Intermolecular Contributions Research Articles

Intermolecular vibrations and fast relaxations in supercooled ionic liquids

Short-time dynamics of ionic liquids has been investigated by low-frequency Raman spectroscopy (4 < ω < 100 cm(-1)) within the supercooled liquid range. Raman spectra are reported for ionic liquids with the same anion, bis(trifluoromethylsulfonyl)imide, and different cations: 1-butyl-3-methylimidazolium, 1-hexyl-3-methylimidazolium, 1-butyl-1-methylpiperidinium, trimethylbutylammonium, and tributylmethylammonium. It is shown that low-frequency Raman spectroscopy provides similar results as optical Kerr effect (OKE) spectroscopy, which has been used to study intermolecular vibrations in ionic liquids. The comparison of ionic liquids containing aromatic and non-aromatic cations identifies the characteristic feature in Raman spectra usually assigned to librational motion of the imidazolium ring. The strength of the fast relaxations (quasi-elastic scattering, QES) and the intermolecular vibrational contribution (boson peak) of ionic liquids with non-aromatic cations are significantly lower than imidazolium ionic liquids. A correlation length assigned to the boson peak vibrations was estimated from the frequency of the maximum of the boson peak and experimental data of sound velocity. The correlation length related to the boson peak (∼19 Å) does not change with the length of the alkyl chain in imidazolium cations, in contrast to the position of the first-sharp diffraction peak observed in neutron and X-ray scattering measurements of ionic liquids. The rate of change of the QES intensity in the supercooled liquid range is compared with data of excess entropy, free volume, and mean-squared displacement recently reported for ionic liquids. The temperature dependence of the QES intensity in ionic liquids illustrates relationships between short-time dynamics and long-time structural relaxation that have been proposed for glass-forming liquids.

Intramolecular and Intermolecular Contributions to the Barriers for Rotation of Methyl Groups in Crystalline Solids: Electronic Structure Calculations and Solid-State NMR Relaxation Measurements

The rotation barriers for 10 different methyl groups in five methyl-substituted phenanthrenes and three methyl-substituted naphthalenes were determined by ab initio electronic structure calculations, both for the isolated molecules and for the central molecules in clusters containing 8-13 molecules. These clusters were constructed computationally using the carbon positions obtained from the crystal structures of the eight compounds and the hydrogen positions obtained from electronic structure calculations. The calculated methyl rotation barriers in the clusters (E(clust)) range from 0.6 to 3.4 kcal/mol. Solid-state (1)H NMR spin-lattice relaxation rate measurements on the polycrystalline solids gave experimental activation energies (E(NMR)) for methyl rotation in the range from 0.4 to 3.2 kcal/mol. The energy differences E(clust) - E(NMR) for each of the ten methyl groups range from -0.2 kcal/mol to +0.7 kcal/mol, with a mean value of +0.2 kcal/mol and a standard deviation of 0.3 kcal/mol. The differences between each of the computed barriers in the clusters (E(clust)) and the corresponding computed barriers in the isolated molecules (E(isol)) provide an estimate of the intermolecular contributions to the rotation barriers in the clusters. The values of E(clust) - E(isol) range from 0.0 to 1.0 kcal/mol.

Singlet state relaxation via intermolecular dipolar coupling

The intermolecular contribution to the relaxation of singlet states has been derived on the basis of a translational-rotational diffusion model that describes molecules as impenetrable spheres which translate and rotate in an isotropic low-viscosity medium. The equations for the relaxation rate constants obtained are discussed and the dependence on physical parameters is exploited. Theoretical predictions are compared with experiments when the intermolecular relaxation is due to both protons and deuterons present in the sample. An agreement between experiments and theory of ±4% was obtained when the physical parameters are estimated from first-principles calculation.

