactions are presented in this paper. From the above data, adiabatic compressibility ( β), intermolecular free length ( L f ) and relative association ( R A ) have been calculated. Other useful parameters such as excess density, excess velocity, excess intermolecular freelength and excess adiabatic compressibility have also been calculated. These parameters have been used to study the nature and extent of intermolecular interactions between component molecules in present binary mixtures.

Rh-Catalyzed Intermolecular Reactions of α-Alkyl-α-Diazo Carbonyl Compounds with Selectivity over β-Hydride Migration.

PubMed

DeAngelis, Andrew; Panish, Robert; Fox, Joseph M

2016-01-19

Rh-carbenes derived from α-diazocarbonyl compounds have found broad utility across a remarkable range of reactivity, including cyclopropanation, cyclopropenation, C-H insertions, heteroatom-hydrogen insertions, and ylide forming reactions. However, in contrast to α-aryl or α-vinyl-α-diazocarbonyl compounds, the utility of α-alkyl-α-diazocarbonyl compounds had been moderated by the propensity of such compounds to undergo intramolecular β-hydride migration to give alkene products. Especially challenging had been intermolecular reactions involving α-alkyl-α-diazocarbonyl compounds. This Account discusses the historical context and prior limitations of Rh-catalyzed reactions involving α-alkyl-α-diazocarbonyl compounds. Early studies demonstrated that ligand and temperature effects could influence chemoselectivity over β-hydride migration. However, effects were modest and conflicting conclusions had been drawn about the influence of sterically demanding ligands on β-hydride migration. More recent advances have led to a more detailed understanding of the reaction conditions that can promote intermolecular reactivity in preference to β-hydride migration. In particular, the use of bulky carboxylate ligands and low reaction temperatures have been key to enabling intermolecular cyclopropenation, cyclopropanation, carbonyl ylide formation/dipolar cycloaddition, indole C-H functionalization, and intramolecular bicyclobutanation with high chemoselectivity over β-hydride migration. Cyclic α-diazocarbonyl compounds have been shown to be particularly resilient toward β-hydride migration and are the first class of compounds that can engage in intermolecular reactivity in the presence of tertiary β-hydrogens. DFT calculations were used to propose that for cyclic α-diazocarbonyl compounds, ring constraints relieve steric interaction for intermolecular reactions and thereby accelerate the rate of intermolecular reactivity relative to intramolecular β-hydride migration. Enantioselective reactions of α-alkyl-α-diazocarbonyl compounds have been developed using bimetallic N-imido-tert-leucinate-derived complexes. The most effective complexes were found by computation and X-ray crystallography to adopt a "chiral crown" conformation in which all of the imido groups are presented on one face of the paddlewheel complex in a chiral arrangement. Insight from computational studies guided the design and synthesis of a mixed ligand paddlewheel complex, Rh2(S-PTTL)3TPA, the structure of which bears similarity to the chiral crown complex Rh2(S-PTTL)4. Rh2(S-PTTL)3TPA engages substrate classes (aliphatic alkynes, silylacetylenes, α-olefins) that are especially challenging in intermolecular reactions of α-alkyl-α-diazoesters and catalyzes enantioselective cyclopropanation, cyclopropenation, and indole C-H functionalization with yields and enantioselectivities that are comparable or superior to Rh2(S-PTTL)4. The work detailed in this Account describes progress toward enabling a more general utility for α-alkyl-α-diazo compounds in Rh-catalyzed carbene reactions. Further studies on ligand design and synthesis will continue to broaden the scope of their selective reactions.

Low-frequency collective dynamics in deep eutectic solvents of acetamide and electrolytes: a femtosecond Raman-induced Kerr effect spectroscopic study.

PubMed

Biswas, Ranjit; Das, Anuradha; Shirota, Hideaki

2014-10-07

In this study, we have investigated the ion concentration dependent collective dynamics in two series of deep eutectic solvent (DES) systems by femtosecond Raman-induced Kerr effect spectroscopy, as well as some physical properties, e.g., shear viscosity (η), density (ρ), and surface tension (γ). The DES systems studied here are [0.75CH3CONH2 + 0.25{f KSCN + (1 - f )NaSCN}] and [0.78CH3CONH2 + 0.22{f LiBr + (1 - f )LiNO3}] with f = 0, 0.2, 0.4, 0.6, 0.8, and 1.0. γ of these DES systems shows near insensitivity to f, while ρ shows a moderate dependence on f. Interestingly, η exhibits a strong dependence on f. In the low-frequency Kerr spectra, obtained via the Fourier transform of the collected Kerr transients, a characteristic band at ∼70 cm(-1) is clear in [0.78CH3CONH2 + 0.22{f LiBr + (1 - f )LiNO3}] DES especially at the larger f. The band is attributed to the intermolecular hydrogen bond of acetamide. Because of less depolarized Raman activities of intermolecular/interionic vibrational motions, which are mostly translational (collision-induced or interaction-induced) motions, of spherical ions, the intermolecular hydrogen-bonding band is clearly observed. In contrast, the intermolecular hydrogen-bonding band is buried in the other intermolecular/interionic vibrational motions, which includes translational and reorientational (librational) motions and their cross-terms, in [0.75CH3CONH2 + 0.25{f KSCN + (1 - f )NaSCN}] system. The first moment (M1) of the intermolecular/interionic vibrational band in these DES systems is much higher than that in typical neutral molecular liquids and shows a weak but contrasting dependence on the bulk parameter √γ/ρ. The time constants for picosecond overdamped Kerr transients in both the DES systems, which are obtained on the basis of the analysis fitted by a triexponential function, are rather insensitive to f for both the DES systems, but all the three time constants (fast: ∼1-3 ps; intermediate: ∼7-20 ps; and slow: ∼100 ps) are different between the [0.78CH3CONH2 + 0.22{f LiBr + (1 - f )LiNO3}] and [0.75CH3CONH2 + 0.25{f KSCN + (1 - f )NaSCN}] systems. These results indicate that the intermolecular/interionic interactions in DES systems is strongly influenced by the ionic species present in these DES systems.

Water pair potential of near spectroscopic accuracy. II. Vibration-rotation-tunneling levels of the water dimer

NASA Astrophysics Data System (ADS)

Groenenboom, G. C.; Wormer, P. E. S.; van der Avoird, A.; Mas, E. M.; Bukowski, R.; Szalewicz, K.

2000-10-01

Nearly exact six-dimensional quantum calculations of the vibration-rotation-tunneling (VRT) levels of the water dimer for values of the rotational quantum numbers J and K ⩽2 show that the SAPT-5s water pair potential presented in the preceding paper (paper I) gives a good representation of the experimental high-resolution far-infrared spectrum of the water dimer. After analyzing the sensitivity of the transition frequencies with respect to the linear parameters in the potential we could further improve this potential by using only one of the experimentally determined tunneling splittings of the ground state in (H2O)2. The accuracy of the resulting water pair potential, SAPT-5st, is established by comparison with the spectroscopic data of both (H2O)2 and (D2O)2: ground and excited state tunneling splittings and rotational constants, as well as the frequencies of the intermolecular vibrations.

Intermolecular Interactions and Electrostatic Properties of the [beta]-Hydroquinone Apohost: Implications for Supramolecular Chemistry

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

Clausen, Henrik F.; Chen, Yu-Sheng; Jayatilaka, Dylan

2012-02-07

The crystal structure of the {beta}-polymorph of hydroquinone ({beta}-HQ), the apohost of a large family of clathrates, is reported with a specific focus on intermolecular interactions and the electrostatic nature of its cavity. Hirshfeld surface analysis reveals subtle close contacts between two interconnecting HQ networks, and the local packing and related close contacts were examined by breakdown of the fingerprint plot. An experimental multipole model containing anisotropic thermal parameters for hydrogen atoms has been successfully refined against 15(2) K single microcrystal synchrotron X-ray diffraction data. The experimental electron density model has been compared with a theoretical electron density calculated withmore » the molecule embedded in its own crystal field. Hirshfeld charges, interaction energies and the electrostatic potential calculated for both models are qualitatively in good agreement, but small differences in the electrostatic potential persist due to charge transfer from all hydrogen atoms to the oxygen atoms in the theoretical model. The electrostatic potential in the center of the cavity is positive, very shallow and highly symmetric, suggesting that the inclusion of polar molecules in the void will involve a balance between opposing effects. The electric field is by symmetry zero in the center of the cavity, increasing to a value of 0.0185 e/{angstrom}{sup 2} (0.27 V/{angstrom}) 1 {angstrom} along the 3-fold axis and 0.0105 e/{angstrom}{sup 2} (0.15 V/{angstrom}) 1 {angstrom} along the perpendicular direction. While these values are substantial in a macroscopic context, they are quite small for a molecular cavity and are not expected to strongly polarize a guest molecule.« less

Local energy decomposition analysis of hydrogen-bonded dimers within a domain-based pair natural orbital coupled cluster study.

PubMed

Altun, Ahmet; Neese, Frank; Bistoni, Giovanni

2018-01-01

The local energy decomposition (LED) analysis allows for a decomposition of the accurate domain-based local pair natural orbital CCSD(T) [DLPNO-CCSD(T)] energy into physically meaningful contributions including geometric and electronic preparation, electrostatic interaction, interfragment exchange, dynamic charge polarization, and London dispersion terms. Herein, this technique is employed in the study of hydrogen-bonding interactions in a series of conformers of water and hydrogen fluoride dimers. Initially, DLPNO-CCSD(T) dissociation energies for the most stable conformers are computed and compared with available experimental data. Afterwards, the decay of the LED terms with the intermolecular distance ( r ) is discussed and results are compared with the ones obtained from the popular symmetry adapted perturbation theory (SAPT). It is found that, as expected, electrostatic contributions slowly decay for increasing r and dominate the interaction energies in the long range. London dispersion contributions decay as expected, as r -6 . They significantly affect the depths of the potential wells. The interfragment exchange provides a further stabilizing contribution that decays exponentially with the intermolecular distance. This information is used to rationalize the trend of stability of various conformers of the water and hydrogen fluoride dimers.

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

Ahart, Muhtar; Aihaiti, Dilare; Hemley, Russell J.

The pressure dependence of the Boson peak (BP) of glycerol, including its behavior across the liquid-glass transition, has been studied under pressure using Raman scattering. A significant increase of the BP frequency was observed with pressure up to 11 GPa at room temperature. The pressure dependence of BP frequency ν BP is proportional to (1+P/P 0) 1/3, where P and P 0 are the pressure and a constant, respectively, the spectra are consistent with a soft potential model. The characteristic length of medium range order is close in size to a cyclic trimer of glycerol molecules, which is predicted asmore » the medium range order of a BP vibration using molecular dynamics simulations. The pressure dependence of a characteristic length of medium range order is nearly constant. The pressure induced structural changes in glycerol can be understood in terms of the shrinkage of voids with cyclic trimers remaining up to at least 11 GPa. Lastly, the pressure dependence of intermolecular O-H stretching mode indicates that the intermolecular hydrogen bond distance gradually decreases below the glass transition pressure of ~5 GPa, while it becomes nearly constant in the glassy state indicating the disappearance of the free volume in the dense glass.« less

Specific noncovalent interactions at protein-ligand interface: implications for rational drug design.

PubMed

Zhou, P; Huang, J; Tian, F

2012-01-01

Specific noncovalent interactions that are indicative of attractive, directional intermolecular forces have always been of key interest to medicinal chemists in their search for the "glue" that holds drugs and their targets together. With the rapid increase in the number of solved biomolecular structures as well as the performance enhancement of computer hardware and software in recent years, it is now possible to give more comprehensive insight into the geometrical characteristics and energetic landscape of certain sophisticated noncovalent interactions present at the binding interface of protein receptors and small ligands based on accumulated knowledge gaining from the combination of two quite disparate but complementary approaches: crystallographic data analysis and quantum-mechanical ab initio calculation. In this perspective, we survey massive body of published works relating to structural characterization and theoretical investigation of three kinds of strong, specific, direct, enthalpy-driven intermolecular forces, including hydrogen bond, halogen bond and salt bridge, involved in the formation of protein-ligand complex architecture in order to characterize their biological functions in conferring affinity and specificity for ligand recognition by host protein. In particular, the biomedical implications of raised knowledge are discussed with respect to potential applications in rational drug design.

Inter-molecular β-sheet structure facilitates lung-targeting siRNA delivery

NASA Astrophysics Data System (ADS)

Zhou, Jihan; Li, Dong; Wen, Hao; Zheng, Shuquan; Su, Cuicui; Yi, Fan; Wang, Jue; Liang, Zicai; Tang, Tao; Zhou, Demin; Zhang, Li-He; Liang, Dehai; Du, Quan

2016-03-01

Size-dependent passive targeting based on the characteristics of tissues is a basic mechanism of drug delivery. While the nanometer-sized particles are efficiently captured by the liver and spleen, the micron-sized particles are most likely entrapped within the lung owing to its unique capillary structure and physiological features. To exploit this property in lung-targeting siRNA delivery, we designed and studied a multi-domain peptide named K-β, which was able to form inter-molecular β-sheet structures. Results showed that K-β peptides and siRNAs formed stable complex particles of 60 nm when mixed together. A critical property of such particles was that, after being intravenously injected into mice, they further associated into loose and micron-sized aggregates, and thus effectively entrapped within the capillaries of the lung, leading to a passive accumulation and gene-silencing. The large size aggregates can dissociate or break down by the shear stress generated by blood flow, alleviating the pulmonary embolism. Besides the lung, siRNA enrichment and targeted gene silencing were also observed in the liver. This drug delivery strategy, together with the low toxicity, biodegradability, and programmability of peptide carriers, show great potentials in vivo applications.

Modeling and simulation of magnetic resonance imaging based on intermolecular multiple quantum coherences

NASA Astrophysics Data System (ADS)

Cai, Congbo; Dong, Jiyang; Cai, Shuhui; Cheng, En; Chen, Zhong

2006-11-01

Intermolecular multiple quantum coherences (iMQCs) have many potential applications since they can provide interaction information between different molecules within the range of dipolar correlation distance, and can provide new contrast in magnetic resonance imaging (MRI). Because of the non-localized property of dipolar field, and the non-linear property of the Bloch equations incorporating the dipolar field term, the evolution behavior of iMQC is difficult to deduce strictly in many cases. In such cases, simulation studies are very important. Simulation results can not only give a guide to optimize experimental conditions, but also help analyze unexpected experimental results. Based on our product operator matrix and the K-space method for dipolar field calculation, the MRI simulation software was constructed, running on Windows operation system. The non-linear Bloch equations are calculated by a fifth-order Cash-Karp Runge-Kutta formulism. Computational time can be efficiently reduced by separating the effects of chemical shifts and strong gradient field. Using this software, simulation of different kinds of complex MRI sequences can be done conveniently and quickly on general personal computers. Some examples were given. The results were discussed.

The formation of quasi-alicyclic rings in alkyl-aromatic compounds

NASA Astrophysics Data System (ADS)

Straka, Pavel; Buryan, Petr; Bičáková, Olga

2018-02-01

The alkyl side chains of n-alkyl phenols, n-alkyl benzenes and n-alkyl naphthalenes are cyclised, as demonstrated by GC measurements, FTIR spectroscopy and molecular mechanics calculations. Cyclisation occurs due to the intramolecular interaction between an aromatic ring (-δ) and a hydrogen of the terminal methyl group (+δ) of an alkyl chain. In fact, conventional molecules are not aliphatic-aromatic, but quasi-alicyclic-aromatic. With the aromatic molecules formed with a quasi-alicyclic ring, the effect of van der Waals attractive forces increases not only intramolecularly but also intermolecularly. This effect is strong in molecules with propyl and higher alkyl substituents. The increase of intermolecular van der Waals attractive forces results in bi-linearity in the GC retention time of the compounds in question, observed in the dependence of the logarithm of the relative retention time on the number of carbons in a molecule in both polar and nonpolar stationary phases with both capillary and packed columns. The role of van der Waals forces has been demonstrated using the potential energies of covalent and noncovalent interactions for 2-n-alkyl phenols, n-alkyl benzenes and 1-n-alkyl- and 2-n-alkyl naphthalenes.

Structure, energetics and vibrational spectra of dimers, trimers, and tetramers of HX (X = Cl, Br, I)

NASA Astrophysics Data System (ADS)

Latajka, Zdzislaw; Scheiner, Steve

1997-03-01

The title complexes are studied by correlated ab initio methods using a pseudopotential double-ζ basis set, augmented by diffuse sp and two sets of polarization functions. The binding energies of the complexes decrease in the order HCl > HBr > HI. In the mixed HX…HX' dimers, the nature of the proton-donor molecule is more important than is the proton-acceptor with respect to the strength of the interaction. Only one minimum is found on the potential energy surface of the trimers and tetramers, which corresponds to the C nh cyclic structure. Enlargement of the complex leads to progressively greater individual H-bond energy and HX bond stretch, coupled with reduced intermolecular separation and smaller nonlinearity of each H-bond. Electron correlation makes a larger contribution as the atomic number of X increases. The highest degree of cooperativity is noted for oligomers of HCl and HBr, as compared to HI. The nonadditivity is dominated by terms present at the SCF level. The vibrational frequencies exhibit trends that generally parallel the energetics and geometry patterns, particularly the red shifts of the HX stretches and the intermolecular modes.

Impact of the A2V Mutation on the Heterozygous and Homozygous Aβ1-40 Dimer Structures from Atomistic Simulations.

PubMed

Nguyen, Phuong H; Sterpone, Fabio; Campanera, Josep M; Nasica-Labouze, Jessica; Derreumaux, Philippe

2016-06-15

The A2V mutation was reported to protect from Alzheimer's disease in its heterozygous form and cause an early Alzheimer's disease type dementia in its homozygous form. Experiments showed that the aggregation rate follows the order A2V > WT (wild-type) > A2V-WT. To understand the impact of this mutation, we carried out replica exchange molecular dynamics simulations of Aβ1-40 WT-A2V and A2V-A2V dimers and compared to the WT dimer. Our atomistic simulations reveal that the mean secondary structure remains constant, but there are substantial differences in the intramolecular and intermolecular conformations upon single and double A2V mutation. Upon single mutation, the intrinsic disorder is reduced, the intermolecular potential energies are reduced, the population of intramolecular three-stranded β-sheets is increased, and the number of all α dimer topologies is decreased. Taken together, these results offer an explanation for the reduced aggregation rate of the Aβ1-40 A2V-WT peptides and the protective effect of A2V in heterozygotes.

Intermolecular hydrogen bond complexes by in situ charge transfer complexation of o-tolidine with picric and chloranilic acids

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; Saad, Hosam A.; Adam, Abdel Majid A.

2011-08-01

A two new charge transfer complexes formed from the interactions between o-tolidine (o-TOL) and picric (PA) or chloranilic (CA) acids, with the compositions, [(o-TOL)(PA) 2] and [(o-TOL)(CA) 2] have been prepared. The 13C NMR, 1H NMR, 1H-Cosy, and IR show that the charge-transfer chelation occurs via the formation of chain structures O-H⋯N intermolecular hydrogen bond between 2NH 2 groups of o-TOL molecule and OH group in each PA or CA units. Photometric titration measurements concerning the two reactions in methanol were performed and the measurements show that the donor-acceptor molar ratio was found to be 1:2 using the modified Benesi-Hildebrand equation. The spectroscopic data were discussed in terms of formation constant, molar extinction coefficient, oscillator strength, dipole moment, standard free energy, and ionization potential. Thermal behavior of both charge transfer complexes showed that the complexes were more stable than their parents. The thermodynamic parameters were estimated from the differential thermogravimetric curves. The results indicated that the formation of molecular charge transfer complexes is spontaneous and endothermic.

Intermolecular hydrogen bond complexes by in situ charge transfer complexation of o-tolidine with picric and chloranilic acids.

PubMed

Refat, Moamen S; Saad, Hosam A; Adam, Abdel Majid A

2011-08-01

A two new charge transfer complexes formed from the interactions between o-tolidine (o-TOL) and picric (PA) or chloranilic (CA) acids, with the compositions, [(o-TOL)(PA)(2)] and [(o-TOL)(CA)(2)] have been prepared. The (13)C NMR, (1)H NMR, (1)H-Cosy, and IR show that the charge-transfer chelation occurs via the formation of chain structures O-H⋯N intermolecular hydrogen bond between 2NH(2) groups of o-TOL molecule and OH group in each PA or CA units. Photometric titration measurements concerning the two reactions in methanol were performed and the measurements show that the donor-acceptor molar ratio was found to be 1:2 using the modified Benesi-Hildebrand equation. The spectroscopic data were discussed in terms of formation constant, molar extinction coefficient, oscillator strength, dipole moment, standard free energy, and ionization potential. Thermal behavior of both charge transfer complexes showed that the complexes were more stable than their parents. The thermodynamic parameters were estimated from the differential thermogravimetric curves. The results indicated that the formation of molecular charge transfer complexes is spontaneous and endothermic. Copyright © 2011 Elsevier B.V. All rights reserved.

Synthetic/Biosynthetic Phase Transfer Polymers for Pollution Minimization, Remediation, and Waste Management

DTIC Science & Technology

1994-01-01

in the viscosity profile is observed. DAMAB induces strong intermolecular associations via hydrophobic interactions . When copolymers of comparable...techniques such as viscosity studies. The AM/DAMAB copolymer series also interacts with surfactants in an interesting manner.’ The surface tension of...in polymer dimensions as hydrophobe is added. The shape of the viscosity curves does not suggest intermolecular interactions , as in typical

Intermolecular vibrations of (CH2)2O-HF and -DF hydrogen bonded complexes investigated by Fourier transform infrared spectroscopy and ab initio calculations.

