The structure of glycerol in the liquid state: a neutron diffraction study

Neutron diffraction coupled with hydrogen/deuterium isotopic substitution has been used to investigate the structure of the pure cryoprotectant glycerol in the liquid state at 298 K and 1 atm. The neutron diffraction data were used to constrain a 3 dimensional computational model that is experimentally relevant using the empirical potential structure refinement (EPSR) technique. These simulations lead to a model structure of the glycerol molecule that is consistent with the experimental data. Interestingly, from interrogation of this structure, it is found that the number of hydrogen bonds per molecule is larger than had previously been suggested. Furthermore, converse to previous work, no evidence for intra-molecular hydrogen bonds is found. These results highlight the importance and relevance of using experimental data to inform computational modelling of even simple liquid systems.     

Optical excitations in star-shaped fluorene molecules

A detailed study of the low-energy optical transitions in two families of star-shaped molecules is presented. Both families have 3-fold rotational symmetry with oligofluorene arms attached to a central core. In one family, the core of the molecule is a rigid meta-linked truxene, while the other is a meta-linked benzene moiety. The low-energy transitions were studied both experimentally and using time-dependent density functional theory (TD-DFT). The optical transitions of these new star-shaped molecules were compared with corresponding linear oligofluorenes. Both families of star-shaped molecules showed higher absorption and fluorescence dipoles and photoluminescence quantum yields than straight chain oligofluorenes. TD-DFT calculations show that absorption takes place across the entire molecule, and after excited state relaxation, the emission results from a single arm. In both theory and experiment the transition dipole moments show an approximate n(0.5) dependence on the number of fluorene units in each arm.     

Structure, dynamics and ordering in structure i ether clathrate hydrates from single-crystal X-ray diffraction and 2H NMR spectroscopy

The structure and dynamics of trimethylene oxide (TMO) and ethylene oxide (EO) structure I (sI) hydrates are reported from single-crystal X-ray diffraction and 2H NMR spectroscopic measurements. The guest molecule positions in the large cage were determined with considerable improvement over previous diffraction work so that a dynamic model that was consistent with these orientations could be developed to explain the 2H NMR data. Reorientations are shown to take place among both symmetry-related and symmetry-independent sites, 16 positions in all. Because of the prochiral nature of the molecules, both guests show 2H NMR line shapes with large asymmetry parameters, rather unusual for guest molecules in the sI hydrate large cage. The results also show that the dipolar axis of the TMO molecule lies close to the 4 bar axis of the cage on average, whereas for EO, this is not the case. For TMO, progressive alignment of the polar axis with decrease of temperature then allows the dipoles to interact more strongly until dipole reversal is quenched at the ordering transition. The lack of ordering of EO is consistent with the much weaker alignment of the molecular dipoles along the 4 bar axis. With the new complementary information on the structure and dynamics from crystallography and NMR, it is possible to understand why the large cage guests order in the large cage of sI hydrate for TMO hydrate but not for EO hydrate.     

Electronic structure of thiazine-indigo pigment on the basis of the crystal structure

Thiazine-indigos are novel hydrogen-bonded pigments developed recently by Clariant that exhibit a variety of shades from yellow to red. Among these, a commercially available chlorinated derivative (THI) gives a color of vivid red, although it is only pale yellow in solution. For this reason, electronic characterization of THI has been carried out on the basis of the crystal structure. There are chains of intermolecular hydrogen bonds between the N-H group of one molecule and the O atom of the neighboring one along the b-axis, forming a two-dimensional hydrogen bond network. The direction of the transition dipole points along the long molecular axis, and the transition dipoles are arranged in "head-to-tail" fashion along the (b,-c) diagonal direction. The large bathochromic shift upon crystallization can be mostly attributed to excitonic interactions between transition dipoles arranged diagonally along the stacking axis as well as those in head-to-tail fashion on the molecular plane.     