Temperature-dependent structure of methyltributylammonium bis(trifluoromethylsulfonyl)amide: X ray scattering and simulations

We report the combined results of computational and x ray scattering studies of amorphous methyltributylammonium bis(trifluoromethylsulfonyl)amide as a function of temperature. These studies included the temperature range for the normal isotropic liquid, a deeply supercooled liquid and the glass. The low q peaks in the range from 0.3 to 1.5 A(-1) in the structure function of this liquid can be properly accounted for by correlations between first and second nearest neighbors. The lowest q peak can be assigned to real space correlations between ions of the same charge, while the second peak arises mostly from nearest neighbors of opposite charge. Peaks at larger q values are mostly intramolecular in nature. While our simulated structure functions provide an excellent match to our experimental results and our experimental findings agree with previous studies reported for this liquid, the prior interpretation of the experimental data in terms of an interdigitated smectic A phase is not supported by our simulations. In this work, we introduce a set of general theoretical partitions of real and reciprocal space correlations that allow for unambiguous analysis of all intra- and interionic contributions to the structure function and coherent scattering intensity. We find that the intermolecular contributions to the x ray scattering intensity are dominated by the anions and cross terms between cations and anions for this ionic liquid.

Self-assembly of Fmoc-tetrapeptides based on the RGDS cell adhesion motif

Self-assembly in aqueous solution has been investigated for two Fmoc [Fmoc = N-(fluorenyl)-9-methoxycarbonyl] tetrapeptides comprising the RGDS cell adhesion motif from fibronectin or the scrambled sequence GRDS. The hydrophobic Fmoc unit confers amphiphilicity on the molecules, and introduces aromatic stacking interactions. Circular dichroism and FTIR spectroscopy show that the self-assembly of both peptides at low concentration is dominated by interactions among Fmoc units, although Fmoc-GRDS shows β-sheet features, at lower concentration than Fmoc-RGDS. Fibre X-ray diffraction indicates β-sheet formation by both peptides at sufficiently high concentration. Strong alignment effects are revealed by linear dichroism experiments for Fmoc-GRDS. Cryo-TEM and small-angle X-ray scattering (SAXS) reveal that both samples form fibrils with a diameter of approximately 10 nm. Both Fmoc-tetrapeptides form self-supporting hydrogels at sufficiently high concentration. Dynamic shear rheometry enabled measurements of the moduli for the Fmoc-GRDS hydrogel, however syneresis was observed for the Fmoc-RGDS hydrogel which was significantly less stable to shear. Molecular dynamics computer simulations were carried out considering parallel and antiparallel β-sheet configurations of systems containing 7 and 21 molecules of Fmoc-RGDS or Fmoc-GRDS, the results being analyzed in terms of both intermolecular structural parameters and energy contributions.

Attractive energy contribution to nanoconfined fluids behavior: the normal pressure tensor

The aim of our research is to demonstrate the role of attractive intermolecular potential energy on normal pressure tensor of confined molecular fluids inside nanoslit pores of two structureless purely repulsive parallel walls in xy plane at z = 0 and z = H, in equilibrium with a bulk homogeneous fluid at the same temperature and at a uniform density. To achieve this we have derived the perturbation theory version of the normal pressure tensor of confined inhomogeneous fluids in nanoslit pores: $$ P_{ZZ} = kT\rho \left( {Z_{1} } \right) + \pi kT\rho \left( {Z_{1} } \right)\int\limits_{ - d}^{0} {\rho \left( {Z_{2} } \right)} Z_{2}^{2} g_{Z,H} (d){\text{d}}Z_{2} - \frac{1}{2}\iint {\int\limits_{0}^{2\pi } {\phi^{\prime } \left( {\vec{r}_{2} } \right)\rho \left( {Z_{1} } \right)\rho \left( {Z_{2} } \right)g_{Z,H} (r_{2} )} }{\frac{{Z_{2}^{2} }}{{(R_{2}^{2} + Z_{2}^{2} )^{{\frac{1}{2}}} }}}R_{2} {\text{d}}R_{2} {\text{d}}Z_{2} {\text{d}}\Uptheta ;\quad \left| {\overset{\lower0.5em\hbox{$\smash{\scriptscriptstyle\rightharpoonup}$}} {r}_{2} } \right| > d $$ In which R, Θ, Z are the cylindrical coordinate’s notations and \( \left| {\vec{r}_{2} } \right| = \sqrt {R_{2}^{2} + Z_{2}^{2} }\). Assuming the truncated-Lennard-Jones potential, the third term represents the attractive intermolecular potential energy contribution to the normal pressure tensor. We report solution of this equation for the truncated-Lennard-Jones confined fluid in nanoslit pores, and we demonstrate the role of attractive potential energy by comparing the results of Lennard-Jones and hard-sphere fluids. Our numerical calculations show that the normal pressure tensor has an oscillatory form versus distance from the walls for all confined fluids. The oscillations increase with reduced bulk density and decrease with fluid–fluid attraction. It also becomes broad and smooth with pore width at constant temperature and density. In comparison with hard-sphere confined fluids, the values of the normal pressure for LJ fluids at all distances from the walls are less than the hard-sphere fluids. This analytic pressure tensor equation is a useful tool to understand the role of attractive and repulsive forces in the normal pressure tensor and to predict phase behavior of nanoconfined fluids.