PubMed

Cirtog, M; Asselin, P; Soulard, P; Madebène, B; Alikhani, M E

2010-10-14

A series of Fourier transform infrared spectra (FTIR) of the hydrogen bonded complexes (CH(2))(2)O-HF and -DF have been recorded in the 50-750 cm(-1) range up to 0.1 cm(-1) resolution in a static cell maintained at near room temperature. The direct observation of three intermolecular transitions enabled us to perform band contour analysis of congested cell spectra and to determine reliable rovibrational parameters such as intermolecular frequencies, rovibrational and anharmonic coupling constants involving two l(1) and l(2) librations and one σ stretching intermolecular motion. Inter-inter anharmonic couplings could be identified between ν(l(1)), ν(l(2)), ν(σ) and the two lowest frequency bending modes. The positive sign of coupling constants (opposite with respect to acid stretching intra-inter ones) reveals a weakening of the hydrogen bond upon intermolecular excitation. The four rovibrational parameters ν(σ) and x(σj) (j = σ, δ(1), δ(2)) derived in the present far-infrared study and also in a previous mid-infrared one [Phys. Chem. Chem. Phys. 2005, 1, 592] make deviations appear smaller than 1% for frequencies and 12% for coupling constants which gives confidence to the reliability of the data obtained. Anharmonic frequencies obtained at the MP2 level with Aug-cc-pvTZ basis set agree well with experimental values over a large set of frequencies and coupling constants. An estimated anharmonic corrected value of the dissociation energy D for both oxirane-HF (2424 cm(-1)) and -DF (2566 cm(-1)) has been derived using a level of theory as high as CCSD(T)/Aug-cc-pvQZ, refining the harmonic value previously calculated for oxirane-HF with the MP2 method and a smaller basis set. Finally, contrary to short predissociation lifetimes evidenced for acid stretching excited states, any homogeneous broadening related to vibrational dynamics of (CH(2))(2)O-HF and -DF has been observed within the three highest frequency intermolecular states, as expected with low excitation energies largely below the dissociation limit as well as a negligible IVR contribution.

Effect of pairwise additivity on finite-temperature behavior of classical ideal gas

NASA Astrophysics Data System (ADS)

Shekaari, Ashkan; Jafari, Mahmoud

2018-05-01

Finite-temperature molecular dynamics simulations have been applied to inquire into the effect of pairwise additivity on the behavior of classical ideal gas within the temperature range of T = 250-4000 K via applying a variety of pair potentials and then examining the temperature dependence of a number of thermodynamical properties. Examining the compressibility factor reveals the most deviation from ideal-gas behavior for the Lennard-Jones system mainly due to the presence of both the attractive and repulsive terms. The systems with either attractive or repulsive intermolecular potentials are found to present no resemblance to real gases, but the most similarity to the ideal one as temperature rises.

Understanding the Phase Behavior of Tetrahydrofuran + Carbon Dioxide, + Methane, and + Water Binary Mixtures from the SAFT-VR Approach.

PubMed

Míguez, J M; Piñeiro, M M; Algaba, J; Mendiboure, B; Torré, J P; Blas, F J

2015-11-05

The high-pressure phase diagrams of the tetrahydrofuran(1) + carbon dioxide(2), + methane(2), and + water(2) mixtures are examined using the SAFT-VR approach. Carbon dioxide molecule is modeled as two spherical segments tangentially bonded, water is modeled as a spherical segment with four associating sites to represent the hydrogen bonding, methane is represented as an isolated sphere, and tetrahydrofuran is represented as a chain of m tangentially bonded spherical segments. Dispersive interactions are modeled using the square-well intermolecular potential. In addition, two different molecular model mixtures are developed to take into account the subtle balance between water-tetrahydrofuran hydrogen-bonding interactions. The polar and quadrupolar interactions present in water, tetrahydrofuran, and carbon dioxide are treated in an effective way via square-well potentials of variable range. The optimized intermolecular parameters are taken from the works of Giner et al. (Fluid Phase Equil. 2007, 255, 200), Galindo and Blas (J. Phys. Chem. B 2002, 106, 4503), Patel et al. (Ind. Eng. Chem. Res. 2003, 42, 3809), and Clark et al. (Mol. Phys. 2006, 104, 3561) for tetrahydrofuran, carbon dioxide, methane, and water, respectively. The phase diagrams of the binary mixtures exhibit different types of phase behavior according to the classification of van Konynenburg and Scott, ranging from types I, III, and VI phase behavior for the tetrahydrofuran(1) + carbon dioxide(2), + methane(2), and + water(2) binary mixtures, respectively. This last type is characterized by the presence of a Bancroft point, positive azeotropy, and the so-called closed-loop curves that represent regions of liquid-liquid immiscibility in the phase diagram. The system exhibits lower critical solution temperatures (LCSTs), which denote the lower limit of immiscibility together with upper critical solution temperatures (UCSTs). This behavior is explained in terms of competition between the incompatibility with the alkyl parts of the tetrahydrofuran ring chain and the hydrogen bonding between water and the ether group. A minimum number of unlike interaction parameters are fitted to give the optimal representation of the most representative features of the binary phase diagrams. In the particular case of tetrahydrofuran(1) + water(2), two sets of intermolecular potential model parameters are proposed to describe accurately either the hypercritical point associated with the closed-loop liquid-liquid immiscibility region or the location of the mixture lower- and upper-critical end-points. The theory is not only able to predict the type of phase behavior of each mixture, but also provides a reasonably good description of the global phase behavior whenever experimental data are available.

Monte Carlo study of one-dimensional confined fluids with Gay-Berne intermolecular potential

NASA Astrophysics Data System (ADS)

Moradi, M.; Hashemi, S.

2011-11-01

The thermodynamic quantities of a one dimensional system of particles with Gay-Berne model potential confined between walls have been obtained by means of Monte Carlo computer simulations. For a number of temperatures, the systems were considered and their density profiles, order parameter, pressure, configurational temperature and average potential energy per particle are reported. The results show that by decreasing the temperature, the soft particles become more ordered and they align to the walls and also they don't show any tendency to be near the walls at very low temperatures. We have also changed the structure of the walls by embedding soft ellipses in them, this change increases the total density near the wall whereas, increasing or decreasing the order parameter depend on the angle of embedded ellipses.

Thioarsenides: A case for long-range Lewis acid-base-directed van der Waals interactions

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

Gibbs, Gerald V.; Wallace, Adam F.; Downs, R. T.

2011-04-01

Electron density distributions, bond paths, Laplacian and local energy density properties have been calculated for a number of As4Sn (n = 3,4,5) thioarsenide molecular crystals. On the basis of the distributions, the intramolecular As-S and As-As interactions classify as shared bonded interactions and the intermolecular As-S, As-As and S-S interactions classify as closed-shell van der Waals bonded interactions. The bulk of the intermolecular As-S bond paths link regions of locally concentrated electron density (Lewis base regions) with aligned regions of locally depleted electron density (Lewis acid regions) on adjacent molecules. The paths are comparable with intermolecular paths reported for severalmore » other molecular crystals that link aligned Lewis base and acid regions in a key-lock fashion, interactions that classified as long range Lewis acid-base directed van der Waals interactions. As the bulk of the intermolecular As-S bond paths (~70%) link Lewis acid-base regions on adjacent molecules, it appears that molecules adopt an arrangement that maximizes the number of As-S Lewis acid-base intermolecular bonded interactions. The maximization of the number of Lewis acid-base interactions appears to be connected with the close-packed array adopted by molecules: distorted cubic close-packed arrays are adopted for alacránite, pararealgar, uzonite, realgar and β-AsS and the distorted hexagonal close-packed arrays adopted by α- and β-dimorphite. A growth mechanism is proposed for thioarsenide molecular crystals from aqueous species that maximizes the number of long range Lewis acid-base vdW As-S bonded interactions with the resulting directed bond paths structuralizing the molecules as a molecular crystal.« less

Energetics of Intermolecular Hydrogen Bonds in a Hydrophobic Protein Cavity

NASA Astrophysics Data System (ADS)

Liu, Lan; Baergen, Alyson; Michelsen, Klaus; Kitova, Elena N.; Schnier, Paul D.; Klassen, John S.

2014-05-01

This work explores the energetics of intermolecular H-bonds inside a hydrophobic protein cavity. Kinetic measurements were performed on the gaseous deprotonated ions (at the -7 charge state) of complexes of bovine β-lactoglobulin (Lg) and three monohydroxylated analogs of palmitic acid (PA): 3-hydroxypalmitic acid (3-OHPA), 7-hydroxypalmitic acid (7-OHPA), and 16-hydroxypalmitic acid (16-OHPA). From the increase in the activation energy for the dissociation of the (Lg + X-OHPA)7- ions, compared with that of the (Lg + PA)7- ion, it is concluded that the -OH groups of the X-OHPA ligands participate in strong (5 - 11 kcal mol-1) intermolecular H-bonds in the hydrophobic cavity of Lg. The results of molecular dynamics (MD) simulations suggest that the -OH groups of 3-OHPA and 16-OHPA act as H-bond donors and interact with backbone carbonyl oxygens, whereas the -OH group of 7-OHPA acts as both H-bond donor and acceptor with nearby side chains. The capacity for intermolecular H-bonds within the Lg cavity, as suggested by the gas-phase measurements, does not necessarily lead to enhanced binding in aqueous solution. The association constant (Ka) measured for 7-OHPA [(2.3 ± 0.2) × 105 M-1] is similar to the value for the PA [(3.8 ± 0.1) × 105 M-1]; Ka for 3-OHPA [(1.1 ± 0.3) × 106 M-1] is approximately three-times larger, whereas Ka for 16-OHPA [(2.3 ± 0.2) × 104 M-1] is an order of magnitude smaller. Taken together, the results of this study suggest that the energetic penalty to desolvating the ligand -OH groups, which is necessary for complex formation, is similar in magnitude to the energetic contribution of the intermolecular H-bonds.

Stabilizing potentials in bound state analytic continuation methods for electronic resonances in polyatomic molecules

DOE PAGES

White, Alec F.; Head-Gordon, Martin; McCurdy, C. William

2017-01-30

The computation of Siegert energies by analytic continuation of bound state energies has recently been applied to shape resonances in polyatomic molecules by several authors. Here, we critically evaluate a recently proposed analytic continuation method based on low order (type III) Padé approximants as well as an analytic continuation method based on high order (type II) Padé approximants. We compare three classes of stabilizing potentials: Coulomb potentials, Gaussian potentials, and attenuated Coulomb potentials. These methods are applied to a model potential where the correct answer is known exactly and to the 2Π g shape resonance of N 2 - whichmore » has been studied extensively by other methods. Both the choice of stabilizing potential and method of analytic continuation prove to be important to the accuracy of the results. We then conclude that an attenuated Coulomb potential is the most effective of the three for bound state analytic continuation methods. With the proper potential, such methods show promise for algorithmic determination of the positions and widths of molecular shape resonances.« less

Stabilizing potentials in bound state analytic continuation methods for electronic resonances in polyatomic molecules

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

White, Alec F.; Head-Gordon, Martin; McCurdy, C. William

The computation of Siegert energies by analytic continuation of bound state energies has recently been applied to shape resonances in polyatomic molecules by several authors. Here, we critically evaluate a recently proposed analytic continuation method based on low order (type III) Padé approximants as well as an analytic continuation method based on high order (type II) Padé approximants. We compare three classes of stabilizing potentials: Coulomb potentials, Gaussian potentials, and attenuated Coulomb potentials. These methods are applied to a model potential where the correct answer is known exactly and to the 2Π g shape resonance of N 2 - whichmore » has been studied extensively by other methods. Both the choice of stabilizing potential and method of analytic continuation prove to be important to the accuracy of the results. We then conclude that an attenuated Coulomb potential is the most effective of the three for bound state analytic continuation methods. With the proper potential, such methods show promise for algorithmic determination of the positions and widths of molecular shape resonances.« less

Intermolecular hydrogen bonds in hetero-complexes of biologically active aromatic molecules probed by the methods of vibrational spectroscopy.

PubMed

Semenov, M A; Blyzniuk, Iu N; Bolbukh, T V; Shestopalova, A V; Evstigneev, M P; Maleev, V Ya

2012-09-01

By the methods of vibrational spectroscopy (Infrared and Raman) the investigation of the hetero-association of biologically active aromatic compounds: flavin-mononucleotide (FMN), ethidium bromide (EB) and proflavine (PRF) was performed in aqueous solutions. It was shown that between the functional groups (CO and NH(2)) the intermolecular hydrogen bonds are formed in the hetero-complexes FMN-EB and FMN-PRF, additionally stabilizing these structures. An estimation of the enthalpy of Н-bonding obtained from experimental shifts of carbonyl vibrational frequencies has shown that the H-bonds do not dominate in the magnitude of experimentally measured total enthalpy of the hetero-association reactions. The main stabilization is likely due to intermolecular interactions of the molecules in these complexes and their interaction with water environment. Copyright © 2012 Elsevier B.V. All rights reserved.

Does a network structure exist in molecular liquid SnI4 and GeI4?

NASA Astrophysics Data System (ADS)

Sakagami, Takahiro; Fuchizaki, Kazuhiro

2017-04-01

The existence of a network structure consisting of electrically neutral tetrahedral molecules in liquid SnI4 and GeI4 at ambient pressure was examined. The liquid structures employed for the examination were obtained from a reverse Monte Carlo analysis. The structures were physically interpreted by introducing an appropriate intermolecular interaction. A ‘bond’ was then defined as an intermolecular connection that minimizes the energy of intermolecular interaction. However, their ‘bond’ energy is too weak for the ‘bond’ and the resulting network structure to be defined statically. The vertex-to-edge orientation between the nearest molecules is so ubiquitous that almost all of the molecules in the system can take part in the network, which is reflected in the appearance of a prepeak in the structure factor.

Evaluating Students' Understanding of Kinetic Particle Theory Concepts Relating to the States of Matter, Changes of State and Diffusion: A Cross-National Study

ERIC Educational Resources Information Center

Treagust, David F.; Chandrasegaran, A. L.; Crowley, Julianne; Yung, Benny H. W.; Cheong, Irene P.-A.; Othman, Jazilah

2010-01-01

This paper reports on the understanding of three key conceptual categories relating to the kinetic particle theory: (1) intermolecular spacing in solids, liquids and gases, (2) changes of state and intermolecular forces and (3) diffusion in liquids and gases, amongst 148 high school students from Brunei, Australia, Hong Kong and Singapore using 11…

Application of terahertz spectroscopy and theoretical calculation in dimethylurea isomers investigation

NASA Astrophysics Data System (ADS)

Zhao, Yonghong; Li, Zhi; Liu, Jianjun; Chen, Tao; Zhang, Huo; Qin, Binyi; Wu, Yifang

2018-03-01

The characteristic absorption spectra of two structural isomers of dimethylurea(DMU) in 0.6-1.8 THz region have been measured using terahertz time-domain spectroscopy (THZ-TDS) at room temperature. Significant differences have been found between their terahertz spectra and implied that the THZ-TDS is an effective means of identifying structural isomers. To simulate their spectra, calculations on single molecule and cluster of 1,1-DMU and 1,3-DMU were performed, and we found that the cluster calculations using DFT-D3 method are better to predict the experimental spectra. Using the normal mode as displacements in redundant internal coordinates and the GaussView program, most observed THz vibrational modes are assigned to bending and rocking modes related to the intermolecular hydrogen bonding interactions, and twisting mode of ethyl groups. The different spectral features of two isomers mainly arise from different intermolecular hydrogen bonds resulting from different atom arrangements in molecules and different molecule arrangements in crystals. Using the reduced-density-gradient (RDG) analysis, the positions and types of intermolecular hydrogen bonding interactions in 1,1-DMU and 1,3-DMU crystals are visualized. Therefore, we can confirm that THz-TDS can be used as an effective means for the recognition of structural isomers and detection of intermolecular hydrogen bonding interactions in these crystals.

Exploring contribution of intermolecular interactions in supramolecular layered assembly of naphthyridine co-crystals: Insights from Hirshfeld surface analysis of their crystalline states

NASA Astrophysics Data System (ADS)

Seth, Saikat Kumar; Das, Nirmal Kumar; Aich, Krishnendu; Sen, Debabrata; Fun, Hoong-Kun; Goswami, Shyamaprasad

2013-09-01

Co-crystals of 1a and 1b have been prepared by slow evaporation of the solutions of mixtures of 2,7-dimethyl-1,8-naphthyridine (1), urea (a) and thiourea (b). The structures of the complexes are determined by the single crystal X-ray diffraction and a detailed investigation of the crystal packing and classification of intermolecular interactions is presented by means of Hirshfeld surface analysis which is of considerable current interest in crystal engineering. The X-ray study reveals that the co-crystal formers are envisioned to produce N-H⋯N hydrogen bond as well as N-H⋯O/N-H⋯S pair-wise hydrogen bonds and also the weaker aromatic π⋯π interactions which cooperatively take part in the crystal packing. The recurring feature of the self-assembly in the compounds is the appearance of the molecular ribbon through multiple hydrogen bonding which are further stacked into molecular layers by π⋯π stacking interactions. Hirshfeld surface analysis for visually analyzing intermolecular interactions in crystal structures employing molecular surface contours and 2D Fingerprint plots have been used to examine molecular shapes. Crystal structure analysis supported with the Hirshfeld surface and fingerprint plots enabled the identification of the significant intermolecular interactions.

Design of a New Concentration Series for the Orthogonal Sample Design Approach and Estimation of the Number of Reactions in Chemical Systems.

PubMed

Shi, Jiajia; Liu, Yuhai; Guo, Ran; Li, Xiaopei; He, Anqi; Gao, Yunlong; Wei, Yongju; Liu, Cuige; Zhao, Ying; Xu, Yizhuang; Noda, Isao; Wu, Jinguang

2015-11-01

A new concentration series is proposed for the construction of a two-dimensional (2D) synchronous spectrum for orthogonal sample design analysis to probe intermolecular interaction between solutes dissolved in the same solutions. The obtained 2D synchronous spectrum possesses the following two properties: (1) cross peaks in the 2D synchronous spectra can be used to reflect intermolecular interaction reliably, since interference portions that have nothing to do with intermolecular interaction are completely removed, and (2) the two-dimensional synchronous spectrum produced can effectively avoid accidental collinearity. Hence, the correct number of nonzero eigenvalues can be obtained so that the number of chemical reactions can be estimated. In a real chemical system, noise present in one-dimensional spectra may also produce nonzero eigenvalues. To get the correct number of chemical reactions, we classified nonzero eigenvalues into significant nonzero eigenvalues and insignificant nonzero eigenvalues. Significant nonzero eigenvalues can be identified by inspecting the pattern of the corresponding eigenvector with help of the Durbin-Watson statistic. As a result, the correct number of chemical reactions can be obtained from significant nonzero eigenvalues. This approach provides a solid basis to obtain insight into subtle spectral variations caused by intermolecular interaction.

Role of dbnd NOH intermolecular interactions in oxime derivatives via Crystal structure, Hirshfeld surface, PIXELC and DFT calculations

NASA Astrophysics Data System (ADS)

Purushothaman, Gayathri; Thiruvenkatam, Vijay

2017-11-01

Oximes are building block of organic synthesis and they have wide range applications in laboratories, industries, and pharmaceutical as antidotes. Herein we report the crystal structures of oxime derivative Beta-p-Dimethylaminodeoxybenzionoxime (I) and o-Chloro-p-dimethylaminodeoxybenzion (II) the precursor molecule of o-Chloro-p-dimethylaminodeoxybenzionoxime and their intermolecular interactions studies through Hirshfeld surface & 2D-fingerprint plot analysis along with PIXELC and DFT calculations. The packing arrangements in I and II are driven by Osbnd H⋯N and Osbnd H⋯C interactions respectively. The Osbnd H⋯N hydrogen bonding in I facilitates the formation of the dimer with the motif of R (22(6)), whereas in II absence of oxime moiety (dbnd NOH) restricts the dimer formation. The 2D-fingerprint plot shows the close contacts for the intermolecular interactions in I & II. The PIXELC calculation of II suggests Osbnd H⋯C contributes for intermolecular interaction that stabilizes the crystal packing with the total energy value of 60.4 kcal/mol. The DFT calculation using B3LYP with 6-311G (d, p) functional set for both the derivatives shows a small deviation in the benzene ring (I) and chlorobenzene ring (II) with the RMSD value of 0.5095 Å and 0.8472 Å respectively.

Low-energy elastic differential scattering of He/++/ by He.

NASA Technical Reports Server (NTRS)

Lam, S. K.; Doverspike, L. D.; Champion, R. L.

1973-01-01

Experimental results are developed for the relative elastic differential scattering of He(++) by He for collision energies in the range 4 equal to or less than E equal to or less than 75 eV. In the analysis of the data, semiclassical considerations are utilized, assuming that the dynamics of the scattering is governed solely by the B and E states of He2(++). It is shown that existing ab initio calculations for the intermolecular potentials predict differential cross sections which are not in particularly good agreement with the experimental data.

Theoretical studies of charge transfer and proton transfer complex formation between 3,5-dinitrobenzic acid and 1,2-dimethylimidazole

NASA Astrophysics Data System (ADS)

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

2018-05-01

Natural atomic charge analysis and molecular electrostatic potential (MEP) surface analysis of hydrogen bonded charge transfer (HBCT) and proton transfer (PT) complex of 3,5-dinitrobenzoic acid (DNBA) and 1,2-dimethylimidazole (DMI) have been investigated by theoretical modelling using widely employed DFT/B3LYP/6-311G(d,p) level of theory. Along with this analysis, Hirshfeld surface study of the intermolecular interactions and associated 2D finger plot for reported PT complex between DNBA and DMI have been explored.

Predicting the Highly Nonlinear Mechanical Properties of Polymeric Materials

NASA Astrophysics Data System (ADS)

Porter, David

2009-06-01

Over the past few years, we have developed models that calculate the highly nonlinear mechanical properties of polymers as a function of temperature, strain and strain rate from their molecular and morphological structure. A review of these models is presented here, with emphasis on combining the fundamental aspects of molecular physics that dictate these properties and the pragmatic need to make realistic predictions for our customers; the designer of new materials and the engineers who use these materials. The models calculate the highly nonlinear mechanical properties of polymers as a function of temperature, strain and strain rate from their molecular structure. The model is based upon the premise that mechanical properties are a direct consequence of energy stored and energy dissipated during deformation of a material. This premise is transformed into a consistent set of structure-property relations for the equation of state, EoS, and the engineering constitutive relations in a polymer by quantifying energy storage and loss at the molecular level of interactions between characteristic groups of atoms in a polymer. These relations are derived from a simple volumetric mean field Lennard-Jones potential function for the potential energy of intermolecular interactions in a polymer. First, properties such as temperature-volume relations and glass transition temperature are calculated directly from the potential function. Then, the `shock' EoS is derived simply by differentiating the potential function with respect to volume, assuming that the molecules cannot relax in the time scales of the deformation. The energy components are then used to predict the dynamic mechanical spectrum of a polymer in terms of temperature and rate. This can be transformed directly into the highly nonlinear stress-strain relations through yield. The constitutive relations are formulated as a set of analytical equations that predict properties directly in terms of a small set of structural parameters that can be calculated directly and independently from the chemical composition and morphology of a polymer. A number of examples are given to illustrate the model and also to show that the method can be applied, with appropriate modifications, to other materials.