Structure and dynamics of methanol in water: a quantum mechanical charge field molecular dynamics study

An ab initio quantum mechanical charge field molecular dynamics simulation was carried out for one methanol molecule in water to analyze the structure and dynamics of hydrophobic and hydrophilic groups. It is found that water molecules around the methyl group form a cage-like structure whereas the hydroxyl group acts as both hydrogen bond donor and acceptor, thus forming several hydrogen bonds with water molecules. The dynamic analyses correlate well with the structural data, evaluated by means of radial distribution functions, angular distribution functions, and coordination number distributions. The overall ligand mean residence time, τ identifies the methanol molecule as structure maker. The relative dynamics data of hydrogen bonds between hydroxyl of methanol and water molecules prove the existence of both strong and weak hydrogen bonds. The results obtained from the simulation are in excellent agreement with the experimental results for dilute solution of CH(3)OH in water. The overall hydration shell of methanol consists in average of 18 water molecules out of which three are hydrogen bonded.     

Spectral investigations on 1,5-dipiperidino anthraquinone

Optical absorption, fluorescence emission and surface enhanced Raman spectra of 1,5-dipiperidino anthraquinone (1,5-DPAQ) have been examined to elucidate the nature of molecule in different environments. Fluorescence emission and optical absorption measurements show that the polarity of the solvent plays a vital role through intermolecular hydrogen bonding and reorientational motion of solvent molecule around excited state fluorophore. Anisotropy measurement gives the angle between absorption and emission transition dipoles. The vibrational features observed in surface enhanced Raman spectroscopy (SERS) suggest that the molecules are chemisorbed. The adsorption of the molecule is through pi electrons in the anthraquinone ring and the axial lone pair of electrons of nitrogen. The orientation of the molecule is found to be 'flat-on'.     

Biodegradable gemini surfactants. Correlation of area per surfactant molecule with surfactant structure

Values of the area per surfactant molecule of various single chain and gemini quaternary ammonium surfactants containing biodegradable amide and ester groups are obtained from the surface tension measurements and they are mutually compared. It was found that surfactant molecules with the ester group in their structure occupy smaller area at the air/water interface than the corresponding molecules with the amide group, mainly due to the higher conformational flexibility of ester groups. In decreasing the area per surfactant molecule value, hydrogen bonding (both inter- and intramolecular) plays a significant role when amide groups are present in the spacer of a gemini molecule. They must be separated by a polymethylene chain or a flexible group such as cyclohexane which is short enough to allow intramolecular hydrogen bonds. The flexible cyclohexane group with the amide group in single chain surfactants may lead to the formation of intermolecular hydrogen bonds among surfactant molecules which also results in the reduction of the area per surfactant molecule.     

Theoretical 13C chemical shift, 14N, and 2H quadrupole coupling- constant studies of hydrogen bonding in L-alanylglycine dipeptide

(13)C chemical shieldings and (14)N and (2)H electric field gradient (EFG) tensors of L-alanylglycine (L-alagly) dipeptide were calculated at RHF/6-31 + + G** and B3LYP/6-31 + + G** levels of theory respectively. For these calculations a crystal structure of this dipeptide obtained from X-ray crystallography was used. Atomic coordinates of different clusters containing several L-alagly molecules were used as input files for calculations. These clusters consist of central and surrounding L-alagly molecules, the latter forming short, strong, hydrogen bonds with the central molecule. Since the calculations did not converge for these clusters, the surrounding L-alagly molecules were replaced by glycine molecules. In order to improve the accuracy of calculated chemical shifts and nuclear quadrupole coupling constants (NQCCs), different geometry-optimization strategies were applied for hydrogen nuclei. Agreement between calculated and experimental data confirms that our optimized coordinates for hydrogen nuclei are more accurate than those obtained by X-ray diffraction.     

High-density hydration layer of lysozymes: molecular dynamics decomposition of solution scattering data

A characterization of the physical properties of protein hydration water is critical for understanding protein structure and function. Recent small-angle X-ray and neutron scattering data indicate that the density of water on the surface of lysozyme is significantly higher than in bulk water. Here, we provide an interpretation of the scattering results using a molecular dynamics simulation, which allows us to make quantitative predictions about density variations in the first hydration shell. The perturbation relative to bulk water involves statistically significant changes in the average water structure in the first hydration layer. The water density in the first hydration shell is increased by 5% with respect to the bulk. In regions of higher water density, the water dipoles align more parallel to each other and the number of hydrogen bonds per water molecule is higher. Increased water density is found for water molecules interacting with hydrogen and carbon atoms in the backbone or with nonpolar or negatively charged side-chain groups.     