Change in heat capacity in melting and glass transition of polymers at high pressures

Equations are reported for calculating the change in the heat capacity in melting and glass transition of polymers. At high pressure, the conformational contribution to the change in the heat capacity of the polymers are almost two times higher in the case of the glass transition than the intermolecular contribution, while the conformational contribution to the change in the heat capacity in melting is more than two times smaller than the intermolecular contribution. The conformational contribution to the change in the heat capacity in the glass transition and melting of polymers changes little with an increase in the pressure.

Geometry Optimization of Large and Flexible van der Waals Dimers: A Fragmentation-Reconstruction Approach.

A novel approach for exploring the energy minima of the potential energy surface of large and flexible van der Waals dimers is proposed and tested. The total dimer energy is divided into intra- and intermolecular contributions, which can be computed at different levels of theory. The intermolecular energy, which is the time-consuming part of the calculation, is computed by means of the fragmentation reconstruction method (FRM), making possible the calculation of the interaction energy of large molecules. The method is validated by performing geometry optimizations through a quasi-Newton technique on two benchmark medium-sized systems, where the comparison with a direct ab initio calculation is still computationally feasible. In both cases, good agreement is achieved between geometries and energies of the resulting energy minima.

Are Long-Chain Alkanes Hydrophilic?

Although short n-alkane chains are classic examples of hydrophobic solutes, mounting evidence points to a hydrophilic crossover for the hydration free energies (DeltaG) of sufficiently long n-alkane chains. Experimental and simulation results for the hydration of n-alkanes from methane (C1) to docosane (C22) are combined with fundamental thermodynamic relations to elucidate intermolecular contributions to DeltaG. Theoretical bounds on the influence of solute conformation on DeltaG are inferred by considering the hydration of idealized linear (all-trans) and globular (spherical) model solutes. More detailed theoretical extrapolations of experimental and simulation results imply that the water-mediated free energy change associated with collapsing an all-trans C100 chain is on the order of -100 kJ/mol and thus that n-alkane chains of this length and longer may be hydrophilic (DeltaG < 0).

Ligand-side tautomer enumeration and scoring for structure-based drug-design

Tautomeric rearrangements of a molecule lead to distinct equilibrated structural states of the same chemical compound that may differ significantly in molecular shape, surface, nature of functional groups, hydrogen-bonding pattern and other derived molecular properties [1]. Especially for the structure-based pharmacophore modeling of ligand-protein complexes [2], knowledge of the most favorable tautomeric ligand states may be crucial for the quality and correctness of the generated pharmacophore models and derived putative binding modes. We will present a ligand-side tautomer enumeration and ranking algorithm that considers both geometrical constraints imposed by the conformation of the bound ligand as well as intra- and inter-molecular energetic contributions to find the preferred tautomeric states of the ligand in the macromolecular environment of the binding-site. The presented tautomer ranking algorithm is based on scores that are derived solely from MMFF94 [3-9] energies (thus the method works for a wide range of organic molecules) and has proven to be able to top-rank known preferred tautomeric states of ligands in a series of investigated protein complexes.