Solid-phase extraction using bis(indolyl)methane-modified silica reinforced with multiwalled carbon nanotubes for the simultaneous determination of flavonoids and aromatic organic acid preservatives.

PubMed

Wang, Na; Liao, Yuan; Wang, Jiamin; Tang, Sheng; Shao, Shijun

2015-12-01

A novel bis(indolyl)methane-modified silica reinforced with multiwalled carbon nanotubes sorbent for solid-phase extraction was designed and synthesized by chemical immobilization of nitro-substituted 3,3'-bis(indolyl)methane on silica modified with multiwalled carbon nanotubes. Coupled with high-performance liquid chromatography analysis, the extraction properties of the sorbent were evaluated for flavonoids and aromatic organic acid compounds. Under optimum conditions, the sorbent can simultaneously extract five flavonoids and two aromatic organic acid preservatives in aqueous solutions in a single-step solid-phase extraction procedure. Wide linear ranges were obtained with correlation coefficients (R(2) ) ranging from 0.9843 to 0.9976, and the limits of detection were in the range of 0.5-5 μg/L for the compounds tested. Compared with the silica modified with multiwalled carbon nanotubes sorbent and the nitro-substituted 3,3'-bis(indolyl)methane-modified silica sorbent, the developed sorbent exhibited higher extraction efficiency toward the selected analytes. The synergistic effect of nitro-substituted 3,3'-bis(indolyl)methane and multiwalled carbon nanotubes not only improved the surface-to-volume ratio but also enhanced multiple intermolecular interactions, such as hydrogen bonds, π-π, and hydrophobic interactions, between the new sorbent and the selected analytes. The as-established solid-phase extraction with high-performance liquid chromatography and diode array detection method was successfully applied to the simultaneous determination of flavonoids and aromatic organic acid preservatives in grape juices with recoveries ranging from 83.9 to 112% for all the selected analytes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Determination of structure and properties of molecular crystals from first principles.

PubMed

Szalewicz, Krzysztof

2014-11-18

CONSPECTUS: Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from first principles. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from first principles, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be extrapolated to such cases. As an alternative to applying SAPT(DFT) in crystal structure calculations, one can use supermolecular DFT interaction energies combined with scaled dispersion energies computed from simple atom-atom functions, that is, use the so-called DFT+D approach. Whereas the standard DFT methods fail for intermolecular interactions, DFT+D performs reasonably well since the dispersion correction is used not only to provide the missing dispersion contribution but also to fix other deficiencies of DFT. The latter cancellation of errors is unphysical and can be avoided by applying the so-called dispersionless density functional, dlDF. In this case, the dispersion energies are added without any scaling. The dlDF+D method is also one of the best performing DFT+D methods. The SAPT(DFT)-based approach has been applied so far only to crystals with rigid monomers. It can be extended to partly flexible monomers, that is, to monomers with only a few internal coordinates allowed to vary. However, the costs will increase relative to rigid monomer cases since the number of grid points increases exponentially with the number of dimensions. One way around this problem is to construct force fields with approximate couplings between inter- and intramonomer degrees of freedom. Another way is to calculate interaction energies (and possibly forces) "on the fly", i.e., in each step of lattice energy minimization procedure. Such an approach would be prohibitively expensive if it replaced analytic force fields at all stages of the crystal predictions procedure, but it can be used to optimize a few dozen candidate structures determined by other methods.

The Ammonia Dimer Revisited

NASA Astrophysics Data System (ADS)

Dawes, Richard; Van Der Avoird, Ad

2012-06-01

The conclusion from microwave spectra by Nelson, Fraser, and Klemperer that the ammonia dimer has a nearly cyclic structure led to much debate about the issue of whether (NH_3)_2 is hydrogen bonded. This structure was surprising because most {ab initio} calculations led to a classical, nearly linear, hydrogen-bonded structure. An obvious explanation of the discrepancy between the outcome of these calculations and the microwave data which led Nelson {et al.} to their ``surprising structure'' might be the effect of vibrational averaging: the electronic structure calculations focus on finding the minimum of the intermolecular potential, the experiment gives a vibrationally averaged structure. Isotope substitution studies seemed to indicate, however, that the complex is nearly rigid. Additional data became available from high-resolution molecular beam far-infrared spectroscopy in the Saykally group. These spectra, displaying large tunneling splittings, indicate that the complex is very floppy. The seemingly contradictory experimental data were explained when it became possible to calculate the vibration-rotation-tunneling (VRT) states of the complex on a six-dimensional intermolecular potential surface. The potential used was a simple model potential, with parameters fitted to the far-infrared data. Now, for the first time, a six-dimensional potential was computed by high level {ab initio} methods and this potential will be used in calculations of the VRT states of (NH_3)_2 and (ND_3)_2. So, we will finally be able to answer the question whether the conclusions from the model calculations are indeed a valid explanation of the experimental data. D. Nelson, G. T. Fraser, and W. Klemperer J. Chem. Phys. 83 6201 (1985) J. G. Loeser, C. A. Schmuttenmaer, R. C. Cohen, M. J. Elrod, D. W. Steyert, R. J. Saykally, R. E. Bumgarner, and G. A. Blake J. Chem. Phys. 97 4727 (1992) E. H. T. Olthof, A. van der Avoird, and P. E. S. Wormer J. Chem. Phys. 101 8430 (1994) E. H. T. Olthof, A. van der Avoird, P. E. S. Wormer, J. G. Loeser, and R. J. Saykally J. Chem. Phys. 101 8443 (1994)

MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures.

PubMed

Caetano, Fabiana A; Dirk, Brennan S; Tam, Joshua H K; Cavanagh, P Craig; Goiko, Maria; Ferguson, Stephen S G; Pasternak, Stephen H; Dikeakos, Jimmy D; de Bruyn, John R; Heit, Bryan

2015-12-01

Our current understanding of the molecular mechanisms which regulate cellular processes such as vesicular trafficking has been enabled by conventional biochemical and microscopy techniques. However, these methods often obscure the heterogeneity of the cellular environment, thus precluding a quantitative assessment of the molecular interactions regulating these processes. Herein, we present Molecular Interactions in Super Resolution (MIiSR) software which provides quantitative analysis tools for use with super-resolution images. MIiSR combines multiple tools for analyzing intermolecular interactions, molecular clustering and image segmentation. These tools enable quantification, in the native environment of the cell, of molecular interactions and the formation of higher-order molecular complexes. The capabilities and limitations of these analytical tools are demonstrated using both modeled data and examples derived from the vesicular trafficking system, thereby providing an established and validated experimental workflow capable of quantitatively assessing molecular interactions and molecular complex formation within the heterogeneous environment of the cell.

An ensemble of paired spin(-1/2) nuclei in a rotating solid: Polarization evolution and NMR spectrum in a wobbling frame.

PubMed

Kundla, Enn

2007-04-01

The evolution of the magnetic polarization of an ensemble of paired spin(-1/2) nuclei in an MAS NMR (nuclear magnetic resonance) experiment and the induced spectrum are described theoretically by means of a Liouville-von Neumann equation representation in a wobbling rotating frame in combination with the averaged Hamiltonian theory. In this method, the effect of a high-intensity external static magnetic field and the effects of the leftover interaction components of the Hamiltonian that commute with the approximate Hamiltonian are taken into account simultaneously and equivalently. This method reproduces details that really exist in the recorded spectra, caused by secular terms in the Hamiltonian, which might otherwise be smoothed out owing to the approximate treatment of the effects of the secular terms. Complete analytical expressions, which describe the whole NMR spectrum including the rotational sideband sets, and which consider all the relevant intermolecular interactions, are obtained.

Relative contribution of combined kinetic and exchange energy terms vs the electronic component of molecular electrostatic potential in hardness potential derivatives.

PubMed

Bhattacharjee, Rituparna; Roy, Ram Kinkar

2013-11-14

The relative contribution of the sum of kinetic [(10/9)CFρ(r)2/3] and exchange energy [(4/9)CXρ(r)1/3] terms to that of the electronic part of the molecular electrostatic potential [Vel(r)] in the variants of hardness potential is investigated to assess the proposed definition of Δ+h(k) = −[VelN+1(k) – VelN(k)] and Δ–h(k) = −[VelN(k) – VelN–1(k)] (Saha; et al. J. Comput. Chem. 2013, 34, 662). Some substituted benzenes and polycyclic aromatic hydrocarbons (PAHs) (undergoing electrophilic aromatic substitution), carboxylic acids, and their derivatives are chosen to carry out the theoretical investigation as stated above. Intra- and intermolecular reactivity trends generated by Δ+h(k) and Δ–h(k) are found to be satisfactory and are correlated reasonably well with experimental results.

Insight into induced charges at metal surfaces and biointerfaces using a polarizable Lennard-Jones potential.

PubMed

Geada, Isidro Lorenzo; Ramezani-Dakhel, Hadi; Jamil, Tariq; Sulpizi, Marialore; Heinz, Hendrik

2018-02-19

Metallic nanostructures have become popular for applications in therapeutics, catalysts, imaging, and gene delivery. Molecular dynamics simulations are gaining influence to predict nanostructure assembly and performance; however, instantaneous polarization effects due to induced charges in the free electron gas are not routinely included. Here we present a simple, compatible, and accurate polarizable potential for gold that consists of a Lennard-Jones potential and a harmonically coupled core-shell charge pair for every metal atom. The model reproduces the classical image potential of adsorbed ions as well as surface, bulk, and aqueous interfacial properties in excellent agreement with experiment. Induced charges affect the adsorption of ions onto gold surfaces in the gas phase at a strength similar to chemical bonds while ions and charged peptides in solution are influenced at a strength similar to intermolecular bonds. The proposed model can be applied to complex gold interfaces, electrode processes, and extended to other metals.

Copper-catalyzed intermolecular and regioselective aminofluorination of styrenes: facile access to β-fluoro-N-protected phenethylamines.

PubMed

Saavedra-Olavarría, Jorge; Arteaga, Gean C; López, Jhon J; Pérez, Edwin G

2015-02-25

A copper-catalyzed regio- and intermolecular aminofluorination of styrenes has been developed. In this reaction Ph-I=N-Ts and Et3N·3HF act as nitrogen and fluorine sources, respectively. The obtained β-fluoro-N-Ts-phenethylamines can be N-alkylated with subsequent deprotection affording the corresponding β-fluoro-N-alkylated phenethylamines, which are interesting building blocks for compounds acting on neuronal targets.

A Closer Look at Trends in Boiling Points of Hydrides: Using an Inquiry-Based Approach to Teach Intermolecular Forces of Attraction

ERIC Educational Resources Information Center

Glazier, Samantha; Marano, Nadia; Eisen, Laura

2010-01-01

We describe how we use boiling-point trends of group IV-VII hydrides to introduce intermolecular forces in our first-year general chemistry classes. Starting with the idea that molecules in the liquid state are held together by some kind of force that must be overcome for boiling to take place, students use data analysis and critical reasoning to…

Chemical gas-dynamics beyond Wang Chang-Uhlenbeck's kinetics

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

Kolesnichenko, Evgeniy G.; Gorbachev, Yuriy E.

Wang Chang-Uhlenbeck equation does not give possibility to take into account intermolecular processes such as redistribution of the energy among different degrees of freedom. The modification of the generalized Wang Chang-Uhlenbeck equation including such processes is proposed. It allows to study for instance the kinetics of non-radiative transitions. Limitations of this approach are connected with the requirements of absence of polarization of rotational momentum and phases of intermolecular vibrations.

Evidence for charge-trapping inducing polymorphic structural-phase transition in pentacene.

PubMed

Ando, Masahiko; Kehoe, Tom B; Yoneya, Makoto; Ishii, Hiroyuki; Kawasaki, Masahiro; Duffy, Claudia M; Minakata, Takashi; Phillips, Richard T; Sirringhaus, Henning

2015-01-07

Trapped-charge-induced transformation of pentacene polymorphs is observed by using in situ Raman spectroscopy and molecular dynamics simulations reveal that the charge should be localized in pentacene molecules at the interface with static intermolecular disorder along the long axis. Quantum chemical calculations of the intermolecular transfer integrals suggest the disorder to be large enough to induce Anderson-type localization. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Regioselectivity in intermolecular Pauson-Khand reactions of dissymmetric fluorinated alkynes.

PubMed

Kizirian, Jean-Claude; Aiguabella, Nuria; Pesquer, Albert; Fustero, Santos; Bello, Paula; Verdaguer, Xavier; Riera, Antoni

2010-12-17

Stoichiometric and catalytic intermolecular Pauson-Khand reactions (PKRs) of dissymmetric fluorinated alkynes were performed, affording regioselectively α-fluorinated cyclopentenones. Ethyl 4,4,4-trifluorobutynoate was an excellent substrate; its reaction with norbornadiene gave the corresponding PKR adduct in good yield and complete regioselectivity. Conjugate addition of nitroalkanes or cyanide to this adduct is stereospecific and entails concomitant loss of a trifluoromethyl group. This reaction can be exploited to prepare cyclopentenones featuring quaternary centers.

Rh(I)-Catalyzed Intermolecular Hydroacylation: Enantioselective Cross-Coupling of Aldehydes and Ketoamides

PubMed Central

2015-01-01

Under Rh(I) catalysis, α-ketoamides undergo intermolecular hydroacylation with aliphatic aldehydes. A newly designed Josiphos ligand enables access to α-acyloxyamides with high atom-economy and enantioselectivity. On the basis of mechanistic and kinetic studies, we propose a pathway in which rhodium plays a dual role in activating the aldehyde for cross-coupling. A stereochemical model is provided to rationalize the sense of enantioinduction observed. PMID:24937681

Langmuir-Blodgett Thin Films of Diketopyrrolopyrrole-Based Amphiphiles.

PubMed

Lo, Chi Kin; Wang, Cheng-Yin; Oosterhout, Stefan D; Zheng, Zilong; Yi, Xueping; Fuentes-Hernandez, Canek; So, Franky; Coropceanu, Veaceslav; Brédas, Jean-Luc; Toney, Michael F; Kippelen, Bernard; Reynolds, John R

2018-04-11

We report on two π-conjugated donor-acceptor-donor (D-A-D) molecules of amphiphilic nature, aiming to promote intermolecular ordering and carrier mobility in organic electronic devices. Diketopyrrolopyrrole was selected as the acceptor moiety that was disubstituted with nonpolar and polar functional groups, thereby providing the amphiphilic structures. This structural design resulted in materials with a strong intermolecular order in the solid state, which was confirmed by differential scanning calorimetry and polarized optical microscopy. Langmuir-Blodgett (LB) films of ordered mono- and multilayers were transferred onto glass and silicon substrates, with layer quality, coverage, and intermolecular order controlled by layer compression pressure on the LB trough. Organic field-effect transistors and organic photovoltaics devices with active layers consisting of the amphiphilic conjugated D-A-D-type molecules were constructed to demonstrate that the LB technique is an effective layer-by-layer deposition approach to fabricate self-assembled, ordered thin films.

Langmuir–Blodgett Thin Films of Diketopyrrolopyrrole-Based Amphiphiles

DOE PAGES

Lo, Chi Kin; Wang, Cheng -Yin; Oosterhout, Stefan D.; ...

2018-03-30

Here, we report on two π-conjugated donor–acceptor–donor (D–A–D) molecules of amphiphilic nature, aiming to promote intermolecular ordering and carrier mobility in organic electronic devices. Diketopyrrolopyrrole was selected as the acceptor moiety that was disubstituted with nonpolar and polar functional groups, thereby providing the amphiphilic structures. This structural design resulted in materials with a strong intermolecular order in the solid state, which was confirmed by differential scanning calorimetry and polarized optical microscopy. Langmuir–Blodgett (LB) films of ordered mono- and multilayers were transferred onto glass and silicon substrates, with layer quality, coverage, and intermolecular order controlled by layer compression pressure on themore » LB trough. Organic field-effect transistors and organic photovoltaics devices with active layers consisting of the amphiphilic conjugated D–A–D-type molecules were constructed to demonstrate that the LB technique is an effective layer-by-layer deposition approach to fabricate self-assembled, ordered thin films.« less

Pressure induced enhancement of the magnetic ordering temperature in rhenium(IV) monomers

NASA Astrophysics Data System (ADS)

Woodall, Christopher H.; Craig, Gavin A.; Prescimone, Alessandro; Misek, Martin; Cano, Joan; Faus, Juan; Probert, Michael R.; Parsons, Simon; Moggach, Stephen; Martínez-Lillo, José; Murrie, Mark; Kamenev, Konstantin V.; Brechin, Euan K.

2016-12-01

Materials that demonstrate long-range magnetic order are synonymous with information storage and the electronics industry, with the phenomenon commonly associated with metals, metal alloys or metal oxides and sulfides. A lesser known family of magnetically ordered complexes are the monometallic compounds of highly anisotropic d-block transition metals; the `transformation' from isolated zero-dimensional molecule to ordered, spin-canted, three-dimensional lattice being the result of through-space interactions arising from the combination of large magnetic anisotropy and spin-delocalization from metal to ligand which induces important intermolecular contacts. Here we report the effect of pressure on two such mononuclear rhenium(IV) compounds that exhibit long-range magnetic order under ambient conditions via a spin canting mechanism, with Tc controlled by the strength of the intermolecular interactions. As these are determined by intermolecular distance, `squeezing' the molecules closer together generates remarkable enhancements in ordering temperatures, with a linear dependence of Tc with pressure.

Synthesis and structural characterization of some trisulfide analoges of thiouracil-based antithyroid drugs

NASA Astrophysics Data System (ADS)

Bhabak, Krishna P.; Bhowmick, Debasish

2012-08-01

Thiourea-based antithyroid drugs are effectively used for the treatment of hyperthyroidism. In this paper, we describe the synthesis of new trisulfides (11-12) from the commonly used thiourea-based antithyroid drugs such as 6-n-propyl-2-thiouracil (PTU) and 6-methyl-2-thiouracil (MTU) in the reaction with I2/KI system. Structural analysis by single crystal X-ray diffraction studies revealed the stabilization of trisulfides by a lactam-lactim tautomerism facilitating effective intramolecular as well as intermolecular non-covalent interactions. Although the structures of both trisulfides were found to be quite similar, a notable difference in the intermolecular interactions was observed between compounds 11 and 12 leading to different structural patterns. Structural stabilization of these trisulfides by tautomerism followed by intramolecular as well as intermolecular H-bonds makes these molecules as perfect examples in molecular recognition with self-complementary donor and acceptor units within a single molecule.

Intermolecular interactions and aggregation of fac-tris(2-phenylpyridinato-C2,N)iridium(III) in nonpolar solvents.

PubMed

Takayasu, Satoshi; Suzuki, Takayoshi; Shinozaki, Kazuteru

2013-08-15

The intermolecular interaction and aggregation of the neutral complex fac-tris(2-phenylpyridinato-C(2),N)iridium(III) (fac-Ir(ppy)3) in solution was investigated. Intermolecular interactions were found to effectively decrease the luminescence lifetime via self-quenching with increasing fac-Ir(ppy)3 concentrations. A Stern-Volmer plot for quenching in acetonitrile was linear, due to bimolecular self-quenching, but curved in toluene as the result of excimer formation. (1)H NMR spectra demonstrated a monomer-aggregate equilibrium which resulted in spectral shifts depending on solvent polarity. X-ray crystallography provided structural information concerning the aggregate, which is based on a tetramer consisting of two Δ-fac-Ir(ppy)3-Λ-fac-Ir(ppy)3 pairs. Offset π-π stacking of ppy ligands and electrostatic dipole-dipole interactions between complex molecules play an important role in the formation of these molecular pairs.

On the interatomic potentials for noble gas mixtures

NASA Astrophysics Data System (ADS)

Watanabe, Kyoko; Allnatt, A. R.; Meath, William J.

1982-07-01

Recently, a relatively simple scheme for the construction of isotropic intermolecular potentials has been proposed and tested for the like species interactions involving He, Ne, Ar, Kr and H 2. The model potential has an adjustable parameter which controls the balance between its exchange and Coulomb energy components. The representation of the Coulomb energy contains a damped multipolar dispersion energy series (which is truncated through O( R-10) and provides additional flexibility through adjustment of the dispersion energy coefficients, particularly C8 and C10, within conservative error estimates. In this paper the scheme is tested further by application to interactions involving unlike noble gas atoms where the parameters in the potential model are determined by fitting mixed second virial coefficient data as a function of temperature. Generally the approach leads to potential of accuracy comparable to the best available literature potentials which are usually determined using a large base of experimental and theoretical input data. Our results also strongly indicate the need of high quality virial data.

Comment on “Isolating the non-polar contributions to the intermolecular potential for water-alkane interactions” [J. Chem. Phys. 141, 064905 (2014)

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

McDaniel, Jesse G.; Yethiraj, Arun

The manuscript by Ballal et al.(Ref 1) presents an interesting study demonstrating the inability of popular force fields with standard combination rules to accurately describe water/alkane interactions. The authors find that the Lorentz-Berthelot combination rules on the SPC/E water and TraPPE alkane potentials give a cross interaction that fails to predict the (low-water content) water solubility in various alkanes. Realizing that both explicit polarization as well as the static octupole moment of methane are missing in these potentials, the authors examine the effect of these terms, but are still unable to resolve the discrepancy. They conclude with the statement thatmore » “the research community lacks a complete picture of water-alkane interactions at the molecular level.« less

Comment on “Isolating the non-polar contributions to the intermolecular potential for water-alkane interactions” [J. Chem. Phys. 141, 064905 (2014)

DOE PAGES

McDaniel, Jesse G.; Yethiraj, Arun

2016-04-06

The manuscript by Ballal et al.(Ref 1) presents an interesting study demonstrating the inability of popular force fields with standard combination rules to accurately describe water/alkane interactions. The authors find that the Lorentz-Berthelot combination rules on the SPC/E water and TraPPE alkane potentials give a cross interaction that fails to predict the (low-water content) water solubility in various alkanes. Realizing that both explicit polarization as well as the static octupole moment of methane are missing in these potentials, the authors examine the effect of these terms, but are still unable to resolve the discrepancy. They conclude with the statement thatmore » “the research community lacks a complete picture of water-alkane interactions at the molecular level.« less

Experimental and theoretical studies of the crystal structures of bis-isoxazole-bis-methylene dinitrate (BIDN) and bis-isoxazole tetramethylene tetranitrate (BITN) by x-ray crystallography and density functional theory

NASA Astrophysics Data System (ADS)

Taylor, Decarlos E.; Sausa, Rosario C.