Simulations of liquid ammonia based on the combined quantum mechanical/molecular mechanical (QM/MM) approach

Two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, namely, HF/MM and B3LYP/MM, have been performed to investigate the local structure and dynamics of liquid ammonia. The most interesting region, a sphere containing a central reference molecule and all its nearest surrounding molecules (first coordination shell), was treated by the Hartree-Fock (HF) and hybrid density functional B3LYP methods, whereas the rest of the system was described by the classical pair potentials. On the basis of both HF and B3LYP methods, it is observed that the hydrogen bonding in this peculiar liquid is weak. The structure and dynamics of this liquid are suggested to be determined by the steric packing effects, rather than by the directional hydrogen bonding interactions. Compared to previous empirical as well as Car-Parrinello (CP) molecular dynamics studies, our QM/MM simulations provide detailed information that is in better agreement with experimental data.     

(5RS)‐5‐(4‐Methoxyphenyl)‐2‐(methylsulfanyl)benzo[g]pyrimido[4,5‐b]quinoline‐4,6,11(3H,5H,12H)‐trione,with Z′ = 3, forms a three‐dimensional hydrogen‐bonded framework containing five types of hydrogen bond

The title compound, C₂₃H₁₇N₃O₄S, crystallizes with Z′ = 3 in the space group P. Two of the three independent molecules are broadly similar in terms of both their molecular conformations and their participation in hydrogen bonds, but the third molecule differs from the other two in both of these respects. The molecules are linked by a combination of N—H...O, N—H...N, C—H...O, C—H...N and C—H...π(arene) hydrogen bonds to form a continuous three‐dimensional framework structure within which a centrosymmetric six‐molecule aggregate can be identified as a key structural element.     

Charge separation in water molecule clusters under thermal fluctuations: 1. Intermolecular interactions

A detailed model of intermolecular interactions in water molecule clusters is developed that makes it possible to describe their disintegration to ions under conditions of finite temperatures by the stochastic simulation methods. In this model, the Hamiltonian in explicit form includes Coulomb, dispersion, exchange, and polarization interactions; many-particle covalent interactions and hydrogen bonds; the interaction of induced dipoles; charge transfers from ions to molecules; and the recombination of counterion charges, as well as the effect of an ion field on the unpaired interactions of molecules. The model is consistent with experimental data on the free energy and entropy of ion hydration in water vapors and the free energy of the hydration of a recombined ion pair.     

The structure of water in p-sulfonatocalix[4]arene

Tetrasodium p-sulfonatocalix[4]arene exists as a hydrate with approximately 14 water molecules and has three polymorphic modifications, all of which contain a water molecule in the molecular cavity that is engaged in OH···π interactions. Single-crystal neutron structures are reported for two of these three forms and reveal a "compressed" water molecule with short OH bonds. Partial atomic charges and hardness analysis (PACHA) calculations based on the neutron coordinates give an OH···π interaction energy of 6.9-7.5 kJ mol(-1). The PACHA analysis also reveals the dominance of the charge-assisted hydrogen bonds from the Na(+)-coordinated water molecules. The instability of the crystal towards dehydration can be traced to an uncoordinated lattice water site. The remarkable calixarene-Na(+)-hydrate motif is conserved almost unchanged across all three polymorphs. A single-crystal neutron structure is also reported for pentasodium p-sulfonatocalix[4]arene·12H(2)O, which exhibits an intracavity water molecule that is engaged in both OH···π and OH···O hydrogen bonding. The shorter covalent bond to the hydrogen atom that forms the interaction with the aromatic ring is again apparent.     

Theoretical study on the reactive sites and intramolecular interactions in taxol and its four analogues

A density‐functional study of the paclitaxel (Taxol) molecule and its four analogues has been performed. The theory of Bader's atoms in molecules (AIM) was applied to examine the electronic structure of these molecules at their ground state. Topological analysis reveals that the esterification of hydroxyl group attached to the oxetane ring results in great change of conformation of the taxane ring, and thus is responsible for bioactivity of the oxetane oxygen atom. It was found that there exists some intramolecular interactions in the molecule, including normal hydrogen bonds (HBs) and double HBs. Visualization of the molecule shows that the central bodies (the four fused rings) of the molecules are wrapped by the intramolecular interactions. It is supposed that these intramolecular interactions lower the aqueous solubility and protect the flexible oxetane ring, which is regarded as the dominating bioactivity site of the drug, from being opened. Our results provide an extended and consistent set of data to gauge classical force fields in view of the atomistic investigations of the interaction of the bioactive molecules. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