N-Type Charge Transport and Mobility of Fluorinated Perylene Bisimide Semiconductors

The intramolecular and intermolecular charge transport parameters are evaluated quantum chemically for three fluorinated derivatives of perylene bisimide (PBI) semiconductors, two of which feature a twisted PBI core. Charge transfer rates are computed within the Marcus-Levich-Jortner formalism including a single effective mode treated quantum mechanically and are injected in a kinetic Monte Carlo scheme to propagate the charge carrier in the crystal and to estimate charge mobilities at room temperature. The relative order of computed mobilities agrees with the observed trend, and the largest mobility is computed for the planar PBI derivative. It is suggested that thermally induced disorder effects should contribute considerably to the observed large mobility of the planar PBI derivative, while a retardation effect induced by the presence of alternating slow and fast jumps along pi-stacked PBI columns is responsible for the lower mobilities of the two twisted derivatives. The computed parameters reveal the subtle interplay between intramolecular and intermolecular contributions to the charge carrier propagation in these organic semiconductors and may guide the design of more efficient architectures.

Observation of Pyridine Aggregation in Aqueous Solution Using Neutron Scattering Experiments and MD Simulations

Neutron diffraction with isotopic substitution (NDIS) experiments have been used to examine the structuring of aqueous solutions of pyridine. A new method is described for extracting the structure factors relating to intermolecular correlations from neutron scattering experiments on liquid solutions of complex molecular species. This approach performs experiments at different concentrations and exploits the intramolecular coordination number concentration invariance (ICNCI) to separate the internal and intermolecular contributions to the total intensities. The ability of this method to deconvolute molecular and intermolecular correlations is tested and demonstrated using simulated neutron scattering results predicted from molecular dynamics simulations of aqueous solutions of the polyatomic solute pyridine in which the inter- and intramolecular terms are known. The method is then implemented using neutron scattering measurements on solutions of pyridine. The results confirm that pyridine shows a significant propensity to aggregate in solution and demonstrate the prospects for the future application of the ICNCI approach to the study of large polyatomic solutes using next-generation neutron sources and detectors.

Features of polymer chain dynamics as revealed by intermolecular nuclear magnetic dipole-dipole interaction: Model calculations and field-cycling NMR relaxometry

Proton NMR phenomena such as spin-lattice relaxation, free-induction decays, and solid echoes are analyzed with respect to contributions by intermolecular dipole-dipole interactions in polymer melts. The intermolecular dipole-dipole correlation function is calculated by taking into account the correlation hole effect characteristic for polymer melts. It is shown that the ratio between the intra- and intermolecular contributions to NMR measurands depends on the degree of isotropy of chain dynamics anticipated in different models. This, in particular, refers to the tube/reptation model that is intrinsically anisotropic in clear contrast to n-renormalized Rouse models, where no such restriction is implied. Due to anisotropy, the tube/reptation model predicts that the intramolecular contribution to the dipole-dipole correlation function increases with time relative to the intermolecular contribution. Therefore, the intramolecular contribution is expected to dominate NMR measurands by tendency at long times (or low frequencies). On the other hand, the isotropic nature of the n-renormalized Rouse model suggests that the intermolecular contribution tends to prevail on long-time scales (or low frequencies). Actually, theoretical estimations and the analysis of experimental spin-lattice relaxation data indicate that the intermolecular contribution to proton NMR measurands is no longer negligible for times longer than 10(-7) s-10(-6) s corresponding to frequencies below the megahertz regime. Interpretations not taking this fact into account need to be reconsidered. The systematic investigation of intermolecular interactions in long-time/low frequency proton NMR promises the revelation of the dynamic features of segment displacements relative to each other in polymer melts.