2018-06-01

The determination of crystal structures plays an important role for model testing and validation, and understanding intra and intermolecular interactions that influence crystal packing. Here, we report the molecular structure of two recently synthesized energetic molecules, 3,3-bis-isoxazole-5,5‧-bis-methylene dinitrate (C8H6N4O8, BIDN) and bis-isoxazole tetramethylene tetranitrate (C10H8N6O14, BITN) determined by single crystal x-ray diffraction and solid state density functional theory (DFT). BIDN is composed of two planar alkyl nitrate groups (r.m.s deviation = 0.0004 (1) Å) bonded to two planar azole rings (r.m.s deviation = 0.001 (1) Å, whereas BITN is composed of four planar alkyl nitrate groups (average r.m.s deviation = 0.002 (1) Å) bonded to two planar azole rings (average r.m.s deviation = 0.002 (1) Å). The theoretical calculations predict very well the planarity of both the alkyl nitrate groups and rings for both compounds. Furthermore, they predict well the bond lengths and angles of both molecules with mean deviation values of 0.018 Å (BIDN) and 0.017 Å (BITN) and 0.481° (BIDN) and 0.747° (BITN). Overall, the DFT determined torsion angles agree well with those determined experimentally for both BIDN (average deviation = 1.139°) and BITN (average deviation = 0.604°). The theoretical cell constant values are in excellent agreement with those determined experimentally for both molecules, with the BIDN a cell value and β angle showing the largest deviation, 2.1% and -1.3%, respectively. Contacts between the atoms N and H dominate the intermolecular interactions of BIDN, whereas contacts involving the atoms O and H dominate the BITN intermolecular interactions. Electrostatic potential calculations at the B3LYP/6-31G* level reveal BIDN exhibits a lower sensitivity to impact compared to BITN.

A programmable optimization environment using the GAMESS-US and MERLIN/MCL packages. Applications on intermolecular interaction energies

NASA Astrophysics Data System (ADS)

Kalatzis, Fanis G.; Papageorgiou, Dimitrios G.; Demetropoulos, Ioannis N.

2006-09-01

The Merlin/MCL optimization environment and the GAMESS-US package were combined so as to offer an extended and efficient quantum chemistry optimization system, capable of implementing complex optimization strategies for generic molecular modeling problems. A communication and data exchange interface was established between the two packages exploiting all Merlin features such as multiple optimizers, box constraints, user extensions and a high level programming language. An important feature of the interface is its ability to perform dimer computations by eliminating the basis set superposition error using the counterpoise (CP) method of Boys and Bernardi. Furthermore it offers CP-corrected geometry optimizations using analytic derivatives. The unified optimization environment was applied to construct portions of the intermolecular potential energy surface of the weakly bound H-bonded complex C 6H 6-H 2O by utilizing the high level Merlin Control Language. The H-bonded dimer HF-H 2O was also studied by CP-corrected geometry optimization. The ab initio electronic structure energies were calculated using the 6-31G ** basis set at the Restricted Hartree-Fock and second-order Moller-Plesset levels, while all geometry optimizations were carried out using a quasi-Newton algorithm provided by Merlin. Program summaryTitle of program: MERGAM Catalogue identifier:ADYB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYB_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: The program is designed for machines running the UNIX operating system. It has been tested on the following architectures: IA32 (Linux with gcc/g77 v.3.2.3), AMD64 (Linux with the Portland group compilers v.6.0), SUN64 (SunOS 5.8 with the Sun Workshop compilers v.5.2) and SGI64 (IRIX 6.5 with the MIPSpro compilers v.7.4) Installations: University of Ioannina, Greece Operating systems or monitors under which the program has been tested: UNIX Programming language used: ANSI C, ANSI Fortran-77 No. of lines in distributed program, including test data, etc.:11 282 No. of bytes in distributed program, including test data, etc.: 49 458 Distribution format: tar.gz Memory required to execute with typical data: Memory requirements mainly depend on the selection of a GAMESS-US basis set and the number of atoms No. of bits in a word: 32 No. of processors used: 1 Has the code been vectorized or parallelized?: no Nature of physical problem: Multidimensional geometry optimization is of great importance in any ab initio calculation since it usually is one of the most CPU-intensive tasks, especially on large molecular systems. For example, the geometric and energetic description of van der Waals and weakly bound H-bonded complexes requires the construction of related important portions of the multidimensional intermolecular potential energy surface (IPES). So the various held views about the nature of these bonds can be quantitatively tested. Method of solution: The Merlin/MCL optimization environment was interconnected with the GAMESS-US package to facilitate geometry optimization in quantum chemistry problems. The important portions of the IPES require the capability to program optimization strategies. The Merlin/MCL environment was used for the implementation of such strategies. In this work, a CP-corrected geometry optimization was performed on the HF-H 2O complex and an MCL program was developed to study portions of the potential energy surface of the C 6H 6-H 2O complex. Restrictions on the complexity of the problem: The Merlin optimization environment and the GAMESS-US package must be installed. The MERGAM interface requires GAMESS-US input files that have been constructed in Cartesian coordinates. This restriction occurs from a design-time requirement to not allow reorientation of atomic coordinates; this rule holds always true when applying the COORD = UNIQUE keyword in a GAMESS-US input file. Typical running time: It depends on the size of the molecular system, the size of the basis set and the method of electron correlation. Execution of the test run took approximately 5 min on a 2.8 GHz Intel Pentium CPU.

Quantum dynamics of the vibrations of helium bound to the nanosurface of a large planar organic molecule: phthalocyanine . He van der Waals complex.

PubMed

Gibbons, Brittney R; Xu, Minzhong; Bacić, Zlatko

2009-04-23

We report rigorous quantum three-dimensional calculations of highly excited intermolecular vibrational states of the van der Waals (vdW) complex phthalocyanine.He (Pc.He). The Pc molecule was treated as rigid and the intermolecular potential energy surface (IPES) was represented as a sum of atom-atom Lennard-Jones pair potentials. The IPES has four equivalent global minima on the diagonals of the square-shaped Pc, inside its five-membered rings, and four slightly shallower local minima between them, creating a distinctive corrugation pattern of the molecular nanosurface. The vdW vibrational states analyzed in this work extend to about two-thirds of the well depth of the IPES. For the assignment of the in-plane (xy) vdW vibrational excitations it was necessary to resort to two sets of quantum numbers, the Cartesian quantum numbers [nu(x), nu(y)] and the quantum numbers (v, l) of the 2D isotropic oscillator, depending on the nodal structure and the symmetry of the wave functions. The delocalization of the He atom parallel to the molecular surface is large already in the ground vdW state. It increases rapidly with the number of quanta in the in-plane vdW vibrations, with the maximum root-mean-square amplitudes Deltax and Deltay of about 7 au at the excitation energies around 40 cm(-1). The wave functions of the highly excited states tend to be delocalized over the entire nanosurface and often have a square shape, reflecting that of the substrate.

The electronegativity equalization method fused with molecular mechanics: a fluctuating charge and flexible body potential function for [Emim][Gly] ionic liquids.

PubMed

Wu, Yang; Li, Yao; Hu, Na; Hong, Mei

2014-02-14

Recently, experimental and theoretical studies on amino acid ionic liquid (AAIL) systems have attracted much attention. A transferable intermolecular potential approach that includes fluctuating charges and a flexible body based on a combination of the electronegativity equalization method and molecular mechanics (EEM/MM), and its application to an AAIL system containing 1-ethyl-3-methylimidazolium ([Emim](+)) and glycine ([Gly](-)) are explored and tested in this study. A consistent integration of EEM with MM requires the input of the EEM charges of all atoms into the MM intermolecular electrostatic interaction term. Compared with ionic liquid (IL) force fields, the EEM/MM model has an outstanding feature: the EEM/MM model not only presents the electrostatic interaction of atoms and their changes in response to different ambient environments but also introduces "the H-bond interaction region" in which a new parameter kHB(RHB) is used to describe the electrostatic interaction of hydrogen atoms in [Emim](+) and oxygen atoms in [Gly](-), which can form hydrogen bonds. The EEM/MM model gives quite accurate predictions for gas-phase state properties of [Emim](+), [Gly](-), and ion pairs, such as optimized geometries, dipole moments, vibrational frequencies, and cluster interaction energies. Due to its explicit description of charges and hydrogen bonds, the EEM/MM model also performs well for the liquid-phase properties of [Emim][Gly] under ambient conditions. The calculated properties, such as density, heat of vaporization, the self-diffusion coefficient, and ionic conductivity, are fairly consistent with available experimental results.

Interaction between polymer constituents and the structure of biopolymers

NASA Technical Reports Server (NTRS)

Rein, R.

1974-01-01

The paper reviews the current status of methods for calculating intermolecular interactions between biopolymer units. The nature of forces contributing to the various domains of intermolecular separations is investigated, and various approximations applicable in the respective regions are examined. The predictive value of current theory is tested by establishing a connection with macroscopic properties and comparing the theoretical predicted values with those derived from experimental data. This has led to the introduction of a statistical model describing DNA.

Highly Stereoselective Intermolecular Haloetherification and Haloesterification of Allyl Amides

PubMed Central

Soltanzadeh, Bardia; Jaganathan, Arvind; Staples, Richard J.

2016-01-01

An organocatalytic and highly regio-, diastereo-, and enantioselective intermolecular haloetherification and haloesterification reaction of allyl amides is reported. A variety of alkene substituents and substitution patterns are compatible with this chemistry. Notably, electronically unbiased alkene substrates exhibit exquisite regio- and diastereoselectivity for the title transformation. We also demonstrate that the same catalytic system can be used in both chlorination and bromination reactions of allyl amides with a variety of nucleophiles with little or no modification. PMID:26110812

A Catalytic, Brønsted Base Strategy for Intermolecular Allylic C—H Amination

PubMed Central

Reed, Sean A.; Mazzotti, Anthony R.; White, M. Christina

2009-01-01

A Brønsted base activation mode for oxidative, Pd(II)/sulfoxide catalyzed, intermolecular C—H allylic amination is reported. N,N-diisopropylethylamine was found to promote amination of unactivated terminal olefins, forming the corresponding linear allylic amine products with high levels of stereo-, regio-, and chemoselectivity. The predictable and high selectivity of this C—H oxidation method enables late-stage incorporation of nitrogen into advanced synthetic intermediates and natural products. PMID:19645492

Singlet Fission via an Excimer-Like Intermediate in 3,6-Bis(thiophen-2-yl)diketopyrrolopyrrole Derivatives.

PubMed

Mauck, Catherine M; Hartnett, Patrick E; Margulies, Eric A; Ma, Lin; Miller, Claire E; Schatz, George C; Marks, Tobin J; Wasielewski, Michael R

2016-09-14

Singlet fission (SF) in polycrystalline thin films of four 3,6-bis(thiophen-2-yl)diketopyrrolopyrrole (TDPP) chromophores with methyl (Me), n-hexyl (C6), triethylene glycol (TEG), and 2-ethylhexyl (EH) substituents at the 2,5-positions is found to involve an intermediate excimer-like state. The four different substituents yield four distinct intermolecular packing geometries, resulting in variable intermolecular charge transfer (CT) interactions in the solid. SF from the excimer state of Me, C6, TEG, and EH takes place in τSF = 22, 336, 195, and 1200 ps, respectively, to give triplet yields of 200%, 110%, 110%, and 70%, respectively. The transient spectra of the excimer-like state and its energetic proximity to the lowest excited singlet state in these derivatives suggests that this state may be the multiexciton (1)(T1T1) state that precedes formation of the uncorrelated triplet excitons. The excimer decay rates correlate well with the SF efficiencies and the degree of intermolecular donor-acceptor interactions resulting from π-stacking of the thiophene donor of one molecule with the DPP core acceptor in another molecule as observed in the crystal structures. Such interactions are found to also increase with the SF coupling energies, as calculated for each derivative. These structural and spectroscopic studies afford a better understanding of the electronic interactions that enhance SF in chromophores having strong intra- and intermolecular CT character.

Intermolecular detergent-membrane protein noes for the characterization of the dynamics of membrane protein-detergent complexes.

PubMed

Eichmann, Cédric; Orts, Julien; Tzitzilonis, Christos; Vögeli, Beat; Smrt, Sean; Lorieau, Justin; Riek, Roland

2014-12-11

The interaction between membrane proteins and lipids or lipid mimetics such as detergents is key for the three-dimensional structure and dynamics of membrane proteins. In NMR-based structural studies of membrane proteins, qualitative analysis of intermolecular nuclear Overhauser enhancements (NOEs) or paramagnetic resonance enhancement are used in general to identify the transmembrane segments of a membrane protein. Here, we employed a quantitative characterization of intermolecular NOEs between (1)H of the detergent and (1)H(N) of (2)H-perdeuterated, (15)N-labeled α-helical membrane protein-detergent complexes following the exact NOE (eNOE) approach. Structural considerations suggest that these intermolecular NOEs should show a helical-wheel-type behavior along a transmembrane helix or a membrane-attached helix within a membrane protein as experimentally demonstrated for the complete influenza hemagglutinin fusion domain HAfp23. The partial absence of such a NOE pattern along the amino acid sequence as shown for a truncated variant of HAfp23 and for the Escherichia coli inner membrane protein YidH indicates the presence of large tertiary structure fluctuations such as an opening between helices or the presence of large rotational dynamics of the helices. Detergent-protein NOEs thus appear to be a straightforward probe for a qualitative characterization of structural and dynamical properties of membrane proteins embedded in detergent micelles.

Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining

PubMed Central

Kukshal, Vandna; Kim, In-Kwon; Hura, Gregory L.; Tomkinson, Alan E.; Tainer, John A.; Ellenberger, Tom

2015-01-01

Mammalian DNA ligase III (LigIII) functions in both nuclear and mitochondrial DNA metabolism. In the nucleus, LigIII has functional redundancy with DNA ligase I whereas LigIII is the only mitochondrial DNA ligase and is essential for the survival of cells dependent upon oxidative respiration. The unique LigIII zinc finger (ZnF) domain is not required for catalytic activity but senses DNA strand breaks and stimulates intermolecular ligation of two DNAs by an unknown mechanism. Consistent with this activity, LigIII acts in an alternative pathway of DNA double strand break repair that buttresses canonical non-homologous end joining (NHEJ) and is manifest in NHEJ-defective cancer cells, but how LigIII acts in joining intermolecular DNA ends versus nick ligation is unclear. To investigate how LigIII efficiently joins two DNAs, we developed a real-time, fluorescence-based assay of DNA bridging suitable for high-throughput screening. On a nicked duplex DNA substrate, the results reveal binding competition between the ZnF and the oligonucleotide/oligosaccharide-binding domain, one of three domains constituting the LigIII catalytic core. In contrast, these domains collaborate and are essential for formation of a DNA-bridging intermediate by adenylated LigIII that positions a pair of blunt-ended duplex DNAs for efficient and specific intermolecular ligation. PMID:26130724

Theoretical investigations of two adamantane derivatives: A combined X-ray, DFT, QTAIM analysis and molecular docking

NASA Astrophysics Data System (ADS)

Al-Wahaibi, Lamya H.; Sujay, Subramaniam; Muthu, Gangadharan Ganesh; El-Emam, Ali A.; Venkataramanan, Natarajan S.; Al-Omary, Fatmah A. M.; Ghabbour, Hazem A.; Percino, Judith; Thamotharan, Subbiah

2018-05-01

A detailed structural analysis of two adamantane derivatives namely, ethyl 2-[(Z)-1-(adamantan-1-yl)-3-(phenyl)isothioureido]acetate I and ethyl 2-[(Z)-1-(adamantan-1-yl)-3-(4-fluorophenyl)isothioureido]acetate II is carried out to understand the effect of fluorine substitution. The introduction of fluorine atom alters the crystal packing and is completely different from its parent compound. The fluorine substitution drastically reduced the intermolecular H⋯H contacts and this reduction is compensated by intermolecular F⋯H and F⋯F contacts. The relative contributions of various intermolecular contacts present in these structures were quantified using Hirshfeld surface analysis. Energetically significant molecular pairs were identified from the crystal structures of these compounds using PIXEL method. The structures of I and II are optimized in gas and solvent phases using the B3LYP-D3/6-311++G(d,p) level of theory. The quantum theory of atoms-in-molecules (QTAIM) analysis was carried out to estimate the strengths of various intermolecular contacts present in these molecular dimers. The results suggest that the Hsbnd H bonding take part in the stabilization of crystal structures. The experimental and theoretical UV-Vis results show the variations in HOMO and LUMO energy levels. In silico docking analysis indicates that both compounds I and II may exhibit inhibitory activity against 11-β-hydroxysteroid dehydrogenase 1 (11-β-HSD1).

Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining.

PubMed

Kukshal, Vandna; Kim, In-Kwon; Hura, Gregory L; Tomkinson, Alan E; Tainer, John A; Ellenberger, Tom

2015-08-18

Mammalian DNA ligase III (LigIII) functions in both nuclear and mitochondrial DNA metabolism. In the nucleus, LigIII has functional redundancy with DNA ligase I whereas LigIII is the only mitochondrial DNA ligase and is essential for the survival of cells dependent upon oxidative respiration. The unique LigIII zinc finger (ZnF) domain is not required for catalytic activity but senses DNA strand breaks and stimulates intermolecular ligation of two DNAs by an unknown mechanism. Consistent with this activity, LigIII acts in an alternative pathway of DNA double strand break repair that buttresses canonical non-homologous end joining (NHEJ) and is manifest in NHEJ-defective cancer cells, but how LigIII acts in joining intermolecular DNA ends versus nick ligation is unclear. To investigate how LigIII efficiently joins two DNAs, we developed a real-time, fluorescence-based assay of DNA bridging suitable for high-throughput screening. On a nicked duplex DNA substrate, the results reveal binding competition between the ZnF and the oligonucleotide/oligosaccharide-binding domain, one of three domains constituting the LigIII catalytic core. In contrast, these domains collaborate and are essential for formation of a DNA-bridging intermediate by adenylated LigIII that positions a pair of blunt-ended duplex DNAs for efficient and specific intermolecular ligation. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Concerted Mitigation of O···H and C(π)···H Interactions Prospects Sixfold Gain in Optical Nonlinearity of Ionic Stilbazolium Derivatives

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

Cole, Jacqueline M.; Lin, Tze-Chia; Edwards, Alison J.

2015-03-04

DAST (4-dimethylamino-N-methyl-4-stilbazolium tosylate) is the most commercially successful organic nonlinear optical (NLO) material for frequency-doubling, integrated optics, and THz wave applications. Its success is predicated on its high optical nonlinearity with concurrent sufficient thermal stability. Many chemical derivatives of DAST have therefore been developed to optimize their properties; yet, to date, none have surpassed the overall superiority of DAST for NLO photonic applications. This is perhaps because DAST is an ionic salt wherein its NLO-active cation is influenced by multiple types of subtle intermolecular forces that are hard to quantify, thus, making difficult the molecular engineering of better functioning DASTmore » derivatives. Here, we establish a model parameter, ηinter, that isolates the influence of intermolecular interactions on second-order optical nonlinearity in DAST and its derivatives, using second-harmonic generation (SHG) as a qualifier; by systematically mapping intercorrelations of all possible pairs of intermolecular interactions to ηinter, we uncover a relationship between concerted intermolecular interactions and SHG output. This correlation reveals that a sixfold gain in the intrinsic second-order NLO performance of DAST is possible, by eliminating the identified interactions. This prediction offers the first opportunity to systematically design next-generation DAST-based photonic device nanotechnology to realize such a prospect.« less

Apparent dynamic contact angle of an advancing gas--liquid meniscus

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

Kalliadasis, S.; Chang, H.

1994-01-01

The steady motion of an advancing meniscus in a gas-filled capillary tube involves a delicate balance of capillary, viscous, and intermolecular forces. The limit of small capillary numbers Ca (dimensionless speeds) is analyzed here with a matched asymptotic analysis that links the outer capillary region to the precursor film in front of the meniscus through a lubricating film. The meniscus shape in the outer region is constructed and the apparent dynamic contact angle [Theta] that the meniscus forms with the solid surface is derived as a function of the capillary number, the capillary radius, and the Hamaker's constant for intermolecularmore » forces, under conditions of weak gas--solid interaction, which lead to fast spreading of the precursor film and weak intermolecular forces relative to viscous forces within the lubricating film. The dependence on intermolecular forces is very weak and the contact angle expression has a tight upper bound tan [Theta]=7.48 Ca[sup 1/3] for thick films, which is independent of the Hamaker constant. This upper bound is in very good agreement with existing experimental data for wetting fluids in any capillary and for partially wetting fluids in a prewetted capillary. Significant correction to the Ca[sup 1/3] dependence occurs only at very low Ca, where the intermolecular forces become more important and tan [Theta] diverges slightly from the above asymptotic behavior toward lower values.« less

Refractive index and thickness determination in Langmuir monolayers of myelin lipids.

PubMed

Pusterla, Julio M; Malfatti-Gasperini, Antonio A; Puentes-Martinez, Ximena E; Cavalcanti, Leide P; Oliveira, Rafael G

2017-05-01

Langmuir monolayers at the air/water interface are widely used as biomembrane models and for amphiphilic molecules studies in general. Under controlled intermolecular organization (lateral molecular area), surface pressure, surface potential, reflectivity (R) and other magnitudes can be precisely determined on these planar monomolecular films. However, some physical parameters such as the refractive index of the monolayer (n) still remain elusive. The refractive index is very relevant because (in combination with R) it allows for the determination of the thickness of the film. The uncertainties of n determine important errors that propagate non-linearly into the calculation of monolayers thickness. Here we present an analytical method for the determination of n in monolayers based on refractive index matching. By using a Brewster angle microscopy (BAM) setup and monolayers spread over subphases with variable refractive index (n 2 ), a minimum in R is search as a function of n 2 . In these conditions, n equals n 2 . The results shown correspond to monolayers of myelin lipids. The n values remain constant at 1.46 upon compression and equals the obtained value for myelin lipid bilayers in suspension. The values for n and R allow for the determination of thickness. We establish comparisons between these thicknesses for the monolayer and those obtained from two X-ray scattering techniques: 1) GIXOS for monolayers at the air/water interface and 2) SAXS for bilayers in bulk suspension. This allows us to conclude that the thickness that we measure by BAM includes the apolar and polar headgroup regions of the monolayer. Copyright © 2017 Elsevier B.V. All rights reserved.