A new lattice-based theory for hydrogen-bonding liquids in uniform electric fields

We propose a new lattice-based, mean-field theory for predicting alignment of molecular dipoles and hydrogen bonds in liquids subject to uniform electric fields. The theory is presently restricted to liquids whose molecules possess one (proton) donor and one acceptor sites each, and wherein the H-bond axis is collinear with the dipole moments of the bonded molecules. The final expressions for hydrogen bond stoichiometry and polarization are free of lattice parameters, are interpretable using simple phenomenological arguments, and reduce to known limiting forms. The theory is applied to understand the internal structure of hydrogen cyanide in the liquid state at different electric fields.     

The structure of liquid tetrahydrofuran

Hydrogen/deuterium isotopic substitution neutron diffraction techniques have been used to measure the structural correlation functions of liquid tetrahydrofuran at room temperature. Empirical potential structure refinement (EPSR) has been used to build a three-dimensional model of the liquid structure that is consistent with the experimental data. Analysis to the level of the orientational correlation functions shows that the liquid displays a preference for T-like configurations between the tetrahydrofuran molecules, a local structure that results in void-like regions of approximately 1.25 angstroms radius within the bulk liquid. The surface chemistry of these voids suggests a slightly positive electrostatic character. These findings are consistent with the known propensity of the liquid to solvate free electrons.     

Nonlinear optical properties in calix[n]arenes: orientation effects of monomers

We investigate the nonlinear optical (NLO) polarizations for various geometric arrangements of the dipolar chromophores in a calix[n]arene geometry. The interactions were studied by using (HF)3 as model compounds both in parallel and frustrated orientations. The interdipolar angle between the monomer molecules is varied so that many different arrangements of the dipoles can be realized which is associated with the opening up of the calix[n]arene rings. Quantum-chemical calculations at both ab initio and semiempirical levels, show that the all-parallel arrangement of the dipoles exhibit the maximum magnitude for the nonlinear optical coefficients at small interdipolar angles for all interdipolar distances. In the frustrated orientations however, the NLO response is maximum at large interdipolar angles corresponding to the flattened calix[n]arene rings. The role of hydrogen bonding in stabilizing these assemblies in various conformations has been investigated. Crystallographic database analysis for calix[3]arenes shows that optical properties in real molecular systems can be modeled based on our simple interaction theory.     

Spatial Effect of C?H Dipoles on the Electron Affinity of Diamond (100)‐2×1 Adsorbed with Organic Molecules

Cycloaddition of allyl organics on the dimer rows of a clean C(100)‐2×1 diamond surface can be used for the controlled functionalization of such a surface. Sticking probability measurements confirm that appreciable uptake of acetylene and butadiene occur on the clean diamond surface at room temperature. The change in electron affinity of the surface as a function of the coverage of the organic molecules is investigated with periodic DFT calculations. The presence of C? H dipoles on these adsorbates modify the surface charge density and gives rise to an induced dipolar layer that modifies the electrostatic potential outside the surface. There is a significant reduction of up to 2.5 eV in electron affinity following the chemisorption of ethylene. Therefore, the adsorbed molecules play the same role as surface hydrogen in inducing the NEA condition on the clean diamond. The change in electron affinity does not scale linearly with the coverage of the organic molecules, because the spatial profile of the C? H dipoles as well as the orientation of the molecules on the surface have a predominant effect on the surface charge density.     

DNA sequencing with titanium nitride electrodes

We construct a hydrogen‐bond based metal–molecule–metal junction, which contains two identical “reader” molecules, one single DNA base as a bridged molecule, and two titanium nitride electrodes. Hydrogen bonds are formed between “reader” molecules and DNA base, whereas titanium–sulfur bonds are formed between “reader” molecules and titanium nitride electrodes. We perform electronic structure calculations for both the bare bridged molecule and the full metal–molecule–metal system. The projected density of states shows that when the molecule is connected to the titanium nitride electrode, the energy levels of the bridged molecule are shifted, with an indirect effect on the hydrogen bonds. This is similar to the case for a gold electrode but with a more pronounced effect. We also calculate the current–voltage characteristics for the molecular junctions containing each DNA base. Results show that titanium nitride as an electrode can generate distinct conductance for each DNA base, providing an alternative electrode for DNA sequencing. © 2013 Wiley Periodicals, Inc.