Effect of hydrogen bonds on polarizability of a water molecule in (H2O)N (N = 6, 10, 20) isomers

Polarizabilities of the low-lying isomers of (H(2)O)(N) (N = 6, 10, 20) clusters were computed by using Density Functional Theory. The global polarizabilities of the water isomers were found to depend mainly on the total number of water molecules rather than their cluster structures. We show that this result hides in fact a strong heterogeneity of the molecular polarizability within the different isomers. The global polarizability of a cluster was divided into a sum of molecular contributions by using the Hirshfeld partitioning scheme. We reveal that the value of the local polarizability of a molecule in the cluster is correlated with the number and type of the hydrogen bonds (HB) the molecule forms. Consequently, the molecules located in the interior of the cluster, which usually form more HBs, have smaller molecular polarizabilities than the molecules at the surface, which form less HBs. The contribution of intermolecular interaction to the global polarizability was analyzed by decomposing the cluster polarizability into intra- and inter-molecular contributions. The former measures the polarization within the molecular basin against the external electric field, while the latter is described as the sum of polarizability caused by charge flow through the HBs. These two contributions vary with the cluster size: the intermolecular contribution decreases with the cluster size on the contrary of the intramolecular contribution which increases.

Ab initio study of van der Waals and hydrogen-bonded molecular crystals with a periodic local-MP2 method

We have studied ab initio the cohesive energy of a set of six molecular crystals with CRYSCOR, a new program implementing a periodic local second-order Moller–Plesset perturbation theory (LMP2) method. The set of studied crystals includes hydrogen-bonded (ice XI, NH3, formic acid, HCN) and van der Waals (CO2, C2H2) crystals. A polarization-augmented triple-zeta quality basis set has been used throughout. The method allows us to obtain cohesive energies in good agreement with the experimental values. Results are also compared to those obtained with a recently proposed B3LYP augmented with an empirical dispersion term (D*) specifically tuned for bulk molecular crystals, and with those obtained through a spin component scaling of the LMP2 results. We finally analyze the correlation contribution to the cohesive energy by separating the intramolecular and intermolecular contribution, according to the distance between correlated electrons, allowing for an interesting insight on the role of weak interactions in the studied systems. In this respect, crystalline formic acid is analyzed in more detail. The investigation of the long range contribution to the cohesive energy also allows us to draw a correspondence between the ab initio LMP2 and empirical approaches used to describe dispersion interaction.

Intermolecular shielding contributions studied by modeling the (13)C chemical-shift tensors of organic single crystals with plane waves.

In order to predict accurately the chemical shift of NMR-active nuclei in solid phase systems, magnetic shielding calculations must be capable of considering the complete lattice structure. Here we assess the accuracy of the density functional theory gauge-including projector augmented wave method, which uses pseudopotentials to approximate the nodal structure of the core electrons, to determine the magnetic properties of crystals by predicting the full chemical-shift tensors of all (13)C nuclides in 14 organic single crystals from which experimental tensors have previously been reported. Plane-wave methods use periodic boundary conditions to incorporate the lattice structure, providing a substantial improvement for modeling the chemical shifts in hydrogen-bonded systems. Principal tensor components can now be predicted to an accuracy that approaches the typical experimental uncertainty. Moreover, methods that include the full solid-phase structure enable geometry optimizations to be performed on the input structures prior to calculation of the shielding. Improvement after optimization is noted here even when neutron diffraction data are used for determining the initial structures. After geometry optimization, the isotropic shift can be predicted to within 1 ppm.

DFT and Local-MP2 Periodic Study of the Structure and Stability of Two Proton-Ordered Polymorphs of Ice

The equilibrium geometry and the formation energy of two periodic polymorphs of Ice have been theoretically studied: the former (Ice XI, crystal group Cmc2(1)) is experimentally observed as the most stable structure at low temperature and pressure; the latter (crystal group Pna2(1)) is the simplest proton-ordered model of ordinary ice. With the Crystal code, the problem is solved using Hartree-Fock (HF), pure Kohn-Sham (PW91), or hybrid (B3LYP) one-electron Hamiltonians. The B3LYP results are those in best agreement with the experiment. Using the B3LYP-optimized geometry and starting from the corresponding HF Crystal solution, the energetics of the two polymorphs have been investigated at an ab initio MP2 level using the Cryscor code, based on a local-correlation approach: these calculations have allowed us not only to confirm the excellent B3LYP results as concerns the formation energy and the relative stability of the two structures but also to analyze the role in this respect of the intra- and intermolecular contributions to the correlation energy. Since both Crystal and Cryscor adopt a basis set of localized Gaussian-type functions and since very small energy differences are involved, utter attention has been paid to correcting for the basis set superposition error in the calculation of formation energies.