New chemical-DSMC method in numerical simulation of axisymmetric rarefied reactive flow

NASA Astrophysics Data System (ADS)

Zakeri, Ramin; Kamali Moghadam, Ramin; Mani, Mahmoud

2017-04-01

The modified quantum kinetic (MQK) chemical reaction model introduced by Zakeri et al. is developed for applicable cases in axisymmetric reactive rarefied gas flows using the direct simulation Monte Carlo (DSMC) method. Although, the MQK chemical model uses some modifications in the quantum kinetic (QK) method, it also employs the general soft sphere collision model and Stockmayer potential function to properly select the collision pairs in the DSMC algorithm and capture both the attraction and repulsion intermolecular forces in rarefied gas flows. For assessment of the presented model in the simulation of more complex and applicable reacting flows, first, the air dissociation is studied in a single cell for equilibrium and non-equilibrium conditions. The MQK results agree well with the analytical and experimental data and they accurately predict the characteristics of the rarefied flowfield with chemical reaction. To investigate accuracy of the MQK chemical model in the simulation of the axisymmetric flow, air dissociation is also assessed in an axial hypersonic flow around two geometries, the sphere as a benchmark case and the blunt body (STS-2) as an applicable test case. The computed results including the transient, rotational and vibrational temperatures, species concentration in the stagnation line, and also the heat flux and pressure coefficient on the surface are compared with those of the other chemical methods like the QK and total collision energy (TCE) models and available analytical and experimental data. Generally, the MQK chemical model properly simulates the chemical reactions and predicts flowfield characteristics more accurate rather than the typical QK model. Although in some cases, results of the MQK approaches match with those of the TCE method, the main point is that the MQK does not need any experimental data or unrealistic assumption of specular boundary condition as used in the TCE method. Another advantage of the MQK model is the significant reduction of computational cost rather than the QK chemical model to reach the same accuracy because of applying more proper collision model and consequently, decrease of the particles collision number.

Big data analytics in healthcare: promise and potential.

PubMed

Raghupathi, Wullianallur; Raghupathi, Viju

2014-01-01

To describe the promise and potential of big data analytics in healthcare. The paper describes the nascent field of big data analytics in healthcare, discusses the benefits, outlines an architectural framework and methodology, describes examples reported in the literature, briefly discusses the challenges, and offers conclusions. The paper provides a broad overview of big data analytics for healthcare researchers and practitioners. Big data analytics in healthcare is evolving into a promising field for providing insight from very large data sets and improving outcomes while reducing costs. Its potential is great; however there remain challenges to overcome.

Synthesis, structure, computational and in-silico anticancer studies of N,N-diethyl-N‧-palmitoylthiourea

NASA Astrophysics Data System (ADS)

Asegbeloyin, Jonnie Niyi; Oyeka, Ebube Evaristus; Okpareke, Obinna; Ibezim, Akachukwu

2018-02-01

A new potential ONS donor ligand N,N-diethyl-N‧-palmitoylthiourea (PACDEA) with the molecular formular C21H42N2OS has been synthesized and characterized by ESI-MS, UV, FTIR 1H and 13C NMR spectroscopy and single X-ray crystallography. The asymmetric molecules crystallized in the centrosymmetric structure of monoclinic crystal system with space group P21/c. In the crystal structure of the compound, molecules are linked in a continuous chain by intermolecular Nsbnd H⋯Odbnd C hydrogen bonds, which stabilized the crystal structure. The palmitoyl moiety and N (2)-ethyl group lie on a plane, while the thiocarbonyl moiety is twisted and lying othorgonal to the plane. Non-covalent interaction (NCI) analysis on the hydrogen bonded solid state structure of the molecule revealed the presence of a significant number of non-covalent interactions including intermolecular hydrogen bonding interactions, Csbnd Hsbnd -lone pair interactions, weak Van der Waals interactions, and steric/ring closure interactions. The NCI analysis also showed the presence of intramolecular stabilizing Csbnd H⋯Odbnd C and Csbnd H⋯Sdbnd C interactions. Docking simulation revealed that the compound interacted favourably with ten selected validated anticancer drug targets, which is an indication that the compound could possess some anticancer properties.

Crystal structure, Hirshfeld surfaces and DFT computation of NLO active (2E)-2-(ethoxycarbonyl)-3-[(1-methoxy-1-oxo-3-phenylpropan-2-yl)amino] prop-2-enoic acid.

PubMed

Venkatesan, Perumal; Thamotharan, Subbiah; Ilangovan, Andivelu; Liang, Hongze; Sundius, Tom

2016-01-15

Nonlinear optical (NLO) activity of the compound (2E)-2-(ethoxycarbonyl)-3-[(1-methoxy-1-oxo-3-phenylpropan-2-yl)amino] prop-2-enoic acid is investigated experimentally and theoretically using X-ray crystallography and quantum chemical calculations. The NLO activity is confirmed by both powder Second Harmonic Generation (SHG) experiment and first hyper polarizability calculation. The title compound displays 8 fold excess of SHG activity when compared with the standard compound KDP. The gas phase geometry optimization and vibrational frequencies calculations are performed using density functional theory (DFT) incorporated in B3LYP with 6-311G++(d,p) basis set. The title compound crystallizes in non-centrosymmetric space group P21. Moreover, the crystal structure is primarily stabilized through intramolecular N-H···O and O-H···O hydrogen bonds and intermolecular C-H···O and C-H···π interactions. These intermolecular interactions are analyzed and quantified using Hirshfeld surface analysis and PIXEL method. The detailed vibrational assignments are performed on the basis of the potential energy distributions (PED) of the vibrational modes. Copyright © 2015 Elsevier B.V. All rights reserved.

Pressure Dependence of the Boson Peak of Glassy Glycerol

DOE PAGES

Ahart, Muhtar; Aihaiti, Dilare; Hemley, Russell J.; ...

2017-05-31

The pressure dependence of the Boson peak (BP) of glycerol, including its behavior across the liquid-glass transition, has been studied under pressure using Raman scattering. A significant increase of the BP frequency was observed with pressure up to 11 GPa at room temperature. The pressure dependence of BP frequency ν BP is proportional to (1+P/P 0) 1/3, where P and P 0 are the pressure and a constant, respectively, the spectra are consistent with a soft potential model. The characteristic length of medium range order is close in size to a cyclic trimer of glycerol molecules, which is predicted asmore » the medium range order of a BP vibration using molecular dynamics simulations. The pressure dependence of a characteristic length of medium range order is nearly constant. The pressure induced structural changes in glycerol can be understood in terms of the shrinkage of voids with cyclic trimers remaining up to at least 11 GPa. Lastly, the pressure dependence of intermolecular O-H stretching mode indicates that the intermolecular hydrogen bond distance gradually decreases below the glass transition pressure of ~5 GPa, while it becomes nearly constant in the glassy state indicating the disappearance of the free volume in the dense glass.« less

Understanding and modulating opalescence and viscosity in a monoclonal antibody formulation

PubMed Central

Salinas, Branden A; Sathish, Hasige A; Bishop, Steven M; Harn, Nick; Carpenter, John F; Randolph, Theodore W

2014-01-01

Opalescence and high viscosities can pose challenges for high concentration formulation of antibodies. Both phenomena result from protein-protein intermolecular interactions that can be modulated with solution ionic strength. We studied a therapeutic monoclonal antibody that exhibits high viscosity in solutions at low ionic strength (~20 centipoise (cP) at 90 mg/mL and 23°C) and significant opalescence at isotonic ionic strength (approximately 100 nephelometric turbidity units at 90 mg/mL and 23°C). The intermolecular interactions responsible for these effects were characterized using membrane osmometry, static light scattering and zeta potential measurements. The net protein-protein interactions were repulsive at low ionic strength (~4 mM) and attractive at isotonic ionic strengths. The high viscosities are attributed to electroviscous forces at low ionic strength and the significant opalescence at isotonic ionic strength is correlated with attractive antibody interactions. Furthermore there appears to be a connection to critical phenomena and it is suggested that the extent of opalescence is dependent on the proximity to the critical point. We demonstrate that by balancing the repulsive and attractive forces via intermediate ionic strengths and by increasing the mAb concentration above the apparent critical concentration both opalescence and viscosity can be simultaneously minimized. PMID:19475558

Temperature-dependent spectroscopic evidences of curcumin in aqueous medium: a mechanistic study of its solubility and stability.

PubMed

Jagannathan, Ramya; Abraham, Priya Mary; Poddar, Pankaj

2012-12-20

In curcumin, keto-enol-enolate equilibrium of the heptadiene-dione moiety determines its physiochemical and antioxidant properties. However, its poor solubility in water at neutral pH and room temperature decreases its bioavailability. Potential therapeutic applications have triggered an interest in manipulating the solubility of curcumin in water as its stability and solubility in water remains poorly understood. Here, the mechanism behind its solubility at various temperatures and the influence of interplay of temperature, intramolecular H-bonding, and intermolecular forces is reported, which leads to aggregation-disaggregation at various temperatures. Remarkable change is observed in temperature-dependent electronic transition behavior of curcumin, however, the absorption spectra after cooling and heating cycles remain unchanged, hinting much better thermal stability of curcumin in water than previously thought. This study indicates that it is perhaps the breaking of intramolecular hydrogen bonding which leads to exposure of polar groups and hence responsible for the dissolution of curcumin at higher temperature. The formation of intermolecular aggregates might be responsible behind a better room temperature stability of the molecules after cooling its aqueous suspension from 90 to 25 °C. These curcumin solubility studies have great application in biological research with reference to bioavailability and to understand target oriented mode of action of curcumin.

Looking for the interactions between omeprazole and amoxicillin in a disordered phase. An experimental and theoretical study.

PubMed

Russo, Marcos G; Sancho, Matias I; Silva, Lorena M A; Baldoni, Hector A; Venancio, Tiago; Ellena, Javier; Narda, Griselda E

2016-03-05

In this paper, co-grinding mixtures of omeprazole-amoxicillin trihydrate (CGM samples) and omeprazole-anhydrous amoxicillin (CGMa samples) at 3:7, 1:1 and 7:3 molar ratios, respectively, were studied with the aim of obtaining a co-amorphous system and determining the potential intermolecular interactions. These systems were fully characterized by differential scanning calorimetry (DSC), FT-infrared spectroscopy (FTIR), X-ray powder diffraction (PXRD), scanning electron microscopy (SEM) and solid state Nuclear Magnetic Resonance (ssNMR). The co-grinding process was not useful to get a co-amorphous system but it led to obtaining the 1:1 CGMa disordered phase. Moreover, in this system both FTIR and ssNMR analysis strongly suggest intermolecular interactions between the sulfoxide group of omeprazole and the primary amine of amoxicillin anhydrous. The solubility measurements were performed in simulated gastric fluid (SGF) to prove the effect of the co-grinding process. Complementarily, we carried out density functional theory calculations (DFT) followed by quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses in order to shed some light on the principles that guide the possible formation of heterodimers at the molecular level, which are supported by spectroscopic experimental findings. Copyright © 2015 Elsevier B.V. All rights reserved.

Field-Assisted Contact Line Motion in Thin Films.

PubMed

Ghosh, Udita Uday; DasGupta, Sunando

2018-04-25

The balance of intermolecular and surface forces plays a critical role in the transport phenomena near the contact line region of an extended meniscus in several technologically important processes. Externally applied fields can alter the equilibrium and stability of the meniscus with concomitant effects on its shape and spreading characteristics and may even lead to an oscillation. This feature article provides a detailed account of the present and past efforts in exploring the behavior of curved thin liquid films subjected to mild thermal perturbations, heat input, and electrical and magnetic fields for pure as well as colloidal suspensions, including the effects of particle charge and polarity. The shape-dependent intermolecular force field has been evaluated in situ by a nonobtrusive optical technique utilizing the interference phenomena and subsequent image processing. The critical role of disjoining pressure is identified along with the determination of the Hamaker constant. The spatial and temporal variations of the capillary forces are evaluated for the advancing and receding menisci. The Maxwell-stress-induced enhanced spreading during electrowetting, at relatively low voltages, and that due to the application of a magnetic field are discussed with respect to their distinctly different characteristics and application potentials. The use of the augmented Young-Laplace equation elicited additional insights into the fundamental physics for flow in ultrathin liquid films.

Modeling the Flow of Rarefied Gases at NASA

NASA Technical Reports Server (NTRS)

Forrest E. Lumpkin, III

2012-01-01

At modest temperatures, the thermal energy of atmospheric diatomic gases such as nitrogen is primarily distributed between only translational and rotational energy modes. Furthermore, these energy modes are fully excited such that the specific heat at constant volume is well approximated by the simple expression C(sub v) = 5/2 R. As a result, classical mechanics provides a suitable approximation at such temperatures of the true quantum mechanical behavior of the inter-molecular collisions of such molecules. Using classical mechanics, the transfer of energy between rotational and translation energy modes is studied. The approach of Lordi and Mates is adopted to compute the trajectories and time dependent rotational orientations and energies during the collision of two non-polar diatomic molecules. A Monte-Carlo analysis is performed collecting data from the results of many such simulations in order to estimate the rotational relaxation time. A Graphical Processing Unit (GPU) is employed to improve the performance of the Monte-Carlo analysis. A comparison of the performance of the GPU implementation to an implementation on traditional computer architecture is made. Effects of the assumed inter-molecular potential on the relaxation time are studied. The seminar will also present highlights of computational analyses performed at NASA Johnson Space Center of heat transfer in rarefied gases.

Resolution enhancement in MR spectroscopy of red bone marrow fat via intermolecular double-quantum coherences

NASA Astrophysics Data System (ADS)

Bao, Jianfeng; Cui, Xiaohong; Huang, Yuqing; Zhong, Jianhui; Chen, Zhong

2015-08-01

High-resolution 1H magnetic resonance spectroscopy (MRS) is generally inaccessible in red bone marrow (RBM) tissues using conventional MRS techniques. This is because signal from these tissues suffers from severe inhomogeneity in the main static B0 field originated from the intrinsic honeycomb structures in trabecular bone. One way to reduce effects of B0 field inhomogeneity is by using the intermolecular double quantum coherence (iDQC) technique, which has been shown in other systems to obtain signals insensitive to B0 field inhomogeneity. In the present study, we employed an iDQC approach to enhance the spectral resolution of RBM. The feasibility and performance of this method for achieving high resolution MRS was verified by experiments on phantoms and pig vertebral bone samples. Unsaturated fatty acid peaks which overlap in the conventional MRS were well resolved and identified in the iDQC spectrum. Quantitative comparison of fractions of three types of fatty acids was performed between iDQC spectra on the in situ RMB and conventional MRS on the extracted fat from the same RBM. Observations of unsaturated fatty acids with iDQC MRS may provide valuable information and may hold potential in diagnosis of diseases such as obesity, diabetes, and leukemia.

Theoretical investigations on the structure and properties of p-n-alkoxy benzoic acid based liquid crystals

NASA Astrophysics Data System (ADS)

Subhapriya, P.; Dhanapal, V.; Sadasivam, K.; Vijayanand, P. S.

2016-05-01

The present study focused on the structural conformations, alkoxy chain lengths and mesogenic properties of two mole of alkoxy benzoic acid(nOBA) and one mole of suberic acid (SA) hydrogen bonded (nOBASA) complexes (n=8 to 10) by density functional theory (DFT) calculations and the Fourier Transform Infrared (FT-IR) spectrum. The intermolecular hydrogen bond formation was confirmed by the optimized geometric bond lengths and bond angles obtained by computation. Using the natural bond orbital (NBO) analysis, the stability of the molecule arising from hyper conjugative interactions and charge delocalization has been analyzed. Results obtained shows that the charge in electron density (ED) in σ*and π* antibonding orbital and second order delocalization energies E(2) authorizes the occurrence of intermolecular charge transfer. The molecular electrostatic potential (MEP) surface map is plotted over the optimized geometry of the molecule to obtain the chemical reactivity of the molecule. From the local charge distributions, the mesomorphic behavior and the nematic phase stabilities for each of the molecule have been predicted. Finally the calculated result is applied to simulated infrared spectra of 8OBASA mesogens which shows good agreement with the observed spectra. The comparison of the theoretical results obtained with the experimental ones shows the reliability of this DFT method.

Nowa, a novel protein with minicollagen Cys-rich domains, is involved in nematocyst formation in Hydra.

PubMed

Engel, Ulrike; Ozbek, Suat; Streitwolf-Engel, Ruth; Petri, Barbara; Lottspeich, Friedrich; Holstein, Thomas W; Oezbek, Suat; Engel, Ruth

2002-10-15

The novel protein Nowa was identified in nematocysts, explosive organelles of Hydra, jellyfish, corals and other CNIDARIA: Biogenesis of these organelles is complex and involves assembly of proteins inside a post-Golgi vesicle to form a double-layered capsule with a long tubule. Nowa is the major component of the outer wall, which is formed very early in morphogenesis. The high molecular weight glycoprotein has a modular structure with an N-terminal sperm coating glycoprotein domain, a central C-type lectin-like domain, and an eightfold repeated cysteine-rich domain at the C-terminus. Interestingly, the cysteine-rich domains are homologous to the cysteine-rich domains of minicollagens. We have previously shown that the cysteines of these minicollagen cysteine-rich domains undergo an isomerization process from intra- to intermolecular disulfide bonds, which mediates the crosslinking of minicollagens to networks in the inner wall of the capsule. The minicollagen cysteine-rich domains present in both proteins provide a potential link between Nowa in the outer wall and minicollagens in the inner wall. We propose a model for nematocyst formation that integrates cytoskeleton rearrangements around the post-Golgi vesicle and protein assembly inside the vesicle to generate a complex structure that is stabilized by intermolecular disulfide bonds.

Lack of habituation of evoked visual potentials in analytic information processing style: evidence in healthy subjects.

PubMed

Buonfiglio, Marzia; Toscano, M; Puledda, F; Avanzini, G; Di Clemente, L; Di Sabato, F; Di Piero, V

2015-03-01

Habituation is considered one of the most basic mechanisms of learning. Habituation deficit to several sensory stimulations has been defined as a trait of migraine brain and also observed in other disorders. On the other hand, analytic information processing style is characterized by the habit of continually evaluating stimuli and it has been associated with migraine. We investigated a possible correlation between lack of habituation of evoked visual potentials and analytic cognitive style in healthy subjects. According to Sternberg-Wagner self-assessment inventory, 15 healthy volunteers (HV) with high analytic score and 15 HV with high global score were recruited. Both groups underwent visual evoked potentials recordings after psychological evaluation. We observed significant lack of habituation in analytical individuals compared to global group. In conclusion, a reduced habituation of visual evoked potentials has been observed in analytic subjects. Our results suggest that further research should be undertaken regarding the relationship between analytic cognitive style and lack of habituation in both physiological and pathophysiological conditions.

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

NASA Astrophysics Data System (ADS)

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. Y5KF211CJ1).

Intermolecular Interaction between Phosphatidylcholine and Sulfobetaine Lipid: A Combination of Lipids with Antiparallel Arranged Headgroup Charge.

PubMed

Aikawa, Tatsuo; Yokota, Keisuke; Kondo, Takeshi; Yuasa, Makoto

2016-10-05

Intermolecular interactions between lipid molecules are important when designing lipid bilayer interfaces, which have many biomedical applications such as in drug delivery vehicles and biosensors. Phosphatidylcholine, a naturally occurring lipid, is the most common lipid found in organisms. Its chemical structure has a negatively charged phosphate linkage, adjacent to an ester linkage in a glycerol moiety, and a positively charged choline group, placed at the terminus of the molecule. Recently, several types of synthetic lipids that have headgroups with the opposite charge to that of phosphatidylcholine have emerged; that is, a positively charged ammonium group is present adjacent to the ester linkage in their glycerol moiety and a negatively charged group is placed at their terminus. These types of lipids constitute a new class of soft material. The aim of this study was to determine how such lipids, with antiparallel arranged headgroup charge, interact with naturally occurring phosphatidylcholines. We synthesized 1,2-dipalmitoyl-sn-glycero-3-sulfobetaine (DPSB) to represent a reversed-head lipid; 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) was used to represent a naturally occurring phospholipid. The intermolecular interaction between these lipids was investigated using surface pressure-area (π-A) isotherms of the lipid monolayer at the air/water interface. We found that the extrapolated area and excess free energy of the mixed monolayer deviated negatively when compared with the ideal values from additivity. Moreover, differential scanning calorimetry of the lipid mixture in aqueous dispersion showed that the gel-to-liquid crystal transition temperature increased compared with that of each pure lipid composition. These results clearly indicate that DPSB preferably interacts with DPPC in the mixture. We believe that the attraction between the oppositely charged headgroups of these lipids reinforces the intermolecular interaction. Our results provide insight into the intermolecular interaction between phospholipids and reversed-head lipids, which may prove useful for the design of lipid-based materials in the future.

Syntheses of organic compounds in the presence of the fused iron catalyst and their mechanisms and kinetics

NASA Astrophysics Data System (ADS)

Glebov, L. S.; Kliger, G. A.

1989-10-01

New synthetic possibilities of the reduced promoted fused iron catalyst in intermolecular and intramolecular amination, cyanation, hydrogenation-dehydrogenation, and hydrodeoxygenation reactions and intermolecular and intramolecular dehydration, polymerisation, and isotope exchange are examined. The mechanisms and kinetics of the reactions leading to the synthesis of amines, alcohols, hydrocarbons, and other organic compunds are discussed. A laser Raman spectroscopic method is described for the investigation of heterogeneous organic catalysis in situ. The bibliography includes 148 references.

Fluorimetric study of the mechanism of molecular association in aqueous solutions of polymethacrylic acid and sodium dodecylbenzenesulfonate

NASA Astrophysics Data System (ADS)

Sachko, A. V.; Zakordonskii, V. P.; Voloshinovskii, A. S.

2013-03-01

Fluorescent spectroscopy is used to investigate the processes of intermolecular association in mixed solutions of polymethacrylic acid (PMAA) and anionic sodium dodecylbenzenesulfonate (SDBS). We propose a model for describing the stage-by-stage mechanism of association processes and conclude that the nature of intermolecular associates depends on the PMAA-SDBS concentration ratio in the solution. Studying the kinetics of fluorescence decay reveals the simultaneous existence of two types of formations capable of pyrene solubilization.

Diastereoselective intermolecular Pauson-Khand reactions of chiral cyclopropenes.

PubMed

Pallerla, Mahesh K; Fox, Joseph M

2005-08-04

In this Letter, it is demonstrated that the unusual reactivity of cyclopropenes can increase the scope and utility of intermolecular Pauson-Khand reactions. The well-defined chiral environment of cyclopropenes has a powerful influence on the diastereoselectivity of the reactions and leads to the production of a single cyclopentenone in each of the described cases. The cyclopropane ring strongly influences the stereochemistry of reactions at the enone, and the three-membered ring can subsequently be cleaved under mild conditions. [reaction: see text

Asymmetric intermolecular Pauson-Khand reaction of symmetrically substituted alkynes.

PubMed

Ji, Yining; Riera, Antoni; Verdaguer, Xavier

2009-10-01

The asymmetric intermolecular Pauson-Khand reaction of symmetric alkynes has been accomplished for the first time. N-Phosphino-p-tolylsulfinamide (PNSO) ligands have been identified as efficient ligands in this process. The chirality of the cobalt S-bonded sulfinyl moiety was found to direct olefin insertion into one of the two possible cobalt-carbon bonds in the alkyne complex. Reaction of symmetric alkynes allows for a simplified experimental protocol since there is no need for separation of diastereomeric complexes.

Tetramethylnorbornadiene, a versatile alkene for cyclopentenone synthesis through intermolecular Pauson-Khand reactions.

PubMed

Revés, Marc; Lledó, Agustí; Ji, Yining; Blasi, Emma; Riera, Antoni; Verdaguer, Xavier

2012-07-06

1,2,3,4-Tetramethyl-bicyclo[2.2.1]hepta-2,5-diene (TMNBD, for tetramethylnorbornadiene) has been prepared and used successfully as an acetylene equivalent in the synthesis of substituted cyclopentenones. TMNBD is easily accessible on a multigram scale and displays excellent reactivity toward the intermolecular Pauson-Khand reaction. Conjugate additions on the resulting tricyclic compounds proceed with exquisite diastereoselectivity. The retro-Diels-Alder reaction of these TMNBD derivatives occurs under much smoother conditions than those required for its norbornadiene homologues.

Palladium-catalyzed Heck-type cross-couplings of unactivated alkyl iodides.

PubMed

McMahon, Caitlin M; Alexanian, Erik J

2014-06-02

A palladium-catalyzed, intermolecular Heck-type coupling of alkyl iodides and alkenes is described. This process is successful with a variety of primary and secondary unactivated alkyl iodides as reaction partners, including those with hydrogen atoms in the β position. The mild catalytic conditions enable intermolecular C-C bond formations with a diverse set of alkyl iodides and alkenes, including substrates containing base- or nucleophile-sensitive functionality. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An intermolecular heterobimetallic system for photocatalytic water reduction.

PubMed

Hansen, Sven; Klahn, Marcus; Beweries, Torsten; Rosenthal, Uwe

2012-04-01

Teamwork: A new intermolecular heterobimetallic system for photocatalytic water reduction, consisting of a photosensitizer of the type [Ru(bpy)(2)(L)](PF(6))(2) (L=bidentate ligand), a dichloro palladium complex PdCl(2)(L) serving as the water reduction catalyst, and triethyl amine as electron donor, is presented. Variations of the ligand as well as of the palladium source results in a significant improvement of the performance of the catalyst system. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Monoclinic modification of 1,1,3,3,5,5-hexa­methyl-cyclo-1,3,5-tris­tannathiane

PubMed Central

Singh, Nanhai; Kumar, Abhinav; Molloy, Kieran C.; Kociok-Köhn, G.

2008-01-01

The asymmetric unit of the title compound, [Sn3(CH3)6S3], contains two molecules with twist-boat conformations. There are intermolecular S⋯H (2.929 Å), S⋯S (3.433 Å), S⋯C (3.465 Å) and C⋯H (2.898 Å) inter­actions in addition to prominent intermolecular Sn⋯S inter­actions of 3.692 and 3.769 Å. PMID:21200475

One-pot stereoselective synthesis of α,β-differentiated diamino esters via the sequence of aminochlorination, aziridination and intermolecular SN2 reaction.

PubMed

Xiong, Yiwen; Qian, Ping; Cao, Chenhui; Mei, Haibo; Han, Jianlin; Li, Guigen; Pan, Yi

2014-01-01

We report here an efficient one-pot method for the synthesis of α,β-differentiated diamino esters directly from cinnamate esters using N,N-dichloro-p-toluenesulfonamide and benzylamine as nitrogen sources. The key transformations include a Cu-catalyzed aminohalogenation and aziridination, followed by an intermolecular SN2 nucleophilic ring opening by benzylamine. The reactions feature a wide scope of substrates and proceed with excellent stereo- and regioselectivity (anti:syn >99:1) .

Synthesis and crystal structure analysis of uranyl triple acetates

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

Klepov, Vladislav V., E-mail: vladislavklepov@gmail.com; Department of Chemistry, Samara National Research University, 443086 Samara; Serezhkina, Larisa B.

2016-12-15

Single crystals of triple acetates NaR[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}·6H{sub 2}O (R=Mg, Co, Ni, Zn), well-known for their use as reagents for sodium determination, were grown from aqueous solutions and their structural and spectroscopic properties were studied. Crystal structures of the mentioned phases are based upon (Na[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}){sup 2–} clusters and [R(H{sub 2}O){sub 6}]{sup 2+} aqua-complexes. The cooling of a single crystal of NaMg[UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 3}·6H{sub 2}O from 300 to 100 K leads to a phase transition from trigonal to monoclinic crystal system. Intermolecular interactions between the structural units and their mutual packing were studiedmore » and compared from the point of view of the stereoatomic model of crystal structures based on Voronoi-Dirichlet tessellation. Using this method we compared the crystal structures of the triple acetates with Na[UO{sub 2}(CH{sub 3}COO){sub 3}] and [R(H{sub 2}O){sub 6}][UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 2} and proposed reasons of triple acetates stability. Infrared and Raman spectra were collected and their bands were assigned. - Graphical abstract: Single crystals of uranium based triple acetates, analytical reagents for sodium determination, were synthesized and structurally, spectroscopically and topologically characterized. The structures were compared with the structures of compounds from preceding families [M(H{sub 2}O){sub 6})][UO{sub 2}(CH{sub 3}COO){sub 3}]{sub 2} (M = Mg, Co, Ni, Zn) and Na[UO{sub 2}(CH{sub 3}COO){sub 3}]. Analysis was performed with the method of molecular Voronoi-Dirichlet polyhedra to reveal a large contribution of the hydrogen bonds into intermolecular interactions which can be a reason of low solubility of studied complexes.« less

Ab initio ground and excited state potential energy surfaces for NO-Kr complex and dynamics of Kr solids with NO impurity

NASA Astrophysics Data System (ADS)

Castro-Palacios, Juan Carlos; Rubayo-Soneira, Jesús; Ishii, Keisaku; Yamashita, Koichi

2007-04-01

The intermolecular potentials for the NO(XΠ2)-Kr and NO(AΣ+2)-Kr systems have been calculated using highly accurate ab initio calculations. The spin-restricted coupled cluster method for the ground 1A'2 state [NO(XΠ2)-Kr ] and the multireference singles and doubles configuration interaction method for the excited 2A'2 state [NO(AΣ+2)-Kr], respectively, were used. The potential energy surfaces (PESs) show two linear wells and one that is almost in the perpendicular position. An analytical representation of the PESs has been constructed for the triatomic systems and used to carry out molecular dynamics (MD) simulations of the NO-doped krypton matrix response after excitation of NO. MD results are shown comparatively for three sets of potentials: (1) anisotropic ab initio potentials [NO molecule direction fixed during the dynamics and considered as a point (its center of mass)], (2) isotropic ab initio potentials (isotropic part in a Legendre polynomial expansion of the PESs), and (3) fitted Kr-NO potentials to the spectroscopic data. An important finding of this work is that the anisotropic and isotropic ab initio potentials calculated for the Kr-NO triatomic system are not suitable for describing the dynamics of structural relaxation upon Rydberg excitation of a NO impurity in the crystal. However, the isotropic ab initio potential in the ground state almost overlaps the published experimental potential, being almost independent of the angle asymmetry. This fact is also manifested in the radial distribution function around NO. However, in the case of the excited state the isotropic ab initio potential differs from the fitted potentials, which indicates that the Kr-NO interaction in the matrix is quite different because of the presence of the surrounding Kr atoms acting on the NO molecule. MD simulations for isotropic potentials reasonably reproduce the experimental observables for the femtosecond response and the bubble size but do not match spectroscopic results. A general overall view of the results suggests that, when the Kr-NO interaction takes place inside the matrix, potentials are rather symmetric and less repulsive than those for the triatomic system. pectroscopy, yields a mean absolute deviation of about 5cm-1 over the 22 levels. The dissociation energy with respect to the lowest vibrational energy is calculated within 30cm-1 of the experimental value of 12953±8cm-1. The reported agreement of the theoretical spectrum and dissociation energy with experiment is contingent upon the inclusion of the effects of core-generated electron correlation, spin-orbit coupling, and scalar relativity. The Dunham analysis [Phys. Rev. 41, 721 (1932)] of the spectrum is found to be very accurate. New values are given for the spectroscopic constants.

A computer model of molecular arrangement in a n-paraffinic liquid

NASA Astrophysics Data System (ADS)

Vacatello, Michele; Avitabile, Gustavo; Corradini, Paolo; Tuzi, Angela

1980-07-01

A computer model of a bulk liquid polymer was built to investigate the problem of local order. The model is made of C30 n-alkane molecules; it is not a lattice model, but it allows for a continuous variability of torsion angles and interchain distances, subject to realistic intra- and intermolecular potentials. Experimental x-ray scattering curves and radial distribution functions are well reproduced. Calculated properties like end-to-end distances, distribution of torsion angles, radial distribution functions, and chain direction correlation parameters, all indicate a random coil conformation and no tendency to form bundles of parallel chains.

Initial Stage of Aerosol Formation from Oversaturated Vapors

NASA Astrophysics Data System (ADS)

Lushnikov, A. A.; Zagainov, V. A.; Lyubovtseva, Yu. S.

2018-03-01

The formation of aerosol particles from oversaturated vapor was considered assuming that the stable nuclei of the new phase contain two (dimers) or three (trimers) condensing vapor molecules. Exact expressions were derived and analyzed for the partition functions of the dimer and trimer suspended in a carrier gas for the rectangular well and repulsive core intermolecular potentials. The equilibrium properties of these clusters and the nucleation rate of aerosol particles were discussed. The bound states of clusters were introduced using a limitation on their total energy: molecular clusters with a negative total energy were considered to exclude configurations with noninteracting fragments.

UV-induced solvent free synthesis of truxillic acid-bile acid conjugates

NASA Astrophysics Data System (ADS)

Koivukorpi, Juha; Kolehmainen, Erkki

2009-07-01

The solvent free UV-induced [2 + 2] intermolecular cycloaddition of two molecules of 3α-cinnamic acid ester of methyl lithocholate produced in 99% yield of α- and ɛ-truxillic acid-bis(methyl lithocholate) isomers, which possess two structurally different potential binding sites. A prerequisite for this effective solid state reaction is a proper self-assembled crystal structure of the starting conjugate crystallized from acetonitrile. The crystallization of cinnamic acid ester of methyl lithocholate from acetonitrile produces two different crystalline forms (polymorphs), which is the reason for the solid state formation of two isomers of truxillic acid-bis(methyl lithocholate).

Pharmaceutical Cocrystals: New Solid Phase Modification Approaches for the Formulation of APIs.

PubMed

Karagianni, Anna; Malamatari, Maria; Kachrimanis, Kyriakos

2018-01-25

Cocrystals can be used as an alternative approach based on crystal engineering to enhance specific physicochemical and biopharmaceutical properties of active pharmaceutical ingredients (APIs) when the approaches to salt or polymorph formation do not meet the expected targets. In this article, an overview of pharmaceutical cocrystals will be presented, with an emphasis on the intermolecular interactions in cocrystals and the methods for their preparation. Furthermore, cocrystals of direct pharmaceutical interest, along with their in vitro properties and available in vivo data and characterization techniques are discussed, highlighting the potential of cocrystals as an attractive route for drug development.

Theoretical predictions of vibration-rotation-tunneling dynamics of the weakly bound trimer (H 2O) 2HCl

NASA Astrophysics Data System (ADS)

Struniewicz, Cezary; Korona, Tatiana; Moszynski, Robert; Milet, Anne

2001-08-01

In this Letter we report a theoretical study of the vibration-rotation-tunneling (VRT) states of the (H 2O) 2HCl trimer. Five degrees of freedom are considered: two angles corresponding to the torsional (flipping) motions of the free, non-hydrogen-bonded, hydrogen atoms in the complex, and three angles describing the overall rotation of the trimer in the space. A two-dimensional potential energy surface is generated ab initio by symmetry-adapted perturbation theory (SAPT). Tunneling splittings, frequencies of the intermolecular vibrations, and vibrational line strengths of spectroscopic transitions are predicted.

Interpreting the nonlinear dielectric response of glass-formers in terms of the coupling model

NASA Astrophysics Data System (ADS)

Ngai, K. L.

2015-03-01

Nonlinear dielectric measurements at high electric fields of glass-forming glycerol and propylene carbonate initially were carried out to elucidate the dynamic heterogeneous nature of the structural α-relaxation. Recently, the measurements were extended to sufficiently high frequencies to investigate the nonlinear dielectric response of faster processes including the so-called excess wing (EW), appearing as a second power law at high frequencies in the loss spectra of many glass formers without a resolved secondary relaxation. While a strong increase of dielectric constant and loss is found in the nonlinear dielectric response of the α-relaxation, there is a lack of significant change in the EW. A surprise to the experimentalists finding it, this difference in the nonlinear dielectric properties between the EW and the α-relaxation is explained in the framework of the coupling model by identifying the EW investigated with the nearly constant loss (NCL) of caged molecules, originating from the anharmonicity of the intermolecular potential. The NCL is terminated at longer times (lower frequencies) by the onset of the primitive relaxation, which is followed sequentially by relaxation processes involving increasing number of molecules until the terminal Kohlrausch α-relaxation is reached. These intermediate faster relaxations, combined to form the so-called Johari-Goldstein (JG) β-relaxation, are spatially and dynamically heterogeneous, and hence exhibit nonlinear dielectric effects, as found in glycerol and propylene carbonate, where the JG β-relaxation is not resolved and in D-sorbitol where it is resolved. Like the linear susceptibility, χ1(f), the frequency dispersion of the third-order dielectric susceptibility, χ3(f), was found to depend primarily on the α-relaxation time, and independent of temperature T and pressure P. I show this property of the frequency dispersions of χ1(f) and χ3(f) is the characteristic of the many-body relaxation dynamics of interacting systems which are governed solely by the intermolecular potential, and thermodynamic condition plays no role in this respect. Although linked to χ3(f), dynamic heterogeneity is one of the parallel consequences of the many-body dynamics, and it should not be considered as the principal control parameter for the other dynamic properties of glassforming systems. Results same as χ3(f) at elevated pressures had been obtained before by molecular dynamics simulations from the four-points correlation function and the intermediate scattering function. Naturally all properties obtained from the computer experiment, including dynamics heterogeneity, frequency dispersion, the relation between the α- and JG β-relaxation, and the breakdown of the Stokes-Einstein relation, are parallel consequences of the many-body relaxation dynamics governed by the intermolecular potential.

GENERAL: The Analytic Solution of Schrödinger Equation with Potential Function Superposed by Six Terms with Positive-power and Inverse-power Potentials

NASA Astrophysics Data System (ADS)

Hu, Xian-Quan; Luo, Guang; Cui, Li-Peng; Li, Fang-Yu; Niu, Lian-Bin

2009-03-01

The analytic solution of the radial Schrödinger equation is studied by using the tight coupling condition of several positive-power and inverse-power potential functions in this article. Furthermore, the precisely analytic solutions and the conditions that decide the existence of analytic solution have been searched when the potential of the radial Schrödinger equation is V(r) = α1r8 + α2r3 + α3r2 + β3r-1 + β2r-3 + β1r-4. Generally speaking, there is only an approximate solution, but not analytic solution for Schrödinger equation with several potentials' superposition. However, the conditions that decide the existence of analytic solution have been found and the analytic solution and its energy level structure are obtained for the Schrödinger equation with the potential which is motioned above in this paper. According to the single-value, finite and continuous standard of wave function in a quantum system, the authors firstly solve the asymptotic solution through the radial coordinate r → and r → 0; secondly, they make the asymptotic solutions combining with the series solutions nearby the neighborhood of irregular singularities; and then they compare the power series coefficients, deduce a series of analytic solutions of the stationary state wave function and corresponding energy level structure by tight coupling among the coefficients of potential functions for the radial Schrödinger equation; and lastly, they discuss the solutions and make conclusions.

A Method to Predict the Structure and Stability of RNA/RNA Complexes.

PubMed

Xu, Xiaojun; Chen, Shi-Jie

2016-01-01

RNA/RNA interactions are essential for genomic RNA dimerization and regulation of gene expression. Intermolecular loop-loop base pairing is a widespread and functionally important tertiary structure motif in RNA machinery. However, computational prediction of intermolecular loop-loop base pairing is challenged by the entropy and free energy calculation due to the conformational constraint and the intermolecular interactions. In this chapter, we describe a recently developed statistical mechanics-based method for the prediction of RNA/RNA complex structures and stabilities. The method is based on the virtual bond RNA folding model (Vfold). The main emphasis in the method is placed on the evaluation of the entropy and free energy for the loops, especially tertiary kissing loops. The method also uses recursive partition function calculations and two-step screening algorithm for large, complicated structures of RNA/RNA complexes. As case studies, we use the HIV-1 Mal dimer and the siRNA/HIV-1 mutant (T4) to illustrate the method.

Optical properties of azobenzene-functionalized self-assembled monolayers: Intermolecular coupling and many-body interactions

NASA Astrophysics Data System (ADS)

Cocchi, Caterina; Moldt, Thomas; Gahl, Cornelius; Weinelt, Martin; Draxl, Claudia

2016-12-01

In a joint theoretical and experimental work, the optical properties of azobenzene-functionalized self-assembled monolayers (SAMs) are studied at different molecular packing densities. Our results, based on density-functional and many-body perturbation theory, as well as on differential reflectance (DR) spectroscopy, shed light on the microscopic mechanisms ruling photo-absorption in these systems. While the optical excitations are intrinsically excitonic in nature, regardless of the molecular concentration, in densely packed SAMs intermolecular coupling and local-field effects are responsible for a sizable weakening of the exciton binding strength. Through a detailed analysis of the character of the electron-hole pairs, we show that distinct excitations involved in the photo-isomerization at low molecular concentrations are dramatically broadened by intermolecular interactions. Spectral shifts in the calculated DR spectra are in good agreement with the experimental results. Our findings represent an important step forward to rationalize the excited-state properties of these complex materials.

Pressure induced enhancement of the magnetic ordering temperature in rhenium(IV) monomers

PubMed Central

Woodall, Christopher H.; Craig, Gavin A.; Prescimone, Alessandro; Misek, Martin; Cano, Joan; Faus, Juan; Probert, Michael R.; Parsons, Simon; Moggach, Stephen; Martínez-Lillo, José; Murrie, Mark; Kamenev, Konstantin V.; Brechin, Euan K.

2016-01-01

Materials that demonstrate long-range magnetic order are synonymous with information storage and the electronics industry, with the phenomenon commonly associated with metals, metal alloys or metal oxides and sulfides. A lesser known family of magnetically ordered complexes are the monometallic compounds of highly anisotropic d-block transition metals; the ‘transformation' from isolated zero-dimensional molecule to ordered, spin-canted, three-dimensional lattice being the result of through-space interactions arising from the combination of large magnetic anisotropy and spin-delocalization from metal to ligand which induces important intermolecular contacts. Here we report the effect of pressure on two such mononuclear rhenium(IV) compounds that exhibit long-range magnetic order under ambient conditions via a spin canting mechanism, with Tc controlled by the strength of the intermolecular interactions. As these are determined by intermolecular distance, ‘squeezing' the molecules closer together generates remarkable enhancements in ordering temperatures, with a linear dependence of Tc with pressure. PMID:28000676

Solvent empirical scales and their importance for the study of intermolecular interactions

NASA Astrophysics Data System (ADS)

Babusca, Daniela; Benchea, Andreea Celia; Morosanu, Ana Cezarina; Dimitriu, Dan Gheorghe; Dorohoi, Dana Ortansa

2017-01-01

The solvent empirical scales were developed in order to classify the solvents regarding their influence on the absorption or fluorescence spectra of different spectrally active molecules. The intermolecular interactions in binary solutions of three molecule having an intramolecular charge transfer visible absorption band are studied in this paper: 5-[2-(1,2,2,4-tetramethyl-1,2,3,4-tetrahydroquinolin-6-yl)-vinyl]-thiophene-2-carbaldehyde (QTC), 1-cyano-2-{5-[2-(1,2,2,4-tetramethyl-1,2,3,4-tetrahydroquinolin-6-yl)-vinyl]-thiophen-2-yl}-vinyl)-phosphonic acid diethyl ester (QTCP) and p-phenyl pyridazinium-p-nitro-phenacylid (PPNP). The solvent empirical scales with a single parameter (Z scale of Kosower, ET (30) or ETN scale of Reichardt and Dimroth) can be used to describe the strength of intermolecular interactions. The contributions of each type of interactions to the total spectral shift are evaluated using the solvent multiple parameters empirical scales defined by Kamlet and Taft and by Catalan et al.

Greenhouse effect in planetary atmospheres caused by molecular symmetry breaking in intermolecular interactions

NASA Astrophysics Data System (ADS)

Vigasin, A. A.; Mokhov, I. I.