The 559-to-600 nm shift observed in red fluorescent protein eqFP611 is attributed to cis–trans isomerization of the chromophore in an anionic protein pocket

Fluorescent proteins are commonly used as molecular labels, noninvasive markers of gene expression, and reporters of environmental conditions in live cells. We investigate the structural and spectroscopic properties of the chromophore of a far-red fluorescent protein eqFP611. Both the cis and trans isomers of the chromophore are examined within the protein for which both anionic and neutral states of protonation are considered. Spectroscopic properties are examined using time-dependent density functional theory (TDDFT), employing the B3LYP, PBE and B3PW91 density functionals. Intermolecular and long-range contributions to the structure and spectroscopy were treated using the own n-layered integrated molecular orbital and molecular mechanics (ONIOM) approach. The results indicated that the chromophore before excitation is in an anionic, protonated state, with the long-range contributions inducing a blue shift in the absorption and fluorescence maxima of the chromophore. Moreover, the calculated changes of the lowest pi-pi* excitation energy upon isomerization match the observed shift from 559 to 600 nm in the absorption maximum of the system following prolonged irradiation. Furthermore, decomposition analysis of the electrostatic contributions from individual residues indicated that the interactions from four residues Arg92, Lys67, Glu145, and His197 to the chromophore play a key role in the absorption and fluorescence spectra of eqFP611, suggesting that mutations at these sites should provide very useful mechanistic information.

Modeling molecular crystals formed by spin-active metal complexes by atom–atom potentials

We apply the atom-atom potentials to molecular crystals of iron(II) complexes with bulky organic ligands. The crystals under study are formed by low-spin or high-spin molecules of Fe(phen)(2)(NCS)(2) (phen = 1,10-phenanthroline), Fe(btz)(2)(NCS)(2) (btz = 5,5',6,6'-tetrahydro-4H,4'H-2,2'-bi-1,3-thiazine), and Fe(bpz)(2)(bipy) (bpz = dihydrobis(1-pyrazolil)borate, and bipy = 2,2'-bipyridine). All molecular geometries are taken from the X-ray experimental data and assumed to be frozen. The unit cell dimensions and angles, positions of the centers of masses of molecules, and the orientations of molecules corresponding to the minimum energy at 1 atm and 1 GPa are calculated. The optimized crystal structures are in a good agreement with the experimental data. Sources of the residual discrepancies between the calculated and experimental structures are discussed. The intermolecular contributions to the enthalpy of the spin transitions are found to be comparable with its total experimental values. It demonstrates that the method of atom-atom potentials is very useful for modeling molecular crystals undergoing the spin transitions.

Unusual halogen-bonded complex FBrδ+⋯Brδ+F and hydrogen-bonded complex FBrδ+⋯Hδ+F formed by interactions between two positively charged atoms of different polar molecules

Using ab initio calculations, the authors' predicted for the first time that the halogen-bonded complex FBrdelta+...delta+BrF and hydrogen-bonded complex FBrdelta+...delta+HF formed by the interactions between two positively charged atoms of different polar molecules can be stable in gas phase. It shows that halogen bond or hydrogen bond not only exists between oppositely charged atoms but also between like-charged atoms. That the attraction arising from the special halogen bond or hydrogen bond can exceed the electrostatic repulsion between two contact positively charged atoms stabilizes the complex. Of course, from the point of view of physics they can consider the interactions in FBrdelta+...delta+BrF and FBrdelta+...delta+HF as mainly the sum of the long range molecular interactions, namely, electrostatic, induction, and dispersion with some short-range repulsion. They found that the intermolecular electron correlation contribution representing dispersion interaction plays a crucial role in the stabilities of seemingly repulsive complexes FBrdelta+...delta+BrF and FBrdelta+...delta+HF.