2017-03-01

It is believed that the greenhouse effect is related to the parameters of absorption spectra of polyatomic molecules, usually trace gases, in planetary atmospheres. The main components of all known atmospheres of celestial bodies are symmetrical molecules that do not possess the dipole-allowed purely rotational (and in the case of diatomic molecules, vibrational-rotational) absorption spectrum. Upon increased pressure, a weak absorption appears, induced by intermolecular interaction, which can lead to a greenhouse effect. The contribution of the induced absorption in radiative forcing of a dense atmosphere may amount to a few or even tens of W/m2. In conditions typical for the atmospheres of terrestrial planets (including paleoatmospheres), the collision-induced absorption and associated greenhouse effect may lead to an increase in surface temperature above the freezing point of water. There is a correlation between the temperature of an atmosphere and the intermolecular bonding energy of gases that dominate in planetary atmospheres of the Solar System.

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

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

Chavda, Bhavin R., E-mail: chavdabhavin9@gmail.com; Dubey, Rahul P.; Patel, Urmila H.

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 –Paulimore » (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.« less

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

DOE PAGES

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

2017-12-21

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

Mapping the force field of a hydrogen-bonded assembly

NASA Astrophysics Data System (ADS)

Sweetman, A. M.; Jarvis, S. P.; Sang, Hongqian; Lekkas, I.; Rahe, P.; Wang, Yu; Wang, Jianbo; Champness, N. R.; Kantorovich, L.; Moriarty, P.

2014-05-01

Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism.

Probing intermolecular interactions in a diethylcarbamazine citrate salt by fast MAS 1H solid-state NMR spectroscopy and GIPAW calculations.

PubMed

Venâncio, Tiago; Oliveira, Lyege Magalhaes; Ellena, Javier; Boechat, Nubia; Brown, Steven P

2017-10-01

Fast magic-angle spinning (MAS) NMR is used to probe intermolecular interactions in a diethylcarbamazine salt, that is widely used as a treatment against adult worms of Wuchereria bancrofti which cause a common disease in tropical countries named filariasis. Specifically, a dihydrogen citrate salt that has improved thermal stability and solubility as compared to the free form is studied. One-dimensional 1 H, 13 C and 15 N and two-dimensional 1 H- 13 C and 14 N- 1 H heteronuclear correlation NMR experiments under moderate and fast MAS together with GIPAW (CASTEP) calculations enable the assignment of the 1 H, 13 C and 14 N/ 15 N resonances. A two-dimensional 1 H- 1 H double-quantum (DQ) -single-quantum (SQ) MAS spectrum recorded with BaBa recoupling at 60kHz MAS identifies specific proton-proton proximities associated with citrate-citrate and citrate-diethylcarbamazine intermolecular interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

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

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

Azar, Richard Julian, E-mail: julianazar2323@berkeley.edu; Head-Gordon, Martin, E-mail: mhg@cchem.berkeley.edu

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 elucidationmore » 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.« less

High-Level Ab Initio Calculations of Intermolecular Interactions: Heavy Main-Group Element π-Interactions.

PubMed

Krasowska, Małgorzata; Schneider, Wolfgang B; Mehring, Michael; Auer, Alexander A

2018-05-02

This work reports high-level ab initio calculations and a detailed analysis on the nature of intermolecular interactions of heavy main-group element compounds and π systems. For this purpose we have chosen a set of benchmark molecules of the form MR 3 , in which M=As, Sb, or Bi, and R=CH 3 , OCH 3 , or Cl. Several methods for the description of weak intermolecular interactions are benchmarked including DFT-D, DFT-SAPT, MP2, and high-level coupled cluster methods in the DLPNO-CCSD(T) approximation. Using local energy decomposition (LED) and an analysis of the electron density, details of the nature of this interaction are unraveled. The results yield insight into the nature of dispersion and donor-acceptor interactions in this type of system, including systematic trends in the periodic table, and also provide a benchmark for dispersion interactions in heavy main-group element compounds. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Small Molecule Activation by Intermolecular Zr(IV)-Phosphine Frustrated Lewis Pairs.

PubMed

Metters, Owen J; Forrest, Sebastian J K; Sparkes, Hazel A; Manners, Ian; Wass, Duncan F

2016-02-17

We report intermolecular transition metal frustrated Lewis pairs (FLPs) based on zirconocene aryloxide and phosphine moieties that exhibit a broad range of small molecule activation chemistry that has previously been the preserve of only intramolecular pairs. Reactions with D2, CO2, THF, and PhCCH are reported. By contrast with previous intramolecular examples, these systems allow facile access to a variety of steric and electronic characteristics at the Lewis acidic and Lewis basic components, with the three-step syntheses of 10 new intermolecular transition metal FLPs being reported. Systematic variation to the phosphine Lewis base is used to unravel steric considerations, with the surprising conclusion that phosphines with relatively small Tolman steric parameters not only give highly reactive FLPs but are often seen to have the highest selectivity for the desired product. DOSY NMR spectroscopic studies on these systems reveal for the first time the nature of the Lewis acid/Lewis base interactions in transition metal FLPs of this type.

Pharmaceutical cocrystals, salts and multicomponent systems; intermolecular interactions and property based design.

PubMed

Berry, David J; Steed, Jonathan W

2017-08-01

As small molecule drugs become harder to develop and less cost effective for patient use, efficient strategies for their property improvement become increasingly important to global health initiatives. Improvements in the physical properties of Active Pharmaceutical Ingredients (APIs), without changes in the covalent chemistry, have long been possible through the application of binary component solids. This was first achieved through the use of pharmaceutical salts, within the last 10-15years with cocrystals and more recently coamorphous systems have also been consciously applied to this problem. In order to rationally discover the best multicomponent phase for drug development, intermolecular interactions need to be considered at all stages of the process. This review highlights the current thinking in this area and the state of the art in: pharmaceutical multicomponent phase design, the intermolecular interactions in these phases, the implications of these interactions on the material properties and the pharmacokinetics in a patient. Copyright © 2017 Elsevier B.V. All rights reserved.

High strength films from oriented, hydrogen-bonded "graphamid" 2D polymer molecular ensembles.

PubMed

Sandoz-Rosado, Emil; Beaudet, Todd D; Andzelm, Jan W; Wetzel, Eric D

2018-02-27

The linear polymer poly(p-phenylene terephthalamide), better known by its tradename Kevlar, is an icon of modern materials science due to its remarkable strength, stiffness, and environmental resistance. Here, we propose a new two-dimensional (2D) polymer, "graphamid", that closely resembles Kevlar in chemical structure, but is mechanically advantaged by virtue of its 2D structure. Using atomistic calculations, we show that graphamid comprises covalently-bonded sheets bridged by a high population of strong intermolecular hydrogen bonds. Molecular and micromechanical calculations predict that these strong intermolecular interactions allow stiff, high strength (6-8 GPa), and tough films from ensembles of finite graphamid molecules. In contrast, traditional 2D materials like graphene have weak intermolecular interactions, leading to ensembles of low strength (0.1-0.5 GPa) and brittle fracture behavior. These results suggest that hydrogen-bonded 2D polymers like graphamid would be transformative in enabling scalable, lightweight, high performance polymer films of unprecedented mechanical performance.

Resonance Raman spectra of organic molecules absorbed on inorganic semiconducting surfaces: Contribution from both localized intramolecular excitation and intermolecular charge transfer excitation

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

Ye, ChuanXiang; Zhao, Yi, E-mail: yizhao@xmu.edu.cn, E-mail: liangwz@xmu.edu.cn; Liang, WanZhen, E-mail: yizhao@xmu.edu.cn, E-mail: liangwz@xmu.edu.cn

2015-10-21

The time-dependent correlation function approach for the calculations of absorption and resonance Raman spectra (RRS) of organic molecules absorbed on semiconductor surfaces [Y. Zhao and W. Z. Liang, J. Chem. Phys. 135, 044108 (2011)] is extended to include the contribution of the intermolecular charge transfer (CT) excitation from the absorbers to the semiconducting nanoparticles. The results demonstrate that the bidirectionally interfacial CT significantly modifies the spectral line shapes. Although the intermolecular CT excitation makes the absorption spectra red shift slightly, it essentially changes the relative intensities of mode-specific RRS and causes the oscillation behavior of surface enhanced Raman spectra withmore » respect to interfacial electronic couplings. Furthermore, the constructive and destructive interferences of RRS from the localized molecular excitation and CT excitation are observed with respect to the electronic coupling and the bottom position of conductor band. The interferences are determined by both excitation pathways and bidirectionally interfacial CT.« less

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

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

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

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

Kim, Sun Ung, E-mail: sunung@umich.edu; Monroe, Charles W., E-mail: cwmonroe@umich.edu

The inverse problem of parameterizing intermolecular potentials given macroscopic transport and thermodynamic data is addressed. Procedures are developed to create arbitrary-precision algorithms for transport collision integrals, using the Lennard-Jones (12–6) potential as an example. Interpolation formulas are produced that compute these collision integrals to four-digit accuracy over the reduced-temperature range 0.3≤T{sup ⁎}≤400, allowing very fast computation. Lennard-Jones parameters for neon, argon, and krypton are determined by simultaneously fitting the observed temperature dependences of their viscosities and second virial coefficients—one of the first times that a thermodynamic and a dynamic property have been used simultaneously for Lennard-Jones parameterization. In addition tomore » matching viscosities and second virial coefficients within the bounds of experimental error, the determined Lennard-Jones parameters are also found to predict the thermal conductivity and self-diffusion coefficient accurately, supporting the value of the Lennard-Jones (12–6) potential for noble-gas transport-property correlation.« less

Cooperativity of anion⋯π and π⋯π interactions regulates the self-assembly of a series of carbene proligands: Towards quantitative analysis of intermolecular interactions with Hirshfeld surface

NASA Astrophysics Data System (ADS)

Samanta, Tapastaru; Dey, Lingaraj; Dinda, Joydev; Chattopadhyay, Shyamal Kumar; Seth, Saikat Kumar

2014-06-01

The cooperative effect of weak non-covalent forces between anions and electron deficient aromatics by π⋯π stacking of a series of carbene proligands (1-3) have been thoroughly explored by crystallographic studies. Structural analysis revealed that the anion⋯π and π⋯π interactions along with intermolecular hydrogen bonding mutually cooperate to facilitate the assembling of the supramolecular framework. The π⋯π and corresponding anion⋯π interactions have been investigated in the title carbene proligands despite their association with counter ions. The presence of the anion in the vicinity of the π-system leads to the formation of anion⋯π/π⋯π/π⋯anion network for an inductive stabilization of the assemblies. To assess the dimensionality of the supramolecular framework consolidated by cooperative anion⋯π/π⋯π interactions and hydrogen bonding, different substituent effects in the carbene backbone have been considered to tune these interactions. These facts show that the supramolecular framework based on these cooperative weak forces may be robust enough for application in molecular recognition. The investigation of close intermolecular interactions between the molecules via Hirshfeld surface analyses is presented in order to reveal subtle differences and similarities in the crystal structures. The decomposition of the fingerprint plot area provides a percentage of each intermolecular interaction, allowing for a quantified analysis of close contacts within each crystal.

Stabilization and Anomalous Hydration of Collagen Fibril under Heating

PubMed Central

Gevorkian, Sasun G.; Allahverdyan, Armen E.; Gevorgyan, David S.; Simonian, Aleksandr L.; Hu, Chin-Kun

2013-01-01

Background Type I collagen is the most common protein among higher vertebrates. It forms the basis of fibrous connective tissues (tendon, chord, skin, bones) and ensures mechanical stability and strength of these tissues. It is known, however, that separate triple-helical collagen macromolecules are unstable at physiological temperatures. We want to understand the mechanism of collagen stability at the intermolecular level. To this end, we study the collagen fibril, an intermediate level in the collagen hierarchy between triple-helical macromolecule and tendon. Methodology/Principal Finding When heating a native fibril sample, its Young’s modulus decreases in temperature range 20–58°C due to partial denaturation of triple-helices, but it is approximately constant at 58–75°C, because of stabilization by inter-molecular interactions. The stabilization temperature range 58–75°C has two further important features: here the fibril absorbs water under heating and the internal friction displays a peak. We relate these experimental findings to restructuring of collagen triple-helices in fibril. A theoretical description of the experimental results is provided via a generalization of the standard Zimm-Bragg model for the helix-coil transition. It takes into account intermolecular interactions of collagen triple-helices in fibril and describes water adsorption via the Langmuir mechanism. Conclusion/Significance We uncovered an inter-molecular mechanism that stabilizes the fibril made of unstable collagen macromolecules. This mechanism can be relevant for explaining stability of collagen. PMID:24244320

Pyromellitamide aggregates and their response to anion stimuli.

PubMed

Webb, James E A; Crossley, Maxwell J; Turner, Peter; Thordarson, Pall

2007-06-06

The N,N',N'',N'''-1,2,4,5-tetra(ethylhexanoate) pyromellitamide is found to be capable of both intermolecular aggregation and binding to small anions. It is synthesized by aminolysis of pyromellitic anhydride with ethanolamine, followed by a reaction with hexanoyl chloride. The single-crystal X-ray structure of the pyromellitamide shows that it forms one-dimensional columnar stacks through an intermolecular hydrogen-bonding network. It also forms self-assembled gels in nonpolar solvents, presumably by a hydrogen-bonding network similar to the solid-state structure as shown by IR and XRD studies. Aggregation by intermolecular hydrogen bonding of the pyromellitamide is also observed by NMR and IR in solution. Fitting of NMR dilution data for pyromellitamide in d6-acetone to a cooperative aggregation model gave KE=232 M-1 and positive cooperativity of aggregation (rho=0.22). The pyromellitamide binds to a range of small anions with the binding strength decreasing in the order chloride>acetate>bromide>nitrate approximately iodide. The data indicate that the pyromellitamide binds two anions and that it displays negative cooperativity. The intermolecular aggregation of the pyromellitamide can also be altered using small anion stimuli; anion addition to preformed self-assembled pyromellitamide gels causes their collapse. The kinetics of anion-induced gel collapse are qualitatively correlated to the binding affinities of the same anions in solution. The cooperative anion binding properties and the sensitivity of the self-assembled gels formed by pyromellitamide toward anions could be useful in the development of sensors and switching/releasing devices.

ReaxFF molecular dynamics simulation of intermolecular structure formation in acetic acid-water mixtures at elevated temperatures and pressures

NASA Astrophysics Data System (ADS)

Sengul, Mert Y.; Randall, Clive A.; van Duin, Adri C. T.

2018-04-01

The intermolecular structure formation in liquid and supercritical acetic acid-water mixtures was investigated using ReaxFF-based molecular dynamics simulations. The microscopic structures of acetic acid-water mixtures with different acetic acid mole fractions (1.0 ≥ xHAc ≥ 0.2) at ambient and critical conditions were examined. The potential energy surface associated with the dissociation of acetic acid molecules was calculated using a metadynamics procedure to optimize the dissociation energy of ReaxFF potential. At ambient conditions, depending on the acetic acid concentration, either acetic acid clusters or water clusters are dominant in the liquid mixture. When acetic acid is dominant (0.4 ≤ xHAc), cyclic dimers and chain structures between acetic acid molecules are present in the mixture. Both structures disappear at increased water content of the mixture. It was found by simulations that the acetic acid molecules released from these dimer and chain structures tend to stay in a dipole-dipole interaction. These structural changes are in agreement with the experimental results. When switched to critical conditions, the long-range interactions (e.g., second or fourth neighbor) disappear and the water-water and acetic acid-acetic acid structural formations become disordered. The simulated radial distribution function for water-water interactions is in agreement with experimental and computational studies. The first neighbor interactions between acetic acid and water molecules are preserved at relatively lower temperatures of the critical region. As higher temperatures are reached in the critical region, these interactions were observed to weaken. These simulations indicate that ReaxFF molecular dynamics simulations are an appropriate tool for studying supercritical water/organic acid mixtures.

Theoretical molecular studies of astrophysical interest

NASA Technical Reports Server (NTRS)

Flynn, George

1991-01-01

When work under this grant began in 1974 there was a great need for state-to-state collisional excitation rates for interstellar molecules observed by radio astronomers. These were required to interpret observed line intensities in terms of local temperatures and densities, but, owing to lack of experimental or theoretical values, estimates then being used for this purpose ranged over several orders of magnitude. A problem of particular interest was collisional excitation of formaldehyde; Townes and Cheung had suggested that the relative size of different state-to-state rates (propensity rules) was responsible for the anomalous absorption observed for this species. We believed that numerical molecular scattering techniques (in particular the close coupling or coupled channel method) could be used to obtain accurate results, and that these would be computationally feasible since only a few molecular rotational levels are populated at the low temperatures thought to prevail in the observed regions. Such calculations also require detailed knowledge of the intermolecular forces, but we thought that those could also be obtained with sufficient accuracy by theoretical (quantum chemical) techniques. Others, notably Roy Gordon at Harvard, had made progress in solving the molecular scattering equations, generally using semi-empirical intermolecular potentials. Work done under this grant generalized Gordon's scattering code, and introduced the use of theoretical interaction potentials obtained by solving the molecular Schroedinger equation. Earlier work had considered only the excitation of a diatomic molecule by collisions with an atom, and we extended the formalism to include excitation of more general molecular rotors (e.g., H2CO, NH2, and H2O) and also collisions of two rotors (e.g., H2-H2).

Infrared Spectra of He-, Ne-, and Ar-C_2D_2 Complexes

NASA Astrophysics Data System (ADS)

Rezai, M.; Moazzen-Ahmadi, N.; McKellar, A. R. W.; Fernandez, Berta; Farrelly, David

2012-06-01

Remarkably, there are no previously published experimental spectra of the helium-acetylene van der Waals complex. Apparently, infrared spectra of He-C_2H_2 were recorded around 1990 in Roger Miller's lab, but a detailed rotational assignment was not possible even with the help of two extensive sets of theoretical predictions. Here, we study rare gas-C_2D_2 complexes in the νb{3} region (˜2439 wn) using a rapid-scan tuneable diode laser spectrometer to probe a pulsed supersonic slit-jet expansion. The He-C_2D_2 assignment problem is readily apparent: most of the absorption is piled-up in a very narrow region around 2440.85 wn, close to the R(0) line of the C_2D_2 monomer. This pile-up is a signature of very weak anisotropy in the helium-acetylene intermolecular potential, leading to almost free internal rotation of the C_2D_2. We are able to achieve a convincing rotational assignment with the help of theoretical energy level calculations based on the intermolecular potential surface of Munteanu and Fernández. So far the results are limited to He-C_2D_2 transitions which correlate with the monomer R(0) transition. Ne-C_2D_2 also shows a free-rotation pile-up of lines near R(0) which makes assignment tricky. In contrast, Ar-C_2D_2 exhibits more conventional behavior and a normal asymmetric rotor analysis is possible. [1] T. Slee, R.J. Le Roy, and C.E. Chuaqui, Mol. Phys. 77, 111 (1992); R. Moszynski, P.E.S. Wormer, and A. van der Avoird, J. Chem. Phys. 102, 8385 (1995). [2] R. Munteanu and B. Fernández, J. Chem. Phys. 123, 014309 (2005).

Far-infrared vibration--rotation-tunneling spectroscopy of Ar--NH sub 3 : Intermolecular vibrations and effective angular potential energy surface

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

Schmuttenmaer, C.A.; Cohen, R.C.; Loeser, J.G.

Two new intermolecular vibration--rotation-tunneling (VRT) bands of Ar--NH{sub 3} have been measured using tunable far infrared laser spectroscopy. We have unambiguously assigned these and a previously measured FIR band (Gwo {ital et} {ital al}., Mol. Phys. {bold 71}, 453 (1990)) as {Pi}(1{sub 0}, {ital n}=0){l arrow}{Sigma}(0{sub 0}, {ital n}=0), {Sigma}(1{sub 0}, {ital n}=0){l arrow}{Sigma}(0{sub 0}, {ital n}=0), and {Sigma}(0{sub 0}, {ital n}=1){l arrow}{Sigma}(0{sub 0}, {ital n}=0). The three upper states of these are found to be strongly mixed by anisotropy and Coriolis effects. A simultaneous least squares fit of all transitions has yielded vibrational frequencies, rotational and centrifugal distortion constants,more » and a Coriolis parameter as well as quadrupole hyperfine coupling constants for the upper states. An effective angular potential energy surface for Ar--NH{sub 3} in its lowest stretching state has been determined from these data, after explicitly accounting for the effects of bend stretch interactions. Features of the surface include a global minimum at the near T-shaped configuration ({theta}=90{degree}), a 30 cm{sup {minus}1} to 60 cm{sup {minus}1} barrier to rotation at {theta}=180{degree} (or 0{degree}), and a very low barrier or possibly a secondary minimum at {theta}=0{degree} (or 180{degree}). Both attractive and repulsive interactions are shown to contribute significantly to the anisotropic forces in the complex. Comparison with {ital ab} {ital initio} calculations are presented.« less

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

Srivastava, Ashish Kumar, E-mail: ashish.memech@gmail.com; Singh, Akhileshwar; Mokhalingam, A.

Atomistic simulations were conducted to estimate the effect of the carbon nanotube (CNT) reinforcement on the mechanical behavior of CNT-reinforced aluminum (Al) nanocomposite. The periodic system of CNT-Al nanocomposite was built and simulated using molecular dynamics (MD) software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). The mechanical properties of the nanocomposite were investigated by the application of uniaxial load on one end of the representative volume element (RVE) and fixing the other end. The interactions between the atoms of Al were modeled using embedded atom method (EAM) potentials, whereas Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential was used for themore » interactions among carbon atoms and these pair potentials are coupled with the Lennard-Jones (LJ) potential. The results show that the incorporation of CNT into the Al matrix can increase the Young’s modulus of the nanocomposite substantially. In the present case, i.e. for approximately 9 with % reinforcement of CNT can increase the axial Young’s modulus of the Al matrix up to 77 % as compared to pure Al.« less

Rh-Catalyzed Intermolecular Reactions of α-Alkyl-α-Diazo Carbonyl Compounds with Selectivity over β-Hydride Migration

PubMed Central

DeAngelis, Andrew; Panish, Robert; Fox, Joseph M.

2016-01-01

CONSPECTUS Rh-carbenes derived from α-diazocarbonyl compounds have found broad utility across a remarkable range of reactivity, including cyclopropanation, cyclopropenation, C–H insertions, heteroatom–H insertions, and ylide forming reactions. However, in contrast to α-aryl or α-vinyl-α-diazocarbonyl compounds, the utility of α-alkyl-α-diazocarbonyl compounds had been moderated by the propensity of such compounds to undergo intramolecular β-hydride migration to give alkene products. Especially challenging had been intermolecular reactions involving α-alkyl-α-diazocarbonyl compounds. PMID:26689221

Iron(II)-catalyzed intermolecular amino-oxygenation of olefins through the N-O bond cleavage of functionalized hydroxylamines.

PubMed

Lu, Deng-Fu; Zhu, Cheng-Liang; Jia, Zhen-Xin; Xu, Hao

2014-09-24

An iron-catalyzed diastereoselective intermolecular olefin amino-oxygenation reaction is reported, which proceeds via an iron-nitrenoid generated by the N-O bond cleavage of a functionalized hydroxylamine. In this reaction, a bench-stable hydroxylamine derivative is used as the amination reagent and oxidant. This method tolerates a range of synthetically valuable substrates that have been all incompatible with existing amino-oxygenation methods. It can also provide amino alcohol derivatives with regio- and stereochemical arrays complementary to known amino-oxygenation methods.

Diazo Esters as Dienophiles in Intramolecular (4 + 2) Cycloadditions: Computational Explorations of Mechanism.

PubMed

Duan, Abing; Yu, Peiyuan; Liu, Fang; Qiu, Huang; Gu, Feng Long; Doyle, Michael P; Houk, K N

2017-02-22

The first experimental examples of Diels-Alder (DA) reactions of diazo compounds as heterodienophiles with dienes have been studied with density functional theory (DFT) using the M06-2X functional. For comparison, the reactivities of diazo esters as dienophiles or 1,3-dipoles with 1,3-dienes in intermolecular model systems have been analyzed by the distortion/interaction model. The 1,3-dipolar cycloaddition is strongly favored for the intermolecular system. The intramolecular example is unique because the tether strongly favors the (4 + 2) cycloaddition.

betaFIT: A computer program to fit pointwise potentials to selected analytic functions

NASA Astrophysics Data System (ADS)

Le Roy, Robert J.; Pashov, Asen

2017-01-01

This paper describes program betaFIT, which performs least-squares fits of sets of one-dimensional (or radial) potential function values to four different types of sophisticated analytic potential energy functional forms. These families of potential energy functions are: the Expanded Morse Oscillator (EMO) potential [J Mol Spectrosc 1999;194:197], the Morse/Long-Range (MLR) potential [Mol Phys 2007;105:663], the Double Exponential/Long-Range (DELR) potential [J Chem Phys 2003;119:7398], and the "Generalized Potential Energy Function (GPEF)" form introduced by Šurkus et al. [Chem Phys Lett 1984;105:291], which includes a wide variety of polynomial potentials, such as the Dunham [Phys Rev 1932;41:713], Simons-Parr-Finlan [J Chem Phys 1973;59:3229], and Ogilvie-Tipping [Proc R Soc A 1991;378:287] polynomials, as special cases. This code will be useful for providing the realistic sets of potential function shape parameters that are required to initiate direct fits of selected analytic potential functions to experimental data, and for providing better analytical representations of sets of ab initio results.

Learning Analytics: Potential for Enhancing School Library Programs

ERIC Educational Resources Information Center

Boulden, Danielle Cadieux

2015-01-01

Learning analytics has been defined as the measurement, collection, analysis, and reporting of data about learners and their contexts, for purposes of understanding and optimizing learning and the environments in which it occurs. The potential use of data and learning analytics in educational contexts has caught the attention of educators and…

Short-time quantum dynamics of sharp boundaries potentials

NASA Astrophysics Data System (ADS)

Granot, Er'el; Marchewka, Avi

2015-02-01

Despite the high prevalence of singular potential in general, and rectangular potentials in particular, in applied scattering models, to date little is known about their short time effects. The reason is that singular potentials cause a mixture of complicated local as well as non-local effects. The object of this work is to derive a generic method to calculate analytically the short-time impact of any singular potential. In this paper it is shown that the scattering of a smooth wavefunction on a singular potential is totally equivalent, in the short-time regime, to the free propagation of a singular wavefunction. However, the latter problem was totally addressed analytically in Ref. [7]. Therefore, this equivalency can be utilized in solving analytically the short time dynamics of any smooth wavefunction at the presence of a singular potentials. In particular, with this method the short-time dynamics of any problem where a sharp boundaries potential (e.g., a rectangular barrier) is turned on instantaneously can easily be solved analytically.

On the use of ionic liquids as mobile phase additives in high-performance liquid chromatography. A review.

PubMed

García-Alvarez-Coque, M C; Ruiz-Angel, M J; Berthod, A; Carda-Broch, S

2015-07-09

The popularity of ionic liquids (ILs) has grown during the last decades in several analytical separation techniques. Consequently, the number of reports devoted to the applications of ILs is still increasing. This review is focused on the use of ILs (mainly imidazolium-based associated to chloride and tetrafluoroborate) as mobile phase additives in high-performance liquid chromatography (HPLC). In this approach, ILs just function as salts, but keep several kinds of intermolecular interactions, which are useful for chromatographic separations. Both cation and anion can be adsorbed on the stationary phase, creating a bilayer. This gives rise to hydrophobic, electrostatic and other specific interactions with the stationary phase and solutes, which modify the retention behaviour and peak shape. This review updates the advances in this field, with emphasis on topics not always deeply considered in the literature, such as the mechanisms of retention, the estimation of the suppressing potency of silanols, modelling and optimisation of the chromatographic performance, and the comparison with other additives traditionally used to avoid the silanol problem. Copyright © 2015 Elsevier B.V. All rights reserved.

Changes in the Coherent Dynamics of Nanoconfined Room Temperature Ionic Liquids

NASA Astrophysics Data System (ADS)

Vallejo, Kevin; Cano, Melissa; Li, Song; Rotner, Gernot; Faraone, Antonio; Banuelos, Jose

Confinement and temperature effects on the coherent dynamics of the room temperature ionic liquid (RTIL) [C10MPy+] [Tf2N-] were investigated using neutron spin-echo (NSE) in two silica matrices with different pore size. Several intermolecular forces give rise to the bulk molecular structure between anions and cations. NSE provided dynamics (via the coherent intermediate scattering function) in the time range of 0.004 to 10 ns, and at Q-values corresponding to intermediate range ordering and inter- and intra-molecular length scales of the RTIL. Pore wall effects were delineated by comparing bulk RTIL dynamics with those of the confined fluid in 2.8 nm and 8 nm pores. Analytical models were applied to the experimental data to extract decay times and amplitudes of each component. We find a fast relaxation outside the experiment time window, a primary relaxation, and slow, surface-induced dynamics, which all speed up with increased temperature, however, the temperature dependence differs between bulk and confinement. This study sheds light on the structure and dynamics of RTILs and is relevant to the optimization of RTILs for green technologies and applications.

Unraveling protein-protein interactions in clathrin assemblies via atomic force spectroscopy.

PubMed

Jin, Albert J; Lafer, Eileen M; Peng, Jennifer Q; Smith, Paul D; Nossal, Ralph

2013-03-01

Atomic force microscopy (AFM), single molecule force spectroscopy (SMFS), and single particle force spectroscopy (SPFS) are used to characterize intermolecular interactions and domain structures of clathrin triskelia and clathrin-coated vesicles (CCVs). The latter are involved in receptor-mediated endocytosis (RME) and other trafficking pathways. Here, we subject individual triskelia, bovine-brain CCVs, and reconstituted clathrin-AP180 coats to AFM-SMFS and AFM-SPFS pulling experiments and apply novel analytics to extract force-extension relations from very large data sets. The spectroscopic fingerprints of these samples differ markedly, providing important new information about the mechanism of CCV uncoating. For individual triskelia, SMFS reveals a series of events associated with heavy chain alpha-helix hairpin unfolding, as well as cooperative unraveling of several hairpin domains. SPFS of clathrin assemblies exposes weaker clathrin-clathrin interactions that are indicative of inter-leg association essential for RME and intracellular trafficking. Clathrin-AP180 coats are energetically easier to unravel than the coats of CCVs, with a non-trivial dependence on force-loading rate. Published by Elsevier Inc.

Screening and structural elucidation of the zwitterionic cocrystal o-picolinic acid with p-nitro aniline

NASA Astrophysics Data System (ADS)

Mekala, R.; Jagdish, P.; Mathammal, R.; Sangeetha, K.

2017-04-01

The cocrystal was screened by solvent drop grinding method and the crystals were grown by slow evaporation method at ambient conditions. The cocrystal formation of o-picolinic acid with p-nitro aniline was initially analysed by powder X-ray diffraction. Further the structural properties of the grown crystal were confirmed by the single X-ray diffraction which indicates that the cocrystal were connected by the strong N+sbnd H-⋯O hydrogen bond interaction. The cell parameters of the grown crystal were a = 14.2144(5) Å, b = 5.7558(2) Å, c = 16.0539(6) Å. The functional groups were identified using Fourier transform infrared and Raman spectral analysis. The excitation and emission state of the sample was analysed by the UV-Visible and Fluorescence studies. The red emission was observed from the Fluorescence studies. NMR studies revealed the chemical shift of the cocrystal. Thermal stability and its melting behaviour were studied by TGA and DSC analytical techniques. Electrical behaviour was studied using the dielectric studies. The intermolecular charge transfer within the molecule were analysed using HOMO- LUMO plots.

Positronium formation studies in crystalline molecular complexes: Triphenylphosphine oxide - Acetanilide

NASA Astrophysics Data System (ADS)

Oliveira, F. C.; Denadai, A. M. L.; Guerra, L. D. L.; Fulgêncio, F. H.; Windmöller, D.; Santos, G. C.; Fernandes, N. G.; Yoshida, M. I.; Donnici, C. L.; Magalhães, W. F.; Machado, J. C.

2013-04-01

Hydrogen bond formation in the triphenylphosphine oxide (TPPO), acetanilide (ACN) supramolecular heterosynton system, named [TPPO0.5·ACN0.5], has been studied by Positron Annihilation Lifetime Spectroscopy (PALS) and supported by several analytical techniques. In toluene solution, Isothermal Titration Calorimetry (ITC) presented a 1:1 stoichiometry and indicated that the complexation process is driven by entropy, with low enthalpy contribution. X-ray structure determination showed the existence of a three-dimensional network of hydrogen bonds, allowing also the confirmation of the existence of a 1:1 crystalline molecular complex in solid state. The results of thermal analysis (TGA, DTA and DSC) and FTIR spectroscopy showed that the interactions in the complex are relatively weaker than those found in pure precursors, leading to a higher positronium formation probability at [TPPO0.5·ACN0.5]. These weak interactions in the complex enhance the possibility of the n- and π-electrons to interact with positrons and consequently, the probability of positronium formation is higher. Through the present work is shown that PALS is a sensible powerful tool to investigate intermolecular interactions in solid heterosynton supramolecular systems.

A theoretical description of the polarization dependence of the sum frequency generation spectroscopy of the water/vapor interface

NASA Astrophysics Data System (ADS)

Perry, Angela; Neipert, Christine; Kasprzyk, Christina Ridley; Green, Tony; Space, Brian; Moore, Preston B.

2005-10-01

An improved time correlation function (TCF) description of sum frequency generation (SFG) spectroscopy was developed and applied to theoretically describing the spectroscopy of the ambient water/vapor interface. A more general TCF expression than was published previously is presented—it is valid over the entire vibrational spectrum for both the real and imaginary parts of the signal. Computationally, earlier time correlation function approaches were limited to short correlation times that made signal processing challenging. Here, this limitation is overcome, and well-averaged spectra are presented for the three independent polarization conditions that are possible for electronically nonresonant SFG. The theoretical spectra compare quite favorably in shape and relative magnitude to extant experimental results in the O H stretching region of water for all polarization geometries. The methodological improvements also allow the calculation of intermolecular SFG spectra. While the intermolecular spectrum of bulk water shows relatively little structure, the interfacial spectra (for polarizations that are sensitive to dipole derivatives normal to the interface—SSP and PPP) show a well-defined intermolecular mode at 875cm-1 that is comparable in intensity to the rest of the intermolecular structure, and has an intensity that is approximately one-sixth of the magnitude of the intense free OH stretching peak. Using instantaneous normal mode methods, the resonance is shown to be due to a wagging mode localized on a single water molecule, almost parallel to the interface, with two hydrogens displaced normal to the interface, and the oxygen anchored in the interface. We have also uncovered the origin of another intermolecular mode at 95cm-1 for the SSP and PPP spectra, and at 220cm-1 for the SPS spectra. These resonances are due to hindered translations perpendicular to the interface for the SSP and PPP spectra, and translations parallel to the interface for the SPS spectra. Further, by examining the real and imaginary parts of the SFG signal, several resonances are shown to be due to a single spectroscopic species while the "donor" OH region is shown to consist of three distinct species—consistent with an earlier experimental analysis.

How Structure Defines Affinity in Protein-Protein Interactions

PubMed Central

Erijman, Ariel; Rosenthal, Eran; Shifman, Julia M.

2014-01-01

Protein-protein interactions (PPI) in nature are conveyed by a multitude of binding modes involving various surfaces, secondary structure elements and intermolecular interactions. This diversity results in PPI binding affinities that span more than nine orders of magnitude. Several early studies attempted to correlate PPI binding affinities to various structure-derived features with limited success. The growing number of high-resolution structures, the appearance of more precise methods for measuring binding affinities and the development of new computational algorithms enable more thorough investigations in this direction. Here, we use a large dataset of PPI structures with the documented binding affinities to calculate a number of structure-based features that could potentially define binding energetics. We explore how well each calculated biophysical feature alone correlates with binding affinity and determine the features that could be used to distinguish between high-, medium- and low- affinity PPIs. Furthermore, we test how various combinations of features could be applied to predict binding affinity and observe a slow improvement in correlation as more features are incorporated into the equation. In addition, we observe a considerable improvement in predictions if we exclude from our analysis low-resolution and NMR structures, revealing the importance of capturing exact intermolecular interactions in our calculations. Our analysis should facilitate prediction of new interactions on the genome scale, better characterization of signaling networks and design of novel binding partners for various target proteins. PMID:25329579

Local structure of ion pair interaction in lapatinib amorphous dispersions characterized by synchrotron x-ray diffraction and pair distribution function analysis

DOE PAGES

de Araujo, Gabriel L. B.; Benmore, Chris J.; Byrn, Stephen R.

2017-04-11

For many years, the idea of analyzing atom-atom contacts in amorphous drug-polymer systems has been of major interest, because this method has always had the potential to differentiate between amorphous systems with domains and amorphous systems which are molecular mixtures. In this study, local structure of ionic and noninonic interactions were studied by High-Energy X-ray Diffraction and Pair Distribution Function (PDF) analysis in amorphous solid dispersions of lapatinib in hypromellose phthalate (HPMCP) and hypromellose (HPMC-E3). The strategy of extracting lapatinib intermolecular drug interactions from the total PDF x-ray pattern was successfully applied allowing the detection of distinct nearest neighbor contactsmore » for the HPMC-E3 rich preparations showing that lapatinib molecules do not cluster in the same way as observed in HPMC-P, where ionic interactions are present. Orientational correlations up to nearest neighbor molecules at about 4.3 Å were observed for polymer rich samples; both observations showed strong correlation to the stability of the systems. Lasty, the superior physical stability of 1:3 LP:HPMCP was consistent with the absence of significant intermolecular interactions in (ΔD inter LP(r)) in the range of 3.0 to 6.0 Å, which are attributed to C-C, C-N and C-O nearest neighbor contacts present in drug-drug interactions.« less

Local structure of ion pair interaction in lapatinib amorphous dispersions characterized by synchrotron x-ray diffraction and pair distribution function analysis

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

de Araujo, Gabriel L. B.; Benmore, Chris J.; Byrn, Stephen R.

For many years, the idea of analyzing atom-atom contacts in amorphous drug-polymer systems has been of major interest, because this method has always had the potential to differentiate between amorphous systems with domains and amorphous systems which are molecular mixtures. In this study, local structure of ionic and noninonic interactions were studied by High-Energy X-ray Diffraction and Pair Distribution Function (PDF) analysis in amorphous solid dispersions of lapatinib in hypromellose phthalate (HPMCP) and hypromellose (HPMC-E3). The strategy of extracting lapatinib intermolecular drug interactions from the total PDF x-ray pattern was successfully applied allowing the detection of distinct nearest neighbor contactsmore » for the HPMC-E3 rich preparations showing that lapatinib molecules do not cluster in the same way as observed in HPMC-P, where ionic interactions are present. Orientational correlations up to nearest neighbor molecules at about 4.3 Å were observed for polymer rich samples; both observations showed strong correlation to the stability of the systems. Lasty, the superior physical stability of 1:3 LP:HPMCP was consistent with the absence of significant intermolecular interactions in (ΔD inter LP(r)) in the range of 3.0 to 6.0 Å, which are attributed to C-C, C-N and C-O nearest neighbor contacts present in drug-drug interactions.« less

Local Structure of Ion Pair Interaction in Lapatinib Amorphous Dispersions characterized by Synchrotron X-Ray diffraction and Pair Distribution Function Analysis

NASA Astrophysics Data System (ADS)

de Araujo, Gabriel L. B.; Benmore, Chris J.; Byrn, Stephen R.

2017-04-01

For many years, the idea of analyzing atom-atom contacts in amorphous drug-polymer systems has been of major interest, because this method has always had the potential to differentiate between amorphous systems with domains and amorphous systems which are molecular mixtures. In this study, local structure of ionic and noninonic interactions were studied by High-Energy X-ray Diffraction and Pair Distribution Function (PDF) analysis in amorphous solid dispersions of lapatinib in hypromellose phthalate (HPMCP) and hypromellose (HPMC-E3). The strategy of extracting lapatinib intermolecular drug interactions from the total PDF x-ray pattern was successfully applied allowing the detection of distinct nearest neighbor contacts for the HPMC-E3 rich preparations showing that lapatinib molecules do not cluster in the same way as observed in HPMC-P, where ionic interactions are present. Orientational correlations up to nearest neighbor molecules at about 4.3 Å were observed for polymer rich samples; both observations showed strong correlation to the stability of the systems. Finally, the superior physical stability of 1:3 LP:HPMCP was consistent with the absence of significant intermolecular interactions in (Δ) in the range of 3.0 to 6.0 Å, which are attributed to C-C, C-N and C-O nearest neighbor contacts present in drug-drug interactions.

Localized-overlap approach to calculations of intermolecular interactions

NASA Astrophysics Data System (ADS)

Rob, Fazle

Symmetry-adapted perturbation theory (SAPT) based on the density functional theory (DFT) description of the monomers [SAPT(DFT)] is one of the most robust tools for computing intermolecular interaction energies. Currently, one can use the SAPT(DFT) method to calculate interaction energies of dimers consisting of about a hundred atoms. To remove the methodological and technical limits and extend the size of the systems that can be calculated with the method, a novel approach has been proposed that redefines the electron densities and polarizabilities in a localized way. In the new method, accurate but computationally expensive quantum-chemical calculations are only applied for the regions where it is necessary and for other regions, where overlap effects of the wave functions are negligible, inexpensive asymptotic techniques are used. Unlike other hybrid methods, this new approach is mathematically rigorous. The main benefit of this method is that with the increasing size of the system the calculation scales linearly and, therefore, this approach will be denoted as local-overlap SAPT(DFT) or LSAPT(DFT). As a byproduct of developing LSAPT(DFT), some important problems concerning distributed molecular response, in particular, the unphysical charge-flow terms were eliminated. Additionally, to illustrate the capabilities of SAPT(DFT), a potential energy function has been developed for an energetic molecular crystal of 1,1-diamino-2,2-dinitroethylene (FOX-7), where an excellent agreement with the experimental data has been found.

The structure of PX3 (X = Cl, Br, I) molecular liquids from X-ray diffraction, molecular dynamics simulations, and reverse Monte Carlo modeling.

PubMed

Pothoczki, Szilvia; Temleitner, László; Pusztai, László

2014-02-07

Synchrotron X-ray diffraction measurements have been conducted on liquid phosphorus trichloride, tribromide, and triiodide. Molecular Dynamics simulations for these molecular liquids were performed with a dual purpose: (1) to establish whether existing intermolecular potential functions can provide a picture that is consistent with diffraction data and (2) to generate reliable starting configurations for subsequent Reverse Monte Carlo modelling. Structural models (i.e., sets of coordinates of thousands of atoms) that were fully consistent with experimental diffraction information, within errors, have been prepared by means of the Reverse Monte Carlo method. Comparison with reference systems, generated by hard sphere-like Monte Carlo simulations, was also carried out to demonstrate the extent to which simple space filling effects determine the structure of the liquids (and thus, also estimating the information content of measured data). Total scattering structure factors, partial radial distribution functions and orientational correlations as a function of distances between the molecular centres have been calculated from the models. In general, more or less antiparallel arrangements of the primary molecular axes that are found to be the most favourable orientation of two neighbouring molecules. In liquid PBr3 electrostatic interactions seem to play a more important role in determining intermolecular correlations than in the other two liquids; molecular arrangements in both PCl3 and PI3 are largely driven by steric effects.

The Far Infrared Vibration-Rotation Spectrum of the Ammonia Dimer.

NASA Astrophysics Data System (ADS)

Loeser, Jennifer Gertrud

1995-11-01

The ammonia dimer has been shown to exhibit unusual weak bonding properties relative to those of the other prototypical second row systems, the hydrogen fluoride dimer and the water dimer. The ultimate goal of the work initiated in this dissertation is to determine a complete intermolecular potential energy surface for the ammonia dimer. It is first necessary to observe its far infrared vibration-rotation-tunneling (VRT) spectrum and to develop a group theoretical model that explains this spectrum in terms of the internal dynamics of the ammonia dimer. These first steps are the subject of this dissertation. First, the current understanding of the ammonia dimer system is reviewed. Group theoretical descriptions of the nature of the ammonia dimer VRT states are explained in detail. An overview of the experimental and theoretical studies of the ammonia dimer made during the last decade is presented. Second, progress on the analysis of the microwave and far infrared spectrum of (ND_3)_2 below 13 cm^{-1} is reported. These spectra directly measure the 'donor -acceptor' interchange splittings in (ND_3) _2, and determine some of the monomer umbrella inversion tunneling splittings. Third, new 80-90 cm^{-1} far infrared spectra of (NH_3)_2 are presented and a preliminary analysis is proposed. Most of the new excited VRT states have been assigned as tunneling sublevels of an out-of-plane intermolecular vibration.